WorldWideScience

Sample records for atomic conformational transition

  1. Conformational Transitions

    Science.gov (United States)

    Czerminski, Ryszard; Roitberg, Adrian; Choi, Chyung; Ulitsky, Alexander; Elber, Ron

    1991-10-01

    on the number of the direct paths between the minima. The influence on the distribution of the barriers and the minima energies is less significant. Calculation of reaction paths in large molecular systems requires new computational techniques. We employed our newly developed reaction path algorithm (SPW) for the study of the B to Z transition in DNA. The SPW (Self Penalty Walk) algorithm is explained in detail. A complex reaction coordinate (the B to Z transition in DNA) is calculated and analyzed. The calculated reaction path is for six basepairs DNA (including all 376 atoms). The path consists of 180° flips of two basepairs from the B DNA conformation to the Z DNA conformation.

  2. The energy profiles of atomic conformational transition intermediates of adenylate kinase.

    Science.gov (United States)

    Feng, Yaping; Yang, Lei; Kloczkowski, Andrzej; Jernigan, Robert L

    2009-11-15

    The elastic network interpolation (ENI) (Kim et al., Biophys J 2002;83:1620-1630) is a computationally efficient and physically realistic method to generate conformational transition intermediates between two forms of a given protein. However it can be asked whether these calculated conformations provide good representatives for these intermediates. In this study, we use ENI to generate conformational transition intermediates between the open form and the closed form of adenylate kinase (AK). Based on C(alpha)-only intermediates, we construct atomic intermediates by grafting all the atoms of known AK structures onto the C(alpha) atoms and then perform CHARMM energy minimization to remove steric conflicts and optimize these intermediate structures. We compare the energy profiles for all intermediates from both the CHARMM force-field and from knowledge-based energy functions. We find that the CHARMM energies can successfully capture the two energy minima representing the open AK and closed AK forms, while the energies computed from the knowledge-based energy functions can detect the local energy minimum representing the closed AK form and show some general features of the transition pathway with a somewhat similar energy profile as the CHARMM energies. The combinatorial extension structural alignment (Shindyalov et al., 1998;11:739-747) and the k-means clustering algorithm are then used to show that known PDB structures closely resemble computed intermediates along the transition pathway.

  3. Transitive conformal holonomy groups

    CERN Document Server

    Alt, Jesse

    2011-01-01

    For $(M,[g])$ a conformal manifold of signature $(p,q)$ and dimension at least three, the conformal holonomy group $\\mathrm{Hol}(M,[g]) \\subset O(p+1,q+1)$ is an invariant induced by the canonical Cartan geometry of $(M,[g])$. We give a description of all possible connected conformal holonomy groups which act transitively on the M\\"obius sphere $S^{p,q}$, the homogeneous model space for conformal structures of signature $(p,q)$. The main part of this description is a list of all such groups which also act irreducibly on $\\R^{p+1,q+1}$. For the rest, we show that they must be compact and act decomposably on $\\R^{p+1,q+1}$, in particular, by known facts about conformal holonomy the conformal class $[g]$ must contain a metric which is locally isometric to a so-called special Einstein product.

  4. Water drives peptide conformational transitions

    CERN Document Server

    Nerukh, Dmitry

    2011-01-01

    Transitions between metastable conformations of a dipeptide are investigated using classical molecular dynamics simulation with explicit water molecules. The distribution of the surrounding water at different moments before the transitions and the dynamical correlations of water with the peptide's configurational motions indicate that water is the main driving force of the conformational changes.

  5. Atomic homodyne detection of weak atomic transitions.

    Science.gov (United States)

    Gunawardena, Mevan; Elliott, D S

    2007-01-26

    We have developed a two-color, two-pathway coherent control technique to detect and measure weak optical transitions in atoms by coherently beating the transition amplitude for the weak transition with that of a much stronger transition. We demonstrate the technique in atomic cesium, exciting the 6s(2)S(1/2) --> 8s(2)S(1/2) transition via a strong two-photon transition and a weak controllable Stark-induced transition. We discuss the enhancement in the signal-to-noise ratio for this measurement technique over that of direct detection of the weak transition rate, and project future refinements that may further improve its sensitivity and application to the measurement of other weak atomic interactions.

  6. Nuclear effects in atomic transitions

    OpenAIRE

    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 ...

  7. Distinguishing Signatures of Multipathway Conformational Transitions

    Science.gov (United States)

    Pierse, Christopher A.; Dudko, Olga K.

    2017-02-01

    The folding and binding of biomolecules into functional conformations are thought to be commonly mediated by multiple pathways rather than a unique route. Yet even in experiments where one can "see" individual conformational transitions, their stochastic nature generally precludes one from determining whether the transitions occurred through one or multiple pathways. We establish model-free, observable signatures in the response of macromolecules to force that unambiguously identify multiple pathways—even when the pathways themselves cannot be resolved. The unified analytical description reveals that, through multiple pathways, the response of molecules to external forces can be shaped in diverse ways, resulting in a rich design space for a tailored biological function already at the single-molecule level.

  8. Conformational transitions of a weak polyampholyte

    KAUST Repository

    Narayanan Nair, Arun Kumar

    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.

  9. Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.

    Science.gov (United States)

    Kulczycka-Mierzejewska, Katarzyna; Trylska, Joanna; Sadlej, Joanna

    2016-01-01

    Molecular dynamics (MD) simulations allow determining internal flexibility of molecules at atomic level. Using ab initio Born-Oppenheimer molecular dynamics (BOMD), one can simulate in a reasonable time frame small systems with hundreds of atoms, usually in vacuum. With quantum mechanics/molecular mechanics (QM/MM) or full-atom molecular dynamics (FAMD), the influence of the environment can also be simulated. Here, we compare three types of MD calculations: ab initio BOMD, hybrid QM/MM, and classical FAMD. As a model system, we use a small antibiotic molecule, clindamycin, which is one of the lincosamide antibiotics. Clindamycin acquires two energetically stable forms and we investigated the transition between these two experimentally known conformers. We performed 60-ps BOMD simulations in vacuum, 50-ps QM/MM, and 100-ns FAMD in explicit water. The transition between two antibiotic conformers was observed using both BOMD and FAMD methods but was not noted in the QM/MM simulations.

  10. 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.

  11. Conformational Transition of Poly (Acrylic Acid) Detected by Microcantilever Sensing

    Institute of Scientific and Technical Information of China (English)

    LI Kai; LIU Hong; ZHANG Qing-Chuan; XUE Chang-Guo; WU Xiao-Ping

    2007-01-01

    Poly (acrylic acid) (PAA) chains are grafted on one side of a microcantilever by the self-assembled method and the deflections of the microcantilever are detected as a function of medium pH from 3 to 11. It is found that when the pH varies, the microcantilever deflects because of the changing surface stress. By analysing the electrostatic repulsive effect, the surface stress change is related to the conformation transition of PAA from a collapse state to a swelling state. This method offers the interaction information among the polymer chains during the conformational transition and affords an alternative way to study conformational change of polymers.

  12. Many-Body Theory of Atomic Transitions

    Science.gov (United States)

    Holmes, Charles Potter

    This dissertation presents a systematic approach to the derivation of transition widths and cross sections for atomic radiative and/or nonradiative processes. By applying the transition theory of Goldberger and Watson ^1, all transition properties are derived from proper solutions of the time-dependent Schrodinger equation. The focus is on situations where initial and final wave functions are nonorthogonal functions that belong to different self-consistent fields. This approach is particularly useful in the treatment of ionizing transitions where the outgoing free electron sees a different atomic potential from that of the initial bound state. Transition amplitudes are expressed as perturbation expansions in which singularities have been removed algebraically. These singularities are due to states which are degenerate with the initial and final states and represent the competing transition channels. The perturbation expansions show clearly the role of the nonorthogonality of the participating states leading to terms representing "shake" processes competing with higher-order electron correlation processes. Transition amplitudes including all second-order processes, are derived for the following transitions: X-ray, Auger, photoionization, radiative recombination, dielectronic recombination, radiative -Auger. Comparisons are made with the expressions frequently used by other workers. Using a Hartree-Fock-Slater model K- and L-shell X-ray and Auger transition widths are calculated for the range 5 Z Theory, (John Wiley & Sons, New York, 1964), Chapter 8, page 424.

  13. Resonant quantum transitions in trapped antihydrogen atoms.

    Science.gov (United States)

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

    2012-03-07

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

  14. Axion dark matter detection using atomic transitions.

    Science.gov (United States)

    Sikivie, P

    2014-11-14

    Dark matter axions may cause transitions between atomic states that differ in energy by an amount equal to the axion mass. Such energy differences are conveniently tuned using the Zeeman effect. It is proposed to search for dark matter axions by cooling a kilogram-sized sample to millikelvin temperatures and count axion induced transitions using laser techniques. This appears to be an appropriate approach to axion dark matter detection in the 10^{-4}  eV mass range.

  15. Axion Dark Matter Detection using Atomic Transitions

    CERN Document Server

    Sikivie, P

    2014-01-01

    Dark matter axions may cause transitions between atomic states that differ in energy by an amount equal to the axion mass. Such energy differences are conveniently tuned using the Zeeman effect. It is proposed to search for dark matter axions by cooling a kilogram-sized sample to milliKelvin temperatures and count axion induced transitions using laser techniques. This appears an appropriate approach to axion dark matter detection in the $10^{-4}$ eV mass range.

  16. de Sitter transitivity, conformal transformations and conservation laws

    CERN Document Server

    Pereira, J G; Savi, L L

    2013-01-01

    Minkowski spacetime is transitive under ordinary translations, a transformation that do not have matrix representations. The de Sitter spacetime, on the other hand, is transitive under a combination of translations and proper conformal transformations, which do have a matrix representation. Such matrix, however, is not by itself a de Sitter generator: it gives rise to a conformal re-scaling of the metric, a transformation not belonging to the de Sitter group, and in general not associated with diffeomorphisms in spacetime. When dealing with variational principles and Noether's theorem in de Sitter spacetime, therefore, it turns out necessary to regularise the transformations in order to eliminate the conformal re-scaling of the metric.

  17. 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...

  18. Molecular motions and conformational transition between different conformational states of HIV-1 gp120 envelope glycoprotein

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The HIV-1 gp120 exterior envelope glycoprotein undergoes a series of conformational rearrangements while sequentially interacting with the receptor CD4 and coreceptor CCR5 or CXCR4 on the surface of host cells to initiate virus entry. Both the crystal structures of the HIV-1 gp120 core bound by the CD4 and antigen 17b and the SIV gp120 core prebound by CD4 are known. Despite the wealth of knowledge on these static snapshots of molecular conformations, the details of molecular motions involved in conformational transition that are crucial to intervention remain elusive. We presented comprehensive comparative analyses of the dynamics behaviors of the gp120 in its CD4-complexed, CD4-free and CD4-unliganded states based on the homology models with modeled V3 and V4 loops by means of CONCOORD computer simulation to generate ensembles of feasible protein structures that were subsequently analysed by essential dynamics analyses to identify preferred concerted motions. The revealed collective fluctuations are dominated by complex modes of combinational motions of the rotation/twisting, flexing/closure, and shortness/elongation between or within the inner, outer, and bridging-sheet domains, and these modes are related to the CD4 association and HIV neutralization avoidance. Further essential subspace overlap analyses were performed to quantitatively distinguish the preference for conformational transitions between the three states, revealing that the unliganded gp120 has a greater potential to translate its conformation into the conformational state adopted by the CD4-complexed gp120 than by the CD4-free gp120, whereas the CD4-free gp120 has a greater potential to translate its conformation into the unliganded state than the CD4-complexed gp120 does. These dy-namics data of gp120 in its different conformations are helpful in understanding the relationship be-tween the molecular motion/conformational transition and the function of gp120, and in gp120-structure-based subunit

  19. Atomic transition probabilities of Nd I

    Science.gov (United States)

    Stockett, M. H.; Wood, M. P.; Den Hartog, E. A.; Lawler, J. E.

    2011-12-01

    Fourier transform spectra are used to determine emission branching fractions for 236 lines of the first spectrum of neodymium (Nd i). These branching fractions are converted to absolute atomic transition probabilities using radiative lifetimes from time-resolved laser-induced fluorescence measurements (Den Hartog et al 2011 J. Phys. B: At. Mol. Opt. Phys. 44 225001). The wavelength range of the data set is from 390 to 950 nm. These transition probabilities from emission and laser measurements are compared to relative absorption measurements in order to assess the importance of unobserved infrared branches from selected upper levels.

  20. Cooperative transition between open and closed conformations in potassium channels.

    Directory of Open Access Journals (Sweden)

    Turkan Haliloglu

    Full Text Available Potassium (K+ ion channels switch between open and closed conformations. The nature of this important transition was revealed by comparing the X-ray crystal structures of the MthK channel from Methanobacterium thermoautotrophicum, obtained in its open conformation, and the KcsA channel from Streptomyces lividans, obtained in its closed conformation. We analyzed the dynamic characteristics and energetics of these homotetrameric structures in order to study the role of the intersubunit cooperativity in this transition. For this, elastic models and in silico alanine-scanning mutagenesis were used, respectively. Reassuringly, the calculations manifested motion from the open (closed towards the closed (open conformation. The calculations also revealed a network of dynamically and energetically coupled residues. Interestingly, the network suggests coupling between the selectivity filter and the gate, which are located at the two ends of the channel pore. Coupling between these two regions was not observed in calculations that were conducted with the monomer, which emphasizes the importance of the intersubunit interactions within the tetrameric structure for the cooperative gating behavior of the channel.

  1. Conformational and phase transitions in DNA--photosensitive surfactant solutions: Experiment and modeling.

    Science.gov (United States)

    Kasyanenko, N; Lysyakova, L; Ramazanov, R; Nesterenko, A; Yaroshevich, I; Titov, E; Alexeev, G; Lezov, A; Unksov, I

    2015-02-01

    DNA binding to trans- and cis-isomers of azobenzene containing cationic surfactant in 5 mM NaCl solution was investigated by the methods of dynamic light scattering (DLS), low-gradient viscometry (LGV), atomic force microscopy (AFM), circular dichroism (CD), gel electrophoresis (GE), flow birefringence (FB), UV-Vis spectrophotometry. Light-responsive conformational transitions of DNA in complex with photosensitive surfactant, changes in DNA optical anisotropy and persistent length, phase transition of DNA into nanoparticles induced by high surfactant concentration, as well as transformation of surfactant conformation under its binding to macromolecule were studied. Computer simulations of micelles formation for cis- and trans-isomers of azobenzene containing surfactant, as well as DNA-surfactant interaction, were carried out. Phase diagram for DNA-surfactant solutions was designed. The possibility to reverse the DNA packaging induced by surfactant binding with the dilution and light irradiation was shown.

  2. 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

  3. 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...

  4. Atomic transition probabilities of Gd i

    Science.gov (United States)

    Lawler, J. E.; Bilty, K. A.; Den Hartog, E. A.

    2011-05-01

    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.

  5. Atomic transition probabilities of Er i

    Science.gov (United States)

    Lawler, J. E.; Wyart, J.-F.; Den Hartog, E. A.

    2010-12-01

    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.

  6. Conformer-specific hydrogen atom tunnelling in trifluoromethylhydroxycarbene

    Science.gov (United States)

    Mardyukov, Artur; Quanz, Henrik; Schreiner, Peter R.

    2017-01-01

    Conformational control of organic reactions is at the heart of the biomolecular sciences. To achieve a particular reactivity, one of many conformers may be selected, for instance, by a (bio)catalyst, as the geometrically most suited and appropriately reactive species. The equilibration of energetically close-lying conformers is typically assumed to be facile and less energetically taxing than the reaction under consideration itself: this is termed the 'Curtin-Hammett principle'. Here, we show that the trans conformer of trifluoromethylhydroxycarbene preferentially rearranges through a facile quantum-mechanical hydrogen tunnelling pathway, while its cis conformer is entirely unreactive. Hence, this presents the first example of a conformer-specific hydrogen tunnelling reaction. The Curtin-Hammett principle is not applicable, due to the high barrier between the two conformers.

  7. Surface immobilization of antibody on silk fibroin through conformational transition.

    Science.gov (United States)

    Lu, Qiang; Wang, Xiaoqin; Zhu, Hesun; Kaplan, David L

    2011-07-01

    In recent studies silk fibroin has been explored as a new material platform for biosensors. Based on these developments, a procedure for the immobilization of antibodies on silk fibroin substrates was developed as a route to functionalizing these biosensor systems. By controlling the conformational transition of the silk fibroin, a primary antibody was immobilized and enriched at the surface of silk fibroin substrates under mild reaction conditions to maintain antibody function. Compared to chemical crosslinking, the immobilization efficiency in the present approach was increased significantly. This method, achieving high loading of antibody while retaining function, improves the feasibility of silk fibroin as a platform material for biosensor applications.

  8. 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.

  9. How and why do transition dipole moment orientations depend on conformer structure?

    Science.gov (United States)

    Brand, Christian; Meerts, W Leo; Schmitt, Michael

    2011-09-01

    A remarkable influence of the orientation of a polar side chain on the direction of the S(1) ← S(0) transition dipole moment of monosubstituted benzenes was previously reported from high-resolution electronic spectroscopy. In search for a more general understanding of this non-Condon behavior, we investigated ethylamino-substituted indole and benzene (tryptamine and 2-phenylethylamine) using ab initio theory and compared the results to rotationally resolved laser-induced fluorescence measurements. The interaction of the ethylamino side chain with the benzene chromophore can evoke a rotation and a change of ordering of the molecular orbitals involved in the excitation, leading to state mixing and large changes in the orientation of the excited-state transition dipole moment. These changes are much less pronounced in tryptamine with the indole chromophore, where a rotation of the transition dipole moment is attributed to Rydberg contributions of the nitrogen atom of the chromophore. For phenylethylamine, a strong dependence of the oscillator strengths of the lowest two singlet states from the conformation of the side chain is found, which makes the use of experimental vibronic intensities for assessment of relative conformer stabilities at least questionable.

  10. Atomic Transition Probabilities for Neutral Cerium

    Science.gov (United States)

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

    2010-01-01

    Among the rare earth species, the spectra of neutral cerium (Ce I) and singly ionized cerium (Ce II) are some of the most complex. Like other rare earth species, Ce has many lines in the visible which are suitable for elemental abundance studies. Recent work on Ce II transition probabilities [1] is now being augmented with similar work on Ce I for future studies using such lines from astrophysical sources. 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 2500 to 3000 lines from 153 upper levels in neutral Ce. Representative data samples and progress to date will be presented. This work was supported by the National Science Foundation's REU program and the Department of Defense's ASSURE program through NSF Award AST-0453442 and NSF Grant CTS0613277. [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). [2] E. A. Den Hartog, K. P. Buettner, and J. E. Lawler, J. Phys. B: Atomic, Molecular & Optical Physics 42, 085006 (7pp) (2009).

  11. Conformational Fluctuations of Polymers in a Melt Associated with Glass Transition

    Science.gov (United States)

    Iwaoka, Nobuyuki; Takano, Hiroshi

    2017-03-01

    The conformational fluctuations of a glassy short polymer melt are studied by coarse-grained molecular dynamics simulations and principal component analysis (PCA). The distribution of PCA eigenvalues, which measure static fluctuations of the polymers, shows a clear difference between above and below the conventional glass transition temperature Tg. The approximate conformational entropy of the polymers also indicates a transition near Tg. This is evidence that the static properties of polymers in the melt signal the glass transition.

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

    Science.gov (United States)

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

    2016-04-15

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

  13. Phase transitions, geometrothermodynamics and critical exponents of black holes with conformal anomaly

    CERN Document Server

    Liu, Jie-Xiong Mo Wen-Biao

    2013-01-01

    We investigate the phase transitions of black holes with conformal anomaly in canonical ensemble from different perspectives. Some interesting and novel phase transition phenomena have been discovered. Firstly, we discuss the behavior of the specific heat and the inverse of the isothermal compressibility. It is shown that there are striking differences in Hawking temperature and phase structure between black holes with conformal anomaly and those without it. In the case with conformal anomaly, there exists local minimum temperature corresponding to the phase transition point. Phase transitions take place not only from an unstable large black hole to a locally stable medium black hole but also from an unstable medium black hole to a locally stable small black hole. Secondly, we probe in details 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 ...

  14. Transition rates in proton - Rydberg atom collisions

    Science.gov (United States)

    Vrinceanu, Daniel

    2016-05-01

    Monte Carlo simulations for energy and angular momentum transfer processes in proton - Ryderg atom collisions were performed and the corresponding rates are reported.The relevance of these rates in the context of cosmological recombination is discussed. The rates are contrasted with the similar rates in electron - Rydberg atom collisions. This work has been supported by National Science Foundation through grants for the Center for Research on Complex Networks (HRD-1137732) and Research Infrastructure for Science and Engineering (RISE) (HRD-1345173).

  15. Electric Field-induced Conformational Transition of Bovine Serum Albumin from α -helix to β -sheet

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    The irreversible conformational transition of bovine serum albumin (BSA) from α -helix to β -sheet, induced by electric field near the electrode surface, was monitored by circular dichroism (CD) with a long optical path thin layer cell (LOPTLC).

  16. Quantum phase transition and entanglement in Li atom system

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    By use of the exact diagonalization method, the quantum phase transition and en- tanglement in a 6-Li atom system are studied. It is found that entanglement appears before the quantum phase transition and disappears after it in this exactly solvable quantum system. The present results show that the von Neumann entropy, as a measure of entanglement, may reveal the quantum phase transition in this model.

  17. The Activation of c-Src Tyrosine Kinase: Conformational Transition Pathway and Free Energy Landscape.

    Science.gov (United States)

    Fajer, Mikolai; Meng, Yilin; Roux, Benoît

    2016-10-28

    Tyrosine kinases are important cellular signaling allosteric enzymes that regulate cell growth, proliferation, metabolism, differentiation, and migration. Their activity must be tightly controlled, and malfunction can lead to a variety of diseases, particularly cancer. The nonreceptor tyrosine kinase c-Src, a prototypical model system and a representative member of the Src-family, functions as complex multidomain allosteric molecular switches comprising SH2 and SH3 domains modulating the activity of the catalytic domain. The broad picture of self-inhibition of c-Src via the SH2 and SH3 regulatory domains is well characterized from a structural point of view, but a detailed molecular mechanism understanding is nonetheless still lacking. Here, we use advanced computational methods based on all-atom molecular dynamics simulations with explicit solvent to advance our understanding of kinase activation. To elucidate the mechanism of regulation and self-inhibition, we have computed the pathway and the free energy landscapes for the "inactive-to-active" conformational transition of c-Src for different configurations of the SH2 and SH3 domains. Using the isolated c-Src catalytic domain as a baseline for comparison, it is observed that the SH2 and SH3 domains, depending upon their bound orientation, promote either the inactive or active state of the catalytic domain. The regulatory structural information from the SH2-SH3 tandem is allosterically transmitted via the N-terminal linker of the catalytic domain. Analysis of the conformational transition pathways also illustrates the importance of the conserved tryptophan 260 in activating c-Src, and reveals a series of concerted events during the activation process.

  18. Control of atomic transition rates via laser light shaping

    CERN Document Server

    Jauregui, R

    2015-01-01

    A modular systematic analysis of the feasibility of modifying atomic transition rates by tailoring the electromagnetic field of an external coherent light source is presented. The formalism considers both the center of mass and internal degrees of freedom of the atom, and all properties of the field: frequency, angular spectrum, and polarization. General features of recoil effects for internal forbidden transitions are discussed. A comparative analysis of different structured light sources is explicitly worked out. It includes spherical waves, Gaussian beams, Laguerre-Gaussian beams, and propagation invariant beams with closed analytical expressions. It is shown that increments in the order of magnitude of the transition rates for Gaussian and Laguerre-Gaussian beams, with respect to those obtained in the paraxial limit, requires waists of the order of the wavelength, while propagation invariant modes may considerably enhance transition rates under more favorable conditions. For transitions that can be natura...

  19. 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...... conformally to the Higgs sector as well as new fermions. We uncover the parameter space leading to a first order phase transition with(out) the Veltman conditions. We also discuss dark (matter) aspects of some of the models and compare with existing literature when appropriate. We observe that to accommodate...

  20. Atomic hydrodynamics of DNA: coil-uncoil-coil transitions in a wall-bounded shear flow.

    Science.gov (United States)

    Sandberg, William C; Wang, Guan M

    2008-12-01

    Extensive experimental work on the response of DNA molecules to externally applied forces and on the dynamics of DNA molecules flowing in microchannels and nanochannels has been carried out over the past two decades, however, there has not been available, until now, any atomic-scale means of analyzing nonequilibrium DNA response dynamics. There has not therefore been any way to investigate how the backbone and side-chain atoms along the length of a DNA molecule interact with the molecules and ions of the flowing solvent and with the atoms of passing boundary surfaces. We report here on the application of the nonequilibrium biomolecular dynamics simulation method that we developed [G. M. Wang and W. C. Sandberg, Nanotechnology 18, 4819 (2007)] to analyze, at the atomic interaction force level, the conformational dynamics of short-chain single-stranded DNA molecules in a shear flow near a surface. This is a direct atomic computational analysis of the hydrodynamic interaction between a biomolecule and a flowing solvent. The DNA molecules are observed to exhibit conformational behaviors including coils, hairpin loops, and figure-eight shapes that have neither been previously measured experimentally nor observed computationally, as far as we know. We relate the conformational dynamics to the atomic interaction forces experienced throughout the length of a molecule as it moves in the flowing solvent past the surface boundary. We show that the DNA conformational dynamics is related to the asymmetry in the molecular environment induced by the motion of the surrounding molecules and the atoms of the passing surface. We also show that while the asymmetry in the environment is necessary, it is not sufficient to produce the observed conformational dynamics. A time variation in the asymmetry, due in our case to a shear flow, must also exist. In order to contrast these results with the usual experimental situation of purely diffusive motion in thermal equilibrium we have also

  1. Allowed and forbidden transitions in artificial hydrogen and helium atoms.

    Science.gov (United States)

    Fujisawa, Toshimasa; Austing, David Guy; Tokura, Yasuhiro; Hirayama, Yoshiro; Tarucha, Seigo

    2002-09-19

    The strength of radiative transitions in atoms is governed by selection rules that depend on the occupation of atomic orbitals with electrons. Experiments have shown similar electron occupation of the quantized energy levels in semiconductor quantum dots--often described as artificial atoms. But unlike real atoms, the confinement potential of quantum dots is anisotropic, and the electrons can easily couple with phonons of the material. Here we report electrical pump-and-probe experiments that probe the allowed and 'forbidden' transitions between energy levels under phonon emission in quantum dots with one or two electrons (artificial hydrogen and helium atoms). The forbidden transitions are in fact allowed by higher-order processes where electrons flip their spin. We find that the relaxation time is about 200 micro s for forbidden transitions, 4 to 5 orders of magnitude longer than for allowed transitions. This indicates that the spin degree of freedom is well separated from the orbital degree of freedom, and that the total spin in the quantum dots is an excellent quantum number. This is an encouraging result for potential applications of quantum dots as basic entities for spin-based quantum information storage.

  2. Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics.

    Science.gov (United States)

    Wang, Jinan; Shao, Qiang; Xu, Zhijian; Liu, Yingtao; Yang, Zhuo; Cossins, Benjamin P; Jiang, Hualiang; Chen, Kaixian; Shi, Jiye; Zhu, Weiliang

    2014-01-09

    Large-scale conformational changes of proteins are usually associated with the binding of ligands. Because the conformational changes are often related to the biological functions of proteins, understanding the molecular mechanisms of these motions and the effects of ligand binding becomes very necessary. In the present study, we use the combination of normal-mode analysis and umbrella sampling molecular dynamics simulation to delineate the atomically detailed conformational transition pathways and the associated free-energy landscapes for three well-known protein systems, viz., adenylate kinase (AdK), calmodulin (CaM), and p38α kinase in the absence and presence of respective ligands. For each protein under study, the transient conformations along the conformational transition pathway and thermodynamic observables are in agreement with experimentally and computationally determined ones. The calculated free-energy profiles reveal that AdK and CaM are intrinsically flexible in structures without obvious energy barrier, and their ligand binding shifts the equilibrium from the ligand-free to ligand-bound conformation (population shift mechanism). In contrast, the ligand binding to p38α leads to a large change in free-energy barrier (ΔΔG ≈ 7 kcal/mol), promoting the transition from DFG-in to DFG-out conformation (induced fit mechanism). Moreover, the effect of the protonation of D168 on the conformational change of p38α is also studied, which reduces the free-energy difference between the two functional states of p38α and thus further facilitates the conformational interconversion. Therefore, the present study suggests that the detailed mechanism of ligand binding and the associated conformational transition is not uniform for all kinds of proteins but correlated to their respective biological functions.

  3. Relativistic Transitions in the Hydrogenic Atoms

    CERN Document Server

    Boudet, R

    2009-01-01

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

  4. 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.

  5. Conformational Transitions in Silver Nanoparticals: DNA and Photoirradiation

    CERN Document Server

    Bregadze, Vasil G; Giorgadze, Tamar G

    2012-01-01

    Photoirradiation of silver nanoparticles in water solution of NaNO3 (0.01M) and in dissolved DNA was investigated by spectrophotometric and thermodynamic kinetic approaches. It is shown that only the irradiated complexes AgNPs-DNA have distinctly expressed isosbestic point. The test with the free AgNPs demonstrates that as a result of photo-irradiation desorption of silver atoms and their oxidation takes place. We have also observed that at photo-irradiation of the complexes by AgNPs-DNA desorption of silver atoms from the surface of AgNPs takes place. Kinetic study of photo-desorption of silver atoms has allowed to estimate desorption rate constant and the heat of adsorption for free AgNPs and AgNPs bound with DNA. On DNA example toxicity of AgNPs at their application to photo-chemo and photo-thermo therapy of cancer is discussed.

  6. Atomic force microscopy evidence for conformational changes of fibronectin adsorbed on unmodified and sulfonated polystyrene surfaces.

    Science.gov (United States)

    Kowalczyńska, Hanna M; Kołos, Robert; Nowak-Wyrzykowska, Małgorzata; Dobkowski, Jacek; Elbaum, Danek; Szczepankiewicz, Andrzej; Kamiński, Jarosław

    2009-12-15

    The effect of polystyrene surface polarity on the conformation of adsorbed fibronectin (FN) has been studied with atomic force microscopy. We demonstrated that bare sulfonated and nonsulfonated polystyrene surfaces featured similar topographies. After the FN adsorption, direct comparison of both types of substrata revealed drastically different topographies, roughness values, and also cell-adhesive properties. This was interpreted in terms of FN conformational changes induced by the surface polarity. At high-solute FN concentrations the multilayer FN adsorption took place resulting, for the sulfonated substratum, in an increase of surface roughness, whereas for the nonsulfonated one the roughness was approximately stable. Conversely, the FN conformation characteristic for the first saturative layer tended to be conserved in the consecutive layers, as evidenced by height histograms. The height of individual FN molecules indicated, consonantly with the derived thickness of the adsorbed protein layer (the latter value being 1.4 nm and 0.6 nm, respectively, for an unmodified and sulfonated polystyrene surface), that molecules are flattened on polar surfaces and more compact on nonsulfonated ones. It was also demonstrated that the FN adsorption and conformation on polymeric substrata, and hence the resultant cell-adhesive properties, depended on the chemistry of the original surface rather than on its topography. Our results also demonstrated the ability of surface polarity to influence the protein conformation and its associated biological activity.

  7. Stabilities and conformational transitions of various proteases in the presence of an organic solvent.

    Science.gov (United States)

    Ogino, Hiroyasu; Gemba, Yuichi; Yutori, Yoshikazu; Doukyu, Noriyuki; Ishimi, Kosaku; Ishikawa, Haruo

    2007-01-01

    The half-life of the activity of the PST-01 protease that was secreted by organic solvent-tolerant Pseudomonas aeruginosa PST-01 was very long in the presence of methanol as compared to that in the absence of methanol. The conformational transitions of the PST-01 protease, alpha-chymotrypsin, thermolysin, and subtilisin in the presence and absence of methanol were monitored by measuring the CD spectra. The conformational stabilities of the PST-01 protease and subtilisin in the presence of methanol were higher than those in the absence of methanol. This resulted in high stability of these proteases in the presence of methanol. Furthermore, it was suggested that the organic solvent stabilities of enzymes were closely related to the secondary structure by monitoring the conformational transitions of polyamino acids, which form the particular conformations, in the presence and absence of methanol.

  8. Spectroscopy Investigation on Conformational Transition of Tea Glycoconjugate from Green Tea

    Institute of Scientific and Technical Information of China (English)

    CHEN,Hai-Xia(陈海霞); ZHANG,Min(张民); XIE,Bi-Jun(谢笔钧)

    2004-01-01

    The conformational transition of a new glycoconjugate,tea glycoconjugate(TGC),was investigated by spectroscopy techniques including circular dichroism(CD)and ultraviolet(UV)spectroscopy.The solution behaviors of TGC inthe mediums of different temperature,pH value,and ions were compared.Results showed that the native conformation of TGC was partially ordered.The CD value and UV absorbance of TGC altered with the change of pH value,temperature,the addition of ions,and also accompanied order-disorder transition.Especially the conditions with temperature higher than the glasstransition temperature(Tg=62℃),higher pH value orlower pH value will have the most impact on the conformation of TGC,which will destroy the hydrogen bonds between the TGC molecules.The results indicated that the outside factors playimportant roles onthe stability of the conformation of TGC.

  9. Minimal Models for a Superconductor-Insulator Conformal Quantum Phase Transition

    CERN Document Server

    Diamantini, M Cristina

    2013-01-01

    Conformal field theories do not only classify 2D classical critical behavior but they also govern a certain class of 2D quantum critical behavior. In this latter case it is the ground state wave functional of the quantum theory that is conformally invariant, rather than the classical action. We show that the superconducting-insulating (SI) quantum phase transition in 2D Josephson junction arrays (JJAs) is a (doubled) $c=1$ Gaussian conformal quantum critical point. The quantum action describing this system is a doubled Maxwell-Chern-Simons model in the strong coupling limit. We also argue that the SI quantum transitions in frustrated JJAs realize the other possible universality classes of conformal quantum critical behavior, corresponding to the unitary minimal models at central charge $c=1-6/m(m+1)$.

  10. Pressure-induced conformation transition of o-phenylene solvated in bulk hydrocarbons.

    Science.gov (United States)

    Riello, Massimo; Doni, Giovanni; Filip, Sorin V; Gold, Martin; De Vita, Alessandro

    2014-11-26

    The conformational behavior of o-phenylene 8-mers and 10-mers solvated in a series of linear alkane solvents by means of classical molecular dynamics and first-principles calculations was studied. Irrespective of the solvent used, we find that at ambient pressure the molecule sits in the well-defined close-helical arrangement previously observed in light polar solvents. However, for pressures greater than 50 atm, and for tetradecane or larger solvent molecules, our simulations predict that o-phenylene undergoes a conformational transition to an uncoiled, extended geometry with a 35% longer head-to-tail distance and a much larger overlap between its lateral aromatic ring groups. The free energy barrier for the transition was studied as a function of pressure and temperature for both solute molecules in butane and hexadecane. Gas-phase density functional theory-based nudged elastic band calculations on 8-mer and 10-mer o-phenylene were used to estimate how the pressure-induced transition energy barrier changes with solute length. Our results indicate that a sufficiently large solvent molecule size is the key factor enabling a configuration transition upon pressure changes and that longer solute molecules associate with higher conformation transition energy barriers. This suggests the possibility of designing systems in which a solute molecule can be selectively "activated" by a controlled conformation transition achieved at a predefined set of pressure and temperature conditions.

  11. Conformal nanocoating of zirconia nanoparticles by atomic layer deposition in a fluidized bed reactor.

    Science.gov (United States)

    Hakim, Luis F; George, Steven M; Weimer, Alan W

    2005-07-01

    Primary zirconia nanoparticles were conformally coated with alumina ultrathin films using atomic layer deposition (ALD) in a fluidized bed reactor. Alternating doses of trimethylaluminium and water vapour were performed to deposit Al(2)O(3) nanolayers on the surface of 26 nm zirconia nanoparticles. Transmission Fourier transform infrared spectroscopy was performed ex situ. Bulk Al(2)O(3) vibrational modes were observed for coated particles after 50 and 70 cycles. Coated nanoparticles were also examined with transmission electron microscopy, high-resolution field emission scanning electron microscopy and energy dispersive spectroscopy. Analysis revealed highly conformal and uniform alumina nanofilms throughout the surface of zirconia nanoparticles. The particle size distribution and surface area of the nanoparticles are not affected by the coating process. Primary nanoparticles are coated individually despite their high aggregation tendency during fluidization. The dynamic aggregation behaviour of zirconia nanoparticles in the fluidized bed plays a key role in the individual coating of nanoparticles.

  12. Highly conformal atomic layer deposition of tantalum oxide using alkylamide precursors

    Energy Technology Data Exchange (ETDEWEB)

    Hausmann, Dennis M.; Rouffignac, Philippe de; Smith, Amethyst; Gordon, Roy; Monsma, Douwe

    2003-10-22

    Atomic layer deposition of highly conformal films of tantalum oxide were studied using tantalum alkylamide precursors and water as the oxygen source. These films also exhibited a very high degree of conformality: 100% step coverage on vias with aspect ratios greater than 35. As deposited, the films were free of detectable impurities with the expected (2.5-1) oxygen to metal ratio and were smooth and amorphous. The films were completely uniform in thickness and composition over the length of the reactor used for depositions. Films were deposited at substrate temperatures from 50 to 350 deg. C from precursors that were vaporized at temperatures from 50 to 120 deg. C. As deposited, the films showed a dielectric constant of 28 and breakdown field consistently greater than 4.5 MV/cm.

  13. Atom-Based Geometrical Fingerprinting of Conformal Two-Dimensional Materials

    Science.gov (United States)

    Mehboudi, Mehrshad

    The shape of two-dimensional materials plays a significant role on their chemical and physical properties. Two-dimensional materials are basic meshes that are formed by mesh points (vertices) given by atomic positions, and connecting lines (edges) between points given by chemical bonds. Therefore the study of local shape and geometry of two-dimensional materials is a fundamental prerequisite to investigate physical and chemical properties. Hereby the use of discrete geometry to discuss the shape of two-dimensional materials is initiated. The local geometry of a surface embodied in 3D space is determined using four invariant numbers from the metric and curvature tensors which indicates how much the surface is stretched and curved under a deformation as compared to a reference pre-deformed conformation. Many different disciplines advance theories on conformal two-dimensional materials by relying on continuum mechanics and fitting continuum surfaces to the shape of conformal two-dimensional materials. However two-dimensional materials are inherently discrete. The continuum models are only applicable when the size of two-dimensional materials is significantly large and the deformation is less than a few percent. In this research, the knowledge of discrete differential geometry was used to tell the local shape of conformal two-dimensional materials. Three kind of two-dimensional materials are discussed: 1) one atom thickness structures such as graphene and hexagonal boron nitride; 2) high and low buckled 2D meshes like stanene, leadene, aluminum phosphate; and, 3) multi layer 2D materials such as Bi2Se3 and WSe2. The lattice structures of these materials were created by designing a mechanical model - the mechanical model was devised in the form of a Gaussian bump and density-functional theory was used to inform the local height; and, the local geometries are also discussed.

  14. 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.

  15. Parallel Cascade Selection Molecular Dynamics (PaCS-MD) to generate conformational transition pathway.

    Science.gov (United States)

    Harada, Ryuhei; Kitao, Akio

    2013-07-21

    Parallel Cascade Selection Molecular Dynamics (PaCS-MD) is proposed as a molecular simulation method to generate conformational transition pathway under the condition that a set of "reactant" and "product" structures is known a priori. In PaCS-MD, the cycle of short multiple independent molecular dynamics simulations and selection of the structures close to the product structure for the next cycle are repeated until the simulated structures move sufficiently close to the product. Folding of 10-residue mini-protein chignolin from the extended to native structures and open-close conformational transition of T4 lysozyme were investigated by PaCS-MD. In both cases, tens of cycles of 100-ps MD were sufficient to reach the product structures, indicating the efficient generation of conformational transition pathway in PaCS-MD with a series of conventional MD without additional external biases. Using the snapshots along the pathway as the initial coordinates, free energy landscapes were calculated by the combination with multiple independent umbrella samplings to statistically elucidate the conformational transition pathways.

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

    Science.gov (United States)

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

    2016-02-01

    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/cm2/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.

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

    Science.gov (United States)

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

    2014-11-12

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

  18. Electronic transitions in highly charged ion-atom collisions

    Science.gov (United States)

    Schmidt-Böcking, H.; Ullrich, J.; Schuch, R.; Olson, R. E.; Dörner, R.

    1989-09-01

    Three different aspects of electronic transitions in fast, highly charged ion-atom collisions are discussed. First, experimental data and n-CTMC calculations for differential multiple ionization cross sections of 1.4 {MeV}/{u} U 32+on rare gas atoms are presented. It is shown that the electronic motion has a dramatic influence on the kinematics of the emitted particles (in particular the nuclei). The possibility is discussed to measure in fast ionizing processes by a recoil ion-projectile coincidence technique the internal sum momentum of "electron clusters" in atoms. This new "technique" opens a new field of atomic structure research at high-energy heavy-ion accelerators. Second, the use of the H-like heavy ions as projectiles is discussed to measure, through observable interference structures, static and dynamic properties of transiently formed superheavy quasimolecular systems. Third, the "ancient" gas target-solid target difference in the impact-parameter dependence of K-shell ionization in nearly symmetric ion-atom collisions is presented. This severe discrepancy between gas and solid still remains an unsolved fundamental problem in the field of inner-shell ionization in the MO regime.

  19. Cyclophilin A inhibition: targeting transition-state-bound enzyme conformations for structure-based drug design.

    Science.gov (United States)

    Nagaraju, Mulpuri; McGowan, Lauren C; Hamelberg, Donald

    2013-02-25

    Human Cyclophilin A (CypA) catalyzes cis-trans isomerization of the prolyl peptide ω-bond in proteins and is involved in many subcellular processes. CypA has, therefore, been identified as a potential drug target in many diseases, and the development of potent inhibitors with high selectivity is a key objective. In computer-aided drug design, selectivity is improved by taking into account the inherent flexibility of the receptor. However, the relevant receptor conformations to focus on in order to develop highly selective inhibitors are not always obvious from available X-ray crystal structures or ensemble of conformations generated using molecular dynamics simulations. Here, we show that the conformation of the active site of CypA varies as the substrate configuration changes during catalytic turnover. We have analyzed the principal modes of the active site dynamics of CypA from molecular dynamics simulations to show that similar ensembles of enzyme conformations recognize diverse inhibitors and bind the different configurations of the peptide substrate. Small nonpeptidomimetic inhibitors with varying activity are recognized by enzyme ensembles that are similar to those that tightly bind the transition state and cis configurations of the substrate. Our results suggest that enzyme-substrate ensembles are more relevant in structure-based drug design for CypA than free enzyme. Of the vast conformational space of the free enzyme, the enzyme conformations of the tightly bound enzyme-substrate complexes are the most important for catalysis. Therefore, functionalizing lead compounds to optimize their interactions with the enzyme's conformational ensemble bound to the substrate in the cis or the transition state could lead to more potent inhibitors.

  20. Multicanonical simulation of biomolecules and microcanonical statistical analysis of conformational transitions

    Science.gov (United States)

    Bachmann, Michael

    2013-05-01

    The simulation of biomolecular structural transitions such as folding and aggregation does not only require adequate models that reflect the key aspects of the cooperative transition behaviour. It is likewise important to employ thermodynamically correct simulation methods and to perform an accurate subsequent statistical analysis of the data obtained in the simulation. The efficient combination of methodology and analysis can be quite sophisticated, but also very instructive in their feedback to a better understanding of the physics of the underlying cooperative processes that drive the conformational transition. We here show that the density of states, which is the central result of multicanonical sampling and any other generalized-ensemble simulation, serves as the optimal basis for the microcanonical statistical analysis of transitions. The microcanonical inflection-point analysis method, which has been introduced for this purpose recently, is a perfect tool for a precise, unique identification and classification of all structural transitions.

  1. A benchmark of excitonic couplings derived from atomic transition charges.

    Science.gov (United States)

    Kistler, Kurt A; Spano, Francis C; Matsika, Spiridoula

    2013-02-21

    In this report we benchmark Coulombic excitonic couplings between various pairs of chromophores calculated using transition charges localized on the atoms of each monomer chromophore, as derived from a Mulliken population analysis of the monomeric transition densities. The systems studied are dimers of 1-methylthymine, 1-methylcytosine, 2-amino-9-methylpurine, all-trans-1,3,5-hexatriene, all-trans-1,3,5,7-octatetraene, trans-stilbene, naphthalene, perylenediimide, and dithia-anthracenophane. Transition densities are taken from different single-reference electronic structure excited state methods: time-dependent density functional theory (TDDFT), configuration-interaction singles (CIS), and semiempirical methods based on intermediate neglect of differential overlap. Comparisons of these results with full ab initio calculations of the electronic couplings using a supersystem are made, as are comparisons with experimental data. Results show that the transition charges do a good job of reproducing the supersystem couplings for dimers with moderate to long-range interchromophore separation. It is also found that CIS supermolecular couplings tend to overestimate the couplings, and often the transition charges approach may be better, due to fortuitous cancellation of errors.

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

    Science.gov (United States)

    Wong, Chung F

    2016-01-01

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

  3. 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

  4. 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.

  5. 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.

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

    OpenAIRE

    Dalgıçdir, Cahit; Şensoy, Özge; Sayar, Mehmet; Peter, Christine

    2013-01-01

    A transferable coarse-grained model for diphenylalanine: How to represent an environment driven conformational transition Cahit Dalgicdir, Ozge Sensoy, Christine Peter, and Mehmet Sayar Citation: The Journal of Chemical Physics 139, 234115 (2013); doi: 10.1063/1.4848675 View online: http://dx.doi.org/10.1063/1.4848675 View Table of Contents: http://scitation.aip.org/content/aip/journal/jcp/139/23?ver=pdfcov Published by the AIP Publishing Articles you may be interested in...

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

    Science.gov (United States)

    Solberg, Jerome Michael

    2012-12-04

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

  8. Notes on Critical Assessment of Theoretical Calculations of Atomic Structure and Transition Probabilities

    OpenAIRE

    Hyun-Kyung Chung; Per Jönsson; Alexander Kramida

    2013-01-01

    Atomic structure and transition probabilities are fundamental physical data required in many fields of science and technology. Atomic physics codes are freely available to other community users to generate atomic data for their interest, but the quality of these data is rarely verified. This special issue addresses estimation of uncertainties in atomic structure and transition probability calculations, and discusses methods and strategies to assess and ensure the quality of theoretical atomic...

  9. 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.

  10. Plasma-assisted atomic layer deposition of conformal Pt films in high aspect ratio trenches

    Science.gov (United States)

    Erkens, I. J. M.; Verheijen, M. A.; Knoops, H. C. M.; Keuning, W.; Roozeboom, F.; Kessels, W. M. M.

    2017-02-01

    To date, conventional thermal atomic layer deposition (ALD) has been the method of choice to deposit high-quality Pt thin films grown typically from (MeCp)PtMe3 vapor and O2 gas at 300 °C. Plasma-assisted ALD of Pt using O2 plasma can offer several advantages over thermal ALD, such as faster nucleation and deposition at lower temperatures. In this work, it is demonstrated that plasma-assisted ALD at 300 °C also allows for the deposition of highly conformal Pt films in trenches with high aspect ratio ranging from 3 to 34. Scanning electron microscopy inspection revealed that the conformality of the deposited Pt films was 100% in trenches with aspect ratio (AR) up to 34. These results were corroborated by high-precision layer thickness measurements by transmission electron microscopy for trenches with an aspect ratio of 22. The role of the surface recombination of O-radicals and the contribution of thermal ALD reactions is discussed.

  11. 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.

  12. 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 (1)C4 and (4)C1 chair conformations. The analysis using RMapViewer allows us to confirm the thermodynamic and kinetic predominance of (4)C1 conformations; that is, the potential energy of the global minimum of (4)C1 is lower than that of (1)C4 (thermodynamic predominance

  13. Conformational Transitions and Glycation of Serum Albumin in Patients with Minimal-Change Glomerulopathy

    Science.gov (United States)

    Hong, Sae Yong; Lee, Eun Young; Yang, Jong Oh; Kim, Tae Yeong; Kim, Eun Hee; Cheong, Mi Young; Kim, Soo Hyun; Cheong, Chae Joon

    2004-01-01

    Background There has been a lack of study on the structural changes of serum albumin in patients with minimal change disease (MCD). To determine whether glycation and/or conformational transitions of albumin are involved in the pathogenesis of albuminuria, nine patients with MCD were enrolled in a prospective follow-up study for comparison of these parameters in serum albumin during the remission and relapse of nephrotic syndrome. Methods Circular dichroism measurements were made with purified albumin. Ellipticities at each wavelength were transformed to mean residue ellipticity. Monosaccharide composition was analyzed by high-pH anion-exchange chromatography with pulsed amperometric detection. Results There was no difference in the proportions of α-helix, β-conformation, and β-turn of albumin between the sera of control patients and those with nephrotic syndrome. However, the proportion of the random configuration was slightly higher in the plasma albumin of patients in relapse than in those in remission. The proportion of the random configuration was lower in the albumin of the serum than in the urine of patients with nephrotic syndrome, but there was no difference in the proportions of α-helix, β-conformation, and β-turn of albumin between their plasma and urine. Conclusion Our results suggest that conformational changes in albumin are involved in albuminuria in patients with MCD. PMID:15481604

  14. Mechanism of Conformational Transition of Silk Fibroin in Alcohol-water Mixtures

    Institute of Scientific and Technical Information of China (English)

    Ma Lin; He Weiren; Huang Aimin; Li Lishuo; Wei Qiaona; Huang Zilun

    2011-01-01

    Circular dichroism, intrinsic fluorescence of protein and exogenous fluorescence probe of 8-anilino-l-naphtha-lenesulfonic acid hemimagnesium salt (ANS) was used to investigate the mechanism of conformational change of silk fibroin (SF) in aqueous alcohol including methanol and ethanol. The conformational transition of SF from ran-dom coil to β-sheet was found to be of a close relationship with the microstructure of the solvent. The alcohol-water mixture at low concentration had little effect on the solvation of the peptide unit, as the inherent water structure was conserved. At high alcohol concentration, the transition from the tetrahedral-like water structure to the chain-like alcohol structure in the mixtures induced a β-sheet conformation of SF, as a result of the formation of intramolecu-lar hydrogen bond between the peptide units in order to eliminate the thermodynamic unfavorite from the contact to the solvent molecules. Meanwhile, the aggregating of hydrophobic side chains was decreased by the alcohol via the destruction of hydrogen bond network of water by alcohol and the binding of alcohol to hydrophobic group.

  15. 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.

  16. Giant modification of atomic transitions probabilities induced by magnetic field: forbidden transitions become predominant

    CERN Document Server

    Sargsyan, A; Hakhumyan, G; Papoyan, A; Mariotti, E; Sarkisyan, D

    2014-01-01

    Magnetic field-induced giant modification of probabilities for seven components of 6S1/2 (Fg=3) - 6P3/2 (Fe=5) transition of Cs D2 line forbidden by selection rules is observed experimentally for the first time. For the case of excitation with circularly-polarized laser radiation, the probability of Fg=3,mF=-3 - Fe=5,mF=-2 transition becomes the largest among 25 transitions of Fg=3 - Fe=2,3,4,5 group in a wide range of magnetic field 200 - 3200 G. Moreover, the modification is the largest among D2 lines of alkali metals. A half-wave-thick cell (length along the beam propagation axis L=426 nm) filled with Cs has been used in order to achieve sub-Doppler resolution which allows for separating the large number of atomic transitions that appear in the absorption spectrum when an external magnetic field is applied. For B > 3 kG the group of seven transitions Fg=3 - Fe=5 is completely resolved and is located at the high frequency wing of Fg=3 - Fe=2,3,4 transitions. The applied theoretical model very well describes...

  17. Enhancing coherence in molecular spin qubits via atomic clock transitions

    Science.gov (United States)

    Shiddiq, Muhandis; Komijani, Dorsa; Duan, Yan; Gaita-Ariño, Alejandro; Coronado, Eugenio; Hill, Stephen

    2016-03-01

    Quantum computing is an emerging area within the information sciences revolving around the concept of quantum bits (qubits). A major obstacle is the extreme fragility of these qubits due to interactions with their environment that destroy their quantumness. This phenomenon, known as decoherence, is of fundamental interest. There are many competing candidates for qubits, including superconducting circuits, quantum optical cavities, ultracold atoms and spin qubits, and each has its strengths and weaknesses. When dealing with spin qubits, the strongest source of decoherence is the magnetic dipolar interaction. To minimize it, spins are typically diluted in a diamagnetic matrix. For example, this dilution can be taken to the extreme of a single phosphorus atom in silicon, whereas in molecular matrices a typical ratio is one magnetic molecule per 10,000 matrix molecules. However, there is a fundamental contradiction between reducing decoherence by dilution and allowing quantum operations via the interaction between spin qubits. To resolve this contradiction, the design and engineering of quantum hardware can benefit from a ‘bottom-up’ approach whereby the electronic structure of magnetic molecules is chemically tailored to give the desired physical behaviour. Here we present a way of enhancing coherence in solid-state molecular spin qubits without resorting to extreme dilution. It is based on the design of molecular structures with crystal field ground states possessing large tunnelling gaps that give rise to optimal operating points, or atomic clock transitions, at which the quantum spin dynamics become protected against dipolar decoherence. This approach is illustrated with a holmium molecular nanomagnet in which long coherence times (up to 8.4 microseconds at 5 kelvin) are obtained at unusually high concentrations. This finding opens new avenues for quantum computing based on molecular spin qubits.

  18. Conformational transitions of a confined lattice protein: A Wang-Landau study

    Science.gov (United States)

    Pattanasiri, Busara; Li, Ying Wai; Landau, David P.; Wüst, Thomas; Triampo, Wannapong

    2012-12-01

    We use Wang-Landau sampling with suitable Monte Carlo trial moves to study a hydrophobic-polar (HP) lattice protein confined between two parallel, attractive walls. The density of states is determined iteratively by a random walk in energy space. Thermodynamic and structural properties, such as specific heat, number of surface contacts and number of H-H monomer pairs, are then calculated. When the surface attraction is comparable to the internal attraction among the hydrophobic monomers in the chain, two conformational “transitions”, adsorption at higher temperature and collapse at lower temperature, have been analyzed based on these properties. This transition behavior depends on the variation of surface separation.

  19. 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.

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

    Science.gov (United States)

    Kim, Woo-Hee; Park, Sang-Joon; Son, Jong-Yeog; Kim, Hyungjun

    2008-01-30

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

  1. Conformational Preference and Donor Atom Interaction Leading to Hexacoordination vs Pentacoordination in Bicyclic Tetraoxyphosphoranes(1).

    Science.gov (United States)

    Sherlock, David J.; Chandrasekaran, A.; Prakasha, T. K.; Day, Roberta O.; Holmes, Robert R.

    1998-01-12

    New bicyclic tetraoxyphosphoranes all containing a six-membered oxaphosphorinane ring, C(6)H(8)(CH(2)O)(2)P(OC(12)H(8))(OXyl) (1), (C(6)H(4)O)(2)P(OC(12)H(8))(OXyl) (2), CH(2)[(t-Bu)(2)C(6)H(2)O](2)P(OC(12)H(8))(OXyl) (3), O(2)S[(t-Bu)MeC(6)H(2)O](2)P(OC(12)H(8))(OXyl) (4), and S[(t-Bu)MeC(6)H(2)O](2)P(OC(12)H(8))(OXyl) (5), were synthesized by the oxidative addition reaction of the cyclic phosphine P(OC(12)H(8))(OXyl) (6) with an appropriate diol in the presence of N-chlorodiisopropylamine. X-ray analysis revealed trigonal bipyramidal (TBP) geometries for 1-4 where the dioxa ring varied in size from six- to eight-membered. With a sulfur donor atom as part of an eight-membered ring in place of a potential oxygen donor atom of a sulfone group as in 4, the X-ray study of 5 showed the formation of a hexacoordinated structure via a P-S interaction. Ring constraints are evaluated to give an order of conformational flexibility associated with the (TBP) tetraoxyphosphoranes 4 > 3 approximately 1 > 2 which parallels the degree of shielding from (31)P NMR chemical shifts: 4 > 3 > 1 > 2. The six- and seven-membered dioxa rings in 1 and 2, respectively, are positioned at axial-equatorial sites, whereas the eight-membered dioxa ring in 3 and 4 occupies diequatorial sites of a TBP. V-T (1)H NMR data give barriers to xylyl group rotation about the C-OXyl bond. The geometry of 5 is located along a coordinate from square pyramidal toward octahedral to the extent of 60.7%. Achieving hexacoordination in bicyclic tetraoxyphosphoranes of reduced electrophilicity relative to bicyclic pentaoxyphosphoranes appears to be dependent on the presence of a sufficiently strong donor atom.

  2. Special Issue on Critical Assessment of Theoretical Calculations of Atomic Structure and Transition Probabilities

    OpenAIRE

    Per Jönsson; Hyun-Kyung Chung

    2013-01-01

    There exist several codes in the atomic physics community to generate atomic structure and transition probabilities freely and readily distributed to researchers outside atomic physics community, in plasma, astrophysical or nuclear physics communities. Users take these atomic physics codes to generate the necessary atomic data or modify the codes for their own applications. However, there has been very little effort to validate and verify the data sets generated by non-expert users. [...

  3. 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.

  4. Origin of the transition voltage in gold-vacuum-gold atomic junctions.

    Science.gov (United States)

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

    2013-01-18

    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.

  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. Conformational transitions of cinnamoyl CoA reductase 1 from Leucaena leucocephala.

    Science.gov (United States)

    Sonawane, Prashant D; Khan, Bashir M; Gaikwad, Sushama M

    2014-03-01

    Conformational transitions of cinnamoyl CoA reductase, a key regulatory enzyme in lignin biosynthesis, from Leucaena leucocephala (Ll-CCRH1) were studied using fluorescence and circular dichroism spectroscopy. The native protein possesses four trp residues exposed on the surface and 66% of helical structure, undergoes rapid structural transitions at and above 45 °C and starts forming aggregates at 55 °C. Ll-CCRH1 was transformed into acid induced (pH 2.0) molten globule like structure, exhibiting altered secondary structure, diminished tertiary structure and exposed hydrophobic residues. The molten globule like structure was examined for the thermal and chemical stability. The altered secondary structure of L1-CCRH1 at pH 2.0 was stable up to 90 °C. Also, in presence of 0.25 M guanidine hydrochloride (GdnHCl), it got transformed into different structure which was stable in the vicinity of 2M GdnHCl (as compared to drastic loss of native structure in 2M GdnHCl) as seen in far UV-CD spectra. The structural transition of Ll-CCRH1 at pH 2.0 followed another transition after readjusting the pH to 8.0, forming a structure with hardly any similarity to that of native protein.

  7. Distinguishing Unfolding and Functional Conformational Transitions of Calmodulin Using Ultraviolet Resonance Raman Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Jones, Eric M.; Balakrishnan, G.; Squier, Thomas C.; Spiro, Thomas

    2014-06-14

    Calmodulin (CaM) is a ubiquitous moderator protein for calcium signaling in all eukaryotic cells. This small calcium-binding protein exhibits a broad range of structural transitions, including domain opening and folding-unfolding, that allow it to recognize a wide variety of binding partners in vivo. While the static structures of CaM associated with its various binding activities are fairly well known, it has been challenging to examine the dynamics of transition between these structures in real-time, due to a lack of suitable spectroscopic probes of CaM structure. In this paper, we examine the potential of ultraviolet resonance Raman (UVRR) spectroscopy for clarifying the nature of structural transitions in CaM. We find that the UVRR spectral change (with 229 nm excitation) due to thermal unfolding of CaM is qualitatively different from that associated with opening of the C-terminal domain in response to Ca2+ binding. This spectral difference is entirely due to differences in teritary contacts at the inter-domain tyrosine residue Tyr138, toward which other spectroscopic methods are not sensitive. We conclude that UVRR is ideally suited to identifying the different types of structural transitions in CaM and other proteins with conformation-sensitive tyrosine residues, opening a path to time-resolved studies of CaM dynamics using Raman spectroscopy.

  8. Lasing and high temperature phase transitions in atomic systems with dressed state polaritons

    CERN Document Server

    Chestnov, I Yu

    2013-01-01

    We consider the fundamental problem of high temperature phase transitions in the system of high density two-level atoms off-resonantly interacting with a pump field in the presence of optical collisions (OCs) and placed in the cavity. OCs are considered in the framework of thermalization of atomic dressed state (DS) population. For the case of a strong atom-field coupling condition we analyze the problem of thermodynamically equilibrium superradiant phase transition for the order parameter representing a real amplitude of cavity mode and taking place as a result of atomic DSs thermalization process. Such transition is also connected with condensed (coherent) properties of low branch (LB) DS-polaritons occurring in the cavity. For describing non-equilibrium phase transitions we derive Maxwell-Bloch like equations which account for cavity decay rate, collisional decay rate and spontaneous emission. Various aspects of transitions to laser field formation by using atomic DS levels for both positive and negative d...

  9. Non-integer Quantum Transition, a True Non-perturbation Effect in Laser-Atom Interaction

    Institute of Scientific and Technical Information of China (English)

    ZHANG Qi-Ren

    2007-01-01

    We show that in the quantum transition of an atom interacting with an intense laser of circular frequencyω, the energy difference between the initial and the final states of the atom is not necessarily an integer multiple of the quantum energy (h)ω. This kind of non-integer transition is a true non-perturbation effect in laser-atom interaction.

  10. Atomic structure of recombinant thaumatin II reveals flexible conformations in two residues critical for sweetness and three consecutive glycine residues.

    Science.gov (United States)

    Masuda, Tetsuya; Mikami, Bunzo; Tani, Fumito

    2014-11-01

    Thaumatin, an intensely sweet-tasting protein used as a sweetener, elicits a sweet taste at 50 nM. Although two major variants designated thaumatin I and thaumatin II exist in plants, there have been few dedicated thaumatin II structural studies and, to date, data beyond atomic resolution had not been obtained. To identify the detailed structural properties explaining why thaumatin elicits a sweet taste, the structure of recombinant thaumatin II was determined at the resolution of 0.99 Å. Atomic resolution structural analysis with riding hydrogen atoms illustrated the differences in the direction of the side-chains more precisely and the electron density maps of the C-terminal regions were markedly improved. Though it had been suggested that the three consecutive glycine residues (G142-G143-G144) have highly flexible conformations, G143, the central glycine residue was successfully modelled in two conformations for the first time. Furthermore, the side chain r.m.s.d. values for two residues (R67 and R82) critical for sweetness exhibited substantially higher values, suggesting that these residues are highly disordered. These results demonstrated that the flexible conformations in two critical residues favoring their interaction with sweet taste receptors are prominent features of the intensely sweet taste of thaumatin.

  11. 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.

  12. Capturing the Membrane-Triggered Conformational Transition of an α-Helical Pore-Forming Toxin.

    Science.gov (United States)

    Giri Rao, V V Hemanth; Desikan, Rajat; Ayappa, K Ganapathy; Gosavi, Shachi

    2016-12-01

    Escherichia coli cytolysin A (ClyA) is an α-helical pore-forming toxin (PFT) which lyses target cells by forming membrane permeabilizing pores. The rate-determining step of this process is the conversion of the soluble ClyA monomer into a membrane inserted protomer. We elucidate the mechanism of this conformational transition using molecular dynamics simulations of coarse-grained models of ClyA and a membrane. We find that a membrane is necessary for the conformational conversion because membrane-protein interactions counteract the loss of the many intraprotein hydrophobic interactions that stabilize the membrane-inserting segments in the ClyA monomer. Of the two membrane-inserting segments, the flexible and highly hydrophobic β-tongue inserts first while the insertion of helix αA1 is membrane assisted. We conclude that the β-tongue is designed to behave as a quick-response membrane sensor, while helix αA1 improves target selectivity for cholesterol-containing cell membranes by acting as a fidelity check.

  13. Water-mediated conformational transitions in nicotinic receptor M2 helix bundles: a molecular dynamics study.

    Science.gov (United States)

    Sankararamakrishnan, R; Sansom, M S

    1995-12-27

    The ion channel of the nicotinic acetylcholine receptor is a water-filled pore formed by five M2 helix segments, one from each subunit. Molecular dynamics simulations on bundles of five M2 alpha 7 helices surrounding a central column of water and with caps of water molecules at either end of the pore have been used to explore the effects of intrapore water on helix packing. Interactions of water molecules with the N-terminal polar sidechains lead to a conformational transition from right- to left-handed supercoils during these stimulations. These studies reveal that the pore formed by the bundle of M2 helices is flexible. A structural role is proposed for water molecules in determining the geometry of bundles of isolated pore-forming helices.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-10-23

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

  15. Interaction between cyclodextrin and neuronal membrane results in modulation of GABA(A) receptor conformational transitions.

    Science.gov (United States)

    Pytel, Maria; Mercik, Katarzyna; Mozrzymas, Jerzy W

    2006-06-01

    Cyclodextrins (CDs) are nanostructures widely applied in biotechnology and chemistry. Owing to partially hydrophobic character, CDs interact with biological membranes. While the mechanisms of CDs interactions with lipids were widely studied, their effects on proteins are less understood. In the present study we investigated the effects of beta cyclodextrin (betaCD) on GABA(A) receptor (GABA(A)R) gating. To reliably resolve the kinetics of conformational transitions, currents were elicited by ultrafast gamma-aminobutyric acid (GABA) applications to outside-out patches from rat cultured hippocampal neurons. betaCD increased the amplitude of responses to saturating GABA concentration ([GABA]) in a dose-dependent manner and this effect was accompanied by profound alterations in the current kinetics. Current deactivation was slowed down by betaCD but this effect was biphasic with a maximum at around 0.5 mM betaCD. While the fast deactivation time constant was monotonically slowed down within considered betaCD concentration range, the slow component first increased and then, at millimolar betaCD concentration, decreased. The rate and extent of desensitization was decreased by betaCD in a dose-dependent manner. The analysis of current responses to nonsaturating [GABA] indicated that betaCD affected the GABA(A)R agonist binding site by slowing down the unbinding rate. Modulation of GABA(A)R desensitization and binding showed different concentration-dependence suggesting different modualtory sites with higher affinity of the latter one. All the betaCD effects were fully reversible indicating that cholesterol uptake into betaCD was not the primary mechanism. We conclude that betaCD is a strong modulator of GABA(A)R conformational transitions.

  16. Interaction between cyclodextrin and neuronal membrane results in modulation of GABAA receptor conformational transitions

    Science.gov (United States)

    Pytel, Maria; Mercik, Katarzyna; Mozrzymas, Jerzy W

    2006-01-01

    Cyclodextrins (CDs) are nanostructures widely applied in biotechnology and chemistry. Owing to partially hydrophobic character, CDs interact with biological membranes. While the mechanisms of CDs interactions with lipids were widely studied, their effects on proteins are less understood. In the present study we investigated the effects of beta cyclodextrin (βCD) on GABAA receptor (GABAAR) gating. To reliably resolve the kinetics of conformational transitions, currents were elicited by ultrafast gamma-aminobutyric acid (GABA) applications to outside-out patches from rat cultured hippocampal neurons. βCD increased the amplitude of responses to saturating GABA concentration ([GABA]) in a dose-dependent manner and this effect was accompanied by profound alterations in the current kinetics. Current deactivation was slowed down by βCD but this effect was biphasic with a maximum at around 0.5 mM βCD. While the fast deactivation time constant was monotonically slowed down within considered βCD concentration range, the slow component first increased and then, at millimolar βCD concentration, decreased. The rate and extent of desensitization was decreased by βCD in a dose-dependent manner. The analysis of current responses to nonsaturating [GABA] indicated that βCD affected the GABAAR agonist binding site by slowing down the unbinding rate. Modulation of GABAAR desensitization and binding showed different concentration-dependence suggesting different modualtory sites with higher affinity of the latter one. All the βCD effects were fully reversible indicating that cholesterol uptake into βCD was not the primary mechanism. We conclude that βCD is a strong modulator of GABAAR conformational transitions. PMID:16702996

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

    Science.gov (United States)

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

    2015-01-20

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

  18. Conformations of Carnosine in Aqueous Solutions by All-Atom Molecular Dynamics Simulations and 2D-NOSEY Spectrum

    Institute of Scientific and Technical Information of China (English)

    Rong Zhang; Dan Wang; Wen-juan Wu

    2013-01-01

    All-atom molecular simulations and two-dimensional nuclear overhauser effect spectrum have been used to study the conformations of carnosine in aqueous solution.Intramolecular distances,root-mean-square deviation,radius of gyration,and solvent-accessible surface are used to characterize the properties of the carnosine.Carnosine can shift between extended and folded states,but exists mostly in extended state in water.Its preference for extension in pure water has been proven by the 2D nuclear magnetic resonance (NMR) experiment.The NMR experimental results are consistent with the molecular dynamics simulations.

  19. 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.

  20. [Dynamics of electron-conformational transitions in proteins and physical mechanisms of biomacromolecule function].

    Science.gov (United States)

    Shaĭtan, K V

    1992-01-01

    The proteins can be considered as a microheterogeneous structured media possessing memory and feedback properties. The conformational energy surface depends on the chemical states of protein groups. Conformational motions are local diffusion with relaxation times much longer than vibrational relaxation times in condensed media. Owing to the hierarchy of relaxation times chemical reaction rates depend on conformation parametrically. Regulation of functional activity by conformational mobility is accomplished via transmission of information in the form of changes in the distribution functions of separate groups along the conformational substates. The interpretation of drastic effects on conformational mobility needs super-stochastic approaches. A possible mechanism of sharp conformational change are discussed in terms of the catastrophe theory.

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

    Science.gov (United States)

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

    2017-01-25

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

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

    CERN Document Server

    Moore, Kaitlin R; Raithel, Georg

    2014-01-01

    Spectroscopy is an essential tool in understanding and manipulating quantum systems, such as atoms and molecules. The model describing spectroscopy includes a multipole-field interaction, which leads to established spectroscopic selection rules, and an interaction that is quadratic in the field, which is often neglected. However, spectroscopy using the quadratic (ponderomotive) interaction promises two significant advantages over spectroscopy using the multipole-field interaction: flexible transition rules and vastly improved spatial addressability of the quantum system. For the first time, we demonstrate ponderomotive spectroscopy by using optical-lattice-trapped Rydberg atoms, pulsating the lattice light at a microwave frequency, and driving a microwave atomic transition that would otherwise be forbidden by established spectroscopic selection rules. This new ability to measure frequencies of previously inaccessible transitions makes possible improved determinations of atomic characteristics and constants un...

  3. 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.

  4. Atomic snapshots of an RNA packaging motor reveal conformational changes linking ATP hydrolysis to RNA translocation.

    Science.gov (United States)

    Mancini, Erika J; Kainov, Denis E; Grimes, Jonathan M; Tuma, Roman; Bamford, Dennis H; Stuart, David I

    2004-09-17

    Many viruses package their genome into preformed capsids using packaging motors powered by the hydrolysis of ATP. The hexameric ATPase P4 of dsRNA bacteriophage phi12, located at the vertices of the icosahedral capsid, is such a packaging motor. We have captured crystallographic structures of P4 for all the key points along the catalytic pathway, including apo, substrate analog bound, and product bound. Substrate and product binding have been observed as both binary complexes and ternary complexes with divalent cations. These structures reveal large movements of the putative RNA binding loop, which are coupled with nucleotide binding and hydrolysis, indicating how ATP hydrolysis drives RNA translocation through cooperative conformational changes. Two distinct conformations of bound nucleotide triphosphate suggest how hydrolysis is activated by RNA binding. This provides a model for chemomechanical coupling for a prototype of the large family of hexameric helicases and oligonucleotide translocating enzymes.

  5. Ccontrolling the Transition Between "Higher" and "Lower" State of OB in Coherent Atomic Mediumntrolling the Transition Between "Higher" and "Lower" State of OB in Coherent Atomic Medium

    Institute of Scientific and Technical Information of China (English)

    WANG Hai; CHANG Hong; WU Haibin; XIE Chande

    2004-01-01

    @@ We present a new experimental demonstration that the threshold points and shape of OB hysteresis curve in a four-level Rb atomic system inside an optical cavity were controllably changed by optical signals.Tuning the triggering optical signal to two different transitions of the atomic system we found that the OB threshold points shift toward different direction and at the same time the shape of the OB curve is also changed.For a given intensity of probe laser the OB system can be reliably inversed from its lower stable state to upper state under the triggering of a suitably tuned optical pulse signal (we named it up-controlling signal).More interesting, the inversed OB state does not drop to its initial lower stable state after the triggering pulse signal has passed, but moves to the upper branch of the initial OB curve and stably stays there until another optical signal tuned on other atomic transition (named down-controlling signal) coming.The result shows that there is the ability of information storage in the OB system.The experiments are reasonably explained with the change of cavity resonant condition resulting from the enhanced third-order nonlinearity in multilevel atomic system owing to atomic coherence.

  6. The Atomic to Molecular Transition in the Interstellar Medium

    Science.gov (United States)

    Goldsmith, Paul F.

    2012-01-01

    Study of H2 in UV and IR continues to surprise us with complexity of excitation state, OPR, and role in astrochemistry. Atomic H in molecular clouds is a very powerful tool suggesting that they are not "young" but that it takes millions of years to convert primarily atomic hydrogen clouds to 99.9% molecular form. Laboratory data suggests that H2 formation is efficient over broader range of temperatures than thought to be the case a few years ago, but range is still limited. Issues of complex grain morphology and surface structure make this a very difficult field in which to obtain definitively meaningful results. Ongoing and future observations of CI and CII will improve our understanding of the structure of clouds, their total mass, and how they have evolved and will continue to do so.

  7. Lattice-Inversion Embedded-Atom-Method Interatomic Potentials for Group-VA Transition Metals

    Institute of Scientific and Technical Information of China (English)

    袁晓俭; 陈难先; 申江

    2011-01-01

    The lattice-inversion embedded-atom-method (LI-EAM) interatomic potential we developed previously [J. Phys.: Condens. Matter 22 (2010) 375503] is extended to group- VA transition metals (V, Nb and Ta). It is found that considering interatomic interactions up to appropriate-distance-neighbor atoms is crucial to constructing accurate EAM potentials, especially for the prediction of surface energy. The LI-EAM interatomic potentials for group-VA transition metals are successfully built by considering interatomic interactions up to the fifth neighbor atoms. These angular-independent potentials drastically promote the accuracy of the predicted surface energies, which match the experimental resuits well.%The lattice-inversion embedded-atom-method(LI-EAM)interatomic potential we developed previously[J.Phys.:Condens.Matter 22(2010)375503]is extended to group-VA transition metals(V,Nb and Ta).It is found that considering interatomic interactions up to appropriate-distance-neighbor atoms is crucial to constructing accurate EAM potentials,especially for the prediction of surface energy.The LI-EAM interatomic potentials for group-VA transition metals are successfully built by considering interatomic interactions up to the fifth neighbor atoms.These angular-independent potentials drastically promote the accuracy of the predicted surface energies,which match the experimental results well.

  8. 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.

  9. 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.

  10. Atomic clock with nuclear transition: current status in TU Wien

    OpenAIRE

    Kazakov, G. A.; Schreitl, M.; Winkler, G.; Sterba, J. H.; Steinhauser, G; Schumm, T.

    2011-01-01

    The nucleus of 229Thorium presents a unique isomer state of very low energy and long lifetime, current estimates are around 7.8 eV and seconds to hours respectively. This nuclear transitions therefore is a promising candidate for a novel type of frequency standard and several groups worldwide have set out to investigate this system. Our aim is to construct a "solid state nuclear clock", i.e. a frequency standard where Thorium ions are implanted into Calciumfluoride crystals transparent in vac...

  11. Radiationless transitions to atomic M 1,2,3 shells - Results of relativistic theory

    Science.gov (United States)

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

    1983-01-01

    Radiationless transitions filling vacancies in atomic M1, M2, and M3 subshells have been calculated relativistically with Dirac-Hartree-Slater wave functions for ten elements with atomic numbers 67-95. Results are compared with those of nonrelativistic calculations and experiment. Relativistic effects are found to be significant. Limitations of an independent-particle model for the calculation of Coster-Kronig rates are noted.

  12. Analysis of the conformation of the androgen receptor in spinal bulbar muscular atrophy by atomic force microscopy.

    Science.gov (United States)

    Jochum, Tobias; Cato, Andrew C B

    2014-01-01

    Spinal bulbar muscular atrophy (SBMA) (also known as Kennedy's disease) is a motor degenerative disease caused by an amplification of the polyglutamine stretch at the N-terminus of the human androgen receptor (AR). Amplifications larger than 40 glutamine residues are thought to lead to the disease. A characteristic feature of this disease is a ligand-dependent misfolding and aggregation of the mutant receptor that lead to the death of motor neurons. Initially, large cytoplasmic and nuclear aggregates reaching sizes of 6 μm were thought to be the pathogenic agents. Later studies have suggested that oligomeric species with sizes of less than 1 μm that occur prior to the formation of the larger aggregates are the toxic agents. However, there have been disagreements regarding the shape of these oligomers, as most studies have been carried out with peptide fragments of the androgen receptor containing different lengths of polyglutamine stretch. We have isolated the wild-type AR with a polyglutamine stretch of 22 (ARQ22) and a mutant receptor with a stretch of 65 (ARQ65) using a baculovirus system and have analyzed the oligomeric structures formed by these receptors with atomic force microscopy. This method has allowed us to determine the conformations of the full-length wild-type and mutant AR and revealed the conformation of the mutant AR that causes SBMA.

  13. Hyperfine-induced electric dipole contributions to the electric octupole and magnetic quadrupole atomic clock transitions

    CERN Document Server

    Dzuba, V A

    2016-01-01

    Hyperfine-induced electric dipole contributions may significantly increase probabilities of otherwise very weak electric octupole and magnetic quadrupole atomic clock transitions (e.g. transitions between $s$ and $f$ electron orbitals). These transitions can be used for exceptionally accurate atomic clocks, quantum information processing and search for dark matter. They are very sensitive to new physics beyond the Standard Model, such as temporal variation of the fine structure constant, the Lorentz invariance and Einstein equivalence principle violation. We formulate conditions under which the hyperfine-induced electric dipole contribution dominates. Due to the hyperfine quenching the electric octupole clock transition in $^{173}$Yb$^+$ is two orders of magnitude stronger than that in currently used $^{171}$Yb$^+$. Some enhancement is found in $^{143}$Nd$^{13+}$, $^{149}$Pm$^{14+}$, $^{147}$Sm$^{14+}$, and $^{147}$Sm$^{15+}$ ions.

  14. 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.

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

    DEFF Research Database (Denmark)

    Miroshnychenko, Yevhen; Mølmer, Klaus

    2013-01-01

    We study the contributions of off-resonant transitions to the dynamics of a system of N multi-level atoms sharing one excitation and interacting with the quantized vector electromagnetic field. The rotating wave approximation significantly simplifies the derivation of the equations of motion...... the photon mode frequencies are extended to incorporate negative values. We explicitly derive the atom–atom interaction for multi-level atoms, coupled to the full vector electromagnetic field, and we recover also in this general case the validity of the results obtained by the extension to negative...

  16. Molecular Dynamics Simulation on the Conformational Transition of the Mad2 Protein from the Open to the Closed State

    Directory of Open Access Journals (Sweden)

    Chaoqun Li

    2014-03-01

    Full Text Available The Mad2 protein, with two distinct conformations of open- and closed-states, is a key player in the spindle checkpoint. The closed Mad2 state is more active than the open one. We carried out conventional and targeted molecular dynamics simulations for the two stable Mad2 states and their conformational transition to address the dynamical transition mechanism from the open to the closed state. The intermediate structure in the transition process shows exposure of the β6 strand and an increase of space around the binding sites of β6 strand due to the unfolding of the β7/8 sheet and movement of the β6/4/5 sheet close to the αC helix. Therefore, Mad2 binding to the Cdc20 protein in the spindle checkpoint is made possible. The interconversion between these two states might facilitate the functional activity of the Mad2 protein. Motion correlation analysis revealed the allosteric network between the β1 strand and β7/8 sheet via communication of the β5-αC loop and the β6/4/5 sheet in this transition process.

  17. 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.

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

    OpenAIRE

    Hirokawa Takatsugu; Ikeda Kazuyoshi; Higo Junichi; Tomii Kentaro

    2008-01-01

    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-l...

  19. Conformal Coating of Three-Dimensional Nanostructures via Atomic Layer Deposition for Development of Advanced Energy Storage Devices and Plasmonic Transparent Conductors

    Science.gov (United States)

    Malek, Gary A.

    Due to the prodigious amount of electrical energy consumed throughout the world, there exists a great demand for new and improved methods of generating electrical energy in a clean and renewable manner as well as finding more effective ways to store it. This enormous task is of great interest to scientists and engineers, and much headway is being made by utilizing three-dimensional (3D) nanostructured materials. This work explores the application of two types of 3D nanostructured materials toward fabrication of advanced electrical energy storage and conversion devices. The first nanostructured material consists of vertically aligned carbon nanofibers. This three-dimensional structure is opaque, electrically conducting, and contains active sites along the outside of each fiber that are conducive to chemical reactions. Therefore, they make the perfect 3D conducting nanostructured substrate for advanced energy storage devices. In this work, the details for transforming vertically aligned carbon nanofiber arrays into core-shell structures via atomic layer deposition as well as into a mesoporous manganese oxide coated supercapacitor electrode are given. Another unique type of three-dimensional nanostructured substrate is nanotextured glass, which is transparent but non-conducting. Therefore, it can be converted to a 3D transparent conductor for possible application in photovoltaics if it can be conformally coated with a conducting material. This work details that transformation as well as the addition of plasmonic gold nanoparticles to complete the transition to a 3D plasmonic transparent conductor.

  20. Ghrelin receptor conformational dynamics regulate the transition from a preassembled to an active receptor:Gq complex.

    Science.gov (United States)

    Damian, Marjorie; Mary, Sophie; Maingot, Mathieu; M'Kadmi, Céline; Gagne, Didier; Leyris, Jean-Philippe; Denoyelle, Séverine; Gaibelet, Gérald; Gavara, Laurent; Garcia de Souza Costa, Mauricio; Perahia, David; Trinquet, Eric; Mouillac, Bernard; Galandrin, Ségolène; Galès, Céline; Fehrentz, Jean-Alain; Floquet, Nicolas; Martinez, Jean; Marie, Jacky; Banères, Jean-Louis

    2015-02-03

    How G protein-coupled receptor conformational dynamics control G protein coupling to trigger signaling is a key but still open question. We addressed this question with a model system composed of the purified ghrelin receptor assembled into lipid discs. Combining receptor labeling through genetic incorporation of unnatural amino acids, lanthanide resonance energy transfer, and normal mode analyses, we directly demonstrate the occurrence of two distinct receptor:Gq assemblies with different geometries whose relative populations parallel the activation state of the receptor. The first of these assemblies is a preassembled complex with the receptor in its basal conformation. This complex is specific of Gq and is not observed with Gi. The second one is an active assembly in which the receptor in its active conformation triggers G protein activation. The active complex is present even in the absence of agonist, in a direct relationship with the high constitutive activity of the ghrelin receptor. These data provide direct evidence of a mechanism for ghrelin receptor-mediated Gq signaling in which transition of the receptor from an inactive to an active conformation is accompanied by a rearrangement of a preassembled receptor:G protein complex, ultimately leading to G protein activation and signaling.

  1. Simple empirical order parameter for a first-order quantum phase transition in atomic nuclei.

    Science.gov (United States)

    Bonatsos, Dennis; McCutchan, E A; Casten, R F; Casperson, R J

    2008-04-11

    A simple, empirical, easy-to-measure effective order parameter of a first-order phase transition in atomic nuclei is presented, namely, the ratio of the energies of the first excited 6+ and 0+ states, distinguishing between first- and second-order transitions, and taking on a special value in the critical region, as data in Nd-Dy show. In the large NB limit of the interacting boson approximation model, a repeating degeneracy between alternate yrast and successive 0+ states is found in the critical region around the line of a first-order phase transition, pointing to a possible underlying symmetry.

  2. 1 and 2 transitions in the ground-state configuration of atomic manganese

    Indian Academy of Sciences (India)

    S Kabakçi; B Karaçoban Usta; L Özdemir

    2015-10-01

    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 transition probabilities between the fine-structure levels in the ground-state configuration of 3d5 4s2 for atomic manganese (Mn I, Z =25). A discussion of these calculations for manganese using MCHF+BP and HFR methods is given here.

  3. A superradiant laser based on two-photon Raman transition of caesium atoms

    CERN Document Server

    Liu, Pengfei

    2013-01-01

    We propose a superradiant laser based on two-photon Raman transition of caesium-133 atoms which collectively emit photons on an ultra narrow transition into the mode of a low Q resonator known as optical bad-cavity regime. The spin-spin correlation which characterizes the collective effect is demonstrated. We theoretically predict that the optical radiation has an extremely narrow linewidth in the 98 (1) *10-2 mHz range, smaller than the transition itself due to collective effects, and a power level of 7 (1)*10-10 W is possible, which can provide a possible new way to realize an optical clock with a millihertz linewidth.

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

    CERN Document Server

    Schunk, Gerhard; Strekalov, Dmitry V; Förtsch, Michael; Sedlmeir, Florian; Schwefel, Harald G L; Göbelt, Manuela; Christiansen, Silke; Leuchs, Gerd; Marquardt, Christoph

    2015-01-01

    Photon-atom coupling, in particular for proposed quantum repeater schemes, requires pure and versatile sources of quantum light. Here we demonstrate coupling to alkali dipole transitions in the near-infrared with a tunable source of photon pairs generated via spontaneous parametric down-conversion in a whispering-gallery mode resonator (WGMR). We have developed novel wavelength tuning mechanisms, which allow for a coarse step-wise central wavelength tuning from 790 nm to 1630 nm as well as continuous tuning with MHz resolution. We demonstrate the compatibility of our source with atomic transitions, such as the D1 line of rubidium at 795 nm (idler at 1608 nm) and cesium at 895\\,nm (idler at 1312 nm). At the cesium D1 transition, we exemplarily show a continuous scanning of the signal wavelength over the Doppler-broadened absorption line, and finally a heralded single photon spectroscopy of the atomic decay. Providing this flexibility in connecting various atomic transitions with telecom wavelengths, we demonst...

  5. Atomic loss and gain as a resource for nonequilibrium phase transitions in optical lattices

    Science.gov (United States)

    Everest, B.; Marcuzzi, M.; Lesanovsky, I.

    2016-02-01

    Recent breakthroughs in the experimental manipulation of strongly interacting atomic Rydberg gases in lattice potentials have opened an avenue for the study of many-body phenomena. Considerable efforts are currently being undertaken to achieve clean experimental settings that show a minimal amount of noise and disorder and are close to zero temperature. A complementary direction investigates the interplay between coherent and dissipative processes. Recent experiments have revealed a glimpse into the emergence of a rich nonequilibrium behavior stemming from the competition of laser excitation, strong interactions, and radiative decay of Rydberg atoms. The aim of the present theoretical work is to show that local incoherent loss and gain of atoms can in fact be the source of interesting out-of-equilibrium dynamics. This perspective opens up paths for the exploration of nonequilibrium critical phenomena and, more generally, phase transitions, some of which so far have been rather difficult to study. To demonstrate the richness of the encountered dynamical behavior we consider here three examples. The first two feature local atom loss and gain together with an incoherent excitation of Rydberg states. In this setting either a continuous or a discontinuous phase transition emerges with the former being reminiscent of genuine nonequilibrium transitions of stochastic processes with multiple absorbing states. The third example considers the regime of coherent laser excitation. Here the many-body dynamics is dominated by an equilibrium transition of the "model A" universality class.

  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. Intrinsic disorder of the bacterial cell division protein ZipA: coil-to-brush conformational transition.

    Science.gov (United States)

    López-Montero, Iván; López-Navajas, Pilar; Mingorance, Jesús; Rivas, Germán; Vélez, Marisela; Vicente, Miguel; Monroy, Francisco

    2013-08-01

    The full-length ZipA protein from Escherichia coli, one of the essential elements of the cell division machinery, was studied in a surface model built as adsorbed monolayers. The interplay between lateral packing and molecular conformation was probed using a combined methodology based on the scaling analysis of the surface pressure isotherms and ellipsometry measurements of the monolayer thickness. The observed behavior is compatible with the one expected for an intrinsically disordered and highly flexible protein that is preferentially structured in a random coil conformation. At low grafting densities, ZipA coils organize in a mushroom-like regime, whereas a coil-to-brush transition occurs on increasing lateral packing. The structural results suggest a functional scenario in which ZipA acts as a flexible tether anchoring bacterial proto-ring elements to the membrane during the earlier stages of division.

  8. Quinacrine and 9-amino acridine inhibit B-Z and B-H(l) form DNA conformational transitions.

    Science.gov (United States)

    Das, Suman; Kundu, Suprabhat; Suresh Kumar, Gopinatha

    2011-07-01

    The interaction of quinacrine and 9-amino acridine with right-handed B-form, left-handed Z-form, and left-handed protonated (H(L))-form structures of polydG-me(5)dC was investigated by circular dichroism and absorption spectral analysis. Both the compounds bind strongly to the B-form structure and convert the Z-form and H(L)-form back to the bound right-handed form. Circular dichroic data revealed that the conformation at the binding site is right-handed even though adjacent regions of the polynucleotide may have left-handed conformation. The rate and extent of B-form-to-Z-form transition were decreased in the presence of these compounds. Scatchard analysis revealed that both quinacrine and 9-amino acridine bind strongly to the polynucleotide in the B-form in a noncooperative manner, in sharp contrast to the highly cooperative binding to the Z-form and H(L)-form. Results indicated that the cooperative binding of these drugs with the Z-form and the H(L)-forms was associated with a sequential conversion of the polynucleotide from a left-handed to a bound right-handed conformation. Experimental data enabled the calculation of the number of base pairs of Z-form (7-8 with quinacrine and 9-amino acridine) and H(L)-form (4 and 25, respectively, with quinacrine and 9-amino acridine) that adopt a right-handed conformation for each bound ligand. As these compounds are known to bind preferentially to alternating guanine--cytosine sequences, which are capable of easily undergoing the B-to-Z or B-to-H(L) transition, these effects may be important in understanding their biological activities.

  9. 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.

  10. Direct visualization of flow-induced conformational transitions of single actin filaments in entangled solutions

    CERN Document Server

    Kirchenbuechler, Inka; Kurniawan, Nicholas A; Koenderink, Gijsje H; Lettinga, M Paul

    2015-01-01

    While semi-flexible polymers and fibers are an important class of material due to their rich mechanical properties, it remains unclear how these properties relate to the microscopic conformation of the polymers. Actin filaments constitute an ideal model polymer system due to their micron-sized length and relatively high stiffness that allow imaging at the single filament level. Here we study the effect of entanglements on the conformational dynamics of actin filaments in shear flow. We directly measure the full three-dimensional conformation of single actin filaments, using confocal microscopy in combination with a counter-rotating cone-plate shear cell. We show that initially entangled filaments form disentangled orientationally ordered hairpins, confined in the flow-vorticity plane. In addition, shear flow causes stretching and shear alignment of the hairpin tails, while the filament length distribution remains unchanged. These observations explain the strain-softening and shear-thinning behavior of entangl...

  11. 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.

  12. Temperature limits in laser cooling of free atoms with three-level cascade transitions

    CERN Document Server

    Cruz, Flavio C; Magno, Wictor C

    2013-01-01

    We employ semiclassical theoretical analysis to study laser cooling of free atoms using three-level cascade transitions, where the upper transition is much weaker than the lower one. This represents an alternate cooling scheme, particularly useful for group II atoms. We find that temperatures below the Doppler limits associated with each of these transitions are expected. The lowest temperatures arise from a remarkable increase in damping and reduced diffusion compared to two-level cooling. They are reached at the two-photon resonance, where there is a crossing between the narrow and the partially-dark dressed states, and can be estimated simply by the usual Doppler limit considering the decay rate of the optical coherence between these states.

  13. Giant perpendicular magnetic anisotropy of an individual atom on two-dimensional transition metal dichalcogenides

    Science.gov (United States)

    Odkhuu, Dorj

    2016-08-01

    Exploring magnetism and magnetic anisotropy in otherwise nonmagnetic two-dimensional materials, such as graphene and transition metal dichalcogenides, is at the heart of spintronics research. Herein, using first-principles calculations we explore the possibility of reaching an atomic-scale perpendicular magnetic anisotropy by carefully exploring the large spin-orbit coupling, orbital magnetism, and ligand field in a suitable choice of a two-dimensional structure with transition metal adatoms. More specifically, we demonstrate perpendicular magnetic anisotropy energies up to an order of 100 meV per atom in individual ruthenium and osmium adatoms at a monosulfur vacancy in molybdenum disulfide. We further propose a phenomenological model where a spin state transition that involves hybridization between molybdenum a1 and adatomic e' orbitals is a possible mechanism for magnetization reversal from an in-plane to perpendicular orientation.

  14. New chemistry for the growth of first-row transition metal films by atomic layer deposition

    Science.gov (United States)

    Klesko, Joseph Peter

    Thin films containing first-row transition metals are widely used in microelectronic, photovoltaic, catalytic, and surface-coating applications. In particular, metallic films are essential for interconnects and seed, barrier, and capping layers in integrated circuitry. Traditional vapor deposition methods for film growth include PVD, CVD, or the use of plasma. However, these techniques lack the requisite precision for film growth at the nanoscale, and thus, are increasingly inadequate for many current and future applications. By contrast, ALD is the favored approach for depositing films with absolute surface conformality and thickness control on 3D architectures and in high aspect ratio features. However, the low-temperature chemical reduction of most first-row transition metal cations to their zero-valent state is very challenging due to their negative electrochemical potentials. A lack of strongly-reducing coreagents has rendered the thermal ALD of metallic films an intractable problem for many elements. Additionally, several established ALD processes for metal films are plagued by low growth rates, impurity incorporation, poor nucleation, high surface roughness, or the need for hazardous coreagents. Finally, stoichiometric control of ternary films grown by ALD is rare, but increasingly important, with emerging applications for metal borate films in catalysis and lithium ion batteries. The research herein is focused toward the development of new ALD processes for the broader application of metal, metal oxide, and metal borate thin films to future nanoscale technologies. These processes display self-limited growth and support the facile nucleation of smooth, continuous, high-purity films. Bis(trimethylsilyl) six-membered rings are employed as strongly-reducing organic coreagents for the ALD of titanium and antimony metal films. Additionally, new processes are developed for the growth of high-purity, low-resistivity cobalt and nickel metal films by exploiting the

  15. Accounting for conformational flexibility and torsional anharmonicity in the H + CH{sub 3}CH{sub 2}OH hydrogen abstraction reactions: A multi-path variational transition state theory study

    Energy Technology Data Exchange (ETDEWEB)

    Meana-Pañeda, Rubén; Fernández-Ramos, Antonio, E-mail: qf.ramos@usc.es [Department of Physical Chemistry and Center for Research in Biological Chemistry and Molecular Materials, University of Santiago de Compostela, 15706 Santiago de Compostela (Spain)

    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.

  16. 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.

  17. 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.

  18. Observation of parity-time symmetry breaking transitions in a dissipative Floquet system of ultracold atoms

    CERN Document Server

    Li, Jiaming; Liu, Ji; de Melo, Leonardo; Joglekar, Yogesh N; Luo, Le

    2016-01-01

    Open physical systems with balanced loss and gain exhibit a transition, absent in their solitary counterparts, which engenders modes that exponentially decay or grow with time and thus spontaneously breaks the parity-time PT symmetry. This PT-symmetry breaking is induced by modulating the strength or the temporal profile of the loss and gain, but also occurs in a pure dissipative system without gain. It has been observed that, in classical systems with mechanical, electrical, and electromagnetic setups with static loss and gain, the PT-symmetry breaking transition leads to extraordinary behavior and functionalities. However, its observation in a quantum system is yet to be realized. Here we report on the first quantum simulation of PT-symmetry breaking transitions using ultracold Li-6 atoms. We simulate static and Floquet dissipative Hamiltonians by generating state-dependent atom loss in a noninteracting Fermi gas, and observe the PT-symmetry breaking transitions by tracking the atom number for each state. W...

  19. 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.

  20. Observation of four-wave mixing in caesium atoms using a noncycling transition

    Institute of Scientific and Technical Information of China (English)

    Wang Li-Rong; Ma Jie; Zhao Jian-Ming; Xiao Lian-Tuan; Jia Suo-Tang

    2006-01-01

    In this paper the generation of four-wave mixing (FWM) signal using a noncycling transition of caesium atoms is investigated when the pumping laser is locked to the transition 6S1/2F = 4 → 6P3/2F' = 4, and meanwhile the probe frequency is scanned across the 6S1/2F = 4 → 6P3/2 transition. The efficiency of the four-wave mixing signal as a function of the intensity of the pumping beams and the detuning of the pumping beams is also studied. In order to increase the detection efficiency, a repumping laser which is resonant with 6S1/2F = 3 → 6P3/2F' = 4 transition is used. A theoretical model is also introduced, and the theoretical results are in qualitative agreement with experimental ones.

  1. The substrate-driven transition to an inward-facing conformation in the functional mechanism of the dopamine transporter.

    Directory of Open Access Journals (Sweden)

    Jufang Shan

    Full Text Available BACKGROUND: The dopamine transporter (DAT, a member of the neurotransmitter:Na(+ symporter (NSS family, terminates dopaminergic neurotransmission and is a major molecular target for psychostimulants such as cocaine and amphetamine, and for the treatment of attention deficit disorder and depression. The crystal structures of the prokaryotic NSS homolog of DAT, the leucine transporter LeuT, have provided critical structural insights about the occluded and outward-facing conformations visited during the substrate transport, but only limited clues regarding mechanism. To understand the transport mechanism in DAT we have used a homology model based on the LeuT structure in a computational protocol validated previously for LeuT, in which steered molecular dynamics (SMD simulations guide the substrate along a pathway leading from the extracellular end to the intracellular (cytoplasmic end. METHODOLOGY/PRINCIPAL FINDINGS: Key findings are (1 a second substrate binding site in the extracellular vestibule, and (2 models of the conformational states identified as occluded, doubly occupied, and inward-facing. The transition between these states involve a spatially ordered sequence of interactions between the two substrate-binding sites, followed by rearrangements in structural elements located between the primary binding site and the cytoplasmic end. These rearrangements are facilitated by identified conserved hinge regions and a reorganization of interaction networks that had been identified as gates. CONCLUSIONS/SIGNIFICANCE: Computational simulations supported by information available from experiments in DAT and other NSS transporters have produced a detailed mechanistic proposal for the dynamic changes associated with substrate transport in DAT. This allosteric mechanism is triggered by the binding of substrate in the S2 site in the presence of the substrate in the S1 site. Specific structural elements involved in this mechanism, and their roles in the

  2. Photoionization Broadening of the 1S-2S Transition in a Beam of Atomic Hydrogen

    CERN Document Server

    Kolachevsky, N; Fischer, M; Haas, M; Herrmann, M; Holzwarth, R; Hänsch, T W; Jentschura, U D; Keitel, C H; Udem, T; Udem, Th.

    2006-01-01

    We consider the excitation dynamics of the two-photon \\sts transition in a beam of atomic hydrogen by 243 nm laser radiation. Specifically, we study the impact of ionization damping on the transition line shape, caused by the possibility of ionization of the $2S$ level by the same laser field. Using a Monte-Carlo simulation, we calculate the line shape of the \\sts transition for the experimental geometry used in the two latest absolute frequency measurements (M. Niering {\\it et al.}, PRL 84, 5496 (2000) and M. Fischer {\\it et al.}, PRL 92, 230802 (2004)). The calculated line shift and line width are in excellent agreement with the experimentally observed values. From this comparison we can verify the values of the dynamic Stark shift coefficient for the \\sts transition for the first time on a level of 15%. We show that the ionization modifies the velocity distribution of the metastable atoms, the line shape of the \\sts transition, and has an influence on the derivation of its absolute frequency.

  3. Narrow-line diode laser system for laser cooling of strontium atoms on the intercombination transition

    Science.gov (United States)

    Li, Y.; Ido, T.; Eichler, T.; Katori, H.

    We report a diode laser system developed for narrow-line cooling and trapping on the 1S0-3P1 intercombination transition of neutral strontium atoms. Doppler cooling on this spin-forbidden transition with a line width of Γ/2π=7.1 kHz enables us to achieve sub-μK temperatures in a two-step cooling process. The required reduction of the laser line width to the kHz level was achieved by locking the laser to a tunable Fabry-Pérot cavity. The long-term drift (>0.1 s) of the reference cavity was compensated by employing the saturated absorption signal obtained from Sr vapor in a heat pipe of novel design. We demonstrate the potential of the system by performing spectroscopy of Sr atoms confined to the Lamb-Dicke regime in a one-dimensional optical lattice.

  4. Temporal Characteristic of M-M Transition Lasers in Strontium Atom Vapour

    Institute of Scientific and Technical Information of China (English)

    CHEN Gang; CHENG Cheng

    2008-01-01

    The kinetic process of Sr atom metastable-metastable transition lasers in He-Sr longitudinal pulsed discharge is analysed and a concise self-consistent physical model is developed. The temporal evolutions of discharge parameters, main particle densities, the electron temperature, and the lasing pulses are numerically calculated.The results provided by the model agree well with the experiment, and the temporal behaviour of each laser pulse is explained successfully by the simulation results.

  5. Atoms and Nanoparticles of Transition Metals as Catalysts for Hydrogen Desorption from Magnesium Hydride

    Directory of Open Access Journals (Sweden)

    N. Bazzanella

    2011-01-01

    Full Text Available The hydrogen desorption kinetics of composite materials made of magnesium hydride with transition metal additives (TM: Nb, Fe, and Zr was studied by several experimental techniques showing that (i a few TM at.% concentrations catalyse the H2 desorption process, (ii the H2 desorption kinetics results stabilized after a few H2 sorption cycles when TM atoms aggregate by forming nanoclusters; (iii the catalytic process occurs also at TM concentration as low as 0.06 at.% when TM atoms clustering is negligible, and (iv mixed Fe and Zr additives produce faster H2 desorption kinetics than single additive. The improved H2 desorption kinetics of the composite materials can be explained by assuming that the interfaces between the MgH2 matrix and the TM nanoclusters act as heterogeneous sites for the nucleation of the Mg phase in the MgH2 matrix and promote the formation of fast diffusion channels for H migrating atoms.

  6. 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.

  7. Atom-photon entanglement in the system with competing k-photon and l-photon transitions

    Institute of Scientific and Technical Information of China (English)

    Wu Qin; Fang Mao-Fa; Hu Yao-Hua

    2007-01-01

    We have investigated the evolution of the atomic quantum entropy and the entanglement of atom-photon in the system with competing k-photon and l-photon transitions by means of fully quantum theory, and examined the effects of competing photon numbers (k and l), the relative coupling strength between the atom and the two-mode field(λ/g),and the initial photon number of the field on the atomic quantum entropy and the entanglement of atom-photon.The results show that the multiphoton competing transitions or the large relative coupling strength can lead to the strong entanglement between atoms and photons. The maximal atom-photon entanglement can be prepared via the appropriate selection of system parameters and interaction time.

  8. Inner-shell magnetic dipole transition in Tm atom as a candidate for optical lattice clocks

    CERN Document Server

    Sukachev, D; Tolstikhina, I; Kalganova, E; Vishnyakova, G; Khabarova, K; Tregubov, D; Golovizin, A; Sorokin, V; Kolachevsky, N

    2016-01-01

    We consider a narrow magneto-dipole transition in the $^{169}$Tm atom at the wavelength of $1.14\\,\\mu$m as a candidate for a 2D optical lattice clock. Calculating dynamic polarizabilities of the two clock levels $[\\text{Xe}]4f^{13}6s^2 (J=7/2)$ and $[\\text{Xe}]4f^{13}6s^2 (J=5/2)$ in the spectral range from $250\\,$nm to $1200\\,$nm, we suggest the "magic" wavelength for the optical lattice at $807\\,$nm. Frequency shifts due to black-body radiation (BBR), the van der Waals interaction, the magnetic dipole-dipole interaction and other effects which can perturb the transition frequency are calculated. The transition at $1.14\\,\\mu$m demonstrates low sensitivity to the BBR shift corresponding to $8\\times10^{-17}$ in fractional units at room temperature which makes it an interesting candidate for high-performance optical clocks. The total estimated frequency uncertainty is less than $5 \\times 10^{-18}$ in fractional units. By direct excitation of the $1.14\\,\\mu$m transition in Tm atoms loaded into an optical dipole ...

  9. X-ray energies of circular transitions and electrons screening in kaonic atoms

    CERN Document Server

    Santos, J P; Desclaux, J P; Indelicato, P J; Parente, F; Indelicato, Paul; ccsd-00002661, ccsd

    2004-01-01

    The QED contribution to the energies of the circular (n,l=n-1), 2 ≤ n ≤ 19 transitions have been calculated for several kaonic atoms throughout the periodic table, using the current world average kaon mass. Calculations were done in the framework of the Klein-Gordon equation, with finite nuclear size and all-order Uelhing vacuum polarization corrections, as well as Kallen and Sabry and Wichmann and Kroll corrections. These energy level values are compared with other computed values. The circular transition energies are compared with available measured and theoretical transition energy. Electron screening is evaluated using a Dirac-Fock model for the electronic part of the wave function. The effect of electronic wavefunction correlation is evaluated for the first time.

  10. The H I Probability Distribution Function and the Atomic-to-molecular Transition in Molecular Clouds

    Science.gov (United States)

    Imara, Nia; Burkhart, Blakesley

    2016-10-01

    We characterize the column-density probability distribution functions (PDFs) of the atomic hydrogen gas, H i, associated with seven Galactic molecular clouds (MCs). We use 21 cm observations from the Leiden/Argentine/Bonn Galactic H i Survey to derive column-density maps and PDFs. We find that the peaks of the H i PDFs occur at column densities in the range ˜1-2 × 1021 {{cm}}-2 (equivalently, ˜0.5-1 mag). The PDFs are uniformly narrow, with a mean dispersion of {σ }{{H}{{I}}}≈ {10}20 {{cm}}-2 (˜0.1 mag). We also investigate the H i-to-H2 transition toward the cloud complexes and estimate H i surface densities ranging from 7 to 16 {M}⊙ {{pc}}-2 at the transition. We propose that the H i PDF is a fitting tool for identifying the H i-to-H2 transition column in Galactic MCs.

  11. The HI Probability Distribution Function and the Atomic-to-Molecular Transition in Molecular Clouds

    CERN Document Server

    Imara, Nia

    2016-01-01

    We characterize the column density probability distributions functions (PDFs) of the atomic hydrogen gas, HI, associated with seven Galactic molecular clouds (MCs). We use 21 cm observations from the Leiden/Argentine/Bonn Galactic HI Survey to derive column density maps and PDFs. We find that the peaks of the HI PDFs occur at column densities ranging from ~1-2$\\times 10^{21}$ cm$^2$ (equivalently, ~0.5-1 mag). The PDFs are uniformly narrow, with a mean dispersion of $\\sigma_{HI}\\approx 10^{20}$ cm$^2$ (~0.1 mag). We also investigate the HI-to-H$_2$ transition towards the cloud complexes and estimate HI surface densities ranging from 7-16 $M_\\odot$ pc$^{-2}$ at the transition. We propose that the HI PDF is a fitting tool for identifying the HI-to-H$_2$ transition column in Galactic MCs.

  12. Atomic data from the Iron Project. LIII. Relativistic allowed and forbidden transition probabilities for Fe XVII

    CERN Document Server

    Nahar, S N; Chen, G X; Pradhan, A K; Nahar, Sultana N.; Eissner, Werner; Chen, Guo-Xin; Pradhan, Anil K.

    2003-01-01

    An extensive set of fine structure levels and corresponding transition probabilities for allowed and forbidden transitions in Fe XVII is presented. A total of 490 bound energy levels of Fe XVII of total angular momenta 0 <= J <= 7 of even and odd parities with 2 <= n <= 10, 0 <= l <= 8, 0 <= L <= 8, and singlet and triplet multiplicities, are obtained. They translate to over 2.6 x 10^4 allowed (E1) transitions that are of dipole and intercombination type, and about 3000 forbidden transitions that include electric quadrupole (E2), magnetic dipole (M1), electric octopole (E3), and magnetic quadrupole (M2) type representing the most detailed calculations to date for the ion. Oscillator strengths f, line strengths S, and coefficients A of spontaneous emission for the E1 type transitions are obtained in the relativistic Breit-Pauli R-matrix approximation. A valus for the forbidden transitions are obtained from atomic structure calculations using codes SUPERSTRUCTURE and GRASP. The energy le...

  13. 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.

  14. Conformation of ceramide 6 molecules and chain-flip transitions in the lipid matrix of the outermost layer of mammalian skin, the stratum corneum

    Science.gov (United States)

    Kiselev, M. A.

    2007-05-01

    Neutron diffraction from oriented multilamellar model stratum corneum (SC) membranes provides information on the internal nanostructure and hydration of the lipid bilayer. The main distinguishing feature of model SC membranes based on ceramide 6 is the extremely small intermembrane space (1 Å). The role of the fully extended (FE) conformation of ceramide 6 molecules in the organization of the nanostructure of the lipid matrix is discussed. The FE conformation gives rise to extremely strong intermembrane attractions (armature reinforcement), which tighten the adjacent bilayers to form steric contacts. Chain-flip transitions in the conformation of ceramide molecules account for structural alterations in native and model SC membranes upon their hydration.

  15. The Physics of Miniature Atomic Clocks: 0-0 Versus "End" Transitions

    Science.gov (United States)

    Post, Amber; Jau, Yuan-Yu; Kuzma, Nicholas; Happer, William

    2003-05-01

    The majority of traditional atomic-clock designs are based on the 0-0 hyperfine transition of a Cs 133 atom. We are currently investigating the advantages of operating a miniature optical atomic clock using the "end" transitions, e.g. connecting states |f=1, mf =+/-1> and |f=2, mf=+/-2> in 87Rb. In our paper we present extensive new measurements of relevant relaxation rates, such as those due to spin-exchange collisions, buffer-gas pressure shifts, Carver Rates and others, which ultimately determine the choices of an operating regime for the miniature optical atomic clock. The relationship between these rates is non-trivial: for example, using higher laser power will increase polarization and reduce the spin-exchange rate [1], but it can simultaneously increase the linewidth due to the optical pumping rate. The dependence of these and other relaxation rates on the cell size, temperature, pressure, a choice of buffer gas, and other parameters will be reported. Based on these measured rates, our modeling can be used to predict the transition linewidths, signal-to-noise ratios and thus the stability of the clock in different operating regimes. The trade-off between the stability of the clock and the desired small cell size and low power consumption needs to be carefully considered in order to optimize our design. In our experiments we used optical, microwave, and radio-frequency excitation to study hyperfine and Zeeman resonance lines in heated glass cells containing pure-isotope alkali-metal vapor and buffer gasses (N2, Ar, He, etc.) at low (0 - 10 G) magnetic fields. Simultaneous use of light, microwave and radio-frequency fields allowed us to calibrate surrounding magnetic fields by observing the corresponding shifts of the resonance, thus leading us to a quantitative understanding of our system. [1] S. Appelt, A. B. Baranga, A. R. Young, W. Happer, Phys. Rev. A 59, 2078 (1999).

  16. Molecular dynamics simulation of phosphorylation-induced conformational transitions in the mycobacterium tuberculosis response regulator PrrA

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Guo [Los Alamos National Laboratory; Mcmahon, Benjamin H [Los Alamos National Laboratory; Tung, Chang - Shung [Los Alamos National Laboratory

    2008-01-01

    Phosphorylation-activated modulation of response regulators (RR) is predominantly used by bacteria as a strategy in regulating their two-component signaling (TCS) systems, the underlying molecular mechanisms are however far from fully understood. In this work we have conducted a molecular dynamics (MD) simulation of the phosphorylation-induced conformational transitions of RRs with the Mycobacterium Tuberculosis PrrA as a particular example. Starting from the full-length inactive structure of PrrA we introduced a local disturbance by phosphorylating the conserved aspartic acid residue, Asp-58, in the regulatory domain. A Go-model-type algorithm packaged with AMBER force fields was then applied to simulate the dynamics upon phosphorylation. The MD simulation shows that the phosphorylation of Asp-58 facilitates PrrA, whose inactive state has a compact conformation with a closed interdomain interface, to open up with its interdomain separation being increased by an average of about 1.5 {angstrom} for a simulation of 20 ns. The trans-activation loop, which is completely buried within the interdomain interface in the inactive PrrA, is found to become more exposed with the phosphorylated structure as well. These results provide more structural details of how the phosphorylation of a local aspartate activates PrrA to undergo a global conformational rearrangement toward its extended active state. This work also indicates that MD simulations can serve as a fast tool to unravel the regulation mechanisms of all RRs, which is especially valuable when the structures of full-length active RRs are currently unavailable.

  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. Coherent Solid-State Phase Transitions with Atomic Diffusion: A Thermomechanical Treatment

    Science.gov (United States)

    Fried, Eliot; Gurtin, Morton E.

    1999-06-01

    Using the framework of modern continuum thermomechanics, we develop sharp- and diffuse-interface theories for coherent solid-state phase transitions. These theories account for atomic diffusion and for deformation. Of essential importance in our formulation of the sharp-interface theory are a system of "configurational forces" and an associated "configurational force balance." These forces, which are distinct from standard Newtonian forces, describe the intrinsic material structure of a body. The configurational balance, when restricted to the interface, leads to a generalization of the classical Gibbs-Thomson relation, a generalization that accounts for the orientation dependence of the interfacial energy density and also for a broad spectrum of dissipative transition kinetics. Our diffuse-interface theory involves nonstandard "microforces" and an associated "microforce balance." These forces arise naturally from an interpretation of the atomic densities as macroscopic parameters that describe atomistic kinematics distinct from the motion of material particles. When supplemented by thermodynamically consistent constitutive relations, the microforce balance yields a generalization of the Cahn-Hilliard relation giving the chemical potentials as variational derivatives of the total free energy with respect to the atomic densities. A formal asymptotic analysis (thickness of the transition layer approaching zero) demonstrates the correspondence between versions of our theories specialized to the case of a single mobile species for situations in which the time scale for interface propagation is small compared to that for bulk diffusion. While the configurational force balance is redundant in the diffuse-interface theory, when integrated over the transition layer, the limit of this balance is the interfacial configurational force balance (i.e., generalized Gibbs-Thomson relation) of the sharp-interface theory.

  19. Large-Scale Conformational Transitions and Dimerization Are Encoded in the Amino-Acid Sequences of Hsp70 Chaperones

    Science.gov (United States)

    Malinverni, Duccio; Marsili, Simone; Barducci, Alessandro; De Los Rios, Paolo

    2015-01-01

    Hsp70s are a class of ubiquitous and highly conserved molecular chaperones playing a central role in the regulation of proteostasis in the cell. Hsp70s assist a myriad of cellular processes by binding unfolded or misfolded substrates during a complex biochemical cycle involving large-scale structural rearrangements. Here we show that an analysis of coevolution at the residue level fully captures the characteristic large-scale conformational transitions of this protein family, and predicts an evolutionary conserved–and thus functional–homo-dimeric arrangement. Furthermore, we highlight that the features encoding the Hsp70 dimer are more conserved in bacterial than in eukaryotic sequences, suggesting that the known Hsp70/Hsp110 hetero-dimer is a eukaryotic specialization built on a pre-existing template. PMID:26046683

  20. Time-of-flight measurements in atomic beam devices using adiabatic high frequency transitions and sextupole magnets

    CERN Document Server

    Baumgarten, C; Brunn, I; Court, G; Ciullo, G; Ferretti, P; Golendukhin, A; Graw, G; Haeberli, W; Henoch, M; Hertenberger, R; Koch, N; Kolster, H; Lenisa, P; Nass, A; Podyachev, S P; Reggiani, D; Rith, K; Simani, M C; Steffens, E; Stewart, J; Wise, T

    2002-01-01

    Atomic beam devices are frequently equipped with sextupole magnets to focus the beam or to act as spin filters in combination with RF-transitions for manipulating the hyperfine population within the atomic beam. A useful tool for the analysis of sextupole systems, the application of time-of-flight (TOF) measurements is presented. TOF measurements are enabled without mechanical beam chopper by utilizing adiabatic radio frequency transitions to select atoms within a certain time interval. This method is especially interesting for the use in atomic beam devices that are already equipped with RF-transitions and sextupole magnets and where space limitations or the required quality of the vacuum do not allow the installation of a mechanical chopper. The measurements presented here were performed with the atomic beam polarimeter of the HERMES polarized deuterium target and the results have been used to optimize the sextupole system of the polarimeter.

  1. 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 ...

  2. 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...

  3. Ultrafast valley dynamics in atomically thin transition metal dichalcogenides (Conference Presentation)

    Science.gov (United States)

    Bratschitsch, Rudolf

    2016-10-01

    Monolayer transition metal dichalcogenides such as MoS2, WS2, MoSe2, WSe2, and MoTe2 received a lot of attention recently due to their atomic thickness in combination with an optical band gap in the visible or infrared. These properties render them a promising material class for new opto-electronic devices. Strong spin-orbit coupling together with the absence of inversion symmetry leads to an emission of polarized photoluminescence after excitation with circularly polarized light. Therefore, the K and K' valley of the semiconductor can be selectively addressed by left and right handed circularly polarized light, which is interesting for valleytronic applications. To understand the mechanisms governing the creation and destruction of valley polarization, time-resolved experiments are necessary. While stationary photoluminescence experiments show nearly perfect valley polarization, indicating very slow intervalley scattering processes, first valley-selective pump-probe experiments yielded a strong signal immediately after optical excitation in both the pumped and unpumped valley, suggesting a small valley polarization. To understand this behavior, we performed a joint experiment-theory study on the time-resolved valley dynamics in atomically thin WS2. We find strong intervalley Coulomb coupling governing the dynamics in the atomically thin semiconductor. Our results are also applicable to the other transition metal dichalcogenides MoS2, MoSe2, and WSe2, where strong intervalley Coulomb coupling is expected.

  4. 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.

  5. Atoms

    Institute of Scientific and Technical Information of China (English)

    刘洪毓

    2007-01-01

    Atoms(原子)are all around us.They are something like the bricks (砖块)of which everything is made. The size of an atom is very,very small.In just one grain of salt are held millions of atoms. Atoms are very important.The way one object acts depends on what

  6. Phase transitions due to interaction between photons and atoms in a cavity system

    CERN Document Server

    Shirai, Tatsuhiko; Miyashita, Seiji

    2012-01-01

    We survey phenomena of a cavity system in which many atoms coherently interact with a single quantized photon mode driven by the AC external field in a dissipative environment. It has been known that a strongly external field causes the so-called optical bistability which is a non-equilibrium phase transition for the balance of excitation and dissipation. On the other hand, a strong interaction causes the Dicke transition, which is a phase transition with a spontaneous appearance of excitations of atoms and photons in the equilibrium system as a consequence of the cooperative phenomena. We study the phenomena in full range of the strength of the interaction and the external field, and present a phase diagram of the stationary state. For the strong interaction region, in order to realize the ground state, appropriate form of the dissipative mechanism in the master equation is necessary instead of the conventional Lindblad form. We provide such an extended master equation. Moreover, the rotating wave approximat...

  7. Immobilization of the distal hinge in the labile serpin plasminogen activator inhibitor 1: identification of a transition state with distinct conformational and functional properties.

    Science.gov (United States)

    De Taeye, Bart; Compernolle, Griet; Dewilde, Maarten; Biesemans, Wouter; Declerck, Paul J

    2003-06-27

    The serpin plasminogen activator inhibitor-1 (PAI-1) plays an important role in the regulation of the fibrinolytic activity in blood. In plasma, PAI-1 circulates mainly in the active conformation. However, PAI-1 spontaneously converts to a latent conformation. This conversion comprises drastic conformational changes in both the distal and the proximal hinge region of the reactive center loop. To study the functional and conformational rearrangements associated solely with the mobility of the proximal hinge, disulfide bonds were introduced to immobilize the distal hinge region. These mutants exhibited specific activities comparable with that of PAI-1-wt. However, the engineered disulfide bond had a major effect on the conformational and associated functional transitions. Strikingly, in contrast to PAI-1-wt, inactivation of these mutants yielded a virtually complete conversion to a substrate-like conformation. Comparison of the digestion pattern (with trypsin and elastase) of the mutants and PAI-1-wt revealed that the inactivated mutants have a conformation differing from that of latent and active PAI-1-wt. Unique trypsin-susceptible cleavage sites arose upon inactivation of these mutants. The localization of these exposed residues provides evidence that a displacement of alphahF has occurred, indicating that the proximal hinge is partly inserted between s3A and s5A. In conclusion, immobilization of the distal hinge region in PAI-1 allowed the identification of an "intermediate" conformation characterized by a partial insertion of the proximal hinge region. We hypothesize that locking PAI-1 in this transition state between active and latent conformations is associated with a displacement of alphahF, subsequently resulting in substrate behavior.

  8. Calculation of Multiphoton Transition in Li Atoms via Chirped Microwave Pulse

    Institute of Scientific and Technical Information of China (English)

    JIA Guang-Rui; ZHANG Xian-Zhou; LIU Yu-Fang; YU Kun; ZHAO Yue-Jin

    2011-01-01

    The position and width of avoided crossings of Li atom energy levels in a static electric field is presented by using the B-spline basis set method combined with the model potential.Using the time-dependent multilevel approach,the population of Li atoms is transferred to the target state completely by one-photon,two-photon or a single multiphoton adiabatic rapid passage,which requires only a small frequency sweep.The calculation results agree well with the experiment and novel explanations are given to understand the experimental results.It is well known that adiabatic rapid passage (ARP) works perfectly in the population transfer of an atomic system.[1-3] Coherent population transfer via ARP in atoms through one-photon[2] or twophoton[4] transitions using chirped pulses has been demonstrated.If the frequency of an external field is swept through the resonance at a rate lower than the square of the Rabi frequency,the population can be transferred through many levels by sequential ARPs with approximately 100% efficiency.%The position and width of avoided crossings of Li atom energy levels in a static electric field is presented by using the B-spline basis set method combined with the model potential Using the time-dependent multilevel approach, the population of Li atoms is transferred to the target state completely by one-photon, two-photon or a single multiphoton adiabatic rapid passage, which requires only a small frequency sweep. The calculation results agree well with the experiment and novel explanations are given to understand the experimental results.

  9. 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...

  10. 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.

  11. The influence of sodium perfluorooctanoate on the conformational transitions of human immunoglobulin.

    Science.gov (United States)

    Messina, Paula V; Prieto, Gerardo; Salgado, Francisco; Varela, Carla; Nogueira, Montserrat; Dodero, Verónica; Ruso, Juan M; Sarmiento, Félix

    2007-07-19

    In the field of bioscience, the study of the interactions between blood proteins and fluorinated materials is very important from both theoretical and applied points of view. Fluorinated materials have potential use in drug delivery, as blood substitutes, and in biotechnology. Using a combination of ultraviolet-visible (UV-vis) and ultraviolet-circular dichroism (UV-CD) spectroscopies and ion-selective electrodes, the complete interaction of sodium perfluorooctanoate (SPFO) and the most important immunoglobulin (on a quantitative basis) in human serum, immunoglobulin G (IgG), has been evaluated. The study has been focused on bulk solution. By the application of an SPFO selective electrode, it was determined that there were true specific unions between surfactant molecules and IgG structure. The experimental data were presented as Koltz and Scatchard plots and analyzed on the basis of an empirical Hill equation. The conformational changes at the bulk solution were well characterized by UV-vis and UV-CD spectroscopies. As a consequence of these changes, the protein structure was affected.

  12. An exacting transition probability measurement - a direct test of atomic many-body theories

    CERN Document Server

    Dutta, T; Yum, D; Rebhi, R; Mukherjee, M

    2016-01-01

    A new protocol for measuring the branching fraction of hydrogenic atoms with only statistically limited uncertainty is proposed and demonstrated for the decay of the P$_{3/2}$ level of the barium ion, with precision below $0.5\\%$. Heavy hydrogenic atoms like the barium ion are test beds for fundamental physics such as atomic parity violation and they also hold the key to understanding nucleo-synthesis in stars. To draw definitive conclusion about possible physics beyond the standard model by measuring atomic parity violation in the barium ion it is necessary to measure the dipole transition probabilities of low-lying excited states with precision better than $1\\%$. Furthermore, enhancing our understanding of the $\\it{barium-puzzle}$ in barium stars requires branching fraction data for proper modelling of nucleo-synthesis. Our measurements are the first to provide a direct test of quantum many-body calculations on the barium ion with precision below one percent and more importantly with no known systematic unc...

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

    Energy Technology Data Exchange (ETDEWEB)

    Apetrei, Alin Marian, E-mail: alin.apetrei@uaic.r [Department of Physics, Alexandru Ioan Cuza University of Iasi, 11 Blvd. Carol I, Iasi 700506 (Romania); Enachescu, Cristian; Tanasa, Radu; Stoleriu, Laurentiu; Stancu, Alexandru [Department of Physics, Alexandru Ioan Cuza University of Iasi, 11 Blvd. Carol I, Iasi 700506 (Romania)

    2010-09-01

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

  14. Conformation of Organic Chain in Phase Transition of Hybrid(Cl2H25NH3)2MnCl4

    Institute of Scientific and Technical Information of China (English)

    GUO Liling; SUN Yubing; MEI Ao; DAI Yadong; LIU Hanxing

    2008-01-01

    The structural change in phase transition of hybrid(C12H25NH3)2MnCl4 was investigated.The temperature and the structures of the phase transition is investigated by thermal gravimetry(TG)and differential scanning calorimetry(DSC),infrared spectrum(IR)and X-ray diffraction(XRD).The results suggest that the phase transition is reversible and the structural change arises from the conformation change of the organic chain.The interlayer distance increases when the hybrid transforms from low temperature phase to high temperature phase.This is explained by the diffusion of gauche-bond along the organic chains and they move away from each other when the phase transition occurs.Combining the experimental data with theoretical calculation,we propose that organic chain of the hybrid in high temperature phase is the conformation of gauche-bond alternating with trans bond(noted as GTG'TGTG'TGTG'T).

  15. Optically excited structural transition in atomic wires on surfaces at the quantum limit.

    Science.gov (United States)

    Frigge, T; Hafke, B; Witte, T; Krenzer, B; Streubühr, C; Samad Syed, A; Mikšić Trontl, V; Avigo, I; Zhou, P; Ligges, M; von der Linde, D; Bovensiepen, U; Horn-von Hoegen, M; Wippermann, S; Lücke, A; Sanna, S; Gerstmann, U; Schmidt, W G

    2017-03-29

    Transient control over the atomic potential-energy landscapes of solids could lead to new states of matter and to quantum control of nuclear motion on the timescale of lattice vibrations. Recently developed ultrafast time-resolved diffraction techniques combine ultrafast temporal manipulation with atomic-scale spatial resolution and femtosecond temporal resolution. These advances have enabled investigations of photo-induced structural changes in bulk solids that often occur on timescales as short as a few hundred femtoseconds. In contrast, experiments at surfaces and on single atomic layers such as graphene report timescales of structural changes that are orders of magnitude longer. This raises the question of whether the structural response of low-dimensional materials to femtosecond laser excitation is, in general, limited. Here we show that a photo-induced transition from the low- to high-symmetry state of a charge density wave in atomic indium (In) wires supported by a silicon (Si) surface takes place within 350 femtoseconds. The optical excitation breaks and creates In-In bonds, leading to the non-thermal excitation of soft phonon modes, and drives the structural transition in the limit of critically damped nuclear motion through coupling of these soft phonon modes to a manifold of surface and interface phonons that arise from the symmetry breaking at the silicon surface. This finding demonstrates that carefully tuned electronic excitations can create non-equilibrium potential energy surfaces that drive structural dynamics at interfaces in the quantum limit (that is, in a regime in which the nuclear motion is directed and deterministic). This technique could potentially be used to tune the dynamic response of a solid to optical excitation, and has widespread potential application, for example in ultrafast detectors.

  16. X-alpha calculation of transition energies in multiply ionized atoms

    Science.gov (United States)

    Ringers, D. A.; Chen, M. H.

    1974-01-01

    It is shown that the accuracy of calculations can be improved if appropriate (different) values of alpha are used for each configuration. Alternatively, the Slater Transition state can be used, wherein a total energy difference is related to a difference in single electron eigenvalues. By a series expansion, the value of alpha for an excited configuration can be related to its value for the ground state configuration. The terms Delta alpha (delta Epsilon/delta alpha) exhibit a similar dependence on atomic number as the ground state values of alpha. Results of sample calculations are reported and compared with experiment.

  17. Magnetism of Metals, Alloys and of Clusters of Transition Metal Atoms

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A condition for local moment formation in metals derived by Stoddart and March (Ann. Phys.NY 1972 64, 174) is first used to discuss the ferromagnetism of body-centred-cubic Fe. A less detailed discussion is also added on Ni and Co. This leads into a treatment of the nonlinear response of such 3d ferromagnets to dilute substitutional impurities. Antiferromagnets responding to local changes in the exchange field caused by such impurities are also studied, Mn in Cr being one such system discussed. The paper concludes with a brief summary of clusters of transition metal atoms, with most attention devoted to Cr and to Mn.

  18. VizieR Online Data Catalog: Atomic transition probabilities of Mn (Den Hartog+, 2011)

    Science.gov (United States)

    den Hartog, E. A.; Lawler, J. E.; Sobeck, J. S.; Sneden, C.; Cowan, J. J.

    2011-08-01

    The goal of the present work is to produce transition probabilities with very low uncertainties for a selected set of multiplets of MnI and MnII. Multiplets are chosen based upon their suitability for stellar abundance analysis. We report on new radiative lifetime measurements for 22 levels of MnI from the e8D, z6P, z6D, z4F, e8S, and e6S terms and six levels of MnII from the z5P and z7P terms using time-resolved laser-induced fluorescence on a slow atom/ion beam. New branching fractions for transitions from these levels, measured using a Fourier-transform spectrometer, are reported. (2 data files).

  19. Design of a nanocarrier with regulated drug release ability utilizing a reversible conformational transition of a peptide, responsive to slight changes in pH.

    Science.gov (United States)

    Murai, Kazuki; Higuchi, Masahiro; Kinoshita, Takatoshi; Nagata, Kenji; Kato, Katsuya

    2013-07-21

    We investigated the drug releasing behavior of a novel nanocarrier system, utilizing a peptide to act as a nanogate to the mesopore, on a mesoporous silica nanoparticle. The surface peptide on mesoporous silica displayed pH-dependant mesopore cap-uncap switching behavior, enabled by the reversible β-sheet-to-random coil conformational transition resulting from slight pH changes between 8.0 and 6.0. The peptide adopted a β-sheet structure under weakly basic conditions (pH 8.0) and a random coil conformation under weakly acidic conditions (pH 6.0). We demonstrated the pH-dependant regulation of the material's drug release property by the reversible conformational transition of the surface peptide. Under basic pH conditions, the drug release from the nanocarrier was significantly inhibited. However, under acidic pH conditions, the drug in the mesopore was gradually released.

  20. Tunneling Hamiltonian description of the atomic-scale 0-{pi} transition in superconductor/ferromagnetic-insulator junctions

    Energy Technology Data Exchange (ETDEWEB)

    Kawabata, S., E-mail: s-kawabata@aist.go.jp [Nanosystem Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568 (Japan)] [CREST, Japan Science and Technology Corporation (JST), Kawaguchi, Saitama 332-0012 (Japan); Tanaka, Y. [Department of Applied Physics, Nagoya University, Nagoya 464-8603 (Japan); Golubov, A.A. [Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE Enschede (Netherlands); Vasenko, A.S. [Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble (France); Kashiwaya, S. [Nanoelectronics Research Institute (NeRI), AIST, Tsukuba, Ibaraki 305-8568 (Japan); Asano, Y. [Department of Applied Physics, Hokkaido University, Sapporo 060-8628 (Japan)

    2011-11-15

    Josephson transport in a superconductor/ferromagnetic-insulator(FI)/superconductor junction is investigated analytically. By using the tunneling Hamiltonian method, we found that the spin-dependent {pi}-phase shift of the electron wave function in a FI layer gives the atomic scale 0-{pi} transition. This observation is consistent with previous numerical results. We show a perturbation theory of the Josephson transport through ferromagnetic insulators (FIs). Recently we have found that the appearance of the atomic scale 0-{pi} transition in such junctions based on numerical calculations. In order to explore the mechanism of this anomalous transition, we have analytically calculated the Josephson current using the tunneling Hamiltonian theory and found that the spin dependent {pi}-phase shift in the FI barrier gives the atomic scale 0-{pi} transition.

  1. Exploring the optical contrast effect in strong atomic lines for exoplanets transiting active stars

    Science.gov (United States)

    Cauley, Paul W.; Redfield, Seth

    2017-01-01

    Transmission spectroscopy is a powerful tool for detecting and characterizing planetary atmospheres. Non-photospheric features on the stellar disk, however, can contaminate the planetary signal: during transit the observed spectrum is weighted towards the features not currently being occulted by the planet. This contrast effect can mimic absorption in the planetary atmosphere for strong atomic lines such as Na I, Ca II, and the hydrogen Balmer lines. While the contrast effect is negligible for quiet stars, contributions to the transmission signal from active stellar surfaces can produce ~1% changes in the line core. It is therefore critical that these contrast signals be differentiated from true absorption features in the planetary atmosphere. Here we present our work on simulating the contrast effect for an active stellar surface. We discuss the particular case of HD 189733 b, a well-studied hot Jupiter orbiting an active K-dwarf, due to the plethora of atomic absorption signals reported in its atmosphere.Specifically, we focus on Hα to address recent suggestions that the measured in-transit signals are a result of stellar activity. In the contrast model we include center-to-limb variations and calculate limb darkening parameters as a function of wavelength across the line of interest. The model includes contributions to the spectrum from spots, faculae and plages, filaments, and the bare stellar photosphere. Stellar rotation is also included. We find that it is very difficult to reproduce the measured in-transit Hα signals for reasonable active region parameters. In addition, it is difficult to create an in-transit contrast signature that lasts for the duration of the transit unless the planet is crossing an active latitudinal belt and is always obscuring active regions. This suggests that the Hα measurements arise predominantly in the planetary atmosphere. However, the contrast effect likely contributes to these signals. Furthermore, our results could be

  2. Hydration and conformational transitions in DNA, RNA, and mixed DNA-RNA triplexes studied by gravimetry and FTIR spectroscopy.

    Science.gov (United States)

    Guzman, M R; Liquier, J; Taillandier, E

    2005-12-01

    We have studied by gravimetric measurements and FTIR spectroscopy the hydration of duplexes and triplexes formed by combinations of dA(n), dT(n), rA(n), and rU(n) strands. Results obtained on hydrated films show important differences in their hydration and in the structural transitions which can be induced by varying the water content of the samples. The number of water molecules per nucleotide (w/n) measured at high relative humidity (98% R.H.) is found to be 21 for dA(n).dT(n) and 15 for rA(n).rU(n). Addition of a third rU(n) strand does not change the number of water molecules per nucleotide: w/n=21 for rU(n)*dA(n).dT(n) and w/n=15 for rU(n)*rA(n).rU(n). On the contrary, the addition of a third dT(n) strand changes the water content but in a different way, depending whether the duplex is DNA or RNA. Thus, a loss of four water molecules per nucleotide is measured for dT(n)*dA(n).dT(n) while an increase of two water molecules per nucleotide is observed for dT(n)*rA(n).rU(n). The final hydration is the same for both triplexes (w/n=17). The desorption profiles obtained by gravimetry and FTIR spectroscopy are similar for the rA(n).rU(n) duplex and the rU(n)*rA(n).rU(n) triplex. On the contrary, the desorption profiles of the dA(n).dT(n) duplex and the triplexes formed with it (rU(n)*dA(n).dT(n) and dT(n)*dA(n).dT(n)) are different from each other. This is correlated with conformational transitions induced by varying the hydration content of the different structures, as shown by FTIR spectroscopy. Modifications of the phosphate group hydration and of the sugar conformation (S to N type repuckering) induced by decrease of the water content are observed in the case of triplexes formed on the dA(n).dT(n) duplex.

  3. Design of Efficient Catalysts with Double Transition Metal Atoms on C2N Layer.

    Science.gov (United States)

    Li, Xiyu; Zhong, Wenhui; Cui, Peng; Li, Jun; Jiang, Jun

    2016-05-05

    Heterogeneous catalysis often involves molecular adsorptions to charged catalyst site and reactions triggered by catalyst charges. Here we use first-principles simulations to design oxygen reduction reaction (ORR) catalyst based on double transition metal (TM) atoms stably supported by 2D crystal C2N. It not only holds characters of low cost and high durability but also effectively accumulates surface polarization charges on TMs and later deliveries to adsorbed O2 molecule. The Co-Co, Ni-Ni, and Cu-Cu catalysts exhibit high adsorption energies and extremely low dissociation barriers for O2, as compared with their single-atom counterparts. Co-Co on C2N presents less than half the value of the reaction barrier of bulk Pt catalysts in the ORR rate-determining steps. These catalytic improvements are well explained by the dependences of charge polarization on various systems, which opens up a new strategy for optimizing TM catalytic performance with the least metal atoms on porous low-dimensional materials.

  4. Tunable electronic and magnetic properties in stanene by 3d transition metal atoms absorption

    Science.gov (United States)

    Xing, Dan-Xu; Ren, Ceng-Ceng; Zhang, Shu-Feng; Feng, Yong; Chen, Xin-Lian; Zhang, Chang-Wen; Wang, Pei-Ji

    2017-03-01

    The electronic and magnetic properties of transition metal (TM) atoms (V, Cr, Mn, Fe, Co, Ni) adsorption on stanene are investigated by first-principles calculations. The results indicate that the TM atoms prefer to be relaxed on a H site on stanene except V atom which lies on the valley site. Fe-absorbed stanene is a spin gapless semiconductor with up-spin electron and down-spin hole carriers allowing the coexistence of charge current and the pure spin current. Co-absorbed stanene lies in the half metal phase. The V-, Cr-, Mn-, and Cu-absorbed stanene turn the stanene into metal, while Ni- and Zn-absorbed stanene open a narrow band gap. For V-, Cr-, Mn-, Fe-, and Co-absorbed stanene, the magnetic moment of the TM will survive while the Ni-, Cu-, and Zn-absorbed stanene will be non-magnetic material. These findings may have great potential in the design of new electrically controllable spintronic devices.

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

    Science.gov (United States)

    Noskov, Boris A

    2014-04-01

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

  6. 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)

  7. Atomic view of the histidine environment stabilizing higher-pH conformations of pH-dependent proteins.

    Science.gov (United States)

    Valéry, Céline; Deville-Foillard, Stéphanie; Lefebvre, Christelle; Taberner, Nuria; Legrand, Pierre; Meneau, Florian; Meriadec, Cristelle; Delvaux, Camille; Bizien, Thomas; Kasotakis, Emmanouil; Lopez-Iglesias, Carmen; Gall, Andrew; Bressanelli, Stéphane; Le Du, Marie-Hélène; Paternostre, Maïté; Artzner, Franck

    2015-07-20

    External stimuli are powerful tools that naturally control protein assemblies and functions. For example, during viral entry and exit changes in pH are known to trigger large protein conformational changes. However, the molecular features stabilizing the higher pH structures remain unclear. Here we elucidate the conformational change of a self-assembling peptide that forms either small or large nanotubes dependent on the pH. The sub-angstrom high-pH peptide structure reveals a globular conformation stabilized through a strong histidine-serine H-bond and a tight histidine-aromatic packing. Lowering the pH induces histidine protonation, disrupts these interactions and triggers a large change to an extended β-sheet-based conformation. Re-visiting available structures of proteins with pH-dependent conformations reveals both histidine-containing aromatic pockets and histidine-serine proximity as key motifs in higher pH structures. The mechanism discovered in this study may thus be generally used by pH-dependent proteins and opens new prospects in the field of nanomaterials.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-11-15

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

  9. Quantum and thermal phase transitions in a bosonic atom-molecule mixture in a two-dimensional optical lattice

    Science.gov (United States)

    de Forges de Parny, L.; Rousseau, V. G.

    2017-01-01

    We study the ground state and the thermal phase diagram of a two-species Bose-Hubbard model, with U(1 ) ×Z2 symmetry, describing atoms and molecules on a two-dimensional optical lattice interacting via a Feshbach resonance. Using quantum Monte Carlo simulations and mean-field theory, we show that the conversion between the two species, coherently coupling the atomic and molecular states, has a crucial impact on the Mott-superfluid transition and stabilizes an insulating phase with a gap controlled by the conversion term—the Feshbach insulator—instead of a standard Mott-insulating phase. Depending on the detuning between atoms and molecules, this model exhibits three phases: the Feshbach insulator, a molecular condensate coexisting with noncondensed atoms, and a mixed atomic-molecular condensate. Employing finite-size scaling analysis, we observe three-dimensional (3D) X Y (3D Ising) transition when U(1 ) (Z2) symmetry is broken, whereas the transition is first order when both U(1 ) and Z2 symmetries are spontaneously broken. The finite-temperature phase diagram is also discussed. The thermal disappearance of the molecular superfluid leads to a Berezinskii-Kosterlitz-Thouless transition with unusual universal jump in the superfluid density. The loss of the quasi-long-range coherence of the mixed atomic and molecular superfluid is more subtle since only atoms exhibit conventional Berezinskii-Kosterlitz-Thouless criticality. We also observe a signal compatible with a classical first-order transition between the mixed superfluid and the normal Bose liquid at low temperature.

  10. 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.

  11. 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

    2017-03-20

    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).

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

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, Shukichi [Kansai Advanced Research Center, National Institute of Information and Communications Technology (KARC-NiCT), 588-2, Iwaoka, Nishi-ku, Kobe 651-2492 (Japan)]. E-mail: tanakas@nict.go.jp; Grevin, Benjamin [Laboratoire de Physique des Metaux Synthetiques UMR5819-SprAM, DRFMC CEA-Grenoble, 17 rue des Martyrs 38054 Grenoble Cedex 9 (France); Rannou, Patrice [Laboratoire de Physique des Metaux Synthetiques UMR5819-SprAM, DRFMC CEA-Grenoble, 17 rue des Martyrs 38054 Grenoble Cedex 9 (France); Suzuki, Hitoshi [Kansai Advanced Research Center, National Institute of Information and Communications Technology (KARC-NiCT), 588-2, Iwaoka, Nishi-ku, Kobe 651-2492 (Japan); Mashiko, Shinro [Kansai Advanced Research Center, National Institute of Information and Communications Technology (KARC-NiCT), 588-2, Iwaoka, Nishi-ku, Kobe 651-2492 (Japan)

    2006-03-21

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

  13. Dipole-forbidden atomic transitions induced by superintense x-ray laser fields

    Science.gov (United States)

    Simonsen, Aleksander Skjerlie; Førre, Morten

    2016-06-01

    A hydrogen atom, initially prepared in the 2 s and/or 2 p (m =±1 ) states, is assumed irradiated by 0.8 keV (1.5 nm) photons in pulses of 1 -250 fs duration and intensities in the range 1020 to 1023W /cm2 . Solving the corresponding time-dependent Schrödinger equation from first principles, we show that the ionization and excitation dynamics of the laser-atom system is strongly influenced by interactions beyond the electric dipole approximation. A beyond-dipole two-photon Raman-like transition between the 2 s and 2 p (m =±1 ) states is found to completely dominate the underlying laser-matter interaction. It turns out that the large difference in the ionization rates of the 2 s and 2 p (m =±1 ) states is important in this context, effectively leading to a symmetry breaking in the corresponding (beyond-dipole) bound-bound dynamics with the result that a net population transfer between the states occurs throughout the laser-matter interaction period. Varying the x-ray exposure time as well as the laser intensity, we probe the phenomenon as the bound wave packet oscillates between having 2 s and 2 p (m =±1 ) character, eventually giving rise to a Rabi-like oscillation pattern in the populations.

  14. Atomic Structure and Doping Response of Grain Boundary in Transition Metal Ni

    Institute of Scientific and Technical Information of China (English)

    王崇愚; 于涛

    1994-01-01

    Based on the coincidence site lattice model and by use of the molecular dynamics method, the relaxation calculations on the atomic structures of the grain boundaries of various generating functions (∑3,∑5,…, ∑19,…,∑33) in the transition metal Ni are performed. The features of atomic structures corresponding to the grain boundaries and the effects of the pre-parameter on the interface structures are given. To study the doping response relating to the properties of materials, the 23 tilt grain boundary is selected. Based on the interstice and vacancy mechanisms, the interface responses doping boron, nitrogen and phosphorus for the grain boundary are investigated. According to the criterion of the energy in molecular dynamics simulation, the most probable positions of doping impurities and effect of doping impurities on the interface structure are given, and the dependence of the fine structure on doping type and the order of the impurity amount are obtained. The analysis of the local energy for the

  15. Evidence of PPII-like helical conformation and glass transition in a self-assembled solid-state polypeptide-surfactant complex: poly(L-histidine)/docylbenzenesulfonic acid.

    Science.gov (United States)

    Ramani, Ramasubbu; Hanski, Sirkku; Laiho, Ari; Tuma, Roman; Kilpeläinen, Simo; Tuomisto, Filip; Ruokolainen, Janne; Ikkala, Olli

    2008-05-01

    We present lamellar self-assembly of cationic poly(L-histidine) (PLH) stoichiometrically complexed with an anionic surfactant, dodecyl benzenesulfonic acid (DBSA), which allows a stabilized conformation reminiscent of polyproline type II (PPII) left-handed helices. Such a conformation has no intrapeptide hydrogen bonds, and it has previously been found to be one source of flexibility, e.g., in collagen and elastin, as well as an intermediate in silk processing. PLH(DBSA)1.0 complexes were characterized by Fourier transform infrared spectroscopy (FTIR), circular dichroism (CD), small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), and differential scanning calorimetry (DSC). The PPII-like conformation in PLH(DBSA)1.0 is revealed by characteristic CD and FTIR spectra, where the latter indicates absence of intrachain peptide hydrogen bonds. In addition, a glass transition was directly verified by DSC at ca. 135 degrees C for PLH(DBSA)1.0 and indirectly by SAXS and TEM in comparison to pure PLH at 165 degrees C, thus indicating plasticization. Glass transitions have not been observed before in polypeptide-surfactant complexes. The present results show that surfactant binding can be a simple scheme to provide steric crowding to stabilize PPII conformation to tune the polypeptide properties, plasticization and flexibility.

  16. 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...

  17. Vibrational properties of vacancy in bcc transition metals using embedded atom method potentials

    Indian Academy of Sciences (India)

    Vandana Gairola; P D Semalty; P N Ram

    2013-06-01

    The embedded atom method (EAM) potentials, with the universal form of the embedding function along with the Morse form of pair potential, have been employed to determine the potential parameters for three bcc transition metals: Fe, Mo, and W, by fitting to Cauchy pressure $(C_{12} − C_{44})/2$, shear constants $G_{v} = (C_{11} − C_{12} + 3C_{44})/5$ and 44, cohesive energy and the vacancy formation energy. The obtained potential parameters are used to calculate the phonon dispersion spectra of these metals. Large discrepancies are found between the calculated results of phonon dispersion using the EAM and the experimental phonon dispersion results. Therefore, to overcome this inadequacy of the EAM model, we employ the modified embedded atom method (MEAM) in which a modified term along with the pair potential and embedding function is added in the total energy. The phonon dispersions calculated using potential parameters obtained from the MEAM show good agreement with experimental results compared to those obtained from the EAM. Using the calculated phonons, we evaluate the local density of states of the neighbours of vacancy using the Green’s function method. The local frequency spectrum of first neighbours of vacancy in Mo shows an increase at higher frequencies and a shift towards the lower frequencies whereas in Fe and W, the frequency spectrum shows a small decrease towards higher frequency and small shift towards lower frequency. For the second neighbours of vacancy in all the three metals, the local frequency spectrum is not much different from that of the host atom. The local density of states of the neighbours of the vacancy has been used to calculate the mean square displacements and the formation entropy of vacancy. The calculated mean square displacements of the first neighbours of vacancy are found to be higher than that of the host atom, whereas it is lower for the second neighbours. The calculated results of the formation entropy of the vacancy

  18. 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.

  19. The Zα domain of fish PKZ facilitates the B-Z conformational transition of oligonucleotide DNAs with d(GC)n inserts

    Institute of Scientific and Technical Information of China (English)

    Puzhong Lu; Shoulong Deng; Youlin Zhu; Yongbin Yan; Yong Liu; Chengyu Hu

    2012-01-01

    PKZ (PKR-like) was discovered as a member of eIF2α kinase family in fish,which possesses a conserved catalytic domain of an eIF2α kinase in C-terminal and also two ZDNA-binding domains (Zα1 and Zα2) in N-terminal.PKZ can be activated through binding of Zα to Z-DNA.However,the regulatory function of PKZ Zα still remains unclear.To investigate a molecular mechanism of how PKZ Zα interacts with Z-DNA,we expressed Zα polypeptide Zα1α2 in Escherichia coli Rosetta strain and purified by affinity chromatography on Ni-NTA resin.Different lengths of oligonucleotide DNAs with various inserts,namely d(GC)n (n =6,8,10,13),d(TA)n (n =6,10),nond(GC),and non-d(TA),were designed and synthesized.Circular dichroism spectrum and gel mobility shift assays were used to investigate the effects of Zα1α2 on the conformational transition of different oligonucleotide DNAs.Results showed that oligonucleotide DNAs retained a conventional B-DNA conformation in the absence of Zα1α2.With the increasing amount of Zα1α2 titration,d(GC)n were recognized and converted to Z-DNA conformation to some degree.With increasing the repeat number (from n =6 to n =13),the tendency of conformational transition became more obvious.However,the conformation of oligonucleotides with d(TA)n inserts changed a little in the presence of Zα1α2,and Zα1α2 had no effect on conformational transition of oligonucleotides with non-d(GC) or non-d(TA) inserts.Gel mobility shift assays further showed that Zα1α2 could bind to oligonucleotide with d(GC)10.In other words,Zα1α2 can turn oligonucleotides with d(GC)n inserts into Z-DNA conformation and bind to it with high affinity.

  20. Pressure-dependent transition from atoms to nanoparticles in magnetron sputtering: Effect on WSi2 film roughness and stress

    OpenAIRE

    2010-01-01

    We report on the transition between two regimes from several-atom clusters to much larger nanoparticles in Ar magnetron sputter deposition of WSi2, and the effect of nanoparticles on the properties of amorphous thin films and multilayers. Sputter deposition of thin films is monitored by in situ x-ray scattering, including x-ray reflectivity and grazing incidence small angle x-ray scattering. The results show an abrupt transition at an Ar background pressure Pc; the transition is associated wi...

  1. 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., eithe

  2. 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., eithe

  3. Theoretical studies of the atomic transitions in boron-like ions: Mg VIII, Si X and S XII

    Energy Technology Data Exchange (ETDEWEB)

    Nataraj, H S [Non-Accelerator Particle Physics Group, Indian Institute of Astrophysics, Bangalore-34 (India); Sahoo, B K [Max Planck Institute for the Physics of Complex Systems, Noethnitzer Street 38, D-01187 Dresden (Germany); Das, B P [Non-Accelerator Particle Physics Group, Indian Institute of Astrophysics, Bangalore-34 (India); Chaudhuri, R K [Non-Accelerator Particle Physics Group, Indian Institute of Astrophysics, Bangalore-34 (India); Mukherjee, D [Department of Physical Chemistry, Indian Association for Cultivation of Science, Kolkata-700 032 (India)

    2007-08-14

    In this paper, we have carried out the calculations of the weighted oscillator strengths and the transition probabilities for a few low-lying transitions of boron-like ions: Mg VIII, Si X and S XII, which are astrophysically important, particularly in the atmosphere of the solar corona. We have employed an all-order relativistic many-body theory called the relativistic coupled-cluster theory to calculate very precisely these atomic quantities of astrophysical interest. We have reported for the first time the transition probabilities for some forbidden transitions which are unavailable in the literature, either theoretically or experimentally. We also discuss the physical effects associated with these transitions. Our data can be used for the identification of spectral lines arising from the coronal atmospheres of the Sun and Sun-like stars having an extended corona.

  4. Highly Anti-UV Properties of Silk Fiber with Uniform and Conformal Nanoscale TiO2 Coatings via Atomic Layer Deposition.

    Science.gov (United States)

    Xiao, Xingfang; Liu, Xin; Chen, Fengxiang; Fang, Dong; Zhang, Chunhua; Xia, Liangjun; Xu, Weilin

    2015-09-30

    In this study, silk fiber was successfully modified via the application of a nanoscale titania coating using atomic layer deposition (ALD), with titanium tetraisopropoxide (TIP) and water as precursors at 100 °C. Scanning electron microscopy, X-ray energy dispersive spectroscopy, X-ray photoelectron spectroscopy, transmission electron microscope, and field emission scanning electron microscope results demonstrated that uniform and conformal titania coatings were deposited onto the silk fiber. The thermal and mechanical properties of the TiO2 silk fiber were then investigated. The results showed that the thermal stability and mechanical properties of this material were superior to those of the uncoated substance. Furthermore, the titania ALD process provided the silk fiber with excellent protection against UV radiation. Specifically, the TiO2-coated silk fibers exhibited significant increases in UV absorbance, considerably less yellowing, and greatly enhanced mechanical properties compared with the uncoated silk fiber after UV exposure.

  5. 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.

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

    Science.gov (United States)

    Sobel, Nicolas; Hess, Christian; Lukas, Manuela; Spende, Anne; Stühn, Bernd; Toimil-Molares, M E; Trautmann, Christina

    2015-01-01

    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.

  7. 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

  8. Modeling the Atomic-to-Molecular Transition and Chemical Distributions of Turbulent Star-Forming Clouds

    CERN Document Server

    Offner, Stella S R; Viti, Serena; Bell, Thomas A

    2013-01-01

    We use 3D-PDR, a three-dimensional astrochemistry code for modeling photodissociation regions (PDRs), to post-process hydrodynamic simulations of turbulent, star-forming clouds. We focus on the transition from atomic to molecular gas, with specific attention to the formation and distribution of H, C+, C, H2 and CO. First, we demonstrate that the details of the cloud chemistry and our conclusions are insensitive to the simulation spatial resolution, to the resolution at the cloud edge, and to the ray angular resolution. We then investigate the effect of geometry and simulation parameters on chemical abundances and find weak dependence on cloud morphology as dictated by gravity and turbulent Mach number. For a uniform external radiation field, we find similar distributions to those derived using a one-dimensional PDR code. However, we demonstrate that a three-dimensional treatment is necessary for a spatially varying external field, and we caution against using one-dimensional treatments for non-symmetric probl...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-06-10

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

  10. Polarization dependence of the direct two photon transitions of 87Rb atoms by erbium: Fiber laser frequency comb

    Science.gov (United States)

    Dai, Shaoyang; Xia, Wei; Zhang, Yin; Zhao, Jianye; Zhou, Dawei; Wang, Qing; Yu, Qi; Li, Kunqian; Qi, Xianghui; Chen, Xuzong

    2016-11-01

    The femtosecond fiber-based optical frequency combs have been proved to be powerful tools for investigating the energy levels of atoms and molecules. In this paper, an Er-doped fiber femtosecond optical frequency comb has been implemented for studying the polarization dependence of 5S-5D two-photon transitions in thermal gas of atomic rubidium 87 using an entirely symmetrical optical configuration. By changing the polarization states of the counter-propagating light beams, the polarization dependence of direct two photon transition spectrum is demonstrated, and a dramatic variation (up to 5.5 times) of the two-photon transitions strength has been observed. The theory for the polarization dependence of two photon transition based on the second-order perturbation was established, which is in good agreement with the experimental results. The measurement results indicate that the polarization state manipulation with the existing frequency comb is used for femtosecond optical frequency comb based two photon transition spectroscopic purposes, which will improve the precision measurement of the absolute transition frequency and related applications.

  11. 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...

  12. 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.

  13. Demonstration of a Sagnac-Type Cold Atom Interferometer with Stimulated Raman Transitions

    Institute of Scientific and Technical Information of China (English)

    WANG Ping; LI Run-Bing; YAN Hui; WANG Jin; ZHAN Ming-Sheng

    2007-01-01

    @@ Cold-matter-wave Sagnac interferometers possess many advantages over their thermal atomic beam counterparts when they are used as precise inertial sensors. We report a realization of a Sagnac-type interferometer with cold atoms.

  14. Interface between light coupled to excited-states transition and ground-state coherence of rubidium atoms

    CERN Document Server

    Parniak, Michał; Wasilewski, Wojciech

    2015-01-01

    We demonstrate an interface between light coupled to transition between excited states of rubidium and long-lived ground-state atomic coherence. In our proof-of-principle experiment a non-linear process of four-wave mixing in an open-loop configuration is used to achieve light emission proportional to independently prepared ground-state atomic coherence. We demonstrate strong correlations between Raman light heralding generation of ground-state coherence and the new four-wave mixing signal. Dependance of the efficiency of the process on laser detunings is studied.

  15. A comparison of transition state of phenol in H-atom abstraction by methyl and methylperoxyl radicals

    Institute of Scientific and Technical Information of China (English)

    SUN YouMin; WU JunSen; LIU ChengBu

    2007-01-01

    DFT method was employed to locate transition state for H-atom transfer from phenol by methyl radical and methylperoxyl radical. The reaction pathway energy profiles and the structure of transition state show that a common feature is the out-of-plane structure of the transition state: in contrast to the energetic minima of a hydrogen-bonded intermediate, the hydrogen bond in transition structures is considerably twisted out of the aromatic ring. From the values of enthalpy (△H) and activation energy (Ea)obtained, it is found that the rate of the reaction of peroxyl radical with phenolic antioxidant is higher than that of alkyl radical with antioxidant. Spin density distributions show that the electron transmission is between methyl (methylperoxyl) radical and phenol.

  16. The Role of 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

    2017-03-20

    Neurotransmitter:sodium symporters (NSS) 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 multi-hydrophobic 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 TM5 (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 (NT) 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.

  17. Secondary structure of prothymosin alpha evidenced for conformational transitions induced by changes in temperature and concentration of n-dodecyltrimethylammonium bromide.

    Science.gov (United States)

    Pombo, C; Suarez, M J; Nogueira, M; Czarnecki, J; Ruso, J M; Sarmiento, F; Prieto, G

    2001-08-01

    Conformational changes of prothymosin alpha (ProTalpha) induced by changes in temperature and concentration of the denaturant n-dodecyltrimethylammonium bromide (C12TAB) were studied by difference spectroscopy. The conformational transition of ProTalpha by C12TAB was followed as a function of denaturant concentration by absorbance measurements at 230 nm and the data were analyzed to obtain the Gibbs energy of the transition in water (deltaG0(w)) and in a hydrophobic environment (deltaG0(hc)) for saturated protein-surfactant complexes. The value of deltaG0(w) was 6.38 kJ mol(-1) and that for deltaG0(hc), which is not affected by temperature, was -18.62 kJ mol(-1). Changes of absorbance at 230 nm of ProTalpha with temperature can be assumed to resemble a transition in the secondary structure. The parameters characterizing the thermodynamics of unfolding, melting temperature (Tm), enthalpy (deltaHm), entropy (deltaSm) and heat capacity (deltaCp) were determined. The values obtained for Tm, deltaHm, and deltaSm are smaller that those found for other globular proteins; deltaCp was found to be much smaller. These results suggest that ProTalpha exhibits some type of secondary structure under these conditions (10 mM glycine buffer, pH 2.4).

  18. Interaction of phospholipase C with liposome: A conformation transition of the enzyme is critical and specific to liposome composition for burst hydrolysis and fusion in concert

    Science.gov (United States)

    Patra, Samir Kumar; Sengupta, Dipta; Deb, Moonmoon; Kar, Swayamsiddha; Kausar, Chahat

    2017-02-01

    Phospholipase C (PLC)1 is known to help the pathogen B. cereus entry to the host cell and human PLC is over expressed in multiple cancers. Knowledge of dynamic activity of the enzyme PLC while in action on membrane lipids is essential and helpful to drug design and delivery. In view of this, interactions of PLC with liposome of various lipid compositions have been visualized by testing enzyme activity and microenvironments around the intrinsic fluorophores of the enzyme. Overall change of the protein's conformation has been monitored by fluorescence spectroscopy and circular dichroism (CD). Liposome aggregation and fusion were predicted by increase in turbidity and vesicle size. PLC in solution has high fluorescence and exhibit appreciable shift in its emission maxima, upon gradual change in excitation wavelength towards the red edge of the absorption band. REES fluorescence studies indicated that certain Trp fluorophores of inactive PLC are in motionally restricted compact/rigid environments in solution conformation. PLC fluorescence decreased in association with liposome and Trps loosed rigidity where liposome aggregation and fusion occurred. We argue that the structural flexibility is the cause of decrease of fluorescence, mostly to gain optimum conformation for maximum activity of the enzyme PLC. Further studies deciphered that the enzyme PLC undergoes change of conformation when mixed to LUVs prepared with specific lipids. CD data at the far-UV and near-UV regions of PLC in solution are in excellent agreement with the previous reports. CD analyses of PLC with LUVs, showed significant reduction of α-helices, increase of β-sheets; and confirmed dramatic change of orientations of Trps. In case of liposome composed of lipid raft like composition, the enzyme binds very fast, hydrolyze PC with higher rate, exhibit highest structural flexibility and promote vesicle fusion. These data strongly suggest marked differences in conformation transition induced PLC

  19. 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.

  20. Magnetic field-induced spectroscopy of forbidden optical transitions with application to lattice-based optical atomic clocks.

    Science.gov (United States)

    Taichenachev, A V; Yudin, V I; Oates, C W; Hoyt, C W; Barber, Z W; Hollberg, L

    2006-03-01

    We develop a method of spectroscopy that uses a weak static magnetic field to enable direct optical excitation of forbidden electric-dipole transitions that are otherwise prohibitively weak. The power of this scheme is demonstrated using the important application of optical atomic clocks based on neutral atoms confined to an optical lattice. The simple experimental implementation of this method--a single clock laser combined with a dc magnetic field--relaxes stringent requirements in current lattice-based clocks (e.g., magnetic field shielding and light polarization), and could therefore expedite the realization of the extraordinary performance level predicted for these clocks. We estimate that a clock using alkaline-earth-like atoms such as Yb could achieve a fractional frequency uncertainty of well below 10(-17) for the metrologically preferred even isotopes.

  1. First application of superconducting transition-edge-sensor microcalorimeters to hadronic-atom x-ray spectroscopy

    CERN Document Server

    Okada, S; Curceanu, C; Doriese, W B; Fowler, J W; Gard, J; Gustafsson, F P; Hashimoto, T; Hayano, R S; Hirenzaki, S; Hays-Wehle, J P; Hilton, G C; Ikeno, N; Iliescu, M; Ishimoto, S; Itahashi, K; Iwasaki, M; Koike, T; Kuwabara, K; Ma, Y; Marton, J; Noda, H; O'Neil, G C; Outa, H; Reintsema, C D; Sato, M; Schmidt, D R; Shi, H; Suzuki, K; Suzuki, T; Swetz, D S; Tatsuno, H; Uhlig, J; Ullom, J N; Widmann, E; Yamada, S; Yamagata-Sekihara, J; Zmeskal, J

    2016-01-01

    High-resolution pionic-atom x-ray spectroscopy was performed with an x-ray spectrometer based on a 240-pixel array of superconducting transition-edge-sensor (TES) microcalorimeters at the piM1 beam line of the Paul Scherrer Institute. X-rays emitted by pionic carbon via the 4f->3d transition and the parallel 4d->3p transition were observed with a full-width-at-half-maximum energy resolution of 6.8 eV at 6.4 keV. Measured x-ray energies are consistent with calculated electromagnetic values which considered the strong-interaction effect assessed via the Seki-Masutani potential for the 3p energy level, and favor the electronic population of two filled 1s electrons in the K-shell. Absolute energy calibration with an uncertainty of 0.1 eV was demonstrated under a high-rate hadron beam condition of 1.45 MHz. This is the first application of a TES spectrometer to hadronic-atom x-ray spectroscopy and is an important milestone towards next-generation high-resolution kaonic-atom x-ray spectroscopy.

  2. Ultra-narrow spectroscopic cells in atomic spectroscopy: reflection, transmission, fluorescence, and nonadiabatic transitions at the walls

    Science.gov (United States)

    Pazgalev, A.; Sarkisyan, D.; Cartaleva, S.; Przhibelskii, S.; Vartanyan, T.

    2014-11-01

    Ultra-narrow cells with the thicknesses in the range from several wavelengths to the small fractions of the wavelength brought a number of new opportunities for atomic spectroscopy. Depending on the cell thickness, spectral lines recorded in ultra-narrow cells are either Doppler-free or Doppler-broadened. With careful selection of the cell thickness hyperfine structure may be easily resolved without resorting on the multibeam nonlinear optical techniques. Moreover, frequent collisions with the walls leads to the important modifications of velocity selective optical pumping resonances. Finally, ultra-narrow cells provide with the unique opportunity to study collisions of the excited atoms with the solid surfaces. In this contribution several examples of the use of the ultra-narrow spectroscopic cells filled with the alkali atomic vapour is presented. First, we discuss general aspects of the transient polarisation that defines all peculiarities of an ultra-narrow cell as a spectroscopic tool. Second, we demonstrate the resolution of the magnetic sublevels in the transition from Zeeman to Paschen-Back regime in the Cs hyperfine structure. Third, new aspects of velocity selective optical pumping resonances in reflection and transmission of resonant radiation by the 6 wavelengths thick cell filled with Cs are discussed. Forth, the experimental evidences of the nonadiabatic transitions between excited states of Rb atoms in the course of collisions with the sapphire surface are presented.

  3. The atomic parameter model for the fifth and sixth transition metal quasicrystal alloys(Mc=0.5)

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    The forming ability of quasicrystal phase has a relationship with the atomic bond factors based on differences in atom size and electron factors.Usually,those factors or their combination are used to describe the forming ability,stability of alloys,etc.In this paper,the quasicrystal alloy forming abilities for the fifth and sixth transition metals(Y,Zr,Nb,Mo,Ru,Rh,Pd and La,Hf,Ta,W,Re,Os,Ir,Pt) based alloys have been studied by the size factor and the atomic parametric function.It has been found that an ellipse curve can be used to separate the quasicrystal formed area from the informed area in the size factor and atomic parameters functional graph.The ellipse curve can be defined by an equation(x-m)2/c2+(y?n)2/d2=1.The overall reliabilities for the model are up to 97.4% and 95.5% for the fifth and the sixth transition metals based quasicrystal alloys,respectively.Also,the ellipse parameters m,n,c and d can be paraphrased by some appropriate parameters for each host metal.

  4. The atomic parameter model for the fifth and sixth transition metal quasicrystal alloys (Mc=0.5)

    Institute of Scientific and Technical Information of China (English)

    LIAO ShuZhi; GUI XuChun; ZHANG Chun; PENG HaoJun; XIE HaoWen; OUYANG YiFang; ZHANG BangWei

    2009-01-01

    The forming ability of quasicrystal phase has a relationship with the atomic bond factors based on differences in atom size and electron factors.Usually,those factors or their combination are used to describe the forming ability,stability of alloys,etc.In this paper,the quasicrystal alloy forming abilities for the fifth and sixth transition metals (Y,Zr,Nb,Mo,Ru,Rh,Pd and La,Hf,Ta,W,Re,Os,Ir,Pt) based alloys have been studied by the size factor and the atomic parametric function.It has been found that an ellipse curve can be used to separate the quasicrystal formed area from the informed area in the size factor and atomic parameters functional graph.The ellipse curve can be defined by an equation(x-m)2/c2+(y-n)2/d2=1.The overall reliabilities for the model are up to 97.4% and 95.5% for the fifth and the sixth transition metals based quasicrystal alloys,respectively.Also,the ellipse parameters m,n,c and d can be paraphrased by some appropriate parameters for each host metal.

  5. 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.; Arnquist, I. J.; Avignone, F. T.; Barabash, A. S.; Bertrand, F. E.; Bradley, A. W.; Brudanin, V.; Busch, M.; Buuck, M.; Caldwell, A. S.; Chan, Y. -D.; Christofferson, C. D.; Chu, P. -H.; Cuesta, C.; Detwiler, J. A.; Dunagan, C.; Efremenko, Yu.; Ejiri, H.; Elliott, S. R.; Finnerty, P. S.; Galindo-Uribarri, A.; Gilliss, T.; Giovanetti, G. K.; Goett, J.; Green, M. P.; Gruszko, J.; Guinn, I. S.; Guiseppe, V. E.; Henning, R.; Hoppe, E. W.; Howard, S.; Howe, M. A.; Jasinski, B. R.; Keeter, K. J.; Kidd, M. F.; Konovalov, S. I.; Kouzes, R. T.; LaFerriere, B. D.; Leon, J.; MacMullin, J.; Martin, R. D.; Massarczyk, R.; Meijer, S. J.; Mertens, S.; Orrell, J. L.; O’Shaughnessy, C.; Poon, A. W. P.; Radford, D. C.; Rager, J.; Rielage, K.; Robertson, R. G. H.; Romero-Romero, E.; Shanks, B.; Shirchenko, M.; Suriano, A. M.; Tedeschi, D.; Trimble, J. E.; Varner, R. L.; Vasilyev, S.; Vetter, K.; Vorren, K.; White, B. R.; Wilkerson, J. F.; Wiseman, C.; Xu, W.; Yakushev, E.; Yu, C. -H.; Yumatov, V.; Zhitnikov, I.

    2016-11-11

    A search for Pauli-exclusion-principle-violating K 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 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 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 Ge, could improve upon these exclusion limits by an order of magnitude after three years of operation.

  6. Optical trapping of ultracold dysprosium atoms: transition probabilities, dynamic dipole polarizabilities and van der Waals C 6 coefficients

    Science.gov (United States)

    Li, H.; Wyart, J.-F.; Dulieu, O.; Nascimbène, S.; Lepers, M.

    2017-01-01

    The efficiency of the optical trapping of ultracold atoms depends 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 levels. 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 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 resonances, the vector and tensor contributions are two-orders-of-magnitude smaller than the scalar contribution, whereas for the imaginary part, the vector and tensor contributions represent a noticeable fraction of the scalar contribution. Finally, our anisotropic C 6 coefficients are much smaller than those published in the literature.

  7. Repumping of ultracold strontium atoms using the ^3P2 - ^3D2 transition

    Science.gov (United States)

    Mickelson, P. G.; Martinez de Escobar, Y. N.; Traverso, A. J.; Killian, T. C.

    2008-05-01

    We discuss recent experiments involving ultracold strontium. Using a commercially-available 3 micron laser, we repump atoms out of the ^3P2 level via the ^3D2 state and gain almost a factor of 10 in the number of atoms in our system. This increase in the signal-to-noise ratio enables improved spectroscopy of strontium in our optical trap.

  8. Structures of the gauche conformers of somE substituted dimethyl ethers. Effect of adjacent atom lone pairs on methyl group asymmetry

    Science.gov (United States)

    Boggs, James E.; Altman, Michael; Cordell, Floyd R.; Dai, Yuanfang

    The complete equilibrium structures of CH 3OCH 3 and of the gauche conformers of CH 30CH 2F, HOCH,F, CH,OCH,Cl and CH,OCH,CN have been determined by ab initio gradient computation at the Hartree-Fock, double zeta-plus-polarization level. The very large asymmetries in CH bond distances previously reported from microwave substitution structures are shown to be non-existent in the equilibrium structures and are presumably artifacts. Small differences, different in direction from those reported from the experiments and nearly an order of magnitude smaller in size, do exist. They reflect three factors: (1) a lengthening of a CH bond which is trans to a lone pair on an adjacent atom, (2) a general shortening of CH bonds originating at a carbon atom bearing a highly electronegative substituent, and (3) a specific interaction in which a CX substituent shortens the nearly parallel CH bond on the other methyl group. The last interaction, not previously reported, is mediated by withdrawal of electron density from the oxygen lone pair which is trans to both groups. Other structural features derived from the microwave studies are supported by the new results. Inclusion of polarization functions in the basis set for oxygen is essential for correct determination of the COC angle and the dihedral angles. The dihedral angles of CH 3OCH 2F and HOCH 2F are not correctly determined by the computation even at this level, although the computed values are improved when d functions are used for oxygen and still more by use of two sets of oxygen d functions. Polarization functions on carbon or on fluorine have no effect on the computed torsional angles. There is no problem in computing the correct dihedral angles with the CI or CN derivatives.

  9. 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.

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

    Science.gov (United States)

    Li, Hui-Ling; Yang, Shu-Zheng; Zu, Xiao-Tao

    2017-01-01

    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.

  11. 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.

  12. Effects of poly (ethylene glycol) chains conformational transition on the properties of mixed DMPC/DMPE-PEG thin liquid films and monolayers.

    Science.gov (United States)

    Georgiev, Georgi As; Sarker, Dipak K; Al-Hanbali, Othman; Georgiev, Georgi D; Lalchev, Zdravko

    2007-10-01

    Foam thin liquid films (TLF) and monolayers at the air-water interface formed by DMPC mixed with DMPE-bonded poly (ethylene glycol)s (DMPE-PEG(550), DMPE-PEG(2000) and DMPE-PEG(5000)) were obtained. The influence of both (i) PEG chain size (evaluated in terms of Mw) and mushroom-to-brush conformational transition and (ii) of the liposome/micelle ratio in the film-forming dispersions, on the interfacial properties of mixed DMPC/DMPE-PEG films was compared. Foam film studies demonstrated that DMPE-PEG addition to foam TLFs caused (i) delayed kinetics of film thinning and black spot expansion and (ii) film stabilization. At the mushroom-to-brush transition, due to steric repulsion increased DMPE-PEG films thickness reached 25 nm while pure DMPC films were only 8 nm thick Newton black films. It was possible to differentiate DMPE-PEG(2000/5000) from DMPE-PEG(550) by the ability to change foam TLF formation mechanism, which could be of great importance for "stealth" liposome design. Monolayer studies showed improved formation kinetics and equilibrium surface tension decrease for DMPE-PEG monolayers compared with DMPC pure films. SEM observations revealed "smoothing" and "sealing" of the defects in the solid-supported layer surface by DMPE-PEGs adsorption, which could explain DMPE-PEGs ability to stabilize TLFs and to decrease monolayer surface tension. All effects in monolayers, foam TLFs and solid-supported layers increased with the increase of PEG Mw and DMPE-PEG concentration. However, at the critical DMPE-PEG concentration (where mushroom-to-brush conformational transition occurred) maximal magnitude of the effects was reached, which only slightly changed at further DMPE-PEG content and micelle/liposome ratio increase.

  13. 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.

  14. 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.

  15. The influence of atomic coherence and dipole–dipole interaction on entanglement of two qubits with nondegenerate two-photon transitions

    Indian Academy of Sciences (India)

    E K Bashkirov; M S Mastyugin

    2015-01-01

    Considering two artificial identical atoms interacting with two-mode thermal field through non-degenerate two-photon transitions, this paper studies the influence of atomic coherence and dipole–dipole interaction on the entanglement of two qubits. It is found that the entanglement is greatly enhanced by these mechanisms.

  16. Structural, electronic, and magnetic properties of transition-metal atom adsorbed two-dimensional GaAs nanosheet

    Science.gov (United States)

    Luo, Jia; Xiang, Gang; Yu, Tian; Lan, Mu; Zhang, Xi

    2016-09-01

    By using first-principles calculations within the framework of density functional theory, the electronic and magnetic properties of 3d transitional metal (TM) atoms (from Sc to Zn) adsorbed monolayer GaAs nanosheets (GaAsNSs) are systematically investigated. Upon TM atom adsorption, GaAsNS, which is a nonmagnetic semiconductor, can be tuned into a magnetic semiconductor (Sc, V, and Fe adsorption), a half-metal (Mn adsorption), or a metal (Co and Cu adsorption). Our calculations show that the strong p-d hybridization between the 3d orbit of TM atoms and the 4p orbit of neighboring As atoms is responsible for the formation of chemical bonds and the origin of magnetism in the GaAsNSs with Sc, V, and Fe adsorption. However, the Mn 3d orbit with more unpaired electrons hybridizes not only with the As 4p orbit but also with the Ga 4p orbit, resulting in a stronger exchange interaction. Our results may be useful for electronic and magnetic applications of GaAsNS-based materials. Project supported by the National Natural Science Foundation of China (Grant No. 11174212).

  17. Determining the quantum-coherent to semiclassical transition in atomic-scale quasi-one-dimensional metals

    Science.gov (United States)

    Weber, Bent; Simmons, Michelle Y.

    2016-08-01

    Atomic-scale silicon wires, patterned by scanning tunneling microscopy (STM) and degenerately doped with phosphorus (P), have attracted significant interest owing to their exceptionally low resistivity and semiclassical Ohmic conduction at temperatures as low as T =4.2 K . Here, we investigate the transition from semiclassical diffusive to quantum-coherent conduction in a 4.6 nm wide wire as we decrease the measurement temperature. By analyzing the temperature dependence of universal conductance fluctuations (UCFs) and one-dimensional (1D) weak localization (WL)—fundamental manifestations of quantum-coherent transport in quasi-1D metals—we show that transport evolves from quantum coherent to semiclassical at T ˜4 K . Remarkably, our study confirms that universal concepts of mesoscopic physics such as UCF and 1D WL retain their validity in quasi-1D metallic conductors down to the atomic scale.

  18. Valence state parameters of all transition metal atoms in metalloproteins--development of ABEEMσπ fluctuating charge force field.

    Science.gov (United States)

    Yang, Zhong-Zhi; Wang, Jian-Jiang; Zhao, Dong-Xia

    2014-09-05

    To promote accuracy of the atom-bond electronegativity equalization method (ABEEMσπ) fluctuating charge polarizable force fields, and extend it to include all transition metal atoms, a new parameter, the reference charge is set up in the expression of the total energy potential function. We select over 700 model molecules most of which model metalloprotein molecules that come from Protein Data Bank. We set reference charges for different apparent valence states of transition metals and calibrate the parameters of reference charges, valence state electronegativities, and valence state hardnesses for ABEEMσπ through linear regression and least square method. These parameters can be used to calculate charge distributions of metalloproteins containing transition metal atoms (Sc-Zn, Y-Cd, and Lu-Hg). Compared the results of ABEEMσπ charge distributions with those obtained by ab initio method, the quite good linear correlations of the two kinds of charge distributions are shown. The reason why the STO-3G basis set in Mulliken population analysis for the parameter calibration is specially explained in detail. Furthermore, ABEEMσπ method can also quickly and quite accurately calculate dipole moments of molecules. Molecular dynamics optimizations of five metalloproteins as the examples show that their structures obtained by ABEEMσπ fluctuating charge polarizable force field are very close to the structures optimized by the ab initio MP2/6–311G method. This means that the ABEEMσπ/MM can now be applied to molecular dynamics simulations of systems that contain metalloproteins with good accuracy.

  19. Structure analysis and conformational transitions of the cell penetrating peptide transportan 10 in the membrane-bound state.

    Directory of Open Access Journals (Sweden)

    Susanne Fanghänel

    Full Text Available Structure analysis of the cell-penetrating peptide transportan 10 (TP10 revealed an exemplary range of different conformations in the membrane-bound state. The bipartite peptide (derived N-terminally from galanin and C-terminally from mastoparan was found to exhibit prominent characteristics of (i amphiphilic α-helices, (ii intrinsically disordered peptides, as well as (iii β-pleated amyloid fibrils, and these conformational states become interconverted as a function of concentration. We used a complementary approach of solid-state (19F-NMR and circular dichroism in oriented membrane samples to characterize the structural and dynamical behaviour of TP10 in its monomeric and aggregated forms. Nine different positions in the peptide were selectively substituted with either the L- or D-enantiomer of 3-(trifluoromethyl-bicyclopent-[1.1.1]-1-ylglycine (CF3-Bpg as a reporter group for (19F-NMR. Using the L-epimeric analogs, a comprehensive three-dimensional structure analysis was carried out in lipid bilayers at low peptide concentration, where TP10 is monomeric. While the N-terminal region is flexible and intrinsically unstructured within the plane of the lipid bilayer, the C-terminal α-helix is embedded in the membrane with an oblique tilt angle of ∼ 55° and in accordance with its amphiphilic profile. Incorporation of the sterically obstructive D-CF3-Bpg reporter group into the helical region leads to a local unfolding of the membrane-bound peptide. At high concentration, these helix-destabilizing C-terminal substitutions promote aggregation into immobile β-sheets, which resemble amyloid fibrils. On the other hand, the obstructive D-CF3-Bpg substitutions can be accommodated in the flexible N-terminus of TP10 where they do not promote aggregation at high concentration. The cross-talk between the two regions of TP10 thus exerts a delicate balance on its conformational switch, as the presence of the α-helix counteracts the tendency of the

  20. Nonequilibrium phase transitions and a nonequilibrium critical point from anti-de Sitter space and conformal field theory correspondence.

    Science.gov (United States)

    Nakamura, Shin

    2012-09-21

    We find novel phase transitions and critical phenomena that occur only outside the linear-response regime of current-driven nonequilibrium states. We consider the strongly interacting (3+1)-dimensional N = 4 large-N(c) SU(N(c)) supersymmetric Yang-Mills theory with a single flavor of fundamental N = 2 hypermultiplet as a microscopic theory. We compute its nonlinear nonballistic quark-charge conductivity by using the AdS/CFT correspondence. We find that the system exhibits a novel nonequilibrium first-order phase transition where the conductivity jumps and the sign of the differential conductivity flips at finite current density. A nonequilibrium critical point is discovered at the end point of the first-order regime. We propose a nonequilibrium steady-state analogue of thermodynamic potential in terms of the gravity-dual theory in order to define the transition point. Nonequilibrium analogues of critical exponents are proposed as well. The critical behavior of the conductivity is numerically confirmed on the basis of these proposals. The present work provides a new example of nonequilibrium phase transitions and nonequilibrium critical points.

  1. Spectral distribution of the 2 → 1 two-photon transition in atoms and few-electron ions

    Indian Academy of Sciences (India)

    Ajay Kumar; S Trotsenko; A V Volotka; D Banaś; H F Beyer; H Bräuning; S Fritzsche; A Gumberidze; S Hagmann; S Hess; C Kozhuharov; R Reuschl; U Spillmann; M Trassinelli; G Weber; Th Stöhlker

    2011-02-01

    The two-photon decay of the 2 state to the ground state in dressed atoms and oneor two-electron ions has been studied for several decades. Relativistic calculations have shown an -dependence of the spectral shape of this two-photon transition in one- or two-electron ions. We have measured the spectral distribution of the 121 0 → 12 1 0 two-photon transition in He-like tin at the ESR storage ring using a new approach for such experiments. In this method, relativistic collisions of initially Li-like projectiles with a gaseous target were used to populate exclusively the first excited state, 12, of He-like tin, which provided a clean two-photon spectrum. The measured two-photon spectral distribution was compared with fully relativistic calculations. The obtained results show very good agreement with the calculations for He-like tin

  2. 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].

  3. Specificity Rendering ‘Hot-Spots’ for Aurora Kinase Inhibitor Design: The Role of Non-Covalent Interactions and Conformational Transitions

    Science.gov (United States)

    Badrinarayan, Preethi; Sastry, G. Narahari

    2014-01-01

    The present study examines the conformational transitions occurring among the major structural motifs of Aurora kinase (AK) concomitant with the DFG-flip and deciphers the role of non-covalent interactions in rendering specificity. Multiple sequence alignment, docking and structural analysis of a repertoire of 56 crystal structures of AK from Protein Data Bank (PDB) has been carried out. The crystal structures were systematically categorized based on the conformational disposition of the DFG-loop [in (DI) 42, out (DO) 5 and out-up (DOU) 9], G-loop [extended (GE) 53 and folded (GF) 3] and αC-helix [in (CI) 42 and out (CO) 14]. The overlapping subsets on categorization show the inter-dependency among structural motifs. Therefore, the four distinct possibilities a) 2W1C (DI, CI, GE) b) 3E5A (DI, CI, GF) c) 3DJ6 (DI, CO, GF) d) 3UNZ (DOU, CO, GF) along with their co-crystals and apo-forms were subjected to molecular dynamics simulations of 40 ns each to evaluate the variations of individual residues and their impact on forming interactions. The non-covalent interactions formed by the 157 AK co-crystals with different regions of the binding site were initially studied with the docked complexes and structure interaction fingerprints. The frequency of the most prominent interactions was gauged in the AK inhibitors from PDB and the four representative conformations during 40 ns. Based on this study, seven major non-covalent interactions and their complementary sites in AK capable of rendering specificity have been prioritized for the design of different classes of inhibitors. PMID:25485544

  4. 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.

  5. 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. PMID:27213086

  6. Ligand field splittings in core level transitions for transition metal (TM) oxides: Tanabe-Sugano diagrams and (TM) dangling bonds in vacated O-atom defects

    Science.gov (United States)

    Lucovsky, Gerry; Wu, Kun; Pappas, Brian; Whitten, Jerry

    2013-04-01

    Defect states in the forbidden band-gap below the conduction band edge are active as electron traps in nano-grain high-) transition metal (TM) oxides with thickness >0.3 nm, e.g., ZrO2 and HfO2. These oxides have received considerable attention as gate-dielectrics in complementary metal oxide semiconductor (CMOS) devices, and more recently are emerging as candidates for charge storage and memory devices. To provide a theoretical basis for device functionality, ab-initio many-electron theory is combined with X-ray absorption spectroscopy (XAS) to study O K edge and TM core level transitions. These studies identify ligand field splittings (ΔLF) for defect state features,. When compared with those obtained from O-atom and TM-atom core spectroscopic transitions, this provides direct information about defect state sun-nm bonding arrangements. comparisons are made for (i) elemental TiO2 and Ti2O3 with different formal ionic charges, Ti4+ and Ti3+ and for (ii) Magneli Phase alloys, TinO2n-1, n is an integer 9>=n>3, and (TiO2)x(HfO2)1-x alloys. The alloys display multi-valent behavior from (i) different ionic-charge states, (ii} local bond-strain, and (iii) metallic hopping transport. The intrinsic bonding defects in TM oxides are identified as pairs of singly occupied dangling bonds. For 6-fold coordinated Ti-oxides defect excited states in 2nd derivative O K pre-edge spectra are essentially the same as single Ti-atom d2 transitions in Tanabe-Sugano (T-S) diagrams. O-vacated site defects in 8-fold coordinated ZrO2 and HfO2 are described by d8 T-S diagrams. T-S defect state ordering and splittings are functions of the coordination and symmetry of vacated site bordering TM atoms. ΔLF values from the analysis of T-S diagrams indicate medium range order (MRO) extending to 3rd and 4th nearest-neighbor (NN) TM-atoms. Values are different for 6-fold Ti, and 8-fold ZrO2 and HfO2, and scale inversely with differences in respective formal ionic radii. O-vacated site bonding

  7. Laser stabilization to an atomic transition using an optically generated dispersive lineshape

    CERN Document Server

    Queiroga, Fabiano; Mestre, Valdeci; Vidal, Itamar; de Silans, Thierry Passerat; Oriá, Marcos; Chevrollier, Martine

    2012-01-01

    We report on a simple and robust technique to generate a dispersive signal which serves as an error signal to electronically stabilize a monomode cw laser emitting around an atomic resonance. We explore nonlinear effects in the laser beam propagation through a resonant vapor by way of spatial filtering. The performance of this technique is validated by locking semiconductor lasers to the cesium and rubidiumD2 line and observing long-term reduction of the emission frequency drifts, making the laser well adapted for many atomic physics applications.

  8. Spin-Statistic Selection Rules for Multi-Equal-Photon Transitions in Atoms: Extension of the Landau-Yang Theorem to Multiphoton Systems

    CERN Document Server

    Zalialiutdinov, T; Labzowsky, L; Plunien, G

    2014-01-01

    We establish the existence of spin-statistic selection rules (SSSR) for multi-equal-photon transitions in atomic systems. These selection rules are similar to those for systems of many equivalent electrons in atomic theory. The latter ones are the direct consequence of Pauli exclusion principle. In this sense the SSSR play the role of the exclusion principle for photons: they forbid some particular states for the photon systems. We established several SSSR for few-photon systems. 1) First rule (SSSR-1): two-equivalent photons involved in any atomic transition can have only even values of the total angular momentum J. This selection rule is an extension of the Landau-Yang theorem to the photons involved in atomic transitions. 2) second rule (SSSR-2): three equivalent dipole photons involved in any atomic transition can have only odd values of the total angular momentum J=1,3. 3) third rule (SSSR-3): four equivalent dipole photons involved in any atomic transition can have only even values of the total angular ...

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

    Directory of Open Access Journals (Sweden)

    Chernykh Elena

    2017-01-01

    Full Text Available 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.

  10. Study of Microwave Multiphoton Transition of Rydberg Potassium Atom by Using B-Spline

    Institute of Scientific and Technical Information of China (English)

    JIN Cheng; ZHOU Xiao-Xin; ZHAO Song-Feng

    2005-01-01

    The B-spline expansion technique and time-dependent two-level approach are applied to study the interaction between the microwave field and potassium atoms in a static electric field. We obtain theoretical multiphoton resonance spectra that can be compared with the experimental data. We also obtain the time evolution of the final state in different microwave fields.

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  12. Quantum noise limited interferometric measurement of atomic noise: towards spin squeezing on the Cs clock transition

    CERN Document Server

    Oblak, D; Tittel, W; Vershovski, A K; Sørensen, J L; Petrov, P G; Alzar, C L G; Polzik, E S; Oblak, Daniel; Mikkelsen, Jens K.; Tittel, Wolfgang; Vershovski, Anton K.; Sorensen, Jens L.; Petrov, Plamen G.; Alzar, Carlos L. Garrido; Polzik, Eugene S.

    2003-01-01

    We investigate theoretically and experimentally a nondestructive interferometric measurement of the state population of an ensemble of laser cooled and trapped atoms. This study is a step towards generation of (quasi-) spin squeezing of cold atoms targeted at the improvement of the Caesium clock performance beyond the limit set by the quantum projection noise of atoms. We propose a protocol for the sequence of operations required to generate and utilize spin squeezing for the improved microwave clock performance via a quantum nondemolition measurement (qnd) on the probe light. We calculate the phase shift and the quantum noise of a near resonant optical probe pulse propagating through a cloud of cold 133Cs atoms. We analyze the figure of merit for a qnd measurement of the collective quasi-spin and show that it can be expressed simply as a product of the ensemble optical depth and the probability of the spontaneous emission caused by the off-resonant probe light. In the experimental part we report on the preli...

  13. Repumping and spectroscopy of laser-cooled Sr atoms using the (5s5p)3P2 - (5s4d)3D2 transition

    CERN Document Server

    Mickelson, P G; Anzel, P; DeSalvo, B J; Nagel, S B; Traverso, A J; Yan, M; Killian, T C

    2009-01-01

    We describe repumping and spectroscopy of laser-cooled strontium (Sr) atoms using the (5s5p)3P2 - (5s4d)3D2 transition. Atom number in a magneto-optical trap is enhanced by driving this transition because Sr atoms that have decayed into the (5s5p)3P2 dark state are repumped back into the (5s2)1S0 ground state. Spectroscopy of 84Sr, 86Sr, 87Sr, and 88Sr improves the value of the (5s5p)3P2 - (5s4d)3D2 transition frequency for 88Sr and determines the isotope shifts for the transition.

  14. Repumping and spectroscopy of laser-cooled Sr atoms using the (5s5p)3P2-(5s4d)3D2 transition

    Science.gov (United States)

    Mickelson, P. G.; Martinez de Escobar, Y. N.; Anzel, P.; De Salvo, B. J.; Nagel, S. B.; Traverso, A. J.; Yan, M.; Killian, T. C.

    2009-12-01

    We describe repumping and spectroscopy of laser-cooled strontium (Sr) atoms using the (5s5p)3P2-(5s4d)3D2 transition. Atom number in a magneto-optical trap is enhanced by driving this transition because Sr atoms that have decayed into the (5s5p)3P2 dark state are repumped back into the (5s2)1S0 ground state. Spectroscopy of 84Sr, 86Sr, 87Sr and 88Sr improves the value of the (5s5p)3P2-(5s4d)3D2 transition frequency and determines the isotope shifts for the transition accurately enough to guide laser-cooling experiments with less abundant isotopes.

  15. The formation of the W43 complex: constraining its atomic-to-molecular transition and searching for colliding clouds

    CERN Document Server

    Motte, F; Schneider, N; Heitsch, F; Glover, S; Carlhoff, P; Hill, T; Bontemps, S; Schilke, P; Louvet, F; Hennemann, M; Didelon, P; Beuther, H

    2014-01-01

    Numerical simulations have explored the possibility to form molecular clouds through either a quasi-static, self-gravitating mechanism or the collision of gas streams or lower-density clouds. They also quantitatively predict the distribution of matter at the transition from atomic to molecular gases. We aim to observationally test these models by studying the environment of W43, a molecular cloud complex near the tip of the Galactic long bar. Using Galaxy-wide HI and 12CO surveys we searched for gas flowing toward the W43 molecular cloud complex. We also estimated the HI and H2 mass surface densities to constrain the transition from atomic to molecular gas around and within W43. We found 3 cloud ensembles within the position-velocity diagrams of 12CO and HI gases. They are separated by 20km/s along the line of sight and extend into the 13CO velocity structure of W43. Since their velocity gradients are consistent with free-fall, they could be nearby clouds attracted by, and streaming toward, the W43 10^7Msun p...

  16. Spectroscopy of ^1S0 -- ^3P1^88Sr Atomic Transition in a 1.06 μm Optical Dipole Trap

    Science.gov (United States)

    Martinez de Escobar, Y. N.; Mickelson, P. G.; Traverso, A. J.; Killian, T. C.

    2008-05-01

    We studied the effects of laser light near-resonant with the ^1S0-- ^3P1^88Sr transition in an optical dipole trap (ODT). We observe laser cooling of our ODT atomic sample as the atoms collide in the presence of red-detuned 689 nm light. Heating of the atoms was also observed at a different range of frequency detunings while performing spectroscopy. Both processes were accompanied with atom loss, but the increase of phase space density observed during 689 nm laser cooling could aid pursuits of quantum degeneracy with Sr.

  17. Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET

    Science.gov (United States)

    Perdios, Louis; Lowe, Alan R.; Saladino, Giorgio; Bunney, Tom D.; Thiyagarajan, Nethaji; Alexandrov, Yuriy; Dunsby, Christopher; French, Paul M. W.; Chin, Jason W.; Gervasio, Francesco Luigi; Tate, Edward W.; Katan, Matilda

    2017-01-01

    Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo.

  18. Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET

    Science.gov (United States)

    Perdios, Louis; Lowe, Alan R.; Saladino, Giorgio; Bunney, Tom D.; Thiyagarajan, Nethaji; Alexandrov, Yuriy; Dunsby, Christopher; French, Paul M. W.; Chin, Jason W.; Gervasio, Francesco Luigi; Tate, Edward W.; Katan, Matilda

    2017-01-01

    Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo. PMID:28045057

  19. Forbidden M1 and E2 transitions in monovalent atoms and ions

    CERN Document Server

    Safronova, U I; Johnson, W R

    2016-01-01

    We carried out a systematic high-precision relativistic study of the forbidden magnetic-dipole and electric-quadrupole transitions in Ca+, Rb, Sr+, Cs, Ba+, Fr, Ra+, Ac2+, and Th3+. This work is motivated by the importance of these transitions for tests of fundamental physics and precision measurements. The relative importance of the relativistic, correlation, Breit correction, and contributions of negative-energy states is investigated. Recommended values of reduced matrix elements are presented together with their uncertainties. The matrix elements and resulting lifetimes are compared with other theoretical values and with experiment where available.

  20. 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...

  1. Dimensionality and Finite Number Effect on BCS Transition of Atomic Fermi Gas

    Institute of Scientific and Technical Information of China (English)

    CUI Hai-Tao; WANG Lin-Cheng; YI Xue-Xi

    2005-01-01

    The effect of finite number and dimensionality has been discussed in this paper. The finite number effect has a negative correction to final temperature for 2D or 3D atomic Fermi gases. The changing of final temperature obtained by scanning from BEC region to BCS region are 10% or so with N ≤ 103 and can be negligible when N > 103.However, in 1D atomic Fermi gas, the effect gives a positive correction which greatly changes the final temperature in Fermi gas. This behavior is completely opposed to the 2D and 3D cases and a proper explanation is still to be found.Dimensionality also has a positive correction, in which the more tightly trapping, the higher final temperature one gets with the same particle number. A discussion is also presented.

  2. Tunable band gap photoluminescence from atomically thin transition-metal dichalcogenide alloys.

    Science.gov (United States)

    Chen, Yanfeng; Xi, Jinyang; Dumcenco, Dumitru O; Liu, Zheng; Suenaga, Kazu; Wang, Dong; Shuai, Zhigang; Huang, Ying-Sheng; Xie, Liming

    2013-05-28

    Band gap engineering of atomically thin two-dimensional (2D) materials is the key to their applications in nanoelectronics, optoelectronics, and photonics. Here, for the first time, we demonstrate that in the 2D system, by alloying two materials with different band gaps (MoS2 and WS2), tunable band gap can be obtained in the 2D alloys (Mo(1-x)W(x)S(2) monolayers, x = 0-1). Atomic-resolution scanning transmission electron microscopy has revealed random arrangement of Mo and W atoms in the Mo(1-x)W(x)S(2) monolayer alloys. Photoluminescence characterization has shown tunable band gap emission continuously tuned from 1.82 eV (reached at x = 0.20) to 1.99 eV (reached at x = 1). Further, density functional theory calculations have been carried out to understand the composition-dependent electronic structures of Mo(1-x)W(x)S(2) monolayer alloys.

  3. Conformal Nets II: Conformal Blocks

    Science.gov (United States)

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

    2017-03-01

    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.

  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. 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...

  6. Thermal and quantum phase transitions in atom-field systems: a microcanonical analysis

    Science.gov (United States)

    Bastarrachea-Magnani, M. A.; Lerma-Hernández, S.; Hirsch, J. G.

    2016-09-01

    The thermodynamical properties of a generalized Dicke model are calculated and related with the critical properties of its energy spectrum, namely the quantum phase transitions (QPT) and excited state quantum phase transitions (ESQPT). The thermal properties are calculated both in the canonical and the microcanonical ensembles. The latter deduction allows for an explicit description of the relation between thermal and energy spectrum properties. While in an isolated system the subspaces with different pseudospin are disconnected, and the whole energy spectrum is accessible, in the statistical ensemble the situation is radically different. The multiplicity of the lowest energy states for each pseudospin completely dominates the thermal behavior, making the set of degenerate states with the smallest pseudospin at a given energy the only ones playing a role in the thermal properties. As a result, the states in the region with positive thermal energy cannot be thermally populated because their negligible probability, making that energy region thermally unreachable at finite temperatures. The quantum phase transitions of the lowest energy states, from a normal to a superradiant phase, produce the thermal transition. The other critical phenomena, the ESQPTs occurring at excited energies, have no manifestation in the thermodynamics, although their effects could be seen in finite size corrections. A new superradiant phase is found, which only exists in the generalized model, and can be relevant in finite size systems.

  7. 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

  8. 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.

  9. 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.)

  10. Search for Pauli Exclusion Principle Violating Atomic Transitions and Electron Decay with a P-type Point Contact Germanium Detector

    CERN Document Server

    Abgrall, N; Avignone, F T; Barabash, A S; Bertrand, F E; Bradley, A W; Brudanin, V; Busch, M; Buuck, M; Caldwell, A S; Chan, Y-D; Christofferson, C D; Chu, P -H; Cuesta, C; Detwiler, J A; Dunagan, C; Efremenko, Yu; Ejiri, H; Elliott, S R; Finnerty, P S; Galindo-Uribarri, A; Gilliss, T; Giovanetti, G K; Goett, J; Green, M P; Gruszko, J; Guinn, I S; Guiseppe, V E; Henning, R; Hoppe, E W; Howard, S; Howe, M A; Jasinski, B R; Keeter, K J; Kidd, M F; Konovalov, S I; Kouzes, R T; LaFerriere, B D; Leon, J; MacMullin, J; Martin, R D; Massarczyk, R; Meijer, S J; Mertens, S; Orrell, J L; O'Shaughnessy, C; Poon, A W P; Radford, D C; Rager, J; Rielage, K; Robertson, R G H; Romero-Romero, E; Shanks, B; Shirchenko, M; Suriano, A M; Tedeschi, D; Trimble, J E; Varner, R L; Vasilyev, S; Vetter, K; Vorren, K; White, B R; Wilkerson, J F; Wiseman, C; Xu, W; Yakushev, E; Yu, C -H; Yumatov, V; Zhitnikov, I

    2016-01-01

    A search for Pauli-exclusion-principle-violating K-alpha 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 5.8x10^30 seconds 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 6.8x10^30 seconds 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 76-Ge, could improve upon these exclusion limits by an order of magnitude after three years of operation.

  11. Lipid-induced conformational transition of the amyloid core fragment Abeta(28-35) and its A30G and A30I mutants.

    Science.gov (United States)

    Nagarajan, Sureshbabu; Ramalingam, Kirubagaran; Neelakanta Reddy, P; Cereghetti, Damiano M; Padma Malar, E J; Rajadas, Jayakumar

    2008-05-01

    The interaction of the beta-amyloid peptide (Abeta) with neuronal membranes could play a key role in the pathogenesis of Alzheimer's disease. Recent studies have focused on the interactions of Abeta oligomers to explain the neuronal toxicity accompanying Alzheimer's disease. In our study, we have investigated the role of lipid interactions with soluble Abeta(28-35) (wild-type) and its mutants A30G and A30I in their aggregation and conformational preferences. CD and Trp fluorescence spectroscopic studies indicated that, immediately on dissolution, these peptides adopted a random coil structure. Upon addition of negatively charged 1,2-dipalmitoyl-syn-glycero-3-phospho-rac-(glycerol) sodium salt (PG) lipid, the wild-type and A30I mutant underwent reorganization into a predominant beta-sheet structure. However, no conformational changes were observed in the A30G mutant on interaction with PG. In contrast, the presence of zwitterionic 1,2-dipalmitoyl-syn-glycero-3-phosphatidylcholine (PC) lipid had no effect on the conformation of these three peptides. These observations were also confirmed with atomic force microscopy and the thioflavin-T assay. In the presence of PG vesicles, both the wild-type and A30I mutant formed fibrillar structures within 2 days of incubation in NaCl/P(i), but not in their absence. Again, no oligomerization was observed with PC vesicles. The Trp studies also revealed that both ends of the three peptides are not buried deep in the vesicle membrane. Furthermore, fluorescence spectroscopy using the environment-sensitive probe 1,6-diphenyl-1,3,5-hexatriene showed an increase in the membrane fluidity upon exposure of the vesicles to the peptides. The latter effect may result from the lipid head group interactions with the peptides. Fluorescence resonance energy transfer experiments revealed that these peptides undergo a random coil-to-sheet conversion in solution on aging and that this process is accelerated by negatively charged lipid vesicles

  12. Protein Conformational Populations and Functionally Relevant Sub-states

    Energy Technology Data Exchange (ETDEWEB)

    Agarwal, Pratul K [ORNL; Burger, Virginia [University of Pittsburgh School of Medicine, Pittsburgh PA; Savol, Andrej [University of Pittsburgh School of Medicine, Pittsburgh PA; Ramanathan, Arvind [ORNL; Chennubhotla, Chakra [University of Pittsburgh School of Medicine, Pittsburgh PA

    2013-01-01

    Functioning proteins do not remain fixed in a unique structure, but instead they sample a range of conformations facilitated by motions within the protein. Even in the native state, a protein exists as a collection of interconverting conformations driven by thermodynamic fluctuations. Motions on the fast time scale allow a protein to sample conformations in the nearby area of its conformational landscape, while motions on slower time scales give it access to conformations in distal areas of the landscape. Emerging evidence indicates that protein landscapes contain conformational substates with dynamic and structural features that support the designated function of the protein. Nuclear magnetic resonance (NMR) experiments provide information about conformational ensembles of proteins. X-ray crystallography allows researchers to identify the most populated states along the landscape, and computational simulations give atom-level information about the conformational substates of different proteins. This ability to characterize and obtain quantitative information about the conformational substates and the populations of proteins within them is allowing researchers to better understand the relationship between protein structure and dynamics and the mechanisms of protein function. In this Account, we discuss recent developments and challenges in the characterization of functionally relevant conformational populations and substates of proteins. In some enzymes, the sampling of functionally relevant conformational substates is connected to promoting the overall mechanism of catalysis. For example, the conformational landscape of the enzyme dihydrofolate reductase has multiple substates, which facilitate the binding and the release of the cofactor and substrate and catalyze the hydride transfer. For the enzyme cyclophilin A, computational simulations reveal that the long time scale conformational fluctuations enable the enzyme to access conformational substates that allow

  13. Regime transition in electromechanical fluid atomization and implications to analyte ionization for mass spectrometric analysis.

    Science.gov (United States)

    Forbes, Thomas P; Degertekin, F Levent; Fedorov, Andrei G

    2010-11-01

    The physical processes governing the transition from purely mechanical ejection to electromechanical ejection to electrospraying are investigated through complementary scaling analysis and optical visualization. Experimental characterization and visualization are performed with the ultrasonically-driven array of micromachined ultrasonic electrospray (AMUSE) ion source to decouple the electrical and mechanical fields. A new dimensionless parameter, the Fenn number, is introduced to define a transition between the spray regimes, in terms of its dependence on the characteristic Strouhal number for the ejection process. A fundamental relationship between the Fenn and Strouhal numbers is theoretically derived and confirmed experimentally in spraying liquid electrolytes of different ionic strength subjected to a varying magnitude electric field. This relationship and the basic understanding of the charged droplet generation physics have direct implications on the optimal ionization efficiency and mass spectrometric response for different types of analytes.

  14. Evaluation of the 'mean frequency' technique. [sum approximation in perturbation theory for atomic transitions

    Science.gov (United States)

    Gaddy, E. M.; Reiss, H. R.

    1976-01-01

    The 'mean frequency' technique, a simple procedure introduced by Bebb and Gold for the approximate evaluation of sums occurring in high-order perturbation theory, represents a useful approximation method. Its predictions compare favorably to exact results obtained by Gontier and Trahin for multiphoton bound-bound transitions in hydrogen. However, the technique can be in error if the 'mean frequency' lies near certain integers.

  15. Structure and Thermodynamic Properties of Liquid Transition Metals with Different Embedded-Atom Method Models

    Institute of Scientific and Technical Information of China (English)

    王金照; 陈民; 过增元

    2002-01-01

    Pair distribution functions and constant-volume heat capacities of liquid copper, silver and nickel have been calculated by molecular dynamics simulations with four different versions of the embedded-atom method (EAM) model, namely, the versions of Johnson, Mei, Cai and Pohlong. The simulated structural properties with the four potential models show reasonable agreement with experiments and have little difference with each other, while the calculated heat capacities with the different EAM versions show remarkable discrepancies. Detailed analyses of the energy of the liquid metallic system show that, to predict successfully the heat capacity, an EAM model should match the state equation first proposed by Rose.

  16. 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.

  17. 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)

  18. [Investigation of enhancing effect for hydride generation-atomic fluorescence of transition metal elements].

    Science.gov (United States)

    Sun, Han-Wen; Suo, Ran

    2008-11-01

    A mechanism of hydride generation based on disassembly reaction of hydrogen-transferred interim state [M(BH4)m]* was developed by investigating the effect of reaction medium acidity on hydride generation. The effects of Co2+ and Ni2+, phenanthroline and 8-hydroxyquinoline on hydride generation-atomic fluorescence signals of Zn, Cd, Cu and Ni were studied, respectively, and their enhancing mechnism was discussed. The enhancing effect Co2+ and Ni2+ on the fluorescence signals of Zn and Cd was due to the increase in transmission efficiency of hydride of Zn and Cd. There was a synergic enhancing effect between phenanthroline or 8-hydroxyquinoline and Co2+ on the fluorescence signals of Zn and Cd, however no synergic enhancing effect between phenanthroline and 8-hydroxyquinoline on the fluorescence signals of Zn and Cd. The simulative action of cationic surfactant, anion surfactant and non-ionic surfactant surfactant to hydride generation was investigated. It is shown that both cationic surfactant and non-ionic surfactant have obvious enhancing effect on the fluorescence signals of analytes because of the decrease in surface tension of reaction solution. The release characteristics of hydride from the absorption solution containing surfactant was ulteriorly examined by using graphite furnace atomic absorption spectrometry, and the mechanism of enhancing effect of surfactant on hydride generation and transmission was proposed.

  19. 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...

  20. Role of Ge Switch in Phase Transition: Approach using Atomically Controlled GeTe/Sb2Te3 Superlattice

    Science.gov (United States)

    Tominaga, Juniji; Fons, Paul; Kolobov, Alexander; Shima, Takayuki; Chong, Tow Chong; Zhao, Rong; Koon Lee, Hock; Shi, Luping

    2008-07-01

    Germanium-antimony-tellurite (GST) is a very attractive material not only for rewritable optical media but also for realizing solid state devices. Recently, the study of the switching mechanism between the amorphous and crystal states has actively been carried out experimentally and theoretically. Now, the role of the flip-flop transition of a Ge atom in a distorted simple-cubic unit cell is the center of discussion. Turning our viewpoint towards a much wider region beyond a unit cell, we can understand that GeSbTe consists of two units: one is a Sb2Te3 layer and the other is a Ge2Te2 layer. On the based of this simple model, we fabricated the superlattice of GST alloys and estimated their thermal properties by differential scanning calorimetry (DSC). In this paper, we discuss the proof of the Ge switch on the basis of thermo-histories.

  1. Adsorption-induced shape transitions in bistable nanopores with atomically thin walls

    Science.gov (United States)

    Shklyaev, Oleg E.; Cole, Milton W.; Crespi, Vincent H.

    2017-01-01

    Atomically thin cylindrical nanopores can change shape in response to physically adsorbed gas inside. Coupled to a gas reservoir, an initially collapsed pore can expand to allow the adsorbed gas to form concentric shells on the inner part of the pore, driven by adsorption energetics, not gas pressure. A lattice gas model describes the evolution of the nanotube pore shape and absorbed gas as a function of gas chemical potential at zero temperature. We found that narrow-enough tubes are always expanded and gas inside adsorbs in sequences of concentric shells as the gas chemical potential increases. Wider tubes, which are collapsed without gas, can expand with one or more concentric shells adsorbed on the inner surface of the expanded region.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-04-21

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

  3. 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...

  4. Atomic Migration Induced Crystal Structure Transformation and Core-Centered Phase Transition in Single Crystal Ge2Sb2Te5 Nanowires.

    Science.gov (United States)

    Lee, Jun-Young; Kim, Jeong-Hyeon; Jeon, Deok-Jin; Han, Jaehyun; Yeo, Jong-Souk

    2016-10-12

    A phase change nanowire holds a promise for nonvolatile memory applications, but its transition mechanism has remained unclear due to the analytical difficulties at atomic resolution. Here we obtain a deeper understanding on the phase transition of a single crystalline Ge2Sb2Te5 nanowire (GST NW) using atomic scale imaging, diffraction, and chemical analysis. Our cross-sectional analysis has shown that the as-grown hexagonal close-packed structure of the single crystal GST NW transforms to a metastable face-centered cubic structure due to the atomic migration to the pre-existing vacancy layers in the hcp structure going through iterative electrical switching. We call this crystal structure transformation "metastabilization", which is also confirmed by the increase of set-resistance during the switching operation. For the set to reset transition between crystalline and amorphous phases, high-resolution imaging indicates that the longitudinal center of the nanowire mainly undergoes phase transition. According to the atomic scale analysis of the GST NW after repeated electrical switching, partial crystallites are distributed around the core-centered amorphous region of the nanowire where atomic migration is mainly induced, thus potentially leading to low power electrical switching. These results provide a novel understanding of phase change nanowires, and can be applied to enhance the design of nanowire phase change memory devices for improved electrical performance.

  5. 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.

  6. Conformational transitions of the catalytic domain of heme-regulated eukaryotic initiation factor 2α kinase, a key translational regulatory molecule.

    Science.gov (United States)

    Sreejith, R K; Suresh, C G; Bhosale, Siddharth H; Bhavnani, Varsha; Kumar, Avinash; Gaikwad, Sushama M; Pal, Jayanta K

    2012-01-01

    In mammalian cells, the heme-regulated inhibitor (HRI) plays a critical role in the regulation of protein synthesis at the initiation step through phosphorylation of α-subunit of the eukaryotic initiation factor 2 (eIF2). In this study we have cloned and performed biophysical characterization of the kinase catalytic domain (KD) of rabbit HRI. The KD described here comprises kinase 1, the kinase insertion domain (KI) and kinase 2. We report here the existence of an active and stable monomer of HRI (KD). The HRI (KD) containing three tryptophan residues was examined for its conformational transitions occurring under various denaturing conditions using steady-state and time-resolved tryptophan fluorescence, circular dichroism (CD) and hydrophobic dye binding. The parameter A and phase diagram analysis revealed multi-state unfolding and existence of three stable intermediates during guanidine hydrochloride (Gdn-HCl) induced unfolding of HRI (KD). The protein treated with 6 M Gdn-HCl showed collisional and static mechanism of acrylamide quenching and the constants (K(sv) = 3.08 M(-1) and K(s)= 5.62 M(-1)) were resolved using time resolved fluorescence titration. Based on pH, guanidine hydrochloride and temperature mediated transitions, HRI (KD) appears to exemplify a rigid molten globule-like intermediate with compact secondary structure, altered tertiary structure and exposed hydrophobic patches at pH 3.0. The results indicate the inherent structural stability of HRI (KD), a member of the class of stress response proteins.

  7. Measurements of transition probabilities for spin-changing lines of atomic ions used in diagnostics of astrophysical plasmas

    Science.gov (United States)

    Smith, P. L.; Johnson, B. C.; Kwong, H. S.; Parkinson, W. H.; Knight, R. D.

    1984-01-01

    The intensities of ultraviolet, spin-changing, 'intersystem' lines of low-Z atomic ions are frequently used in determinations of electron densities and temperatures in astrophysical plasmas as well as in measurements of element abundances in the interstellar gas. The transition probabilities (A-values) of these lines, which are about five orders of magnitude weaker than allowed lines, have not been measured heretofore and various calculations produce A-values for these lines that differ by as much as 50 percent A radio-frequency ion trap has been used for the first measurements of transition probabilities for intersystem lines seen in astronomical spectra. The measurement procedure is discussed and results for Si III, O III, N II, and C III are reviewed and compared to calculated values. Discrepancies exist; these indicate that some of the calculated A-values may be less reliable than has been beleived and that revisions to the electron densities determined for some astrophysical plasmas may be required.

  8. Forbidden 2 P- nP and 2 P- nF transitions in the energy spectrum of ultracold Rydberg lithium-7 atoms

    Science.gov (United States)

    Zelener, B. B.; Saakyan, S. A.; Sautenkov, V. A.; Manykin, E. A.; Zelener, B. V.; Fortov, V. E.

    2016-04-01

    Forbidden 2 P- nP and 2 P- nF transitions in the ranges of the principal quantum number n = 42-114 and n = 38-48 have been detected in the optical spectra of ultracold highly excited lithium-7 atoms. The presence of forbidden transitions is due to induced external electric fields. The quantum defects and ionization energy obtained in various experiments and predicted theoretically have been discussed.

  9. On the Roles of Substrate Binding and Hinge Unfolding in Conformational Changes of Adenylate Kinase

    Energy Technology Data Exchange (ETDEWEB)

    Brokaw, Jason B.; Chu, Jhih-wei

    2010-11-17

    We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier works of coarse-grained modeling. The trajectories of the all-atom molecular-dynamics simulations revealed the complexity of protein dynamics and the coupling between different domains during conformational change. Calculations of solvent density and density fluctuations surrounding AK did not show prominent variation during the transition between closed and open forms. Finally, we characterized the effects of local unfolding of an important hinge near Pro177 on the closed-to-open transition of AK and identified a novel mechanism by which hinge unfolding modulates protein conformational change. The local unfolding of Pro177 hinge induces alternative tertiary contacts that stabilize the closed structure and prevent the opening transition.

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

    Science.gov (United States)

    Yang, Fei; Xu, Ling; Zhang, Rui; Geng, Lei; Tong, Liang; Xu, Jun; Su, Weining; Yu, Yao; Ma, Zhongyuan; Chen, Kunji

    2012-10-01

    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 °C to 300 °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.

  11. Atomic-to-molecular gas phase transition triggered by the radio jet in Centaurus A

    CERN Document Server

    Salomé, Quentin; Combes, Françoise; Hamer, Stephen

    2016-01-01

    NGC 5128 (Centaurus A) is one of the best example to study AGN-feedback in the local Universe. At 13.5 kpc from the galaxy, optical filaments with recent star formation are lying along the radio-jet direction. We used the Atacama Pathfinder EXperiment (APEX) to map the CO(2-1) emission all along the filament structure. Molecular gas mass of 8.2x10^7 Msun was found over the 4.2 kpc-structure which represents about 3% of the total gas mass of the NGC 5128 cold gas content. Two dusty mostly molecular structure are identified, following the optical filaments. The region corresponds to the crossing of the radio jet with the Northern HI shell, coming from a past galaxy merger. One filament is located at the border of the HI shell, while the other is entirely molecular, and devoid of HI gas. The molecular mass is comparable to the HI mass in the shell, suggesting a scenario where the atomic gas was shocked and transformed in molecular clouds by the radio jet. Comparison with combined FIR Herschel and UV GALEX estima...

  12. 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...

  13. 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

    2015-03-01

    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.

  14. Spontaneous transitions in atomic system in the presence of high-intensity laser field

    Science.gov (United States)

    Bogatskaya, Anna; Volkova, Ekaterina; Popov, Alexander

    2016-10-01

    A new approach to the study of the spontaneous emission of the quantum system driven by a high-intensity laser field is developed. This approach is based on the accurate consideration of quantum system interaction with vacuum quantized field modes in the first order of perturbation theory, while the intense laser field is considered classically beyond the perturbation theory which allows to observe any-order stimulated processes governed by classical field. The proposed approach is applied to the study of a number of quantum systems in intense laser field. The obtained data are compared with those obtained in the frames of semiclassical approximation typically used for analyzing of the strong-field dynamic. It is found that the applicability of the semiclassical approach is strictly limited. It is valid for calculation of transitions to the initially populated state only if the population of this state is close to unity during the pulse and in the after-pulse regime. If its population is depleted, the semiclassical approach fails.

  15. Theory and computation of electromagnetic transition matrix elements in the continuous spectrum of atoms

    Science.gov (United States)

    Komninos, Yannis; Mercouris, Theodoros; Nicolaides, Cleanthes A.

    2017-01-01

    The present study examines the mathematical properties of the free-free ( f - f) matrix elements of the full electric field operator, O E (κ, r̅), of the multipolar Hamiltonian. κ is the photon wavenumber. Special methods are developed and applied for their computation, for the general case where the scattering wavefunctions are calculated numerically in the potential of the term-dependent ( N - 1) electron core, and are energy-normalized. It is found that, on the energy axis, the f - f matrix elements of O E (κ, r̅) have singularities of first order, i.e., as ɛ' → ɛ, they behave as ( ɛ - ɛ')-1. The numerical applications are for f - f transitions in hydrogen and neon, obeying electric dipole and quadrupole selection rules. In the limit κ = 0, O E (κ, r̅) reduces to the length form of the electric dipole approximation (EDA). It is found that the results for the EDA agree with those of O E (κ, r̅), with the exception of a wave-number region k' = k ± κ about the point k' = k.

  16. Solid-state ensemble of highly entangled photon sources at rubidium atomic transitions

    CERN Document Server

    Keil, Robert; Chen, Yan; Hoefer, Bianca; Zhang, Jiaxiang; Ding, Fei; Schmidt, Oliver G

    2016-01-01

    Semiconductor InAs/GaAs quantum dots grown by the Stranski-Krastanov method are among the leading candidates for the deterministic generation of polarization entangled photon pairs. Despite remarkable progress in the last twenty years, many challenges still remain for this material, such as the extremely low yield (<1% quantum dots can emit entangled photons), the low degree of entanglement, and the large wavelength distribution. Here we show that, with an emerging family of GaAs/AlGaAs quantum dots grown by droplet etching and nanohole infilling, it is possible to obtain a large ensemble (close to 100%) of polarization-entangled photon emitters on a wafer without any post-growth tuning. Under pulsed resonant two-photon excitation, all measured quantum dots emit single pairs of entangled photons with ultra-high purity, high degree of entanglement (fidelity up to F=0.91, with a record high concurrence C=0.90), and ultra-narrow wavelength distribution at rubidium transitions. Therefore, a solid-state quantum...

  17. 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.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2010-11-14

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

  19. Two-dimensional percolation transition at finite temperature: Phase boundary for in-plane magnetism in films with two atomic layers of Fe on W(110)

    Science.gov (United States)

    Belanger, R.; Venus, D.

    2017-02-01

    A two-dimensional (2D) percolation transition in Fe/W(110) ultrathin magnetic films occurs when islands in the second atomic layer percolate and resolve a frustrated magnetic state to produce long-range in-plane ferromagnetic order. Novel measurements of percolation using the magnetic susceptibility χ (θ ) as the films are deposited at a constant temperature, allow the long-range percolation transition to be observed as a sharp peak consistent with a critical phase transition. The measurements are used to trace the paramagnetic-to-ferromagnetic phase boundary between the T =0 percolation magnetic transition and the thermal Curie magnetic transition of the undiluted film. A quantitative comparison to critical scaling theory is made by fitting the functional form of the phase boundary. The fitted parameters are then used in theoretical expressions for χ (T ) in the critical region of the paramagnetic state to provide an excellent, independent representation of the experimental measurements.

  20. Use of surface plasmon resonance for real-time measurements of the global conformational transition in human phenylalanine hydroxylase in response to substrate binding and catalytic activation.

    Science.gov (United States)

    Flatmark, T; Stokka, A J; Berge, S V

    2001-07-15

    In the present study the optical biosensor technique, based on the surface plasmon resonance (SPR) phenomenon, was used for real-time measurements of the reversible binding of the pterin cofactor (6R)-l-erythro-5,6,7,8-tetrahydrobiopterin (BH(4)) and l-phenylalanine (l-Phe) to human phenylalanine hydroxylase (hPAH). When BH(4) (241 Da) was injected over the sensor chip with immobilized tetrameric wt-hPAH a positive DeltaRU response was observed with a square-wave type of sensorgram and a saturable response (about 25 RU/(pmol subunit/mm(2)) with a [S](0.5) value of 5.6 +/- 0.8 microM for the pterin cofactor. The rapid on-and-off rates were, however, not possible to determine. By contrast, when l-Phe (165 Da) was injected a time-dependent increase in RU (up to about 3 min) and a much higher saturable DeltaRU response (about 75 RU/(pmol subunit/mm(2)) at 2 mM l-Phe) than expected (i.e., <5 RU/(pmol subunit/mm(2))) from the low molecular mass of l-Phe were observed in the sensorgram. The half-time for the on-and-off rates were 6 +/- 2 and 9 +/- 1 s, respectively, at 2 mM l-Phe. The steady-state (apparent equilibrium) response revealed a hyperbolic concentration dependence with a [S](0.5) value of 98 +/- 7 microM. The [S](0.5) values of both pterin cofactor and l-Phe were lower than those determined by steady-state enzyme kinetic analysis. Evidence is presented that the DeltaRU response to l-Phe is accounted for by the global conformational transition which occurs in the enzyme upon l-Phe binding, i.e., by the slow reversible transition from a low activity state ("T"-state) to a high activity state ("R"-state) characteristic of this hysteretic enzyme.

  1. 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.

  2. Direct measurement of transition frequencies in isolated pHe+ atoms, and new CPT-violation limits on the antiproton charge and mass.

    Science.gov (United States)

    Hori, M; Eades, J; Hayano, R S; Ishikawa, T; Pirkl, W; Widmann, E; Yamaguchi, H; Torii, H A; Juhász, B; Horváth, D; Yamazaki, T

    2003-09-19

    A radio frequency quadrupole decelerator and achromatic momentum analyzer were used to decelerate antiprotons and produce p4He+ and p3He+ atoms in ultra-low-density targets, where collision-induced shifts of the atomic transition frequencies were negligible. The frequencies at near-vacuo conditions were measured by laser spectroscopy to fractional precisions of (6-19) x 10(-8). By comparing these with QED calculations and the antiproton cyclotron frequency, we set a new limit of 1 x 10(-8) on possible differences between the antiproton and proton charges and masses.

  3. Chiral nonracemic late-transition-metal organometallics with a metal-bonded stereogenic carbon atom: development of new tools for asymmetric organic synthesis.

    Science.gov (United States)

    Malinakova, Helena C

    2004-06-07

    Transition-metal-catalyzed cross-coupling reactions and the Heck reaction have evolved into powerful tools for the construction of carbon-carbon bonds. In most cases, the reactive organometallic intermediates feature a carbon-transition-metal sigma bond between a sp(2)-hybridized carbon atom and the transition metal (Csp(2)--TM). New, and potentially more powerful approach to transition-metal-catalyzed asymmetric organic synthesis would arise if catalytic chiral nonracemic organometallic intermediates with a stereogenic sp(3)-hybridized carbon atoms directly bonded to the transition metal (C*sp(3)--TM bond) could be formed from racemic or achiral organic substrates, and subsequently participate in the formation of a new carbon-carbon bond (C*sp(3)-C) with retention of the stereochemical information. To date, only a few catalytic processes that are based on this concept, have been developed. In this account, both "classical" and recent studies on preparation and reactivity of stable chiral nonracemic organometallics with a metal-bonded stereogenic carbon, which provide the foundation for the future design of new synthetic transformations exploiting the outlined concept, are discussed, along with examples of relevant catalytic processes.

  4. Conformal Infinity

    Science.gov (United States)

    Frauendiener, Jörg

    2004-12-01

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

  5. 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.

  6. 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.

  7. Sensitive search for the temporal variation of the fine structure constant using radio-frequency E1 transitions in atomic dysprosium

    CERN Document Server

    Nguyen, A T; Lamoreaux, S K; Torgerson, J R

    2003-01-01

    It has been proposed that the radio-frequency electric-dipole (E1) transition between two nearly degenerate opposite-parity states in atomic dysprosium should be highly sensitive to possible temporal variation of the fine structure constant ($\\alpha$) [V. A. Dzuba, V. V. Flambaum, and J. K. Webb, Phys. Rev. A {\\bf 59}, 230 (1999)]. We discuss here an experimental realization of the proposed search, which involves monitoring the E1 transition frequency over a period of time using direct frequency counting techniques. We estimate that a statistical sensitivity of $|\\adota| \\sim 10^{-18}$/yr may be achieved and discuss possible systematic effects in such a measurement.

  8. Doping anatase TIO_{2} with group V-b and VI-b transition metal atoms : a hybrid functional first-principles study

    OpenAIRE

    Matsubara, Masahiko; Saniz, Rolando; Partoens, Bart; Lamoen, Dirk

    2017-01-01

    Abstract: We investigate the role of transition metal atoms of group V-b (V, Nb, and Ta) and VI-b (Cr, Mo, and W) as n- or p-type dopants in anatase TiO2 using thermodynamic principles and density functional theory with the HeydScuseriaErnzerhof HSE06 hybrid functional. The HSE06 functional provides a realistic value for the band gap, which ensures a correct classification of dopants as shallow or deep donors or acceptors. Defect formation energies and thermodynamic transition levels are calc...

  9. Atomic sulfur: Frequency measurement of the J = 0 left arrow 1 fine-structure transition at 56.3 microns by laser magnetic resonance

    Science.gov (United States)

    Brown, John M.; Evenson, Kenneth M.; Zink, Lyndon R.

    1994-01-01

    The J = 0 left arrow 1 fine-structure transition in atomic sulfur (S I) in its ground (3)P state has been detected in the laboratory by far-infrared laser magnetic resonance. The fine-structure interval has been measured accurately as 5,322,492.9 +/- 2.8 MHz which corresponds to a wavelength of 56.325572 +/- 0.000030 micrometers.

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

    Directory of Open Access Journals (Sweden)

    X. D. Li

    2015-05-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Chang, Shan-Yan [Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 (China); Liu, Fu-Feng, E-mail: fufengliu@tju.edu.cn, E-mail: ysun@tju.edu.cn; Dong, Xiao-Yan; Sun, Yan, E-mail: fufengliu@tju.edu.cn, E-mail: ysun@tju.edu.cn [Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072 (China); Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072 (China)

    2013-12-14

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

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

    Science.gov (United States)

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

    2013-12-01

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

  13. Method of making dense, conformal, ultra-thin cap layers for nanoporous low-k ILD by plasma assisted atomic layer deposition

    Science.gov (United States)

    Jiang, Ying-Bing; Cecchi, Joseph L.; Brinker, C. Jeffrey

    2011-05-24

    Barrier layers and methods for forming barrier layers on a porous layer are provided. The methods can include chemically adsorbing a plurality of first molecules on a surface of the porous layer in a chamber and forming a first layer of the first molecules on the surface of the porous layer. A plasma can then be used to react a plurality of second molecules with the first layer of first molecules to form a first layer of a barrier layer. The barrier layers can seal the pores of the porous material, function as a diffusion barrier, be conformal, and/or have a negligible impact on the overall ILD k value of the porous material.

  14. 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....

  15. Atom probe study of Cu-poor to Cu-rich transition during Cu(In,Ga)Se2 growth

    Science.gov (United States)

    Couzinie-Devy, F.; Cadel, E.; Barreau, N.; Arzel, L.; Pareige, P.

    2011-12-01

    Atomic scale chemistry of polycrystalline Cu(In,Ga)Se2 (CIGSe) thin film has been characterized at key points of the 3-stage process using atom probe tomography. 3D atom distributions have been reconstructed when the layer is Cu-poor ([Cu]/([Ga] + [In]) 1), and at the end of the process. Particular attention has been devoted to grain boundary composition and Na atomic distribution within the CIGSe layer. Significant variation of composition is highlighted during the growing process, providing fundamental information helping the understanding of high efficiency CIGSe formation.

  16. Conformational changes at the highly reactive cystein and lysine regions of skeletal muscle myosin induced by formation of transition state analogues.

    Science.gov (United States)

    Maruta, S; Homma, K; Ohki, T

    1998-09-01

    Myosin forms stable ternary complexes with Mg2+-ADP and phosphate analogues of aluminum fluoride (AlF4-), beryllium fluoride (BeFn), and scandium fluoride (ScFn). These complexes are distinct from each other and may mimic different transient states in the ATPase cycle [Maruta et al. (1993) J. Biol. Chem. 268, 7093-7100]. Regions of skeletal muscle myosin containing the highly reactive residues Cys 707 (SH1), Cys 697 (SH2), and lysine 83 (RLR) dramatically alter their local conformation when myosin hydrolyzes ATP, and these changes may reflect formation of a series of transient intermediates during ATP hydrolysis. We used the fluorescent probes 4-fluoro-7-sulfamoylbezofurazan, 2-(4'-maleimidylanilino)naphthalene-6-sulfonic acid, and trinitrobenzene-sulfonate, which bind to SH1, SH2, and RLR, respectively, to examine differences in local conformations within myosin.ADP.phosphate analogue (BeFn, Vi, AlF4-, and ScFn) complexes. It was observed that the ternary complexes had SH1 conformations similar to those seen on S-1 in the presence of ATP. In contrast, local conformations in the SH2 and RLR regions of S-1.ADP.BeFn were different from those in corresponding regions of S-1.ADP.AlF4- or ScFn. These results suggest that SH1 and SH2 move distinctly during ATP hydrolysis and that the local conformations of the SH2 and RLR regions more sensitively reflect different transient states.

  17. Predicting the size- and shape-dependent cohesive energy and order-disorder transition temperature of Co-Pt nanoparticles by embedded-atom-method potential.

    Science.gov (United States)

    Liu, Chenze; Qi, Weihong; Ouyang, Bin; Wang, Xing; Huang, Baiyun

    2013-02-01

    The cohesive energy (CE) of CoPt nanoparticles (NPs) with different sizes and shapes have been calculated by embedded-atom-method (EAM) potential. It is shown that CE of NPs with order or disorder structures decreases with the decrease of particle size, while the shape effects become obvious only at small size. The CE difference per atom between order and disorder structures decreases with the decrease of particle size, indicating that the possibility of order-disorder transition in small size becomes larger compared with these in large size. Significantly, the CE difference varies in proportion to order-disorder transition temperature (T(c)), which suggests that one can predict order-disorder transition of NPs by calculation the cohesive energy. The present calculated T(c) of CoPt NPs is consistent with recent experiments, simulation and theoretical predictions, and the method can also be applied to study the order-disorder transition of FePt, FePd, and so on.

  18. Cytoskeletal re-arrangement in TGF-β1-induced alveolar epithelial-mesenchymal transition studied by atomic force microscopy and high-content analysis.

    Science.gov (United States)

    Buckley, Stephen T; Medina, Carlos; Davies, Anthony M; Ehrhardt, Carsten

    2012-04-01

    Epithelial-mesenchymal transition (EMT) is closely implicated in the pathogenesis of idiopathic pulmonary fibrosis. Associated with this phenotypic transition is the acquisition of an elongated cell morphology and establishment of stress fibers. The extent to which these EMT-associated changes influence cellular mechanics is unclear. We assessed the biomechanical properties of alveolar epithelial cells (A549) following exposure to TGF-β1. Using atomic force microscopy, changes in cell stiffness and surface membrane features were determined. Stimulation with TGF-β1 gave rise to a significant increase in stiffness, which was augmented by a collagen I matrix. Additionally, TGF-β1-treated cells exhibited a rougher surface profile with notable protrusions. Simultaneous quantitative examination of the morphological attributes of stimulated cells using an image-based high-content analysis system revealed dramatic alterations in cell shape, F-actin content and distribution. Together, these investigations point to a strong correlation between the cytoskeletal-associated cellular architecture and the mechanical dynamics of alveolar epithelial cells undergoing EMT. From the Clinical Editor: Epithelial-mesenchymal transition is implicated in the pathogenesis of pulmonary fibrosis. Using atomic force microscopy, the authors demonstrate a strong correlation between the cytoskeletal-associated cellular architecture and the mechanical dynamics of alveolar epithelial cells undergoing mesenchymal transition.

  19. Conformational re-analysis of (+)-meptazinol: an opioid with mixed analgesic pharmacophores

    Institute of Scientific and Technical Information of China (English)

    Wei LI; Xing-hai WANG; Choi-wan LAU; Yun TANG; Qiong XIE; Zhui-bai QIU

    2006-01-01

    Aim: To further investigate the analgesic pharmacophore of (+)-meptazinol. Methods: Two different opioid pharmacophores, Pharm-Ⅰ and Pharm-Ⅱ, were established from structures of nine typical opiates and meperidine by using molecular modeling approaches according to their different structure activity relationship properties. They were further validated by a set of conformationally constrained arylpiperidines. Two conformers of (+)-meptazinol (Conformer-Ⅰ and Con-former-Ⅱ) detected in solution were then fitted into the pharmacophores, respectively, by Fit Atoms facilities available in SYBYL, a computational modeling tool kit for molecular design and analysis. Results: Conformer-Ⅰ fit Pharm-Ⅰ from typical opiates well. However, Conformer-Ⅱ fit none of these pharmacophores. Instead, it was found to be similar to another potent analgesic, benzofuro[2,3-c] pyridin-6-ol, whose pharmacophore was suggested to hold the transitional state between the two established pharmacophores. Unlike typical analgesics derived from 4-aryl piperidine (eg, meperidine) with one conformer absolutely overwhelming, the (+)-meptazinol exists in two conformers with similar amounts in solution. Furthermore, both conformers can not transform to each other freely in ordinary conditions based on our NMR results. Conclusion: (+)-meptazinol was suggested to be an opioid with mixed analgesic pharmacophores, which may account for the complicated pharmacological properties of meptazinol.

  20. Conduction electrons as dissipation channel in friction experiments at the metal-metal transition of LSMO measured by contact-resonance atomic force microscopy

    Science.gov (United States)

    Pfahl, V.; Phani, M. K.; Büchsenschütz-Göbeler, M.; Kumar, A.; Moshnyaga, V.; Arnold, W.; Samwer, K.

    2017-01-01

    We report on friction measurements on a La0.6Sr0.4MnO3 (LSMO) thin film using atomic force microscopy cantilever contact-resonances. There is a contribution to the damping of the cantilever oscillations, which is caused by micro-sliding of the cantilever tip on the surface of the thin film. This frictional part decreases with temperature parallel to the increase in the resistivity of the thin film. The LSMO is well-known for a ferromagnetic to paramagnetic phase transition that occurs without changes in the rhombohedral (R-3c) crystalline structure. The magnetic transition at the Curie temperature TC ˜ 360 K is accompanied by a metal-to-metal transition with a large increase in electrical resistivity. The behavior of the cantilever damping constant demonstrates that there is a direct coupling between mechanical friction and the mobility of the electrons in the LSMO film.

  1. 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.

  2. Luminescence spectroscopy of matrix-isolated atomic manganese: excitation of the "forbidden" a6D(J)a6S transitions.

    Science.gov (United States)

    Collier, Martin A; Ryan, Maryanne C; McCaffrey, John G

    2005-07-22

    Laser-induced excitation spectra recorded for the electric-quadrupole 3d(6)4s a6D(J)transitions of atomic Mn, allow assignment of the red emission features, previously observed in Mn/RG (RG=Ar, Kr and Xe) matrices with resonance 3d(5)4s4pz6P(5/2)transition from the J=9/2 spin-orbit level. Temperature dependent emission scans lead to the identification of the zero phonon line for the a6D(9/2)-->a6S(5/2) transition at 585.75 nm. The identified matrix-shift of +20 cm(-1) allows an assessment of the extent of the ground state stabilization in the red (secondary) site of atomic Mn isolation in solid Kr. Emission produced with direct a6D state excitation yielded both the 585.75 and 626 nm features. The former band arises for Mn atoms occupying the red site--the latter from blue site occupancy in solid Kr. The excitation linewidths recorded for these two sites differ greatly, with the blue site yielding a broad featureless profile, in contrast to the narrow, structured features of the red site. The corresponding red site a6D(J)a6S(5/2) transitions in Ar and Xe matrices are broader than in Kr--a difference considered to originate from the site sizes available in these hosts and the interatomic Mn x RG potentials. The millisecond decay times recorded for the red emission bands in the Mn/RG systems are all much shorter than the 3 s value predicted for the gas phase a6D(9/2)-->a6S(5/2) transition. This enhancement allows optical pumping of the forbidden a6D(J)a6S transitions with low laser powers when atomic manganese is isolated in the solid state. However all the emission decays are complex, exhibiting triple exponential decays. This behavior may be related to the dependence of the excitation linewidths on the J value, indicating removal of the J degeneracy due to weak matrix-induced, crystal field splitting.

  3. Autler-Townes doublet in the absorption spectra for the transition between excited states of cold cesium atoms

    Institute of Scientific and Technical Information of China (English)

    Liang Qiang-Bing; Yang Bao-Dong; Yang Jian-Feng; Zhang Tian-Cai; Wang Jun-Min

    2010-01-01

    Autler-Townes splitting in absorption spectra of the excited states 6 2P3/2 - 82S1/2 of cold cesium atoms confined in a magneto-optical trap has been observed.Experimental data of the Autler-Townes splitting fit well to the dressedatom theory,by which the fact of the cold atoms dressed by cooling/trapping laser beams is revealed.The results of the theoretical fitting with experiment not only told us the effective Rabi frequency cold atoms experienced,but also could be used for measuring the probability amplitudes of the dressed states.

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

    Energy Technology Data Exchange (ETDEWEB)

    Yan, Pengfei [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Zheng, Jianming [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lv, Dongping [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Wei, Yi [Peking Univ., Beijing (China); Zheng, Jiaxin [Peking Univ., Beijing (China); Wang, Zhiguo [Univ. of Electronic Science and Technology of China, Chengdu (China); Kuppan, Saravanan [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Yu, Jianguo [Idaho National Lab. (INL), Idaho Falls, ID (United States); Luo, Langli [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Edwards, Danny J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Olszta, Matthew J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Amine, Khalil [Argonne National Lab. (ANL), Argonne, IL (United States); Liu, Jun [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Xiao, Jie [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Pan, Feng [Peking Univ., Beijing (China); Chen, Guoying [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Zhang, Jiguang [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Wang, Chong M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-07-06

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

  5. 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...

  6. Conformational changes in biopolymers

    Science.gov (United States)

    Ivanov, Vassili

    2005-12-01

    Biopolymer conformational changes are involved in many biological processes. This thesis summarizes some theoretical and experimental approaches which I have taken at UCLA to explore conformational changes in biopolymers. The reversible thermal denaturation of the DNA double helix is, perhaps, the simplest example of biopolymer conformational change. I have developed a statistical mechanics model of DNA melting with reduced degrees of freedom, which allows base stacking interaction to be taken into account and treat base pairing and stacking separately. Unlike previous models, this model describes both the unpairing and unstacking parts of the experimental melting curves and explains the observed temperature dependence of the effective thermodynamic parameters used in models of the nearest neighbor type. I developed a basic kinetic model for irreversible thermal denaturation of F-actin, which incorporates depolymerization of F-actin from the ends and breaking of F-actin fiber in the middle. The model explains the cooperativity of F-actin thermal denaturation observed by D. Pavlov et al. in differential calorimetry measurements. CG-rich DNA sequences form left-handed Z-DNA at high ionic strength or upon binding of polyvalent ions and some proteins. I studied experimentally the B-to-Z transition of the (CG)6 dodecamer. Improvement of the locally linearized model used to interpret the data gives evidence for an intermediate state in the B-to-Z transition of DNA, contrary to previous research on this subject. In the past 15 years it has become possible to study the conformational changes of biomolecules using single-molecule techniques. In collaboration with other lab members I performed a single-molecule experiment, where we monitored the displacement of a micrometer-size bead tethered to a surface by a DNA probe undergoing the conformational change. This technique allows probing of conformational changes with subnanometer accuracy. We applied the method to detect

  7. Atomic scale visualization of novel magnetic phase transitions in Fe-based superconductor Sr4V2O6Fe2As2

    Science.gov (United States)

    Choi, Seokhwan; Jang, Won-Jun; Ok, Jong Mok; Choi, Hyun Woo; Lee, Hyun Jung; Jung, Jin Oh; Son, Dong Hyun; Suh, Hwan Soo; Kim, Jun Sung; Semertzidis, Yannis K.; Lee, Jhinhwan

    Sr4V2O6Fe2As2 consists of superconducting FeAs layers and Mott insulating Sr2VO3 layers, and exhibits superconductivity with Tc near 30 K despite being a parent compound material. Unlike normal Fe-based superconductors, the magnetism of Sr4V2O6Fe2As2 has complexity due to the presence of two magnetic atomic layers of V and Fe; therefore, the issue of magnetism has been actively debated. In this work, we studied the orbital and magnetic phase transitions in the range of 4 K to 180 K using spin-polarized scanning tunneling microscope. We directly observed the changes of charge density waves of V atomic layer related to the nematicity at 150 K, and spin density waves of V atomic layer resulting from spin ordering of underlying Fe atomic layer below 50 K. Moreover, controlling the sample bias voltage, the hysteresis of magnetic domain is observed at 4 K. Our results show key clues to solve controversy about the magnetism of Sr4V2O6Fe2As2.

  8. Fine splits of photon emission spectrum of hydrogen atom caused by transitions between different dressed states in intense high frequency laser field

    Institute of Scientific and Technical Information of China (English)

    Zhou Zhao-Yan; Yuan Jian-Min

    2008-01-01

    The photon emission spectrum of the hydrogen atoms in an intense high-frequency laser pulse is simulated by using one-dimensional soft Coulomb potential. Regular fine structures appear on the two sides of both the odd and even multiples of photon energy of the laser field besides the ordinary odd harmonic peaks. It is proved that the splits of the fine structures are responsible for hyper-Raman lines and the energy spacing between the odd harmonic lines is equal to the difference in energy between the eigenstates with the same parity of the time averaged Krameters-Henneberger (KH) potential. By analysing the features of the fine structures, we also verify that the so-called even order harmonics under the stabilization condition are indeed hyper-Raman lines caused by the transitions between the dressed atomic states with different values of parity.

  9. 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 properties according to specific functionality targets. The differences in the spectra could be used to identify relative abundances of isomers with different spins in experimental studies. As a salient feature, this theoretical spectroscopic analysis predicts the metallization of the infinite (Ti......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...... of layers, including infinite chains, are considered. The lowest excitation energy peaks in the spectra are characteristic of the robust bonding in these complexes. The excitation energies vary in a systematic way with the metal atoms and with the cluster size, and so these materials could be used to tune...

  10. Probing the conformation and 2D-distribution of pyrene-terminated redox-labeled poly(ethylene glycol) chains end-adsorbed on HOPG using cyclic voltammetry and atomic force electrochemical microscopy.

    Science.gov (United States)

    Anne, Agnès; Bahri, Mohamed Ali; Chovin, Arnaud; Demaille, Christophe; Taofifenua, Cécilia

    2014-03-14

    The present paper aims at illustrating how end-attachment of water-soluble flexible chains bearing a terminal functional group onto graphene-like surfaces has to be carefully tuned to ensure the proper positioning of the functional moiety with respect to the anchoring surface. The model experimental system considered here consists of a layer of poly(ethylene glycol) (PEG) chains, bearing an adsorbing pyrene foot and a ferrocene (Fc) redox functional head, self-assembled onto highly oriented pyrolytic graphite (HOPG). Cyclic voltammetry is used to accurately measure the chain coverage and gain insights into the microenvironment experienced by the Fc heads. Molecule-touching atomic force electrochemical microscopy (Mt/AFM-SECM) is used to simultaneously probe the chain conformation and the position of the Fc heads within the layer, and also to map the 2D-distribution of the chains over the surface. This multiscale electrochemical approach allows us to show that whereas Fc-PEG-pyrene readily self-assembles to form extremely homogeneous layers, the strongly hydrophobic nature of graphite planes results in a complex coverage-dependent structure of the PEG layer due to the interaction of the ferrocene label with the HOPG surface. It is shown that, even though pyrene is known to adsorb particularly strongly onto HOPG, the more weakly adsorbing terminal ferrocene can also act as the chain anchoring moiety especially at low coverage. However we show that beyond a critical coverage value the Fc-PEG-pyrene chains adopt an ideal "foot-on" end-attached conformation allowing the Fc head to explore a volume away from the surface solely limited by the PEG chain elasticity.

  11. Interaction-induced quantum phase revivals and evidence for the transition to the quantum chaotic regime in 1D atomic Bloch oscillations.

    Science.gov (United States)

    Meinert, F; Mark, M J; Kirilov, E; Lauber, K; Weinmann, P; Gröbner, M; Nägerl, H-C

    2014-05-16

    We study atomic Bloch oscillations in an ensemble of one-dimensional tilted superfluids in the Bose-Hubbard regime. For large values of the tilt, we observe interaction-induced coherent decay and matter-wave quantum phase revivals of the Bloch oscillating ensemble. We analyze the revival period dependence on interactions by means of a Feshbach resonance. When reducing the value of the tilt, we observe the disappearance of the quasiperiodic phase revival signature towards an irreversible decay of Bloch oscillations, indicating the transition from regular to quantum chaotic dynamics.

  12. Electromagnetically induced absorption due to transfer of coherence and coherence population oscillation for the Fg = 3 →Fe = 4 transition in 85Rb atoms

    Science.gov (United States)

    Rehman, Hafeez Ur; Mohsin, Muhammad Qureshi; Noh, Heung-Ryoul; Kim, Jin-Tae

    2016-12-01

    Lineshapes for the electromagnetically induced absorption (EIA) of thermal 85Rb atoms in a degenerate two-level system have been investigated using matching (σ∥σ , π∥π) and orthogonal (σ ⊥ σ , π ⊥ π) polarization configurations of coupling and probe beams. EIA signals, which result from coherence population oscillation and transfer of coherence of the excited state, are obtained in detail theoretically and experimentally. The observed EIA linewidths, which are limited due to the decoherence rate between the magnetic sublevels in the ground state from transit-time relaxation, match well with the calculated ones. Decompositions of the absorption signals analyzed with respect to magnetic sublevels of the ground state show that enhanced or decreased absorption signals for each component of magnetic sublevels in the ground state depend on several factors. These factors include the decay rates and transition strengths, which determine the overall absorption spectral profile.

  13. 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 types......, 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......C, delta-MoC, TaC, and WC (in NaCl structure) and the adsorbates H, B, C, N, O, F, NH, NH2, and NH3. 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...

  14. Joined X-ray, spectroscopic and theoretical study of potential antibacterial cyano group containing fluoroquinolone drugs precursors with the focus on the conformational behavior

    Science.gov (United States)

    Dorotíková, Sandra; Kucková, Lenka; Malček, Michal; Plevová, Kristína; Kožíšek, Jozef; Milata, Viktor; Dvoranová, Dana; Bučinský, Lukáš

    2016-12-01

    Conformational behavior of 3-fluorophenylaminoethylene precursors of potential antibacterial fluoroquinolone drugs are investigated by the comparison of obtained experimental X-ray structures, IR vibrational frequencies and UV-vis transitions with B3LYP/6-311++G** theoretical calculations. Theoretical investigations of the conformational behavior are extended for the rotational energy barriers between ZZa-EZa and ZZa-ZEa conformers which are investigated along with the change of bond critical points characteristics and delocalization indices of quantum theory of atoms in molecules (including atomic and formal functional group charges). Subsequently, molecular dynamics simulations are presenting a critical assessment of the dynamics of distinguished dihedral angles which are related to the conformational behavior.

  15. A double-interferometer laser system for cold 87Rb atom gyroscopes based on stimulated Raman transitions

    CERN Document Server

    Song, Ningfang; Li, Wei; Li, Yang; Liu, Jixun; Xu, Xiaobin; Pan, Xiong

    2014-01-01

    We proposed and implemented a double-interferometer laser system to manipulate cold 87Rb atoms to interfere. A frequency-modulated continuous-wave technique was applied to determine and compensate the optical path difference between the two Raman beams. With a coherent self-heterodyne method, the beat signal's FWHM linewidth was measured and the obtained linewidth of ~1Hz mainly limited by the resolution bandwidth of the spectrum analyzer indicates a good coherence degree of the two Raman beams, paving the way to realize a highly sensitive atom gyroscope.

  16. The Transition from Atomic to Molecular Hydrogen in Interstellar Clouds: 21cm Signature of the Evolution of Cold Atomic Hydrogen in Dense Clouds

    CERN Document Server

    Goldsmith, P F; Krco, M; Goldsmith, Paul F.; Li, Di; Krco, Marko

    2006-01-01

    We have investigated the time scale for formation of molecular clouds by examining the conversion of HI to H2 using a time-dependent model. H2 formation on dust grains and cosmic ray and photo destruction are included in one-dimensional model slab clouds which incorporate time-independent density and temperature distributions. We calculate 21cm spectral line profiles seen in absorption against a background provided by general Galactic HI emission, and compare the model spectra with HI Narrow Self-Absorption, or HINSA, profiles absorbed in a number of nearby molecular clouds. The time evolution of the HI and H2 densities is dramatic, with the atomic hydrogen disappearing in a wave propagating from the central, denser regions which have a shorter H2 formation time scale, to the edges, where the density is lower and the time scale for H2 formation longer. The model 21cm spectra are characterized by very strong absorption at early times, when the HI column density through the model clouds is extremely large. The ...

  17. Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

    Science.gov (United States)

    Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

    2016-08-25

    Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and

  18. 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.

  19. Remote sensing of atomic oxygen - Some observational difficulties in the use of the forbidden O I 1173-A and O I 1641-A transitions

    Science.gov (United States)

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

    1987-01-01

    Recent sounding rocket and satellite studies suggest that simultaneous measurements of the O I 989-A and 1304-A resonance lines and of the forbidden 1172.6-A and 1641.3-A transitions would form the basis of a useful remote sensing technique for measuring the O I density and optical opacity of a planetary or stellar atmosphere. Because the 1172.6-A and 1641.3-A emissions are weak lines and are emitted in a wavelength region rich in spectral features, it is important to determine whether typical flight instruments can make measurements with sufficient spectral purity so that the remote sensing observations will yield accurate results. A detailed, high-resolution study of the far UV emission features in the regions surrounding the atomic oxygen transitions at 1172.6 and 1641.3 A was made. These spectra, which were excited by electron impact on O2 and N2, are presented in an attempt to display some potential sources of interference in aeronomical measurements of these O I lines. Both atomic and molecular emissions are found, and the spectral resolution necessary to make unambiguous measurements is discussed.

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

    Science.gov (United States)

    Chu, S.

    1976-10-01

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

  1. 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.

  2. Suppression of angular momentum transfer in cold collisions of transition metal atoms in ground States with nonzero orbital angular momentum.

    Science.gov (United States)

    Hancox, Cindy I; Doret, S Charles; Hummon, Matthew T; Krems, Roman V; Doyle, John M

    2005-01-14

    The Zeeman relaxation rate in cold collisions of Ti(3d(2)4s(2) 3F2) with He is measured. We find that collisional transfer of angular momentum is dramatically suppressed due to the presence of the filled 4s(2) shell. The degree of electronic interaction anisotropy, which is responsible for Zeeman relaxation, is estimated to be about 200 times smaller in the Ti-He complex than in He complexes with typical non-S-state atoms.

  3. Four complete turns of a curved 3₁₀-helix at atomic resolution: the crystal structure of the peptaibol trichovirin I-4A in a polar environment suggests a transition to α-helix for membrane function.

    Science.gov (United States)

    Gessmann, Renate; Axford, Danny; Owen, Robin L; Brückner, Hans; Petratos, Kyriacos

    2012-02-01

    The first crystal structure of a member of peptaibol antibiotic subfamily 4, trichovirin I-4A (14 residues), has been determined by direct methods and refined at atomic resolution. The monoclinic unit cell has two molecules in the asymmetric unit. Both molecules assume a 3₁₀ right-handed helical conformation and are significantly bent. The molecules pack loosely along the crystallographic twofold axis, forming two large tunnels between symmetry-related molecules in which no ordered solvent could be located. Carbonyl O atoms which are not involved in intramolecular hydrogen bonding participate in close van der Waals interactions with apolar groups. The necessary amphipathicity for biological activity of peptaibols is not realised in the crystal structure. Hence, a structural change of trichovirin to an α-helical conformation is proposed for membrane integration and efficient water/ion transportation across the lipid bilayer.

  4. 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)

  5. Conformal invariant saturation

    CERN Document Server

    Navelet, H

    2002-01-01

    We show that, in onium-onium scattering at (very) high energy, a transition to saturation happens due to quantum fluctuations of QCD dipoles. This transition starts when the order alpha^2 correction of the dipole loop is compensated by its faster energy evolution, leading to a negative interference with the tree level amplitude. After a derivation of the the one-loop dipole contribution using conformal invariance of the elastic 4-gluon amplitude in high energy QCD, we obtain an exact expression of the saturation line in the plane (Y,L) where Y is the total rapidity and L, the logarithm of the onium scale ratio. It shows universal features implying the Balitskyi - Fadin - Kuraev - Lipatov (BFKL) evolution kernel and the square of the QCD triple Pomeron vertex. For large L, only the higher BFKL Eigenvalue contributes, leading to a saturation depending on leading log perturbative QCD characteristics. For initial onium scales of same order, however, it involves an unlimited summation over all conformal BFKL Eigen...

  6. On the stochastic dynamics of molecular conformation

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    An important functioning mechanism of biological macromolecules is the transition between different conformed states due to thermal fluctuation. In the present paper, a biological macromolecule is modeled as two strands with side chains facing each other, and its stochastic dynamics including the statistics of stationary motion and the statistics of conformational transition is studied by using the stochastic averaging method for quasi Hamiltonian systems. The theoretical results are confirmed with the results from Monte Carlo simulation.

  7. Theoretical expression of the internal conversion coefficient of a M{sub 1} transition between two atomic states; Expression theorique du coefficient de conversion interne entre deux etats atomiques lies par une transition M{sub 1}

    Energy Technology Data Exchange (ETDEWEB)

    Attallah, F.; Chemin, J.F.; Scheurer, J.N.; Karpeshin, F.; Harston, M. [Centre d`Etudes Nucleaires, Bordeaux-1 Univ., 33 Gradignan (France)

    1997-06-01

    We have established a general relation for the expression of the internal conversion of an M{sub 1} transition a 1s electronic state to an empty ns electronic bound state. Under the hypothesis that the density of the electron level {rho}{sub n} satisfies the condition {rho}{sub n}{Gamma} >> 1 (where {Gamma} is the total width of the excited atomic state) a calculation in the first order gives a relation for the internal conversion coefficient.This relation shows that the internal conversion coefficient takes a resonant character when the nuclear energy transition is smaller than the binding energy of the 1s electron. An application of this relation to an M{sub 1} transition in the case of the ion {sup 125}T{sub e} with a charge state Q = 45 and an 1s electron binding energy E{sub B}{sup 45} = 35.581 KeV gives the value for the internal conversion coefficient R = 5.7 3 refs.

  8. 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.

  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 physics

    Energy Technology Data Exchange (ETDEWEB)

    Livingston, A.E.; Kukla, K.; Cheng, S. [Univ. of Toledo, OH (United States)] [and others

    1995-08-01

    In a collaboration with the Atomic Physics group at Argonne and the University of Toledo, the Atomic Physics group at the University of Notre Dame is measuring the fine structure transition energies in highly-charged lithium-like and helium-like ions using beam-foil spectroscopy. Precise measurements of 2s-2p transition energies in simple (few-electron) atomic systems provide stringent tests of several classes of current atomic- structure calculations. Analyses of measurements in helium-like Ar{sup 16+} have been completed, and the results submitted for publication. A current goal is to measure the 1s2s{sup 3}S{sub 1} - 1s2p{sup 3}P{sub 0} transition wavelength in helium-like Ni{sup 26+}. Measurements of the 1s2s{sup 2}S{sub 1/2} - 1s2p{sup 2}P{sub 1/2,3/2} transition wavelengths in lithium-like Kr{sup 33+} is planned. Wavelength and lifetime measurements in copper-like U{sup 63+} are also expected to be initiated. The group is also participating in measurements of forbidden transitions in helium-like ions. A measurement of the lifetime of the 1s2s{sup 3}S{sub 1} state in Kr{sup 34+} was published recently. In a collaboration including P. Mokler of GSI, Darmstadt, measurements have been made of the spectral distribution of the 2E1 decay continuum in helium-like Kr{sup 34+}. Initial results have been reported and further measurements are planned.

  11. Simulating Protein Conformations through Global Optimization

    CERN Document Server

    Mucherino, A; Pardalos, P M

    2008-01-01

    Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein conformations. This simple model is based on the idea of imposing few geometric requirements on chains of atoms representing the backbone of a protein conformation. The model leads to the formulation of a global optimization problem, whose solutions correspond to conformations satisfying the desired requirements. The global optimization problem is solved by the recently proposed Monkey Search algorithm. The simplicity of the optimization problem and the effectiveness of the used meta-heuristic search allowed the simulation of a large set of high-quality conformations. We show that, even though only few geometric requirements are imposed, some of the simulated conformation results to be similar (in terms of RMSD) to conformations real proteins actually have in nature.

  12. Dopant-induced 2D-3D transition in small Au-containing clusters: DFT-global optimisation of 8-atom Au-Ag nanoalloys.

    Science.gov (United States)

    Heiles, Sven; Logsdail, Andrew J; Schäfer, Rolf; Johnston, Roy L

    2012-02-21

    A genetic algorithm (GA) coupled with density functional theory (DFT) calculations is used to perform global optimisations for all compositions of 8-atom Au-Ag bimetallic clusters. The performance of this novel GA-DFT approach for bimetallic nanoparticles is tested for structures reported in the literature. New global minimum structures for various compositions are predicted and the 2D-3D transition is located. Results are explained with the aid of an analysis of the electronic density of states. The chemical ordering of the predicted lowest energy isomers are explained via a detailed analysis of the charge separation and mixing energies of the bimetallic clusters. Finally, dielectric properties are computed and the composition and dimensionality dependence of the electronic polarizability and dipole moment is discussed, enabling predictions to be made for future electric beam deflection experiments.

  13. Crossing the dividing surface of transition state theory. II. Recrossing times for the atom-diatom interaction

    Science.gov (United States)

    Lorquet, J. C.

    2014-04-01

    We consider a triatomic system with zero total angular momentum and demonstrate that, no matter how complicated the anharmonic part of the potential energy function, classical dynamics in the vicinity of a saddle point is constrained by symmetry properties. At short times and at not too high energies, recrossing dynamics is largely determined by elementary local structural parameters and thus can be described in configuration space only. Conditions for recrossing are given in the form of inequalities involving structural parameters only. Explicit expressions for recrossing times, valid for microcanonical ensembles, are shown to obey interesting regularities. In a forward reaction, when the transition state is nonlinear and tight enough, one-fourth of the trajectories are expected to recross the plane R = R* (where R* denotes the position of the saddle point) within a short time. Another fourth of them are expected to have previously recrossed at a short negative time, i.e., close to the saddle point. These trajectories do not contribute to the reaction rate. The reactive trajectories that obey the transition state model are to be found in the remaining half. However, no conclusion can be derived for them, except that if recrossings occur, then they must either take place in the distant future or already have taken place in the remote past, i.e., far away from the saddle point. Trajectories that all cross the plane R = R* at time t = 0, with the same positive translational momentum P_{R_* } can be partitioned into two sets, distinguished by the parity of their initial conditions; both sets have the same average equation of motion up to and including terms cubic in time. Coordination is excellent in the vicinity of the saddle point but fades out at long (positive or negative) times, i.e., far away from the transition state.

  14. 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.

  15. Magnetic dipolar and quadrupolar transitions in two-electron atoms under exponential-cosine-screened Coulomb potential

    Energy Technology Data Exchange (ETDEWEB)

    Modesto-Costa, Lucas; Canuto, Sylvio [Instituto de Física, Universidade de São Paulo, CP 66318, 05314-970 São Paulo (Brazil); Mukherjee, Prasanta K., E-mail: profpkmukherjee@gmail.com [Department of Physics, Ramakrishna Mission Vivekananda University, P.O. Belur Math, Howrah, West Bengal 711202 (India)

    2015-03-15

    A detailed investigation of the magnetic dipolar and quadrupolar excitation energies and transition probabilities of helium isoelectronic He, Be{sup 2+}, C{sup 4+}, and O{sup 6+} have been performed under exponential cosine screened Coulomb potential generated in a plasma environment. The low-lying excited states 1s{sup 2}:{sup 1}S{sup e} → 1sns:{sup 3}S{sup e}{sub 0}, and 1snp:{sup 3}P{sup o}{sub 2} (n = 2, 3, 4, and 5) are considered. The variational time-dependent coupled Hartree-Fock scheme has been used. The effect of the confinement produced by the potential on the structural properties is investigated for increasing coupling strength of the plasma. It is noted that there is a gradual destabilization of the energy of the system with the reduction of the ionization potential and the number of excited states. The effect of the screening enhancement on the excitation energies and transition probabilities has also been investigated and the results compared with those available for the free systems and under the simple screened Coulomb potential.

  16. Measurement of the scalar polarizability within the 5P1/2-6S1/2, 410 nm transition in atomic indium

    CERN Document Server

    Ranjit, G; Lorenzo, A T; Schneider, A E; Majumder, P K

    2013-01-01

    We have completed a new measurement of the Stark shift in 115In within the 410 nm 5P1/2- 6S1/2 transition. We measure the Stark shift constant to be kS= - 122.92(33)kHz/(kV/cm)^2, corresponding to a difference in the 6S1/2 and 5P1/2 state polarizabilities, \\Delta\\alpha_0, of 1000.2 (2.7) a.u.(in atomic units). This result is a factor of 30 more precise than previous measurements and is in excellent agreement with a new theoretical value based on an ab initio calculation of the wave functions in this three-valence-electron system. The measurement was performed in an indium atomic beam apparatus, used a GaN laser diode system, and exploited an FM spectroscopy technique to extract laser transmission spectra under conditions where our interaction region optical depth was typically less than 10^-3.

  17. Electronic structures and magnetic properties of the transition-metal atoms (Mn, Fe, Co and Ni) doped WS2: A first-principles study

    Science.gov (United States)

    Xie, Ling-Yun; Zhang, Jian-Min

    2016-10-01

    The spin-polarized first-principles calculations are performed to study the electronic structures and magnetic properties of a single or double identical transition metal (TM) atoms X (X = Mn, Fe, Co and Ni) doped monolayer WS2 systems. Although the pristine monolayer WS2 system is a nonmagnetic semiconductor with a direct band gap of 1.820 eV, a single Mn, Fe, Co or Ni doped WS2 systems exhibit the magnetic half-metallic (HM) characters with the total magnetic moments Mtot of 1, 2, 3 and 4 μB and the smaller spin-down gaps Eg of 1.262, 1.154, 1.407 and 1.073 eV, respectively. For double identical TM atoms doped monolayer WS2 systems, except for the cases of two Ni atoms doped at the first (0,1), second (0,2) and third (0,3) nearest-neighbor cation configuration which are antiferromagnetic (AFM), ferromagnetic (FM) and FM metals, respectively, the other cases are all HM ferromagnets, and the total magnetic moment Mtot increases not only for double identical TM dopants Mn, Fe, Co and Ni (except for (0,1) AFM case) successively at the same nearest-neighbor cation configuration but also for each of the double identical TM dopants at the first (0,1), second (0,2) and third (0,3) nearest-neighbor cation configurations successively. These results provide a theoretical guide to choose new two-dimensional HM ferromagnetic materials in spintronic applications.

  18. Conformal transformations and conformal invariance in gravitation

    CERN Document Server

    Dabrowski, Mariusz P; Blaschke, David B

    2008-01-01

    Conformal transformations are frequently used tools in order to study relations between various theories of gravity and Einstein relativity. Because of that, in this paper we discuss the rules of conformal transformations for geometric quantities in general relativity. In particular, we discuss the conformal transformations of the matter energy-momentum tensor. We thoroughly discuss the latter and show the subtlety of the conservation law (i.e., the geometrical Bianchi identity) imposed in one of the conformal frames in reference to the other. The subtlety refers to the fact that conformal transformation ``creates'' an extra matter term composed of the conformal factor which enters the conservation law. In an extreme case of the flat original spacetime the matter is ``created'' due to work done by the conformal transformation to bend the spacetime which was originally flat. We also discuss how to construct the conformally invariant gravity which, in the simplest version, is a special case of the Brans-Dicke t...

  19. 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.

  20. 利用受激Raman跃迁制备的原子激光的相干性%Coherent properties of a atom laser originating from stimulated Raman transition

    Institute of Scientific and Technical Information of China (English)

    贺慧勇; 黄春佳

    2009-01-01

    研究了利用原子玻色-爱因斯坦凝聚体与制备的原子激光的二阶相干性质. 结果表明,这种原子激光是反聚束的,在一定条件下,是二阶相干的.%The coherent properties of a atom laser originating from stimulated Raman transition of the atoms in Bose-Einstein condensate interacting with light fields is studied. The results show that this atom laser is antibunching, but in some conditions it is second-order coherent.

  1. Interlayer Transition and Infrared Photodetection in Atomically Thin Type-II MoTe₂/MoS₂ van der Waals Heterostructures.

    Science.gov (United States)

    Zhang, Kenan; Zhang, Tianning; Cheng, Guanghui; Li, Tianxin; Wang, Shuxia; Wei, Wei; Zhou, Xiaohao; Yu, Weiwei; Sun, Yan; Wang, Peng; Zhang, Dong; Zeng, Changgan; Wang, Xingjun; Hu, Weida; Fan, Hong Jin; Shen, Guozhen; Chen, Xin; Duan, Xiangfeng; Chang, Kai; Dai, Ning

    2016-03-22

    We demonstrate the type-II staggered band alignment in MoTe2/MoS2 van der Waals (vdW) heterostructures and an interlayer optical transition at ∼1.55 μm. The photoinduced charge separation between the MoTe2/MoS2 vdW heterostructure is verified by Kelvin probe force microscopy (KPFM) under illumination, density function theory (DFT) simulations and photoluminescence (PL) spectroscopy. Photoelectrical measurements of MoTe2/MoS2 vdW heterostructures show a distinct photocurrent response in the infrared regime (1550 nm). The creation of type-II vdW heterostructures with strong interlayer coupling could improve our fundamental understanding of the essential physics behind vdW heterostructures and help the design of next-generation infrared optoelectronics.

  2. Conformal isoparametric hypersurfaces with two distinct conformal principal curvatures in conformal space

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The conformal geometry of regular hypersurfaces in the conformal space is studied.We classify all the conformal isoparametric hypersurfaces with two distinct conformal principal curvatures in the conformal space up to conformal equivalence.

  3. Real-time visualization of conformational changes within single MloK1 cyclic nucleotide-modulated channels.

    Science.gov (United States)

    Rangl, Martina; Miyagi, Atsushi; Kowal, Julia; Stahlberg, Henning; Nimigean, Crina M; Scheuring, Simon

    2016-09-20

    Eukaryotic cyclic nucleotide-modulated (CNM) ion channels perform various physiological roles by opening in response to cyclic nucleotides binding to a specialized cyclic nucleotide-binding domain. Despite progress in structure-function analysis, the conformational rearrangements underlying the gating of these channels are still unknown. Here, we image ligand-induced conformational changes in single CNM channels from Mesorhizobium loti (MloK1) in real-time, using high-speed atomic force microscopy. In the presence of cAMP, most channels are in a stable conformation, but a few molecules dynamically switch back and forth (blink) between at least two conformations with different heights. Upon cAMP depletion, more channels start blinking, with blinking heights increasing over time, suggestive of slow, progressive loss of ligands from the tetramer. We propose that during gating, MloK1 transitions from a set of mobile conformations in the absence to a stable conformation in the presence of ligand and that these conformations are central for gating the pore.

  4. The Atomic to Molecular Transition and its Relation to the Scaling Properties of Galaxy Disks in the Local Universe

    CERN Document Server

    Fu, Jian; Kauffmann, Guinevere; Krumholz, Mark R

    2010-01-01

    We extend existing semi-analytic models of galaxy formation to track atomic and molecular gas in disk galaxies. Simple recipes for processes such as cooling, star formation, supernova feedback, and chemical enrichment of the stars and gas are grafted on to dark matter halo merger trees derived from the Millennium Simulation. Each galactic disk is represented by a series of concentric rings. We assume that surface density profile of infalling gas in a dark matter halo is exponential, with scale radius r_d that is proportional to the virial radius of the halo times its spin parameter $\\lambda$. As the dark matter haloes grow through mergers and accretion, disk galaxies assemble from the inside out. We include two simple prescriptions for molecular gas formation processes in our models: one is based on the analytic calculations by Krumholz, McKee & Tumlinson (2008), and the other is a prescription where the H_2 fraction is determined by the kinematic pressure of the ISM. Motivated by the observational result...

  5. Atoms Talking to SQUIDs

    CERN Document Server

    Hoffman, J E; Kim, Z; Wood, A K; Anderson, J R; Dragt, A J; Hafezi, M; Lobb, C J; Orozco, L A; Rolston, S L; Taylor, J M; Vlahacos, C P; Wellstood, F C

    2011-01-01

    We present a scheme to couple trapped $^{87}$Rb atoms to a superconducting flux qubit through a magnetic dipole transition. We plan to trap atoms on the evanescent wave outside an ultrathin fiber to bring the atoms to less than 10 $\\mu$m above the surface of the superconductor. This hybrid setup lends itself to probing sources of decoherence in superconducting qubits. Our current plan has the intermediate goal of coupling the atoms to a superconducting LC resonator.

  6. Resolving the Transition from Molecular to Atomic at 1/5 Solar Metallicity in the Small Magellanic Cloud

    Science.gov (United States)

    Jameson, Katherine E.; Bolatto, Alberto D.; Wolfire, Mark; Rubio, Monica; Camus, Rodrigo Herrera; Aff003

    At a distance of 61 kpc, the Small Magellanic Cloud (SMC) affords an absolutely unique view of the low metallicity star-forming interstellar medium, providing the nearest laboratory to study processes relevant to star formation at high redshifts. We present new ALMA 7m-array maps of CO and 12CO (2-1) for one of the four observed regions in the Southwest Bar of the SMC. These maps are the first high-resolution (~6'' ~ 1.7 pc) images of CO in a molecular cloud at 1/5 Solar metallicity. We show the structure of photodissociation regions for the first time at 1/5 Solar metallicity by combining the new ALMA data with Herschel maps of [C ii] and [O i]. We present preliminary evidence that there is extended, faint 12CO (2-1) emission near where we expect the Hi-to-H2 transition. We also compare our data to the low metallicity 3D simulations by Glover & Mac Low (2011) and Shetty et al. (2011).

  7. 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.

  8. Principles of Atomic Structure and the Valence Electron Configurations of the Transition Elements%原子构造原理与过渡元素原子的价电子组态

    Institute of Scientific and Technical Information of China (English)

    刘承东

    2001-01-01

    According to the Aufbau build-up principle and the order of filling atomic orbits, the valence electron configuration of ground state atoms of the d-block transition elements seems only to be (n-1) dx-2ns2(x here denotes the number of the electron in (n-1) d and ns orbits). But the result of the spectra test shows that the atomic electron structure of the d-block transition elements also has the configurations (n-1) dx-1 ns1 and (n-1) dx nso. These two types of electron configurations are usually considered as "out of the ordinary". In addition, the another important phenomenon is that the electronic structure of the atoms for all of the elements can not attain the configuration (n-1)d6 ns1. The reasons why these exceptional electron configurations can be formed and why the configuration (n-1) d 6 ns1 can not exist are not properly understood and at present no theory of the many-electron atom structure is entirely satisfactory[1-7]. For this, it seems that the theoretical difficulty lies in accounting for the diversification of electron configurations and for the non-existence of configuration (n-1) d6 ns1 as we did not pay more attention to the control effect of symmetry principle in atom structure. We know that the stability of a mass system depends on the mechanics conservation law in the system and each conservation law is always relative to the invariance of the certain symmetry. In atom structure, the main interaction is the electromagnetic interaction. So the stability of atom structure system must be bounded up with the symmetry of the electromagnetic interaction in the atom system. The direct expression of this interconnection is that,when the electrons are allotted to the orbits with energy equivalent or close to one another in many-electron atoms, they would always distribute themselves in such a way that there is a relative highest symmetry configuration. That is to say, the way of the distribution of electrons(include electron spin states) in orbits is

  9. EFFECTS OF METAL IONS ON THE CONFORMATIONAL CHANGES OF DNA

    Institute of Scientific and Technical Information of China (English)

    G. Q. Liu; Y.Y. Meng; S.H. Liu; Y.H. Hu

    2005-01-01

    DNA takes on multi-different conformations such as A-, B-, C-, D- and Z-form. These conformations can transit to one another when DNA deposited in some metal ions solutions or when changing the concentrations of the same metal ions. Here, several major conformational transitions of DNA induced by metal ions under different environment were introduced and the mechanism of the interaction of metal ions with DNA was discuss in detail.

  10. Holographic multiverse and conformal invariance

    Energy Technology Data Exchange (ETDEWEB)

    Garriga, Jaume [Departament de Física Fonamental i Institut de Ciències del Cosmos, Universitat de Barcelona, Martí i Franquès 1, 08193 Barcelona (Spain); Vilenkin, Alexander, E-mail: jaume.garriga@ub.edu, E-mail: vilenkin@cosmos.phy.tufts.edu [Institute of Cosmology, Department of Physics and Astronomy, Tufts University, 212 College Ave., Medford, MA 02155 (United States)

    2009-11-01

    We consider a holographic description of the inflationary multiverse, according to which the wave function of the universe is interpreted as the generating functional for a lower dimensional Euclidean theory. We analyze a simple model where transitions between inflationary vacua occur through bubble nucleation, and the inflating part of spacetime consists of de Sitter regions separated by thin bubble walls. In this model, we present some evidence that the dual theory is conformally invariant in the UV.

  11. 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

  12. The Atomic-to-Molecular Transition in Galaxies. III. A New Method for Determining the Molecular Content of Primordial and Dusty Clouds

    CERN Document Server

    McKee, Christopher F

    2009-01-01

    Understanding the molecular content of galaxies is a critical problem in star formation and galactic evolution. Here we present a new method, based on a Stromgren-type analysis, to calculate the amount of HI that surrounds a molecular cloud irradiated by an isotropic radiation field. We consider both planar and spherical clouds, and H_2 formation either in the gas phase or catalyzed by dust grains. Under the assumption that the transition from atomic to molecular gas is sharp, our method gives the solution without any reference to the photodissociation cross section. We test our results for the planar case against those of a PDR code, and find typical accuracies of about 10%. Our results are also consistent with the scaling relations found in Paper I of this series, but they apply to a wider range of physical conditions. We present simple, accurate analytic fits to our results that are suitable for comparison to observations and to implementation in numerical and semi-analytic models.

  13. Electronic structure and local atomic arrangement of transition metal ions in nanoporous iron-substituted nickel phosphates, VSB-1 and VSB-5.

    Science.gov (United States)

    Kim, Tae Woo; Oh, Eun-Jin; Jhung, Sung Hwa; Chang, Jong-San; Hwang, Seong-Ju

    2010-01-01

    The electronic structure and local atomic arrangement of transition metal ions in nanoporous iron-substituted nickel phosphates VSB-1 and VSB-5 have been investigated using X-ray absorption near-edge structure (XANES) spectroscopy at Fe K- and Ni K-edges. The Fe K-edge XANES study clearly demonstrated that substituted iron ions were stabilized in octahedral nickel sites of nanoporous nickel phosphate lattice. A comparison with several Fe-references revealed that the substituted irons have mixed Fe2+/Fe3+ oxidation state with the average valence of +2.8-3.0. According to the Ni K-edge XANES analysis, the aliovalent substitution of Ni2+ with Fe2+/Fe3+ induced a slight reduction of divalent nickel ions in VSB-5 to meet a charge balance. On the contrary, Fe substitution for the VSB-1 phase did not cause notable decrease in the oxidation state of nickel ions, which would be related either to the accompanying decrease of pentavalent phosphorus cations or to the increase of oxygen anions. In conclusion, the present findings clearly demonstrated that the nanoporous lattice of nickel phosphate can accommodate effectively iron ions in its octahedral nickel sites.

  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

    2016-05-26

    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. 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.

  16. Representation of target-bound drugs by computed conformers: implications for conformational libraries

    Directory of Open Access Journals (Sweden)

    Goede Andrean

    2006-06-01

    Full Text Available Abstract Background The increasing number of known protein structures provides valuable information about pharmaceutical targets. Drug binding sites are identifiable and suitable lead compounds can be proposed. The flexibility of ligands is a critical point for the selection of potential drugs. Since computed 3D structures of millions of compounds are available, the knowledge of their binding conformations would be a great benefit for the development of efficient screening methods. Results Integration of two public databases allowed superposition of conformers for 193 approved drugs with 5507 crystallised target-bound counterparts. The generation of 9600 drug conformers using an atomic force field was carried out to obtain an optimal coverage of the conformational space. Bioactive conformations are best described by a conformational ensemble: half of all drugs exhibit multiple active states, distributed over the entire range of the reachable energy and conformational space. A number of up to 100 conformers per drug enabled us to reproduce the bound states within a similarity threshold of 1.0 Å in 70% of all cases. This fraction rises to about 90% for smaller or average sized drugs. Conclusion Single drugs adopt multiple bioactive conformations if they interact with different target proteins. Due to the structural diversity of binding sites they adopt conformations that are distributed over a broad conformational space and wide energy range. Since the majority of drugs is well represented by a predefined low number of conformers (up to 100 this procedure is a valuable method to compare compounds by three-dimensional features or for fast similarity searches starting with pharmacophores. The underlying 9600 generated drug conformers are downloadable from the Super Drug Web site 1. All superpositions are visualised at the same source. Additional conformers (110,000 of 2400 classified WHO-drugs are also available.

  17. Structural Dynamics and Conformational Equilibria of SERCA Regulatory Proteins in Membranes by Solid-State NMR Restrained Simulations

    Science.gov (United States)

    De Simone, Alfonso; Mote, Kaustubh R.; Veglia, Gianluigi

    2014-01-01

    Solid-state NMR spectroscopy is emerging as a powerful approach to determine structure, topology, and conformational dynamics of membrane proteins at the atomic level. Conformational dynamics are often inferred and quantified from the motional averaging of the NMR parameters. However, the nature of these motions is difficult to envision based only on spectroscopic data. Here, we utilized restrained molecular dynamics simulations to probe the structural dynamics, topology and conformational transitions of regulatory membrane proteins of the calcium ATPase SERCA, namely sarcolipin and phospholamban, in explicit lipid bilayers. Specifically, we employed oriented solid-state NMR data, such as dipolar couplings and chemical shift anisotropy measured in lipid bicelles, to refine the conformational ensemble of these proteins in lipid membranes. The samplings accurately reproduced the orientations of transmembrane helices and showed a significant degree of convergence with all of the NMR parameters. Unlike the unrestrained simulations, the resulting sarcolipin structures are in agreement with distances and angles for hydrogen bonds in ideal helices. In the case of phospholamban, the restrained ensemble sampled the conformational interconversion between T (helical) and R (unfolded) states for the cytoplasmic region that could not be observed using standard structural refinements with the same experimental data set. This study underscores the importance of implementing NMR data in molecular dynamics protocols to better describe the conformational landscapes of membrane proteins embedded in realistic lipid membranes. PMID:24940774

  18. 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)

  19. 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.

  20. Atomic-level characterization of the activation mechanism of SERCA by calcium.

    Directory of Open Access Journals (Sweden)

    L Michel Espinoza-Fonseca

    Full Text Available We have performed molecular dynamics (MD simulations to elucidate, in atomic detail, the mechanism by which the sarcoplasmic reticulum Ca(2+-ATPase (SERCA is activated by Ca(2+. Crystal structures suggest that activation of SERCA occurs when the cytoplasmic head-piece, in an open (E1 conformation stabilized by Ca(2+, undergoes a large-scale open-to-closed (E1 to E2 transition that is induced by ATP binding. However, spectroscopic measurements in solution suggest that these structural states (E1 and E2 are not tightly coupled to biochemical states (defined by bound ligands; the closed E2 state predominates even in the absence of ATP, in both the presence and absence of Ca(2+. How is this loose coupling consistent with the high efficiency of energy transduction in the Ca(2+-ATPase? To provide insight into this question, we performed long (500 ns all-atom MD simulations starting from the open crystal structure, including a lipid bilayer and water. In both the presence and absence of Ca(2+, we observed a large-scale open-to-closed conformational transition within 400 ns, supporting the weak coupling between structural and biochemical states. However, upon closer inspection, it is clear that Ca(2+ is necessary and sufficient for SERCA to reach the precise geometrical arrangement necessary for activation of ATP hydrolysis. Contrary to suggestions from crystal structures, but in agreement with solution spectroscopy, the presence of ATP is not required for this activating transition. Principal component analysis showed that Ca(2+ reshapes the free energy landscape of SERCA to create a path between the open conformation and the activated closed conformation. Thus the malleability of the free energy landscape is essential for SERCA efficiency, ensuring that ATP hydrolysis is tightly coupled to Ca(2+ transport. These results demonstrate the importance of real-time dynamics in the formation of catalytically competent conformations of SERCA, with broad

  1. Conformation of 1,2-Dimethoxyethane in Water

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    To understand the conformation of 1,2-dimethoxyethane (DME) in water, a system of two kinds of molecules, DME and H2O, was focused. The interaction of various conformers of DME with water was studied by means of ab initio molecular orbital calculation with 6-31G(d)basis set. It is shown that there are two forms of interactions between the two molecules in the sys tem, the close touched (H2O attaches to the two oxygen atoms of DME) and the open touched (H2O attaches to one oxygen atom of DME) structures. The conformation of DME is remark ably influenced by the interactions. Instead the ttt conformer is preferred in the gas state, with a close touched H2O the tgt conformer becomes the most stable one. The obtained hydration ener gies show that the stabilized order of DME conformers by water is tgt>tgg'>ttt.

  2. Atomic magnetometer

    Science.gov (United States)

    Schwindt, Peter [Albuquerque, NM; Johnson, Cort N [Albuquerque, NM

    2012-07-03

    An atomic magnetometer is disclosed which uses a pump light beam at a D1 or D2 transition of an alkali metal vapor to magnetically polarize the vapor in a heated cell, and a probe light beam at a different D2 or D1 transition to sense the magnetic field via a polarization rotation of the probe light beam. The pump and probe light beams are both directed along substantially the same optical path through an optical waveplate and through the heated cell to an optical filter which blocks the pump light beam while transmitting the probe light beam to one or more photodetectors which generate electrical signals to sense the magnetic field. The optical waveplate functions as a quarter waveplate to circularly polarize the pump light beam, and as a half waveplate to maintain the probe light beam linearly polarized.

  3. UV light induced insulator-metal transition in ultra-thin ZnO/TiOx stacked layer grown by atomic layer deposition

    Science.gov (United States)

    Saha, D.; Misra, P.; Joshi, M. P.; Kukreja, L. M.

    2016-08-01

    In the present study, atomic layer deposition has been used to grow a series of Ti incorporated ZnO thin films by vertically stacking different numbers (n = 1-7) of ZnO/TiOx layers on (0001) sapphire substrates. The effects of defect states mediated chemisorption of O2 and/OH groups on the electrical properties of these films have been investigated by illuminating the samples under UV light inside a high vacuum optical cryostat. The ultra-thin film having one stacked layer (n = 1) did not show any change in its electrical resistance upon UV light exposure. On the contrary, marginal drop in the electrical resistivity was measured for the samples with n ≥ 3. Most surprisingly, the sample with n = 2 (thickness ˜ 12 nm) showed an insulator to metal transition upon UV light exposure. The temperature dependent electrical resistivity measurement on the as grown film (n = 2) showed insulating behaviour, i.e., diverging resistivity on extrapolation to T→ 0 K. However, upon UV light exposure, it transformed to a metallic state, i.e., finite resistivity at T → 0 K. Such an insulator-metal transition plausibly arises due to the de-trapping of conduction electrons from the surface defect sites which resulted in an upward shift of the Fermi level above the mobility edge. The low-temperature electron transport properties on the insulating film (n = 2) were investigated by a combined study of zero field electrical resistivity ρ(T) and magnetoresistance (MR) measurements. The observed negative MR was found to be in good agreement with the magnetic field induced suppression of quantum interference between forward-going paths of tunnelling electrons. Both ρ(T) and MR measurements provided strong evidence for the Efros-Shklovskii type variable range hopping conduction in the low-temperature (≤40 K) regime. Such studies on electron transport in ultra-thin n-type doped ZnO films are crucial to achieve optimum functionality with long term reliability of ZnO based transparent

  4. Unearthing the transition rates between photoreceptor conformers

    NARCIS (Netherlands)

    Smith, Robert W.; Helwig, Britta; Westphal, Adrie H.; Pel, Eran; Hörner, Maximilian; Beyer, Hannes M.; Samodelov, Sophia L.; Weber, Wilfried; Zurbriggen, Matias D.; Borst, Janwillem; Fleck, Christian

    2016-01-01

    Background: Obtaining accurate estimates of biological or enzymatic reaction rates is critical in understanding the design principles of a network and how biological processes can be experimentally manipulated on demand. In many cases experimental limitations mean that some enzymatic rates cannot

  5. 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.

  6. Microchip-Based Trapped-Atom Clocks

    CERN Document Server

    Vuletic, Vladan; Schleier-Smith, Monika H

    2011-01-01

    This is a chapter of a recently published book entitled Atom Chips, edited by Jakob Reichel and Vladan Vuletic. The contents of this chapter include: Basic Principles; Atomic-Fountain versus Trapped-Atom Clocks; Optical-Transition Clocks versus Microwave Clocks; Clocks with Magnetically Trapped Atoms--Fundamental Limits and Experimental Demonstrations; Readout in Trapped-Atom Clocks; and Spin Squeezing.

  7. Atom probe study of Cu-poor to Cu-rich transition during Cu(In,Ga)Se{sub 2} growth

    Energy Technology Data Exchange (ETDEWEB)

    Couzinie-Devy, F.; Cadel, E.; Pareige, P. [Groupe de Physique des Materiaux (GPM), UMR 6634 CNRS, Universite et INSA de Rouen, Avenue de l' Universite BP 12, 76801 Saint Etienne du Rouvray (France); Barreau, N.; Arzel, L. [Institut des Materiaux Jean Rouxel (IMN), UMR 6502 CNRS, 2 rue de la Houssiniere BP 32229, 44322 Nantes cedex 3 (France)

    2011-12-05

    Atomic scale chemistry of polycrystalline Cu(In,Ga)Se{sub 2} (CIGSe) thin film has been characterized at key points of the 3-stage process using atom probe tomography. 3D atom distributions have been reconstructed when the layer is Cu-poor ([Cu]/([Ga] + [In]) < 1), Cu-rich ([Cu]/([Ga] + [In]) > 1), and at the end of the process. Particular attention has been devoted to grain boundary composition and Na atomic distribution within the CIGSe layer. Significant variation of composition is highlighted during the growing process, providing fundamental information helping the understanding of high efficiency CIGSe formation.

  8. Is there adequate ionization mechanism of the spontaneous transitions? Quantum-chemical investigation

    OpenAIRE

    Hovorun D. M.; Zhurakivsky R. O.; Brovarets’ O. O.

    2010-01-01

    Aim. To investigate theoretically the adequacy of the ionization mechanism of the spontaneous transitions appearance, using simple molecular models – DNA base pairs, one of which is ionized, and electroneutral and ionized DNA-like conformers of canonical nucleosides. Methods. Non-empirical quantum chemistry, physicochemical kinetics and analysis of the electron density by means of Bader’s atoms in molecules (AIM) theory were used. Results. It is established at base pairs that the ionization m...

  9. 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.

  10. Toward TeV Conformality

    Energy Technology Data Exchange (ETDEWEB)

    Appelquist, T; Avakian, A; Babich, R; Brower, R C; Cheng, M; Clark, M A; Cohen, S D; Fleming, G T; Kiskis, J; Neil, E T; Osborn, J C; Rebbi, C; Schaich, D; Soltz, R; Vranas, P

    2009-11-30

    We study the chiral condensate <{bar {psi}}{psi}> for an SU(3) gauge theory with N{sub f} massless Dirac fermions in the fundamental representation when N{sub f} is increased from 2 to 6. For N{sub f} = 2, our lattice simulations of <{bar {psi}}{psi}>/F{sup 3}, where F is the Nambu-Goldstone-boson decay constant, agree with the measured QCD value. For N{sub f} = 6, this ratio shows significant enhancement, presaging an even larger enhancement anticipated as N{sub f} increases further, toward the critical value for transition from confinement to infrared conformality.

  11. DNA polymerase conformational dynamics and the role of fidelity-conferring residues: Insights from computational simulations

    Directory of Open Access Journals (Sweden)

    Massimiliano eMeli

    2016-05-01

    Full Text Available Herein we investigate the molecular bases of DNA polymerase I conformational dynamics that underlie the replication fidelity of the enzyme. Such fidelity is determined by conformational changes that promote the rejection of incorrect nucleotides before the chemical ligation step. We report a comprehensive atomic resolution study of wild type and mutant enzymes in different bound states and starting from different crystal structures, using extensive molecular dynamics (MD simulations that cover a total timespan of ~ 5 microseconds. The resulting trajectories are examined via a combination of novel methods of internal dynamics and energetics analysis, aimed to reveal the principal molecular determinants for the (destabilization of a certain conformational state. Our results show that the presence of fidelity-decreasing mutations or the binding of incorrect nucleotides in ternary complexes tend to favor transitions from closed towards open structures, passing through an ensemble of semi-closed intermediates. The latter ensemble includes the experimentally observed ajar conformation which, consistent with previous experimental observations, emerges as a molecular checkpoint for the selection of the correct nucleotide to incorporate. We discuss the implications of our results for the understanding of the relationships between the structure, dynamics and function of DNA polymerase I at the atomistic level.

  12. The effect of the electronic structure, phase transition, and localized dynamics of atoms in the formation of tiny particles of gold

    Science.gov (United States)

    Ali, Mubarak; Lin, I.-Nan

    2017-01-01

    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.

  13. 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.

  14. Is there adequate ionization mechanism of the spontaneous transitions? Quantum-chemical investigation

    Directory of Open Access Journals (Sweden)

    Hovorun D. M.

    2010-09-01

    Full Text Available Aim. To investigate theoretically the adequacy of the ionization mechanism of the spontaneous transitions appearance, using simple molecular models – DNA base pairs, one of which is ionized, and electroneutral and ionized DNA-like conformers of canonical nucleosides. Methods. Non-empirical quantum chemistry, physicochemical kinetics and analysis of the electron density by means of Bader’s atoms in molecules (AIM theory were used. Results. It is established at base pairs that the ionization mechanism of transitions origin doesn’t imply any advantages in comparison with other mechanisms described in literature. However, the protonation/deprotonation of base in any canonical nucleoside significantly perturbs DNA-like conformations of the latter. Conclusions. The ionization mechanism can’t explain entirely the nature of the spontaneous transitions.

  15. [Dosimetric evaluation of conformal radiotherapy: conformity factor].

    Science.gov (United States)

    Oozeer, R; Chauvet, B; Garcia, R; Berger, C; Felix-Faure, C; Reboul, F

    2000-01-01

    The aim of three-dimensional conformal therapy (3DCRT) is to treat the Planning Target Volume (PTV) to the prescribed dose while reducing doses to normal tissues and critical structures, in order to increase local control and reduce toxicity. The evaluation tools used for optimizing treatment techniques are three-dimensional visualization of dose distributions, dose-volume histograms, tumor control probabilities (TCP) and normal tissue complication probabilities (NTCP). These tools, however, do not fully quantify the conformity of dose distributions to the PTV. Specific tools were introduced to measure this conformity for a given dose level. We have extended those definitions to different dose levels, using a conformity index (CI). CI is based on the relative volumes of PTV and outside the PTV receiving more than a given dose. This parameter has been evaluated by a clinical study including 82 patients treated for lung cancer and 82 patients treated for prostate cancer. The CI was low for lung dosimetric studies (0.35 at the prescribed dose 66 Gy) due to build-up around the GTV and to spinal cord sparing. For prostate dosimetric studies, the CI was higher (0.57 at the prescribed dose 70 Gy). The CI has been used to compare treatment plans for lung 3DCRT (2 vs 3 beams) and prostate 3DCRT (4 vs 7 beams). The variation of CI with dose can be used to optimize dose prescription.

  16. 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.

  17. Nuclear physics: Elusive transition spotted in thorium

    Science.gov (United States)

    Safronova, Marianna

    2016-05-01

    The highly precise atomic clocks used in science and technology are based on electronic transitions in atoms. The discovery of a nuclear transition in thorium-229 raises hopes of making nuclear clocks a reality. See Article p.47

  18. 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....

  19. 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....

  20. Evanescent Wave Atomic Mirror

    Science.gov (United States)

    Ghezali, S.; Taleb, A.

    2008-09-01

    A research project at the "Laboratoire d'électronique quantique" consists in a theoretical study of the reflection and diffraction phenomena via an atomic mirror. This poster presents the principle of an atomic mirror. Many groups in the world have constructed this type of atom optics experiments such as in Paris-Orsay-Villetaneuse (France), Stanford-Gaithersburg (USA), Munich-Heidelberg (Germany), etc. A laser beam goes into a prism with an incidence bigger than the critical incidence. It undergoes a total reflection on the plane face of the prism and then exits. The transmitted resulting wave out of the prism is evanescent and repulsive as the frequency detuning of the laser beam compared to the atomic transition δ = ωL-ω0 is positive. The cold atomic sample interacts with this evanescent wave and undergoes one or more elastic bounces by passing into backward points in its trajectory because the atoms' kinetic energy (of the order of the μeV) is less than the maximum of the dipolar potential barrier ℏΩ2/Δ where Ω is the Rabi frequency [1]. In fact, the atoms are cooled and captured in a magneto-optical trap placed at a distance of the order of the cm above the prism surface. The dipolar potential with which interact the slow atoms is obtained for a two level atom in a case of a dipolar electric transition (D2 Rubidium transition at a wavelength of 780nm delivered by a Titane-Saphir laser between a fundamental state Jf = l/2 and an excited state Je = 3/2). This potential is corrected by an attractive Van der Waals term which varies as 1/z3 in the Lennard-Jones approximation (typical atomic distance of the order of λ0/2π where λ0 is the laser wavelength) and in 1/z4 if the distance between the atom and its image in the dielectric is big in front of λ0/2π. This last case is obtained in a quantum electrodynamic calculation by taking into account an orthornormal base [2]. We'll examine the role of spontaneous emission for which the rate is inversely

  1. EC declaration of conformity.

    Science.gov (United States)

    Donawa, M E

    1996-05-01

    The CE-marking procedure requires that manufacturers draw up a written declaration of conformity before placing their products on the market. However, some companies do not realize that this is a requirement for all devices. Also, there is no detailed information concerning the contents and format of the EC declaration of conformity in the medical device Directives or in EC guidance documentation. This article will discuss some important aspects of the EC declaration of conformity and some of the guidance that is available on its contents and format.

  2. Intrinsic α-helical and β-sheet conformational preferences: a computational case study of alanine.

    Science.gov (United States)

    Caballero, Diego; Määttä, Jukka; Zhou, Alice Qinhua; Sammalkorpi, Maria; O'Hern, Corey S; Regan, Lynne

    2014-07-01

    A fundamental question in protein science is what is the intrinsic propensity for an amino acid to be in an α-helix, β-sheet, or other backbone dihedral angle ( ϕ-ψ) conformation. This question has been hotly debated for many years because including all protein crystal structures from the protein database, increases the probabilities for α-helical structures, while experiments on small peptides observe that β-sheet-like conformations predominate. We perform molecular dynamics (MD) simulations of a hard-sphere model for Ala dipeptide mimetics that includes steric interactions between nonbonded atoms and bond length and angle constraints with the goal of evaluating the role of steric interactions in determining protein backbone conformational preferences. We find four key results. For the hard-sphere MD simulations, we show that (1) β-sheet structures are roughly three and half times more probable than α-helical structures, (2) transitions between α-helix and β-sheet structures only occur when the backbone bond angle τ (NCα C) is greater than 110°, and (3) the probability distribution of τ for Ala conformations in the "bridge" region of ϕ-ψ space is shifted to larger angles compared to other regions. In contrast, (4) the distributions obtained from Amber and CHARMM MD simulations in the bridge regions are broader and have increased τ compared to those for hard sphere simulations and from high-resolution protein crystal structures. Our results emphasize the importance of hard-sphere interactions and local stereochemical constraints that yield strong correlations between ϕ-ψ conformations and τ.

  3. Animal culture: chimpanzee conformity?

    Science.gov (United States)

    van Schaik, Carel P

    2012-05-22

    Culture-like phenomena in wild animals have received much attention, but how good is the evidence and how similar are they to human culture? New data on chimpanzees suggest their culture may even have an element of conformity.

  4. 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.

  5. Conformally Coupled Inflation

    Directory of Open Access Journals (Sweden)

    Valerio Faraoni

    2013-07-01

    Full Text Available A massive scalar field in a curved spacetime can propagate along the light cone, a causal pathology, which can, in principle, be eliminated only if the scalar couples conformally to the Ricci curvature of spacetime. This property mandates conformal coupling for the field driving inflation in the early universe. During slow-roll inflation, this coupling can cause super-acceleration and, as a signature, a blue spectrum of primordial gravitational waves.

  6. 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....

  7. Conformism and Wealth Distribution

    OpenAIRE

    Mino, Kazuo; Nakamoto, Yasuhiro

    2014-01-01

    This paper explores the role of consumption externalities in a neoclassical growth model in which households have heterogeneous preferences. We fi?nd that the degree of conformism in consumption held by each household signifi?cantly affects the speed of convergence of the aggregate economy as well as the patterns of wealth distribution in the steady state equilibrium. In particular, a higher degree of consumption conformism accelerates the convergence speed of the economy towards the steady s...

  8. 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.)

  9. Conformally coupled inflation

    CERN Document Server

    Faraoni, Valerio

    2013-01-01

    A massive scalar field in a curved spacetime can propagate along the light cone, a causal pathology, which can, in principle, be eliminated only if the scalar couples conformally to the Ricci curvature of spacetime. This property mandates conformal coupling for the field driving inflation in the early universe. During slow-roll inflation, this coupling can cause super-acceleration and, as a signature, a blue spectrum of primordial gravitational waves.

  10. Two-dimensional heterospectral correlation analysis of the redox-induced conformational transition in cytochrome c using surface-enhanced Raman and infrared absorption spectroscopies on a two-layer gold surface.

    Science.gov (United States)

    Zou, Changji; Larisika, Melanie; Nagy, Gabor; Srajer, Johannes; Oostenbrink, Chris; Chen, Xiaodong; Knoll, Wolfgang; Liedberg, Bo; Nowak, Christoph

    2013-08-22

    The heme protein cytochrome c adsorbed to a two-layer gold surface modified with a self-assembled monolayer of 2-mercaptoethanol was analyzed using a two-dimensional (2D) heterospectral correlation analysis that combined surface-enhanced infrared absorption spectroscopy (SEIRAS) and surface-enhanced Raman spectroscopy (SERS). Stepwise increasing electric potentials were applied to alter the redox state of the protein and to induce conformational changes within the protein backbone. We demonstrate herein that 2D heterospectral correlation analysis is a particularly suitable and useful technique for the study of heme-containing proteins as the two spectroscopies address different portions of the protein. Thus, by correlating SERS and SEIRAS data in a 2D plot, we can obtain a deeper understanding of the conformational changes occurring at the redox center and in the supporting protein backbone during the electron transfer process. The correlation analyses are complemented by molecular dynamics calculations to explore the intramolecular interactions.

  11. A reoptimized GROMOS force field for hexopyranose-based carbohydrates accounting for the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers.

    Science.gov (United States)

    Hansen, Halvor S; Hünenberger, Philippe H

    2011-04-30

    This article presents a reoptimization of the GROMOS 53A6 force field for hexopyranose-based carbohydrates (nearly equivalent to 45A4 for pure carbohydrate systems) into a new version 56A(CARBO) (nearly equivalent to 53A6 for non-carbohydrate systems). This reoptimization was found necessary to repair a number of shortcomings of the 53A6 (45A4) parameter set and to extend the scope of the force field to properties that had not been included previously into the parameterization procedure. The new 56A(CARBO) force field is characterized by: (i) the formulation of systematic build-up rules for the automatic generation of force-field topologies over a large class of compounds including (but not restricted to) unfunctionalized polyhexopyranoses with arbritrary connectivities; (ii) the systematic use of enhanced sampling methods for inclusion of experimental thermodynamic data concerning slow or unphysical processes into the parameterization procedure; and (iii) an extensive validation against available experimental data in solution and, to a limited extent, theoretical (quantum-mechanical) data in the gas phase. At present, the 56A(CARBO) force field is restricted to compounds of the elements C, O, and H presenting single bonds only, no oxygen functions other than alcohol, ether, hemiacetal, or acetal, and no cyclic segments other than six-membered rings (separated by at least one intermediate atom). After calibration, this force field is shown to reproduce well the relative free energies of ring conformers, anomers, epimers, hydroxymethyl rotamers, and glycosidic linkage conformers. As a result, the 56A(CARBO) force field should be suitable for: (i) the characterization of the dynamics of pyranose ring conformational transitions (in simulations on the microsecond timescale); (ii) the investigation of systems where alternative ring conformations become significantly populated; (iii) the investigation of anomerization or epimerization in terms of free-energy differences

  12. Conformational changes in glycine tri- and hexapeptide

    CERN Document Server

    Yakubovitch, A V; Solovyov, A V; Solovyov, I A; Greiner, Walter; Solov'yov, Andrey V.; Solov'yov, Ilia A.; Yakubovitch, Alexander V.

    2005-01-01

    We have investigated the potential energy surfaces for glycine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles phi and psi, which are widely used for the characterization of the polypeptide chains. These particular degrees of freedom are essential for the characterization of proteins folding process. Calculations have been carried out within ab initio theoretical framework based on the density functional theory and accounting for all the electrons in the system. We have determined stable 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 and with the available experimental data extracted from the Protein Data Base. This comparison demonstrates a reasonable co...

  13. Magnetoelectric Jones Dichroism in Atoms

    CERN Document Server

    Budker, D

    2003-01-01

    The authors suggest that atomic experiments measuring the interference between magnetic-dipole and electric-field-induced electric-dipole transition amplitudes may provide a valuable system to study magnetoelectric Jones effects.

  14. Effects of dark atom excitations

    CERN Document Server

    Cudell, Jean-René; Wallemacq, Quentin

    2014-01-01

    New stable quarks and charged leptons may exist and be hidden from detection, as they are bound by Coulomb interaction in neutral dark atoms of composite dark matter. This possibility leads to fundamentally new types of indirect effects related to the excitation of such dark atoms followed by their electromagnetic de-excitation. Stable -2 charged particles, bound to primordial helium in O-helium (OHe) atoms, represent the simplest model of dark atoms. Here we consider the structure of OHe atomic levels which is a necessary input for the indirect tests of such composite dark matter scenarios, and we give the spectrum of electromagnetic transitions from the levels excited in OHe collisions.

  15. Differential steric effects in Cl reactions with aligned CHD3(v1 = 1) by the R(0) and Q(1) transitions. II. Abstracting the unexcited D-atoms

    Science.gov (United States)

    Wang, Fengyan; Liu, Kopin

    2016-10-01

    A complete set of four polarization-dependent differential cross sections in the reactions of Cl + aligned-CHD 3 ( v 1 = 1 , |" separators=" jK > ) → DCl ( v = 0 ) + CHD 2 ( v 1 = 1 ) is reported here for two different, rotationally polarized states with j = 1: specifically the |" separators=" jK > = |" separators=" 10 > state prepared via the R(0) excitation and the |" separators=" 1 ± 1 > state via Q(1). In stark contrast to the complicated situation of the HCl(v) + CD3(v = 0) channel reported in Paper-I, the stereo-requirement of this isotopic channel for both polarized reactants appears quite straightforward and consistent with a direct rebound mechanism. The extent of steric effects is moderate and relatively smaller than the alternative H-atom abstraction channel. All major findings reported here can qualitatively be understood by first noting that the present reaction invokes abstracting a D-atom, which is the spectator in the IR-excitation process. Next, it is recognized that the directional properties of two polarized states of CHD 3 ( v 1 = 1 , |" separators=" jK > ) should manifest primarily in the IR-excited C-H bond, leaving secondary imprints in the unexcited CD3-moiety. The stereo-specificity of the DCl + CHD2 product channel is further reduced by the fact that the abstraction can occur with any one of the three spatially distinct D-atoms.

  16. 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.

  17. 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...

  18. Conformation of α,α,α'-Trisubstituted Cyclododecanone

    Institute of Scientific and Technical Information of China (English)

    WANG,Ming-An; ZHANG,Ning; LU,Hui-Zhe; WANG,Dao-Quan

    2007-01-01

    Ten α,α,α'-trisubstituted cyclododecanones were synthesized and characterized by elemental analyses, infrared,1H NMR and 13C NMR spectra, and X-ray diffraction. NMR data could not give conformational information clearly,but some of their ring skeleton conformations of cyclododecanone moiety were showed to remain the unchanged [3333]-2-one conformation with little distortion, while the others were changed to the [3324]-2-one conformation in their crystal structures. These are consistent with the results of molecular mechanics calculation with Sybyl 6.9 software and Tripos force field, and semi-empirical quantum calculation with AM1 method in Gaussian 98 software.Two geminal substituting groups are located at α-comer carbon atom, and the third group is at α-side-exo carbon atom in both conformations. Both [3333]-2-one and [3324]-2-one conformations are present in a dynamic equilibrium in the solution, but only one preferred conformation exists in the crystal solid.

  19. Satellite and hypersatellite structures of Lα1,2 and Lβ1 x-ray transitions in mid-Z atoms multiply ionized by fast oxygen ions

    OpenAIRE

    Czarnota, M.; Banaś, D; Berset, Michel; Chmielewska, D; Dousse, Jean-Claude; Hoszowska, Joanna; Maillard, Yves-Patrick; Mauron, Olivier; Pajek, M.; Polasik, M.; Raboud, Pierre-Alexandre; Rzadkiewicz, J.; Słabkowska, K.; Sujkowski, Z.

    2014-01-01

    A detailed investigation of the Lα1,2 (L3→M4,5) and Lβ1 (L2→M4) x-ray satellite and hypersatellite structures in zirconium, molybdenum, and palladium atoms multiply ionized by impact with 278.6-MeV oxygen ions is reported. The x-ray spectra were measured with a high-resolution von Hamos bent crystal spectrometer. For the interpretation of the complex spectral features, relativistic multiconfiguration Dirac-Fock calculations were performed for all multivacancy configurations expected to contri...

  20. Boundary Conformal Field Theory

    CERN Document Server

    Cardy, J L

    2004-01-01

    Boundary conformal field theory (BCFT) is simply the study of conformal field theory (CFT) in domains with a boundary. It gains its significance because, in some ways, it is mathematically simpler: the algebraic and geometric structures of CFT appear in a more straightforward manner; and because it has important applications: in string theory in the physics of open strings and D-branes, and in condensed matter physics in boundary critical behavior and quantum impurity models. In this article, however, I describe the basic ideas from the point of view of quantum field theory, without regard to particular applications nor to any deeper mathematical formulations.

  1. Transfer-Free Growth of Atomically Thin Transition Metal Disulfides Using a Solution Precursor by a Laser Irradiation Process and Their Application in Low-Power Photodetectors.

    Science.gov (United States)

    Huang, Chi-Chih; Medina, Henry; Chen, Yu-Ze; Su, Teng-Yu; Li, Jian-Guang; Chen, Chia-Wei; Yen, Yu-Ting; Wang, Zhiming M; Chueh, Yu-Lun

    2016-04-13

    Although chemical vapor deposition is the most common method to synthesize transition metal dichalcogenides (TMDs), several obstacles, such as the high annealing temperature restricting the substrates used in the process and the required transfer causing the formation of wrinkles and defects, must be resolved. Here, we present a novel method to grow patternable two-dimensional (2D) transition metal disulfides (MS2) directly underneath a protective coating layer by spin-coating a liquid chalcogen precursor onto the transition metal oxide layer, followed by a laser irradiation annealing process. Two metal sulfides, molybdenum disulfide (MoS2) and tungsten disulfide (WS2), are investigated in this work. Material characterization reveals the diffusion of sulfur into the oxide layer prior to the formation of the MS2. By controlling the sulfur diffusion, we are able to synthesize continuous MS2 layers beneath the top oxide layer, creating a protective coating layer for the newly formed TMD. Air-stable and low-power photosensing devices fabricated on the synthesized 2D WS2 without the need for a further transfer process demonstrate the potential applicability of TMDs generated via a laser irradiation process.

  2. Determination of magic wavelengths for the $7s ~ {^2}S_{1/2}-7p ~ {^2}P_{3/2,1/2}$ transitions in Fr atom

    CERN Document Server

    Singh, Sukhjit; Arora, Bindiya

    2016-01-01

    Magic wavelengthsfor the $7S_{1/2}-7P_{1/2,3/2}$ transitions in Fr were reported by Dammalapati \\textit{et al.} in [Phys. Rev. A 93, 043407 (2016)]. These $\\lambda_{\\rm{magic}}$ were determined by plotting dynamic polarizabilities ($\\alpha$) of the involved states with the above transitions against a desired range of wavelength. Electric dipole (E1) matrix elements listed in [J. Phys. Chem. Ref. Data 36, 497 (2007)], from the measured lifetimes of the $7P_{1/2,3/2}$ states and from the calculations considering core-polarization effects in the relativistic Hartree-Fock (HFR) method, were used to determine $\\alpha$. However, contributions from core correlation effects and from the E1 matrix elements of the $7P-7S$, $7P-8S$ and $7P-6D$ transitions to $\\alpha$ of the $7P$ states were ignored. In this work, we demonstrate importance of these contributions and improve accuracies of $\\alpha$ further by replacing the E1 matrix elements taken from the HFR method by the values obtained employing relativistic coupled-cl...

  3. Structural, Conformational and Vibrational Studies of Isocyanocyclopentane from Infrared, Raman Spectra and AB Initio Calculations

    Science.gov (United States)

    Sawant, Dattatray K.; Klaassen, Joshua J.; Durig, James R.

    2013-06-01

    The infrared and Raman spectra (3200 to 50 cm^{-1}) of the gas, liquid or solution, and solid have been recorded of isocyanocyclopentane, _{c}-C_{5}H_{9}NC. FT-microwave studies have also been carried out and 23 transitions were recorded for the envelope-axial (Ax) conformer. Variable temperature (-55 to -100°C) studies of the infrared spectra (3200 to 400 cm^{-1}) dissolved in liquid xenon have been carried out. From these data, both the Ax and envelope-equatorial (Eq) conformers have been identified and their relative stabilities obtained. The enthalpy difference has been determined to be 102 ± 10 cm^{-1} (1.21 ± 0.03 kJ mol^{-1}) with the Ax conformer the more stable form. The percentage of the Eq conformer is estimated to be 38 ± 1% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing several different basis sets up to aug-cc-pVTZ from both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been made for the observed bands for both conformers with initial predictions by MP2(full)/6-31G(d) ab initio calculations to obtain harmonic force constants, wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. The heavy atom distances (Å): C≡N = 1.176 ; C_{α}-N≡C= 1.432; C_{α}-C_{β},C_{β}' = 1.534; C_{β}-C_{γ}, C_{γ}' = 1.542; C_{γ}-C_{γ}' = 1.554 and angles (°:angleC_{α}-N≡C = 177.8; angleC_{β}C_{α}-N≡C = 110.4; angleC_{β}C_{α}C_{β}'= 102.9; angleC_{α}C_{β}C_{γ} = 103.6; angleC_{β}C_{γ}C_{γ}' = 105.9. The results are discussed and compared to the corresponding properties of some related molecules.

  4. Synthesis, characterization and biological approach of metal chelates of some first row transition metal ions with halogenated bidentate coumarin Schiff bases containing N and O donor atoms.

    Science.gov (United States)

    Prabhakara, Chetan T; Patil, Sangamesh A; Toragalmath, Shivakumar S; Kinnal, Shivashankar M; Badami, Prema S

    2016-04-01

    The impregnation of halogen atoms in a molecule is an emerging trend in pharmaceutical chemistry. The presence of halogens (Cl, Br, I and F) increases the lipophilic nature of molecule and improves the penetration of lipid membrane. The presence of electronegative halogen atoms increases the bio- activity of core moiety. In the present study, Co(II), Ni(II) and Cu(II) complexes are synthesised using Schiff bases (HL(I) and HL(II)), derived from 8-formyl-7-hydroxy-4-methylcoumarin/3-chloro-8-formyl-7-hydroxy-4-methylcoumarin with 2,4-difluoroaniline/o-toluidine respectively. The synthesized compounds were characterized by spectral (IR, NMR, UV-visible, Mass, ESI-MS, ESR), thermal, fluorescence and molar conductivity studies. All the synthesized metal complexes are completely soluble in DMF and DMSO. The non-electrolytic nature of the metal complexes was confirmed by molar conductance studies. Elemental analysis study suggest [ML2(H2O)2] stoichiometry, here M=Co(II), Ni(II) and Cu(II), L=deprotonated ligand. The obtained IR data supports the binding of metal ion to Schiff base. Thermal study suggests the presence of coordinated water molecules. Electronic spectral results reveal six coordinated geometry for the synthesized metal complexes. The Schiff bases and their metal complexes were evaluated for antibacterial (Pseudomonas aureginosa and Proteus mirabilis), antifungal (Aspergillus niger and Rhizopus oryzae), anthelmintic (Pheretima posthuma) and DNA cleavage (Calf Thymus DNA) activities.

  5. Conformal General Relativity

    CERN Document Server

    Pervushin, V

    2001-01-01

    The inflation-free solution of problems of the modern cosmology (horizon, cosmic initial data, Planck era, arrow of time, singularity,homogeneity, and so on) is considered in the conformal-invariant unified theory given in the space with geometry of similarity where we can measure only the conformal-invariant ratio of all quantities. Conformal General Relativity is defined as the $SU_c(3)\\times SU(2)\\times U(1)$-Standard Model where the dimensional parameter in the Higgs potential is replaced by a dilaton scalar field described by the negative Penrose-Chernikov-Tagirov action. Spontaneous SU(2) symmetry breaking is made on the level of the conformal-invariant angle of the dilaton-Higgs mixing, and it allows us to keep the structure of Einstein's theory with the equivalence principle. We show that the lowest order of the linearized equations of motion solves the problems mentioned above and describes the Cold Universe Scenario with the constant temperature T and z-history of all masses with respect to an obser...

  6. Conformal cloak for waves

    CERN Document Server

    Chen, Huanyang; Tyc, Tomas

    2011-01-01

    Conformal invisibility devices are only supposed to work within the validity range of geometrical optics. Here we show by numerical simulations and analytical arguments that for certain quantized frequencies they are nearly perfect even in a regime that clearly violates geometrical optics. The quantization condition follows from the analogy between the Helmholtz equation and the stationary Schrodinger equation.

  7. Conformal supermultiplets without superpartners

    CERN Document Server

    Jarvis, Peter

    2011-01-01

    We consider polynomial deformations of Lie superalgebras and their representations. For the class A(n-1,0) ~ sl(n/1), we identify families of superalgebras of quadratic and cubic type, consistent with Jacobi identities. For such deformed superalgebras we point out the possibility of zero step supermultiplets, carried on a single, irreducible representation of the even (Lie) subalgebra. For the conformal group SU(2,2) in 1+3-dimensional spacetime, such irreducible (unitary) representations correspond to standard conformal fields (j_1,j_2;d), where (j_1,j_2) is the spin and d the conformal dimension; in the massless class j_1 j_2=0, and d=j_1+j_2+1. We show that these repesentations are zero step supermultiplets for the superalgebra SU_(2)(2,2/1), the quadratic deformation of conformal supersymmetry SU(2,2/1). We propose to elevate SU_(2)(2,2/1) to a symmetry of the S-matrix. Under this scenario, low-energy standard model matter fields (leptons, quarks, Higgs scalars and gauge fields) descended from such confor...

  8. A CONFORMATIONAL ELASTICITY THEORY

    Institute of Scientific and Technical Information of China (English)

    1998-01-01

    A new statistical theory based on the rotational isomeric state model describing the chain conformational free energy has been proposed. This theory can be used to predict different tensions of rubber elongation for chemically different polymers, and the energy term during the elongation of natural rubber coincides with the experimental one.

  9. 金属离子导致的丝素蛋白的构象转变%The Effect of Metal Ions on the Conformation Transition of Silk Fibroin

    Institute of Scientific and Technical Information of China (English)

    李贵阳; 孙尧俊; 等

    2001-01-01

    How the silkworm spins out such an excellent silk fiber has been a hot topic. The issue here is to know how the coil chains in the gland of silkworm transform to β-sheet in silk fiber. We used the regenerated silk fibroin to imitate the silk fibroin of the gland to investigate the effect of metal ion(Ca2+. Cu2+) on the silk spinning process of Bombyx mori silkworm. The solutions or gel obtained from hte mixture of regenerated silk fibroin and metal ions were dried for mimicking the gradual loss of water in the spinning process. The 13C NMR spectrum simulation for Cβ nucleus of alanine quantitatively demonstrated that the conformation of the regenerated silk fibroin is dominantly of silk Ⅰ, whereas the fibroin with metal ions has more silk Ⅱ conformation. Raman spectroscopies show the consistent results with that of NMR. The binding of metal ion with carbonyl and amide in protein backbone allows the protein chain to array regularly, therefore leading to the β-sheet formation.

  10. 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.

  11. Atom chips

    CERN Document Server

    Reichel, Jakob

    2010-01-01

    This book provides a stimulating and multifaceted picture of a rapidly developing field. The first part reviews fundamentals of atom chip research in tutorial style, while subsequent parts focus on the topics of atom-surface interaction, coherence on atom chips, and possible future directions of atom chip research. The articles are written by leading researchers in the field in their characteristic and individual styles.

  12. Atomic energy

    CERN Multimedia

    1996-01-01

    Interviews following the 1991 co-operation Agreement between the Department of Atomic Energy (DAE) of the Government of India and the European Organization for Nuclear Research (CERN) concerning the participation in the Large Hadron Collider Project (LHC) . With Chidambaram, R, Chairman, Atomic Energy Commission and Secretary, Department of Atomic Energy, Department of Atomic Energy (DAE) of the Government of India and Professor Llewellyn-Smith, Christopher H, Director-General, CERN.

  13. 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

  14. Potential Energy Surfaces for Reactions of X Metal Atoms (X = Cu, Zn, Cd, Ga, Al, Au, or Hg with YH4 Molecules (Y = C, Si, or Ge and Transition Probabilities at Avoided Crossings in Some Cases

    Directory of Open Access Journals (Sweden)

    Octavio Novaro

    2012-01-01

    Full Text Available We review ab initio studies based on quantum mechanics on the most important mechanisms of reaction leading to the C–H, Si–H, and Ge–H bond breaking of methane, silane, and germane, respectively, by a metal atom in the lowest states in Cs symmetry: X(2nd excited state, 1st excited state and ground state + YH4→ H3XYH → H + XYH3 and XH + YH3. with X = Au, Zn, Cd, Hg, Al, and G, and Y = C, Si, and Ge. Important issues considered here are (a the role that the occupation of the d-, s-, or p-shells of the metal atom plays in the interactions with a methane or silane or germane molecule, (b the role of either singlet or doublet excited states of metals on the reaction barriers, and (c the role of transition probabilities for different families of reacting metals with these gases, using the H–X–Y angle as a reaction coordinate. The breaking of the Y–H bond of YH4 is useful in the production of amorphous hydrogenated films, necessary in several fields of industry.

  15. Gravity duals for nonrelativistic conformal field theories.

    Science.gov (United States)

    Balasubramanian, Koushik; McGreevy, John

    2008-08-08

    We attempt to generalize the anti-de Sitter/conformal field theory correspondence to nonrelativistic conformal field theories which are invariant under Galilean transformations. Such systems govern ultracold atoms at unitarity, nucleon scattering in some channels, and, more generally, a family of universality classes of quantum critical behavior. We construct a family of metrics which realize these symmetries as isometries. They are solutions of gravity with a negative cosmological constant coupled to pressureless dust. We discuss realizations of the dust, which include a bulk superconductor. We develop the holographic dictionary and find two-point correlators of the correct form. A strange aspect of the correspondence is that the bulk geometry has two extra noncompact dimensions.

  16. A probabilistic model of RNA conformational space

    DEFF Research Database (Denmark)

    Frellsen, Jes; Moltke, Ida; Thiim, Martin;

    2009-01-01

    The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling......, the discrete nature of the fragments necessitates the use of carefully tuned, unphysical energy functions, and their non-probabilistic nature impairs unbiased sampling. We offer a solution to the sampling problem that removes these important limitations: a probabilistic model of RNA structure that allows...... conformations for 9 out of 10 test structures, solely using coarse-grained base-pairing information. In conclusion, the method provides a theoretical and practical solution for a major bottleneck on the way to routine prediction and simulation of RNA structure and dynamics in atomic detail....

  17. How to distinguish conformational selection and induced fit based on chemical relaxation rates

    CERN Document Server

    Paul, Fabian

    2016-01-01

    Protein binding often involves conformational changes. Important questions are whether a conformational change occurs prior to a binding event ('conformational selection') or after a binding event ('induced fit'), and how conformational transition rates can be obtained from experiments. In this article, we present general results for the chemical relaxation rates of conformational-selection and induced-fit binding processes that hold for all concentrations of proteins and ligands and, thus, go beyond the standard pseudo-first-order approximation of large ligand concentration. These results allow to distinguish conformational-selection from induced-fit processes - also in cases in which such a distinction is not possible under pseudo-first-order conditions - and to extract conformational transition rates of proteins from chemical relaxation data.

  18. Dipole moment surfaces of the CH4 + •X → CH3• + HX (X = F, Cl) reactions from atomic dipole moment surfaces, and the origins of the sharp extrema of the dipole moments near the transition states.

    Science.gov (United States)

    Matta, Chérif F; Sowlati-Hashjin, Shahin; Bandrauk, André D

    2013-08-15

    The partitioning of the dipole moment of an isolated molecule or that of a reacting system is reviewed and applied to a dynamic reacting system whereby the system's dipole moment surface is constructed in parallel to its potential energy surface. The dipole moment surface is then decomposed into two origin-independent surfaces: (1) an atomic polarization (AP) surface and a charge transfer (CT) surface. The dipole moment surface as well as its two composing AP and CT surfaces are all further broken down into atomic and/or group contributions with the aid of the quantum theory of atoms in molecules (QTAIM). This approach is applied to the title's laser-induced chemical reactions [CH4 + (•)X → CH3(•) + HX (X = F, Cl)] previously studied by Bandrauk et al. [ J. Chem. Phys. 2004 , 121 , 7764 - 7775 ], and which were found to exhibit marked peaks in the dipole moment and in the polarizability tensor component at (or near) the transition state. These peaks afford a means to control the kinetics of these reactions with the proper adjustment of an external laser field intensity and phase. The entrance channel potentials of these reactions have recently been probed by photodetachment spectroscopy by Bowman and collaborators [ J. Chem. Phys. 2011 , 134 , 191102_1 - 4 ]. The understanding of the origin of the peaks in the dipole moment can provide, eventually, an additional layer of control in the design of reactions tunable by external fields through the proper selection of the reactants to maximize the field-molecule interaction.

  19. Probing conformation and conformational change in proteins is optimally undertaken in relative mode.

    Science.gov (United States)

    Errington, Neil; Rowe, Arthur J

    2003-08-01

    Hydrodynamic bead modelling has been widely used in attempts to assess the 3D conformation of proteins in solution. Initially, simple models employing only a small number of beads were used, with a considerable degree of success. Latterly, high-resolution bead models based upon atomic coordinates have been developed, and much more sophisticated questions can in principle be addressed. A detailed analysis is presented of the errors involved in the generation of such models and associated prediction of (translational friction) parameters, and in the practical measurement of these parameters for comparison. It is shown that in most cases, for a particle of only moderate asymmetry, the errors are such that it is not feasible to determine, on an absolute basis, which of a range of candidate conformers is the "correct" one. However, when the properties of the candidate conformers can be compared in relation to those of a "paradigm conformer", whose structure in solution, on the basis of external evidence, can be accepted as correct, then errors cancel and very precise comparisons become possible. The generation of 3D bead models (and hence 3D data files) for a range of candidate conformers is a simple matter, using the existing program MacBEADS, further facilitated by a 3D display module (pro Fit).

  20. 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.

  1. A Conformal Extension Theorem based on Null Conformal Geodesics

    CERN Document Server

    Lübbe, Christian

    2008-01-01

    In this article we describe the formulation of null geodesics as null conformal geodesics and their description in the tractor formalism. A conformal extension theorem through an isotropic singularity is proven by requiring the boundedness of the tractor curvature and its derivatives to sufficient order along a congruence of null conformal geodesic. This article extends earlier work by Tod and Luebbe.

  2. Emission Probability of the Cascade Three-Level-Atom Mazer with Injected Atomic Coherence

    Institute of Scientific and Technical Information of China (English)

    熊锦; 张智明

    2002-01-01

    We investigate the effects of the injected atomic coherence on the atomic emission probability of the micromaser injected with ultracold cascade three-level atoms by considering that the atoms are initially in the coherent superposition states of the two upper levels. We show that there is no interference between the transitions from the two upper levels to the lowest level. In the large atom-field-detuning case, the atomic emission probability decreases as the coherent parameter increases. In the zero atom-field-detuning case, the atomic emission probability has three sets of resonance peaks. The reason for these results has been explained.

  3. 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.

  4. A DFT study on the correlation between topology and Bader charges: Part IV, on the change of atomic charges in polymorphic transitions - A case study on CaCl2

    Science.gov (United States)

    Beck, Horst P.

    2016-02-01

    Referring to the experimental results of high pressure experiments of Léger et al. (1998) we have calculated the energies of all phases observed for CaCl2 within the DFT formalism using the VASP package, and we have retrieved enthalpies and transition pressures. All phases can be considerably compressed or dilated without much change in energy. This energetic "softness" could even be quantified. We classify the high temperature TiO2-type structure and the PbCl2-type one at highest pressures as the energetically "softest" ones and the SrI2-type one as the "hardest". We furthermore discuss the energy density (E/V) of the different phases and redefine it as a fictive cohesive pressure within these structures. Pursuing our earlier approaches we have analysed the charges of the atoms in the different CaCl2 phases and their change on compression or dilation. On comparing the gradients of the charge curves we define a sort of "charge hardness" which will generally depend on the type of cation-anion pair but also on their topological connection in the respective structures. We speculate that exhausting the "charge softness or hardness" of individual ions in such arrangements may initiate the structural reorganization at the transition pressures.

  5. 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

  6. Src kinase conformational activation: thermodynamics, pathways, and mechanisms.

    Directory of Open Access Journals (Sweden)

    Sichun Yang

    2008-03-01

    Full Text Available Tyrosine kinases of the Src-family are large allosteric enzymes that play a key role in cellular signaling. Conversion of the kinase from an inactive to an active state is accompanied by substantial structural changes. Here, we construct a coarse-grained model of the catalytic domain incorporating experimental structures for the two stable states, and simulate the dynamics of conformational transitions in kinase activation. We explore the transition energy landscapes by constructing a structural network among clusters of conformations from the simulations. From the structural network, two major ensembles of pathways for the activation are identified. In the first transition pathway, we find a coordinated switching mechanism of interactions among the alphaC helix, the activation-loop, and the beta strands in the N-lobe of the catalytic domain. In a second pathway, the conformational change is coupled to a partial unfolding of the N-lobe region of the catalytic domain. We also characterize the switching mechanism for the alphaC helix and the activation-loop in detail. Finally, we test the performance of a Markov model and its ability to account for the structural kinetics in the context of Src conformational changes. Taken together, these results provide a broad framework for understanding the main features of the conformational transition taking place upon Src activation.

  7. Computation of conformational coupling in allosteric proteins.

    Directory of Open Access Journals (Sweden)

    Brian A Kidd

    2009-08-01

    Full Text Available In allosteric regulation, an effector molecule binding a protein at one site induces conformational changes, which alter structure and function at a distant active site. Two key challenges in the computational modeling of allostery are the prediction of the structure of one allosteric state starting from the structure of the other, and elucidating the mechanisms underlying the conformational coupling of the effector and active sites. Here we approach these two challenges using the Rosetta high-resolution structure prediction methodology. We find that the method can recapitulate the relaxation of effector-bound forms of single domain allosteric proteins into the corresponding ligand-free states, particularly when sampling is focused on regions known to change conformation most significantly. Analysis of the coupling between contacting pairs of residues in large ensembles of conformations spread throughout the landscape between and around the two allosteric states suggests that the transitions are built up from blocks of tightly coupled interacting sets of residues that are more loosely coupled to one another.

  8. Correcting mitochondrial fusion by manipulating mitofusin conformations

    Science.gov (United States)

    Franco, Antonietta; Kitsis, Richard N.; Fleischer, Julie A.; Gavathiotis, Evripidis; Kornfeld, Opher S.; Gong, Guohua; Biris, Nikolaos; Benz, Ann; Qvit, Nir; Donnelly, Sara K; Chen, Yun; Mennerick, Steven; Hodgson, Louis; Mochly-Rosen, Daria; Dorn, Gerald W

    2017-01-01

    Summary Mitochondria are dynamic organelles, remodeling and exchanging contents during cyclic fusion and fission. Genetic mutations of mitofusin (Mfn) 2 interrupt mitochondrial fusion and cause the untreatable neurodegenerative condition, Charcot Marie Tooth disease type 2A (CMT2A). It has not been possible to directly modulate mitochondrial fusion, in part because the structural basis of mitofusin function is incompletely understood. Here we show that mitofusins adopt either a fusion-constrained or fusion-permissive molecular conformation directed by specific intramolecular binding interactions, and demonstrate that mitofusin-dependent mitochondrial fusion can be regulated by targeting these conformational transitions. Based on this model we engineered a cell-permeant minipeptide to destabilize fusion-constrained mitofusin and promote the fusion-permissive conformation, reversing mitochondrial abnormalities in cultured fibroblasts and neurons harboring CMT2A gene defects. The relationship between mitofusin conformational plasticity and mitochondrial dynamism uncovers a central mechanism regulating mitochondrial fusion whose manipulation can correct mitochondrial pathology triggered by defective or imbalanced mitochondrial dynamics. PMID:27775718

  9. Spatial atomic layer deposition: a route towards further industrialization of atomic layer deposition

    NARCIS (Netherlands)

    Poodt, P.W.G.; Cameron, D.C.; Dickey, E.; George, S.M.; Kuznetsov, V.; Parsons, G.N.; Roozeboom, F.; Sundaram, G.; Vermeer, A.

    2012-01-01

    Atomic layer deposition (ALD) is a technique capable of producing ultrathin conformal films with atomic level control over thickness. A major drawback of ALD is its low deposition rate, making ALD less attractive for applications that require high throughput processing. An approach to overcome this

  10. 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.

  11. From integrable to conformal theory

    Energy Technology Data Exchange (ETDEWEB)

    Babelon, O. (Paris-6 Univ., 75 (France). Lab. de Physique Theorique et Hautes Energies)

    1990-12-01

    Working in the context of Toda field theory, we establish the relationship between their integrability properties and their conformal structure, thereby clarifying the role of the Yang-Baxter equation in conformal field theory. (orig.).

  12. 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.

  13. Conformal Complementarity Maps

    CERN Document Server

    Barbón, José L F

    2013-01-01

    We study quantum cosmological models for certain classes of bang/crunch singularities, using the duality between expanding bubbles in AdS with a FRW interior cosmology and perturbed CFTs on de Sitter space-time. It is pointed out that horizon complementarity in the AdS bulk geometries is realized as a conformal transformation in the dual deformed CFT. The quantum version of this map is described in full detail in a toy model involving conformal quantum mechanics. In this system the complementarity map acts as an exact duality between eternal and apocalyptic Hamiltonian evolutions. We calculate the commutation relation between the Hamiltonians corresponding to the different frames. It vanishes only on scale invariant states.

  14. Conformational flexibility of aspartame.

    Science.gov (United States)

    Toniolo, Claudio; Temussi, Pierandrea

    2016-05-01

    L-Aspartyl-L-phenylalanine methyl ester, better known as aspartame, is not only one of the most used artificial sweeteners, but also a very interesting molecule with respect to the correlation between molecular structure and taste. The extreme conformational flexibility of this dipeptide posed a huge difficulty when researchers tried to use it as a lead compound to design new sweeteners. In particular, it was difficult to take advantage of its molecular model as a mold to infer the shape of the, then unknown, active site of the sweet taste receptor. Here, we follow the story of the 3D structural aspects of aspartame from early conformational studies to recent docking into homology models of the receptor. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 376-384, 2016.

  15. On conformal lenses

    CERN Document Server

    Chen, Huanyang; Li, Hui

    2011-01-01

    Plane mirror can make one object into two for observers on the object's side. Yet, there seems no way to achieve the same effect for observers from all directions. In this letter, we will design a new class of gradient index lenses from multivalued optical conformal mapping. We shall call them the conformal lenses. Such lenses can transform one source into two (or even many) omnidirectionally. Like the overlapped illusion optics does, they can even transform multiple sources into one. Rather than using negative index materials, implementation here only needs isotropic positive index materials like other gradient index lenses. One obvious drawback however, is that they have singular permittivity values which restrict them to functioning at one single frequency. This however, needs not be the case when applying transmutation methods, which enable the lenses to work in a broadband frequency range.

  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. On the difference between breakdown and quench voltages of argon plasma and its relation to $4p-4s$ atomic state transitions

    CERN Document Server

    Forati, Ebrahim; Sievenpiper, Dan

    2014-01-01

    Using a relaxation oscillator circuit, breakdown ($V_{\\mathrm{BD}}$) and quench ($V_{\\mathrm{Q}}$) voltages of a DC discharge microplasma between two needle probes are measured. High resolution modified Paschen curves are obtained for argon microplasmas including a quench voltage curve representing the voltage at which the plasma turns off. It is shown that, for a point to point microgap (e.g. the microgap between two needle probes) which describes many realistic microdevices, neither Paschen's law applies nor field emission is noticeable. Although normally $V_{\\mathrm{BD}}>V_{\\mathrm{Q}}$, it is observed that depending on environmental parameters of argon, such as pressure and the driving circuitry, plasma can exist in a different state with equal $V_{\\mathrm{BD}}$ and $V_{\\mathrm{Q}}$. Using emission line spectroscopy, it is shown that $V_{\\mathrm{BD}}$ and $V_{\\mathrm{Q}}$ are equal if the atomic excitation by the electric field dipole moment dominantly leads to one of the argon's metastable states ($4P_{5...

  18. On the difference between breakdown and quench voltages of argon plasma and its relation to 4p–4s atomic state transitions

    Energy Technology Data Exchange (ETDEWEB)

    Forati, Ebrahim, E-mail: forati@ieee.org; Piltan, Shiva; Sievenpiper, Dan, E-mail: dsievenpiper@ucsd.edu [University of California San Diego, La Jolla, California 92093 (United States)

    2015-02-02

    Using a relaxation oscillator circuit, breakdown (V{sub BD}) and quench (V{sub Q}) voltages of a DC discharge microplasma between two needle probes are measured. High resolution modified Paschen curves are obtained for argon microplasmas including a quench voltage curve representing the voltage at which the plasma turns off. It is shown that for a point to point microgap (e.g., the microgap between two needle probes) which describes many realistic microdevices, neither Paschen's law applies nor field emission is noticeable. Although normally V{sub BD} > V{sub Q,} it is observed that depending on environmental parameters of argon, such as pressure and the driving circuitry, plasma can exist in a different state with equal V{sub BD} and V{sub Q.} Using emission line spectroscopy, it is shown that V{sub BD} and V{sub Q} are equal if the atomic excitation by the electric field dipole moment dominantly leads to one of the argon's metastable states (4P{sub 5} in our study)

  19. Design Rules for Non-Atomic Implementations of PRS

    OpenAIRE

    Papadantonakis, Karl

    2005-01-01

    Martin Synthesis yields quasi--delay-insensitive (QDI) circuits, expressed in production--rule-set (PRS) form. Under an atomic circuit evaluation model, these circuits are provably correct. However, not all physical circuit implementations provide the atomic transitions needed to satisfy the atomic circuit model. This can cause operational failures in real circuits, as we illustrate. Nonetheless, circuits with non-atomic transitions can faithfully implement the atomic circuit model when comb...

  20. Two Additional Remarks on Conformism

    OpenAIRE

    Schlicht, Ekkehart

    2014-01-01

    Abstract This note offers two comments on the article “Social Influences towards Conformism in Economic Experiments” by Hargreaves Heap that is to appear in the Economics e-Journal. One relates to the concept of conformism, the other lines out some phenomena where an explicit recognition of group processes, such as conformism, may be analytically helpful.

  1. 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

    2016-12-23

    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.

  2. Two-dimensional atom localization via probe absorption in a four-level atomic system

    Institute of Scientific and Technical Information of China (English)

    Wang Zhi-Ping; Ge Qiang; Ruan Yu-Hua; Yu Ben-Li

    2013-01-01

    We have investigated the two-dimensional (2D) atom localization via probe absorption in a coherently driven fourlevel atomic system by means of a radio-frequency field driving a hyperfine transition.It is found that the detecting probability and precision of 2D atom localization can be significantly improved via adjusting the system parameters.As a result,our scheme may be helpful in laser cooling or the atom nano-lithography via atom localization.

  3. Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility

    Energy Technology Data Exchange (ETDEWEB)

    Pancera, Marie; Majeed, Shahzad; Ban, Yih-En Andrew; Chen, Lei; Huang, Chih-chin; Kong, Leopold; Kwon, Young Do; Stuckey, Jonathan; Zhou, Tongqing; Robinson, James E.; Schief, William R.; Sodroski, Joseph; Wyatt, Richard; Kwong, Peter D. (UWASH); (NIH); (Tulane); (DFCI)

    2010-04-15

    The viral spike of HIV-1 is composed of three gp120 envelope glycoproteins attached noncovalently to three gp41 transmembrane molecules. Viral entry is initiated by binding to the CD4 receptor on the cell surface, which induces large conformational changes in gp120. These changes not only provide a model for receptor-triggered entry, but affect spike sensitivity to drug- and antibody-mediated neutralization. Although some of the details of the CD4-induced conformational change have been visualized by crystal structures and cryoelectron tomograms, the critical gp41-interactive region of gp120 was missing from previous atomic-level characterizations. Here we determine the crystal structure of an HIV-1 gp120 core with intact gp41-interactive region in its CD4-bound state, compare this structure to unliganded and antibody-bound forms to identify structurally invariant and plastic components, and use ligand-oriented cryoelectron tomograms to define component mobility in the viral spike context. Newly defined gp120 elements proximal to the gp41 interface complete a 7-stranded {beta}-sandwich, which appeared invariant in conformation. Loop excursions emanating from the sandwich form three topologically separate - and structurally plastic - layers, topped off by the highly glycosylated gp120 outer domain. Crystal structures, cryoelectron tomograms, and interlayer chemistry were consistent with a mechanism in which the layers act as a shape-changing spacer, facilitating movement between outer domain and gp41-associated {beta}-sandwich and providing for conformational diversity used in immune evasion. A 'layered' gp120 architecture thus allows movement among alternative glycoprotein conformations required for virus entry and immune evasion, whereas a {beta}-sandwich clamp maintains gp120-gp41 interaction and regulates gp41 transitions.

  4. Unbiased simulations reveal the inward-facing conformation of the human serotonin transporter and Na+ ion release

    DEFF Research Database (Denmark)

    Koldsø, Heidi; Noer, Pernille Rimmer; Grouleff, Julie;

    2011-01-01

    . The simulations reveal a transition of hSERT from an outward-facing occluded conformation to an inward-facing conformation in a one-substrate-bound state. Simulations with a second substrate in the proposed symport effector site did not lead to conformational changes associated with translocation. The central...

  5. 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...

  6. Simple, yet powerful methodologies for conformational sampling of proteins.

    Science.gov (United States)

    Harada, Ryuhei; Takano, Yu; Baba, Takeshi; Shigeta, Yasuteru

    2015-03-07

    Several biological functions, such as molecular recognition, enzyme catalysis, signal transduction, allosteric regulation, and protein folding, are strongly related to conformational transitions of proteins. These conformational transitions are generally induced as slow dynamics upon collective motions, including biologically relevant large-amplitude fluctuations of proteins. Although molecular dynamics (MD) simulation has become a powerful tool for extracting conformational transitions of proteins, it might still be difficult to reach time scales of the biological functions because the accessible time scales of MD simulations are far from biological time scales, even if straightforward conventional MD (CMD) simulations using massively parallel computers are employed. Thus, it is desirable to develop efficient methods to achieve canonical ensembles with low computational costs. From this perspective, we review several enhanced conformational sampling techniques of biomolecules developed by us. In our methods, multiple independent short-time MD simulations are employed instead of single straightforward long-time CMD simulations. Our basic strategy is as follows: (i) selection of initial seeds (initial structures) for the conformational sampling in restarting MD simulations. Here, the seeds should be selected as candidates with high potential to transit. (ii) Resampling from the selected seeds by initializing velocities in restarting short-time MD simulations. A cycle of these simple protocols might drastically promote the conformational transitions of biomolecules. (iii) Once reactive trajectories extracted from the cycles of short-time MD simulations are obtained, a free energy profile is evaluated by means of umbrella sampling (US) techniques with the weighted histogram analysis method (WHAM) as a post-processing technique. For the selection of the initial seeds, we proposed four different choices: (1) Parallel CaScade molecular dynamics (PaCS-MD), (2) Fluctuation

  7. 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.

  8. Atomic Structure Theory Lectures on Atomic Physics

    CERN Document Server

    Johnson, Walter R

    2007-01-01

    Atomic Structure Theory is a textbook for students with a background in quantum mechanics. The text is designed to give hands-on experience with atomic structure calculations. Material covered includes angular momentum methods, the central field Schrödinger and Dirac equations, Hartree-Fock and Dirac-Hartree-Fock equations, multiplet structure, hyperfine structure, the isotope shift, dipole and multipole transitions, basic many-body perturbation theory, configuration interaction, and correlation corrections to matrix elements. Numerical methods for solving the Schrödinger and Dirac eigenvalue problems and the (Dirac)-Hartree-Fock equations are given as well. B-spline basis sets are used to carry out sums arising in higher-order many-body calculations. Illustrative problems are provided, together with solutions. FORTRAN programs implementing the numerical methods in the text are included.

  9. 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.

  10. Leaf growth is conformal

    Science.gov (United States)

    Alim, Karen; Armon, Shahaf; Shraiman, Boris I.; Boudaoud, Arezki

    2016-10-01

    Growth pattern dynamics lie at the heart of morphogenesis. Here, we investigate the growth of plant leaves. We compute the conformal transformation that maps the contour of a leaf at a given stage onto the contour of the same leaf at a later stage. Based on the mapping we predict the local displacement field in the leaf blade and find it to agree with the experimentally measured displacement field to 92%. This approach is applicable to any two-dimensional system with locally isotropic growth, enabling the deduction of the whole growth field just from observation of the tissue contour.

  11. Leaf growth is conformal

    CERN Document Server

    Alim, Karen; Shraiman, Boris I; Boudaoud, Arezki

    2016-01-01

    Growth pattern dynamics lie at the heart of morphogenesis. Here, we investigate the growth of plant leaves. We compute the conformal transformation that maps the contour of a leaf at a given stage onto the contour of the same leaf at a later stage. Based on the mapping we predict the local displacement field in the leaf blade and find it to agree with the experimentally measured displacement field to 92%. This approach is applicable to any two-dimensional system with locally isotropic growth, enabling the deduction of the whole growth field just from observation of the tissue contour.

  12. 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....

  13. Conformal fluid dynamics

    CERN Document Server

    Jarvis, P D

    2006-01-01

    We present a conformal theory of a dissipationless relativistic fluid in 2 space-time dimensions. The theory carries with it a representation of the algebra of 2-$D$ area-preserving diffeomorphisms in the target space of the complex scalar potentials. A complete canonical description is given, and the central charge of the current algebra is calculated. The passage to the quantum theory is discussed in some detail; as a result of operator ordering problems, full quantization at the level of the fields is as yet an open problem.

  14. 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.

  15. Atomic physics

    CERN Document Server

    Born, Max

    1989-01-01

    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.

  16. 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.

  17. Regioselective sulfation of Artemisia sphaerocephala polysaccharide: Solution conformation and antioxidant activities in vitro.

    Science.gov (United States)

    Wang, Junlong; Yang, Wen; Tang, YinYing; Xu, Qing; Huang, Shengli; Yao, Jian; Zhang, Ji; Lei, Ziqiang

    2016-01-20

    Regioselective modification is an effective approach to synthesize polysaccharides with different structure features and improved properties. In this study, regioselective sulfation of Artemisia sphaerocephala polysaccharide (SRSASP) was prepared by using triphenylchloromethane (TrCl) as protecting precursor. The decrease in fractal dimension (df) values (1.56-2.04) of SRSASP was observed in size-exclusion chromatography combined with multi angle laser light scattering (SEC-MALLS) analysis. Compared to sample substituted at C-6, SRSASP showed a more expanded conformation of random coil, which was attributed to the breakup of hydrogen bonds and elastic contributions. Circular dichroism (CD), methylene blue (MB) and congo red (CR) spectrophotometric method and atomic force microscopy (AFM) results confirmed the conformational transition and stiffness of the chains after sulfation. SRSASP exhibited enhanced antioxidant activities in the DPPH, superoxide and hydroxyl radical scavenging assay. Sulfation at C-2 or C-3 was favorable for the chelation which might prevent the generation of hydroxyl radicals. It concluded that the degree of substitution and substitution position were the factors influencing biological activities of sulfated polysaccharides.

  18. 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.

  19. Hot Conformal Gauge Theories

    CERN Document Server

    Mojaza, Matin; Sannino, Francesco

    2010-01-01

    We compute the nonzero temperature free energy up to the order g^6 \\ln(1/g) in the coupling constant for vector like SU(N) gauge theories featuring matter transforming according to different representations of the underlying gauge group. The number of matter fields, i.e. flavors, is arranged in such a way that the theory develops a perturbative stable infrared fixed point at zero temperature. Due to large distance conformality we trade the coupling constant with its fixed point value and define a reduced free energy which depends only on the number of flavors, colors and matter representation. We 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 o...

  20. 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.

  1. 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.

  2. 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.

  3. Photoregulation of polymer conformation. A modelstudy for biology

    NARCIS (Netherlands)

    Veen, Gerlof van der

    1972-01-01

    SUMMARY A conformational transition of a macromolecule is often postulated to occur in biological energy transductions. When +he energy of a photon is transduced, a photochromic ligand mediates in the transfer of energy from the sun to the macromolecule. In this thesis the molecular mechanism of tho

  4. Conformational Transformation of Five-Membered Rings: the Gas Phase Structure of 2-METHYLTETRAHYDROFURAN

    Science.gov (United States)

    Van, Vinh; Nguyen, Ha Vinh Lam; Stahl, Wolfgang

    2015-06-01

    2-Methyltetrahydrofuran (2-MeTHF) is a promising environmentally friendly solvent and biofuel component which is derived from renewable resources. Following the principles of Green Chemistry, 2-MeTHF has been evaluated in various fields like organometallics, metathesis, and biosynthesis on the way to more eco-friendly syntheses. Cyclopentane as the prototype of five-membered rings is well-known to exist as twist or envelope structures. However, the conformational analysis of its heterocyclic derivative 2-methyl-tetrahydrothiophene (MTTP) yielded two stable twist conformers and two envelope transition states. Here, we report on the heavy atom r_s structure of the oxygen-analog of MTTP, 2-MeTHF, studied by a combination of molecular beam Fourier transform microwave spectroscopy and quantum chemistry. One conformer of 2-MeTHF was observed and highly accurate molecular parameters were determined using the XIAM program. In addition, all 13C-isotopologues were assigned in natural abundance of 1%. A structural determination based on the r_s positions of all carbon atoms was achieved via Kraitchman's equations. The methyl group in 2-MeTHF undergoes internal rotation and causes A-E splittings of the rotational lines. The barrier was calculated to be 1142 wn at the MP2/6-311++G(d,p) level of theory, which is rather high. Accordingly, narrow A-E splittings could be observed for only a few transitions. However, the barrier height could be fitted while the angles between the internal rotor axis and the principal axes of inertia were taken from the experimental geometry. V. Pace, P. Hoyos, L. Castoldi, P. Domínguez de María, A. R. Alcántara, ChemSusChem 5 (2012), 1369-1379. a) D. F. Aycock, Org. Process Res. Dev. 11 (2007),156-159. b) M. Smoleń, M. Kȩdziorek, K. Grela, Catal. Commun. 44 (2014), 80-84. V. Van, C. Dindic, H.V.L. Nguyen, W. Stahl, ChemPhysChem 16 (2015), 291-294. H. Hartwig, H. Dreizler, Z. Naturforsch. A 51 (1996), 923-932. J. Kraitchman, Am. J. Phys. 21

  5. 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.

  6. Subtleties Concerning Conformal Tractor Bundles

    CERN Document Server

    Graham, C Robin

    2012-01-01

    The realization of tractor bundles as associated bundles in conformal geometry is studied. It is shown that different natural choices of principal bundle with normal Cartan connection corresponding to a given conformal manifold can give rise to topologically distinct associated tractor bundles for the same inducing representation. Consequences for homogeneous models and conformal holonomy are described. A careful presentation is made of background material concerning standard tractor bundles and equivalence between parabolic geometries and underlying structures.

  7. Dimensional Reduction for Conformal Blocks

    CERN Document Server

    Hogervorst, Matthijs

    2016-01-01

    We consider the dimensional reduction of a CFT, breaking multiplets of the d-dimensional conformal group SO(d+1,1) up into multiplets of SO(d,1). This leads to an expansion of d-dimensional conformal blocks in terms of blocks in d-1 dimensions. In particular, we obtain a formula for 3d conformal blocks as an infinite sum over 2F1 hypergeometric functions with closed-form coefficients.

  8. Loop Virasoro Lie conformal algebra

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Henan, E-mail: wuhenanby@163.com; Chen, Qiufan; Yue, Xiaoqing [Department of Mathematics, Tongji University, Shanghai 200092 (China)

    2014-01-15

    The Lie conformal algebra of loop Virasoro algebra, denoted by CW, is introduced in this paper. Explicitly, CW is a Lie conformal algebra with C[∂]-basis (L{sub i} | i∈Z) and λ-brackets [L{sub i} {sub λ} L{sub j}] = (−∂−2λ)L{sub i+j}. Then conformal derivations of CW are determined. Finally, rank one conformal modules and Z-graded free intermediate series modules over CW are classified.

  9. Reflections on Conformal Spectra

    CERN Document Server

    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

  10. Conformal frames in cosmology

    CERN Document Server

    Domènech, Guillem

    2016-01-01

    From higher dimensional theories, e.g. string theory, one expects the presence of non-minimally coupled scalar fields. We review the notion of conformal frames in cosmology and emphasize their physical equivalence, which holds at least at a classical level. Furthermore, if there is a field, or fields, which dominates the universe, as it is often the case in cosmology, we can use such notion of frames to treat our system, matter and gravity, as two different sectors. On one hand, the gravity sector which describes the dynamics of the geometry and on the other hand the matter sector which has such geometry as a playground. We use this interpretation to build a model where the fact that a curvaton couples to a particular frame metric could leave an imprint in the CMB.

  11. Reflections on Conformal Spectra

    CERN Document Server

    Kim, Hyungrok; Ooguri, Hirosi

    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 $\\Delta_0$ 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 $\\Delta_0$ as well as for large $\\Delta_0$. 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.

  12. Energy levels and quantum states of [Leu]enkephalin conformations based on theoretical and experimental investigations

    DEFF Research Database (Denmark)

    Abdali, Salim; Jensen, Morten Østergaard; Bohr, Henrik

    2003-01-01

    This paper describes a theoretical and experimental study of [Leu]enkephalin conformations with respect to the quantum estates of the atomic structure of the peptide. Results from vibrational absorption measurements and quantum calculations are used to outline a quantum picture and to assign...... vibrational modes to the different conformations. The energy landscape of the conformations is reported as a function of a Hamming distance in Ramachandran space. Molecular dynamics simulations reveal a pronounced stability of the so-called single-bend low-energy conformation, which supports the derived...... quantum picture of this peptide....

  13. Conformation Switching in Gas-Phase Complexes of Histidine with Alkaline Earth Ions

    NARCIS (Netherlands)

    Dunbar, R. C.; Hopkinson, A. C.; Oomens, J.; Siu, C. K.; Siu, K. W. M.; Steill, J. D.; Verkerk, U. H.; Zhao, J. F.

    2009-01-01

    Infrared multiple photon dissociation spectroscopy of gas-phase doubly charged alkaline earth complexes of histidine reveals a transition from dominance of the zwitterion (salt bridge, SB) conformation with Ba2+ to substantial presence of the canonical (charge-solvated, CS) conformation with Ca2+. T

  14. DFT study of conformational and vibrational characteristics of 2-(2-hydroxyphenyl)benzothiazole molecule

    Science.gov (United States)

    Pandey, Urmila; Srivastava, Mayuri; Singh, R. P.; Yadav, R. A.

    2014-08-01

    The conformational and IR and Raman spectral studies of 2-(2-hydroxyphenyl)benzothiazole have been carried out by using the DFT method at the B3LYP/6-311++G** level. The detailed vibrational assignments have been done on the basis of calculated potential energy distributions. Comparative studies of molecular geometries, atomic charges and vibrational fundamentals of all the conformers have been made. There are four possible conformers for this molecule. The optimized geometrical parameters obtained by B3LYP/6-311++G** method showed good agreement with the experimental X-ray data. The atomic polar tensor (APT) charges, Mulliken atomic charges, natural bond orbital (NBO) analysis and HOMO-LUMO energy gap of HBT and its conformers were also computed.

  15. Study of the conformal region of the SU(3) gauge theory with domain-wall fermions

    CERN Document Server

    Noaki, J; Ishikawa, K-I; Iwasaki, Y; Yoshie, T

    2015-01-01

    We investigate the phase structure of the SU(3) gauge theory with $N_f=8$ by numerical simulations employing the massless Domain-Wall fermions.Our aim is to study directly the massless quark region, since it is the most important region to clarify the properties of conformal theories. When the number of flavor is within the conformal window, it is claimed recently with Wilson quarks that there is the conformal region at the small quark mass region in the parameter space in addition to the confining phase and the deconfining phase. We study the properties of the conformal region investing the spatial Polyakov loops and the temporal meson propagators. Our data imply that there is the conformal region, and a phase transition between the confining phase and the conformal region takes place. These results are consistent with the claim that the conformal window is between $7$ and $16$. Progress reports on other related studies are also presented.

  16. Correlative atomic force and confocal fluorescence microscopy: single molecule imaging and force induced spectral shifts (Conference Presentation)

    Science.gov (United States)

    Basché, Thomas; Hinze, Gerald; Stöttinger, Sven

    2016-09-01

    A grand challenge in nanoscience is to correlate structure or morphology of individual nano-sized objects with their photo-physical properties. An early example have been measurements of the emission spectra and polarization of single semiconductor quantum dots as well as their crystallographic structure by a combination of confocal fluorescence microscopy and transmission electron microscopy.[1] Recently, the simultaneous use of confocal fluorescence and atomic force microscopy (AFM) has allowed for correlating the morphology/conformation of individual nanoparticle oligomers or molecules with their photo-physics.[2, 3] In particular, we have employed the tip of an AFM cantilever to apply compressive stress to single molecules adsorbed on a surface and follow the effect of the impact on the electronic states of the molecule by fluorescence spectroscopy.[3] Quantum mechanical calculations corroborate that the spectral changes induced by the localized force can be associated to transitions among the different possible conformers of the adsorbed molecule.

  17. Intrinsic conformational plasticity of native EmrE provides a pathway for multidrug resistance.

    Science.gov (United States)

    Cho, Min-Kyu; Gayen, Anindita; Banigan, James R; Leninger, Maureen; Traaseth, Nathaniel J

    2014-06-04

    EmrE is a multidrug resistance efflux pump with specificity to a wide range of antibiotics and antiseptics. To obtain atomic-scale insight into the attributes of the native state that encodes the broad specificity, we used a hybrid of solution and solid-state NMR methods in lipid bilayers and bicelles. Our results indicate that the native EmrE dimer oscillates between inward and outward facing structural conformations at an exchange rate (k(ex)) of ~300 s(-1) at 37 °C (millisecond motions), which is ~50-fold faster relative to the tetraphenylphosphonium (TPP(+)) substrate-bound form of the protein. These observables provide quantitative evidence that the rate-limiting step in the TPP(+) transport cycle is not the outward-inward conformational change in the absence of drug. In addition, using differential scanning calorimetry, we found that the width of the gel-to-liquid crystalline phase transition was 2 °C broader in the absence of the TPP(+) substrate versus its presence, which suggested that changes in transporter dynamics can impact the phase properties of the membrane. Interestingly, experiments with cross-linked EmrE showed that the millisecond inward-open to outward-open dynamics was not the culprit of the broadening. Instead, the calorimetry and NMR data supported the conclusion that faster time scale structural dynamics (nanosecond-microsecond) were the source and therefore impart the conformationally plastic character of native EmrE capable of binding structurally diverse substrates. These findings provide a clear example how differences in membrane protein transporter structural dynamics between drug-free and bound states can have a direct impact on the physical properties of the lipid bilayer in an allosteric fashion.

  18. 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.

  19. 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.

  20. 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.