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Sample records for atomic conformational transition

  1. Nuclear effects in atomic transitions

    CERN Document Server

    Pálffy, Adriana

    2011-01-01

    Atomic electrons are sensitive to the properties of the nucleus they are bound to, such as nuclear mass, charge distribution, spin, magnetization distribution, or even excited level scheme. These nuclear parameters are reflected in the atomic transition energies. A very precise determination of atomic spectra may thus reveal information about the nucleus, otherwise hardly accessible via nuclear physics experiments. This work reviews theoretical and experimental aspects of the nuclear effects that can be identified in atomic structure data. An introduction to the theory of isotope shifts and hyperfine splitting of atomic spectra is given, together with an overview of the typical experimental techniques used in high-precision atomic spectroscopy. More exotic effects at the borderline between atomic and nuclear physics, such as parity violation in atomic transitions due to the weak interaction, or nuclear polarization and nuclear excitation by electron capture, are also addressed.

  2. 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.

  3. 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.

  4. Atomic inner-shell transitions

    Science.gov (United States)

    Crasemann, B.; Chen, M. H.; Mark, H.

    1984-01-01

    Atomic inner-shell processes have quite different characteristics, in several important aspects, from processes in the optical regime. Energies are large, e.g., the 1s binding energy reaches 100 keV at Z = 87; relativistic and quantum-electrodynamic effects therefore are strong. Radiationless transitions vastly dominate over photon emission in most cases. Isolated inner-shell vacancies have pronounced single-particle character, with correlations generally contributing only approximately 1 eV to the 1s and 2p binding energies; the structure of such systems is thus well tractable by independent-particle self-consistent-field atomic models. For systems containing multiple deep inner-shell vacancies, or for highly stripped ions, the importance of relativistic intermediate coupling and configuration interaction becomes pronounced. Cancellation of the Coulomb interaction can lead to strong manifestations of the Breit interaction in such phenomena as multiplet splitting and hypersatellite X-ray shifts. Unique opportunities arise for the test of theory.

  5. 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.

  6. Factor Va alternative conformation reconstruction using atomic force microscopy.

    Science.gov (United States)

    Chaves, R C; Dahmane, S; Odorico, M; Nicolaes, G A F; Pellequer, J-L

    2014-12-01

    Protein conformational variability (or dynamics) for large macromolecules and its implication for their biological function attracts more and more attention. Collective motions of domains increase the ability of a protein to bind to partner molecules. Using atomic force microscopy (AFM) topographic images, it is possible to take snapshots of large multi-component macromolecules at the single molecule level and to reconstruct complete molecular conformations. Here, we report the application of a reconstruction protocol, named AFM-assembly, to characterise the conformational variability of the two C domains of human coagulation factor Va (FVa). Using AFM topographic surfaces obtained in liquid environment, it is shown that the angle between C1 and C2 domains of FVa can vary between 40° and 166°. Such dynamical variation in C1 and C2 domain arrangement may have important implications regarding the binding of FVa to phospholipid membranes.

  7. Atomic Force Microscopy Study of Conformational Change of Immobilized Calmodulin

    OpenAIRE

    Trajkovic, Sanja; Zhang, Xiaoning; Daunert, Sylvia; Cai, Yuguang

    2011-01-01

    Maintaining the biological functionality of immobilized proteins is the key to the success of numerous protein-based biomedical devices. To that end, we studied conformational change of calmodulin (CaM) immobilized on chemical patterns. 1-cysteine mutated calmodulin was immobilized on a mercapto-terminated surface through the cysteine-Hg-mercapto coupling. Utilizing Atomic Force Microscope (AFM), the average height of the immobilized calmodulin was determined to be 1.87 ± 0.19 nm. After incub...

  8. Atomic Force Microscopy Study of Conformational Change of Immobilized Calmodulin

    Science.gov (United States)

    Trajkovic, Sanja; Zhang, Xiaoning; Daunert, Sylvia

    2011-01-01

    Maintaining the biological functionality of immobilized proteins is the key to the success of numerous protein-based biomedical devices. To that end, we studied conformational change of calmodulin (CaM) immobilized on chemical patterns. 1-cysteine mutated calmodulin was immobilized on a mercapto-terminated surface through the cysteine-Hg-mercapto coupling. Utilizing Atomic Force Microscope (AFM), the average height of the immobilized calmodulin was determined to be 1.87 ± 0.19 nm. After incubation in EGTA solution, the average height of protein changed to 2.26 ± 0.21 nm, indicating conformational change of CaM to Apo-CaM. The immobilized CaM also demonstrated conformational change upon the reaction with known calmodulin antagonist chlorpromazine (CPZ). After incubation in CPZ solution, the average height of CPZ-bound CaM increased to 2.32 ± 0.20 nm, demonstrating the immobilized CaM still has the similar response as in bulk solution. These results show that immobilization of calmodulin on a solid support does not interfere with the ability of the protein to bind calcium and calmodulin antagonists. Our results demonstrate the feasibility of employing AFM to probe and understand protein conformational changes. PMID:21766850

  9. 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.

  10. Transition energies of atomic lawrencium

    Energy Technology Data Exchange (ETDEWEB)

    Borschevsky, A.; Eliav, E.; Kaldor, U. [Tel Aviv Univ., School of Chemistry (Israel); Vilkas, M.J.; Ishikawa, Y. [Puerto Rico Univ., Dept. of Chemistry (United States)

    2007-10-15

    Transition energies of the superheavy element lawrencium, including the ionization potential, excitation energies and electron affinities, are calculated by the intermediate Hamiltonian coupled cluster method. A large basis set (37s31p26d21f16g11h6i) is used, as well as an extensive P space (6s5p4d2f1g). The outer 43 electrons are correlated. Accuracy is monitored by applying the same approach to lutetium, the lighter homologue of Lr, and comparing with experimentally known energies. QED corrections are included. The main goal is to predict excitation energies, in anticipation of planned spectroscopy of Lr. The ground state of Lr is 7s{sup 2}7p {sup 2}P(1/2), unlike the 5d6s{sup 2} {sup 2}D(3/2) of Lu. Predicted Lr excitations with large transition moments in the prime range for the planned experiment, 20.000-30.000 cm{sup -1}, are 7p {yields} 8s at 20.100 cm{sup -1} and 7p {yields} 7d at 28.100 cm{sup -1}. The average absolute error of 20 excitation energies of Lu is 423 cm{sup -1}, and the error limits for Lr are put at 700 cm{sup -1}. The two electron affinities measured recently for Lu are reproduced within 55 cm{sup -1}, and a third bound state of Lu{sup -} is predicted. (authors)

  11. Structural plasticity and conformational transitions of HIV envelope glycoprotein gp120.

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    Anil Korkut

    Full Text Available HIV envelope glycoproteins undergo large-scale conformational changes as they interact with cellular receptors to cause the fusion of viral and cellular membranes that permits viral entry to infect targeted cells. Conformational dynamics in HIV gp120 are also important in masking conserved receptor epitopes from being detected for effective neutralization by the human immune system. Crystal structures of HIV gp120 and its complexes with receptors and antibody fragments provide high-resolution pictures of selected conformational states accessible to gp120. Here we describe systematic computational analyses of HIV gp120 plasticity in such complexes with CD4 binding fragments, CD4 mimetic proteins, and various antibody fragments. We used three computational approaches: an isotropic elastic network analysis of conformational plasticity, a full atomic normal mode analysis, and simulation of conformational transitions with our coarse-grained virtual atom molecular mechanics (VAMM potential function. We observe collective sub-domain motions about hinge points that coordinate those motions, correlated local fluctuations at the interfacial cavity formed when gp120 binds to CD4, and concerted changes in structural elements that form at the CD4 interface during large-scale conformational transitions to the CD4-bound state from the deformed states of gp120 in certain antibody complexes.

  12. 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...

  13. Capturing Transition Paths and Transition States for Conformational Rearrangements in the Ribosome

    Science.gov (United States)

    Noel, Jeffrey; Chahine, Jorge; Leite, Vitor; Whitford, Paul

    2015-03-01

    To reveal the molecular determinants of biological function, one seeks to characterize the interactions that are formed in conformational and chemical transition states. In other words, what interactions govern the molecule's energy landscape? To accomplish this, it is necessary to determine which degrees of freedom can unambiguously identify each transition state. Here, we perform simulations of large-scale aminoacyl-tRNA (aa-tRNA) rearrangements during accommodation on the ribosome and project the dynamics along experimentally-accessible atomic distances. From this analysis, we obtain evidence for which coordinates capture the correct number of barrier-crossing events and accurately indicate when the aa-tRNA is on a transition path. While a currently-used coordinate in single-molecule experiments performs poorly, this study implicates alternative coordinates along which rearrangements are accurately described as diffusive movements across a one-dimensional free-energy profile. From this, we provide the theoretical foundation required for single-molecule techniques to uncover the energy landscape governing aa-tRNA selection by the ribosome. More details can be found at doi:10.1529/biophysj.106.090944.

  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. Probing the conformal Calabrese-Cardy scaling with cold atoms

    CERN Document Server

    Unmuth-Yockey, J; Preiss, P M; Yang, Li-Ping; Tsai, S -W; Meurice, Y

    2016-01-01

    We demonstrate that current experiments using cold bosonic atoms trapped in one-dimensional optical lattices and designed to measure the second-order Renyi entanglement entropy S_2, can be used to verify detailed predictions of conformal field theory (CFT) and estimate the central charge c. We discuss the adiabatic preparation of the ground state at half-filling where we expect a CFT with c=1. This can be accomplished with a very small hoping parameter J, in contrast to existing studies with density one where a much larger J is needed. We provide two complementary methods to estimate and subtract the classical entropy generated by the experimental preparation and imaging processes. We compare numerical calculations for the classical O(2) model with a chemical potential on a 1+1 dimensional lattice, and the quantum Bose-Hubbard Hamiltonian implemented in the experiments. S_2 is very similar for the two models and follows closely the Calabrese-Cardy scaling, (c/8)\\ln(N_s), for N_s sites with open boundary condi...

  16. Atomic transition probabilities of Er i

    Energy Technology Data Exchange (ETDEWEB)

    Lawler, J E; Den Hartog, E A [Department of Physics, University of Wisconsin, 1150 University Ave., Madison, WI 53706 (United States); Wyart, J-F, E-mail: jelawler@wisc.ed, E-mail: jean-francois.wyart@lac.u-psud.f, E-mail: eadenhar@wisc.ed [Laboratoire Aime Cotton, CNRS (UPR3321), Bat. 505, Centre Universitaire Paris-Sud, 91405-Orsay (France)

    2010-12-14

    Atomic transition probabilities for 562 lines of the first spectrum of erbium (Er i) are reported. These data are from new branching fraction measurements on Fourier transform spectra normalized with previously reported radiative lifetimes from time-resolved laser-induced fluorescence measurements (Den Hartog et al 2010 J. Phys. B: At. Mol. Opt. Phys. 43 155004). The wavelength range of the data set is from 298 to 1981 nm. In this work we explore the utility of parametric fits based on the Cowan code in assessing branching fraction errors due to lines connecting to unobserved lower levels.

  17. Atomic transition probabilities of Gd i

    Energy Technology Data Exchange (ETDEWEB)

    Lawler, J E; Den Hartog, E A [Department of Physics, University of Wisconsin, 1150 University Avenue, Madison, WI 53706 (United States); Bilty, K A, E-mail: jelawler@wisc.edu, E-mail: biltyka@uwec.edu, E-mail: eadenhar@wisc.edu [Department of Physics and Astronomy, University of Wisconsin-Eau Claire, Eau Claire, WI 54702 (United States)

    2011-05-14

    Fourier transform spectra are used to determine emission branching fractions for 1290 lines of the first spectrum of gadolinium (Gd i). These branching fractions are converted to absolute atomic transition probabilities using previously reported radiative lifetimes from time-resolved laser-induced-fluorescence measurements (Den Hartog et al 2011 J. Phys. B: At. Mol. Opt. Phys. 44 055001). The wavelength range of the data set is from 300 to 1850 nm. A least squares technique for separating blends of the first and second spectra lines is also described and demonstrated in this work.

  18. Atomic Transition Probabilities in TiI

    Science.gov (United States)

    Nitz, David E.; Siewert, Lowell K.; Schneider, Matthew N.

    2001-05-01

    We have measured branching fractions and atomic transition probabilities in TiI for 50 visible and near-IR transitions which connect odd-parity levels lying 25000 cm-1 to 27000 cm-1 above the ground state to low-lying even parity levels. Branching fractions are obtained from the analysis of six hollow cathode emission spectra recorded using the Fourier transform spectrometer at the National Solar Observatory, supplemented in cases susceptible to radiation-trapping problems by conventional emission spectroscopy using a commercial sealed lamp operated at very low discharge current. The absolute scale for normalizing the branching fractions is established using radiative lifetimes from time-resolved laser-induced fluorescence measurements.(S. Salih and J.E. Lawler, Astronomy and Astrophysics 239, 407 (1990).) Uncertainties of the transition probabilities range from ±5% for the stronger branches to ±20% for the weaker ones. Among the 16 lines for which previously-measured transition probabilities are listed in the NIST critical compilation,(G. A. Martin, J. R. Fuhr, and W. L. Wiese, J. Phys. Chem. Ref. Data 17, Suppl. 3, 85 (1988).) several significant discrepancies are noted.

  19. Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces.

    Science.gov (United States)

    Ikeda, Kazuyoshi; Hirokawa, Takatsugu; Higo, Junichi; Tomii, Kentaro

    2008-08-13

    Many studies have examined rules governing two aspects of protein structures: short segments and proteins' structural domains. Nevertheless, the organization and nature of the conformational space of segments with intermediate length between short segments and domains remain unclear. Conformational spaces of intermediate length segments probably differ from those of short segments. We investigated the identification and characterization of the boundary(s) between peptide-like (short segment) and protein-like (long segment) distributions. We generated ensembles embedded in globular proteins comprising segments 10-50 residues long. We explored the relationships between the conformational distribution of segments and their lengths, and also protein structural classes using principal component analysis based on the intra-segment Calpha-Calpha atomic distances. Our statistical analyses of segment conformations and length revealed critical dual transitions in their conformational distribution with segments derived from all four structural classes. Dual transitions were identified with the intermediate phase between the short segments and domains. Consequently, protein segment universes were categorized. i) Short segments (10-22 residues) showed a distribution with a high frequency of secondary structure clusters. ii) Medium segments (23-26 residues) showed a distribution corresponding to an intermediate state of transitions. iii) Long segments (27-50 residues) showed a distribution converging on one huge cluster containing compact conformations with a smaller radius of gyration. This distribution reflects the protein structures' organization and protein domains' origin. Three major conformational components (radius of gyration, structural symmetry with respect to the N-terminal and C-terminal halves, and single-turn/two-turn structure) well define most of the segment universes. Furthermore, we identified several conformational components that were unique to each

  20. Protein-segment universe exhibiting transitions at intermediate segment length in conformational subspaces

    Directory of Open Access Journals (Sweden)

    Hirokawa Takatsugu

    2008-08-01

    Full Text Available Abstract Background Many studies have examined rules governing two aspects of protein structures: short segments and proteins' structural domains. Nevertheless, the organization and nature of the conformational space of segments with intermediate length between short segments and domains remain unclear. Conformational spaces of intermediate length segments probably differ from those of short segments. We investigated the identification and characterization of the boundary(s between peptide-like (short segment and protein-like (long segment distributions. We generated ensembles embedded in globular proteins comprising segments 10–50 residues long. We explored the relationships between the conformational distribution of segments and their lengths, and also protein structural classes using principal component analysis based on the intra-segment Cα-Cα atomic distances. Results Our statistical analyses of segment conformations and length revealed critical dual transitions in their conformational distribution with segments derived from all four structural classes. Dual transitions were identified with the intermediate phase between the short segments and domains. Consequently, protein segment universes were categorized. i Short segments (10–22 residues showed a distribution with a high frequency of secondary structure clusters. ii Medium segments (23���26 residues showed a distribution corresponding to an intermediate state of transitions. iii Long segments (27–50 residues showed a distribution converging on one huge cluster containing compact conformations with a smaller radius of gyration. This distribution reflects the protein structures' organization and protein domains' origin. Three major conformational components (radius of gyration, structural symmetry with respect to the N-terminal and C-terminal halves, and single-turn/two-turn structure well define most of the segment universes. Furthermore, we identified several

  1. 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

  2. Atomic Transition Probabilities for Neutral Cerium

    Science.gov (United States)

    Lawler, J. E.; den Hartog, E. A.; Wood, M. P.; Nitz, D. E.; Chisholm, J.; Sobeck, J.

    2009-10-01

    The spectra of neutral cerium (Ce I) and singly ionized cerium (Ce II) are more complex than spectra of other rare earth species. The resulting high density of lines in the visible makes Ce ideal for use in metal halide (MH) High Intensity Discharge (HID) lamps. Inclusion of cerium-iodide in a lamp dose can improve both the Color Rendering Index and luminous efficacy of a MH-HID lamp. Basic spectroscopic data including absolute atomic transition probabilities for Ce I and Ce II are needed for diagnosing and modeling these MH-HID lamps. Recent work on Ce II [1] is now being augmented with similar work on Ce I. Radiative lifetimes from laser induced fluorescence measurements [2] on neutral Ce are being combined with emission branching fractions from spectra recorded using a Fourier transform spectrometer. A total of 14 high resolution spectra are being analyzed to determine branching fractions for 2000 to 3000 lines from 153 upper levels in neutral Ce. Representative data samples and progress to date will be presented. [4pt] [1] J. E. Lawler, C. Sneden, J. J. Cowan, I. I. Ivans, and E. A. Den Hartog, Astrophys. J. Suppl. Ser. 182, 51-79 (2009). [0pt] [2] E. A. Den Hartog, K. P. Buettner, and J. E. Lawler, J. Phys. B: Atomic, Molecular & Optical Physics 42, 085006 (7pp) (2009).

  3. Conformational transition pathway in the activation process of allosteric glucokinase.

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    Min Huang

    Full Text Available Glucokinase (GK is a glycolytic enzyme that plays an important role in regulating blood glucose level, thus acting as a potentially attractive target for drug discovery in the treatment of diabetes of the young type 2 and persistent hyperinsulinemic hypoglycemia of infancy. To characterize the activation mechanism of GK from the super-open state (inactive state to the closed state (active state, a series of conventional molecular dynamics (MD and targeted MD (TMD simulations were performed on this enzyme. Conventional MD simulation showed a specific conformational ensemble of GK when the enzyme is inactive. Seven TMD simulations depicted a reliably conformational transition pathway of GK from the inactive state to the active state, and the components important to the conformational change of GK were identified by analyzing the detailed structures of the TMD trajectories. In combination with the inactivation process, our findings showed that the whole conformational pathway for the activation-inactivation-activation of GK is a one-direction circulation, and the active state is less stable than the inactive state in the circulation. Additionally, glucose was demonstrated to gradually modulate its binding pose with the help of residues in the large domain and connecting region of GK during the activation process. Furthermore, the obtained energy barriers were used to explain the preexisting equilibrium and the slow binding kinetic process of the substrate by GK. The simulated results are in accordance with the recent findings from the mutagenesis experiments and kinetic analyses. Our observations reveal a complicated conformational process in the allosteric protein, resulting in new knowledge about the delicate mechanisms for allosteric biological macromolecules that will be useful in drug design for targeting allosteric proteins.

  4. Nuclear polarizability of helium isotopes in atomic transitions

    OpenAIRE

    Pachucki, K.; Moro, A. M.

    2006-01-01

    We estimate the nuclear polarizability correction to atomic transition frequencies in various helium isotopes. This effect is non-negligible for high precision tests of quantum electrodynamics or accurate determination of the nuclear charge radius from spectroscopic measurements in helium atoms and ions. In particular, it amounts to $28(3)$ kHz for 1S-2S transition in 4He+.

  5. Conformational transitions upon ligand binding: holo-structure prediction from apo conformations.

    Directory of Open Access Journals (Sweden)

    Daniel Seeliger

    2010-01-01

    Full Text Available Biological function of proteins is frequently associated with the formation of complexes with small-molecule ligands. Experimental structure determination of such complexes at atomic resolution, however, can be time-consuming and costly. Computational methods for structure prediction of protein/ligand complexes, particularly docking, are as yet restricted by their limited consideration of receptor flexibility, rendering them not applicable for predicting protein/ligand complexes if large conformational changes of the receptor upon ligand binding are involved. Accurate receptor models in the ligand-bound state (holo structures, however, are a prerequisite for successful structure-based drug design. Hence, if only an unbound (apo structure is available distinct from the ligand-bound conformation, structure-based drug design is severely limited. We present a method to predict the structure of protein/ligand complexes based solely on the apo structure, the ligand and the radius of gyration of the holo structure. The method is applied to ten cases in which proteins undergo structural rearrangements of up to 7.1 A backbone RMSD upon ligand binding. In all cases, receptor models within 1.6 A backbone RMSD to the target were predicted and close-to-native ligand binding poses were obtained for 8 of 10 cases in the top-ranked complex models. A protocol is presented that is expected to enable structure modeling of protein/ligand complexes and structure-based drug design for cases where crystal structures of ligand-bound conformations are not available.

  6. Conformational conversion during amyloid formation at atomic resolution.

    Science.gov (United States)

    Eichner, Timo; Kalverda, Arnout P; Thompson, Gary S; Homans, Steve W; Radford, Sheena E

    2011-01-21

    Numerous studies of amyloid assembly have indicated that partially folded protein species are responsible for initiating aggregation. Despite their importance, the structural and dynamic features of amyloidogenic intermediates and the molecular details of how they cause aggregation remain elusive. Here, we use ΔN6, a truncation variant of the naturally amyloidogenic protein β(2)-microglobulin (β(2)m), to determine the solution structure of a nonnative amyloidogenic intermediate at high resolution. The structure of ΔN6 reveals a major repacking of the hydrophobic core to accommodate the nonnative peptidyl-prolyl trans-isomer at Pro32. These structural changes, together with a concomitant pH-dependent enhancement in backbone dynamics on a microsecond-millisecond timescale, give rise to a rare conformer with increased amyloidogenic potential. We further reveal that catalytic amounts of ΔN6 are competent to convert nonamyloidogenic human wild-type β(2)m (Hβ(2)m) into a rare amyloidogenic conformation and provide structural evidence for the mechanism by which this conformational conversion occurs. Copyright © 2011 Elsevier Inc. All rights reserved.

  7. Conformal phase transition as a new perspective on conventional superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Nogueira, Flavio [Theoretische Physik III, Ruhr-Universitaet Bochum (Germany); Sudbo, Asle [Dept. of Physics, Norwegian University of Science and Technology (Norway)

    2015-07-01

    We argue that the phase transition in strong type I superconductors features charged fluctuations, meaning that it is essentially driven by thermal fluctuations of the magnetic field. This is simply a consequence of the small value of the Ginzburg parameter in the deep type I regime. We substantiate this conclusion by a generalization of the Ginzburg criterion to include charged fluctuations. Finally, we demonstrate by means of a renormalization group analysis that the correlation length actually does not obey a power law as function of T-T{sub c}. Rather it features an essential singularity at T{sub c}, which is characteristic of a so called conformal phase transition, one known example of it being the Berezinski-Kosterliz-Thouless (BKT) phase transition in two-dimensional superfluids. We argue that a similar behavior happens in three-dimensional strongly type I superconductors. One important prediction from our theory that may be tested experimentally by microwave measurement is a universal discontinuous jump in the superfluid density.

  8. Joint Space-Time Coherent Vibration Driven Conformational Transitions in a Single Molecule

    Science.gov (United States)

    Li, Shaowei; Chen, Siyu; Li, Jie; Wu, Ruqian; Ho, W.

    2017-10-01

    We report single-molecule conformational transitions with joint angstrom-femtosecond resolution by irradiating the junction of a scanning tunneling microscope with femtosecond laser pulses. An isolated pyrrolidine molecule adsorbed on a Cu(001) surface undergoes reversible transitions between two conformational states. The transition rate decays in time and exhibits sinusoidal oscillations with periods of specific molecular vibrations. The dynamics of this transition depends sensitively on the molecular environment, as exemplified by the effects of another molecule in proximity.

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

    Science.gov (United States)

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

    2017-05-01

    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. Supported by the National Natural Science Foundation of China under Grant Nos. 11275118, 11404198, 91430109, 61505100, 51502189, and the Scientific and Technological Innovation Programs of Higher Education Institutions in Shanxi Province (STIP) under Grant No. 2014102, and the Launch of the Scientific Research of Shanxi University under Grant No. 011151801004, and the National Fundamental Fund of Personnel Training under Grant No. J1103210. The Natural Science Foundation of Shanxi Province under Grant No. 2015011008

  10. HIV-1 TAR RNA spontaneously undergoes relevant apo-to-holo conformational transitions in molecular dynamics and constrained geometrical simulations.

    Science.gov (United States)

    Fulle, Simone; Christ, Nina Alexandra; Kestner, Eva; Gohlke, Holger

    2010-08-23

    We report all-atom molecular dynamics and replica exchange molecular dynamics simulations on the unbound human immunodeficiency virus type-1 (HIV-1) transactivation responsive region (TAR) RNA structure and three TAR RNA structures in bound conformations of, in total, approximately 250 ns length. We compare the extent of observed conformational sampling with that of the conceptually simpler and computationally much cheaper constrained geometrical simulation approach framework rigidity optimized dynamic algorithm (FRODA). Atomic fluctuations obtained by replica-exchange molecular dynamics (REMD) simulations agree quantitatively with those obtained by molecular dynamics (MD) and FRODA simulations for the unbound TAR structure. Regarding the stereochemical quality of the generated conformations, backbone torsion angles and puckering modes of the sugar-phosphate backbone were reproduced equally well by MD and REMD simulations, but further improvement is needed in the case of FRODA simulations. Essential dynamics analysis reveals that all three simulation approaches show a tendency to sample bound conformations when starting from the unbound TAR structure, with MD and REMD simulations being superior with respect to FRODA. These results are consistent with the experimental view that bound TAR RNA conformations are transiently sampled in the free ensemble, following a conformation selection model. The simulation-generated TAR RNA conformations have been successfully used as receptor structures for docking. This finding has important implications for RNA-ligand docking in that docking into an ensemble of simulation-generated RNA structures is shown to be a valuable means to cope with large apo-to-holo conformational transitions of the receptor structure.

  11. Mechanism of Catalytic Microtubule Depolymerization via KIF2-Tubulin Transitional Conformation

    Directory of Open Access Journals (Sweden)

    Tadayuki Ogawa

    2017-09-01

    Full Text Available Microtubules (MTs are dynamic structures that are fundamental for cell morphogenesis and motility. MT-associated motors work efficiently to perform their functions. Unlike other motile kinesins, KIF2 catalytically depolymerizes MTs from the peeled protofilament end during ATP hydrolysis. However, the detailed mechanism by which KIF2 drives processive MT depolymerization remains unknown. To elucidate the catalytic mechanism, the transitional KIF2-tubulin complex during MT depolymerization was analyzed through multiple methods, including atomic force microscopy, size-exclusion chromatography, multi-angle light scattering, small-angle X-ray scattering, analytical ultracentrifugation, and mass spectrometry. The analyses outlined the conformation in which one KIF2core domain binds tightly to two tubulin dimers in the middle pre-hydrolysis state during ATP hydrolysis, a process critical for catalytic MT depolymerization. The X-ray crystallographic structure of the KIF2core domain displays the activated conformation that sustains the large KIF2-tubulin 1:2 complex.

  12. 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....

  13. Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase

    Directory of Open Access Journals (Sweden)

    Schmid Rolf D

    2009-05-01

    Full Text Available Abstract Background The characteristic of most lipases is the interfacial activation at a lipid interface or in non-polar solvents. Interfacial activation is linked to a large conformational change of a lid, from a closed to an open conformation which makes the active site accessible for substrates. While for many lipases crystal structures of the closed and open conformation have been determined, the pathway of the conformational transition and possible bottlenecks are unknown. Therefore, molecular dynamics simulations of a closed homology model and an open crystal structure of Burkholderia cepacia lipase in water and toluene were performed to investigate the influence of solvents on structure, dynamics, and the conformational transition of the lid. Results The conformational transition of B. cepacia lipase was dependent on the solvent. In simulations of closed B. cepacia lipase in water no conformational transition was observed, while in three independent simulations of the closed lipase in toluene the lid gradually opened during the first 10–15 ns. The pathway of conformational transition was accessible and a barrier was identified, where a helix prevented the lid from opening to the completely open conformation. The open structure in toluene was stabilized by the formation of hydrogen bonds. In simulations of open lipase in water, the lid closed slowly during 30 ns nearly reaching its position in the closed crystal structure, while a further lid opening compared to the crystal structure was observed in toluene. While the helical structure of the lid was intact during opening in toluene, it partially unfolded upon closing in water. The closing of the lid in water was also observed, when with eight intermediate structures between the closed and the open conformation as derived from the simulations in toluene were taken as starting structures. A hydrophobic β-hairpin was moving away from the lid in all simulations in water, which was not

  14. A High-Temperature Order-Disorder Phase Transition Coupled With Conformational Change in the Hybrid Material [C6 H13 NH]2 ⋅ZnBr4.

    Science.gov (United States)

    Khan, Tariq; Asghar, Muhammad Adnan; Sun, Zhihua; Zeb, Aurang; Li, Lina; Sijie, Liu; Zhao, Sangen; Ji, Chengmin; Luo, Junhua

    2016-10-20

    A new high-temperature, hybrid, phase-transition material, 1-methylpiperidinium tetrabromozincate (1), that shows a reversible transition at 345 K was synthesized. Differential scanning calorimetry and specific heat capacity measurements confirmed this reversible transformation with a large heat hysteresis of 25 K, which describes a typical first-order phase transition in 1. The dielectric constant exhibited a steplike anomaly and showed high and low dielectric states in the high- and room-temperature phases, respectively, and therefore, this hybrid might be considered as a potential switchable dielectric material. The variable-temperature powder X-ray diffraction patterns displayed remarkable shifts between the experimental patterns at the two different phases. Single-crystal X-ray diffraction analyses at various temperatures revealed that the origin of this transformation could be attributed to disordering of the bromine atoms in the anion and the nitrogen atom of the cation. The cation also assumed a conformational change, which was likely induced by the disordered nitrogen atom. The conformational onset of the transformation of the cation from a planar conformer into a relaxed chair also occurred upon decreasing the temperature below transition point; thus, the combined order-disorder and conformational change induced the structural transformation and the change in symmetry. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Measurement of "optical" transition probabilities in the silver atom

    NARCIS (Netherlands)

    Terpstra, J.; Smit, J.A.

    1958-01-01

    For 22 spectral lines of the silver atom the probability of spontaneous transition has been derived from measurements of the emission intensity of the line and the population of the corresponding upper level. The medium of excitation was the column of a vertical arc discharge in air of atmospheric

  16. 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.

  17. Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI

    Science.gov (United States)

    Ovchinnikov, Victor; Karplus, Martin; Vanden-Eijnden, Eric

    2011-01-01

    A set of techniques developed under the umbrella of the string method is used in combination with all-atom molecular dynamics simulations to analyze the conformation change between the prepowerstroke (PPS) and rigor (R) structures of the converter domain of myosin VI. The challenges specific to the application of these techniques to such a large and complex biomolecule are addressed in detail. These challenges include (i) identifying a proper set of collective variables to apply the string method, (ii) finding a suitable initial string, (iii) obtaining converged profiles of the free energy along the transition path, (iv) validating and interpreting the free energy profiles, and (v) computing the mean first passage time of the transition. A detailed description of the PPS↔R transition in the converter domain of myosin VI is obtained, including the transition path, the free energy along the path, and the rates of interconversion. The methodology developed here is expected to be useful more generally in studies of conformational transitions in complex biomolecules. PMID:21361558

  18. Atomic force microscopy study of the conformational change in immobilized calmodulin.

    Science.gov (United States)

    Trajkovic, Sanja; Zhang, Xiaoning; Daunert, Sylvia; Cai, Yuguang

    2011-09-06

    Maintaining the biological functionality of immobilized proteins is the key to the success of numerous protein-based biomedical devices. To that end, we studied the conformational change in calmodulin (CaM) immobilized on chemical patterns. 1-Cysteine-mutated calmodulin was immobilized on a mercapto-terminated surface through cysteine-Hg-mercapto coupling. Utilizing atomic force microscopy (AFM), the average height of immobilized calmodulin was determined to be 1.87 ± 0.19 nm. After incubation in EGTA solution, the average height of the protein changed to 2.26 ± 0.21 nm, indicating the conformational change of CaM to Apo-CaM. Immobilized CaM also demonstrated a conformational change upon the reaction with known calmodulin antagonist chlorpromazine (CPZ). After incubation in CPZ solution, the average height of CPZ-bound CaM increased to 2.32 ± 0.20 nm, demonstrating that immobilized CaM has a similar response to that in bulk solution. These results show that the immobilization of calmodulin on a solid support does not interfere with the ability of the protein to bind calcium and calmodulin antagonists. Our results demonstrate the feasibility of employing AFM to probe and understand protein conformational changes. © 2011 American Chemical Society

  19. 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.

  20. Atomic transition probabilities of Ce I from Fourier transform spectra

    Science.gov (United States)

    Lawler, J. E.; Chisholm, J.; Nitz, D. E.; Wood, M. P.; Sobeck, J.; Den Hartog, E. A.

    2010-04-01

    Atomic transition probabilities for 2874 lines of the first spectrum of cerium (Ce I) are reported. These data are from new branching fraction measurements on Fourier transform spectra normalized with previously reported radiative lifetimes from time-resolved laser-induced-fluorescence measurements (Den Hartog et al 2009 J. Phys. B: At. Mol. Opt. Phys. 42 085006). The wavelength range of the data set is from 360 to 1500 nm. Comparisons are made to previous investigations which are less extensive. Accurate Ce i transition probabilities are needed for lighting research and development on metal halide high-intensity discharge lamps.

  1. Atomic transition probabilities of Ce I from Fourier transform spectra

    Energy Technology Data Exchange (ETDEWEB)

    Lawler, J E; Wood, M P; Den Hartog, E A [Department of Physics, University of Wisconsin, 1150 University Ave., Madison, WI 53706 (United States); Chisholm, J [Department of Physics, Boston College, 140 Commonwealth Ave., Chestnut Hill, MA 02467 (United States); Nitz, D E [Department of Physics, St. Olaf College, 1520 St. Olaf Ave., Northfield, MN 55057 (United States); Sobeck, J, E-mail: jelawler@wisc.ed, E-mail: chishojd@bc.ed, E-mail: nitz@stolaf.ed, E-mail: mpwood@wisc.ed, E-mail: jsobeck@uchicago.ed, E-mail: eadenhar@wisc.ed [Department of Astronomy and Astrophysics, University of Chicago, 5640 Ellis Ave., Chicago, IL 60637 (United States)

    2010-04-28

    Atomic transition probabilities for 2874 lines of the first spectrum of cerium (Ce I) are reported. These data are from new branching fraction measurements on Fourier transform spectra normalized with previously reported radiative lifetimes from time-resolved laser-induced-fluorescence measurements (Den Hartog et al 2009 J. Phys. B: At. Mol. Opt. Phys. 42 085006). The wavelength range of the data set is from 360 to 1500 nm. Comparisons are made to previous investigations which are less extensive. Accurate Ce i transition probabilities are needed for lighting research and development on metal halide high-intensity discharge lamps.

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

    Energy Technology Data Exchange (ETDEWEB)

    Golrokhi, Zahra; Chalker, Sophia; Sutcliffe, Christopher J.; Potter, Richard J., E-mail: rjpott@liverpool.ac.uk

    2016-02-28

    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{sup 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. Impurity effects on solid-solid transitions in atomic clusters.

    Science.gov (United States)

    Husic, B E; Schebarchov, D; Wales, D J

    2016-11-03

    We use the harmonic superposition approach to examine how a single atom substitution affects low-temperature anomalies in the vibrational heat capacity (CV) of model nanoclusters. Each anomaly is linked to competing solidlike "phases", where crossover of the corresponding free energies defines a solid-solid transition temperature (Ts). For selected Lennard-Jones clusters we show that Ts and the corresponding CV peak can be tuned over a wide range by varying the relative atomic size and binding strength of the impurity, but excessive atom-size mismatch can destroy a transition and may produce another. In some tunable cases we find up to two additional CV peaks emerging below Ts, signalling one- or two-step delocalisation of the impurity within the ground-state geometry. Results for Ni74X and Au54X clusters (X = Au, Ag, Al, Cu, Ni, Pd, Pt, Pb), modelled by the many-body Gupta potential, further corroborate the possibility of tuning, engineering, and suppressing finite-system analogues of a solid-solid transition in nanoalloys.

  4. Improved Tracking of an Atomic-Clock Resonance Transition

    Science.gov (United States)

    Prestage, John D.; Chung, Sang K.; Tu, Meirong

    2010-01-01

    An improved method of making an electronic oscillator track the frequency of an atomic-clock resonance transition is based on fitting a theoretical nonlinear curve to measurements at three oscillator frequencies within the operational frequency band of the transition (in other words, at three points within the resonance peak). In the measurement process, the frequency of a microwave oscillator is repeatedly set at various offsets from the nominal resonance frequency, the oscillator signal is applied in a square pulse of the oscillator signal having a suitable duration (typically, of the order of a second), and, for each pulse at each frequency offset, fluorescence photons of the transition in question are counted. As described below, the counts are used to determine a new nominal resonance frequency. Thereafter, offsets are determined with respect to the new resonance frequency. The process as described thus far is repeated so as to repeatedly adjust the oscillator to track the most recent estimate of the nominal resonance frequency.

  5. 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.)

  6. Quantitative analyses of RAG-RSS interactions and conformations revealed by atomic force microscopy.

    Science.gov (United States)

    Pavlicek, Jeffrey W; Lyubchenko, Yuri L; Chang, Yung

    2008-10-28

    During V(D)J recombination, site specific DNA excision is dictated by the binding of RAG1/2 proteins to the conserved recombination signal sequence (RSS) within the genome. The interaction between RAG1/2 and RSS is thought to involve a large DNA distortion that is permissive for DNA cleavage. In this study, using atomic force microscopy imaging (AFM), we analyzed individual RAG-RSS complexes, in which the bending angle of RAG-associated RSS substrates could be visualized and quantified. We provided the quantitative measurement on the conformations of specific RAG-12RSS complexes. Previous data indicating the necessity of RAG2 for recombination implies a structural role in the RAG-RSS complex. Surprisingly, however, no significant difference was observed in conformational bending with AFM between RAG1-12RSS and RAG1/2-12RSS. RAG1 was found sufficient to induce DNA bending, and the addition of RAG2 did not change the bending profile. In addition, a prenicked 12RSS bound by RAG1/2 proteins displayed a conformation similar to the one observed with the intact 12RSS, implying that no greater DNA bending occurs after the nicking step in the signal complex. Taken together, the quantitative AFM results on the components of the recombinase emphasize a tightly held complex with a bend angle value near 60 degrees , which may be a prerequisite step for the site-specific nicking by the V(D)J recombinase.

  7. Conformation transitions of a polyelectrolyte chain: a replica-exchange Monte-Carlo study.

    Science.gov (United States)

    Chi, Peng; Li, Baohui; Shi, An-Chang

    2011-08-01

    The thermodynamic behavior of a strongly charged polyelectrolyte chain immersed in a salt-free solution is studied using replica-exchange Monte-Carlo simulations. The results reveal that the chain can assume a variety of conformations, and it undergoes two phase transitions upon cooling. The first transition is identified as a continuous counterion condensation transition while the second one as a first-order coil-globule transition. In the globular state, the counterions and the charged chain segments are densely packed forming a three-dimensional Wigner crystal.

  8. 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.

  9. 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.

  10. Supramolecular chemical shift reagents inducing conformational transitions: NMR analysis of carbohydrate homooligomer mixtures

    DEFF Research Database (Denmark)

    Beeren, Sophie; Meier, Sebastian

    2015-01-01

    We introduce the concept of supramolecular chemical shift reagents as a tool to improve signal resolution for the NMR analysis of homooligomers. Non-covalent interactions with the shift reagent can constrain otherwise flexible analytes inducing a conformational transition that results in signal...

  11. 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.

  12. 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

  13. 4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening

    Directory of Open Access Journals (Sweden)

    Jahn Andreas

    2011-07-01

    Full Text Available Abstract 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.

  14. Shrinking light to allow forbidden transitions on the atomic scale

    Science.gov (United States)

    Rivera, Nicholas; Kaminer, Ido; Zhen, Bo; Joannopoulos, John D.; Soljačić, Marin

    2016-07-01

    The diversity of light-matter interactions accessible to a system is limited by the small size of an atom relative to the wavelength of the light it emits, as well as by the small value of the fine-structure constant. We developed a general theory of light-matter interactions with two-dimensional systems supporting plasmons. These plasmons effectively make the fine-structure constant larger and bridge the size gap between atom and light. This theory reveals that conventionally forbidden light-matter interactions—such as extremely high-order multipolar transitions, two-plasmon spontaneous emission, and singlet-triplet phosphorescence processes—can occur on very short time scales comparable to those of conventionally fast transitions. Our findings may lead to new platforms for spectroscopy, sensing, and broadband light generation, a potential testing ground for quantum electrodynamics (QED) in the ultrastrong coupling regime, and the ability to take advantage of the full electronic spectrum of an emitter.

  15. LDRD Project 52523 final report :Atomic layer deposition of highly conformal tribological coatings.

    Energy Technology Data Exchange (ETDEWEB)

    Jungk, John Michael (University of Minnesota); Dugger, Michael Thomas; George, Steve M. (University of Colorado); Prasad, Somuri V.; Grubbs, Robert K.; Moody, Neville Reid; Mayer, Thomas Michael; Scharf, Thomas W.; Goeke, Ronald S.; Gerberich, William W. (University of Minnesota)

    2005-10-01

    Friction and wear are major concerns in the performance and reliability of micromechanical (MEMS) devices. While a variety of lubricant and wear resistant coatings are known which we might consider for application to MEMS devices, the severe geometric constraints of many micromechanical systems (high aspect ratios, shadowed surfaces) make most deposition methods for friction and wear-resistance coatings impossible. In this program we have produced and evaluate highly conformal, tribological coatings, deposited by atomic layer deposition (ALD), for use on surface micromachined (SMM) and LIGA structures. ALD is a chemical vapor deposition process using sequential exposure of reagents and self-limiting surface chemistry, saturating at a maximum of one monolayer per exposure cycle. The self-limiting chemistry results in conformal coating of high aspect ratio structures, with monolayer precision. ALD of a wide variety of materials is possible, but there have been no studies of structural, mechanical, and tribological properties of these films. We have developed processes for depositing thin (<100 nm) conformal coatings of selected hard and lubricious films (Al2O3, ZnO, WS2, W, and W/Al{sub 2}O{sub 3} nanolaminates), and measured their chemical, physical, mechanical and tribological properties. A significant challenge in this program was to develop instrumentation and quantitative test procedures, which did not exist, for friction, wear, film/substrate adhesion, elastic properties, stress, etc., of extremely thin films and nanolaminates. New scanning probe and nanoindentation techniques have been employed along with detailed mechanics-based models to evaluate these properties at small loads characteristic of microsystem operation. We emphasize deposition processes and fundamental properties of ALD materials, however we have also evaluated applications and film performance for model SMM and LIGA devices.

  16. Tracing Conformational Transition of Abnormal Prion Proteins during Interspecies Transmission by Using Novel Antibodies*

    OpenAIRE

    Ushiki-Kaku, Yuko; Endo, Ryo; Iwamaru, Yoshifumi; Shimizu, Yoshihisa; Imamura, Morikazu; Masujin, Kentaro; Yamamoto, Takuji; Hattori, Shunji; Itohara, Shigeyoshi; Irie, Shinkichi; Yokoyama, Takashi

    2010-01-01

    Conformational differences in abnormal prion proteins (PrPSc) have been postulated to produce different prion phenotypes. During the interspecies transmission of prions, the conformation of PrPSc may change with passage; however, little is known about the mechanism of PrPSc transition. In this study, novel PrPSc-specific monoclonal antibodies (mAbs) were developed that could detect the PrPSc of mouse but not that of sheep. By using these mAbs, we attempted to examine PrPSc accumulated in mice...

  17. 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

  18. 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.

  19. 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....

  20. Area-Selective Atomic Layer Deposition: Conformal Coating, Subnanometer Thickness Control, and Smart Positioning.

    Science.gov (United States)

    Fang, Ming; Ho, Johnny C

    2015-09-22

    Transistors have already been made three-dimensional (3D), with device channels (i.e., fins in trigate field-effect transistor (FinFET) technology) that are taller, thinner, and closer together in order to enhance device performance and lower active power consumption. As device scaling continues, these transistors will require more advanced, fabrication-enabling technologies for the conformal deposition of high-κ dielectric layers on their 3D channels with accurate position alignment and thickness control down to the subnanometer scale. Among many competing techniques, area-selective atomic layer deposition (AS-ALD) is a promising method that is well suited to the requirements without the use of complicated, complementary metal-oxide semiconductor (CMOS)-incompatible processes. However, further progress is limited by poor area selectivity for thicker films formed via a higher number of ALD cycles as well as the prolonged processing time. In this issue of ACS Nano, Professor Stacy Bent and her research group demonstrate a straightforward self-correcting ALD approach, combining selective deposition with a postprocess mild chemical etching, which enables selective deposition of dielectric films with thicknesses and processing times at least 10 times larger and 48 times shorter, respectively, than those obtained by conventional AS-ALD processes. These advances present an important technological breakthrough that may drive the AS-ALD technique a step closer toward industrial applications in electronics, catalysis, and photonics, etc. where more efficient device fabrication processes are needed.

  1. Recent Progress in Atomic Layer Deposition of Multifunctional Oxides and Two-Dimensional Transition Metal Dichalcogenides

    Science.gov (United States)

    Liu, Hongfei

    Atomic layer deposition (ALD) has long been developed for conformal coating thin films on planar surfaces and complex structured substrates based on its unique sequential process and self-limiting surface chemistry. In general, the coated thin films can be dielectrics, semiconductors, conductors, metals, etc., while the targeted surface can vary from those of particles, wires, to deep pores, through holes, and so on. The ALD coating technique, itself, was developed from gas-phase chemical vapor deposition, but now it has been extended even to liquid phase coating/growth. Because the thickness of ALD growth is controlled in atomic level (˜0.1nm), it has recently been employed for producing two-dimensional (2D) materials, typically semiconducting nanosheets of transition metal dichalcogenides (TMDCs). In this paper, we briefly introduce recent progress in ALD of multifunctional oxides and 2D TMDCs with the focus being placed on suitable ALD precursors and their ALD processes (for both binary compounds and ternary alloys), highlighting the remaining challenges and promising potentials.

  2. The intramolecular impact to the sequence specificity of B-->A transition: low energy conformational variations in AA/TT and GG/CC steps.

    Science.gov (United States)

    Il'icheva, I A; Vlasov, P K; Esipova, N G; Tumanyan, V G

    2010-04-01

    It is well known, that local B--> A transformation in DNA is involved in several biological processes. In vitro B A transition is sequence-specific. The physical basis of this specificity is not known yet. Here we analyze the effect of intramolecular interactions on the structural behavior of the GG/CC and AA/TT steps. These steps exemplify sequence specific bias to the B- or A-form structure. Optimization of potential energy of the molecular systems composed of an octanucleotide, neutralized by Na(+) and solvated with TIP3P water molecules in rectangular box with periodic boundary conditions gives the statistically representative sets of low energy structures for GG/CC and AA/TT steps in the middle of the diverse flanking sequences. Permissible 3D variations of GG/CC and AA/TT, and correlation of the relative motion of base pairs in these steps were analyzed. AA/TT step permits high variability for low energy conformers in the B-form DNA and small variability for low energy conformers in the A-form DNA. In contrast GG/CC step permits high variability for low energy conformers in the A-form DNA and small variability for low energy conformers in the B-form DNA. The relative motion of base pairs in GG/CC step is high correlated, while in AA/TT step this correlation is notably less. Atom-atom interactions inside-the-step always favors the B-form and their component - stacking interactions (atom-atom interactions between nucleic bases) is crucial for the duplex stabilization. Formation of the A-form for both steps is a result of interactions with the flanking sequences and water-cation environment in the box. The average energy difference between conformations presenting B-form and A-form for the GG/CC step is high, while for the AA/TT step it is rather low. Thus, intramolecular interactions in GG/CC and AA/TT steps affect the possible conformational diversity ("conformational entropy") of the A- and B- type structures of DNA step. This determines the known bias of the

  3. Schlieren imaging of nano-scale atom-surface inelastic transition using a Fresnel biprism atom interferometer

    Science.gov (United States)

    Grucker, J.; Baudon, J.; Perales, F.; Dutier, G.; Bocvarski, V.; Karam, J.-C.; Vassilev, G.; Ducloy, M.

    2008-05-01

    Surface-induced exo-energetic inelastic transitions among atomic Zeeman states in a magnetic field (“van der Waals Zeeman” transitions) are useable as tuneable beam splitters. A transversally coherent atom beam impinging a pair of opposite surfaces (e.g. 2 edges of a slit or of an ensemble of periodic slits) gives rise to two coherently diffracted wave packets. Within the wave packet overlap, non-localised interference fringes of the Young-slit type are predicted. From the diffraction pattern observed in the Fraunhofer regime (Schlieren image), detailed information about the transition amplitude on a scale of a few nanometers should be derived.

  4. Tracking Ca2+-dependent and Ca2+-independent conformational transitions in syntaxin 1A during exocytosis in neuroendocrine cells.

    Science.gov (United States)

    Greitzer-Antes, Dafna; Barak-Broner, Noa; Berlin, Shai; Oron, Yoram; Chikvashvili, Dodo; Lotan, Ilana

    2013-07-01

    A key issue for understanding exocytosis is elucidating the various protein interactions and the associated conformational transitions underlying soluble N-ethylmeleimide-sensitive factor attachment protein receptor (SNARE) protein assembly. To monitor dynamic changes in syntaxin 1A (Syx) conformation along exocytosis, we constructed a novel fluorescent Syx-based probe that can be efficiently incorporated within endogenous SNARE complexes, support exocytosis, and report shifts in Syx between 'closed' and 'open' conformations by fluorescence resonance energy transfer analysis. Using this probe we resolve two distinct Syx conformational transitions during membrane depolarization-induced exocytosis in PC12 cells: a partial 'opening' in the absence of Ca(2+) entry and an additional 'opening' upon Ca(2+) entry. The Ca(2+)-dependent transition is abolished upon neutralization of the basic charges in the juxtamembrane regions of Syx, which also impairs exocytosis. These novel findings provide evidence of two conformational transitions in Syx during exocytosis, which have not been reported before: one transition directly induced by depolarization and an additional transition that involves the juxtamembrane region of Syx. The superior sensitivity of our probe also enabled detection of subtle Syx conformational changes upon interaction with VAMP2, which were absolutely dependent on the basic charges of the juxtamembrane region. Hence, our results further suggest that the Ca(2+)-dependent transition in Syx involves zippering between the membrane-proximal juxtamembrane regions of Syx and VAMP2 and support the recently implied existence of this zippering in the final phase of SNARE assembly to catalyze exocytosis.

  5. 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.

  6. Potential Energy Surface-Based Automatic Deduction of Conformational Transition Networks and Its Application on Quantum Mechanical Landscapes of d-Glucose Conformers.

    Science.gov (United States)

    Satoh, Hiroko; Oda, Tomohiro; Nakakoji, Kumiyo; Uno, Takeaki; Tanaka, Hiroaki; Iwata, Satoru; Ohno, Koichi

    2016-11-08

    This paper describes our approach that is built upon the potential energy surface (PES)-based conformational analysis. This approach automatically deduces a conformational transition network, called a conformational reaction route map (r-map), by using the Scaled Hypersphere Search of the Anharmonic Downward Distortion Following method (SHS-ADDF). The PES-based conformational search has been achieved by using large ADDF, which makes it possible to trace only low transition state (TS) barriers while restraining bond lengths and structures with high free energy. It automatically performs sampling the minima and TS structures by simply taking into account the mathematical feature of PES without requiring any a priori specification of variable internal coordinates. An obtained r-map is composed of equilibrium (EQ) conformers connected by reaction routes via TS conformers, where all of the reaction routes are already confirmed during the process of the deduction using the intrinsic reaction coordinate (IRC) method. The postcalculation analysis of the deduced r-map is interactively carried out using the RMapViewer software we have developed. This paper presents computational details of the PES-based conformational analysis and its application to d-glucose. The calculations have been performed for an isolated glucose molecule in the gas phase at the RHF/6-31G level. The obtained conformational r-map for α-d-glucose is composed of 201 EQ and 435 TS conformers and that for β-d-glucose is composed of 202 EQ and 371 TS conformers. For the postcalculation analysis of the conformational r-maps by using the RMapViewer software program we have found multiple minimum energy paths (MEPs) between global minima of 1C4 and 4C1 chair conformations. The analysis using RMapViewer allows us to confirm the thermodynamic and kinetic predominance of 4C1 conformations; that is, the potential energy of the global minimum of 4C1 is lower than that of 1C4 (thermodynamic predominance) and that

  7. Blocking of diffusion transitions of metal atoms at excitation of weakly attenuating plasmons

    CERN Document Server

    Gorelov, B M; Ogenko, V M; Shalyapina, G M

    2001-01-01

    One studies blocking transitions of metal atoms in YBa sub 2 Cu sub 3 O sub 7 high-temperature superconductor at excitation of weakly attenuating acoustic plasmons and at thermodesorption of 01 atoms. Ni and Au atoms were as diffusates. YBa sub 2 Cu sub 3 O sub 7 sub - subdelta specimens were irradiated by 9.4 GHz frequency and 10 sup 4 W power pulsed UHF-field. Temperature dependences of diffusion coefficient of Ni and Au atoms prior and subsequent to UHF irradiation and thermodesorption of 0 atoms are analyzed. It is pointed out that subsequent to UHF irradiation resistance of a specimen increases near transition into superconducting state. One makes a conclusion that blocking of space and surface transitions of Ni and Au atoms results from accumulation a large number of interstitial atoms in the surface layer of crystallites

  8. Direct measurement of sequence-dependent transition path times and conformational diffusion in DNA duplex formation.

    Science.gov (United States)

    Neupane, Krishna; Wang, Feng; Woodside, Michael T

    2017-02-07

    The conformational diffusion coefficient, D, sets the timescale for microscopic structural changes during folding transitions in biomolecules like nucleic acids and proteins. D encodes significant information about the folding dynamics such as the roughness of the energy landscape governing the folding and the level of internal friction in the molecule, but it is challenging to measure. The most sensitive measure of D is the time required to cross the energy barrier that dominates folding kinetics, known as the transition path time. To investigate the sequence dependence of D in DNA duplex formation, we measured individual transition paths from equilibrium folding trajectories of single DNA hairpins held under tension in high-resolution optical tweezers. Studying hairpins with the same helix length but with G:C base-pair content varying from 0 to 100%, we determined both the average time to cross the transition paths, τtp, and the distribution of individual transit times, PTP(t). We then estimated D from both τtp and PTP(t) from theories assuming one-dimensional diffusive motion over a harmonic barrier. τtp decreased roughly linearly with the G:C content of the hairpin helix, being 50% longer for hairpins with only A:T base pairs than for those with only G:C base pairs. Conversely, D increased linearly with helix G:C content, roughly doubling as the G:C content increased from 0 to 100%. These results reveal that G:C base pairs form faster than A:T base pairs because of faster conformational diffusion, possibly reflecting lower torsional barriers, and demonstrate the power of transition path measurements for elucidating the microscopic determinants of folding.

  9. Conformational transitions of plasmid ds-DNA on ultrathin films of alkylamines on graphite

    Science.gov (United States)

    Falk, Caroline; Liang, Hua; Severin, Nikolai; Zhuang, Wei; Zauscher, Stefan; Rabe, Jürgen P.

    2015-03-01

    DNA replication is an important process in the human body. Replication of double-stranded (ds)-DNA requires its local melting into two single strands. DNA, when stretched in solution, overwinds and melts. This was argued to give insight onto the replication mechanism. It is difficult, however, to access the direct conformational changes during stretching in solution. Recent work demonstrated that this transition can be imaged with scanning force microscopy on a graphite surface that is coated with an alkylamine layer. ds-DNA can be controlled by an amphiphilic layer, since the DNA conformation depends on the amphiphile concentration. In particular we analyzed different DNA lengths on the same surface, and we found that at a specific concentration of octadecylamine the ds-DNA pUC19 plasmid ring splits into two single strands at one position. We will discuss methods to mark the DNA to determine the exact location at which the plasmid ring splits.

  10. 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. Tunnel ionization takes place when the electric field changes the atomic potential and electron sees a very small mod- ified potential and can tunnel through it. Keldysh [4] made the first attempt to perform a general analysis of ionization of atoms by laser radiation as ...

  11. Accounting for conformational flexibility and torsional anharmonicity in the H + CH3CH2OH hydrogen abstraction reactions: a multi-path variational transition state theory study.

    Science.gov (United States)

    Meana-Pañeda, Rubén; Fernández-Ramos, Antonio

    2014-05-07

    This work reports a detailed theoretical study of the hydrogen abstraction reactions from ethanol by atomic hydrogen. The calculated thermal rate constants take into account torsional anharmonicity and conformational flexibility, in addition to the variational and tunneling effects. Specifically, the kinetics calculations were performed by using multi-path canonical variational transition state theory with least-action path tunneling corrections, to which we have added the two-dimensional non-separable method to take into account torsional anharmonicity. The multi-path thermal rate constant is expressed as a sum over conformational reaction channels. Each of these channels includes all the transition states that can be reached by internal rotations. The results show that, in the interval of temperatures between 250 and 2500 K, the account for multiple paths leads to higher thermal rate constants with respect to the single path approach, mainly at low and at high temperatures. In addition, torsional anharmonicity enhances the slope of the Arrhenius plot in this range of temperatures. Finally, we show that the incorporation of tunneling into the hydrogen abstraction reactions substantially changes the contribution of each of the transition states to the conformational reaction channel.

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

    Science.gov (United States)

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

    2012-05-01

    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 N2∗(3Σu+), transitions among magnetic sub-levels in the presence of a magnetic field.

  13. Force induced conformational transition in a system of interacting stiff polymer: Application to unfolding

    OpenAIRE

    Kumar, Sanjay; Giri, Debaprasad

    2007-01-01

    We consider a stiff polymer chain in poor solvent and apply a force at one end of the chain. We find that by varying the stiffness parameter, polymer undergoes a transition from the globule state to the folded like state. The conformation of folded state mimics the $\\beta$-sheet as seen in titin molecule. Using exact enumeration technique, we study the extension-force and force-temperature diagrams of such a system. Force-temperature diagram shows the re-entrance behaviour for flexible chain....

  14. Conformational transitions during FtsK translocase activation of individual XerCD-dif recombination complexes.

    Science.gov (United States)

    Zawadzki, Pawel; May, Peter F J; Baker, Rachel A; Pinkney, Justin N M; Kapanidis, Achillefs N; Sherratt, David J; Arciszewska, Lidia K

    2013-10-22

    Three single-molecule techniques have been used simultaneously and in tandem to track the formation in vitro of single XerCD-dif recombination complexes. We observed the arrival of the FtsK translocase at individual preformed synaptic complexes and demonstrated the conformational change that occurs during their activation. We then followed the reaction intermediate transitions as Holliday junctions formed through catalysis by XerD, isomerized, and were converted by XerC to reaction products, which then dissociated. These observations, along with the calculated intermediate lifetimes, inform the reaction mechanism, which plays a key role in chromosome unlinking in most bacteria with circular chromosomes.

  15. Conformation transitions of a single polyelectrolyte chain in a poor solvent: a replica-exchange lattice Monte-Carlo study.

    Science.gov (United States)

    Wang, Lang; Wang, Zheng; Jiang, Run; Yin, Yuhua; Li, Baohui

    2017-03-15

    The thermodynamic behaviors of a strongly charged polyelectrolyte chain in a poor solvent are studied using replica-exchange Monte-Carlo simulations on a lattice model, focusing on the effects of finite chain length and the solvent quality on the chain conformation and conformation transitions. The neutralizing counterions and solvent molecules are considered explicitly. The thermodynamic quantities that vary continuously with temperature over a wide range are computed using the multiple histogram reweighting method. Our results suggest that the strength of the short-range hydrophobic interaction, the chain length, and the temperature of the system, characterized by ε, N, and T, respectively, are important parameters that control the conformations of a charged chain. When ε is moderate, the competition between the electrostatic energy and the short-range hydrophobic interaction leads to rich conformations and conformation transitions for a longer chain with a fixed length. Our results have unambiguously demonstrated the stability of the n-pearl-necklace structures, where n has a maximum value and decreases with decreasing temperature. The maximum n value increases with increasing chain length. Our results have also demonstrated the first-order nature of the conformation transitions between the m-pearl and the (m-1)-pearl necklaces. With the increase of ε, the transition temperature increases and the first-order feature becomes more pronounced. It is deduced that at the thermodynamic limit of infinitely long chain length, the conformational transitions between the m-pearl and the (m-1)-pearl necklaces may remain first order when ε > 0 and m = 2 or 3. Pearl-necklace conformations cannot be observed when either ε is too large or N is too small. To observe a pearl-necklace conformation, the T value needs to be carefully chosen for simulations performed at only a single temperature.

  16. Initiation of the 3':5'-AMP-induced protein kinase A Iα regulatory subunit conformational transition. Part II. Inhibition by Rp-3':5'-AMPS.

    Science.gov (United States)

    Rogacheva, O N; Shchegolev, B F; Stefanov, V E; Savvateeva-Popova, E V

    2012-05-01

    Protein-ligand docking and ab initio calculations have shown that the 3':5'-AMP phosphorothioate analog (Rp-3':5'-AMPS) blocks the A326 amide group displacement typical of transition from the H- to B-conformation within the B-domain of protein kinase A Iα R-subunit. This behavior of Rp-3':5'-AMPS leads to the inhibition of initial stages of hydrophobic relay operation. In accordance with the proposed hypothesis, Rp-3':5'-AMPS similarly to 3':5'-AMP forms a hydrogen bond with the amide group of A326; however, the properties of this bond together with the position of the sulfur atom prevent the movement of A326. Finally, the Rp-3':5'-AMPS-bound domain appears to be locked in the H-conformation, which is in agreement with the X-ray data.

  17. Thermoelectric material including conformal oxide layers and method of making the same using atomic layer deposition

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Jung Young; Ahn, Dongjoon; Salvador, James R.; Meisner, Gregory P.

    2016-06-07

    A thermoelectric material includes a substrate particle and a plurality of conformal oxide layers formed on the substrate particle. The plurality of conformal oxide layers has a total oxide layer thickness ranging from about 2 nm to about 20 nm. The thermoelectric material excludes oxide nanoparticles. A method of making the thermoelectric material is also disclosed herein.

  18. Efficiency of Adaptive Temperature-Based Replica Exchange for Sampling Large-Scale Protein Conformational Transitions.

    Science.gov (United States)

    Zhang, Weihong; Chen, Jianhan

    2013-06-11

    Temperature-based replica exchange (RE) is now considered a principal technique for enhanced sampling of protein conformations. It is also recognized that existence of sharp cooperative transitions (such as protein folding/unfolding) can lead to temperature exchange bottlenecks and significantly reduce the sampling efficiency. Here, we revisit two adaptive temperature-based RE protocols, namely, exchange equalization (EE) and current maximization (CM), that were previously examined using atomistic simulations (Lee and Olson, J. Chem. Physics2011, 134, 24111). Both protocols aim to overcome exchange bottlenecks by adaptively adjusting the simulation temperatures, either to achieve uniform exchange rates (in EE) or to maximize temperature diffusion (CM). By designing a realistic yet computationally tractable coarse-grained protein model, one can sample many reversible folding/unfolding transitions using conventional constant temperature molecular dynamics (MD), standard REMD, EE-REMD, and CM-REMD. This allows rigorous evaluation of the sampling efficiency, by directly comparing the rates of folding/unfolding transitions and convergence of various thermodynamic properties of interest. The results demonstrate that both EE and CM can indeed enhance temperature diffusion compared to standard RE, by ∼3- and over 10-fold, respectively. Surprisingly, the rates of reversible folding/unfolding transitions are similar in all three RE protocols. The convergence rates of several key thermodynamic properties, including the folding stability and various 1D and 2D free energy surfaces, are also similar. Therefore, the efficiency of RE protocols does not appear to be limited by temperature diffusion, but by the inherent rates of spontaneous large-scale conformational rearrangements. This is particularly true considering that virtually all RE simulations of proteins in practice involve exchange attempt frequencies (∼ps(-1)) that are several orders of magnitude faster than the

  19. Effects of Cofactors on Conformation Transition of Random Peptides Consisting of a Reduced Amino Acid Alphabet.

    Science.gov (United States)

    Lu, Ming-Feng; Xie, Ying; Zhang, Yue-Jie; Xing, Xue-Yan

    2015-01-01

    This study aims to explore the structure characteristic of random polypeptides constructed by origin early amino acid alphabet, as well as the effects of cofactors on conformation transition of random peptides. DNA library R8-4 encoding VNM random peptides were constructed by small cassette strategy. Subsequently, a random polypeptide library was constructed using in vitro translation. Expression and purification of VNM random peptides were also performed by a conventional method of recombinant. CD spectrum analysis indicated that VNM random polypeptides have a secondary structure characteristic of protein, such as the content of α-helix is greater than 60%, random coil is about 20% β sheet, and β turn is less than 10%. CD spectrum changed with the addition of 10-40 µM ATP and NADP, but slightly changed by NAD; no influence was observed with MgSO4. Bis-ANS binding assay indicated that fluorescent intensity of bis-ANS was strengthened slightly by 10 VNM random peptides. Fluorescent intensity was strengthened fourfold by adding 10-40 µM ATP, NAD, and NADH, whereas the inducing effect of NADPH and MgSO4 were negligible. VNM random peptides have a classic secondary structure and hydrophobic domain in water solution. Moreover, conformation transition and hydrophobic domain could be induced by cofactor, indicating the preliminary evidence for the hypothesis that "the origin of primitive protein was induced by small molecule."

  20. Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2

    Directory of Open Access Journals (Sweden)

    Gu Jenny

    2007-02-01

    Full Text Available Abstract Background The mechanisms underlying protein function and associated conformational change are dominated by a series of local entropy fluctuations affecting the global structure yet are mediated by only a few key residues. Transitional Dynamic Analysis (TDA is a new method to detect these changes in local protein flexibility between different conformations arising from, for example, ligand binding. Additionally, Positional Impact Vertex for Entropy Transfer (PIVET uses TDA to identify important residue contact changes that have a large impact on global fluctuation. We demonstrate the utility of these methods for Cyclin-dependent kinase 2 (CDK2, a system with crystal structures of this protein in multiple functionally relevant conformations and experimental data revealing the importance of local fluctuation changes for protein function. Results TDA and PIVET successfully identified select residues that are responsible for conformation specific regional fluctuation in the activation cycle of Cyclin Dependent Kinase 2 (CDK2. The detected local changes in protein flexibility have been experimentally confirmed to be essential for the regulation and function of the kinase. The methodologies also highlighted possible errors in previous molecular dynamic simulations that need to be resolved in order to understand this key player in cell cycle regulation. Finally, the use of entropy compensation as a possible allosteric mechanism for protein function is reported for CDK2. Conclusion The methodologies embodied in TDA and PIVET provide a quick approach to identify local fluctuation change important for protein function and residue contacts that contributes to these changes. Further, these approaches can be used to check for possible errors in protein dynamic simulations and have the potential to facilitate a better understanding of the contribution of entropy to protein allostery and function.

  1. Unconventional thermal transport enhancement with large atom mass: a comparative study of 2D transition dichalcogenides

    Science.gov (United States)

    Wang, Huimin; Qin, Guangzhao; Li, Guojian; Wang, Qiang; Hu, Ming

    2018-01-01

    2D layered transition dichalcogenides have attracted tremendous attention for their excellent properties and multifarious applications. In particular, NbSe2 and TaSe2 are the canonical systems to study superconductivity and charge density waves. Here, we perform a comparative study of the thermal transport properties of 2D NbSe2 and TaSe2 for both 1T and 2H phases based on first-principles calculations. Usually, the lattice thermal conductivity ({{κ }L} ) is smaller with larger average atom mass. However, it is contrary for the comparison between TaSe2 and NbSe2, despite the heavier Ta than Nb. The abnormally larger {{κ }L} of TaSe2 originates from the weakened phonon–phonon scattering due to the combination of large phonon bandgap and bunching of the acoustic phonon branches, which is caused by the larger mass difference. On one hand, the large bandgap hinders the acoustic–optical phonon scattering. On the other hand, the bunching of the acoustic phonon branches hampers Umklapp process by weakening the high frequency acoustic–acoustic phonon scattering. The special characteristics of phonon transport are further conformed by mode level analysis and scattering channels of phonon–phonon scattering. Moreover, lower κ L of 1T phase for both Nb and Ta selenides compared to 2H phase are also reported, which stems from the stronger anharmonicity.

  2. The Intramolecular Impact to the Sequence Specificity of B→A Transition: Low Energy Conformational Variations in AA/TT and GG/CC Steps.

    Science.gov (United States)

    Il'icheva, I A; Vlasov, P K; Esipova, N G; Tumanyan, V G

    2010-04-01

    Abstract It is well known, that local B→A transformation in DNA is involved in several biological processes. In vitro B↔A transition is sequence-specific. The physical basis of this specificity is not known yet. Here we analyze the effect of intramolecular interactions on the structural behavior of the GG/CC and AA/TT steps. These steps exemplify sequence specific bias to the B- or A-form structure. Optimization of potential energy of the molecular systems composed of an octanucle-otide, neutralized by Na(+) and solvated with TIP3P water molecules in rectangular box with periodic boundary conditions gives the statistically representative sets of low energy structures for GG/CC and AA/TT steps in the middle of the diverse flanking sequences. Permissible 3D variations of GG/CC and AA/TT, and correlation of the relative motion of base pairs in these steps were analyzed. AA/TT step permits high variability for low energy conformers in the B-form DNA and small variability for low energy conformers in the A-form DNA. In contrast GG/CC step permits high variability for low energy conformers in the A-form DNA and small variability for low energy conformers in the B-form DNA. The relative motion of base pairs in GG/CC step is high correlated, while in AA/TT step this correlation is notably less. Atom-atom interactions inside-the-step always favors the B-form and their component - stacking interactions (atomatom interactions between nucleic bases) is crucial for the duplex stabilization. Formation of the A-form for both steps is a result of interactions with the flanking sequences and water-cation environment in the box. The average energy difference between conformations presenting B-form and A-form for the GG/CC step is high, while for the AA/TT step it is rather low. Thus, intramolecular interactions in GG/CC and AA/TT steps affect the possible conformational diversity ("conformational entropy") of the A- and B- type structures of DNA step. This determines the known

  3. Conformational transition of DNA by dinuclear Pt(II) complexes causes cooperative inhibition of gene expression

    Science.gov (United States)

    Shimizu, Yuta; Yoshikawa, Yuko; Kenmotsu, Takahiro; Komeda, Seiji; Yoshikawa, Kenichi

    2017-06-01

    Recently, it was reported that a cationic tetrazolato-bridged dinuclear Pt(II) complex, 5-H-Y, is a promising anticancer drug candidate. Here, we investigated the effects of a series of tetrazolato-bridged dinuclear Pt(II) complexes on the higher-order structure of DNA by using fluorescence and atomic force microscopies. The results showed that these dinuclear Pt(II) complexes cause marked shrinkage on the conformation of genomic DNA. We also found highly cooperative inhibitory effects of these drugs on in vitro gene expression. The unique mechanism of action of these dinuclear Pt(II) complexes is discussed in terms of their bridging effect on DNA segments.

  4. Additive Mixing and Conformal Coating of Noniridescent Structural Colors with Robust Mechanical Properties Fabricated by Atomization Deposition.

    Science.gov (United States)

    Li, Qingsong; Zhang, Yafeng; Shi, Lei; Qiu, Huihui; Zhang, Suming; Qi, Ning; Hu, Jianchen; Yuan, Wei; Zhang, Xiaohua; Zhang, Ke-Qin

    2018-02-15

    Artificial structural colors based on short-range-ordered amorphous photonic structures (APSs) have attracted great scientific and industrial interest in recent years. However, the previously reported methods of self-assembling colloidal nanoparticles lack fine control of the APS coating and fixation on substrates and poorly realize three-dimensional (3D) conformal coatings for objects with irregular or highly curved surfaces. In this paper, atomization deposition of silica colloidal nanoparticles with poly(vinyl alcohol) as the additive is proposed to solve the above problems. By finely controlling the thicknesses of APS coatings, additive mixing of noniridescent structural colors is easily realized. Based on the intrinsic omnidirectional feature of atomization, a one-step 3D homogeneous conformal coating is also readily realized on various irregular or highly curved surfaces, including papers, resins, metal plates, ceramics, and flexible silk fabrics. The vivid coatings on silk fabrics by atomization deposition possess robust mechanical properties, which are confirmed by rubbing and laundering tests, showing great potential in developing an environmentally friendly coloring technique in the textile industry.

  5. Prothrombin requires two sequential metal-dependent conformational transitions to bind phospholipid. Conformation-specific antibodies directed against the phospholipid-binding site on prothrombin

    Energy Technology Data Exchange (ETDEWEB)

    Borowski, M.; Furie, B.C.; Bauminger, S.; Furie, B.

    1986-11-15

    Prothrombin is a gamma-carboxyglutamic acid-containing protein that binds to phospholipid vesicles in the presence of calcium ions after undergoing a metal ion-induced conformational transition. To integrate recent data into a scheme that is compatible with our knowledge of prothrombin-metal interaction, we have proposed a new model of prothrombin structure. In this model prothrombin undergoes two metal-dependent conformational transitions: PT----PT'----PT*. The first transition is not cation-specific, but the second transition is metal-selective for Ca(II), Sr(II), or Ba(II). Only the PT* conformer binds to phospholipid surfaces. To test this model, anti-prothrombin antibodies that only bind to prothrombin in the presence of Ca(II) but not Mg(II) (PT*-specific) were isolated, and termed anti-prothrombin X Ca(II)-specific. Half-maximal binding of antibody to prothrombin was observed at 0.1 mM CaCl/sub 2/ or 1 mM SrCl/sub 2/, but no binding was observed with Mg(II), Mn(II), or Ba(II). However, prothrombin in the presence of both Mg(II)/Ba(II) or Mn(II)/Ba(II) demonstrated significant interaction with the antibody. Prothrombin binding to phospholipid vesicles was inhibited by the anti-prothrombin X Ca(II)-specific antibody or its Fab fragment, but was not inhibited by anti-prothrombin X Mg(II) antibody or its Fab fragment directed at the PT' conformer. These results support this three-state model for prothrombin. The metal specificity characteristic of prothrombin-phospholipid interaction is a property required for the expression of the phospholipid-binding site in the binary prothrombin-metal complex.

  6. Force-induced conformational transition in a system of interacting stiff polymers: application to unfolding.

    Science.gov (United States)

    Kumar, Sanjay; Giri, Debaprasad

    2005-11-01

    We consider a stiff polymer chain in poor solvent and apply a force at one end of the chain. We find that by varying the stiffness parameter, the polymer undergoes a transition from the globule state to the foldedlike state. The conformation of the folded state mimics the beta sheet as seen in the titin molecule. Using the exact enumeration technique, we study the extension-force and force-temperature diagrams of such a system. The force-temperature diagram shows the re-entrance behavior for a flexible chain. However, for a stiff chain this re-entrance behavior is absent and there is an enhancement in theta temperature with the rise of stiffness. We further propose that the internal information about the frozen structure of a polymer can be read from the distribution of end-to-end distance which shows a sawtoothlike behavior.

  7. On the equivalence of conformational and enantiomeric changes of atomic configuration for vibrational circular dichroism

    NARCIS (Netherlands)

    Heshmat, M.; Nicu, V.P.; Baerends, E.J.

    2012-01-01

    We study systematically the vibrational circular dichroism (VCD) spectra of the conformers of a simple chiral molecule, with one chiral carbon and an "achiral" alkyl substituent of varying length. The vibrational modes can be divided into a group involving the chiral center and its direct neighbors

  8. Molecular dynamics simulations on the conformational transitions from the GA 98 (GA 88) to GB 98 (GB 88) proteins.

    Science.gov (United States)

    Song, Chunnian; Wang, Qing; Xue, Tuo; Wang, Yan; Chen, Guangju

    2016-12-01

    We performed conventional and targeted molecular dynamics simulations to address the dynamic transition mechanisms of the conformational transitions from the GA 98 protein with only 1 mutation of Leu45Tyr to GB 98 and from the GA 88 protein with 7 mutations of Gly24Ala, Ile25Thr, Ile30Phe, Ile33Tyr, Leu45Tyr, Ile49Thr, and Leu50Lys to GB 88. The results show that the conformational transition mechanism from the mutated 3α GA 98 (GA 88) state to the α+4β GB 98 (GB 88) state via several intermediate conformations involves the bending of loops at the N and C termini firstly, the unfolding of αA and αC, then the traversing of αB, and the formation of the 4β layer with the conversion of the hydrophobic core. The bending of loops at the N and C termini and the formation of the crucial transition conformation with the full unfolded structure are key factors in their transition processes. The communication of the interaction network, the bending directions of loops, and the traversing site of αB in the transition of GA 98 to GB 98 are markedly different from those in GA 88 to GB 88 because of the different mutated residues. The analysis of the correlations and the calculated mass center distances between some segments further supported their conformational transition mechanisms. These results could help people to better understand the Paracelsus challenge. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  9. DNA conformational transitions inferred from re-evaluation of m|Fo| - D|Fc| electron-density maps.

    Science.gov (United States)

    Sunami, Tomoko; Chatake, Toshiyuki; Kono, Hidetoshi

    2017-07-01

    Conformational flexibility of DNA plays important roles in biological processes such as transcriptional regulation and DNA packaging etc. To understand the mechanisms of these processes, it is important to analyse when, where and how DNA shows conformational variations. Recent analyses have indicated that conventional refinement methods do not always provide accurate models of crystallographic heterogeneities and that some information on polymorphism has been overlooked in previous crystallographic studies. In the present study, the m|Fo| - D|Fc| electron-density maps of double-helical DNA crystal structures were calculated at a resolution equal to or better than 1.5 Å and potential conformational transitions were found in 27% of DNA phosphates. Detailed analyses of the m|Fo| - D|Fc| peaks indicated that some of these unassigned densities correspond to ZI ↔ ZII or A/B → BI conformational transitions. A relationship was also found between ZI/ZII transitions and metal coordination in Z-DNA from the detected peaks. The present study highlights that frequent transitions of phosphate backbones occur even in crystals and that some of these transitions are affected by the local molecular environment.

  10. Strong Coupling on a Forbidden Transition in Strontium and Nondestructive Atom Counting

    CERN Document Server

    Norcia, Matthew A

    2015-01-01

    We observe strong collective coupling between an optical cavity and the forbidden spin singlet to triplet optical transition $^1$S$_0$ to $^3$P$_1$ in an ensemble of $^{88}$Sr. Despite the transition being 1000 times weaker than a typical dipole transition, we observe a well resolved vacuum Rabi splitting. We use the observed vacuum Rabi splitting to make non-destructive measurements of atomic population with the equivalent of projection-noise limited sensitivity and minimal heating ($<0.01$ photon recoils/atom). This technique may be used to enhance the performance of optical lattice clocks by generating entangled states and reducing dead time.

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

    Energy Technology Data Exchange (ETDEWEB)

    Baudon, J., E-mail: jacques.baudon@univ-paris13.fr [Laboratoire de Physique des Lasers, CNRS-UMR 7538, Universite Paris 13, Villetaneuse (France); Hamamda, M. [Laboratoire de Physique des Lasers, CNRS-UMR 7538, Universite Paris 13, Villetaneuse (France); Boustimi, M. [Umm Al-Qura University, Makkah (Saudi Arabia); Bocvarski, V. [Institute of Physics, University of Belgrade (Serbia); Taillandier-Loize, T.; Dutier, G.; Perales, F.; Ducloy, M. [Laboratoire de Physique des Lasers, CNRS-UMR 7538, Universite Paris 13, Villetaneuse (France)

    2012-05-15

    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{sup Asterisk-Operator }, Kr{sup Asterisk-Operator }), rovibrational transitions in N{sub 2}{sup Asterisk-Operator }({sup 3}{Sigma}{sub u}{sup +}), transitions among magnetic sub-levels in the presence of a magnetic field.

  12. Ranking the Stability of Transition-Metal Complexes by On-Surface Atom Exchange.

    Science.gov (United States)

    Rieger, Alexandra; Schnidrig, Stephan; Probst, Benjamin; Ernst, Karl-Heinz; Wäckerlin, Christian

    2017-12-21

    Surface-adsorbed macrocycles exhibit a number of interesting physical and chemical properties; many of them are determined by their transition-metal centers. The hierarchical exchange of the central metal atom in such surface-adsorbed complexes is demonstrated, specifically in the porphyrin-like macrocycle pyrphyrin adsorbed on Cu(111). Using scanning tunneling microscopy and X-ray photoelectron spectroscopy, we show that Cu as central metal atom is easily exchanged with Ni or Fe atoms supplied in trace amounts to the surface. Atom exchange of Ni centers with Fe atoms also occurs, with moderate yield. These results allow ranking the stability of the surface-adsorbed Cu, Ni, and Fe complexes. The fact that the atom exchange occurs at 423 K shows that surface-adsorbed macrocycles can be surprisingly easily transformed.

  13. Probing an Excited-State Atomic Transition Using Hyperfine Quantum Beat Spectroscopy

    CERN Document Server

    Wade, Christopher G; Keaveney, James; Adams, Charles S; Weatherill, Kevin J

    2014-01-01

    We describe a method to observe the dynamics of an excited-state transition in a room temperature atomic vapor using hyperfine quantum beats. Our experiment using cesium atoms consists of a pulsed excitation of the D2 transition, and continuous-wave driving of an excited-state transition from the 6P$_{3/2}$ state to the 7S$_{1/2}$ state. We observe quantum beats in the fluorescence from the 6P$_{3/2}$ state which are modified by the driving of the excited-state transition. The Fourier spectrum of the beat signal yields evidence of Autler-Townes splitting of the 6P$_{3/2}$, F = 5 hyperfine level and Rabi oscillations on the excited-state transition. A detailed model provides qualitative agreement with the data, giving insight to the physical processes involved.

  14. Conformal and atomic characterization of ultrathin CdSe platelets with a helical shape

    NARCIS (Netherlands)

    Hutter, Eline M.; Bladt, Eva; Goris, Bart; Pietra, Francesca; Van Der Bok, Johanna C.; Boneschanscher, Mark P.; De Mello Donegá, Celso; Bals, Sara; Vanmaekelbergh, Daniël

    2014-01-01

    Currently, ultrathin colloidal CdSe semiconductor nanoplatelets (NPLs) with a uniform thickness that is controllable up to the atomic scale can be prepared. The optical properties of these 2D semiconductor systems are the subject of extensive research. Here, we reveal their natural morphology and

  15. Tight conformational coupling between the domains of the enterotoxigenic Escherichia coli fimbrial adhesin CfaE regulates binding state transition.

    Science.gov (United States)

    Liu, Yang; Esser, Lothar; Interlandi, Gianluca; Kisiela, Dagmara I; Tchesnokova, Veronika; Thomas, Wendy E; Sokurenko, Evgeni; Xia, Di; Savarino, Stephen J

    2013-04-05

    CfaE, the tip adhesin of enterotoxigenic Escherichia coli colonization factor antigen I fimbriae, initiates binding of this enteropathogen to the small intestine. It comprises stacked β-sandwich adhesin (AD) and pilin (PD) domains, with the putative receptor-binding pocket at one pole and an equatorial interdomain interface. CfaE binding to erythrocytes is enhanced by application of moderate shear stress. A G168D replacement along the AD facing the CfaE interdomain region was previously shown to decrease the dependence on shear by increasing binding at lower shear forces. To elucidate the structural basis for this functional change, we studied the properties of CfaE G168D (with a self-complemented donor strand) and solved its crystal structure at 2.6 Å resolution. Compared with native CfaE, CfaE G168D showed a downward shift in peak erythrocyte binding under shear stress and greater binding under static conditions. The thermal melting transition of CfaE G168D occurred 10 °C below that of CfaE. Compared with CfaE, the atomic structure of CfaE G168D revealed a 36% reduction in the buried surface area at the interdomain interface. Despite the location of this single modification in the AD, CfaE G168D exhibited structural derangements only in the adjoining PD compared with CfaE. In molecular dynamics simulations, the G168D mutation was associated with weakened interdomain interactions under tensile force. Taken together, these findings indicate that the AD and PD of CfaE are conformationally tightly coupled and support the hypothesis that opening of the interface plays a critical modulatory role in the allosteric activation of CfaE.

  16. Polyelectrolyte conformational transition in aqueous solvent mixture influenced by hydrophobic interactions and hydrogen bonding effects: PAA-water-ethanol.

    Science.gov (United States)

    Sappidi, Praveenkumar; Natarajan, Upendra

    2016-03-01

    Molecular dynamics simulations of poly(acrylic acid) PAA chain in water-ethanol mixture were performed for un-ionized and ionized cases at different degree-of-ionization 0%, 80% and 100% of PAA chain by Na(+) counter-ions and co-solvent (ethanol) concentration in the range 0-90vol% ethanol. Aspects of structure and dynamics were investigated via atom pair correlation functions, number and relaxation of hydrogen bonds, nearest-neighbor coordination numbers, and dihedral angle distribution function for back-bone and side-groups of the chain. With increase in ethanol concentration, chain swelling is observed for un-ionized chain (f=0) and on the contrary chain shrinkage is observed for partially and fully ionized cases (i.e., f=0.8 and 1). For un-ionized PAA, with increase in ethanol fraction ϕeth the number of PAA-ethanol hydrogen bonds increases while PAA-water decreases. Increase in ϕeth leads to PAA chain expansion for un-ionized case and chain shrinkage for ionized case, in agreement with experimental observations on this system. For ionized-PAA case, chain shrinkage is found to be influenced by intermolecular hydrogen bonding with water as well as ethanol. The localization of ethanol molecules near the un-ionized PAA backbone at higher levels of ethanol is facilitated by a displacement of water molecules indicating presence of specific ethanol hydration shell, as confirmed by results of the RDF curves and coordination number calculations. This behavior, controlled by hydrogen bonding provides a significant contribution to such a conformational transition behavior of the polyelectrolyte chain. The interactions between counter-ions and charges on the PAA chain also influence chain collapse. The underlying origins of polyelectrolyte chain collapse in water-alcohol mixtures are brought out for the first time via explicit MD simulations by this study. Copyright © 2016 Elsevier Inc. All rights reserved.

  17. Further investigation on potassium-induced conformation transition of Nephila spidroin film with two-dimensional infrared correlation spectroscopy.

    Science.gov (United States)

    Peng, Xianneng; Shao, Zhengzhong; Chen, Xin; Knight, David P; Wu, Peiyi; Vollrath, Fritz

    2005-01-01

    We used two-dimensional (2D) correlation infrared spectroscopy to study further the potassium-induced conformation transition in Nephila spidroin films. It provided increased resolution and important new information on the sequence of events in the conformation transition process, showing that beta-sheet formed from the helical component before they formed from random coil. It also showed more evidence that formation of the 1691 cm(-1) (turn/bend) peak did not proceed with the same kinetics as the 1620 cm(-1) (antiparallel beta-sheet component) one, so we attribute the 1691 cm(-1) peak to turns which formed with different kinetics as the antiparallel beta-sheets. We present a single coherent and detailed hypothesis for the assembly and secondary structural transition of silk proteins in vivo and in vitro based on our findings and on evidence from other laboratories.

  18. Structural factors that control conformational transitions and serotype specificity in type 3 poliovirus.

    Science.gov (United States)

    Filman, D J; Syed, R; Chow, M; Macadam, A J; Minor, P D; Hogle, J M

    1989-01-01

    The three-dimensional structure of the Sabin strain of type 3 poliovirus has been determined at 2.4 A resolution. Significant structural differences with the Mahoney strain of type 1 poliovirus are confined to loops and terminal extensions of the capsid proteins, occur in all of the major antigenic sites of the virion and typically involve insertions, deletions or the replacement of prolines. Several newly identified components of the structure participate in assembly-dependent interactions which are relevant to the biologically important processes of viral assembly and uncoating. These include two sites of lipid substitution, two putative nucleotides and a beta sheet formed by the N-termini of capsid proteins VP4 and VP1. The structure provides an explanation for the temperature sensitive phenotype of the P3/Sabin strain. Amino acids that regulate temperature sensitivity in type 3 poliovirus are located in the interfaces between promoters, in the binding site for a lipid substituent and in an assembly-dependent extended beta sheet that stabilizes the association of pentamers. Several lines of evidence indicate that these structural components also control conformational transitions at various stages of the viral life cycle. Images PMID:2548847

  19. Tuning the electronic and magnetic properties of borophene by 3d transition-metal atom adsorption

    Science.gov (United States)

    Li, J. Y.; Lv, H. Y.; Lu, W. J.; Shao, D. F.; Xiao, R. C.; Sun, Y. P.

    2016-12-01

    The electronic and magnetic properties of borophene functionalized by 3d transition metal (TM) atom adsorption are investigated by using first-principles calculations. The results show that the 3d TM atoms can be adsorbed on borophene with high binding energies ranging between 5.9 and 8.3 eV. Interestingly, the originally nonmagnetic borophene tends to be ferromagnetic when Ti, V, Cr, Mn, and Fe atoms are adsorbed, and the magnetic moments are dominated by the TM atoms. The origin of the ferromagnetism is discussed based on the Stoner criterion. Our results indicate that the magnetic properties of borophene can be effectively tuned through the adsorption of 3d TM atoms, which could have promising applications in spintronics and nanoelectronics.

  20. Temperature-Dependent Conformational Properties of Human Neuronal Calcium Sensor-1 Protein Revealed by All-Atom Simulations.

    Science.gov (United States)

    Zhu, Yuzhen; Ma, Buyong; Qi, Ruxi; Nussinov, Ruth; Zhang, Qingwen

    2016-04-14

    Neuronal calcium sensor-1 (NCS-1) protein has orthologues from Saccharomyces cerevisiae to human with highly conserved amino acid sequences. NCS-1 is an important factor controlling the animal's response to temperature change. This leads us to investigate the temperature effects on the conformational dynamics of human NCS-1 at 310 and 316 K by all-atom molecular dynamics (MD) simulations and dynamic community network analysis. Four independent 500 ns MD simulations show that secondary structure content at 316 K is similar to that at 310 K, whereas the global protein structure is expanded. Loop 3 (L3) adopts an extended state occuping the hydrophobic crevice, and the number of suboptimal communication paths between residue D176 and V190 is reduced at 316 K. The dynamic community network analysis suggests that the interdomain correlation is weakened, and the intradomain coupling is strengthened at 316 K. The elevated temperature reduces the number of the salt bridges, especially in C-domain. This study suggests that the elevated temperature affects the conformational dynamics of human NCS-1 protein. Comparison of the structural dynamics of R102Q mutant and Δ176-190 truncated NCS-1 suggests that the structural and dynamical response of NCS-1 protein to elevated temperature may be one of its intrinsic functional properties.

  1. Tuning the electronic and magnetic properties of borophene by 3d transition-metal atom adsorption

    Energy Technology Data Exchange (ETDEWEB)

    Li, J.Y. [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China); University of Science and Technology of China, Hefei, 230026 (China); Lv, H.Y. [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China); Lu, W.J., E-mail: wjlu@issp.ac.cn [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China); Shao, D.F. [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China); Xiao, R.C. [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China); University of Science and Technology of China, Hefei, 230026 (China); Sun, Y.P. [Key Laboratory of Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China); High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031 (China)

    2016-12-01

    Highlights: • Electronic and magnetic properties of borophene can be effectively tuned by the adsorption of 3d transition metal atoms. • The borophene tends to be ferromagnetic when Ti, V, Cr, Mn, and Fe atoms are adsorbed. • The origin of the ferromagnetism is analyzed based on the Stoner itinerant ferromagnetic model. - Abstract: The electronic and magnetic properties of borophene functionalized by 3d transition metal (TM) atom adsorption are investigated by using first-principles calculations. The results show that the 3d TM atoms can be adsorbed on borophene with high binding energies ranging between 5.9 and 8.3 eV. Interestingly, the originally nonmagnetic borophene tends to be ferromagnetic when Ti, V, Cr, Mn, and Fe atoms are adsorbed, and the magnetic moments are dominated by the TM atoms. The origin of the ferromagnetism is discussed based on the Stoner criterion. Our results indicate that the magnetic properties of borophene can be effectively tuned through the adsorption of 3d TM atoms, which could have promising applications in spintronics and nanoelectronics.

  2. Precision measurement of the 1S-2S transition in atomic hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Parthey, Christian G.; Matveev, Arthur; Alnis, Janis; Beyer, Axel; Kolachevsky, Nikolai; Pohl, Randolf; Udem, Thomas [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); Haensch, Theodor W. [Max-Planck-Institut fuer Quantenoptik, 85748 Garching (Germany); Ludwig-Maximilians-Universitaet, 80799 Muenchen (Germany)

    2011-07-01

    Precision spectroscopy of the 1S-2S transition in atomic hydrogen has been used to test quantum electrodynamics (QED), determine the Rydberg constant and the proton charge radius. It can also be used to set limits on possible Lorentz-boost invariance violations. Here we report on a new measurement of the 1S-2S transition pushing the uncertainty to the 10{sup -15} level.

  3. 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.

  4. Local Softening as a Universal Feature of Conformational Transitions of Biological Macromolecules

    OpenAIRE

    Qu, Hao

    2012-01-01

    Conformational changes are essential to biological macromolecules because they are tightly coupled to function and dynamics of these macromolecules. In cells, under most occasions, the macromolecules are deformed rather than in free states as in solution, due to mechanical stresses exposed. It is therefore of great interest and importance to understand conformational changes associated with the macromolecules. More in details, the conformational changes of two types of macromolecules, DNA and...

  5. Glutamate dehydrogenase of the unicellular green alga Scenedesmus acutus : Substrate-induced conformational transition.

    Science.gov (United States)

    Shatilov, V R; Sund, H

    1983-07-01

    The coenzyme-non-specific glutamate dehydrogenase (EC 1.4.1.3) from Scenedesmus acutus in inhibited by p-hydroxymercuribenzoate only in the deamination reaction. From this result and from its stability in the presence of urea it is concluded that this enzyme exhibits and equilibrium between three conformations: aminating and deaminating conformations induced by NADH-2-oxoglutarate and NAD(+)-glutamate, respectively, and the "native" conformation in the absence of substrates.

  6. Interaction of 3d transition metal atoms with charged ion projectiles from Electron Nuclear Dynamics computation

    Science.gov (United States)

    Hagelberg, Frank

    2003-03-01

    Computational results on atomic scattering between charged projectiles and transition metal target atoms are presented. This work aims at obtaining detailed information about charge, spin and energy transfer processes that occur between the interacting particles. An in-depth understanding of these phenomena is expected to provide a theoretical basis for the interpretation of various types of ion beam experiments, ranging from gas phase chromatography to spectroscopic observations of fast ions in ferromagnetic media. This contribution focuses on the scattering of light projectiles ranging from He to O, that are prepared in various initial charge states, by 3d transition metal atoms. The presented computations are performed in the framework of Electron Nuclear Dynamics (END)^1 theory which incorporates the coupling between electronic and nuclear degrees of freedom without reliance on the computationally cumbersome and frequently intractable determination of potential energy surfaces. In the present application of END theory to ion - transition metal atom scattering, a supermolecule approach is utilized in conjunction with a spin-unrestricted single determinantal wave function describing the electronic system. Integral scattering, charge and spin exchange cross sections are discussed as functions of the elementary parameters of the problem, such as projectile and target atomic numbers as well as projectile charge and initial kinetic energy. ^1 E.Deumens, A.Diz, R.Longo, Y.Oehrn, Rev.Mod.Phys. 66, 917 (1994)

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

    Indian Academy of Sciences (India)

    In calculations, various configuration sets are considered for including correlation effects. We have considered the valence–valence correlation and used the. MCHF and HFR atomic codes [14,15] in .... absorption or emission of electromagnetic radiations in transitions between energy levels. For absorption, the oscillator ...

  8. Strong coupling on a forbidden transition in strontium and nondestructive atom counting

    Science.gov (United States)

    Norcia, Matthew A.; Thompson, James K.

    2016-02-01

    We observe strong collective coupling between an optical cavity and the forbidden spin singlet to triplet optical transition S10 to P31 in an ensemble of 88Sr. Despite the transition being 1000 times weaker than a typical dipole transition, we observe a well-resolved vacuum Rabi splitting. We use the observed vacuum Rabi splitting to make nondestructive measurements of atomic population with the equivalent of projection-noise limited sensitivity between subsequent measurements and with minimal heating [lattice clocks by generating entangled states and reducing dead time.

  9. 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

  10. 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.

  11. Assessing Uncertainties of Theoretical Atomic Transition Probabilities with Monte Carlo Random Trials

    Directory of Open Access Journals (Sweden)

    Alexander Kramida

    2014-04-01

    Full Text Available This paper suggests a method of evaluation of uncertainties in calculated transition probabilities by randomly varying parameters of an atomic code and comparing the results. A control code has been written to randomly vary the input parameters with a normal statistical distribution around initial values with a certain standard deviation. For this particular implementation, Cowan’s suite of atomic codes (R.D. Cowan, The Theory of Atomic Structure and Spectra, Berkeley, CA: University of California Press, 1981 was used to calculate radiative rates of magnetic-dipole and electric-quadrupole transitions within the ground configuration of titanium-like iron, Fe V. The Slater parameters used in the calculations were adjusted to fit experimental energy levels with Cowan’s least-squares fitting program, RCE. The standard deviations of the fitted parameters were used as input of the control code providing the distribution widths of random trials for these parameters. Propagation of errors through the matrix diagonalization and summation of basis state expansions leads to significant variations in the resulting transition rates. These variations vastly differ in their magnitude for different transitions, depending on their sensitivity to errors in parameters. With this method, the rate uncertainty can be individually assessed for each calculated transition.

  12. Narrow-linewidth cooling of $^{6}$Li atoms using the 2S-3P transition

    CERN Document Server

    Chen, Hao-Ze; Wu, Yu-Ping; Liu, Xiang-Pei; Wang, Xiao-Qiong; Chen, Yu-Ao; Pan, Jian-Wei

    2016-01-01

    We report on a narrow-linewidth cooling of $^{6}$Li atoms using the $2S_{1/2}\\to 3P_{3/2}$ transition in the ultraviolet (UV) wavelength regime. By combining the traditional red magneto-optical trap (MOT) at 671 nm and the UV MOT at 323 nm, we obtain a cold sample of $1.3\\times10^9$ atoms with a temperature of 58 $\\mu$K. Furthermore, we demonstrate a high efficiency magnetic transport for $^{6}$Li atoms with the help of the UV MOT. Finally, we obtain $8.1\\times10^8$ atoms with a temperature of 296 $\\mu$K at a magnetic gradient of 198 G/cm in the science chamber with a good vacuum environment and large optical access.

  13. Ionic Hamiltonians for transition metal atoms: effective exchange coupling and Kondo temperature

    Science.gov (United States)

    Flores, F.; Goldberg, E. C.

    2017-02-01

    An ionic Hamiltonian for describing the interaction between a metal and a d-shell transition metal atom having an orbital singlet state is introduced and its properties analyzed using the Schrieffer-Wolf transformation (exchange coupling) and the poor man’s scaling method (Kondo temperature). We find that the effective exchange coupling between the metal and the atom has an antiferromagnetic or a ferromagnetic interaction depending on the kind of atomic fluctuations, either S\\to S-1/2 or S\\to S+1/2 , associated with the metal-atom coupling. We present a general scheme for all those processes and calculate, for the antiferromagnetic interaction, the corresponding Kondo-temperature.

  14. Ion-Controlled Conformational Dynamics in the Outward-Open Transition from an Occluded State of LeuT

    Science.gov (United States)

    Zhao, Chunfeng; Stolzenberg, Sebastian; Gracia, Luis; Weinstein, Harel; Noskov, Sergei; Shi, Lei

    2012-01-01

    Neurotransmitter:sodium symporter (NSS) proteins are secondary Na+-driven active transporters that terminate neurotransmission by substrate uptake. Despite the availability of high-resolution crystal structures of a bacterial homolog of NSSs—Leucine Transporter (LeuT)—and extensive computational and experimental structure-function studies, unanswered questions remain regarding the transport mechanisms. We used microsecond atomistic molecular-dynamics (MD) simulations and free-energy computations to reveal ion-controlled conformational dynamics of LeuT in relation to binding affinity and selectivity of the more extracellularly positioned Na+ binding site (Na1 site). In the course of MD simulations starting from the occluded state with bound Na+, but in the absence of substrate, we find a spontaneous transition of the extracellular vestibule of LeuT into an outward-open conformation. The outward opening is enhanced by the absence of Na1 and modulated by the protonation state of the Na1-associated Glu-290. Consistently, the Na+ affinity for the Na1 site is inversely correlated with the extent of outward-open character and is lower than in the occluded state with bound substrate; however, the Na1 site retains its selectivity for Na+ over K+ in such conformational transitions. To the best of our knowledge, our findings shed new light on the Na+-driven transport cycle and on the symmetry in structural rearrangements for outward- and inward-open transitions. PMID:23009837

  15. 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.

  16. Dynamics of the His79-heme Alkaline Transition of Yeast Iso-1-cytochrome c Probed by Conformationally-gated Electron Transfer with Co(II)bis(terpyridine)†

    Science.gov (United States)

    Cherney, Melisa M.; Junior, Carolyn C.; Bergquist, Bryan B.; Bowler, Bruce E.

    2013-01-01

    Alkaline conformers of cytochrome c may be involved in both its electron transport and apoptotic functions. We use cobalt(II)bis(terpyridine), Co(terpy)22+, as a reagent for conformationally-gated electron transfer (gated ET) experiments to study the alkaline conformational transition of K79H variants of yeast iso-1-cytochrome c expressed in Escherichia coli, WT*K79H, with alanine at position 72, and Saccharomyces cerevisiae, yK79H, with trimethyllysine (Tml) at position 72. Co(terpy)22+ is well-suited to the 100 ms to 1 s time scale of the His79-mediated alkaline conformational transition of these variants. Reduction of the His79-heme alkaline conformer by Co(terpy)22+ occurs primarily by gated ET, which involves conversion to the native state followed by reduction, with a small fraction of the His79- heme alkaline conformer directly reduced by Co(terpy)22+. The gated ET experiments show that the mechanism of formation of the His79-heme alkaline conformer involves only two ionizable groups. In previous work, we showed that the mechanism of the His73-mediated alkaline conformational transition requires three ionizable groups. Thus, the mechanism of heme crevice opening depends upon the position of the ligand mediating the process. The microscopic rate constants provided by gated ET studies show that mutation of Tml72 (yK79H variant) in the heme crevice loop to Ala72 (WT*K79H variant) affects the dynamics of heme crevice opening through a small destabilization of both the native conformer and the transition state relative to the His79-heme alkaline conformer. Previous pH jump data had indicated that the Tml72→Ala mutation primarily stabilized the transition state for the His79-mediated alkaline conformational transition. PMID:23899348

  17. Circular dichroism in free-free transitions of high energy electron-atom scattering

    CERN Document Server

    Cionga, Aurelia; Zloh, Gabriela; 10.1103/PhysRevA.62.063406

    2013-01-01

    We consider high energy electron scattering by hydrogen atoms in the presence of a laser field of moderate power and higher frequencies. If the field is a superposition of a linearly and a circularly polarized laser beam in a particular configuration, then we can show that circular dichroism in two photon transitions can be observed not only for the differential but also for the integrated cross sections, provided the laser-dressing of the atomic target is treated in second order perturbation theory and the coupling between hydrogenic bound and continuum states is involved.

  18. Gel--sol transition in kappa-carrageenan systems: microviscosity of hydrophobic microdomains, dynamic rheology and molecular conformation.

    Science.gov (United States)

    Hugerth, A; Nilsson, S; Sundelöf, L O

    1999-10-01

    The effect of gel-sol transition in kappa-carrageenan systems on the microviscosity of hydrophobic microdomains, as well as its relation to macroscopic rheology and molecular conformation, was studied in kappa-carrageenan systems. The microdomains were probed by 1,3-di(-1-pyrenyl)propane (P3P) for which the excimer intensity (Ie) provides relative measures of the microviscosity in the immediate probe surroundings. In particular the applicability of P3P to monitor the gel--sol transition was proved, the results showing a dramatic decrease in microviscosity in the vicinity of the transition point. The corresponding changes in rheological properties and carrageenan conformation were investigated by dynamic viscometry (DV) and optical rotation (OR), respectively. The temperature of onset of the transition as indicated by the microviscosity data (T0) was found to correlate well with the OR and DV-results. The application of microviscosity and OR-measurements allowed an estimation of the helical content at T0 to be determined. P3P-data indicate a microenvironment viscosity for the probe sites in the kappa-carrageenan system comparable to that found in SDS micelles.

  19. Excitonlike exchange in two-photon transitions of pairs of cold Rb Rydberg atoms

    Science.gov (United States)

    Lee, Jeonghun; Kongkhambut, Phatthamon; Gallagher, T. F.

    2017-12-01

    We have observed an excitonlike exchange in two-photon microwave transitions between pairs of cold Rb Rydberg atoms, specifically, transitions in which a n s1 /2n s1 /2 pair undergoes the transition to the n p1 /2n p3 /2 and n p3 /2n p1 /2 states. This transition occurs due to the excitonlike n s1 /2n pj↔n pjn s1 /2 exchange in the intermediate states, and the process can be thought of as a Förster resonant energy transfer between Floquet, or dressed, states. In addition, the measurements provide clear evidence of the importance of the three-dimensional nature of the dipole-dipole interaction.

  20. 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

  1. Landau-Zener transition in photoassociation of cold atoms: strong interaction limit

    Energy Technology Data Exchange (ETDEWEB)

    Ishkhanyan, Artur [Engineering Center of NAS of Armenia, Ashtarak-2, 0203 (Armenia); Javanainen, Juha [University of Connecticut, Storrs, CT 06269-3046 (United States); Nakamura, Hiroki [Institute for Molecular Science, Okazaki 444-8585 (Japan)

    2006-12-01

    The nonlinear Landau-Zener problem for two-mode photoassociation of cold atoms is studied. Based on an exact nonlinear Volterra integral equation for molecular state probability, a limit nonlinear first-order differential equation is applied to construct the first-order approximation to the solution of the problem at a strong coupling limit. An accurate approximate expression for the final transition probability to the molecular state is derived. The non-transition probability turns out to be inversely proportional to the Landau-Zener parameter in contrast to the linear two-state case when the dependence is exponential.

  2. 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.

  3. 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

    wavelength-tuning mechanisms that allow a coarse tuning to either the cesium or rubidium wavelength, with subsequent continuous fine-tuning to the desired transition. As a demonstration of the functionality of the source, we performed a heralded single-photon measurement of the atomic decay. We present......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...... problem for most available sources of quantum light. Here we demonstrate the coupling of alkali dipole transitions with a tunable source of photon pairs. Our source is based on spontaneous parametric downconversion in a triply resonant whispering gallery mode resonator. For this, we have developed novel...

  4. 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.

  5. Anomalous Insulator-Metal Transition in Boron Nitride-Graphene Hybrid Atomic Layers

    Science.gov (United States)

    2012-08-13

    hexagonal boron nitride (h-BNC) constitute a new kind of disordered 2D electronic system. Magnetoelectric transport measurements performed at low...Magnetoelectric transport measurements performed at low temperature in vapor phase synthesized h-BNC atomic layers show a clear and anomalous transition from...Tallahassee, Florida 32310, USA 3Nano-Bio Spectroscopy Group and ETSF Scientific Development Centre, Departamento de Fı́sica de Materiales , Centro de Fı́sica

  6. Role of the Subunits Interactions in the Conformational Transitions in Adult Human Hemoglobin: an Explicit Solvent Molecular Dynamics Study

    CERN Document Server

    Yusuff, Olaniyi K; Bussi, Giovanni; Raugei, Simone

    2012-01-01

    Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solutes present under physiological conditions. In the present study, the dynamical and quaternary structural changes occurring in two unligated (deoxy-) T structures, and two fully ligated (oxy-) R, R2 structures of adult human hemoglobin were investigated with molecular dynamics. It is shown that, in the sub-microsecond time scale, there is no marked difference in the global dynamics of the amino acids residues in both the oxy- and the deoxy- forms of the individual structures. In addition, the R, R2 are relatively stable and do not present quaternary conformational changes within the time scale of our simulations while the T structure is dynamically more flexible and exhibited the T\\rightarrow R quaternary conformational transition, which is propagated by the relative rotation of the residues at the {\\alpha}1{\\beta}2 and {\\alpha}2{\\b...

  7. Ultrathin and Atomically Flat Transition-Metal Oxide: Promising Building Blocks for Metal-Insulator Electronics.

    Science.gov (United States)

    Cui, Qingsong; Sakhdari, Maryam; Chamlagain, Bhim; Chuang, Hsun-Jen; Liu, Yi; Cheng, Mark Ming-Cheng; Zhou, Zhixian; Chen, Pai-Yen

    2016-12-21

    We present a new and viable template-assisted thermal synthesis method for preparing amorphous ultrathin transition-metal oxides (TMOs) such as TiO2 and Ta2O5, which are converted from crystalline two-dimensional (2D) transition-metal dichalcogenides (TMDs) down to a few atomic layers. X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and scanning transmission electron microscopy (STEM) were used to characterize the chemical composition and bonding, surface morphology, and atomic structure of these ultrathin amorphous materials to validate the effectiveness of our synthesis approach. Furthermore, we have fabricated metal-insulator-metal (MIM) diodes using the TiO2 and Ta2O5 as ultrathin insulating layers with low potential barrier heights. Our MIM diodes show a clear transition from direct tunneling to Fowler-Nordheim tunneling, which was not observed in previously reported MIM diodes with TiO2 or Ta2O5 as the insulating layer. We attribute the improved performance of our MIM diodes to the excellent flatness and low pinhole/defect densities in our TMO insulting layers converted from 2D TMDs, which enable the low-threshold and controllable electron tunneling transport. We envision that it is possible to use the ultrathin TMOs converted from 2D TMDs as the insulating layer of a wide variety of metal-insulator and field-effect electronic devices for various applications ranging from microwave mixing, parametric conversion, infrared photodetection, emissive energy harvesting, to ultrafast electronic switching.

  8. Effect of Doped Transition Metal Atoms on Structure and Nonlinear Optical Properties of Decaborane

    Science.gov (United States)

    Beigi, Motahareh Noormohammad; Shamlouei, Hamid Reza; Omidi, Masoome; Jalalvandi, Esmat

    2017-11-01

    In this study, electrical and nonlinear optical properties of decaborane (B10H14) were investigated using the density functional theory method when transition metal atoms (scandium, titanium and vanadium) were doped on the structure. Hydrogen and boron atoms in B10H14 were substituted by the transition metals. This doping process resulted in a drastic reduction in the energy gap of decaborane. First, the hyperpolarizability ( β 0) of B10H14 dramatically increased in the presence of titanium (Ti) in the place of hydrogen atoms. The highest value of β 0 (≈ 98,387.90 a.u.) was obtained for B10TiH13 (in the S3 position) and calculated to be 1700 times larger than the β 0 value for B10H14 (≈57.82 a.u.). Therefore, the Ti-doped systems showed a significantly larger non-linear optical (NLO) response than the other studied transition metals, suggesting that its system might be useful as a promising NLO material.

  9. Effect of graphene oxide on the conformational transitions of amyloid beta peptide: A molecular dynamics simulation study.

    Science.gov (United States)

    Baweja, Lokesh; Balamurugan, Kanagasabai; Subramanian, Venkatesan; Dhawan, Alok

    2015-09-01

    The interactions between nanomaterials (NMs) and amyloid proteins are central to the nanotechnology-based diagnostics and therapy in neurodegenerative disorders such as Alzheimer's and Parkinson's. Graphene oxide (GO) and its derivatives have shown to modulate the aggregation pattern of disease causing amyloid beta (Aβ) peptide. However, the mechanism is still not well understood. Using molecular dynamics simulations, the effect of graphene oxide (GO) and reduced graphene oxide (rGO) having carbon:oxygen ratio of 4:1 and 10:1, respectively, on the conformational transitions (alpha-helix to beta-sheet) and the dynamics of the peptide was investigated. GO and rGO decreased the beta-strand propensity of amino acid residues in Aβ. The peptide displayed different modes of adsorption on GO and rGO. The adsorption on GO was dominated by electrostatic interactions, whereas on rGO, both van der Waals and electrostatic interactions contributed in the adsorption of the peptide. Our study revealed that the slight increase in the hydrophobic patches on rGO made it more effective inhibitor of conformational transitions in the peptide. Alpha helix-beta sheet transition in Aβ peptide could be one of the plausible mechanism by which graphene oxide may inhibit amyloid fibrillation. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Residues in the gp41 Ectodomain Regulate HIV-1 Envelope Glycoprotein Conformational Transitions Induced by gp120-Directed Inhibitors.

    Science.gov (United States)

    Pacheco, Beatriz; Alsahafi, Nirmin; Debbeche, Olfa; Prévost, Jérémie; Ding, Shilei; Chapleau, Jean-Philippe; Herschhorn, Alon; Madani, Navid; Princiotto, Amy; Melillo, Bruno; Gu, Christopher; Zeng, Xin; Mao, Youdong; Smith, Amos B; Sodroski, Joseph; Finzi, Andrés

    2017-03-01

    Interactions between the gp120 and gp41 subunits of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) trimer maintain the metastable unliganded form of the viral spike. Binding of gp120 to the receptor, CD4, changes the Env conformation to promote gp120 interaction with the second receptor, CCR5 or CXCR4. CD4 binding also induces the transformation of Env into the prehairpin intermediate, in which the gp41 heptad repeat 1 (HR1) coiled coil is assembled at the trimer axis. In nature, HIV-1 Envs must balance the requirements to maintain the noncovalent association of gp120 with gp41 and to evade the host antibody response with the need to respond to CD4 binding. Here we show that the gp41 HR1 region contributes to gp120 association with the unliganded Env trimer. Changes in particular amino acid residues in the gp41 HR1 region decreased the efficiency with which Env moved from the unliganded state. Thus, these gp41 changes decreased the sensitivity of HIV-1 to cold inactivation and ligands that require Env conformational changes to bind efficiently. Conversely, these gp41 changes increased HIV-1 sensitivity to small-molecule entry inhibitors that block Env conformational changes induced by CD4. Changes in particular gp41 HR1 amino acid residues can apparently affect the relative stability of the unliganded state and CD4-induced conformations. Thus, the gp41 HR1 region contributes to the association with gp120 and regulates Env transitions from the unliganded state to downstream conformations.IMPORTANCE The development of an efficient vaccine able to prevent HIV infection is a worldwide priority. Knowledge of the envelope glycoprotein structure and the conformational changes that occur after receptor engagement will help researchers to develop an immunogen able to elicit antibodies that block HIV-1 transmission. Here we identify residues in the HIV-1 transmembrane envelope glycoprotein that stabilize the unliganded state by modulating the

  11. Application of MCR-ALS to reveal intermediate conformations in the thermally induced α-β transition of poly-L-lysine monitored by FT-IR spectroscopy

    Science.gov (United States)

    Alcaráz, Mirta R.; Schwaighofer, Andreas; Goicoechea, Héctor; Lendl, Bernhard

    2017-10-01

    Temperature-induced conformational transitions of poly-L-lysine were monitored with Fourier-transform infrared (FT-IR) spectroscopy between 10 °C and 70 °C. Chemometric analysis of dynamic IR spectra was performed by multivariate curve analysis-alternating least squares (MCR-ALS) of the amide I‧ and amide II‧ spectral region. With this approach, the pure spectral and concentration profiles of the conformational transition were obtained. Beside the initial α-helical, the intermediate random coil/extended helices and the final β-sheet structure, an additional intermediate PLL conformation was identified and attributed to a transient β-sheet structure.

  12. 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.

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

    Directory of Open Access Journals (Sweden)

    Kim Hyunyoung Y.

    2018-01-01

    Full Text Available 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.

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

    KAUST Repository

    Wang, Ruiqi

    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.

  15. Probing Magnetism in 2D Molecular Networks after in Situ Metalation by Transition Metal Atoms.

    Science.gov (United States)

    Schouteden, K; Ivanova, Ts; Li, Z; Iancu, V; Janssens, E; Van Haesendonck, C

    2015-03-19

    Metalated molecules are the ideal building blocks for the bottom-up fabrication of, e.g., two-dimensional arrays of magnetic particles for spintronics applications. Compared to chemical synthesis, metalation after network formation by an atom beam can yield a higher degree of control and flexibility and allows for mixing of different types of magnetic atoms. We report on successful metalation of tetrapyridyl-porphyrins (TPyP) by Co and Cr atoms, as demonstrated by scanning tunneling microscopy experiments. For the metalation, large periodic networks formed by the TPyP molecules on a Ag(111) substrate are exposed in situ to an atom beam. Voltage-induced dehydrogenation experiments support the conclusion that the porphyrin macrocycle of the TPyP molecule incorporates one transition metal atom. The newly synthesized Co-TPyP and Cr-TPyP complexes exhibit striking differences in their electronic behavior, leading to a magnetic character for Cr-TPyP only as evidenced by Kondo resonance measurements.

  16. A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy

    OpenAIRE

    García-Sacristán, Ana; Moreno Molina, Miguel; Ariza-Mateos, Ascensión; López-Camacho, Elena; Jáudenes, Rosa M.; Vázquez, Luis; Gómez, Jordi; Martín-Gago, José A.; Briones, Carlos

    2014-01-01

    The 5? untranslated region of hepatitis C virus (HCV) genomic RNA contains an internal ribosome entry site (IRES) element, composed of domains II?IV, which is required for cap-independent translation initiation. Little information on the 3D structure of the whole functional HCV IRES is still available. Here, we use atomic force microscopy to visualize the HCV IRES conformation in its natural sequence context, which includes the upstream domain I and the essential, downstream domains V and VI....

  17. Adsorption of alkali, alkaline-earth, and 3d transition metal atoms on silicene

    Science.gov (United States)

    Sahin, H.; Peeters, F. M.

    2013-02-01

    The adsorption characteristics of alkali, alkaline-earth, and transition metal adatoms on silicene, a graphene-like monolayer structure of silicon are analyzed by means of first-principles calculations. In contrast to graphene, interaction between the metal atoms and the silicene surface is quite strong due to its highly reactive buckled hexagonal structure. In addition to structural properties, we also calculate the electronic band dispersion, net magnetic moment, charge transfer, work function, and dipole moment of the metal adsorbed silicene sheets. Alkali metals, Li, Na, and K, adsorb to hollow sites without any lattice distortion. As a consequence of the significant charge transfer from alkalis to silicene, metalization of silicene takes place. Trends directly related to atomic size, adsorption height, work function, and dipole moment of the silicene/alkali adatom system are also revealed. We found that the adsorption of alkaline-earth metals on silicene is entirely different from their adsorption on graphene. The adsorption of Be, Mg, and Ca turns silicene into a narrow gap semiconductor. Adsorption characteristics of eight transition metals Ti, V, Cr, Mn, Fe, Co, Mo, and W are also investigated. As a result of their partially occupied d orbital, transition metals show diverse structural, electronic, and magnetic properties. Upon the adsorption of transition metals, depending on the adatom type and atomic radius, the system can exhibit metal, half-metal, and semiconducting behavior. For all metal adsorbates, the direction of the charge transfer is from adsorbate to silicene, because of its high surface reactivity. Our results indicate that the reactive crystal structure of silicene provides a rich playground for functionalization at nanoscale.

  18. Characterizing rapid, activity-linked conformational transitions in proteins via sub-second hydrogen deuterium exchange mass spectrometry.

    Science.gov (United States)

    Resetca, Diana; Wilson, Derek J

    2013-11-01

    This review outlines the application of time-resolved electrospray ionization mass spectrometry (TRESI-MS) and hydrogen-deuterium exchange (HDX) to study rapid, activity-linked conformational transitions in proteins. The method is implemented on a microfluidic chip which incorporates all sample-handling steps required for a 'bottom-up' HDX workflow: a capillary mixer for sub-second HDX labeling, a static mixer for HDX quenching, a microreactor for rapid protein digestion, and on-chip electrospray. By combining short HDX labeling pulses with rapid digestion, this approach provides a detailed characterization of the structural transitions that occur during protein folding, ligand binding, post-translational modification and catalytic turnover in enzymes. This broad spectrum of applications in areas largely inaccessible to conventional techniques means that microfluidics-enabled TRESI-MS/HDX is a unique and powerful approach for investigating the dynamic basis of protein function. © 2013 FEBS.

  19. 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.

  20. Search for magnetism in transition metal atoms doped tetragonal graphene: A DFT approach

    Science.gov (United States)

    Chowdhury, Suman; Majumdar, Arnab; Jana, Debnarayan

    2017-11-01

    The discovery of different two-dimensional (2D) materials both theoretically and experimentally, can change the scenario of the current electronic industry because of their intriguing properties. Among the 2D materials, the first one which was discovered experimentally was graphene. In this work we have studied the electronic and magnetic properties of a new allotrope of disordered graphene, which is not hexagonal, rather possesses tetragonal symmetry known as T-graphene (TG). Density functional theory (DFT) has been thoroughly employed to study the relevant electronic properties. In previous works, it has been reported that pristine TG is non-magnetic. It is also known that, introducing transition metal (TM) atoms is a feasible way to control the electronic and magnetic properties. Here we have reported the relevant properties of four TM atoms i.e. Sc, V, Cr and Mn doped TG. From the defect formation energy study, it has been noticed that all the structures are endothermic in nature. For each case, we have found appreciable amount of magnetic moment. With increasing atomic weight of the dopant atom, the magnitude of the magnetic moment also increases. We have tried to explain this magnetic ordering with the help of spin-polarized partial density of states (PDOS). Controlling spin degrees of freedom is important for building spintronic devices. From that point of view, we hope this study will be useful to build TG based spintronic devices.

  1. 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.

  2. Generation of non-Abelian geometric phases in degenerate atomic transitions

    Science.gov (United States)

    Simeonov, Lachezar S.; Vitanov, Nikolay V.

    2017-09-01

    A popular quantum system, in which the Pancharatnam-Berry non-Abelian geometric phase has been generated and exploited, is the atomic tripod system. It is conveniently created by linking a single atomic state with three other states by three electromagnetic fields. Such a linkage pattern naturally emerges between the magnetic sublevels of two atomic levels with angular momenta J =0 and J =1 , although tripod implementations between other suitable sublevels are also used. Here we go beyond the limitation of a tripod system and show that it is possible to generate the non-Abelian geometric phase in a quantum system composed of N lower and N -2 upper sublevels. The theoretical instrument is the Morris-Shore transformation which reveals the existence of two uncoupled (dark) states composed of the lower sublevels only. A possible physical implementation is the atomic transition J ↔J -1 , with J arbitrary, which is driven, as in the case of tripod system, by three electromagnetic fields of different polarizations. This generalization considerably broadens the range of systems that can be used to generate a geometric phase, with the the same experimental complexity as in the tripod system. Specific calculations of the non-Abelian geometric phase are presented for J =3/2 ↔J =1/2 and J =2 ↔J =1 systems. A method for measuring the geometric phase is proposed.

  3. Fine-structure transitions of interstellar atomic sulfur and silicon induced by collisions with helium.

    Science.gov (United States)

    Lique, F; Kłos, J; Le Picard, S D

    2017-10-02

    Atomic sulfur and silicon are important constituents of the interstellar matter and are both used as tracers of the physical conditions in interstellar shocks and outflows. We present an investigation of the spin-orbit (de-)excitation of S((3)P) and Si((3)P) atoms induced by collisions with helium with the aim to improve the determination of atomic sulfur and silicon abundances in the interstellar medium from S and Si emission spectra. Quantum-mechanical calculations have been performed in order to determine rate coefficients for the fine-structure transitions in the 5-1000 K temperature range. The scattering calculations are based on new highly correlated ab initio potentials. The theoretical results show that the (de-)excitation of Si is much faster than that of S. The rate coefficients deduced from this study are in good agreement with previous experimental and theoretical findings despite some deviations at low temperatures. From the computation of critical densities defined as the ratios between Einstein coefficients and the sum of the relevant collisional de-excitation rate coefficients, we show that local thermodynamic equilibrium conditions are not fulfilled for analyzing S and Si emission spectra observed in the interstellar medium. Hence, the present rate coefficients will be extremely useful for the accurate determination of interstellar atomic sulfur and silicon abundances.

  4. Density functional theory calculations on transition metal atoms adsorbed on graphene monolayers

    Science.gov (United States)

    Dimakis, Nicholas; Flor, Fernando Antonio; Salgado, Andres; Adjibi, Kolade; Vargas, Sarah; Saenz, Justin

    2017-11-01

    Transition metal atom adsorption on graphene monolayers has been elucidated using periodic density functional theory under hybrid and generalized gradient approximation functionals. More specifically, we examined the adsorption of Cu, Fe, Zn, Ru, and Os on graphene monolayers by calculating, among others, the electronic density-of-states spectra of the adatom-graphene system and the overlap populations of the adatom with the nearest adsorbing graphene carbon atoms. These calculations reveal that Cu form primarily covalent bonds with graphene atoms via strong hybridization between the adatom orbitals and the sp band of the graphene substrate, whereas the interaction of the Ru and Os with graphene also contain ionic parts. Although the interaction of Fe with graphene atoms is mostly covalent, some charge transfer to graphene is also observed. The interaction of Zn with graphene is weak. Mulliken population analysis and charge contour maps are used to elucidate charge transfers between the adatom and the substrate. The adsorption strength is correlated with the metal adsorption energy and the height of the metal adatom from the graphene plane for the geometrically optimized adatom-graphene system. Our analysis shows that show that metal adsorption strength follows the adatom trend Ru ≈ Os > Fe > Cu > Zn, as verified by corresponding changes in the adsorption energies. The increased metal-carbon orbital overlap for the Ru relative to Os adatom is attributed to hybridization defects.

  5. DFT studies of the conformation and relative energies of alpha-maltotetraose (DP-4): An amylose fragment at atomic resolution

    Science.gov (United States)

    DFT optimization studies of more than one hundred conformations of a-maltotetraose have been carried out at the B3LYP/6-311++G** level of theory. The DP-4 fragments of predominately 4C1 chair residues include tightly bent forms, helix, band-flips, kinks, boat, and some 1C4 conformers. The three do...

  6. DFT Conformation and Energies of Amylose Fragments at Atomic Resolution Part I: Syn Forms of Alpha-Maltotetraose

    Science.gov (United States)

    DFT optimization studies of ninety syn '-maltotetraose (DP-4) amylose fragments have been carried out at the B3LYP/6-311++G** level of theory. The DP-4 fragments studied include V-helix, tightly bent conformations, a boat, and a 1C4 conformer. The standard hydroxymethyl rotamers (gg, gt, tg) were ...

  7. Adsorption of 3d, 4d, and 5d transition metal atoms on β 12-Borophene.

    Science.gov (United States)

    Alvarez-Quiceno, J C; Schleder, G R; Marinho, E; Fazzio, A

    2017-08-02

    We perform an ab initio study of the electronic structure and magnetic properties of 3d, 4d and 5d transition metals (TM) adsorbed on freestanding and Ag(1 1 1)-supported [Formula: see text]-borophene. The stability of TM adsorption is high for all atoms and increases with the period. For the 3d TM adsorption we observed strong exchange effects. The Ag(1 1 1)-surface induced small effects on the calculated properties. Studying the magnetic interaction between TMs, VIB atoms showed direct exchange, while VIIB and Fe showed 2p(B)-mediated indirect exchange. In the ultimate case of a one-dimensional TM array, Ru and Os also show direct exchange effects.

  8. Strain-induced metal-semiconductor transition observed in atomic carbon chains.

    Science.gov (United States)

    La Torre, A; Botello-Mendez, A; Baaziz, W; Charlier, J-C; Banhart, F

    2015-03-30

    Carbyne, the sp(1)-hybridized phase of carbon, is still a missing link in the family of carbon allotropes. While the bulk phases of carbyne remain elusive, the elementary constituents, that is, linear chains of carbon atoms, have already been observed using the electron microscope. Isolated atomic chains are highly interesting one-dimensional conductors that have stimulated considerable theoretical work. Experimental information, however, is still very limited. Here we show electrical measurements and first-principles transport calculations on monoatomic carbon chains. When the 1D system is under strain, the chains are semiconducting corresponding to the polyyne structure with alternating bond lengths. Conversely, when the chain is unstrained, the ohmic behaviour of metallic cumulene with uniform bond lengths is observed. This confirms the recent prediction of a metal-insulator transition that is induced by strain. The key role of the contacting leads explains the rectifying behaviour measured in monoatomic carbon chains in a nonsymmetric contact configuration.

  9. Strain-induced metal–semiconductor transition observed in atomic carbon chains

    Science.gov (United States)

    La Torre, A.; Botello-Mendez, A.; Baaziz, W.; Charlier, J. -C.; Banhart, F.

    2015-01-01

    Carbyne, the sp1-hybridized phase of carbon, is still a missing link in the family of carbon allotropes. While the bulk phases of carbyne remain elusive, the elementary constituents, that is, linear chains of carbon atoms, have already been observed using the electron microscope. Isolated atomic chains are highly interesting one-dimensional conductors that have stimulated considerable theoretical work. Experimental information, however, is still very limited. Here we show electrical measurements and first-principles transport calculations on monoatomic carbon chains. When the 1D system is under strain, the chains are semiconducting corresponding to the polyyne structure with alternating bond lengths. Conversely, when the chain is unstrained, the ohmic behaviour of metallic cumulene with uniform bond lengths is observed. This confirms the recent prediction of a metal–insulator transition that is induced by strain. The key role of the contacting leads explains the rectifying behaviour measured in monoatomic carbon chains in a nonsymmetric contact configuration. PMID:25818506

  10. Repetitively pulsed SPER laser using transitions in Cd atoms. [Segmented plasma source of metal vapor

    Energy Technology Data Exchange (ETDEWEB)

    Apollonov, V.V.; Sirotkin, A.A. (Institut Obshchei Fiziki, Moscow (USSR))

    1989-08-01

    The repetitively pulsed operation of a laser with a segmented plasma source of metal vapor using transitions in Cd I atoms (at wavelengths of 1.43 and 3.955 microns) is reported. The mean power of laser radiation at the pump pulse repetition rate of 2 kHz amounted to 36 and 20 mW for 1.43 and 3.955 microns, respectively. Mechanisms which limit the maximum pulse repetition rate are considered, and ways to enhance the laser output energy characteristics are proposed. 7 refs.

  11. Chain conformation and nano-patterning of polymer brushes prepared by surface-initiated atom transfer radical polymerization

    Science.gov (United States)

    Gao, Xiang

    Over the past decade, the development of surface-initiated living polymerization methods has brought a breakthrough to surface modification owing to their control ability. Surface-initiated atom transfer radical polymerization (si-ATRP), as the most popular one, has been widely employed to give novel polymer structures and functionalities to various surfaces for the purposes of tailoring surface properties, introducing new functions, or preparing so-called "smart surfaces", which can respond to external stimuli such as solvent type, pH, temperature, electric and magnetic fields etc. In this thesis, the mechanistic study of the si-ATRP was first carried out through modeling to gain good understanding of si-ATRP. Si-ATRP was then employed to prepare different types of polymer brushes to produce "smart surfaces". The kinetic model was developed using the method of moment. Combined with experimental data, a quantitative analysis was carried out for the si-ATRP mechanism. All information of grafted polymer chains, including active chain concentration, radical concentration, chain length, polydispersity, was illustrated. A new radical termination mechanism, termed as migration-termination, was proposed for si-ATRP. Si-ATRP was then employed to graft poly(oligo(ethylene glycol) methacrylate) (POEGMA) block poly(methyl methacrylate) (PMMA) brushes on silicon wafer surfaces. Simple solvent treatment gave nanoscale patterns via the phase segregation of POEGMA and PMMA segments. Various patterns including spherical aggregates, wormlike aggregates, stripe patterns, perforated layers and complete overlayers, were obtained by adjusting the upper block layer thickness. Furthermore, these nanopatterns had a unique stimuli-responsive property, i.e., switching between different morphologies reversibly after being treated with selective solvents. POEGMA-block-poly(2-(methacryloyloxy)ethyl trimethylammonium chloride) (PMETAC) brushes, having two hydrophilic segments, were synthesized

  12. Atom-surface interaction at the nanometre scale: van der Waals-Zeeman transitions in a magnetic field

    Science.gov (United States)

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

    2012-04-01

    van der Waals-Zeeman transitions between magnetic states of metastable rare-gas atoms Ar*, Kr* and Xe* (3P2) induced by a solid surface in the presence of a magnetic field, are investigated theoretically and experimentally. By use of a Zeeman slower, metastable argon atoms with various velocities ranging from 170 to 560 m/s allow us to investigate the small impact parameter range (3-7 nm) within which these transitions occur, as well as the effect of atom polarisation on the sharing out of the M states.

  13. 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....

  14. 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.

  15. Electronic and magnetic properties of 3D transition-metal atom adsorbed arsenene

    Science.gov (United States)

    Liu, Ming-Yang; Chen, Qing-Yuan; Huang, Yang; Li, Ze-Yu; Cao, Chao; He, Yao

    2018-03-01

    To utilize arsenene as the electronic and spintronic material, it is important to enrich its electronic properties and induce useful magnetic properties in it. In this paper, we theoretically studied the electronic and magnetic properties of arsenene functionalized by 3D transition-metal (TM) atoms (TM@As). Although pristine arsenene is a nonmagnetic material, the dilute magnetism can be produced upon TM atoms chemisorption, where the magnetism mainly originates from TM adatoms. We find that the magnetic properties can be tuned by a moderate external strain. The chemisorption of 3D TM atoms also enriches the electronic properties of arsenene, such as metallic, half-metallic, and semiconducting features. Interestingly, we can classify the semiconducting feature into three types according to the band-gap contribution of spin channels. On the other hand, the chemisorption properties can be modified by introducing monovacancy defect in arsenene. Present results suggest that TM-adsorbed arsenene may be a promising candidate for electronic and spintronic applications.

  16. Atomic structure of the adsorption of transition metals on silicon surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Cocoletzi, G.H. [IF-BUAP, 72000 Puebla (Mexico); Takeuchi, N. [CCMC-UNAM, Ensenada, BCN (Mexico)

    2007-07-01

    Full text: Solid state devices are useful for their high sensitivity in a small volume. Applications of such devices as dose materials include semi-conducting dose-rate, and dose-reading measuring devices. Transition metals (TM) have electronic and atomic properties similar to those of rare earth elements when they are adsorbed on silicon surfaces. The interfaces of transition metals silicides with Si (111) have very small lattice mismatches, sharp interfaces, and low Schottky barrier, making them ideal in electronic devices, such as infrared detectors and rectifying contacts. In this work we shall describe our first principles total energy calculations to investigate structural properties of bulk ScSi and YSi, the two dimensional arrangement of ScSi{sub 2} and YSi{sub 2} on the Si(111) surface, and the growth of a few layers of ScSi{sub 1.7} and YSi{sub 1.7} on the Si(111) surface. Our calculated bulk structural parameters are in excellent agreement with experimental values. It will be shown that one monolayer of a TM on Si( l l 1) yields a two dimensional phase with (lxl) periodicity consisting of a layer of TM atoms on T4 sites and a Si bilayer on top. This double layer of Si atoms is very close to ideal Si(111)-(1x1) surface, but rotated 180 with respect to the rest of the crystal. More layers of TM silicide epitaxially grown on Si(l 11) result in a hexagonal structure similar to bulk ScSi2 and YSi2: graphite-like Si planes (with vacancies) intercalated with TM planes, and forming a ({radical}3x{radical}3) arrangement with a ScSi{sub 1.7} and YSi{sub 1.7} stoichiometry. The top Si layer does not contain vacancies and it does not present a graphite-like structure, but forms a bilayer arrangement as in bulk Si. (Author)

  17. Structural characterization and pH-induced conformational transition of full-length KcsA.

    Science.gov (United States)

    Zimmer, Jochen; Doyle, Declan A; Grossmann, J Günter

    2006-03-01

    The bacterial K+ channel KcsA from Streptomyces lividans was analyzed by neutron and x-ray small-angle solution scattering. The C-terminally truncated version of KcsA, amenable to crystallographic studies, was compared with the full-length channel. Analyzing the scattering data in terms of radius of gyration reveals differences between both KcsA species of up to 13.2 A. Equally, the real-space distance distribution identifies a 40 to 50 A extension of full-length KcsA compared to its C-terminally truncated counterpart. We show that the x-ray and neutron scattering data are amenable for molecular shape reconstruction of full-length KcsA. The molecular envelopes calculated display an hourglass-shaped structure within the C-terminal intracellular domain. The C-terminus extends the membrane spanning region of KcsA by 54-70 A, with a central constriction 10-30 A wide. Solution scattering techniques were further employed to characterize the KcsA channel under acidic conditions favoring its open conformation. The full-length KcsA at pH 5.0 shows the characteristics of a dumbbell-shaped macromolecular structure, originating from dimerization of the tetrameric K+ channel. Since C-terminally truncated KcsA measured under the same low pH conditions remains tetrameric, oligomerization of full-length KcsA seems to proceed via structurally changed C-terminal domains. The determined maximum dimensions of the newly formed complex increase by 50-60%. Shape reconstruction of the pseudooctameric complex indicates the pH-induced conformational reorganization of the intracellular C-terminal domain.

  18. Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: Insights from all-atom simulations

    Science.gov (United States)

    Nam, Hoang Bao; Kouza, Maksim; Zung, Hoang; Li, Mai Suan

    2010-04-01

    Despite much progress in understanding the aggregation process of biomolecules, the factors that govern its rates have not been fully understood. This problem is of particular importance since many conformational diseases such as Alzheimer, Parkinson, and type-II diabetes are associated with the protein oligomerization. Having performed all-atom simulations with explicit water and various force fields for two short peptides KFFE and NNQQ, we show that their oligomer formation times are strongly correlated with the population of the fibril-prone conformation in the monomeric state. The larger the population the faster the aggregation process. Our result not only suggests that this quantity plays a key role in the self-assembly of polypeptide chains but also opens a new way to understand the fibrillogenesis of biomolecules at the monomeric level. The nature of oligomer ordering of NNQQ is studied in detail.

  19. Calcium-Induced Conformational Transition of Trout Ependymins Monitored by Tryptophan Fluorescence

    OpenAIRE

    Ganss, Bernhard; Hoffmann, Werner

    2009-01-01

    Ependymins are secretory, calcium-binding sialoproteins which are the predominant constituents of the cerebrospinal fluid of many teleost fish. A bound form of these regeneration-responsive glycoproteins is associated with collagen fibrils of the extracellular matrix. Here, the tryptophan fluorescence of ependymins was monitored at various Ca2+ concentrations. Two distinct states were identified with a relatively sharp transition at about 1 mM Ca2+. In agreement with previous circular dichroi...

  20. Effects of forcefield and sampling method in all-atom simulations of inherently disordered proteins: Application to conformational preferences of human amylin.

    Directory of Open Access Journals (Sweden)

    Enxi Peng

    Full Text Available Although several computational modelling studies have investigated the conformational behaviour of inherently disordered protein (IDP amylin, discrepancies in identifying its preferred solution conformations still exist between various forcefields and sampling methods used. Human islet amyloid polypeptide has long been a subject of research, both experimentally and theoretically, as the aggregation of this protein is believed to be the lead cause of type-II diabetes. In this work, we present a systematic forcefield assessment using one of the most advanced non-biased sampling techniques, Replica Exchange with Solute Tempering (REST2, by comparing the secondary structure preferences of monomeric amylin in solution. This study also aims to determine the ability of common forcefields to sample a transition of the protein from a helical membrane bound conformation into the disordered solution state of amylin. Our results demonstrated that the CHARMM22* forcefield showed the best ability to sample multiple conformational states inherent for amylin. It is revealed that REST2 yielded results qualitatively consistent with experiments and in quantitative agreement with other sampling methods, however far more computationally efficiently and without any bias. Therefore, combining an unbiased sampling technique such as REST2 with a vigorous forcefield testing could be suggested as an important step in developing an efficient and robust strategy for simulating IDPs.

  1. Single-Molecule Analysis of Protein Large-Amplitude Conformational Transitions

    Science.gov (United States)

    Yang, Haw

    2011-03-01

    Proteins have evolved to harness thermal fluctuations, rather than frustrated by them, to carry out chemical transformations and mechanical work. What are, then, the operation and design principles of protein machines? To frame the problem in a tractable way, several basic questions have been formulated to guide the experimental design: (a) How many conformational states can a protein sample on the functionally important timescale? (b) What are the inter-conversion rates between states? (c) How do ligand binding or interactions with other proteins modulate the motions? (d) What are the structural basis of flexibility and its underlying molecular mechanics? Guided by this framework, we have studied protein tyrosine phosphatase B, PtpB, from M. tuberculosis (a virulence factor of tuberculosis and a potential drug target) and adenylate kinase, AK, from E. coli (a ubiquitous energy-balancing enzyme in cells). These domain movements have been followed in real time on their respective catalytic timescales using high-resolution single-molecule Förster resonance energy transfer (FRET) spectroscopy. It is shown quantitatively that both PtpB and AK are capable of dynamically sampling two distinct states that correlate well with those observed by x-ray crystallography. Integrating these microscopic dynamics into macroscopic kinetics allows us to place the experimentally measured free-energy landscape in the context of enzymatic turnovers.

  2. In situ atom scale visualization of domain wall dynamics in VO2 insulator-metal phase transition.

    Science.gov (United States)

    He, Xinfeng; Xu, Tao; Xu, Xiaofeng; Zeng, Yijie; Xu, Jing; Sun, Litao; Wang, Chunrui; Xing, Huaizhong; Wu, Binhe; Lu, Aijiang; Liu, Dingquan; Chen, Xiaoshuang; Chu, Junhao

    2014-10-08

    A domain wall, as a device, can bring about a revolution in developing manipulation of semiconductor heterostructures devices at the atom scale. However, it is a challenge for these new devices to control domain wall motion through insulator-metal transition of correlated-electron materials. To fully understand and harness this motion, it requires visualization of domain wall dynamics in real space. Here, domain wall dynamics in VO2 insulator-metal phase transition was observed directly by in situ TEM at atom scale. Experimental results depict atom scale evolution of domain morphologies and domain wall exact positions in (202) and (040) planes referring to rutile structure at 50°C. In addition, microscopic mechanism of domain wall dynamics and accurate lattice basis vector relationship of two domains were investigated with the assistance of X-ray diffraction, ab initio calculations and image simulations. This work offers a route to atom scale tunable heterostructure device application.

  3. The influence of ligand conformation on the thermal spin transitions in iron(III) saltrien complexes.

    Science.gov (United States)

    Pritchard, Ruth; Barrett, Simon A; Kilner, Colin A; Halcrow, Malcolm A

    2008-06-28

    We report the syntheses of six new salts of the iron(III) complexes of four hexadentate Schiff bases of the saltrien-type derived from 1,8-diamino-3,6-diazaoctane and 2 equiv. of the appropriate salicylaldehyde derivative. Three of these new compounds undergo gradual spin-transitions centred between 155-204 K in the solid state, that proceed to 35-50% completeness. One of the other compounds remains high-spin on cooling, another is low-spin, while the last undergoes spin-crossover centred above room temperature. This spin-state variability is typical of solid compounds of this type. As an aid to understanding this behaviour, the crystal structures and magnetochemistry of the known spin-crossover salts [Fe(saltrien)]PF6, [Fe(saltrien)]ClO4 and [Fe(saltrien)]BPh4 have also been reexamined. The structural chemistry of all three salts was found to differ significantly from what has been previously reported. Correlation of the crystal structures and magnetic behaviour of the compounds in this and previous work suggests that the disposition of the two ligand phenoxy groups plays an important role in determining whether high-spin [Fe(saltrien)]+ complexes can undergo thermal spin-transitions.

  4. Length-dependent conformational transitions of polyglutamine repeats as molecular origin of fibril initiation.

    Science.gov (United States)

    Heck, Benjamin S; Doll, Franziska; Hauser, Karin

    2014-01-01

    Polyglutamine (polyQ) sequences are found in a variety of proteins with normal function. However, their repeat expansion is associated with a number of neurodegenerative diseases, also called polyQ diseases. The length of the polyQ sequence, varying in the number of consecutive glutamines among different diseases, is critical for inducing fibril formation. We performed a systematic spectroscopic study to analyze the conformation of polyQ model peptides in dependence of the glutamine sequence lengths (K2QnK2 with n=10, 20, 30). Complementary FTIR- and CD-spectra were measured in a wide concentration range and repeated heating and cooling cycles revealed the thermal stability of formed β-sheets. The shortest glutamine sequence K2Q10K2 shows solely random structure for concentrations up to 10 mg/ml. By increasing the peptide length to K2Q20K2, a significant fraction of β-sheet is observed even at low concentrations of 0.01 mg/ml. The higher the concentration, the more the structural composition is dominated by the intermolecular β-sheet. The formation of highly thermostable β-sheet is much more pronounced in K2Q30K2. K2Q30K2 precipitates at a concentration of 0.3 mg/ml. Our spectroscopic study shows that the aggregation tendency is enhanced with increased glutamine repeat expansion and that the concentration plays another critical factor in the β-sheet formation. Copyright © 2013 Elsevier B.V. All rights reserved.

  5. Atomically resolved phase transition of fullerene cations solvated in helium droplets

    Science.gov (United States)

    Kuhn, M.; Renzler, M.; Postler, J.; Ralser, S.; Spieler, S.; Simpson, M.; Linnartz, H.; Tielens, A. G. G. M.; Cami, J.; Mauracher, A.; Wang, Y.; Alcamí, M.; Martín, F.; Beyer, M. K.; Wester, R.; Lindinger, A.; Scheier, P.

    2016-11-01

    Helium has a unique phase diagram and below 25 bar it does not form a solid even at the lowest temperatures. Electrostriction leads to the formation of a solid layer of helium around charged impurities at much lower pressures in liquid and superfluid helium. These so-called `Atkins snowballs' have been investigated for several simple ions. Here we form HenC60+ complexes with n exceeding 100 via electron ionization of helium nanodroplets doped with C60. Photofragmentation of these complexes is measured by merging a tunable narrow-bandwidth laser beam with the ions. A switch from red- to blueshift of the absorption frequency of HenC60+ on addition of He atoms at n=32 is associated with a phase transition in the attached helium layer from solid to partly liquid (melting of the Atkins snowball). Elaborate molecular dynamics simulations using a realistic force field and including quantum effects support this interpretation.

  6. Trypsinogen-trypsin transition: a molecular dynamics study of induced conformational change in the activation domain.

    Science.gov (United States)

    Brünger, A T; Huber, R; Karplus, M

    1987-08-11

    The trypsinogen to trypsin transition has been investigated by a stochastic boundary molecular dynamics simulation that included a major portion of the trypsin molecule and the surrounding solvent. Attention focused on the "activation domain", which crystallographic studies have shown to be ordered in trypsin and disordered in its zymogen, trypsinogen. The chain segments that form the activation domain were found to exhibit large fluctuations during the simulation of trypsin. To model a difference between trypsin and trypsinogen, the N-terminal residues Ile-16 and Val-17 were removed in the former and replaced by water molecules. As a result of the perturbation, a structural drift of 1-2 A occurred that is limited to the activation domain. Glycine residues are found to act as hinges for the displaced chain segments.

  7. Manipulating the Architecture of Atomically Thin Transition Metal (Hydr)oxides for Enhanced Oxygen Evolution Catalysis.

    Science.gov (United States)

    Dou, Yuhai; Zhang, Lei; Xu, Jiantie; He, Chun-Ting; Xu, Xun; Sun, Ziqi; Liao, Ting; Nagy, Balázs; Liu, Porun; Dou, Shi Xue

    2018-02-27

    Graphene-like nanomaterials have received tremendous research interest due to their atomic thickness and fascinating properties. Previous studies mainly focus on the modulation of their electronic structures, which undoubtedly optimizes the electronic properties, but is not the only determinant of performance in practical applications. Herein, we propose a generalized strategy to incrementally manipulate the architectures of several atomically thin transition metal (hydr)oxides, and study their effects on catalytic water oxidation. The results demonstrate the obvious superiority of a wrinkled nanosheet architecture in both catalytic activity and durability. For instance, wrinkled Ni(OH) 2 nanosheets display a low overpotential of 358.2 mV at 10 mA cm -2 , a high current density of 187.2 mA cm -2 at 500 mV, a small Tafel slope of 54.4 mV dec -1 , and excellent long-term durability with gradually optimized performance, significantly outperforming other nanosheet architectures and previously reported catalysts. The outstanding catalytic performance is mainly attributable to the 3D porous network structure constructed by wrinkled nanosheets, which not only provides sufficient contact between electrode materials and current collector, but also offers highly accessible channels for facile electrolyte diffusion and efficient O 2 escape. Our study provides a perspective on improving the performance of graphene-like nanomaterials in a wide range of practical applications.

  8. Investigation of Ag-TiO2 Interfacial Reaction of Highly Stable Ag Nanowire Transparent Conductive Film with Conformal TiO2 Coating by Atomic Layer Deposition.

    Science.gov (United States)

    Yeh, Ming-Hua; Chen, Po-Hsun; Yang, Yi-Ching; Chen, Guan-Hong; Chen, Hsueh-Shih

    2017-03-29

    The atomic layer deposition (ALD) technique is applied to coat Ag nanowires (NWs) with a highly uniform and conformal TiO2 layer to improve the stability and sustainability of Ag NW transparent conductive films (TCFs) at high temperatures. The TiO2 layer can be directly deposited on Ag NWs with a surface polyvinylpyrrolidone (PVP) coat that acts a bed for TiO2 seeding in the ALD process. The ALD TiO2 layer significantly enhances the thermal stability at least 100 fold when aged between 200-400 °C and also provides an extra function of violet-blue light filtration for Ag NW TCFs. Investigation into the interaction between TiO2 and Ag reveals that the conformal TiO2 shell could effectively prevent Ag from 1D-to-3D ripening. However, Ag could penetrate the conformal TiO2 shell and form nanocrystals on the TiO2 shell surface when it is aged at 400 °C. According to experimental data and thermodynamic evaluation, the Ag penetration leads to an interlayer composed of mixed Ag-Ag2O-amorphous carbon phases and TiO2-x at the Ag-TiO2 interface, which is thought to be caused by extremely high vapor pressure of Ag at the Ag-TiO2 interface at a higher temperature (e.g., 400 °C).

  9. Optical trapping of ultracold dysprosium atoms: transition probabilities, dynamic dipole polarizabilities and van der Waals $C_6$ coefficients

    CERN Document Server

    Li, Hui; Dulieu, Olivier; Nascimbene, Sylvain; Lepers, Maxence

    2016-01-01

    The efficiency of optical trapping of ultracold atoms depend on the atomic dynamic dipole polarizability governing the atom-field interaction. In this article, we have calculated the real and imaginary parts of the dynamic dipole polarizability of dysprosium in the ground and first excited level. Due to the high electronic angular momentum of those two states, the polarizabilities possess scalar, vector and tensor contributions that we have computed, on a wide range of trapping wavelengths, using the sum-over-state formula. Using the same formalism, we have also calculated the $C_6$ coefficients characterizing the van der Waals interaction between two dysprosium atoms in the two lowest levels. We have computed the energies of excited states and the transition probabilities appearing in the sums, using a combination of \\textit{ab initio} and least-square-fitting techniques provided by the Cowan codes and extended in our group. Regarding the real part of the polarizability, for field frequencies far from atomic...

  10. Electronic structures, magnetic properties and band alignments of 3d transition metal atoms doped monolayer MoS2

    Science.gov (United States)

    Wu, Maokun; Yao, Xiaolong; Hao, Yuan; Dong, Hong; Cheng, Yahui; Liu, Hui; Lu, Feng; Wang, Weichao; Cho, Kyeongjae; Wang, Wei-Hua

    2018-01-01

    Utilizing first-principles calculations, the electronic structures, magnetic properties and band alignments of monolayer MoS2 doped by 3d transition metal atoms have been investigated. It is found that in V, Cr, Mn, Fe-doped monolayers, the nearest neighboring S atoms (SNN) are antiferromagnetically polarized with the doped atoms. While in Co, Ni, Cu, Zn-doped systems, the SNN are ferromagnetically coupled with the doped atoms. Moreover, the nearest neighboring Mo atoms also demonstrate spin polarization. Compared with pristine monolayer MoS2, little change is found for the band edges' positions in the doped systems. The Fermi level is located in the spin-polarized impurity bands, implying a half-metallic state. These results provide fundamental insights for doped monolayer MoS2 applying in spintronic, optoelectronic and electronic devices.

  11. Ligand-specific conformational transitions and intracellular transport required for atypical chemokine receptor 3-mediated chemokine scavenging.

    Science.gov (United States)

    Montpas, Nicolas; St-Onge, Geneviève; Nama, Nassr; Rhainds, David; Benredjem, Besma; Girard, Mélanie; Hickson, Gilles; Pons, Véronique; Heveker, Nikolaus

    2017-11-27

    The atypical chemokine receptor ACKR3 contributes to chemotaxis by binding, internalizing, and degrading the chemokines CXCL11 and CXCL12 to shape and terminate chemotactic gradients during development and immune responses. Although unable to trigger G protein activation, both ligands activate G protein-independent ACKR3 responses and prompt arrestin recruitment. This offers a model to specifically study ligand-specific receptor conformations leading to G protein-independent signaling, and to functional parameters such as receptor transport and chemokine degradation. We here show chemokine specificity in arrestin recruitment, by different effects of single amino acid substitutions in ACKR3 on arrestin in response to CXCL12 or CXCL11. Chemokine specificity in receptor transport was also observed, as CXCL11 induced faster receptor internalization, slower recycling, and longer intracellular sojourn of ACKR3 than CXCL12. Internalization and recycling rates of the ACKR3-R1423.50A substitution in response to each chemokine were similar; however, ACKR3-R1423.50A degraded only CXCL12, but not CXCL11. This suggests that ligand-specific intracellular receptor transport is required for chemokine degradation. Remarkably, failure of ACKR3-R1423.50A to degrade CXCL11 was not caused by the lacking arrestin recruitment; rather, arrestin was entirely dispensable for scavenging of either chemokine. This suggests involvement of another, yet unidentified, ACKR3 effector in scavenging. In summary, our study correlates ACKR3 ligand-specific conformational transitions with chemokine-dependent receptor transport dynamics and points toward unexpected ligand specificity in the mechanisms of chemokine degradation. Copyright © 2017, The American Society for Biochemistry and Molecular Biology.

  12. Properties of kinetic transition networks for atomic clusters and glassy solids.

    Science.gov (United States)

    Morgan, John W R; Mehta, Dhagash; Wales, David J

    2017-09-27

    A database of minima and transition states corresponds to a network where the minima represent nodes and the transition states correspond to edges between the pairs of minima they connect via steepest-descent paths. Here we construct networks for small clusters bound by the Morse potential for a selection of physically relevant parameters, in two and three dimensions. The properties of these unweighted and undirected networks are analysed to examine two features: whether they are small-world, where the shortest path between nodes involves only a small number or edges; and whether they are scale-free, having a degree distribution that follows a power law. Small-world character is present, but statistical tests show that a power law is not a good fit, so the networks are not scale-free. These results for clusters are compared with the corresponding properties for the molecular and atomic structural glass formers ortho-terphenyl and binary Lennard-Jones. These glassy systems do not show small-world properties, suggesting that such behaviour is linked to the structure-seeking landscapes of the Morse clusters.

  13. Radiative Lifetimes and Atomic Transition Probabilities for Rare-Earth Elements

    Science.gov (United States)

    den Hartog, E. A.; Curry, J. J.; Anderson, Heidi M.; Wickliffe, M. E.; Lawler, J. E.

    1997-10-01

    Interest in rare-earth elements has been on the rise in recent years in both the lighting and astrophysics communities. The lighting industry is increasingly using rare-earths in high-intensity discharge (HID) lamps and require comprehensive sets of accurate oscillator strengths for the modelling of these lamps. Spectroscopic data on rare-earths is also needed in astrophysical studies such as those dealing with the evolution of chemically-peculiar stars. The present work is addressing this need with extensive radiative lifetime and branching fraction measurements, which when combined will yield a large database of absolute transition probabilities of the elements thulium, dysprosium, and holmium. Radiative lifetimes are measured using laser-induced fluorescence of a slow atomic/ionic beam. Branching fractions are determined from spectra recorded using the 1.0 meter Fourier-transform spectrometer at the National Solar Observatory. Lifetimes for 298 levels of Tm I and Tm II and 440 levels of Dy I and Dy II are complete. Branching fractions have been measured for 522 transitions of Tm I and Tm II. Work is underway on lifetimes of Ho and branching fractions of Dy. Representative lifetime and branching fraction data will be presented and discussed.

  14. Investigation of structural transition of dsDNA on various substrates studied by atomic force microscopy.

    Science.gov (United States)

    Nguyen, T H; Kim, Y U; Kim, K J; Choi, S S

    2009-03-01

    Structural transition of single dsDNA molecule which is immobilized on 3-aminopropyltriethoxysilane (APTES) treated substrate (APTES/substrate) or alkylthiol treated substrate (alkylthiol/substrate) has been investigated by atomic force microscopy (AFM). The obtained force versus distance (F-D) curves are used to dissect the transition from B-form to S-form, the melting from double stranded (ds) to single stranded (ss) DNA, and its Young's modulus as well as persistence length. The melt from dsDNA to ssDNA is evidenced by fitting with freely jointed chain (FJC) model. FJC fit and Young's modulus or persistence length values when the molecules are fixed on alkylthiol/substrate are more agreeable with other studies than those on APTES. We have clarified the different results of those experiments by analyzing the binding force between DNA molecules and APTES or alkylthiol linkers on the substrate. The DNA binding to APTES linker is much stronger than that on alkylthiol/substrate.

  15. 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.

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

    Science.gov (United States)

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

    2017-03-18

    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. Copyright © 2017 Elsevier Inc. All rights reserved.

  17. Claisen rearrangement of allyl phenyl ether: heavy-atom kinetic isotope effects and bond orders in the transition structure

    Energy Technology Data Exchange (ETDEWEB)

    Kupczyk-Subotkowska, L.; Saunders, W.H. Jr.; Shine, H.J.

    1988-10-12

    Kinetic isotope effects (KIE) were measured for the rearrangement at 220/degree/C of allyl ether (1) which was labeled successively at its oxygen atom ((/sup 18/O)-1), /alpha/-carbon atom ((/alpha/-/sup 14/C)-1), /gamma/-carbon atom ((/gamma/-/sup 14/C)-1), and ortho-carbon atom ((2-/sup 14/C)-1). The KIE were 1.0297 (/sup 18/O), 1.0306 (/alpha/-/sup 14/C), 1.0362 (/gamma/-/sup 14/C), and 1.0375 (2-/sup 14/C). KIE were determined from isotopic abundances in the product, o-allylphenol (2), which were measured by multiscan mass spectrometry (/sup 18/O) and scintillation counting (/sup 14/C). A model of the transition structure was then developed, whose bond orders gave calculated KIE in reasonably good agreement not only with the experimentally determined heavy-atom KIE but also with the deuterium KIE reported earlier by McMichael and Korver. A loose transition structure was thus found for the rearrangement of 1 into 2. In this transition structure the C/sub /alpha//-O bond is 50-60% broken while the C/sub /gamma//-C/sub ortho/ bond is only 10-20% complete. The results thus define this concerted, nonsynchronous rearrangement more explicitly than hitherto possible. 40 references, 8 tables.

  18. ATOMIC-FORCE MICROSCOPY IMAGING OF TRANSITION-METAL LAYERED COMPOUNDS - A 2-DIMENSIONAL STICK-SLIP SYSTEM

    NARCIS (Netherlands)

    Kerssemakers, J.W J; de Hosson, J.T.M.

    1995-01-01

    Various layered transition metal dichalcogenides were scanned with an optical-lever atomic force microscope (AFM). The microscopic images indicate the occurrence of strong lateral stick-slip effects. In this letter, two models are presented to describe the observations due to stick-slip, i.e.,

  19. Atomic force microscopy imaging of transition metal layered compounds : A two-dimensional stick–slip system

    NARCIS (Netherlands)

    Kerssemakers, J.; Hosson, J.Th.M. De

    1995-01-01

    Various layered transition metal dichalcogenides were scanned with an optical-lever atomic force microscope (AFM). The microscopic images indicate the occurrence of strong lateral stick–slip effects. In this letter, two models are presented to describe the observations due to stick–slip, i.e.,

  20. Interaction-induced conducting-non-conducting transition of ultra-cold atoms in one-dimensional optical lattices

    Science.gov (United States)

    Chien, Chih-Chun; Gruss, Daniel; Di Ventra, Massimiliano; Zwolak, Michael

    2013-06-01

    The study of time-dependent, many-body transport phenomena is increasingly within reach of ultra-cold atom experiments. We show that the introduction of spatially inhomogeneous interactions, e.g., generated by optically controlled collisions, induce negative differential conductance in the transport of atoms in one-dimensional optical lattices. Specifically, we simulate the dynamics of interacting fermionic atoms via a micro-canonical transport formalism within both a mean-field and a higher-order approximation, as well as with a time-dependent density-matrix renormalization group (DMRG). For weakly repulsive interactions, a quasi-steady-state atomic current develops that is similar to the situation occurring for electronic systems subject to an external voltage bias. At the mean-field level, we find that this atomic current is robust against the details of how the interaction is switched on. Further, a conducting-non-conducting transition exists when the interaction imbalance exceeds some threshold from both our approximate and time-dependent DMRG simulations. This transition is preceded by the atomic equivalent of negative differential conductivity observed in transport across solid-state structures.

  1. 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.

  2. 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

  3. Conformal SiO2 coating of sub-100 nm diameter channels of polycarbonate etched ion-track channels by atomic layer deposition

    Directory of Open Access Journals (Sweden)

    Nicolas Sobel

    2015-02-01

    Full Text Available Polycarbonate etched ion-track membranes with about 30 µm long and 50 nm wide cylindrical channels were conformally coated with SiO2 by atomic layer deposition (ALD. The process was performed at 50 °C to avoid thermal damage to the polymer membrane. Analysis of the coated membranes by small angle X-ray scattering (SAXS reveals a homogeneous, conformal layer of SiO2 in the channels at a deposition rate of 1.7–1.8 Å per ALD cycle. Characterization by infrared and X-ray photoelectron spectroscopy (XPS confirms the stoichiometric composition of the SiO2 films. Detailed XPS analysis reveals that the mechanism of SiO2 formation is based on subsurface crystal growth. By dissolving the polymer, the silica nanotubes are released from the ion-track membrane. The thickness of the tube wall is well controlled by the ALD process. Because the track-etched channels exhibited diameters in the range of nanometres and lengths in the range of micrometres, cylindrical tubes with an aspect ratio as large as 3000 have been produced.

  4. Electronic and magnetic properties of 1T-HfS2 by doping transition-metal atoms

    Science.gov (United States)

    Zhao, Xu; Wang, Tianxing; Wang, Guangtao; Dai, Xianqi; Xia, Congxin; Yang, Lin

    2016-10-01

    We explored the electronic and magnetic properties of 1T-HfS2 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-HfS2. Numerical results show that the pristine 1T-HfS2 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-HfS2 can be a metal, semiconductor or half-metal. Analysis of the band structure and magnetic properties indicates that TM-doped HfS2 (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 HfS2 under S-rich experimental conditions. In contrast, V-doped HfS2 has relatively wide half-metallic gap and low formation energy. So V-doped 1T-HfS2 is ideal for spin injection, which is important for application in semiconductor spintronics.

  5. A New Rb Lamp Exciter Circuit for Rb atomic clocks and Studies on Transition from Ring to Red mode

    CERN Document Server

    Singh, Savita; Saxena, G M

    2010-01-01

    In this paper we describe the development of novel RF exciter circuit for electrode less Rb lamp. The lamp exciter circuit is a RF oscillator with a a new configuration operating at 60 to 65 MHz frequency with 3 to 4 watt power. The Rb lamp is used in exciting the ground state hyperfine transitions in Rb atom in a glass cell placed inside a tuned microwave cavity, As the frequency of these hyperfine transitions is very stable it is used in the development of Rb atomic clock by phase locking the oven controlled crystal oscillator (OCXO) to this atomic transition frequency. The details of the Rb lamp exciter are presented in the paper.The Lamp is ideally operated in ring mode as in this mode the linewidth is narrow and there is no self reversal. However, high temperature and RF excitation power may drive the Rb lamp to red mode which gives rise to line broadening and self reversal. It is the experience that mode change from ring to red deteriorates the atomic signal strength and S/N. In this paper the reasons o...

  6. External Ba2+ block of the two-pore domain potassium channel TREK-1 defines conformational transition in its selectivity filter.

    Science.gov (United States)

    Ma, Xiao-Yun; Yu, Jin-Mei; Zhang, Shu-Zhuo; Liu, Xiao-Yan; Wu, Bao-Hong; Wei, Xiao-Li; Yan, Jia-Qing; Sun, Hong-Liang; Yan, Hai-Tao; Zheng, Jian-Quan

    2011-11-18

    TREK-1 is a member of the two-pore domain potassium channel family that is known as a leak channel and plays a key role in many physiological and pathological processes. The conformational transition of the selectivity filter is considered as an effective strategy for potassium channels to control the course of potassium efflux. It is well known that TREK-1 is regulated by a large volume of extracellular and intracellular signals. However, until now, little was known about the selectivity filter gating mechanism of the channel. In this research, it was found that Ba(2+) blocked the TREK-1 channel in a concentration- and time-dependent manner. A mutagenesis analysis showed that overlapped binding of Ba(2+) at the assumed K(+) binding site 4 (S4) within the selectivity filter was responsible for the inhibitory effects on TREK-1. Then, Ba(2+) was used as a probe to explore the conformational transition in the selectivity filter of the channel. It was confirmed that collapsed conformations were induced by extracellular K(+)-free and acidification at the selectivity filters, leading to nonconductive to permeable ions. Further detailed characterization demonstrated that the two conformations presented different properties. Additionally, the N-terminal truncated isoform (ΔN41), a product derived from alternative translation initiation, was identified as a constitutively nonconductive variant. Together, these results illustrate the important role of selectivity filter gating in the regulation of TREK-1 by the extracellular K(+) and proton.

  7. External Ba2+ Block of the Two-pore Domain Potassium Channel TREK-1 Defines Conformational Transition in Its Selectivity Filter*

    Science.gov (United States)

    Ma, Xiao-Yun; Yu, Jin-Mei; Zhang, Shu-Zhuo; Liu, Xiao-Yan; Wu, Bao-Hong; Wei, Xiao-Li; Yan, Jia-Qing; Sun, Hong-Liang; Yan, Hai-Tao; Zheng, Jian-Quan

    2011-01-01

    TREK-1 is a member of the two-pore domain potassium channel family that is known as a leak channel and plays a key role in many physiological and pathological processes. The conformational transition of the selectivity filter is considered as an effective strategy for potassium channels to control the course of potassium efflux. It is well known that TREK-1 is regulated by a large volume of extracellular and intracellular signals. However, until now, little was known about the selectivity filter gating mechanism of the channel. In this research, it was found that Ba2+ blocked the TREK-1 channel in a concentration- and time-dependent manner. A mutagenesis analysis showed that overlapped binding of Ba2+ at the assumed K+ binding site 4 (S4) within the selectivity filter was responsible for the inhibitory effects on TREK-1. Then, Ba2+ was used as a probe to explore the conformational transition in the selectivity filter of the channel. It was confirmed that collapsed conformations were induced by extracellular K+-free and acidification at the selectivity filters, leading to nonconductive to permeable ions. Further detailed characterization demonstrated that the two conformations presented different properties. Additionally, the N-terminal truncated isoform (ΔN41), a product derived from alternative translation initiation, was identified as a constitutively nonconductive variant. Together, these results illustrate the important role of selectivity filter gating in the regulation of TREK-1 by the extracellular K+ and proton. PMID:21965685

  8. Charge Versus Energy Transfer in Atomically Thin Graphene-Transition Metal Dichalcogenide van der Waals Heterostructures

    Science.gov (United States)

    Froehlicher, Guillaume; Lorchat, Etienne; Berciaud, Stéphane

    2018-01-01

    Made from stacks of two-dimensional materials, van der Waals heterostructures exhibit unique light-matter interactions and are promising for novel optoelectronic devices. The performance of such devices is governed by near-field coupling through, e.g., interlayer charge and/or energy transfer. New concepts and experimental methodologies are needed to properly describe two-dimensional heterointerfaces. Here, we report an original study of interlayer charge and energy transfer in atomically thin metal-semiconductor [i.e., graphene-transition metal dichalcogenide (TMD, here molybdenum diselenide, MoSe2 )] heterostructures using a combination of microphotoluminescence and Raman scattering spectroscopies. The photoluminescence intensity in graphene /MoSe2 is quenched by more than 2 orders of magnitude and rises linearly with the incident photon flux, demonstrating a drastically shortened (about 1 ps) room-temperature MoSe2 exciton lifetime. Key complementary insights are provided from a comprehensive analysis of the graphene and MoSe2 Raman modes, which reveals net photoinduced electron transfer from MoSe2 to graphene and hole accumulation in MoSe2 . Remarkably, the steady-state Fermi energy of graphene saturates at 290 ±15 meV above the Dirac point. This reproducible behavior is observed both in ambient air and in vacuum and is discussed in terms of intrinsic factors (i.e., band offsets) and environmental effects. In this saturation regime, balanced photoinduced flows of electrons and holes may transfer to graphene, a mechanism that effectively leads to energy transfer. Using a broad range of incident photon fluxes and diverse environmental conditions, we find that the presence of net photoinduced charge transfer has no measurable impact on the near-unity photoluminescence quenching efficiency in graphene /MoSe2 . This absence of correlation strongly suggests that energy transfer to graphene (either in the form of electron exchange or dipole-dipole interaction) is the

  9. Charge Versus Energy Transfer in Atomically Thin Graphene-Transition Metal Dichalcogenide van der Waals Heterostructures

    Directory of Open Access Journals (Sweden)

    Guillaume Froehlicher

    2018-01-01

    Full Text Available Made from stacks of two-dimensional materials, van der Waals heterostructures exhibit unique light-matter interactions and are promising for novel optoelectronic devices. The performance of such devices is governed by near-field coupling through, e.g., interlayer charge and/or energy transfer. New concepts and experimental methodologies are needed to properly describe two-dimensional heterointerfaces. Here, we report an original study of interlayer charge and energy transfer in atomically thin metal-semiconductor [i.e., graphene-transition metal dichalcogenide (TMD, here molybdenum diselenide, MoSe_{2}] heterostructures using a combination of microphotoluminescence and Raman scattering spectroscopies. The photoluminescence intensity in graphene/MoSe_{2} is quenched by more than 2 orders of magnitude and rises linearly with the incident photon flux, demonstrating a drastically shortened (about 1 ps room-temperature MoSe_{2} exciton lifetime. Key complementary insights are provided from a comprehensive analysis of the graphene and MoSe_{2} Raman modes, which reveals net photoinduced electron transfer from MoSe_{2} to graphene and hole accumulation in MoSe_{2}. Remarkably, the steady-state Fermi energy of graphene saturates at 290±15  meV above the Dirac point. This reproducible behavior is observed both in ambient air and in vacuum and is discussed in terms of intrinsic factors (i.e., band offsets and environmental effects. In this saturation regime, balanced photoinduced flows of electrons and holes may transfer to graphene, a mechanism that effectively leads to energy transfer. Using a broad range of incident photon fluxes and diverse environmental conditions, we find that the presence of net photoinduced charge transfer has no measurable impact on the near-unity photoluminescence quenching efficiency in graphene/MoSe_{2}. This absence of correlation strongly suggests that energy transfer to graphene (either in the form of electron

  10. Conformation transition in silk protein films monitored by time-resolved Fourier transform infrared spectroscopy: effect of potassium ions on Nephila spidroin films.

    Science.gov (United States)

    Chen, Xin; Knight, David P; Shao, Zhengzhong; Vollrath, Fritz

    2002-12-17

    We used time-resolved Fourier transform infrared spectroscopy (FTIR) to follow a conformation transition in Nephila spidroin film from random coil and/or helical structures to beta-sheet induced by the addition of KCl from 0.01 to 1.0 mol/L in D(2)O. Time series difference spectra showed parallel increases in absorption at 1620 and 1691 cm(-)(1), indicating formation of beta-sheet, together with a coincident loss of intensity of approximately 1650 cm(-)(1), indicating decrease of random coil and/or helical structures. Increase in KCl concentration produced an increased rate of the conformation transition that may attributable to weakening of hydrogen bonds within spidroin macromolecules. The conformation transition was a biphasic process with [KCl] > or = 0.3 mol/L but monophasic with [KCl] < or = 0.1 mol/L. This suggests that, at high KCl concentrations, segments of the molecular chain are adjusted first and then the whole molecule undergoes rearrangement. We discuss the possible significance of these findings to an understanding of the way that spiders spin silk.

  11. 5,10-Methylene-5,6,7,8-tetrahydrofolate conformational transitions upon binding to thymidylate synthase: molecular mechanics and continuum solvent studies

    Science.gov (United States)

    Jarmuła, Adam; Cieplak, Piotr; Montfort, William R.

    2005-02-01

    We applied the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach to evaluate relative stability of the extended (flat) and C-shaped (bent) solution conformational forms of the 5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) molecule in aqueous solution. Calculations indicated that both forms have similar free energies in aqueous solution but detailed energy components are different. The bent solution form has lower intramolecular electrostatic and van der Waals interaction energies. The flat form has more favorable solvation free energy and lower contribution from the bond, angle and torsion angle molecular mechanical internal energies. We exploit these results and combine them with known crystallographic data to provide a model for the progressive binding of the mTHF molecule, a natural cofactor of thymidylate synthase (TS), to the complex forming in the TS-catalyzed reaction. We propose that at the time of initial weak binding in the open enzyme the cofactor molecule remains in a close balance between the flat and bent solution conformations, with neither form clearly favored. Later, thymidylate synthase undergoes conformational change leading to the closure of the active site and the mTHF molecule is withdrawn from the solvent. That effect shifts the thermodynamic equilibrium of the mTHF molecule toward the bent solution form. At the same time, burying the cofactor molecule in the closed active site produces numerous contacts between mTHF and protein that render change in the shape of the mTHF molecule. As a result, the bent solution conformer is converted to more strained L-shaped bent enzyme conformer of the mTHF molecule. The strain in the bent enzyme conformation allows for the tight binding of the cofactor molecule to the productive ternary complex that forms in the closed active site, and facilitates the protonation of the imidazolidine N10 atom, which promotes further reaction.

  12. 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.

  13. Reversible 2D Phase Transition Driven By an Electric Field: Visualization and Control on the Atomic Scale.

    Science.gov (United States)

    Wortmann, B; van Vörden, D; Graf, P; Robles, R; Abufager, P; Lorente, N; Bobisch, C A; Möller, R

    2016-01-13

    We report on a reversible structural phase transition of a two-dimensional system that can be locally induced by an external electric field. Two different structural configurations may coexist within a CO monolayer on Cu(111). The balance between the two phases can be shifted by an external electric field, causing the domain boundaries to move, increasing the area of the favored phase controllable both in location and size. If the field is further enhanced new domains nucleate. The arrangement of the CO molecules on the Cu surface is observed in real time and real space with atomic resolution while the electric field driving the phase transition is easily varied over a broad range. Together with the well-known molecular manipulation of CO adlayers, our findings open exciting prospects for combining spontaneous long-range order with man-made CO structures such as "molecule cascades" or "molecular graphene". Our new manipulation mode permits us to bridge the gap between fundamental concepts and the fabrication of arbitrary atomic patterns in large scale, by providing unprecedented insight into the physics of structural phase transitions on the atomic scale.

  14. A conformational polymorphic transition in the high-temperature epsilon-form of chlorpropamide on cooling: a new epsilon'-form.

    Science.gov (United States)

    Drebushchak, Tatiana N; Chesalov, Yury A; Boldyreva, Elena V

    2009-12-01

    Structural changes in the high-temperature -polymorph of chlorpropamide, 4-chloro-N-(propylaminocarbonyl)benzenesulfonamide, C(10)H(13)ClN(2)O(3)S, on cooling down to 100 K and on reverse heating were followed by single-crystal X-ray diffraction. At temperatures below 200 K the phase transition into a new polymorph (termed the epsilon'-form) has been observed for the first time. The polymorphic transition preserves the space group Pna2(1), is reversible and is accompanied by discontinuous changes in the cell volume and parameters, resulting from changes in molecular conformation. As shown by IR spectroscopy and X-ray powder diffraction, the phase transition in a powder sample is inhomogeneous throughout the bulk, and the two phases co-exist in a wide temperature range. The cell parameters and the molecular conformation in the new polymorph are close to those in the previously known alpha-polymorph, but the packing of the z-shaped molecular ribbons linked by hydrogen bonds inherits that of the epsilon-form and is different from the packing in the alpha-polymorph. A structural study of the alpha-polymorph in the same temperature range has revealed no phase transitions.

  15. 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

  16. 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.

  17. 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.

  18. The role of transmembrane segment 5 (TM5) in Na2 release and the conformational transition of neurotransmitter:sodium symporters toward the inward-open state.

    Science.gov (United States)

    Stolzenberg, Sebastian; Li, Zheng; Quick, Matthias; Malinauskaite, Lina; Nissen, Poul; Weinstein, Harel; Javitch, Jonathan A; Shi, Lei

    2017-05-05

    Neurotransmitter:sodium symporters (NSSs) terminate neurotransmission by the reuptake of released neurotransmitters. This active accumulation of substrate against its concentration gradient is driven by the transmembrane Na+ gradient and requires that the transporter traverses several conformational states. LeuT, a prokaryotic NSS homolog, has been crystallized in outward-open, outward-occluded, and inward-open states. Two crystal structures of another prokaryotic NSS homolog, the multihydrophobic amino acid transporter (MhsT) from Bacillus halodurans, have been resolved in novel inward-occluded states, with the extracellular vestibule closed and the intracellular portion of transmembrane segment 5 (TM5i) in either an unwound or a helical conformation. We have investigated the potential involvement of TM5i in binding and unbinding of Na2, i.e. the Na+ bound in the Na2 site, by carrying out comparative molecular dynamics simulations of the models derived from the two MhsT structures. We find that the helical TM5i conformation is associated with a higher propensity for Na2 release, which leads to the repositioning of the N terminus and transition to an inward-open state. By using comparative interaction network analysis, we also identify allosteric pathways connecting TM5i and the Na2 binding site to the extracellular and intracellular regions. Based on our combined computational and mutagenesis studies of MhsT and LeuT, we propose that TM5i plays a key role in Na2 binding and release associated with the conformational transition toward the inward-open state, a role that is likely to be shared across the NSS family. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  19. Lead-Free Hybrid Material with an Exceptional Dielectric Phase Transition Induced by a Chair-to-Boat Conformation Change of the Organic Cation.

    Science.gov (United States)

    Han, Shiguo; Zhang, Jing; Sun, Zhihua; Ji, Chengmin; Zhang, Weichuan; Wang, Yuyin; Tao, Kewen; Teng, Bing; Luo, Junhua

    2017-11-06

    Hybrid organic-inorganic perovskite materials have demonstrated great potential in the field of photovoltaics and photoelectronics. On the basis of the high degree of structural flexibility and compatibility, diverse molecular functional materials have been assembled by modifying the length of the organic components and/or dimensionality of the inorganic frameworks. In this paper, we present a chiral lead-free organic-inorganic hybrid, (piperidinium)2SbCl5 (1), which follows the one-dimensional inorganic frameworks of the corner-sharing SbCl6 octahedra. Strikingly, 1 displays a dielectric phase transition at Tc = 338 K, changing from the chiral space group of P212121 to polar Pna21 upon heating. Crystal structure analyses reveal that an unusual thermally activated conformation change of the piperidinium cations affords the driving force to the phase transition of 1. That is, organic piperidinium moieties display a chairlike conformation below Tc, which transforms to a boatlike structure above Tc. Such an unprecedented change is strongly coupled to the dielectric transition along with notable steplike anomalies, which suggest that 1 could be used as a potential switchable dielectric material. Besides, the temperature-dependent conductivity and theoretical analysis of its electronic structure disclose the semiconducting behavior of 1. This study paves the pathway to the design of new lead-free semiconducting perovskites with targeted properties for optoelectronic application.

  20. Full characterization of the quantum linear-zigzag transition in atomic chains

    OpenAIRE

    Silvi, Pietro; De Chiara, Gabriele; Calarco, Tommaso; Morigi, Giovanna; Montangero, Simone

    2013-01-01

    A string of repulsively interacting particles exhibits a phase transition to a zigzag structure, by reducing the transverse trap potential or the interparticle distance. The transition is driven by transverse, short wavelength vibrational modes. Based on the emergent symmetry Z_2 it has been argued that this instability is a quantum phase transition, which can be mapped to an Ising model in transverse field. We perform an extensive Density Matrix Renormalization Group analysis of the behaviou...

  1. Spatial-temporal characteristics of a SPER laser using transitions of the Cd,Zn,In atoms. [Segmented-Plasma-Excitation-Recombination

    Energy Technology Data Exchange (ETDEWEB)

    Apollonov, V.V.; Derzhavin, S.I.; Prokhorov, A.M.; Sirotkin, A.A. (Institut Obshchei Fiziki, Moscow (USSR))

    1989-05-01

    An experimental study of a SPER (segmented-plasma-excitation-recombination) laser using transitions of Cd,Zn,In atoms shows that the stretching of the pump pulse trailing edge results in a increased energy output. The recombination pump mechanism in the atomic-transition SPER laser is confirmed. The feasibility of the repetitively pulsed operation of the SPER laser is examined, and it is found that the maximum pulse repetition rate can amount to 10 kHz. 9 refs.

  2. Critical Assessment of Theoretical Calculations of Atomic Structure and Transition Probabilities: An Experimenter’s View

    Directory of Open Access Journals (Sweden)

    Elmar Träbert

    2014-03-01

    Full Text Available The interpretation of atomic observations by theory and the testing of computational predictions by experiment are interactive processes. It is necessary to gain experience with “the other side” before claims of achievement can be validated and judged. The discussion covers some general problems in the field as well as many specific examples, mostly organized by isoelectronic sequence, of what level of accuracy recently has been reached or which atomic structure or level lifetime problem needs more attention.

  3. Atomic-scale study of the amorphous-to-crystalline phase transition mechanism in GeTe thin films.

    Science.gov (United States)

    Mantovan, R; Fallica, 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

    2017-08-15

    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 bonds, with a net electronic charge density transfer of  ~ 1.6 e/a0 between FeGe and neighboring Te atoms. This charge transfer accounts for a lowering of the covalent character during crystallization. The results are corroborated by theoretical calculations within the framework of density functional theory. The observed atomic-scale chemical-structural changes are directly connected to the macroscopic phase transition and resistivity switch of GeTe thin films.

  4. Effect of photoions on the line shape of the Foerster resonance lines and microwave transitions in cold rubidium Rydberg atoms

    Energy Technology Data Exchange (ETDEWEB)

    Tretyakov, D. B.; Beterov, I. I.; Entin, V. M.; Yakshina, E. A.; Ryabtsev, I. I., E-mail: ryabtsev@isp.nsc.ru [Russian Academy of Sciences, Institute of Semiconductor Physics, Siberian Branch (Russian Federation); Dyubko, S. F.; Alekseev, E. A.; Pogrebnyak, N. L. [National Academy of Sciences of Ukraine, Institute of Radio Astronomy (Ukraine); Bezuglov, N. N. [St. Petersburg State University (Russian Federation); Arimondo, E. [Universita di Pisa (Italy)

    2012-01-15

    Experiments are carried out on the spectroscopy of the Foerster resonance lines Rb(37P) + Rb(37P) {yields} Rb(37S) + Rb(38S) and microwave transitions nP {yields} n Prime S, n Prime D between Rydberg states of cold rubidium atoms in a magneto-optical trap (MOT). Under ordinary conditions, all spectra exhibit a linewidth of 2-3 MHz irrespective of the interaction time between atoms or between atoms and microwave radiation, although the limit resonance width should be determined by the inverse interaction time. The analysis of experimental conditions has shown that the main source of line broadening is the inhomogeneous electric field of cold photoions that are generated under the excitation of initial nP Rydberg states by broadband pulsed laser radiation. The application of an additional electric-field pulse that rapidly extracts photoions produced by a laser pulse leads to a considerable narrowing of lines of microwave resonances and the Foerster resonance. Various sources of line broadening in cold Rydberg atoms are analyzed.

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

    Indian Academy of Sciences (India)

    Using the multiconfiguration Hartree–Fock approximation within the framework of the Breit–Pauli Hamiltonian (MCHF+BP) and the relativistic Hartree–Fock (HFR) approximation, we have calculated the forbidden transition (1 and 2) parameters such as transition energies, logarithmic weighted oscillator strengths and ...

  6. Adsorption of 3d, 4d, and 5d transition metal atoms on β 12—Borophene

    Science.gov (United States)

    Alvarez-Quiceno, J. C.; Schleder, G. R.; Marinho, E., Jr.; Fazzio, A.

    2017-08-01

    We perform an ab initio study of the electronic structure and magnetic properties of 3d, 4d and 5d transition metals (TM) adsorbed on freestanding and Ag(1 1 1)-supported {β12} -borophene. The stability of TM adsorption is high for all atoms and increases with the period. For the 3d TM adsorption we observed strong exchange effects. The Ag(1 1 1)-surface induced small effects on the calculated properties. Studying the magnetic interaction between TMs, VIB atoms showed direct exchange, while VIIB and Fe showed 2p(B)-mediated indirect exchange. In the ultimate case of a one-dimensional TM array, Ru and Os also show direct exchange effects.

  7. Cooper minima in the transitions from low-excited and Rydberg states of alkali-metal atoms

    OpenAIRE

    Beterov, I. I.; Mansell, C. W.; Yakshina, E. A.; Ryabtsev, I. I.; Tretyakov, D. B.; Entin, V. M.; MacCormick, C.; Piotrowicz, M. J.; Kowalczyk, A.; Bergamini, S.

    2012-01-01

    The structure of the Cooper minima in the transition probabilities and photoionization cross-sections for low-excited and Rydberg nS, nP, nD and nF states of alkali-metal atoms has been studied using a Coulomb approximation and a quasiclassical model. The range of applicability of the quasiclassical model has been defined from comparison with available experimental and theoretical data on dipole moments, oscillator strengths, and photoionization cross-sections. A new Cooper minimum for transi...

  8. Electronic and magnetic behaviors of graphene with 5d series transition metal atom substitutions: A first-principles study

    Science.gov (United States)

    Sun, Minglei; Tang, Wencheng; Ren, Qingqiang; Zhao, Yiming; Wang, Sake; Yu, Jin; Du, Yanhui; Hao, Yitong

    2016-06-01

    The electronic structures and magnetic behaviors of graphene with 5d series transition metal atom substitutions are investigated by performing first-principles calculations. All the impurities are tightly bonded to single vacancy in a graphene sheet. The substitutions of La and Ta lead to Fermi level shifting to valence and conduction band, respectively. Both the two substitutions result in metallic properties. Moreover, the Hf, Os and Pt-substituted systems exhibit semiconductor properties, while the Re and Ir-substituted ones exhibit robust half-metallic properties. Interestingly, W-substituted system shows dilute magnetic semiconductor property. On the other hand, the substitution of Ta, W, Re and Ir induce 0.86 μB, 2 μB, 1 μB and 0.99 μB magnetic moment, respectively. Our studies demonstrate that the 5d series transition metal substituted graphene have potential applications in nanoelectronics, spintronics and magnetic storage devices.

  9. Symmetry-protected topological phase transition in one-dimensional Kondo lattice and its realization with ultracold atoms

    Science.gov (United States)

    Nakagawa, Masaya; Kawakami, Norio

    2017-10-01

    We propose that ultracold alkaline-earth-like atoms confined in one-dimensional optical lattice can realize a Kondo lattice model which hosts a symmetry-protected topological (SPT) phase and an associated quantum phase transition in a controllable manner. The symmetry protection of the phase transition is discussed from two different viewpoints: topological properties related to spatial patterns of Kondo singlets and symmetry eigenvalues of the spin states. We uncover the role of various symmetries in the phase diagram of this system by combining a weak-coupling approach by Abelian bosonization and strong-coupling pictures of ground states. Furthermore, we show that the bosonization approach correctly describes a crossover from a fermionic SPT phase to a bosonic SPT phase and an associated change of protecting symmetries as the charge degrees of freedom are frozen by the Hubbard repulsion.

  10. Thermally-induced phase transition of pseudorotaxane crystals: changes in conformation and interaction of the molecules and optical properties of the crystals.

    Science.gov (United States)

    Horie, Masaki; Suzaki, Yuji; Hashizume, Daisuke; Abe, Tomoko; Wu, Tiendi; Sassa, Takafumi; Hosokai, Takuya; Osakada, Kohtaro

    2012-10-31

    This paper presents a pseudorotaxane that acts as a thermally driven molecular switch in the single-crystal state. Crystals of the cationic pseudorotaxane consisting of dibenzo[24]crown-8 (DB24C8) and N-(xylylammonium)-methylferrocene as the cyclic and axle component molecules, respectively, undergo crystalline-phase transition at 128 °C with heating and 116 °C with cooling, according to differential-scanning-calorimetry measurements. X-ray crystallographic analyses revealed that the phase transition was accompanied by rotation of the 4-methylphenyl group of the axle component molecule and a simultaneous shift in the position of the PF(6)(-) counteranion. Crystalline phase transition changes the conformation and position of the DB24C8 molecule relative to the ammonium cation partially; the interaction between the cyclic component and the PF(6)(-) anion in the crystal changes to a greater extent. Moreover, there are changes in the vibration angle (θ) and birefringence (Δn) on the (001) face of the crystal transitionally; θ is rotated by +12°, and Δn is decreased from 0.070 to 0.059 upon heating across the phase transition temperature. The phase transition and accompanying change in the optical properties of the crystal occur reversibly and repeatedly upon heating and cooling processes. The switching rotation of the aromatic plane of the molecule induces a change in the optical anisotropy of the crystal, which is regarded as a demonstration of a new type of optical crystal. Partial replacement of the PF(6)(-) anion with the bulkier AsF(6)(-) anion forms crystals with similar crystallographic parameters. An increase in the AsF(6)(-) content decreases the reversible-phase-transition temperature gradually down to 99 °C (T(end)) and 68 °C (T(exo)) ([AsF(6)(-)]:[PF(6)(-)] = 0.4:0.6).

  11. Unraveling the solid-liquid-vapor phase transition dynamics at the atomic level with ultrafast x-ray absorption near-edge spectroscopy.

    Science.gov (United States)

    Dorchies, F; Lévy, A; Goyon, C; Combis, P; Descamps, D; Fourment, C; Harmand, M; Hulin, S; Leguay, P M; Petit, S; Peyrusse, O; Santos, J J

    2011-12-09

    X-ray absorption near-edge spectroscopy (XANES) is a powerful probe of electronic and atomic structures in various media, ranging from molecules to condensed matter. We show how ultrafast time resolution opens new possibilities to investigate highly nonequilibrium states of matter including phase transitions. Based on a tabletop laser-plasma ultrafast x-ray source, we have performed a time-resolved (∼3  ps) XANES experiment that reveals the evolution of an aluminum foil at the atomic level, when undergoing ultrafast laser heating and ablation. X-ray absorption spectra highlight an ultrafast transition from the crystalline solid to the disordered liquid followed by a progressive transition of the delocalized valence electronic structure (metal) down to localized atomic orbitals (nonmetal-vapor), as the average distance between atoms increases.

  12. Determination of the Glass Transition Temperature of Freestanding and Supported Azo-Polymer Thin Films by Thermal Assisted Atomic Force Microscopy

    Science.gov (United States)

    Chernykh, Elena; Kharintsev, Sergey; Fishman, Alexandr; Alekseev, Alexander; Salakhov, Myakzuym

    2017-03-01

    In this paper we introduce and apply the method for determination of the glass transition temperature of the sub-100 nm thick freestanding and supported polymer films based on thermally assisted atomic force microscopy (AFM). In proposed approach changes of the phase of an oscillating AFM cantilever are used to determine glass transition temperature. An anomalous decrease of the glass transition temperature for both free-standing and supported azobenzene-functionalized polymer thin films is shown.

  13. Forbidden transitions in the microwave spectrum of the trans conformer of the (CD3)2CDOH molecule

    Science.gov (United States)

    Kazimova, S. B.

    2013-07-01

    We searched for forbidden transitions in the microwave rotational spectrum of the (CD3)2CDOH molecule in the frequency range 17030-79050 MHz. The (CD3)2CDOH molecule has a symmetry plane containing the dipole moment components μ b and μ c , while μ a = 0. As a result of centrifugal distortion, in this type of molecule an induced dipole moment component μ a may appear perpendicular to the symmetry plane. We have observed forbidden "centrifugal" transitions in the (CD3)2CDOH molecule arising as a result of the induced component of the dipole moment. We have identified 92 μ a -transitions.

  14. 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.

  15. Aminomethyl-bipyridine bearing two flexible nitronyl-nitroxide arms: a new podand for complexation of transition metals in a facial or meridional conformation.

    Science.gov (United States)

    Stroh, Christophe; Belorizky, Elie; Turek, Philippe; Bolvin, Hélène; Ziessel, Raymond

    2003-05-05

    Transition metal complexes of 6-aminomethyl-bis[methyl-2-(4,5-dihydro-4,4,5,5- tetramethylimidazolinyl-3-oxide-l-oxy)]-2,2'-bipyridine, bpyN(NIT)(2), 1, have been synthesized and characterized by FAB-MS, UV-vis, FT-IR, and EPR spectroscopies, elemental analysis, and susceptibility measurements. Single-crystal X-ray diffraction studies have been performed on all compounds giving the following crystal data: bpyN(NIT)(2), 1, triclinic, P(-)1, Z = 2, a = 10.7224(4) A, b = 11.0995(4) A, c = 13.1134(3) A, alpha = 114.101(9) degrees, beta = 97.476(9) degrees, gamma = 99.667(9) degrees; ZnbpyN(NIT)(2), 2, hexagonal, P3(2), Z = 3, a = 15.4545(3) A, b = 15.4545(3) A, c = 13.5594(3) A; NibpyN(NIT)(2), 3, hexagonal, P3(2), Z = 3, a = 15.2867(1) A, b = 15.2867(1) A, c = 13.7160(1) A; CubpyN(NIT)(2), 4, triclinic, P(-)l, Z = 2, a = 11.8640(4) A, b = 13.2023(4) A, c = 13.2661(5) A, alpha = 90.539(9) degrees, beta = 104.983(9) degrees, gamma = 113.252(9) degrees. The two radicals of the free ligand 1 are almost perpendicular to one another in the solid state, favoring a weak ferromagnetic interaction (J/k(B) = 8.8 K). The complexes obtained by wrapping the ligand around a single metal center gave rise to two different coordination schemes where the two radicals of 1 adopt a ON(3)O meridional (with Ni and Zn) or a ON(3)O facial conformation (with Cu), which strongly affects the magnetic and electronic properties (O accounts for the coordinated oxygen atoms of the nitroxide radicals and N(3) accounts for the tertiary amine). For 2, a model of a dimer has been used giving rise to a weak antiferromagnetic interaction between the radicals (J/k(B) = -5.3 K). For 3, a very strong intramolecular antiferromagnetic coupling has been found and estimated at J/k(B) = -230 K and J'/k(B) = -110 K between the nickel and each radical using an asymmetric model of a trimer. For 4, an unusual magnetic behavior is observed, dominated by antiferromagnetic interactions with a residual plateau at chi

  16. Ab initio calculations for structural, electronic and magnetic behaviors of nitrogenized monolayer graphene decorated with 5d transition metal atoms

    Science.gov (United States)

    Rafique, Muhammad; Shuai, Yong; Xu, Meng; Zhang, Guohua; Guo, Yanming

    2017-09-01

    Graphene-based magnetic materials have revealed great potential for developing high-performance electronic units at sub-nanometer such as spintronic data storage devices. However, a significant ferromagnetism behavior and ample band gap in the electronic structure of graphene is required before it can be used for actual engineering applications. Based on first-principles calculations, here we demonstrate the structural, electronic and magnetic behaviors of 5d transition metal (TM) atom-substituted nitrogenized monolayer graphene. We find that, during TMN(3)4 cluster-substitution, tight bonding occurs between impurity atoms and graphene with significant binding energies. Charge transfer occurs from graphene layer to the TMN(3)4 clusters. Interestingly, PtN3, TaN4 and ReN4 cluster-doped graphene structures exhibit dilute magnetic semiconductor behavior with 1.00 μB, 1.04 μB and 1.05 μB magnetic moments, respectively. While, OsN4 and PtN4 cluster-doped structures display nonmagnetic direct band gap semiconductor behavior. Remaining, TMN(3)4 cluster-doped graphene complexes exhibit half metal properties. Detailed analysis of density of states (DOS) plots indicate that d orbitals of TM atoms should be responsible for arising magnetic moments in graphene. Given results pave a new route for potential applications of dilute magnetic semiconductors and half-metals in spintronic devices by employing TMN(3)4 cluster-doped graphene complexes.

  17. 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.

  18. An Improved Limit on Pauli-Exclusion-Principle Forbidden Atomic Transitions

    Science.gov (United States)

    Elliott, S. R.; LaRoque, B. H.; Gehman, V. M.; Kidd, M. F.; Chen, M.

    2012-08-01

    We have examined the atomic theory behind recent constraints on the violation of the Pauli Exclusion Principle derived from experiments that look for X-rays emitted from conductors while a large current is present. We also re-examine the assumptions underlying such experiments. We use the results of these studies to assess pilot measurements to develop an improved test of the Principle. We present an improved limit of 1/2β2 Messiah-Greenberg symmetrization-postulate selection rule.

  19. 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

  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. Spectral distribution of the 2S → 1S two-photon transition in atoms ...

    Indian Academy of Sciences (India)

    electron ions. We have measured the spectral ... the photon field operator and ωi is the frequency of transition i. The frequency .... two-photon decay continuum was normalized to the measured spectra at the reduced pho- ton energy of 0.50, i.e., ...

  2. Atomically Thin Ordered Alloys of Transition Metal Dichalcogenides: Stability and Band Structures

    DEFF Research Database (Denmark)

    Pandey, Mohnish; Jacobsen, Karsten Wedel; Thygesen, Kristian Sommer

    2016-01-01

    We explore the possibility of modulating the electronic band edges of the transition metal dichalcogenides (TMD) via alloying of different semiconductors within the same group (intra-group alloying). The stability of the ordered alloys is assessed from the calculated mixing enthalpy which is found...

  3. 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...

  4. A Computational Model of Word Segmentation from Continuous Speech Using Transitional Probabilities of Atomic Acoustic Events

    Science.gov (United States)

    Rasanen, Okko

    2011-01-01

    Word segmentation from continuous speech is a difficult task that is faced by human infants when they start to learn their native language. Several studies indicate that infants might use several different cues to solve this problem, including intonation, linguistic stress, and transitional probabilities between subsequent speech sounds. In this…

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

    Energy Technology Data Exchange (ETDEWEB)

    Borschevsky, A.; Eliav, E.; Kaldor, U. [School of Chemistry, Tel Aviv University, 69978 Tel Aviv, (Israel); Vilkas, M.J.; Ishikawa, Y. [Department of Chemistry, University of Puerto Rico, P.O. Box 23346, San Juan, Puerto Rico 00931-3346 (United States)

    2007-07-01

    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{sup -1}, and the error limits for Lr are therefore put at 700 cm{sup -1}. Predicted Lr excitations with large transition moments in the prime range for the planned experiment, 20,000-30,000 cm{sup -1}, are 7p {yields} 8s at 20,100 cm{sup -1} and 7p {yields}p 7d at 28,100 cm{sup -1}. In case of Yb, the calculated ionization potential was within 20 cm{sup -1} of the experiment, and the average error of the 20 lowest calculated excitations was about 300 cm{sup -1}. Hence, the

  6. DFT Conformation and Energies of Amylose Fragments at Atomic Resolution Part 2: “Band-flip” and “Kink” Forms of Alpha-Maltotetraose

    Science.gov (United States)

    In Part 2 of this series of DFT optimization studies of '-maltotetraose, we present results at the B3LYP/6-311++G** level of theory for conformations denoted “band-flips” and “kinks”. Recent experimental X-ray studies have found examples of amylose fragments with conformations distorted from the us...

  7. 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.)

  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. 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)

  10. Atomically Thin Transition-Metal Dinitrides: High-Temperature Ferromagnetism and Half-Metallicity.

    Science.gov (United States)

    Wu, Fang; Huang, Chengxi; Wu, Haiping; Lee, Changhoon; Deng, Kaiming; Kan, Erjun; Jena, Puru

    2015-12-09

    High-temperature ferromagnetic two-dimensional (2D) materials with flat surfaces have been a long-sought goal due to their potential in spintronics applications. Through comprehensive first-principles calculations, we show that the recently synthesized MoN2 monolayer is such a material; it is ferromagnetic with a Curie temperature of nearly 420 K, which is higher than that of any flat 2D magnetic materials studied to date. This novel property, made possible by the electron-deficient nitrogen ions, render transition-metal dinitrides monolayers with unique electronic properties which can be switched from the ferromagnetic metals in MoN2, ZrN2, and TcN2 to half-metallic ones in YN2. Transition-metal dinitrides monolayers may, therefore, serve as good candidates for spintronics devices.

  11. Strength fragmentation of Gamow-Teller transitions and delayed neutron emission of atomic nuclei

    Science.gov (United States)

    Severyukhin, A. P.

    2017-11-01

    Starting from a Skyrme interaction with tensor terms, the β-decay rates of 52Ca have been studied within a microscopic model including the 2 p - 2 h configuration effects. We observe a redistribution of the strength of Gamow-Teller transitions due to the 2 p - 2 h fragmentation. Taking into account this effect results in a satisfactory description of the neutron emission probability of the β-decay in 52Ca.

  12. 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.

  13. Structural, electronic and magnetic properties of transition metal atom-doped ZnS dilute magnetic semiconductors: A first-principles study

    Energy Technology Data Exchange (ETDEWEB)

    Yin, Zhu-Hua [College of Physics and Information Technology, Shaanxi Normal University, Xian, 710119, Shaanxi (China); Zhang, Jian-Min, E-mail: jmzhang@snnu.edu.cn [College of Physics and Information Technology, Shaanxi Normal University, Xian, 710119, Shaanxi (China); Xu, Ke-Wei [State Key Laboratory for Mechanical Behavior of Materials, Xian Jiaotong University, Xian, 710049, Shaanxi (China)

    2016-11-01

    The spin-polarized first-principles calculations are performed to study the structural, electronic and magnetic properties of a single and two identical transition metal (TM) atoms X (X = V, Cr, Mn, Fe, Co and Ni) doped ZnS dilute magnetic semiconductors (DMS). The single V-, Cr-, Fe- and Ni-doped ZnS systems exhibit the magnetic half-metallic (HM) characters, while Mn- and Co-doped ZnS systems display magnetic semiconducting characters. For two identical TM atoms doped ZnS systems, the two identical V, Cr and Ni atoms are in a ferromagnetic (FM) coupling under the double-exchange (DE) mechanism, leading V-, Cr- and Ni-doped ZnS systems to be HM with FM coupling. While two identical Mn- and Co-doped ZnS systems are semiconductors with antiferromagnetic (AFM) coupling consisting with the superexchange (SE) mechanism. Specifically, two identical Fe atoms display a competition between the SE and DE mechanisms. The Zn{sub 70}Fe{sub 2}S{sub 72} system is metal with AFM coupling at the nearest separation of two Fe atoms while HM with FM coupling at the farther separations of two Fe atoms. - Graphical abstract: The 3 × 2 × 3 supercell containing 72 formula units of zincblende ZnS. Red (Green) balls represent the S (Zn) atoms. One TM atom or two identical TM atoms X (X = V, Cr, Mn, Fe, Co or Ni) to substitute for one Zn atom at position 0 or two Zn atoms at positions 0 and i (i = 1, 2, 3 or 4). - Highlights: • A single V, Cr, Fe or Ni (Mn or Co) atoms doped ZnS are magnetic HM (magnetic semiconductor). • Two V, Cr or Ni (two Mn or Co) atoms doped ZnS are FM HM (AFM semiconductor). • Two Fe atoms doped ZnS are AFM metal (FM HM) at the nearest (farther) separations.

  14. Data supporting the involvement of the adenine nucleotide translocase conformation in opening the Tl+-induced permeability transition pore in Ca2+-loaded rat liver mitochondria

    Directory of Open Access Journals (Sweden)

    Sergey M. Korotkov

    2016-06-01

    Full Text Available There we made available information about the effects of the adenine nucleotide translocase (ANT ‘c’ conformation fixers (phenylarsine oxide (PAO, tert-butylhydroperoxide (tBHP, and carboxyatractyloside as well as thiol reagent (4,4′-diisothiocyanostilbene-2,2′-disulfonate (DIDS on isolated rat liver mitochondria. We observed a decrease in A540 (mitochondrial swelling and respiratory control rates (RCRADP [state 3/state 4] and RCRDNP [2,4-dinitrophenol-uncoupled state/basal state or state 4], as well as an increase in Ca2+-induced safranin fluorescence (F485/590, arbitrary units, showed a dissipation in the inner membrane potential (ΔΨmito, in experiments with energized rat liver mitochondria, injected into the buffer containing 25–75 mM TlNO3, 125 mM KNO3, and 100 µM Ca2+. The fixers and DIDS, in comparison to Ca2+ alone, greatly increased A540 decline and the rate of Ca2+-induced ΔΨmito dissipation. These reagents also markedly decreased RCRADP and RCRDNP. The MPTP inhibitors (ADP, cyclosporin A, bongkrekic acid, and N-ethylmaleimide fixing the ANT in ‘m’ conformation significantly hindered the above-mentioned effects of the fixers and DIDS. A more complete scientific analysis of these findings may be obtained from the manuscript “To involvement the conformation of the adenine nucleotide translocase in opening the Tl+-induced permeability transition pore in Ca2+-loaded rat liver mitochondria” (Korotkov et al., 2016 [1].

  15. 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.

  16. 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.

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

    Science.gov (United States)

    López-Moreno, S; Romero, A H

    2015-04-21

    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 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. Electromagnetic transition matrix elements in the continuous spectrum of atoms: theory and computation

    CERN Document Server

    Komninos, Yannis; Nicolaides, Cleanthes A

    2014-01-01

    In a variety of problems concerning the coupling of atomic and molecular states to strong and or short electromagnetic pulses, it is necessary to solve the time-dependent Schroedinger equation nonperturbatively. To this purpose, we have proposed and applied to various problems the state-specific expansion approach. Its implementation requires the computation of bound-bound, bound-free and free-free N-electron matrix elements of the operator that describes the coupling of the electrons to the external electromagnetic field. The present study penetrates into the mathematical properties of the free-free matrix elements of the full electric field operator of the multipolar Hamiltonian. kk is the photon wavenumber, and the field is assumed linearly polarized, propagating along the z axis. Special methods are developed and applied for the computation of such matrix elements using energy-normalized, numerical scattering wavefunctions. It is found that, on the momentum (energy) axis, the free-free matrix elements hav...

  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. pH- and thermal-dependent conformational transition of PGAIPG, a repeated hexapeptide sequence from tropoelastin.

    Science.gov (United States)

    Lin, Shan-Yang; Hsieh, Tzu-Feng; Wei, Yen-Shan

    2005-04-01

    The secondary structure of PGAIPG (Pro-Gly-Ala-IIe-Pro-Gly), a repeated hexapeptide of tropoelastin, in buffer solution of different pH was determined by using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy. The thermal-dependent structural change of PGAIPG in aqueous solution or in solid state was also examined by thermal FTIR microspectroscopy. The conformation of PGAIPG in aqueous solution exhibited a pH-dependent structural characterization. A predominant peak at 1614 cm(-1) (aggregated beta-sheet) with a shoulder near 1560 cm(-1) (beta-sheet) appeared in pH 5.5-8.5 buffer solutions. A new broad shoulder at 1651 cm(-1) (random coil and/or alpha-helix) with 1614 cm(-1) was observed in the pH 4.5 buffer solution. However, the broad shoulder at 1651 cm(-1) was converted to a maximum peak at 1679 cm(-1) (beta-turn/antiparallel beta-sheet) when the pH shifted from 4.5 to 3.5, but the original pronounced peak at 1614 cm(-1) became a shoulder. Once the pH was lowered to 2.5, the IR spectrum of PGAIPG was dominated by major absorption at 1679 cm(-1) with a minor peak at 1552 cm(-1) (alpha-helix/random coil). The result indicates that the pH was a predominant factor to transform PGAIPG structure from aggregated beta-sheet (pH 8.5) to beta-turn/intermolecular antiparallel beta-sheet (pH 2.5). Moreover, a partial conformation of PGAIPG with minor alpha-helix/random coil structures was also explored in the lower pH buffer solution. There was no thermal-dependent structural change for solid-state PGAIPG. The thermal-induced formation of aggregated beta-sheet for PGAIPG in aqueous solution was found from 28 to 30 degrees C, however, which might be correlated with the formation of an opaque gel that turned from clear solution. The formation of aggregated beta-sheet structure for PGAIPG beyond 30 degrees C might be due to the intermolecular hydrogen bonded interaction between the hydrophobic PGAIPG fragments induced by coacervation.

  1. Conformational cooling dynamics in matrix-isolated 1,3-butanediol.

    Science.gov (United States)

    Rosado, Mário T S; Jesus, António J Lopes; Reva, Igor D; Fausto, Rui; Redinha, José S

    2009-07-02

    The complete conformational space of monomeric 1,3-butanediol has been characterized theoretically, and 73 unique stable conformers were found at the MP2/6-311++G(d,p) level. These were classified into nine families whose members share the same heavy atom backbone configurations and differ in the hydrogen atom orientations. The first and third most populated backbone families are governed by the formation of an intramolecular hydrogen bond; however, the second precludes this type of interaction and was frequently overlooked in previous studies. Its stability is determined by the relatively high entropy of its main conformers. The hydrogen bonding of four of the most important conformers was characterized by means of atoms in molecules (AIM, also known as QTAIM) and natural bond orbital (NBO) analyses. Using appropriate isodesmic reactions, hydrogen bonding energy stabilizations of 12-14 kJ mol(-1) have been found. Experimentally, monomeric molecules of 1,3-butanediol were isolated in low-temperature inert matrixes, and their infrared spectra were analyzed from the viewpoint of the conformational distribution. All the relevant transition states for the conformational interconversion reaction paths were characterized at the same level of theory to interpret the conformational cooling dynamics observed in the low-temperature matrixes. The energy barriers for rotation of the OH groups were calculated to be very low (conformers. Further increase in the substrate temperature (up to 40 K, Xe matrix) resulted in conformational cooling where the medium-height barriers (approximately 13 kJ mol(-1)) could be surmounted and all conformational population converted to the ground conformational state. Remarkably, this state turned to consist of two forms of the most stable hydrogen bonded family, which were predicted by calculations to be accidentally degenerated and were found in the annealed matrix in equal amounts. All of these experimentally observed conformational cooling

  2. Temperature and electric field induced metal-insulator transition in atomic layer deposited VO2 thin films

    Science.gov (United States)

    Tadjer, Marko J.; Wheeler, Virginia D.; Downey, Brian P.; Robinson, Zachary R.; Meyer, David J.; Eddy, Charles R.; Kub, Fritz J.

    2017-10-01

    Amorphous vanadium oxide (VO2) films deposited by atomic layer deposition (ALD) were crystallized with an ex situ anneal at 660-670 °C for 1-2 h under a low oxygen pressure (10-4 to 10-5 Torr). Under these conditions the crystalline VO2 phase was maintained, while formation of the V2O5 phase was suppressed. Electrical transition from the insulator to the metallic phase was observed in the 37-60 °C range, with an ROFF/RON ratio of up to about 750 and ΔTC ≅ 7-10 °C. Lateral electric field applied across two-terminal device structures induced a reversible phase change, with a room temperature transition field of about 25 kV/cm in the VO2 sample processed with the 2 h long O2 anneal. Both the width and slope of the field induced MIT I-V hysteresis were dependent upon the VO2 crystalline quality.

  3. Magnetism of 3d transition metal atoms on W(001): submonolayer films

    Energy Technology Data Exchange (ETDEWEB)

    Ondracek, M [Institute of Physics, Academy of Sciences of the Czech Republic, Prague, CZ (Czech Republic); Kudrnovsky, J [Institute of Physics, Academy of Sciences of the Czech Republic, Prague, CZ (Czech Republic); Turek, I [Institute of Physics of Materials, Academy of Sciences of the Czech Republic, Brno, CZ (Czech Republic); Maca, F [Institute of Physics, Academy of Sciences of the Czech Republic, Prague, CZ (Czech Republic)

    2007-04-15

    We have investigated random submonolayer films of 3d transition metals on W(001). The tight-binding linear muffin-tin orbital method combined with the coherent potential approximation was employed to calculate the electronic structure of the films. We have estimated local magnetic moments and the stability of different magnetic structures, namely the ferromagnetic order, the disordered local moments and the non-magnetic state, by comparing the total energies of the corresponding systems. It has been found that the magnetic moments of V and Cr decrease and eventually disappear with decreasing coverage. On the other hand, Fe retains approximately the same magnetic moment throughout the whole concentration range from a single impurity to the monolayer coverage. Mn is an intermediate case between Cr and Fe since it is non-magnetic at very low coverages and (ferro)magnetic otherwise.

  4. Dynamic conformational transitions of the EGF receptor in living mammalian cells determined by FRET and fluorescence lifetime imaging microscopy.

    Science.gov (United States)

    Ziomkiewicz, Iwona; Loman, Anastasia; Klement, Reinhard; Fritsch, Cornelia; Klymchenko, Andrey S; Bunt, Gertrude; Jovin, Thomas M; Arndt-Jovin, Donna J

    2013-09-01

    We have revealed a reorientation of ectodomain I of the epidermal growth factor receptor (EGFR; ErbB1; Her1) in living CHO cells expressing the receptor, upon binding of the native ligand EGF. The state of the unliganded, nonactivated EGFR was compared to that exhibited after ligand addition in the presence of a kinase inhibitor that prevents endocytosis but does not interfere with binding or the ensuing conformational rearrangements. To perform these experiments, we constructed a transgene EGFR with an acyl carrier protein sequence between the signal peptide and the EGFR mature protein sequence. This protein, which behaves similarly to wild-type EGFR with respect to EGF binding, activation, and internalization, can be labeled at a specific serine in the acyl carrier tag with a fluorophore incorporated into a 4'-phosphopantetheine (P-pant) conjugate transferred enzymatically from the corresponding CoA derivative. By measuring Förster resonance energy transfer between a molecule of Atto390 covalently attached to EGFR in this manner and a novel lipid probe NR12S distributed exclusively in the outer leaflet of the plasma membrane, we determined the apparent relative separation of ectodomain I from the membrane under nonactivating and activating conditions. The data indicate that the unliganded domain I of the EGFR receptor is situated much closer to the membrane before EGF addition, supporting the model of a self-inhibited configuration of the inactive receptor in quiescent cells. Copyright © 2013 International Society for Advancement of Cytometry.

  5. Alkali metal and simple gas atom adsorption and coadsorption on transition metal surfaces

    CERN Document Server

    Norris, A G

    2000-01-01

    system is formed by adsorption of potassium or cesium on the Ni(100)c(2x2)-O overlayer. The difficulty of the structural fit is compounded' by the size of the unit cell. In this study, Anomalous Scattering was used to investigate whether there is a contribution from the nickel substrate to the reconstruction. Measurements of the fractional order rods at 10 eV and 200 eV below the nickel K edge (8333 eV) showed no discernible differences and involvement of the nickel substrate in the reconstruction can be eliminated. Alkali metal coadsorption systems represent a step along the pathway from simple model adsorbate overlayers to more technologically relevant real systems. Such is their complexity, however, that very few systems have been solved structurally. Presented here are SXRD and STM investigations of two such systems. The first study involves potassium adsorption on the Ni(100)(2x2)p4g-N surface, where a clock reconstruction is present with the nickel substrate atoms rotated in alternate clockwise and anti...

  6. Atomically thin arsenene and antimonene: semimetal-semiconductor and indirect-direct band-gap transitions.

    Science.gov (United States)

    Zhang, Shengli; Yan, Zhong; Li, Yafei; Chen, Zhongfang; Zeng, Haibo

    2015-03-02

    The typical two-dimensional (2D) semiconductors MoS2, MoSe2, WS2, WSe2 and black phosphorus have garnered tremendous interest for their unique electronic, optical, and chemical properties. However, all 2D semiconductors reported thus far feature band gaps that are smaller than 2.0 eV, which has greatly restricted their applications, especially in optoelectronic devices with photoresponse in the blue and UV range. Novel 2D mono-elemental semiconductors, namely monolayered arsenene and antimonene, with wide band gaps and high stability were now developed based on first-principles calculations. Interestingly, although As and Sb are typically semimetals in the bulk, they are transformed into indirect semiconductors with band gaps of 2.49 and 2.28 eV when thinned to one atomic layer. Significantly, under small biaxial strain, these materials were transformed from indirect into direct band-gap semiconductors. Such dramatic changes in the electronic structure could pave the way for transistors with high on/off ratios, optoelectronic devices working under blue or UV light, and mechanical sensors based on new 2D crystals. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. 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.

  8. NMR elucidation of monomer-dimer transition and conformational heterogeneity in histone-like DNA binding protein of Helicobacter pylori.

    Science.gov (United States)

    Jaiswal, Nancy; Raikwal, Nisha; Pandey, Himanshu; Agarwal, Nipanshu; Arora, Ashish; Poluri, Krishna Mohan; Kumar, Dinesh

    2017-12-14

    Helicobacter pylori (H. pylori) colonizes under harsh acidic/oxidative stress conditions of human gastrointestinal tract and can survive there for infinitely longer durations of host life. The bacterium expresses several harbinger proteins to facilitate its persistent colonization under such conditions. One such protein in H. pylori is histone-like DNA binding protein (Hup), which in its homo-dimeric form binds to DNA to perform various DNA dependent cellular activities. Further, it also plays an important role in protecting the genomic DNA from oxidative stress and acidic denaturation. Legitimately, if the binding of Hup to DNA is suppressed, it will directly impact on the survival of the bacterium, thus making Hup a potential therapeutic target for developing new anti-H. pylori agents. However, to inhibit the binding of Hup to DNA, it is necessary to gain detailed insights into the molecular and structural basis of Hup-dimerization and its binding mechanism to DNA. As a first step in this direction, we report here the nuclear magnetic resonance (NMR) assignments and structural features of Hup at pH 6.0. The study revealed the occurrence of dynamic equilibrium between its monomer and dimer conformations. The dynamic equilibrium was found to shifting towards dimer both at low temperature and low pH; whereas DNA binding studies evidenced that the protein binds to DNA in its dimeric form. These preliminary investigations correlate very well with the diverse functionality of protein and will form the basis for future studies aiming to develop novel anti-H. pylori agents employing structure-based-rational drug discovery approach. Copyright © 2017 John Wiley & Sons, Ltd.

  9. NIR Laser Radiation Induced Conformational Changes and Tunneling Lifetimes of High-Energy Conformers of Amino Acids in Low-Temperature Matrices

    Science.gov (United States)

    Bazso, Gabor; Najbauer, Eszter E.; Magyarfalvi, Gabor; Tarczay, Gyorgy

    2013-06-01

    We review our recent results on combined matrix isolation FT-IR and NIR laser irradiation studies on glycine alanine, and cysteine. The OH and the NH stretching overtones of the low-energy conformers of these amino acids deposited in Ar, Kr, Xe, and N_{2} matrices were irradiated. At the expense of the irradiated conformer, other conformers were enriched and new, high-energy, formerly unobserved conformers were formed in the matrices. This enabled the separation and unambiguous assignment of the vibrational transitions of the different conformers. The main conversion paths and their efficiencies are described qualitatively showing that there are significant differences in different matrices. It was shown that the high-energy conformer decays in the matrix by H-atom tunneling. The lifetimes of the high-energy conformers in different matrices were measured. Based on our results we conclude that some theoretically predicted low-energy conformers of amino acids are likely even absent in low-energy matrices due to fast H-atom tunneling. G. Bazso, G. Magyarfalvi, G. Tarczay J. Mol. Struct. 1025 (Light-Induced Processes in Cryogenic Matrices Special Issue) 33-42 (2012). G. Bazso, G. Magyarfalvi, G. Tarczay J. Phys. Chem. A 116 (43) 10539-10547 (2012). G. Bazso, E. E. Najbauer, G. Magyarfalvi, G. Tarczay J. Phys. Chem. A in press, DOI: 10.1021/jp400196b. E. E. Najbauer, G. Bazso, G. Magyarfalvi, G. Tarczay in preparation.

  10. 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.

  11. 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...

  12. 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.

  13. All-Atom Multiscale Molecular Dynamics Theory and Simulation of Self-Assembly, Energy Transfer and Structural Transition in Nanosystems

    Science.gov (United States)

    Espinosa Duran, John Michael

    The study of nanosystems and their emergent properties requires the development of multiscale computational models, theories and methods that preserve atomic and femtosecond resolution, to reveal details that cannot be resolved experimentally today. Considering this, three long time scale phenomena were studied using molecular dynamics and multiscale methods: self-assembly of organic molecules on graphite, energy transfer in nanosystems, and structural transition in vault nanoparticles. Molecular dynamics simulations of the self-assembly of alkoxybenzonitriles with different tail lengths on graphite were performed to learn about intermolecular interactions and phases exhibited by self-organized materials. This is important for the design of ordered self-assembled organic photovoltaic materials with greater efficiency than the disordered blends. Simulations revealed surface dynamical behaviors that cannot be resolved experimentally today due to the lack of spatiotemporal resolution. Atom-resolved structures predicted by simulations agreed with scanning tunneling microscopy images and unit cell measurements. Then, a multiscale theory based on the energy density as a field variable is developed to study energy transfer in nanoscale systems. For applications like photothermal microscopy or cancer phototherapy is required to understand how the energy is transferred to/from nanosystems. This multiscale theory could be applied in this context and here is tested for cubic nanoparticles immersed in water for energy being transferred to/from the nanoparticle. The theory predicts the energy transfer dynamics and reveals phenomena that cannot be described by current phenomenological theories. Finally, temperature-triggered structural transitions were revealed for vault nanoparticles using molecular dynamics and multiscale simulations. Vault is a football-shaped supramolecular assembly very distinct from the commonly observed icosahedral viruses. It has very promising

  14. 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...

  15. 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.

  16. First-principles studies of BN sheets with absorbed transition metal single atoms or dimers: stabilities, electronic structures, and magnetic properties.

    Science.gov (United States)

    Ma, Dongwei; Lu, Zhansheng; Ju, Weiwei; Tang, Yanan

    2012-04-11

    BN sheets with absorbed transition metal (TM) single atoms, including Fe, Co, and Ni, and their dimers have been investigated by using a first-principles method within the generalized gradient approximation. All of the TM atoms studied are found to be chemically adsorbed on BN sheets. Upon adsorption, the binding energies of the Fe and Co single atoms are modest and almost independent of the adsorption sites, indicating the high mobility of the adatoms and isolated particles to be easily formed on the surface. However, Ni atoms are found to bind tightly to BN sheets and may adopt a layer-by-layer growth mode. The Fe, Co, and Ni dimers tend to lie (nearly) perpendicular to the BN plane. Due to the wide band gap of the pure BN sheet, the electronic structures of the BN sheets with TM adatoms are determined primarily by the distribution of TM electronic states around the Fermi level. Very interesting spin gapless semiconductors or half-metals can be obtained in the studied systems. The magnetism of the TM atoms is preserved well on the BN sheet, very close to that of the corresponding free atoms and often weakly dependent on the adsorption sites. The present results indicate that BN sheets with adsorbed TM atoms have potential applications in fields such as spintronics and magnetic data storage due to the special spin-polarized electronic structures and magnetic properties they possess.

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

    Science.gov (United States)

    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

    2017-07-01

    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.

  18. Surface conformations of anti-ricin aptamer and its affinity to ricin determined by atomic force microscopy and surface plasmon resonance

    Science.gov (United States)

    The specific interactions between ricin and anti-ricin aptamer were measured with atomic force microscopy (AFM) and surface plasmon resonance (SPR) spectrometry and the results were compared. In AFM, a single-molecule experiment with ricin functionalized AFM tip was used for scanning the aptamer mol...

  19. 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

  20. Effect of Glow-to-Arc Transition on Loss Mechanism of Ba Atoms from Electrode of Fluorescent Lamp

    Science.gov (United States)

    Ueda, Takashi; Samir, Ahmed; Egashira, Yuichi; Yamashita, Go; Shimada, Shozaburo; Yamagata, Yukihiko; Uchino, Kiichiro; Manabe, Yoshio

    2007-10-01

    The loss of Ba atoms from the electrode of a fluorescent lamp was measured while the lamp was operated in the glow and arc discharge modes at 60 Hz. A laser-induced fluorescence (LIF) technique was applied to the measurements of the temporal and spatial distributions of Ba atoms in the vicinity of the electrode. Ground-state (61S0) Ba atoms were excited to a 51P1 level by a frequency-doubled dye laser beam (350.1 nm), and the subsequent fluorescence (51P1-51D2, 582.6 nm) was detected. The temporal and spatial distributions of Ba atoms were found to be completely different in the two discharge modes. Temporally; in the arc discharge mode, the density of the Ba atoms was found to have two peaks, and the number of Ba atoms emitted in the anode half-cycle was about twofold larger than that emitted in the cathode half-cycle. In the glow discharge mode, the number of Ba atoms emitted in the anode half-cycle was found to be negligible compared with that emitted in the cathode half-cycle. Spatially; in the arc discharge mode, Ba atoms were found to be emitted mainly from the hot spot of the filament electrode. In the glow discharge mode, Ba atoms were found to be emitted from all parts of the filament electrodes homogeneously. The mechanism of Ba atom loss in both modes was discussed.

  1. The influence of higher spatial harmonics of atomic polarization on the saturated absorption resonance upon excitation of open dipole transitions by a field of counterpropagating waves

    Science.gov (United States)

    Brazhnikov, D. V.; Novokreshchenov, A. S.

    2017-04-01

    The effect of a double structure of saturated absorption resonance in the field of counterpropagating light waves interacting with an atomic gas is studied. The experimental observation of this effect was first reported in 2011 in a work by our colleagues at the P.N. Lebedev Physical Institute of the Russian Academy of Sciences (Laboratory of Frequency Standards). The essence of the effect lies in the fact that, on exciting an open dipole transition, another, narrower, resonance of an opposite sign can be observed at the center of the ordinary saturated absorption resonance. A theoretical analysis of this effect has also been performed in this work in terms of a simple spectroscopic model of an atom with two nondegenerate energy levels without taking into account higher spatial harmonics of atomic polarization and polarizations of light waves (scalar model). The present work is devoted to the development of a theory of the formation of a central narrow resonance for the example of a real F g = 1 → F e = 1 atomic transition and to the study of its main characteristics (amplitude, width, contrast, and amplitude-to-width ratio). In addition, the theoretical results obtained without taking into account the influence of higher spatial harmonics and with inclusion of the influence of first higher harmonics are compared. This comparison shows that their influence on the parameters of the new nonlinear resonance is strong even in moderately intense light fields ( R γ, where R is the Rabi frequency). The results of this study can be of interest for quantum metrology, as well as for many experiments in which the laser-radiation frequency is stabilized by the saturated absorption resonance on open dipole transitions in atoms and molecules.

  2. 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.

  3. The solid-state and solution-state reassigned structures of tagitinin A, a 3,10-epoxy-germacrolide from Tithonia diversifolia, and the interconversion of 3,10-epoxy-germacrolide conformational families via a ring-atom flip mechanism

    Energy Technology Data Exchange (ETDEWEB)

    Glaser, Robert [Ben-Gurion University of the Negev (Israel). Dept. of Chemistry]. E-mail: rglaser@bgumail.bgu.ac.il; Garcia, Abraham; Chavez, Maria Isabel; Delgado, Guillermo [Universidad Nacional Autonoma de Mexico, Mexico, D.F. (Mexico). Inst. de Quimica]. E-mail: delgado@servidor.unam.mx

    2005-05-15

    Tagitinin A (2), a known 3,10-epoxy-germacrolide-6,7-trans-lactone isolated from Tithonia diversifolia, was investigated by single crystal X-ray diffraction analysis. It was found to have a 1{beta},4{alpha},6{alpha},7{beta},8{beta} relative configuration which differed at C(1) from the 1a-orientation originally reported in the literature which was determined by Horeau's Rule. Analysis of the 1H NMR spectrum of 2 shows the molecule to maintain its crystallographically observed twist-chair-boat (TCB) nine-membered ring conformation in acetone-d6 solution. The twist-chair-boat/skew-chair-boat type 3 conformations of saturated/unsaturated nine-membered rings within 3,10-epoxy-germacrolides can be interconverted to the skew-chair-chair (SCC) conformation by means of a C(9) ring atom flip mechanism. As a result of this conformational change, the orientation of the C(1) atom and the C(8)-oxycarbonyl moiety are transformed from diequatorial to diaxial. The reported stereochemistry of 3,10-epoxy-germacrolide lactone structures, and the DFT B3LYP/6-31g(d) modeling findings in this work indicate that tetrahedral C(1) atoms stabilize the TCB/SCB type 3 conformations, while their trigonal counterparts stabilize the SCC conformation. (author)

  4. Structural stability and O2 dissociation on nitrogen-doped graphene with transition metal atoms embedded: A first-principles study

    Directory of Open Access Journals (Sweden)

    Mingye Yang

    2015-06-01

    Full Text Available By using first-principles calculations, we investigate the structural stability of nitrogen-doped (N-doped graphene with graphitic-N, pyridinic-N and pyrrolic-N, and the transition metal (TM atoms embedded into N-doped graphene. The structures and energetics of TM atoms from Sc to Ni embedded into N-doped graphene are studied. The TM atoms at N4V 2 forming a 4N-centered structure shows the strongest binding and the binding energies are more than 7 eV. Finally, we investigate the catalytic performance of N-doped graphene with and without TM embedding for O2 dissociation, which is a fundamental reaction in fuel cells. Compared to the pyridinic-N, the graphitic-N is more favorable to dissociate O2 molecules with a relatively low reaction barrier of 1.15 eV. However, the catalytic performance on pyridinic-N doped structure can be greatly improved by embedding TM atoms, and the energy barrier can be reduced to 0.61 eV with V atom embedded. Our results provide the stable structure of N-doped graphene and its potential applications in the oxygen reduction reactions.

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

    Science.gov (United States)

    Watanabe, Shinta; Sawada, Yuki; Nakaya, Masato; Yoshino, Masahito; Nagasaki, Takanori; Kameyama, Tatsuya; Torimoto, Tsukasa; Inaba, Yusuke; Takahashi, Hideharu; Takeshita, Kenji; Onoe, Jun

    2016-06-01

    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 Fe2+ to Fe3+ but also the 3d-3d intra-transitions of Fe3+ ions. In addition, the spin crossover transition of Fe3+ 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 Fe2+ ions. In contrast to the Fe and Co ferrocyanides, Ni ferrocyanide showed that the absorption peaks originated from the 3d-3d intra-transitions of Ni3+ ions in a low-energy region, while from both the 3d-3d intra-transitions of Fe2+ ions and the charge-transfer transitions from Fe2+ to Ni3+ 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Data set for fabrication of conformal two-dimensional TiO2 by atomic layer deposition using tetrakis (dimethylamino titanium (TDMAT and H2O precursors

    Directory of Open Access Journals (Sweden)

    Serge Zhuiykov

    2017-08-01

    Full Text Available The data and complementary information presented hare are related to the research article of “http://dx.doi.org/10.1016/j.matdes.2017.02.016; Materials and Design 120 (2017 99–108” [1]. The article provides data and information on the case of atomic layer deposition (ALD of ultra-thin two-dimensional TiO2 film. The chemical structure of precursors, and the fabrication process were illustrated. The data of spectral ellipsometric measurements and the methods of calculations were presented. Data of root mean square roughness and the average roughness of the ADL TiO2 film are presented. The method of bandgap measurements and the bandgap calculation are also explained in the present data article.

  13. 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

    as ligand binding in this region can accelerate or decelerate the conformational inactivation. Plasticity in this region may thus be mechanistically linked to the conformational change, possibly through facilitation of further unfolding of the hydrophobic core, as previously reported. This study provides...... a promising example of how computer simulations can help tether out mechanisms of serpin function and dysfunction at a spatial and temporal resolution that is far beyond the reach of any experiment....

  14. Study of the 5p3/2 -> 6p3/2 electric dipole forbidden transition in atomic rubidium using optical-optical double resonance spectroscopy

    CERN Document Server

    Ponciano-Ojeda, Francisco; López-Hernández, Oscar; Mojica-Casique, Cristian; Colín-Rodríguez, Ricardo; Ramírez-Martínez, Fernando; Flores-Mijangos, Jesús; Sahagún, Daniel; Jáuregui, Rocío; Jiménez-Mier, José

    2015-01-01

    Direct evidence of excitation of the 5p3/2 -> 6p3/2 electric dipole forbidden transition in atomic rubidium is presented. The experiments were performed in a room temperature rubidium cell with continuous wave extended cavity diode lasers. Optical-optical double resonance spectroscopy with counterpropagating beams allows the detection of the non-dipole transition free of Doppler broadening. The 5p3/2 state is prepared by excitation with a laser locked to the maximum F cyclic transition of the D2 line, and the forbidden transition is produced by excitation with a 911 nm laser. Production of the forbidden transition is monitored by detection of the 420 nm fluorescence that results from decay of the 6p3/2 state. Spectra with three narrow lines (~ 13 MHz FWHM) with the characteristic F - 1, F and F + 1 splitting of the 6p3/2 hyperfine structure in both rubidium isotopes were obtained. The results are in very good agreement with a direct calculation that takes into account the 5s -> 5p3/2 preparation dynamics, the...

  15. 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.

  16. Spin-dependent structural, electronic and transport properties of armchair graphyne nanoribbons doped with single transition-metal atom, using DFT calculations

    Science.gov (United States)

    Golafrooz Shahri, S.; Roknabadi, M. R.; Radfar, R.

    2017-12-01

    In this present paper, the non-equilibrium Green function (NEGF) method along with the density functional theory (DFT) were used to investigate the effect of doping a single transition-metal atom on transport and electronic properties of armchair graphyne (γ-graphyne) nanoribbons. It can be deduced from the results that among the doped TM atoms, Mn and Fe cause stronger polarized currents comparing to Co and Ni. Mn-AGyNR represents the features of a half-semiconductor and behaves like a semiconductor in both up and down spin channels. On the other hand, Fe-AGyNR shows a great potential in spintronic applications due to its half-metal properties. Also our results show the promising application of armchair graphyne nanoribbons in nano-electrical devices.

  17. 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....

  18. Conformations and Conformational Processes of Hexahydrobenzazocines by NMR and DFT Studies.

    Science.gov (United States)

    Musielak, Bogdan; Holak, Tad A; Rys, Barbara

    2015-09-18

    Conformational processes that occur in hexahydrobenzazocines have been studied with the (1)H and (13)C dynamic nuclear magnetic resonance (DNMR) spectroscopy. The coalescence effects are assigned to two different conformational processes: the ring-inversion of the ground-state conformations and the interconversion between two different conformers. The barriers for these processes are in the range of 42-52 and 42-43 kJ mol(-1), respectively. Molecular modeling on the density functional theory (DFT) level and the gauge invariant atomic orbitals (GIAO)-DFT calculations of isotropic shieldings and coupling constants for the set of low-energy conformations were compared with the experimental NMR data. The ground-state of all compounds in solution is the boat-chair (BC) conformation. The BC form adopts two different conformations because the nitrogen atom can be in the boat or chair parts of the BC structure. These two conformers are engaged in the interconversion process.

  19. Saturated-absorption spectroscopy revisited: atomic transitions in strong magnetic fields ($>$20 mT) with a micrometer-thin cell

    OpenAIRE

    Sargsyan, A.; Tonoyan, A.(Department for Physics and Technology, University of Bergen, Bergen, Norway); Mirzoyan, R.; Sarkisyan, D; Stabrawa, A. M. Wojciechowski A.; Gawlik, W.

    2014-01-01

    The existence of cross-over resonances makes saturated-absorption spectra very complicated when external magnetic field B is applied. It is demonstrated for the first time that the use of micrometric-thin cells (MTC, $L\\approx40\\,\\mu$m) allows application of SA for quantitative studies of frequency splittings and shifts of the Rb atomic transitions in a wide range of external magnetic fields, from 0.2 up to 6 kG (20-600 mT). We compare the SA spectra obtained with the MTC with those obtained ...

  20. Spectroscopie de l'atome d'hydrogène. Vers une mesure absolue de la fréquence de la transition 1S-3S.

    OpenAIRE

    Hagel, Gaëtan

    2001-01-01

    The subject of this thesis is the 1S-3S two-photons transition frequency measurement in hydrogen. For that one needs a 205 nm radiation obtained from a titane-sapphire laser by two frequency doubling steps.The chapter 1 of this thesis deals with the scectroscopy of the hydrogen atom since the last twenty years. In the chapters 3 and 4 the experimental set-up is described in details. One can see in these parts that one of the important point of the work was devoted to the rise-up of the signal...

  1. Detection of the Direct Hyperfine Transition of Positronium Atoms using sub-THz High-power Radiation

    OpenAIRE

    Suehara, T.; Miyazaki, A.; Yamazaki, T; G. Akimoto; Ishida, A; NAMBA, T; Asai, S.; Kobayashi, T; Saito, H.(Institute of Physics, Graduate School of Arts and Sciences, University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan); Yoshida, M.; IDEHARA, T; Ogawa, I.; Urushizaki, Y.; SABCHEVSKI, S

    2010-01-01

    Hyperfine splitting of positronium is an important parameter for particle physics. This paper gives experimental techniques and results of R&D studies of our experiment to observe direct hyperfine transition of ortho-positronium to para-positronium.

  2. Calculation of state-to-state differential and integral cross sections for atom-diatom reactions with transition-state wave packets.

    Science.gov (United States)

    Zhao, Bin; Sun, Zhigang; Guo, Hua

    2014-06-21

    A recently proposed transition-state wave packet method [R. Welsch, F. Huarte-Larrañaga, and U. Manthe, J. Chem. Phys. 136, 064117 (2012)] provides an efficient and intuitive framework to study reactive quantum scattering at the state-to-state level. It propagates a few transition-state wave packets, defined by the eigenfunctions of the low-rank thermal flux operator located near the transition state, into the asymptotic regions of the reactant and product arrangement channels separately using the corresponding Jacobi coordinates. The entire S-matrix can then be assembled from the corresponding flux-flux cross-correlation functions for all arrangement channels. Since the transition-state wave packets can be defined in a relatively small region, its transformation into either the reactant or product Jacobi coordinates is accurate and efficient. Furthermore, the grid/basis for the propagation, including the maximum helicity quantum number K, is much smaller than that required in conventional wave packet treatments of state-to-state reactive scattering. This approach is implemented for atom-diatom reactions using a time-dependent wave packet method and applied to the H + D2 reaction with all partial waves. Excellent agreement with benchmark integral and differential cross sections is achieved.

  3. 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

  4. Plastic-to-Elastic Transition in Aggregated Emulsion Networks, Studied with Atomic Force Microscopy-Confocal Scanning Laser Microscopy Microrheology

    NARCIS (Netherlands)

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

    2006-01-01

    In this paper, we demonstrate how the simultaneous application of atomic force microscopy (AFM) and confocal scanning laser microscopy (CSLM) can be used to characterize the (local) rheological properties of soft condensed matter at micrometer length scales. Measurement of AFM force curves as a

  5. Repumping and spectroscopy of laser-cooled Sr atoms using the (5s5p){sup 3}P{sub 2}-(5s4d){sup 3}D{sub 2} transition

    Energy Technology Data Exchange (ETDEWEB)

    Mickelson, P G; De Escobar, Y N Martinez; Anzel, P; DeSalvo, B J; Nagel, S B; Traverso, A J; Yan, M; Killian, T C, E-mail: killian@rice.ed [Department of Physics and Astronomy, Rice University, Houston, TX 77251 (United States)

    2009-12-14

    We describe repumping and spectroscopy of laser-cooled strontium (Sr) atoms using the (5s5p){sup 3}P{sub 2}-(5s4d){sup 3}D{sub 2} transition. Atom number in a magneto-optical trap is enhanced by driving this transition because Sr atoms that have decayed into the (5s5p){sup 3}P{sub 2} dark state are repumped back into the (5s{sup 2}){sup 1}S{sub 0} ground state. Spectroscopy of {sup 84}Sr, {sup 86}Sr, {sup 87}Sr and {sup 88}Sr improves the value of the (5s5p){sup 3}P{sub 2}-(5s4d){sup 3}D{sub 2} transition frequency and determines the isotope shifts for the transition accurately enough to guide laser-cooling experiments with less abundant isotopes.

  6. Study of the atom-phonon coupling model for (SC) partition function: first order phase transition for an infinite linear chain

    Science.gov (United States)

    Nasser, Jamil A.; Chassagne, Luc; Topçu, Suat; Linares, Jorge; Alayli, Yasser

    2014-03-01

    In spin-conversion (SC) compounds containing molecules organized around an iron (II) ion the fundamental level of the ion is low spin (LS), S = 0, and its first excited one is high spin (HS), S = 2. This energy diagram is due to the ligands field interaction on 3d electrons and to the spin pairing energy. Heating the compound increases the magnetic susceptibility which corresponds to a change of populations of both levels and consequently a change of spin value of the molecules. This mechanism, called spin conversion (SC), can be accompagnied by thermal hysteresis observed by studying magnetic susceptibility or high spin fraction. In that case one considers that the (SC) takes place through a first-order phase transition due to intermolecular interactions. In the atom-phonon coupling model the molecules are considered as two-level systems, or two-level atoms, and it is assumed that the elastic force constant value of the spring which links two atoms first neighbours is depending on the electronic states of both atoms. In this study we calculate the partition function of a linear chain of N atoms (N ≤ 16) and we describe the role of phonons and that of the parameter Δ which corresponds to the distance in energy between both levels. The chain free-energy function is Fatph. We introduce for the chain a free-energy function defined by the set (FHS, FLS, Fbarr) and we show that Fatph tends towards the previous set when N → ∞. The previous set allows to describe a first order phase transition between a (LS) phase and a (HS) one. At the crossing point between the function FLS and FHS, and around this point, there is an intermediate free-energy barrier which prevents the chain to change phase which can lead to thermal hysteresis. The energy gap between the free-energy function Fatph and that defined by the set (FHS, FLS, Fbarr) is small. So we can expect that a nanoparticule takes for free-energy function that defined by the set and then displays a thermal

  7. 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.

  8. Two Keggin-type heteropolytungstates with transition metal as a central atom: Crystal structure and magnetic study with 2D-IR correlation spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Chai, Feng [Department of Chemistry, Fuzhou University, Fuzhou 350108 (China); Chen, YiPing, E-mail: ypchen007@sina.com [Department of Chemistry, Fuzhou University, Fuzhou 350108 (China); State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002 (China); You, ZhuChai; Xia, ZeMin; Ge, SuZhi; Sun, YanQiong; Huang, BiHua [Department of Chemistry, Fuzhou University, Fuzhou 350108 (China)

    2013-06-01

    Two Keggin-type heteropolytungstates, [Co(phen)₃]₃[CoW₁₂O₄₀]·9H₂O 1 (phen=1,10-phenanthroline) and [Fe(phen)₃]₂[FeW₁₂O₄₀]·H₃O·H₂O 2, have been synthesized via the hydrothermal technique and characterized by single crystal X-ray diffraction analyses, IR, XPS, TG analysis, UV–DRS, XRD, thermal-dependent and magnetic-dependent 2D-COS IR (two-dimensional infrared correlation spectroscopy). Crystal structure analysis reveals that the polyanions in compound 1 are linked into 3D supramolecule through hydrogen bonding interactions between lattice water molecules and terminal oxygen atoms of polyanion units, and [Co(phen)₃]²⁺ cations distributed in the polyanion framework with many hydrogen bonding interactions. The XPS spectra indicate that all the Co atoms in 1 are +2 oxidation state, the Fe atoms in 2 existing with +2 and +3 mixed oxidation states. - Graphical abstract: The magnetic-dependent synchronous 2D correlation IR spectra of 1 (a), 2 (b) over 0–50 mT in the range of 600–1000 cm⁻¹, the obvious response indicate two Keggin polyanions skeleton susceptible to applied magnetic field. Highlights: • Two Keggin-type heteropolytungstates with transition metal as a central atom has been obtained. • Compound 1 forms into 3D supramolecular architecture through hydrogen bonding between water molecules and polyanions. • Magnetic-dependent 2D-IR correlation spectroscopy was introduced to discuss the magnetism of polyoxometalate.

  9. Self-assembly in a near-frictionless granular material: Conformational structures and transitions in uniaxial cyclic compression of hydrogel spheres

    NARCIS (Netherlands)

    Walker, D.M.; Tordesillas, A.; Brodu, N.; Dijksman, J.A.; Behringer, R.P.; Froyland, G.

    2015-01-01

    We use a Markov transition matrix-based analysis to explore the structures and structural transitions in a three-dimensional assembly of hydrogel spheres under cyclic uniaxial compression. We apply these methods on experimental data obtained from a packing of nearly frictionless hydrogel balls. This

  10. High efficiency optical modulation at a telecom wavelength using the quantum Zeno effect in a ladder transition in Rb atoms.

    Science.gov (United States)

    Krishnamurthy, Subramanian; Wang, Y; Tu, Y; Tseng, S; Shahriar, M S

    2012-06-18

    We demonstrate a high-efficiency optical modulator at ~1323 nm using the quantum Zeno effect in a ladder transition in a Rb vapor cell. The lower leg of the transitions represents the control beam while the upper leg of the transitions represents the signal beam. The cross-modulation of the signal beam transmission is observed as the control beam is intensity modulated, and is explained in terms of the quantum Zeno effect. We observe a modulation depth of near 100% at frequencies up to 1 MHz and demonstrate modulation at speeds up to 75 MHz, with a 3 dB bandwidth of about 5 MHz, limited by the homogeneous linewidth of the intermediate state. We also describe how much higher modulation speeds could be realized by using a buffer gas to broaden the transitions. We identify and explain the special conditions needed for optimizing the modulation efficiency. Numerical simulations of modulation at ~1 GHz are presented. The maximum modulation speed is found to scale with the pressure-broadened linewidth of the intermediate state, so that much higher speeds should be attainable.

  11. Numerical calculations of the probabilities for quantum transitions in atoms and molecules by the path integral method

    Science.gov (United States)

    Biryukov, Alexander; Degtyareva, Yana

    2017-10-01

    The probabilities of molecular quantum transitions induced by electromagnetic field are expressed as path integrals of a real alternating functional. We propose a new method for computing these integrals by means of recurrence relations. We apply this approach to description of the two-photon Rabi oscillations.

  12. Dissecting Local Atomic and Intermolecular Interactions of Transition-Metal Ions in Solution with Selective X-ray Spectroscopy

    NARCIS (Netherlands)

    Wernet, Philippe; Kunnus, Kristjan; Schreck, Simon; Quevedo, Wilson; Kurian, Reshmi|info:eu-repo/dai/nl/331322056; Techert, Simone; de Groot, Frank M. F.|info:eu-repo/dai/nl/08747610X; Odelius, Michael; Foehlisch, Alexander

    2012-01-01

    Determining covalent and charge-transfer contributions to bonding in solution has remained an experimental challenge. Here, the quenching of fluorescence decay channels as expressed in dips in the L-edge X-ray spectra of solvated 3d transition-metal ions and complexes was reported as a probe. With a

  13. 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)

  14. Phase transitions and adiabatic preparation of a fractional Chern insulator in a boson cold-atom model

    Science.gov (United States)

    Motruk, Johannes; Pollmann, Frank

    2017-10-01

    We investigate the fate of hardcore bosons in a Harper-Hofstadter model which was experimentally realized by Aidelsburger et al. [Nat. Phys. 11, 162 (2015), 10.1038/nphys3171] at half-filling of the lowest band. We discuss the stability of an emergent fractional Chern insulator (FCI) state in a finite region of the phase diagram that is separated from a superfluid state by a first-order transition when tuning the band topology following the protocol used in the experiment. Since crossing a first-order transition is unfavorable for adiabatically preparing the FCI state, we extend the model to stabilize a featureless insulating state. The transition between this phase and the topological state proves to be continuous, providing a path in parameter space along which an FCI state could be adiabatically prepared. To further corroborate this statement, we perform time-dependent DMRG calculations which demonstrate that the FCI state may indeed be reached by adiabatically tuning a simple product state.

  15. 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.

  16. α-Helical to β-Helical Conformation Change in the C-Terminal of the Mammalian Prion Protein

    Science.gov (United States)

    Singh, Jesse; Whitford, Paul; Hayre, Natha; Cox, Daniel; Onuchic, José.

    2011-03-01

    We employ all-atom structure-based models with mixed basis contact maps to explore whether there are any significant geometric or energetic constraints limiting conjectured conformational transitions between the alpha-helical (α H) and the left handed beta helical (LHBH) conformations for the C-terminal (residues 166-226) of the mammalian prion protein. The LHBH structure has been proposed to describe infectious oligomers and one class of in vitro grown fibrils, as well as possibly self- templating the conversion of normal cellular prion protein to the infectious form. Our results confirm that the kinetics of the conformation change are not strongely limited by large scale geometry modification and there exists an overall preference for the LHBH conformation.

  17. 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

    This study explores atomic and molecular adsorption on a number of early transition-metal carbides (TMCs) in NaCl structure by means of density-functional theory calculations. The investigated substrates are the TM-terminated TMC(111) surfaces, of interest because of the presence of different typ...... CCM to this larger class of substrates and adsorbates. Implications for other classes of materials, for catalysis, and for other surface processes are discussed....... of surface resonances (SRs) on them and because of their technological importance in growth processes. Also, TM compounds have shown potential in catalysis applications. Trend studies are conducted with respect to both period and group in the periodic table, choosing the substrates ScC, TiC, VC, ZrC, Nb...

  18. Saturated-absorption spectroscopy revisited: atomic transitions in strong magnetic fields (>20  mT) with a micrometer-thin cell.

    Science.gov (United States)

    Sargsyan, A; Tonoyan, A; Mirzoyan, R; Sarkisyan, D; Wojciechowski, A M; Stabrawa, A; Gawlik, W

    2014-04-15

    The existence of crossover resonances makes saturated-absorption (SA) spectra very complicated when external magnetic field B is applied. It is demonstrated for the first time, to the best of our knowledge, that the use of micrometric-thin cells (MTCs, L≈40  μm) allows application of SA for quantitative studies of frequency splitting and shifts of the Rb atomic transitions in a wide range of external magnetic fields, from 0.2 up to 6 kG (20-600 mT). We compare the SA spectra obtained with the MTC with those obtained with other techniques and present applications for optical magnetometry with micrometer spatial resolution and a broadly tunable optical frequency lock.

  19. Valence correlation in the s2dn, sdn + 1, and dn + 2 states of the first-row transition metal atoms

    Science.gov (United States)

    Botch, Beatrice H.; Dunning, Thom. H., Jr.; Harrison, James F.

    1981-10-01

    The major differential valence correlation effects of the lowest lying states arising from the s2dn, sdn+1, and dn+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 4s2 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 sdn+1 and dn+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 (˜0.2 eV in Sc-Cr and ˜0.5 eV in Mn-Cu for the sdn+1-s2dn excitation energy), yet still is of a form which lends itself easily to molecular calculations.

  20. Mapping the temperature-dependent conformational landscapes of the dynamic enzymes cyclophilin A and urease

    Science.gov (United States)

    Thorne, Robert; Keedy, Daniel; Warkentin, Matthew; Fraser, James; Moreau, David; Atakisi, Hakan; Rau, Peter

    Proteins populate complex, temperature-dependent ensembles of conformations that enable their function. Yet in X-ray crystallographic studies, roughly 98% of structures have been determined at 100 K, and most refined to only a single conformation. A combination of experimental methods enabled by studies of ice formation and computational methods for mining low-density features in electron density maps have been applied to determine the evolution of the conformational landscapes of the enzymes cyclophilin A and urease between 300 K and 100 K. Minority conformations of most side chains depopulate on cooling from 300 to ~200 K, below which subsequent conformational evolution is quenched. The characteristic temperatures for this depopulation are highly heterogeneous throughout each enzyme. The temperature-dependent ensemble of the active site flap in urease has also been mapped. These all-atom, site-resolved measurements and analyses rule out one interpretation of the protein-solvent glass transition, and give an alternative interpretation of a dynamical transition identified in site-averaged experiments. They demonstrate a powerful approach to structural characterization of the dynamic underpinnings of protein function. Supported by NSF MCB-1330685.

  1. A quantitative measure for protein conformational heterogeneity.

    Science.gov (United States)

    Lyle, Nicholas; Das, Rahul K; Pappu, Rohit V

    2013-09-28

    Conformational heterogeneity is a defining characteristic of proteins. Intrinsically disordered proteins (IDPs) and denatured state ensembles are extreme manifestations of this heterogeneity. Inferences regarding globule versus coil formation can be drawn from analysis of polymeric properties such as average size, shape, and density fluctuations. Here we introduce a new parameter to quantify the degree of conformational heterogeneity within an ensemble to complement polymeric descriptors. The design of this parameter is guided by the need to distinguish between systems that couple their unfolding-folding transitions with coil-to-globule transitions and those systems that undergo coil-to-globule transitions with no evidence of acquiring a homogeneous ensemble of conformations upon collapse. The approach is as follows: Each conformation in an ensemble is converted into a conformational vector where the elements are inter-residue distances. Similarity between pairs of conformations is quantified using the projection between the corresponding conformational vectors. An ensemble of conformations yields a distribution of pairwise projections, which is converted into a distribution of pairwise conformational dissimilarities. The first moment of this dissimilarity distribution is normalized against the first moment of the distribution obtained by comparing conformations from the ensemble of interest to conformations drawn from a Flory random coil model. The latter sets an upper bound on conformational heterogeneity thus ensuring that the proposed measure for intra-ensemble heterogeneity is properly calibrated and can be used to compare ensembles for different sequences and across different temperatures. The new measure of conformational heterogeneity will be useful in quantitative studies of coupled folding and binding of IDPs and in de novo sequence design efforts that are geared toward controlling the degree of heterogeneity in unbound forms of IDPs.

  2. 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).

  3. 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.

  4. Multiconfiguration Dirac-Hartree-Fock energy levels, oscillator strengths, transition probabilities, hyperfine constants and Landé g-factor of intermediate Rydberg series in neutral argon atom

    Science.gov (United States)

    Salah, Wa'el; Hassouneh, Ola

    2017-04-01

    We computed the energy levels, oscillator strengths f_{ij}, the radiative transition rates A_{ij}, the Landé g -factor, the magnetic dipole moment and the electric quadrupole hyperfine constants of the intermediate Rydberg series ns [k]J ( 4 ≤ n ≤ 6), nd [k]J (3 ≤ n ≤ 4), np [k]J (4 ≤ n ≤ 5) relative to the ground state 3p6 1S0 for neutral argon atom spectra. The values are obtained in the framework of the multiconfiguration Dirac-Hartree-Fock (MCDHF) approach. In this approach, Breit interaction, leading quantum electrodynamics (QED) effects and self-energy correction are taken into account. Moreover, these spectroscopic parameters have been calculated for many levels belonging to the configuration 3p54s, 3p55s, 3p56s, 3p53d, 3p54d, 3p54p, 3p55p as well as for transitions between levels 3p54s-3p54p, 3p54p-3p53d, 3p54p-3p55s, 3p55s-3p55p and 3p55p-3p56s. The large majority of the lines from the 4p-5s and 4p-3d, 5s-5p and 5p-6s transition arrays have been observed and the calculations are consistent with the J -file-sum rule. The obtained theoretical values are compared with previous experimental and theoretical data available in the literature. An overall satisfactory agreement is noticed allowing assessing the reliability of our data.

  5. Solid state conformational classification of eight-membered rings

    DEFF Research Database (Denmark)

    Pérez, J.; García, L.; Kessler, M.

    2005-01-01

    A statistical classification of the solid state conformation in the title complexes using data retrieved from the Cambridge Structural Database (CSD) has been made. Phosphate and phosphinate complexes show a chair conformation preferably. In phosphonate complexes, the most frequent conformations ...... are found to be boat–chair, chair and boat–boat; in all the boat–chair cases, the phosphorus atoms appear connected by a bridging carbon atom....

  6. Pressure dependence of human fibrinogen correlated to the conformational alpha-helix to beta-sheet transition: an Fourier transform infrared study microspectroscopic study.

    Science.gov (United States)

    Lin, Shan-Yang; Wei, Yen-Shan; Hsieh, Tzu-Feng; Li, Mei-Jane

    2004-12-05

    We used Fourier transform infrared (FTIR) microspectroscopy to investigate pressure-induced conformational changes in secondary structure of fibrinogen (FBG). Solid state FBG was compressed on a KBr pellet (1KBr method) or between two KBr pellets (2KBr method). The peak positions of the original and second-derivative ir spectra of compressed FBG samples prepared by the 1KBr method were similar to FBG sample without pressure. When FBG was prepared by the 2KBr method and pressure was increased up to 400 kg/cm(2), peaks at 1625 (intermolecular beta-sheet) and 1611 (beta-sheet aggregates structure and/or the side-chain absorption of the tyrosine residues) cm(-1) were enhanced. The peaks near 1661 (beta-sheet) and 1652 (alpha-helix) cm(-1) also exhibited a marked change with pressure. A linear correlation was found between the peak intensity ratio of 1611/1652 cm(-1) (r = 0.9879) or 1625/1652 cm(-1) (r = 0.9752) and applied pressure. The curve-fitted compositional changes in secondary structure of FBG also indicate that the composition of the alpha-helix structure (1657-1659 cm(-1)) was gradually reduced with the increase in compression pressure, but the composition of the beta-sheet structure (1681, 1629, and 1609 cm(-1)) gradually increased. This indicates that pressure-induced conformational changes in FBG include not only transformations from alpha-helix to beta-sheet structure, but also unfolding and denaturation of FBG and the formation of aggregates. Copyright 2004 Wiley Periodicals, Inc.

  7. 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...

  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. Non-conformable, partial and conformable transposition

    DEFF Research Database (Denmark)

    König, Thomas; Mäder, Lars Kai

    2013-01-01

    Although member states are obliged to transpose directives into domestic law in a conformable manner and receive considerable time for their transposition activities, we identify three levels of transposition outcomes for EU directives: conformable, partially conformable and non-conformable...... 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...

  10. Atomic and molecular adsorption on transition-metal carbide (111) surfaces from density-functional theory: a trend study of surface electronic factors.

    Science.gov (United States)

    Vojvodic, A; Ruberto, C; Lundqvist, B I

    2010-09-22

    This study explores atomic and molecular adsorption on a number of early transition-metal carbides (TMCs) in NaCl structure by means of density-functional theory calculations. The investigated substrates are the TM-terminated TMC(111) surfaces, of interest because of the presence of different types of surface resonances (SRs) on them and because of their technological importance in growth processes. Also, TM compounds have shown potential in catalysis applications. Trend studies are conducted with respect to both period and group in the periodic table, choosing the substrates ScC, TiC, VC, ZrC, NbC, δ-MoC, TaC, and WC (in NaCl structure) and the adsorbates H, B, C, N, O, F, NH, NH(2), and NH(3). Trends in adsorption strength are explained in terms of surface electronic factors, by correlating the calculated adsorption-energy values with the calculated surface electronic structures. The results are rationalized by use of a concerted-coupling model (CCM), which has previously been applied successfully to the description of adsorption on TiC(111) and TiN(111) surfaces (Ruberto et al 2007 Solid State Commun. 141 48). First, the clean TMC(111) surfaces are characterized by calculating surface energies, surface relaxations, Bader charges, and surface-localized densities of states (DOSs). Detailed comparisons between surface and bulk DOSs reveal the existence of transition-metal localized SRs (TMSRs) in the pseudogap and of several C-localized SRs (CSRs) in the upper valence band on all considered TMC(111) 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 reveals a presence of both adsorbate-TMSR and adsorbate-CSRs interactions, of varying strengths depending on the surface and the adsorbate. These variations are

  11. 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.

  12. Universal bosonic tetramers of dimer-atom-atom structure

    OpenAIRE

    Deltuva, A.

    2012-01-01

    Unstable four-boson states having an approximate dimer-atom-atom structure are studied using momentum-space integral equations for the four-particle transition operators. For a given Efimov trimer the universal properties of the lowest associated tetramer are determined. The impact of this tetramer on the atom-trimer and dimer-dimer collisions is analyzed. The reliability of the three-body dimer-atom-atom model is studied.

  13. Binding, conformational transition and dimerization of amyloid-β peptide on GM1-containing ternary membrane: insights from molecular dynamics simulation.

    Directory of Open Access Journals (Sweden)

    Moutusi Manna

    Full Text Available Interactions of amyloid-β (Aβ with neuronal membrane are associated with the progression of Alzheimer's disease (AD. Ganglioside GM1 has been shown to promote the structural conversion of Aβ and increase the rate of peptide aggregation; but the exact nature of interaction driving theses processes remains to be explored. In this work, we have carried out atomistic-scale computer simulations (totaling 2.65 µs to investigate the behavior of Aβ monomer and dimers in GM1-containing raft-like membrane. The oligosaccharide head-group of GM1 was observed to act as scaffold for Aβ-binding through sugar-specific interactions. Starting from the initial helical peptide conformation, a β-hairpin motif was formed at the C-terminus of the GM1-bound Aβ-monomer; that didn't appear in absence of GM1 (both in fluid POPC and liquid-ordered cholesterol/POPC bilayers and also in aqueous medium within the simulation time span. For Aβ-dimers, the β-structure was further enhanced by peptide-peptide interactions, which might influence the propensity of Aβ to aggregate into higher-ordered structures. The salt-bridges and inter-peptide hydrogen bonds were found to account for dimer stability. We observed spontaneous formation of intra-peptide D(23-K(28 salt-bridge and a turn at V(24GSN(27 region - long been accepted as characteristic structural-motifs for amyloid self-assembly. Altogether, our results provide atomistic details of Aβ-GM1 and Aβ-Aβ interactions and demonstrate their importance in the early-stages of GM1-mediated Aβ-oligomerisation on membrane surface.

  14. 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.

  15. Conformal basis for flat space amplitudes

    Science.gov (United States)

    Pasterski, Sabrina; Shao, Shu-Heng

    2017-09-01

    We study solutions of the Klein-Gordon, Maxwell, and linearized Einstein equations in R1 ,d +1 that transform as d -dimensional conformal primaries under the Lorentz group S O (1 ,d +1 ). Such solutions, called conformal primary wavefunctions, are labeled by a conformal dimension Δ and a point in Rd, rather than an on-shell (d +2 )-dimensional momentum. We show that the continuum of scalar conformal primary wavefunctions on the principal continuous series Δ ∈d/2 +i R of S O (1 ,d +1 ) spans a complete set of normalizable solutions to the wave equation. In the massless case, with or without spin, the transition from momentum space to conformal primary wavefunctions is implemented by a Mellin transform. As a consequence of this construction, scattering amplitudes in this basis transform covariantly under S O (1 ,d +1 ) as d -dimensional conformal correlators.

  16. 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)

  17. On conformally related -waves

    Indian Academy of Sciences (India)

    Conformal transformations; conformal Killing vectors; -waves. Abstract. Brinkmann [1] has shown that conformally related distinct Ricci flat solutions are -waves. Brinkmann's result has been generalized to include the conformally invariant source terms. It has been shown that [4] if g i k and g ¯ i k ( = − 2 g i k , : a ...

  18. Dimer-atom-atom recombination in the universal four-boson system

    OpenAIRE

    Deltuva, A.

    2012-01-01

    The dimer-atom-atom recombination process in the system of four identical bosons with resonant interactions is studied. The description uses the exact Alt, Grassberger and Sandhas equations for the four-particle transition operators that are solved in the momentum-space framework. The dimer-dimer and atom-trimer channel contributions to the ultracold dimer-atom-atom recombination rate are calculated. The dimer-atom-atom recombination rate greatly exceeds the three-atom recombination rate.

  19. Maximally Atomic Languages

    Directory of Open Access Journals (Sweden)

    Janusz Brzozowski

    2014-05-01

    Full Text Available The atoms of a regular language are non-empty intersections of complemented and uncomplemented quotients of the language. Tight upper bounds on the number of atoms of a language and on the quotient complexities of atoms are known. We introduce a new class of regular languages, called the maximally atomic languages, consisting of all languages meeting these bounds. We prove the following result: If L is a regular language of quotient complexity n and G is the subgroup of permutations in the transition semigroup T of the minimal DFA of L, then L is maximally atomic if and only if G is transitive on k-subsets of 1,...,n for 0 <= k <= n and T contains a transformation of rank n-1.

  20. A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding.

    Science.gov (United States)

    Hu, Jie; Chen, Tao; Wang, Moye; Chan, Hue Sun; Zhang, Zhuqing

    2017-05-31

    Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations. The conformations in the unfolded state in common Gō models are more extended, and are thus more in line with experiment, than those from all-atom MD simulations. Nevertheless, the structural features of transition states obtained by the two types of models are largely similar. In contrast, the folding transition paths are significantly more sensitive to modeling details. In particular, when common Gō-like models are augmented with nonnative interactions, the predicted dimensions of the unfolded conformations become similar to those computed using all-atom MD. With this connection, the large deviations of all-atom MD from simple diffusion theory are likely caused in part by the presence of significant nonnative effects in folding processes modelled by current atomic force fields. The ramifications of our findings to the application of coarse-grained modeling to more complex biomolecular systems are discussed.

  1. 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 S1 state, with the aid of relative stabilization energies of each conformer in the S0 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 S1 in the conformer in which an oxygen atom of the meta-OH group is close to the ammonium group.

  2. Frequency response of a protein to local conformational perturbations.

    Directory of Open Access Journals (Sweden)

    Dilek Eren

    Full Text Available Signals created by local perturbations are known to propagate long distances through proteins via backbone connectivity and nonbonded interactions. In the current study, signal propagation from the flexible ligand binding loop to the rest of Protein Tyrosine Phosphatase 1B (PTP1B was investigated using frequency response techniques. Using restrained Targeted Molecular Dynamics (TMD potential on WPD and R loops, PTP1B was driven between its crystal structure conformations at different frequencies. Propagation of the local perturbation signal was manifested via peaks at the fundamental frequency and upper harmonics of 1/f distributed spectral density of atomic variables, such as Cα atoms, dihedral angles, or polar interaction distances. Frequency of perturbation was adjusted high enough (simulation length >∼10×period of a perturbation cycle not to be clouded by random diffusional fluctuations, and low enough (<∼0.8 ns(-1 not to attenuate the propagating signal and enhance the contribution of the side-chains to the dissipation of the signals. Employing Discrete Fourier Transform (DFT to TMD simulation trajectories of 16 cycles of conformational transitions at periods of 1.2 to 5 ns yielded Cα displacements consistent with those obtained from crystal structures. Identification of the perturbed atomic variables by statistical t-tests on log-log scale spectral densities revealed the extent of signal propagation in PTP1B, while phase angles of the filtered trajectories at the fundamental frequency were used to cluster collectively fluctuating elements. Hydrophobic interactions were found to have a higher contribution to signal transduction between side-chains compared to the role of polar interactions. Most of in-phase fluctuating residues on the signaling pathway were found to have high identity among PTP domains, and located over a wide region of PTP1B including the allosteric site. Due to its simplicity and efficiency, the suggested technique

  3. Unraveling the differential structural stability and dynamics features of T7 endolysin partially folded conformations.

    Science.gov (United States)

    Sharma, Meenakshi; Kumar, Dinesh; Poluri, Krishna Mohan

    2018-04-01

    Characterization of partially collapsed protein conformations at atomic level is a daunting task due to their inherent flexibility and conformational heterogeneity. T7 bacteriophage endolysin (T7L) is a single-domain amidase that facilitates the lysis of Gram-negative bacteria. T7L exhibits a pH-dependent structural transition from native state to partially folded (PF) conformation. In the pH range 5-3, T7L PF states display differential ANS binding characteristics. CD, fluorescence, NMR spectroscopy and lysis assays were used to investigate the structure-stability- dynamics relationships of T7L PF conformations. Structural studies indicated a partial loss of secondary/tertiary structures compared to its native state. The loss in the tertiary structure and the hydrophobic core opening increases upon decrease of pH from 5 to 3. Thermal denaturation experiments delineated that the pH 5 conformation is thermally irreversible in contrast to pH 3, depicting that hydrophobic core opening is essential for thermal reversibility. Further, urea dependent unfolding features of PF state at pH 5 and 4 evidenced for a collapsed conformation at intermediate urea concentrations. Residue level studies revealed that α1-helix and β3-β4 segment of T7L are the major contributors for such a structural collapse and inherent dynamics. The results suggested that the low pH PF states of T7L are heterogeneous and exhibits differential structural, unfolding, thermal reversibility, and dynamic features. Unraveling the structure-stability characteristics of different endolysin conformations is essential for designing novel chimeric and engineered phage endolysins as broadband antimicrobial agents over a varied pH range. Copyright © 2018 Elsevier B.V. All rights reserved.

  4. Exploring the conformational space of cysteine by matrix isolation spectroscopy combined with near-infrared laser induced conformational change.

    Science.gov (United States)

    Najbauer, Eszter E; Bazsó, Gábor; Góbi, Sándor; Magyarfalvi, Gábor; Tarczay, György

    2014-02-27

    Six conformers of α-cysteine were identified by matrix isolation IR spectroscopy combined with NIR laser irradiation. Five of these conformers are identical with the five out of six conformers that have recently been identified by microwave spectroscopy. The sixth conformer observed in the present study is a short-lived conformer, which decays by H-atom tunneling; its half-life in a 12 K N2 matrix is (1.1 ± 0.5) × 10(3) s. This study proves that matrix isolation IR spectroscopy combined with NIR laser irradiation is a suitable method to identify conformers of a complex system for which computations predict several dozens of conformers, and that the reliability of this method for conformational assignment is comparable to that of microwave spectroscopy.

  5. 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...

  6. 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.

  7. Conformational Properties of β-PrP*

    Science.gov (United States)

    Hosszu, Laszlo L. P.; Trevitt, Clare R.; Jones, Samantha; Batchelor, Mark; Scott, David J.; Jackson, Graham S.; Collinge, John; Waltho, Jonathan P.; Clarke, Anthony R.

    2009-01-01

    Prion propagation involves a conformational transition of the cellular form of prion protein (PrPC) to a disease-specific isomer (PrPSc), shifting from a predominantly α-helical conformation to one dominated by β-sheet structure. This conformational transition is of critical importance in understanding the molecular basis for prion disease. Here, we elucidate the conformational properties of a disulfide-reduced fragment of human PrP spanning residues 91–231 under acidic conditions, using a combination of heteronuclear NMR, analytical ultracentrifugation, and circular dichroism. We find that this form of the protein, which similarly to PrPSc, is a potent inhibitor of the 26 S proteasome, assembles into soluble oligomers that have significant β-sheet content. The monomeric precursor to these oligomers exhibits many of the characteristics of a molten globule intermediate with some helical character in regions that form helices I and III in the PrPC conformation, whereas helix II exhibits little evidence for adopting a helical conformation, suggesting that this region is a likely source of interaction within the initial phases of the transformation to a β-rich conformation. This precursor state is almost as compact as the folded PrPC structure and, as it assembles, only residues 126–227 are immobilized within the oligomeric structure, leaving the remainder in a mobile, random-coil state. PMID:19369250

  8. Conformational properties of beta-PrP.

    Science.gov (United States)

    Hosszu, Laszlo L P; Trevitt, Clare R; Jones, Samantha; Batchelor, Mark; Scott, David J; Jackson, Graham S; Collinge, John; Waltho, Jonathan P; Clarke, Anthony R

    2009-08-14

    Prion propagation involves a conformational transition of the cellular form of prion protein (PrPC) to a disease-specific isomer (PrPSc), shifting from a predominantly alpha-helical conformation to one dominated by beta-sheet structure. This conformational transition is of critical importance in understanding the molecular basis for prion disease. Here, we elucidate the conformational properties of a disulfide-reduced fragment of human PrP spanning residues 91-231 under acidic conditions, using a combination of heteronuclear NMR, analytical ultracentrifugation, and circular dichroism. We find that this form of the protein, which similarly to PrPSc, is a potent inhibitor of the 26 S proteasome, assembles into soluble oligomers that have significant beta-sheet content. The monomeric precursor to these oligomers exhibits many of the characteristics of a molten globule intermediate with some helical character in regions that form helices I and III in the PrPC conformation, whereas helix II exhibits little evidence for adopting a helical conformation, suggesting that this region is a likely source of interaction within the initial phases of the transformation to a beta-rich conformation. This precursor state is almost as compact as the folded PrPC structure and, as it assembles, only residues 126-227 are immobilized within the oligomeric structure, leaving the remainder in a mobile, random-coil state.

  9. Calculation of the state-to-state S-matrix for tetra-atomic reactions with transition-state wave packets: H₂/D₂ + OH → H/D + H₂O/HOD.

    Science.gov (United States)

    Zhao, Bin; Sun, Zhigang; Guo, Hua

    2014-10-21

    This work is concerned with the calculation of state-to-state S-matrix elements for four-atom reactions using a recently proposed method based on the quantum transition-state theory. In this approach, the S-matrix elements are computed from the thermal flux cross-correlation functions obtained in both the reactant and product arrangement channels. Since transition-state wave packets are propagated with only single arrangement channels, the bases/grids required are significantly smaller than those needed in state-to-state approaches based on a single set of scattering coordinates. Furthermore, the propagation of multiple transition-state wave packets can be carried out in parallel. This method is demonstrated for the H2/D2 + OH → H/D + H2O/HOD reactions (J = 0) and the reaction probabilities are in excellent agreement with benchmark results.

  10. 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....

  11. 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.

  12. An All-Atom Model of the Pore-Like Structure of Hexameric VP40 from Ebola: Structural Insights into the Monomer-Hexamer Transition

    National Research Council Canada - National Science Library

    Nguyen, Tam L; Schoehn, Guy; Weissenhorn, Winfried; Hermone, Ann R; Burnett, James C; Panchal, Rekha G; McGrath, Connor; Zaharevitz, Dan W; Aman, M. J; Gussio, Rick; Bavari, Sina

    2005-01-01

    ...) to a resolution of approximately 30A. In this paper, we present the refinement of the EM reconstruction of truncated hexameric VP40 to approximately 20A and the construction of an all-atom model (residues 44-212...

  13. 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.

  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. 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.

  16. Molecular mechanism of melting of a helical polymer crystal: Role of conformational order, packing and mobility of polymers

    Science.gov (United States)

    Cheerla, Ramesh; Krishnan, Marimuthu

    2018-03-01

    The molecular mechanism of melting of a superheated helical polymer crystal has been investigated using isothermal-isobaric molecular dynamics simulation that allows anisotropic deformation of the crystal lattice. A detailed microscopic analysis of the onset and progression of melting and accompanying changes in the polymer conformational order, translational, and orientation order of the solid along the melting pathway is presented. Upon gradual heating from room temperature to beyond the melting point at ambient pressure, the crystal exhibits signatures of premelting well below the solid-to-liquid melting transition at the melting point. The melting transition is manifested by abrupt changes in the crystal volume, lattice energy, polymer conformation, and dynamical properties. In the premelting stage, the crystal lattice structure and backbone orientation of the polymer chains are retained but with the onset of weakening of long-range helical order and interchain packing of polymers perpendicular to the fibre axis of the crystal. The premelting also marks the onset of conformational defects and anisotropic solid-state diffusion of polymers along the fibre axis. The present study underscores the importance of the interplay between intermolecular packing, interactions, and conformational dynamics at the atomic level in determining the macroscopic melting behavior of polymer crystals.

  17. Ensemble refinement shows conformational flexibility in crystal structures of human complement factor D

    Energy Technology Data Exchange (ETDEWEB)

    Forneris, Federico; Burnley, B. Tom; Gros, Piet, E-mail: p.gros@uu.nl [Utrecht University, Padualaan 8, 3584 CH Utrecht (Netherlands)

    2014-03-01

    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{sup +} 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{sup +} 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.

  18. Transition state complexes of the Klebsiella pneumoniae nitrogenase proteins. Spectroscopic properties of aluminium fluoride-stabilized and beryllium fluoride-stabilized MgADP complexes reveal conformational differences of the Fe protein.

    Science.gov (United States)

    Miller, R W; Eady, R R; Fairhurst, S A; Gormal, C A; Smith, B E

    2001-02-01

    Stable inactive 2 : 1 complexes of the Klebsiella pneumoniae nitrogenase components (Kp2/Kp1) were prepared with ADP or the fluorescent ADP analogue, 2'(3')-O-[N-methylanthraniloyl] ADP and AlF(4)(-) or BeF(3)(-) ions. By analogy with published crystallographic data [Schindelin et al. (1997) Nature 387, 370-376)], we suggest that the metal fluoride ions replaced phosphate at the two ATP-binding sites of the iron protein, Kp2. The beryllium (BeF(x)) and aluminium (AlF(4)(-)) containing complexes are proposed to correspond to the ATP-bound state and the hydrolytic transition states, respectively, by analogy with the equivalent complexes of myosin [Fisher et al. (1995) Biochemistry 34, 8960-8972]. (31)P NMR spectroscopy showed that during the initial stages of complex formation, MgADP bound to the complexed Kp2 in a manner similar to that reported for isolated Kp2. This process was followed by a second step that caused broadening of the (31)P NMR signals and, in the case of the AlF4- complex, slow hydrolysis of some of the excess ADP to AMP and inorganic phosphate. The purified BeFx complex contained 3.8 +/- 0.1 MgADP per mol Kp1. With the AlF(4)(-) complex, MgAMP and adenosine (from MgAMP hydrolysis) replaced part of the bound MgADP although four AlF(4)(-) ions were retained, demonstrating that full occupancy by MgADP is not required for the stability of the complex. The fluorescence emission maximum of 2'(3')-O-[N-methylanthraniloyl] ADP was blue-shifted by 6-8 nm in both metal fluoride complexes and polarization was 6-9 times that of the free analogue. The fluorescence yield of bound 2'(3')-O-[N-methylanthraniloyl] ADP was enhanced by 40% in the AlF(4)(-) complex relative to the solvent but no increase in fluorescence was observed in the BeFx complex. Resonance energy transfer from conserved tyrosine residues located in proximity to the Kp2 nucleotide-binding pocket was marked in the AlF(4)(-) complex but minimal in the BeFx fluoride complex, illustrating a clear

  19. 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.

  20. Structural phase transitions of (Bi1-xSbx)2(Te1-ySey)3 compounds under high pressure and the influence of the atomic radius on the compression processes of tetradymites.

    Science.gov (United States)

    Zhao, Jinggeng; Yu, Zhenhai; Hu, Qingyang; Wang, Yong; Schneeloch, John; Li, Chunyu; Zhong, Ruidan; Wang, Yi; Liu, Zhiguo; Gu, Genda

    2017-01-18

    Recently, A2B3-type tetradymites have developed into a hot topic in physical and material research fields, where the A and B atoms represent V and VI group elements, respectively. In this study, in situ angle-dispersive X-ray diffraction measurements were performed on Bi2Te2Se, BiSbTeSe2, and Sb2Te2Se tetradymites under high pressure. Bi2Te2Se transforms from a layered rhombohedral structure (phase I) into 7-fold monoclinic (phase II) and body-centered tetragonal (phase IV) structures at about 8.0 and 14.3 GPa, respectively, without an 8-fold monoclinic structure (phase III) similar to that in Bi2Te3. Thus, the compression behavior of Bi2Te2Se is the same as that of Bi2Se3, which could also be obtained from first-principles calculations and in situ high-pressure electrical resistance measurements. Under high pressure, BiSbTeSe2 and Sb2Te2Se undergo similar structural phase transitions to Bi2Te2Se, which indicates that the compression process of tellurides can be modulated by doping Se in Te sites. According to these high-pressure investigations of A2B3-type tetradymites, the decrease of the B-site atomic radius shrinks the stable pressure range of phase III and expands that of phase II, whereas the decrease of the A-site atomic radius induces a different effect, i.e. expanding the stable pressure range of phase III and shrinking that of phase II. The influence of the atomic radius on the compression process of tetradymites is closely related to the chemical composition and the atom arrangement in the quintuple layer.

  1. Conformal Carroll groups

    OpenAIRE

    Duval, C.; Gibbons, G W; Horvathy, P. A.

    2014-01-01

    Conformal extensions of Levy-Leblond's Carroll group, based on geometric properties analogous to those of Newton-Cartan space-time are proposed. The extensions are labelled by an integer $k$. This framework includes and extends our recent study of the Bondi-Metzner-Sachs (BMS) and Newman-Unti (NU) groups. The relation to Conformal Galilei groups is clarified. Conformal Carroll symmetry is illustrated by "Carrollian photons". Motion both in the Newton-Cartan and Carroll spaces may be related t...

  2. FAC: Flexible Atomic Code

    Science.gov (United States)

    Gu, Ming Feng

    2018-02-01

    FAC calculates various atomic radiative and collisional processes, including radiative transition rates, collisional excitation and ionization by electron impact, energy levels, photoionization, and autoionization, and their inverse processes radiative recombination and dielectronic capture. The package also includes a collisional radiative model to construct synthetic spectra for plasmas under different physical conditions.

  3. 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...

  4. Conformational stability of calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, Charlotte S; Trandum, Christa; Larsen, Nanna Brink

    2005-01-01

    The conformational stability of calreticulin was investigated. Apparent unfolding temperatures (Tm) 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 alpha-helix was of major importance to the conformational stability of calreticulin....

  5. 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....

  6. 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.

  7. 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

  8. NMR studies of dynamic biomolecular conformational ensembles.

    Science.gov (United States)

    Torchia, Dennis A

    2015-02-01

    Multidimensional heteronuclear NMR approaches can provide nearly complete sequential signal assignments of isotopically enriched biomolecules. The availability of assignments together with measurements of spin relaxation rates, residual spin interactions, J-couplings and chemical shifts provides information at atomic resolution about internal dynamics on timescales ranging from ps to ms, both in solution and in the solid state. However, due to the complexity of biomolecules, it is not possible to extract a unique atomic-resolution description of biomolecular motions even from extensive NMR data when many conformations are sampled on multiple timescales. For this reason, powerful computational approaches are increasingly applied to large NMR data sets to elucidate conformational ensembles sampled by biomolecules. In the past decade, considerable attention has been directed at an important class of biomolecules that function by binding to a wide variety of target molecules. Questions of current interest are: "Does the free biomolecule sample a conformational ensemble that encompasses the conformations found when it binds to various targets; and if so, on what time scale is the ensemble sampled?" This article reviews recent efforts to answer these questions, with a focus on comparing ensembles obtained for the same biomolecules by different investigators. A detailed comparison of results obtained is provided for three biomolecules: ubiquitin, calmodulin and the HIV-1 trans-activation response RNA. Published by Elsevier B.V.

  9. 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

  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. 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.

  12. Coherent Atom Optics with fast metastable rare gas atoms

    Science.gov (United States)

    Grucker, J.; Baudon, J.; Karam, J.-C.; Perales, F.; Bocvarski, V.; Vassilev, G.; Ducloy, M.

    2006-12-01

    Coherent atom optics experiments making use of an ultra-narrow beam of fast metastable atoms generated by metastability exchange are reported. The transverse coherence of the beam (coherence radius of 1.7 μm for He*, 1.2 μm for Ne*, 0.87 μm for Ar*) is demonstrated via the atomic diffraction by a non-magnetic 2μm-period reflection grating. The combination of the non-scalar van der Waals (vdW) interaction with the Zeeman interaction generated by a static magnetic field gives rise to "vdW-Zeeman" transitions among Zeeman sub-levels. Exo-energetic transitions of this type are observed with Ne*(3P2) atoms traversing a copper micro-slit grating. They can be used as a tunable beam splitter in an inelastic Fresnel bi-prism atom interferometer.

  13. Discovering conformational sub-states relevant to protein function.

    Directory of Open Access Journals (Sweden)

    Arvind Ramanathan

    2011-01-01

    Full Text Available Internal motions enable proteins to explore a range of conformations, even in the vicinity of native state. The role of conformational fluctuations in the designated function of a protein is widely debated. Emerging evidence suggests that sub-groups within the range of conformations (or sub-states contain properties that may be functionally relevant. However, low populations in these sub-states and the transient nature of conformational transitions between these sub-states present significant challenges for their identification and characterization.To overcome these challenges we have developed a new computational technique, quasi-anharmonic analysis (QAA. QAA utilizes higher-order statistics of protein motions to identify sub-states in the conformational landscape. Further, the focus on anharmonicity allows identification of conformational fluctuations that enable transitions between sub-states. QAA applied to equilibrium simulations of human ubiquitin and T4 lysozyme reveals functionally relevant sub-states and protein motions involved in molecular recognition. In combination with a reaction pathway sampling method, QAA characterizes conformational sub-states associated with cis/trans peptidyl-prolyl isomerization catalyzed by the enzyme cyclophilin A. In these three proteins, QAA allows identification of conformational sub-states, with critical structural and dynamical features relevant to protein function.Overall, QAA provides a novel framework to intuitively understand the biophysical basis of conformational diversity and its relevance to protein function.

  14. Atomic Force Microscopy Studies on DNA Structural Changes Induced by Vincristine Sulfate and Aspirin

    Science.gov (United States)

    Zhu, Yi; Zeng, Hu; Xie, Jianming; Ba, Long; Gao, Xiang; Lu, Zuhong

    2004-04-01

    We report that atomic force microscopy (AFM) studies on structural variations of a linear plasmid DNA interact with various concentrations of vincristine sulfate and aspirin. The different binding images show that vincrinstine sulfate binding DNA chains caused some loops and cleavages of the DNA fragments, whereas aspirin interaction caused the width changes and conformational transition of the DNA fragments. Two different DNA structural alternations could be explained by the different mechanisms of the interactions with these two components. Our work indicates that the AFM is a powerful tool in studying the interaction between DNA and small molecules.

  15. Linear Atom Guides: Guiding Rydberg Atoms and Progress Toward an Atom Laser

    Science.gov (United States)

    Traxler, Mallory A.

    In this thesis, I explore a variety of experiments within linear, two-wire, magnetic atom guides. Experiments include guiding of Rydberg atoms; transferring between states while keeping the atoms contained within the guide; and designing, constructing, and testing a new experimental apparatus. The ultimate goal of the atom guiding experiments is to develop a continuous atom laser. The guiding of 87Rb 59D5/2 Rydberg atoms is demonstrated. The evolution of the atoms is driven by the combined effects of dipole forces acting on the center-of-mass degree of freedom as well as internal-state transitions. Time delayed microwave and state-selective field ionization, along with ion detection, are used to investigate the evolution of the internal-state distribution as well as the Rydberg atom motion while traversing the guide. The observed decay time of the guided-atom signal is about five times that of the initial state. A population transfer between Rydberg states contributes to this lengthened lifetime, and also broadens the observed field ionization spectrum. The population transfer is attributed to thermal transitions and, to a lesser extent, initial state-mixing due to Rydberg-Rydberg collisions. Characteristic signatures in ion time-of-flight signals and spatially resolved images of ion distributions, which result from the coupled internal-state and center-of-mass dynamics, are discussed. Some groups have used a scheme to make BECs where atoms are optically pumped from one reservoir trap to a final state trap, irreversibly transferring those atoms from one trap to the other. In this context, transfer from one guided ground state to another is studied. In our setup, before the atoms enter the guide, they are pumped into the | F = 1, mF = --1> state. Using two repumpers, one tuned to the F = 1 → F' = 0 transition (R10) and the other tuned to the F = 1 → F' = 2 transition (R12), the atoms are pumped between these guided states. Magnetic reflections within the guide

  16. Conformal expansions and renormalons

    CERN Document Server

    Brodsky, S J; Grunberg, G; Rathsman, J; Brodsky, Stanley J.; Gardi, Einan; Grunberg, Georges; Rathsman, Johan

    2001-01-01

    The coefficients in perturbative expansions in gauge theories are factoriallyincreasing, predominantly due to renormalons. This type of factorial increaseis not expected in conformal theories. In QCD conformal relations betweenobservables can be defined in the presence of a perturbative infraredfixed-point. Using the Banks-Zaks expansion we study the effect of thelarge-order behavior of the perturbative series on the conformal coefficients.We find that in general these coefficients become factorially increasing.However, when the factorial behavior genuinely originates in a renormalonintegral, as implied by a postulated skeleton expansion, it does not affect theconformal coefficients. As a consequence, the conformal coefficients willindeed be free of renormalon divergence, in accordance with previousobservations concerning the smallness of these coefficients for specificobservables. We further show that the correspondence of the BLM method with theskeleton expansion implies a unique scale-setting procedure. Th...

  17. Conformal expansions and renormalons

    CERN Document Server

    Gardi, E; Gardi, Einan; Grunberg, Georges

    2001-01-01

    The large-order behaviour of QCD is dominated by renormalons. On the other hand renormalons do not occur in conformal theories, such as the one describing the infrared fixed-point of QCD at small beta_0 (the Banks--Zaks limit). Since the fixed-point has a perturbative realization, all-order perturbative relations exist between the conformal coefficients, which are renormalon-free, and the standard perturbative coefficients, which contain renormalons. Therefore, an explicit cancellation of renormalons should occur in these relations. The absence of renormalons in the conformal limit can thus be seen as a constraint on the structure of the QCD perturbative expansion. We show that the conformal constraint is non-trivial: a generic model for the large-order behaviour violates it. We also analyse a specific example, based on a renormalon-type integral over the two-loop running-coupling, where the required cancellation does occur.

  18. Group Size and Conformity

    OpenAIRE

    Bond, Rod

    2005-01-01

    Abstract This paper reviews theory and research on the relationship between group size and conformity and presents a meta-analysis of 125 Asch-type conformity studies. It questions the assumption of a single function made in formal models of social influence and proposes instead that the function will vary depending on which social influence process predominates. It is argued that normative influence is lik...

  19. 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.

  20. Quantum massive conformal gravity

    Energy Technology Data Exchange (ETDEWEB)

    Faria, F.F. [Universidade Estadual do Piaui, Centro de Ciencias da Natureza, Teresina, PI (Brazil)

    2016-04-15

    We first find the linear approximation of the second plus fourth order derivative massive conformal gravity action. Then we reduce the linearized action to separated second order derivative terms, which allows us to quantize the theory by using the standard first order canonical quantization method. It is shown that quantum massive conformal gravity is renormalizable but has ghost states. A possible decoupling of these ghost states at high energies is discussed. (orig.)

  1. 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....

  2. An atomic model for neutral and singly ionized uranium

    Science.gov (United States)

    Maceda, E. L.; Miley, G. H.

    1979-01-01

    A model for the atomic levels above ground state in neutral, U(0), and singly ionized, U(+), uranium is described based on identified atomic transitions. Some 168 states in U(0) and 95 in U(+) are found. A total of 1581 atomic transitions are used to complete this process. Also discussed are the atomic inverse lifetimes and line widths for the radiative transitions as well as the electron collisional cross sections.

  3. Intramolecular inversions, structure and conformational behavior of gaseous and liquid N-cyanopiperidine. Comparison with other 1-cyanoheterocyclohexanes

    Science.gov (United States)

    Shlykov, Sergey A.; Phien, Tran Dinh; Weber, Peter M.

    2017-06-01

    The molecular structure and intramolecular inversions of N-cyanopiperidine (CNP) were studied by various quantum chemical methods and using synchronous gas electron diffraction/mass spectrometry (GED/MS) and IR spectroscopy. The contribution of the equatorial conformer was found GED 52(6), IR 60(6), B3LYP 77, B3LYP-D3 67, M062X 59, MP2 54%. Interpolation using CCSD(T)-F12/CBS predicts Eax-Eeq = 0.26 kcal/mol. The NBO analysis shows a strong conjugation of the nitrogen atom lone pair with the triple bond making the r(N-CCN) = 1.355(3) Å distance as short as a typical sesquilateral bond. A low energy barrier for the Eq→Ax transition of 1.0-2.3 kcal/mol in CNP leads to difficulties in NMR conformational ratio studies. This leaves the GED method almost as the only experimental method to study both structural and conformational properties. Conformational properties of the related compounds are found to depend on the X-CCN bond distance and conjugation between the CN group and the lone pair on the heteroatom. The contribution of the axial form of 1-cyano-heterocyclohexanes increases in the series of heteroatoms X in the cyclohexane ring: N→C→Si→P.

  4. Carbonyl Activation by Borane Lewis Acid Complexation: Transition States of H2Splitting 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.

  5. Detailed mapping of the local Ir4+ dimers through the metal-insulator transitions of CuIr2S4 thiospinel by X-ray atomic pair distribution function measurements.

    Science.gov (United States)

    Božin, E S; Masadeh, A S; Hor, Y S; Mitchell, J F; Billinge, S J L

    2011-01-28

    The evolution of the short-range structural signature of the Ir4+ dimer state in CuIr2S4 thiospinel has been studied across the metal-insulator phase transitions as the metallic state is induced by temperature, Cr doping, and x-ray fluence. An atomic pair distribution function (PDF) approach reveals that there are no local dimers that survive into the metallic phase when this is invoked by temperature and doping. The PDF shows Ir4+ dimers when they exist, regardless of whether or not they are long-range ordered. At 100 K, exposure to a 98 keV x-ray beam melts the long-range dimer order within a few seconds, though the local dimers remain intact. This shows that the metallic state accessed on warming and doping is qualitatively different from the state obtained under x-ray irradiation.

  6. Detection of the level of fluoride in the commercially available toothpaste using laser induced breakdown spectroscopy with the marker atomic transition line of neutral fluorine at 731.1 nm

    Science.gov (United States)

    Gondal, M. A.; Maganda, Y. W.; Dastageer, M. A.; Al Adel, F. F.; Naqvi, A. A.; Qahtan, T. F.

    2014-04-01

    Fourth harmonic of a pulsed Nd:YAG laser (wavelength 266 nm) in combination with high resolution spectrograph equipped with Gated ICCD camera has been employed to design a high sensitive analytical system. This detection system is based on Laser Induced Breakdown Spectroscopy and has been tested first time for analysis of semi-fluid samples to detect fluoride content present in the commercially available toothpaste samples. The experimental parameters were optimized to achieve an optically thin and in local thermo dynamic equilibrium plasma. This improved the limits of detection of fluoride present in tooth paste samples. The strong atomic transition line of fluorine at 731.102 nm was used as the marker line to quantify the fluoride concentration levels. Our LIBS system was able to detect fluoride concentration levels in the range of 1300-1750 ppm with a detection limit of 156 ppm.

  7. 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.

  8. Optically controlled waveplate at a telecom wavelength using a ladder transition in Rb atoms for all-optical switching and high speed Stokesmetric imaging.

    Science.gov (United States)

    Krishnamurthy, Subramanian; Tu, Y; Wang, Y; Tseng, S; Shahriar, M S

    2014-11-17

    We demonstrate an optically controlled waveplate at ~1323 nm using the 5S(1/2)-5P(1/2)-6S(1/2) ladder transition in a Rb vapor cell. The lower leg of the transitions represents the control beam, while the upper leg represents the signal beam. We show that we can place the signal beam in any arbitrary polarization state with a suitable choice of polarization of the control beam. Specifically, we demonstrate a differential phase retardance of ~180 degrees between the two circularly polarized components of a linearly polarized signal beam. We also demonstrate that the system can act as a Quarter Wave plate. The optical activity responsible for the phase retardation process is explained in terms of selection rules involving the Zeeman sublevels. As such, the system can be used to realize a fast Stokesmetric imaging system with a speed of ~3 MHz. When implemented using a tapered nano fiber embedded in a vapor cell, this system can be used to realize an ultra-low power all-optical switch as well as a Quantum Zeno Effect based all-optical logic gate by combining it with an optically controlled polarizer, previously demonstrated by us. We present numerical simulations of the system using a comprehensive model which incorporates all the relevant Zeeman sub-levels in the system, using a novel algorithm recently developed by us for efficient computation of the evolution of an arbitrary large scale quantum system.

  9. Dynamics of DNA conformations and DNA-protein interaction

    DEFF Research Database (Denmark)

    Metzler, R.; Ambjörnsson, T.; Lomholt, Michael Andersen

    2005-01-01

    Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA denaturat......Optical tweezers, atomic force microscopes, patch clamping, or fluorescence techniques make it possible to study both the equilibrium conformations and dynamics of single DNA molecules as well as their interaction with binding proteins. In this paper we address the dynamics of local DNA...

  10. Atomic physics

    CERN Document Server

    Born, Max

    1969-01-01

    The Nobel Laureate's brilliant exposition of the kinetic theory of gases, elementary particles, the nuclear atom, wave-corpuscles, atomic structure and spectral lines, electron spin and Pauli's principle, quantum statistics, molecular structure and nuclear physics. Over 40 appendices, a bibliography, numerous figures and graphs.

  11. Early Atomism

    Indian Academy of Sciences (India)

    http://www.ias.ac.in/article/fulltext/reso/015/10/0905-0925. Keywords. Atomic theory; Avogadro's hypothesis; atomic weights; periodic table; valence; molecular weights; molecular formula; isomerism. Author Affiliations. S Ramasesha1. Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560 012, ...

  12. Conformal invariance of curvature perturbation

    CERN Document Server

    Gong, Jinn-Ouk; Park, Wan Il; Sasaki, Misao; Song, Yong-Seon

    2011-01-01

    We show that in the single component situation all perturbation variables in the comoving gauge are conformally invariant to all perturbation orders. Generally we identify a special time slicing, the uniform-conformal transformation slicing, where all perturbations are again conformally invariant to all perturbation orders. We apply this result to the delta N formalism, and show its conformal invariance.

  13. Conformal invariance of curvature perturbation

    Energy Technology Data Exchange (ETDEWEB)

    Gong, Jinn-Ouk [Theory Division, CERN, CH-1211 Genève 23 (Switzerland); Hwang, Jai-chan [Department of Astronomy and Atmospheric Sciences, Kyungpook National University, Daegu 702-701 (Korea, Republic of); Park, Wan Il; Sasaki, Misao; Song, Yong-Seon, E-mail: jinn-ouk.gong@cern.ch, E-mail: jchan@knu.ac.kr, E-mail: wipark@kias.re.kr, E-mail: misao@yukawa.kyoto-u.ac.jp, E-mail: ysong@kias.re.kr [Korea Institute for Advanced Study, Seoul 130-722 (Korea, Republic of)

    2011-09-01

    We show that in the single component situation all perturbation variables in the comoving gauge are conformally invariant to all perturbation orders. Generally we identify a special time slicing, the uniform-conformal transformation slicing, where all perturbations are again conformally invariant to all perturbation orders. We apply this result to the δN formalism, and show its conformal invariance.

  14. 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).

  15. 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) is a cost effective nano-manufacturing technique that allows for the conformal coating of substrates with atomic control in a benign...

  16. Hot Conformal Gauge Theories

    DEFF Research Database (Denmark)

    Mojaza, Matin; Pica, Claudio; Sannino, Francesco

    2010-01-01

    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...... show that the reduced free energy changes sign, at the second, fifth and sixth order in the coupling, when decreasing the number of flavors from the upper end of the conformal window. If the change in sign is interpreted as signal of an instability of the system then we infer a critical number...... 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...

  17. Periodic systems of N-atom molecules

    Science.gov (United States)

    Hefferlin, R. A.; Zhuvikin, G. V.; Caviness, K. E.; Duerksen, P. J.

    1984-10-01

    The atoms have long been classified into a periodic system, which is now based on quantum mechanics and group theory. A classification of molecules containing any number (N) of atoms is proposed. It is an extension of the periodic system of the atoms. The approach in this paper is that of group theory, although the proposed system has been subjected to exhaustive comparison with experimental and ab initio computational results for diatomic molecules, and conforms to the commonly known behaviors of molecules with larger N. Orthonormal transformations are performed so that the molecules can be arranged according to their numbers of electrons and to the differences of atomic numbers of the constituent atoms. These arrangements parallel the physical reality of atomic bonding and permit partial three-dimensional models of the systems to be constructed for molecules with as many as four atoms.

  18. Infrared study on annealing effect on conformation of zinc stearate.

    Science.gov (United States)

    Ishioka, Tsutomu; Kiritani, Atsushi; Kojima, Takuya

    2007-04-01

    The molecular conformation and thermal transition behavior of two zinc stearate specimens, unannealed one and annealed one, were compared. The unannealed specimen has one thermal transition at 134 degrees C. Annealing was made by increasing temperature to 150 degrees C and cooling to room temperature slowly. This annealed specimen has an exothermic peak at 103 degrees C, and endothermic shoulders and a peak at 118, 124 and 131 degrees C, respectively. The observed frequencies of all bands of the unannealed specimen at room temperature are assigned to the all-trans conformation. We found new bands at 858, 823, 793, 766, 688, and 604 cm-1 for the annealed specimen. Based on the normal mode analyses, these bands are assigned to the TGT conformation at the COO end, where T means trans and G means gauche. The annealed specimen consists of almost all-trans molecule but partial molecules have the TGT conformation.

  19. Spinor product computations for protein conformations.

    Science.gov (United States)

    Chys, Pieter; Chacón, Pablo

    2012-08-05

    Spinor operators in geometric algebra (GA) can efficiently describe conformational changes of proteins by ordered products that act on individual bonds and represent their net rotations. Backward propagation through the protein backbone yields all rotational spinor axes in advance allowing the efficient computation of atomic coordinates from internal coordinates. The introduced mathematical framework enables to efficiently manipulate and generate protein conformations to any arbitrary degree. Moreover, several new formulations in the context of rigid body motions are added. Emphasis is placed on the intimate relationship between spinors and quaternions, which can be recovered from within the GA approach. The spinor methodology is implemented and tested versus the state of the art algorithms for both protein construction and coordinate updating. Spinor calculations have a smaller computational cost and turn out to be slightly faster than current alternatives. Copyright © 2012 Wiley Periodicals, Inc.

  20. 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.

  1. Interplay between α-relaxation and morphology transition of perfluorosulfonate ionomer membranes

    Science.gov (United States)

    Matos, Bruno R.; Santiago, Elisabete I.; Muccillo, Reginaldo; Velasco-Davalos, Ivan A.; Ruediger, Andreas; Tavares, Ana C.; Fonseca, Fabio C.

    2015-10-01

    Nafion α-relaxation is the subject of intense investigations as it regulates the performance of electric actuators and polymer electrolyte fuel cells. Dielectric spectroscopy and atomic force microscopy measurements of Nafion membranes allow identifying the conformation transition of the polymeric aggregates as the process underlying the α-transition. The dielectric permittivity curves of Nafion membranes show that for relative humidity higher than ∼60% and for temperatures higher than ∼120 °C, the α-relaxation displaces to lower frequencies. Such unusual behavior is attributed to an elongation of Nafion polymeric aggregates occurring at high temperatures (T > 120 °C) and is in perfect agreement with morphological changes inferred from atomic force microscopy analyses.

  2. Conformal Relativity versus Brans–Dicke and Superstring Theories

    Directory of Open Access Journals (Sweden)

    David B. Blaschke

    2012-10-01

    Full Text Available We show how conformal relativity is related to Brans–Dicke theory and to low-energy-effective superstring theory. Conformal relativity or the Hoyle–Narlikar theory is invariant with respect to conformal transformations of the metric. We show that the conformal relativity action is equivalent to the transformed Brans–Dicke action for ω = -3/2 (which is the border between standard scalar field and ghost in contrast to the reduced (graviton-dilaton low-energy-effective superstring action which corresponds to the Brans–Dicke action with ω = -1. We show that like in ekpyrotic/cyclic models, the transition through the singularity in conformal cosmology in the string frame takes place in the weak coupling regime. We also find interesting self-duality and duality relations for the graviton-dilaton actions.

  3. 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

  4. Galilean conformal and superconformal symmetries

    Energy Technology Data Exchange (ETDEWEB)

    Lukierski, J., E-mail: lukier@ift.uni.wroc.pl [University of Wroclaw, Institute for Theoretical Physics (Poland)

    2012-10-15

    Firstly we discuss briefly three different algebras named as nonrelativistic (NR) conformal: Schroedinger, Galilean conformal, and infinite algebra of local NR conformal isometries. Further we shall consider in some detail Galilean conformal algebra (GCA) obtained in the limit c{yields}{infinity} from relativistic conformal algebraO(d+1, 2) (d-number of space dimensions). Two different contraction limits providing GCA and some recently considered realizations will be briefly discussed. Finally by considering NR contraction of D = 4 superconformal algebra the Galilei conformal superalgebra (GCSA) is obtained, in the formulation using complexWeyl supercharges.

  5. Targeting the Conformal Window: Scalars on the Lattice

    CERN Document Server

    Weinberg, Evan; Hasenfratz, Anna; Rebbi, Claudio; Witzel, Oliver

    2014-01-01

    The light Higgs boson of the Standard Model could arise as the consequence of the weakly broken conformal symmetry in a strongly interacting gauge theory. Here we present a novel idea to study the transition from conformal to confining behavior using an SU(3) gauge theory with four light and eight heavy flavors. This system interpolates between the 12-flavor conformal and the 4 flavor chirally broken theory as the mass of the heavy flavors are varied. We show first results on our determination of the iso-singlet 0++ state.

  6. A conformational study of proline derivatives | Kamwaya | Bulletin of ...

    African Journals Online (AJOL)

    From the study of the structures and molecular conformations of a number of proline derivatives, some conclusions were drawn. The widening effect of angle C-C'-N' is caused by steric repulsion between a hydrogen atom at C of the preceding prolyl residue with any other at either C or C of the pyrrolidine ring cis to it.

  7. Atom mapping with constraint programming.

    Science.gov (United States)

    Mann, Martin; Nahar, Feras; Schnorr, Norah; Backofen, Rolf; Stadler, Peter F; Flamm, Christoph

    2014-01-01

    Chemical reactions are rearrangements of chemical bonds. Each atom in an educt molecule thus appears again in a specific position of one of the reaction products. This bijection between educt and product atoms is not reported by chemical reaction databases, however, so that the "Atom Mapping Problem" of finding this bijection is left as an important computational task for many practical applications in computational chemistry and systems biology. Elementary chemical reactions feature a cyclic imaginary transition state (ITS) that imposes additional restrictions on the bijection between educt and product atoms that are not taken into account by previous approaches. We demonstrate that Constraint Programming is well-suited to solving the Atom Mapping Problem in this setting. The performance of our approach is evaluated for a manually curated subset of chemical reactions from the KEGG database featuring various ITS cycle layouts and reaction mechanisms.

  8. 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

  9. 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.

  10. Atom-atom interactions around the band edge of a photonic crystal waveguide.

    Science.gov (United States)

    Hood, Jonathan D; Goban, Akihisa; Asenjo-Garcia, Ana; Lu, Mingwu; Yu, Su-Peng; Chang, Darrick E; Kimble, H J

    2016-09-20

    Tailoring the interactions between quantum emitters and single photons constitutes one of the cornerstones of quantum optics. Coupling a quantum emitter to the band edge of a photonic crystal waveguide (PCW) provides a unique platform for tuning these interactions. In particular, the cross-over from propagating fields [Formula: see text] outside the bandgap to localized fields [Formula: see text] within the bandgap should be accompanied by a transition from largely dissipative atom-atom interactions to a regime where dispersive atom-atom interactions are dominant. Here, we experimentally observe this transition by shifting the band edge frequency of the PCW relative to the [Formula: see text] line of atomic cesium for [Formula: see text] atoms trapped along the PCW. Our results are the initial demonstration of this paradigm for coherent atom-atom interactions with low dissipation into the guided mode.

  11. 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.

  12. Dynamical spacetimes in conformal gravity

    National Research Council Canada - National Science Library

    Hongsheng Zhang; Yi Zhang; Xin-Zhou Li

    2017-01-01

    The conformal gravity remarkably boosts our prehension of gravity theories. We find a series of dynamical solutions in the W2-conformal gravity, including generalized Schwarzschild–Friedmann–Robertson–Walker (GSFRW...

  13. Multiscale conformal pattern transfer

    Science.gov (United States)

    Lodewijks, Kristof; Miljkovic, Vladimir; Massiot, Inès; Mekonnen, Addis; Verre, Ruggero; Olsson, Eva; Dmitriev, Alexandre

    2016-06-01

    We demonstrate a method for seamless transfer from a parent flat substrate of basically any lithographic top-down or bottom-up pattern onto essentially any kind of surface. The nano- or microscale patterns, spanning macroscopic surface areas, can be transferred with high conformity onto a large variety of surfaces when such patterns are produced on a thin carbon film, grown on top of a sacrificial layer. The latter allows lifting the patterns from the flat parent substrate onto a water-air interface to be picked up by the host surface of choice. We illustrate the power of this technique by functionalizing broad range of materials including glass, plastics, metals, rough semiconductors and polymers, highlighting the potential applications in in situ colorimetry of the chemistry of materials, anti-counterfeit technologies, biomolecular and biomedical studies, light-matter interactions at the nanoscale, conformal photovoltaics and flexible electronics.

  14. Multiscale conformal pattern transfer.

    Science.gov (United States)

    Lodewijks, Kristof; Miljkovic, Vladimir; Massiot, Inès; Mekonnen, Addis; Verre, Ruggero; Olsson, Eva; Dmitriev, Alexandre

    2016-06-22

    We demonstrate a method for seamless transfer from a parent flat substrate of basically any lithographic top-down or bottom-up pattern onto essentially any kind of surface. The nano- or microscale patterns, spanning macroscopic surface areas, can be transferred with high conformity onto a large variety of surfaces when such patterns are produced on a thin carbon film, grown on top of a sacrificial layer. The latter allows lifting the patterns from the flat parent substrate onto a water-air interface to be picked up by the host surface of choice. We illustrate the power of this technique by functionalizing broad range of materials including glass, plastics, metals, rough semiconductors and polymers, highlighting the potential applications in in situ colorimetry of the chemistry of materials, anti-counterfeit technologies, biomolecular and biomedical studies, light-matter interactions at the nanoscale, conformal photovoltaics and flexible electronics.

  15. Atomic theories

    CERN Document Server

    Loring, FH

    2014-01-01

    Summarising the most novel facts and theories which were coming into prominence at the time, particularly those which had not yet been incorporated into standard textbooks, this important work was first published in 1921. The subjects treated cover a wide range of research that was being conducted into the atom, and include Quantum Theory, the Bohr Theory, the Sommerfield extension of Bohr's work, the Octet Theory and Isotopes, as well as Ionisation Potentials and Solar Phenomena. Because much of the material of Atomic Theories lies on the boundary between experimentally verified fact and spec

  16. 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....

  17. Conformal block study and bounding OPE in conformal field theories

    CERN Document Server

    Yvernay, Pierre

    2015-01-01

    During the past few years, the re-emergence of conformal bootstrap as a numerical tool to solve conformal field theory allowed more precise estimation of several presumed conformal field theory among which we could cite the 3D Ising model. This work intends to provide insight on conformal blocks which are elementary objects in the conformal bootstrap approach. These are considered in Euclidian space where we study fields of all equal dimension. This study allows us to improve bounds derived in \\cite{OPEconv}.

  18. Polymer Conformation under Confinement

    Directory of Open Access Journals (Sweden)

    Stavros Bollas

    2017-02-01

    Full Text Available The conformation of polymer chains under confinement is investigated in intercalated polymer/layered silicate nanocomposites. Hydrophilic poly(ethylene oxide/sodium montmorillonite, PEO/Na+-MMT, hybrids were prepared utilizing melt intercalation with compositions where the polymer chains are mostly within the ~1 nm galleries of the inorganic material. The polymer chains are completely amorphous in all compositions even at temperatures where the bulk polymer is highly crystalline. Attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR is utilized to investigate the conformation of the polymer chains over a broad range of temperatures from below to much higher than the bulk polymer melting temperature. A systematic increase of the gauche conformation relatively to the trans is found with decreasing polymer content both for the C–C and the C–O bonds that exist along the PEO backbone indicating that the severe confinement and the proximity to the inorganic surfaces results in a more disordered state of the polymer.

  19. 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.

  20. High-level direct-dynamics variational transition state theory calculations including multidimensional tunneling of the thermal rate constants, branching ratios, and kinetic isotope effects of the hydrogen abstraction reactions from methanol by atomic hydrogen.

    Science.gov (United States)

    Meana-Pañeda, Rubén; Truhlar, Donald G; Fernández-Ramos, Antonio

    2011-03-07

    We report a detailed theoretical study of the hydrogen abstraction reaction from methanol by atomic hydrogen. The study includes the analysis of thermal rate constants, branching ratios, and kinetic isotope effects. Specifically, we have performed high-level computations at the MC3BB level together with direct dynamics calculations by canonical variational transition state theory (CVT) with the microcanonically optimized multidimensional tunneling (μOMT) transmission coefficient (CVT/μOMT) to study both the CH(3)OH+H→CH(2)OH+H(2) (R1) reaction and the CH(3)OH+H→CH(3)O+H(2) (R2) reaction. The CVT/μOMT calculations show that reaction R1 dominates in the whole range 298≤T (K)≤2500 and that anharmonic effects on the torsional mode about the C-O bond are important, mainly at high temperatures. The activation energy for the total reaction sum of R1 and R2 reactions changes substantially with temperature and, therefore, the use of straight-line Arrhenius plots is not valid. We recommend the use of new expressions for the total R1 + R2 reaction and for the R1 and R2 individual reactions. © 2011 American Institute of Physics.

  1. Atomic Power

    African Journals Online (AJOL)

    Atomic Power. By Denis Taylor: Dr. Taylor was formerly Chief UNESCO Advisor at the University. College, Nairobi, Kenya and is now Professor of Electrical Engineering in the Uni- versity of ... method of producing radioactive isotopes, which are materials .... the sealing and the pressure balancing, all can be carried out ...

  2. Conformational biosensor for diagnosis of prion diseases.

    Science.gov (United States)

    Tcherkasskaya, Olga; Davidson, Eugene A; Schmerr, Mary Jo; Orser, Cindy S

    2005-05-01

    A fluorescence technology to monitor the proliferation of amyloidogenic neurological disorders is proposed. A crude brain homogenate (0.01%) from animals infected with a transmissible spongiform encephalopathy is employed as a catalytic medium initiating conformational changes in 520 nM polypeptide biosensors (Tris/trifluoroethanol 50% mixture at pH 7). The fluorescence methods utilize pyrene residues covalently attached to the peptide ends. The coil-to-beta-strand transitions in biosensor molecules cause elevation of a distinct fluorescence band of the pyrene aggregates (i.e. excimers). This approach enables the detection of infectious prion proteins at fmol, does not require antibody binding or protease treatment. Technology might be adopted for diagnosing a large variety of conformational disorders as well as for generic high-throughput screening of the amyloidogenic potential in plasma.

  3. Storage of Quantum Variables in Atomic Media

    DEFF Research Database (Denmark)

    Cviklinski, J.; Ortalo, J.; Josse, V.

    2007-01-01

    Storage and read-out of non classical states of light is a critical element for quantum information networks. Simultaneous storage of two non-commuting variables carried by light and subsequent read-out is shown to be possible in atomic ensembles. Interaction of light fields with three......-level systems allows direct mapping the quantum state of light into long lived coherences in the atomic ground state. We show that excess noise linked to atomic transitions can be made negligible. Experimental developments are discussed for atomic vapours and cold atoms....

  4. 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

  5. Atomic physics: Cold gases venture into Flatland

    Science.gov (United States)

    Burnett, Keith

    2007-09-01

    Vortex structures have revealed a lot about the nature of three-dimensional Bose-Einstein condensates. They play an even bigger part in two-dimensional cold atomic gases and drive a fundamentally different phase transition.

  6. Conformal Janus on Euclidean sphere

    Energy Technology Data Exchange (ETDEWEB)

    Bak, Dongsu [Physics Department, University of Seoul,Seoul 02504 (Korea, Republic of); B.W. Lee Center for Fields, Gravity & Strings, Institute for Basic Sciences,Daejeon 34047 (Korea, Republic of); Gustavsson, Andreas [School of Physics, Korea Institute for Advanced Study,Seoul 02455 (Korea, Republic of); Rey, Soo-Jong [School of Physics & Astronomy and Center for Theoretical Physics,Seoul National University,Seoul 08826 (Korea, Republic of); Center for Theoretical Physics, College of Physical Sciences, Sichuan University,Chengdu 610064 P.R. (China); B.W. Lee Center for Fields, Gravity & Strings, Institute for Basic Sciences,Daejeon 34047 (Korea, Republic of)

    2016-12-07

    We interpret Janus as an interface in a conformal field theory and study its properties. The Janus is created by an exactly marginal operator and we study its effect on the interface conformal field theory on the Janus. We do this by utilizing the AdS/CFT correspondence. We compute the interface free energy both from leading correction to the Euclidean action in the dual gravity description and from conformal perturbation theory in the conformal field theory. We find that the two results agree each other and that the interface free energy scales precisely as expected from the conformal invariance of the Janus interface.

  7. Magnetism of a single atom

    NARCIS (Netherlands)

    Otte, Alexander Ferdinand

    2008-01-01

    A low-temperature scanning tunneling microscope is used to perform spin-excitations on individual magnetic transition metal atoms when placed onto a crystal surface. By following these excitations while applying external magnetic fields the precise influence of the anisotropic crystal field on the

  8. Atoms and molecules interacting with light atomic physics for the laser era

    CERN Document Server

    Straten, Peter van der

    2016-01-01

    This in-depth textbook with a focus on atom-light interactions prepares students for research in a fast-growing and dynamic field. Intended to accompany the laser-induced revolution in atomic physics, it is a comprehensive text for the emerging era in atomic, molecular and optical science. Utilising an intuitive and physical approach, the text describes two-level atom transitions, including appendices on Ramsey spectroscopy, adiabatic rapid passage and entanglement. With a unique focus on optical interactions, the authors present multi-level atomic transitions with dipole selection rules, and M1/E2 and multiphoton transitions. Conventional structure topics are discussed in some detail, beginning with the hydrogen atom and these are interspersed with material rarely found in textbooks such as intuitive descriptions of quantum defects. The final chapters examine modern applications and include many references to current research literature. The numerous exercises and multiple appendices throughout enable advanc...

  9. Chameleon Induced Atomic Afterglow

    CERN Document Server

    Brax, Philippe

    2010-01-01

    The chameleon is a scalar field whose mass depends on the density of its environment. Chameleons are necessarily coupled to matter particles and will excite transitions between atomic energy levels in an analogous manner to photons. When created inside an optical cavity by passing a laser beam through a constant magnetic field, chameleons are trapped between the cavity walls and form a standing wave. This effect will lead to an afterglow phenomenon even when the laser beam and the magnetic field have been turned off, and could be used to probe the interactions of the chameleon field with matter.

  10. Cosmological Perturbations in Conformal Gravity

    CERN Document Server

    Mannheim, Philip D

    2011-01-01

    We present the first steps needed for an analysis of the perturbations that occur in the cosmology associated with the conformal gravity theory. We discuss the implications of conformal invariance for perturbative coordinate gauge choices, and show that in the conformal theory the trace of the metric fluctuation kinematically decouples from the first-order gravitational fluctuation equations. We determine the equations that describe first-order metric fluctuations around the illustrative conformally flat de Sitter background. Via a conformal transformation we show that such fluctuations can be constructed from fluctuations around a flat background, even though the fluctuations themselves are associated with a perturbative geometry that is not itself conformal to flat. We extend the analysis to fluctuations around other cosmologically relevant backgrounds, such as the conformally-flat Robertson-Walker background, and find tensor fluctuations that grow far more rapidly than those that occur in the analogous sta...

  11. WIZARD: AI in conformational analysis

    Science.gov (United States)

    Dolata, Daniel P.; Leach, Andrew R.; Prout, Keith

    1987-04-01

    A program which utilizes the techniques of Artificial Intelligence and Expert Systems to solve problems in the area of Conformational Analysis is described. The program searches conformational space in a systematic fashion, based on the technique known as heuristic state-space search. The program proceeds by recognizing conformational units, assigning one or more conformational templates to each unit, and joining them to form conformational suggestions. These suggestions are criticized to discover logical inconsistencies, and any resulting stresses are resolved. The resulting conformational suggestions are sometimes accurate enough for immediate use, or may be further refined by a numerical program. The latter combination is shown to be quite efficient compared to purely numerical conformational search techniques.

  12. Effects of carbon nanofiller characteristics on PTT chain conformation and dynamics: A computational study

    Science.gov (United States)

    Asadinezhad, Ahmad; Kelich, Payam

    2017-01-01

    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.

  13. From heavy ions to exotic atoms

    OpenAIRE

    Indelicato, Paul; Trassinelli, Martino

    2005-01-01

    We review a number of experiments and theoretical calculations on heavy ions and exotic atoms, which aim at providing informations on fundamental interactions. Among those are propositions of experiments for parity violation measurements in heavy ions and high-precision mesurements of He-like transition energies in highly charged ions. We also describe recent experiments on pionic atoms, that make use of highly-charged ion transitions to obtain accurate measurements of strong interaction shif...

  14. Atomic energy levels and Grotrian diagrams

    CERN Document Server

    Bashkin, Stanley

    1975-01-01

    Atomic Energy Levels and Grotrian Diagrams, Volume I: Hydrogen I - Phosphorus XV presents diagrams of various elements that show their energy level and electronic transitions. The book covers the first 15 elements according to their atomic number. The text will be of great use to researchers and practitioners of fields such as astrophysics that requires pictorial representation of the energy levels and electronic transitions of elements.

  15. Comparative structural and vibrational study of the four lowest energy conformers of serotonin

    Science.gov (United States)

    Jha, Omkant; Yadav, T. K.; Yadav, R. A.

    2017-02-01

    A computational investigation of all possible lowest energy conformers of serotonin was carried out at the B3LYP/6-311 ++G** level. Out of the 14 possible lowest energy conformers, the first 4 conformers were investigated thoroughly for the optimized geometries, fundamental frequencies, the potential energy distributions, APT and natural charges, natural bond orbital (NBO) analysis, MEP, Contour map, total density array, HOMO, LUMO energies. The second third and fourth conformers are energetically at higher temperatures of 78, 94 and 312 K respectively with respect to the first one. Bond angles and bond lengths do not show significant variations while the dihedral angles vary significantly in going from one conformer to the other. Some of the vibrational modes of the indole moiety are conformation dependent to some extent whereas most of the normal modes of vibration of amino-ethyl side chain vary significantly in going from one conformer to conformer. The MEP for the four conformers suggested that the sites of the maximum positive and negative ESP change on changing the conformation. The charges at some atomic sites also change significantly from conformer to conformer.

  16. Electronic structure of atoms: atomic spectroscopy information system

    Science.gov (United States)

    Kazakov, V. V.; Kazakov, V. G.; Kovalev, V. S.; Meshkov, O. I.; Yatsenko, A. S.

    2017-10-01

    The article presents a Russian atomic spectroscopy, information system electronic structure of atoms (IS ESA) (http://grotrian.nsu.ru), and describes its main features and options to support research and training. The database contains over 234 000 records, great attention paid to experimental data and uniform filling of the database for all atomic numbers Z, including classified levels and transitions of rare earth and transuranic elements and their ions. Original means of visualization of scientific data in the form of spectrograms and Grotrian diagrams have been proposed. Presentation of spectral data in the form of interactive color charts facilitates understanding and analysis of properties of atomic systems. The use of the spectral data of the IS ESA together with its functionality is effective for solving various scientific problems and training of specialists.

  17. Movement of elongation factor G between compact and extended conformations.

    Science.gov (United States)

    Salsi, Enea; Farah, Elie; Netter, Zoe; Dann, Jillian; Ermolenko, Dmitri N

    2015-01-30

    Previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor G (EF-G). Here, we follow the movement of domain IV of EF-G relative to domain II of EF-G using ensemble and single-molecule Förster resonance energy transfer. Our results indicate that ribosome-free EF-G predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain IV moves away from domain II. By contrast, ribosome-bound EF-G predominantly adopts an extended conformation regardless of whether it is interacting with pretranslocation ribosomes or with posttranslocation ribosomes. Our data suggest that ribosome-bound EF-G may also occasionally sample at least one more compact conformation. GTP hydrolysis catalyzed by EF-G does not affect the relative stability of the observed conformations in ribosome-free and ribosome-bound EF-G. Our data support a model suggesting that, upon binding to a pretranslocation ribosome, EF-G moves from a compact to a more extended conformation. This transition is not coupled to but likely precedes both GTP hydrolysis and mRNA/tRNA translocation. Copyright © 2014. Published by Elsevier Ltd.

  18. Movement of Elongation Factor G between Compact and Extended Conformations

    Science.gov (United States)

    Salsi, Enea; Farah, Elie; Netter, Zoe; Dann, Jillian; Ermolenko, Dmitri N.

    2014-01-01

    Previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor G (EF-G). Here, we follow the movement of domain IV of EF-G relative to domain II of EF-G using ensemble and single-molecule Förster resonance energy transfer (smFRET). Our results indicate that ribosome-free EF-G predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain IV moves away from domain II. By contrast, ribosome-bound EF-G predominantly adopts an extended conformation regardless of whether it is interacting with pre- or posttranslocation ribosomes. Our data suggest that ribosome-bound EF-G may also occasionally sample at least one more compact conformation. GTP hydrolysis catalyzed by EF-G does not affect the relative stability of the observed conformations in ribosome-free and ribosome-bound EF-G. Our data support a model suggesting that, upon binding to a pretranslocation ribosome, EF-G moves from a compact to a more extended conformation. This transition is not coupled to, but likely precedes both GTP hydrolysis and mRNA/tRNA translocation. PMID:25463439

  19. Conformance and Deviance

    DEFF Research Database (Denmark)

    Gjerdrum Pedersen, Esben Rahbek; Neergaard, Peter; Thusgaard Pedersen, Janni

    2013-01-01

    This paper analyses how large Danish companies are responding to new governmental regulation which requires them to report on corporate social responsibility (CSR). The paper is based on an analysis of 142 company annual reports required by the new Danish regulation regarding CSR reporting, plus ...... in CSR reporting practices. Finally, it is argued that non-conformance with the new regulatory requirements is not solely about conscious resistance but may also be caused by, for example, lack of awareness, resource limitations, misinterpretations, and practical difficulties....

  20. Atomic arias

    Science.gov (United States)

    Crease, Robert P.

    2009-01-01

    The American composer John Adams uses opera to dramatize controversial current events. His 1987 work Nixon in China was about the landmark meeting in 1972 between US President Richard Nixon and Chairman Mao Zedong of China; The Death of Klinghoffer (1991) was a musical re-enactment of an incident in 1985 when Palestinian terrorists kidnapped and murdered a wheelchair-bound Jewish tourist on a cruise ship. Adams's latest opera, Doctor Atomic, is also tied to a controversial event: the first atomic-bomb test in Alamogordo, New Mexico, on 16 June 1945. The opera premièred in San Francisco in 2005, had a highly publicized debut at the Metropolitan Opera in New York in 2008, and will have another debut on 25 February - with essentially the same cast - at the English National Opera in London.

  1. Atomic rivals

    Energy Technology Data Exchange (ETDEWEB)

    Goldschmidt, B.

    1990-01-01

    This book is a memoir of rivalries among the Allies over the bomb, by a participant and observer. Nuclear proliferation began in the uneasy wartime collaboration of the United States, England, Canada, and Free France to produce the atom bomb. Through the changes of history, a young French chemist had a role in almost every act of this international drama. This memoir is based on Goldschmidt's own recollections, interviews with other leading figures, and 3,000 pages of newly declassified documents in Allied archives. From his own start as Marie Curie's lab assistant, Goldschmidt's career was closely intertwined with Frances complicated rise to membership in the nuclear club. As a refugee from the Nazis, he became part of the wartime nuclear energy project in Canada and found himself the only French scientist to work (although briefly) on the American atom bomb project.

  2. Atomic displacements in bcc dilute alloys

    Indian Academy of Sciences (India)

    Home; Journals; Pramana – Journal of Physics; Volume 68; Issue 4. Atomic displacements in bcc ... 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.

  3. pH dependence of the conformation of small peptides investigated with two-dimensional vibrational spectroscopy.

    Science.gov (United States)

    Huerta-Viga, Adriana; Shaw, Daniel J; Woutersen, Sander

    2010-11-25

    We investigate how the conformation of small peptides is influenced by the presence or absence of charge on the C-terminus and on the side groups. To this purpose, the conformations of two tripeptides, with acidic and basic side groups, is determined at several pD values using two-dimensional infrared (2DIR) spectroscopy. The investigated pD values are chosen relative to the C-terminal and side-chain pK(a) values in such a way that the C-terminus and side groups are in well-defined protonation states. The measurements are analyzed quantitatively using an excitonic model for the Amide I' mode. From the vibrational coupling and the angle between the Amide I' transition dipoles obtained in this way, the dihedral angles (φ,ψ) of the central C(α) atom are determined. Interestingly, our measurements show that the backbone structure of the peptides is remarkably stable against changing the charges of both the side groups and the C-terminal carboxylate groups. This is probably a consequence of effective screening of the Coulomb interactions between the charged groups by the water molecules between them. We also find that the (φ,ψ) confidence regions obtained from 2DIR measurements can have highly irregular shapes as a consequence of the nonlinear relation between the dihedral angles and the experimentally determined Amide I' coupling and transition-dipole angle.

  4. Quantum gates between superconducting and atomic qubits

    Science.gov (United States)

    Saffman, Mark; Wilhelm, Frank; McDermott, Robert

    2009-05-01

    We propose methods for performing entangling gate operations between superconducting phase qubits and neutral atom hyperfine qubits. The gate is mediated by mapping the superconducting qubit onto a microwave excitation of a coplanar waveguide resonator (CPW). The large transition dipole moments of atomic Rydberg states at microwave frequencies enable bidirectional entanglement between a single atom and a single CPW photon. Specific gate protocols and fidelity calculations are presented for experimentally realistic geometries.

  5. Collective light forces on atoms in resonators

    Energy Technology Data Exchange (ETDEWEB)

    Black, Adam T; Thompson, James K; Vuletic, Vladan [Department of Physics, MIT-Harvard Center for Ultracold Atoms, and Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)

    2005-05-14

    We study resonator-induced light forces arising from cooperative atom-light interaction. For such collective processes, the force on the sample can be orders of magnitude larger than the sum of conventional light forces on individual atoms. Since resonator-induced light forces can be dissipative even when the incident light is far detuned from atomic transitions, they may be applicable to target particles with a complex level structure.

  6. 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.

  7. 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.

  8. 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

  9. Atomic form factor for twisted vortex photons interacting with atoms

    Science.gov (United States)

    Guthrey, Pierson; Kaplan, Lev; McGuire, J. H.

    2014-04-01

    The relatively new atomic form factor for twisted (vortex) beams, which carry orbital angular momentum (OAM), is considered and compared to the conventional atomic form factor for plane-wave beams that carry only spin angular momentum. Since the vortex symmetry of a twisted photon is more complex that that of a plane wave, evaluation of the atomic form factor is also more complex for twisted photons. On the other hand, the twisted photon has additional parameters, including the OAM quantum number, ℓ, the nodal radial number, p, and the Rayleigh range, zR, which determine the cone angle of the vortex. This Rayleigh range may be used as a variable parameter to control the interaction of twisted photons with matter. Here we address (i) normalization of the vortex atomic form factor, (ii) displacement of target atoms away from the center of the beam vortex, and (iii) formulation of transition probabilities for a variety of photon-atom processes. We attend to features related to experiments that can test the range of validity and accuracy of calculations of these variations of the atomic form factor. Using the absolute square of the form factor for vortex beams, we introduce a vortex factor that can be directly measured.

  10. Properties of Transition Metal Atoms and Ions

    Energy Technology Data Exchange (ETDEWEB)

    Donald, Beck, R.

    2008-03-18

    Accomplishments of this project include: (1) improvement of the accuracy and efficiency of the RCI methodology to permit it to tackle almost all TM properties, and making good progress in extending these gains to the RE. Our improvements have stimulated improvements in the GRASP package, done by Froese Fischer. RCI efficiency gains are estimated to be {approx} 200x since the start of the project - about 10x from hardware improvements (originally DOE funded) and about 20x from software improvements. The net result is that currently the longest runs don't exceed 1 day. (2) identification and removal of systematic errors in several TM properties. To some extent, the PI became a 'court of last resort' for experimenters who wondered why certain theoretical-experimental discrepancies existed. Auxiliary analysis codes were written and successfully used to improve the systematic understanding of correlation effects in TM and RE. This improved efficiency and a priori understanding of what new projects might involve. [Unsurprisingly, there are several cases which the PI was unable to resolve. Work on these is unpublished]. (3) education and training of graduate students and postdocs.

  11. 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.

  12. Unruh Effect Revisited: Poincare {theta}-Vacua as Coherent States of Conformal Zero Modes

    Energy Technology Data Exchange (ETDEWEB)

    Calixto, M [Departamento de Matematica Aplicada, Universidad de Granada, Facultad de Ciencias, Campus de Fuentenueva, 18071 Granada (Spain); Perez-Romero, E; Aldaya, V, E-mail: calixto@ugr.es [Instituto de Astrofisica de Andalucia (IAA-CSIC), Apartado Postal 3004, 18080 Granada (Spain)

    2011-09-22

    We report on a group-theoretical revision of the Unruh effect based on the conformal group SO (4, 2), which has been developed by the authors and collaborators. Special Conformal Transformations (SCT) are interpreted as transitions to relativistic uniformly accelerated frames. Poincare invariant {theta}-vacua (which turn out to be coherent states of conformal zero modes) are destabilized by SCT and radiate as a black body.

  13. Probing conformational changes in rhodopsin using hydrogen-deuterium exchange coupled to mass spectrometry.

    Science.gov (United States)

    Orban, Tivadar; Tsybovsky, Yaroslav

    2015-01-01

    Hydrogen-deuterium exchange coupled to mass spectrometry is a powerful tool to evaluate changes in protein conformation between two or more states. Here, we describe a complete methodology that can be used to assess conformational changes in rhodopsin accompanying its transition from the inactive to activated state upon light exposure. This approach may be employed to investigate the structure and conformational changes of various membrane proteins.

  14. On the hydration and conformation of cocaine in solution

    Science.gov (United States)

    Gillams, Richard J.; Lorenz, Christian D.; McLain, Sylvia E.

    2017-05-01

    In order to develop theories relating to the mechanism through which cocaine can diffuse across the blood-brain barrier, it is important to understand the interplay between the hydration of the molecule and the adopted conformation. Here key differences in the hydration of cocaine hydrochloride (CHC) and freebase cocaine (CFB) are highlighted on the atomic scale in solution, through the use of molecular dynamics simulations. By adopting different conformations, CHC and CFB experience differing hydration environments. The interplay between these two factors may account for the vast difference in solubility of these two molecules.

  15. Exploring the early stages of the pH-induced conformational change of influenza hemagglutinin.

    Science.gov (United States)

    Zhou, Yu; Wu, Chao; Zhao, Lifeng; Huang, Niu

    2014-10-01

    Hemagglutinin (HA) mediates the membrane fusion process of influenza virus through its pH-induced conformational change. However, it remains challenging to study its structure reorganization pathways in atomic details. Here, we first applied continuous constant pH molecular dynamics approach to predict the pK(a) values of titratable residues in H2 subtype HA. The calculated net-charges in HA1 globular heads increase from 0e (pH 7.5) to +14e (pH 4.5), indicating that the charge repulsion drives the detrimerization of HA globular domains. In HA2 stem regions, critical pH sensors, such as Glu103(2), His18(1), and Glu89(1), are identified to facilitate the essential structural reorganizations in the fusing pathways, including fusion peptide release and interhelical loop transition. To probe the contribution of identified pH sensors and unveil the early steps of pH-induced conformational change, we carried out conventional molecular dynamics simulations in explicit water with determined protonation state for each titratable residue in different environmental pH conditions. Particularly, energy barriers involving previously uncharacterized hydrogen bonds and hydrophobic interactions are identified in the fusion peptide release pathway. Nevertheless, comprehensive comparisons across HA family members indicate that different HA subtypes might employ diverse pH sensor groups along with different fusion pathways. Finally, we explored the fusion inhibition mechanism of antibody CR6261 and small molecular inhibitor TBHQ, and discovered a novel druggable pocket in H2 and H5 subtypes. Our results provide the underlying mechanism for the pH-driven conformational changes and also novel insight for anti-flu drug development. © 2014 Wiley Periodicals, Inc.

  16. Conformal Methods in General Relativity

    Science.gov (United States)

    Valiente Kroon, Juan A.

    2016-07-01

    List of symbols; Preface; 1. Introduction; Part I. Geometric Tools: 2. Differential Geometry; 3. Spacetime spinors; 4. Space spinors; 5. Conformal Geometry; Part II. General Relativity and Conformal Geometry: 6. Conformal extensions of exact solutions; 7. Asymptotic simplicity; 8. The conformal Einstein field equations; 9. Matter models; 10. Asymptotics; Part III. Methods of PDE Theory: 11. The conformal constraint equations; 12. Methods of the theory of hyperbolic differential equations; 13. Hyperbolic reductions; 14. Causality and the Cauchy problem in General Relativity; Part IV. Applications: 15. De Sitter-like spacetimes; 16. Minkowski-like spacetimes; 17. Anti-de Sitter-like spacetimes; 18. Characteristic problems for the conformal field equations; 19. Static solutions; 20. Spatial infinity; 21. Perspectives; References; Index.

  17. Tracing conformational changes in proteins

    OpenAIRE

    Haspel, Nurit; Moll, Mark; Baker, Matthew L; Chiu, Wah; Kavraki, Lydia E.

    2010-01-01

    Background Many proteins undergo extensive conformational changes as part of their functionality. Tracing these changes is important for understanding the way these proteins function. Traditional biophysics-based conformational search methods require a large number of calculations and are hard to apply to large-scale conformational motions. Results In this work we investigate the application of a robotics-inspired method, using backbone and limited side chain representation and a coarse grain...

  18. Two separable conformers of TATP and analogues exist at room temperature.

    Science.gov (United States)

    Denekamp, C; Gottlieb, L; Tamiri, T; Tsoglin, A; Shilav, R; Kapon, M

    2005-06-09

    [reaction: see text] TATP gives rise to two separable conformations because the barrier for interconversion between them is relatively high at room temperature. This kind of behavior is rare in cyclic organic systems and is the result of poor overlap in the "flip-flop" transition state. The crystal structure of the analogous tricyclohexanone triperoxide also indicates the presence of two conformers.

  19. Resonant interaction modified by the atomic environment

    Energy Technology Data Exchange (ETDEWEB)

    Sainz, I; Klimov, A B; Chumakov, S M [Departamento de Fisica, Universidad de Guadalajara, Revolucion 1500, 44410, Guadalajara, Jal. (Mexico)

    2003-04-01

    The dynamics of a resonant atom interacting with a quantum cavity field in the presence of many off-resonant atoms is studied. In the framework of the effective Hamiltonian approach we show that the results of elimination of non-resonant transitions are (a) a dynamical Stark shift of the field frequency, dependent on the populations of non-resonant atoms, (b) dependence of the coupling constant between the resonant atom and the field on the populations of non-resonant atoms, and (c) an effective dipole-dipole interaction between non-resonant atoms. Two effects (the coherent influence and dephasing) of the off-resonant environment on the dynamics of the resonant atom are discussed.

  20. Conformal Fermi Coordinates

    CERN Document Server

    Dai, Liang; Schmidt, Fabian

    2015-01-01

    Fermi Normal Coordinates (FNC) are a useful frame for isolating the locally observable, physical effects of a long-wavelength spacetime perturbation. Their cosmological application, however, is hampered by the fact that they are only valid on scales much smaller than the horizon. We introduce a generalization that we call Conformal Fermi Coordinates (CFC). CFC preserve all the advantages of FNC, but in addition are valid outside the horizon. They allow us to calculate the coupling of long- and short-wavelength modes on all scales larger than the sound horizon of the cosmological fluid, starting from the epoch of inflation until today, by removing the complications of the second order Einstein equations to a large extent, and eliminating all gauge ambiguities. As an application, we present a calculation of the effect of long-wavelength tensor modes on small scale density fluctuations. We recover previous results, but clarify the physical content of the individual contributions in terms of locally measurable ef...

  1. Reflections on conformal spectra

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Hyungrok; Kravchuk, Petr [Walter Burke Institute for Theoretical Physics, Caltech,Pasadena, California 91125 (United States); School of Natural Sciences, Institute for Advanced Study,Princeton, New Jersey 08540 (United States); Ooguri, Hirosi [Walter Burke Institute for Theoretical Physics, Caltech,Pasadena, California 91125 (United States); School of Natural Sciences, Institute for Advanced Study,Princeton, New Jersey 08540 (United States); Kavli Institute for the Physics and Mathematics of the Universe (WPI),University of Tokyo,Kashiwa 277-8583 (Japan)

    2016-04-29

    We use modular invariance and crossing symmetry of conformal field theory to reveal approximate reflection symmetries in the spectral decompositions of the partition function in two dimensions in the limit of large central charge and of the four-point function in any dimension in the limit of large scaling dimensions Δ{sub 0} of external operators. We use these symmetries to motivate universal upper bounds on the spectrum and the operator product expansion coefficients, which we then derive by independent techniques. Some of the bounds for four-point functions are valid for finite Δ{sub 0} as well as for large Δ{sub 0}. We discuss a similar symmetry in a large spacetime dimension limit. Finally, we comment on the analogue of the Cardy formula and sparse light spectrum condition for the four-point function.

  2. Conformal (In)Equality

    Science.gov (United States)

    Hyun, Young-Hwan; Kim, Yoonbai; Lee, Seokcheon

    2018-01-01

    The current accelerating expansion of the Universe is explained either by dark energy or by modified gravity theories. Both of them can explain exactly the same background evolution of the Universe, however this degeneracy may be broken when the observation of large scale structure formation is taken into account. Two observables are parameterized by the so-called dark energy equation of state, ω and the growth index parameter, γ. From these observed parameters, one may reconstruct the model parameters of the so-called scalar-tensor gravity theory, one of the modified gravity theories. Especially, the scalar-tensor gravity theory is described both in Jordan frame and in Einstein frame. If cosmological observations are interpreted in one frame, then all of the observables should also be interpreted in that frame. This explicitly shows conformal inequality of cosmological observables.

  3. Conformal (InEquality

    Directory of Open Access Journals (Sweden)

    Hyun Young-Hwan

    2018-01-01

    Full Text Available The current accelerating expansion of the Universe is explained either by dark energy or by modified gravity theories. Both of them can explain exactly the same background evolution of the Universe, however this degeneracy may be broken when the observation of large scale structure formation is taken into account. Two observables are parameterized by the so-called dark energy equation of state, ω and the growth index parameter, γ. From these observed parameters, one may reconstruct the model parameters of the so-called scalar-tensor gravity theory, one of the modified gravity theories. Especially, the scalar-tensor gravity theory is described both in Jordan frame and in Einstein frame. If cosmological observations are interpreted in one frame, then all of the observables should also be interpreted in that frame. This explicitly shows conformal inequality of cosmological observables.

  4. Reflections on Conformal Spectra

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    We use modular invariance and crossing symmetry of conformal field theory to reveal approximate reflection symmetries in the spectral decompositions of the partition function in two dimensions in the limit of large central charge and of the four-point function in any dimension in the limit of large scaling dimensions Δ0 of external operators. We use these symmetries to motivate universal upper bounds on the spectrum and the operator product expansion coefficients, which we then derive by independent techniques. Some of the bounds for four-point functions are valid for finite Δ0 as well as for large Δ0. We discuss a similar symmetry in a large spacetime dimension limit. Finally, we comment on the analogue of the Cardy formula and sparse light spectrum condition for the four-point function. (based on 1510.08772 with Kim & Ooguri). This seminar will be given via videolink

  5. Physical nature of interactions in Zn(II) complexes with 2,2'-bipyridyl: quantum theory of atoms in molecules (QTAIM), interacting quantum atoms (IQA), noncovalent interactions (NCI), and extended transition state coupled with natural orbitals for chemical valence (ETS-NOCV) comparative studies.

    Science.gov (United States)

    Cukrowski, Ignacy; de Lange, Jurgens H; Mitoraj, Mariusz

    2014-01-23

    In the present account factors determining the stability of ZnL, ZnL2, and ZnL3 complexes (L = bpy, 2,2′-bipyridyl) were characterized on the basis of various techniques: the quantum theory of atoms in molecules (QTAIM), energy decomposition schemes based on interacting quantum atoms (IQA), and extended transition state coupled with natural orbitals for chemical valence (ETS-NOCV). Finally, the noncovalent interactions (NCI) index was also applied. All methods consistently indicated that the strength of the coordination bonds, Zn–O and Zn–N, decreases from ZnL to ZnL3. Importantly, it has been identified that the strength of secondary intramolecular heteropolar hydrogen bonding interactions, CH···O and CH···N, increases when going from ZnL to ZnL3. A similar trend appeared to be valid for the π-bonding as well as electrostatic stabilization. In addition to the above leading bonding contributions, all techniques suggested the existence of very subtle, but non-negligible additional stabilization from the CH···HC electronic exchange channel; these interactions are the weakest among all considered here. From IQA it was found that the local diatomic interaction energy, Eint(H,H), amounts at HF to −2.5, −2.7, and −2.9 kcal mol(–1) for ZnL, ZnL2, and ZnL3, respectively (−2.1 kcal mol(–1) for ZnL at MP2). NOCV-based deformation density channels showed that formation of CH--HC contacts in Zn complexes causes significant polarization of σ(C–H) bonds, which accordingly leads to charge accumulation in the CH···HC bay region. Charge depletion from σ(C–H) bonds was also reflected in the calculated spin–spin (1)J(C–H) coupling constants, which decrease from 177.06 Hz (ZnL) to 173.87 Hz (ZnL3). This last result supports our findings of an increase in the local electronic CH···HC stabilization from ZnL to ZnL3 found from QTAIM, IQA, and ETS-NOCV. Finally, this work unites for the first time the results from four methods that are widely

  6. Conformations of some large-ring cyclodextrins derived from conformational search with molecular dynamics simulations and principal component analysis.

    Science.gov (United States)

    Ivanov, Petko M

    2010-03-04

    Principal component analysis (PCA) was applied for postprocessing of trajectories from conformational search, based on 50.0 ns molecular dynamics (MD) simulations, with the purpose to elucidate the conformations of some large-ring cyclodextrins (LR-CDs), CDn (n = 24, 25, 26, 27, 28, 29). The dominant PCA modes for concerted motions of the macroring atoms were monitored in a lower-dimension subspace. The first 10 lowest indexed modes describe more than 90% of the total atomic motions in all cases, with about 85% (CD27, CD29) to more than 90% (CD24, CD25) contribution coming from the six highest-eigenvalue principal components. Representative average geometries of the cyclodextrin macrorings were also obtained for the whole simulation and for the five 10.0 ns time intervals of the simulation. Two conformations for CD26, the largest LR-CD for which X-ray data is available, are characterized by possessing, respectively, one and two helical turns. Resemblance to computed representative conformations of CD26 in water was found for CD27 and CD28, with the similarity being better expressed for the former case. Only CD24, among the two smaller size LR-CDs, displays resemblance during short simulation intervals to one of the conformations of CD26. The formation of small loops of six to seven glucose units is a favorable deformation mode of the macrorings. Besides, once a small loop of six to seven glucoses is formed, the next natural mode for deformation of the macromolecule is toward the creation of a short helix that further enhances the stability of the structure. The average geometry of CD29 has no likeness at all to the conformations of CD26. Thus, the difference of three glucose units between CD26 and CD29 already influences significantly the shape of the most probable conformation.

  7. Shape: automatic conformation prediction of carbohydrates using a genetic algorithm

    Directory of Open Access Journals (Sweden)

    Rosen Jimmy

    2009-09-01

    Full Text Available Abstract Background Detailed experimental three dimensional structures of carbohydrates are often difficult to acquire. Molecular modelling and computational conformation prediction are therefore commonly used tools for three dimensional structure studies. Modelling procedures generally require significant training and computing resources, which is often impractical for most experimental chemists and biologists. Shape has been developed to improve the availability of modelling in this field. Results The Shape software package has been developed for simplicity of use and conformation prediction performance. A trivial user interface coupled to an efficient genetic algorithm conformation search makes it a powerful tool for automated modelling. Carbohydrates up to a few hundred atoms in size can be investigated on common computer hardware. It has been shown to perform well for the prediction of over four hundred bioactive oligosaccharides, as well as compare favourably with previously published studies on carbohydrate conformation prediction. Conclusion The Shape fully automated conformation prediction can be used by scientists who lack significant modelling training, and performs well on computing hardware such as laptops and desktops. It can also be deployed on computer clusters for increased capacity. The prediction accuracy under the default settings is good, as it agrees well with experimental data and previously published conformation prediction studies. This software is available both as open source and under commercial licenses.

  8. Shape: automatic conformation prediction of carbohydrates using a genetic algorithm

    Science.gov (United States)

    2009-01-01

    Background Detailed experimental three dimensional structures of carbohydrates are often difficult to acquire. Molecular modelling and computational conformation prediction are therefore commonly used tools for three dimensional structure studies. Modelling procedures generally require significant training and computing resources, which is often impractical for most experimental chemists and biologists. Shape has been developed to improve the availability of modelling in this field. Results The Shape software package has been developed for simplicity of use and conformation prediction performance. A trivial user interface coupled to an efficient genetic algorithm conformation search makes it a powerful tool for automated modelling. Carbohydrates up to a few hundred atoms in size can be investigated on common computer hardware. It has been shown to perform well for the prediction of over four hundred bioactive oligosaccharides, as well as compare favourably with previously published studies on carbohydrate conformation prediction. Conclusion The Shape fully automated conformation prediction can be used by scientists who lack significant modelling training, and performs well on computing hardware such as laptops and desktops. It can also be deployed on computer clusters for increased capacity. The prediction accuracy under the default settings is good, as it agrees well with experimental data and previously published conformation prediction studies. This software is available both as open source and under commercial licenses. PMID:20298520

  9. New open conformation of SMYD3 implicates conformational selection and allostery

    Directory of Open Access Journals (Sweden)

    Nicholas Spellmon

    2016-12-01

    Full Text Available SMYD3 plays a key role in cancer cell viability, adhesion, migration and invasion. SMYD3 promotes formation of inducible regulatory T cells and is involved in reducing autoimmunity. However, the nearly “closed” substrate-binding site and poor in vitro H3K4 methyltransferase activity have obscured further understanding of this oncogenically related protein. Here we reveal that SMYD3 can adopt an “open” conformation using molecular dynamics simulation and small-angle X-ray scattering. This ligand-binding-capable open state is related to the crystal structure-like closed state by a striking clamshell-like inter-lobe dynamics. The two states are characterized by many distinct structural and dynamical differences and the conformational transition pathway is mediated by a reversible twisting motion of the C-terminal domain (CTD. The spontaneous transition from the closed to open states suggests two possible, mutually non-exclusive models for SMYD3 functional regulation and the conformational selection mechanism and allostery may regulate the catalytic or ligand binding competence of SMYD3. This study provides an immediate clue to the puzzling role of SMYD3 in epigenetic gene regulation.

  10. Atom Skimmers and Atom Lasers Utilizing Them

    Science.gov (United States)

    Hulet, Randall; Tollett, Jeff; Franke, Kurt; Moss, Steve; Sackett, Charles; Gerton, Jordan; Ghaffari, Bita; McAlexander, W.; Strecker, K.; Homan, D.

    2005-01-01

    Atom skimmers are devices that act as low-pass velocity filters for atoms in thermal atomic beams. An atom skimmer operating in conjunction with a suitable thermal atomic-beam source (e.g., an oven in which cesium is heated) can serve as a source of slow atoms for a magneto-optical trap or other apparatus in an atomic-physics experiment. Phenomena that are studied in such apparatuses include Bose-Einstein condensation of atomic gases, spectra of trapped atoms, and collisions of slowly moving atoms. An atom skimmer includes a curved, low-thermal-conduction tube that leads from the outlet of a thermal atomic-beam source to the inlet of a magneto-optical trap or other device in which the selected low-velocity atoms are to be used. Permanent rare-earth magnets are placed around the tube in a yoke of high-magnetic-permeability material to establish a quadrupole or octupole magnetic field leading from the source to the trap. The atoms are attracted to the locus of minimum magnetic-field intensity in the middle of the tube, and the gradient of the magnetic field provides centripetal force that guides the atoms around the curve along the axis of the tube. The threshold velocity for guiding is dictated by the gradient of the magnetic field and the radius of curvature of the tube. Atoms moving at lesser velocities are successfully guided; faster atoms strike the tube wall and are lost from the beam.

  11. Synthesis of selenium-containing Artemisia sphaerocephala polysaccharides: Solution conformation and anti-tumor activities in vitro.

    Science.gov (United States)

    Wang, Junlong; Li, Qingyao; Bao, Aijuan; Liu, Xiurong; Zeng, Junyuan; Yang, Xiaopin; Yao, Jian; Zhang, Ji; Lei, Ziqiang

    2016-11-05

    It has been reported in our previous work that selenized Artemisia sphaerocephala polysaccharides (SeASPs) with the Se content range of 168-1703μg/g were synthesized by using Na2SeO3/HNO3/BaCl2 system. In the present work, the solution property of SeASP was studied by using size exclusion chromatography combined with multi angle laser light scattering (SEC-MALLS). A decrease in df values indicated that SeASPs with different conformational features that were highly dependent on MW. SeASPs exhibited a more rigid conformation (df value of 1.29-1.52) in low molecular weight range (MW of 1.026-1.426×10(4)g/mol) and compact spherical conformation in high molecular weight range (MW of 2.268-4.363×10(4)g/mol). It could be due to the degradation of polysaccharide chains in HNO3, which was supported in monosaccharide composition analysis. Congo red (CR) spectrophotometric method and atomic force microscopy (AFM) results also confirmed the conformational transition and the evidence on the shape of the rigid chains. In vitro anti-tumor assays, SeASP2 displayed greater anti-proliferative effects against three tumor cell lines (hepatocellular carcinoma HepG-2 cells, lung adenocarcinom A549 cells and cervical squamous carcinoma Hela cells) in a dose-dependent manner. This suggested that selenylation could significantly enhance the anti-tumor activities of polysaccharide derivatives in vitro. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Exploration of conformational changes in lactose permease upon sugar binding and proton transfer through coarse-grained simulations.

    Science.gov (United States)

    Jewel, Yead; Dutta, Prashanta; Liu, Jin

    2017-10-01

    Escherichia coli lactose permease (LacY) actively transports lactose and other galactosides across cell membranes through lactose/H(+) symport process. Lactose/H(+) symport is a highly complex process that involves sugar translocation, H(+) transfer, and large-scale protein conformational changes. The complete picture of lactose/H(+) symport is largely unclear due to the complexity and multiscale nature of the process. In this work, we develop the force field for sugar molecules compatible with PACE, a hybrid and coarse-grained force field that couples the united-atom protein models with the coarse-grained MARTINI water/lipid. After validation, we implement the new force field to investigate the binding of a β-d-galactopyranosyl-1-thio- β-d-galactopyranoside (TDG) molecule to a wild-type LacY. Results show that the local interactions between TDG and LacY at the binding pocket are consistent with the X-ray experiment. Transitions from inward-facing to outward-facing conformations upon TDG binding and protonation of Glu269 have been achieved from ∼5.5 µs simulations. Both the opening of the periplasmic side and closure of the cytoplasmic side of LacY are consistent with double electron-electron resonance and thiol cross-linking experiments. Our analysis suggests that the conformational changes of LacY are a cumulative consequence of interdomain H-bonds breaking at the periplasmic side, interdomain salt-bridge formation at the cytoplasmic side, and the TDG orientational changes during the transition. © 2017 Wiley Periodicals, Inc.

  13. Atomic displacements due to interstitial hydrogen in Cu and Pd

    Indian Academy of Sciences (India)

    The density functional theory (DFT) is used to study the atomic interactions in transition metal-based interstitial alloys. The strain field is calculated in the discrete lattice model using Kanzaki method. The total energy and hence atomic forces between interstitial hydrogen and transition metal hosts are calculated using DFT.

  14. Atomic displacements due to interstitial hydrogen in Cu and Pd

    Indian Academy of Sciences (India)

    Abstract. The density functional theory (DFT) is used to study the atomic interac- tions in transition metal-based interstitial alloys. The strain field is calculated in the discrete lattice model using Kanzaki method. The total energy and hence atomic forces between interstitial hydrogen and transition metal hosts are calculated ...

  15. Replacement between conformity and counter-conformity in consumption decisions.

    Science.gov (United States)

    Chou, Ting-Jui; Chang, En-Chung; Dai, Qi; Wong, Veronica

    2013-02-01

    This study assessed, in a Chinese context, how self-esteem interacts with perceived similarity and uniqueness to yield cognitive dissonance, and whether the dissonance leads to self-reported conformity or counter-conformity behavior. Participants were 408 respondents from 4 major Chinese cities (M age = 33.0 yr., SD = 4.3; 48% men). Self-perceptions of uniqueness, similarity, cognitive dissonance, self-esteem and need to behave in conformity or counter-conformity were measured. A theoretical model was assessed in four situations, relating the ratings of self-esteem and perceived similarity/uniqueness to the way other people at a wedding were dressed, and the resultant cognitive dissonance and conformity/ counter-conformity behavior. Regardless of high or low self-esteem, all participants reported cognitive dissonance when they were told that they were dressed extremely similarly to or extremely differently from the other people attending the wedding. However, the conforming/counter-conforming strategies used by participants to resolve the cognitive dissonance differed. When encountering dissonance induced by the perceived extreme uniqueness of dress, participants with low self-esteem tended to say they would dress next time so as to conform with the way others were dressed, while those with high self-esteem indicated they would continue their counter-conformity in attire. When encountering dissonance induced by the perceived extreme similarity to others, both those with high and low self-esteem tended to say they would dress in an unorthodox manner to surprise other people in the future.

  16. Acceleration effects on atomic clocks

    CERN Document Server

    Dahia, F

    2014-01-01

    We consider a free massive particle inside a box which is dragged by Rindler observers. Admitting that the particle obeys the Klein-Gordon equation, we find the frequencies of the stationary states of this system. Transitions between the stationary states are employed to set a standard frequency for a toy atomic clock. Comparing the energy spectrum of the accelerated system with the energy spectrum of an identical system in an inertial frame, we determine the influence of the instantaneous acceleration on the rate of atomic clocks. We argue that our result does not violate the clock hypothesis.

  17. Binary cluster collision dynamics and minimum energy conformations

    Energy Technology Data Exchange (ETDEWEB)

    Muñoz, Francisco [Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle (Germany); Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y Nanotecnología, CEDENNA, Avenida Ecuador 3493, Santiago (Chile); Rogan, José; Valdivia, J.A. [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y Nanotecnología, CEDENNA, Avenida Ecuador 3493, Santiago (Chile); Varas, A. [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Nano-Bio Spectroscopy Group, ETSF Scientific Development Centre, Departamento de Física de Materiales, Universidad del País Vasco UPV/EHU, Av. Tolosa 72, E-20018 San Sebastián (Spain); Kiwi, Miguel, E-mail: m.kiwi.t@gmail.com [Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago (Chile); Centro para el Desarrollo de la Nanociencia y Nanotecnología, CEDENNA, Avenida Ecuador 3493, Santiago (Chile)

    2013-10-15

    The collision dynamics of one Ag or Cu atom impinging on a Au{sub 12} cluster is investigated by means of DFT molecular dynamics. Our results show that the experimentally confirmed 2D to 3D transition of Au{sub 12}→Au{sub 13} is mostly preserved by the resulting planar Au{sub 12}Ag and Au{sub 12}Cu minimum energy clusters, which is quite remarkable in view of the excess energy, well larger than the 2D–3D potential barrier height. The process is accompanied by a large s−d hybridization and charge transfer from Au to Ag or Cu. The dynamics of the collision process mainly yields fusion of projectile and target, however scattering and cluster fragmentation also occur for large energies and large impact parameters. While Ag projectiles favor fragmentation, Cu favors scattering due to its smaller mass. The projectile size does not play a major role in favoring the fragmentation or scattering channels. By comparing our collision results with those obtained by an unbiased minimum energy search of 4483 Au{sub 12}Ag and 4483 Au{sub 12}Cu configurations obtained phenomenologically, we find that there is an extra bonus: without increase of computer time collisions yield the planar lower energy structures that are not feasible to obtain using semi-classical potentials. In fact, we conclude that phenomenological potentials do not even provide adequate seeds for the search of global energy minima for planar structures. Since the fabrication of nanoclusters is mainly achieved by synthesis or laser ablation, the set of local minima configurations we provide here, and their distribution as a function of energy, are more relevant than the global minimum to analyze experimental results obtained at finite temperatures, and is consistent with the dynamical coexistence of 2D and 3D liquid Au clusters conformations obtained previously.

  18. Advances in atomic, molecular, and optical physics

    CERN Document Server

    Berman, Paul R; Arimondo, Ennio

    2006-01-01

    Volume 54 of the Advances Series contains ten contributions, covering a diversity of subject areas in atomic, molecular and optical physics. The article by Regal and Jin reviews the properties of a Fermi degenerate gas of cold potassium atoms in the crossover regime between the Bose-Einstein condensation of molecules and the condensation of fermionic atom pairs. The transition between the two regions can be probed by varying an external magnetic field. Sherson, Julsgaard and Polzik explore the manner in which light and atoms can be entangled, with applications to quantum information processing

  19. Structure and conformational dynamics of scaffolded DNA origami nanoparticles.

    Science.gov (United States)

    Pan, Keyao; Bricker, William P; Ratanalert, Sakul; Bathe, Mark

    2017-06-20

    Synthetic DNA is a highly programmable nanoscale material that can be designed to self-assemble into 3D structures that are fully determined by underlying Watson-Crick base pairing. The double crossover (DX) design motif has demonstrated versatility in synthesizing arbitrary DNA nanoparticles on the 5-100 nm scale for diverse applications in biotechnology. Prior computational investigations of these assemblies include all-atom and coarse-grained modeling, but modeling their conformational dynamics remains challenging due to their long relaxation times and associated computational cost. We apply all-atom molecular dynamics and coarse-grained finite element modeling to DX-based nanoparticles to elucidate their fine-scale and global conformational structure and dynamics. We use our coarse-grained model with a set of secondary structural motifs to predict the equilibrium solution structures of 45 DX-based DNA origami nanoparticles including a tetrahedron, octahedron, icosahedron, cuboctahedron and reinforced cube. Coarse-grained models are compared with 3D cryo-electron microscopy density maps for these five DNA nanoparticles and with all-atom molecular dynamics simulations for the tetrahedron and octahedron. Our results elucidate non-intuitive atomic-level structural details of DX-based DNA nanoparticles, and offer a general framework for efficient computational prediction of global and local structural and mechanical properties of DX-based assemblies that are inaccessible to all-atom based models alone. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Recent advancements in conformal gravity

    Science.gov (United States)

    O'Brien, James G.; Chaykov, Spasen S.; Dentico, Jeremy; Stulge, Modestas; Stefanski, Brian; Moss, Robert J.

    2017-05-01

    In recent years, due to the lack of direct observed evidence of cold dark matter, coupled with the shrinking parameter space to search for new dark matter particles, there has been increased interest in Alternative Gravitational theories. This paper, addresses three recent advances in conformal gravity, a fourth order renormalizable metric theory of gravitation originally formulated by Weyl, and later advanced by Mannheim and Kazanas. The first section of the paper applies conformal gravity to the rotation curves of the LITTLE THINGS survey, extending the total number of rotation curves successfully fit by conformal gravity to well over 200 individual data sets without the need for additional dark matter. Further, in this rotation curve study, we show how MOND and conformal gravity compare for each galaxy in the sample. Second, we look at the original Zwicky problem of applying the virial theorem to the Coma cluster in order to get an estimate for the cluster mass. However, instead of using the standard Newtonian potential, here we use the weak field approximation of conformal gravity. We show that in the conformal case we can get a much smaller mass estimate and thus there is no apparent need to include dark matter. We then show that this calculation is in agreement with the observational data from other well studied clusters. Last, we explore the calculation of the deflection of starlight through conformal gravity, as a first step towards applying conformal gravity to gravitaitonal lensing.

  1. Solvent Induced Conformational Kinetics (SICK)

    NARCIS (Netherlands)

    Jonkman, Leffert; Kommandeur, Jan

    1970-01-01

    Specific conformations of molecules may be induced by the solvent when a large free volume is associated with the oonformational change. The conformational energy barrier is then a property of the solvent, rather than of the molecule. Such effects are reported for several substituted

  2. Counselor Identity: Conformity or Distinction?

    Science.gov (United States)

    McLaughlin, Jerry E.; Boettcher, Kathryn

    2009-01-01

    The authors explore 3 debates in other disciplines similar to counseling's identity debate in order to learn about common themes and outcomes. Conformity, distinction, and cohesion emerged as common themes. They conclude that counselors should retain their distinctive, humanistic approach rather than conforming to the dominant, medical approach.

  3. Conformational dynamics of Thermus aquaticus DNA polymerase I during catalysis.

    Science.gov (United States)

    Xu, Cuiling; Maxwell, Brian A; Suo, Zucai

    2014-08-12

    Despite the fact that DNA polymerases have been investigated for many years and are commonly used as tools in a number of molecular biology assays, many details of the kinetic mechanism they use to catalyze DNA synthesis remain unclear. Structural and kinetic studies have characterized a rapid, pre-catalytic open-to-close conformational change of the Finger domain during nucleotide binding for many DNA polymerases including Thermus aquaticus DNA polymerase I (Taq Pol), a thermostable enzyme commonly used for DNA amplification in PCR. However, little has been performed to characterize the motions of other structural domains of Taq Pol or any other DNA polymerase during catalysis. Here, we used stopped-flow Förster resonance energy transfer to investigate the conformational dynamics of all five structural domains of the full-length Taq Pol relative to the DNA substrate during nucleotide binding and incorporation. Our study provides evidence for a rapid conformational change step induced by dNTP binding and a subsequent global conformational transition involving all domains of Taq Pol during catalysis. Additionally, our study shows that the rate of the global transition was greatly increased with the truncated form of Taq Pol lacking the N-terminal domain. Finally, we utilized a mutant of Taq Pol containing a de novo disulfide bond to demonstrate that limiting protein conformational flexibility greatly reduced the polymerization activity of Taq Pol. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Size-controlled conformal nanofabrication of biotemplated three-dimensional TiO₂ and ZnO nanonetworks

    National Research Council Canada - National Science Library

    Ceylan, Hakan; Ozgit-Akgun, Cagla; Erkal, Turan S; Donmez, Inci; Garifullin, Ruslan; Tekinay, Ayse B; Usta, Hakan; Biyikli, Necmi; Guler, Mustafa O

    2013-01-01

    A solvent-free fabrication of TiO₂ and ZnO nanonetworks is demonstrated by using supramolecular nanotemplates with high coating conformity, uniformity, and atomic scale size control. Deposition of TiO₂...

  5. Recursion Relations for Conformal Blocks

    CERN Document Server

    Penedones, João; Yamazaki, Masahito

    2016-09-12

    In the context of conformal field theories in general space-time dimension, we find all the possible singularities of the conformal blocks as functions of the scaling dimension $\\Delta$ of the exchanged operator. In particular, we argue, using representation theory of parabolic Verma modules, that in odd spacetime dimension the singularities are only simple poles. We discuss how to use this information to write recursion relations that determine the conformal blocks. We first recover the recursion relation introduced in 1307.6856 for conformal blocks of external scalar operators. We then generalize this recursion relation for the conformal blocks associated to the four point function of three scalar and one vector operator. Finally we specialize to the case in which the vector operator is a conserved current.

  6. Conformal Organohalide Perovskites Enable Lasing on Spherical Resonators

    KAUST Repository

    Sutherland, Brandon R.

    2014-10-28

    © 2014 American Chemical Society. Conformal integration of semiconductor gain media is broadly important in on-chip optical communication technology. Here we deploy atomic layer deposition to create conformally deposited organohalide perovskites-an attractive semiconducting gain medium-with the goal of achieving coherent light emission on spherical optical cavities. We demonstrate the high quality of perovskite gain media fabricated with this method, achieving optical gain in the nanosecond pulse regime with a threshold for amplified spontaneous emission of 65 ± 8 μJ cm-2. Through variable stripe length measurements, we report a net modal gain of 125 ± 22 cm-1 and a gain bandwidth of 50 ± 14 meV. Leveraging the high quality of the gain medium, we conformally coat silica microspheres with perovskite to form whispering gallery mode optical cavities and achieve lasing.

  7. High Atom Number in Microsized Atom Traps

    Science.gov (United States)

    2015-12-14

    Final Performance Report on ONR Grant N00014-12-1-0608 High atom number in microsized atom traps for the period 15 May 2012 through 14 September...TYPE Final Technical Report 3. DATES COVERED (From - To) 05/15/2012-09/14/2012 4. TITLE AND SUBTITLE High atom number in microsized atom traps...forces for implementing a small-footprint, large-number atom -chip instrument. Bichromatic forces rely on absorption and stimulated emission to produce

  8. Rydberg Atom Quantum Hybrid Systems

    Science.gov (United States)

    Chao, Yuanxi; Sheng, Jiteng; Kumar, Santosh; Bigelow, Nicholas P.; Shaffer, James P.

    2017-04-01

    We report on our recent experimental and theoretical work with Rydberg atom-cavity and Rydberg atom-surface hybrid quantum systems. In the atom-cavity system, Rb contained in a dipole trap is transported into a high-finesse optical cavity using a focus-tunable lens. Cavity assisted Rydberg EIT is observed in the cavity transmission and used to characterize the electric fields in the cavity. The electric fields are attributed to surface adsorbates adhering to the cavity mirrors. We also investigate the coupling of a Rydberg atom ensemble to surface phonon polaritons (SPhPs) propagating on piezoelectric superlattices made from thin film ferroelectric materials. Strong coupling between the atomic and surface excitations can be achieved, due to the large Rydberg transition dipole moments and the local field enhancement of the SPhP modes. The system has many advantages for information transport since the atoms need only be placed at distances on the order of mms from the surface and the SPhPs do not couple to free space electro-magnetic fields. Experimental progress will be discussed, including the fabrication of submicron-period periodically poled Lithium Niobate using the direct e-beam writing technique. This work is supported by AFOSR.

  9. Theoretical and conformational studies of a series of cannabinoids

    Science.gov (United States)

    Da Silva, Albérico B. F.; Trsic, Milan

    1995-11-01

    The MNDO semi-empirical method is applied to the study of a series of cannabinoids with the aim of providing an improved understanding of the structure-activity relationship (SAR). The conformation of some groups that seem important in the biological activity (psychoactivity) of these compounds is characterized. Some electronic properties, such as atomic net charges and HOMO and LUMO energies, are correlated with the psychoactive effect.

  10. Imaging of conformational changes

    Energy Technology Data Exchange (ETDEWEB)

    Michl, Josef [Univ. of Colorado, Boulder, CO (United States)

    2016-03-13

    Control of intramolecular conformational change in a small number of molecules or even a single one by an application of an outside electric field defined by potentials on nearby metal or dielectric surfaces has potential applications in both 3-D and 2-D nanotechnology. Specifically, the synthesis, characterization, and understanding of designed solids with controlled built-in internal rotational motion of a dipole promises a new class of materials with intrinsic dielectric, ferroelectric, optical and optoelectronic properties not found in nature. Controlled rotational motion is of great interest due to its expected utility in phenomena as diverse as transport, current flow in molecular junctions, diffusion in microfluidic channels, and rotary motion in molecular machines. A direct time-resolved observation of the dynamics of motion on ps or ns time scale in a single molecule would be highly interesting but is also very difficult and has yet to be accomplished. Much can be learned from an easier but still challenging comparison of directly observed initial and final orientational states of a single molecule, which is the basis of this project. The project also impacts the understanding of surface-enhanced Raman spectroscopy (SERS) and single-molecule spectroscopic detection, as well as the synthesis of solid-state materials with tailored properties from designed precursors.

  11. Conformational analysis and circular dichroism of bilirubin, the yellow pigment of jaundice

    Science.gov (United States)

    Lightner, David A.; Person, Richard; Peterson, Blake; Puzicha, Gisbert; Pu, Yu-Ming; Bojadziev, Stefan

    1991-06-01

    Conformational analysis of (4Z, 15Z)-bilirubin-IX(alpha) by molecular mechanics computations reveals a global energy minimum folded conformation. Powerful added stabilization is achieved through intramolecular hydrogen bonding. Theoretical treatment of bilirubin as a molecular exciton predicts an intense bisignate circular dichroism spectrum for the folded conformation: (Delta) (epsilon) is congruent to 270 L (DOT) mole-1 (DOT) cm-1 for the $OM450 nm electronic transition(s). Synthesis of bilirubin analogs with propionic acid groups methylated at the (alpha) or (beta) position introduces an allosteric effect that allows for an optical resolution of the pigments, with enantiomers exhibiting the theoretically predicted circular dichroism.

  12. BOOK REVIEW: Computational Atomic Structure

    Science.gov (United States)

    Post, Douglass E.

    1998-02-01

    The primary purpose of `Computational Atomic Structure' is to give a potential user of the Multi-Configuration Hartree-Fock (MCHF) Atomic Structure Package an outline of the physics and computational methods in the package, guidance on how to use the package, and information on how to interpret and use the computational results. The book is successful in all three aspects. In addition, the book provides a good overview and review of the physics of atomic structure that would be useful to the plasma physicist interested in refreshing his knowledge of atomic structure and quantum mechanics. While most of the subjects are covered in greater detail in other sources, the book is reasonably self-contained, and, in most cases, the reader can understand the basic material without recourse to other sources. The MCHF package is the standard package for computing atomic structure and wavefunctions for single or multielectron ions and atoms. It is available from a number of ftp sites. When the code was originally written in FORTRAN 77, it could only be run on large mainframes. With the advances in computer technology, the suite of codes can now be compiled and run on present day workstations and personal computers and is thus available for use by any physicist, even those with extremely modest computing resources. Sample calculations in interactive mode are included in the book to illustrate the input needed for the code, what types of results and information the code can produce, and whether the user has installed the code correctly. The user can also specify the calculational level, from simple Hartree-Fock to multiconfiguration Hartree-Fock. The MCHF method begins by finding approximate wavefunctions for the bound states of an atomic system. This involves minimizing the energy of the bound state using a variational technique. Once the wavefunctions have been determined, other atomic properties, such as the transition rates, can be determined. The book begins with an

  13. An Introduction to Atomic Layer Deposition

    Science.gov (United States)

    Dwivedi, Vivek H.

    2017-01-01

    Atomic Layer Deposition has been instrumental in providing a deposition method for multiple space flight applications. It is well known that ALD is a cost effective nanoadditive-manufacturing technique that allows for the conformal coating of substrates with atomic control in a benign temperature and pressure environment. Through the introduction of paired precursor gases, thin films can be deposited on a myriad of substrates from flat surfaces to those with significant topography. By providing atomic layer control, where single layers of atoms can be deposited, the fabrication of metal transparent films, precise nano-laminates, and coatings of nano-channels, pores and particles is achievable. The feasibility of this technology for NASA line of business applications range from thermal systems, optics, sensors, to environmental protection. An overview of this technology will be presented.

  14. Cooling Atomic Gases With Disorder

    Science.gov (United States)

    Paiva, Thereza; Khatami, Ehsan; Yang, Shuxiang; Rousseau, Valéry; Jarrell, Mark; Moreno, Juana; Hulet, Randall G.; Scalettar, Richard T.

    2015-12-01

    Cold atomic gases have proven capable of emulating a number of fundamental condensed matter phenomena including Bose-Einstein condensation, the Mott transition, Fulde-Ferrell-Larkin-Ovchinnikov pairing, and the quantum Hall effect. Cooling to a low enough temperature to explore magnetism and exotic superconductivity in lattices of fermionic atoms remains a challenge. We propose a method to produce a low temperature gas by preparing it in a disordered potential and following a constant entropy trajectory to deliver the gas into a nondisordered state which exhibits these incompletely understood phases. We show, using quantum Monte Carlo simulations, that we can approach the Néel temperature of the three-dimensional Hubbard model for experimentally achievable parameters. Recent experimental estimates suggest the randomness required lies in a regime where atom transport and equilibration are still robust.

  15. A nanoscale quantum interface for single atoms

    Science.gov (United States)

    Tiecke, Tobias; Thompson, Jeff; Feist, Johannes; Yu, Chun; Akimov, Alexey; Chang, Darrick; Zibrov, Alexander; Vuletic, Vladan; Park, Hongkun; Lukin, Mikhail

    2012-02-01

    Neutral atoms are ideal quantum systems: they have long ground-state coherence times and strong optical cycling transitions that enable state detection and preparation. Building quantum networks of atoms interacting through photons is challenging, however, as many schemes for atom-photon interaction are inefficient or hard to scale. We propose a scheme to trap neutral atoms near silver nanowires, which are tightly confining waveguides for surface plasmons. The nanowire tip is used to generate a near-field optical trapping potential, and to enhance and efficiently collect spontaneous emission from the atom. We present experimental results on using the atom to sense the optical field at submicron distances from the wire and our current efforts towards loading the nanotrap.

  16. Première observation de la transition fortement interdite 1S0-3P0 du strontium, pour une horloge optique à atomes piégés

    OpenAIRE

    Courtillot, Irene

    2003-01-01

    Rapporteurs : François Biraben et Jacques Vigué Examinateurs : Robin Kaiser, E. Peik Président du jury : Jean-Michel Raimond Invité : Cristophe Salomon; 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 1S...

  17. Locally conformal symplectic manifolds

    Directory of Open Access Journals (Sweden)

    Izu Vaisman

    1985-01-01

    Full Text Available A locally conformal symplectic (l. c. s. manifold is a pair (M2n,Ω where M2n(n>1 is a connected differentiable manifold, and Ω a nondegenerate 2-form on M such that M=⋃αUα (Uα- open subsets. Ω/Uα=eσαΩα, σα:Uα→ℝ, dΩα=0. Equivalently, dΩ=ω∧Ω for some closed 1-form ω. L. c. s. manifolds can be seen as generalized phase spaces of Hamiltonian dynamical systems since the form of the Hamilton equations is, in fact, preserved by homothetic canonical transformations. The paper discusses first Hamiltonian vector fields, and infinitesimal automorphisms (i. a. on l. c. s. manifolds. If (M,Ω has an i. a. X such that ω(X≠0, we say that M is of the first kind and Ω assumes the particular form Ω=dθ−ω∧θ. Such an M is a 2-contact manifold with the structure forms (ω,θ, and it has a vertical 2-dimensional foliation V. If V is regular, we can give a fibration theorem which shows that M is a T2-principal bundle over a symplectic manifold. Particularly, V is regular for some homogeneous l. c. s, manifolds, and this leads to a general construction of compact homogeneous l. c. s, manifolds. Various related geometric results, including reductivity theorems for Lie algebras of i. a. are also given. Most of the proofs are adaptations of corresponding proofs in symplectic and contact geometry. The paper ends with an Appendix which states an analogous fibration theorem in Riemannian geometry.

  18. Could Atomic clocks be affected by neutrinos?

    CERN Document Server

    Hanafi, Hanaa

    2016-01-01

    An atomic clock is a clock device that uses an electronic transition frequency of the electromagnetic spectrum of atoms as a frequency standard in order to derive a time standard since time is the reciprocal of frequency. If the electronic transition frequencies are in an "optical region", we are talking in this case about optical atomic clocks. If they are in an "microwave region" these atomic clocks are made of the metallic element cesium so they are called Cesium atomic clocks. Atomic clocks are the most accurate time and frequency standards known despite the different perturbations that can affect them, a lot of researches were made in this domain to show how the transitions can be different for different type of perturbations..Since atomic clocks are very sensitive devices, based on coherent states (A coherent state tends to loose coherence after interacting). One question can arise (from a lot of questions) which is why cosmic neutrinos are not affecting these clocks? The answer to this question requir...

  19. Asymmetrical two-atom entanglement in a coated microsphere

    Energy Technology Data Exchange (ETDEWEB)

    Burlak, G.N. [Center for Research on Engineering and Applied Sciences, Autonomous State University of Morelos, Cuernavaca, Mor. 62210 (Mexico)]. E-mail: gburlak@uaem.mx; Klimov, A.B. [Departamento de Fisica, Universidad de Guadalajara, Revolucion 1500, Guadalajara, Jalisco, 44420 (Mexico)]. E-mail: klimov@cencar.udg.mx

    2006-12-25

    We study evolution of entanglement of two two-level atoms placed inside a multilayered microsphere. We show that due to inhomogeneity of the optical field modes this entanglement essentially depends on the atomic positions (asymmetrical entanglement) and also on the detuning between the atomic transitions and field frequencies. The robust and complete entanglement can be achieved even in the resonant case when the atoms have different effective coupling constants, and it can be extended in time if the detuning is large enough.

  20. Delay in atomic photoionization

    CERN Document Server

    Kheifets, A S

    2010-01-01

    We analyze the time delay between emission of photoelectrons from the outer valence $ns$ and $np$ sub-shells in noble gas atoms following absorption of an attosecond XUV pulse. By solving the time dependent Schr\\"odinger equation and carefully examining the time evolution of the photoelectron wave packet, we establish the apparent "time zero" when the photoelectron leaves the atom. Various processes such as elastic scattering of the photoelectron on the parent ion and many-electron correlation affect the quantum phase of the dipole transition matrix element, the energy dependence of which defines the emission timing. This qualitatively explains the time delay between photoemission from the $2s$ and $2p$ sub-shells of Ne as determined experimentally by attosecond streaking [{\\em Science} {\\bf 328}, 1658 (2010)]. However, with our extensive numerical modeling, we were only able to account for less than a half of the measured time delay of $21\\pm5$~as. We argue that the XUV pulse alone cannot produce such a larg...

  1. "Bohr's Atomic Model."

    Science.gov (United States)

    Willden, Jeff

    2001-01-01

    "Bohr's Atomic Model" is a small interactive multimedia program that introduces the viewer to a simplified model of the atom. This interactive simulation lets students build an atom using an atomic construction set. The underlying design methodology for "Bohr's Atomic Model" is model-centered instruction, which means the central model of the…

  2. Transparent ferrimagnetic semiconducting CuCr2O4 thin films by atomic layer deposition

    Science.gov (United States)

    Tripathi, T. S.; Yadav, C. S.; Karppinen, M.

    2016-04-01

    We report the magnetic and optical properties of CuCr2O4 thin films fabricated by atomic layer deposition (ALD) from Cu(thd)2, Cr(acac)3, and ozone; we deposit 200 nm thick films and anneal them at 700 °C in oxygen atmosphere to crystallize the spinel phase. A ferrimagnetic transition at 140 K and a direct bandgap of 1.36 eV are determined for the films from magnetic and UV-vis spectrophotometric measurements. Electrical transport measurements confirm the p-type semiconducting behavior of the films. As the ALD technique allows the deposition of conformal pin-hole-free coatings on complex 3D surfaces, our CuCr2O4 films are interesting material candidates for various frontier applications.

  3. Transparent ferrimagnetic semiconducting CuCr2O4 thin films by atomic layer deposition

    Directory of Open Access Journals (Sweden)

    T. S. Tripathi

    2016-04-01

    Full Text Available We report the magnetic and optical properties of CuCr2O4 thin films fabricated by atomic layer deposition (ALD from Cu(thd2, Cr(acac3, and ozone; we deposit 200 nm thick films and anneal them at 700 °C in oxygen atmosphere to crystallize the spinel phase. A ferrimagnetic transition at 140 K and a direct bandgap of 1.36 eV are determined for the films from magnetic and UV-vis spectrophotometric measurements. Electrical transport measurements confirm the p-type semiconducting behavior of the films. As the ALD technique allows the deposition of conformal pin-hole-free coatings on complex 3D surfaces, our CuCr2O4 films are interesting material candidates for various frontier applications.

  4. On Surface-Initiated Atom Transfer Radical Polymerization Using Diazonium Chemistry To Introduce the Initiator Layer

    DEFF Research Database (Denmark)

    Iruthayaraj, Joseph; Chernyy, Sergey; Lillethorup, Mie

    2011-01-01

    of bromine shows a gradual transition from mushroom to brush-type conformation of the surface anchored chains in both polar and nonpolar reaction medium. Interestingly, it is revealed that very thick polymer brushes, on the order of 1 μm, can be obtained at high bromine content of the initiator layer......This work features the controllability of surface-initiated atom transfer radical polymerization (SI-ATRP) of methyl methacrylate, initiated by a multilayered 2-bromoisobutyryl moiety formed via diazonium chemistry. The thickness as a function of polymerization time has been studied by varying...... Cu(II)/Cu(I) complexes (L = Me(6)TREN, PMDETA, and BIPY). It is also observed that the ability of polymer brushes to reinitiate depends on the initial thickness and the solvent used for generating it....

  5. Elucidating the backbone conformation of photoswitchable foldamers using vibrational circular dichroism.

    Science.gov (United States)

    Domingos, Sérgio R; Roeters, Steven J; Amirjalayer, Saeed; Yu, Zhilin; Hecht, Stefan; Woutersen, Sander

    2013-10-28

    The backbone conformation of amphiphilic oligo(azobenzene) foldamers is investigated using vibrational circular dichroism (VCD) spectroscopy on a mode involving the stretching of the N=N bonds in the backbone. From denaturation experiments, we find that the VCD response in the helical conformation arises mainly from through-space interaction between the N=N-stretch transition-dipole moments, so that the coupled-oscillator model can be used to predict the VCD spectrum associated with a particular conformation. Using this approach, we elucidate the origin of the VCD signals in the folded conformation, and can assign the observed partial loss of VCD signals upon photo-induced unfolding to specific conformational changes. Our results show that the N=N-stretch VCD response provides an excellent probe of the helical conformation of the N=N bonds in this type of switchable molecular system.

  6. Towards an Approximate Conformance Relation for Hybrid I/O Automata

    Directory of Open Access Journals (Sweden)

    Morteza Mohaqeqi

    2016-12-01

    Full Text Available Several notions of conformance have been proposed for checking the behavior of cyber-physical systems against their hybrid systems models. In this paper, we explore the initial idea of a notion of approximate conformance that allows for comparison of both observable discrete actions and (sampled continuous trajectories. As such, this notion will consolidate two earlier notions, namely the notion of Hybrid Input-Output Conformance (HIOCO by M. van Osch and the notion of Hybrid Conformance by H. Abbas and G.E. Fainekos. We prove that our proposed notion of conformance satisfies a semi-transitivity property, which makes it suitable for a step-wise proof of conformance or refinement.

  7. Thin films of protein (BSA, lysozyme) - Polyelectrolyte (PSS) complexes show larger red-shift in optical emissions irrespective of protein conformation

    Science.gov (United States)

    Talukdar, Hrishikesh; Kundu, Sarathi

    2017-09-01

    Protein-polyelectrolyte complexes (PPC) are prepared using globular proteins (BSA, lysozyme) and optically active polyelectrolyte poly (sodium 4-styrenesulfonate) (PSS) in aqueous solutions and as thin films on solid substrates to explore their structures and optical behaviors. Out-of-plane structures of PPC films having ≈15-60 nm thicknesses are investigated from X-ray reflectivity and their relatively smooth surface morphologies are obtained from atomic force microscopy. ATR-FTIR spectroscopy confirms that the conformation of BSA proteins inside the films of PSSB (PSS+BSA) is nearly same with pure BSA but for lysozyme inside PSSL (PSS+lysozyme) conformation modifies which is evidenced from the shifting of the amide-I band of each protein. However, irrespective of the conformation variation of proteins larger red-shifts of ≈30 nm in optical emissions are obtained from the thin films of PPC. Relatively enhance dissipation of energy thorough non-radiative transition of the fluorophore residues in the dry state is the most probable reason for such larger optical red-shifts.

  8. Some Progress in Conformal Geometry

    Directory of Open Access Journals (Sweden)

    Sun-Yung A. Chang

    2007-12-01

    Full Text Available This is a survey paper of our current research on the theory of partial differential equations in conformal geometry. Our intention is to describe some of our current works in a rather brief and expository fashion. We are not giving a comprehensive survey on the subject and references cited here are not intended to be complete. We introduce a bubble tree structure to study the degeneration of a class of Yamabe metrics on Bach flat manifolds satisfying some global conformal bounds on compact manifolds of dimension 4. As applications, we establish a gap theorem, a finiteness theorem for diffeomorphism type for this class, and diameter bound of the $sigma_2$-metrics in a class of conformal 4-manifolds. For conformally compact Einstein metrics we introduce an eigenfunction compactification. As a consequence we obtain some topological constraints in terms of renormalized volumes.

  9. Steady states in conformal theories

    CERN Multimedia

    CERN. Geneva

    2015-01-01

    A novel conjecture regarding the steady state behavior of conformal field theories placed between two heat baths will be presented. Some verification of the conjecture will be provided in the context of fluid dynamics and holography.

  10. Conformity Adequacy Review: Region 5

    Science.gov (United States)

    Resources are for air quality and transportation government and community leaders. Information on the conformity SIP adequacy/inadequacy of state implementation plans (SIPs) in EPA Region 5 (IL, IN, MI, OH, WI) is provided here.

  11. Perovskite Thin Films via Atomic Layer Deposition

    KAUST Repository

    Sutherland, Brandon R.

    2014-10-30

    © 2014 Wiley-VCH Verlag GmbH & Co. KGaA. (Graph Presented) A new method to deposit perovskite thin films that benefit from the thickness control and conformality of atomic layer deposition (ALD) is detailed. A seed layer of ALD PbS is place-exchanged with PbI2 and subsequently CH3NH3PbI3 perovskite. These films show promising optical properties, with gain coefficients of 3200 ± 830 cm-1.

  12. Falsification of Mannheim's conformal gravity

    CERN Document Server

    Yoon, Youngsub

    2013-01-01

    We show that Mannheim's conformal gravity, whose potential has a term proportional to $1/r$ and another term proportional to $r$, doesn't reduce to Newtonian gravity at short distances. Therefore, despite the claim that it successfully explains galaxy rotation curves, it seems falsified by numerous Cavendish-type experiments performed at laboratories on Earth whose work haven't found any deviations from Newton's theory. Moreover, when Mannheim used his potential to fit the galaxy rotation curve, he used the Newtonian formula to calculate the effects of the term proportional to $1/r$, not the conformal gravity one. So, he lacked consistency. After all, he would not have been able to use the conformal gravity one either since it deviates so much from the Newtonian one, which the conformal gravity one should reduce to. We also give a couple of other similar reasons why Mannheim's conformal gravity is wrong. For example, the gravitational potential of conformal gravity doesn't reduce to the Newtonian one even in ...

  13. Efficient transfer of francium atoms

    Science.gov (United States)

    Aubin, Seth; Behr, John; Gorelov, Alexander; Pearson, Matt; Tandecki, Michael; Collister, Robert; Gwinner, Gerald; Shiells, Kyle; Gomez, Eduardo; Orozco, Luis; Zhang, Jiehang; Zhao, Yanting; FrPNC Collaboration

    2016-05-01

    We report on the progress of the FrPNC collaboration towards Parity Non Conservation Measurements (PNC) using francium atoms at the TRIUMF accelerator. We demonstrate efficient transfer (higher than 40%) to the science vacuum chamber where the PNC measurements will be performed. The transfer uses a downward resonant push beam from the high-efficiency capture magneto optical trap (MOT) towards the science chamber where the atoms are recaptured in a second MOT. The transfer is very robust with respect to variations in the parameters (laser power, detuning, alignment, etc.). We accumulate a growing number of atoms at each transfer pulse (limited by the lifetime of the MOT) since the push beam does not eliminate the atoms already trapped in the science MOT. The number of atoms in the science MOT is on track to meet the requirements for competitive PNC measurements when high francium rates (previously demonstrated) are delivered to our apparatus. The catcher/neutralizer for the ion beam has been tested reliably to 100,000 heating/motion cycles. We present initial tests on the direct microwave excitation of the ground hyperfine transition at 45 GHz. Support from NSERC and NRC from Canada, NSF and Fulbright from USA, and CONACYT from Mexico.

  14. Analysis of polarizability measurements made with atom interferometry

    CERN Document Server

    Gregoire, Maxwell D; Trubko, Raisa; Cronin, Alexander D

    2016-01-01

    We present revised measurements of the static electric dipole polarizabilities of K, Rb, and Cs based on atom interferometer experiments presented in [Phys. Rev. A 2015, 92, 052513] but now re-analyzed with new calibrations for the magnitude and geometry of the applied electric field gradient. The resulting polarizability values did not change, but the uncertainties were significantly reduced. Then we interpret several measurements of alkali metal atomic polarizabilities in terms of atomic oscillator strengths $f_{ik}$, Einstein coefficients $A_{ik}$, state lifetimes $\\tau_{k}$, transition dipole matrix elements $D_{ik}$, line strengths $S_{ik}$, and van der Waals $C_6$ coefficients. Finally, we combine atom interferometer measurements of polarizabilities with independent measurements of lifetimes and $C_6$ values in order to quantify the residual contribution to polarizability due to all atomic transitions other than the principal $ns$-$np_J$ transitions for alkali metal atoms.

  15. Teach us atom structure

    Energy Technology Data Exchange (ETDEWEB)

    Lim, Suh Yeon

    2006-08-15

    This book is written to teach atom structure in very easy way. It is divided into nine chapters, which indicates what is the components of matter? when we divide matter continuously, it becomes atom, what did atom look like? particles comprised of matter is not only atom, discover of particles comprised of atom, symbol of element, various radiation, form alchemy to nuclear transmutation, shape of atom is evolving. It also has various pictures in each chapters to explain easily.

  16. Playing pinball with atoms.

    Science.gov (United States)

    Saedi, Amirmehdi; van Houselt, Arie; van Gastel, Raoul; Poelsema, Bene; Zandvliet, Harold J W

    2009-05-01

    We demonstrate the feasibility of controlling an atomic scale mechanical device by an external electrical signal. On a germanium substrate, a switching motion of pairs of atoms is induced by electrons that are directly injected into the atoms with a scanning tunneling microscope tip. By precisely controlling the tip current and distance we make two atom pairs behave like the flippers of an atomic-sized pinball machine. This atomic scale mechanical device exhibits six different configurations.

  17. Fisher zeros and conformality in lattice models

    CERN Document Server

    Meurice, Yannick; Berg, Bernd A; Du, Daping; Denbleyker, Alan; Liu, Yuzhi; Sinclair, Donald K; Unmuth-Yockey, Judah; Zou, Haiyuan

    2012-01-01

    Fisher zeros are the zeros of the partition function in the beta=2N_c/g^2 complex plane. When they pinch the real axis, finite size scaling allows to distinguish between first and second order transition and to estimate exponents. On the other hand, a gap signals confinement and the method can be used to explore the boundary of the conformal window. We present recent numerical results for 2D O(N) sigma models, 4D U(1) and SU(2) pure gauge and SU(3) with N_f=4and 12 flavors. We discuss attempts to understand some of these results using analytical methods. We discuss the 2-lattice matching and qualitative aspects of the renormalization group (RG) flows in the Migdal-Kadanoff approximation. We consider the effects of the boundary conditions on the nonperturbative part of the average energy in the 1D O(2) model

  18. CONFORMANCE IMPROVEMENT USING GELS

    Energy Technology Data Exchange (ETDEWEB)

    Randall S. Seright

    2003-09-01

    This report describes work performed during the second year of the project, ''Conformance Improvement Using Gels.'' The project has two objectives. The first objective is to identify gel compositions and conditions that substantially reduce flow through fractures that allow direct channeling between wells, while leaving secondary fractures open so that high fluid injection and production rates can be maintained. The second objective is to optimize treatments in fractured production wells, where the gel must reduce permeability to water much more than that to oil. Pore-level images from X-ray computed microtomography were re-examined for Berea sandstone and porous polyethylene. This analysis suggests that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than a gel-ripping mechanism. This finding helps to explain why aqueous gels can reduce permeability to water more than to oil. We analyzed a Cr(III)-acetate-HPAM gel treatment in a production well in the Arbuckle formation. The availability of accurate pressure data before, during, and after the treatment was critical for the analysis. After the gel treatment, water productivity was fairly constant at about 20% of the pre-treatment value. However, oil productivity was stimulated by a factor of 18 immediately after the treatment. During the six months after the treatment, oil productivity gradually decreased to approach the pre-treatment value. To explain this behavior, we proposed that the fracture area open to oil flow was increased substantially by the gel treatment, followed by a gradual closing of the fractures during subsequent production. For a conventional Cr(III)-acetate-HPAM gel, the delay between gelant preparation and injection into a fracture impacts the placement, leakoff, and permeability reduction behavior. Formulations placed as partially formed gels showed relatively low pressure gradients during placement, and yet substantially reduced the

  19. CONFORMANCE IMPROVEMENT USING GELS

    Energy Technology Data Exchange (ETDEWEB)

    Randall S. Seright

    2004-09-30

    This report describes work performed during the third and final year of the project, ''Conformance Improvement Using Gels.'' Corefloods revealed throughput dependencies of permeability reduction by polymers and gels that were much more prolonged during oil flow than water flow. This behavior was explained using simple mobility ratio arguments. A model was developed that quantitatively fits the results and predicts ''clean up'' times for oil productivity when production wells are returned to service after application of a polymer or gel treatment. X-ray computed microtomography studies of gels in strongly water-wet Berea sandstone and strongly oil-wet porous polyethylene suggested that oil penetration through gel-filled pores occurs by a gel-dehydration mechanism, rather than gel-ripping or gel-displacement mechanisms. In contrast, analysis of data from the University of Kansas suggests that the gel-ripping or displacement mechanisms are more important in more permeable, strongly water-wet sandpacks. These findings help to explain why aqueous gels can reduce permeability to water more than to oil under different conditions. Since cement is the most commonly used material for water shutoff, we considered when gels are preferred over cements. Our analysis and experimental results indicated that cement cannot be expected to completely fill (top to bottom) a vertical fracture of any width, except near the wellbore. For vertical fractures with apertures less than 4 mm, the cement slurry will simply not penetrate very far into the fracture. For vertical fractures with apertures greater than 4 mm, the slurry may penetrate a substantial distance into the bottom part of the fracture. However, except near the wellbore, the upper part of the fracture will remain open due to gravity segregation. We compared various approaches to plugging fractures using gels, including (1) varying polymer content, (2) varying placement (extrusion) rate

  20. PubChem atom environments.

    Science.gov (United States)

    Hähnke, Volker D; Bolton, Evan E; Bryant, Stephen H

    2015-01-01

    Atom environments and fragments find wide-spread use in chemical information and cheminformatics. They are the basis of prediction models, an integral part in similarity searching, and employed in structure search techniques. Most of these methods were developed and evaluated on the relatively small sets of chemical structures available at the time. An analysis of fragment distributions representative of most known chemical structures was published in the 1970s using the Chemical Abstracts Service data system. More recently, advances in automated synthesis of chemicals allow millions of chemicals to be synthesized by a single organization. In addition, open chemical databases are readily available containing tens of millions of chemical structures from a multitude of data sources, including chemical vendors, patents, and the scientific literature, making it possible for scientists to readily access most known chemical structures. With this availability of information, one can now address interesting questions, such as: what chemical fragments are known today? How do these fragments compare to earlier studies? How unique are chemical fragments found in chemical structures? For our analysis, after hydrogen suppression, atoms were characterized by atomic number, formal charge, implicit hydrogen count, explicit degree (number of neighbors), valence (bond order sum), and aromaticity. Bonds were differentiated as single, double, triple or aromatic bonds. Atom environments were created in a circular manner focused on a central atom with radii from 0 (atom types) up to 3 (representative of ECFP_6 fragments). In total, combining atom types and atom environments that include up to three spheres of nearest neighbors, our investigation identified 28,462,319 unique fragments in the 46 million structures found in the PubChem Compound database as of January 2013. We could identify several factors inflating the number of environments involving transition metals, with many