Sample records for zundel-like transition state

  1. Nitranilic acid hexahydrate, a novel benchmark system of the Zundel cation in an intrinsically asymmetric environment: spectroscopic features and hydrogen bond dynamics characterised by experimental and theoretical methods.

    PubMed

    Molčanov, Krešimir; Stare, Jernej; Vener, Mikhail V; Kojić-Prodić, Biserka; Mali, Gregor; Grdadolnik, Jože; Mohaček-Grošev, Vlasta

    2014-01-21

    Nitranilic acid (2,5-dihydroxy-3,6-dinitro-2,5-cyclohexadiene-1,4-dione) as a strong dibasic acid in acidic aqueous media creates the Zundel cation, H5O2(+). The structural unit in a crystal comprises (H5O2)2(+) (2,5-dihydroxy-3,6-dinitro-1,4-benzoquinonate)(2-) dihydrate where the Zundel cation reveals no symmetry, being an ideal case for studying proton dynamics and its stability. The Zundel cation and proton transfer dynamics are studied by variable-temperature X-ray diffraction, IR and solid-state NMR spectroscopy, and various quantum chemical methods, including periodic DFT calculations, ab initio molecular dynamics simulation, and quantization of nuclear motion along three fully coupled internal coordinates. The Zundel cation features a short H-bond with the O···O distance of 2.433(2) Å with an asymmetric placement of hydrogen. The proton potential is of a single well type and, due to the non-symmetric surroundings, of asymmetric shape. The formation of the Zundel cation is facilitated by the electronegative NO2 groups. The employed spectroscopic techniques supported by calculations confirm the presence of a short H-bond with a complex proton dynamics.

  2. Structure and spectral features of H+(H2O)7: Eigen versus Zundel forms.

    PubMed

    Shin, Ilgyou; Park, Mina; Min, Seung Kyu; Lee, Eun Cheol; Suh, Seung Bum; Kim, Kwang S

    2006-12-21

    The two dimensional (2D) to three dimensional (3D) transition for the protonated water cluster has been controversial, in particular, for H(+)(H(2)O)(7). For H(+)(H(2)O)(7) the 3D structure is predicted to be lower in energy than the 2D structure at most levels of theory without zero-point energy (ZPE) correction. On the other hand, with ZPE correction it is predicted to be either 2D or 3D depending on the calculational levels. Although the ZPE correction favors the 3D structure at the level of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using the aug-cc-pVDZ basis set, the result based on the anharmonic zero-point vibrational energy correction favors the 2D structure. Therefore, the authors investigated the energies based on the complete basis set limit scheme (which we devised in an unbiased way) at the resolution of the identity approximation Moller-Plesset second order perturbation theory and CCSD(T) levels, and found that the 2D structure has the lowest energy for H(+)(H(2)O)(7) [though nearly isoenergetic to the 3D structure for D(+)(D(2)O)(7)]. This structure has the Zundel-type configuration, but it shows the quantum probabilistic distribution including some of the Eigen-type configuration. The vibrational spectra of MP2/aug-cc-pVDZ calculations and Car-Parrinello molecular dynamics simulations, taking into account the thermal and dynamic effects, show that the 2D Zundel-type form is in good agreement with experiments.

  3. Structure and spectral features of H+(H2O)7: Eigen versus Zundel forms

    NASA Astrophysics Data System (ADS)

    Shin, Ilgyou; Park, Mina; Min, Seung Kyu; Lee, Eun Cheol; Suh, Seung Bum; Kim, Kwang S.

    2006-12-01

    The two dimensional (2D) to three dimensional (3D) transition for the protonated water cluster has been controversial, in particular, for H+(H2O)7. For H+(H2O)7 the 3D structure is predicted to be lower in energy than the 2D structure at most levels of theory without zero-point energy (ZPE) correction. On the other hand, with ZPE correction it is predicted to be either 2D or 3D depending on the calculational levels. Although the ZPE correction favors the 3D structure at the level of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using the aug-cc-pVDZ basis set, the result based on the anharmonic zero-point vibrational energy correction favors the 2D structure. Therefore, the authors investigated the energies based on the complete basis set limit scheme (which we devised in an unbiased way) at the resolution of the identity approximation Møller-Plesset second order perturbation theory and CCSD(T) levels, and found that the 2D structure has the lowest energy for H+(H2O)7 [though nearly isoenergetic to the 3D structure for D+(D2O)7]. This structure has the Zundel-type configuration, but it shows the quantum probabilistic distribution including some of the Eigen-type configuration. The vibrational spectra of MP2/aug-cc-pVDZ calculations and Car-Parrinello molecular dynamics simulations, taking into account the thermal and dynamic effects, show that the 2D Zundel-type form is in good agreement with experiments.

  4. Capturing the state transitions of seizure-like events using Hidden Markov models.

    PubMed

    Guirgis, Mirna; Serletis, Demitre; Carlen, Peter L; Bardakjian, Berj L

    2011-01-01

    The purpose of this study was to investigate the number of states present in the progression of a seizure-like event (SLE). Of particular interest is to determine if there are more than two clearly defined states, as this would suggest that there is a distinct state preceding an SLE. Whole-intact hippocampus from C57/BL mice was used to model epileptiform activity induced by the perfusion of a low Mg(2+)/high K(+) solution while extracellular field potentials were recorded from CA3 pyramidal neurons. Hidden Markov models (HMM) were used to model the state transitions of the recorded SLEs by incorporating various features of the Hilbert transform into the training algorithm; specifically, 2- and 3-state HMMs were explored. Although the 2-state model was able to distinguish between SLE and nonSLE behavior, it provided no improvements compared to visual inspection alone. However, the 3-state model was able to capture two distinct nonSLE states that visual inspection failed to discriminate. Moreover, by developing an HMM based system a priori knowledge of the state transitions was not required making this an ideal platform for seizure prediction algorithms.

  5. IR spectroscopy of protonation in benzene-water nanoclusters: hydronium, zundel, and eigen at a hydrophobic interface.

    PubMed

    Cheng, Timothy C; Bandyopadhyay, Biswajit; Mosley, Jonathan D; Duncan, Michael A

    2012-08-08

    The structure of ions in water at a hydrophobic interface influences important processes throughout chemistry and biology. However, experiments to measure these structures are limited by the distribution of configurations present and the inability to selectively probe the interfacial region. Here, protonated nanoclusters containing benzene and water are produced in the gas phase, size-selected, and investigated with infrared laser spectroscopy. Proton stretch, free OH, and hydrogen-bonding vibrations uniquely define protonation sites and hydrogen-bonding networks. The structures consist of protonated water clusters binding to the hydrophobic interface of neutral benzene via one or more π-hydrogen bonds. Comparison to the spectra of isolated hydronium, zundel, or eigen ions reveals the inductive effects and local ordering induced by the interface. The structures and interactions revealed here represent key features expected for aqueous hydrophobic interfaces.

  6. A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy

    PubMed Central

    Munder, Matthias Christoph; Midtvedt, Daniel; Franzmann, Titus; Nüske, Elisabeth; Otto, Oliver; Herbig, Maik; Ulbricht, Elke; Müller, Paul; Taubenberger, Anna; Maharana, Shovamayee; Malinovska, Liliana; Richter, Doris; Guck, Jochen; Zaburdaev, Vasily; Alberti, Simon

    2016-01-01

    Cells can enter into a dormant state when faced with unfavorable conditions. However, how cells enter into and recover from this state is still poorly understood. Here, we study dormancy in different eukaryotic organisms and find it to be associated with a significant decrease in the mobility of organelles and foreign tracer particles. We show that this reduced mobility is caused by an influx of protons and a marked acidification of the cytoplasm, which leads to widespread macromolecular assembly of proteins and triggers a transition of the cytoplasm to a solid-like state with increased mechanical stability. We further demonstrate that this transition is required for cellular survival under conditions of starvation. Our findings have broad implications for understanding alternative physiological states, such as quiescence and dormancy, and create a new view of the cytoplasm as an adaptable fluid that can reversibly transition into a protective solid-like state. DOI: http://dx.doi.org/10.7554/eLife.09347.001 PMID:27003292

  7. Radiative transition of hydrogen-like ions in quantum plasma

    NASA Astrophysics Data System (ADS)

    Hu, Hongwei; Chen, Zhanbin; Chen, Wencong

    2016-12-01

    At fusion plasma electron temperature and number density regimes of 1 × 103-1 × 107 K and 1 × 1028-1 × 1031/m3, respectively, the excited states and radiative transition of hydrogen-like ions in fusion plasmas are studied. The results show that quantum plasma model is more suitable to describe the fusion plasma than the Debye screening model. Relativistic correction to bound-state energies of the low-Z hydrogen-like ions is so small that it can be ignored. The transition probability decreases with plasma density, but the transition probabilities have the same order of magnitude in the same number density regime.

  8. Two-Photon Transitions in Hydrogen-Like Atoms

    NASA Astrophysics Data System (ADS)

    Martinis, Mladen; Stojić, Marko

    Different methods for evaluating two-photon transition amplitudes in hydrogen-like atoms are compared with the improved method of direct summation. Three separate contributions to the two-photon transition probabilities in hydrogen-like atoms are calculated. The first one coming from the summation over discrete intermediate states is performed up to nc(max) = 35. The second contribution from the integration over the continuum states is performed numerically. The third contribution coming from the summation from nc(max) to infinity is calculated in an approximate way using the mean level energy for this region. It is found that the choice of nc(max) controls the numerical error in the calculations and can be used to increase the accuracy of the results much more efficiently than in other methods.

  9. Transition States and transition state analogue interactions with enzymes.

    PubMed

    Schramm, Vern L

    2015-04-21

    Enzymatic transition states have lifetimes of a few femtoseconds (fs). Computational analysis of enzyme motions leading to transition state formation suggests that local catalytic site motions on the fs time scale provide the mechanism to locate transition states. An experimental test of protein fs motion and its relation to transition state formation can be provided by isotopically heavy proteins. Heavy enzymes have predictable mass-altered bond vibration states without altered electrostatic properties, according to the Born-Oppenheimer approximation. On-enzyme chemistry is slowed in most heavy proteins, consistent with altered protein bond frequencies slowing the search for the transition state. In other heavy enzymes, structural changes involved in reactant binding and release are also influenced. Slow protein motions associated with substrate binding and catalytic site preorganization are essential to allow the subsequent fs motions to locate the transition state and to facilitate the efficient release of products. In the catalytically competent geometry, local groups move in stochastic atomic motion on the fs time scale, within transition state-accessible conformations created by slower protein motions. The fs time scale for the transition state motions does not permit thermodynamic equilibrium between the transition state and stable enzyme states. Isotopically heavy enzymes provide a diagnostic tool for fast coupled protein motions to transition state formation and mass-dependent conformational changes. The binding of transition state analogue inhibitors is the opposite in catalytic time scale to formation of the transition state but is related by similar geometries of the enzyme-transition state and enzyme-inhibitor interactions. While enzymatic transition states have lifetimes as short as 10(-15) s, transition state analogues can bind tightly to enzymes with release rates greater than 10(3) s. Tight-binding transition state analogues stabilize the rare but

  10. Enzymatic Transition States, Transition-State Analogs, Dynamics, Thermodynamics, and Lifetimes

    PubMed Central

    Schramm, Vern L.

    2017-01-01

    Experimental analysis of enzymatic transition-state structures uses kinetic isotope effects (KIEs) to report on bonding and geometry differences between reactants and the transition state. Computational correlation of experimental values with chemical models permits three-dimensional geometric and electrostatic assignment of transition states formed at enzymatic catalytic sites. The combination of experimental and computational access to transition-state information permits (a) the design of transition-state analogs as powerful enzymatic inhibitors, (b) exploration of protein features linked to transition-state structure, (c) analysis of ensemble atomic motions involved in achieving the transition state, (d) transition-state lifetimes, and (e) separation of ground-state (Michaelis complexes) from transition-state effects. Transition-state analogs with picomolar dissociation constants have been achieved for several enzymatic targets. Transition states of closely related isozymes indicate that the protein’s dynamic architecture is linked to transition-state structure. Fast dynamic motions in catalytic sites are linked to transition-state generation. Enzymatic transition states have lifetimes of femtoseconds, the lifetime of bond vibrations. Binding isotope effects (BIEs) reveal relative reactant and transition-state analog binding distortion for comparison with actual transition states. PMID:21675920

  11. Transition Probabilities for Hydrogen-Like Atoms

    NASA Astrophysics Data System (ADS)

    Jitrik, Oliverio; Bunge, Carlos F.

    2004-12-01

    E1, M1, E2, M2, E3, and M3 transition probabilities for hydrogen-like atoms are calculated with point-nucleus Dirac eigenfunctions for Z=1-118 and up to large quantum numbers l=25 and n=26, increasing existing data more than a thousandfold. A critical evaluation of the accuracy shows a higher reliability with respect to previous works. Tables for hydrogen containing a subset of the results are given explicitly, listing the states involved in each transition, wavelength, term energies, statistical weights, transition probabilities, oscillator strengths, and line strengths. The complete results, including 1 863 574 distinct transition probabilities, lifetimes, and branching fractions are available at http://www.fisica.unam.mx/research/tables/spectra/1el

  12. Transition energies and polarizabilities of hydrogen like ions in plasma

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Das, Madhusmita

    2012-09-15

    Effect of plasma screening on various properties like transition energy, polarizability (dipole and quadrupole), etc. of hydrogen like ions is studied. The bound and free state wave functions and transition matrix elements are obtained by numerically integrating the radial Schrodinger equation for appropriate plasma potential. We have used adaptive step size controlled Runge-Kutta method to perform the numerical integration. Debye-Huckel potential is used to investigate the variation in transition lines and polarizabilities (dipole and quadrupole) with increasing plasma screening. For a strongly coupled plasma, ion sphere potential is used to show the variation in excitation energy with decreasing ion spheremore » radius. It is observed that plasma screening sets in phenomena like continuum lowering and pressure ionization, which are unique to ions in plasma. Of particular interest is the blue (red) shift in transitions conserving (non-conserving) principal quantum number. The plasma environment also affects the dipole and quadrupole polarizability of ions in a significant manner. The bound state contribution to polarizabilities decreases with increase in plasma density whereas the continuum contribution is significantly enhanced. This is a result of variation in the behavior of bound and continuum state wave functions in the presence of plasma. We have compared the results with existing theoretical and experimental data wherever present.« less

  13. Calibration of state and transition models with FVS

    Treesearch

    Melinda Moeur; Don Vandendriesche

    2010-01-01

    The Interagency Mapping and Assessment Project (IMAP), a partnership between federal and state agencies, is developing mid-scale vegetation data and state and transition models (STM) for comparing the likely outcomes of alternative management policies on forested landscapes across the Pacific Northwest Region. In an STM, acres within a forested ecosystem transition...

  14. Quantum phase transition between cluster and antiferromagnetic states

    NASA Astrophysics Data System (ADS)

    Son, W.; Amico, L.; Fazio, R.; Hamma, A.; Pascazio, S.; Vedral, V.

    2011-09-01

    We study a Hamiltonian system describing a three-spin-1/2 cluster-like interaction competing with an Ising-like exchange. We show that the ground state in the cluster phase possesses symmetry protected topological order. A continuous quantum phase transition occurs as result of the competition between the cluster and Ising terms. At the critical point the Hamiltonian is self-dual. The geometric entanglement is also studied and used to investigate the quantum phase transition. Our findings in one dimension corroborate the analysis of the two-dimensional generalization of the system, indicating, at a mean-field level, the presence of a direct transition between an antiferromagnetic and a valence bond solid ground state.

  15. Hyperfine induced transition probabilities from 4{f}^{14}5s5p{}^{3}{{\\rm{P}}}_{0,2}^{o} states in Sm-like ions

    NASA Astrophysics Data System (ADS)

    Zhou, Fuyang; Li, Jiguang; Qu, Yizhi; Wang, Jianguo

    2017-11-01

    The hyperfine induced 4{f}145s5p{}3{{{P}}}0,2o-4{f}145{s}2{}1{{{S}}}0 transition probabilities for highly charged Sm-like ions are calculated within the framework of the multiconfiguration Dirac-Hartree-Fock method. Electron correlation, the Breit interaction and quantum electrodynamical effects are taken into account. For ions ranging from Z = 79 to Z=94,4{f}145s5p{}3{{{P}}}0o is the first excited state, and the hyperfine induced transition (HIT) is a dominant decay channel. For the 4{f}145s5p{}3{{{P}}}2o state, the HIT rates of Sm-like ions with Z=82-94 are reported as well as the magnetic dipole (M1) {}3{{{P}}}2o-{}3{{{P}}}1o, the electric quadrupole (E2) {}3{{{P}}}2o-{}3{{{P}}}0,1o, and the magnetic quadrupole (M2) {}3{{{P}}}2o-{}1{{{S}}}0 transition probabilities. It is found that M1 transition from the 4{f}145s5p{}3{{{P}}}2o state is the most important decay channel in this range on Z≥slant 82.

  16. A molten globule-like intermediate state detected in the thermal transition of cytochrome c under low salt concentration.

    PubMed

    Nakamura, Shigeyoshi; Baba, Takayuki; Kidokoro, Shun-Ichi

    2007-04-01

    To understand the stabilization mechanism of the transient intermediate state in protein folding, it is very important to understand the structure and stability of the molten globule state under a native condition, in which the native state exists stably. The thermal transitions of horse cytochrome c were thermodynamically evaluated by highly precise differential scanning calorimetry (DSC) at pH 3.8-5.0. The heat capacity functions were analyzed using double deconvolution and the nonlinear least-squares method. An intermediate (I) state is clearly confirmed in the thermal native (N)-to-denatured (D) transition of horse cytochrome c. The mole fraction of the intermediate state shows the largest value, 0.4, at nearly 70 degrees C at pH 4.1. This intermediate state was also detected by the circular dichroism (CD) method and was found to have the properties of the molten globule-like structure by three-state analysis of the CD data. The Gibbs free-energy change between N and I, DeltaG(NI), and that between N and D, DeltaG(ND), were evaluated to be 9-22 kJ mol(-1) and 41-45 kJ mol(-1), respectively at 15( ) degrees C and pH 4.1.

  17. Solid-liquid like phase transition in a confined granular suspension

    NASA Astrophysics Data System (ADS)

    Sakai, Nariaki; Lechenault, Frederic; Adda Bedia, Mokhtar

    We present an experimental study of a liquid-solid like phase transition in a two-dimensional granular media. Particles are placed in a vertical Hele-Show cell filled with a denser solution of cesium-chloride. Thus, when the cell is rotated around its axis, hydrostatic pressure exerts a centripetal force on the particles which confines them towards the center. This force is in competition with gravity, thus by modifying the rotation rate, it is possible to transform continuously and reversibly the sample from a disordered loose state to an ordered packed state. The system presents many similarities with thermal systems at equilibrium like density and interface fluctuations, and the transition between the two phases goes through a coexistence state, where there is nucleation and growth of locally ordered domains which are captured by the correlation function of the hexatic order parameter. We discuss the possibility to extend the grand-canonical formalism to out-of equilibrium systems, in order to uncover a state equation between the density and the pressure in the medium.

  18. Energy Landscape and Transition State of Protein-Protein Association

    NASA Astrophysics Data System (ADS)

    Alsallaq, Ramzi; Zhou, Huan-Xiang

    2006-11-01

    Formation of a stereospecific protein complex is favored by specific interactions between two proteins but disfavored by the loss of translational and rotational freedom. Echoing the protein folding process, we have previously proposed a transition state for protein-protein association. Here we clarify the specification of the transition state by working with two toy models for protein association. The models demonstrate that a sharp transition between the bound state with numerous short-range interactions but restricted translation and rotational freedom and the unbound state with at most a small number of interactions but expanded configurational freedom. This transition sets the outer boundary of the bound state as well as the transition state for association. The energy landscape is funnel-like, with the deep well of the bound state surrounded by a broad shallow basin. This formalism of protein-protein association is applied to four protein-protein complexes, and is found to give accurate predictions for the effects of charge mutations and ionic strength on the association rates.

  19. Saddle-like topological surface states on the T T'X family of compounds (T , T' = Transition metal, X =Si , Ge)

    NASA Astrophysics Data System (ADS)

    Singh, Bahadur; Zhou, Xiaoting; Lin, Hsin; Bansil, Arun

    2018-02-01

    Topological nodal-line semimetals are exotic conductors that host symmetry-protected conducting nodal lines in their bulk electronic spectrum and nontrivial drumhead states on the surface. Based on first-principles calculations and an effective model analysis, we identify the presence of topological nodal-line semimetal states in the low crystalline symmetric T T'X family of compounds (T ,T' = transition metal, X = Si or Ge) in the absence of spin-orbit coupling (SOC). Taking ZrPtGe as an exemplar system, we show that owing to small lattice symmetry this material harbors a single nodal line on the ky=0 plane with large energy dispersion and unique drumhead surface state with a saddlelike energy dispersion. When the SOC is included, the nodal line gaps out and the system transitions to a strong topological insulator state with Z2=(1 ;000 ) . The topological surface state evolves from the drumhead surface state via the sharing of its saddlelike energy dispersion within the bulk energy gap. These features differ remarkably from those of the currently known topological surface states in topological insulators such as Bi2Se3 with Dirac-cone-like energy dispersions.

  20. Enhancement of the radiative transitions between the ground and the 3.5-EV isomer states in the hydrogen-like 229TH89+ ion

    NASA Astrophysics Data System (ADS)

    Karpeshin, F. F.; Wycech, S.; Band, I. M.; Trzhaskovskaya, M. B.; Pfützner, M.; Żylicz, J.

    1998-12-01

    Lifetimes for the M1 transitions from the isomeric 3.5 eV 3/2+ state to the ground state are predicted to be enhanced in the hydrogen-like 229Th89+ relative to the bare 229Th nucleus by several orders of magnitude. A possibility of experimental study of this phenomenon is discussed.

  1. Ground-State Hyperfine Structure of Heavy Hydrogen-Like Ions

    NASA Astrophysics Data System (ADS)

    Kühl, T.; Borneis, S.; Dax, A.; Engel, T.; Faber, S.; Gerlach, M.; Holbrow, C.; Huber, G.; Marx, D.; Merz, P.; Quint, W.; Schmitt, F.; Seelig, P.; Tomaselli, M.; Winter, H.; Wuertz, M.; Beckert, K.; Franzke, B.; Nolden, F.; Reich, H.; Steck, M.

    Contributions of quantum electrodynamics (QED) to the combined electric and magnetic interaction between the electron and the nucleus can be studied by optical spectroscopy in high-Z hydrogen-like heavy ions. The transition studied is the ground-state hyperfine structure transition, well known from the 21 cm line in atomic hydrogen. The hyperfine splitting of the is ground state of hydrogen-like systems constitutes the simplest and most basic magnetic interaction in atomic physics. The Z3-increase leads to a transition energy in the UV-region of the optical spectrum for the case of Bi82+. At the same time, the QED correction rises to nearly 1 fraction of higher order contributions. This situation is particularly useful for a comparison with non-perturbative QED calculations. The combination of exceptionally intense electric and magnetic fields electric and magnetic fields is unique. This transition has become accessible to precision laser spectroscopy at the high-energy heavy-ion storage ring at GSI-Darmstadt in the hydrogen-like 209Bi82+ and 207Pb81+. In the meantime, 165Ho66+ and 185,187Re74+ were also studied with reduced resolution by conventional optical spectroscopy at the SuperEBIT ion trap at Lawrence Livermore National Laboratory.

  2. Stabilization of fullerene-like boron cages by transition metal encapsulation

    NASA Astrophysics Data System (ADS)

    Lv, Jian; Wang, Yanchao; Zhang, Lijun; Lin, Haiqing; Zhao, Jijun; Ma, Yanming

    2015-06-01

    The stabilization of fullerene-like boron (B) cages in the free-standing form has been long sought after and a challenging problem. Studies that have been carried out for more than a decade have confirmed that the planar or quasi-planar polymorphs are energetically favored ground states over a wide range of small and medium-sized B clusters. Recently, the breakthroughs represented by Nat. Chem., 2014, 6, 727 established that the transition from planar/quasi-planar to cage-like Bn clusters occurs around n = ~38-40, paving the way for understanding the intriguing chemistry of B-fullerene. We herein demonstrate that the transition demarcation, n, can be significantly reduced with the help of transition metal encapsulation. We explore via extensive first-principles swarm-intelligence based structure searches the free energy landscapes of B24 clusters doped by a series of transition metals and find that the low-lying energy regime is generally dominated by cage-like isomers. This is in sharp contrast to that of bare B24 clusters, where the quasi-planar and rather irregular polyhedrons are prevalent. Most strikingly, a highly symmetric B cage with D3h symmetry is discovered in the case of Mo or W encapsulation. The endohedral D3h cages exhibit robust thermodynamic, dynamic and chemical stabilities, which can be rationalized in terms of their unique electronic structure of an 18-electron closed-shell configuration. Our results indicate that transition metal encapsulation is a feasible route for stabilizing medium-sized B cages, offering a useful roadmap for the discovery of more B fullerene analogues as building blocks of nanomaterials.The stabilization of fullerene-like boron (B) cages in the free-standing form has been long sought after and a challenging problem. Studies that have been carried out for more than a decade have confirmed that the planar or quasi-planar polymorphs are energetically favored ground states over a wide range of small and medium-sized B clusters

  3. Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes.

    PubMed

    Formoso, Elena; Matxain, Jon M; Lopez, Xabier; York, Darrin M

    2010-06-03

    The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally, it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study, we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, to study the conformational dynamics, structural relaxation, and differential solvation that occur at discrete stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogues. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3',5'-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen-bond patterns is presented and compared. The integrity of the overall backbone structure is preserved in the simulations and supports a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen-bond donation to the nonbridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step.

  4. Molecular Dynamics Simulation of Bovine Pancreatic Ribonuclease A - CpA and Transition State-like Complexes

    PubMed Central

    Formoso, Elena; Matxain, Jon M.; Lopez, Xabier; York, Darrin M.

    2010-01-01

    The mechanisms of enzymes are intimately connected with their overall structure and dynamics in solution. Experimentally it is considerably challenging to provide detailed atomic level information about the conformational events that occur at different stages along the chemical reaction path. Here, theoretical tools may offer new potential insights that complement those obtained from experiments that may not yield an unambiguous mechanistic interpretation. In this study we apply molecular dynamics simulations of bovine pancreatic ribonuclease A, an archetype ribonuclease, in order to study the conformational dynamics, structural relaxation, and differential solvation that occurs at discreet stages of the transesterification and cleavage reaction. Simulations were performed with explicit solvation with rigorous electrostatics, and utilize recently developed molecular mechanical force field parameters for transphosphorylation and hydrolysis transition state analogs. Herein, we present results for the enzyme complexed with the dinucleotide substrate cytidilyl-3′,5′-adenosine (CpA) in the reactant, and transphosphorylation and hydrolysis transition states. A detailed analysis of active site structures and hydrogen bond patterns are presented and compared. The integrity of the overall backbone structure is preserved in the simulations, and support a mechanism whereby His12 stabilizes accumulating negative charge at the transition states through hydrogen bond donation to the non-bridge oxygens. Lys41 is shown to be highly versatile along the reaction coordinate, and can aid in the stabilization of the dianionic transition state, while being poised to act as a general acid catalyst in the hydrolysis step. PMID:20455590

  5. Stabilization of fullerene-like boron cages by transition metal encapsulation.

    PubMed

    Lv, Jian; Wang, Yanchao; Zhang, Lijun; Lin, Haiqing; Zhao, Jijun; Ma, Yanming

    2015-06-21

    The stabilization of fullerene-like boron (B) cages in the free-standing form has been long sought after and a challenging problem. Studies that have been carried out for more than a decade have confirmed that the planar or quasi-planar polymorphs are energetically favored ground states over a wide range of small and medium-sized B clusters. Recently, the breakthroughs represented by Nat. Chem., 2014, 6, 727 established that the transition from planar/quasi-planar to cage-like Bn clusters occurs around n = ∼38-40, paving the way for understanding the intriguing chemistry of B-fullerene. We herein demonstrate that the transition demarcation, n, can be significantly reduced with the help of transition metal encapsulation. We explore via extensive first-principles swarm-intelligence based structure searches the free energy landscapes of B24 clusters doped by a series of transition metals and find that the low-lying energy regime is generally dominated by cage-like isomers. This is in sharp contrast to that of bare B24 clusters, where the quasi-planar and rather irregular polyhedrons are prevalent. Most strikingly, a highly symmetric B cage with D3h symmetry is discovered in the case of Mo or W encapsulation. The endohedral D3h cages exhibit robust thermodynamic, dynamic and chemical stabilities, which can be rationalized in terms of their unique electronic structure of an 18-electron closed-shell configuration. Our results indicate that transition metal encapsulation is a feasible route for stabilizing medium-sized B cages, offering a useful roadmap for the discovery of more B fullerene analogues as building blocks of nanomaterials.

  6. Variational Transition State Theory

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Truhlar, Donald G.

    2016-09-29

    This is the final report on a project involving the development and applications of variational transition state theory. This project involved the development of variational transition state theory for gas-phase reactions, including optimized multidimensional tunneling contributions and the application of this theory to gas-phase reactions with a special emphasis on developing reaction rate theory in directions that are important for applications to combustion. The development of variational transition state theory with optimized multidimensional tunneling as a useful computational tool for combustion kinetics involved eight objectives.

  7. Energy, fine structure, hyperfine structure, and radiative transition rates of the high-lying multi-excited states for B-like neon

    NASA Astrophysics Data System (ADS)

    Zhang, Chun Mei; Chen, Chao; Sun, Yan; Gou, Bing Cong; Shao, Bin

    2015-04-01

    The Rayleigh-Ritz variational method with multiconfiguration interaction wave functions is used to obtain the energies of high-lying multi-excited quartet states 1 s 22 s2 pnl and 1 s 22 p 2 nl 4Pe,o ( n ≥ 2) in B-like neon, including the mass polarization and relativistic corrections. The fine structure and hyperfine structure of the excited quartet states for this system are investigated. Configuration structures of the high-lying multi-excited series are further identified by relativistic corrections and fine structure splittings. The transition rates and wavelengths are also calculated. Calculated wavelengths include the quantum electrodynamic effects. The results are compared with other theoretical and experimental data in the literature.

  8. Conformational transition in signal transduction: metastable states and transition pathways in the activation of a signaling protein.

    PubMed

    Banerjee, Rahul; Yan, Honggao; Cukier, Robert I

    2015-06-04

    Signal transduction is of vital importance to the growth and adaptation of living organisms. The key to understand mechanisms of biological signal transduction is elucidation of the conformational dynamics of its signaling proteins, as the activation of a signaling protein is fundamentally a process of conformational transition from an inactive to an active state. A predominant form of signal transduction for bacterial sensing of environmental changes in the wild or inside their hosts is a variety of two-component systems, in which the conformational transition of a response regulator (RR) from an inactive to an active state initiates responses to the environmental changes. Here, RR activation has been investigated using RR468 as a model system by extensive unbiased all-atom molecular dynamics (MD) simulations in explicit solvent, starting from snapshots along a targeted MD trajectory that covers the conformational transition. Markov state modeling, transition path theory, and geometric analyses of the wealth of the MD data have provided a comprehensive description of the RR activation. It involves a network of metastable states, with one metastable state essentially the same as the inactive state and another very similar to the active state that are connected via a small set of intermediates. Five major pathways account for >75% of the fluxes of the conformational transition from the inactive to the active-like state. The thermodynamic stability of the states and the activation barriers between states are found, to identify rate-limiting steps. The conformal transition is initiated predominantly by movements of the β3α3 loop, followed by movements of the β4α4-loop and neighboring α4 helix region, and capped by additional movements of the β3α3 loop. A number of transient hydrophobic and hydrogen bond interactions are revealed, and they may be important for the conformational transition.

  9. X-ray transitions studied for decelerated bare and H-like uranium ions at the ESR electron cooler

    NASA Astrophysics Data System (ADS)

    Gumberidze, A.; Stöhlker, Th.; Bednarz, G.; Beyer, H. F.; Bosch, F.; Cai, X.; Hagmann, S.; Klepper, O.; Kozhuharov, C.; Liesen, D.; Ma, X.; Mokler, P. H.; Sierpowski, D.; Stachura, Z.; Steck, M.; Toleikis, S.; Warczak, A.; Zou, Y.

    2003-05-01

    Here we report on X-ray spectra induced by spontaneous capture of free electrons into decelerated bare- and hydrogen-like uranium ions which we measured recently at the cooler section of the ESR storage ring. The most intense lines observed in spectra can be attributed to direct transition of electrons into the K shell of the projectile ions and to characteristic L → K (Lyα) transitions. Radiative recombination lines into the K shell of bare and H-like uranium can be exploited for measuring the two-electron contribution to the ground state binding energy in helium-like uranium. The goal is to probe for high-Z ions bound-state QED corrections which are of the order of α2. Besides the dominant characteristic L → K transitions, the strongly reduced Bremsstrahlung (due to the low cooler voltage applied to the decelerated ions) allowed us to observe for the very first time RR transitions into the L shell as well as the balmer radiation located at the low-energy part of the spectra.

  10. Steps for Implementing a State-Level Professional Development Plan for Secondary Transition

    ERIC Educational Resources Information Center

    Mazzotti, Valerie L.; Rowe, Dawn A.; Simonsen, Monica; Boaz, Bonnie; VanAvery, Cynthia

    2018-01-01

    To scale up and sustain the use of evidence-based practices, it is imperative that state education agencies systematically implement professional development that represents best practice. By delivering quality professional development to local districts, it is more likely that transition personnel will implement transition programs and practices…

  11. Cross-National Differences in Disability Among Elders: Transitions in Disability in Mexico and the United States

    PubMed Central

    Wong, Rebeca; Michaels-Obregon, Alejandra; Palloni, Alberto

    2015-01-01

    Objectives. Little is known about how exposure to a combination of infectious and chronic conditions throughout the lifecourse could impact disability in old age. This paper compares 2 cohorts of adults who have aged under very different country contexts by contrasting disability transitions among elders in Mexico with elders in the United States. Methods. Data comes from the Mexican Health and Aging Study (MHAS) and the U.S. Health and Retirement Study (HRS). Estimated probabilities of 2-year transitions among disability states and mortality are presented for adults aged 50 and older. Results. The levels of disability prevalence and 2 year transitions are consistent with a higher rate of disability for the United States compared to Mexico. In 2-year transitions, the U.S. sample was more likely to transition to a disabled state or increase the number of disabilities than the Mexican counterparts, while Mexicans are more likely to move out of disability or reduce the number of disabilities reported. Discussion. The findings suggest that the current rate of disability in old age is lower for a less developed country compared with a developed society. We discuss implications, possible explanations, and likely future scenarios. PMID:25633135

  12. Transition probabilities of health states for workers in Malaysia using a Markov chain model

    NASA Astrophysics Data System (ADS)

    Samsuddin, Shamshimah; Ismail, Noriszura

    2017-04-01

    The aim of our study is to estimate the transition probabilities of health states for workers in Malaysia who contribute to the Employment Injury Scheme under the Social Security Organization Malaysia using the Markov chain model. Our study uses four states of health (active, temporary disability, permanent disability and death) based on the data collected from the longitudinal studies of workers in Malaysia for 5 years. The transition probabilities vary by health state, age and gender. The results show that men employees are more likely to have higher transition probabilities to any health state compared to women employees. The transition probabilities can be used to predict the future health of workers in terms of a function of current age, gender and health state.

  13. Epigenetic modulation of the miR-200 family is associated with transition to a breast cancer stem-cell-like state.

    PubMed

    Lim, Yat-Yuen; Wright, Josephine A; Attema, Joanne L; Gregory, Philip A; Bert, Andrew G; Smith, Eric; Thomas, Daniel; Lopez, Angel F; Drew, Paul A; Khew-Goodall, Yeesim; Goodall, Gregory J

    2013-05-15

    The miR-200 family is a key regulator of the epithelial-mesenchymal transition, however, its role in controlling the transition between cancer stem-cell-like and non-stem-cell-like phenotypes is not well understood. We utilized immortalized human mammary epithelial (HMLE) cells to investigate the regulation of the miR-200 family during their conversion to a stem-like phenotype. HMLE cells were found to be capable of spontaneous conversion from a non-stem to a stem-like phenotype and this conversion was accompanied by the loss of miR-200 expression. Stem-like cell fractions isolated from metastatic breast cancers also displayed loss of miR-200 indicating similar molecular changes may occur during breast cancer progression. The phenotypic change observed in HMLE cells was directly controlled by miR-200 because restoration of its expression decreased stem-like properties while promoting a transition to an epithelial phenotype. Investigation of the mechanisms controlling miR-200 expression revealed both DNA methylation and histone modifications were significantly altered in the stem-like and non-stem phenotypes. In particular, in the stem-like phenotype, the miR-200b-200a-429 cluster was silenced primarily through polycomb group-mediated histone modifications whereas the miR-200c-141 cluster was repressed by DNA methylation. These results indicate that the miR-200 family plays a crucial role in the transition between stem-like and non-stem phenotypes and that distinct epigenetic-based mechanisms regulate each miR-200 gene in this process. Therapy targeted against miR-200 family members and epigenetic modifications might therefore be applicable to breast cancer.

  14. Walking associated with public transit: moving toward increased physical activity in the United States.

    PubMed

    Freeland, Amy L; Banerjee, Shailendra N; Dannenberg, Andrew L; Wendel, Arthur M

    2013-03-01

    We assessed changes in transit-associated walking in the United States from 2001 to 2009 and documented their importance to public health. We examined transit walk times using the National Household Travel Survey, a telephone survey administered by the US Department of Transportation to examine travel behavior in the United States. People are more likely to transit walk if they are from lower income households, are non-White, and live in large urban areas with access to rail systems. Transit walkers in large urban areas with a rail system were 72% more likely to transit walk 30 minutes or more per day than were those without a rail system. From 2001 to 2009, the estimated number of transit walkers rose from 7.5 million to 9.6 million (a 28% increase); those whose transit-associated walking time was 30 minutes or more increased from approximately 2.6 million to 3.4 million (a 31% increase). Transit walking contributes to meeting physical activity recommendations. Study results may contribute to transportation-related health impact assessment studies evaluating the impact of proposed transit systems on physical activity, potentially influencing transportation planning decisions.

  15. Dynamic Functional Connectivity States Reflecting Psychotic-like Experiences.

    PubMed

    Barber, Anita D; Lindquist, Martin A; DeRosse, Pamela; Karlsgodt, Katherine H

    2018-05-01

    Psychotic-like experiences (PLEs) are associated with lower social and occupational functioning, and lower executive function. Emerging evidence also suggests that PLEs reflect neural dysfunction resembling that of psychotic disorders. The present study examined dynamic connectivity related to a measure of PLEs derived from the Achenbach Adult Self-Report, in an otherwise-healthy sample of adults from the Human Connectome Project. A total of 76 PLE-endorsing and 153 control participants were included in the final sample. To characterize network dysfunction, dynamic connectivity states were examined across large-scale resting-state networks using dynamic conditional correlation and k-means clustering. Three dynamic states were identified. The PLE-endorsing group spent more time than the control group in state 1, a state reflecting hyperconnectivity within visual regions and hypoconnectivity within the default mode network, and less time in state 2, a state characterized by robust within-network connectivity for all networks and strong default mode network anticorrelations. Within the PLE-endorsing group, worse executive function was associated with more time spent in and more transitions into state 1 and less time spent in and fewer transitions into state 3. PLEs are associated with altered large-scale brain dynamics, which tip the system away from spending more time in states reflecting more "typical" connectivity patterns toward more time in states reflecting visual hyperconnectivity and default mode hypoconnectivity. Copyright © 2017 Society of Biological Psychiatry. Published by Elsevier Inc. All rights reserved.

  16. Employment outcomes of transition-aged adults with autism spectrum disorders: a state of the States report.

    PubMed

    Burgess, Sloane; Cimera, Robert E

    2014-01-01

    The primary purpose of this study was to evaluate the employment outcomes of transition-aged adults with autism spectrum disorders (ASD) served by vocational rehabilitation services (VR) over the last 10 years by state. A secondary purpose was to compare employment outcomes of individuals with ASD to those of the overall transition-aged population served by VR for the same time period. Although there was variability both within and among states, the results of this study indicate that, over time, the number of young adults with ASD seeking VR services has increased; however, employment outcomes including the percent of adults with ASD achieving employment, the number of hours worked, and wages earned have not improved for this group. The cost to provide VR services to transition-aged adults with ASD was relatively stable over time. Transition-aged adults with ASD were more likely to become successfully employed as a result of receiving VR services than the overall population of transition-aged adults served by VR. However, the employed transition-aged adults consistently worked fewer hours and earned lower wages than those in the overall population. Factors that may influence variability within and among states, and between groups, and implications for research and practice are discussed.

  17. Three key residues form a critical contact network in a protein folding transition state

    NASA Astrophysics Data System (ADS)

    Vendruscolo, Michele; Paci, Emanuele; Dobson, Christopher M.; Karplus, Martin

    2001-02-01

    Determining how a protein folds is a central problem in structural biology. The rate of folding of many proteins is determined by the transition state, so that a knowledge of its structure is essential for understanding the protein folding reaction. Here we use mutation measurements-which determine the role of individual residues in stabilizing the transition state-as restraints in a Monte Carlo sampling procedure to determine the ensemble of structures that make up the transition state. We apply this approach to the experimental data for the 98-residue protein acylphosphatase, and obtain a transition-state ensemble with the native-state topology and an average root-mean-square deviation of 6Å from the native structure. Although about 20 residues with small positional fluctuations form the structural core of this transition state, the native-like contact network of only three of these residues is sufficient to determine the overall fold of the protein. This result reveals how a nucleation mechanism involving a small number of key residues can lead to folding of a polypeptide chain to its unique native-state structure.

  18. Simulation Studies of LCST-like Phase Transitions in Elastin-like Polypeptides (ELPs) and Conjugates of ELP with Rigid Macromolecules

    NASA Astrophysics Data System (ADS)

    Condon, Joshua; Martin, Tyler; Jayaraman, Arthi

    We use atomistic (AA) and coarse-grained (CG) molecular dynamics simulations to elucidate the thermodynamic driving forces governing lower critical solution temperature (LCST)-like phase transition exhibited by elastin-like peptides (ELPs) and conjugates of ELP with other macromolecules. In the AA simulations, we study ELP oligomers in explicit water, and mark the transition as the temperature at which they undergo a change in ``hydration'' state. While AA simulations are restricted to small systems of short ELPs and do not capture the chain aggregation observed in experiments of ELPs, they guide the phenomenological CG model development by highlighting the solvent induced polymer-polymer effective interactions with changing temperature. In the CG simulations, we capture the LCST polymer aggregation by increasing polymer-polymer effective attractive interactions in an implicit solvent. We examine the impact of conjugating a block of LCST polymer to another rigid unresponsive macromolecular block on the LCST-like transition. We find that when multiple LCST polymers are conjugated to a rigid polymer block, increased crowding of the LCST polymers shifts the onset of chain aggregation to smaller effective polymer-polymer attraction compared to the free LCST polymers. These simulation results provide guidance on the design of conjugated bio-mimetic thermoresponsive materials, and shape the fundamental understanding of the impact of polymer crowding on phase behavior in thermoresponsive LCST polymer systems.

  19. Wetting transition on patterned surfaces: transition states and energy barriers.

    PubMed

    Ren, Weiqing

    2014-03-18

    We study the wetting transition on microstructured hydrophobic surfaces. We use the string method [J. Chem. Phys. 2007, 126, 164103; J. Chem. Phys. 2013, 138, 134105] to accurately compute the transition states, the energy barriers, and the minimum energy paths for the wetting transition from the Cassie-Baxter state to the Wenzel state. Numerical results are obtained for the wetting of a hydrophobic surface textured with a square lattice of pillars. It is found that the wetting of the solid substrate occurs via infiltration of the liquid in a single groove, followed by lateral propagation of the liquid front. The propagation of the liquid front proceeds in a stepwise manner, and a zipping mechanism is observed during the infiltration of each layer. The minimum energy path for the wetting transition goes through a sequence of intermediate metastable states, whose wetted areas reflect the microstructure of the patterned surface. We also study the dependence of the energy barrier on the drop size and the gap between the pillars.

  20. The Effects of Hydrogen-Like Impurity and Temperature on State Energies and Transition Frequency of Strong-Coupling Bound Polaron in an Asymmetric Gaussian Potential Quantum Well

    NASA Astrophysics Data System (ADS)

    Xiao, Jing-lin

    2018-02-01

    In the present work, we study the ground state energy, the first excited state energy and the transition frequency (TF) between the two states of the strong-coupling impurity bound polaron in an asymmetric Gaussian potential quantum well (AGPQW) by using the variational method of the Pekar type. By employing quantum statistics theory, the temperature effect on the state energies (SEs) and the TF are also calculated with a hydrogen-like impurity at the coordinate origin of the AGPQW. According to the obtained results, we found that the SEs and the TF are increasing functions of the temperature, whereas they are decreasing ones of the Coulombic impurity potential.

  1. Quantum phase transitions between a class of symmetry protected topological states

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tsui, Lokman; Jiang, Hong-Chen; Lu, Yuan-Ming

    2015-07-01

    The subject of this paper is the phase transition between symmetry protected topological states (SPTs). We consider spatial dimension d and symmetry group G so that the cohomology group, Hd+1(G,U(1)), contains at least one Z2n or Z factor. We show that the phase transition between the trivial SPT and the root states that generate the Z2n or Z groups can be induced on the boundary of a (d+1)-dimensional View the MathML source-symmetric SPT by a View the MathML source symmetry breaking field. Moreover we show these boundary phase transitions can be “transplanted” to d dimensions and realized in lattice modelsmore » as a function of a tuning parameter. The price one pays is for the critical value of the tuning parameter there is an extra non-local (duality-like) symmetry. In the case where the phase transition is continuous, our theory predicts the presence of unusual (sometimes fractionalized) excitations corresponding to delocalized boundary excitations of the non-trivial SPT on one side of the transition. This theory also predicts other phase transition scenarios including first order transition and transition via an intermediate symmetry breaking phase.« less

  2. Quantum phase transitions between a class of symmetry protected topological states

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tsui, Lokman; Jiang, Hong -Chen; Lu, Yuan -Ming

    2015-04-30

    The subject of this paper is the phase transition between symmetry protected topological states (SPTs). We consider spatial dimension d and symmetry group G so that the cohomology group, H d+1(G,U(1)), contains at least one Z 2n or Z factor. We show that the phase transition between the trivial SPT and the root states that generate the Z 2n or Z groups can be induced on the boundary of a (d+1)-dimensional G x Z T 2-symmetric SPT by a Z T 2 symmetry breaking field. Moreover we show these boundary phase transitions can be “transplanted” to d dimensions and realizedmore » in lattice models as a function of a tuning parameter. The price one pays is for the critical value of the tuning parameter there is an extra non-local (duality-like) symmetry. In the case where the phase transition is continuous, our theory predicts the presence of unusual (sometimes fractionalized) excitations corresponding to delocalized boundary excitations of the non-trivial SPT on one side of the transition. This theory also predicts other phase transition scenarios including first order transition and transition via an intermediate symmetry breaking phase.« less

  3. Pediatricians Transitioning Practices, Youth With Special Health Care Needs in New York State.

    PubMed

    Davidson, Lynn F; Chhabra, Rosy; Cohen, Hillel W; Lechuga, Claudia; Diaz, Patricia; Racine, Andrew

    2015-10-01

    To assess current practices of New York State pediatricians as they transition youth with special health care needs to adult-oriented medical care. A survey of New York State pediatricians included 6 critical steps from 2002 consensus statement, 11 essential steps adapted from recent literature, and questions targeting age of starting transition and availability of transition policy. Of 181 respondents, only 11% have a transition policy. Most assist patients in transition process; identify an adult provider (92%); and create portable medical summary (57%). Only 3% start planning process at recommended age. No respondents are compliant with all 6 critical steps; subspecialists were more likely to report compliance to more than 4 steps. Participating pediatricians are making gains, yet effort is needed, to incorporate the essential steps into practice for transitioning youth with special health care needs. Recognition of barriers, use of electronic tools, and clarifying subspecialist's approach, may improve compliance with transition recommendations. © The Author(s) 2015.

  4. Optimal trajectories of brain state transitions

    PubMed Central

    Gu, Shi; Betzel, Richard F.; Mattar, Marcelo G.; Cieslak, Matthew; Delio, Philip R.; Grafton, Scott T.; Pasqualetti, Fabio; Bassett, Danielle S.

    2017-01-01

    The complexity of neural dynamics stems in part from the complexity of the underlying anatomy. Yet how white matter structure constrains how the brain transitions from one cognitive state to another remains unknown. Here we address this question by drawing on recent advances in network control theory to model the underlying mechanisms of brain state transitions as elicited by the collective control of region sets. We find that previously identified attention and executive control systems are poised to affect a broad array of state transitions that cannot easily be classified by traditional engineering-based notions of control. This theoretical versatility comes with a vulnerability to injury. In patients with mild traumatic brain injury, we observe a loss of specificity in putative control processes, suggesting greater susceptibility to neurophysiological noise. These results offer fundamental insights into the mechanisms driving brain state transitions in healthy cognition and their alteration following injury. PMID:28088484

  5. Characterizing Transitions Between Decadal States of the Tropical Pacific using State Space Reconstruction

    NASA Astrophysics Data System (ADS)

    Ramesh, N.; Cane, M. A.

    2017-12-01

    The complex coupled ocean-atmosphere system of the Tropical Pacific generates variability on timescales from intraseasonal to multidecadal. Pacific Decadal Variability (PDV) is among the key drivers of global climate, with effects on hydroclimate on several continents, marine ecosystems, and the rate of global mean surface temperature rise under anthropogenic greenhouse gas forcing. Predicting phase shifts in the PDV would therefore be highly useful. However, the small number of PDV phase shifts that have occurred in the observational record pose a substantial challenge to developing an understanding of the mechanisms that underlie decadal variability. In this study, we use a 100,000-year unforced simulation from an intermediate-complexity model of the Tropical Pacific region that has been shown to produce PDV comparable to that in the real world. We apply the Simplex Projection method to the NINO3 index from this model to reconstruct a shadow manifold that preserves the topology of the true attractor of this system. We find that the high- and low-variance phases of PDV emerge as a pair of regimes in a 3-dimensional state space, and that the transitions between decadal states lie in a highly predictable region of the attractor. We then use a random forest algorithm to develop a physical interpretation of the processes associated with these highly-predictable transitions. We find that transitions to low-variance states are most likely to occur approximately 2.5 years after an El Nino event, and that ocean-atmosphere variables in the southeastern Tropical Pacific play a crucial role in driving these transitions.

  6. Relativistic many-body calculations of excitation energies, oscillator strengths, transition rates, and lifetimes in samarium like ions

    NASA Astrophysics Data System (ADS)

    Safronova, Ulyana; Safronova, Alla; Beiersdorfer, Peter

    2013-05-01

    Excitation energies, oscillator strengths, transition probabilities, and lifetimes are calculated for (5s2 + 5p2 + 5d2 + 5 s 5 d + 5 s 5 g + 5 p 5 f) - (5 s 5 p + 5 s 5 f + 5 p 5 d + 5 p 5 g) electric dipole transitions in Sm-like ions with nuclear charge Z ranging from 74 to 100. Relativistic many-body perturbation theory (RMBPT), including the Breit interaction, is used to evaluate retarded E1 matrix elements in length and velocity forms. The calculations start from a 1s2 2s2 2p6 3s2 3p6 3d10 4s2 4p6 4d10 4f14 Dirac-Fock potential. First-order perturbation theory is used to obtain intermediate coupling coefficients, and the second-order RMBPT is used to determine the matrix elements. The contributions from negative-energy states are included in the second-order E1 matrix elements to achieve agreement between length-form and velocity-form amplitudes. The resulting transition energies and transition probabilities, and lifetimes for Sm-like W12+ are compared with results obtained by the relativistic Hartree-Fock approximation (COWAN code) to estimate contribution of the 4 f -core-excited states. Trends of excitation energies and oscillator strengths as function of nuclear charge Z are shown graphically for selected states and transitions. This work provides a number of yet unmeasured properti. This research was sponsored by the grant DE-FG02-08ER54951.

  7. An inhibitory gate for state transition in cortex

    PubMed Central

    Zucca, Stefano; D’Urso, Giulia; Pasquale, Valentina; Vecchia, Dania; Pica, Giuseppe; Bovetti, Serena; Moretti, Claudio; Varani, Stefano; Molano-Mazón, Manuel; Chiappalone, Michela; Panzeri, Stefano; Fellin, Tommaso

    2017-01-01

    Large scale transitions between active (up) and silent (down) states during quiet wakefulness or NREM sleep regulate fundamental cortical functions and are known to involve both excitatory and inhibitory cells. However, if and how inhibition regulates these activity transitions is unclear. Using fluorescence-targeted electrophysiological recording and cell-specific optogenetic manipulation in both anesthetized and non-anesthetized mice, we found that two major classes of interneurons, the parvalbumin and the somatostatin positive cells, tightly control both up-to-down and down-to-up state transitions. Inhibitory regulation of state transition was observed under both natural and optogenetically-evoked conditions. Moreover, perturbative optogenetic experiments revealed that the inhibitory control of state transition was interneuron-type specific. Finally, local manipulation of small ensembles of interneurons affected cortical populations millimetres away from the modulated region. Together, these results demonstrate that inhibition potently gates transitions between cortical activity states, and reveal the cellular mechanisms by which local inhibitory microcircuits regulate state transitions at the mesoscale. DOI: http://dx.doi.org/10.7554/eLife.26177.001 PMID:28509666

  8. Reliable Transition State Searches Integrated with the Growing String Method.

    PubMed

    Zimmerman, Paul

    2013-07-09

    The growing string method (GSM) is highly useful for locating reaction paths connecting two molecular intermediates. GSM has often been used in a two-step procedure to locate exact transition states (TS), where GSM creates a quality initial structure for a local TS search. This procedure and others like it, however, do not always converge to the desired transition state because the local search is sensitive to the quality of the initial guess. This article describes an integrated technique for simultaneous reaction path and exact transition state search. This is achieved by implementing an eigenvector following optimization algorithm in internal coordinates with Hessian update techniques. After partial convergence of the string, an exact saddle point search begins under the constraint that the maximized eigenmode of the TS node Hessian has significant overlap with the string tangent near the TS. Subsequent optimization maintains connectivity of the string to the TS as well as locks in the TS direction, all but eliminating the possibility that the local search leads to the wrong TS. To verify the robustness of this approach, reaction paths and TSs are found for a benchmark set of more than 100 elementary reactions.

  9. Improving Upon String Methods for Transition State Discovery.

    PubMed

    Chaffey-Millar, Hugh; Nikodem, Astrid; Matveev, Alexei V; Krüger, Sven; Rösch, Notker

    2012-02-14

    Transition state discovery via application of string methods has been researched on two fronts. The first front involves development of a new string method, named the Searching String method, while the second one aims at estimating transition states from a discretized reaction path. The Searching String method has been benchmarked against a number of previously existing string methods and the Nudged Elastic Band method. The developed methods have led to a reduction in the number of gradient calls required to optimize a transition state, as compared to existing methods. The Searching String method reported here places new beads on a reaction pathway at the midpoint between existing beads, such that the resolution of the path discretization in the region containing the transition state grows exponentially with the number of beads. This approach leads to favorable convergence behavior and generates more accurate estimates of transition states from which convergence to the final transition states occurs more readily. Several techniques for generating improved estimates of transition states from a converged string or nudged elastic band have been developed and benchmarked on 13 chemical test cases. Optimization approaches for string methods, and pitfalls therein, are discussed.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kharchenko, V.F., E-mail: vkharchenko@bitp.kiev.ua

    2015-04-15

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

  11. Disorder-Induced Topological State Transition in Photonic Metamaterials

    NASA Astrophysics Data System (ADS)

    Liu, Changxu; Gao, Wenlong; Yang, Biao; Zhang, Shuang

    2017-11-01

    The topological state transition has been widely studied based on the quantized topological band invariant such as the Chern number for the system without intense randomness that may break the band structures. We numerically demonstrate the disorder-induced state transition in the photonic topological systems for the first time. Instead of applying the ill-defined topological band invariant in a disordered system, we utilize an empirical parameter to unambiguously illustrate the state transition of the topological metamaterials. Before the state transition, we observe a robust surface state with well-confined electromagnetic waves propagating unidirectionally, immune to the disorder from permittivity fluctuation up to 60% of the original value. During the transition, a hybrid state composed of a quasiunidirectional surface mode and intensively localized hot spots is established, a result of the competition between the topological protection and Anderson localization.

  12. Intrinsic exciton-state mixing and nonlinear optical properties in transition metal dichalcogenide monolayers

    NASA Astrophysics Data System (ADS)

    Glazov, M. M.; Golub, L. E.; Wang, G.; Marie, X.; Amand, T.; Urbaszek, B.

    2017-01-01

    Optical properties of transition metal dichalcogenides monolayers are controlled by Wannier-Mott excitons forming a series of 1 s ,2 s ,2 p ,... hydrogen-like states. We develop the theory of the excited excitonic states energy spectrum fine structure. We predict that p - and s -shell excitons are mixed due to the specific D3 h point symmetry of the transition metal dichalcogenide monolayers. Hence, both s - and p -shell excitons are active in both single- and two-photon processes, providing an efficient mechanism of second harmonic generation. The corresponding contribution to the nonlinear susceptibility is calculated.

  13. Transition state analysis of Trypanosoma cruzi uridine phosphorylase-catalyzed arsenolysis of uridine

    PubMed Central

    Silva, Rafael G.; Vetticatt, Mathew J.; Merino, Emilio F.; Cassera, Maria B.; Schramm, Vern L.

    2011-01-01

    Uridine phosphorylase catalyzes the reversible phosphorolysis of uridine and 2′-deoxyuridine to generate uracil and (2-deoxy)ribose 1-phosphate, an important step in the pyrimidine salvage pathway. The coding sequence annotated as a putative nucleoside phosphorylase in the Trypanosoma cruzi genome was overexpressed in Escherichia coli, purified to homogeneity, and shown to be a homodimeric uridine phosphorylase, with similar specificity for uridine and 2′-deoxyuridine, and undetectable activity towards thymidine and purine nucleosides. Competitive kinetic isotope effects (KIEs) were measured and corrected for a forward commitment factor using arsenate as the nucleophile. The intrinsic KIEs are: 1′-14C = 1.103, 1,3-15N2 = 1.034, 3-15N = 1.004, 1-15N = 1.030, 1′-3H = 1.132, 2′-2H = 1.086 and 5′-3H2 = 1.041 for this reaction. Density functional theory was employed to quantitatively interpret the KIEs in terms of transition state structure and geometry. Matching of experimental KIEs to proposed transition state structures suggests an almost synchronous, SN2-like transition state model, in which the ribosyl moiety possesses significant bond order to both nucleophile and leaving group. Natural bond orbital analysis allowed a comparison of the charge distribution pattern between the ground state and the transition state model. PMID:21599004

  14. Estimation of State Transition Probabilities: A Neural Network Model

    NASA Astrophysics Data System (ADS)

    Saito, Hiroshi; Takiyama, Ken; Okada, Masato

    2015-12-01

    Humans and animals can predict future states on the basis of acquired knowledge. This prediction of the state transition is important for choosing the best action, and the prediction is only possible if the state transition probability has already been learned. However, how our brains learn the state transition probability is unknown. Here, we propose a simple algorithm for estimating the state transition probability by utilizing the state prediction error. We analytically and numerically confirmed that our algorithm is able to learn the probability completely with an appropriate learning rate. Furthermore, our learning rule reproduced experimentally reported psychometric functions and neural activities in the lateral intraparietal area in a decision-making task. Thus, our algorithm might describe the manner in which our brains learn state transition probabilities and predict future states.

  15. Resonant coherent excitation of hydrogen-like ions planar channeled in a crystal; Transition into the first excited state

    NASA Astrophysics Data System (ADS)

    Babaev, A.; Pivovarov, Yu. L.

    2012-03-01

    The presented program is designed to simulate the characteristics of resonant coherent excitation of hydrogen-like ions planar-channeled in a crystal. The program realizes the numerical algorithm to solve the Schrödinger equation for the ion-bound electron at a special resonance excitation condition. The calculated wave function of the bound electron defines probabilities for the ion to be in the either ground or first excited state, or to be ionized. Finally, in the outgoing beam the fractions of ions in the ground state, in the first excited state, and ionized by collisions with target electrons, are defined. The program code is written on C++ and is designed for multiprocessing systems (clusters). The output data are presented in the table. Program summaryProgram title: RCE_H-like_1 Catalogue identifier: AEKX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 2813 No. of bytes in distributed program, including test data, etc.: 34 667 Distribution format: tar.gz Programming language: C++ (g++, icc compilers) Computer: Multiprocessor systems (clusters) Operating system: Any OS based on LINUX; program was tested under Novell SLES 10 Has the code been vectorized or parallelized?: Yes. Contains MPI directives RAM: <1 MB per processor Classification: 2.1, 2.6, 7.10 External routines: MPI library for GNU C++, Intel C++ compilers Nature of problem: When relativistic hydrogen-like ion moves in the crystal in the planar channeling regime, in the ion rest frame the time-periodic electric field acts on the bound electron. If the frequency of this field matches the transition frequency between electronic energy levels, the resonant coherent excitation can take place. Therefore, ions in the different states may be

  16. Origin of Transitions between Metallic and Insulating States in Simple Metals

    DOE PAGES

    Naumov, Ivan I.; Hemley, Russell J.

    2015-04-17

    Unifying principles that underlie recently discovered transitions between metallic and insulating states in elemental solids under pressure are developed. Using group theory arguments and first principles calculations, we show that the electronic properties of the phases involved in these transitions are controlled by symmetry principles not previously recognized. The valence bands in these systems are described by simple and composite band representations constructed from localized Wannier functions centered on points unoccupied by atoms, and which are not necessarily all symmetrical. The character of the Wannier functions is closely related to the degree of s-p(-d) hybridization and reflects multi-center chemical bondingmore » in these insulating states. The conditions under which an insulating state is allowed for structures having an integer number of atoms per primitive unit cell as well as re-entrant (i.e., metal-insulator-metal) transition sequences are detailed, resulting in predictions of novel behavior such as phases having three-dimensional Dirac-like points. The general principles developed are tested and applied to the alkali and alkaline earth metals, including elements where high-pressure insulating phases have been identified or reported (e.g., Li, Na, and Ca).« less

  17. A hierarchical transition state search algorithm

    NASA Astrophysics Data System (ADS)

    del Campo, Jorge M.; Köster, Andreas M.

    2008-07-01

    A hierarchical transition state search algorithm is developed and its implementation in the density functional theory program deMon2k is described. This search algorithm combines the double ended saddle interpolation method with local uphill trust region optimization. A new formalism for the incorporation of the distance constrain in the saddle interpolation method is derived. The similarities between the constrained optimizations in the local trust region method and the saddle interpolation are highlighted. The saddle interpolation and local uphill trust region optimizations are validated on a test set of 28 representative reactions. The hierarchical transition state search algorithm is applied to an intramolecular Diels-Alder reaction with several internal rotors, which makes automatic transition state search rather challenging. The obtained reaction mechanism is discussed in the context of the experimentally observed product distribution.

  18. State-transition diagrams for biologists.

    PubMed

    Bersini, Hugues; Klatzmann, David; Six, Adrien; Thomas-Vaslin, Véronique

    2012-01-01

    It is clearly in the tradition of biologists to conceptualize the dynamical evolution of biological systems in terms of state-transitions of biological objects. This paper is mainly concerned with (but obviously not limited too) the immunological branch of biology and shows how the adoption of UML (Unified Modeling Language) state-transition diagrams can ease the modeling, the understanding, the coding, the manipulation or the documentation of population-based immune software model generally defined as a set of ordinary differential equations (ODE), describing the evolution in time of populations of various biological objects. Moreover, that same UML adoption naturally entails a far from negligible representational economy since one graphical item of the diagram might have to be repeated in various places of the mathematical model. First, the main graphical elements of the UML state-transition diagram and how they can be mapped onto a corresponding ODE mathematical model are presented. Then, two already published immune models of thymocyte behavior and time evolution in the thymus, the first one originally conceived as an ODE population-based model whereas the second one as an agent-based one, are refactored and expressed in a state-transition form so as to make them much easier to understand and their respective code easier to access, to modify and run. As an illustrative proof, for any immunologist, it should be possible to understand faithfully enough what the two software models are supposed to reproduce and how they execute with no need to plunge into the Java or Fortran lines.

  19. State-Transition Diagrams for Biologists

    PubMed Central

    Bersini, Hugues; Klatzmann, David; Six, Adrien; Thomas-Vaslin, Véronique

    2012-01-01

    It is clearly in the tradition of biologists to conceptualize the dynamical evolution of biological systems in terms of state-transitions of biological objects. This paper is mainly concerned with (but obviously not limited too) the immunological branch of biology and shows how the adoption of UML (Unified Modeling Language) state-transition diagrams can ease the modeling, the understanding, the coding, the manipulation or the documentation of population-based immune software model generally defined as a set of ordinary differential equations (ODE), describing the evolution in time of populations of various biological objects. Moreover, that same UML adoption naturally entails a far from negligible representational economy since one graphical item of the diagram might have to be repeated in various places of the mathematical model. First, the main graphical elements of the UML state-transition diagram and how they can be mapped onto a corresponding ODE mathematical model are presented. Then, two already published immune models of thymocyte behavior and time evolution in the thymus, the first one originally conceived as an ODE population-based model whereas the second one as an agent-based one, are refactored and expressed in a state-transition form so as to make them much easier to understand and their respective code easier to access, to modify and run. As an illustrative proof, for any immunologist, it should be possible to understand faithfully enough what the two software models are supposed to reproduce and how they execute with no need to plunge into the Java or Fortran lines. PMID:22844438

  20. Distinct Mechanisms Underlie Quiescence during Two Caenorhabditis elegans Sleep-Like States

    PubMed Central

    Trojanowski, Nicholas F.; Nelson, Matthew D.; Flavell, Steven W.

    2015-01-01

    Electrophysiological recordings have enabled identification of physiologically distinct yet behaviorally similar states of mammalian sleep. In contrast, sleep in nonmammals has generally been identified behaviorally and therefore regarded as a physiologically uniform state characterized by quiescence of feeding and locomotion, reduced responsiveness, and rapid reversibility. The nematode Caenorhabditis elegans displays sleep-like quiescent behavior under two conditions: developmentally timed quiescence (DTQ) occurs during larval transitions, and stress-induced quiescence (SIQ) occurs in response to exposure to cellular stressors. Behaviorally, DTQ and SIQ appear identical. Here, we use optogenetic manipulations of neuronal and muscular activity, pharmacology, and genetic perturbations to uncover circuit and molecular mechanisms of DTQ and SIQ. We find that locomotion quiescence induced by DTQ- and SIQ-associated neuropeptides occurs via their action on the nervous system, although their neuronal target(s) and/or molecular mechanisms likely differ. Feeding quiescence during DTQ results from a loss of pharyngeal muscle excitability, whereas feeding quiescence during SIQ results from a loss of excitability in the nervous system. Together these results indicate that, as in mammals, quiescence is subserved by different mechanisms during distinct sleep-like states in C. elegans. SIGNIFICANCE STATEMENT Sleep behavior is characterized by cessation of feeding and locomotion, reduced responsiveness, and rapid reversibility. In mammals and birds, there are sleep states that have fundamentally different electrophysiology despite outwardly similar behavior. However, it is not clear whether behavioral sleep is a uniform state in animals in which electrophysiology is not readily possible. The nematode Caenorhabditis elegans displays sleep-like behavior under two conditions: during development and after exposure to environmental stressors. Here, we show that feeding and locomotion

  1. First Born amplitude for transitions from a circular state to a state of large (l, m)

    NASA Astrophysics Data System (ADS)

    Dewangan, D. P.

    2005-01-01

    The use of cylindrical polar coordinates instead of the conventional spherical polar coordinates enables us to derive compact expressions of the first Born amplitude for some selected sets of transitions from an arbitrary initial circular \\big|\\psi_{n_i,n_i-1,n_i-1}\\big\\rangle state to a final \\big|\\psi_{n_f,l_f,m_f}\\big\\rangle state of large (lf, mf). The formulae for \\big|\\psi_{n_i,n_i-1,n_i-1}\\big\\rangle \\longrightarrow \\big|\\psi_{n_f,n_f-1,n_f-2}\\big\\rangle and \\big|\\psi_{n_i,n_i-1,n_i-1}\\big\\rangle \\longrightarrow \\big|\\psi_{n_f,n_f-1,n_f-3}\\big\\rangle transitions are expressed in terms of the Jacobi polynomials which serve as suitable starting points for constructing complete solutions over the bound energy levels of hydrogen-like atoms. The formulae for \\big|\\psi_{n_i,n_i-1,n_i-1}\\big\\rangle \\longrightarrow \\big|\\psi_{n_f,n_f-1,-(n_f-2)}\\big\\rangle and \\big|\\psi_{n_i,n_i-1,n_i-1}\\big\\rangle \\longrightarrow \\big|\\psi_{n_f,n_f-1,-(n_f-3)}\\big\\rangle transitions are in simple algebraic forms and are directly applicable to all possible values of ni and nf. It emerges that the method can be extended to evaluate the first Born amplitude for many other transitions involving states of large (l, m).

  2. Field-controlled magnetic order with insulator-metal transitions in a periodic Anderson-like organic polymer.

    PubMed

    Ding, L J; Yao, K L; Fu, H H

    2011-01-07

    The zero- and low-temperature behaviors of a quasi-one-dimensional organic polymer proposed as a symmetrical periodic Anderson-like chain model, in which the localized f orbitals hybridize with the conduction orbitals at even sites, are investigated by means of many-body Green's function theory. In the absence of magnetic field, the ground state of the system turns out to be ferrimagnetic. The temperature-induced phase diagrams have been explored, where the competition between the Hubbard repulsion U on the localized f orbital and the hybridization strength V makes an important impact on the transition temperature. In a magnetic field, it is found that a 1/3 magnetization plateau appears and two critical fields indicating the insulator-metal transitions at zero temperature emerge, which are closely related to the energy bands. Furthermore, the single-site entanglement entropy is a good indicator of quantum phase transitions. The temperature-field-induced phase diagram has also been attained, wherein the magnetization plateau state, the gapless phase and the spin polarized state are revealed. The temperature dependence of thermodynamic quantities such as the magnetization, susceptibility and specific heat are calculated to characterize the corresponding phases. It is also found that the up-spin and down-spin hole excitations are responsible for the thermodynamic properties.

  3. Variational Identification of Markovian Transition States

    NASA Astrophysics Data System (ADS)

    Martini, Linda; Kells, Adam; Covino, Roberto; Hummer, Gerhard; Buchete, Nicolae-Viorel; Rosta, Edina

    2017-07-01

    We present a method that enables the identification and analysis of conformational Markovian transition states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented by using both analytical models and examples from MD simulations of the benchmark system helix-forming peptide Ala5 , and of larger, biomedically important systems: the 15-lipoxygenase-2 enzyme (15-LOX-2), the epidermal growth factor receptor (EGFR) protein, and the Mga2 fungal transcription factor. The analysis of 15-LOX-2 uses data generated exclusively from biased umbrella sampling simulations carried out at the hybrid ab initio density functional theory (DFT) quantum mechanics/molecular mechanics (QM/MM) level of theory. In all cases, our method automatically identifies the corresponding transition states and metastable conformations in a variationally optimal way, with the input of a set of relevant coordinates, by accurately reproducing the intrinsic slowest relaxation rate of each system. Our approach offers a general yet easy-to-implement analysis method that provides unique insight into the molecular mechanism and the rare but crucial (i.e., rate-limiting) transition states occurring along conformational transition paths in complex dynamical systems such as molecular trajectories.

  4. Walk, Bicycle, and Transit Trips of Transit-Dependent and Choice Riders in the 2009 United States National Household Travel Survey.

    PubMed

    Lachapelle, Ugo

    2015-08-01

    Previous research has shown that public transit use may be associated with active transportation. Access to a car may influence active transportation of transit riders. Using the 2009 United States National Household Travel Survey (NHTS), transit users ≥ 16 years old (n = 25,550) were categorized according to driver status and number of cars and drivers in the household. This typology ranged from choice transit riders (ie, "fully motorized drivers") to transit-dependent riders (ie, "unmotorized nondriver"). Transit trips, walking trips, and bicycling trips of transit users are estimated in negative binomial models against the car availability typology. Sixteen percent of participants took transit in the past month; most (86%) lived in car-owning households. As income increased, car availability also increased. Transit user groups with lower car availability were generally more likely than fully motorized drivers to take more public transit, walking, and bicycle trips. Transit riders have varying levels of vehicle access; their use of combinations of alternative modes of transportation fluctuates accordingly. Transit-dependent individuals without cars or sharing cars used active transportation more frequently than car owners. Policies to reduce vehicle ownership in households may enable increases in the use of alternative modes of transportation for transit users, even when cars are still owned.

  5. Travel Patterns And Characteristics Of Transit Users In New York State

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hwang, Ho-Ling; Wilson, Daniel W.; Reuscher, Tim

    This research is a detailed examination of the travel behaviors and patterns of transit users within New York State (NYS), primarily based on travel data provided by the National Household Travel Survey (NHTS) in 2009 and the associated Add-on sample households purchased by the New York State Department of Transportation (NYSDOT). Other data sources analyzed in this study include: NYS General Transit Feed Specification (GTFS) to assist in analyzing spatial relationships for access to transit and the creation of Transit Shed geographic areas of 1, 2.5, and 5 miles from transit stop locations, LandScan population database to understand transit coverage,more » and Census Bureau s American Community Survey (ACS) data to examine general transit patterns and trends in NYS over time. The majority of analyses performed in this research aimed at identifying transit trip locations, understanding differences in transit usage by traveler demographics, as well as producing trip/mode-specific summary statistics including travel distance, trip duration, time of trip, and travel purpose of transit trips made by NYS residents, while also analyzing regional differences and unique travel characteristics and patterns. The analysis was divided into two aggregated geographic regions: New York Metropolitan Transportation Council (NYMTC) and NYS minus NYMTC (Rest of NYS). The inclusion of NYMTC in all analysis would likely produce misleading conclusions for other regions in NYS. TRANSIT COVERAGE The NYS transit network has significant coverage in terms of transit stop locations across the state s population. Out of the 19.3 million NYS population in 2011, about 15.3 million (or 79%) resided within the 1-mile transit shed. This NYS population transit coverage increased to 16.9 million (or 88%) when a 2.5-mile transit shed was considered; and raised to 17.7 million (or 92%) when the 5-mile transit shed was applied. KEY FINDINGS Based on 2009 NHTS data, about 40% of NYMTC households used

  6. Design of biomimetic catalysts by molecular imprinting in synthetic polymers: the role of transition state stabilization.

    PubMed

    Wulff, Günter; Liu, Junqiu

    2012-02-21

    The impressive efficiency and selectivity of biological catalysts has engendered a long-standing effort to understand the details of enzyme action. It is widely accepted that enzymes accelerate reactions through their steric and electronic complementarity to the reactants in the rate-determining transition states. Thus, tight binding to the transition state of a reactant (rather than to the corresponding substrate) lowers the activation energy of the reaction, providing strong catalytic activity. Debates concerning the fundamentals of enzyme catalysis continue, however, and non-natural enzyme mimics offer important additional insight in this area. Molecular structures that mimic enzymes through the design of a predetermined binding site that stabilizes the transition state of a desired reaction are invaluable in this regard. Catalytic antibodies, which can be quite active when raised against stable transition state analogues of the corresponding reaction, represent particularly successful examples. Recently, synthetic chemistry has begun to match nature's ability to produce antibody-like binding sites with high affinities for the transition state. Thus, synthetic, molecularly imprinted polymers have been engineered to provide enzyme-like specificity and activity, and they now represent a powerful tool for creating highly efficient catalysts. In this Account, we review recent efforts to develop enzyme models through the concept of transition state stabilization. In particular, models for carboxypeptidase A were prepared through the molecular imprinting of synthetic polymers. On the basis of successful experiments with phosphonic esters as templates to arrange amidinium groups in the active site, the method was further improved by combining the concept of transition state stabilization with the introduction of special catalytic moieties, such as metal ions in a defined orientation in the active site. In this way, the imprinted polymers were able to provide both an

  7. Spatial correlations, clustering and percolation-like transitions in homicide crimes

    NASA Astrophysics Data System (ADS)

    Alves, L. G. A.; Lenzi, E. K.; Mendes, R. S.; Ribeiro, H. V.

    2015-07-01

    The spatial dynamics of criminal activities has been recently studied through statistical physics methods; however, models and results have been focusing on local scales (city level) and much less is known about these patterns at larger scales, e.g. at a country level. Here we report on a characterization of the spatial dynamics of the homicide crimes along the Brazilian territory using data from all cities (˜5000) in a period of more than thirty years. Our results show that the spatial correlation function in the per capita homicides decays exponentially with the distance between cities and that the characteristic correlation length displays an acute increasing trend in the latest years. We also investigate the formation of spatial clusters of cities via a percolation-like analysis, where clustering of cities and a phase-transition-like behavior describing the size of the largest cluster as a function of a homicide threshold are observed. This transition-like behavior presents evolutive features characterized by an increasing in the homicide threshold (where the transitions occur) and by a decreasing in the transition magnitudes (length of the jumps in the cluster size). We believe that our work sheds new light on the spatial patterns of criminal activities at large scales, which may contribute for better political decisions and resources allocation as well as opens new possibilities for modeling criminal activities by setting up fundamental empirical patterns at large scales.

  8. Tables of branching ratios for electric dipole transitions between arbitrary levels of hydrogen-like atoms

    NASA Technical Reports Server (NTRS)

    Omidvar, K.

    1977-01-01

    The branching ratios in hydrogen-like atoms due to the electric-dipole transitions are tabulated for the initial principal and azimuthal quantum numbers n prime l prime, and final principal and azimuthal quantum numbers n l. Average values with respect to l prime are given. The branching ratios not tabulated, including the initial states n prime yields infinity l prime corresponding to the threshold of the continuum, could be obtained by extrapolation.

  9. Relativistic distorted-wave collision strengths for Δn = 0 transitions in the 67 Li-like, F-like and Na-like ions with 26 ≤ Z ≤ 92

    NASA Astrophysics Data System (ADS)

    Fontes, Christopher J.; Zhang, Hong Lin

    2017-01-01

    Relativistic distorted-wave collision strengths have been calculated for all possible Δn = 0 transitions, where n denotes the valence shell of the ground level, in the 67 Li-like, F-like and Na-like ions with Z in the range 26 ≤ Z ≤ 92. This choice produces 3 transitions with n = 2 in the Li-like and F-like ions, and 10 transitions with n = 3 in the Na-like ions. For the Li-like and F-like ions, the calculations were made for the six final, or scattered, electron energies E‧ = 0.008 , 0.04 , 0.10 , 0.21 , 0.41, and 0.75, where E‧ is in units of Zeff2 Ry with Zeff = Z - 1.66 for Li-like ions and Zeff = Z - 6.667 for F-like ions. For the Na-like ions, the calculations were made for the six final electron energies E‧ = 0.0025 , 0.015 , 0.04 , 0.10 , 0.21, and 0.40, with Zeff = Z - 8.34. In the present calculations, an improved "top-up" method, which employs relativistic plane waves, was used to obtain the high partial-wave contribution for each transition, in contrast to the partial-relativistic Coulomb-Bethe approximation used in previous works by Zhang, Sampson and Fontes [H.L. Zhang, D.H. Sampson, C.J. Fontes, At. Data Nucl. Data Tables 44 (1990) 31; H.L. Zhang, D.H. Sampson, C.J. Fontes, At. Data Nucl. Data Tables 48 (1991) 25; D.H. Sampson, H.L. Zhang, C.J. Fontes, At. Data Nucl. Data Tables 44 (1990) 209]. In those previous works, collision strengths were also provided for Li-, F- and Na-like ions, but for a more comprehensive set of transitions. The collision strengths covered in the present work should be more accurate than the corresponding data given in those previous works and are presented here to replace those earlier results.

  10. Relativistic distorted-wave collision strengths for Δn = 0 transitions in the 67 Li-like, F-like and Na-like ions with 26 ≤ Z ≤ 92

    DOE PAGES

    Fontes, Christopher J.; Zhang, Hong Lin

    2017-01-01

    We calculated relativistic distorted-wave collision strength for all possible Δn=0 transitions, where n denotes the valence shell of the ground level, in the 67 Li-like, F-like and Na-like ions with Z in the range 26 ≤ Z ≤92. This choice produces 3 transitions with n=2 in the Li-like and F-like ions, and 10 transitions with n=3 in the Na-like ions. Moreover, for the Li-like and F-like ions, the calculations were made for the six final, or scattered, electron energies E'=0.008,0.04,0.10,0.21,0.41, and 0.75, where E' is in units of Zmore » $$2\\atop{eff}$$ Ry with Z eff = Z- 1.66 for Li-like ions and Z eff= Z- 6.667 for F-like ions. For the Na-like ions, the calculations were made for the six final electron energies E'=0.0025,0.015,0.04,0.10,0.21, and 0.40, with Z eff = Z- 8.34. In the present calculations, an improved “top-up” method, which employs relativistic plane waves, was used to obtain the high partial-wave contribution for each transition, in contrast to the partial-relativistic Coulomb–Bethe approximation used in previous works by Zhang, Sampson and Fontes [H.L. Zhang, D.H. Sampson, C.J. Fontes, At. Data Nucl. Data Tables 44 (1990) 31; H.L. Zhang, D.H. Sampson, C.J. Fontes, At. Data Nucl. Data Tables 48 (1991) 25; D.H. Sampson, H.L. Zhang, C.J. Fontes, At. Data Nucl. Data Tables 44 (1990) 209]. In those previous works, collision strengths were also provided for Li-, F- and Na-like ions, but for a more comprehensive set of transitions. Finally, the collision strengths covered in the present work should be more accurate than the corresponding data given in those previous works and are presented here to replace those earlier results.« less

  11. Successive magnetic phase transitions in α -RuCl3 : XY-like frustrated magnet on the honeycomb lattice

    NASA Astrophysics Data System (ADS)

    Kubota, Yumi; Tanaka, Hidekazu; Ono, Toshio; Narumi, Yasuo; Kindo, Koichi

    2015-03-01

    The layered compound α -RuCl3 is composed of a honeycomb lattice of magnetic Ru3 + ions with the 4 d5 electronic state. We have investigated the magnetic properties of α -RuCl3 via magnetization and specific heat measurements using single crystals. It was observed that α -RuCl3 undergoes a structural phase transition at Tt≃150 K accompanied by fairly large hysteresis. This structural phase transition is expected to be similar to that observed in closely related CrCl3. The magnetizations and magnetic susceptibilities are strongly anisotropic, which mainly arise from the anisotropic g factors, i.e., ga b≃2.5 and gc≃0.4 for magnetic fields parallel and perpendicular to the a b plane, respectively. These g factors and the obtained entropy indicate that the effective spin of Ru3 + is one-half, which results from the low-spin state. Specific heat data show that magnetic ordering occurs in four steps at zero magnetic field. The successive magnetic phase transitions should be ascribed to the competition among exchange interactions. The magnetic phase diagram for H ∥a b is obtained. We discuss the strongly anisotropic g factors in α -RuCl3 and deduce that the exchange interaction is strongly XY-like. α -RuCl3 is magnetically described as a three-dimensionally coupled XY-like frustrated magnet on a honeycomb lattice.

  12. Localized-to-extended-states transition below the Fermi level

    NASA Astrophysics Data System (ADS)

    Tito, M. A.; Pusep, Yu. A.

    2018-05-01

    Time-resolved photoluminescence is employed to examine a transition from localized to extended electron states below the Fermi level in multiple narrow quantum well GaAs/AlGaAs heterostructures, where disorder was generated by interface roughness. Such a transition resembles the metal-insulator transition profoundly investigated by electric transport measurements. An important distinction distinguishes the localized-to-extended-states transition studied here: it takes place below the Fermi level in an electron system with a constant concentration, which implies unchanging Coulomb correlations. Moreover, for such a localized-to-extended-states transition the temperature is shown to be irrelevant. In the insulating regime the magnetic field was found to cause an additional momentum relaxation which considerably enhanced the recombination rate. Thus, we propose a method to explore the evolution of the localized electron states in a system with a fixed disorder and Coulomb interaction.

  13. Spectroscopy of M-shell x-ray transitions in Zn-like through Co-like W

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Clementson, J; Beiersdorfer, P; Brown, G V

    2009-07-08

    The M-shell x-ray emission of highly charged tungsten ions has been investigated at the Livermore electron beam ion trap facility. Using the SuperEBIT electron beam ion trap and a NASA x-ray calorimeter array, transitions connecting the ground configurations in the 1500-3600 eV spectral range of zinc-like W{sup 44+} through cobalt-like W{sup 47+} have been measured. The measured spectra are compared with theoretical line positions and emissivities calculated using the FAC code.

  14. State-to-State Mode Specificity: Energy Sequestration and Flow Gated by Transition State.

    PubMed

    Zhao, Bin; Sun, Zhigang; Guo, Hua

    2015-12-23

    Energy flow and sequestration at the state-to-state level are investigated for a prototypical four-atom reaction, H2 + OH → H + H2O, using a transition-state wave packet (TSWP) method. The product state distribution is found to depend strongly on the reactant vibrational excitation, indicating mode specificity at the state-to-state level. From a local-mode perspective, it is shown that the vibrational excitation of the H2O product derives from two different sources, one attributable to the energy flow along the reaction coordinate into the newly formed OH bond and the other due to the sequestration of the vibrational energy in the OH spectator moiety during the reaction. The analysis provided a unified interpretation of some seemingly contradicting experimental observations. It is further shown that the transfer of vibrational energy from the OH reactant to H2O product is gated by the transition state, accomplished coherently by multiple TSWPs with the corresponding OH vibrational excitation.

  15. State transitions of GRS 1739-278 in the 2014 outburst

    NASA Astrophysics Data System (ADS)

    Wang, Sili; Kawai, Nobuyuki; Shidatsu, Megumi; Tachibana, Yutaro; Yoshii, Taketoshi; Sudo, Masayuki; Kubota, Aya

    2018-05-01

    We report on the X-ray spectral analysis and time evolution of GRS 1739-278 during its 2014 outburst, based on MAXI/GSC and Swift/XRT observations. Over the course of the outburst, a transition from the low/hard state to the high/soft state and then back to the low/hard state was seen. During the high/soft state, the innermost disk temperature mildly decreased, while the innermost radius estimated with the multi-color disk model remained constant at ˜18 (D/8.5 kpc)(cos i/cos 30°)-1/2 km, where D is the source distance and i is the inclination of observation. This small innermost radius of the accretion disk suggests that the central object is more likely to be a Kerr black hole rather than a Schwardzschild black hole. Applying a relativistic disk emission model to the high/soft state spectra, a mass upper limit of 18.3 M⊙ was obtained based on the inclination limit i < 60° for an assumed distance of 8.5 kpc. Using the empirical relation of the transition luminosity to the Eddington limit, the mass is constrained to 4.0-18.3 M⊙ for the same distance. The mass can be further constrained to be no larger than 9.5 M⊙ by adopting the constraints based on the fits to the NuSTAR spectra with relativistically blurred disk reflection models (Miller et al. 2015, ApJ, 799, L6).

  16. Transition State Geometry Measurements from 13C Isotope Effects. The Experimental Transition State for the Epoxidation of Alkenes with Oxaziridines

    PubMed Central

    Hirschi, Jennifer S.; Takeya, Tetsuya; Hang, Chao; Singleton, Daniel A.

    2009-01-01

    We suggest here and evaluate a methodology for the measurement of specific interatomic distances from a combination of theoretical calculations and experimentally measured 13C kinetic isotope effects. This process takes advantage of a broad diversity of transition structures available for the epoxidation of 2-methyl-2-butene with oxaziridines. From the isotope effects calculated for these transition structures, a theory-independent relationship between the C-O bond distances of the newly forming bonds and the isotope effects is established. Within the precision of the measurement, this relationship in combination with the experimental isotope effects provides a highly accurate picture of the C-O bonds forming at the transition state. The diversity of transition structures also allows an evaluation of the Schramm process for defining transition state geometries based on calculations at non-stationary points, and the methodology is found to be reasonably accurate. PMID:19146405

  17. Do state-and-transition models derived from vegetation succession also represent avian succession in restored mine pits?

    PubMed

    Craig, Michael D; Stokes, Vicki L; Fontaine, Joseph B; Hardy, Giles E StJ; Grigg, Andrew H; Hobbs, Richard J

    2015-10-01

    State-and-transition models are increasingly used as a tool to inform management of post-disturbance succession and effective conservation of biodiversity in production landscapes. However, if they are to do this effectively, they need to represent faunal, as well as vegetation, succession. We assessed the congruence between vegetation and avian succession by sampling avian communities in each state of a state-and-transition model used to inform management of post-mining restoration in a production landscape in southwestern Australia. While avian communities differed significantly among states classified as on a desirable successional pathway, they did not differ between desirable and deviated states of the same post-mining age. Overall, we concluded there was poor congruence between vegetation and avian succession in this state-and-transition model. We identified four factors that likely contributed to this lack of congruence, which were that long-term monitoring of succession in restored mine pits was not used to update and improve models, states were not defined based on ecological processes and thresholds, states were not defined by criteria that were important in structuring the avian community, and states were not based on criteria that related to values in the reference community. We believe that consideration of these four factors in the development of state-and-transition models should improve their ability to accurately represent faunal, as well as vegetation, succession. Developing state-and-transition models that better incorporate patterns of faunal succession should improve the ability to manage post-disturbance succession across a range of ecosystems for biodiversity conservation.

  18. Electrophoretic-like gating used to control metal-insulator transitions in electronically phase separated manganite wires.

    PubMed

    Guo, Hangwen; Noh, Joo H; Dong, Shuai; Rack, Philip D; Gai, Zheng; Xu, Xiaoshan; Dagotto, Elbio; Shen, Jian; Ward, T Zac

    2013-08-14

    Electronically phase separated manganite wires are found to exhibit controllable metal-insulator transitions under local electric fields. The switching characteristics are shown to be fully reversible, polarity independent, and highly resistant to thermal breakdown caused by repeated cycling. It is further demonstrated that multiple discrete resistive states can be accessed in a single wire. The results conform to a phenomenological model in which the inherent nanoscale insulating and metallic domains are rearranged through electrophoretic-like processes to open and close percolation channels.

  19. Detecting critical state before phase transition of complex systems by hidden Markov model

    NASA Astrophysics Data System (ADS)

    Liu, Rui; Chen, Pei; Li, Yongjun; Chen, Luonan

    Identifying the critical state or pre-transition state just before the occurrence of a phase transition is a challenging task, because the state of the system may show little apparent change before this critical transition during the gradual parameter variations. Such dynamics of phase transition is generally composed of three stages, i.e., before-transition state, pre-transition state, and after-transition state, which can be considered as three different Markov processes. Thus, based on this dynamical feature, we present a novel computational method, i.e., hidden Markov model (HMM), to detect the switching point of the two Markov processes from the before-transition state (a stationary Markov process) to the pre-transition state (a time-varying Markov process), thereby identifying the pre-transition state or early-warning signals of the phase transition. To validate the effectiveness, we apply this method to detect the signals of the imminent phase transitions of complex systems based on the simulated datasets, and further identify the pre-transition states as well as their critical modules for three real datasets, i.e., the acute lung injury triggered by phosgene inhalation, MCF-7 human breast cancer caused by heregulin, and HCV-induced dysplasia and hepatocellular carcinoma.

  20. Morphological transitions of brain sphingomyelin are determined by the hydration protocol: ripples re-arrange in plane, and sponge-like networks disintegrate into small vesicles.

    PubMed

    Meyer, H W; Bunjes, H; Ulrich, A S

    1999-06-01

    The phase transition of hydrated brain sphingomyelin occurs at around 35 degrees C, which is close to the physiological temperature. Freeze-fracture electron microscopy is used to characterize different gel state morphologies in terms of solid-ordered and liquid-ordered phase states, according to the occurrence of ripples and other higher-dimensional bilayer deformations. Evidently, the natural mixed-chain sphingomyelin does not assume the flat L beta, phase but instead the rippled P beta, phase, with symmetric and asymmetric ripples as well as macroripples and an egg-carton pattern, depending on the incubation conditions. An unexpected difference was observed between samples that are hydrated above and below the phase transition temperature. When the lipid is hydrated at low temperature, a sponge-like network of bilayers is formed in the gel state, next to some normal lamellae. The network loses its ripples during cold-incubation, which indicates the formation of a liquid-ordered (lo) gel phase. Ripples re-appear upon warming and the sponge-like network disintegrates spontaneously and irreversibly into small vesicles above the phase transition.

  1. Mixed state dynamical quantum phase transitions

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Utso; Bandyopadhyay, Souvik; Dutta, Amit

    2017-11-01

    Preparing an integrable system in a mixed state described by a thermal density matrix, we subject it to a sudden quench and explore the subsequent unitary dynamics. To address the question of whether the nonanalyticities, namely, the dynamical quantum phase transitions (DQPTs), persist when the initial state is mixed, we consider two versions of the generalized Loschmidt overlap amplitude (GLOA). Our study shows that the GLOA constructed using the Uhlmann approach does not show any signature of DQPTs at any nonzero initial temperature. On the other hand, a GLOA defined in the interferometric phase approach through the purifications of the time-evolved density matrix, indeed shows that nonanalyiticies in the corresponding "dynamical free-energy density" persist, thereby establishing the existence of mixed state dynamical quantum phase transitions (MSDQPTs). Our work provides a framework that perfectly reproduces both the nonanalyticities and also the emergent topological structure in the pure state limit. These claims are corroborated by analyzing the nonequilibrium dynamics of a transverse Ising chain initially prepared in a thermal state and subjected to a sudden quench of the transverse field.

  2. Energy levels and radiative rates for transitions in B-like to F-like Kr ions (Kr XXXII XXVIII)

    NASA Astrophysics Data System (ADS)

    Aggarwal, K. M.; Keenan, F. P.; Lawson, K. D.

    2008-05-01

    Energy levels, radiative rates, oscillator strengths, line strengths, and lifetimes have been calculated for transitions in B-like to F-like Kr ions, Kr XXXIII-XXVIII. For the calculations, the fully relativistic GRASP code has been adopted, and results are reported for all electric dipole (E1), electric quadrupole (E2), magnetic dipole (M1), and magnetic quadrupole (M2) transitions among the lowest 125, 236, 272, 226, and 113 levels of Kr XXXII, Kr XXXI, Kr XXX, Kr XXIX, and Kr XXVIII, respectively, belonging to the n ⩽ 3 configurations. Comparisons are made with earlier available theoretical and experimental results, and some discrepancies have been noted and explained.

  3. CellTrans: An R Package to Quantify Stochastic Cell State Transitions.

    PubMed

    Buder, Thomas; Deutsch, Andreas; Seifert, Michael; Voss-Böhme, Anja

    2017-01-01

    Many normal and cancerous cell lines exhibit a stable composition of cells in distinct states which can, e.g., be defined on the basis of cell surface markers. There is evidence that such an equilibrium is associated with stochastic transitions between distinct states. Quantifying these transitions has the potential to better understand cell lineage compositions. We introduce CellTrans, an R package to quantify stochastic cell state transitions from cell state proportion data from fluorescence-activated cell sorting and flow cytometry experiments. The R package is based on a mathematical model in which cell state alterations occur due to stochastic transitions between distinct cell states whose rates only depend on the current state of a cell. CellTrans is an automated tool for estimating the underlying transition probabilities from appropriately prepared data. We point out potential analytical challenges in the quantification of these cell transitions and explain how CellTrans handles them. The applicability of CellTrans is demonstrated on publicly available data on the evolution of cell state compositions in cancer cell lines. We show that CellTrans can be used to (1) infer the transition probabilities between different cell states, (2) predict cell line compositions at a certain time, (3) predict equilibrium cell state compositions, and (4) estimate the time needed to reach this equilibrium. We provide an implementation of CellTrans in R, freely available via GitHub (https://github.com/tbuder/CellTrans).

  4. The transition state structure for binding between TAZ1 of CBP and the disordered Hif-1α CAD.

    PubMed

    Lindström, Ida; Andersson, Eva; Dogan, Jakob

    2018-05-18

    Intrinsically disordered proteins (IDPs) are common in eukaryotes. However, relatively few experimental studies have addressed the nature of the rate-limiting transition state for the coupled binding and folding reactions involving IDPs. By using site-directed mutagenesis in combination with kinetics measurements we have here characterized the transition state for binding between the globular TAZ1 domain of CREB binding protein and the intrinsically disordered C-terminal activation domain of Hif-1α (Hif-1α CAD). A total of 17 Hif-1α CAD point-mutations were generated and a Φ-value binding analysis was carried out. We found that native hydrophobic binding interactions are not formed at the transition state. We also investigated the effect the biologically important Hif-1α CAD Asn-803 hydroxylation has on the binding kinetics, and found that the whole destabilization effect due the hydroxylation is within the dissociation rate constant. Thus, the rate-limiting transition state is "disordered-like", with native hydrophobic binding contacts being formed cooperatively after the rate-limiting barrier, which is clearly shown by linear free energy relationships. The same behavior was observed in a previously characterized TAZ1/IDP interaction, which may suggest common features for the rate-limiting transition state for TAZ1/IDP interactions.

  5. Policy to Performance: State ABE Transition Systems Report. Transitioning Adults to Opportunity

    ERIC Educational Resources Information Center

    Alamprese, Judith A.

    2012-01-01

    The U.S. Department of Education's Policy to Performance project was funded in 2009 to build the capacity of state adult basic education (ABE) staff to develop and implement policies and practices that would support an ABE transition system. Policy to Performance states were selected though a competitive process. State adult education directors…

  6. Estimating state-transition probabilities for unobservable states using capture-recapture/resighting data

    USGS Publications Warehouse

    Kendall, W.L.; Nichols, J.D.

    2002-01-01

    Temporary emigration was identified some time ago as causing potential problems in capture-recapture studies, and in the last five years approaches have been developed for dealing with special cases of this general problem. Temporary emigration can be viewed more generally as involving transitions to and from an unobservable state, and frequently the state itself is one of biological interest (e.g., 'nonbreeder'). Development of models that permit estimation of relevant parameters in the presence of an unobservable state requires either extra information (e.g., as supplied by Pollock's robust design) or the following classes of model constraints: reducing the order of Markovian transition probabilities, imposing a degree of determinism on transition probabilities, removing state specificity of survival probabilities, and imposing temporal constancy of parameters. The objective of the work described in this paper is to investigate estimability of model parameters under a variety of models that include an unobservable state. Beginning with a very general model and no extra information, we used numerical methods to systematically investigate the use of ancillary information and constraints to yield models that are useful for estimation. The result is a catalog of models for which estimation is possible. An example analysis of sea turtle capture-recapture data under two different models showed similar point estimates but increased precision for the model that incorporated ancillary data (the robust design) when compared to the model with deterministic transitions only. This comparison and the results of our numerical investigation of model structures lead to design suggestions for capture-recapture studies in the presence of an unobservable state.

  7. Recognition of human activity characteristics based on state transitions modeling technique

    NASA Astrophysics Data System (ADS)

    Elangovan, Vinayak; Shirkhodaie, Amir

    2012-06-01

    Human Activity Discovery & Recognition (HADR) is a complex, diverse and challenging task but yet an active area of ongoing research in the Department of Defense. By detecting, tracking, and characterizing cohesive Human interactional activity patterns, potential threats can be identified which can significantly improve situation awareness, particularly, in Persistent Surveillance Systems (PSS). Understanding the nature of such dynamic activities, inevitably involves interpretation of a collection of spatiotemporally correlated activities with respect to a known context. In this paper, we present a State Transition model for recognizing the characteristics of human activities with a link to a prior contextbased ontology. Modeling the state transitions between successive evidential events determines the activities' temperament. The proposed state transition model poses six categories of state transitions including: Human state transitions of Object handling, Visibility, Entity-entity relation, Human Postures, Human Kinematics and Distance to Target. The proposed state transition model generates semantic annotations describing the human interactional activities via a technique called Casual Event State Inference (CESI). The proposed approach uses a low cost kinect depth camera for indoor and normal optical camera for outdoor monitoring activities. Experimental results are presented here to demonstrate the effectiveness and efficiency of the proposed technique.

  8. X-ray spectroscopy of E2 and M3 transitions in Ni-like W

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Clementson, J.; Beiersdorfer, P.; Gu, M. F.

    2010-01-15

    The electric quadrupole (E2) and magnetic octupole (M3) ground-state transitions in Ni-like W{sup 46+} have been measured using high-resolution crystal spectroscopy at the LLNL electron-beam ion trap facility. The lines fall in the soft x-ray region near 7.93 A and were originally observed as an unresolved feature in tokamak plasmas. Using flat ammonium dihydrogen phosphate and quartz crystals, the wavelengths, intensities, and polarizations of the two lines have been measured for various electron-beam energies and compared to intensity and polarization calculations performed using the Flexible Atomic Code (FAC).

  9. X-ray Spectroscopy of E2 and M3 Transitions in Ni-like W

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Clementson, J; Beiersdorfer, P; Gu, M F

    2009-11-09

    The electric quadrupole (E2) and magnetic octupole (M3) ground state transitions in Ni-like W{sup 46+} have been measured using high-resolution crystal spectroscopy at the Livermore electron beam ion trap facility. The lines fall in the soft x-ray region near 7.93 {angstrom} and were originally observed as an unresolved feature in tokamak plasmas. Using flat ADP and quartz crystals the wavelengths, intensities, and polarizations of the two lines have been measured for various electron beam energies and compared to intensity and polarization calculations performed using the Flexible Atomic Code (FAC).

  10. Epitaxial strain-mediated spin-state transitions: can we switch off magnetism?

    NASA Astrophysics Data System (ADS)

    Rondinelli, James; Spaldin, Nicola

    2008-03-01

    We use first-principles density functional theory calculations to explore spin-state transitions in epitaxially strained LaCoO3. While high-spin to low-spin state transitions in minerals are common in geophysics, where pressures can reach over 200 GPa, we explore whether heteroepitaxial strain can achieve similar transitions with moderate strain in thin films. LaCoO3 is known to undergo a low-spin (S=0, t2g^6eg^0) to intermediate-spin (S=1, t2g^5eg^1) or high-spin (S=2, t2g^4eg^2) state transition with increasing temperature, and thus makes it a promising candidate material for strain-mediated spin transitions. Here we discuss the physics of the low-spin transition and changes in the electronic structure of LaCoO3, most notably, the metal-insulator transition that accompanies the spin-state transitions with epitaxial strain. As thin film growth techniques continue to reach atomic-level precision, we suggest this is another approach for controlling magnetism in complex oxide heterostructures.

  11. Ashkin-Teller criticality and weak first-order behavior of the phase transition to a fourfold degenerate state in two-dimensional frustrated Ising antiferromagnets

    NASA Astrophysics Data System (ADS)

    Liu, R. M.; Zhuo, W. Z.; Chen, J.; Qin, M. H.; Zeng, M.; Lu, X. B.; Gao, X. S.; Liu, J.-M.

    2017-07-01

    We study the thermal phase transition of the fourfold degenerate phases (the plaquette and single-stripe states) in the two-dimensional frustrated Ising model on the Shastry-Sutherland lattice using Monte Carlo simulations. The critical Ashkin-Teller-like behavior is identified both in the plaquette phase region and the single-stripe phase region. The four-state Potts critical end points differentiating the continuous transitions from the first-order ones are estimated based on finite-size-scaling analyses. Furthermore, a similar behavior of the transition to the fourfold single-stripe phase is also observed in the anisotropic triangular Ising model. Thus, this work clearly demonstrates that the transitions to the fourfold degenerate states of two-dimensional Ising antiferromagnets exhibit similar transition behavior.

  12. A Model of Mental State Transition Network

    NASA Astrophysics Data System (ADS)

    Xiang, Hua; Jiang, Peilin; Xiao, Shuang; Ren, Fuji; Kuroiwa, Shingo

    Emotion is one of the most essential and basic attributes of human intelligence. Current AI (Artificial Intelligence) research is concentrating on physical components of emotion, rarely is it carried out from the view of psychology directly(1). Study on the model of artificial psychology is the first step in the development of human-computer interaction. As affective computing remains unpredictable, creating a reasonable mental model becomes the primary task for building a hybrid system. A pragmatic mental model is also the fundament of some key topics such as recognition and synthesis of emotions. In this paper a Mental State Transition Network Model(2) is proposed to detect human emotions. By a series of psychological experiments, we present a new way to predict coming human's emotions depending on the various current emotional states under various stimuli. Besides, people in different genders and characters are taken into consideration in our investigation. According to the psychological experiments data derived from 200 questionnaires, a Mental State Transition Network Model for describing the transitions in distribution among the emotions and relationships between internal mental situations and external are concluded. Further more the coefficients of the mental transition network model were achieved. Comparing seven relative evaluating experiments, an average precision rate of 0.843 is achieved using a set of samples for the proposed model.

  13. Operationalizing resilience using state and transition models

    USDA-ARS?s Scientific Manuscript database

    In management, restoration, and policy contexts, the notion of resilience can be confusing. Systematic development of conceptual models of ecological state change (state transition models; STMs) can help overcome semantic confusion and promote a mechanistic understanding of resilience. Drawing on ex...

  14. Two drastically different climate states on an Earth-like terra-planet

    NASA Astrophysics Data System (ADS)

    Kalidindi, Sirisha; Reick, Christian H.; Raddatz, Thomas; Claussen, Martin

    2018-06-01

    We study an Earth-like terra-planet (water-limited terrestrial planet) with an overland recycling mechanism bringing fresh water back from the high latitudes to the low latitudes. By performing model simulations for such a planet we find two drastically different climate states for the same set of boundary conditions and parameter values: a cold and wet (CW) state with dominant low-latitude precipitation and a hot and dry (HD) state with only high-latitude precipitation. We notice that for perpetual equinox conditions, both climate states are stable below a certain threshold value of background soil albedo while above the threshold only the CW state is stable. Starting from the HD state and increasing background soil albedo above the threshold causes an abrupt shift from the HD state to the CW state resulting in a sudden cooling of about 35 °C globally, which is of the order of the temperature difference between present day and the Snowball Earth state. When albedo starting from the CW state is reduced down to zero the terra-planet does not shift back to the HD state (no closed hysteresis). This is due to the high cloud cover in the CW state hiding the surface from solar irradiation so that surface albedo has only a minor effect on the top of the atmosphere radiation balance. Additional simulations with present-day Earth's obliquity all lead to the CW state, suggesting a similar abrupt transition from the HD state to the CW state when increasing obliquity from zero. Our study also has implications for the habitability of Earth-like terra-planets. At the inner edge of the habitable zone, the higher cloud cover in the CW state cools the planet and may prevent the onset of a runaway greenhouse state. At the outer edge, the resupply of water at low latitudes stabilizes the greenhouse effect and keeps the planet in the HD state and may prevent water from getting trapped at high latitudes in frozen form. Overall, the existence of bistability in the presence of an

  15. Transition State Analysis of Thymidine Hydrolysis by Human Thymidine Phosphorylase*

    PubMed Central

    Schwartz, Phillip A.; Vetticatt, Mathew; Schramm, Vern L.

    2010-01-01

    Human thymidine phosphorylase (hTP) is responsible for thymidine (dT) homeostasis and its action promotes angiogenesis. In the absence of phosphate, hTP catalyzes a slow hydrolytic depyrimidination of dT yielding thymine and 2-deoxyribose (dRib). Its transition state was characterized using multiple kinetic isotope effect (KIE) measurements. Isotopically enriched thymidines were synthesized enzymatically from glucose or (deoxy)ribose and intrinsic KIEs were used to interpret the transition state structure. KIEs from [1′-14C]-, [1-15N]-, [1′-3H]-, [2′R-3H]-, [2′S-3H]-, [4′-3H]-, [5′-3H]dTs provided values of 1.033 ± 0.002, 1.004 ± 0.002, 1.325 ± 0.003, 1.101 ± 0.004, 1.087 ± 0.005, 1.040 ± 0.003, and 1.033 ± 0.003, respectively. Transition state analysis revealed a stepwise mechanism with a 2-deoxyribocation formed early and a higher energetic barrier for nucleophilic attack of a water molecule on the high energy intermediate. An equilibrium exists between the deoxyribocation and reactants prior to the irreversible nucleophilic attack by water. The results establish activation of the thymine leaving group without requirement for phosphate. A transition state constrained to match the intrinsic KIEs was found using density functional theory. An active site histidine (His116) is implicated as the catalytic base for activation of the water nucleophile at the rate-limiting transition state. The distance between the water nucleophile and the anomeric carbon (rC-O) is predicted to be 2.3 Å at the transition state. The transition state model predicts that deoxyribose adopts a mild 3′-endo confirmation during nucleophilic capture. These results differ from the concerted bimolecular mechanism reported for the arsenolytic reaction PMID:20804144

  16. A residue in helical conformation in the native state adopts a β-strand conformation in the folding transition state despite its high and canonical Φ-value.

    PubMed

    Zarrine-Afsar, Arash; Dahesh, Samira; Davidson, Alan R

    2012-05-01

    Delineating structures of the transition states in protein folding reactions has provided great insight into the mechanisms by which proteins fold. The most common method for obtaining this information is Φ-value analysis, which is carried out by measuring the changes in the folding and unfolding rates caused by single amino acid substitutions at various positions within a given protein. Canonical Φ-values range between 0 and 1, and residues displaying high values within this range are interpreted to be important in stabilizing the transition state structure, and to elicit this stabilization through native-like interactions. Although very successful in defining the general features of transition state structures, Φ-value analysis can be confounded when non-native interactions stabilize this state. In addition, direct information on backbone conformation within the transition state is not provided. In the work described here, we have investigated structure formation at a conserved β-bulge (with helical conformation) in the Fyn SH3 domain by characterizing the effects of substituting all natural amino acids at one position within this structural motif. By comparing the effects on folding rates of these substitutions with database-derived local structure propensity values, we have determined that this position adopts a non-native backbone conformation in the folding transition state. This result is surprising because this position displays a high and canonical Φ-value of 0.7. This work emphasizes the potential role of non-native conformations in folding pathways and demonstrates that even positions displaying high and canonical Φ-values may, nevertheless, adopt a non-native conformation in the transition state. Copyright © 2012 Wiley Periodicals, Inc.

  17. Deacylation transition states of a bacterial DD-peptidase.

    PubMed

    Adediran, S A; Kumar, I; Pratt, R F

    2006-10-31

    Beta-lactam antibiotics restrict bacterial growth by inhibiting DD-peptidases. These enzymes catalyze the final transpeptidation step in bacterial cell wall biosynthesis. Although much structural information is now available for these enzymes, the mechanism of the actual transpeptidation reaction has not been studied in detail. The reaction is known to involve a double-displacement mechanism with an acyl-enzyme intermediate, which can be attacked by water, specific amino acids, peptides, and other acyl acceptors. We describe in this paper an investigation of acyl acceptor specificity and assess the need for general base catalysis in the deacylation transition state of the Streptomyces R61 DD-peptidase. We show, by the criterion of solvent deuterium kinetic isotope effect measurements and proton inventories, that the transition states of specific and nonspecific substrates are very similar, at least with respect to proton motion. The transition states for attack (tetrahedral intermediate formation) by d-amino acids and Gly-l-Xaa dipeptides do not include a general base catalyst, while such catalysis is essential for reaction with water and d-alpha-hydroxy acids. D-Alpha-hydroxy acids act as acyl acceptors for glycyl substrates but not for more specific d-alanyl substrates; hydroxy acids actually behave, more generally, as mixed inhibitors of the DD-peptidase. The structural and mechanistic bases of these observations are discussed; they should inform transition state analogue design.

  18. The transition from the open minimum to the ring minimum on the ground state and on the lowest excited state of like symmetry in ozone: A configuration interaction study

    DOE PAGES

    Theis, Daniel; Ivanic, Joseph; Windus, Theresa L.; ...

    2016-03-10

    The metastable ring structure of the ozone 1 1A 1 ground state, which theoretical calculations have shown to exist, has so far eluded experimental detection. An accurate prediction for the energy difference between this isomer and the lower open structure is therefore of interest, as is a prediction for the isomerization barrier between them, which results from interactions between the lowest two 1A 1 states. In the present work, valence correlated energies of the 1 1A 1 state and the 2 1A 1 state were calculated at the 1 1A 1 open minimum, the 1 1A 1 ring minimum, themore » transition state between these two minima, the minimum of the 2 1A 1 state, and the conical intersection between the two states. The geometries were determined at the full-valence multi-configuration self-consistent-field level. Configuration interaction (CI) expansions up to quadruple excitations were calculated with triple-zeta atomic basis sets. The CI expansions based on eight different reference configuration spaces were explored. To obtain some of the quadruple excitation energies, the method of CorrelationEnergy Extrapolation by Intrinsic Scaling was generalized to the simultaneous extrapolation for two states. This extrapolation method was shown to be very accurate. On the other hand, none of the CI expansions were found to have converged to millihartree (mh) accuracy at the quadruple excitation level. The data suggest that convergence to mh accuracy is probably attained at the sextuple excitation level. On the 11A1 state, the present calculations yield the estimates of (ring minimum—open minimum) ~45–50 mh and (transition state—open minimum) ~85–90 mh. For the (2 1A 1– 1A 1) excitation energy, the estimate of ~130–170 mh is found at the open minimum and 270–310 mh at the ring minimum. At the transition state, the difference (2 1A 1– 1A 1) is found to be between 1 and 10 mh. The geometry of the transition state on the 11A1 surface and that of the minimum on the 2 1A 1

  19. The transition from the open minimum to the ring minimum on the ground state and on the lowest excited state of like symmetry in ozone: A configuration interaction study

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Theis, Daniel; Ivanic, Joseph; Windus, Theresa L.

    The metastable ring structure of the ozone 1 1A 1 ground state, which theoretical calculations have shown to exist, has so far eluded experimental detection. An accurate prediction for the energy difference between this isomer and the lower open structure is therefore of interest, as is a prediction for the isomerization barrier between them, which results from interactions between the lowest two 1A 1 states. In the present work, valence correlated energies of the 1 1A 1 state and the 2 1A 1 state were calculated at the 1 1A 1 open minimum, the 1 1A 1 ring minimum, themore » transition state between these two minima, the minimum of the 2 1A 1 state, and the conical intersection between the two states. The geometries were determined at the full-valence multi-configuration self-consistent-field level. Configuration interaction (CI) expansions up to quadruple excitations were calculated with triple-zeta atomic basis sets. The CI expansions based on eight different reference configuration spaces were explored. To obtain some of the quadruple excitation energies, the method of CorrelationEnergy Extrapolation by Intrinsic Scaling was generalized to the simultaneous extrapolation for two states. This extrapolation method was shown to be very accurate. On the other hand, none of the CI expansions were found to have converged to millihartree (mh) accuracy at the quadruple excitation level. The data suggest that convergence to mh accuracy is probably attained at the sextuple excitation level. On the 11A1 state, the present calculations yield the estimates of (ring minimum—open minimum) ~45–50 mh and (transition state—open minimum) ~85–90 mh. For the (2 1A 1– 1A 1) excitation energy, the estimate of ~130–170 mh is found at the open minimum and 270–310 mh at the ring minimum. At the transition state, the difference (2 1A 1– 1A 1) is found to be between 1 and 10 mh. The geometry of the transition state on the 11A1 surface and that of the minimum on the 2 1A 1

  20. Typology of State Types: Persistence and Transition

    DTIC Science & Technology

    2015-04-28

    is the lack of positive transition among the weakest states. Our findings are derived from a minimalist construct of a refined time series dataset...states based on a „ minimalist ‟ construct of the Country Indicators for Foreign Policy (CIFP) fragile states project and its core structural...begin with the rationale for developing a minimalist construct of a state typology model (STM), similar to the approach taken by Gravingholt, Ziaja

  1. Relationship of Topology, Multiscale Phase Synchronization, and State Transitions in Human Brain Networks

    PubMed Central

    Kim, Minkyung; Kim, Seunghwan; Mashour, George A.; Lee, UnCheol

    2017-01-01

    How the brain reconstitutes consciousness and cognition after a major perturbation like general anesthesia is an important question with significant neuroscientific and clinical implications. Recent empirical studies in animals and humans suggest that the recovery of consciousness after anesthesia is not random but ordered. Emergence patterns have been classified as progressive and abrupt transitions from anesthesia to consciousness, with associated differences in duration and electroencephalogram (EEG) properties. We hypothesized that the progressive and abrupt emergence patterns from the unconscious state are associated with, respectively, continuous and discontinuous synchronization transitions in functional brain networks. The discontinuous transition is explainable with the concept of explosive synchronization, which has been studied almost exclusively in network science. We used the Kuramato model, a simple oscillatory network model, to simulate progressive and abrupt transitions in anatomical human brain networks acquired from diffusion tensor imaging (DTI) of 82 brain regions. To facilitate explosive synchronization, distinct frequencies for hub nodes with a large frequency disassortativity (i.e., higher frequency nodes linking with lower frequency nodes, or vice versa) were applied to the brain network. In this simulation study, we demonstrated that both progressive and abrupt transitions follow distinct synchronization processes at the individual node, cluster, and global network levels. The characteristic synchronization patterns of brain regions that are “progressive and earlier” or “abrupt but delayed” account for previously reported behavioral responses of gradual and abrupt emergence from the unconscious state. The characteristic network synchronization processes observed at different scales provide new insights into how regional brain functions are reconstituted during progressive and abrupt emergence from the unconscious state. This

  2. Relationship of Topology, Multiscale Phase Synchronization, and State Transitions in Human Brain Networks.

    PubMed

    Kim, Minkyung; Kim, Seunghwan; Mashour, George A; Lee, UnCheol

    2017-01-01

    How the brain reconstitutes consciousness and cognition after a major perturbation like general anesthesia is an important question with significant neuroscientific and clinical implications. Recent empirical studies in animals and humans suggest that the recovery of consciousness after anesthesia is not random but ordered. Emergence patterns have been classified as progressive and abrupt transitions from anesthesia to consciousness, with associated differences in duration and electroencephalogram (EEG) properties. We hypothesized that the progressive and abrupt emergence patterns from the unconscious state are associated with, respectively, continuous and discontinuous synchronization transitions in functional brain networks. The discontinuous transition is explainable with the concept of explosive synchronization, which has been studied almost exclusively in network science. We used the Kuramato model, a simple oscillatory network model, to simulate progressive and abrupt transitions in anatomical human brain networks acquired from diffusion tensor imaging (DTI) of 82 brain regions. To facilitate explosive synchronization, distinct frequencies for hub nodes with a large frequency disassortativity (i.e., higher frequency nodes linking with lower frequency nodes, or vice versa) were applied to the brain network. In this simulation study, we demonstrated that both progressive and abrupt transitions follow distinct synchronization processes at the individual node, cluster, and global network levels. The characteristic synchronization patterns of brain regions that are "progressive and earlier" or "abrupt but delayed" account for previously reported behavioral responses of gradual and abrupt emergence from the unconscious state. The characteristic network synchronization processes observed at different scales provide new insights into how regional brain functions are reconstituted during progressive and abrupt emergence from the unconscious state. This theoretical

  3. The Galactic Black Hole Transient H1743-322 During Outburst Decay Connections Between Timing Noise, State Transitions, And Radio Emission

    NASA Technical Reports Server (NTRS)

    Kalemci, E.; Tomsick, J. A.; Corbel; Kaaret, P.; Rothschild, R. E.; Pottschmidt, K.

    2006-01-01

    Multiwavelength observations of Galactic black hole transients during outburst decay are instrumental for our understanding of the accretion geometry and the formation of outflows around black hole systems. H1743-322, a black hole transient observed intensely in X-rays and also covered in the radio band during its 2003 decay, provides clues about the changes in accretion geometry during state transitions and also the general properties of X-ray emission during the intermediate and low-hard states. In this work, we report on the evolution of spectral and temporal properties in X-rays and the flux in the radio band, with the goal of understanding the nature of state transitions observed in this source. We concentrate on the transition from the thermal dominant state to the intermediate state that occurs on a timescale of 1 day. We show that the state transition is associated with a sudden increase in power-law flux. We determine that the ratio of the power-law flux to the overall flux in the 3-25 keV band must exceed 0.6 for us to observe strong timing noise. Even after the state transition, once this ratio was below 0.6, the system transited back to the thermal dominant state for 1 day. We show that the emission from the compact radio core does not turn on during the transition from the thermal dominant state to the intermediate state but does turn on when the source reaches the low-hard state, as seen in 4U 1543-47 and GX 339-4. We find that the photon index correlates strongly with the QPO frequency and anticorrelates with the rms amplitude of variability. We also show that the variability is more likely to be associated with the power-law emission than the disk emission.

  4. Near-optimal energy transitions for energy-state trajectories of hypersonic aircraft

    NASA Technical Reports Server (NTRS)

    Ardema, M. D.; Bowles, J. V.; Terjesen, E. J.; Whittaker, T.

    1992-01-01

    A problem of the instantaneous energy transition that occurs in energy-state approximation is considered. The transitions are modeled as a sequence of two load-factor bounded paths (either climb-dive or dive-climb). The boundary-layer equations associated with the energy-state dynamic model are analyzed to determine the precise location of the transition.

  5. Youth and administrator perspectives on transition in Kentucky's state agency schools.

    PubMed

    Marshall, Amy; Powell, Norman; Pierce, Doris; Nolan, Ronnie; Fehringer, Elaine

    2012-01-01

    Students, a large percentage with disabilities, are at high risk for poor post-secondary outcomes in state agency education programs. This mixed-methods study describes the understandings of student transitions in state agency education programs from the perspectives of youth and administrators. Results indicated that: transition is more narrowly defined within alternative education programs; key strengths of transition practice are present in nontraditional schools; and the coordination barriers within this fluid inter-agency transition system are most apparent in students' frequent inter-setting transitions between nontraditional and home schools.

  6. Constrained proper sampling of conformations of transition state ensemble of protein folding

    PubMed Central

    Lin, Ming; Zhang, Jian; Lu, Hsiao-Mei; Chen, Rong; Liang, Jie

    2011-01-01

    Characterizing the conformations of protein in the transition state ensemble (TSE) is important for studying protein folding. A promising approach pioneered by Vendruscolo [Nature (London) 409, 641 (2001)] to study TSE is to generate conformations that satisfy all constraints imposed by the experimentally measured ϕ values that provide information about the native likeness of the transition states. Faísca [J. Chem. Phys. 129, 095108 (2008)] generated conformations of TSE based on the criterion that, starting from a TS conformation, the probabilities of folding and unfolding are about equal through Markov Chain Monte Carlo (MCMC) simulations. In this study, we use the technique of constrained sequential Monte Carlo method [Lin , J. Chem. Phys. 129, 094101 (2008); Zhang Proteins 66, 61 (2007)] to generate TSE conformations of acylphosphatase of 98 residues that satisfy the ϕ-value constraints, as well as the criterion that each conformation has a folding probability of 0.5 by Monte Carlo simulations. We adopt a two stage process and first generate 5000 contact maps satisfying the ϕ-value constraints. Each contact map is then used to generate 1000 properly weighted conformations. After clustering similar conformations, we obtain a set of properly weighted samples of 4185 candidate clusters. Representative conformation of each of these cluster is then selected and 50 runs of Markov chain Monte Carlo (MCMC) simulation are carried using a regrowth move set. We then select a subset of 1501 conformations that have equal probabilities to fold and to unfold as the set of TSE. These 1501 samples characterize well the distribution of transition state ensemble conformations of acylphosphatase. Compared with previous studies, our approach can access much wider conformational space and can objectively generate conformations that satisfy the ϕ-value constraints and the criterion of 0.5 folding probability without bias. In contrast to previous studies, our results show that

  7. Amoeba-like self-oscillating polymeric fluids with autonomous sol-gel transition

    NASA Astrophysics Data System (ADS)

    Onoda, Michika; Ueki, Takeshi; Tamate, Ryota; Shibayama, Mitsuhiro; Yoshida, Ryo

    2017-07-01

    In the field of polymer science, many kinds of polymeric material systems that show a sol-gel transition have been created. However, most systems are unidirectional stimuli-responsive systems that require physical signals such as a change in temperature. Here, we report on the design of a block copolymer solution that undergoes autonomous and periodic sol-gel transition under constant conditions without any on-off switching through external stimuli. The amplitude of this self-oscillation of the viscosity is about 2,000 mPa s. We also demonstrate an intermittent forward motion of a droplet of the polymer solution synchronized with the autonomous sol-gel transition. This polymer solution bears the potential to become the base for a type of slime-like soft robot that can transform its shape kaleidoscopically and move autonomously, which is associated with the living amoeba that moves forward by a repeated sol-gel transition.

  8. The Variable Transition State in Polar Additions to Pi Bonds

    ERIC Educational Resources Information Center

    Weiss, Hilton M.

    2010-01-01

    A vast majority of polar additions of Bronsted acids to alkynes involve a termolecular transition state. With strong acids, considerable positive charge is developed on carbon and Markovnikov addition predominates. In less acidic solutions, however, the reaction is much slower and the transition state more closely resembles the olefinic product.…

  9. Enriching mission planning approach with state transition graph heuristics for deep space exploration

    NASA Astrophysics Data System (ADS)

    Jin, Hao; Xu, Rui; Xu, Wenming; Cui, Pingyuan; Zhu, Shengying

    2017-10-01

    As to support the mission of Mars exploration in China, automated mission planning is required to enhance security and robustness of deep space probe. Deep space mission planning requires modeling of complex operations constraints and focus on the temporal state transitions of involved subsystems. Also, state transitions are ubiquitous in physical systems, but have been elusive for knowledge description. We introduce a modeling approach to cope with these difficulties that takes state transitions into consideration. The key technique we build on is the notion of extended states and state transition graphs. Furthermore, a heuristics that based on state transition graphs is proposed to avoid redundant work. Finally, we run comprehensive experiments on selected domains and our techniques present an excellent performance.

  10. The transition from the open minimum to the ring minimum on the ground state and on the lowest excited state of like symmetry in ozone: A configuration interaction study

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Theis, Daniel; Windus, Theresa L.; Ruedenberg, Klaus

    The metastable ring structure of the ozone 1{sup 1}A{sub 1} ground state, which theoretical calculations have shown to exist, has so far eluded experimental detection. An accurate prediction for the energy difference between this isomer and the lower open structure is therefore of interest, as is a prediction for the isomerization barrier between them, which results from interactions between the lowest two {sup 1}A{sub 1} states. In the present work, valence correlated energies of the 1{sup 1}A{sub 1} state and the 2{sup 1}A{sub 1} state were calculated at the 1{sup 1}A{sub 1} open minimum, the 1{sup 1}A{sub 1} ring minimum,more » the transition state between these two minima, the minimum of the 2{sup 1}A{sub 1} state, and the conical intersection between the two states. The geometries were determined at the full-valence multi-configuration self-consistent-field level. Configuration interaction (CI) expansions up to quadruple excitations were calculated with triple-zeta atomic basis sets. The CI expansions based on eight different reference configuration spaces were explored. To obtain some of the quadruple excitation energies, the method of Correlation Energy Extrapolation by Intrinsic Scaling was generalized to the simultaneous extrapolation for two states. This extrapolation method was shown to be very accurate. On the other hand, none of the CI expansions were found to have converged to millihartree (mh) accuracy at the quadruple excitation level. The data suggest that convergence to mh accuracy is probably attained at the sextuple excitation level. On the 1{sup 1}A{sub 1} state, the present calculations yield the estimates of (ring minimum—open minimum) ∼45–50 mh and (transition state—open minimum) ∼85–90 mh. For the (2{sup 1}A{sub 1}–{sup 1}A{sub 1}) excitation energy, the estimate of ∼130–170 mh is found at the open minimum and 270–310 mh at the ring minimum. At the transition state, the difference (2{sup 1}A{sub 1}–{sup 1}A{sub 1

  11. The transition to the metallic state in low density hydrogen

    DOE PAGES

    McMinis, Jeremy; Morales, Miguel A.; Ceperley, David M.; ...

    2015-11-18

    Solid atomic hydrogen is one of the simplest systems to undergo a metal-insulator transition. Near the transition, the electronic degrees of freedom become strongly correlated and their description provides a difficult challenge for theoretical methods. As a result, the order and density of the phase transition are still subject to debate. In this work we use diffusion quantum Monte Carlo to benchmark the transition between the paramagnetic and anti-ferromagnetic phases of ground state body centered cubic atomic hydrogen. We locate the density of the transition by computing the equation of state for these two phases and identify the phase transitionmore » order by computing the band gap near the phase transition. These benchmark results show that the phase transition is continuous and occurs at a Wigner-Seitz radius of r s = 2.27(3)a 0. As a result, we compare our results to previously reported density functional theory, Hedin s GW approximation, and dynamical mean field theory results.« less

  12. The Aromaticity of Pericyclic Reaction Transition States

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2007-01-01

    An approach is presented that starts from two fundamental concepts in organic chemistry, chirality and aromaticity, and combines them into a simple rule for stating selection rules for pericyclic reactions in terms of achiral Huckel-aromatic and chiral Mobius-aromatic transition states. This is illustrated using an example that leads to apparent…

  13. Getting College-Ready during State Transition toward the Common Core State Standards

    ERIC Educational Resources Information Center

    Xu, Zeyu; Cepa, Kennan

    2018-01-01

    Background: As of 2016, 42 states and the District of Columbia have adopted the Common Core State Standards (CCSS). Tens of millions of students across the country completed high school before their schools were able to fully implement the CCSS. As with previous standards-based reforms, the transition to the CCSS-aligned state education standards…

  14. Predicting landscape vegetation dynamics using state-and-transition simulation models

    Treesearch

    Colin J. Daniel; Leonardo Frid

    2012-01-01

    This paper outlines how state-and-transition simulation models (STSMs) can be used to project changes in vegetation over time across a landscape. STSMs are stochastic, empirical simulation models that use an adapted Markov chain approach to predict how vegetation will transition between states over time, typically in response to interactions between succession,...

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Qiao, Qin, E-mail: qqiao@ust.hk; Zhang, Hou-Dao; Huang, Xuhui, E-mail: xuhuihuang@ust.hk

    2016-04-21

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

  17. MRCI study on transition dipole moments and transition probabilities of 18 low-lying states of CP+ cation

    NASA Astrophysics Data System (ADS)

    Zhou, Dan; Wang, Kedong; Li, Xue

    2018-07-01

    This study calculates the potential energy curves of 18 Λ-S and 50 Ω states, which arise from the C(3Pg) + P+(3Pg) dissociation channel of the CP+ cation. The calculations are made using the CASSCF method, followed by the icMRCI approach with the Davidson correction. Core-valence correlation and scalar relativistic corrections, as well as extrapolation to the complete basis set limit are included. The transition dipole moments are computed for 25 pairs of Λ-S states. The spin-orbit coupling effect on the spectroscopic and vibrational properties is evaluated. The Franck-Condon factors and Einstein coefficients of emissions are calculated. Radiative lifetimes are obtained for several vibrational levels of some states. The transitions are evaluated and spectroscopic measurement schemes for observing these Λ-S states are proposed. The potential energy curves, spectroscopic constants, vibrational levels, transition dipole moments, and transition probabilities reported in this paper can be considered to be very accurate and reliable. Because no experimental observations are currently available, the results obtained here can be used as guidelines for the detection of these states in appropriate spectroscopy experiments, in particular for observations in stellar atmospheres and in interstellar space.

  18. Transition state-finding strategies for use with the growing string method.

    PubMed

    Goodrow, Anthony; Bell, Alexis T; Head-Gordon, Martin

    2009-06-28

    Efficient identification of transition states is important for understanding reaction mechanisms. Most transition state search algorithms require long computational times and a good estimate of the transition state structure in order to converge, particularly for complex reaction systems. The growing string method (GSM) [B. Peters et al., J. Chem. Phys. 120, 7877 (2004)] does not require an initial guess of the transition state; however, the calculation is still computationally intensive due to repeated calls to the quantum mechanics code. Recent modifications to the GSM [A. Goodrow et al., J. Chem. Phys. 129, 174109 (2008)] have reduced the total computational time for converging to a transition state by a factor of 2 to 3. In this work, three transition state-finding strategies have been developed to complement the speedup of the modified-GSM: (1) a hybrid strategy, (2) an energy-weighted strategy, and (3) a substring strategy. The hybrid strategy initiates the string calculation at a low level of theory (HF/STO-3G), which is then refined at a higher level of theory (B3LYP/6-31G(*)). The energy-weighted strategy spaces points along the reaction pathway based on the energy at those points, leading to a higher density of points where the energy is highest and finer resolution of the transition state. The substring strategy is similar to the hybrid strategy, but only a portion of the low-level string is refined using a higher level of theory. These three strategies have been used with the modified-GSM and are compared in three reactions: alanine dipeptide isomerization, H-abstraction in methanol oxidation on VO(x)/SiO(2) catalysts, and C-H bond activation in the oxidative carbonylation of toluene to p-toluic acid on Rh(CO)(2)(TFA)(3) catalysts. In each of these examples, the substring strategy was proved most effective by obtaining a better estimate of the transition state structure and reducing the total computational time by a factor of 2 to 3 compared to the

  19. Automated Transition State Search and Its Application to Diverse Types of Organic Reactions.

    PubMed

    Jacobson, Leif D; Bochevarov, Art D; Watson, Mark A; Hughes, Thomas F; Rinaldo, David; Ehrlich, Stephan; Steinbrecher, Thomas B; Vaitheeswaran, S; Philipp, Dean M; Halls, Mathew D; Friesner, Richard A

    2017-11-14

    Transition state search is at the center of multiple types of computational chemical predictions related to mechanistic investigations, reactivity and regioselectivity predictions, and catalyst design. The process of finding transition states in practice is, however, a laborious multistep operation that requires significant user involvement. Here, we report a highly automated workflow designed to locate transition states for a given elementary reaction with minimal setup overhead. The only essential inputs required from the user are the structures of the separated reactants and products. The seamless workflow combining computational technologies from the fields of cheminformatics, molecular mechanics, and quantum chemistry automatically finds the most probable correspondence between the atoms in the reactants and the products, generates a transition state guess, launches a transition state search through a combined approach involving the relaxing string method and the quadratic synchronous transit, and finally validates the transition state via the analysis of the reactive chemical bonds and imaginary vibrational frequencies as well as by the intrinsic reaction coordinate method. Our approach does not target any specific reaction type, nor does it depend on training data; instead, it is meant to be of general applicability for a wide variety of reaction types. The workflow is highly flexible, permitting modifications such as a choice of accuracy, level of theory, basis set, or solvation treatment. Successfully located transition states can be used for setting up transition state guesses in related reactions, saving computational time and increasing the probability of success. The utility and performance of the method are demonstrated in applications to transition state searches in reactions typical for organic chemistry, medicinal chemistry, and homogeneous catalysis research. In particular, applications of our code to Michael additions, hydrogen abstractions

  20. Amoeba-like self-oscillating polymeric fluids with autonomous sol-gel transition

    PubMed Central

    Onoda, Michika; Ueki, Takeshi; Tamate, Ryota; Shibayama, Mitsuhiro; Yoshida, Ryo

    2017-01-01

    In the field of polymer science, many kinds of polymeric material systems that show a sol-gel transition have been created. However, most systems are unidirectional stimuli-responsive systems that require physical signals such as a change in temperature. Here, we report on the design of a block copolymer solution that undergoes autonomous and periodic sol-gel transition under constant conditions without any on–off switching through external stimuli. The amplitude of this self-oscillation of the viscosity is about 2,000 mPa s. We also demonstrate an intermittent forward motion of a droplet of the polymer solution synchronized with the autonomous sol-gel transition. This polymer solution bears the potential to become the base for a type of slime-like soft robot that can transform its shape kaleidoscopically and move autonomously, which is associated with the living amoeba that moves forward by a repeated sol-gel transition. PMID:28703123

  1. Specificity in Transition State Binding: The Pauling Model Revisited

    PubMed Central

    Amyes, Tina L.; Richard, John P.

    2013-01-01

    Linus Pauling proposed that the large rate accelerations for enzymes are due to the high specificity of the protein catalyst for binding the reaction transition state. The observation that stable analogs of the transition states for enzymatic reactions often act as tight-binding binding inhibitors provided early support for this simple and elegant proposal. We review experimental results which support the proposal that Pauling’s model provides a satisfactory explanation for the rate accelerations for many heterolytic enzymatic reactions through high energy reaction intermediates, such as proton transfer and decarboxylation. Specificity in transition state binding is obtained when the total intrinsic binding energy of the substrate is significantly larger than the binding energy observed at the Michaelis complex. The results of recent studies to characterize the specificity in binding of the enolate oxygen at the transition state for the 1,3-isomerization reaction catalyzed by ketosteroid isomerase are reviewed. Interactions between pig heart succinyl-CoA:3-oxoacid coenzyme A transferase (SCOT) and the nonreacting portions of CoA are responsible for a rate increase of 3 × 1012-fold, which is close to the estimated total 5 × 1013-fold enzymatic rate acceleration. Studies that partition the interactions between SCOT and CoA into their contributing parts are reviewed. Interactions of the protein with the substrate phosphodianion group provide a ca. 12 kcal/mol stabilization of the transition state for the reactions catalyzed by triosephosphate isomerase, orotidine 5′-monophosphate decarboxylase and α-glycerol phosphate dehydrogenase. The interactions of these enzymes with the substrate piece phosphite dianion provide a 6 – 8 kcal/mol stabilization of the transition state for reaction of the appropriate truncated substrate. Enzyme activation by phosphite dianion reflects the higher dianion affinity for binding to the enzyme-transition state complex compared

  2. Catching Up on State Transitions in Cygnus X-1

    NASA Technical Reports Server (NTRS)

    Boeck, Moritz; Hanke, Manfred; Wilms, Joern; Pirner, Stefan; Grinberg, Victoria; Markoff, Sera; Pottschmidt, Katja; Nowak, Michael A.; Pooley, Guy

    2008-01-01

    In 2005 February we observed Cygnus X-1 over a period of 10 days quasi-continuously with the Rossi X-ray Timing Explorer and the Ryle telescope. We present the results of the spectral and timing analysis on a timescale of 90 min and show that the behavior of Cyg X-1 is similar to that found during our years long monitoring campaign. As a highlight we present evidence for a full transition from the hard to the soft state that happened during less than three hours. The observation provided a more complete picture of a state transition than before, especially concerning the evolution of the time lags, due to unique transition coverage and analysis with high time resolution.

  3. State transitions of actin cortices in vitro and in vivo

    NASA Astrophysics Data System (ADS)

    Tan, Tzer Han; Keren, Kinneret; Mackintosh, Fred; Schmidt, Christoph; Fakhri, Nikta

    Most animal cells are enveloped by a thin layer of actin cortex which governs the cell mechanics. A functional cortex must be rigid to provide mechanical support while being flexible to allow for rapid restructuring events such as cell division. To satisfy these requirements, the actin cortex is highly dynamic with fast actin turnover and myosin-driven contractility. The regulatory mechanism responsible for the transition between a mechanically stable state and a restructuring state is not well understood. Here, we develop a technique to map the dynamics of reconstituted actin cortices in emulsion droplets using IR fluorescent single-walled carbon nanotubes (SWNTs). By increasing crosslinker concentration, we find that a homogeneous cortex transitions to an intermediate state with broken rotational symmetry and a globally contractile state which further breaks translational symmetry. We apply this new dynamic mapping technique to cortices of live starfish oocytes in various developmental stages. To identify the regulatory mechanism for steady state transitions, we subject the oocytes to actin and myosin disrupting drugs.

  4. Likely transiting exocomets detected by Kepler

    NASA Astrophysics Data System (ADS)

    Rappaport, S.; Vanderburg, A.; Jacobs, T.; LaCourse, D.; Jenkins, J.; Kraus, A.; Rizzuto, A.; Latham, D. W.; Bieryla, A.; Lazarevic, M.; Schmitt, A.

    2018-02-01

    We present the first good evidence for exocomet transits of a host star in continuum light in data from the Kepler mission. The Kepler star in question, KIC 3542116, is of spectral type F2V and is quite bright at Kp = 10. The transits have a distinct asymmetric shape with a steeper ingress and slower egress that can be ascribed to objects with a trailing dust tail passing over the stellar disc. There are three deeper transits with depths of ≃ 0.1 per cent that last for about a day, and three that are several times more shallow and of shorter duration. The transits were found via an exhaustive visual search of the entire Kepler photometric data set, which we describe in some detail. We review the methods we use to validate the Kepler data showing the comet transits, and rule out instrumental artefacts as sources of the signals. We fit the transits with a simple dust-tail model, and find that a transverse comet speed of ˜35-50 km s-1 and a minimum amount of dust present in the tail of ˜1016 g are required to explain the larger transits. For a dust replenishment time of ˜10 d, and a comet lifetime of only ˜300 d, this implies a total cometary mass of ≳3 × 1017 g, or about the mass of Halley's comet. We also discuss the number of comets and orbital geometry that would be necessary to explain the six transits detected over the 4 yr of Kepler prime-field observations. Finally, we also report the discovery of a single comet-shaped transit in KIC 11084727 with very similar transit and host-star properties.

  5. Probing excitons in transition metal dichalcogenides by Drude-like exciton intraband absorption.

    PubMed

    Zhao, Siqi; He, Dawei; He, Jiaqi; Zhang, Xinwu; Yi, Lixin; Wang, Yongsheng; Zhao, Hui

    2018-05-24

    Understanding excitonic dynamics in two-dimensional semiconducting transition metal dichalcogenides is important for developing their optoelectronic applications. Recently, transient absorption techniques based on resonant excitonic absorption have been used to study various aspects of excitonic dynamics in these materials. The transient absorption in such measurements originates from phase-space state filling, bandgap renormalization, or screening effects. Here we report a new method to probe excitonic dynamics based on exciton intraband absorption. In this Drude-like process, probe photons are absorbed by excitons in their intraband excitation to higher energy states, causing a transient absorption signal. Although the magnitude of the transient absorption is lower than that of the resonant techniques, the new method is less restrictive on the selection of probe wavelength, has a larger linear range, and can provide complementary information on photocarrier dynamics. Using the WS2 monolayer and bulk samples as examples, we show that the new method can probe exciton-exciton annihilation at high densities and reveal exciton formation processes. We also found that the exciton intraband absorption cross section of the WS2 monolayer is on the order of 10-18 cm2.

  6. Towards Automatic Classification of Exoplanet-Transit-Like Signals: A Case Study on Kepler Mission Data

    NASA Astrophysics Data System (ADS)

    Valizadegan, Hamed; Martin, Rodney; McCauliff, Sean D.; Jenkins, Jon Michael; Catanzarite, Joseph; Oza, Nikunj C.

    2015-08-01

    Building new catalogues of planetary candidates, astrophysical false alarms, and non-transiting phenomena is a challenging task that currently requires a reviewing team of astrophysicists and astronomers. These scientists need to examine more than 100 diagnostic metrics and associated graphics for each candidate exoplanet-transit-like signal to classify it into one of the three classes. Considering that the NASA Explorer Program's TESS mission and ESA's PLATO mission survey even a larger area of space, the classification of their transit-like signals is more time-consuming for human agents and a bottleneck to successfully construct the new catalogues in a timely manner. This encourages building automatic classification tools that can quickly and reliably classify the new signal data from these missions. The standard tool for building automatic classification systems is the supervised machine learning that requires a large set of highly accurate labeled examples in order to build an effective classifier. This requirement cannot be easily met for classifying transit-like signals because not only are existing labeled signals very limited, but also the current labels may not be reliable (because the labeling process is a subjective task). Our experiments with using different supervised classifiers to categorize transit-like signals verifies that the labeled signals are not rich enough to provide the classifier with enough power to generalize well beyond the observed cases (e.g. to unseen or test signals). That motivated us to utilize a new category of learning techniques, so-called semi-supervised learning, that combines the label information from the costly labeled signals, and distribution information from the cheaply available unlabeled signals in order to construct more effective classifiers. Our study on the Kepler Mission data shows that semi-supervised learning can significantly improve the result of multiple base classifiers (e.g. Support Vector Machines, Ada

  7. Transition state theory for enzyme kinetics

    PubMed Central

    Truhlar, Donald G.

    2015-01-01

    This article is an essay that discusses the concepts underlying the application of modern transition state theory to reactions in enzymes. Issues covered include the potential of mean force, the quantization of vibrations, the free energy of activation, and transmission coefficients to account for nonequilibrium effect, recrossing, and tunneling. PMID:26008760

  8. Exotic and excited-state radiative transitions in charmonium from lattice QCD

    DOE PAGES

    Dudek, Jozef J.; Edwards, Robert G.; Thomas, Christopher E.

    2009-05-01

    We compute, for the first time using lattice QCD methods, radiative transition rates involving excited charmonium states, states of high spin and exotics. Utilizing a large basis of interpolating fields we are able to project out various excited state contributions to three-point correlators computed on quenched anisotropic lattices. In the first lattice QCD calculation of the exoticmore » $$1^{-+}$$ $$\\eta_{c1}$$ radiative decay, we find a large partial width $$\\Gamma(\\eta_{c1} \\to J/\\psi \\gamma) \\sim 100 \\,\\mathrm{keV}$$. We find clear signals for electric dipole and magnetic quadrupole transition form factors in $$\\chi_{c2} \\to J/\\psi \\gamma$$, calculated for the first time in this framework, and study transitions involving excited $$\\psi$$ and $$\\chi_{c1,2}$$ states. We calculate hindered magnetic dipole transition widths without the sensitivity to assumptions made in model studies and find statistically significant signals, including a non-exotic vector hybrid candidate $Y_{\\mathrm{hyb?}} \\to \\et« less

  9. Folding of a LysM Domain: Entropy-Enthalpy Compensation in the Transition State of an Ideal Two-state Folder

    PubMed Central

    Nickson, Adrian A.; Stoll, Kate E.; Clarke, Jane

    2008-01-01

    Protein-engineering methods (Φ-values) were used to investigate the folding transition state of a lysin motif (LysM) domain from Escherichia coli membrane-bound lytic murein transglycosylase D. This domain consists of just 48 structured residues in a symmetrical βααβ arrangement and is the smallest αβ protein yet investigated using these methods. An extensive mutational analysis revealed a highly robust folding pathway with no detectable transition state plasticity, indicating that LysM is an example of an ideal two-state folder. The pattern of Φ-values denotes a highly polarised transition state, with significant formation of the helices but no structure within the β-sheet. Remarkably, this transition state remains polarised after circularisation of the domain, and exhibits an identical Φ-value pattern; however, the interactions within the transition state are uniformly weaker in the circular variant. This observation is supported by results from an Eyring analysis of the folding rates of the two proteins. We propose that the folding pathway of LysM is dominated by enthalpic rather than entropic considerations, and suggest that the lower entropy cost of formation of the circular transition state is balanced, to some extent, by the lower enthalpy of contacts within this structure. PMID:18538343

  10. Can dead zones create structures like a transition disk?

    NASA Astrophysics Data System (ADS)

    Pinilla, Paola; Flock, Mario; Ovelar, Maria de Juan; Birnstiel, Til

    2016-12-01

    Context. Regions of low ionisation where the activity of the magneto-rotational instability is suppressed, the so-called dead zones, have been suggested to explain gaps and asymmetries of transition disks. Dead zones are therefore a potential cause for the observational signatures of transition disks without requiring the presence of embedded planets. Aims: We investigate the gas and dust evolution simultaneously assuming simplified prescriptions for a dead zone and a magnetohydrodynamic (MHD) wind acting on the disk. We explore whether the resulting gas and dust distribution can create signatures similar to those observed in transition disks. Methods: We imposed a dead zone and/or an MHD wind in the radial evolution of gas and dust in protoplanetary disks. For the dust evolution, we included the transport, growth, and fragmentation of dust particles. To compare with observations, we produced synthetic images in scattered optical light and in thermal emission at mm wavelengths. Results: In all models with a dead zone, a bump in the gas surface density is produced that is able to efficiently trap large particles (≳ 1 mm) at the outer edge of the dead zone. The gas bump reaches an amplitude of a factor of 5, which can be enhanced by the presence of an MHD wind that removes mass from the inner disk. While our 1D simulations suggest that such a structure can be present only for 1 Myr, the structure may be maintained for a longer time when more realistic 2D/3D simulations are performed. In the synthetic images, gap-like low-emission regions are seen at scattered light and in thermal emission at mm wavelengths, as previously predicted in the case of planet-disk interaction. Conclusions: Main signatures of transition disks can be reproduced by assuming a dead zone in the disk, such as gap-like structure in scattered light and millimetre continuum emission, and a lower gas surface density within the dead zone. Previous studies showed that the Rossby wave instability can

  11. Probing the transition state for nucleic acid hybridization using phi-value analysis.

    PubMed

    Kim, Jandi; Shin, Jong-Shik

    2010-04-27

    Genetic regulation by noncoding RNA elements such as microRNA and small interfering RNA (siRNA) involves hybridization of a short single-stranded RNA with a complementary segment in a target mRNA. The physical basis of the hybridization process between the structured nucleic acids is not well understood primarily because of the lack of information about the transition-state structure. Here we use transition-state theory, inspired by phi-value analysis in protein folding studies, to provide quantitative analysis of the relationship between changes in the secondary structure stability and the activation free energy. Time course monitoring of the hybridization reaction was performed under pseudo-steady-state conditions using a single fluorophore. The phi-value analysis indicates that the native secondary structure remains intact in the transition state. The nativelike transition state was confirmed via examination of the salt dependence of the hybridization kinetics, indicating that the number of sodium ions associated with the transition state was not substantially affected by changes in the native secondary structure. These results propose that hybridization between structured nucleic acids undergoes a transition state leading to formation of a nucleation complex and then is followed by sequential displacement of preexisting base pairings involving successive small energy barriers. The proposed mechanism might provide new insight into physical processes during small RNA-mediated gene silencing, which is essential to selection of a target mRNA segment for siRNA design.

  12. Specificity in transition state binding: the Pauling model revisited.

    PubMed

    Amyes, Tina L; Richard, John P

    2013-03-26

    Linus Pauling proposed that the large rate accelerations for enzymes are caused by the high specificity of the protein catalyst for binding the reaction transition state. The observation that stable analogues of the transition states for enzymatic reactions often act as tight-binding inhibitors provided early support for this simple and elegant proposal. We review experimental results that support the proposal that Pauling's model provides a satisfactory explanation for the rate accelerations for many heterolytic enzymatic reactions through high-energy reaction intermediates, such as proton transfer and decarboxylation. Specificity in transition state binding is obtained when the total intrinsic binding energy of the substrate is significantly larger than the binding energy observed at the Michaelis complex. The results of recent studies that aimed to characterize the specificity in binding of the enolate oxygen at the transition state for the 1,3-isomerization reaction catalyzed by ketosteroid isomerase are reviewed. Interactions between pig heart succinyl-coenzyme A:3-oxoacid coenzyme A transferase (SCOT) and the nonreacting portions of coenzyme A (CoA) are responsible for a rate increase of 3 × 10(12)-fold, which is close to the estimated total 5 × 10(13)-fold enzymatic rate acceleration. Studies that partition the interactions between SCOT and CoA into their contributing parts are reviewed. Interactions of the protein with the substrate phosphodianion group provide an ~12 kcal/mol stabilization of the transition state for the reactions catalyzed by triosephosphate isomerase, orotidine 5'-monophosphate decarboxylase, and α-glycerol phosphate dehydrogenase. The interactions of these enzymes with the substrate piece phosphite dianion provide a 6-8 kcal/mol stabilization of the transition state for reaction of the appropriate truncated substrate. Enzyme activation by phosphite dianion reflects the higher dianion affinity for binding to the enzyme-transition

  13. Multi-state succession in wetlands: a novel use of state and transition models

    USGS Publications Warehouse

    Zweig, Christa L.; Kitchens, Wiley M.

    2009-01-01

    The complexity of ecosystems and mechanisms of succession are often simplified by linear and mathematical models used to understand and predict system behavior. Such models often do not incorporate multivariate, nonlinear feedbacks in pattern and process that include multiple scales of organization inherent within real-world systems. Wetlands are ecosystems with unique, nonlinear patterns of succession due to the regular, but often inconstant, presence of water on the landscape. We develop a general, nonspatial state and transition (S and T) succession conceptual model for wetlands and apply the general framework by creating annotated succession/management models and hypotheses for use in impact analysis on a portion of an imperiled wetland. The S and T models for our study area, Water Conservation Area 3A South (WCA3), Florida, USA, included hydrologic and peat depth values from multivariate analyses and classification and regression trees. We used the freeware Vegetation Dynamics Development Tool as an exploratory application to evaluate our S and T models with different management actions (equal chance [a control condition], deeper conditions, dry conditions, and increased hydrologic range) for three communities: slough, sawgrass (Cladium jamaicense), and wet prairie. Deeper conditions and increased hydrologic range behaved similarly, with the transition of community states to deeper states, particularly for sawgrass and slough. Hydrology is the primary mechanism for multi-state transitions within our study period, and we show both an immediate and lagged effect on vegetation, depending on community state. We consider these S and T succession models as a fraction of the framework for the Everglades. They are hypotheses for use in adaptive management, represent the community response to hydrology, and illustrate which aspects of hydrologic variability are important to community structure. We intend for these models to act as a foundation for further restoration

  14. Edge states in the climate system: exploring global instabilities and critical transitions

    NASA Astrophysics Data System (ADS)

    Lucarini, Valerio; Bódai, Tamás

    2017-07-01

    Multistability is a ubiquitous feature in systems of geophysical relevance and provides key challenges for our ability to predict a system’s response to perturbations. Near critical transitions small causes can lead to large effects and—for all practical purposes—irreversible changes in the properties of the system. As is well known, the Earth climate is multistable: present astronomical and astrophysical conditions support two stable regimes, the warm climate we live in, and a snowball climate characterized by global glaciation. We first provide an overview of methods and ideas relevant for studying the climate response to forcings and focus on the properties of critical transitions in the context of both stochastic and deterministic dynamics, and assess strengths and weaknesses of simplified approaches to the problem. Following an idea developed by Eckhardt and collaborators for the investigation of multistable turbulent fluid dynamical systems, we study the global instability giving rise to the snowball/warm multistability in the climate system by identifying the climatic edge state, a saddle embedded in the boundary between the two basins of attraction of the stable climates. The edge state attracts initial conditions belonging to such a boundary and, while being defined by the deterministic dynamics, is the gate facilitating noise-induced transitions between competing attractors. We use a simplified yet Earth-like intermediate complexity climate model constructed by coupling a primitive equations model of the atmosphere with a simple diffusive ocean. We refer to the climatic edge states as Melancholia states and provide an extensive analysis of their features. We study their dynamics, their symmetry properties, and we follow a complex set of bifurcations. We find situations where the Melancholia state has chaotic dynamics. In these cases, we have that the basin boundary between the two basins of attraction is a strange geometric set with a nearly zero

  15. SUPPRESSION OF THE EPITHELIAL-MESENCHYMAL TRANSITION BY GRAINYHEAD-LIKE-2

    PubMed Central

    Cieply, Benjamin; Riley, Philip; Pifer, Phillip M.; Widmeyer, Joseph; Addison, Joseph B.; Ivanov, Alexey V.; Denvir, James; Frisch, Steven M.

    2012-01-01

    Grainyhead genes are involved in wound healing and developmental neural tube closure. In light of the high degree of similarity between the epithelial-mesenchymal transitions (EMT) occurring in wound healing processes and the cancer stem cell-like compartment of tumors, including TGF-β-dependence, we investigated the role of the Grainyhead gene, Grainyhead-Like-2 (GRHL2) in oncogenic EMT. GRHL2 was down-regulated specifically in the claudin-low subclass breast tumors and in basal-B subclass breast cancer cell lines. GRHL2 suppressed TGF-β-induced, Twist-induced or spontaneous EMT, enhanced anoikis-sensitivity, and suppressed mammosphere generation in mammary epithelial cells. These effects were mediated in part by suppression of ZEB1 expression via direct repression of the ZEB1 promoter. GRHL2 also inhibited Smad-mediated transcription and it upregulated mir200b/c as well as the TGF-β receptor antagonist, BMP2. Lastly, ectopic expression of GRHL2 in MDA-MB-231 breast cancer cells triggered a mesenchymal-to-epithelial transition and restored sensitivity to anoikis. Taken together, our findings define a major role for GRHL2 in the suppression of oncogenic EMT in breast cancer cells. PMID:22379025

  16. Laboratory Measurements of the Dielectronic Recombination Satellite Transitions of He-Like FE XXV and H-Like FE XXVI

    NASA Technical Reports Server (NTRS)

    Gu, M. F.; Beiersdorfer, P.; Brown, G. V.; Graf, A.; Kelley, R. I.; Kilbourne, C. A.; Porter, F. S.; Kahn, S. M,

    2012-01-01

    We present laboratory spectra of dielectronic recombination (DR) satellite transitions attached to the He-like and H-like iron resonance lines obtained with the NASA Goddard Space Flight Center X-ray calorimeter and produced by a thermal plasma simu1ation technique on the EBIT-I electron beam ion trap at the Lawrence Livermore National Laboratory. We demonstrate that the calorimeter has sufficient spectral resolution in the 6-9 keV range to provide reliable measurements not only of standard DR satellite to resonance line intensities but also of DR satellite to DR satellite ratios that can be used to diagnose nonthermal electron distributions. Electron temperatures derived from the measured line intensities are consistent with the temperature of the simulated plasma. Temperature measurements based on DR satellite transitions have significant advantages over those based on collisional ionization equilibrium or continuum shape. Thus, successful demonstration of this method with the X-ray calorimeter is an important step fur its application in X-ray astronomy.

  17. Detection of the MW Transition Between Ortho and Para States

    NASA Astrophysics Data System (ADS)

    Kanamori, Hideto; Dehghani, Zeinab Tafti; Mizoguchi, Asao; Endo, Yasuki

    2017-06-01

    Thorough the detailed analysis of the hyperfine resolved rotational transitions, we have been pointed out that there exists not a little interaction between ortho and para states in the molecular Hamiltonian of S_2Cl_2. Using the ortho-para mixed molecular wavefunctions derived from the Hamiltonian, we calculated the transition moment and frequency of the ortho-para forbidden transitions in the cm- and mm-wave region, and picked up some promising candidate transitions for the spectroscopic detection. In the experiment, the S_2Cl_2 vapor with Ar buffer gas in a supersonic jet condition was used with FTMW spectrometer at National Chiao Tung University. As a result, seven hyperfine resolved rotational transitions in the cm-wave region were detected as the ortho-para transition at the predicted frequency within the experimental error range. The observed intensity was 10^{-3} smaller than that of an allowed transition, which is also consistent with the prediction. This is the first time the electric dipole transition between ortho and para states has been detected in a free isolated molecule. A. Mizoguchi, S. Ota, H. Kanamori, Y. Sumiyoshi, and Y. Endo, J. Mol. Spectrosc, 250, 86 (2008) Z. T. Dehghani, S. Ota, A. Mizoguchi and H. Kanamori, J. Phys. Chem. A, 117(39), 10041, (2013)

  18. MOST Detects Transits of HD 97658b, a Warm, Likely Volatile-rich Super-Earth

    NASA Astrophysics Data System (ADS)

    Dragomir, Diana; Matthews, Jaymie M.; Eastman, Jason D.; Cameron, Chris; Howard, Andrew W.; Guenther, David B.; Kuschnig, Rainer; Moffat, Anthony F. J.; Rowe, Jason F.; Rucinski, Slavek M.; Sasselov, Dimitar; Weiss, Werner W.

    2013-07-01

    Through photometric monitoring of the extended transit window of HD 97658b with the MOST space telescope, we have found that this exoplanet transits with an ephemeris consistent with that predicted from radial velocity measurements. The mid-transit times are 5.6σ earlier than those of the unverified transit-like signals reported in 2011, and we find no connection between the two sets of events. The transit depth together with our determined stellar radius (R_\\star = 0.703^{+0.039}_{-0.034}\\ R_\\odot) indicates a 2.34^{+0.18}_{-0.15} R ⊕ super-Earth. When combined with the radial velocity determined mass of 7.86 ± 0.73 M ⊕, our radius measure allows us to derive a planet density of 3.44^{+0.91}_{-0.82} g cm-3. Models suggest that a planet with our measured density has a rocky core that is enveloped in an atmosphere composed of lighter elements. The star of the HD 97658 system is the second brightest known to host a transiting super-Earth, facilitating follow-up studies of this not easily daunted, warm and likely volatile-rich exoplanet. Based on data from the MOST satellite, a Canadian Space Agency mission operated by Microsatellite Systems Canada Inc. (MSCI; former Dynacon Inc.) and the Universities of Toronto and British Columbia, with the assistance of the University of Vienna.

  19. Rangifer management controls a climate-sensitive tundra state transition.

    PubMed

    Bråthen, Kari Anne; Ravolainen, Virve Tuulia; Stien, Audun; Tveraa, Torkild; Ims, Rolf A

    2017-12-01

    Rangifer (caribou/reindeer) management has been suggested to mitigate the temperature-driven transition of Arctic tundra into a shrubland state, yet how this happens is uncertain. Here we study this much focused ecosystem state transition in riparian areas, where palatable willows (Salix) are dominant tall shrubs and highly responsive to climate change. For the state transition to take place, small life stages must become tall and abundant. Therefore we predicted that the performance of small life stages (potential recruits) of the tall shrubs were instrumental to the focal transition, where Rangifer managed at high population density would keep the small-stage shrubs in a "browse trap" independent of summer temperature. We used a large-scale quasi-experimental study design that included real management units that spanned a wide range of Rangifer population densities and summer temperatures in order to assess the relative importance of these two driving variables. Ground surveys provided data on density and height of the small shrub life stages, while the distributional limit (shrubline) of established shrublands (the tall shrub life stage) was derived from aerial photographs. Where Rangifer densities were above a threshold of approximately 5 animals/km 2 , we found, in accordance with the expectation of a "browse trap," that the small life stages of shrubs in grasslands were at low height and low abundance. At Rangifer densities below this threshold, the small life stages of shrubs were taller and more abundant indicating Rangifer were no longer in control of the grassland state. For the established shrubland state, we found that the shrubline was at a 100-m lower elevation in the management units where Rangifer had been browsing in summer as opposed to the migratory ranges with no browsing in summer. In both seasonal ranges, the shrubline increased 100 m per 1°C increment in temperature. Our study supports the proposal that Rangifer management within a

  20. Magnetoelectric Effect in a Spin-State Transition System

    NASA Astrophysics Data System (ADS)

    Naka, Makoto; Mizoguchi, Eriko; Nasu, Joji; Ishihara, Sumio

    2018-06-01

    Magnetic, dielectric, and magnetoelectric properties in a spin-state transition system are examined, motivated by the recent discovery of multiferroic behavior in a cobalt oxide. We construct an effective model Hamiltonian on the basis of the two-orbital Hubbard model, in which the spin-state degrees of freedom in magnetic ions couple with ferroelectric-type lattice distortions. A phase transition occurs from the high-temperature low-spin phase to the low-temperature high-spin ferroelectric phase with an accompanying increase in spin entropy. The calculated results are consistent with the experimental pressure-temperature phase diagram. We predict the magnetic-field induced electric polarization in the low-spin paraelectric phase near the ferroelectric phase boundary.

  1. Resonant Coherent Excitation of Hydrogen-Like Ar Ions to the n =: 3 States

    NASA Astrophysics Data System (ADS)

    Azuma, T.; Ito, T.; Takabayashi, Y.; Komaki, K.; Yamazaki, Y.; Yamazaki, Y.; Takada, E.; Murakami, T.

    We have succeeded in observing resonant coherent excitaion (RCE) of 1s electrons to the n = 3 states in 390 MeV/u hydrogen-like Ar17+ ions planar channeled in a silicon crystal through measurements of the charge-state distribution of ions transmitting the crystal. Furthermore, we directly confirmed RCE to the n = 3 states by observing the enhancement of the de-excitation X-rays, i.e., Kβ X-rays under the resonance condition. The resonance profiles of the charge-state distribution as functions of the incident angle to the crystal, which uniquely relates with the transition energy, have a characteristic structure consisting of several peaks. Compared with the profile of RCE to the n = 2 states, the present profiles show a large peak shift from the j = 1/2 and 3/2 levels in vacuum, and the profiles are much wider than those expected from the Stark-split level structure of the n = 3 manifolds due to the position- (distance from the channel center in the planar channel) dependent strong static field in the crystal.

  2. Perovskite-like fluorides and oxyfluorides: Phase transitions and caloric effects

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Flerov, I. N., E-mail: flerov@iph.krasn.ru; Gorev, M. V., E-mail: gorev@iph.krasn.ru; Tressaud, A.

    2011-01-15

    An analysis of the effect that chemical and hydrostatic pressures have on the thermodynamic properties of perovskite-like fluorine-oxygen compounds A{sub 2}A Prime MeO{sub x}F{sub 6-x} has revealed that materials under-going order-disorder transitions and having significant external-pressure compliance have the highest caloric efficiency. Some of the fluorides and oxyfluorides under study can be considered promising solid coolants.

  3. Eigenfunction fractality and pseudogap state near the superconductor-insulator transition.

    PubMed

    Feigel'man, M V; Ioffe, L B; Kravtsov, V E; Yuzbashyan, E A

    2007-01-12

    We develop a theory of a pseudogap state appearing near the superconductor-insulator (SI) transition in strongly disordered metals with an attractive interaction. We show that such an interaction combined with the fractal nature of the single-particle wave functions near the mobility edge leads to an anomalously large single-particle gap in the superconducting state near SI transition that persists and even increases in the insulating state long after the superconductivity is destroyed. We give analytic expressions for the value of the pseudogap in terms of the inverse participation ratio of the corresponding localization problem.

  4. Digital soil mapping as a tool for quantifying state-and-transition models

    USDA-ARS?s Scientific Manuscript database

    Ecological sites and associated state-and-transition models (STMs) are rapidly becoming important land management tools in rangeland systems in the US and around the world. Descriptions of states and transitions are largely developed from expert knowledge and generally accepted species and community...

  5. Still states of bistable lattices, compatibility, and phase transition

    NASA Astrophysics Data System (ADS)

    Cherkaev, Andrej; Kouznetsov, Andrei; Panchenko, Alexander

    2010-09-01

    We study a two-dimensional triangular lattice made of bistable rods. Each rod has two equilibrium lengths, and thus its energy has two equal minima. A rod undergoes a phase transition when its elongation exceeds a critical value. The lattice is subject to a homogeneous strain and is periodic with a sufficiently large period. The effective strain of a periodic element is defined. After phase transitions, the lattice rods are in two different states and lattice strain is inhomogeneous, the Cauchy-Born rule is not applicable. We show that the lattice has a number of deformed still states that carry no stresses. These states densely cover a neutral region in the space of entries of effective strains. In this region, the minimal energy of the periodic lattice is asymptotically close to zero. When the period goes to infinity, the effective energy of such lattices has the “flat bottom” which we explicitly describe. The compatibility of the partially transited lattice is studied. We derive compatibility conditions for lattices and demonstrate a family of compatible lattices (strips) that densely covers the flat bottom region. Under an additional assumption of the small difference of two equilibrium lengths, we demonstrate that the still structures continuously vary with the effective strain and prove a linear dependence of the average strain on the concentration of transited rods.

  6. Energy Levels, Lifetimes, and Transition Rates for P-like Ions from Cr X to Zn XVI from Large-scale Relativistic Multiconfiguration Calculations

    NASA Astrophysics Data System (ADS)

    Wang, K.; Jönsson, P.; Gaigalas, G.; Radžiūtė, L.; Rynkun, P.; Del Zanna, G.; Chen, C. Y.

    2018-04-01

    The fully relativistic multiconfiguration Dirac–Hartree–Fock method is used to compute excitation energies and lifetimes for the 143 lowest states of the 3{s}23{p}3, 3s3p 4, 3{s}23{p}23d, 3s3p 33d, 3p 5, 3{s}23p3{d}2 configurations in P-like ions from Cr X to Zn XVI. Multipole (E1, M1, E2, M2) transition rates, line strengths, oscillator strengths, and branching fractions among these states are also given. Valence–valence and core–valence electron correlation effects are systematically accounted for using large basis function expansions. Computed excitation energies are compared with the NIST ASD and CHIANTI compiled values and previous calculations. The mean average absolute difference, removing obvious outliers, between computed and observed energies for the 41 lowest identified levels in Fe XII, is only 0.057%, implying that the computed energies are accurate enough to aid identification of new emission lines from the Sun and other astrophysical sources. The amount of energy and transition data of high accuracy are significantly increased for several P-like ions of astrophysics interest, where experimental data are still very scarce.

  7. Continuity of states between the cholesteric → line hexatic transition and the condensation transition in DNA solutions

    DOE PAGES

    Yasar, Selcuk; Podgornik, Rudolf; Valle-Orero, Jessica; ...

    2014-11-05

    A new method of finely temperature-tuning osmotic pressure allows one to identify the cholesteric → line hexatic transition of oriented or unoriented long-fragment DNA bundles in monovalent salt solutions as first order, with a small but finite volume discontinuity. This transition is similar to the osmotic pressure-induced expanded → condensed DNA transition in polyvalent salt solutions at small enough polyvalent salt concentrations. Therefore there exists a continuity of states between the two. This finding with the corresponding empirical equation of state, effectively relates the phase diagram of DNA solutions for monovalent salts to that for polyvalent salts and sheds somemore » light on the complicated interactions between DNA molecules at high densities.« less

  8. E1 transitions from octupole vibration states

    NASA Astrophysics Data System (ADS)

    Cottle, P. D.

    1993-04-01

    Electric dipole moments are extracted from data for E1 transitions deexciting octupole vibration states in nineteen nuclei. The moments are then compared to values calculated using the droplet model prescription of Dorso, Myers, and Swiatecki. It is found that the E1 moments in quadrupole deformed nuclei can be reproduced with the droplet model using the same model parameters that reproduce atomic masses and fission barriers. This result supports the suggestion of Butler and Nazarewicz that single particle effects are usually much smaller than macroscopic effects in E1 transitions associated with octupole vibrations in reflection symmetric deformed nuclei.

  9. Infrared photodissociation spectroscopy of H(+)(H2O)6·M(m) (M = Ne, Ar, Kr, Xe, H2, N2, and CH4): messenger-dependent balance between H3O(+) and H5O2(+) core isomers.

    PubMed

    Mizuse, Kenta; Fujii, Asuka

    2011-04-21

    Although messenger mediated spectroscopy is a widely-used technique to study gas phase ionic species, effects of messengers themselves are not necessarily clear. In this study, we report infrared photodissociation spectroscopy of H(+)(H(2)O)(6)·M(m) (M = Ne, Ar, Kr, Xe, H(2), N(2), and CH(4)) in the OH stretch region to investigate messenger(M)-dependent cluster structures of the H(+)(H(2)O)(6) moiety. The H(+)(H(2)O)(6), the protonated water hexamer, is the smallest system in which both the H(3)O(+) (Eigen) and H(5)O(2)(+) (Zundel) hydrated proton motifs coexist. All the spectra show narrower band widths reflecting reduced internal energy (lower vibrational temperature) in comparison with bare H(+)(H(2)O)(6). The Xe-, CH(4)-, and N(2)-mediated spectra show additional band features due to the relatively strong perturbation of the messenger. The observed band patterns in the Ar-, Kr-, Xe-, N(2)-, and CH(4)-mediated spectra are attributed mainly to the "Zundel" type isomer, which is more stable. On the other hand, the Ne- and H(2)-mediated spectra are accounted for by a mixture of the "Eigen" and "Zundel" types, like that of bare H(+)(H(2)O)(6). These results suggest that a messenger sometimes imposes unexpected isomer-selectivity even though it has been thought to be inert. Plausible origins of the isomer-selectivity are also discussed.

  10. Tables of Transition Probabilities and Branching Ratios for Electric Dipole Transitions Between Arbitrary Levels of Hydrogen-Like Atoms

    NASA Technical Reports Server (NTRS)

    Omidvar, K.

    1980-01-01

    Branching ratios in hydrogen-like atoms due to electric-dipole transitions are tabulated for the initial principal and angular momentum quantum number n, lambda, and final principal and angular momentum quantum numbers n, lambda. In table 1, transition probabilities are given for transitions n, lambda, yields n, where sums have been made with respect to lambda. In this table, 2 or = n' or = 10, o or = lambda' or = n'-1, and 1 or = n or = n'-1. In addition, averages with respect to lambda' and sums with respect to n, and lifetimes are given. In table 2, branching ratios are given for transitions n' lambda' yields ni, where sums have been made with respect to lambda. In these tables, 2 or = n' or = 10, 0 or = lambda', n'-1, and 1 or = n or = n'-1. Averages with respect to lambda' are also given. In table 3, branching ratios are given for transitions n' lambda' yields in lambda, where 1 or = n or = 5, 0 or = lambda or = n-1, n n' or = 15, and 0 or = lambda' or = n(s), where n(s), is the smaller of the two numbers n'-1 and 6. Averages with respect to lambda' are given.

  11. What can one learn from experiments about the elusive transition state?

    PubMed Central

    Chang, Iksoo; Cieplak, Marek; Banavar, Jayanth R.; Maritan, Amos

    2004-01-01

    We present the results of an exact analysis of a model energy landscape of a protein to clarify the idea of the transition state and the physical meaning of the φ values determined in protein engineering experiments. We benchmark our findings to various theoretical approaches proposed in the literature for the identification and characterization of the transition state. PMID:15295118

  12. Spectroscopic parameters, vibrational levels, transition dipole moments and transition probabilities of the 9 low-lying states of the NCl+ cation

    NASA Astrophysics Data System (ADS)

    Yin, Yuan; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2018-03-01

    This work calculates the potential energy curves of 9 Λ-S and 28 Ω states of the NCl+ cation. The technique employed is the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with the Davidson correction. The Λ-S states are X2Π, 12Σ+, 14Π, 14Σ+, 14Σ-, 24Π, 14Δ, 16Σ+, and 16Π, which are yielded from the first two dissociation channels of NCl+ cation. The Ω states are generated from these Λ-S states. The 14Π, 14Δ, 16Σ+, and 16Π states are inverted with the spin-orbit coupling effect included. The 14Σ+, 16Σ+, and 16Π states are very weakly bound, whose well depths are only several-hundred cm- 1. One avoided crossing of PECs occurs between the 12Σ+ and 22Σ+ states. To improve the quality of potential energy curves, core-valence correlation and scalar relativistic corrections are included. The potential energies are extrapolated to the complete basis set limit. The spectroscopic parameters and vibrational levels are calculated. The transition dipole moments are computed. The Franck-Condon factors, Einstein coefficients, and radiative lifetimes of many transitions are determined. The spectroscopic approaches are proposed for observing these states according to the transition probabilities. The spin-orbit coupling effect on the spectroscopic and vibrational properties is evaluated. The spectroscopic parameters, vibrational levels, transition dipole moments, as well as transition probabilities reported in this paper could be considered to be very reliable.

  13. Intramolecular fluorine migration via four-member cyclic transition states

    PubMed

    Nguyen; Mayer; Morton

    2000-11-17

    expected: the transition state becomes more product-like as the metathesis becomes increasingly exothermic. This reversal of the naive interpretation of the Hammond postulate is accounted for by the relative positions of the potential energy wells that precede and follow the central barrier.

  14. Effects of hydrogen-like impurity and electromagnetic field on quantum transition of an electron in a Gaussian potential with QD thickness

    NASA Astrophysics Data System (ADS)

    Xin, Wei; Zhao, Yu-Wei; Sudu; Eerdunchaolu

    2018-05-01

    Considering Hydrogen-like impurity and the thickness effect, the eigenvalues and eigenfunctions of the electronic ground and first exited states in a quantum dot (QD) are derived by using the Lee-Low-Pins-Pekar variational method with the harmonic and Gaussian potentials as the transverse and longitudinal confinement potentials, respectively. A two-level system is constructed on the basis of those two states, and the electronic quantum transition affected by an electromagnetic field is discussed in terms of the two-level system theory. The results indicate the Gaussian potential reflects the real confinement potential more accurately than the parabolic one; the influence of the thickness of the QD on the electronic transition probability is interesting and significant, and cannot be ignored; the electronic transition probability Γ is influenced significantly by some physical quantities, such as the strength of the electron-phonon coupling α, the electric-field strength F, the magnetic-field cyclotron frequency ωc , the barrier height V0 and confinement range L of the asymmetric Gaussian potential, suggesting the transport and optical properties of the QD can be manipulated further though those physical quantities.

  15. Extended calculations of energies, transition rates, and lifetimes for F-like Kr XXVIII

    NASA Astrophysics Data System (ADS)

    Zhang, C. Y.; Si, R.; Yao, K.; Gu, M. F.; Wang, K.; Chen, C. Y.

    2018-02-01

    The excitation energies, lifetimes, wavelengths and E1, E2, M1 and M2 transition rates for the lowest 389 levels of the 2l7, 2l63l‧, 2l64l‧, and 2l65l‧ configurations from second-order many-body perturbation theory (MBPT) calculations, and the results for the lowest 200 states of the 2l7, 2l63l‧, and 2l64l‧ configurations from multi-configuration Dirac-Hartree-Fock (MCDHF) calculations in F-like Kr XXVIII are presented in this work. The relative differences between our two sets of level energies are mostly within 0.005% for the lowest 200 levels. Comparisons are made with experimental and other available theoretical results to assess the reliability and accuracy of the present calculations. We believe them to be the most complete and accurate results for Kr XXVIII at present.

  16. Decoding brain state transitions in the pedunculopontine nucleus: cooperative phasic and tonic mechanisms

    PubMed Central

    Petzold, Anne; Valencia, Miguel; Pál, Balázs; Mena-Segovia, Juan

    2015-01-01

    Cholinergic neurons of the pedunculopontine nucleus (PPN) are most active during the waking state. Their activation is deemed to cause a switch in the global brain activity from sleep to wakefulness, while their sustained discharge may contribute to upholding the waking state and enhancing arousal. Similarly, non-cholinergic PPN neurons are responsive to brain state transitions and their activation may influence some of the same targets of cholinergic neurons, suggesting that they operate in coordination. Yet, it is not clear how the discharge of distinct classes of PPN neurons organize during brain states. Here, we monitored the in vivo network activity of PPN neurons in the anesthetized rat across two distinct levels of cortical dynamics and their transitions. We identified a highly structured configuration in PPN network activity during slow-wave activity that was replaced by decorrelated activity during the activated state (AS). During the transition, neurons were predominantly excited (phasically or tonically), but some were inhibited. Identified cholinergic neurons displayed phasic and short latency responses to sensory stimulation, whereas the majority of non-cholinergic showed tonic responses and remained at high discharge rates beyond the state transition. In vitro recordings demonstrate that cholinergic neurons exhibit fast adaptation that prevents them from discharging at high rates over prolonged time periods. Our data shows that PPN neurons have distinct but complementary roles during brain state transitions, where cholinergic neurons provide a fast and transient response to sensory events that drive state transitions, whereas non-cholinergic neurons maintain an elevated firing rate during global activation. PMID:26582977

  17. Hyperfine quenching of the 2s2 2p5 3 s3P2 state of Ne-like ions

    NASA Astrophysics Data System (ADS)

    Safronova, U. I.; Stafford, A.; Safronova, A. S.

    2017-04-01

    The many-body perturbation theory (RMBPT) is used to calculate energies and multipole matrix elements to evaluate hyperfine quenching of the 2s2 2p5 3 s 3P2 state in Ne-like ions. In particular, the 3P2 excited state decays to the 1S0 ground state by M2 emission, while both 1P1 and 3P1 states decay to the ground-state by E1 emission, which is substantially faster. For odd-A nuclei, the hyperfine interaction induces admixtures of 3P1 and 1P1 states into the 3P2 state, resulting in an increase of the 3P2 transition rate and a corresponding reduction of the 3P2 lifetime. We consider 22 Ne like ions with Z = 14 - 94 and nuclear moment I =1/2. We found that the largess hyperfine quenching contribution by a factor of 2 are for Ne-like 31P and 203Tl. The smallest (less than 1%) induced contribution are the following Ne-like ions: 57Fe, 107Ag, 109Ag, 183W, and 187Os ions. For another 15 Ne-like ions the hyperfine quenching contribution is between 15% and 35%. Applications to x-ray line polarization of Ne-like lines is considered. This work is supported by the Department of Energy, National Nuclear Security Administration, under Award Number DE-NA0002954.

  18. An Integrated Approach to Winds, Jets, and State Transitions

    NASA Astrophysics Data System (ADS)

    Neilsen, Joseph

    2017-09-01

    We propose a large multiwavelength campaign (120 ks Chandra HETGS, NuSTAR, INTEGRAL, JVLA/ATCA, Swift, XMM, Gemini) on a black hole transient to study the influence of ionized winds on relativistic jets and state transitions. With a reimagined observing strategy based on new results on integrated RMS variability and a decade of radio/X-ray monitoring, we will search for winds during and after the state transition to test their influence on and track their coevolution with the disk and the jet over the next 2-3 months. Our spectral and timing constraints will provide precise probes of the accretion geometry and accretion/ejection physics.

  19. Structure of vortices in superfluid 3He A-like phase in uniaxially stretched aerogel

    NASA Astrophysics Data System (ADS)

    Aoyama, Kazushi; Ikeda, Ryusuke

    2009-02-01

    Possible vortex-core transitions in A-like phase of superfluid 3He in uniaxially stretched aerogel are investigated. Since the global anisotropy in this system induces the polar pairing state in a narrow range close to the superfluid transition in addition to the A-like and B-like phases, the polar state may occur in the core of a vortex in the A-like phase identified with the ABM pairing state, like in the case of the bulk B phase where a core including the ABM state is realized at higher pressures. We examine the core structure of a single vortex under the boundary condition compatible with the Mermin-Ho vortex in the presence of the dipole interaction. Following Salomaa and Volovik's approach, we numerically solve the Ginzburg-Landau equation for an axially symmetric vortex and, by examining its stability against nonaxisymmetric perturbations, discuss possible vortex core states. It is found that a first order transition on core states may occur on warming from an axisymmetric vortex with a nonunitary core to a singular vortex with the polar core.

  20. Enzyme architecture: optimization of transition state stabilization from a cation-phosphodianion pair.

    PubMed

    Reyes, Archie C; Koudelka, Astrid P; Amyes, Tina L; Richard, John P

    2015-04-29

    The side chain cation of R269 lies at the surface of l-glycerol 3-phosphate dehydrogenase (GPDH) and forms an ion pair to the phosphodianion of substrate dihydroxyacetone phosphate (DHAP), which is buried at the nonpolar protein interior. The R269A mutation of GPDH results in a 110-fold increase in K(m) (2.8 kcal/mol effect) and a 41,000-fold decrease in k(cat) (6.3 kcal/mol effect), which corresponds to a 9.1 kcal/mol destabilization of the transition state for GPDH-catalyzed reduction of DHAP by NADH. There is a 6.7 kcal/mol stabilization of the transition state for the R269A mutant GPDH-catalyzed reaction by 1.0 M guanidinium ion, and the transition state for the reaction of the substrate pieces is stabilized by an additional 2.4 kcal/mol by their covalent attachment at wildtype GPDH. These results provide strong support for the proposal that GPDH invests the 11 kcal/mol intrinsic phosphodianion binding energy of DHAP in trapping the substrate at a nonpolar active site, where strong electrostatic interactions are favored, and obtains a 9 kcal/mol return from stabilizing interactions between the side chain cation and transition state trianion. We propose a wide propagation for the catalytic motif examined in this work, which enables strong transition state stabilization from enzyme-phosphodianion pairs.

  1. Time-dependent evolution of cosmic-ray-modified shock structure: Transition to steady state

    NASA Astrophysics Data System (ADS)

    Donohue, D. J.; Zank, G. P.; Webb, G. M.

    1994-03-01

    Steady state solutions to the two-fluid equations of cosmic-ray-modified shock structure were investigated first by Drury and Volk (1981). Their analysis revealed, among other properties, that there exist regions of upstream parameter space where the equations possess three different downstream solutions for a given upstream state. In this paper we investigate whether or not all these solutions can occur as time-asymptotic states in a physically realistic evolution. To do this, we investigate the time-dependent evolution of the two-fluid cosmic-ray equations in going from a specified initial condition to a steady state. Our results indicate that the time-asymptotic solution is strictly single-valued, and it undergoes a transition from weakly to strongly cosmic-ray-modified at a critical value of the upstream cosmic ray energy density. The expansion of supernova remnant shocks is considered as an example, and it is shown that the strong to weak transition is in fact more likely. The third intermediate solution is shown to influence the time-dependent evolution of the shock, but it is not found to be a stable time-asymptotic state. Timescales for convergence to these states and their implications for the efficiency of shock acceleration are considered. We also investigate the effects of a recently introduced model for the injection of seed particles into the shock accelerated cosmic-ray population. The injection is found to result in a more strongly cosmic-ray-dominated shock, which supports our conclusion that for most classes of intermediate and strong cosmic-ray-modified shocks, the downstream cosmic-ray pressure component is at least as large as the thermal gas pressure, independent of the upstream state. As a result, cosmic rays almost always play a significant role in determining the shock structure and dissipation and they cannot be regarded as test particles.

  2. Time-dependent evolution of cosmic-ray-modified shock structure: Transition to steady state

    NASA Technical Reports Server (NTRS)

    Donohue, D. J.; Zank, G. P.; Webb, G. M.

    1994-01-01

    Steady state solutions to the two-fluid equations of cosmic-ray-modified shock structure were investigated first by Drury and Volk (1981). Their analysis revealed, among other properties, that there exist regions of upstream parameter space where the equations possess three different downstream solutions for a given upstream state. In this paper we investigate whether or not all these solutions can occur as time-asymptotic states in a physically realistic evolution. To do this, we investigate the time-dependent evolution of the two-fluid cosmic-ray equations in going from a specified initial condition to a steady state. Our results indicate that the time-asymptotic solution is strictly single-valued, and it undergoes a transition from weakly to strongly cosmic-ray-modified at a critical value of the upstream cosmic ray energy density. The expansion of supernova remnant shocks is considered as an example, and it is shown that the strong to weak transition is in fact more likely. The third intermediate solution is shown to influence the time-dependent evolution of the shock, but it is not found to be a stable time-asymptotic state. Timescales for convergence to these states and their implications for the efficiency of shock acceleration are considered. We also investigate the effects of a recently introduced model for the injection of seed particles into the shock accelerated cosmic-ray population. The injection is found to result in a more strongly cosmic-ray-dominated shock, which supports our conclusion that for most classes of intermediate and strong cosmic-ray-modified shocks, the downstream cosmic-ray pressure component is at least as large as the thermal gas pressure, independent of the upstream state. As a result, cosmic rays almost always play a significant role in determining the shock structure and dissipation and they cannot be regarded as test particles.

  3. Solid-to-fluid – like DNA transition in viruses facilitates infection

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, Ting; Sae-Ueng, Udom; Li, Dong

    2014-10-14

    Releasing the packaged viral DNA into the host cell is an essential process to initiate viral infection. In many double-stranded DNA bacterial viruses and herpesviruses, the tightly packaged genome is hexagonally ordered and stressed in the protein shell, called the capsid. DNA condensed in this state inside viral capsids has been shown to be trapped in a glassy state, with restricted molecular motion in vitro. This limited intracapsid DNA mobility is caused by the sliding friction between closely packaged DNA strands, as a result of the repulsive interactions between the negative charges on the DNA helices. It had been unclearmore » how this rigid crystalline structure of the viral genome rapidly ejects from the capsid, reaching rates of 60,000 bp/s. Through a combination of single- molecule and bulk techniques, we determined how the structure and energy of the encapsidated DNA in phage λ regulates the mobility required for its ejection. Our data show that packaged λ -DNA undergoes a solid-to-fluid – like disordering transition as a function of temperature, resultin g locally in less densely packed DNA, reducing DNA – DNA repulsions. This p rocess leads to a sig- nificant increase in genome mobility or fluidity, which facilitates genome release at temperatures close to that of viral infection (37 °C), suggesting a remarkab le physical adaptation of bac- terial viruses to the environment of Escherichia coli cells in a human host.« less

  4. Parameter optimization for transitions between memory states in small arrays of Josephson junctions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Rezac, Jacob D.; Imam, Neena; Braiman, Yehuda

    Coupled arrays of Josephson junctions possess multiple stable zero voltage states. Such states can store information and consequently can be utilized for cryogenic memory applications. Basic memory operations can be implemented by sending a pulse to one of the junctions and studying transitions between the states. In order to be suitable for memory operations, such transitions between the states have to be fast and energy efficient. Here in this article we employed simulated annealing, a stochastic optimization algorithm, to study parameter optimization of array parameters which minimizes times and energies of transitions between specifically chosen states that can be utilizedmore » for memory operations (Read, Write, and Reset). Simulation results show that such transitions occur with access times on the order of 10–100 ps and access energies on the order of 10 -19–5×10 -18 J. Numerical simulations are validated with approximate analytical results.« less

  5. Transit Car Performance Comparison, State-of-the-Art Car vs. PATCO Transit Car, NYCTA R-46, MBTA Silverbirds

    DOT National Transportation Integrated Search

    1978-02-01

    The first phase of this contract authorized the design, development, and demonstration of two State-Of-The-Art Cars (SOAC). This document reports on the gathering of comparative test data on existing in-service transit cars. The three transit cars se...

  6. A Semi-analytical Model for Wind-fed Black Hole High-mass X-Ray Binaries: State Transition Triggered by Magnetic Fields from the Companion Star

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yaji, Kentaro; Yamada, Shinya; Masai, Kuniaki

    We propose a mechanism of state transition in wind-fed black hole (BH) binaries (high-mass X-ray binaries) such as Cyg X-1 and LMC X-1. Modeling a line-driven stellar wind from the companion by two-dimensional hydrodynamical calculations, we investigate the processes of wind capture by, and accretion onto, the BH. We assume that the wind acceleration is terminated at the He ii ionization front because ions responsible for line-driven acceleration are ionized within the front, i.e., the He iii region. It is found that the mass accretion rate inferred from the luminosity is remarkably smaller than the capture rate. Considering the difference,more » we construct a model for the state transition based on the accretion flow being controlled by magnetorotational instability. The outer flow is torus-like, and plays an important role to trigger the transition. The model can explain why state transition does occur in Cyg X-1, while not in LMC X-1. Cyg X-1 exhibits a relatively low luminosity, and then the He ii ionization front is located and can move between the companion and BH, depending on its ionizing photon flux. On the other hand, LMC X-1 exhibits too high luminosity for the front to move considerably; the front is too close to the companion atmosphere. The model also predicts that each state of high-soft or low-hard would last fairly long because the luminosity depends weakly on the wind velocity. In the context of the model, the state transition is triggered by a fluctuation of the magnetic field when its amplitude becomes comparable to the field strength in the torus-like outer flow.« less

  7. Accurate potential energy curves, spectroscopic parameters, transition dipole moments, and transition probabilities of 21 low-lying states of the CO+ cation

    NASA Astrophysics Data System (ADS)

    Xing, Wei; Shi, Deheng; Zhang, Jicai; Sun, Jinfeng; Zhu, Zunlue

    2018-05-01

    This paper calculates the potential energy curves of 21 Λ-S and 42 Ω states, which arise from the first two dissociation asymptotes of the CO+ cation. The calculations are conducted using the complete active space self-consistent field method, which is followed by the valence internally contracted multireference configuration interaction approach with the Davidson correction. To improve the reliability and accuracy of the potential energy curves, core-valence correlation and scalar relativistic corrections, as well as the extrapolation of potential energies to the complete basis set limit are taken into account. The spectroscopic parameters and vibrational levels are determined. The spin-orbit coupling effect on the spectroscopic parameters and vibrational levels is evaluated. To better study the transition probabilities, the transition dipole moments are computed. The Franck-Condon factors and Einstein coefficients of some emissions are calculated. The radiative lifetimes are determined for a number of vibrational levels of several states. The transitions between different Λ-S states are evaluated. Spectroscopic routines for observing these states are proposed. The spectroscopic parameters, vibrational levels, transition dipole moments, and transition probabilities reported in this paper can be considered to be very reliable and can be used as guidelines for detecting these states in an appropriate spectroscopy experiment, especially for the states that were very difficult to observe or were not detected in previous experiments.

  8. Site-directed mutagenesis reveals transition-state stabilization as a general catalytic mechanism for aminoacyl-tRNA synthetases.

    PubMed

    Borgford, T J; Gray, T E; Brand, N J; Fersht, A R

    1987-11-17

    Some aminoacyl-tRNA synthetases of almost negligible homology do have a small region of similarity around four-residue sequence His-Ile(or Leu or Met)-Gly-His(or Asn), the HIGH sequence. The first histidine in this sequence in the tyrosyl-tRNA synthetase, His-45, has been shown to form part of a binding site for the gamma-phosphate of ATP in the transition state for the reaction as does Thr-40. Residue His-56 in the valyl-tRNA synthetase begins a HIGH sequence, and there is a threonine at position 52, one position closer to the histidine than in the tyrosyl-tRNA synthetase. The mutants Thr----Ala-52 and His----Asn-56 have been made and their complete free energy profiles for the formation of valyl adenylate determined. Difference energy diagrams have been constructed by comparison with the reaction of wild-type enzyme. The difference energy profiles are very similar to those for the mutants Thr----Ala-40 and His----Asn-45 of the tyrosyl-tRNA synthetase. Thr-52 and His-56 of the valyl-tRNA synthetase contribute little binding energy to valine, ATP, and Val-AMP. Instead, the wild-type enzyme binds the transition state and pyrophosphate some 6 kcal/mol more tightly than do the mutants. Preferential transition-state stabilization is thus an important component of catalysis by the valyl-tRNA synthetase. Further, by analogy to the tyrosyl-tRNA synthetase, the valyl-tRNA synthetase has a binding site for the gamma-phosphate of ATP in the transition state, and this is likely to be a general feature of aminoacyl-tRNA synthetases that have a HIGH region.

  9. Transitional millisecond pulsars in the low-level accretion state

    NASA Astrophysics Data System (ADS)

    Jaodard, Amruta D.; Hessels, Jason W. T.; Archibald, Anne; Bogdanov, Slavko; Deller, Adam; Hernandez Santisteban, Juan; Patruno, Alessandro; D'Angelo, Caroline; Bassa, Cees; Amruta Jaodand

    2018-01-01

    In the canonical pulsar recycling scenario, a slowly spinning neutron star can be rejuvenated to rapid spin rates by the transfer of angular momentum and mass from a binary companion star. Over the last decade, the discovery of three transitional millisecond pulsars (tMSPs) has allowed us to study recycling in detail. These systems transition between accretion-powered (X-ray) and rotation-powered (radio) pulsar states within just a few days, raising questions such as: what triggers the state transition, when does the recycling process truly end, and what will the radio pulsar’s final spin rate be? Systematic multi-wavelength campaigns over the last decade have provided critical insights: multi-year-long, low-level accretion states showing coherent X-ray pulsations; extremely stable, bi-modal X-ray light curves; outflows probed by radio continuum emission; a surprising gamma-ray brightening during accretion, etc. In my thesis I am trying to bring these clues together to understand the low-level accretion process that recycles a pulsar. For example, recently we timed PSR J1023+0038 in the accretion state and found it to be spinning down ~26% faster compared to the non-accreting radio pulsar state. We are currently conducting simultaneous multi-wavelength campaigns (XMM, HST, Kepler and VLA) to understand the global variability of the accretion flow, as well as high-energy Fermi-LAT observations to probe the gamma-ray emission mechanism. I will highlight these recent developments, while also presenting a broad overview of tMSPs as exciting new laboratories to test low-level accretion onto magnetized neutron stars.

  10. Statistical Mechanical Foundation for the Two-State Transition in Protein Folding of Small Globular Proteins

    NASA Astrophysics Data System (ADS)

    Iguchi, Kazumoto

    We discuss the statistical mechanical foundation for the two-state transition in the protein folding of small globular proteins. In the standard arguments of protein folding, the statistical search for the ground state is carried out from astronomically many conformations in the configuration space. This leads us to the famous Levinthal's paradox. To resolve the paradox, Gō first postulated that the two-state transition - all-or-none type transition - is very crucial for the protein folding of small globular proteins and used the Gō's lattice model to show the two-state transition nature. Recently, there have been accumulated many experimental results that support the two-state transition for small globular proteins. Stimulated by such recent experiments, Zwanzig has introduced a minimal statistical mechanical model that exhibits the two-state transition. Also, Finkelstein and coworkers have discussed the solution of the paradox by considering the sequential folding of a small globular protein. On the other hand, recently Iguchi have introduced a toy model of protein folding using the Rubik's magic snake model, in which all folded structures are exactly known and mathematically represented in terms of the four types of conformations: cis-, trans-, left and right gauche-configurations between the unit polyhedrons. In this paper, we study the relationship between the Gō's two-state transition, the Zwanzig's statistical mechanics model and the Finkelsteinapos;s sequential folding model by applying them to the Rubik's magic snake models. We show that the foundation of the Gō's two-state transition model relies on the search within the equienergy surface that is labeled by the contact order of the hydrophobic condensation. This idea reproduces the Zwanzig's statistical model as a special case, realizes the Finkelstein's sequential folding model and fits together to understand the nature of the two-state transition of a small globular protein by calculating the

  11. Bistability and State Transition of a Delay Differential Equation Model of Neutrophil Dynamics

    NASA Astrophysics Data System (ADS)

    Ma, Suqi; Zhu, Kaiyi; Lei, Jinzhi

    This paper studies the existence of bistable states and control strategies to induce state transitions of a delay differential equation model of neutrophil dynamics. We seek the conditions that a stable steady state and an oscillatory state coexist in the neutrophil dynamical system. Physiologically, stable steady state represents the healthy state, while oscillatory state is usually associated with diseases such as cyclical neutropenia. We study the control strategies to induce the transitions from the disease state to the healthy state by introducing temporal perturbations to system parameters. This study is valuable in designing clinical protocols for the treatment of cyclical neutropenia.

  12. Towards autonomous locomotion: CPG-based control of smooth 3D slithering gait transition of a snake-like robot.

    PubMed

    Bing, Zhenshan; Cheng, Long; Chen, Guang; Röhrbein, Florian; Huang, Kai; Knoll, Alois

    2017-04-04

    Snake-like robots with 3D locomotion ability have significant advantages of adaptive travelling in diverse complex terrain over traditional legged or wheeled mobile robots. Despite numerous developed gaits, these snake-like robots suffer from unsmooth gait transitions by changing the locomotion speed, direction, and body shape, which would potentially cause undesired movement and abnormal torque. Hence, there exists a knowledge gap for snake-like robots to achieve autonomous locomotion. To address this problem, this paper presents the smooth slithering gait transition control based on a lightweight central pattern generator (CPG) model for snake-like robots. First, based on the convergence behavior of the gradient system, a lightweight CPG model with fast computing time was designed and compared with other widely adopted CPG models. Then, by reshaping the body into a more stable geometry, the slithering gait was modified, and studied based on the proposed CPG model, including the gait transition of locomotion speed, moving direction, and body shape. In contrast to sinusoid-based method, extensive simulations and prototype experiments finally demonstrated that smooth slithering gait transition can be effectively achieved using the proposed CPG-based control method without generating undesired locomotion and abnormal torque.

  13. Radiative one- and two-electron transitions into the empty K shell of He-like ions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kadrekar, Riddhi; Natarajan, L.

    2011-12-15

    The branching ratios between the single and double electron radiative transitions to empty K shell in He-like ions with 2s2p configuration are evaluated for 15 ions with 4{<=}Z{<=}26 using fully relativistic multiconfiguration Dirac-Fock wavefunctions in the active space approximation. The effects of configuration interaction and Breit contributions on the transition parameters have been analyzed in detail. Though the influence of Breit interaction on the electric dipole allowed one-electron radiative transitions is negligible, it substantially changes the spin-forbidden rates and the two-electron one-photon transition probabilities. Also, while the single electron transition rates are gauge independent, the correlated double-electron probabilities are foundmore » to be gauge sensitive. The probable uncertainties in the computed transition rates have been evaluated by considering the line strengths and the differences between the calculated and experimental transition energies as accuracy indicators. The present results are compared with other available experimental and theoretical data.« less

  14. Cell Fate Decision as High-Dimensional Critical State Transition

    PubMed Central

    Zhou, Joseph; Castaño, Ivan G.; Leong-Quong, Rebecca Y. Y.; Chang, Hannah; Trachana, Kalliopi; Giuliani, Alessandro; Huang, Sui

    2016-01-01

    Cell fate choice and commitment of multipotent progenitor cells to a differentiated lineage requires broad changes of their gene expression profile. But how progenitor cells overcome the stability of their gene expression configuration (attractor) to exit the attractor in one direction remains elusive. Here we show that commitment of blood progenitor cells to the erythroid or myeloid lineage is preceded by the destabilization of their high-dimensional attractor state, such that differentiating cells undergo a critical state transition. Single-cell resolution analysis of gene expression in populations of differentiating cells affords a new quantitative index for predicting critical transitions in a high-dimensional state space based on decrease of correlation between cells and concomitant increase of correlation between genes as cells approach a tipping point. The detection of “rebellious cells” that enter the fate opposite to the one intended corroborates the model of preceding destabilization of a progenitor attractor. Thus, early warning signals associated with critical transitions can be detected in statistical ensembles of high-dimensional systems, offering a formal theory-based approach for analyzing single-cell molecular profiles that goes beyond current computational pattern recognition, does not require knowledge of specific pathways, and could be used to predict impending major shifts in development and disease. PMID:28027308

  15. Efficient Transition State Optimization of Periodic Structures through Automated Relaxed Potential Energy Surface Scans.

    PubMed

    Plessow, Philipp N

    2018-02-13

    This work explores how constrained linear combinations of bond lengths can be used to optimize transition states in periodic structures. Scanning of constrained coordinates is a standard approach for molecular codes with localized basis functions, where a full set of internal coordinates is used for optimization. Common plane wave-codes for periodic boundary conditions almost exlusively rely on Cartesian coordinates. An implementation of constrained linear combinations of bond lengths with Cartesian coordinates is described. Along with an optimization of the value of the constrained coordinate toward the transition states, this allows transition optimization within a single calculation. The approach is suitable for transition states that can be well described in terms of broken and formed bonds. In particular, the implementation is shown to be effective and efficient in the optimization of transition states in zeolite-catalyzed reactions, which have high relevance in industrial processes.

  16. Charge states of ions, and mechanisms of charge ordering transitions

    NASA Astrophysics Data System (ADS)

    Pickett, Warren E.; Quan, Yundi; Pardo, Victor

    2014-07-01

    To gain insight into the mechanism of charge ordering transitions, which conventionally are pictured as a disproportionation of an ion M as 2Mn+→M(n+1)+ + M(n-1)+, we (1) review and reconsider the charge state (or oxidation number) picture itself, (2) introduce new results for the putative charge ordering compound AgNiO2 and the dual charge state insulator AgO, and (3) analyze the cationic occupations of the actual (not formal) charge, and work to reconcile the conundrums that arise. We establish that several of the clearest cases of charge ordering transitions involve no disproportion (no charge transfer between the cations, and hence no charge ordering), and that the experimental data used to support charge ordering can be accounted for within density functional-based calculations that contain no charge transfer between cations. We propose that the charge state picture retains meaning and importance, at least in many cases, if one focuses on Wannier functions rather than atomic orbitals. The challenge of modeling charge ordering transitions with model Hamiltonians isdiscussed.

  17. Tegotae-based decentralised control scheme for autonomous gait transition of snake-like robots.

    PubMed

    Kano, Takeshi; Yoshizawa, Ryo; Ishiguro, Akio

    2017-08-04

    Snakes change their locomotion patterns in response to the environment. This ability is a motivation for developing snake-like robots with highly adaptive functionality. In this study, a decentralised control scheme of snake-like robots that exhibited autonomous gait transition (i.e. the transition between concertina locomotion in narrow aisles and scaffold-based locomotion on unstructured terrains) was developed. Additionally, the control scheme was validated via simulations. A key insight revealed is that these locomotion patterns were not preprogrammed but emerged by exploiting Tegotae, a concept that describes the extent to which a perceived reaction matches a generated action. Unlike local reflexive mechanisms proposed previously, the Tegotae-based feedback mechanism enabled the robot to 'selectively' exploit environments beneficial for propulsion, and generated reasonable locomotion patterns. It is expected that the results of this study can form the basis to design robots that can work under unpredictable and unstructured environments.

  18. Topological phase transition and evolution of edge states in In-rich InGaN/GaN quantum wells under hydrostatic pressure

    NASA Astrophysics Data System (ADS)

    Łepkowski, S. P.; Bardyszewski, W.

    2017-02-01

    Combining the k · p method with the third-order elasticity theory, we perform a theoretical study of the pressure-induced topological phase transition and the pressure evolution of topologically protected edge states in InN/GaN and In-rich InGaN/GaN quantum wells. We show that for a certain range of the quantum well parameters, thanks to a negative band gap pressure coefficient, it is possible to continuously drive the system from the normal insulator state through the topological insulator into the semimetal phase. The critical pressure for the topological phase transition depends not only on the quantum well thickness but also on the width of the Hall bar, which determines the coupling between the edge states localized at the opposite edges. We also find that in narrow Hall bar structures, near the topological phase transition, a significant Rashba-type spin splitting of the lower and upper branches of the edge state dispersion curve appears. This effect originates from the lack of the mirror symmetry of the quantum well potential caused by the built-in electric field, and can be suppressed by increasing the Hall bar width. When the pressure increases, the energy dispersion of the edge states becomes more parabolic-like and the spin splitting decreases. A further increase of pressure leads to the transition to a semimetal phase, which occurs due to the closure of the indirect 2D bulk band gap. The difference between the critical pressure at which the system becomes semimetallic, and the pressure for the topological phase transition, correlates with the variation of the pressure coefficient of the band gap in the normal insulator state.

  19. Topological phase transition and evolution of edge states in In-rich InGaN/GaN quantum wells under hydrostatic pressure.

    PubMed

    Łepkowski, S P; Bardyszewski, W

    2017-02-08

    Combining the k · p method with the third-order elasticity theory, we perform a theoretical study of the pressure-induced topological phase transition and the pressure evolution of topologically protected edge states in InN/GaN and In-rich InGaN/GaN quantum wells. We show that for a certain range of the quantum well parameters, thanks to a negative band gap pressure coefficient, it is possible to continuously drive the system from the normal insulator state through the topological insulator into the semimetal phase. The critical pressure for the topological phase transition depends not only on the quantum well thickness but also on the width of the Hall bar, which determines the coupling between the edge states localized at the opposite edges. We also find that in narrow Hall bar structures, near the topological phase transition, a significant Rashba-type spin splitting of the lower and upper branches of the edge state dispersion curve appears. This effect originates from the lack of the mirror symmetry of the quantum well potential caused by the built-in electric field, and can be suppressed by increasing the Hall bar width. When the pressure increases, the energy dispersion of the edge states becomes more parabolic-like and the spin splitting decreases. A further increase of pressure leads to the transition to a semimetal phase, which occurs due to the closure of the indirect 2D bulk band gap. The difference between the critical pressure at which the system becomes semimetallic, and the pressure for the topological phase transition, correlates with the variation of the pressure coefficient of the band gap in the normal insulator state.

  20. A clock transition in a solid-state system

    NASA Astrophysics Data System (ADS)

    Edge, G. J. A.; Potnis, S.; Vutha, A. C.

    2017-04-01

    With the impending redefinition of the SI second based on optical frequency standards, new secondary frequency standards are needed in order to form clock ensembles. Ideally such secondary standards will offer enhanced robustness, portability and high signal-to-noise ratios (SNR), to enable rapid and precise comparisons to be made against primary standards. A clock based on a narrow optical transition, in atoms that are doped into a solid-state host, offers the experimental simplicity and large SNR to satisfy these requirements. The intra-configuration 7F0 ->5D0 transition, in Sm2+ ions doped into a host crystal, is an attractive candidate for such secondary standards due to its low susceptibility to perturbations from the crystal environment. We present results from the interrogation of this clock transition with a narrow linewidth laser.

  1. Densification and state transition across the Missouri Ozarks landscape

    Treesearch

    Brice B. Hanberry; John M. Kabrick; Hong S. He

    2014-01-01

    World-wide, some biomes are densifying, or increasing in dense woody vegetation, and shifting to alternative stable states. We quantified densification and state transition between forests ecosystems in historical (ca. 1815-1850) and current (2004-2008) surveys of the Missouri Ozark Highlands, a 5-million ha landscape in southern Missouri, USA. To estimate density of...

  2. Modeling the dynamic responses of riparian vegetation and salmon habitat in the Oregon Coast Range with state-and-transition models

    Treesearch

    Steven M. Wondzell; Agnieszka Przeszlowska; Dirk Pflugmacher; Miles A. Hemstrom; Peter A. Bisson

    2012-01-01

    Interactions between landuse and ecosystem change are complex, especially in riparian zones. To date, few models are available to project the influence of alternative landuse practices, natural disturbance and plant succession on the likely future conditions of riparian zones and aquatic habitats across large spatial extents. A state and transition approach was used to...

  3. DEPRESSIVE SYMPTOMS AND FUNCTIONAL TRANSITIONS OVER TIME IN OLDER PERSONS

    PubMed Central

    Barry, Lisa C.; Murphy, Terrence E.; Gill, Thomas M.

    2010-01-01

    Objective We determined the association between clinically significant depressive symptoms, often referred to as depression, and subsequent transitions between no disability, mild disability, severe disability, and death. Design Prospective cohort study. Setting General community in greater New Haven, Connecticut, from March 23, 1998, to December 31, 2008. Participants Seven-hundred fifty four persons, aged 70 years or older. Measurements Monthly assessments of disability in essential activities of daily living and assessments of depressive symptoms every 18 months using a short-form of the Center for Epidemiologic Studies of Depression Scale for up to 129 months. Results Depressed participants were more likely than those who were non-depressed to transition from a state of no disability to mild (HR= 1.52; 95% CI 1.25, 1.85) and severe disability (HR=1.57; 95% CI 1.22, 2.01), and from a state of mild disability to severe disability (HR=1.33; 95% CI 1.06, 1.65); and were less likely to transition from a state of mild disability to no disability (HR=0.69; 95% CI 0.57, 0.85) and from a state of severe disability to no disability (HR=0.50; 95% CI 0.31, 0.79). Conclusions Depressive symptoms are associated with transitions into and out of disabled states, and with increased likelihood of transitioning from mild to severe disability. More broadly, our findings underscore the complexity of the relationship between depressive symptoms and disability. Future work is needed to evaluate the likely reciprocal relationship between depression and functional transitions in older persons. PMID:21873834

  4. Movement-related and steady-state electromyographic activity of human elbow flexors in slow transition movements between two equilibrium states.

    PubMed

    Tal'nov, A N; Cherkassky, V L; Kostyukov, A I

    1997-08-01

    The electromyograms were recorded in healthy human subjects by surface electrodes from the mm. biceps brachii (caput longum et. brevis), brachioradialis, and triceps brachii (caput longum) during slow transition movements in elbow joint against a weak extending torque. The test movements (flexion transitions between two steady-states) were fulfilled under visual control through combining on a monitor screen a signal from a joint angle sensor with a corresponding command generated by a computer. Movement velocities ranged between 5 and 80 degrees/s, subjects were asked to move forearm without activation of elbow extensors. Surface electromyograms were full-wave rectified, filtered and averaged within sets of 10 identical tests. Amplitudes of dynamic and steady-state components of the electromyograms were determined in dependence on a final value of joint angle, slow and fast movements were compared. An exponential-like increase of dynamic component was observed in electromyograms recorded from m. biceps brachii, the component had been increased with movement velocity and with load increment. In many experiments a statistically significant decrease of static component could be noticed within middle range of joint angles (40-60 degrees) followed by a well expressed increment for larger movements. This pattern of the static component in electromyograms could vary in different experiments even in the same subjects. A steady discharge in m. brachioradialis at ramp phase has usually been recorded only under a notable load. Variable and quite often unpredictable character of the static components of the electromyograms recorded from elbow flexors in the transition movements makes it difficult to use the equilibrium point hypothesis to describe the central processes of movement. It has been assumed that during active muscle shortening the dynamic components in arriving efferent activity should play a predominant role. A simple scheme could be proposed for transition to a

  5. Communication: Electronic flux induced by crossing the transition state

    NASA Astrophysics Data System (ADS)

    Jia, Dongming; Manz, Jörn; Yang, Yonggang

    2018-01-01

    We present a new effect of chemical reactions, e.g., isomerizations, that occurs when the reactants pass along the transition state, on the way to products. It is based on the well-known fact that at the transition state, the electronic structure of one isomer changes to the other. We discover that this switch of electronic structure causes a strong electronic flux that is well distinguishable from the usual flux of electrons that travel with the nuclei. As a simple but clear example, the effect is demonstrated here for bond length isomerization of Na2 (21Σu+), with adiabatic crossing the barrier between the inner and outer wells of the double minimum potential that support different "Rydberg" and "ionic" type electronic structures, respectively.

  6. Transforming high-dimensional potential energy surfaces into sum-of-products form using Monte Carlo methods

    NASA Astrophysics Data System (ADS)

    Schröder, Markus; Meyer, Hans-Dieter

    2017-08-01

    We propose a Monte Carlo method, "Monte Carlo Potfit," for transforming high-dimensional potential energy surfaces evaluated on discrete grid points into a sum-of-products form, more precisely into a Tucker form. To this end we use a variational ansatz in which we replace numerically exact integrals with Monte Carlo integrals. This largely reduces the numerical cost by avoiding the evaluation of the potential on all grid points and allows a treatment of surfaces up to 15-18 degrees of freedom. We furthermore show that the error made with this ansatz can be controlled and vanishes in certain limits. We present calculations on the potential of HFCO to demonstrate the features of the algorithm. To demonstrate the power of the method, we transformed a 15D potential of the protonated water dimer (Zundel cation) in a sum-of-products form and calculated the ground and lowest 26 vibrationally excited states of the Zundel cation with the multi-configuration time-dependent Hartree method.

  7. State-and-transition simulation models: a framework for forecasting landscape change

    USGS Publications Warehouse

    Daniel, Colin; Frid, Leonardo; Sleeter, Benjamin M.; Fortin, Marie-Josée

    2016-01-01

    SummaryA wide range of spatially explicit simulation models have been developed to forecast landscape dynamics, including models for projecting changes in both vegetation and land use. While these models have generally been developed as separate applications, each with a separate purpose and audience, they share many common features.We present a general framework, called a state-and-transition simulation model (STSM), which captures a number of these common features, accompanied by a software product, called ST-Sim, to build and run such models. The STSM method divides a landscape into a set of discrete spatial units and simulates the discrete state of each cell forward as a discrete-time-inhomogeneous stochastic process. The method differs from a spatially interacting Markov chain in several important ways, including the ability to add discrete counters such as age and time-since-transition as state variables, to specify one-step transition rates as either probabilities or target areas, and to represent multiple types of transitions between pairs of states.We demonstrate the STSM method using a model of land-use/land-cover (LULC) change for the state of Hawai'i, USA. Processes represented in this example include expansion/contraction of agricultural lands, urbanization, wildfire, shrub encroachment into grassland and harvest of tree plantations; the model also projects shifts in moisture zones due to climate change. Key model output includes projections of the future spatial and temporal distribution of LULC classes and moisture zones across the landscape over the next 50 years.State-and-transition simulation models can be applied to a wide range of landscapes, including questions of both land-use change and vegetation dynamics. Because the method is inherently stochastic, it is well suited for characterizing uncertainty in model projections. When combined with the ST-Sim software, STSMs offer a simple yet powerful means for developing a wide range of models of

  8. Transition of vegetation states positively affects harvester ants in the Great Basin, United States

    USGS Publications Warehouse

    Holbrook, Joseph D.; Pilliod, David S.; Arkle, Robert; Rachlow, Janet L.; Vierling, Kerri T.; Wiest, Michelle M.

    2016-01-01

    Invasions by non-native plants can alter ecosystems such that new ecological states are reached, but less is known about how these transitions influence animal populations. Sagebrush (Artemisia tridentata) ecosystems are experiencing state changes because of fire and invasion by exotic annual grasses. Our goal was to study the effects of these state changes on the Owyhee and western harvester ants (Pogonomyrmex salinusOlsen and P. occidentalis Cresson, respectively). We sampled 358 1-ha plots across the northern Great Basin, which captured unburned and burned conditions across 1 −≥31 years postfire. Our results indicated an immediate and consistent change in vegetation states from shrubland to grassland between 1 and 31 years postfire. Harvester ant occupancy was unrelated to time since fire, whereas we observed a positive effect of fire on nest density. Similarly, we discovered that fire and invasion by exotic annuals were weak predictors of harvester ant occupancy but strong predictors of nest density. Occupancy of harvester ants was more likely in areas with finer-textured soils, low precipitation, abundant native forbs, and low shrub cover. Nest density was higher in arid locations that recently burned and exhibited abundant exotic annual and perennial (exotic and native) grasses. Finally, we discovered that burned areas that received postfire restoration had minimal influence on harvester ant occupancy or nest density compared with burned and untreated areas. These results suggest that fire-induced state changes from native shrublands to grasslands dominated by non-native grasses have a positive effect on density of harvester ants (but not occupancy), and that postfire restoration does not appear to positively or negatively affect harvester ants. Although wildfire and invasion by exotic annual grasses may negatively affect other species, harvester ants may indeed be one of the few winners among a myriad of losers linked to vegetation state changes within

  9. Chimera-like states in structured heterogeneous networks

    NASA Astrophysics Data System (ADS)

    Li, Bo; Saad, David

    2017-04-01

    Chimera-like states are manifested through the coexistence of synchronous and asynchronous dynamics and have been observed in various systems. To analyze the role of network topology in giving rise to chimera-like states, we study a heterogeneous network model comprising two groups of nodes, of high and low degrees of connectivity. The architecture facilitates the analysis of the system, which separates into a densely connected coherent group of nodes, perturbed by their sparsely connected drifting neighbors. It describes a synchronous behavior of the densely connected group and scaling properties of the induced perturbations.

  10. Energies, Wavelengths, and Transition Rates for Ga-Like Ions (Nd XXX-Tb XXXV)

    NASA Astrophysics Data System (ADS)

    El-Sayed, Fatma; Attia, S. M.

    2016-03-01

    Energies, wavelengths, transition probabilities, oscillator strengths, and line strengths have been calculated for 4s24p-4s4p2 and 4s24p-4s24d transitions in gallium-like ions from Z = 60 to 65, for Nd XXX, Pm XXXI, Sm XXXII, Eu XXXIII, Gd XXXIV, and Tb XXXV using the fully relativistic multiconfi guration Dirac-Fock method. The correlation with the n = 4 complex and the quantum electrodynamic effects have been considered in the calculations. The obtained results have been compared with the available experimental and other theoretical results.

  11. The structure and energetics of the HCN → HNC transition state

    NASA Astrophysics Data System (ADS)

    Lee, Timothy J.; Rendell, Alistair P.

    1991-03-01

    The optimum geometries and quadratic force constants of HCN, HNC and the transition state connecting them have been determined at the single and double excitation coupled-cluster (CCSD) and CCSD(T) levels of theory. Energy differences were evaluated using the CCSD and CCSD(T) methods in conjunction with large atomic natural orbital basis sets containing g-type basis functions on the heavy atoms and f-type functions on hydrogen. The most reliable structure obtained for the transition state has bond distances of 1.194, 1.188 and 1.389 Å for rCN, rCH and rNH, respectively. Including a correction for zero-point vibrational energies, the transition state is predicted to be 44.6 ± 1.0 kcal/mol above the HCN isomer, while HNC is predicted to be 14.4 ± 1.0 kcal/mol above HCN. The latter value is in excellent agreement with the most recent experimental determination (14.8 ± 2.0 kcal/mol).

  12. Genome-wide chromatin state transitions associated with developmental and environmental cues.

    PubMed

    Zhu, Jiang; Adli, Mazhar; Zou, James Y; Verstappen, Griet; Coyne, Michael; Zhang, Xiaolan; Durham, Timothy; Miri, Mohammad; Deshpande, Vikram; De Jager, Philip L; Bennett, David A; Houmard, Joseph A; Muoio, Deborah M; Onder, Tamer T; Camahort, Ray; Cowan, Chad A; Meissner, Alexander; Epstein, Charles B; Shoresh, Noam; Bernstein, Bradley E

    2013-01-31

    Differences in chromatin organization are key to the multiplicity of cell states that arise from a single genetic background, yet the landscapes of in vivo tissues remain largely uncharted. Here, we mapped chromatin genome-wide in a large and diverse collection of human tissues and stem cells. The maps yield unprecedented annotations of functional genomic elements and their regulation across developmental stages, lineages, and cellular environments. They also reveal global features of the epigenome, related to nuclear architecture, that also vary across cellular phenotypes. Specifically, developmental specification is accompanied by progressive chromatin restriction as the default state transitions from dynamic remodeling to generalized compaction. Exposure to serum in vitro triggers a distinct transition that involves de novo establishment of domains with features of constitutive heterochromatin. We describe how these global chromatin state transitions relate to chromosome and nuclear architecture, and discuss their implications for lineage fidelity, cellular senescence, and reprogramming. Copyright © 2013 Elsevier Inc. All rights reserved.

  13. Tobacco use transitions in the United States: The National Longitudinal Study of Adolescent Health

    PubMed Central

    Kaufman, Annette R.; Land, Stephanie; Parascandola, Mark; Augustson, Erik; Backinger, Cathy L.

    2015-01-01

    Objectives The purpose of this study is to evaluate and describe transitions in cigarette and smokeless tobacco (ST) use, including dual use, prospectively from adolescence into young adulthood. Methods The current study utilizes four waves of the National Longitudinal Study of Adolescent Health (Add Health) to examine patterns of cigarette and ST use (within 30 days of survey) over time among a cohort in the United States beginning in 7th–12th grade (1995) into young adulthood (2008–2009). Transition probabilities were estimated using Markov modeling. Results Among the cohort (N = 20,774), 48.7% reported using cigarettes, 12.8% reported using ST, and 7.2% reported dual use (cigarettes and ST in the same wave) in at least one wave. In general, the risk for transitioning between cigarettes and ST was higher for males and those who were older. Dual users exhibited a high probability (81%) of continuing dual use over time. Conclusions Findings suggest that adolescents who use multiple tobacco products are likely to continue such use as they move into young adulthood. When addressing tobacco use among adolescents and young adults, multiple forms of tobacco use should be considered. PMID:26361752

  14. Status of Credentialing Structures Related to Secondary Transition: A State-Level Policy Analysis

    ERIC Educational Resources Information Center

    Simonsen, Monica L.; Novak, Jeanne A.; Mazzotti, Valerie L.

    2018-01-01

    To understand the current status of transition-related credentialing systems in driving personnel preparation, it is necessary to identify which state education and rehabilitation services agencies are currently providing certification and licensure in the area of secondary transition. The purpose of this study was to examine the current state of…

  15. Topological quantum phase transitions and edge states in spin-orbital coupled Fermi gases.

    PubMed

    Zhou, Tao; Gao, Yi; Wang, Z D

    2014-06-11

    We study superconducting states in the presence of spin-orbital coupling and Zeeman field. It is found that a phase transition from a Fulde-Ferrell-Larkin-Ovchinnikov state to the topological superconducting state occurs upon increasing the spin-orbital coupling. The nature of this topological phase transition and its critical property are investigated numerically. Physical properties of the topological superconducting phase are also explored. Moreover, the local density of states is calculated, through which the topological feature may be tested experimentally.

  16. Role of entropy and structural parameters in the spin-state transition of LaCoO3

    NASA Astrophysics Data System (ADS)

    Chakrabarti, Bismayan; Birol, Turan; Haule, Kristjan

    2017-11-01

    The spin-state transition in LaCoO3 has eluded description for decades despite concerted theoretical and experimental effort. In this study, we approach this problem using fully charge self-consistent density functional theory + embedded dynamical mean field theory (DFT+DMFT). We show from first principles that LaCoO3 cannot be described by a single, pure spin state at any temperature. Instead, we observe a gradual change in the population of higher-spin multiplets with increasing temperature, with the high-spin multiplets being excited at the onset of the spin-state transition followed by the intermediate-spin multiplets being excited at the metal-insulator-transition temperature. We explicitly elucidate the critical role of lattice expansion and oxygen octahedral rotations in the spin-state transition. We also reproduce, from first principles, that the spin-state transition and the metal-insulator transition in LaCoO3 occur at different temperature scales. In addition, our results shed light on the importance of electronic entropy in driving the spin-state transition, which has so far been ignored in all first-principles studies of this material.

  17. IR spectral assignments for the hydrated excess proton in liquid water.

    PubMed

    Biswas, Rajib; Carpenter, William; Fournier, Joseph A; Voth, Gregory A; Tokmakoff, Andrei

    2017-04-21

    The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We find there is a wide distribution of vibrational frequencies spanning 1200-3000 cm -1 for every local proton configuration, with the region 2000-2600 cm -1 being mostly governed by the distorted Eigen-like configuration. We find a continuous red shift of the special-pair O⋯H + ⋯O stretching frequency, and an increase in the flanking water bending intensity with decreasing δ. Also, we find that the flanking water stretch mode of the Zundel-like species is strongly mixed with the flanking water bend, and the special pair proton oscillation band is strongly coupled with the bend modes of the central H 5 O2+moiety.

  18. IR spectral assignments for the hydrated excess proton in liquid water

    NASA Astrophysics Data System (ADS)

    Biswas, Rajib; Carpenter, William; Fournier, Joseph A.; Voth, Gregory A.; Tokmakoff, Andrei

    2017-04-01

    The local environmental sensitivity of infrared (IR) spectroscopy to a hydrogen-bonding structure makes it a powerful tool for investigating the structure and dynamics of excess protons in water. Although of significant interest, the line broadening that results from the ultrafast evolution of different solvated proton-water structures makes the assignment of liquid-phase IR spectra a challenging task. In this work, we apply a normal mode analysis using density functional theory of thousands of proton-water clusters taken from reactive molecular dynamics trajectories of the latest generation multistate empirical valence bond proton model (MS-EVB 3.2). These calculations are used to obtain a vibrational density of states and IR spectral density, which are decomposed on the basis of solvated proton structure and the frequency dependent mode character. Decompositions are presented on the basis of the proton sharing parameter δ, often used to distinguish Eigen and Zundel species, the stretch and bend character of the modes, the mode delocalization, and the vibrational mode symmetry. We find there is a wide distribution of vibrational frequencies spanning 1200-3000 cm-1 for every local proton configuration, with the region 2000-2600 cm-1 being mostly governed by the distorted Eigen-like configuration. We find a continuous red shift of the special-pair O⋯H+⋯O stretching frequency, and an increase in the flanking water bending intensity with decreasing δ. Also, we find that the flanking water stretch mode of the Zundel-like species is strongly mixed with the flanking water bend, and the special pair proton oscillation band is strongly coupled with the bend modes of the central H5+O2 moiety.

  19. Experimental and computational analysis of the transition state for ribonuclease A-catalyzed RNA 2′-O-transphosphorylation

    PubMed Central

    Gu, Hong; Zhang, Shuming; Wong, Kin-Yiu; Radak, Brian K.; Dissanayake, Thakshila; Kellerman, Daniel L.; Dai, Qing; Miyagi, Masaru; Anderson, Vernon E.; York, Darrin M.; Piccirilli, Joseph A.; Harris, Michael E.

    2013-01-01

    Enzymes function by stabilizing reaction transition states; therefore, comparison of the transition states of enzymatic and nonenzymatic model reactions can provide insight into biological catalysis. Catalysis of RNA 2′-O-transphosphorylation by ribonuclease A is proposed to involve electrostatic stabilization and acid/base catalysis, although the structure of the rate-limiting transition state is uncertain. Here, we describe coordinated kinetic isotope effect (KIE) analyses, molecular dynamics simulations, and quantum mechanical calculations to model the transition state and mechanism of RNase A. Comparison of the 18O KIEs on the 2′O nucleophile, 5′O leaving group, and nonbridging phosphoryl oxygens for RNase A to values observed for hydronium- or hydroxide-catalyzed reactions indicate a late anionic transition state. Molecular dynamics simulations using an anionic phosphorane transition state mimic suggest that H-bonding by protonated His12 and Lys41 stabilizes the transition state by neutralizing the negative charge on the nonbridging phosphoryl oxygens. Quantum mechanical calculations consistent with the experimental KIEs indicate that expulsion of the 5′O remains an integral feature of the rate-limiting step both on and off the enzyme. Electrostatic interactions with positively charged amino acid site chains (His12/Lys41), together with proton transfer from His119, render departure of the 5′O less advanced compared with the solution reaction and stabilize charge buildup in the transition state. The ability to obtain a chemically detailed description of 2′-O-transphosphorylation transition states provides an opportunity to advance our understanding of biological catalysis significantly by determining how the catalytic modes and active site environments of phosphoryl transferases influence transition state structure. PMID:23878223

  20. Complex transitions between spike, burst or chaos synchronization states in coupled neurons with coexisting bursting patterns

    NASA Astrophysics Data System (ADS)

    Gu, Hua-Guang; Chen, Sheng-Gen; Li, Yu-Ye

    2015-05-01

    We investigated the synchronization dynamics of a coupled neuronal system composed of two identical Chay model neurons. The Chay model showed coexisting period-1 and period-2 bursting patterns as a parameter and initial values are varied. We simulated multiple periodic and chaotic bursting patterns with non-(NS), burst phase (BS), spike phase (SS), complete (CS), and lag synchronization states. When the coexisting behavior is near period-2 bursting, the transitions of synchronization states of the coupled system follows very complex transitions that begins with transitions between BS and SS, moves to transitions between CS and SS, and to CS. Most initial values lead to the CS state of period-2 bursting while only a few lead to the CS state of period-1 bursting. When the coexisting behavior is near period-1 bursting, the transitions begin with NS, move to transitions between SS and BS, to transitions between SS and CS, and then to CS. Most initial values lead to the CS state of period-1 bursting but a few lead to the CS state of period-2 bursting. The BS was identified as chaos synchronization. The patterns for NS and transitions between BS and SS are insensitive to initial values. The patterns for transitions between CS and SS and the CS state are sensitive to them. The number of spikes per burst of non-CS bursting increases with increasing coupling strength. These results not only reveal the initial value- and parameter-dependent synchronization transitions of coupled systems with coexisting behaviors, but also facilitate interpretation of various bursting patterns and synchronization transitions generated in the nervous system with weak coupling strength. Project supported by the National Natural Science Foundation of China (Grant Nos. 11372224 and 11402039) and the Fundamental Research Funds for Central Universities designated to Tongji University (Grant No. 1330219127).

  1. Critical high-dimensional state transitions in cell populations or why cancers follow the principle ``What does not kill me makes me stronger''

    NASA Astrophysics Data System (ADS)

    Huang, Sui

    Transitions between high-dimensional attractor states in the quasi-potential landscape of the gene regulatory network, induced by environmental perturbations and/or facilitated by mutational rewiring of the network, underlie cell phenotype switching in development as well as in cancer progression, including acquisition of drug-resistant phenotypes. Considering heterogeneous cell populations as statistical ensembles of cells, and single-cell resolution gene expression profiling of cell populations undergoing a cell phenotype shift allow us now to map the topography of the landscape and its distortion. From snapshots of single-cell expression patterns of a cell population measured during major transitions we compute a quantity that identifies symmetry-breaking destabilization of attractors (bifurcation) and concomitant dimension-reduction of the state space manifold (landscape distortion) which precede critical transitions to new attractor states. The model predicts, and we show experimentally, the almost inevitable generation of aberrant cells associated with such critical transitions in multi-attractor landscapes: therapeutic perturbations which seek to push cancer cells to the apoptotic state, almost always produce ``rebellious'' cells which move in the ``opposite direction'': instead of dying they become more stem-cell-like and malignant. We show experimentally that the inadvertent generation of more malignant cancer cells by therapy indeed results from transition of surviving (but stressed) cells into unforeseen attractor states and not simply from selection of inherently more resistant cells. Thus, cancer cells follow not so much Darwin, as generally thought (survival of the fittest), but rather Nietzsche (What does not kill me makes me stronger). Supported by NIH (NCI, NIGMS), Alberta Innovates.

  2. Grassland to shrubland state transitions enhance carbon sequestration in the northern Chihuahuan Desert

    Treesearch

    M. D. Petrie; S. L. Collins; A. M. Swann; P. L. Ford; M. E. Litvak

    2015-01-01

    The replacement of native C4-dominated grassland by C3-dominated shrubland is considered an ecological state transition where different ecological communities can exist under similar environmental conditions. These state transitions are occurring globally, and may be exacerbated by climate change. One consequence of the global increase in woody vegetation may be...

  3. A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms

    PubMed Central

    Chandrasekaran, Srinivas Niranj; Das, Jhuma; Dokholyan, Nikolay V.; Carter, Charles W.

    2016-01-01

    PATH rapidly computes a path and a transition state between crystal structures by minimizing the Onsager-Machlup action. It requires input parameters whose range of values can generate different transition-state structures that cannot be uniquely compared with those generated by other methods. We outline modifications to estimate these input parameters to circumvent these difficulties and validate the PATH transition states by showing consistency between transition-states derived by different algorithms for unrelated protein systems. Although functional protein conformational change trajectories are to a degree stochastic, they nonetheless pass through a well-defined transition state whose detailed structural properties can rapidly be identified using PATH. PMID:26958584

  4. Magnetocaloric effect and negative thermal expansion in hexagonal Fe doped MnNiGe compounds with a magnetoelastic AFM-FM-like transition

    PubMed Central

    Xu, Kun; Li, Zhe; Liu, Enke; Zhou, Haichun; Zhang, Yuanlei; Jing, Chao

    2017-01-01

    We report a detailed study of two successive first-order transitions, including a martensitic transition (MT) and an antiferromagnetic (AFM)-ferromagnetic (FM)-like transition, in Mn1-xFexNiGe (x = 0, 0.06, 0.11) alloys by X-ray diffraction, differential scanning calorimetry, magnetization and linear thermal expansion measurements. Such an AFM-FM-like transition occurring in the martensitic state has seldom been observed in the M(T) curves. The results of Arrott plot and linear relationship of the critical temperature with M2 provide explicit evidence of its first-order magnetoelastic nature. On the other hand, their performances as magnetocaloric and negative thermal expansion materials were characterized. The isothermal entropy change for a field change of 30 kOe reaches an impressive value of −25.8 J/kg K at 203 K for x = 0.11 compared to the other two samples. It demonstrates that the magneto-responsive ability has been significantly promoted since an appropriate amount of Fe doping can break the local Ni-6Mn AFM configuration. Moreover, the Fe-doped samples reveal both the giant negative thermal expansion and near-zero thermal expansion for different temperature ranges. For instance, the average thermal expansion coefficient ā of x = 0.06 reaches −60.7 × 10−6/K over T = 231–338 K and 0.6 × 10−6/K over T = 175–231 K during cooling. PMID:28134355

  5. An Overview of State Mass Transit Assistance Programs: Financing and Distribution Mechanisms

    DOT National Transportation Integrated Search

    1987-11-01

    In FY 1987, thirty states provided a total of approximately $2.5 billion in : state operating assistance to public transit. The level of state operating : assistance ranges from $75,000 in the state of Montanna to $941 million in New : York state. Th...

  6. Employment Outcomes of Transition-Aged Adults with Autism Spectrum Disorders: A State of the States Report

    ERIC Educational Resources Information Center

    Burgess, Sloane; Cimera, Robert E.

    2014-01-01

    The primary purpose of this study was to evaluate the employment outcomes of transition-aged adults with autism spectrum disorders (ASD) served by vocational rehabilitation services (VR) over the last 10 years by state. A secondary purpose was to compare employment outcomes of individuals with ASD to those of the overall transition-aged population…

  7. The Transition from State Care to Adulthood: International Examples of Best Practices

    ERIC Educational Resources Information Center

    Reid, Carrie

    2007-01-01

    The issue of outcomes for youth who transition from state care to adulthood is not unique to any one country. Youth exiting the child welfare system, or aging out, face a plethora of problems and issues associated with the transition to adulthood. For the majority of youth, the transition to adulthood represents a process that takes place over a…

  8. State Transition to High-Quality, College/Career-Ready Assessments: A Workbook for State Action on Key Policy, Legal, and Technical Issues. Updated

    ERIC Educational Resources Information Center

    Achieve, Inc., 2013

    2013-01-01

    Over the next few years, states will be transitioning to new, high-quality assessments aligned to the Common Core State Standards (CCSS) or other state college- and career-ready (CCR) standards. States are committed to making this transition in a manner that is determined and thoughtful--to help transform teaching and learning, advance CCR…

  9. AN ENIGMATIC POINT-LIKE FEATURE WITHIN THE HD 169142 TRANSITIONAL DISK ,

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Biller, Beth A.; Males, Jared; Morzinski, Katie

    2014-09-01

    We report the detection of a faint point-like feature possibly related to ongoing planet-formation in the disk of the transition disk star HD 169142. The point-like feature has a Δmag(L) ∼ 6.4, at a separation of ∼0.''11 and position angle ∼0°. Given its lack of an H or K{sub S} counterpart despite its relative brightness, this candidate cannot be explained by purely photospheric emission and must be a disk feature heated by an as yet unknown source. Its extremely red colors make it highly unlikely to be a background object, but future multi-wavelength follow up is necessary for confirmation and characterization ofmore » this feature.« less

  10. Transition metal decorated graphene-like zinc oxide monolayer: A first-principles investigation

    NASA Astrophysics Data System (ADS)

    Lei, Jie; Xu, Ming-Chun; Hu, Shu-Jun

    2015-09-01

    Transition metal (TM) atoms have been extensively employed to decorate the two-dimensional materials, endowing them with promising physical properties. Here, we have studied the adsorption of TM atoms (V, Cr, Mn, Fe, and Co) on graphene-like zinc oxide monolayer (g-ZnO) and the substitution of Zn by TM using first-principles calculations to search for the most likely configurations when TM atoms are deposited on g-ZnO. We found that when a V atom is initially placed on the top of Zn atom, V will squeeze out Zn from the two-dimensional plane then substitute it, which is a no barrier substitution process. For heavier elements (Cr to Co), although the substitution configurations are more stable than the adsorption ones, there is an energy barrier for the adsorption-substitution transition with the height of tens to hundreds meV. Therefore, Cr to Co prefers to be adsorbed on the hollow site or the top of oxygen, which is further verified by the molecular dynamics simulations. The decoration of TM is revealed to be a promising approach in terms of tuning the work function of g-ZnO in a large energy range.

  11. Identifying intrinsically disordered protein regions likely to undergo binding-induced helical transitions.

    PubMed

    Glover, Karen; Mei, Yang; Sinha, Sangita C

    2016-10-01

    Many proteins contain intrinsically disordered regions (IDRs) lacking stable secondary and ordered tertiary structure. IDRs are often implicated in macromolecular interactions, and may undergo structural transitions upon binding to interaction partners. However, as binding partners of many protein IDRs are unknown, these structural transitions are difficult to verify and often are poorly understood. In this study we describe a method to identify IDRs that are likely to undergo helical transitions upon binding. This method combines bioinformatics analyses followed by circular dichroism spectroscopy to monitor 2,2,2-trifluoroethanol (TFE)-induced changes in secondary structure content of these IDRs. Our results demonstrate that there is no significant change in the helicity of IDRs that are not predicted to fold upon binding. IDRs that are predicted to fold fall into two groups: one group does not become helical in the presence of TFE and includes examples of IDRs that form β-strands upon binding, while the other group becomes more helical and includes examples that are known to fold into helices upon binding. Therefore, we propose that bioinformatics analyses combined with experimental evaluation using TFE may provide a general method to identify IDRs that undergo binding-induced disorder-to-helix transitions. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Liquid-Gas-Like Phase Transition in Sand Flow Under Microgravity

    NASA Astrophysics Data System (ADS)

    Huang, Yu; Zhu, Chongqiang; Xiang, Xiang; Mao, Wuwei

    2015-06-01

    In previous studies of granular flow, it has been found that gravity plays a compacting role, causing convection and stratification by density. However, there is a lack of research and analysis of the characteristics of different particles' motion under normal gravity contrary to microgravity. In this paper, we conduct model experiments on sand flow using a model test system based on a drop tower under microgravity, within which the characteristics and development processes of granular flow under microgravity are captured by high-speed cameras. The configurations of granular flow are simulated using a modified MPS (moving particle simulation), which is a mesh-free, pure Lagrangian method. Moreover, liquid-gas-like phase transitions in the sand flow under microgravity, including the transitions to "escaped", "jumping", and "scattered" particles are highlighted, and their effects on the weakening of shear resistance, enhancement of fluidization, and changes in particle-wall and particle-particle contact mode are analyzed. This study could help explain the surface geology evolution of small solar bodies and elucidate the nature of granular interaction.

  13. Exploring the Conformational Transitions of Biomolecular Systems Using a Simple Two-State Anisotropic Network Model

    PubMed Central

    Jo, Sunhwan; Bahar, Ivet; Roux, Benoît

    2014-01-01

    Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver ANMPathway results

  14. MHD simulation of relaxation transition to a flipped relaxed state in spherical torus

    NASA Astrophysics Data System (ADS)

    Kanki, Takashi; Nagata, Masayoshi; Kagei, Yasuhiro

    2008-11-01

    Recently, it has been demonstrated in the HIST device that in spite of the violation of the Kruskal-Shafranov stability condition, a normal spherical torus (ST) plasma has relaxed to a flipped ST state through a transient reversed-field pinch-like state when the vacuum toroidal field is decreased and its direction is reversed [1]. It has been also observed during this relaxation transition process that not only the toroidal field but also the poloidal field reverses polarity spontaneously and that the ion flow velocity is strongly fluctuated and abruptly increased up to > 50 km/s. The purpose of the present study is to investigate the plasma flows and the relevant MHD relaxation phenomena to elucidate this transition mechanism by using three-dimensional MHD simulations [2]. It is found from the numerical results that the magnetic reconnection between the open and closed field lines occurs due to the non-linear growth of the n=1 kink instability of the central open flux, generating the toroidal flow ˜ 60 km/s in the direction of the toroidal current. The n=1 kink instability and the plasma flows driven by the magnetic reconnection are consider to be responsible for the self-reversal of the magnetic fields. [1] M. Nagata el al., Phys. Rev. Lett. 90, 225001 (2003). [2] Y. Kagei el al., Plasma. Phys. Control. Fusion 45, L17 (2003).

  15. Tables of stark level transition probabilities and branching ratios in hydrogen-like atoms

    NASA Technical Reports Server (NTRS)

    Omidvar, K.

    1980-01-01

    The transition probabilities which are given in terms of n prime k prime and n k are tabulated. No additional summing or averaging is necessary. The electric quantum number k plays the role of the angular momentum quantum number l in the presence of an electric field. The branching ratios between stark levels are also tabulated. Necessary formulas for the transition probabilities and branching ratios are given. Symmetries are discussed and selection rules are given. Some disagreements for some branching ratios are found between the present calculation and the measurement of Mark and Wierl. The transition probability multiplied by the statistical weight of the initial state is called the static intensity J sub S, while the branching ratios are called the dynamic intensity J sub D.

  16. Exact transition probabilities in a 6-state Landau–Zener system with path interference

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sinitsyn, Nikolai A.

    2015-04-23

    In this paper, we identify a nontrivial multistate Landau–Zener (LZ) model for which transition probabilities between any pair of diabatic states can be determined analytically and exactly. In the semiclassical picture, this model features the possibility of interference of different trajectories that connect the same initial and final states. Hence, transition probabilities are generally not described by the incoherent successive application of the LZ formula. Finally, we discuss reasons for integrability of this system and provide numerical tests of the suggested expression for the transition probability matrix.

  17. Defining and characterizing the critical transition state prior to the type 2 diabetes disease

    PubMed Central

    Zhu, Chunqing; Zhou, Xin; Chen, Pei; Fu, Tianyun; Hu, Zhongkai; Wu, Qian; Liu, Wei; Liu, Daowei; Yu, Yunxian; Zhang, Yan; McElhinney, Doff B.; Li, Yu-Ming; Culver, Devore S; Alfreds, Shaun T.; Stearns, Frank; Sylvester, Karl G.; Widen, Eric

    2017-01-01

    Background Type 2 diabetes mellitus (T2DM), with increased risk of serious long-term complications, currently represents 8.3% of the adult population. We hypothesized that a critical transition state prior to the new onset T2DM can be revealed through the longitudinal electronic medical record (EMR) analysis. Method We applied the transition-based network entropy methodology which previously identified a dynamic driver network (DDN) underlying the critical T2DM transition at the tissue molecular biological level. To profile pre-disease phenotypical changes that indicated a critical transition state, a cohort of 7,334 patients was assembled from the Maine State Health Information Exchange (HIE). These patients all had their first confirmative diagnosis of T2DM between January 1, 2013 and June 30, 2013. The cohort’s EMRs from the 24 months preceding their date of first T2DM diagnosis were extracted. Results Analysis of these patients’ pre-disease clinical history identified a dynamic driver network (DDN) and an associated critical transition state six months prior to their first confirmative T2DM state. Conclusions This 6-month window before the disease state provides an early warning of the impending T2DM, warranting an opportunity to apply proactive interventions to prevent or delay the new onset of T2DM. PMID:28686739

  18. 31 CFR 560.406 - Transshipment or transit through United States prohibited.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... or transit, of Iranian-origin goods or goods owned or controlled by the Government of Iran which are... transit of foreign goods through the United States which are intended or destined for Iran or the Government of Iran, including entities owned or controlled by the Government of Iran. [64 FR 20172, Apr. 26...

  19. 31 CFR 560.406 - Transshipment or transit through United States prohibited.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... or transit, of Iranian-origin goods or goods owned or controlled by the Government of Iran which are... transit of foreign goods through the United States which are intended or destined for Iran or the Government of Iran, including entities owned or controlled by the Government of Iran. [64 FR 20172, Apr. 26...

  20. 31 CFR 560.406 - Transshipment or transit through United States prohibited.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... or transit, of Iranian-origin goods or goods owned or controlled by the Government of Iran which are... transit of foreign goods through the United States which are intended or destined for Iran or the Government of Iran, including entities owned or controlled by the Government of Iran. [64 FR 20172, Apr. 26...

  1. Quantum Teleportation of a Two Qubit State Using GHZ- Like State

    NASA Astrophysics Data System (ADS)

    Nandi, Kaushik; Mazumdar, Chandan

    2014-04-01

    Recently Yang et al. (Int. J. Theor. Phys. 48:516, 2009) had shown that using a particular type of GHZ- Like state as quantum channel, it is possible to teleport an arbitrary unknown qubit. We investigate this channel for the teleportation of a particular type of two qubit state.

  2. A Pipelined Non-Deterministic Finite Automaton-Based String Matching Scheme Using Merged State Transitions in an FPGA

    PubMed Central

    Choi, Kang-Il

    2016-01-01

    This paper proposes a pipelined non-deterministic finite automaton (NFA)-based string matching scheme using field programmable gate array (FPGA) implementation. The characteristics of the NFA such as shared common prefixes and no failure transitions are considered in the proposed scheme. In the implementation of the automaton-based string matching using an FPGA, each state transition is implemented with a look-up table (LUT) for the combinational logic circuit between registers. In addition, multiple state transitions between stages can be performed in a pipelined fashion. In this paper, it is proposed that multiple one-to-one state transitions, called merged state transitions, can be performed with an LUT. By cutting down the number of used LUTs for implementing state transitions, the hardware overhead of combinational logic circuits is greatly reduced in the proposed pipelined NFA-based string matching scheme. PMID:27695114

  3. A Pipelined Non-Deterministic Finite Automaton-Based String Matching Scheme Using Merged State Transitions in an FPGA.

    PubMed

    Kim, HyunJin; Choi, Kang-Il

    2016-01-01

    This paper proposes a pipelined non-deterministic finite automaton (NFA)-based string matching scheme using field programmable gate array (FPGA) implementation. The characteristics of the NFA such as shared common prefixes and no failure transitions are considered in the proposed scheme. In the implementation of the automaton-based string matching using an FPGA, each state transition is implemented with a look-up table (LUT) for the combinational logic circuit between registers. In addition, multiple state transitions between stages can be performed in a pipelined fashion. In this paper, it is proposed that multiple one-to-one state transitions, called merged state transitions, can be performed with an LUT. By cutting down the number of used LUTs for implementing state transitions, the hardware overhead of combinational logic circuits is greatly reduced in the proposed pipelined NFA-based string matching scheme.

  4. Grassland-shrubland state transitions in arid rangelands: Competition matters

    USDA-ARS?s Scientific Manuscript database

    Background: State transition from grassland to shrubland is synonymous with desertification in many arid rangeland systems. Traditional desertification models emphasize abiotic feedbacks that modify the physical environment in ways that promote shrub proliferation and impede grass survival. Inherent...

  5. Communication: State-to-state dynamics of the Cl + H2O → HCl + OH reaction: Energy flow into reaction coordinate and transition-state control of product energy disposal.

    PubMed

    Zhao, Bin; Sun, Zhigang; Guo, Hua

    2015-06-28

    Quantum state-to-state dynamics of a prototypical four-atom reaction, namely, Cl + H2O → HCl + OH, is investigated for the first time in full dimensionality using a transition-state wave packet method. The state-to-state reactivity and its dependence on the reactant internal excitations are analyzed and found to share many similarities both energetically and dynamically with the H + H2O → H2 + OH reaction. The strong enhancement of reactivity by the H2O stretching vibrational excitations in both reactions is attributed to the favorable energy flow into the reaction coordinate near the transition state. On the other hand, the insensitivity of the product state distributions with regard to reactant internal excitation stems apparently from the transition-state control of product energy disposal.

  6. Evolution of the phonon density of states of LaCoO3 over the spin state transition

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Golosova, N. O.; Kozlenko, D. P.; Kolesnikov, Alexander I

    2011-01-01

    The phonon spectra of LaCoO3 were studied by inelastic neutron scattering in the temperature range of 4 120 K. The DFT calculations of the lattice dynamics have been made for interpretation of the experimental data. The observed and calculated phonon frequencies were found to be in a reasonable agreement. The evolution of the phonon density of states over the spin state transition was analyzed. In the low-temperature range (T < 50 K), an increase in the energy of resolved breathing, stretching, and bending phonon modes was found, followed by their softening and broadening at higher temperatures due to the spinmore » state transition and relevant orbital-phonon coupling.« less

  7. Non-Markovian Complexity in the Quantum-to-Classical Transition

    PubMed Central

    Xiong, Heng-Na; Lo, Ping-Yuan; Zhang, Wei-Min; Feng, Da Hsuan; Nori, Franco

    2015-01-01

    The quantum-to-classical transition is due to environment-induced decoherence, and it depicts how classical dynamics emerges from quantum systems. Previously, the quantum-to-classical transition has mainly been described with memory-less (Markovian) quantum processes. Here we study the complexity of the quantum-to-classical transition through general non-Markovian memory processes. That is, the influence of various reservoirs results in a given initial quantum state evolving into one of the following four scenarios: thermal state, thermal-like state, quantum steady state, or oscillating quantum nonstationary state. In the latter two scenarios, the system maintains partial or full quantum coherence due to the strong non-Markovian memory effect, so that in these cases, the quantum-to-classical transition never occurs. This unexpected new feature provides a new avenue for the development of future quantum technologies because the remaining quantum oscillations in steady states are decoherence-free. PMID:26303002

  8. Adiabatic quantum games and phase-transition-like behavior between optimal strategies

    NASA Astrophysics Data System (ADS)

    de Ponte, M. A.; Santos, Alan C.

    2018-06-01

    In this paper we propose a game of a single qubit whose strategies can be implemented adiabatically. In addition, we show how to implement the strategies of a quantum game through controlled adiabatic evolutions, where we analyze the payment of a quantum player for various situations of interest: (1) when the players receive distinct payments, (2) when the initial state is an arbitrary superposition, and (3) when the device that implements the strategy is inefficient. Through a graphical analysis, it is possible to notice that the curves that represent the gains of the players present a behavior similar to the curves that give rise to a phase transition in thermodynamics. These transitions are associated with optimal strategy changes and occur in the absence of entanglement and interaction between the players.

  9. THE ROLE OF METASTABLE STATES IN POLYMER PHASE TRANSITIONS: Concepts, Principles, and Experimental Observations

    NASA Astrophysics Data System (ADS)

    Cheng, Stephen Z. D.; Keller, Andrew

    1998-08-01

    Polymer phases can be described in the same way as phases in other condensed matter using a number density operator and its correlation functions. This description requires the understanding of symmetry operations and order at different atomic and molecular levels. Statistical mechanics provides a link between the microscopic description of the structure and motion and the macroscopic thermodynamic properties. Within the limits of the laws of thermodynamics, polymers exhibit a rich variety of phase transition behaviors. By definition, a first-order phase transition describes a transformation that involves a sudden change of thermodynamic properties at its transition temperature, whereas higher-order phase transitions are classified as critical phenomena. Of special interest is the role of metastability in phase and phase transition behaviors. Although a metastable state possesses a local free energy minimum, it is not at the global equilibrium. Furthermore, metastable states can also be associated with phase sizes. Metastable behavior is also observed in phase transformations that are impeded by kinetic limitations along the pathway to thermodynamic equilibrium. This is illustrated in structural and morphological investigations of crystallization and mesophase transitions, liquid-liquid phase separation, vitrification, and gel formation, as well as combinations of transformation processes. In these cases, the metastable state often becomes the dominant state for the entire system and is observed over a range of time and size scales. This review describes the general principles of metastability in polymer phases and phase transitions and provides illustrations from current experimental works in selected areas.

  10. Plasma effect on fast-electron-impact-ionization from 2p state of hydrogen-like ions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Qi, Y. Y.; Ning, L. N.; Wang, J. G.

    2013-12-15

    Plasma effects on the high-energy electron-impact ionization process from 2p orbital of Hydrogen-like ions embedded in weakly coupled plasmas are investigated in the first Born approximation. The plasma screening of the Coulomb interaction between charged particles is represented by the Debye Hückel model. The screening of Coulomb interactions decreases the ionization energies and varies the wave functions for not only the bound orbital but also the continuum; the number of the summation for the angular-momentum states in the generalized oscillator strength densities is reduced with the plasma screening stronger when the ratio of ε/I{sub 2p} (I{sub 2p} is the ionizationmore » energy of 2p state and ε is the energy of the continuum electron) is kept, and then the contribution from the lower-angular-momentum states dominates the generalized oscillator strength densities, so the threshold phenomenon in the generalized oscillator strength densities and the double differential cross sections are remarkable: The accessional minima, the outstanding enhancement, and the resonance peaks emerge a certain energy region, whose energy position and width are related to the vicinity between δ and the critical value δ{sub nl}{sup c}, corresponding to the special plasma condition when the bound state |nl just enters the continuum; the multiple virtual-state enhancement and the multiple shape resonances in a certain energy domain also appear in the single differential cross section whenever the plasma screening parameter passes through a critical value δ{sub nl}{sup c}, which is similar to the photo-ionization process but different from it, where the dipole transition only happens, but multi-pole transition will occur in the electron-impact ionization process, so its multiple virtual-state enhancements and the multiple shape resonances appear more frequently than the photo-ionization process.« less

  11. Plasma effect on fast-electron-impact-ionization from 2p state of hydrogen-like ions

    NASA Astrophysics Data System (ADS)

    Qi, Y. Y.; Ning, L. N.; Wang, J. G.; Qu, Y. Z.

    2013-12-01

    Plasma effects on the high-energy electron-impact ionization process from 2p orbital of Hydrogen-like ions embedded in weakly coupled plasmas are investigated in the first Born approximation. The plasma screening of the Coulomb interaction between charged particles is represented by the Debye Hückel model. The screening of Coulomb interactions decreases the ionization energies and varies the wave functions for not only the bound orbital but also the continuum; the number of the summation for the angular-momentum states in the generalized oscillator strength densities is reduced with the plasma screening stronger when the ratio of ɛ /I2p (I2p is the ionization energy of 2p state and ɛ is the energy of the continuum electron) is kept, and then the contribution from the lower-angular-momentum states dominates the generalized oscillator strength densities, so the threshold phenomenon in the generalized oscillator strength densities and the double differential cross sections are remarkable: The accessional minima, the outstanding enhancement, and the resonance peaks emerge a certain energy region, whose energy position and width are related to the vicinity between δ and the critical value δnlc, corresponding to the special plasma condition when the bound state |nl⟩ just enters the continuum; the multiple virtual-state enhancement and the multiple shape resonances in a certain energy domain also appear in the single differential cross section whenever the plasma screening parameter passes through a critical value δnlc, which is similar to the photo-ionization process but different from it, where the dipole transition only happens, but multi-pole transition will occur in the electron-impact ionization process, so its multiple virtual-state enhancements and the multiple shape resonances appear more frequently than the photo-ionization process.

  12. California's Transition to the Common Core State Standards: The State's Role in Local Capacity Building

    ERIC Educational Resources Information Center

    Warren, Paul; Murphy, Patrick

    2014-01-01

    The Common Core State Standards (CCSS) and the Local Control Funding Formula are introducing major changes to California's K-12 system. Implementation of new curricula and instruction is under way at the district level, but California started its transition relatively late and it has taken a more decentralized approach than most other states.…

  13. Grassland-shrubland state transitions in arid lands: Competition matters

    USDA-ARS?s Scientific Manuscript database

    Background/Question/Methods: State transition from grassland to shrubland is synonymous with desertification in many dryland systems. The classic desertification model emphasizes abiotic feedbacks that modify the physical environment in ways that promote shrub proliferation and impede grass survival...

  14. Protons in non-ionic aqueous reverse micelles.

    PubMed

    Rodriguez, Javier; Martí, Jordi; Guàrdia, Elvira; Laria, Daniel

    2007-05-03

    Using molecular dynamics techniques, we investigate the solvation of an excess proton within an aqueous reverse micelle in vacuo, with the neutral surfactant diethylene glycol monodecyl ether [CH3(CH2)11(OC2H4)2OH]. The simulation experiments were performed using a multistate empirical valence bond Hamiltonian model. Our results show that the stable solvation environments for the excess proton are located in the water-surfactant interface and that its first solvation shell is composed exclusively by water molecules. The relative prevalence of Eigen- versus Zundel-like solvation structures is investigated; compared to bulk results, Zundel-like structures in micelles become somewhat more stable. Characteristic times for the proton translocation jumps have been computed using population relaxation time correlation functions. The micellar rate for proton transfer is approximately 40x smaller than that found in bulk water at ambient conditions. Differences in the computed rates are examined in terms of the hydrogen-bond connectivity involving the first solvation shell of the excess charge with the rest of the micellar environment. Simulation results would indicate that proton transfers are correlated with rare episodes during which the HB connectivity between the first and second solvation shells suffers profound modifications.

  15. Characterizing longitudinal health state transitions among heroin, cocaine, and methamphetamine users

    PubMed Central

    Nosyk, B; Li, L; Evans, E; Huang, D; Min, J; Kerr, T; Brecht, ML; Hser, YI

    2014-01-01

    Aims Characterize longitudinal patterns of drug use careers and identify determinants of drug use frequency across cohorts of primary heroin, methamphetamine (MA) and cocaine users. Design Pooled analysis of prospective cohort studies. Settings Illicit drug users recruited from community, criminal justice and drug treatment settings in California, USA. Participants We used longitudinal data on from five observational cohort studies featuring primary users of heroin (N=629), cocaine (N=694) and methamphetamine (N=474). The mean duration of follow-up was 20.9 years. Measurements Monthly longitudinal data was arranged according to five health states (incarceration, drug treatment, abstinence, non-daily and daily use). We fitted proportional hazards (PH) frailty models to determine independent differences in successive episode durations. We then executed multi-state Markov (MSM) models to estimate probabilities of transitioning between health states, and the determinants of these transitions. Findings Across primary drug use types, PH frailty models demonstrated durations of daily use diminished in successive episodes over time. MSM models revealed primary stimulant users had more erratic longitudinal patterns of drug use, transitioning more rapidly between periods of treatment, abstinence, non-daily and daily use. MA users exhibited relatively longer durations of high-frequency use. Criminal engagement had a destabilizing effect on health state durations across drug types. Longer incarceration histories were associated with delayed transitions towards cessation. Conclusions PH frailty and MSM modeling techniques provided complementary information on longitudinal patterns of drug abuse. This information can inform clinical practice and policy, and otherwise be used in health economic simulation models, designed to inform resource allocation decisions. PMID:24837584

  16. Multi-path variational transition state theory for chemical reaction rates of complex polyatomic species: ethanol + OH reactions.

    PubMed

    Zheng, Jingjing; Truhlar, Donald G

    2012-01-01

    Complex molecules often have many structures (conformations) of the reactants and the transition states, and these structures may be connected by coupled-mode torsions and pseudorotations; some but not all structures may have hydrogen bonds in the transition state or reagents. A quantitative theory of the reaction rates of complex molecules must take account of these structures, their coupled-mode nature, their qualitatively different character, and the possibility of merging reaction paths at high temperature. We have recently developed a coupled-mode theory called multi-structural variational transition state theory (MS-VTST) and an extension, called multi-path variational transition state theory (MP-VTST), that includes a treatment of the differences in the multi-dimensional tunneling paths and their contributions to the reaction rate. The MP-VTST method was presented for unimolecular reactions in the original paper and has now been extended to bimolecular reactions. The MS-VTST and MP-VTST formulations of variational transition state theory include multi-faceted configuration-space dividing surfaces to define the variational transition state. They occupy an intermediate position between single-conformation variational transition state theory (VTST), which has been used successfully for small molecules, and ensemble-averaged variational transition state theory (EA-VTST), which has been used successfully for enzyme kinetics. The theories are illustrated and compared here by application to three thermal rate constants for reactions of ethanol with hydroxyl radical--reactions with 4, 6, and 14 saddle points.

  17. On the behavior of Bronsted-Evans-Polanyi Relations for Transition Metal Oxides

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Vojvodic, Aleksandra

    2011-08-22

    Versatile Broensted-Evans-Polanyi (BEP) relations are found from density functional theory for a wide range of transition metal oxides including rutiles and perovskites. For oxides, the relation depends on the type of oxide, the active site and the dissociating molecule. The slope of the BEP relation is strongly coupled to the adsorbate geometry in the transition state. If it is final state-like the dissociative chemisorption energy can be considered as a descriptor for the dissociation. If it is initial state-like, on the other hand, the dissociative chemisorption energy is not suitable as descriptor for the dissociation. Dissociation of molecules with strongmore » intramolecular bonds belong to the former and molecules with weak intramolecular bonds to the latter group. We show, for the prototype system La-perovskites, that there is a 'cyclic' behavior in the transition state characteristics upon change of the active transition metal of the oxide.« less

  18. Tautomeric transition between wobble A·C DNA base mispair and Watson-Crick-like A·C* mismatch: microstructural mechanism and biological significance.

    PubMed

    Brovarets', Ol'ha O; Hovorun, Dmytro M

    2015-06-21

    Here, we use MP2/DFT quantum-chemical methods combined with Quantum Theory of Atoms in Molecules to study the tautomeric transition between wobble A·C(w) mismatch and Watson-Crick-like A·C*(WC) base mispair, proceeding non-dissociatively via sequential proton transfer between bases through the planar, highly stable and zwitterionic TS(A∙C-)(A∙C(W)<-->A∙C&(WC)) transition state joined by the participation of (A)N6(+)H∙∙∙N4(-)(C), (A)N1(+)H∙∙∙N4(-)(C) and (A)C2(+)H∙∙∙N3(-)(C) H-bonds. Notably, the A·C(w) ↔ A·C*(WC) tautomerization reaction is accompanied by 10 unique patterns of the specific intermolecular interactions that consistently replace each other. Our data suggest that biologically significant A·C(w) → A·C*(WC) tautomerization is a kinetically controlled pathway for formation of the enzymatically competent Watson-Crick-like A·C*(WC) DNA base mispair in the essentially hydrophobic recognition pocket of the high-fidelity DNA-polymerase, responsible for the occurrence of spontaneous point AC/CA incorporation errors during DNA biosynthesis.

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

    NASA Astrophysics Data System (ADS)

    Pal'Chikov, V. G.

    2000-08-01

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

  20. The competition of hydrogen-like and isotropic interactions on polymer collapse

    NASA Astrophysics Data System (ADS)

    Krawczyk, J.; Owczarek, A. L.; Prellberg, T.

    2007-09-01

    We investigate a lattice model of polymers where the nearest neighbour monomer monomer interaction strengths differ according to whether the local configurations have so-called 'hydrogen-like' formations or not. If the interaction strengths are all the same then the classical θ-point collapse transition occurs on lowering the temperature, and the polymer enters the isotropic liquid drop phase known as the collapsed globule. On the other hand, strongly favouring the hydrogen-like interactions gives rise to an anisotropic folded (solid-like) phase on lowering the temperature. We use Monte Carlo simulations up to a length of 256 to map out the phase diagram in the plane of parameters and determine the order of the associated phase transitions. We discuss the connections to semi-flexible polymers and other polymer models. Importantly, we demonstrate that for a range of energy parameters, two phase transitions occur on lowering the temperature, the second being a transition from the globule state to the crystal state. We argue from our data that this globule-to-crystal transition is continuous in two dimensions in accord with field-theory arguments concerning Hamiltonian walks, but is first order in three dimensions.

  1. Nematic order-disorder state transition in a liquid crystal analogue formed by oriented and migrating amoeboid cells

    NASA Astrophysics Data System (ADS)

    Kemkemer, R.; Teichgräber, V.; Schrank-Kaufmann, S.; Kaufmann, D.; Gruler, H.

    2000-10-01

    In cell culture, liquid crystal analogues are formed by elongated, migrating, and interacting amoeboid cells. An apolar nematic liquid crystal analogue is formed by different cell types like human melanocytes (=pigment cells of the skin), human fibroblasts (=connective tissue cells), human osteoblasts (=bone cells), human adipocytes (=fat cells), etc. The nematic analogue is quite well described by i) a stochastic machine equation responsible for cell orientation and ii) a self-organized extracellular guiding signal, E_2, which is proportional to the orientational order parameter as well as to the cell density. The investigations were mainly made with melanocytes. The transition to an isotropic state analogue can be accomplished either by changing the strength of interaction (e.g. variation of the cell density) or by influencing the cellular machinery by an externally applied signal: i) An isotropic gaseous state analogue is observed at low cell density (ρ < 110melanocytes/mm^2) and a nematic liquid crystal state analogue at higher cell density. ii) The nematic state analogue disappears if the bipolar shaped melanocytes are forced to become a star-like shape (induced by colchicine or staurosporine). The analogy between nematic liquid crystal state analogue formed by elongated, migrating and interacting cells and the nematic liquid crystal phase formed by interacting elongated molecules is discussed.

  2. A specific transition state for S-peptide combining with folded S-protein and then refolding

    PubMed Central

    Goldberg, Jonathan M.; Baldwin, Robert L.

    1999-01-01

    We measured the folding and unfolding kinetics of mutants for a simple protein folding reaction to characterize the structure of the transition state. Fluorescently labeled S-peptide analogues combine with S-protein to form ribonuclease S analogues: initially, S-peptide is disordered whereas S-protein is folded. The fluorescent probe provides a convenient spectroscopic probe for the reaction. The association rate constant, kon, and the dissociation rate constant, koff, were both determined for two sets of mutants. The dissociation rate constant is measured by adding an excess of unlabeled S-peptide analogue to a labeled complex (RNaseS*). This strategy allows kon and koff to be measured under identical conditions so that microscopic reversibility applies and the transition state is the same for unfolding and refolding. The first set of mutants tests the role of the α-helix in the transition state. Solvent-exposed residues Ala-6 and Gln-11 in the α-helix of native RNaseS were replaced by the helix destabilizing residues glycine or proline. A plot of log kon vs. log Kd for this series of mutants is linear over a very wide range, with a slope of −0.3, indicating that almost all of the molecules fold via a transition state involving the helix. A second set of mutants tests the role of side chains in the transition state. Three side chains were investigated: Phe-8, His-12, and Met-13, which are known to be important for binding S-peptide to S-protein and which also contribute strongly to the stability of RNaseS*. Only the side chain of Phe-8 contributes significantly, however, to the stability of the transition state. The results provide a remarkably clear description of a folding transition state. PMID:10051587

  3. Transition metal decorated graphene-like zinc oxide monolayer: A first-principles investigation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lei, Jie; School of Science, Qilu University of Technology, Jinan, Shandong 250353; Xu, Ming-Chun

    Transition metal (TM) atoms have been extensively employed to decorate the two-dimensional materials, endowing them with promising physical properties. Here, we have studied the adsorption of TM atoms (V, Cr, Mn, Fe, and Co) on graphene-like zinc oxide monolayer (g-ZnO) and the substitution of Zn by TM using first-principles calculations to search for the most likely configurations when TM atoms are deposited on g-ZnO. We found that when a V atom is initially placed on the top of Zn atom, V will squeeze out Zn from the two-dimensional plane then substitute it, which is a no barrier substitution process. Formore » heavier elements (Cr to Co), although the substitution configurations are more stable than the adsorption ones, there is an energy barrier for the adsorption-substitution transition with the height of tens to hundreds meV. Therefore, Cr to Co prefers to be adsorbed on the hollow site or the top of oxygen, which is further verified by the molecular dynamics simulations. The decoration of TM is revealed to be a promising approach in terms of tuning the work function of g-ZnO in a large energy range.« less

  4. Phase Transitions in Definite Total Spin States of Two-Component Fermi Gases.

    PubMed

    Yurovsky, Vladimir A

    2017-05-19

    Second-order phase transitions have no latent heat and are characterized by a change in symmetry. In addition to the conventional symmetric and antisymmetric states under permutations of bosons and fermions, mathematical group-representation theory allows for non-Abelian permutation symmetry. Such symmetry can be hidden in states with defined total spins of spinor gases, which can be formed in optical cavities. The present work shows that the symmetry reveals itself in spin-independent or coordinate-independent properties of these gases, namely as non-Abelian entropy in thermodynamic properties. In weakly interacting Fermi gases, two phases appear associated with fermionic and non-Abelian symmetry under permutations of particle states, respectively. The second-order transitions between the phases are characterized by discontinuities in specific heat. Unlike other phase transitions, the present ones are not caused by interactions and can appear even in ideal gases. Similar effects in Bose gases and strong interactions are discussed.

  5. Self-photopumped x-ray lasers from elements in the Ne-like and Ni-like ionization state

    DOE PAGES

    Siegrist, Michael; Staub, Felix; Jia, Fei; ...

    2016-08-11

    In this paper, we report on experiments on the self-photopumped 3d 1P 1→3p 1P 1 and 4f 1P 1→4d 1P 1 laser transitions in Ne-like and Ni-like ions, respectively. Lasing on the self-photopumped laser line has been observed for the first time for a number of elements including Ne-like V, Cr, Fe, and Co as well as Ni-like Ru and Pd. We have investigated the lasing process by varying the prepulse delay, which shows a shift of the optimum main pulse to second prepulse delays towards lower values with higher atomic number Z. Time-resolved measurements showed that self-photopumped and monopolemore » collision-pumped lasing emission occurs essentially simultaneously. Finally, accurate wavelength measurements and calculations are shown to be in excellent agreement.« less

  6. Advances in the Kepler Transit Search Engine and Automated Approaches to Identifying Likely Planet Candidates in Transit Surveys

    NASA Astrophysics Data System (ADS)

    Jenkins, Jon Michael

    2015-08-01

    Twenty years ago, no planets were known outside our own solar system. Since then, the discoveries of ~1500 exoplanets have radically altered our views of planets and planetary systems. This revolution is due in no small part to the Kepler Mission, which has discovered >1000 of these planets and >4000 planet candidates. While Kepler has shown that small rocky planets and planetary systems are quite common, the quest to find Earth’s closest cousins and characterize their atmospheres presses forward with missions such as NASA Explorer Program’s Transiting Exoplanet Survey Satellite (TESS) slated for launch in 2017 and ESA’s PLATO mission scheduled for launch in 2024.These future missions pose daunting data processing challenges in terms of the number of stars, the amount of data, and the difficulties in detecting weak signatures of transiting small planets against a roaring background. These complications include instrument noise and systematic effects as well as the intrinsic stellar variability of the subjects under scrutiny. In this paper we review recent developments in the Kepler transit search pipeline improving both the yield and reliability of detected transit signatures.Many of the phenomena in light curves that represent noise can also trigger transit detection algorithms. The Kepler Mission has expended great effort in suppressing false positives from its planetary candidate catalogs. While over 18,000 transit-like signatures can be identified for a search across 4 years of data, most of these signatures are artifacts, not planets. Vetting all such signatures historically takes several months’ effort by many individuals. We describe the application of machine learning approaches for the automated vetting and production of planet candidate catalogs. These algorithms can improve the efficiency of the human vetting effort as well as quantifying the likelihood that each candidate is truly a planet. This information is crucial for obtaining valid planet

  7. Radiationless Transitions and Excited-State Absorption in Tunable Laser Materials

    DTIC Science & Technology

    1992-09-01

    chromium - doped halide elpasolites K2 NaGaF 6 , K2 NaScF6 and Cs2NaYCl 6 , and on the laser-active TI0 (l) color center in KCI. Luminescence lifetime...Non-radiative transitions, transition metals, chromium , ¶SLWmER o E tunable lasers, high pressure, luminescence, color centers ൙. SECURITY O...quenching and excited-state absorption are major loss mechanisms. Low-crystal-field chromium complexes in ordered perovskites of cubic elpasolite structure

  8. Transitions between sleep and feeding states in rat ventral striatum neurons

    PubMed Central

    Tellez, Luis A.; Perez, Isaac O.; Simon, Sidney A.

    2012-01-01

    Neurons in the nucleus accumbens (NAc) have been shown to participate in several behavioral states, including feeding and sleep. However, it is not known if the same neuron participates in both states and, if so, how similar are the responses. In addition, since the NAc contains several cell types, it is not known if each type participates in the transitions associated with feeding and sleep. Such knowledge is important for understanding the interaction between two different neural networks. For these reasons we recorded ensembles of NAc neurons while individual rats volitionally transitioned between the following states: awake and goal directed, feeding, quiet-awake, and sleeping. We found that during both feeding and sleep states, the same neurons could increase their activity (be activated) or decrease their activity (be inactivated) by feeding and/or during sleep, thus indicating that the vast majority of NAc neurons integrate sleep and feeding signals arising from spatially distinct neural networks. In contrast, a smaller population was modulated by only one of the states. For the majority of neurons in either state, we found that when one population was excited, the other was inhibited, suggesting that they act as a local circuit. Classification of neurons into putative interneurons [fast-spiking interneurons (pFSI) and choline acetyltransferase interneurons (pChAT)] and projection medium spiny neurons (pMSN) showed that all three types are modulated by transitions to and from feeding and sleep states. These results show, for the first time, that in the NAc, those putative inhibitory interneurons respond similarly to pMSN projection neurons and demonstrate interactions between NAc networks involved in sleep and feeding. PMID:22745464

  9. Kinetic isotope effects reveal early transition state of protein lysine methyltransferase SET8

    PubMed Central

    Linscott, Joshua A.; Kapilashrami, Kanishk; Wang, Zhen; Senevirathne, Chamara; Bothwell, Ian R.; Blum, Gil; Luo, Minkui

    2016-01-01

    Protein lysine methyltransferases (PKMTs) catalyze the methylation of protein substrates, and their dysregulation has been linked to many diseases, including cancer. Accumulated evidence suggests that the reaction path of PKMT-catalyzed methylation consists of the formation of a cofactor(cosubstrate)–PKMT–substrate complex, lysine deprotonation through dynamic water channels, and a nucleophilic substitution (SN2) transition state for transmethylation. However, the molecular characters of the proposed process remain to be elucidated experimentally. Here we developed a matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) method and corresponding mathematic matrix to determine precisely the ratios of isotopically methylated peptides. This approach may be generally applicable for examining the kinetic isotope effects (KIEs) of posttranslational modifying enzymes. Protein lysine methyltransferase SET8 is the sole PKMT to monomethylate histone 4 lysine 20 (H4K20) and its function has been implicated in normal cell cycle progression and cancer metastasis. We therefore implemented the MS-based method to measure KIEs and binding isotope effects (BIEs) of the cofactor S-adenosyl-l-methionine (SAM) for SET8-catalyzed H4K20 monomethylation. A primary intrinsic 13C KIE of 1.04, an inverse intrinsic α-secondary CD3 KIE of 0.90, and a small but statistically significant inverse CD3 BIE of 0.96, in combination with computational modeling, revealed that SET8-catalyzed methylation proceeds through an early, asymmetrical SN2 transition state with the C-N and C-S distances of 2.35–2.40 Å and 2.00–2.05 Å, respectively. This transition state is further supported by the KIEs, BIEs, and steady-state kinetics with the SAM analog Se-adenosyl-l-selenomethionine (SeAM) as a cofactor surrogate. The distinct transition states between protein methyltransferases present the opportunity to design selective transition-state analog inhibitors. PMID

  10. New Transition in the Vortex Liquid State: intrinsic limit of the irreversibility line

    NASA Astrophysics Data System (ADS)

    Kwok, Wai-Kwong; Paulius, Lisa; Figueras, Jordi

    2005-03-01

    We have carried out angular dependent magneto-transport measurements on optimally doped, untwinned YBCO crystals irradiated with high energy heavy ions to determine the onset of vortex line tension in the vortex liquid state. The matching field was controlled and kept at a low level to partially preserve the first order vortex lattice melting transition. A Bose glass transition is observed below the lower critical point which then transforms into a first order phase transition near 5 Tesla. The locus of points which indicate the onset of vortex line tension overlaps with the Bose glass transition line at low fields and then deviates at higher fields, indicating a new transition line in the vortex liquid state. This new line in the vortex liquid phase extends beyond the upper critical point.This work was supported by the U.S. Department of Energy, BES, Materials Science under Contract No. W-31-109-ENG-38 at Argonne National Laboratory.

  11. Vocational Rehabilitation Transition Outcomes of Youth with Disabilities from a Midwestern State

    ERIC Educational Resources Information Center

    Awsumb, Jessica M.; Balcazar, Fabricio E.; Alvarado, Francisco

    2016-01-01

    Purpose: To examine the outcomes (rehabilitated vs. nonrehabilitated) of youth with disabilities (ages 14-22 years) participating in the transition program from a midwestern state. Method: Five years of vocational rehabilitation transition data (N = 6,252) were analyzed to determine what demographic and system-level factors were related to…

  12. Mechanisms of proton transfer in Nafion: elementary reactions at the sulfonic acid groups.

    PubMed

    Sagarik, Kritsana; Phonyiem, Mayuree; Lao-ngam, Charoensak; Chaiwongwattana, Sermsiri

    2008-04-21

    Proton transfer reactions at the sulfonic acid groups in Nafion were theoretically studied, using complexes formed from triflic acid (CF3SO3H), H3O+ and H2O, as model systems. The investigations began with searching for potential precursors and transition states at low hydration levels, using the test-particle model (T-model), density functional theory (DFT) and ab initio calculations. They were employed as starting configurations in Born-Oppenheimer molecular dynamics (BOMD) simulations at 298 K, from which elementary reactions were analyzed and categorized. For the H3O+-H2O complexes, BOMD simulations suggested that a quasi-dynamic equilibrium could be established between the Eigen and Zundel complexes, and that was considered to be one of the most important elementary reactions in the proton transfer process. The average lifetime of H3O+ obtained from BOMD simulations is close to the lowest limit, estimated from low-frequency vibrational spectroscopy. It was demonstrated that proton transfer reactions at -SO3H are not concerted, due to the thermal energy fluctuation and the existence of various quasi-dynamic equilibria, and -SO3H could directly and indirectly mediate proton transfer reactions through the formation of proton defects, as well as the -SO3- and -SO3H2+ transition states.

  13. Grassland to shrubland state transitions enhance carbon sequestration in the northern Chihuahuan Desert.

    PubMed

    Petrie, M D; Collins, S L; Swann, A M; Ford, P L; Litvak, M E

    2015-03-01

    The replacement of native C4 -dominated grassland by C3 -dominated shrubland is considered an ecological state transition where different ecological communities can exist under similar environmental conditions. These state transitions are occurring globally, and may be exacerbated by climate change. One consequence of the global increase in woody vegetation may be enhanced ecosystem carbon sequestration, although the responses of arid and semiarid ecosystems may be highly variable. During a drier than average period from 2007 to 2011 in the northern Chihuahuan Desert, we found established shrubland to sequester 49 g C m(-2) yr(-1) on average, while nearby native C4 grassland was a net source of 31 g C m(-2) yr(-1) over this same period. Differences in C exchange between these ecosystems were pronounced--grassland had similar productivity compared to shrubland but experienced higher C efflux via ecosystem respiration, while shrubland was a consistent C sink because of a longer growing season and lower ecosystem respiration. At daily timescales, rates of carbon exchange were more sensitive to soil moisture variation in grassland than shrubland, such that grassland had a net uptake of C when wet but lost C when dry. Thus, even under unfavorable, drier than average climate conditions, the state transition from grassland to shrubland resulted in a substantial increase in terrestrial C sequestration. These results illustrate the inherent tradeoffs in quantifying ecosystem services that result from ecological state transitions, such as shrub encroachment. In this case, the deleterious changes to ecosystem services often linked to grassland to shrubland state transitions may at least be partially offset by increased ecosystem carbon sequestration. © 2014 John Wiley & Sons Ltd.

  14. Cooperative structural transitions in amyloid-like aggregation

    NASA Astrophysics Data System (ADS)

    Steckmann, Timothy; Bhandari, Yuba R.; Chapagain, Prem P.; Gerstman, Bernard S.

    2017-04-01

    Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's, and others. Although proteins that undergo aggregation vary widely in their primary structure, they all produce a cross-β motif with the proteins in β-strand conformations perpendicular to the fibril axis. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. To better understand the molecular basis of the protein structural transitions and aggregation, we report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccβ, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow β-hairpin proteins to straighten, and the subsequent formation of interchain H-bonds during aggregation into amyloid fibrils. For our MD simulations, we found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccβ protein experiences during the process of forming protofibrillar structures. This temperature dependence allows us to investigate the dynamics on a molecular level. We report on the thermodynamics and cooperativity of the transformations. The structural transitions that occurred in a specific temperature window for ccβ in our investigations may also occur in other amyloid forming proteins but with biochemical parameters controlling the dynamics rather than temperature.

  15. Identification of the protein folding transition state from molecular dynamics trajectories

    NASA Astrophysics Data System (ADS)

    Muff, S.; Caflisch, A.

    2009-03-01

    The rate of protein folding is governed by the transition state so that a detailed characterization of its structure is essential for understanding the folding process. In vitro experiments have provided a coarse-grained description of the folding transition state ensemble (TSE) of small proteins. Atomistic details could be obtained by molecular dynamics (MD) simulations but it is not straightforward to extract the TSE directly from the MD trajectories, even for small peptides. Here, the structures in the TSE are isolated by the cut-based free-energy profile (cFEP) using the network whose nodes and links are configurations sampled by MD and direct transitions among them, respectively. The cFEP is a barrier-preserving projection that does not require arbitrarily chosen progress variables. First, a simple two-dimensional free-energy surface is used to illustrate the successful determination of the TSE by the cFEP approach and to explain the difficulty in defining boundary conditions of the Markov state model for an entropically stabilized free-energy minimum. The cFEP is then used to extract the TSE of a β-sheet peptide with a complex free-energy surface containing multiple basins and an entropic region. In contrast, Markov state models with boundary conditions defined by projected variables and conventional histogram-based free-energy profiles are not able to identify the TSE of the β-sheet peptide.

  16. Quantization of Space-like States in Lorentz-Violating Theories

    NASA Astrophysics Data System (ADS)

    Colladay, Don

    2018-01-01

    Lorentz violation frequently induces modified dispersion relations that can yield space-like states that impede the standard quantization procedures. In certain cases, an extended Hamiltonian formalism can be used to define observer-covariant normalization factors for field expansions and phase space integrals. These factors extend the theory to include non-concordant frames in which there are negative-energy states. This formalism provides a rigorous way to quantize certain theories containing space-like states and allows for the consistent computation of Cherenkov radiation rates in arbitrary frames and avoids singular expressions.

  17. H2S induces a suspended animation-like state in mice.

    PubMed

    Blackstone, Eric; Morrison, Mike; Roth, Mark B

    2005-04-22

    Mammals normally maintain their core body temperature (CBT) despite changes in environmental temperature. Exceptions to this norm include suspended animation-like states such as hibernation, torpor, and estivation. These states are all characterized by marked decreases in metabolic rate, followed by a loss of homeothermic control in which the animal's CBT approaches that of the environment. We report that hydrogen sulfide can induce a suspended animation-like state in a nonhibernating species, the house mouse (Mus musculus). This state is readily reversible and does not appear to harm the animal. This suggests the possibility of inducing suspended animation-like states for medical applications.

  18. Magnetic states, correlation effects and metal-insulator transition in FCC lattice

    NASA Astrophysics Data System (ADS)

    Timirgazin, M. A.; Igoshev, P. A.; Arzhnikov, A. K.; Irkhin, V. Yu

    2016-12-01

    The ground-state magnetic phase diagram (including collinear and spiral states) of the single-band Hubbard model for the face-centered cubic lattice and related metal-insulator transition (MIT) are investigated within the slave-boson approach by Kotliar and Ruckenstein. The correlation-induced electron spectrum narrowing and a comparison with a generalized Hartree-Fock approximation allow one to estimate the strength of correlation effects. This, as well as the MIT scenario, depends dramatically on the ratio of the next-nearest and nearest electron hopping integrals {{t}\\prime}/t . In contrast with metallic state, possessing substantial band narrowing, insulator one is only weakly correlated. The magnetic (Slater) scenario of MIT is found to be superior over the Mott one. Unlike simple and body-centered cubic lattices, MIT is the first order transition (discontinuous) for most {{t}\\prime}/t . The insulator state is type-II or type-III antiferromagnet, and the metallic state is spin-spiral, collinear antiferromagnet or paramagnet depending on {{t}\\prime}/t . The picture of magnetic ordering is compared with that in the standard localized-electron (Heisenberg) model.

  19. Molecular Remodeling of Photosystem II during State Transitions in Chlamydomonas reinhardtii[W

    PubMed Central

    Iwai, Masakazu; Takahashi, Yuichiro; Minagawa, Jun

    2008-01-01

    State transitions, or the redistribution of light-harvesting complex II (LHCII) proteins between photosystem I (PSI) and photosystem II (PSII), balance the light-harvesting capacity of the two photosystems to optimize the efficiency of photosynthesis. Studies on the migration of LHCII proteins have focused primarily on their reassociation with PSI, but the molecular details on their dissociation from PSII have not been clear. Here, we compare the polypeptide composition, supramolecular organization, and phosphorylation of PSII complexes under PSI- and PSII-favoring conditions (State 1 and State 2, respectively). Three PSII fractions, a PSII core complex, a PSII supercomplex, and a multimer of PSII supercomplex or PSII megacomplex, were obtained from a transformant of the green alga Chlamydomonas reinhardtii carrying a His-tagged CP47. Gel filtration and single particles on electron micrographs showed that the megacomplex was predominant in State 1, whereas the core complex was predominant in State 2, indicating that LHCIIs are dissociated from PSII upon state transition. Moreover, in State 2, strongly phosphorylated LHCII type I was found in the supercomplex but not in the megacomplex. Phosphorylated minor LHCIIs (CP26 and CP29) were found only in the unbound form. The PSII subunits were most phosphorylated in the core complex. Based on these observations, we propose a model for PSII remodeling during state transitions, which involves division of the megacomplex into supercomplexes, triggered by phosphorylation of LHCII type I, followed by LHCII undocking from the supercomplex, triggered by phosphorylation of minor LHCIIs and PSII core subunits. PMID:18757554

  20. Supersymmetrical bounding of asymmetric states and quantum phase transitions by anti-crossing of symmetric states

    PubMed Central

    Afzal, Muhammad Imran; Lee, Yong Tak

    2016-01-01

    Von Neumann and Wigner theorized the bounding and anti-crossing of eigenstates. Experiments have demonstrated that owing to anti-crossing and similar radiation rates, the graphene-like resonance of inhomogeneously strained photonic eigenstates can generate a pseudomagnetic field, bandgaps and Landau levels, whereas exponential or dissimilar rates induce non-Hermicity. Here, we experimentally demonstrate higher-order supersymmetry and quantum phase transitions by resonance between similar one-dimensional lattices. The lattices consisted of inhomogeneous strain-like phases of triangular solitons. The resonance created two-dimensional, inhomogeneously deformed photonic graphene. All parent eigenstates were annihilated. Eigenstates of mildly strained solitons were annihilated at similar rates through one tail and generated Hermitian bounded eigenstates. The strongly strained solitons with positive phase defects were annihilated at exponential rates through one tail, which bounded eigenstates through non-Hermitianally generated exceptional points. Supersymmetry was evident, with preservation of the shapes and relative phase differences of the parent solitons. Localizations of energies generated from annihilations of mildly and strongly strained soliton eigenstates were responsible for geometrical (Berry) and topological phase transitions, respectively. Both contributed to generating a quantum Zeno phase, whereas only strong twists generated topological (Anderson) localization. Anti-bunching-like condensation was also observed. PMID:27966596

  1. Adhesion and Wetting of Soft Nanoparticles on Textured Surfaces: Transition between Wenzel and Cassie-Baxter States

    DOE PAGES

    Cao, Zhen; Stevens, Mark J.; Carrillo, Jan-Michael Y.; ...

    2015-01-16

    We use a combination of the molecular dynamics simulations and scaling analysis to study interactions between gel-like nanoparticles and substrates covered with rectangular shape posts. Our simulations have shown that nanoparticle in contact with substrate undergo first order transition between Wenzel and Cassie-Baxter state which location depends on nanoparticle shear modulus, the strength of nanoparticle-substrate interactions, height of the substrate posts and nanoparticle size, R p. There is a range of system parameters where these two states coexist such that the average indentation δ produced by substrate posts changes monotonically with nanoparticle shear modulus, G p. We have developed amore » scaling model that describes deformation of nanoparticle in contact with patterned substrate. In the framework of this model the effect of the patterned substrate can be taken into account by introducing an effective work of adhesion, W eff, which describes the first order transition between Wenzel and Cassie-Baxter states. There are two different shape deformation regimes for nanoparticles with shear modulus G p and surface tension γ p. Shape of small nanoparticles with size R p < γ p 3/2G p -1 W eff -1/2 is controlled by capillary forces while deformation of large nanoparticles, R p > γ p 3/2G p -1 W eff -1/2« less

  2. 19 CFR 123.42 - Truck shipments transiting the United States.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...; DEPARTMENT OF THE TREASURY CBP RELATIONS WITH CANADA AND MEXICO United States and Canada In-Transit Truck... the manifest shall validate it by stamping each copy in the lower right hand corner to show the port...

  3. Enhancing transit polio vaccination in collaboration with targeted stakeholders in Kaduna State, Nigeria: Lessons learnt: 2014-2015.

    PubMed

    Musa, Audu; Abba, Bashir; Ningi, Adamu M I; Gali, Emanuel; Bawa, Samuel; Manneh, Fadninding; Mkanda, Pascal; Banda, Richard; Yehuluashet, Yared G; Tegegne, Sisay G; Umeh, Gregory; Nsubuga, Peter; Etsano, Andrew; Shuaib, Faisal; Mohammed, Ado; Vaz, Rui G

    2016-10-10

    In Kaduna State of Nigeria, the high influx of people from neighboring states with eligible children for polio vaccination represents a significant proportion of the target population. Many of these children are often missed by the vaccination team. The purpose of the study was to determine the contribution of targeted stakeholders in transit polio vaccination. We used the trends of vaccinated children at transit points, motor parks and markets, well as total children vaccinated by transit teams in Chikun, Igabi and Sabon Gari Local Government Areas (LGAs) of Kaduna State, Nigeria, four rounds before and after the introduction of transit polio vaccination with targeted stakeholders in Kaduna State. A total of 87,502 under-5 children were vaccinated by the various transit teams in the three LGAs, which accounted for 3.2% of the total 2,781,162 children vaccinated by the three LGAs. For transit point vaccination, the number of vaccinated children increased from 1026 to 19,289 (302%), while motor park vaccination increased from 1289 to 4106 (318%) and market vaccination increased from 10,488 to 14,511 (138%), four rounds after the introduction of transit polio vaccination with targeted stakeholders. Engagement of targeted stakeholders significantly enhanced transit polio vaccination in Kaduna State, Nigeria. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  4. Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ho, Meng-Chiao; Sturm, Matthew B.; Almo, Steven C.

    2010-01-12

    Ricin A-chain (RTA) and saporin-L1 (SAP) catalyze adenosine depurination of 28S rRNA to inhibit protein synthesis and cause cell death. We present the crystal structures of RTA and SAP in complex with transition state analogue inhibitors. These tight-binding inhibitors mimic the sarcin-ricin recognition loop of 28S rRNA and the dissociative ribocation transition state established for RTA catalysis. RTA and SAP share unique purine-binding geometry with quadruple {pi}-stacking interactions between adjacent adenine and guanine bases and 2 conserved tyrosines. An arginine at one end of the {pi}-stack provides cationic polarization and enhanced leaving group ability to the susceptible adenine. Common featuresmore » of these ribosome-inactivating proteins include adenine leaving group activation, a remarkable lack of ribocation stabilization, and conserved glutamates as general bases for activation of the H{sub 2}O nucleophile. Catalytic forces originate primarily from leaving group activation evident in both RTA and SAP in complex with transition state analogues.« less

  5. Theoretical studies of the transition state structures and free energy barriers for base-catalyzed hydrolysis of amides

    PubMed Central

    Xiong, Ying; Zhan, Chang-Guo

    2010-01-01

    The transition state structures and free energy barriers for the rate-determining step (i.e. the formation of a tetrahedral intermediate) of base-catalyzed hydrolysis of a series of amides in aqueous solution have been studied by performing first-principle electronic structure calculations using a hybrid supermolecule-polarizable continuum approach. The calculated results and a revisit of recently reported experimental proton inventory data reveal that the favorable transition state structure optimized for the tetrahedral intermediate formation of hydroxide ion-catalyzed hydrolysis of formamide may have three solvating water molecules remaining on the attacking hydroxide oxygen and two additional water molecules attached to the carbonyl oxygen of formamide. The calculated results have also demonstrated interesting substituent effects on the optimized transition state geometries, on the transition-state stabilization, and on the calculated free energy barriers for the base-catalyzed hydrolysis of amides. When some or all of the hydrogen atoms of formamide are replaced by methyl groups, the total number of water molecules hydrogen-bonding with the attacking hydroxide in the transition state decreases from three for formamide to two for N-methylacetamide, N,N-dimethylformamide (DMF), and N,N-dimethylacetamide (DMA). The larger substituents of the amide hinder the solvent water molecules approaching the attacking hydroxide oxygen in the transition state and, therefore, destabilize the transition state structure and increase the free energy barrier. By using the optimized most favorable transition state structures, the calculated free energy barriers, i.e. 21.6 (or 21.7), 22.7, 23.1, and 26.0 kcal/mol for formamide, N-methylacetamide, DMF, and DMA, respectively, are in good agreement with the available experimental free energy barriers, i.e. 21.2, 21.5, 22.6, and 24.1 kcal/mol for formamide, N-methylacetamide, DMF, and DMA, respectively. PMID:17107116

  6. Pseudo-direct bandgap transitions in silicon nanocrystals: effects on optoelectronics and thermoelectrics

    NASA Astrophysics Data System (ADS)

    Singh, Vivek; Yu, Yixuan; Sun, Qi-C.; Korgel, Brian; Nagpal, Prashant

    2014-11-01

    While silicon nanostructures are extensively used in electronics, the indirect bandgap of silicon poses challenges for optoelectronic applications like photovoltaics and light emitting diodes (LEDs). Here, we show that size-dependent pseudo-direct bandgap transitions in silicon nanocrystals dominate the interactions between (photoexcited) charge carriers and phonons, and hence the optoelectronic properties of silicon nanocrystals. Direct measurements of the electronic density of states (DOS) for different sized silicon nanocrystals reveal that these pseudo-direct transitions, likely arising from the nanocrystal surface, can couple with the quantum-confined silicon states. Moreover, we demonstrate that since these transitions determine the interactions of charge carriers with phonons, they change the light emission, absorption, charge carrier diffusion and phonon drag (Seebeck coefficient) in nanoscaled silicon semiconductors. Therefore, these results can have important implications for the design of optoelectronics and thermoelectric devices based on nanostructured silicon.While silicon nanostructures are extensively used in electronics, the indirect bandgap of silicon poses challenges for optoelectronic applications like photovoltaics and light emitting diodes (LEDs). Here, we show that size-dependent pseudo-direct bandgap transitions in silicon nanocrystals dominate the interactions between (photoexcited) charge carriers and phonons, and hence the optoelectronic properties of silicon nanocrystals. Direct measurements of the electronic density of states (DOS) for different sized silicon nanocrystals reveal that these pseudo-direct transitions, likely arising from the nanocrystal surface, can couple with the quantum-confined silicon states. Moreover, we demonstrate that since these transitions determine the interactions of charge carriers with phonons, they change the light emission, absorption, charge carrier diffusion and phonon drag (Seebeck coefficient) in

  7. The folding transition state of Protein L is extensive with non-native interactions (and not small and polarized)

    PubMed Central

    Yoo, Tae Yeon; Adhikari, Aashish; Xia, Zhen; Huynh, Tien; Freed, Karl F.; Zhou, Ruhong; Sosnick, Tobin R.

    2012-01-01

    Progress in understanding protein folding relies heavily upon an interplay between experiment and theory. In particular, readily interpretable experimental data are required that can be meaningfully compared to simulations. According to standard mutational φ analysis, the transition state for Protein L contains only a single hairpin. However, we demonstrate here using ψ analysis with engineered metal ion binding sites that the transition state is extensive, containing the entire four-stranded β sheet. Underreporting of the structural content of the transition state by φ analysis also occurs for acyl phosphatase1, ubiquitin2 and BdpA3. The carboxy terminal hairpin in the transition state of Protein L is found to be non-native, a significant result that agrees with our PDB-based backbone sampling and all-atom simulations. The non-native character partially explains the failure of accepted experimental and native-centric computational approaches to adequately describe the transition state. Hence, caution is required even when an apparent agreement exists between experiment and theory, thus highlighting the importance of having alternative methods for characterizing transition states. PMID:22522126

  8. Boundary layer turbulence in transitional and developed states

    NASA Astrophysics Data System (ADS)

    Park, George Ilhwan; Wallace, James M.; Wu, Xiaohua; Moin, Parviz

    2012-03-01

    Using the recent direct numerical simulations by Wu and Moin ["Transitional and turbulent boundary layer with heat transfer," Phys. Fluids 22, 85 (2010)] of a flat-plate boundary layer with a passively heated wall, statistical properties of the turbulence in transition at Reθ ≈ 300, from individual turbulent spots, and at Reθ ≈ 500, where the spots merge (distributions of the mean velocity, Reynolds stresses, kinetic energy production, and dissipation rates, enstrophy and its components) have been compared to these statistical properties for the developed boundary layer turbulence at Reθ = 1840. When the distributions in the transitional regions are conditionally averaged so as to exclude locations and times when the flow is not turbulent, they closely resemble the distributions in the developed turbulent state at the higher Reynolds number, especially in the buffer layer. Skin friction coefficients, determined in this conditional manner at the two Reynolds numbers in the transitional flow are, of course, much larger than when their values are obtained by including both turbulent and non-turbulent information there, and the conditional averaged values are consistent with the 1/7th power law approximation. An octant analysis based on the combinations of signs of the velocity and temperature fluctuations, u, v, and θ shows that the momentum and heat fluxes are predominantly of the mean gradient type in both the transitional and developed regions. The fluxes appear to be closely associated with vortices that transport momentum and heat toward and away from the wall in both regions of the flow. The results suggest that there may be little fundamental difference between the nonlinear processes involved in the formation of turbulent spots that appear in transition and those that sustain the turbulence when it is developed. They also support the view that the transport processes and the vortical structures that drive them in developed and transitional boundary

  9. Transition State Gauche Effects Control the Torquoselectivities of the Electrocyclizations of Chiral 1-Azatrienes.

    PubMed

    Patel, Ashay; Vella, Joseph R; Ma, Zhi-Xiong; Hsung, R P; Houk, K N

    2015-12-04

    Hsung et al. have reported a series of torquoselective electrocyclizations of chiral 1-azahexa-1E,3Z,5E-trienes that yield functionalized dihydropyridines. To understand the origins of the torquoselectivities of these azaelectrocyclizations, we modeled these electrocyclic ring closures using the M06-2X density functional. A new stereochemical model that rationalizes the observed 1,2 stereoinduction emerges from these computations. This model is an improvement and generalization of the "inside-alkoxy" model used to rationalize stereoselectivities of the 1,3-dipolar cycloaddition of chiral allyl ethers and emphasizes a stabilizing hyperconjugative effect, which we have termed a transition state gauche effect. This stereoelectronic effect controls the conformational preferences at the electrocyclization transition states, and only in one of the allowed disrotatory electrocyclization transition states is the ideal stereoelectronic arrangement achieved without the introduction of a steric clash. Computational experiments confirm the role of this effect as a stereodeterminant since substrates with electropositive groups and electronegative groups have different conformational preferences at the transition state and undergo ring closure with divergent stereochemical outcomes. This predicted reversal of stereoselectivity for the ring closures of several silyl substituted azatrienes have been demonstrated experimentally.

  10. State Accountability in the Transition to Common Core. Updated

    ERIC Educational Resources Information Center

    Sears, Victoria

    2014-01-01

    The Common Core is at a critical juncture. While many surveys show that support for the standards themselves remains strong, implementation has not been without major challenges. "State Accountability in the Transition to Common Core," a new policy brief from the Thomas B. Fordham Institute, provides cautionary advice about what key…

  11. Generating multi-photon W-like states for perfect quantum teleportation and superdense coding

    NASA Astrophysics Data System (ADS)

    Li, Ke; Kong, Fan-Zhen; Yang, Ming; Ozaydin, Fatih; Yang, Qing; Cao, Zhuo-Liang

    2016-08-01

    An interesting aspect of multipartite entanglement is that for perfect teleportation and superdense coding, not the maximally entangled W states but a special class of non-maximally entangled W-like states are required. Therefore, efficient preparation of such W-like states is of great importance in quantum communications, which has not been studied as much as the preparation of W states. In this paper, we propose a simple optical scheme for efficient preparation of large-scale polarization-based entangled W-like states by fusing two W-like states or expanding a W-like state with an ancilla photon. Our scheme can also generate large-scale W states by fusing or expanding W or even W-like states. The cost analysis shows that in generating large-scale W states, the fusion mechanism achieves a higher efficiency with non-maximally entangled W-like states than maximally entangled W states. Our scheme can also start fusion or expansion with Bell states, and it is composed of a polarization-dependent beam splitter, two polarizing beam splitters and photon detectors. Requiring no ancilla photon or controlled gate to operate, our scheme can be realized with the current photonics technology and we believe it enable advances in quantum teleportation and superdense coding in multipartite settings.

  12. MRCI study on the spectroscopic parameters, transition dipole moments and transition probabilities of 16 low-lying states of the BeB radical

    NASA Astrophysics Data System (ADS)

    Zhou, Dan; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2018-03-01

    In this work, we calculate the potential energy curves of 16 Λ-S and 36 Ω states of beryllium boride (BeB) radical using the complete active space self-consistent field method, followed by the valence internally contracted multireference configuration interaction approach with Davidson correction. The 16 Λ-S states are the X2Π, A2Σ+, B2Π, C2Δ, D2Ʃ-, E2Σ+, G2Π, I2Σ+, a4Σ-, b4Π, c4Σ-, d4Δ, e4Σ+, g4Π, h4Π, and 24Σ+, which are obtained from the first three dissociation channels of the BeB radical. The Ω states are obtained from the Λ-S states. Of the Λ-S states, the G2Π, I2Σ+, and h4Π states exhibit double well curves. The G2Π, b4Π, and g4Π states are inverted with the spin-orbit coupling effect included. The d4Δ, e4Σ+, and g4Π states as well as the second well of the h4Π state are very weakly bound. Avoided crossings exist between the G2Π and H2Π states, the A2Σ+ and E2Σ+ states, the c4Σ- and f4Σ- states, the g4Π and h4Π states, the I2Σ+ and 42Σ+ states, as well as the 24Σ+ and 34Σ+ states. To improve the quality of the potential energy curves, core-valence correlation and scalar relativistic corrections, as well as the extrapolation of the potential energies to the complete basis set limit, are included. The transition dipole moments are computed. Spectroscopic parameters and vibrational levels are determined along with Franck-Condon factors, Einstein coefficients, and radiative lifetimes of many electronic transitions. The transition probabilities are evaluated. The spin-orbit coupling effect on the spectroscopic parameters and vibrational levels is discussed. The spectroscopic parameters, vibrational levels, and transition probabilities reported in this paper can be considered very reliable and can be employed to predict these states in an appropriate spectroscopy experiment.

  13. Thermodynamics phase transition and Hawking radiation of the Schwarzschild black hole with quintessence-like matter and a deficit solid angle

    NASA Astrophysics Data System (ADS)

    Rodrigue, Kamiko Kouemeni Jean; Saleh, Mahamat; Thomas, Bouetou Bouetou; Kofane, Timoleon Crepin

    2018-05-01

    In this paper, we investigate the thermodynamics and Hawking radiation of Schwarzschild black hole with quintessence-like matter and deficit solid angle. From the metric of the black hole, we derive the expressions of temperature and specific heat using the laws of black hole thermodynamics. Using the null geodesics method and Parikh-Wilczeck tunneling method, we derive the expressions of Boltzmann factor and the change of Bekenstein-Hawking entropy for the black hole. The behaviors of the temperature, specific heat, Boltzmann factor and the change of Bekenstein entropy versus the deficit solid angle (ɛ 2) and the density of static spherically symmetric quintessence-like matter (ρ 0) were explicitly plotted. The results show that, when the deficit solid angle (ɛ 2) and the density of static spherically symmetric quintessence-like matter at r=1 (ρ 0) vanish (ρ 0=ɛ =0), these four thermodynamics quantities are reduced to those obtained for the simple case of Schwarzschild black hole. For low entropies, the presence of quintessence-like matter induces a first order phase transition of the black hole and for the higher values of the entropies, we observe the second order phase transition. When increasing ρ 0, the transition points are shifted to lower entropies. The same thing is observed when increasing ɛ 2. In the absence of quintessence-like matter (ρ 0=0), these transition phenomena disappear. Moreover the rate of radiation decreases when increasing ρ 0 or (ɛ ^2).

  14. MAXI/GSC detection of an undergoing soft-to-hard state transition of MAXI J1535-571

    NASA Astrophysics Data System (ADS)

    Negoro, H.; Sugawara, Y.; Nakajima, M.; Sakamaki, A.; Maruyama, W.; Mihara, T.; Nakahira, S.; Yatabe, F.; Takao, Y.; Matsuoka, M.; Kawai, N.; Sugizaki, M.; Tachibana, Y.; Morita, K.; Sakamoto, T.; Serino, M.; Sugita, S.; Kawakubo, Y.; Hashimoto, T.; Yoshida, A.; Ueno, S.; Tomida, H.; Ishikawa, M.; Isobe, N.; Shimomukai, R.; Ueda, Y.; Tanimoto, A.; Morita, T.; Yamada, S.; Tsuboi, Y.; Iwakiri, W.; Sasaki, R.; Kawai, H.; Sato, T.; Tsunemi, H.; Yoneyama, T.; Yamauchi, M.; Hidaka, K.; Iwahori, S.; Kawamuro, T.; Yamaoka, K.; Shidatsu, M.

    2018-06-01

    We report an undergoing soft-to-hard state transition of the black hole candidate MAXI J1535-571 in outburst (ATel #10699). After the unexpectedly rapid decrease in the X-ray flux remaining in the soft state from 2018 April 16 (ATel #11568), the source underwent a hard state transition around April 30 (ATel #11611).

  15. A transition in brain state during propofol-induced unconsciousness.

    PubMed

    Mukamel, Eran A; Pirondini, Elvira; Babadi, Behtash; Wong, Kin Foon Kevin; Pierce, Eric T; Harrell, P Grace; Walsh, John L; Salazar-Gomez, Andres F; Cash, Sydney S; Eskandar, Emad N; Weiner, Veronica S; Brown, Emery N; Purdon, Patrick L

    2014-01-15

    Rhythmic oscillations shape cortical dynamics during active behavior, sleep, and general anesthesia. Cross-frequency phase-amplitude coupling is a prominent feature of cortical oscillations, but its role in organizing conscious and unconscious brain states is poorly understood. Using high-density EEG and intracranial electrocorticography during gradual induction of propofol general anesthesia in humans, we discovered a rapid drug-induced transition between distinct states with opposite phase-amplitude coupling and different cortical source distributions. One state occurs during unconsciousness and may be similar to sleep slow oscillations. A second state occurs at the loss or recovery of consciousness and resembles an enhanced slow cortical potential. These results provide objective electrophysiological landmarks of distinct unconscious brain states, and could be used to help improve EEG-based monitoring for general anesthesia.

  16. Comparative Analysis of Light-Harvesting Antennae and State Transition in chlorina and cpSRP Mutants.

    PubMed

    Wang, Peng; Grimm, Bernhard

    2016-11-01

    State transitions in photosynthesis provide for the dynamic allocation of a mobile fraction of light-harvesting complex II (LHCII) to photosystem II (PSII) in state I and to photosystem I (PSI) in state II. In the state I-to-state II transition, LHCII is phosphorylated by STN7 and associates with PSI to favor absorption cross-section of PSI. Here, we used Arabidopsis (Arabidopsis thaliana) mutants with defects in chlorophyll (Chl) b biosynthesis or in the chloroplast signal recognition particle (cpSRP) machinery to study the flexible formation of PS-LHC supercomplexes. Intriguingly, we found that impaired Chl b biosynthesis in chlorina1-2 (ch1-2) led to preferentially stabilized LHCI rather than LHCII, while the contents of both LHCI and LHCII were equally depressed in the cpSRP43-deficient mutant (chaos). In view of recent findings on the modified state transitions in LHCI-deficient mutants (Benson et al., 2015), the ch1-2 and chaos mutants were used to assess the influence of varying LHCI/LHCII antenna size on state transitions. Under state II conditions, LHCII-PSI supercomplexes were not formed in both ch1-2 and chaos plants. LHCII phosphorylation was drastically reduced in ch1-2, and the inactivation of STN7 correlates with the lack of state transitions. In contrast, phosphorylated LHCII in chaos was observed to be exclusively associated with PSII complexes, indicating a lack of mobile LHCII in chaos Thus, the comparative analysis of ch1-2 and chaos mutants provides new evidence for the flexible organization of LHCs and enhances our understanding of the reversible allocation of LHCII to the two photosystems. © 2016 American Society of Plant Biologists. All Rights Reserved.

  17. An Analytical State Transition Matrix for Orbits Perturbed by an Oblate Spheroid

    NASA Technical Reports Server (NTRS)

    Mueller, A. C.

    1977-01-01

    An analytical state transition matrix and its inverse, which include the short period and secular effects of the second zonal harmonic, were developed from the nonsingular PS satellite theory. The fact that the independent variable in the PS theory is not time is in no respect disadvantageous, since any explicit analytical solution must be expressed in the true or eccentric anomaly. This is shown to be the case for the simple conic matrix. The PS theory allows for a concise, accurate, and algorithmically simple state transition matrix. The improvement over the conic matrix ranges from 2 to 4 digits accuracy.

  18. States Pave the Way for Smoother Transitions to Kindergarten

    ERIC Educational Resources Information Center

    Loewenberg, Aaron

    2018-01-01

    Children enter kindergarten with a wide range of previous education experiences: Some have participated in pre-K programs: private, state-funded, or part of Head Start. Others have spent time in a family child care setting or in informal arrangements with family, friends, and neighbors. Regardless, this transition is fraught with stress and…

  19. Roles of JnRAP2.6-like from the transition zone of black walnut in hormone signaling

    Treesearch

    Zhonglian Huang; Peng Zhao; Jose Medina; Richard Meilan; Keith Woeste

    2013-01-01

    An EST sequence, designated JnRAP2-like, was isolated from tissue at the heartwood/sapwood transition zone (TZ) in black walnut (Juglans nigra L). The deduced amino acid sequence of JnRAP2-like protein consists of a single AP2- containing domain with significant similarity to conserved AP2/ERF DNA-binding domains in other...

  20. Energy levels, wavelengths, and radiative transition probabilities for the Na-like ions with 38 [le] Z [le] 45

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ying Zhang; Qiren Zhu; Shoufu Pan

    1992-11-01

    The investigation by Z.-Q Zhang et al. (Acta Optica Sinica 11, 193, 1991) shows that it is possible to realize soft X-ray lasing in the water window 23.3-43.8 [Angstrom] with the Na-like recombination scheme, which requires a lower pumping power at a high-power laser facility than that with other schemes. The fine-structure levels with n [le] 15 and l [le] 6 in Na-like ions with 38 [le] Z [le] 45 and the probabilities for radiative transitions between these levels are calculated using the multiconfiguration Dirac-Fock approach. The calculations show that the wavelengths of the anticipated laser transitions 6 f-4d andmore » 6g-4f in the Na-like ions with 38 [le] Z [le] 43 and 5f-4d and 5g-4f in the Na-like ions with 40 [le] Z [le] 45 lie in the region of the water window.« less

  1. Interference between two resonant transitions with distinct initial and final states connected by radiative decay

    NASA Astrophysics Data System (ADS)

    Marsman, A.; Horbatsch, M.; Hessels, E. A.

    2017-12-01

    The resonant line shape from driving a transition between two states, |a 〉 and |b 〉 , can be distorted due to a quantum-mechanical interference effect involving a resonance between two different states, |c 〉 and |d 〉 , if |c 〉 has a decay path to |a 〉 and |d 〉 has a decay path to |b 〉 . This interference can cause a shift of the measured resonance, despite the fact that the two resonances do not have a common initial or final state. As an example, we demonstrate that such a shift affects measurements of the atomic hydrogen 2 S1 /2 -to-2 P1 /2 Lamb-shift transition due to 3 S -to-3 P transitions if the 3 S1 /2 state has some initial population.

  2. Direct Reprogramming of Fibroblasts via a Chemically Induced XEN-like State.

    PubMed

    Li, Xiang; Liu, Defang; Ma, Yantao; Du, Xiaomin; Jing, Junzhan; Wang, Lipeng; Xie, Bingqing; Sun, Da; Sun, Shaoqiang; Jin, Xueqin; Zhang, Xu; Zhao, Ting; Guan, Jingyang; Yi, Zexuan; Lai, Weifeng; Zheng, Ping; Huang, Zhuo; Chang, Yanzhong; Chai, Zhen; Xu, Jun; Deng, Hongkui

    2017-08-03

    Direct lineage reprogramming, including with small molecules, has emerged as a promising approach for generating desired cell types. We recently found that during chemical induction of induced pluripotent stem cells (iPSCs) from mouse fibroblasts, cells pass through an extra-embryonic endoderm (XEN)-like state. Here, we show that these chemically induced XEN-like cells can also be induced to directly reprogram into functional neurons, bypassing the pluripotent state. The induced neurons possess neuron-specific expression profiles, form functional synapses in culture, and further mature after transplantation into the adult mouse brain. Using similar principles, we were also able to induce hepatocyte-like cells from the XEN-like cells. Cells in the induced XEN-like state were readily expandable over at least 20 passages and retained genome stability and lineage specification potential. Our study therefore establishes a multifunctional route for chemical lineage reprogramming and may provide a platform for generating a diverse range of cell types via application of this expandable XEN-like state. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. The effects of refraction on transit transmission spectroscopy: application to Earth-like exoplanets

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Misra, Amit; Meadows, Victoria; Crisp, Dave, E-mail: amit0@astro.washington.edu

    2014-09-01

    We quantify the effects of refraction in transit transmission spectroscopy on spectral absorption features and on temporal variations that could be used to obtain altitude-dependent spectra for planets orbiting stars of different stellar types. We validate our model against altitude-dependent transmission spectra of the Earth from ATMOS and against lunar eclipse spectra from Pallé et al. We perform detectability studies to show the potential effects of refraction on hypothetical observations of Earth analogs with the James Webb Space Telescope NIRSPEC. Due to refraction, there will be a maximum tangent pressure level that can be probed during transit for each givenmore » planet-star system. We show that because of refraction, for an Earth-analog planet orbiting in the habitable zone of a Sun-like star only the top 0.3 bars of the atmosphere can be probed, leading to a decrease in the signal-to-noise ratio (S/N) of absorption features by 60%, while for an Earth-analog planet orbiting in the habitable zone of an M5V star it is possible to probe almost the entire atmosphere with minimal decreases in S/N. We also show that refraction can result in temporal variations in the transit transmission spectrum which may provide a way to obtain altitude-dependent spectra of exoplanet atmospheres. Additionally, the variations prior to ingress and subsequent to egress provide a way to probe pressures greater than the maximum tangent pressure that can be probed during transit. Therefore, probing the maximum range of atmospheric altitudes, and in particular the near-surface environment of an Earth-analog exoplanet, will require looking at out-of-transit refracted light in addition to the in-transit spectrum.« less

  4. M1 transitions between low-lying states in the sdg-IBM-2

    NASA Astrophysics Data System (ADS)

    Casperson, Robert; Werner, Volker

    2006-10-01

    The interplay between collective and single-particle degrees of freedom for nuclei in the A=90 region have recently been under investigation. In Molybdenum and Ruthenium nuclei, collective symmetric and mixed-symmetric structures have been identified, while in Zirconium, underlying shell-structure plays an enhanced role. Collective symmetric structures appear when protons and neutrons are in phase, whereas mixed-symmetric structures occur when they are not. The one-phonon 2^+ mixed-symmetric state was identified from strong M1 transitions to the 2^+1 state. Similar transitions were observed between higher-spin states, and are predicted by the shell model. These phenomena will be investigated within the sdg Interacting Boson Model 2 in order to obtain a better understanding about the structure of the states involved, and results from first model calculations will be presented. Work supported by US DOE under grant number DE-FG02-91ER-40609.

  5. Transition properties of the Be-like Kα X-ray from Mg IX

    NASA Astrophysics Data System (ADS)

    Hu, Feng; Zhang, Shufang; Sun, Yan; Mei, Maofei; Sang, Cuicui; Yang, Jiamin

    2017-12-01

    Energy levels among the lowest 40 fine-structure levels in Be-like Mg IX are calculated using grasp2K code. The wavelengths, oscillator strengths, radiative rates and lifetimes for all possible Kα transitions have been calculated using the multiconfiguration Dirac-Fock method. The accuracy of the results is determined through extensive comparisons with the existing laboratory measurements and theoretical results. The present data can be used reliably for many purposes, such as the line identification of the observed spectra, and modelling and diagnostics of magnesium plasma.

  6. Role of Entropy and Structural Parameters in the Spin State Transition of LaCoO3

    NASA Astrophysics Data System (ADS)

    Chakrabarti, Bismayan; Birol, Turan; Haule, Kristjan

    The spin state transition in LaCoO3 has eluded description for decades despite concerted theoretical and experimental effort. In this study, we approach this problem using fully charge consistent Density Functional Theory + Dynamical Mean Field Theory (DFT+DMFT). We show, from first principles, that LaCoO3 cannot be described by a single, pure spin state at any temperature, but instead shows a gradual change in the population of higher spin multiples as temperature is increased. We explicitly elucidate the critical role of the lattice expansion and oxygen octahedral rotations in the spin state transition. We also show that the spin state transition and the metal-insulator transition in the compound occur at different temperatures. In addition, our results shed light on the importance of electronic entropy, which has so far been ignored in all first principles studies of this material.

  7. Electrostatic transition state stabilization rather than reactant destabilization provides the chemical basis for efficient chorismate mutase catalysis.

    PubMed

    Burschowsky, Daniel; van Eerde, André; Ökvist, Mats; Kienhöfer, Alexander; Kast, Peter; Hilvert, Donald; Krengel, Ute

    2014-12-09

    For more than half a century, transition state theory has provided a useful framework for understanding the origins of enzyme catalysis. As proposed by Pauling, enzymes accelerate chemical reactions by binding transition states tighter than substrates, thereby lowering the activation energy compared with that of the corresponding uncatalyzed process. This paradigm has been challenged for chorismate mutase (CM), a well-characterized metabolic enzyme that catalyzes the rearrangement of chorismate to prephenate. Calculations have predicted the decisive factor in CM catalysis to be ground state destabilization rather than transition state stabilization. Using X-ray crystallography, we show, in contrast, that a sluggish variant of Bacillus subtilis CM, in which a cationic active-site arginine was replaced by a neutral citrulline, is a poor catalyst even though it effectively preorganizes chorismate for the reaction. A series of high-resolution molecular snapshots of the reaction coordinate, including the apo enzyme, and complexes with substrate, transition state analog and product, demonstrate that an active site, which is only complementary in shape to a reactive substrate conformer, is insufficient for effective catalysis. Instead, as with other enzymes, electrostatic stabilization of the CM transition state appears to be crucial for achieving high reaction rates.

  8. Synaptic plasticity modulates autonomous transitions between waking and sleep states: Insights from a Morris-Lecar model

    NASA Astrophysics Data System (ADS)

    Ciszak, Marzena; Bellesi, Michele

    2011-12-01

    The transitions between waking and sleep states are characterized by considerable changes in neuronal firing. During waking, neurons fire tonically at irregular intervals and a desynchronized activity is observed at the electroencephalogram. This activity becomes synchronized with slow wave sleep onset when neurons start to oscillate between periods of firing (up-states) and periods of silence (down-states). Recently, it has been proposed that the connections between neurons undergo potentiation during waking, whereas they weaken during slow wave sleep. Here, we propose a dynamical model to describe basic features of the autonomous transitions between such states. We consider a network of coupled neurons in which the strength of the interactions is modulated by synaptic long term potentiation and depression, according to the spike time-dependent plasticity rule (STDP). The model shows that the enhancement of synaptic strength between neurons occurring in waking increases the propensity of the network to synchronize and, conversely, desynchronization appears when the strength of the connections become weaker. Both transitions appear spontaneously, but the transition from sleep to waking required a slight modification of the STDP rule with the introduction of a mechanism which becomes active during sleep and changes the proportion between potentiation and depression in accordance with biological data. At the neuron level, transitions from desynchronization to synchronization and vice versa can be described as a bifurcation between two different states, whose dynamical regime is modulated by synaptic strengths, thus suggesting that transition from a state to an another can be determined by quantitative differences between potentiation and depression.

  9. Use of the forest vegetation simulator to quantify disturbance activities in state and transition models

    Treesearch

    Reuben Weisz; Don Vandendriesche

    2012-01-01

    The Forest Vegetation Simulator (FVS) has been used to provide rates of natural growth transitions under endemic conditions for use in State and Transition Models (STMs). This process has previously been presented. This paper expands on that work by citing the methods used to capture resultant vegetation states following disturbance activities; be it of natural causes...

  10. How Well Can Modern Density Functionals Predict Internuclear Distances at Transition States?

    PubMed

    Xu, Xuefei; Alecu, I M; Truhlar, Donald G

    2011-06-14

    We introduce a new database called TSG48 containing 48 transition state geometrical data (in particular, internuclear distances in transition state structures) for 16 main group reactions. The 16 reactions are the 12 reactions in the previously published DBH24 database (which includes hydrogen transfer reactions, heavy-atom transfer reactions, nucleophilic substitution reactions, and association reactions plus one unimolecular isomerization) plus four H-transfer reactions in which a hydrogen atom is abstracted by the methyl or hydroperoxyl radical from the two different positions in methanol. The data in TSG48 include data for four reactions that have previously been treated at a very high level in the literature. These data are used to test and validate methods that are affordable for the entire test suite, and the most accurate of these methods is found to be the multilevel BMC-CCSD method. The data that constitute the TSG48 database are therefore taken to consist of these very high level calculations for the four reactions where they are available and BMC-CCSD calculations for the other 12 reactions. The TSG48 database is used to assess the performance of the eight Minnesota density functionals from the M05-M08 families and 26 other high-performance and popular density functionals for locating transition state geometries. For comparison, the MP2 and QCISD wave function methods have also been tested for transition state geometries. The MC3BB and MC3MPW doubly hybrid functionals and the M08-HX and M06-2X hybrid meta-GGAs are found to have the best performance of all of the density functionals tested. M08-HX is the most highly recommended functional due to the excellent performance for all five subsets of TSG48, as well as having a lower cost when compared to doubly hybrid functionals. The mean absolute errors in transition state internuclear distances associated with breaking and forming bonds as calculated by the B2PLYP, MP2, and B3LYP methods are respectively

  11. Experiences of Japanese Visiting Scholars in the United States: An Exploration of Transition

    ERIC Educational Resources Information Center

    Shimmi, Yukiko

    2014-01-01

    The purpose of this study is to examine the reasons why Japanese visiting scholars visited the United States, their activities and experiences during their visits, their challenges and support for their transition, and personal and contextual factors that affected their transition in different stages. Although short-term international scholar…

  12. Ionic and Covalent Stabilization of Intermediates and Transition States in Catalysis by Solid Acids

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Deshlahra, Prashant; Carr, Robert T.; Iglesia, Enrique

    Reactivity descriptors describe catalyst properties that determine the stability of kinetically relevant transition states and adsorbed intermediates. Theoretical descriptors, such as deprotonation energies (DPE), rigorously account for Brønsted acid strength for catalytic solids with known structure. Here, mechanistic interpretations of methanol dehydration turnover rates are used to assess how charge reorganization (covalency) and electrostatic interactions determine DPE and how such interactions are recovered when intermediates and transition states interact with the conjugate anion in W and Mo polyoxometalate (POM) clusters and gaseous mineral acids. Turnover rates are lower and kinetically relevant species are less stable on Mo than W POMmore » clusters with similar acid strength, and such species are more stable on mineral acids than that predicted from W-POM DPE–reactivity trends, indicating that DPE and acid strength are essential but incomplete reactivity descriptors. Born–Haber thermochemical cycles indicate that these differences reflect more effective charge reorganization upon deprotonation of Mo than W POM clusters and the much weaker reorganization in mineral acids. Such covalency is disrupted upon deprotonation but cannot be recovered fully upon formation of ion pairs at transition states. Predictive descriptors of reactivity for general classes of acids thus require separate assessments of the covalent and ionic DPE components. Here, we describe methods to estimate electrostatic interactions, which, taken together with energies derived from density functional theory, give the covalent and ionic energy components of protons, intermediates, and transition states. In doing so, we provide a framework to predict the reactive properties of protons for chemical reactions mediated by ion-pair transition states.« less

  13. Dynamically Switching the Polarization State of Light Based on the Phase Transition of Vanadium Dioxide

    NASA Astrophysics Data System (ADS)

    Jia, Zhi-Yong; Shu, Fang-Zhou; Gao, Ya-Jun; Cheng, Feng; Peng, Ru-Wen; Fan, Ren-Hao; Liu, Yongmin; Wang, Mu

    2018-03-01

    There have been great endeavors devoted to manipulating the polarization state of light by plasmonic nanostructures in recent decades. However, the topic of active polarizers has attracted much less attention. We present a composite plasmonic nanostructure consisting of vanadium dioxide that can dynamically modulate the polarization state of the reflected light through a thermally induced phase transition of vanadium dioxide. We design a system consisting of anisotropic plasmonic nanostructures with vanadium dioxide that exhibits distinct reflections subjected to different linearly polarized incidence at room temperature and in the heated state. Under a particular linearly polarized incidence, the polarization state of the reflected light changes at room temperature, and reverts to its original polarization state above the phase-transition temperature. The composite structure can also be used to realize a dynamically switchable infrared image, wherein a pattern can be visualized at room temperature while it disappears above the phase-transition temperature. The composite structure could be potentially used for versatile optical modulators, molecular detection, and polarimetric imaging.

  14. Fine-structure calculations of energy levels, oscillator strengths, and transition probabilities for sulfur-like iron, Fe XI

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Abou El-Maaref, A., E-mail: aahmh@hotmail.com; Ahmad, Mahmoud; Allam, S.H.

    Energy levels, oscillator strengths, and transition probabilities for transitions among the 14 LS states belonging to configurations of sulfur-like iron, Fe XI, have been calculated. These states are represented by configuration interaction wavefunctions and have configurations 3s{sup 2}3p{sup 4}, 3s3p{sup 5}, 3s{sup 2}3p{sup 3}3d, 3s{sup 2}3p{sup 3}4s, 3s{sup 2}3p{sup 3}4p, and 3s{sup 2}3p{sup 3}4d, which give rise to 123 fine-structure energy levels. Extensive configuration interaction calculations using the CIV3 code have been performed. To assess the importance of relativistic effects, the intermediate coupling scheme by means of the Breit–Pauli Hamiltonian terms, such as the one-body mass correction and Darwin term,more » and spin–orbit, spin–other-orbit, and spin–spin corrections, are incorporated within the code. These incorporations adjusted the energy levels, therefore the calculated values are close to the available experimental data. Comparisons between the present calculated energy levels as well as oscillator strengths and both experimental and theoretical data have been performed. Our results show good agreement with earlier works, and they might be useful in thermonuclear fusion research and astrophysical applications. -- Highlights: •Accurate atomic data of iron ions are needed for identification of solar corona. •Extensive configuration interaction wavefunctions including 123 fine-structure levels have been calculated. •The relativistic effects by means of the Breit–Pauli Hamiltonian terms are incorporated. •This incorporation adjusts the energy levels, therefore the calculated values are close to experimental values.« less

  15. Theory of Interface States at Silicon / Transition - - Silicide Interfaces.

    NASA Astrophysics Data System (ADS)

    Lim, Hunhwa

    The Si/NiSi(,2)(111) interface is of both fundamental and techno- logical interest: From the fundamental point of view, it is the best characterized of all semiconductor/metal interfaces, with two well-determined geometries (A and B) involving nearly perfect bonding. (This is because Si and NiSi(,2) have nearly the same lattice spacing.) Consequently, a theoretical treatment of this system makes sense--as it would not for messier systems--and one can have some confidence that the theoretical predictions are relevant to experimental observa- tions. From the technological point of view, Si/NiSi(,2) is representative of the class of semiconductor/metal interfaces that are currently of greatest interest in regard to electronic devices--Si/transition -metal-silicide interfaces. The calculations of this dissertation are for the intrinsic interface states of Si/NiSi(,2)-A geometry. These calculations also provide a foundation for later studies of defects at this interface, and for studies of other related systems, such as CoSi(,2). The calculations employ empirical tight-binding Hamiltonians for both Si and NiSi(,2) (with the parameters fitted to prior calculations of the bulk band structures, which appear to be in agreement with the available experimental data on bulk Si and NiSi(,2)). They also employ Green's function techniques--in particular, the subspace Hamiltonian technique. Our principal results are the following: (1) Interface state disper- sion curves are predicted along the symmetry lines (')(GAMMA)(')M, (')M(')K and (')K(')(GAMMA) of the surface Brillouin zone. (2) A prominent band of interface states is found which disperses downward from an energy within the Si band gap to an energy below the Si valence band edge E(,(upsilon)) as the planar wavevector (')k increases from (')(GAMMA) ((')k = 0) to (')M or (')K (symmetry points at boundary of the surface Brillouin zone). This band of inter- face states should be observable. It produces a peak in the surface

  16. Markov-chain model of classified atomistic transition states for discrete kinetic Monte Carlo simulations.

    PubMed

    Numazawa, Satoshi; Smith, Roger

    2011-10-01

    Classical harmonic transition state theory is considered and applied in discrete lattice cells with hierarchical transition levels. The scheme is then used to determine transitions that can be applied in a lattice-based kinetic Monte Carlo (KMC) atomistic simulation model. The model results in an effective reduction of KMC simulation steps by utilizing a classification scheme of transition levels for thermally activated atomistic diffusion processes. Thermally activated atomistic movements are considered as local transition events constrained in potential energy wells over certain local time periods. These processes are represented by Markov chains of multidimensional Boolean valued functions in three-dimensional lattice space. The events inhibited by the barriers under a certain level are regarded as thermal fluctuations of the canonical ensemble and accepted freely. Consequently, the fluctuating system evolution process is implemented as a Markov chain of equivalence class objects. It is shown that the process can be characterized by the acceptance of metastable local transitions. The method is applied to a problem of Au and Ag cluster growth on a rippled surface. The simulation predicts the existence of a morphology-dependent transition time limit from a local metastable to stable state for subsequent cluster growth by accretion. Excellent agreement with observed experimental results is obtained.

  17. Jamming transitions in cancer

    NASA Astrophysics Data System (ADS)

    Oswald, Linda; Grosser, Steffen; Smith, David M.; Käs, Josef A.

    2017-12-01

    The traditional picture of tissues, where they are treated as liquids defined by properties such as surface tension or viscosity has been redefined during the last few decades by the more fundamental question: under which conditions do tissues display liquid-like or solid-like behaviour? As a result, basic concepts arising from the treatment of tissues as solid matter, such as cellular jamming and glassy tissues, have shifted into the current focus of biophysical research. Here, we review recent works examining the phase states of tissue with an emphasis on jamming transitions in cancer. When metastasis occurs, cells gain the ability to leave the primary tumour and infiltrate other parts of the body. Recent studies have shown that a linkage between an unjamming transition and tumour progression indeed exists, which could be of importance when designing surgery and treatment approaches for cancer patients.

  18. Unambiguously identifying spin states of transition-metal ions in the Earth (Invited)

    NASA Astrophysics Data System (ADS)

    Hsu, H.

    2010-12-01

    The spin state of a transition-metal ion in crystalline solids, defined by the number of unpaired electrons in the ion’s incomplete 3d shell, may vary with many factors, such as temperature, pressure, strain, and the local atomic configuration, to name a few. Such a phenomenon, known as spin-state crossover, plays a crucial role in spintronic materials. Recently, the pressure-induced spin-state crossover in iron-bearing minerals has been recognized to affect the minerals’ structural and elastic properties. However, the detailed mechanism of such crossover in iron-bearing magnesium silicate perovskite, the most abundant mineral in the Earth, remains unclear. A significant part of this confusion arises from the difficulty in reliably extracting the spin state from experiments. For the same reason, the thermally-induced spin-state crossover in lanthanum cobaltite (LaCoO3) has been controversial for more than four decades. In this talk, I will discuss how first-principle calculations can help clarifying these long-standing controversies. In addition to the total energy, equation of state, and elastic properties of each spin state, first-principle calculations also predict the electric field gradient (EFG) at the nucleus of each transition-metal ion. Our calculations showed that the nuclear EFG, a quantity that can be measured via Mössbauer or nuclear magnetic resonance (NMR) spectroscopy, depends primarily on the spin state, irrespective of the concentration or configuration of transition-metal ions. Such robustness makes EFG a unique fingerprint to identify the spin state. The combination of first-principle calculations and Mössbauer/NMR spectroscopy can therefore be a reliable and efficient approach in tackling spin-state crossover problems in the Earth. This work was primarily supported by the MRSEC Program of NSF under Awards Number DMR-0212302 and DMR-0819885, and partially supported by NSF under ATM-0428774 (V-Lab), EAR-1019853, and EAR-0810272. The

  19. How Accurate Are Transition States from Simulations of Enzymatic Reactions?

    PubMed Central

    2015-01-01

    The rate expression of traditional transition state theory (TST) assumes no recrossing of the transition state (TS) and thermal quasi-equilibrium between the ground state and the TS. Currently, it is not well understood to what extent these assumptions influence the nature of the activated complex obtained in traditional TST-based simulations of processes in the condensed phase in general and in enzymes in particular. Here we scrutinize these assumptions by characterizing the TSs for hydride transfer catalyzed by the enzyme Escherichia coli dihydrofolate reductase obtained using various simulation approaches. Specifically, we compare the TSs obtained with common TST-based methods and a dynamics-based method. Using a recently developed accurate hybrid quantum mechanics/molecular mechanics potential, we find that the TST-based and dynamics-based methods give considerably different TS ensembles. This discrepancy, which could be due equilibrium solvation effects and the nature of the reaction coordinate employed and its motion, raises major questions about how to interpret the TSs determined by common simulation methods. We conclude that further investigation is needed to characterize the impact of various TST assumptions on the TS phase-space ensemble and on the reaction kinetics. PMID:24860275

  20. Kinetic Analysis for Macrocyclizations Involving Anionic Template at the Transition State

    PubMed Central

    Martí-Centelles, Vicente; Burguete, M. Isabel; Luis, Santiago V.

    2012-01-01

    Several kinetic models for the macrocyclization of a C2 pseudopeptide with a dihalide through a SN2 reaction have been developed. These models not only focus on the kinetic analysis of the main macrocyclization reaction, but also consider the competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes. PMID:22666148

  1. Career Transitions and Professional Development of Bulgarian Immigrants in the United States

    ERIC Educational Resources Information Center

    Angelova, Iva

    2016-01-01

    This paper focuses on job transitions and professional development of immigrants in the United States. Using narrative as a method and exploring Bulgarian immigrants' personal experience stories, this report shares some of the findings from the author's dissertation. Upon coming to the United States, the Bulgarian immigrants experienced a…

  2. State Switching of the X-Ray/Radio Transitional Millisecond Pulsar

    NASA Astrophysics Data System (ADS)

    Shang, Lun-Hua; Zhang, Cheng-Min; Li, Di; Wang, De-Hua; Wang, Shuang-Qiang; Wang, Pei; Pan, Yuan-Yue; Yang, Yi-Yan; Zhi, Qi-Jun

    2017-11-01

    PSR J1023+0038 is a known transitional pulsar, which switches between the accretion-powered X-ray pulsar state and the rotation-powered radio millisecond pulsar (MSP) state. Here, we study the conditions for its state transition by ascribing ˜GHz radio pulse emission to the plasma cutoff oscillation frequency at the magnetosphere, which depends on the plasma density or accretion rate. With the accretion X-ray luminosity declining fromhigh to low state (e.g., ˜ {10}35 erg s-1 to ˜ {10}32 erg s-1), the magnetosphere boundary expands to the light cylinder, where the plasma density is low enough to permit the emission of radio waves at the several-GHz frequency band. Thus, for a sufficiently low accretion-rate state (˜ {10}32 erg s-1), the radio emission at the several-GHz band is not blocked by the plasma, and the radio pulsar can be detected in the favored “observational windows,” I.e., the L band (1-2 GHz), S band (2-4 GHz), and C band (4-8 GHz). Furthermore, to evaluate the penetration characteristics of the outgoing radio wave of low frequency, we calculate its skin depth, which is found to be a couple of centimeters for the low X-ray luminosity of {10}34{--}{10}32 erg s-1, a scale that is much shorter than the light cylinder radius of about 100 km for MSPs.

  3. Role of Chemical Reactivity and Transition State Modeling for Virtual Screening.

    PubMed

    Karthikeyan, Muthukumarasamy; Vyas, Renu; Tambe, Sanjeev S; Radhamohan, Deepthi; Kulkarni, Bhaskar D

    2015-01-01

    Every drug discovery research program involves synthesis of a novel and potential drug molecule utilizing atom efficient, economical and environment friendly synthetic strategies. The current work focuses on the role of the reactivity based fingerprints of compounds as filters for virtual screening using a tool ChemScore. A reactant-like (RLS) and a product- like (PLS) score can be predicted for a given compound using the binary fingerprints derived from the numerous known organic reactions which capture the molecule-molecule interactions in the form of addition, substitution, rearrangement, elimination and isomerization reactions. The reaction fingerprints were applied to large databases in biology and chemistry, namely ChEMBL, KEGG, HMDB, DSSTox, and the Drug Bank database. A large network of 1113 synthetic reactions was constructed to visualize and ascertain the reactant product mappings in the chemical reaction space. The cumulative reaction fingerprints were computed for 4000 molecules belonging to 29 therapeutic classes of compounds, and these were found capable of discriminating between the cognition disorder related and anti-allergy compounds with reasonable accuracy of 75% and AUC 0.8. In this study, the transition state based fingerprints were also developed and used effectively for virtual screening in drug related databases. The methodology presented here provides an efficient handle for the rapid scoring of molecular libraries for virtual screening.

  4. δ-Deuterium Isotope Effects as Probes for Transition-State Structures of Isoprenoid Substrates

    PubMed Central

    2015-01-01

    The biosynthetic pathways to isoprenoid compounds involve transfer of the prenyl moiety in allylic diphosphates to electron-rich (nucleophilic) acceptors. The acceptors can be many types of nucleophiles, while the allylic diphosphates only differ in the number of isoprene units and stereochemistry of the double bonds in the hydrocarbon moieties. Because of the wide range of nucleophilicities of naturally occurring acceptors, the mechanism for prenyltransfer reactions may be dissociative or associative with early to late transition states. We have measured δ-secondary kinetic isotope effects operating through four bonds for substitution reactions with dimethylallyl derivatives bearing deuterated methyl groups at the distal (C3) carbon atom in the double bond under dissociative and associative conditions. Computational studies with density functional theory indicate that the magnitudes of the isotope effects correlate with the extent of bond formation between the allylic moiety and the electron-rich acceptor in the transition state for alkylation and provide insights into the structures of the transition states for associative and dissociative alkylation reactions. PMID:24665882

  5. Integrating continuous stocks and flows into state-and-transition simulation models of landscape change

    USGS Publications Warehouse

    Daniel, Colin J.; Sleeter, Benjamin M.; Frid, Leonardo; Fortin, Marie-Josée

    2018-01-01

    State-and-transition simulation models (STSMs) provide a general framework for forecasting landscape dynamics, including projections of both vegetation and land-use/land-cover (LULC) change. The STSM method divides a landscape into spatially-referenced cells and then simulates the state of each cell forward in time, as a discrete-time stochastic process using a Monte Carlo approach, in response to any number of possible transitions. A current limitation of the STSM method, however, is that all of the state variables must be discrete.Here we present a new approach for extending a STSM, in order to account for continuous state variables, called a state-and-transition simulation model with stocks and flows (STSM-SF). The STSM-SF method allows for any number of continuous stocks to be defined for every spatial cell in the STSM, along with a suite of continuous flows specifying the rates at which stock levels change over time. The change in the level of each stock is then simulated forward in time, for each spatial cell, as a discrete-time stochastic process. The method differs from the traditional systems dynamics approach to stock-flow modelling in that the stocks and flows can be spatially-explicit, and the flows can be expressed as a function of the STSM states and transitions.We demonstrate the STSM-SF method by integrating a spatially-explicit carbon (C) budget model with a STSM of LULC change for the state of Hawai'i, USA. In this example, continuous stocks are pools of terrestrial C, while the flows are the possible fluxes of C between these pools. Importantly, several of these C fluxes are triggered by corresponding LULC transitions in the STSM. Model outputs include changes in the spatial and temporal distribution of C pools and fluxes across the landscape in response to projected future changes in LULC over the next 50 years.The new STSM-SF method allows both discrete and continuous state variables to be integrated into a STSM, including interactions between

  6. Transitional Child Care: State Experiences and Emerging Policies under the Family Support Act.

    ERIC Educational Resources Information Center

    Ebb, Nancy; And Others

    This guide is designed to provide information about transitional child care (TCC) program policies and operations and to offer recommendations to policymakers and advocates. Transitional child care is a new federal child care program that every state must implement by April 1, 1990. Established by the Family Support Act (FSA) of 1988, TCC is…

  7. Transitioning youth with rheumatic conditions: perspectives of pediatric rheumatology providers in the United States and Canada.

    PubMed

    Chira, Peter; Ronis, Tova; Ardoin, Stacy; White, Patience

    2014-04-01

    To assess North American pediatric rheumatology providers' perspectives on practices, barriers, and opportunities concerning the transition from pediatric-centered to adult-centered care. Childhood Arthritis and Rheumatology Research Alliance (CARRA) members completed a 25-item survey assessing current transition practices, transition policy awareness, and transitional care barriers and needs. Results were compared to the American Academy of Pediatrics (AAP) 2008 survey on transitional care. Over half (158/288, 55%) of CARRA members completed the survey. Fewer than 10% are very familiar with AAP guidelines about transition care for youth with special healthcare needs. Eight percent have a formal written transition policy, but 42% use an informal approach. Patient request (75%) most frequently initiates transfer to adult care. Two major barriers to transition are fragmented adult medical care and lack of sufficient time to provide services. Compared with AAP survey participants, pediatric rheumatology providers are significantly more likely to help youth find an adult specialist (63% vs 45%) and discuss confidentiality and consent before age 18 (45% vs 33%), but are less likely to help with medical summary creation (16% vs 27%) or find a primary care provider (25% vs 47%). Outcomes ranked as "very important" in defining a successful transition are survival (76%), seeing an adult rheumatologist within 6 months of final pediatric rheumatology visit (66%), and maintaining insurance coverage (57%). This comprehensive survey of North American pediatric rheumatology providers regarding transitional care practices demonstrates deficiencies in education, resources, and a formalized process. Respondents support development of standardized rheumatology-specific transition practices.

  8. Quantum Teleportation of an Arbitrary N-qubit State via GHZ-like States

    NASA Astrophysics Data System (ADS)

    Zhang, Bo; Liu, Xing-tong; Wang, Jian; Tang, Chao-jing

    2016-03-01

    Recently Zhu (Int. J. Theor. Phys. 53, 4095, 2014) had shown that using GHZ-like states as quantum channel, it is possible to teleport an arbitrary unknown two-qubit state. We investigate this channel for the teleportation of an arbitrary N-qubit state. The strict proof through mathematical induction is presented and the rule for the receiver to reconstruct the desired state is explicitly derived in the most general case. We also discuss that if a system of quantum secret sharing of classical message is established, our protocol can be transformed to a N-qubit perfect controlled teleportation scheme from the controller's point of view.

  9. 19 CFR 123.65 - Domestic baggage transiting Canada or Mexico between ports in the United States.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Domestic baggage transiting Canada or Mexico... MEXICO Baggage § 123.65 Domestic baggage transiting Canada or Mexico between ports in the United States... transported from one port in the United States to another through Canada or through Mexico in accord with the...

  10. Transition between morule-like and solid components may occur in solid-predominant adenocarcinoma of the lung: report of 2 cases with EGFR and KRAS mutations.

    PubMed

    Tajima, Shogo; Koda, Kenji

    2015-01-01

    A limited number of pulmonary adenocarcinoma cases with morule-like components have been described to date, and the most frequent histological subtype is papillary-predominant adenocarcinoma. Occasionally, this type of adenocarcinoma is associated with solid-predominant adenocarcinoma. EGFR mutations are predominant in adenocarcinoma with morule-like components, followed by ALK rearrangements. Herein, we present 2 cases of solid-predominant adenocarcinoma with morule-like components harboring either an EGFR or KRAS mutation. This KRAS-mutant case is the first to be associated with morule-like components, to the best of our knowledge. Both cases showed transition between micropapillary and morule-like components. Transition between morule-like and solid components was also observed in both cases. Although a few cases of solid-predominant adenocarcinoma have been shown to harbor morule-like components, this type of transition has not been previously well described. We surmised that the solid components of some EGFR-mutant adenocarcinomas might be derived from morule-like components.

  11. Structural and topological phase transitions on the German Stock Exchange

    NASA Astrophysics Data System (ADS)

    Wiliński, M.; Sienkiewicz, A.; Gubiec, T.; Kutner, R.; Struzik, Z. R.

    2013-12-01

    We find numerical and empirical evidence for dynamical, structural and topological phase transitions on the (German) Frankfurt Stock Exchange (FSE) in the temporal vicinity of the worldwide financial crash. Using the Minimal Spanning Tree (MST) technique, a particularly useful canonical tool of the graph theory, two transitions of the topology of a complex network representing the FSE were found. The first transition is from a hierarchical scale-free MST representing the stock market before the recent worldwide financial crash, to a superstar-like MST decorated by a scale-free hierarchy of trees representing the market’s state for the period containing the crash. Subsequently, a transition is observed from this transient, (meta)stable state of the crash to a hierarchical scale-free MST decorated by several star-like trees after the worldwide financial crash. The phase transitions observed are analogous to the ones we obtained earlier for the Warsaw Stock Exchange and more pronounced than those found by Onnela-Chakraborti-Kaski-Kertész for the S&P 500 index in the vicinity of Black Monday (October 19, 1987) and also in the vicinity of January 1, 1998. Our results provide an empirical foundation for the future theory of dynamical, structural and topological phase transitions on financial markets.

  12. Land management in the American southwest: a state-and-transition approach to ecosystem complexity.

    PubMed

    Bestelmeyer, Brandon T; Herrick, Jeffrey E; Brown, Joel R; Trujillo, David A; Havstad, Kris M

    2004-07-01

    State-and-transition models are increasingly being used to guide rangeland management. These models provide a relatively simple, management-oriented way to classify land condition (state) and to describe the factors that might cause a shift to another state (a transition). There are many formulations of state-and-transition models in the literature. The version we endorse does not adhere to any particular generalities about ecosystem dynamics, but it includes consideration of several kinds of dynamics and management response to them. In contrast to previous uses of state-and-transition models, we propose that models can, at present, be most effectively used to specify and qualitatively compare the relative benefits and potential risks of different management actions (e.g., fire and grazing) and other factors (e.g., invasive species and climate change) on specified areas of land. High spatial and temporal variability and complex interactions preclude the meaningful use of general quantitative models. Forecasts can be made on a case-by-case basis by interpreting qualitative and quantitative indicators, historical data, and spatially structured monitoring data based on conceptual models. We illustrate how science- based conceptual models are created using several rangeland examples that vary in complexity. In doing so, we illustrate the implications of designating plant communities and states in models, accounting for varying scales of pattern in vegetation and soils, interpreting the presence of plant communities on different soils and dealing with our uncertainty about how those communities were assembled and how they will change in the future. We conclude with observations about how models have helped to improve management decision-making.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Soh, Daniel Beom Soo

    We calculated the optical nonlinearities of the atomically thin monolayer transition metal dichalcogenide material (particularly MoS 2), particularly for those linear and nonlinear transition processes that utilize the bound exciton states. We adopted the bound and the unbound exciton states as the basis for the Hilbert space, and derived all the dynamical density matrices that provides the induced current density, from which the nonlinear susceptibilities can be drawn order-by-order via perturbative calculations. We provide the nonlinear susceptibilities for the linear, the second-harmonic, the third-harmonic, and the kerr-type two-photon processes.

  14. Line strengths of QED-sensitive forbidden transitions in B-, Al-, F- and Cl-like ions

    NASA Astrophysics Data System (ADS)

    Bilal, M.; Volotka, A. V.; Beerwerth, R.; Fritzsche, S.

    2018-05-01

    The magnetic dipole (M 1 ) line strength between the fine-structure levels of the ground configurations in B-, F-, Al-, and Cl-like ions are calculated for the four elements argon, iron, molybdenum, and tungsten. Systematically enlarged multiconfiguration Dirac-Hartree-Fock (MCDHF) wave functions are employed to account for the interelectronic interaction with the Breit interaction included in first-order perturbation theory. The QED corrections are evaluated to all orders in α Z utilizing an effective potential approach. The calculated line strengths are compared with the results of other theories. The M 1 transition rates are reported using accurate energies from the literature. Moreover, the lifetimes in the range of millisecond to picosecond are predicted including the contributions from the transition rate due to the E 2 transition channel. The discrepancies of the predicted rates from those available from the literature are discussed and a benchmark data set of theoretical lifetimes is provided to support future experiments.

  15. Computer Series 41: Potential-Energy Surfaces and Transition-State Theory.

    ERIC Educational Resources Information Center

    Moss, S. J.; Coady, C. J.

    1983-01-01

    Describes computer programs involving the London-Eyring-Polany-Sato method (LEPS). The programs provide a valuable means of introducing students to potential energy surfaces and to the foundations of transition state theory. Program listings (with copies of student scripts) or programs on DOS 3.3 disc are available from authors. (JN)

  16. Test of the Chevallier-Polarski-Linder parametrization for rapid dark energy equation of state transitions

    NASA Astrophysics Data System (ADS)

    Linden, Sebastian; Virey, Jean-Marc

    2008-07-01

    We test the robustness and flexibility of the Chevallier-Polarski-Linder (CPL) parametrization of the dark energy equation of state w(z)=w0+wa(z)/(1+z) in recovering a four-parameter steplike fiducial model. We constrain the parameter space region of the underlying fiducial model where the CPL parametrization offers a reliable reconstruction. It turns out that non-negligible biases leak into the results for recent (z<2.5) rapid transitions, but that CPL yields a good reconstruction in all other cases. The presented analysis is performed with supernova Ia data as forecasted for a space mission like SNAP/JDEM, combined with future expectations for the cosmic microwave background shift parameter R and the baryonic acoustic oscillation parameter A.

  17. Victimization and PTSD-like states in an Icelandic youth probability sample.

    PubMed

    Bödvarsdóttir, Iris; Elklit, Ask

    2007-10-01

    Although adolescence in many cases is a period of rebellion and experimentation with new behaviors and roles, the exposure of adolescents to life-threatening and violent events has rarely been investigated in national probability studies using a broad range of events. In an Icelandic national representative sample of 206 9th-grade students (mean = 14.5 years), the prevalence of 20 potentially traumatic events and negative life events was reported, along with the psychological impact of these events. Seventy-four percent of the girls and 79 percent of the boys were exposed to at least one event. The most common events were the death of a family member, threat of violence, and traffic accidents. The estimated lifetime prevalence of posttraumatic stress disorder-like states (PTSD; DSM-IV, APA, 1994 1) was 16 percent, whereas another 12 percent reached a sub-clinical level of PTSD-like states (missing the full diagnosis with one symptom). Following exposure, girls suffered from PTSD-like states almost twice as often as boys. Gender, mothers' education, and single-parenthood were associated with specific events. The odds ratios and 95% CI for PTSD-like states given a specific event are reported. Being exposed to multiple potentially traumatic events was associated with an increase in PTSD-like states. The findings indicate substantial mental health problems in adolescents that are associated with various types of potentially traumatic exposure.

  18. P-20 Education Policy: School to College Transition Policy in Washington State

    ERIC Educational Resources Information Center

    Pitre, Paul E.

    2011-01-01

    This study examines Washington State's attempt to move toward an integrated, P-20 system of education that enhances student transitions from high school to college. In analyzing Washington as a single case study, a profile of the state is developed on key access related characteristics. Data for this study were gathered utilizing fundamental case…

  19. Radiative rates and electron impact excitation rate coefficients for Ne-like selenium, Se XXV

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wang, K.; Chen, C.Y., E-mail: chychen@fudan.edu.cn; Huang, M.

    2011-07-15

    In this article we report calculations of energy levels, radiative rates, electron impact collision strengths, and effective collision strengths for transitions among the 241 fine-structure levels arising from 2l{sup 8} and 2l{sup 7}n{sup '}l{sup '} (n{sup '{<=}}6 and l{sup '{<=}}n{sup '}-1) configurations of Ne-like Se XXV using the Flexible Atomic Code. Energy levels and radiative rates are calculated within the relativistic configuration-interaction method. Direct excitation collision strengths are calculated using the relativistic distorted-wave approximation and high-energy collision strengths are obtained in the relativistic plane-wave approximation. Resonance contributions through the relevant Na-like doubly-excited configurations 2l{sup 7}n'l'n''l'' (3{<=}n'{<=}7, l'{<=}n'-1, n'{<=}n''{<=}50, and l''{<=}8)more » are explicitly taken into account via the independent-process and isolated-resonance approximation using distorted waves. Resonant stabilizing transitions and possibly important radiative decays from the resonances toward low-lying autoionizing levels are considered. In addition, the resonance contributions from Na-like 2l{sup 6}3l'3l'''n''' (n'''=3-6) configurations are included and found to be predominant for many transitions among the singly-excited states in Ne-like Se XXV. We present the radiative rates, oscillator strengths, and line strengths for all electric dipole, magnetic dipole, electric quadrupole, magnetic quadrupole, electric octopole, and magnetic octopole transitions among the 241 levels. The effective collision strengths are reported for all 28920 transitions among the 241 levels over a wide temperature range up to 10 keV. To assess the reliability and accuracy of the present collisional data, we have performed a 27-state close-coupling calculation, employing the Dirac R-matrix theory. The results from the close-coupling calculation and the independent-process calculation for the identical target states are found to be in good

  20. Vibrational energy transfer near a dissociative adsorption transition state: State-to-state study of HCl collisions at Au(111).

    PubMed

    Geweke, Jan; Shirhatti, Pranav R; Rahinov, Igor; Bartels, Christof; Wodtke, Alec M

    2016-08-07

    In this work we seek to examine the nature of collisional energy transfer between HCl and Au(111) for nonreactive scattering events that sample geometries near the transition state for dissociative adsorption by varying both the vibrational and translational energy of the incident HCl molecules in the range near the dissociation barrier. Specifically, we report absolute vibrational excitation probabilities for HCl(v = 0 → 1) and HCl(v = 1 → 2) scattering from clean Au(111) as a function of surface temperature and incidence translational energy. The HCl(v = 2 → 3) channel could not be observed-presumably due to the onset of dissociation. The excitation probabilities can be decomposed into adiabatic and nonadiabatic contributions. We find that both contributions strongly increase with incidence vibrational state by a factor of 24 and 9, respectively. This suggests that V-T as well as V-EHP coupling can be enhanced near the transition state for dissociative adsorption at a metal surface. We also show that previously reported HCl(v = 0 → 1) excitation probabilities [Q. Ran et al., Phys. Rev. Lett. 98, 237601 (2007)]-50 times smaller than those reported here-were influenced by erroneous assignment of spectroscopic lines used in the data analysis.

  1. Comparative Analysis of Light-Harvesting Antennae and State Transition in chlorina and cpSRP Mutants1[OPEN

    PubMed Central

    Wang, Peng

    2016-01-01

    State transitions in photosynthesis provide for the dynamic allocation of a mobile fraction of light-harvesting complex II (LHCII) to photosystem II (PSII) in state I and to photosystem I (PSI) in state II. In the state I-to-state II transition, LHCII is phosphorylated by STN7 and associates with PSI to favor absorption cross-section of PSI. Here, we used Arabidopsis (Arabidopsis thaliana) mutants with defects in chlorophyll (Chl) b biosynthesis or in the chloroplast signal recognition particle (cpSRP) machinery to study the flexible formation of PS-LHC supercomplexes. Intriguingly, we found that impaired Chl b biosynthesis in chlorina1-2 (ch1-2) led to preferentially stabilized LHCI rather than LHCII, while the contents of both LHCI and LHCII were equally depressed in the cpSRP43-deficient mutant (chaos). In view of recent findings on the modified state transitions in LHCI-deficient mutants (Benson et al., 2015), the ch1-2 and chaos mutants were used to assess the influence of varying LHCI/LHCII antenna size on state transitions. Under state II conditions, LHCII-PSI supercomplexes were not formed in both ch1-2 and chaos plants. LHCII phosphorylation was drastically reduced in ch1-2, and the inactivation of STN7 correlates with the lack of state transitions. In contrast, phosphorylated LHCII in chaos was observed to be exclusively associated with PSII complexes, indicating a lack of mobile LHCII in chaos. Thus, the comparative analysis of ch1-2 and chaos mutants provides new evidence for the flexible organization of LHCs and enhances our understanding of the reversible allocation of LHCII to the two photosystems. PMID:27663408

  2. Experiences of Nigerian Internationally Educated Nurses Transitioning to United States Health Care Settings.

    PubMed

    Iheduru-Anderson, Kechinyere C; Wahi, Monika M

    2018-04-01

    Successful transition to practice of internationally educated nurses (IENs) can critically affect quality of care. The aim of this study was to characterize the facilitators and barriers to transition of Nigerian IENs (NIENs) to the United States health care setting. Using a descriptive phenomenology approach, 6 NIENs were interviewed about their transitional experiences in the United States. Thematic methods were used for data analysis. The three major themes identified from the participants' stories were "fear/anger and disappointment" (FAD), "road/journey to success/overcoming challenges" (RJO), and "moving forward" (MF). The FAD theme predominated, including experiences of racism, bullying, and inequality. The RJO theme included resilience, and the MF theme encompassed personal growth. NIENs face personal and organizational barriers to adaptation, especially fear, anger and disappointment. Future research should seek to develop a model for optimal adaptation that focuses on improving both personal and organizational facilitators and decreasing barriers.

  3. Wnt/β-catenin signaling promotes self-renewal and inhibits the primed state transition in naïve human embryonic stem cells.

    PubMed

    Xu, Zhuojin; Robitaille, Aaron M; Berndt, Jason D; Davidson, Kathryn C; Fischer, Karin A; Mathieu, Julie; Potter, Jennifer C; Ruohola-Baker, Hannele; Moon, Randall T

    2016-10-18

    In both mice and humans, pluripotent stem cells (PSCs) exist in at least two distinct states of pluripotency, known as the naïve and primed states. Our understanding of the intrinsic and extrinsic factors that enable PSCs to self-renew and to transition between different pluripotent states is important for understanding early development. In mouse embryonic stem cells (mESCs), Wnt proteins stimulate mESC self-renewal and support the naïve state. In human embryonic stem cells (hESCs), Wnt/β-catenin signaling is active in naïve-state hESCs and is reduced or absent in primed-state hESCs. However, the role of Wnt/β-catenin signaling in naïve hESCs remains largely unknown. Here, we demonstrate that inhibition of the secretion of Wnts or inhibition of the stabilization of β-catenin in naïve hESCs reduces cell proliferation and colony formation. Moreover, we show that addition of recombinant Wnt3a partially rescues cell proliferation in naïve hESCs caused by inhibition of Wnt secretion. Notably, inhibition of Wnt/β-catenin signaling in naïve hESCs did not cause differentiation. Instead, it induced primed hESC-like proteomic and metabolic profiles. Thus, our results suggest that naïve hESCs secrete Wnts that activate autocrine or paracrine Wnt/β-catenin signaling to promote efficient self-renewal and inhibit the transition to the primed state.

  4. Quantum transition state dynamics of the cyclooctatetraene unimolecular reaction on ab initio potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Tokizaki, Chihiro; Yoshida, Takahiko; Takayanagi, Toshiyuki

    2016-05-01

    The cyclooctatetraene (COT) anion has a stable D4h structure that is similar to the transition state configurations of the neutral C-C bond-alternation (D4h ↔ D8h ↔ D4h) and ring-inversion (D2d ↔ D4h ↔ D2d) unimolecular reactions. The previously measured photodetachment spectrum of COT- revealed the reaction dynamics in the vicinity of the two transition states on the neutral potential energy surface. In this work, the photodetachment spectrum is calculated quantum mechanically on ab initio-level potential energy surfaces within a three degree-of-freedom reduced-dimensionality model. Very good agreement has been obtained between theory and experiment, providing reliable interpretations for the experimental spectrum. A detailed picture of the reactive molecular dynamics of the COT unimolecular reaction in the transition state region is also discussed.

  5. Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins

    PubMed Central

    Calosci, Nicoletta; Chi, Celestine N.; Richter, Barbara; Camilloni, Carlo; Engström, Åke; Eklund, Lars; Travaglini-Allocatelli, Carlo; Gianni, Stefano; Vendruscolo, Michele; Jemth, Per

    2008-01-01

    The energy landscape theory provides a general framework for describing protein folding reactions. Because a large number of studies, however, have focused on two-state proteins with single well-defined folding pathways and without detectable intermediates, the extent to which free energy landscapes are shaped up by the native topology at the early stages of the folding process has not been fully characterized experimentally. To this end, we have investigated the folding mechanisms of two homologous three-state proteins, PTP-BL PDZ2 and PSD-95 PDZ3, and compared the early and late transition states on their folding pathways. Through a combination of Φ value analysis and molecular dynamics simulations we obtained atomic-level structures of the transition states of these homologous three-state proteins and found that the late transition states are much more structurally similar than the early ones. Our findings thus reveal that, while the native state topology defines essentially in a unique way the late stages of folding, it leaves significant freedom to the early events, a result that reflects the funneling of the free energy landscape toward the native state. PMID:19033470

  6. Solar wind charge exchange in laboratory - Observation of forbidden X-ray transitions

    NASA Astrophysics Data System (ADS)

    Numadate, Naoki; Shimaya, Hirofumi; Ishida, Takuya; Okada, Kunihiro; Nakamura, Nobuyuki; Tanuma, Hajime

    2017-10-01

    We have reproduced solar wind charge exchange collisions of hydrogen-like O7+ ions with He gas at collision energies of 42 keV in the laboratory and observed the forbidden transition of 1s21S0 -1s2s 3S1 in helium-like O6+ ions produced by single electron capture. The measured soft X-ray spectrum had a peak at 560 eV which corresponds to the energy of the forbidden 1s21S0 -1s2s 3S1 transition in the O6+ ion, and a reasonable energy difference between peak positions of the forbidden and resonance lines was found, which ensured that we succeeded in observing the forbidden transition of O6+ ions. The dominant electron capture level in the collision of O7+ ions with He can be estimated to be a principal quantum number n = 4 by the classical over barrier model and the two-center atomic orbital close coupling method. After the charge exchange, the population of the 1s2s state becomes large due to cascade transitions from the higher excited states, so the long-lived forbidden transition to the 1s21S0 ground state is one of main features observed in the charge exchange spectra.

  7. Transitions in Gambling Participation during Late Adolescence and Young Adulthood

    PubMed Central

    Bray, Bethany C.; Lee, Grace P.; Liu, Weiwei; Storr, Carla L.; Ialongo, Nicholas S.; Martins, Silvia S.

    2014-01-01

    Purpose The purpose of this study was to examine transitions in gambling participation from late adolescence into emerging adulthood, and to identify factors (i.e., gender, race, intervention status, lunch status, conduct disorder, parental monitoring, neighborhood environment, and substance use) that might influence these transitions. Methods Markov modeling was used to describe movement between past-year gambling states (i.e., non-gambling and gambling) over five years. Annual data on past-year gambling behavior and substance use were collected from 515 young men and women starting at age 17. Results Past-year gambling declined from 51% prevalence at age 17 to 21% prevalence at age 22. Participants who reported no past-year gambling at a particular annual assessment had more than an 80% probability of also reporting no past-year gambling at the following assessment. Men were 1.07–2.82 times more likely than women to transition from past-year non-gambling to gambling year-to-year, and women were 1.27–5.26 times more likely than men to transition from past-year gambling to non-gambling year-to-year. In addition, gender and past-year tobacco use interacted such that men who used tobacco were most likely (and men who did not use tobacco least likely) to gamble at baseline. Conclusions Transition rates between gambling states appear to be relatively stable over time from late adolescence into emerging adulthood; however, men and those who engage in substance use may be at increased risk for gambling participation. Implications and Contribution The current study provides important information about the naturalistic transitions in gambling behavior during late adolescence and emerging adulthood among an urban, mainly ethnic minority population. The finding that approximately half of past-year gamblers do not gamble during the following year suggests that gambling follows a variable developmental course. PMID:24656449

  8. Transient transition from free carrier metallic state to exciton insulating state in GaAs by ultrafast photoexcitation

    NASA Astrophysics Data System (ADS)

    Nie, X. C.; Song, Hai-Ying; Zhang, Xiu; Gu, Peng; Liu, Shi-Bing; Li, Fan; Meng, Jian-Qiao; Duan, Yu-Xia; Liu, H. Y.

    2018-03-01

    We present systematic studies of the transient dynamics of GaAs by ultrafast time-resolved reflectivity. In photoexcited non-equilibrium states, we found a sign reverse in reflectivity change ΔR/R, from positive around room temperature to negative at cryogenic temperatures. The former corresponds to a free carrier metallic state, while the latter is attributed to an exciton insulating state, in which the transient electronic properties is mostly dominated by excitons, resulting in a transient metal–insulator transition (MIT). Two transition temperatures (T 1 and T 2) are well identified by analyzing the intensity change of the transient reflectivity. We found that photoexcited MIT starts emerging at T 1 as high as ∼ 230 K, in terms of a dip feature at 0.4 ps, and becomes stabilized below T 2 that is up to ∼ 180 K, associated with a negative constant after 40 ps. Our results address a phase diagram that provides a framework for the inducing of MIT through temperature and photoexcitation, and may shed light on the understanding of light-semiconductor interaction and exciton physics.

  9. On helium-like 1s2l-1snl prime transitions in solar flare spectra

    NASA Technical Reports Server (NTRS)

    Kastner, S. O.; Neupert, W. M.; Swartz, M.

    1974-01-01

    Expected wavelengths and intensities are computed for 1s2l-1snl prime transitions in helium-like ions of the abundant elements from oxygen to iron under coronal conditions. Probable observations of some of these lines in the spectra of solar flares are discussed, and attention is called to a possible reversal of singlet and triplet intensities as compared to laboratory observations.

  10. Invariant criteria for bound states, degree of ionization, and plasma phase transition

    NASA Technical Reports Server (NTRS)

    Girardeau, M. D.

    1990-01-01

    Basis invariant characterizations of bound states and bound fraction of a partially ionized hydrogen plasma are given in terms of properties of the spectrum of eigenvalues and eigenfunctions of the equilibrium quantum statistical one-proton-one-electron reduced density matrix. It is suggested that these can be used to place theories of a proposed plasma-ionization phase transition on a firm foundation. This general approach may be relevant to cosmological questions such as the quark deconfinement-confinement transition.

  11. Recycling nicotinamide. The transition-state structure of human nicotinamide phosphoribosyltransferase

    PubMed Central

    Burgos, Emmanuel S.; Vetticatt, Mathew J.; Schramm, Vern L.

    2013-01-01

    Human nicotinamide phosphoribosyltransferase (NAMPT) replenishes the NAD pool and controls the activities of sirtuins (SIRT), mono- and poly-(ADP-ribose) polymerases (PARP) and NAD nucleosidase (CD38). The nature of the enzymatic transition-state (TS) is central to understanding the function of NAMPT. We determined the TS structure for pyrophosphorolysis of nicotinamide mononucleotide (NMN) by kinetic isotope effects (KIEs). With the natural substrates, NMN and pyrophosphate (PPi), the intrinsic KIEs of [1′-14C], [1-15N], [1′-3H] and [2′-3H] are 1.047, 1.029, 1.154 and 1.093, respectively. A unique quantum computational approach was used for TS analysis that included structural elements of the catalytic site. Without constraints (e.g. imposed torsion angles), the theoretical and experimental data are in good agreement. The quantum-mechanical calculations incorporated a crucial catalytic site residue (D313), two magnesium atoms and coordinated water molecules. The transition state model predicts primary 14C, α-secondary 3H, β-secondary 3H and primary 15N KIE close to the experimental values. The analysis reveals significant ribocation character at the TS. The attacking PPi nucleophile is weakly interacting (rC-O = 2.60 Å) and the N-ribosidic C1′-N bond is highly elongated at the TS (rC-N = 2.35 Å), consistent with an ANDN mechanism. Together with the crystal structure of the NMN•PPi•Mg2•enzyme complex, the reaction coordinate is defined. The enzyme holds the nucleophile and leaving group in relatively fixed positions to create a reaction coordinate with C1′-anomeric migration from nicotinamide to the PPi. The transition state is reached by a 0.85 Å migration of C1′. PMID:23373462

  12. Excitation energies, radiative and autoionization rates, dielectronic satellite lines, and dielectronic recombination rates for excited states of Rb-like W from Kr-like W [Relativistic atomic data for Rb-like tungsten

    DOE PAGES

    Safronova, U. I.; Safronova, A. S.; Beiersdorfer, P.

    2016-11-02

    Energy levels, radiative transition probabilities, and autoionization rates for [Ni]more » $$4{s}^{2}4{p}^{6}{nl}$$, [Ni]$$4{s}^{2}4{p}^{5}4l^{\\prime} {nl}$$ ($$l^{\\prime} =d,f,n$$ = 4–7), [Ni]$$4s4{p}^{6}4l^{\\prime} {nl}$$, ($$l^{\\prime} =d,f,n$$ = 4–7), [Ni]$$4{s}^{2}4{p}^{5}5l^{\\prime} {nl}$$ (n = 5–7), and [Ni]$$4s4{p}^{6}6l^{\\prime} {nl}$$ (n = 6–7) states in Rb-like tungsten (W37+) are calculated using the relativistic many-body perturbation theory method (RMBPT code) and the Hartree–Fock-relativistic method (COWAN code). Autoionizing levels above the [Ni]$$4{s}^{2}4{p}^{6}$$ threshold are considered. It is found that configuration mixing among [Ni]$$4{s}^{2}4{p}^{5}4l^{\\prime} {nl}$$ and [Ni]$$4s4{p}^{6}4l^{\\prime} {nl}$$ plays an important role for all atomic characteristics. Branching ratios relative to the first threshold and intensity factors are calculated for satellite lines, and dielectronic recombination (DR) rate coefficients are determined for the [Ni]$$4{s}^{2}4{p}^{6}{nl}$$ (n = 4–7) singly excited states, as well as the [Ni]$$4{s}^{2}4{p}^{5}4{dnl}$$, [Ni]$$4{s}^{2}4{p}^{5}4{fnl}$$, [Ni]$$4s4{p}^{6}4{dnl}$$, [Ni]$$4{s}^{2}4{p}^{6}4{fnl}$$, (n = 4–6), and [Ni]$$4{s}^{2}4{p}^{5}5l^{\\prime} 5l$$ doubly excited nonautoionizing states in Rb-like W37+ ion. Contributions from the [Ni]$$4s24{p}^{6}4{fnl}$$ (n = 6–7), [Ni]$$4{s}^{2}4{p}^{5}5l^{\\prime} {nl}$$ (n = 5–6), and [Ni]$$4{s}^{2}4{p}^{5}6l^{\\prime} {nl}$$ (n = 6–7) doubly excited autoionizing states are evaluated numerically. The high-n state (with n up to 500) contributions are very important for high temperatures. These contributions are determined by using a scaling procedure. Synthetic dielectronic satellite spectra from Rb-like W are simulated in a broad spectral range from 8 to 70 Å. Here, these calculations provide highly accurate values for a number of W 37+ properties useful for a variety of applications including for fusion applications.« less

  13. State-and-transition model archetypes: a global taxonomy of rangeland change

    USDA-ARS?s Scientific Manuscript database

    State and transition models (STMs) synthesize science-based and local knowledge to formally represent the dynamics of rangeland and other ecosystems. Mental models or concepts of ecosystem dynamics implicitly underlie all management decisions in rangelands and thus how people influence rangeland sus...

  14. Transitions between states of labor-force participation among older Israelis.

    PubMed

    Achdut, Leah; Tur-Sinai, Aviad; Troitsky, Rita

    2015-03-01

    The study examines the labor-force behavior of Israelis at older ages, focusing on the determinants of the transitions between states of labor-force participation between 2005 and 2010. The study uses panel data from the first two waves of the SHARE-Israel longitudinal survey. A multinomial logit model is used to examine the impact of sociodemographic characteristics, health state, and economic resources on labor-force transitions of people aged 50-67. The results emphasize the role of age and poor health in "pushing" older people out of the labor force or "keeping" them there. Spouse's participation is found to encourage individuals to leave the labor force or to refrain from joining it. However, living with a participating spouse is negatively associated with staying out of the labor force, consistent with the dominance of the complementarity of leisure effect found in the literature. Wealth as an economic resource available to individuals for retirement is also found to encourage individuals to leave the labor force or to refrain from joining it.

  15. Dynamics of harpooning studied by transition state spectroscopy. II. LiṡṡFH

    NASA Astrophysics Data System (ADS)

    Hudson, A. J.; Oh, H. B.; Polanyi, J. C.; Piecuch, P.

    2000-12-01

    The van der Waals complex LiṡṡFH was formed in crossed beams and the transition state of the excited-state reaction, Li*(2p 2P)+HF→LiF+H, was accessed by photoexcitation of this complex. The dynamics of the excited-state reaction were probed by varying the excitation wavelength over the range 570-970 nm while recording the photodepletion of the complex. The findings were interpreted using high-level ab initio calculations of the ground and lowest excited-state potential-energy surfaces.

  16. Pseudo-direct bandgap transitions in silicon nanocrystals: effects on optoelectronics and thermoelectrics.

    PubMed

    Singh, Vivek; Yu, Yixuan; Sun, Qi-C; Korgel, Brian; Nagpal, Prashant

    2014-12-21

    While silicon nanostructures are extensively used in electronics, the indirect bandgap of silicon poses challenges for optoelectronic applications like photovoltaics and light emitting diodes (LEDs). Here, we show that size-dependent pseudo-direct bandgap transitions in silicon nanocrystals dominate the interactions between (photoexcited) charge carriers and phonons, and hence the optoelectronic properties of silicon nanocrystals. Direct measurements of the electronic density of states (DOS) for different sized silicon nanocrystals reveal that these pseudo-direct transitions, likely arising from the nanocrystal surface, can couple with the quantum-confined silicon states. Moreover, we demonstrate that since these transitions determine the interactions of charge carriers with phonons, they change the light emission, absorption, charge carrier diffusion and phonon drag (Seebeck coefficient) in nanoscaled silicon semiconductors. Therefore, these results can have important implications for the design of optoelectronics and thermoelectric devices based on nanostructured silicon.

  17. Generic finite size scaling for discontinuous nonequilibrium phase transitions into absorbing states

    NASA Astrophysics Data System (ADS)

    de Oliveira, M. M.; da Luz, M. G. E.; Fiore, C. E.

    2015-12-01

    Based on quasistationary distribution ideas, a general finite size scaling theory is proposed for discontinuous nonequilibrium phase transitions into absorbing states. Analogously to the equilibrium case, we show that quantities such as response functions, cumulants, and equal area probability distributions all scale with the volume, thus allowing proper estimates for the thermodynamic limit. To illustrate these results, five very distinct lattice models displaying nonequilibrium transitions—to single and infinitely many absorbing states—are investigated. The innate difficulties in analyzing absorbing phase transitions are circumvented through quasistationary simulation methods. Our findings (allied to numerical studies in the literature) strongly point to a unifying discontinuous phase transition scaling behavior for equilibrium and this important class of nonequilibrium systems.

  18. Graphene and graphene-like layered transition metal dichalcogenides in energy conversion and storage.

    PubMed

    Wang, Hua; Feng, Hongbin; Li, Jinghong

    2014-06-12

    Being confronted with the energy crisis and environmental problems, the exploration of clean and renewable energy materials as well as their devices are urgently demanded. Two-dimensional (2D) atomically-thick materials, graphene and grpahene-like layered transition metal dichalcogenides (TMDs), have showed vast potential as novel energy materials due to their unique physicochemical properties. In this Review, we outline the typical application of graphene and grpahene-like TMDs in energy conversion and storage fields, and hope to promote the development of 2D TMDs in this field through the analysis and comparisons with the relatively natural graphene. First, a brief introduction of electronic structures and basic properties of graphene and TMDs are presented. Then, we summarize the exciting progress of these materials made in both energy conversion and storage field including solar cells, electrocatalysis, supercapacitors and lithium ions batteries. Finally, the prospects and further developments in these exciting fields of graphene and graphene-like TMDs materials are also suggested. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Transition-State Ensembles Navigate the Pathways of Enzyme Catalysis.

    PubMed

    Mickert, Matthias J; Gorris, Hans H

    2018-06-07

    Transition-state theory (TST) provides an important framework for analyzing and explaining the reaction rates of enzymes. TST, however, needs to account for protein dynamic effects and heterogeneities in enzyme catalysis. We have analyzed the reaction rates of β-galactosidase and β-glucuronidase at the single molecule level by using large arrays of femtoliter-sized chambers. Heterogeneities in individual reaction rates yield information on the intrinsic distribution of the free energy of activation (Δ G ‡ ) in an enzyme ensemble. The broader distribution of Δ G ‡ in β-galactosidase compared to β-glucuronidase is attributed to β-galactosidase's multiple catalytic functions as a hydrolase and a transglycosylase. Based on the catalytic mechanism of β-galactosidase, we show that transition-state ensembles do not only contribute to enzyme catalysis but can also channel the catalytic pathway to the formation of different products. We conclude that β-galactosidase is an example of natural evolution, where a new catalytic pathway branches off from an established enzyme function. The functional division of work between enzymatic substates explains why the conformational space represented by the enzyme ensemble is larger than the conformational space that can be sampled by any given enzyme molecule during catalysis.

  20. Transition of multidiffusive states in a biased periodic potential

    NASA Astrophysics Data System (ADS)

    Zhang, Jia-Ming; Bao, Jing-Dong

    2017-03-01

    We study a frequency-dependent damping model of hyperdiffusion within the generalized Langevin equation. The model allows for the colored noise defined by its spectral density, assumed to be proportional to ωδ -1 at low frequencies with 0 <δ <1 (sub-Ohmic damping) or 1 <δ <2 (super-Ohmic damping), where the frequency-dependent damping is deduced from the noise by means of the fluctuation-dissipation theorem. It is shown that for super-Ohmic damping and certain parameters, the diffusive process of the particle in a titled periodic potential undergos sequentially four time regimes: thermalization, hyperdiffusion, collapse, and asymptotical restoration. For analyzing transition phenomenon of multidiffusive states, we demonstrate that the first exist time of the particle escaping from the locked state into the running state abides by an exponential distribution. The concept of an equivalent velocity trap is introduced in the present model; moreover, reformation of ballistic diffusive system is also considered as a marginal situation but does not exhibit the collapsed state of diffusion.

  1. Experimentally demonstrate the surface state and optical topological phase transition of one dimensional hyperbolic metamaterials in Otto and KR configuration (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Wei, Chih Chung; Un, Leng-Wai; Yen, Ta-Jen

    2017-05-01

    One-dimension hyperbolic metamaterials (1DHMMs) possess marvelous and considerable applications: hyperlens, spontaneous emission engineering and nonlinear optics. Conventionally, effective medium theory, which is only valid for long wavelength limit, was used to predict and analyze the optical properties and applications. In our previous works, we considered a binary 1DHMM which consists of alternative metallic and dielectric layers, and rigorously demonstrated the existence of surface states and bulk-interface correspondence with the plasmonic band theory from the coupled surface plasmon point of view. In the plasmonic band structure, we can classify 1DHMMs into two classes: metallic-like and dielectric-like, depending on the formation of the surface states with dielectric and metallic material, respectively. Band crossing exists only when the dielectric layers are thicker than the metallic ones, which is independent from the dielectric constants. Furthermore, the 1DHMMs are all metallic-like without band crossing. On the other hand, the 1DHMMs with band crossing are metal-like before the band crossing point, while they are dielectric-like after the band crossing point. In this work, we measure the surface states formed by dielectric material and 1DHMMs with band crossing in Otto configuration. With white light source and fixed incident angle, we measure the reflectance to investigate the existence of the surface states of 1DHMMs with various thickness ratio of metallic to dielectric layers. Conclusively, our results show that the surface states of 1DHMMs exist only when the thickness ratio is larger than 0.15. The disappearance of the surface states indicates the topological phase transition of 1DHMMs. Our experimental results will benefit new applications for manipulating light on the surface of hyperbolic metamaterials.

  2. Ground state transitions in vertically coupled N-layer single electron quantum dots

    NASA Astrophysics Data System (ADS)

    Xie, Wenfang; Wang, Anmei

    2003-12-01

    A method is proposed to exactly diagonalize the Hamiltonian of a N-layer quantum dot containing a single electron in each dot in arbitrary magnetic fields. For N=4, the energy spectra of the dot are calculated as a function of the applied magnetic field. We find discontinuous ground-state energy transitions induced by an external magnetic field in the case of strong coupling. However, in the case of weak coupling, such a transition does not occur and the angular momentum remains zero.

  3. Comparison of qubit and qutrit like entangled squeezed and coherent states of light

    NASA Astrophysics Data System (ADS)

    Najarbashi, G.; Mirzaei, S.

    2016-10-01

    Squeezed state of light is one of the important subjects in quantum optics which is generated by optical nonlinear interactions. In this paper, we especially focus on qubit like entangled squeezed states (ESS's) generated by beam splitters, phase-shifter and cross Kerr nonlinearity. Moreover the Wigner function of two-mode qubit and qutrit like ESS are investigated. We will show that the distances of peaks of Wigner functions for two-mode ESS are entanglement sensitive and can be a witness for entanglement. Like the qubit cases, monogamy inequality is fulfilled for qutrit like ESS. These trends are compared with those obtained for qubit and qutrit like entangled coherent states (ECS).

  4. A Conserved Behavioral State Barrier Impedes Transitions between Anesthetic-Induced Unconsciousness and Wakefulness: Evidence for Neural Inertia

    PubMed Central

    Friedman, Eliot B.; Sun, Yi; Moore, Jason T.; Hung, Hsiao-Tung; Meng, Qing Cheng; Perera, Priyan; Joiner, William J.; Thomas, Steven A.; Eckenhoff, Roderic G.; Sehgal, Amita; Kelz, Max B.

    2010-01-01

    One major unanswered question in neuroscience is how the brain transitions between conscious and unconscious states. General anesthetics offer a controllable means to study these transitions. Induction of anesthesia is commonly attributed to drug-induced global modulation of neuronal function, while emergence from anesthesia has been thought to occur passively, paralleling elimination of the anesthetic from its sites in the central nervous system (CNS). If this were true, then CNS anesthetic concentrations on induction and emergence would be indistinguishable. By generating anesthetic dose-response data in both insects and mammals, we demonstrate that the forward and reverse paths through which anesthetic-induced unconsciousness arises and dissipates are not identical. Instead they exhibit hysteresis that is not fully explained by pharmacokinetics as previously thought. Single gene mutations that affect sleep-wake states are shown to collapse or widen anesthetic hysteresis without obvious confounding effects on volatile anesthetic uptake, distribution, or metabolism. We propose a fundamental and biologically conserved concept of neural inertia, a tendency of the CNS to resist behavioral state transitions between conscious and unconscious states. We demonstrate that such a barrier separates wakeful and anesthetized states for multiple anesthetics in both flies and mice, and argue that it contributes to the hysteresis observed when the brain transitions between conscious and unconscious states. PMID:20689589

  5. Epithelial-mesenchymal transition and tumor suppression are controlled by a reciprocal feedback loop between ZEB1 and Grainyhead-like-2

    PubMed Central

    Cieply, Benjamin; Farris, Joshua; Denvir, James; Ford, Heide; Frisch, Steven M.

    2013-01-01

    Epithelial-mesenchymal transition (EMT) in carcinoma cells enhances malignant progression by promoting invasion and survival. EMT is induced by microenvironmental factors including TGF-β and Wnt agonists, and by the E-box-binding transcription factors Twist, Snail and ZEB. Grainyhead-like-2 (GRHL2), a member of the mammalian Grainyhead family of wound healing regulatory transcription factors, suppresses EMT and restores sensitivity to anoikis by repressing ZEB1 expression and inhibiting TGF-β signaling. In this study, we elucidate the functional relationship between GRHL2 and ZEB1 in EMT/MET and tumor biology. At least three homeodomain proteins, Six1, LBX1, and HoxA5, transactivated the ZEB1 promoter, in the case of Six1, through direct protein-promoter interaction. GRHL2 altered the Six1-DNA complex, inhibiting this transactivation. Correspondingly, GRHL2 expression prevented tumor initiation in xenograft assays, sensitized breast cancer cells to paclitaxel and suppressed the emergence of CD44highCD24low cells (defining the cancer stem cell phenotype in the cell type studied). GRHL2 was down-regulated in recurrent mouse tumors that had evolved to an oncogene-independent, EMT-like state, supporting a role for GRHL2 down-regulation in this phenotypic transition, modeling disease recurrence. The combination of TGF-β and Wnt activation repressed GRHL2 expression by direct interaction of ZEB1 with the GRHL2 promoter, inducing EMT. Together, our observations indicate that a reciprocal feedback loop between GRHL2 and ZEB1 controls epithelial vs. mesenchymal phenotypes and EMT-driven tumor progression. PMID:23943797

  6. Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar

    PubMed Central

    Baxa, Michael C.; Yu, Wookyung; Adhikari, Aashish N.; Ge, Liang; Xia, Zhen; Zhou, Ruhong; Freed, Karl F.; Sosnick, Tobin R.

    2015-01-01

    Experimental and computational folding studies of Proteins L & G and NuG2 typically find that sequence differences determine which of the two hairpins is formed in the transition state ensemble (TSE). However, our recent work on Protein L finds that its TSE contains both hairpins, compelling a reassessment of the influence of sequence on the folding behavior of the other two homologs. We characterize the TSEs for Protein G and NuG2b, a triple mutant of NuG2, using ψ analysis, a method for identifying contacts in the TSE. All three homologs are found to share a common and near-native TSE topology with interactions between all four strands. However, the helical content varies in the TSE, being largely absent in Proteins G & L but partially present in NuG2b. The variability likely arises from competing propensities for the formation of nonnative β turns in the naturally occurring proteins, as observed in our TerItFix folding algorithm. All-atom folding simulations of NuG2b recapitulate the observed TSEs with four strands for 5 of 27 transition paths [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517–520]. Our data support the view that homologous proteins have similar folding mechanisms, even when nonnative interactions are present in the transition state. These findings emphasize the ongoing challenge of accurately characterizing and predicting TSEs, even for relatively simple proteins. PMID:26100906

  7. Optical transitions in two-dimensional topological insulators with point defects

    NASA Astrophysics Data System (ADS)

    Sablikov, Vladimir A.; Sukhanov, Aleksei A.

    2016-12-01

    Nontrivial properties of electronic states in topological insulators are inherent not only to the surface and boundary states, but to bound states localized at structure defects as well. We clarify how the unusual properties of the defect-induced bound states are manifested in optical absorption spectra in two-dimensional topological insulators. The calculations are carried out for defects with short-range potential. We find that the defects give rise to the appearance of specific features in the absorption spectrum, which are an inherent property of topological insulators. They have the form of two or three absorption peaks that are due to intracenter transitions between electron-like and hole-like bound states.

  8. Cyclic electron flow is redox-controlled but independent of state transition.

    PubMed

    Takahashi, Hiroko; Clowez, Sophie; Wollman, Francis-André; Vallon, Olivier; Rappaport, Fabrice

    2013-01-01

    Photosynthesis is the biological process that feeds the biosphere with reduced carbon. The assimilation of CO2 requires the fine tuning of two co-existing functional modes: linear electron flow, which provides NADPH and ATP, and cyclic electron flow, which only sustains ATP synthesis. Although the importance of this fine tuning is appreciated, its mechanism remains equivocal. Here we show that cyclic electron flow as well as formation of supercomplexes, thought to contribute to the enhancement of cyclic electron flow, are promoted in reducing conditions with no correlation with the reorganization of the thylakoid membranes associated with the migration of antenna proteins towards Photosystems I or II, a process known as state transition. We show that cyclic electron flow is tuned by the redox power and this provides a mechanistic model applying to the entire green lineage including the vast majority of the cases in which state transition only involves a moderate fraction of the antenna.

  9. The failed state transition of the ATOLL source GRS 1724-308

    NASA Astrophysics Data System (ADS)

    Tarana, A.; Capitanio, F.; Cocchi, M.

    2018-07-01

    The 2004-2012 X-ray time history of the NS LMXB GRS 1724-308 shows, along with the episodic brightenings associated with the low-high state transitions typical of the ATOLL sources, a peculiar, long lasting (˜300 d) flaring event, observed in 2008. This rare episode, characterized by a high-flux hard state, has never been observed before for GRS 1724-308, and in any case is not common among ATOLL sources. We discuss here different hypotheses on the origin of this peculiar event that displayed the spectral signatures of a failed transition, similar in shape and duration to those rarely observed in black hole binaries. We also suggest the possibility that the atypical flare occurred in coincidence with a new rising phase of the 12-yr superorbital modulation that has been previously reported by other authors. The analysed data also confirm for GRS 1724-308 the already reported orbital period of ˜90 d.

  10. Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily.

    PubMed

    Hou, Guanhua; Cui, Qiang

    2013-07-17

    The first step for the hydrolysis of a phosphate monoester (pNPP(2-)) in enzymes of the alkaline phosphatase (AP) superfamily, R166S AP and wild-type NPP, is studied using QM/MM simulations based on an approximate density functional theory (SCC-DFTBPR) and a recently introduced QM/MM interaction Hamiltonian. The calculations suggest that similar loose transition states are involved in both enzymes, despite the fact that phosphate monoesters are the cognate substrates for AP but promiscuous substrates for NPP. The computed loose transition states are clearly different from the more synchronous ones previously calculated for diester reactions in the same AP enzymes. Therefore, our results explicitly support the proposal that AP enzymes are able to recognize and stabilize different types of transition states in a single active site. Analysis of the structural features of computed transition states indicates that the plastic nature of the bimetallic site plays a minor role in accommodating multiple types of transition states and that the high degree of solvent accessibility of the AP active site also contributes to its ability to stabilize diverse transition-state structures without the need of causing large structural distortions of the bimetallic motif. The binding mode of the leaving group in the transition state highlights that vanadate may not always be an ideal transition state analog for loose phosphoryl transfer transition states.

  11. Insights from the structure of a smallpox virus topoisomerase-DNA transition state mimic

    PubMed Central

    Perry, Kay; Hwang, Young; Bushman, Frederic D.; Van Duyne, Gregory D.

    2010-01-01

    Summary Poxviruses encode their own type IB topoisomerases (TopIBs) which release superhelical tension generated by replication and transcription of their genomes. To investigate the reaction catalyzed viral TopIBs, we have determined the structure of a variola virus topoisomerase-DNA complex trapped as a vanadate transition state mimic. The structure reveals how the viral TopIB enzymes are likely to position the DNA duplex for ligation following relaxation of supercoils and identifies the sources of friction observed in single molecule experiments that argue against free rotation. The structure also identifies a conformational change in the leaving group sugar that must occur prior to cleavage and reveals a mechanism for promoting ligation following relaxation of supercoils that involves a novel Asp-minor groove interaction. Overall, the new structural data support a common catalytic mechanism for the TopIB superfamily but indicate distinct methods for controlling duplex rotation in the small vs. large enzyme subfamilies. PMID:20152159

  12. Mechanical properties of 4d transition metals in molten state

    NASA Astrophysics Data System (ADS)

    Singh, Deobrat; Sonvane, Yogesh; Thakor, P. B.

    2016-05-01

    Mechanical properties of 4d transition metals in molten state have been studied in the present study. We have calculated mechanical properties such as isothermal bulk modulus (B), modulus of rigidity (G), Young's modulus (Y) and Hardness have also been calculated from the elastic part of the Phonon dispersion curve (PDC). To describe the structural information, we have used different structure factor S(q) using Percus-Yevick hard sphere (PYHS) reference systems along with our newly constructed parameter free model potential.To see the influence of exchange and correlation effect on the above said properties of 3d liquid transition metals, we have used Sarkar et al (S)local field correction functions. Present results have been found good in agreement with available experimental data.

  13. Direct Conversion of an Enzyme from Native-like to Amyloid-like Aggregates within Inclusion Bodies.

    PubMed

    Elia, Francesco; Cantini, Francesca; Chiti, Fabrizio; Dobson, Christopher Martin; Bemporad, Francesco

    2017-06-20

    The acylphosphatase from Sulfolobus solfataricus (Sso AcP) is a globular protein able to aggregate in vitro from a native-like conformational ensemble without the need for a transition across the major unfolding energy barrier. This process leads to the formation of assemblies in which the protein retains its native-like structure, which subsequently convert into amyloid-like aggregates. Here, we investigate the mechanism by which Sso AcP aggregates in vivo to form bacterial inclusion bodies after expression in E. coli. Shortly after the initiation of expression, Sso AcP is incorporated into inclusion bodies as a native-like protein, still exhibiting small but significant enzymatic activity. Additional experiments revealed that this overall process of aggregation is enhanced by the presence of the unfolded N-terminal region of the sequence and by destabilization of the globular segment of the protein. At later times, the Sso AcP molecules in the inclusion bodies lose their native-like properties and convert into β-sheet-rich amyloid-like structures, as indicated by their ability to bind thioflavin T and Congo red. These results show that the aggregation behavior of this protein is similar in vivo to that observed in vitro, and that, at least for a predominant part of the protein population, the transition from a native to an amyloid-like structure occurs within the aggregate state. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  14. Status of quarkonia-like negative and positive parity states in a relativistic confinement scheme

    NASA Astrophysics Data System (ADS)

    Bhavsar, Tanvi; Shah, Manan; Vinodkumar, P. C.

    2018-03-01

    Properties of quarkonia-like states in the charm and bottom sector have been studied in the frame work of relativistic Dirac formalism with a linear confinement potential. We have computed the mass spectroscopy and decay properties (vector decay constant and leptonic decay width) of several quarkonia-like states. The present study is also intended to identify some of the unexplained states as mixed P-wave and mixed S-D-wave states of charmonia and bottomonia. The results indicate that the X(4140) state can be an admixture of two P states of charmonium. And the charmonium-like states X(4630) and X(4660) are the admixed state of S-D-waves. Similarly, the X(10610) state recently reported by Belle II can be mixed P-states of bottomonium. In the relativistic framework we have computed the vector decay constant and the leptonic decay width for S wave charmonium and bottomonium. The leptonic decay widths for the J^{PC} = 1^{-} mixed states are also predicted. Further, both the masses and the leptonic decay width are considered for the identification of the quarkonia-like states.

  15. Energy levels and radiative rates for transitions in Cr-like Co IV and Ni V

    NASA Astrophysics Data System (ADS)

    Aggarwal, K. M.; Bogdanovich, P.; Karpuškienė, R.; Keenan, F. P.; Kisielius, R.; Stancalie, V.

    2016-01-01

    We report calculations of energy levels and radiative rates (A-values) for transitions in Cr-like Co IV and Ni V. The quasi-relativistic Hartree-Fock (QRHF) code is adopted for calculating the data although GRASP (general-purpose relativistic atomic structure package) and flexible atomic code (FAC) have also been employed for comparison purposes. No radiative rates are available in the literature to compare with our results, but our calculated energies are in close agreement with those compiled by NIST for a majority of the levels. However, there are discrepancies for a few levels of up to 3%. The A-values are listed for all significantly contributing E1, E2 and M1 transitions, and the corresponding lifetimes reported, although unfortunately no previous theoretical or experimental results exist to compare with our data.

  16. A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

    NASA Astrophysics Data System (ADS)

    Nguyen, Trong-Nghia; Putikam, Raghunath; Lin, M. C.

    2015-03-01

    We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH2OO and anti/syn-CH3C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH2OO and anti-CH3C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH3C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C-H bonds. For syn-CH3C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH3 group by the terminal O atom producing CH2C(H)O-OH. At 298 K, the intramolecular insertion process in CH2OO was found to be 600 times faster than the commonly assumed ring-closing reaction.

  17. The role of autophagy in the cross-talk between epithelial-mesenchymal transitioned tumor cells and cancer stem-like cells.

    PubMed

    Marcucci, Fabrizio; Ghezzi, Pietro; Rumio, Cristiano

    2017-01-30

    Epithelial-mesenchymal transition (EMT) and cancer stem-like cells (CSC) are becoming highly relevant targets in anticancer drug discovery. A large body of evidence suggests that epithelial-mesenchymal transitioned tumor cells (EMT tumor cells) and CSCs have similar functions. There is also an overlap regarding the stimuli that can induce the generation of EMT tumor cells and CSCs. Moreover, direct evidence has been brought that EMT can give rise to CSCs. It is unclear however, whether EMT tumor cells should be considered CSCs or if they have to undergo further changes. In this article we summarize available evidence suggesting that, indeed, additional programs must be engaged and we propose that macroautophagy (hereafter, autophagy) represents a key trait distinguishing CSCs from EMT tumor cells. Thus, CSCs have often been reported to be in an autophagic state and blockade of autophagy inhibits CSCs. On the other hand, there is ample evidence showing that EMT and autophagy are distinct events. CSCs, however, represent, by themselves, a heterogeneous population. Thus, CSCs have been distinguished in predominantly non-cycling and cycling CSCs, the latter representing CSCs that self-renew and replenish the pool of differentiated tumor cells. We now suggest that the non-cycling CSC subpopulation is in an autophagic state. We propose also two models to explain the relationship between EMT tumor cells and these two major CSC subpopulations: a branching model in which EMT tumor cells can give rise to cycling or non-cycling CSCs, respectively, and a hierarchical model in which EMT tumor cells are first induced to become autophagic CSCs and, subsequently, cycling CSCs. Finally, we address the therapeutic consequences of these insights.

  18. Transition in coupled replicas may not imply a finite-temperature ideal glass transition in glass-forming systems.

    PubMed

    Garrahan, Juan P

    2014-03-01

    A key open question in the glass transition field is whether a finite temperature thermodynamic transition to the glass state exists or not. Recent simulations of coupled replicas in atomistic models have found signatures of a static transition as a function of replica coupling. This can be viewed as evidence of an associated thermodynamic glass transition in the uncoupled system. We demonstrate here that a different interpretation is possible. We consider the triangular plaquette model, an interacting spin system which displays (East model-like) glassy dynamics in the absence of any static transition. We show that when two replicas are coupled, there is a curve of equilibrium phase transitions, between phases of small and large overlap, in the temperature-coupling plane (located on the self-dual line of an exact temperature-coupling duality of the system) which ends at a critical point. Crucially, in the limit of vanishing coupling the finite temperature transition disappears, and the uncoupled system is in the disordered phase at all temperatures. We discuss an interpretation of atomistic simulations in light of this result.

  19. Relativistic many-body calculation of energies, multipole transition rates, and lifetimes in tungsten ions

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

    Atomic properties of Cd-like W26 +, In-like W25 +, and Sn-like W24 + ions are evaluated by using a relativistic CI+all -order approach that combines configuration-interaction and the coupled-cluster methods. The energies, transition rates, and lifetimes of low-lying levels are calculated and compared with available theoretical and experimental values. The magnetic-dipole transition rates are calculated to determine the branching ratios and lifetimes for the 4 f3 states in W25 + and for the 4 f4 states in W24 + ions. Excellent agreement of the CI+all -order values provided a benchmark test of this method for the 4 fn configurations validating the recommended values of tungsten ion properties calculated in this work.

  20. Direct control of transitions between different mode-locking states of a fiber laser

    NASA Astrophysics Data System (ADS)

    Ilday, Fatih; Teamir, Tesfay; Iegorov, Roman; Makey, Ghaith

    Mode-locking corresponds to a far-from-equilibrium steady state of a laser, whereby extremely short pulses can be produced. Capability to directly control mode-locking states can be used to improve laser performance with numerous applications, as well as shed light on their far-from-equilibrium physics using the laser as an experimental platform. Here, we demonstrate direct control of the mode-locking state using spectral pulse shaping by incorporating a spatial light modulator at a Fourier plane inside the cavity of an Yb-doped fiber laser. We show that we can halt and restart mode-locking, suppress instabilities, induce controlled reversible and irreversible transitions between mode-locking states, and perform advanced pulse shaping on pulses as short as 40 fs. This capability can be used to experimentally investigate bifurcations, reversible and irreversible transitions, by selecting, steering, and even competing various mode-locking states. Such studies can explore collective dynamics of dissipative soliton molecules, and ultimately test emerging theories about far-from-equilibrium physics, where there is an acute lack of experimental systems that are sufficiently well controlled. ERC CoG 617521, TUBITAK 113F319.

  1. Transition energy measurements in hydrogenlike and heliumlike ions strongly supporting bound-state QED calculations

    NASA Astrophysics Data System (ADS)

    Kubiček, K.; Mokler, P. H.; Mäckel, V.; Ullrich, J.; López-Urrutia, J. R. Crespo

    2014-09-01

    For the hydrogenlike Ar17+ ion, the 1s Lamb shift was absolutely determined with a 1.4% accuracy based on Lyman-α wavelength measurements that have negligible uncertainties from nuclear size effects. The result agrees with state-of-the-art quantum electrodynamics (QED) calculations, and demonstrates the suitability of Lyman-α transitions in highly charged ions as x-ray energy standards, accurate at the five parts-per-million level. For the heliumlike Ar16+ ion the transition energy for the 1s2p1P1→1s21S0 line was also absolutely determined on an even higher level of accuracy. Additionally, we present relative measurements of transitions in S15+,S14+, and Fe24+ ions. The data for the heliumlike S14+,Ar16+, and Fe24+ ions stringently confirm advanced bound-state QED predictions including screened QED terms that had recently been contested.

  2. Rates of transition between amyloid and neurodegeneration biomarker states and to dementia among non-demented individuals: a population-based cohort study

    PubMed Central

    Jack, Clifford R.; Therneau, Terry M.; Wiste, Heather J.; Weigand, Stephen D.; Knopman, David S.; Lowe, Val J.; Mielke, Michelle M.; Vemuri, Prashanthi; Roberts, Rosebud O.; Machulda, Mary M.; Senjem, Matthew L.; Gunter, Jeffrey L.; Rocca, Walter A.; Petersen, Ronald C.

    2016-01-01

    Summary Background We previously observed in a cross-sectional analysis that frequencies of amyloid and neurodegeneration biomarker states varied greatly by age among cognitively non-impaired participants, suggesting dynamic within-person processes. Our objective in this longitudinal study was to estimate rates of transitioning from a less- to a more-abnormal biomarker state by age among non-demented individuals, as well as rates of transitioning to dementia by biomarker state. Methods All participants (n=4049) were non-demented at baseline. A subset of 1541 underwent multi-modality imaging. Amyloid PET was used to classify individuals as amyloid positive (A+) or negative (A−). FDG PET and MRI were used to classify individuals as neurodegeneration positive (N+) or negative (N−). All observations from the 4049 individuals were used in a multi-state model to estimate four different age-specific biomarker state transition rates among non-demented individuals: A−N− to A+N−; A−N− to A−N+ (suspected non-Alzheimer pathology, SNAP); A+N− to A+N+; A−N+ (SNAP) to A+N+. We also estimated two age-specific rates to dementia: A+N+ to dementia; and A−N+ (SNAP) to dementia. Using these state-to-state transition rates, we estimated biomarker state frequencies by age. Findings All transition rates were low at age 50 and (with one exception) were well-characterized by an exponential increase with age. The rates per 100-person years at ages 65 versus 85 were 1.6 versus 17.2 for A−N− to A−N+, 6.1 versus 20.8 for A+N− to A+N+, 2.6 versus 13.2 for A−N+ to A+N+, 0.8 versus 7.0 for A+N+ to dementia, and 0.6 versus 1.7 for A−N+ to dementia. The one exception to an exponential increase with age was the transition rate from A−N− to A+N− which increased from 4.0 transitions per 100 person-years at age 65 to approximately 7 transitions per 100 person-years in the 70s and then plateaued beyond that age. Estimated biomarker frequencies by age from the

  3. A Search for Transitions between States in Redbacks and Black Widows Using Seven Years of Fermi-LAT Observations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Torres, Diego F.; Ji, Long; Li, Jian

    Considering about seven years of Fermi-Large Area Telescope (LAT) data, we present a systematic search for variability that is possibly related to transitions between states in redbacks and black widow systems. In addition, the transitions are characterized by sudden and significant changes in the gamma-ray flux that persist on a timescale that is much larger than the orbital period. This phenomenology was already detected in the case of two redback systems, PSR J1023+0038 and PSR J1227-4853, which we present here. We show the existence of only one transition for each of these systems over the past seven years. We determinemore » their spectra, establishing high-energy cutoffs at a few GeV for the high gamma-ray state of PSR J1023+0038, and for both states of PSR J1227-4853. The surveying capability of the Fermi-LAT allows further study of whether similar phenomenology has occurred in other sources. Although we have not found any evidence of a state transition for most of the studied pulsars, we note two black-widow systems, PSR J2234+0944 and PSR J1446-4701, whose apparent variabilities are reminiscent of the transitions in PSR J1023+0038 and PSR J1227-4853. Finally, for the other systems, we set limits on potential transitions in their measured gamma-ray light curves.« less

  4. A Search for Transitions between States in Redbacks and Black Widows Using Seven Years of Fermi -LAT Observations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Torres, Diego F.; Li, Jian; Rea, Nanda

    Considering about seven years of Fermi -Large Area Telescope (LAT) data, we present a systematic search for variability that is possibly related to transitions between states in redbacks and black widow systems. The transitions are characterized by sudden and significant changes in the gamma-ray flux that persist on a timescale that is much larger than the orbital period. This phenomenology was already detected in the case of two redback systems, PSR J1023+0038 and PSR J1227−4853, which we present here. We show the existence of only one transition for each of these systems over the past seven years. We determine theirmore » spectra, establishing high-energy cutoffs at a few GeV for the high gamma-ray state of PSR J1023+0038, and for both states of PSR J1227−4853. The surveying capability of the Fermi -LAT allows further study of whether similar phenomenology has occurred in other sources. Although we have not found any evidence of a state transition for most of the studied pulsars, we note two black-widow systems, PSR J2234+0944 and PSR J1446−4701, whose apparent variabilities are reminiscent of the transitions in PSR J1023+0038 and PSR J1227−4853. For the other systems, we set limits on potential transitions in their measured gamma-ray light curves.« less

  5. A Search for Transitions between States in Redbacks and Black Widows Using Seven Years of Fermi-LAT Observations

    DOE PAGES

    Torres, Diego F.; Ji, Long; Li, Jian; ...

    2017-02-08

    Considering about seven years of Fermi-Large Area Telescope (LAT) data, we present a systematic search for variability that is possibly related to transitions between states in redbacks and black widow systems. In addition, the transitions are characterized by sudden and significant changes in the gamma-ray flux that persist on a timescale that is much larger than the orbital period. This phenomenology was already detected in the case of two redback systems, PSR J1023+0038 and PSR J1227-4853, which we present here. We show the existence of only one transition for each of these systems over the past seven years. We determinemore » their spectra, establishing high-energy cutoffs at a few GeV for the high gamma-ray state of PSR J1023+0038, and for both states of PSR J1227-4853. The surveying capability of the Fermi-LAT allows further study of whether similar phenomenology has occurred in other sources. Although we have not found any evidence of a state transition for most of the studied pulsars, we note two black-widow systems, PSR J2234+0944 and PSR J1446-4701, whose apparent variabilities are reminiscent of the transitions in PSR J1023+0038 and PSR J1227-4853. Finally, for the other systems, we set limits on potential transitions in their measured gamma-ray light curves.« less

  6. Energy levels, oscillator strengths, and transition probabilities for sulfur-like scandium, Sc VI

    NASA Astrophysics Data System (ADS)

    El-Maaref, A. A.; Abou Halaka, M. M.; Saddeek, Yasser B.

    2017-09-01

    Energy levels, Oscillator strengths, and transition probabilities for sulfur-like scandium are calculated using CIV3 code. The calculations have been executed in an intermediate coupling scheme using Breit-Pauli Hamiltonian. The present calculations have been compared with the experimental data and other theoretical calculations. LANL code has been used to confirm the accuracy of the present calculations, where the calculations using CIV3 code agree well with the corresponding values by LANL code. The calculated energy levels and oscillator strengths are in reasonable agreement with the published experimental data and theoretical values. We have calculated lifetimes of some excited levels, as well.

  7. A multi-state model examining patterns of transitioning among states of engagement in care in HIV-positive individuals initiating combination antiretroviral therapy

    PubMed Central

    Gillis, Jennifer; Loutfy, Mona; Bayoumi, Ahmed M; Antoniou, Tony; Burchell, Ann N; Walmsley, Sharon; Cooper, Curtis; Klein, Marina B.; Machouf, Nima; Montaner, Julio SG; Rourke, Sean B.; Tsoukas, Christos; Hogg, Robert; Raboud, Janet

    2016-01-01

    Background Common measures of engagement in care fail to acknowledge that infrequent follow-up may occur either intentionally among patients with sustained virologic suppression or unintentionally among patients with poor clinical outcomes. Methods Five states of HIV care were defined within the Canadian Observational Cohort (CANOC) Collaboration following combination antiretroviral therapy (cART) initiation: (1) guidelines HIV care (suppressed viral load (VL) and CD4 >200 cells/mm3, no gaps in cART >3 months, no gaps in CD4 or VL measurement >6 months), (2) successful care with decreased frequency of follow-up (as above except no gaps in CD4 or VL measurement >12 months), (3) suboptimal care (unsuppressed VL, CD4<200 cells/mm3 on 2 consecutive visits, ≥1 gap in cART >3 months, or ≥1 gap in CD4 or VL measurement >12 months), (4) loss to follow-up (no contact for 18 months), and (5) death. Multi-state models were used to determine factors associated with transitioning among states. Results 7810 participants were included. Younger age, female gender, Indigenous ethnicity and people who have injected drugs (PWID) were associated with increased likelihoods of transitioning from guidelines to suboptimal care and decreased likelihoods of transitioning from suboptimal to guidelines care. One-fifth of individuals in successful, decreased follow-up after cART initiation (mean sojourn time 0.72 years) were in suboptimal care in subsequent years. Conclusions Using routinely collected data, we have developed a flexible framework that characterizes patient transitions among states of HIV clinical care. We have demonstrated that multi-state models provide a useful approach to supplement ‘cascade of care’ work. PMID:27851713

  8. Different secondary structure elements as scaffolds for protein folding transition states of two homologous four-helix bundles.

    PubMed

    Teilum, Kaare; Thormann, Thorsten; Caterer, Nigel R; Poulsen, Heidi I; Jensen, Peter H; Knudsen, Jens; Kragelund, Birthe B; Poulsen, Flemming M

    2005-04-01

    Comparison of the folding processes for homologue proteins can provide valuable information about details in the interactions leading to the formation of the folding transition state. Here the folding kinetics of 18 variants of yACBP and 3 variants of bACBP have been studied by Phi-value analysis. In combination with Phi-values from previous work, detailed insight into the transition states for folding of both yACBP and bACBP has been obtained. Of the 16 sequence positions that have been studied in both yACBP and bACBP, 5 (V12, I/L27, Y73, V77, and L80) have high Phi-values and appear to be important for the transition state formation in both homologues. Y31, A34, and A69 have high Phi-values only in yACBP, while F5, A9, and I74 have high Phi-values only in bACBP. Thus, additional interactions between helices A2 and A4 appear to be important for the transition state of yACBP, whereas additional interactions between helices A1 and A4 appear to be important for the transition state of bACBP. To examine whether these differences could be assigned to different packing of the residues in the native state, a solution structure of yACBP was determined by NMR. Small changes in the packing of the hydrophobic side-chains, which strengthen the interactions between helices A2 and A4, are observed in yACBP relative to bACBP. It is suggested that different structure elements serve as scaffolds for the folding of the 2 ACBP homologues. (c) 2005 Wiley-Liss, Inc.

  9. Dynamical transitions in large systems of mean field-coupled Landau-Stuart oscillators: Extensive chaos and cluster states.

    PubMed

    Ku, Wai Lim; Girvan, Michelle; Ott, Edward

    2015-12-01

    In this paper, we study dynamical systems in which a large number N of identical Landau-Stuart oscillators are globally coupled via a mean-field. Previously, it has been observed that this type of system can exhibit a variety of different dynamical behaviors. These behaviors include time periodic cluster states in which each oscillator is in one of a small number of groups for which all oscillators in each group have the same state which is different from group to group, as well as a behavior in which all oscillators have different states and the macroscopic dynamics of the mean field is chaotic. We argue that this second type of behavior is "extensive" in the sense that the chaotic attractor in the full phase space of the system has a fractal dimension that scales linearly with N and that the number of positive Lyapunov exponents of the attractor also scales linearly with N. An important focus of this paper is the transition between cluster states and extensive chaos as the system is subjected to slow adiabatic parameter change. We observe discontinuous transitions between the cluster states (which correspond to low dimensional dynamics) and the extensively chaotic states. Furthermore, examining the cluster state, as the system approaches the discontinuous transition to extensive chaos, we find that the oscillator population distribution between the clusters continually evolves so that the cluster state is always marginally stable. This behavior is used to reveal the mechanism of the discontinuous transition. We also apply the Kaplan-Yorke formula to study the fractal structure of the extensively chaotic attractors.

  10. Dynamical transitions in large systems of mean field-coupled Landau-Stuart oscillators: Extensive chaos and cluster states

    NASA Astrophysics Data System (ADS)

    Ku, Wai Lim; Girvan, Michelle; Ott, Edward

    2015-12-01

    In this paper, we study dynamical systems in which a large number N of identical Landau-Stuart oscillators are globally coupled via a mean-field. Previously, it has been observed that this type of system can exhibit a variety of different dynamical behaviors. These behaviors include time periodic cluster states in which each oscillator is in one of a small number of groups for which all oscillators in each group have the same state which is different from group to group, as well as a behavior in which all oscillators have different states and the macroscopic dynamics of the mean field is chaotic. We argue that this second type of behavior is "extensive" in the sense that the chaotic attractor in the full phase space of the system has a fractal dimension that scales linearly with N and that the number of positive Lyapunov exponents of the attractor also scales linearly with N. An important focus of this paper is the transition between cluster states and extensive chaos as the system is subjected to slow adiabatic parameter change. We observe discontinuous transitions between the cluster states (which correspond to low dimensional dynamics) and the extensively chaotic states. Furthermore, examining the cluster state, as the system approaches the discontinuous transition to extensive chaos, we find that the oscillator population distribution between the clusters continually evolves so that the cluster state is always marginally stable. This behavior is used to reveal the mechanism of the discontinuous transition. We also apply the Kaplan-Yorke formula to study the fractal structure of the extensively chaotic attractors.

  11. Educational Transitions in the United States: Reflections on the American Dream

    ERIC Educational Resources Information Center

    Crawford, Paul T.

    2012-01-01

    Education involves socialization so that individuals become productive members of society. At present, in the United States, educational transitions are primarily viewed in terms of their location in an outcomes-oriented process and framed as helping people achieve the American Dream, but in terms of the status quo national economic interest. But…

  12. State safety oversight program : audit of the tri-state oversight committee and the Washington metropolitan area transit authority, final audit report, March 4, 2010.

    DOT National Transportation Integrated Search

    2010-03-04

    The Federal Transit Administration (FTA) conducted an on-site audit of the safety program implemented by the Washington Metropolitan Area Transit Authority (WMATA) and overseen by the Tri-State Oversight Committee (TOC) between December 14 and 17, 20...

  13. Mechanical induction of transitions into mesenchymal and amoeboid states

    NASA Astrophysics Data System (ADS)

    Liphardt, Jan

    One of the fundamental mysteries of biology lies in the ability of cells to convert from one phenotype to another in response to external control inputs. We have been studying the Epithelial-to-Mesenchymal Transition (EMT), which allows organized assemblies of epithelial cells to scatter into lone mesenchymal cells. EMT is critical for normal development and wound healing, and may be important for cancer metastasis. I'll present recent data on disorganizing mammary epithelial structures. We have used CRISPR to insert fluorescent tags directly into eight EMT-related genes (such as E-cadherin and Vimentin), which allows us to monitor the dynamics of the transition in real time, subject only to delays imposed by fluorophore folding/maturation times. With this information, we can begin to order events in time (temporal resolution 30 minutes), starting with external signal inputs and proceeding through a secession of intracellular changes of gene expression on the path to the mesenchymal state.

  14. Columbus State University Global Observation and Outreach for the 2012 Transit of Venus

    NASA Astrophysics Data System (ADS)

    Perry, Matthew; McCarty, C.; Bartow, M.; Hood, J. C.; Lodder, K.; Johnson, M.; Cruzen, S. T.; Williams, R. N.

    2013-01-01

    Faculty, staff and students from Columbus State University’s (CSU’s) Coca-Cola Space Science Center presented a webcast of the 2012 Transit of Venus from three continents to a global audience of 1.4 million unique viewers. Team members imaged the transit with telescopes using white-light, hydrogen-alpha, and calcium filters, from Alice Springs, Australia; the Gobi Desert, Mongolia; Bryce Canyon, UT; and Columbus, GA. Images were webcast live during the transit in partnership with NASA’s Sun-Earth Day program, and Science Center staff members were featured on NASA TV. Local members of the public were brought in for a series of outreach initiatives, in both Georgia and Australia, before and during the transit. The data recorded from the various locations have been archived for use in demonstrating principles such as the historical measurement of the astronomical unit.

  15. Status in calculating electronic excited states in transition metal oxides from first principles.

    PubMed

    Bendavid, Leah Isseroff; Carter, Emily Ann

    2014-01-01

    Characterization of excitations in transition metal oxides is a crucial step in the development of these materials for photonic and optoelectronic applications. However, many transition metal oxides are considered to be strongly correlated materials, and their complex electronic structure is challenging to model with many established quantum mechanical techniques. We review state-of-the-art first-principles methods to calculate charged and neutral excited states in extended materials, and discuss their application to transition metal oxides. We briefly discuss developments in density functional theory (DFT) to calculate fundamental band gaps, and introduce time-dependent DFT, which can model neutral excitations. Charged excitations can be described within the framework of many-body perturbation theory based on Green's functions techniques, which predominantly employs the GW approximation to the self-energy to facilitate a feasible solution to the quasiparticle equations. We review the various implementations of the GW approximation and evaluate each approach in its calculation of fundamental band gaps of many transition metal oxides. We also briefly review the related Bethe-Salpeter equation (BSE), which introduces an electron-hole interaction between GW-derived quasiparticles to describe accurately neutral excitations. Embedded correlated wavefunction theory is another framework used to model localized neutral or charged excitations in extended materials. Here, the electronic structure of a small cluster is modeled within correlated wavefunction theory, while its coupling to its environment is represented by an embedding potential. We review a number of techniques to represent this background potential, including electrostatic representations and electron density-based methods, and evaluate their application to transition metal oxides.

  16. Computation of rare transitions in the barotropic quasi-geostrophic equations

    NASA Astrophysics Data System (ADS)

    Laurie, Jason; Bouchet, Freddy

    2015-01-01

    We investigate the theoretical and numerical computation of rare transitions in simple geophysical turbulent models. We consider the barotropic quasi-geostrophic and two-dimensional Navier-Stokes equations in regimes where bistability between two coexisting large-scale attractors exist. By means of large deviations and instanton theory with the use of an Onsager-Machlup path integral formalism for the transition probability, we show how one can directly compute the most probable transition path between two coexisting attractors analytically in an equilibrium (Langevin) framework and numerically otherwise. We adapt a class of numerical optimization algorithms known as minimum action methods to simple geophysical turbulent models. We show that by numerically minimizing an appropriate action functional in a large deviation limit, one can predict the most likely transition path for a rare transition between two states. By considering examples where theoretical predictions can be made, we show that the minimum action method successfully predicts the most likely transition path. Finally, we discuss the application and extension of such numerical optimization schemes to the computation of rare transitions observed in direct numerical simulations and experiments and to other, more complex, turbulent systems.

  17. Raman study of transition-metal oxides with perovskite-like structure

    NASA Astrophysics Data System (ADS)

    Kolev, Nikolay Iliev

    Perovskite-like oxides exhibit a rich variety of properties of fundamental scientific interest and potential application value. The motivation for this work is to contribute to our knowledge of perovskite-like systems and strongly correlated systems in general. The polarized Raman spectra of single crystal and thin film CaCu3Ti4O12, single crystal and thin film CaRuO3, microcrystals of La0.5Ca 0.5MnO3, and ceramic and thin film CaMnO3 have been investigated. In close comparison to results from lattice dynamics calculations most of the Raman lines in the CaCu3Ti4O12, CaRuO3, La0.5Ca0.5MnO3 and CaMnO 3 spectra, have been assigned to definite phonon modes. The validity of the model for twin orientation in the Pnma structure for CaRuO3 and La0.5Ca0.5MnO3 is confirmed. The analysis of the CaMnO3 spectra contributed to the development of a model, based on four basic distortions of the (distorted) perovskite structure. The temperature behavior of the CaCu3Ti4O 12 spectra shows that there is no evidence for structural phase transition in the temperature range 20--600 K, so such a transition cannot be responsible for the sharp drop in the dielectric constant below 100 K. The Raman spectra indirectly support the mechanism of formation of barrier layer capacitances in CaCu3Ti4O12.The observation of additional Raman mode of nominal Ag symmetry is discussed in terms of coexistence of domains of different atomic arrangement, or alternatively of non-stoichiometry (Cu deficiency). In the case of the thin film, the tetragonal distortions could be responsible for the greater separation of the additional Ag line. No anomalies in the temperature behavior of the Raman lines of CaRuO3 is observed, which is an indirect evidence for its lack of long-range magnetic ordering at low temperatures (depending on whether this ordering would be observable by Raman spectroscopy through spin-phonon coupling). In La0.5Ca0.5MnO 3 the appearance of several Raman lines below TN is analyzed in terms of

  18. 19 CFR 123.64 - Baggage in transit through the United States between ports in Canada or in Mexico.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... between ports in Canada or in Mexico. 123.64 Section 123.64 Customs Duties U.S. CUSTOMS AND BORDER... MEXICO Baggage § 123.64 Baggage in transit through the United States between ports in Canada or in Mexico. (a) Procedure. Baggage in transit from point to point in Canada or Mexico through the United States...

  19. The Role of Leadership in Transitional States: The Cases of Lebanon, Israel-Palestine

    DTIC Science & Technology

    2014-11-01

    Using authoritarian, democratic, and laissez - faire leadership styles as a basis for this work, it was concluded that some leaders were more people...NOV 2014 2. REPORT TYPE 3. DATES COVERED 00-00-2014 to 00-00-2014 4. TITLE AND SUBTITLE The Role of Leadership in Transitional States: The Cases...Prescribed by ANSI Std Z39-18 The United States Army War College U.S. ARMY WAR COLLEGE CENTER for STRATEGIC LEADERSHIP and DEVELOPMENT The United States

  20. Variational transition state theory: theoretical framework and recent developments.

    PubMed

    Bao, Junwei Lucas; Truhlar, Donald G

    2017-12-11

    This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications. The theoretical methods reviewed here include multidimensional quantum mechanical tunneling, multistructural VTST (MS-VTST), multi-path VTST (MP-VTST), both reaction-path VTST (RP-VTST) and variable reaction coordinate VTST (VRC-VTST), system-specific quantum Rice-Ramsperger-Kassel theory (SS-QRRK) for predicting pressure-dependent rate constants, and VTST in the solid phase, liquid phase, and enzymes. We also provide some perspectives regarding the general applicability of VTST.

  1. Dynamical transitions in large systems of mean field-coupled Landau-Stuart oscillators: Extensive chaos and cluster states

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ku, Wai Lim; Girvan, Michelle; Ott, Edward

    In this paper, we study dynamical systems in which a large number N of identical Landau-Stuart oscillators are globally coupled via a mean-field. Previously, it has been observed that this type of system can exhibit a variety of different dynamical behaviors. These behaviors include time periodic cluster states in which each oscillator is in one of a small number of groups for which all oscillators in each group have the same state which is different from group to group, as well as a behavior in which all oscillators have different states and the macroscopic dynamics of the mean field ismore » chaotic. We argue that this second type of behavior is “extensive” in the sense that the chaotic attractor in the full phase space of the system has a fractal dimension that scales linearly with N and that the number of positive Lyapunov exponents of the attractor also scales linearly with N. An important focus of this paper is the transition between cluster states and extensive chaos as the system is subjected to slow adiabatic parameter change. We observe discontinuous transitions between the cluster states (which correspond to low dimensional dynamics) and the extensively chaotic states. Furthermore, examining the cluster state, as the system approaches the discontinuous transition to extensive chaos, we find that the oscillator population distribution between the clusters continually evolves so that the cluster state is always marginally stable. This behavior is used to reveal the mechanism of the discontinuous transition. We also apply the Kaplan-Yorke formula to study the fractal structure of the extensively chaotic attractors.« less

  2. Facilitating a Major Staffing Transition in a State Psychiatric Hospital With Changes to Nursing Orientation.

    PubMed

    Birnbaum, Shira; Sperber-Weiss, Doreen; Dimitrios, Timothy; Eckel, Donald; Monroy-Miller, Cherry; Monroe, Janet J; Friedman, Ross; Ologbosele, Mathias; Epo, Grace; Sharpe, Debra; Zarski, Yongsuk

    A large state psychiatric hospital experienced a state-mandated Reduction in Force that resulted in the abrupt loss and rapid turnover of more than 40% of its nursing and paraprofessional staff. The change exemplified current national trends toward downsizing and facility closure. This article describes revisions to the nursing orientation program that supported cost containment and fidelity to mission and clinical practices during the transition. An existing nursing orientation program was reconfigured in alignment with principles of rational instructional design and a core-competencies model of curriculum development, evidence-based practices that provided tactical clarity and commonality of purpose during a complex and emotionally charged transition period. Program redesign enabled efficiencies that facilitated the transition, with no evidence of associated negative effects. The process described here offers an example for hospitals facing similar workforce reorganization in an era of public sector downsizing.

  3. A Visualization System for Predicting Learning Activities Using State Transition Graphs

    ERIC Educational Resources Information Center

    Okubo, Fumiya; Shimada, Atsushi; Taniguchi, Yuta

    2017-01-01

    In this paper, we present a system for visualizing learning logs of a course in progress together with predictions of learning activities of the following week and the final grades of students by state transition graphs. Data are collected from 236 students attending the course in progress and from 209 students attending the past course for…

  4. Image Charge and Electric Field Effects on Hydrogen-like Impurity-bound Polaron Energies and Oscillator Strengths in a Quantum Dot

    NASA Astrophysics Data System (ADS)

    Vardanyan, L. A.; Vartanian, A. L.; Asatryan, A. L.; Kirakosyan, A. A.

    2016-11-01

    By using Landau-Pekar variational method, the ground and the first excited state energies and the transition frequencies between the ground and the first excited states of a hydrogen-like impurity-bound polaron in a spherical quantum dot (QD) have been studied by taking into account the image charge effect (ICE). We employ the dielectric continuum model to describe the phonon confinement effects. The oscillator strengths (OSs) of transitions from the 1 s-like state to excited states of 2 s, 2 p x , and 2 p z symmetries are calculated as functions of the applied electric field and strength of the confinement potential. We have shown that with and without image charge effect, the increase of the strength of the parabolic confinement potential leads to the increase of the oscillator strengths of 1 s - 2 p x and 1 s - 2 p z transitions. This indicates that the energy differences between 1 s- and 2 p x - as well as 1 s- and 2 p z -like states have a dominant role determining the oscillator strength. Although there is almost no difference in the oscillator strengths for transitions 1 s - 2 p x and 1 s -2 p z when the image charge effect is not taken into account, it becomes significant with the image charge effect.

  5. Diels–Alder Reactions of Allene with Benzene and Butadiene: Concerted, Stepwise, and Ambimodal Transition States

    PubMed Central

    2015-01-01

    Multiconfigurational complete active space methods (CASSCF and CASPT2) have been used to investigate the (4 + 2) cycloadditions of allene with butadiene and with benzene. Both concerted and stepwise radical pathways were examined to determine the mechanism of the Diels–Alder reactions with an allene dienophile. Reaction with butadiene occurs via a single ambimodal transition state that can lead to either the concerted or stepwise trajectories along the potential energy surface, while reaction with benzene involves two separate transition states and favors the concerted mechanism relative to the stepwise mechanism via a diradical intermediate. PMID:25216056

  6. Safety and Automated Train Control for Rail Rapid Transit Systems

    DOT National Transportation Integrated Search

    1974-07-01

    The anticipated construction and expansion of rail rapid transit system in the United States over the next 10-15 years implies major capital expenditures. A significant level of automation in train cntrol is likely to be central to these systems. The...

  7. Electron impact excitation of the electronic states of N2. III - Transitions in the 12.5-14.2-eV energy-loss region at incident energies of 40 and 60 eV

    NASA Technical Reports Server (NTRS)

    Chutjian, A.; Trajmar, S.; Cartwright, D. C.

    1977-01-01

    Analysis of electron energy-loss data at incident electron energies of 40 and 60 eV has led to the determination of normalized absolute differential cross sections for electron-impact excitation of five optically-allowed singlet states, two known triplet states, and two unknown triplet-like states of N2, lying in the energy-loss range 12.5-14.2 eV. The range of scattering angles was 5 to 138 deg. The optically allowed transitions and the known triplet excitations are identified. Cross sections for excitation to two unidentified triplet-like states at 13.155 and 13.395 eV were also obtained. The relationship of the generalized oscillator strength for the dipole-allowed states obtained from the described data to known optical oscillator strengths is discussed.

  8. Engineered bi-histidine metal chelation sites map the structure of the mechanical unfolding transition state of an elastomeric protein domain GB1.

    PubMed

    Shen, Tao; Cao, Yi; Zhuang, Shulin; Li, Hongbin

    2012-08-22

    Determining the structure of the transition state is critical for elucidating the mechanism behind how proteins fold and unfold. Due to its high free energy, however, the transition state generally cannot be trapped and studied directly using traditional structural biology methods. Thus, characterizing the structure of the transition state that occurs as proteins fold and unfold remains a major challenge. Here, we report a novel (to our knowledge) method that uses engineered bi-histidine (bi-His) metal-binding sites to directly map the structure of the mechanical unfolding transition state of proteins. This method is adapted from the traditional ψ-value analysis, which uses engineered bi-His metal chelation sites to probe chemical (un)folding transition-state structure. The φ(M2+)(U)-value is defined as ΔΔG(‡-N)/ΔΔG(U-N), which is the energetic effects of metal chelation by the bi-His site on the unfolding energy barrier (ΔG(‡-N)) relative to its thermodynamic stability (ΔG(U-N)) and can be used to obtain information about the transition state in the mutational site. As a proof of principle, we used the small protein GB1 as a model system and set out to map its mechanical unfolding transition-state structure. Using single-molecule atomic force microscopy and spectrofluorimetry, we directly quantified the effect of divalent metal ion binding on the mechanical unfolding free energy and thermodynamic stability of GB1, which allowed us to quantify φ(M2+)(U)-values for different sites in GB1. Our results enabled us to map the structure of the mechanical unfolding transition state of GB1. Within GB1's mechanical unfolding transition state, the interface between force-bearing β-strands 1 and 4 is largely disrupted, and the first β-hairpin is partially disordered while the second β-hairpin and the α-helix remain structured. Our results demonstrate the unique application of ψ-value analysis in elucidating the structure of the transition state that occurs

  9. Regimes of radiative and nonradiative transitions in transport through an electronic system in a photon cavity reaching a steady state

    NASA Astrophysics Data System (ADS)

    Gudmundsson, Vidar; Jonsson, Thorsteinn H.; Bernodusson, Maria Laura; Abdullah, Nzar Rauf; Sitek, Anna; Goan, Hsi-Sheng; Tang, Chi-Shung; Manolescu, Andrei

    2017-01-01

    We analyze how a multilevel many-electron system in a photon cavity approaches the steady state when coupled to external leads. When a plunger gate is used to lower cavity photon dressed one- and two-electron states below the bias window defined by the external leads, we can identify one regime with nonradiative transitions dominating the electron transport, and another regime with radiative transitions. Both transitions trap the electrons in the states below the bias bringing the system into a steady state. The order of the two regimes and their relative strength depends on the location of the bias window in the energy spectrum of the system and the initial conditions.

  10. Characterization of Dynamical Phase Transitions in Quantum Jump Trajectories Beyond the Properties of the Stationary State

    NASA Astrophysics Data System (ADS)

    Lesanovsky, Igor; van Horssen, Merlijn; Guţă, Mădălin; Garrahan, Juan P.

    2013-04-01

    We describe how to characterize dynamical phase transitions in open quantum systems from a purely dynamical perspective, namely, through the statistical behavior of quantum jump trajectories. This approach goes beyond considering only properties of the steady state. While in small quantum systems dynamical transitions can only occur trivially at limiting values of the controlling parameters, in many-body systems they arise as collective phenomena and within this perspective they are reminiscent of thermodynamic phase transitions. We illustrate this in open models of increasing complexity: a three-level system, the micromaser, and a dissipative version of the quantum Ising model. In these examples dynamical transitions are accompanied by clear changes in static behavior. This is however not always the case, and, in general, dynamical phases need to be uncovered by observables which are strictly dynamical, e.g., dynamical counting fields. We demonstrate this via the example of a class of models of dissipative quantum glasses, whose dynamics can vary widely despite having identical (and trivial) stationary states.

  11. Characterization of dynamical phase transitions in quantum jump trajectories beyond the properties of the stationary state.

    PubMed

    Lesanovsky, Igor; van Horssen, Merlijn; Guţă, Mădălin; Garrahan, Juan P

    2013-04-12

    We describe how to characterize dynamical phase transitions in open quantum systems from a purely dynamical perspective, namely, through the statistical behavior of quantum jump trajectories. This approach goes beyond considering only properties of the steady state. While in small quantum systems dynamical transitions can only occur trivially at limiting values of the controlling parameters, in many-body systems they arise as collective phenomena and within this perspective they are reminiscent of thermodynamic phase transitions. We illustrate this in open models of increasing complexity: a three-level system, the micromaser, and a dissipative version of the quantum Ising model. In these examples dynamical transitions are accompanied by clear changes in static behavior. This is however not always the case, and, in general, dynamical phases need to be uncovered by observables which are strictly dynamical, e.g., dynamical counting fields. We demonstrate this via the example of a class of models of dissipative quantum glasses, whose dynamics can vary widely despite having identical (and trivial) stationary states.

  12. MHD Simulation for Investigating the Dynamic State Transition Responsible for a Solar Eruption in Active Region 12158

    NASA Astrophysics Data System (ADS)

    Lee, Hwanhee; Magara, Tetsuya

    2018-06-01

    We present a magnetohydrodynamic model of solar eruption based on the dynamic state transition from the quasi-static state to the eruptive state of an active region (AR) magnetic field. For the quasi-static state before an eruption, we consider the existence of a slow solar wind originating from an AR, which may continuously make the AR magnetic field deviate from mechanical equilibrium. In this model, we perform a three-dimensional magnetohydrodynamic simulation of AR 12158 producing a coronal mass ejection, where the initial magnetic structure of the simulation is given by a nonlinear force-free field derived from an observed photospheric vector magnetic field. We then apply a pressure-driven outflow to the upper part of the magnetic structure to achieve a quasi-static pre-eruptive state. The simulation shows that the eruptive process observed in this AR may be caused by the dynamic state transition of an AR magnetic field, which is essentially different from the destabilization of a static magnetic field. The dynamic state transition is determined from the shape evolution of the magnetic field line according to the κH-mechanism. This work demonstrates how the mechanism works to produce a solar eruption in the dynamic solar corona governed by the gravitational field and the continuous outflows of solar wind.

  13. Interplay of the Glass Transition and the Liquid-Liquid Phase Transition in Water

    PubMed Central

    Giovambattista, Nicolas; Loerting, Thomas; Lukanov, Boris R.; Starr, Francis W.

    2012-01-01

    Water has multiple glassy states, often called amorphous ices. Low-density (LDA) and high-density (HDA) amorphous ice are separated by a dramatic, first-order like phase transition. It has been argued that the LDA-HDA transformation connects to a first-order liquid-liquid phase transition (LLPT) above the glass transition temperature Tg. Direct experimental evidence of the LLPT is challenging to obtain, since the LLPT occurs at conditions where water rapidly crystallizes. In this work, we explore the implications of a LLPT on the pressure dependence of Tg(P) for LDA and HDA by performing computer simulations of two water models – one with a LLPT, and one without. In the absence of a LLPT, Tg(P) for all glasses nearly coincide. When there is a LLPT, different glasses exhibit dramatically different Tg(P) which are directly linked with the LLPT. Available experimental data for Tg(P) are only consistent with the scenario including a LLPT. PMID:22550566

  14. Interplay of the Glass Transition and the Liquid-Liquid Phase Transition in Water

    NASA Astrophysics Data System (ADS)

    Giovambattista, Nicolas; Loerting, Thomas; Lukanov, Boris R.; Starr, Francis W.

    2012-05-01

    Water has multiple glassy states, often called amorphous ices. Low-density (LDA) and high-density (HDA) amorphous ice are separated by a dramatic, first-order like phase transition. It has been argued that the LDA-HDA transformation connects to a first-order liquid-liquid phase transition (LLPT) above the glass transition temperature Tg. Direct experimental evidence of the LLPT is challenging to obtain, since the LLPT occurs at conditions where water rapidly crystallizes. In this work, we explore the implications of a LLPT on the pressure dependence of Tg(P) for LDA and HDA by performing computer simulations of two water models - one with a LLPT, and one without. In the absence of a LLPT, Tg(P) for all glasses nearly coincide. When there is a LLPT, different glasses exhibit dramatically different Tg(P) which are directly linked with the LLPT. Available experimental data for Tg(P) are only consistent with the scenario including a LLPT.

  15. A United States regulator's perspective on the ongoing chlorofluorocarbon transition.

    PubMed

    Meyer, R J

    1999-12-01

    The Food and Drug Administration (FDA) put in place a general ban on the use of chlorofluorocarbons for the products it regulates (medical devices, drugs, and foods) in 1978, exempting those products where chlorofluorocarbon use was determined to be essential for the public health. In the intervening years, as the international commitment to a full transition away from all chlorofluorocarbon use took shape under the Montreal Protocol, the FDA has worked with industry to facilitate the development and testing of alternative technologies and products for inhalation drug products. As these alternative products begin to move from testing through the approval process and into marketing, the FDA is working collaboratively with the Environmental Protection Agency, other governmental agencies, and nongovernmental stakeholders to develop a transition policy for the United States. The transition policy for metered dose inhalers must be one that achieves the dual aims of first protecting the patients who rely on these vital medical products, while also achieving the public health need of protecting the ozone layer. As a part of developing such a transition strategy, the FDA published an advance notice of proposed rulemaking (ANPRM) in March 1997. The ANPRM proposed mechanisms by which the FDA could determine when chlorofluorocarbon use in a drug product could no longer be considered essential. The ANPRM resulted in a large amount of valuable public debate and input. The FDA is now working to incorporate the knowledge gained from these public comments as it continues the rule-making process.

  16. Do Hegemons Distribute Private Goods?: A Test of Power-Transition Theory

    ERIC Educational Resources Information Center

    Bussmann, Margit; Oneal, John R.

    2007-01-01

    According to power-transition theory, war is most likely when the leading state is challenged by a rapidly growing, dissatisfied rival. Challengers are said to be dissatisfied because the hegemon manages the status quo for its own benefit, rewarding its allies and penalizing rivals. We assess the leading state's ability to distribute the private…

  17. Review of State Policies and Programs to Support Young People Transitioning Out of Foster Care

    ERIC Educational Resources Information Center

    Dworsky, Amy; Havlicek, Judy

    2009-01-01

    This comprehensive review of policies and programs designed to support youth transitioning out of foster care spans all 50 states and the District of Columbia. As part of the review, Chapin Hall administered a web-based survey of state independent living services coordinators to collect up-to-date information about their state's policies and…

  18. Engineering electrocatalytic activity in nanosized perovskite cobaltite through surface spin-state transition

    PubMed Central

    Zhou, Shiming; Miao, Xianbing; Zhao, Xu; Ma, Chao; Qiu, Yuhao; Hu, Zhenpeng; Zhao, Jiyin; Shi, Lei; Zeng, Jie

    2016-01-01

    The activity of electrocatalysts exhibits a strongly dependence on their electronic structures. Specifically, for perovskite oxides, Shao-Horn and co-workers have reported a correlation between the oxygen evolution reaction activity and the eg orbital occupation of transition-metal ions, which provides guidelines for the design of highly active catalysts. Here we demonstrate a facile method to engineer the eg filling of perovskite cobaltite LaCoO3 for improving the oxygen evolution reaction activity. By reducing the particle size to ∼80 nm, the eg filling of cobalt ions is successfully increased from unity to near the optimal configuration of 1.2 expected by Shao-Horn's principle. Consequently, the activity is significantly enhanced, comparable to those of recently reported cobalt oxides with eg∼1.2 configurations. This enhancement is ascribed to the emergence of spin-state transition from low-spin to high-spin states for cobalt ions at the surface of the nanoparticles, leading to more active sites with increased reactivity. PMID:27187067

  19. The nature of photoinduced phase transition and metastable states in vanadium dioxide

    PubMed Central

    Tao, Zhensheng; Zhou, Faran; Han, Tzong-Ru T.; Torres, David; Wang, Tongyu; Sepulveda, Nelson; Chang, Kiseok; Young, Margaret; Lunt, Richard R.; Ruan, Chong-Yu

    2016-01-01

    Photoinduced threshold switching processes that lead to bistability and the formation of metastable phases in photoinduced phase transition of VO2 are elucidated through ultrafast electron diffraction and diffusive scattering techniques with varying excitation wavelengths. We uncover two distinct regimes of the dynamical phase change: a nearly instantaneous crossover into an intermediate state and its decay led by lattice instabilities over 10 ps timescales. The structure of this intermediate state is identified to be monoclinic, but more akin to M2 rather than M1 based on structure refinements. The extinction of all major monoclinic features within just a few picoseconds at the above-threshold-level (~20%) photoexcitations and the distinct dynamics in diffusive scattering that represents medium-range atomic fluctuations at two photon wavelengths strongly suggest a density-driven and nonthermal pathway for the initial process of the photoinduced phase transition. These results highlight the critical roles of electron correlations and lattice instabilities in driving and controlling phase transformations far from equilibrium. PMID:27982066

  20. The nature of photoinduced phase transition and metastable states in vanadium dioxide

    NASA Astrophysics Data System (ADS)

    Tao, Zhensheng; Zhou, Faran; Han, Tzong-Ru T.; Torres, David; Wang, Tongyu; Sepulveda, Nelson; Chang, Kiseok; Young, Margaret; Lunt, Richard R.; Ruan, Chong-Yu

    2016-12-01

    Photoinduced threshold switching processes that lead to bistability and the formation of metastable phases in photoinduced phase transition of VO2 are elucidated through ultrafast electron diffraction and diffusive scattering techniques with varying excitation wavelengths. We uncover two distinct regimes of the dynamical phase change: a nearly instantaneous crossover into an intermediate state and its decay led by lattice instabilities over 10 ps timescales. The structure of this intermediate state is identified to be monoclinic, but more akin to M2 rather than M1 based on structure refinements. The extinction of all major monoclinic features within just a few picoseconds at the above-threshold-level (~20%) photoexcitations and the distinct dynamics in diffusive scattering that represents medium-range atomic fluctuations at two photon wavelengths strongly suggest a density-driven and nonthermal pathway for the initial process of the photoinduced phase transition. These results highlight the critical roles of electron correlations and lattice instabilities in driving and controlling phase transformations far from equilibrium.

  1. Proceedings of the First Landscape State-and-Transition Simulation Modeling Conference, June 14–16, 2011, Portland, Oregon

    Treesearch

    Becky K. Kerns; Ayn J. Shlisky; Colin J. Daniel

    2012-01-01

    The first ever Landscape State-and-Transition Simulation Modeling Conference was held from June 14–16, 2011, in Portland Oregon. The conference brought together over 70 users of state-and-transition simulation modeling tools—the Vegetation Dynamics Development Tool (VDDT), the Tool for Exploratory Landscape Analysis (TELSA) and the Path Landscape Model. The goal of the...

  2. State transition storyboards: A tool for designing the Goldstone solar system radar data acquisition system user interface software

    NASA Technical Reports Server (NTRS)

    Howard, S. D.

    1987-01-01

    Effective user interface design in software systems is a complex task that takes place without adequate modeling tools. By combining state transition diagrams and the storyboard technique of filmmakers, State Transition Storyboards were developed to provide a detailed modeling technique for the Goldstone Solar System Radar Data Acquisition System human-machine interface. Illustrations are included with a description of the modeling technique.

  3. Valley-selective photon-dressed states in transition metal dichalcogenides

    NASA Astrophysics Data System (ADS)

    LaMountain, Trevor; Chen, Yen-Jung; Stanev, Teodor K.; Stern, Nathaniel P.

    2018-02-01

    When electronic excitations in a semiconductor interact with light, the relevant quasiparticles are hybrid lightmatter dressed states, or exciton-polaritons. In monolayer transition metal dichalcogenides, a class of 2D direct bandgap semiconductors, optical excitations selectively populate distinct momentum valleys with correlated spin projection. The combination of this spin-valley locking with photon dressed states can lead to new optical phenomena in these materials. We present spectroscopic measurements of valley-specific exciton-polaritons in monolayer 2D materials in distinct regimes. When a monolayer is embedded in a dielectric microcavity, strong coupling exciton-polaritons are achieved. Cavity-modified dynamics of the dressed states are inferred from emission. Polarization persists up to room temperature in monolayer MoS2, in contrast with bare material. We also show that distinct regimes of valley-polarized exciton-polaritons can be accessed with microcavity engineering by tuning system parameters such as cavity decay rate and exciton-photon coupling strength. Further, we report results showing that polarization-sensitive ultrafast spectroscopy can enable sensitive measurements of the valley optical Stark shift, a light-induced dressed state energy shift, in monolayer semiconductors such as WSe2 and MoS2. These findings demonstrate distinct approaches to manipulating the picosecond dynamics of valleysensitive dressed states in monolayer semiconductors.

  4. 19 CFR 123.65 - Domestic baggage transiting Canada or Mexico between ports in the United States.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 19 Customs Duties 1 2011-04-01 2011-04-01 false Domestic baggage transiting Canada or Mexico... PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CBP RELATIONS WITH CANADA AND MEXICO Baggage § 123.65 Domestic baggage transiting Canada or Mexico between ports in the United States. (a...

  5. 19 CFR 123.65 - Domestic baggage transiting Canada or Mexico between ports in the United States.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 19 Customs Duties 1 2013-04-01 2013-04-01 false Domestic baggage transiting Canada or Mexico... PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CBP RELATIONS WITH CANADA AND MEXICO Baggage § 123.65 Domestic baggage transiting Canada or Mexico between ports in the United States. (a...

  6. 19 CFR 123.65 - Domestic baggage transiting Canada or Mexico between ports in the United States.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 19 Customs Duties 1 2014-04-01 2014-04-01 false Domestic baggage transiting Canada or Mexico... PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CBP RELATIONS WITH CANADA AND MEXICO Baggage § 123.65 Domestic baggage transiting Canada or Mexico between ports in the United States. (a...

  7. 19 CFR 123.65 - Domestic baggage transiting Canada or Mexico between ports in the United States.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 19 Customs Duties 1 2012-04-01 2012-04-01 false Domestic baggage transiting Canada or Mexico... PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CBP RELATIONS WITH CANADA AND MEXICO Baggage § 123.65 Domestic baggage transiting Canada or Mexico between ports in the United States. (a...

  8. Electric Monopole Transition Strengths in the Stable Nickel Isotopes

    NASA Astrophysics Data System (ADS)

    Evitts, Lee John

    A series of measurements of stable nickel isotopes were performed at the Australian National University in Canberra. Excited states in 58,60,62Ni were populated via inelastic scattering of proton beams delivered by the 14UD Pelletron accelerator. Multiple setups were used in order to determine the structure of low-lying states. The CAESAR array of Compton-suppressed HPGe detectors was used to measure the (E2/M1) mixing ratio of transitions from angular distributions of gamma rays. The Super-e spectrometer was used to measure conversion coefficients for a number of J to J transitions. The data obtained from both devices was combined with previously measured parent lifetimes and branching ratios to determine E0 transition strengths between J-pi transitions. The E0 transition strength for the second 0+ to first 0+ transitions in 60,62Ni have been measured for the first time through internal conversion electron detection. The experimental value of 132(+59,-70) for 62Ni agrees within 2 sigma of the previous result obtained from internal pair formation. However it is likely that the previous experimental results used an outdated theoretical model for internal pair formation emission. This work also represents the first measurements of E0 transition strengths between 2+ states in Ni isotopes. There is generally large E0 strength between the 2+ states, particularly in the second 2+ to first 2+ transition, however there is also a large uncertainty in the measurements owing to the difficulties involved in measuring conversion coefficients. In 62Ni, the E0 transition strength of 172(+62,-77) for the second 2+ to first 2+ transition gives further weight to the argument against the spherical vibrator model, as an E0 transition is forbidden if there is a change of only one phonon. The large measurement also indicates the presence of shape coexistence, complementing the recent experimental work carried out in the neutron-rich Ni isotopes.

  9. Bond-length fluctuations and the spin-state transition in LCoO3 (L=La, Pr, and Nd)

    NASA Astrophysics Data System (ADS)

    Yan, J.-Q.; Zhou, J.-S.; Goodenough, J. B.

    2004-04-01

    The temperature dependence of thermal conductivity, κ(T), and magnetic susceptibility, χ(T), have been measured on single crystals of LCoO3 (L=La, Pr, Nd) grown by the floating-zone method. The susceptibility measurement shows a progressive stabilization of the low-spin (LS) state of Co(III) with decreasing size of the L3+ ion, and the population of excited intermediate-spin (IS) or high-spin (HS) state Co(III) ions begins to increase at 200 K and 300 K for PrCoO3 and NdCoO3 compared with 35 K in LaCoO3. The low-temperature Curie-Weiss paramagnetic susceptibility of LCoO3 is an intrinsic property arising from surface cobalt and, possibly, a LS ground state bearing some IS character caused by the virtual excitation to the IS state. The transition from a LS to a IS/HS state introduces bond-length fluctuations that suppress the phonon contribution to κ(T) below 300 K. The suppressed κ(T) could be further reduced by dynamic Jahn-Teller distortions associated with the IS/HS species. A smooth transition in ρ(T) and α(T) and a nearly temperature independent α(T)≈20 μV/K above 600 K do not support a thermally induced, homogeneous Mott-Hubbard transition model for the high-temperature transition of LaCoO3 from an insulating to a conductive state. A two-phase process is proposed for the interval 300 Kstates with localized e electrons that are stabilized by Jahn-Teller distortions that may be dynamic.

  10. Reduced probabilities for E2 transitions between excited collective states of triaxial even–even nuclei

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nadyrbekov, M. S., E-mail: nodirbekov@inp.uz; Bozarov, O. A.

    Reduced probabilities for intra- and interband E2 transitions in excited collective states of even–even lanthanide and actinide nuclei are analyzed on the basis of a model that admits an arbitrary triaxiality. They are studied in detail in the energy spectra of {sup 154}Sm, {sup 156}Gd, {sup 158}Dy, {sup 162,164}Er, {sup 230,232}Th, and {sup 232,234,236,238}U even–even nuclei. Theoretical and experimental values of the reduced probabilities for the respective E2 transitions are compared. This comparison shows good agreement for all states, including high-spin ones. The ratios of the reduced probabilities for the E2 transitions in question are compared with results following frommore » the Alaga rules. These comparisons make it possible to assess the sensitivity of the probabilities being considered to the presence of quadrupole deformations.« less

  11. Investigation of transition States in bulk and freestanding film polymer glasses.

    PubMed

    Jain, Tushar S; de Pablo, Juan J

    2004-04-16

    We have performed transition state searches on the potential energy landscape for bulk and freestanding film polymer glasses and identified connected minima. An analysis of the displacements between minima shows that the sites that undergo the greatest displacement are highly localized in space for both the bulk and the thin-film systems studied. In the case of the thin film, the clusters originate at the surface and penetrate into the center of the film thereby coupling the relaxation in the center of the film to the mobile surface layer. Furthermore, the energy barriers between minima are lower in the thin film than in the bulk system. These findings can rationalize the experimentally observed depression of the glass transition temperature in freestanding polymer films.

  12. Integrating Ecosystem Carbon Dynamics into State-and-Transition Simulation Models of Land Use/Land Cover Change

    NASA Astrophysics Data System (ADS)

    Sleeter, B. M.; Daniel, C.; Frid, L.; Fortin, M. J.

    2016-12-01

    State-and-transition simulation models (STSMs) provide a general approach for incorporating uncertainty into forecasts of landscape change. Using a Monte Carlo approach, STSMs generate spatially-explicit projections of the state of a landscape based upon probabilistic transitions defined between states. While STSMs are based on the basic principles of Markov chains, they have additional properties that make them applicable to a wide range of questions and types of landscapes. A current limitation of STSMs is that they are only able to track the fate of discrete state variables, such as land use/land cover (LULC) classes. There are some landscape modelling questions, however, for which continuous state variables - for example carbon biomass - are also required. Here we present a new approach for integrating continuous state variables into spatially-explicit STSMs. Specifically we allow any number of continuous state variables to be defined for each spatial cell in our simulations; the value of each continuous variable is then simulated forward in discrete time as a stochastic process based upon defined rates of change between variables. These rates can be defined as a function of the realized states and transitions of each cell in the STSM, thus providing a connection between the continuous variables and the dynamics of the landscape. We demonstrate this new approach by (1) developing a simple IPCC Tier 3 compliant model of ecosystem carbon biomass, where the continuous state variables are defined as terrestrial carbon biomass pools and the rates of change as carbon fluxes between pools, and (2) integrating this carbon model with an existing LULC change model for the state of Hawaii, USA.

  13. Anomalous structural transition of confined hard squares.

    PubMed

    Gurin, Péter; Varga, Szabolcs; Odriozola, Gerardo

    2016-11-01

    Structural transitions are examined in quasi-one-dimensional systems of freely rotating hard squares, which are confined between two parallel walls. We find two competing phases: one is a fluid where the squares have two sides parallel to the walls, while the second one is a solidlike structure with a zigzag arrangement of the squares. Using transfer matrix method we show that the configuration space consists of subspaces of fluidlike and solidlike phases, which are connected with low probability microstates of mixed structures. The existence of these connecting states makes the thermodynamic quantities continuous and precludes the possibility of a true phase transition. However, thermodynamic functions indicate strong tendency for the phase transition and our replica exchange Monte Carlo simulation study detects several important markers of the first order phase transition. The distinction of a phase transition from a structural change is practically impossible with simulations and experiments in such systems like the confined hard squares.

  14. Spectral properties near the Mott transition in the two-dimensional Hubbard model

    NASA Astrophysics Data System (ADS)

    Kohno, Masanori

    2013-03-01

    Single-particle excitations near the Mott transition in the two-dimensional (2D) Hubbard model are investigated by using cluster perturbation theory. The Mott transition is characterized by the loss of the spectral weight from the dispersing mode that leads continuously to the spin-wave excitation of the Mott insulator. The origins of the dominant modes of the 2D Hubbard model near the Mott transition can be traced back to those of the one-dimensional Hubbard model. Various anomalous spectral features observed in cuprate high-temperature superconductors, such as the pseudogap, Fermi arc, flat band, doping-induced states, hole pockets, and spinon-like and holon-like branches, as well as giant kink and waterfall in the dispersion relation, are explained in a unified manner as properties near the Mott transition in a 2D system.

  15. Titan-Like Exoplanets: Variations in Geometric Albedo and Effective Transit Height with Haze Production Rate

    NASA Technical Reports Server (NTRS)

    Checlair, Jade; McKay, Christopher P.; Imanaka, Hiroshi

    2016-01-01

    Extensive studies characterizing Titan present an opportunity to study the atmospheric properties of Titan-like exoplanets. Using an existing model of Titan's atmospheric haze, we computed geometric albedo spectra and effective transit height spectra for six values of the haze production rate (zero haze to twice present) over a wide range of wavelengths (0.2-2 microns). In the geometric albedo spectra, the slope in the UV-visible changes from blue to red when varying the haze production rate values from zero to twice the current Titan value. This spectral feature is the most effective way to characterize the haze production rates. Methane absorption bands in the visible-NIR compete with the absorbing haze, being more prominent for smaller haze production rates. The effective transit heights probe a region of the atmosphere where the haze and gas are optically thin and that is thus not effectively probed by the geometric albedo. The effective transit height decreases smoothly with increasing wavelength, from 376 km to 123 km at 0.2 and 2 microns, respectively. When decreasing the haze production rate, the methane absorption bands become more prominent, and the effective transit height decreases with a steeper slope with increasing wavelength. The slope of the geometric albedo in the UV-visible increases smoothly with increasing haze production rate, while the slope of the effective transit height spectra is not sensitive to the haze production rate other than showing a sharp rise when the haze production rate increases from zero. We conclude that geometric albedo spectra provide the most sensitive indicator of the haze production rate and the background Rayleigh gas. Our results suggest that important and complementary information can be obtained from the geometric albedo and motivates improvements in the technology for direct imaging of nearby exoplanets.

  16. Nature of phase transitions in Axelrod-like coupled Potts models in two dimensions

    NASA Astrophysics Data System (ADS)

    Gandica, Yerali; Chiacchiera, Silvia

    2016-03-01

    We study F coupled q -state Potts models in a two-dimensional square lattice. The interaction between the different layers is attractive to favor a simultaneous alignment in all of them, and its strength is fixed. The nature of the phase transition for zero field is numerically determined for F =2 ,3 . Using the Lee-Kosterlitz method, we find that it is continuous for F =2 and q =2 , whereas it is abrupt for higher values of q and/or F . When a continuous or a weakly first-order phase transition takes place, we also analyze the properties of the geometrical clusters. This allows us to determine the fractal dimension D of the incipient infinite cluster and to examine the finite-size scaling of the cluster number density via data collapse. A mean-field approximation of the model, from which some general trends can be determined, is presented too. Finally, since this lattice model has been recently considered as a thermodynamic counterpart of the Axelrod model of social dynamics, we discuss our results in connection with this one.

  17. Nature of phase transitions in Axelrod-like coupled Potts models in two dimensions.

    PubMed

    Gandica, Yerali; Chiacchiera, Silvia

    2016-03-01

    We study F coupled q-state Potts models in a two-dimensional square lattice. The interaction between the different layers is attractive to favor a simultaneous alignment in all of them, and its strength is fixed. The nature of the phase transition for zero field is numerically determined for F = 2,3. Using the Lee-Kosterlitz method, we find that it is continuous for F = 2 and q = 2, whereas it is abrupt for higher values of q and/or F. When a continuous or a weakly first-order phase transition takes place, we also analyze the properties of the geometrical clusters. This allows us to determine the fractal dimension D of the incipient infinite cluster and to examine the finite-size scaling of the cluster number density via data collapse. A mean-field approximation of the model, from which some general trends can be determined, is presented too. Finally, since this lattice model has been recently considered as a thermodynamic counterpart of the Axelrod model of social dynamics, we discuss our results in connection with this one.

  18. Diabetes insipidus-like state complicating percutaneous transluminal renal stenting for transplant renal artery stenosis.

    PubMed

    Tian, Lu; He, Yangyan; Zhang, Hongkun; Wu, Ziheng; Li, Donglin; Chen, Shanwen

    2014-07-01

    To report the incidence, etiology, and treatments of diabetes insipidus-like state that complicate percutaneous transluminal renal stenting (PTRS) for transplant renal artery stenosis (TRAS). Data from 7 patients on whom PTRS for TRAS was performed between October 2008 and March 2012 were reviewed retrospectively. The parameters investigated included blood flow velocity, blood pressure, and creatinine levels before and after the intervention. The procedural success rate was 100%. Three cases developed a diabetes insipidus-like state in the immediate postprocedural period. Urine output returned to normal within 2 weeks after treatment. The median blood flow velocity was significantly reduced from 4.51 m/sec (4.31-4.61 m/sec) at the time of TRAS diagnosis to 1.33 m/sec (1.31-1.51 m/sec) at the most recent follow-up of the group with a diabetes insipidus-like state. The ratio of median blood flow velocity before and after stenting in the group with a diabetes insipidus-like state was significantly higher than that in the group without a diabetes insipidus-like state (3.39 vs. 1.93). Diabetes insipidus-like state that complicates PTRS for TRAS is not an uncommon event, but appears to be underreported in the medical literature. A high ratio of pre- and poststenting median blood flow velocity may be a predictor for a postprocedural diabetes insipidus-like state. The most probable cause may be the marked increase in renal arterial flow. Early recognition of the condition is essential to avoid dehydration and electrolyte imbalance. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. Efficient dynamical correction of the transition state theory rate estimate for a flat energy barrier.

    PubMed

    Mökkönen, Harri; Ala-Nissila, Tapio; Jónsson, Hannes

    2016-09-07

    The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch between the initial and final state energy wells while the polymer beads undergo diffusive motion back and forth over the barrier. We present an efficient method for evaluating the correction factor by constructing a sequence of hyperplanes starting at the transition state and calculating the probability that the system advances from one hyperplane to another towards the product. This is analogous to what is done in forward flux sampling except that there the hyperplane sequence starts at the initial state. The method is applied to the escape of polymers with up to 64 beads from a potential well. For high temperature, the results are compared with direct Langevin dynamics simulations as well as forward flux sampling and excellent agreement between the three rate estimates is found. The use of a sequence of hyperplanes in the evaluation of the recrossing correction speeds up the calculation by an order of magnitude as compared with the traditional approach. As the temperature is lowered, the direct Langevin dynamics simulations as well as the forward flux simulations become computationally too demanding, while the harmonic transition state theory estimate corrected for recrossings can be calculated without significant increase in the computational effort.

  20. Methods used to parameterize the spatially-explicit components of a state-and-transition simulation model

    USGS Publications Warehouse

    Sleeter, Rachel; Acevedo, William; Soulard, Christopher E.; Sleeter, Benjamin M.

    2015-01-01

    Spatially-explicit state-and-transition simulation models of land use and land cover (LULC) increase our ability to assess regional landscape characteristics and associated carbon dynamics across multiple scenarios. By characterizing appropriate spatial attributes such as forest age and land-use distribution, a state-and-transition model can more effectively simulate the pattern and spread of LULC changes. This manuscript describes the methods and input parameters of the Land Use and Carbon Scenario Simulator (LUCAS), a customized state-and-transition simulation model utilized to assess the relative impacts of LULC on carbon stocks for the conterminous U.S. The methods and input parameters are spatially explicit and describe initial conditions (strata, state classes and forest age), spatial multipliers, and carbon stock density. Initial conditions were derived from harmonization of multi-temporal data characterizing changes in land use as well as land cover. Harmonization combines numerous national-level datasets through a cell-based data fusion process to generate maps of primary LULC categories. Forest age was parameterized using data from the North American Carbon Program and spatially-explicit maps showing the locations of past disturbances (i.e. wildfire and harvest). Spatial multipliers were developed to spatially constrain the location of future LULC transitions. Based on distance-decay theory, maps were generated to guide the placement of changes related to forest harvest, agricultural intensification/extensification, and urbanization. We analyze the spatially-explicit input parameters with a sensitivity analysis, by showing how LUCAS responds to variations in the model input. This manuscript uses Mediterranean California as a regional subset to highlight local to regional aspects of land change, which demonstrates the utility of LUCAS at many scales and applications.

  1. Relaxation mode analysis and Markov state relaxation mode analysis for chignolin in aqueous solution near a transition temperature

    NASA Astrophysics Data System (ADS)

    Mitsutake, Ayori; Takano, Hiroshi

    2015-09-01

    It is important to extract reaction coordinates or order parameters from protein simulations in order to investigate the local minimum-energy states and the transitions between them. The most popular method to obtain such data is principal component analysis, which extracts modes of large conformational fluctuations around an average structure. We recently applied relaxation mode analysis for protein systems, which approximately estimates the slow relaxation modes and times from a simulation and enables investigations of the dynamic properties underlying the structural fluctuations of proteins. In this study, we apply this relaxation mode analysis to extract reaction coordinates for a system in which there are large conformational changes such as those commonly observed in protein folding/unfolding. We performed a 750-ns simulation of chignolin protein near its folding transition temperature and observed many transitions between the most stable, misfolded, intermediate, and unfolded states. We then applied principal component analysis and relaxation mode analysis to the system. In the relaxation mode analysis, we could automatically extract good reaction coordinates. The free-energy surfaces provide a clearer understanding of the transitions not only between local minimum-energy states but also between the folded and unfolded states, even though the simulation involved large conformational changes. Moreover, we propose a new analysis method called Markov state relaxation mode analysis. We applied the new method to states with slow relaxation, which are defined by the free-energy surface obtained in the relaxation mode analysis. Finally, the relaxation times of the states obtained with a simple Markov state model and the proposed Markov state relaxation mode analysis are compared and discussed.

  2. Metformin inhibits TGF-β1-induced epithelial-to-mesenchymal transition-like process and stem-like properties in GBM via AKT/mTOR/ZEB1 pathway.

    PubMed

    Song, Yang; Chen, Yong; Li, Yunqian; Lyu, Xiaoyan; Cui, Jiayue; Cheng, Ye; Zhao, Liyan; Zhao, Gang

    2018-01-23

    Glioblastoma (GBM) is the most frequent and aggressive brain tumor in adults. In spite of advances in diagnosis and therapy, the prognosis is still relatively poor. The invasive property of GBM is the major cause of death in patients. Epithelial-to-mesenchymal transition-like process (EMT-like process) is considered to play an important role in the invasive property. Metformin has been reported as a regulator of EMT-like process. In this study, we confirmed that metformin inhibited TGF-β1-induced EMT-like process and EMT-associated migration and invasion in LN18 and U87 GBM cells. Our results also showed that metformin significantly suppressed self-renewal capacity of glioblastoma stem cells (GSCs), and expression of stem cell markers Bmi1, Sox2 and Musashi1, indicating that metformin can inhibit cancer stem-like properties of GBM cells. We further clarified that metformin specifically inhibited TGF-β1 activated AKT, the downstream molecular mTOR and the leading transcription factor ZEB1. Taken together, our data demonstrate that metformin inhibits TGF-β1-induced EMT-like process and cancer stem-like properties in GBM cells via AKT/mTOR/ZEB1 pathway and provide evidence of metformin for further clinical investigation targeted GBM.

  3. A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Nguyen, Trong-Nghia; Department of Physical Chemistry, Hanoi University of Science and Technology, Hanoi; Putikam, Raghunath

    2015-03-28

    We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH{sub 2}OO and anti/syn-CH{sub 3}C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH{sub 2}OO and anti-CH{sub 3}C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH{sub 3}C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C–H bonds. For syn-CH{sub 3}C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH{sub 3} groupmore » by the terminal O atom producing CH{sub 2}C(H)O–OH. At 298 K, the intramolecular insertion process in CH{sub 2}OO was found to be 600 times faster than the commonly assumed ring-closing reaction.« less

  4. Ab initio MCHF structural calculations of Mg-like cerium

    NASA Astrophysics Data System (ADS)

    Wajid, Abdul; Jabeen, S.; Husain, Abid

    2018-05-01

    Energy levels and emission line wavelengths of high-Z materials are useful for impurity diagnostics in the next generation fusion devices. For this here we have calculated E1, M2 transitions, oscillator strengths, and transition probabilities for transitions among the terms belonging to the 2p63s2, 2p63s3p, 2p63p2 and 2p63s3d for the Magnesium like cerium (Ce XLVII) using the GRASP2K package based on the fully relativistic multi-configuration Dirac-Fock method. The electron correlation effects, Breit interaction and quantum electrodynamics effects to the atomic state wave functions and the corresponding energies have been taken into account.

  5. Manganese Deficiency Leads to Genotype-Specific Changes in Fluorescence Induction Kinetics and State Transitions1[C][OA

    PubMed Central

    Husted, Søren; Laursen, Kristian H.; Hebbern, Christopher A.; Schmidt, Sidsel B.; Pedas, Pai; Haldrup, Anna; Jensen, Poul E.

    2009-01-01

    Barley (Hordeum vulgare) genotypes display a marked difference in their ability to tolerate growth at low manganese (Mn) concentrations, a phenomenon designated as differential Mn efficiency. Induction of Mn deficiency in two genotypes differing in Mn efficiency led to a decline in the quantum yield efficiency for both, although faster in the Mn-inefficient genotype. Leaf tissue and thylakoid Mn concentrations were reduced under Mn deficiency, but no difference between genotypes was observed and no visual Mn deficiency symptoms were developed. Analysis of the fluorescence induction kinetics revealed that in addition to the usual O-J-I-P steps, clear K and D steps were developed in the Mn-inefficient genotype under Mn deficiency. These marked changes indicated damages to photosystem II (PSII). This was further substantiated by state transition measurements, indicating that the ability of plants to redistribute excitation energy was reduced. The percentage change in state transitions for control plants with normal Mn supply of both genotypes was 9% to 11%. However, in Mn-deficient leaves of the Mn-inefficient genotypes, state transitions were reduced to less than 1%, whereas no change was observed for the Mn-efficient genotypes. Immunoblotting and the chlorophyll a/b ratio confirmed that Mn deficiency in general resulted in a significant reduction in abundance of PSII reaction centers relative to the peripheral antenna. In addition, PSII appeared to be significantly more affected by Mn limitation than PSI. However, the striking genotypic differences observed in Mn-deficient plants, when analyzing state transitions and fluorescence induction kinetics, could not be correlated with specific changes in photosystem proteins. Thus, there is no simple linkage between protein expression and the differential reduction in state transition and fluorescence induction kinetics observed for the genotypes under Mn deficiency. PMID:19369593

  6. On the Ising character of the quantum-phase transition in LiHoF4

    NASA Astrophysics Data System (ADS)

    Skomski, R.

    2016-05-01

    It is investigated how a transverse magnetic field affects the quantum-mechanical character of LiHoF4, a system generally considered as a textbook example for an Ising-like quantum-phase transition. In small magnetic fields, the low-temperature behavior of the ions is Ising-like, involving the nearly degenerate low-lying Jz = ± 8 doublet. However, as the transverse field increases, there is a substantial admixture of states having |Jz| < 8. Near the quantum-phase-transition field, the system is distinctively non-Ising like, and all Jz eigenstates yield ground-state contributions of comparable magnitude. A classical analog to this mechanism is the micromagnetic single point in magnets with uniaxial anisotropy. Since Ho3+ has J = 8, the ion's behavior is reminiscent of the classical limit (J = ∞), but quantum corrections remain clearly visible.

  7. GaAs-oxide interface states - Gigantic photoionization via Auger-like process

    NASA Technical Reports Server (NTRS)

    Lagowski, J.; Kazior, T. E.; Gatos, H. C.; Walukiewicz, W.; Siejka, J.

    1981-01-01

    Spectral and transient responses of photostimulated current in MOS structures were employed for the study of GaAs-anodic oxide interface states. Discrete deep traps at 0.7 and 0.85 eV below the conduction band were found with concentrations of 5 x 10 to the 12th/sq cm and 7 x 10 to the 11th/sq cm, respectively. These traps coincide with interface states induced on clean GaAs surfaces by oxygen and/or metal adatoms (submonolayer coverage). In contrast to surfaces with low oxygen coverage, the GaAs-thick oxide interfaces exhibited a high density (about 10 to the 14th/sq cm) of shallow donors and acceptors. Photoexcitation of these donor-acceptor pairs led to a gigantic photoionization of deep interface states with rates 1000 times greater than direct transitions into the conduction band. The gigantic photoionization is explained on the basis of energy transfer from excited donor-acceptor pairs to deep states.

  8. Equation of state and QCD transition at finite temperature

    NASA Astrophysics Data System (ADS)

    Bazavov, A.; Bhattacharya, T.; Cheng, M.; Christ, N. H.; Detar, C.; Ejiri, S.; Gottlieb, Steven; Gupta, R.; Heller, U. M.; Huebner, K.; Jung, C.; Karsch, F.; Laermann, E.; Levkova, L.; Miao, C.; Mawhinney, R. D.; Petreczky, P.; Schmidt, C.; Soltz, R. A.; Soeldner, W.; Sugar, R.; Toussaint, D.; Vranas, P.

    2009-07-01

    We calculate the equation of state in 2+1 flavor QCD at finite temperature with physical strange quark mass and almost physical light quark masses using lattices with temporal extent Nτ=8. Calculations have been performed with two different improved staggered fermion actions, the asqtad and p4 actions. Overall, we find good agreement between results obtained with these two O(a2) improved staggered fermion discretization schemes. A comparison with earlier calculations on coarser lattices is performed to quantify systematic errors in current studies of the equation of state. We also present results for observables that are sensitive to deconfining and chiral aspects of the QCD transition on Nτ=6 and 8 lattices. We find that deconfinement and chiral symmetry restoration happen in the same narrow temperature interval. In an appendix we present a simple parametrization of the equation of state that can easily be used in hydrodynamic model calculations. In this parametrization we include an estimate of current uncertainties in the lattice calculations which arise from cutoff and quark mass effects.

  9. Vibrational states and optical transitions in hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Johannsen, P. G.

    1998-03-01

    Proton energies in hydrogen bonds are mostly calculated using a double Morse potential (the DMP model). This form, however, does not reproduce the experimentally observed correlation between the proton stretching frequency and the bond length in an extended bond-length region sufficiently well. An alternative potential is proposed in the present paper. The quantum states of this non-symmetric double-well potential are calculated numerically using the Numerov (Fox-Goodwin) algorithm. It is shown that the optical spectra of hydrogen bonds in various substances can be well approximated on the basis of the transition frequencies and intensities predicted by the present model. For weakly interacting OH impurities in 0953-8984/10/10/008/img1, the overtone spectrum and line intensities are well reproduced, whereas the line broadenings and the decrease of the fundamental stretching frequencies in intermediate and strong hydrogen bonds are traced back to the influence of the reduced height of the central barrier. The model is also extrapolated to the range of symmetric hydrogen bonds, and the calculated transition frequencies are discussed with respect to most recent infra-red experiments on ice under strong compression. A possible artificial infra-red signal from strained diamond anvils is thereby noted.

  10. Spatiotemporal dynamics of HSV genome nuclear entry and compaction state transitions using bioorthogonal chemistry and super-resolution microscopy

    PubMed Central

    2017-01-01

    We investigated the spatiotemporal dynamics of HSV genome transport during the initiation of infection using viruses containing bioorthogonal traceable precursors incorporated into their genomes (HSVEdC). In vitro assays revealed a structural alteration in the capsid induced upon HSVEdC binding to solid supports that allowed coupling to external capture agents and demonstrated that the vast majority of individual virions contained bioorthogonally-tagged genomes. Using HSVEdC in vivo we reveal novel aspects of the kinetics, localisation, mechanistic entry requirements and morphological transitions of infecting genomes. Uncoating and nuclear import was observed within 30 min, with genomes in a defined compaction state (ca. 3-fold volume increase from capsids). Free cytosolic uncoated genomes were infrequent (7–10% of the total uncoated genomes), likely a consequence of subpopulations of cells receiving high particle numbers. Uncoated nuclear genomes underwent temporal transitions in condensation state and while ICP4 efficiently associated with condensed foci of initial infecting genomes, this relationship switched away from residual longer lived condensed foci to increasingly decondensed genomes as infection progressed. Inhibition of transcription had no effect on nuclear entry but in the absence of transcription, genomes persisted as tightly condensed foci. Ongoing transcription, in the absence of protein synthesis, revealed a distinct spatial clustering of genomes, which we have termed genome congregation, not seen with non-transcribing genomes. Genomes expanded to more decondensed forms in the absence of DNA replication indicating additional transitional steps. During full progression of infection, genomes decondensed further, with a diffuse low intensity signal dissipated within replication compartments, but frequently with tight foci remaining peripherally, representing unreplicated genomes or condensed parental strands of replicated DNA. Uncoating and nuclear

  11. The transiting dust clumps in the evolved disc of the Sun-like UXor RZ Psc

    PubMed Central

    Kenworthy, Matthew A.; Pepper, Joshua; Rodriguez, Joseph E.; Siverd, Robert J.; Stassun, Keivan G.; Wyatt, Mark C.

    2017-01-01

    RZ Psc is a young Sun-like star, long associated with the UXor class of variable stars, which is partially or wholly dimmed by dust clumps several times each year. The system has a bright and variable infrared excess, which has been interpreted as evidence that the dimming events are the passage of asteroidal fragments in front of the host star. Here, we present a decade of optical photometry of RZ Psc and take a critical look at the asteroid belt interpretation. We show that the distribution of light curve gradients is non-uniform for deep events, which we interpret as possible evidence for an asteroidal fragment-like clump structure. However, the clumps are very likely seen above a high optical depth midplane, so the disc’s bulk clumpiness is not revealed. While circumstantial evidence suggests an asteroid belt is more plausible than a gas-rich transition disc, the evolutionary status remains uncertain. We suggest that the rarity of Sun-like stars showing disc-related variability may arise because (i) any accretion streams are transparent and/or (ii) turbulence above the inner rim is normally shadowed by a flared outer disc. PMID:28280566

  12. The transiting dust clumps in the evolved disc of the Sun-like UXor RZ Psc

    NASA Astrophysics Data System (ADS)

    Kennedy, Grant M.; Kenworthy, Matthew A.; Pepper, Joshua; Rodriguez, Joseph E.; Siverd, Robert J.; Stassun, Keivan G.; Wyatt, Mark C.

    2017-01-01

    RZ Psc is a young Sun-like star, long associated with the UXor class of variable stars, which is partially or wholly dimmed by dust clumps several times each year. The system has a bright and variable infrared excess, which has been interpreted as evidence that the dimming events are the passage of asteroidal fragments in front of the host star. Here, we present a decade of optical photometry of RZ Psc and take a critical look at the asteroid belt interpretation. We show that the distribution of light curve gradients is non-uniform for deep events, which we interpret as possible evidence for an asteroidal fragment-like clump structure. However, the clumps are very likely seen above a high optical depth midplane, so the disc's bulk clumpiness is not revealed. While circumstantial evidence suggests an asteroid belt is more plausible than a gas-rich transition disc, the evolutionary status remains uncertain. We suggest that the rarity of Sun-like stars showing disc-related variability may arise because (i) any accretion streams are transparent and/or (ii) turbulence above the inner rim is normally shadowed by a flared outer disc.

  13. The transiting dust clumps in the evolved disc of the Sun-like UXor RZ Psc.

    PubMed

    Kennedy, Grant M; Kenworthy, Matthew A; Pepper, Joshua; Rodriguez, Joseph E; Siverd, Robert J; Stassun, Keivan G; Wyatt, Mark C

    2017-01-01

    RZ Psc is a young Sun-like star, long associated with the UXor class of variable stars, which is partially or wholly dimmed by dust clumps several times each year. The system has a bright and variable infrared excess, which has been interpreted as evidence that the dimming events are the passage of asteroidal fragments in front of the host star. Here, we present a decade of optical photometry of RZ Psc and take a critical look at the asteroid belt interpretation. We show that the distribution of light curve gradients is non-uniform for deep events, which we interpret as possible evidence for an asteroidal fragment-like clump structure. However, the clumps are very likely seen above a high optical depth midplane, so the disc's bulk clumpiness is not revealed. While circumstantial evidence suggests an asteroid belt is more plausible than a gas-rich transition disc, the evolutionary status remains uncertain. We suggest that the rarity of Sun-like stars showing disc-related variability may arise because (i) any accretion streams are transparent and/or (ii) turbulence above the inner rim is normally shadowed by a flared outer disc.

  14. Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble

    PubMed Central

    Fisher, Kaitlin M.; Haglund, Ellinor; Noel, Jeffrey K.; Hailey, Kendra L.; Onuchic, José N.; Jennings, Patricia A.

    2015-01-01

    Interleukin-33 (IL-33) is currently the focus of multiple investigations into targeting pernicious inflammatory disorders. This mediator of inflammation plays a prevalent role in chronic disorders such as asthma, rheumatoid arthritis, and progressive heart disease. In order to better understand the possible link between the folding free energy landscape and functional regions in IL-33, a combined experimental and theoretical approach was applied. IL-33 is a pseudo- symmetrical protein composed of three distinct structural elements that complicate the folding mechanism due to competition for nucleation on the dominant folding route. Trefoil 1 constitutes the majority of the binding interface with the receptor whereas Trefoils 2 and 3 provide the stable scaffold to anchor Trefoil 1. We identified that IL-33 folds with a three-state mechanism, leading to a rollover in the refolding arm of its chevron plots in strongly native conditions. In addition, there is a second slower refolding phase that exhibits the same rollover suggesting similar limitations in folding along parallel routes. Characterization of the intermediate state and the rate limiting steps required for folding suggests that the rollover is attributable to a moving transition state, shifting from a post- to pre-intermediate transition state as you move from strongly native conditions to the midpoint of the transition. On a structural level, we found that initially, all independent Trefoil units fold equally well until a QCA of 0.35 when Trefoil 1 will backtrack in order to allow Trefoils 2 and 3 to fold in the intermediate state, creating a stable scaffold for Trefoil 1 to fold onto during the final folding transition. The formation of this intermediate state and subsequent moving transition state is a result of balancing the difficulty in folding the functionally important Trefoil 1 onto the remainder of the protein. Taken together our results indicate that the functional element of the protein is

  15. Domain Walls and Macroscopic Spin-Flip-Like States in GdxCo1-x/GdyCo1-y Bilayers

    NASA Astrophysics Data System (ADS)

    Martin, Jose I.

    2005-03-01

    Exchange coupled double layers (ECDL) made of rare earth -- transition metal amorphous alloys are of basic and technological interest, as they present different magnetization configurations when the composition is changed or when the temperature is varied crossing the compensation temperatures (Tcomp) of both ferrimagnetic alloys. In this work, amorphous GdxCo1-x(100 nm)/GdyCo1-y(100 nm) ECDL have been prepared to investigate the magnetization reversal and the stable magnetic configurations when the compositions of both layers are similar: x = 0.22, y = 0.24. The samples have been grown by co-sputtering on corning glass substrates, which has allowed to analyze the behaviour within each layer by transverse Kerr effect measurements. A rich variety of behaviours has been found in the temperature range between the Tcomp of both layers, including magnetization reversal by annihilation/creation of a Bloch wall across the sample thickness, and a macroscopic spin-flip-like metamagnetic state where the magnetic moments form a double antiferromagnetic state with the presence of a N'eel-like wall when the magnetizations of both layers are similar [1]. The whole observed behavior can be understood in terms of a deduced general magnetic field -- temperature phase diagram. [1] R. Morales et al. Phys. Rev. B 70, 174440 (2004). Work supported by Spanish CICYT.

  16. Anchoring transition metal elements on graphene-like ZnO monolayer by CO molecule to obtain spin gapless semiconductor

    NASA Astrophysics Data System (ADS)

    Lei, Jie; Xu, Ming-Chun; Hu, Shu-Jun

    2017-09-01

    Graphene-like zinc oxide monolayer (g-ZnO) is a newfound two-dimensional material. Here we utilize the transition metal (TM) elements (Cr, Mn, Fe, Co, Ni, and Cu) to functionalize the g-ZnO with the aim of designing novel spintronics materials by using first-principles calculations. Our results show that although the adsorption of TM atoms can endow g-ZnO with magnetization and impurity states in the bandgap, the interaction between TM elements and g-ZnO is weak. We found that the attachment of CO molecule on TM is able to stabilize the TM elements on g-ZnO based on the 'donation and back-donation' mechanism. As a result, the adsorption energy of the CO-TM complex on g-ZnO is as high as 1.41-2.11 eV. Furthermore, the incorporation of CO molecule modulates the magnetic and electronic properties of the TM-decorated g-ZnO. In particular, the CO-Mn-g-ZnO is predicted to be a spin gapless semiconductor.

  17. GH therapy in transition age: state of the art and future perspectives.

    PubMed

    Cappa, M; Caruso, M; Saggese, G; Salerno, M C; Tonini, G

    2015-03-01

    Growth hormone (GH) has been recently approved by the Italian Health Authorities for use in transition patients with childhood onset-growth hormone deficiency (CO-GHD). GH in addition to promote linear growth influences several key metabolic processes. In particular, in the transition period, from late adolescent to early adulthood, GH plays an important role in the achievement of a complete somatic development including body composition, muscle mass maturation, full skeletal mineralization and reproductive maturation, as well as in the prevention of metabolic and cardiovascular risk. Therefore, GH replacement should be restarted if a GH stimulation test at the re-evaluation fulfills established criteria. Endocrinologists experienced in the care of GHD adolescent patients held a workshop in Rome, Italy in July 2012 to review in detail the literature data and compare experiences of five Italian endocrinological centers on the negative consequences of interrupting GH treatment and the positive effects of continued GH replacement on intermediary metabolism, heart, muscle, pubertal development, and bone. The aim of the meeting was to delineate the state of the art on GH therapy in transition age and provide suggestions to pediatric and adult endocrinologists for a smooth transition care.

  18. Signature of chaos in the 4 f -core-excited states for highly-charged tungsten ions

    NASA Astrophysics Data System (ADS)

    Safronova, Ulyana; Safronova, Alla

    2014-05-01

    We evaluate radiative and autoionizing transition rates in highly charged W ions in search for the signature of chaos. In particularly, previously published results for Ag-like W27+, Tm-like W5+, and Yb-like W4+ ions as well as newly obtained for I-like W21+, Xe-like W20+, Cs-like W19+, and La-like W17+ ions (with ground configuration [Kr] 4d10 4fk with k = 7, 8, 9, and 11, respectively) are considered that were calculated using the multiconfiguration relativistic Hebrew University Lawrence Livermore Atomic Code (HULLAC code) and the Hartree-Fock-Relativistic method (COWAN code). The main emphasis was on verification of Gaussian statistics of rates as a function of transition energy. There was no evidence of such statistics for above mentioned previously published results as well as for the transitions between the excited and autoionizing states for newly calculated results. However, we did find the Gaussian profile for the transitions between excited states such as the [Kr] 4d10 4fk - [Kr] 4d10 4f k - 1 5 d transitions , for newly calculated W ions. This work is supported in part by DOE under NNSA Cooperative Agreement DE-NA0001984.

  19. Pressure-induced magneto-structural transition in iron via a modified solid-state nudged elastic band method

    NASA Astrophysics Data System (ADS)

    Zarkevich, Nikolai A.; Johnson, Duane D.

    2015-03-01

    Materials under pressure may exhibit critical electronic and structural transitions that affect equation of states, as known for superconductors and the magneto-structural transformations of iron with both geophysical and planetary implications. While experiments often use constant-pressure (diamond-anvil cell, DAC) measurements, many theoretical results address a constant-volume transitions, which avoid issues with magnetic collapse but cannot be directly compared to experiment. We establish a modified solid-state nudge elastic band (MSS-NEB) method to handle magnetic systems that may exhibit moment (and volume) collapse during transformation. We apply it to the pressure-induced transformation in iron between the low-pressure body-centered cubic (bcc) and the high-pressure hexagonal close-packed (hcp) phases, find the bcc-hcp equilibrium coexistence pressure and a transitional pathway, and compare to shock and DAC experiments. We use methods developed with support by the U.S. Department of Energy (DE-FG02-03ER46026 and DE-AC02-07CH11358). Ames Laboratory is operated for the DOE by Iowa State University under contract DE-AC02-07CH11358.

  20. Improved transition path sampling methods for simulation of rare events

    NASA Astrophysics Data System (ADS)

    Chopra, Manan; Malshe, Rohit; Reddy, Allam S.; de Pablo, J. J.

    2008-04-01

    The free energy surfaces of a wide variety of systems encountered in physics, chemistry, and biology are characterized by the existence of deep minima separated by numerous barriers. One of the central aims of recent research in computational chemistry and physics has been to determine how transitions occur between deep local minima on rugged free energy landscapes, and transition path sampling (TPS) Monte-Carlo methods have emerged as an effective means for numerical investigation of such transitions. Many of the shortcomings of TPS-like approaches generally stem from their high computational demands. Two new algorithms are presented in this work that improve the efficiency of TPS simulations. The first algorithm uses biased shooting moves to render the sampling of reactive trajectories more efficient. The second algorithm is shown to substantially improve the accuracy of the transition state ensemble by introducing a subset of local transition path simulations in the transition state. The system considered in this work consists of a two-dimensional rough energy surface that is representative of numerous systems encountered in applications. When taken together, these algorithms provide gains in efficiency of over two orders of magnitude when compared to traditional TPS simulations.

  1. First-Class State Change in Plaid

    DTIC Science & Technology

    2011-10-01

    conceptual state change. State change is pervasive in the natural world; as a dramatic example, consider the state transition from egg, to caterpillar ...All this raises a natural question: why not support abstract states in programming languages? We previously proposed Typestate-Oriented Programming as...well as trait-like state composition. Plaid has been implemented, and has proven effective for writing a diverse set of small and medium- sized (up to

  2. Physiologic Measures of Animal Stress during Transitional States of Consciousness

    PubMed Central

    Meyer, Robert E.

    2015-01-01

    Simple Summary The humaneness, and therefore suitability, of any particular agent or method used to produce unconsciousness in animals, whether for anesthesia, euthanasia, humane slaughter, or depopulation, depends on the experience of pain or distress prior to loss of consciousness. Commonly reported physiologic measures of animal stress, including physical movement and vocalization, heart rate and ECG, electroencephalographic activity, and plasma and neuronal stress markers are discussed within this context. Abstract Determination of the humaneness of methods used to produce unconsciousness in animals, whether for anesthesia, euthanasia, humane slaughter, or depopulation, relies on our ability to assess stress, pain, and consciousness within the contexts of method and application. Determining the subjective experience of animals during transitional states of consciousness, however, can be quite difficult; further, loss of consciousness with different agents or methods may occur at substantially different rates. Stress and distress may manifest behaviorally (e.g., overt escape behaviors, approach-avoidance preferences [aversion]) or physiologically (e.g., movement, vocalization, changes in electroencephalographic activity, heart rate, sympathetic nervous system [SNS] activity, hypothalamic-pituitary axis [HPA] activity), such that a one-size-fits-all approach cannot be easily applied to evaluate methods or determine specific species applications. The purpose of this review is to discuss methods of evaluating stress in animals using physiologic methods, with emphasis on the transition between the conscious and unconscious states. PMID:26479382

  3. Relativistic many-body calculation of energies, transition rates, lifetimes, and multipole polarizabilities in Cs-like La iii

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

    Excitation energies of the [Xe]nd (n =5-9), [Xe]ns (n =6-10), [Xe]np (n =6-9), [Xe]nf (n =4-8), and [Xe]ng (n =5-8) states in La iii, where [Xe] = 1s22s22p63s23p63d104s24p64d105s25p6, are evaluated. Electric dipole matrix elements for the allowed transitions between the low-lying [Xe]nd, [Xe]ns, [Xe]np, [Xe]nf, and [Xe]ng states in the La iii ion are calculated using the high-precision relativistic all-order method where all single, double, and partial triple excitations of the Dirac-Fock wave functions are included to all orders of perturbation theory. Recommended values are provided for a large number of electric dipole matrix elements, oscillator strengths, transition rates, and lifetimes. Scalar and tensor polarizabilities of the states listed above are evaluated. The uncertainties of the recommended values are estimated. Electric quadrupole and magnetic dipole matrix elements are calculated to determine lifetimes of the 5d5/2 and 6s metastable levels. The ground-state E1, E2, and E3 static polarizabilities are calculated. This work provides recommended values critically evaluated for their accuracy for a number of La iii atomic properties for use in planning and analysis of various experiments as well as theoretical modeling.

  4. Transition Dipole Moments and Transition Probabilities of the CN Radical

    NASA Astrophysics Data System (ADS)

    Yin, Yuan; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2018-04-01

    This paper studies the transition probabilities of electric dipole transitions between 10 low-lying states of the CN radical. These states are X2Σ+, A2Π, B2Σ+, a4Σ+, b4Π, 14Σ‑, 24Π, 14Δ, 16Σ+, and 16Π. The potential energy curves are calculated using the CASSCF method, which is followed by the icMRCI approach with the Davidson correction. The transition dipole moments between different states are calculated. To improve the accuracy of potential energy curves, core–valence correlation and scalar relativistic corrections, as well as the extrapolation of potential energies to the complete basis set limit are included. The Franck–Condon factors and Einstein coefficients of emissions are calculated. The radiative lifetimes are determined for the vibrational levels of the A2Π, B2Σ+, b4Π, 14Σ‑, 24Π, 14Δ, and 16Π states. According to the transition probabilities and radiative lifetimes, some guidelines for detecting these states spectroscopically are proposed. The spin–orbit coupling effect on the spectroscopic and vibrational properties is evaluated. The splitting energy in the A2Π state is determined to be 50.99 cm‑1, which compares well with the experimental ones. The potential energy curves, transition dipole moments, spectroscopic parameters, and transition probabilities reported in this paper can be considered to be very reliable. The results obtained here can be used as guidelines for detecting these transitions, in particular those that have not been measured in previous experiments or have not been observed in the Sun, comets, stellar atmospheres, dark interstellar clouds, and diffuse interstellar clouds.

  5. A universal indicator of critical state transitions in noisy complex networked systems

    PubMed Central

    Liang, Junhao; Hu, Yanqing; Chen, Guanrong; Zhou, Tianshou

    2017-01-01

    Critical transition, a phenomenon that a system shifts suddenly from one state to another, occurs in many real-world complex networks. We propose an analytical framework for exactly predicting the critical transition in a complex networked system subjected to noise effects. Our prediction is based on the characteristic return time of a simple one-dimensional system derived from the original higher-dimensional system. This characteristic time, which can be easily calculated using network data, allows us to systematically separate the respective roles of dynamics, noise and topology of the underlying networked system. We find that the noise can either prevent or enhance critical transitions, playing a key role in compensating the network structural defect which suffers from either internal failures or environmental changes, or both. Our analysis of realistic or artificial examples reveals that the characteristic return time is an effective indicator for forecasting the sudden deterioration of complex networks. PMID:28230166

  6. Transitions between strongly correlated and random steady-states for catalytic CO-oxidation on surfaces at high-pressure

    DOE PAGES

    Liu, Da -Jiang; Evans, James W.

    2015-04-02

    We explore simple lattice-gas reaction models for CO-oxidation on 1D and 2D periodic arrays of surface adsorption sites. The models are motivated by studies of CO-oxidation on RuO 2(110) at high-pressures. Although adspecies interactions are neglected, the effective absence of adspecies diffusion results in kinetically-induced spatial correlations. A transition occurs from a random mainly CO-populated steady-state at high CO-partial pressure p CO, to a strongly-correlated near-O-covered steady-state for low p CO as noted. In addition, we identify a second transition to a random near-O-covered steady-state at very low p CO.

  7. Semi-Markov models for interval censored transient cognitive states with back transitions and a competing risk

    PubMed Central

    Wei, Shaoceng; Kryscio, Richard J.

    2015-01-01

    Continuous-time multi-state stochastic processes are useful for modeling the flow of subjects from intact cognition to dementia with mild cognitive impairment and global impairment as intervening transient, cognitive states and death as a competing risk (Figure 1). Each subject's cognition is assessed periodically resulting in interval censoring for the cognitive states while death without dementia is not interval censored. Since back transitions among the transient states are possible, Markov chains are often applied to this type of panel data. In this manuscript we apply a Semi-Markov process in which we assume that the waiting times are Weibull distributed except for transitions from the baseline state, which are exponentially distributed and in which we assume no additional changes in cognition occur between two assessments. We implement a quasi-Monte Carlo (QMC) method to calculate the higher order integration needed for likelihood estimation. We apply our model to a real dataset, the Nun Study, a cohort of 461 participants. PMID:24821001

  8. Semi-Markov models for interval censored transient cognitive states with back transitions and a competing risk.

    PubMed

    Wei, Shaoceng; Kryscio, Richard J

    2016-12-01

    Continuous-time multi-state stochastic processes are useful for modeling the flow of subjects from intact cognition to dementia with mild cognitive impairment and global impairment as intervening transient cognitive states and death as a competing risk. Each subject's cognition is assessed periodically resulting in interval censoring for the cognitive states while death without dementia is not interval censored. Since back transitions among the transient states are possible, Markov chains are often applied to this type of panel data. In this manuscript, we apply a semi-Markov process in which we assume that the waiting times are Weibull distributed except for transitions from the baseline state, which are exponentially distributed and in which we assume no additional changes in cognition occur between two assessments. We implement a quasi-Monte Carlo (QMC) method to calculate the higher order integration needed for likelihood estimation. We apply our model to a real dataset, the Nun Study, a cohort of 461 participants. © The Author(s) 2014.

  9. Update: Transitional Bilingual Instruction Program (TBIP), 2012-2013

    ERIC Educational Resources Information Center

    Malagon, Helen; McCold, Paul; Nelson, Joan Johnston

    2013-01-01

    This report provides an update on the Transitional Bilingual Instruction Program (TBIP). In 2012-13, 104,025 English language learners (ELLs) received state services through the TBIP. This was an increase of just over 9% from the previous year. Most students live in urban areas along Interstate 5 corridor and in rural areas like the Yakima Valley.…

  10. Evaluating transition state structures of vanadium-phosphatase protein complexes using shape analysis.

    PubMed

    Sánchez-Lombardo, Irma; Alvarez, Santiago; McLauchlan, Craig C; Crans, Debbie C

    2015-06-01

    Shape analysis of coordination complexes is well-suited to evaluate the subtle distortions in the trigonal bipyramidal (TBPY-5) geometry of vanadium coordinated in the active site of phosphatases and characterized by X-ray crystallography. Recent studies using the tau (τ) analysis support the assertion that vanadium is best described as a trigonal bipyramid, because this geometry is the ideal transition state geometry of the phosphate ester substrate hydrolysis (C.C. McLauchlan, B.J. Peters, G.R. Willsky, D.C. Crans, Coord. Chem. Rev. http://dx.doi.org/10.1016/j.ccr.2014.12.012 ; D.C. Crans, M.L. Tarlton, C.C. McLauchlan, Eur. J. Inorg. Chem. 2014, 4450-4468). Here we use continuous shape measures (CShM) analysis to investigate the structural space of the five-coordinate vanadium-phosphatase complexes associated with mechanistic transformations between the tetrahedral geometry and the five-coordinate high energy TBPY-5 geometry was discussed focusing on the protein tyrosine phosphatase 1B (PTP1B) enzyme. No evidence for square pyramidal geometries was observed in any vanadium-protein complexes. The shape analysis positioned the metal ion and the ligands in the active site reflecting the mechanism of the cleavage of the organic phosphate in a phosphatase. We identified the umbrella distortions to be directly on the reaction path between tetrahedral phosphate and the TBPY-5-types of high-energy species. The umbrella distortions of the trigonal bipyramid are therefore identified as being the most relevant types of transition state structures for the phosphoryl group transfer reactions for phosphatases and this may be related to the possibility that vanadium is an inhibitor for enzymes that support both exploded and five-coordinate transition states. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Hydrogen-bonded intermediates and transition states during spontaneous and acid-catalyzed hydrolysis of the carcinogen (+)-anti-BPDE.

    PubMed

    Palenik, Mark C; Rodriguez, Jorge H

    2014-07-07

    Understanding mechanisms of (+)-anti-BPDE detoxification is crucial for combating its mutagenic and potent carcinogenic action. However, energetic-structural correlations of reaction intermediates and transition states during detoxification via hydrolysis are poorly understood. To gain mechanistic insight we have computationally characterized intermediate and transition species associated with spontaneous and general-acid catalyzed hydrolysis of (+)-anti-BPDE. We studied the role of cacodylic acid as a proton donor in the rate limiting step. The computed activation energy (ΔG‡) is in agreement with the experimental value for hydrolysis in a sodium cacodylate buffer. Both types of, spontaneous and acid catalyzed, BPDE hydrolysis can proceed through low-entropy hydrogen bonded intermediates prior to formation of transition states whose energies determine reaction activation barriers and rates.

  12. Empirical models of transitions between coral reef states: effects of region, protection, and environmental change.

    PubMed

    Lowe, Phillip K; Bruno, John F; Selig, Elizabeth R; Spencer, Matthew

    2011-01-01

    There has been substantial recent change in coral reef communities. To date, most analyses have focussed on static patterns or changes in single variables such as coral cover. However, little is known about how community-level changes occur at large spatial scales. Here, we develop Markov models of annual changes in coral and macroalgal cover in the Caribbean and Great Barrier Reef (GBR) regions. We analyzed reef surveys from the Caribbean and GBR (1996-2006). We defined a set of reef states distinguished by coral and macroalgal cover, and obtained Bayesian estimates of the annual probabilities of transitions between these states. The Caribbean and GBR had different transition probabilities, and therefore different rates of change in reef condition. This could be due to differences in species composition, management or the nature and extent of disturbances between these regions. We then estimated equilibrium probability distributions for reef states, and coral and macroalgal cover under constant environmental conditions. In both regions, the current distributions are close to equilibrium. In the Caribbean, coral cover is much lower and macroalgal cover is higher at equilibrium than in the GBR. We found no evidence for differences in transition probabilities between the first and second halves of our survey period, or between Caribbean reefs inside and outside marine protected areas. However, our power to detect such differences may have been low. We also examined the effects of altering transition probabilities on the community state equilibrium, along a continuum from unfavourable (e.g., increased sea surface temperature) to favourable (e.g., improved management) conditions. Both regions showed similar qualitative responses, but different patterns of uncertainty. In the Caribbean, uncertainty was greatest about effects of favourable changes, while in the GBR, we are most uncertain about effects of unfavourable changes. Our approach could be extended to provide

  13. Goos-Hänchen-like shift in biased silicene

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Zhu, Bang-Shan; Wang, Yu, E-mail: ywang@semi.ac.cn; Lou, Yi-Yi

    2016-04-28

    We have theoretically studied the Goos-Hänchen-like shift of spinor-unpolarized beams tunneling through various gate-biased silicene nanostructures. Following the stationary-phase method, lateral displacement in single-, dual-, and multiple-gated silicene systems has been systematically demonstrated. It is shown for simple single-gated silicene that lateral displacement can be generally enhanced by Fabry-Perot interference, and near the transition point turning on the evanescent mode a very large lateral shift could be observed. For the dual-gated structure, we have also shown the crucial role of localized modes like quantum well states in enhancing the beam lateral displacement, while for the multiple gate-biased systems the resultingmore » superlattice subbands are also favorable for lateral displacement enhancement. Importantly, including the degeneracy-broken mechanisms such as gate-field and magnetic modulations, a fully spinor-resolved beam can be distinguished from the rest counterparts by aligning the incident beam with a proper spinor-resolved transition point, localized state, and subband, all of which can be flexibly modulated via electric means, offering the very desirable strategies to achieve the fully spinor-polarized beam for functional electronic applications.« less

  14. Potential Energy Curves, Transition Dipole Moments, and Franck-Condon Factors of the 12 Low-Lying States of BrO- Anion.

    PubMed

    Yin, Yuan; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2017-11-02

    This work investigates the spectroscopic parameters, vibrational levels, and transition probabilities of 12 low-lying states, which are generated from the first dissociation limit, Br( 2 P u ) + O - ( 2 P u ), of the BrO - anion. The 12 states are X 1 Σ + , 2 1 Σ + , 1 1 Σ - , 1 1 Π, 2 1 Π, 1 1 Δ, a 3 Π, 1 3 Σ + , 2 3 Σ + , 1 3 Σ - , 2 3 Π, and 1 3 Δ. The potential energy curves are calculated with the complete active-space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with Davidson modification. The dissociation energy D 0 of X 1 Σ + state is determined to be approximately 26876.44 cm -1 , which agrees well with the experimental one of 26494.50 cm -1 . Of these 12 states, the 2 1 Σ + , 1 1 Σ - , 2 1 Π, 1 1 Δ, 1 3 Σ + , 2 3 Σ + , 2 3 Π, and 1 3 Δ states are very weakly bound states, whose well depths are only several-hundred cm -1 . The a 3 Π, 2 3 Π, and 1 3 Δ states are inverted and account for the spin-orbit coupling effect. No states are repulsive regardless of whether the spin-orbit coupling effect is included. The spectroscopic parameters and vibrational levels are determined. The transition dipole moments of 12-pair electronic states are calculated. Franck-Condon factors of a number of transitions of more than 20-pair electronic states are evaluated. The electronic transitions are discussed. The spin-orbit coupling effect on the spectroscopic parameters and vibrational properties is profound for all the states except for X 1 Σ + , a 3 Π, and 1 1 Π. The spectroscopic parameters and transition probabilities obtained in this paper can provide some powerful guidelines for observing these states in a proper spectroscopy experiment, in particular the states that have very shallow potential wells.

  15. The nature of photoinduced phase transition and metastable states in vanadium dioxide

    DOE PAGES

    Tao, Zhensheng; Zhou, Faran; Han, Tzong-Ru T.; ...

    2016-12-16

    Photoinduced threshold switching processes that lead to bistability and the formation of metastable phases in photoinduced phase transition of VO 2 are elucidated through ultrafast electron diffraction and diffusive scattering techniques with varying excitation wavelengths. We uncover two distinct regimes of the dynamical phase change: a nearly instantaneous crossover into an intermediate state and its decay led by lattice instabilities over 10 ps timescales. The structure of this intermediate state is identified to be monoclinic, but more akin to M 2 rather than M1 based on structure refinements. The extinction of all major monoclinic features within just a few picosecondsmore » at the above-threshold-level (~20%) photoexcitations and the distinct dynamics in diffusive scattering that represents medium-range atomic fluctuations at two photon wavelengths strongly suggest a density-driven and nonthermal pathway for the initial process of the photoinduced phase transition. These results highlight the critical roles of electron correlations and lattice instabilities in driving and controlling phase transformations far from equilibrium.« less

  16. The Perceived Readiness of the Graduates of Delaware State University to Transition into the Workforce

    ERIC Educational Resources Information Center

    Scott-Cheatham, Lawita Germaine

    2013-01-01

    This study was designed to explore the perceived readiness of the graduating seniors at Delaware State University to transition from the classroom into the workforce. Delaware State University's undergraduate graduating class of 2012, 547 undergraduate seniors, were invited to participate in an online survey comprised of 23 items--derived from the…

  17. Phase transitions of sodium niobate powder and ceramics, prepared by solid state synthesis

    NASA Astrophysics Data System (ADS)

    Koruza, J.; Tellier, J.; Malič, B.; Bobnar, V.; Kosec, M.

    2010-12-01

    Phase transitions of sodium niobate, prepared by the solid state synthesis method, were examined using dielectric measurements, differential scanning calorimetry, and high temperature x-ray diffraction, in order to contribute to the clarification of its structural behavior below 400 °C. Four phase transitions were detected in the ceramic sample using dielectric measurements and differential scanning calorimetry and the obtained temperatures were in a good agreement with previous reports for the transitions of the P polymorph. The anomaly observed by dielectric measurements in the vicinity of 150 °C was frequency dependent and could be related to the dynamics of the ferroelectric nanoregions. The phase transitions of the as-synthesized NaNbO3 powder were investigated using differential scanning calorimetry and high temperature x-ray diffraction. The results show the existence of the Q polymorph at room temperature, not previously reported for the powder, which undergoes a transition to the R polymorph upon heating through a temperature region between 265 and 326.5 °C. This transition is mainly related to the displacement of Na into a more symmetric position and a minor change in the tilting system. The structures at room temperature, 250, 300, and 420 °C were refined by the Rietveld method and the evolution of the tilting system of the octahedral network and cationic displacement are reported.

  18. Estimating transition probabilities in unmarked populations --entropy revisited

    USGS Publications Warehouse

    Cooch, E.G.; Link, W.A.

    1999-01-01

    The probability of surviving and moving between 'states' is of great interest to biologists. Robust estimation of these transitions using multiple observations of individually identifiable marked individuals has received considerable attention in recent years. However, in some situations, individuals are not identifiable (or have a very low recapture rate), although all individuals in a sample can be assigned to a particular state (e.g. breeding or non-breeding) without error. In such cases, only aggregate data (number of individuals in a given state at each occasion) are available. If the underlying matrix of transition probabilities does not vary through time and aggregate data are available for several time periods, then it is possible to estimate these parameters using least-squares methods. Even when such data are available, this assumption of stationarity will usually be deemed overly restrictive and, frequently, data will only be available for two time periods. In these cases, the problem reduces to estimating the most likely matrix (or matrices) leading to the observed frequency distribution of individuals in each state. An entropy maximization approach has been previously suggested. In this paper, we show that the entropy approach rests on a particular limiting assumption, and does not provide estimates of latent population parameters (the transition probabilities), but rather predictions of realized rates.

  19. Zooplankton community structure during a transition from dry to wet state in a shallow, subtropical estuarine lake

    NASA Astrophysics Data System (ADS)

    Carrasco, Nicola K.; Perissinotto, Renzo

    2015-12-01

    Lake St Lucia is among the most important shallow ecosystems globally and Africa's largest estuarine lake. It has long been regarded as a resilient system, oscillating through periods of hypersalinity and freshwater conditions, depending on the prevailing climate. The alteration of the system's catchment involving the diversion of the Mfolozi River away from Lake St Lucia, however, challenged the resilience of the system, particularly during the most recent drought (2002-2011), sacrificing much of its biodiversity. This study reports on the transition of the St Lucia zooplankton community from a dry hypersaline state to a new wet phase. Sampling was undertaken during routine quarterly surveys at five representative stations along the lake system from February 2011 to November 2013. A total of 54 taxa were recorded during the study period. The zooplankton community was numerically dominated by the calanoid copepods Acartiella natalensis and Pseudodiaptomus stuhlmanni and the cyclopoid copepod Oithona brevicornis. While the mysid Mesopodopsis africana was still present in the system during the wet phase, it was not found in the swarming densities that were recorded during the previous dry phase, possibly due to increased predation pressure, competition with other taxa and or the reconnection with the Mfolozi River via a beach spillway. The increase in zooplankton species richness recorded during the present study shows that the system has undergone a transition to wet state, with the zooplankton community structure reflecting that recorded during the past. It is likely, though, that only a full restoration of natural mouth functioning will result in further diversity increases.

  20. Transition paths of Met-enkephalin from Markov state modeling of a molecular dynamics trajectory.

    PubMed

    Banerjee, Rahul; Cukier, Robert I

    2014-03-20

    Conformational states and their interconversion pathways of the zwitterionic form of the pentapeptide Met-enkephalin (MetEnk) are identified. An explicit solvent molecular dynamics (MD) trajectory is used to construct a Markov state model (MSM) based on dihedral space clustering of the trajectory, and transition path theory (TPT) is applied to identify pathways between open and closed conformers. In the MD trajectory, only four of the eight backbone dihedrals exhibit bistable behavior. Defining a conformer as the string XXXX with X = "+" or "-" denoting, respectively, positive or negative values of a given dihedral angle and obtaining the populations of these conformers shows that only four conformers are highly populated, implying a strong correlation among these dihedrals. Clustering in dihedral space to construct the MSM finds the same four bistable dihedral angles. These state populations are very similar to those found directly from the MD trajectory. TPT is used to obtain pathways, parametrized by committor values, in dihedral state space that are followed in transitioning from closed to open states. Pathway costs are estimated by introducing a kinetics-based procedure that orders pathways from least (shortest) to greater cost paths. The least costly pathways in dihedral space are found to only involve the same XXXX set of dihedral angles, and the conformers accessed in the closed to open transition pathways are identified. For these major pathways, a correlation between reaction path progress (committors) and the end-to-end distance is identified. A dihedral space principal component analysis of the MD trajectory shows that the first three modes capture most of the overall fluctuation, and pick out the same four dihedrals having essentially all the weight in those modes. A MSM based on root-mean-square backbone clustering was also carried out, with good agreement found with dihedral clustering for the static information, but with results that differ

  1. Interfacial states and far-from-equilibrium transitions in the epitaxial growth and erosion on (110) crystal surfaces

    NASA Astrophysics Data System (ADS)

    Levandovsky, Artem; Golubović, Leonardo; Moldovan, Dorel

    2006-12-01

    We discuss the far-from-equilibrium interfacial phenomena occurring in the multilayer homoepitaxial growth and erosion on (110) crystal surfaces. Experimentally, these rectangular symmetry surfaces exhibit a multitude of interesting nonequilibrium interfacial structures, such as the rippled one-dimensional periodic states that are not present in the homoepitaxial growth and erosion on the high symmetry (100) and (111) crystal surfaces. Within a unified phenomenological model, we reveal and elucidate this multitude of states on (110) surfaces as well as the transitions between them. By analytic arguments and numerical simulations, we address experimentally observed transitions between two types of rippled states on (110) surfaces. We discuss several intermediary interface states intervening, via consecutive transitions, between the two rippled states. One of them is the rhomboidal pyramid state, theoretically predicted by Golubovic [Phys. Rev. Lett. 89, 266104 (2002)] and subsequently seen, by de Mongeot and co-workers, in the epitaxial erosion of Cu(110) and Rh(110) surfaces [A. Molle , Phys. Rev. Lett. 93, 256103 (2004), and A. Molle , Phys. Rev. B 73, 155418 (2006)]. In addition, we find a number of interesting intermediary states having structural properties somewhere between those of rippled and pyramidal states. Prominent among them are the rectangular rippled states of long rooflike objects (huts) recently seen on Ag(110) surface. We also predict the existence of a striking interfacial structure that carries nonzero, persistent surface currents. Periodic surface currents vortex lattice formed in this so-called buckled rippled interface state is a far-from-equilibrium relative of the self-organized convective flow patterns in hydrodynamic systems. We discuss the coarsening growth of the multitude of the interfacial states on (110) crystal surfaces.

  2. Transitioning to Performance-Based State Funding: Concerns, Commitment, and Cautious Optimism

    ERIC Educational Resources Information Center

    Wayt, Lindsay K.; LaCost, Barbara Y.

    2016-01-01

    The introduction of performance-based state funding of higher education can be traced to the late 1970s which eliminated bonuses, and replaced regular state funding in part or completely, with funding tied to achievement of state-defined performance goals, which often include student outcomes, like graduation and retention rates. In this article,…

  3. Optical study of phase transitions in single-crystalline RuP

    NASA Astrophysics Data System (ADS)

    Chen, R. Y.; Shi, Y. G.; Zheng, P.; Wang, L.; Dong, T.; Wang, N. L.

    2015-03-01

    RuP single crystals of MnP-type orthorhombic structure were synthesized by the Sn flux method. Temperature-dependent x-ray diffraction measurements reveal that the compound experiences two structural phase transitions, which are further confirmed by enormous anomalies shown in temperature-dependent resistivity and magnetic susceptibility. Particularly, the resistivity drops monotonically upon temperature cooling below the second transition, indicating that the material shows metallic behavior, in sharp contrast with the insulating ground state of polycrystalline samples. Optical conductivity measurements were also performed in order to unravel the mechanism of these two transitions. The measurement revealed a sudden reconstruction of band structure over a broad energy scale and a significant removal of conducting carriers below the first phase transition, while a charge-density-wave-like energy gap opens below the second phase transition.

  4. (14)N overtone transition in double rotation solid-state NMR.

    PubMed

    Haies, Ibraheem M; Jarvis, James A; Brown, Lynda J; Kuprov, Ilya; Williamson, Philip T F; Carravetta, Marina

    2015-10-07

    Solid-state NMR transitions involving outer energy levels of the spin-1 (14)N nucleus are immune, to first order in perturbation theory, to the broadening caused by the nuclear quadrupole interaction. The corresponding overtone spectra, when acquired in conjunction with magic-angle sample spinning, result in lines, which are just a few kHz wide, permitting the direct detection of nitrogen compounds without the need for labeling. Despite the success of this technique, "overtone" resonances are still broadened due to indirect, second order effects arising from the large quadrupolar interaction. Here we demonstrate that another order of magnitude in spectral resolution may be gained by using double rotation. This brings the width of the (14)N solid-state NMR lines much closer to the region commonly associated with high-resolution solid-state NMR spectroscopy of (15)N and demonstrates the improvements in resolution that may be possible through the development of pulsed methodologies to suppress these second order effects.

  5. Theory of pure rotational transitions in doubly degenerate torsional states of ethane

    NASA Technical Reports Server (NTRS)

    Rosenberg, A.; Susskind, J.

    1979-01-01

    It is shown that pure rotational transitions in doubly degenerate torsional states of C2H6 (with selection rules Delta K = 0, plus or minus 1) are made allowed by Coriolis interaction between torsion and dipole-allowed vibrations. Expressions are presented for integrated intensities from which strengths of lines in the millimeter region can be calculated.

  6. Inducing and destruction of chimeras and chimera-like states by an external harmonic force

    NASA Astrophysics Data System (ADS)

    Shepelev, I. A.; Vadivasova, T. E.

    2018-03-01

    We study the phenomena of chimera destruction and inducing of chimera-like states in an ensemble of nonlocally coupled chaotic Rössler oscillators under an external harmonic force. The localized harmonic influence can lead to both destruction and changing of the spatial topology of chimeras. At the same time this influence can cause the emergence of stable chimera-like states (induced chimeras) for the regime of partial coherent chaos. Induced chimeras are also observed for the global influence. We show the possibility of controlling the chimera-like state topology by varying the parameters of localized external harmonic influence.

  7. Precise Determination of the Lyman-1 Transition Energy in Hydrogen-like Gold Ions with Microcalorimeters

    NASA Astrophysics Data System (ADS)

    Kraft-Bermuth, S.; Andrianov, V.; Bleile, A.; Echler, A.; Egelhof, P.; Grabitz, P.; Kilbourne, C.; Kiselev, O.; McCammon, D.; Scholz, P.

    2014-09-01

    The precise determination of the transition energy of the Lyman-1 line in hydrogen-like heavy ions provides a sensitive test of quantum electrodynamics in very strong Coulomb fields. We report the determination of the Lyman-1 transition energy of gold ions (Au) with microcalorimeters at the experimental storage ring at GSI. X-rays produced by the interaction of 125 MeV/u Au ions with an internal argon gas-jet target were detected. The detector array consisted of 14 pixels with silicon thermistors and Sn absorbers, for which an energy resolution of 50 eV for an X-ray energy of 59.5 keV was obtained in the laboratory. The Lyman-1 transition energy was determined for each pixel in the laboratory frame, then transformed into the emitter frame and averaged. A Dy-159 source was used for energy calibration. The absolute positions of the detector pixels, which are needed for an accurate correction of the Doppler shift, were determined by topographic measurements and by scanning a collimated Am-241 source across the cryostat window. The energy of the Lyman-1 line in the emitter frame is eV, in good agreement with theoretical predictions. The systematic error is dominated by the uncertainty in the position of the cryostat relative to the interaction region of beam and target.

  8. Insights into the nature of DNA binding of AbrB-like transcription factors

    PubMed Central

    Sullivan, Daniel M.; Bobay, Benjamin G.; Kojetin, Douglas J.; Thompson, Richele J.; Rance, Mark; Strauch, Mark A.; Cavanagh, John

    2008-01-01

    Summary Understanding the DNA recognition and binding by the AbrB-like family of transcriptional regulators is of significant interest since these proteins enable bacteria to elicit the appropriate response to diverse environmental stimuli. Although these ‘transition-state regulator’ proteins have been well characterized at the genetic level, the general and specific mechanisms of DNA binding remain elusive. We present RDC-refined NMR solution structures and dynamic properties of the DNA-binding domains of three Bacillus subtilis transition-state regulators AbrB, Abh, and SpoVT. We combined previously investigated DNase I footprinting, DNA methylation, gel shift assays, mutagenic and NMR studies to generate a structural model of the complex between AbrBN55 and its cognate promoter, abrB8. These investigations have enabled us to generate the first model for the specific nature of the transition-state regulator-DNA interaction. PMID:19000822

  9. Nature of the transition between a ferromagnetic metal and a spin-glass insulator in pyrochlore molybdates.

    PubMed

    Hanasaki, N; Watanabe, K; Ohtsuka, T; Kézsmárki, I; Iguchi, S; Miyasaka, S; Tokura, Y

    2007-08-24

    The metal-insulator transition has been investigated for pyrochlore molybdates R(2)Mo(2)O(7) with nonmagnetic rare-earth ions R. The dynamical scaling analysis of ac susceptibility reveals that the geometrical frustration causes the atomic spin-glass state. The reentrant spin-glass phase exists below the ferromagnetic transition. The electronic specific heat is enhanced as compared to the band calculation result, perhaps due to the orbital fluctuation in the half-metallic ferromagnetic state. The large specific heat is rather reduced upon the transition, likely because the short-range antiferromagnetic fluctuation shrinks the Fermi surface.

  10. Steady-state and transitional aerodynamic characteristics of a wing in simulated heavy rain

    NASA Technical Reports Server (NTRS)

    Campbell, Bryan A.; Bezos, Gaudy M.

    1989-01-01

    The steady-state and transient effects of simulated heavy rain on the subsonic aerodynamic characteristics of a wing model were determined in the Langley 14- by 22-Foot Subsonic Tunnel. The 1.29 foot chord wing was comprised of a NACA 23015 airfoil and had an aspect ratio of 6.10. Data were obtained while test variables of liquid water content, angle of attack, and trailing edge flap angle were parametrically varied at dynamic pressures of 10, 30, and 50 psf (i.e., Reynolds numbers of .76x10(6), 1.31x10(6), and 1.69x10(6)). The experimental results showed reductions in lift and increases in drag when in the simulated rain environment. Accompanying this was a reduction of the stall angle of attack by approximately 4 deg. The transient aerodynamic performance during transition from dry to wet steady-state conditions varied between a linear and a nonlinear transition.

  11. Multistate empirical valence bond study of temperature and confinement effects on proton transfer in water inside hydrophobic nanochannels.

    PubMed

    Tahat, Amani; Martí, Jordi

    2016-07-01

    Microscopic characteristics of an aqueous excess proton in a wide range of thermodynamic states, from low density amorphous ices (down to 100 K) to high temperature liquids under the critical point (up to 600 K), placed inside hydrophobic graphene slabs at the nanometric scale (with interplate distances between 3.1 and 0.7 nm wide) have been analyzed by means of molecular dynamics simulations. Water-proton and carbon-proton forces were modeled with a multistate empirical valence bond method. Densities between 0.07 and 0.02 Å(-3) have been considered. As a general trend, we observed a competition between effects of confinement and temperature on structure and dynamical properties of the lone proton. Confinement has strong influence on the local structure of the proton, whereas the main effect of temperature on proton properties is observed on its dynamics, with significant variation of proton transfer rates, proton diffusion coefficients, and characteristic frequencies of vibrational motions. Proton transfer is an activated process with energy barriers between 1 and 10 kJ/mol for both proton transfer and diffusion, depending of the temperature range considered and also on the interplate distance. Arrhenius-like behavior of the transfer rates and of proton diffusion are clearly observed for states above 100 K. Spectral densities of proton species indicated that in all states Zundel-like and Eigen-like complexes survive at some extent. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  12. Study on the spectroscopic parameters and transition probabilities of 25 low-lying states of the AlC+ cation

    NASA Astrophysics Data System (ADS)

    Zhang, Jicai; Shi, Deheng; Xing, Wei; Sun, Jinfeng; Zhu, Zunlue

    2017-11-01

    This paper investigates the spectroscopic parameters and transition probabilities of 25 low-lying states, which come from the first five dissociation channels of AlC+ cation. The potential energy curves are calculated with the complete active space self-consistent field method, which is followed by the valence internally contracted multireference configuration interaction approach with Davidson correction. Of these 25 states, only the 35Σ-state is repulsive; the c1Σ+, f1Π, and 15Π states have the double well; the first well of c1Σ+ state and the second well of 15Π state are very weakly bound; the first well of c1Σ+ state has no vibrational levels; the 25Π state and the double well of f1Π state have only several vibrational states; the B3Σ-, E3Σ+, D3Π, 15Σ+, 25Σ-, and 15Π states are inverted when the spin-orbit coupling effect is included. The avoided crossings exist between the B3Σ- and 33Σ- states, the c1Σ+ and d1Σ+ states, the f1Π and 31Π states, the 15Π and 25Π states, as well as the 25Π and 35Π states. Core-valence correlation and scalar relativistic corrections are considered. The extrapolation of potential energies to the complete basis set limit is done. The spectroscopic parameters and vibrational levels are determined for all the Λ-S and Ω bound states. The transition dipole moments are calculated. Franck-Condon factors of a great number of electronic transitions are evaluated. On the whole, the spin-orbit coupling effect on the spectroscopic parameters and vibrational levels is small except for very few states. The results determined in this paper could provide some powerful guidelines to observe these states in a spectroscopy experiment.

  13. Downscaling global land-use/land-cover projections for use in region-level state-and-transition simulation modeling

    USGS Publications Warehouse

    Sherba, Jason T.; Sleeter, Benjamin M.; Davis, Adam W.; Parker, Owen P.

    2015-01-01

    Global land-use/land-cover (LULC) change projections and historical datasets are typically available at coarse grid resolutions and are often incompatible with modeling applications at local to regional scales. The difficulty of downscaling and reapportioning global gridded LULC change projections to regional boundaries is a barrier to the use of these datasets in a state-and-transition simulation model (STSM) framework. Here we compare three downscaling techniques to transform gridded LULC transitions into spatial scales and thematic LULC classes appropriate for use in a regional STSM. For each downscaling approach, Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathway (RCP) LULC projections, at the 0.5 × 0.5 cell resolution, were downscaled to seven Level III ecoregions in the Pacific Northwest, United States. RCP transition values at each cell were downscaled based on the proportional distribution between ecoregions of (1) cell area, (2) land-cover composition derived from remotely-sensed imagery, and (3) historic LULC transition values from a LULC history database. Resulting downscaled LULC transition values were aggregated according to their bounding ecoregion and “cross-walked” to relevant LULC classes. Ecoregion-level LULC transition values were applied in a STSM projecting LULC change between 2005 and 2100. While each downscaling methods had advantages and disadvantages, downscaling using the historical land-use history dataset consistently apportioned RCP LULC transitions in agreement with historical observations. Regardless of the downscaling method, some LULC projections remain improbable and require further investigation.

  14. Light rail transit : state-of-the-art overview

    DOT National Transportation Integrated Search

    1977-05-01

    This document presents an overview of light rail transit, an urban transit alternative which has the potential to help fill the need for flexibility in public transportation. Existing and proposed U.S. and Canadian light rail transit systems are desc...

  15. Imaging metal-like monoclinic phase stabilized by surface coordination effect in vanadium dioxide nanobeam

    PubMed Central

    Li, Zejun; Wu, Jiajing; Hu, Zhenpeng; Lin, Yue; Chen, Qi; Guo, Yuqiao; Liu, Yuhua; Zhao, Yingcheng; Peng, Jing; Chu, Wangsheng; Wu, Changzheng; Xie, Yi

    2017-01-01

    In correlated systems, intermediate states usually appear transiently across phase transitions even at the femtosecond scale. It therefore remains an open question how to determine these intermediate states—a critical issue for understanding the origin of their correlated behaviour. Here we report a surface coordination route to successfully stabilize and directly image an intermediate state in the metal-insulator transition of vanadium dioxide. As a prototype metal-insulator transition material, we capture an unusual metal-like monoclinic phase at room temperature that has long been predicted. Coordinate bonding of L-ascorbic acid molecules with vanadium dioxide nanobeams induces charge-carrier density reorganization and stabilizes metallic monoclinic vanadium dioxide, unravelling orbital-selective Mott correlation for gap opening of the vanadium dioxide metal–insulator transition. Our study contributes to completing phase-evolution pathways in the metal-insulator transition process, and we anticipate that coordination chemistry may be a powerful tool for engineering properties of low-dimensional correlated solids. PMID:28613281

  16. Free-end adaptive nudged elastic band method for locating transition states in minimum energy path calculation.

    PubMed

    Zhang, Jiayong; Zhang, Hongwu; Ye, Hongfei; Zheng, Yonggang

    2016-09-07

    A free-end adaptive nudged elastic band (FEA-NEB) method is presented for finding transition states on minimum energy paths, where the energy barrier is very narrow compared to the whole paths. The previously proposed free-end nudged elastic band method may suffer from convergence problems because of the kinks arising on the elastic band if the initial elastic band is far from the minimum energy path and weak springs are adopted. We analyze the origin of the formation of kinks and present an improved free-end algorithm to avoid the convergence problem. Moreover, by coupling the improved free-end algorithm and an adaptive strategy, we develop a FEA-NEB method to accurately locate the transition state with the elastic band cut off repeatedly and the density of images near the transition state increased. Several representative numerical examples, including the dislocation nucleation in a penta-twinned nanowire, the twin boundary migration under a shear stress, and the cross-slip of screw dislocation in face-centered cubic metals, are investigated by using the FEA-NEB method. Numerical results demonstrate both the stability and efficiency of the proposed method.

  17. Effect of non-stationary accretion on spectral state transitions: An example of a persistent neutron star LMXB 4U1636–536

    NASA Astrophysics Data System (ADS)

    Zhang, Hui; Yu, Wen-Fei

    2018-03-01

    Observations of black hole and neutron star X-ray binaries show that the luminosity of the hard-to-soft state transition is usually higher than that of the soft-to-hard state transition, indicating additional parameters other than mass accretion rate are required to interpret spectral state transitions. It has been found in some individual black hole or neutron star soft X-ray transients that the luminosity corresponding to the hard-to-soft state transition is positively correlated with the peak luminosity of the following soft state. In this work, we report the discovery of the same correlation in the single persistent neutron star low mass X-ray binary (LMXB) 4U 1636–536 based on data from the All Sky Monitor (ASM) on board RXTE, the Gas Slit Camera (GSC) on board MAXI and the Burst Alert Telescope (BAT) on board Swift. We also found such a positive correlation holds in this persistent neutron star LMXB in a luminosity range spanning about a factor of four. Our results indicate that non-stationary accretion also plays an important role in driving X-ray spectral state transitions in persistent accreting systems with small accretion flares, which is much less dramatic compared with the bright outbursts seen in many Galactic LMXB transients.

  18. Family Structure States and Transitions: Associations with Children's Well-Being during Middle Childhood

    ERIC Educational Resources Information Center

    Magnuson, Katherine; Berger, Lawrence M.

    2009-01-01

    Using longitudinal data from the Maternal and Child Supplement of the National Longitudinal Survey of Youth (N = 3,862) and Hierarchical Linear Models, we estimated associations of family structure states and transitions with children's achievement and behavior trajectories during middle childhood. Results suggest that residing in a single-mother…

  19. Urodynamic function during sleep-like brain states in urethane anesthetized rats.

    PubMed

    Crook, J; Lovick, T

    2016-01-28

    The aim was to investigate urodynamic parameters and functional excitability of the periaqueductal gray matter (PAG) during changes in sleep-like brain states in urethane anesthetized rats. Simultaneous recordings of detrusor pressure, external urethral sphincter (EUS) electromyogram (EMG), cortical electroencephalogram (EEG), and single-unit activity in the PAG were made during repeated voiding induced by continuous infusion of saline into the bladder. The EEG cycled between synchronized, high-amplitude slow wave activity (SWA) and desynchronized low-amplitude fast activity similar to slow wave and 'activated' sleep-like brain states. During (SWA, 0.5-1.5 Hz synchronized oscillation of the EEG waveform) voiding became more irregular than in the 'activated' brain state (2-5 Hz low-amplitude desynchronized EEG waveform) and detrusor void pressure threshold, void volume threshold and the duration of bursting activity in the external urethral sphincter EMG were raised. The spontaneous firing rate of 23/52 neurons recorded within the caudal PAG and adjacent tegmentum was linked to the EEG state, with the majority of responsive cells (92%) firing more slowly during SWA. Almost a quarter of the cells recorded (12/52) showed phasic changes in firing rate that were linked to the occurrence of voids. Inhibition (n=6), excitation (n=4) or excitation/inhibition (n=2) was seen. The spontaneous firing rate of 83% of the micturition-responsive cells was sensitive to changes in EEG state. In nine of the 12 responsive cells (75%) the responses were reduced during SWA. We propose that during different sleep-like brain states changes in urodynamic properties occur which may be linked to changing excitability of the micturition circuitry in the periaqueductal gray. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  20. Unexpected rewards induce dopamine-dependent positive emotion-like state changes in bumblebees.

    PubMed

    Perry, Clint J; Baciadonna, Luigi; Chittka, Lars

    2016-09-30

    Whether invertebrates exhibit positive emotion-like states and what mechanisms underlie such states remain poorly understood. We demonstrate that bumblebees exhibit dopamine-dependent positive emotion-like states across behavioral contexts. After training with one rewarding and one unrewarding cue, bees that received pretest sucrose responded in a positive manner toward ambiguous cues. In a second experiment, pretest consumption of sucrose solution resulted in a shorter time to reinitiate foraging after a simulated predator attack. These behavioral changes were abolished with topical application of the dopamine antagonist fluphenazine. Further experiments established that pretest sucrose does not simply cause bees to become more exploratory. Our findings present a new opportunity for understanding the fundamental neural elements of emotions and may alter the view of how emotion states affect decision-making in animals. Copyright © 2016, American Association for the Advancement of Science.

  1. Folding mechanism of β-hairpin trpzip2: heterogeneity, transition state and folding pathways.

    PubMed

    Xiao, Yi; Chen, Changjun; He, Yi

    2009-06-22

    We review the studies on the folding mechanism of the beta-hairpin tryptophan zipper 2 (trpzip2) and present some additional computational results to refine the picture of folding heterogeneity and pathways. We show that trpzip2 can have a two-state or a multi-state folding pattern, depending on whether it folds within the native basin or through local state basins on the high-dimensional free energy surface; Trpzip2 can fold along different pathways according to the packing order of tryptophan pairs. We also point out some important problems related to the folding mechanism of trpzip2 that still need clarification, e.g., a wide distribution of the computed conformations for the transition state ensemble.

  2. Mutational analysis of the folding transition state of the C-terminal domain of ribosomal protein L9: a protein with an unusual beta-sheet topology.

    PubMed

    Li, Ying; Gupta, Ruchi; Cho, Jae-Hyun; Raleigh, Daniel P

    2007-01-30

    The C-terminal domain of ribosomal protein L9 (CTL9) is a 92-residue alpha-beta protein which contains an unusual three-stranded mixed parallel and antiparallel beta-sheet. The protein folds in a two-state fashion, and the folding rate is slow. It is thought that the slow folding may be caused by the necessity of forming this unusual beta-sheet architecture in the transition state for folding. This hypothesis makes CTL9 an interesting target for folding studies. The transition state for the folding of CTL9 was characterized by phi-value analysis. The folding of a set of hydrophobic core mutants was analyzed together with a set of truncation mutants. The results revealed a few positions with high phi-values (> or = 0.5), notably, V131, L133, H134, V137, and L141. All of these residues were found in the beta-hairpin region, indicating that the formation of this structure is likely to be the rate-limiting step in the folding of CTL9. One face of the beta-hairpin docks against the N-terminal helix. Analysis of truncation mutants of this helix confirmed its importance in folding. Mutations at other sites in the protein gave small phi-values, despite the fact that some of them had major effects on stability. The analysis indicates that formation of the antiparallel hairpin is critical and its interactions with the first helix are also important. Thus, the slow folding is not a consequence of the need to fully form the unusual three-stranded beta-sheet in the transition state. Analysis of the urea dependence of the folding rates indicates that mutations modulate the unfolded state. The folding of CTL9 is broadly consistent with the nucleation-condensation model of protein folding.

  3. Promoting Singlet/triplet Exciton Transformation in Organic Optoelectronic Molecules: Role of Excited State Transition Configuration.

    PubMed

    Chen, Runfeng; Tang, Yuting; Wan, Yifang; Chen, Ting; Zheng, Chao; Qi, Yuanyuan; Cheng, Yuanfang; Huang, Wei

    2017-07-24

    Exciton transformation, a non-radiative process in changing the spin multiplicity of an exciton usually between singlet and triplet forms, has received much attention recently due to its crucial effects in manipulating optoelectronic properties for various applications. However, current understanding of exciton transformation mechanism does not extend far beyond a thermal equilibrium of two states with different multiplicity and it is a significant challenge to probe what exactly control the transformation between the highly active excited states. Here, based on the recent developments of three types of purely organic molecules capable of efficient spin-flipping, we perform ab initio structure/energy optimization and similarity/overlap extent analysis to theoretically explore the critical factors in controlling the transformation process of the excited states. The results suggest that the states having close energy levels and similar exciton characteristics with same transition configurations and high heteroatom participation are prone to facilitating exciton transformation. A basic guideline towards the molecular design of purely organic materials with facile exciton transformation ability is also proposed. Our discovery highlights systematically the critical importance of vertical transition configuration of excited states in promoting the singlet/triplet exciton transformation, making a key step forward in excited state tuning of purely organic optoelectronic materials.

  4. State-change in the "transition" binary millisecond pulsar J1023+0038

    NASA Astrophysics Data System (ADS)

    Stappers, B. W.; Archibald, A.; Bassa, C.; Hessels, J.; Janssen, G.; Kaspi, V.; Lyne, A.; Patruno, A.; Hill, A. B.

    2013-10-01

    We report a change in the state of PSR J1023+0038, a source which is believed to be transitioning from an X-ray binary to an eclipsing binary radio millisecond pulsar (Archibald et al. 2009, Science, 324, 1411). The system was known to contain an accretion disk in 2001 but has shown no signs of it, or of accretion, since then, rather exhibiting all the properties of an eclipsing binary millisecond radio pulsar (MSP).

  5. Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States

    NASA Astrophysics Data System (ADS)

    de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M.

    2018-03-01

    Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

  6. Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States.

    PubMed

    de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M

    2018-03-23

    Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

  7. Chapter 5: Application of state-and-transition models to evaluate wildlife habitat

    Treesearch

    Anita T. Morzillo; Pamela Comeleo; Blair Csuti; Stephanie Lee

    2014-01-01

    Wildlife habitat analysis often is a central focus of natural resources management and policy. State-and-transition models (STMs) allow for simulation of landscape level ecological processes, and for managers to test “what if” scenarios of how those processes may affect wildlife habitat. This chapter describes the methods used to link STM output to wildlife habitat to...

  8. Toward a social justice theory of demographic transition: lessons from India's Kerala State.

    PubMed

    Ratcliffe, J W

    1983-06-01

    Recent research evidence, which suggests that observed demographic trends and patterns are largely consequences of broad structural changes in society, has raised serious doubts about the validity of traditional demographic theory and the framework for action it has generated. This theoretical essay 1st recasts classical demographic transition theory in general systems terms in order to make it consistent with the evidence and to place the processes of fertility and mortality in a larger social context. The demographic transition experience of Kerala State, India is then recounted to provide a concrete example of the demographic response in society to structural reforms based primarily on equity considerations.

  9. Vibrational density of states and thermodynamics at the nanoscale: the 3D-2D transition in gold nanostructures

    NASA Astrophysics Data System (ADS)

    Carles, R.; Benzo, P.; Pécassou, B.; Bonafos, C.

    2016-12-01

    Surface enhanced Raman scattering (SERS) is generally and widely used to enhance the vibrational fingerprint of molecules located at the vicinity of noble metal nanoparticles. In this work, SERS is originally used to enhance the own vibrational density of states (VDOS) of nude and isolated gold nanoparticles. This offers the opportunity of analyzing finite size effects on the lattice dynamics which remains unattainable with conventional techniques based on neutron or x-ray inelastic scattering. By reducing the size down to few nanometers, the role of surface atoms versus volume atoms become dominant, and the “text-book” 3D-2D transition on the dynamical behavior is experimentally emphasized. “Anomalies” that have been predicted by a large panel of simulations at the atomic scale, are really observed, like the enhancement of the VDOS at low frequencies or the occurrence of localized modes at frequencies beyond the cut-off in bulk. Consequences on the thermodynamic properties at the nanoscale, like the reduction of the Debye temperature or the excess of the specific heat, have been evaluated. Finally the high sensitivity of reminiscent bulk-like phonons on the arrangements at the atomic scale is used to access the morphology and internal disorder of the nanoparticles.

  10. Vibrational density of states and thermodynamics at the nanoscale: the 3D-2D transition in gold nanostructures

    PubMed Central

    Carles, R.; Benzo, P.; Pécassou, B.; Bonafos, C.

    2016-01-01

    Surface enhanced Raman scattering (SERS) is generally and widely used to enhance the vibrational fingerprint of molecules located at the vicinity of noble metal nanoparticles. In this work, SERS is originally used to enhance the own vibrational density of states (VDOS) of nude and isolated gold nanoparticles. This offers the opportunity of analyzing finite size effects on the lattice dynamics which remains unattainable with conventional techniques based on neutron or x-ray inelastic scattering. By reducing the size down to few nanometers, the role of surface atoms versus volume atoms become dominant, and the “text-book” 3D-2D transition on the dynamical behavior is experimentally emphasized. “Anomalies” that have been predicted by a large panel of simulations at the atomic scale, are really observed, like the enhancement of the VDOS at low frequencies or the occurrence of localized modes at frequencies beyond the cut-off in bulk. Consequences on the thermodynamic properties at the nanoscale, like the reduction of the Debye temperature or the excess of the specific heat, have been evaluated. Finally the high sensitivity of reminiscent bulk-like phonons on the arrangements at the atomic scale is used to access the morphology and internal disorder of the nanoparticles. PMID:27982080

  11. Elastic anomalies and acoustic dissipation associated with spin state transitions in LnCoO3 (Ln=La, Nd, Gd) and Co3O4: analogue behaviour for spin state transitions in minerals

    NASA Astrophysics Data System (ADS)

    Zhang, Z.; Carpenter, M. A.; Koppensteiner, J.; Schranz, W.

    2010-12-01

    Iron ions in lower mantle minerals magnesiowüstitue (Mg,Fe)O, perovskite (Mg,Fe)(Si,Al)O3 and post-perovskite phases undergo electronic spin state transitions from high spin (HS) to low spin (LS) or intermediate spin (IS) at high pressures and high temperatures. These spin state transitions give rise to changes in bulk and shear moduli which have significant implications for the physical and chemical properties of the lower mantle. However, the possibility of increased attenuation does not appear to have been considered yet. Co3+ is isoelectronic with Fe2+ and shows analogous HS/LS behaviour at ambient pressure in a temperature range which is easily accessible for in-situ investigations. We have studied spin state transitions in cobalt perovskites LaCoO3, NdCoO3, GdCoO3 and in Co3O4 using resonant ultrasound spectroscopy (RUS) at high frequencies 0.1-1.5 MHz, and dynamic mechanical analysis (DMA) at low frequencies 0.1-50 Hz, in the temperature range 10-1200 K. The specific objectives were to characterize anomalies in the shear moduli and in acoustic attenuation accompanying changes in the spin state of Co3+. Anomalies in shear moduli have been observed at ~110 K and ~590 K for LaCoO3, ~325 K and ~695 K for NdCoO3, ~720 K for GdCoO3, and ~30 K for Co3O4. For LaCoO3, a spin order parameter qspin is expected to couple with volume strain ea as λeaqspin and with shear strain es as λes2qspin. As a consequence of linear/quadratic coupling with es, the shear modulus is expected to vary linearly with qspin. This appears to be approximately the case for LaCoO3. Changes in spin state do not appear to give rise to acoustic attenuation at either DMA frequencies (~1 Hz) or RUS frequencies (~1 MHz), consistent with the expectation that spin/lattice relaxation is rapid in comparison with the time scale of applied stress in each case. On the other hand, for LaCoO3 there is a peak in dissipation near 590 K at low frequencies, which is attributed to freezing of ferroelastic twin

  12. Development of state and transition model assumptions used in National Forest Plan revision

    Treesearch

    Eric B. Henderson

    2008-01-01

    State and transition models are being utilized in forest management analysis processes to evaluate assumptions about disturbances and succession. These models assume valid information about seral class successional pathways and timing. The Forest Vegetation Simulator (FVS) was used to evaluate seral class succession assumptions for the Hiawatha National Forest in...

  13. Interface states, negative differential resistance, and rectification in molecular junctions with transition-metal contacts

    NASA Astrophysics Data System (ADS)

    Dalgleish, Hugh; Kirczenow, George

    2006-06-01

    We present a theory of nonlinear transport phenomena in molecular junctions where single thiolated organic molecules bridge transition metal nanocontacts whose densities of states have strong d orbital components near the Fermi level. At moderate bias, we find electron transmission between the contacts to be mediated by interface states within the molecular highest-occupied-molecular-orbital-lowest-unoccupied-molecular-orbital gap that arise from hybridization between the thiol-terminated ends of the molecules and the d orbitals of the transition metals. Because these interface states are localized mainly within the metal electrodes, we find their energies to accurately track the electrochemical potentials of the contacts when a variable bias is applied across the junction. We predict resonant enhancement and reduction of the interface state transmission as the applied bias is varied, resulting in negative differential resistance (NDR) in molecular junctions with Pd nanocontacts. We show that these nonlinear phenomena can be tailored by suitably choosing the nanocontact materials: If a Rh electrode is substituted for one Pd contact, we predict enhancement of these NDR effects. The same mechanism is also predicted to give rise to rectification in Pd/molecule/Au junctions. The dependences of the interface state resonances on the orientation of the metal interface, the adsorption site of the molecule, and the separation between the thiolated ends of the molecule and the metal contacts are also discussed.

  14. Quantum Phase Transitions and Collective Modes in d-Wave Superconductors

    NASA Astrophysics Data System (ADS)

    Vojta, Matthias; Sachdev, Subir

    Fluctuations near second-order quantum phase transitions in d-wave superconductors can cause strong damping of fermionic excitations, as observed in photoemission experiments. The damping of the gapless nodal quasiparticles can arise naturally in the quantum-critical region of a transition with an additional spin-singlet, zero momentum order parameter; we argue that the transition to a dx^2-y^2+ i dxy pairing state is the most likely possibility in this category. On the other hand, the gapped antinodal quasiparticles can be strongly damped by the coupling to antiferromagnetic spin fluctuations arising from the proximity to a Neel-ordered state. We review some aspects of the low-energy field theories for both transitions and the corresponding quantum-critical behavior.In addition, we discuss the spectral properties of the collective modes associated with the proximity to a superconductor with dx^2-y^2+ i dxy symmetry, and implications for experiments.

  15. Magnetic Phase Transitions in NdCoAsO

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    McGuire, Michael A; Gout, Delphine J; Garlea, Vasile O

    2010-01-01

    NdCoAsO undergoes three magnetic phase transitions below room temperature. Here we report the results of our experimental investigation of this compound, including determination of the crystal and magnetic structures using powder neutron diffraction, as well as measurements of electrical resistivity, thermal conductivity, Seebeck coefficient, magnetization, and heat capacity. These results show that upon cooling a ferromagnetic state emerges near 69 K with a small saturation moment of -0.2{micro}{sub B}, likely on Co atoms. At 14 K the material enters an antiferromagnetic state with propagation vector (0 0 1/2) and small ordered moments (-0.4{micro}{sub B}) on Co and Nd. Near 3.5more » K a third transition is observed, and corresponds to the antiferromagnetic ordering of larger moments on Nd, with the same propagation vector. The ordered moment on Nd reaches 1.39(5){micro}{sub B} at 300 mK. Anomalies in the magnetization, electrical resistivity, and heat capacity are observed at all three magnetic phase transitions.« less

  16. Transition state region in the A-Band photodissociation of allyl iodide—A femtosecond extreme ultraviolet transient absorption study

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bhattacherjee, Aditi, E-mail: abhattacherjee@berkeley.edu, E-mail: andrewattar@berkeley.edu; Attar, Andrew R., E-mail: abhattacherjee@berkeley.edu, E-mail: andrewattar@berkeley.edu; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720

    2016-03-28

    Femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy based on a high-harmonic generation source is used to study the 266 nm induced A-band photodissociation dynamics of allyl iodide (CH{sub 2} =CHCH{sub 2}I). The photolysis of the C—I bond at this wavelength produces iodine atoms both in the ground ({sup 2}P{sub 3/2}, I) and spin-orbit excited ({sup 2}P{sub 1/2}, I*) states, with the latter as the predominant channel. Using XUV absorption at the iodine N{sub 4/5} edge (45–60 eV), the experiments constitute a direct probe of not only the long-lived atomic iodine reaction products but also the fleeting transition state region ofmore » the repulsive n{sub I}σ{sup ∗}{sub C—I} excited states. Specifically, three distinct features are identified in the XUV transient absorption spectrum at 45.3 eV, 47.4 eV, and 48.4 eV (denoted transients A, B, and C, respectively), which arise from the repulsive valence-excited nσ{sup ∗} states and project onto the high-lying core-excited states of the dissociating molecule via excitation of 4d(I) core electrons. Transients A and B originate from 4d(I) → n(I) core-to-valence transitions, whereas transient C is best assigned to a 4d(I) →σ{sup ∗}(C—I) transition. The measured differential absorbance of these new features along with the I/I* branching ratios known from the literature is used to suggest a more definitive assignment, albeit provisional, of the transients to specific dissociative states within the A-band manifold. The transients are found to peak around 55 fs–65 fs and decay completely by 145 fs–185 fs, demonstrating the ability of XUV spectroscopy to map the evolution of reactants into products in real time. The similarity in the energies of transients A and B with analogous features observed in methyl iodide [Attar et al. J. Phys. Chem. Lett. 6, 5072, (2015)] together with the new observation of transient C in the present work provides a more complete picture of the valence

  17. Spirometric variability in smokers: transitions in COPD diagnosis in a five-year longitudinal study.

    PubMed

    Sood, Akshay; Petersen, Hans; Qualls, Clifford; Meek, Paula M; Vazquez-Guillamet, Rodrigo; Celli, Bartolome R; Tesfaigzi, Yohannes

    2016-11-10

    Spirometrically-defined chronic obstructive pulmonary disease (COPD) is considered progressive but its natural history is inadequately studied. We hypothesized that spirometrically-defined COPD states could undergo beneficial transitions. Participants in the Lovelace Smokers' Cohort (n = 1553), primarily women, were longitudinally studied over 5 years. Spirometric states included normal postbronchodilator spirometry, COPD Stage I, Unclassified state, and COPD Stage II+, as defined by GOLD guidelines. Beneficial transitions included either a decrease in disease severity, including resolution of spirometric abnormality, or maintenance of non-diseased state. 'All smokers' (n = 1553) and subgroups with normal and abnormal spirometry at baseline (n = 956 and 597 respectively) were separately analyzed. Markov-like model of transition probabilities over an average follow-up period of 5 years were calculated. Among 'all smokers', COPD Stage I, Unclassified, and COPD Stage II+ states were associated with probabilities of 16, 39, and 22 % respectively for beneficial transitions, and of 16, 35, and 4 % respectively for resolution. Beneficial transitions were more common for new-onset disease than for pre-existing disease (p < 0.001). Beneficial transitions were less common among older smokers, men, or those with bronchial hyperresponsiveness but more common among Hispanics and smokers with excess weight. This observational study of ever smokers, shows that spirometrically-defined COPD states, may not be uniformly progressive and can improve or resolve over time. The implication of these findings is that the spirometric diagnosis of COPD can be unstable. Furthermore, COPD may have a pre-disease state when interventions might help reverse or change its natural history. NA.

  18. Political transition and emergent forest-conservation issues in Myanmar.

    PubMed

    Prescott, Graham W; Sutherland, William J; Aguirre, Daniel; Baird, Matthew; Bowman, Vicky; Brunner, Jake; Connette, Grant M; Cosier, Martin; Dapice, David; De Alban, Jose Don T; Diment, Alex; Fogerite, Julia; Fox, Jefferson; Hlaing, Win; Htun, Saw; Hurd, Jack; LaJeunesse Connette, Katherine; Lasmana, Felicia; Lim, Cheng Ling; Lynam, Antony; Maung, Aye Chan; McCarron, Benjamin; McCarthy, John F; McShea, William J; Momberg, Frank; Mon, Myat Su; Myint, Than; Oberndorf, Robert; Oo, Thaung Naing; Phelps, Jacob; Rao, Madhu; Schmidt-Vogt, Dietrich; Speechly, Hugh; Springate-Baginski, Oliver; Steinmetz, Robert; Talbott, Kirk; Than, Maung Maung; Thaung, Tint Lwin; Thawng, Salai Cung Lian; Thein, Kyaw Min; Thein, Shwe; Tizard, Robert; Whitten, Tony; Williams, Guy; Wilson, Trevor; Woods, Kevin; Ziegler, Alan D; Zrust, Michal; Webb, Edward L

    2017-12-01

    Political and economic transitions have had substantial impacts on forest conservation. Where transitions are underway or anticipated, historical precedent and methods for systematically assessing future trends should be used to anticipate likely threats to forest conservation and design appropriate and prescient policy measures to counteract them. Myanmar is transitioning from an authoritarian, centralized state with a highly regulated economy to a more decentralized and economically liberal democracy and is working to end a long-running civil war. With these transitions in mind, we used a horizon-scanning approach to assess the 40 emerging issues most affecting Myanmar's forests, including internal conflict, land-tenure insecurity, large-scale agricultural development, demise of state timber enterprises, shortfalls in government revenue and capacity, and opening of new deforestation frontiers with new roads, mines, and hydroelectric dams. Averting these threats will require, for example, overhauling governance models, building capacity, improving infrastructure- and energy-project planning, and reforming land-tenure and environmental-protection laws. Although challenges to conservation in Myanmar are daunting, the political transition offers an opportunity for conservationists and researchers to help shape a future that enhances Myanmar's social, economic, and environmental potential while learning and applying lessons from other countries. Our approach and results are relevant to other countries undergoing similar transitions. © 2017 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

  19. Applying Ecological Site Concepts and State-and-Transition Models to a Grazed Riparian Rangeland

    USDA-ARS?s Scientific Manuscript database

    Ecological site and state-and-transition models are useful tools for generating and testing hypotheses about drivers of vegetation composition in non-equilibrium systems, and have been widely implemented on rangelands. Compared to upland areas, little attention has been given to developing ecologica...

  20. Col1A1 Production and Apoptotic Resistance in TGF-β1-Induced Epithelial-to-Mesenchymal Transition-Like Phenotype of 603B Cells

    PubMed Central

    Liu, Jun; Eischeid, Alex N.; Chen, Xian-Ming

    2012-01-01

    Recent studies have suggested that proliferating cholangiocytes have an important role in the induction of fibrosis, either directly via epithelial-to-mesenchymal transition (EMT), or indirectly via activation of other liver cell types. Transforming growth factor beta 1 (TGF-β1), a critical fibrotic cytokine for hepatic fibrosis, is a potent EMT inducer. This study aimed to clarify the potential contributions of TGF-β1-induced EMT-like cholangiocyte phenotype to collagen production and cell survival of cholangiocytes in vitro. Mouse cholangiocytes (603B cells) were treated with TGF-β1 and EMT-like phenotype alterations were monitored by morphological changes and expression of EMT-associated genes. Alterations in Col1A1 gene, Col1A1-associated miR-29s, and pro-apoptotic genes were measured in TGF-β1-treated 603B cells. Snail1 knockdown was achieved using shRNA to evaluate the contribution of EMT-associated changes to Col1A1 production and cell survival. We found TGF-β1 treatment induced partial EMT-like phenotype transition in 603B cells in a Snail1-dependent manner. TGF-β1 also stimulated collagen α1(I) expression in 603B cells. However, this induction was not parallel to the EMT-like alterations and independent of Snail1 or miR-29 expression. Cells undergoing EMT-like changes showed a modest down-regulation of multiple pro-apoptotic genes and displayed resistance to TNF-α-induced apoptosis. TGF-β1-induced apoptosis resistance was attenuated in Snail1 knockdown 603B cells. TGF-β1-induced Col1A1 production seems to be independent of EMT-like transition and miR-29 expression. Nevertheless, TGF-β1-induced EMT may contribute to the increased survival capacity of cholangiocytes via modulating the expression of pro-apoptotic genes. PMID:23236489