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.

Kinetic mechanism for reversible structural transition in MoTe2 induced by excess charge carriers

NASA Astrophysics Data System (ADS)

Rubel, O.

2018-06-01

Kinetic of a reversible structural transition between insulating (2H) and metallic (1T ') phases in a monolayer MoTe2 due to an electrostatic doping is studied using first-principle calculations. The driving force for the structural transition is the energy gained by transferring excess electrons from the bottom of the conduction band to lower energy gapless states in the metallic phase as have been noticed in earlier studies. The corresponding structural transformation involves dissociation of Mo-Te bonds (one per formula unit), which results in a kinetic energy barrier of 0.83 eV. The transformation involves a consecutive movement of atoms similar to a domain wall motion. The presence of excess charge carriers modifies not only the total energy of the initial and final states, but also lowers an energy of the transition state. An experimentally observed hysteresis in the switching process can be attributed to changes in the kinetic energy barrier due to its dependence on the excess carrier density.

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.

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.

Absorption spectra and optical transitions in InAs/GaAs self-assembled quantum dots

NASA Astrophysics Data System (ADS)

Cusack, M. A.; Briddon, P. R.; Jaros, M.

1997-08-01

We have applied the multiband effective mass/valence force field method to the calculation of optical transitions and absorption spectra in InAs/GaAs self-organized dots of different sizes. We have found that the apparently conflicting assignments of luminescence features to optical transitions in different experiments are in fact entirely compatible with each other. Whether the optical signature of a dot is constructed from transitions between states of the same quantum numbers, or via additional processes between the ground conduction state and a low-lying valence state depends on the aspect ratio of the quantum dot radius and height. The states involved can be predicted from a simple particle in a rigid rectangular box model.

Impact of the Valence Charge of Transition Metals on the Cobalt- and Rhodium-Catalyzed Synthesis of Indenamines, Indenols, and Isoquinolinium Salts: A Catalytic Cycle Involving MIII/MV [M = Co, Rh] for [4+2] Annulation.

PubMed

Chiou, Mong-Feng; Jayakumar, Jayachandran; Cheng, Chien-Hong; Chuang, Shih-Ching

2018-06-13

Reaction mechanisms for the synthesis of indenamines, indenols, and isoquinolinium salts through cobalt- and rhodium-catalysis were investigated using density functional theory calculations. We found that the valence charge of transition metals dramatically influences the reaction pathways. Catalytic reactions involving lower-oxidation-state transition metals (M I /M III , M = Co and Rh) generally favor a [3+2] cyclization pathway, whereas those involving higher oxidation states (M III /M V ) proceed through a [4+2] cyclization pathway. A catalytic cycle with novel M III /M V as a crucial species was successfully revealed for isoquinolinium salts synthesis, which highly valent M V was not only encountered in the [RhCp*]-catalysis but also in the [CoCp*]-catalysis.

Highly excited symmetry-breaking infrared and THz transitions in methanol-D 1

NASA Astrophysics Data System (ADS)

Mukhopadhyay, Indranath

2004-06-01

In this paper, symmetry-breaking transitions have been identified in the Fourier transform infrared (FTIR) and Terra Hertz (THz) fast scan spectra of asymmetrically deuterated methanol CH 2DOH involving three quanta of the lowest lying vibrational state ( ν1). These transitions have an upper state belonging to highly excited torsional state with the torsional quantum number v=11 (e 5) (with the axial component of total rotational angular momentum K=5 and 6) in the Internal Axis Method (IAM) formalism developed by Quade and his co-workers [J. Mol. Spectrosc. 146 (1991) 238; J. Mol. Spectrosc. 146 (1991) 252], which was later extended by Mukhopadhyay [Spectrochim. Acta A 53 (1997) 2457; Spectrochim. Acta A 53 (1997) 1947] to include highly excited torsional-rotational states. The originating lower states belong to the o 1 ( v=3) with K=4 and 5. In analogy with pure methanol these transitions terminate to the third excited torsional state, which has very small torsional matrix elements to be observable in normal FTIR spectra. The location of the e 5 states suggests that the calculated energy levels using the parameters of Liu and Quade [J. Mol. Spectrosc. 146 (1991) 252] are reasonable and very helpful to assign such highly excited transitions, considering that their studies include low angular momentum states. In addition the very existence of these transitions proves that the matrix elements calculated by Mukhopadhyay [Spectrochim. Acta A 53 (1997) 1947] are very useful and dependable. Thus they represent a valuable tool for entangling the complex spectrum of this asymmetrically deuterated methanol. In order to provide confirmatory evidence the THz spectra obtained using the Fast Scanning Submillimeter Spectroscopy Technique (FASSST) at the Ohio State University [Rev. Instr. 68 (1997) 1675; Anal. Chem. 70 (1998) 719A] were searched for the ground state transitions that can be calculated precisely from IR combination relations. All the transitions that can be predicted with K=4 and 5 in the o 1 states are indeed identified in the FASSST spectrum. To our knowledge this is the first reported work involving direct transitions to such highly excited torsional state of CH 2DOH. This work will enable the determination of higher order barrier terms and provide enough understanding of the energy levels for the identification of many unidentified transitions. To our knowledge, this is the first time such high frequency symmetry-breaking transitions have been observed in asymmetrically deuterated methanol.

Approaches to incorporating climate change effects in state and transition simulation models of vegetation

Treesearch

Becky K. Kerns; Miles A. Hemstrom; David Conklin; Gabriel I. Yospin; Bart Johnson; Dominique Bachelet; Scott Bridgham

2012-01-01

Understanding landscape vegetation dynamics often involves the use of scientifically-based modeling tools that are capable of testing alternative management scenarios given complex ecological, management, and social conditions. State-and-transition simulation model (STSM) frameworks and software such as PATH and VDDT are commonly used tools that simulate how landscapes...

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.

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

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

Factors associated with successful transition among children with disabilities in eight European countries

PubMed Central

2017-01-01

Introduction This research paper aims to assess factors reported by parents associated with the successful transition of children with complex additional support requirements that have undergone a transition between school environments from 8 European Union member states. Methods Quantitative data were collected from 306 parents within education systems from 8 EU member states (Bulgaria, Cyprus, Greece, Ireland, the Netherlands, Romania, Spain and the UK). The data were derived from an online questionnaire and consisted of 41 questions. Information was collected on: parental involvement in their child’s transition, child involvement in transition, child autonomy, school ethos, professionals’ involvement in transition and integrated working, such as, joint assessment, cooperation and coordination between agencies. Survey questions that were designed on a Likert-scale were included in the Principal Components Analysis (PCA), additional survey questions, along with the results from the PCA, were used to build a logistic regression model. Results Four principal components were identified accounting for 48.86% of the variability in the data. Principal component 1 (PC1), ‘child inclusive ethos,’ contains 16.17% of the variation. Principal component 2 (PC2), which represents child autonomy and involvement, is responsible for 8.52% of the total variation. Principal component 3 (PC3) contains questions relating to parental involvement and contributed to 12.26% of the overall variation. Principal component 4 (PC4), which involves transition planning and coordination, contributed to 11.91% of the overall variation. Finally, the principal components were included in a logistic regression to evaluate the relationship between inclusion and a successful transition, as well as whether other factors that may have influenced transition. All four principal components were significantly associated with a successful transition, with PC1 being having the most effect (OR: 4.04, CI: 2.43–7.18, p<0.0001). Discussion To support a child with complex additional support requirements through transition from special school to mainstream, governments and professionals need to ensure children with additional support requirements and their parents are at the centre of all decisions that affect them. It is important that professionals recognise the educational, psychological, social and cultural contexts of a child with additional support requirements and their families which will provide a holistic approach and remove barriers for learning. PMID:28636649

Factors associated with successful transition among children with disabilities in eight European countries.

PubMed

Ravenscroft, John; Wazny, Kerri; Davis, John M

2017-01-01

This research paper aims to assess factors reported by parents associated with the successful transition of children with complex additional support requirements that have undergone a transition between school environments from 8 European Union member states. Quantitative data were collected from 306 parents within education systems from 8 EU member states (Bulgaria, Cyprus, Greece, Ireland, the Netherlands, Romania, Spain and the UK). The data were derived from an online questionnaire and consisted of 41 questions. Information was collected on: parental involvement in their child's transition, child involvement in transition, child autonomy, school ethos, professionals' involvement in transition and integrated working, such as, joint assessment, cooperation and coordination between agencies. Survey questions that were designed on a Likert-scale were included in the Principal Components Analysis (PCA), additional survey questions, along with the results from the PCA, were used to build a logistic regression model. Four principal components were identified accounting for 48.86% of the variability in the data. Principal component 1 (PC1), 'child inclusive ethos,' contains 16.17% of the variation. Principal component 2 (PC2), which represents child autonomy and involvement, is responsible for 8.52% of the total variation. Principal component 3 (PC3) contains questions relating to parental involvement and contributed to 12.26% of the overall variation. Principal component 4 (PC4), which involves transition planning and coordination, contributed to 11.91% of the overall variation. Finally, the principal components were included in a logistic regression to evaluate the relationship between inclusion and a successful transition, as well as whether other factors that may have influenced transition. All four principal components were significantly associated with a successful transition, with PC1 being having the most effect (OR: 4.04, CI: 2.43-7.18, p<0.0001). To support a child with complex additional support requirements through transition from special school to mainstream, governments and professionals need to ensure children with additional support requirements and their parents are at the centre of all decisions that affect them. It is important that professionals recognise the educational, psychological, social and cultural contexts of a child with additional support requirements and their families which will provide a holistic approach and remove barriers for learning.

Realization of a Λ System with Metastable States of a Capacitively Shunted Fluxonium.

PubMed

Earnest, N; Chakram, S; Lu, Y; Irons, N; Naik, R K; Leung, N; Ocola, L; Czaplewski, D A; Baker, B; Lawrence, Jay; Koch, Jens; Schuster, D I

2018-04-13

We realize a Λ system in a superconducting circuit, with metastable states exhibiting lifetimes up to 8 ms. We exponentially suppress the tunneling matrix elements involved in spontaneous energy relaxation by creating a "heavy" fluxonium, realized by adding a capacitive shunt to the original circuit design. The device allows for both cavity-assisted and direct fluorescent readouts, as well as state preparation schemes akin to optical pumping. Since direct transitions between the metastable states are strongly suppressed, we utilize Raman transitions for coherent manipulation of the states.

Realization of a Λ System with Metastable States of a Capacitively Shunted Fluxonium

NASA Astrophysics Data System (ADS)

Earnest, N.; Chakram, S.; Lu, Y.; Irons, N.; Naik, R. K.; Leung, N.; Ocola, L.; Czaplewski, D. A.; Baker, B.; Lawrence, Jay; Koch, Jens; Schuster, D. I.

2018-04-01

We realize a Λ system in a superconducting circuit, with metastable states exhibiting lifetimes up to 8 ms. We exponentially suppress the tunneling matrix elements involved in spontaneous energy relaxation by creating a "heavy" fluxonium, realized by adding a capacitive shunt to the original circuit design. The device allows for both cavity-assisted and direct fluorescent readouts, as well as state preparation schemes akin to optical pumping. Since direct transitions between the metastable states are strongly suppressed, we utilize Raman transitions for coherent manipulation of the states.

Speeding Up Sigmatropic Shifts-To Halve or to Hold.

PubMed

Tantillo, Dean J

2016-04-19

Catalysis is common. Rational catalyst design, however, is at the frontier of chemical science. Although the histories of physical organic and synthetic organic chemistry boast key chapters involving [3s,3s] sigmatropic shifts, catalysis of these reactions is much less common than catalysis of ostensibly more complex processes. The comparative dearth of catalysts for sigmatropic shifts is perhaps a result of the perception that transition state structures for these reactions, like their reactants, are nonpolar and therefore not amenable to selective stabilization and its associated barrier lowering. However, as demonstrated in this Account, transition state structures for [3s,3s] sigmatropic shifts can in fact have charge distributions that differ significantly from those of reactants, even for hydrocarbon substrates, allowing for barriers to be decreased and rates increased. In some cases, differences in charge distribution result from the inclusion of heteroatoms at specific positions in reactants, but in other cases differences are actually induced by catalysts. Perhaps surprisingly, strategies for complexation of transition state structures that remain nonpolar are also possible. In general, the strategies for catalysis employed can be characterized as involving either mechanistic intervention, where a catalyst induces a change from the concerted mechanism expected for a [3s,3s] sigmatropic shift to a multistep process (cutting the transformation into halves or smaller pieces) whose overall barrier is decreased relative to the concerted process, or transition state complexation, where a catalyst simply binds (holds) more tightly to the transition state structure for a [3s,3s] sigmatropic shift than to the reactant, leading to a lower barrier in the presence of the catalyst. Both of these strategies can be considered to be biomimetic in that enzymes frequently induce multistep processes and utilize selective transition state stabilization for the steps involved. In addition, transition state complexation was the principle around which catalytic antibodies were originally designed. The field of catalysis of sigmatropic shifts is now ready for rational design. The studies described here all provide evidence for the origins of rate acceleration, derived in large part from the results of quantum chemical calculations, that can now be applied to the design of new catalysts for [3s,3s] and other sigmatropic shifts.

An intermittency route to global instability in low-density jets

NASA Astrophysics Data System (ADS)

Murugesan, Meenatchidevi; Zhu, Yuanhang; Li, Larry K. B.

2017-11-01

Above a critical Reynolds number (Re), a low-density jet can become globally unstable, transitioning from a steady state (i.e. a fixed point) to a self-excited oscillatory state (i.e. a limit cycle) via a Hopf bifurcation. In this experimental study, we show that this transition can sometimes involve intermittency. When Re is just slightly above the critical point, intermittent bursts of high-amplitude periodic oscillations emerge amidst a background of low-amplitude aperiodic fluctuations. As Re increases further, these intermittent bursts persist longer in time until they dominate the overall dynamics, causing the jet to transition fully to a periodic limit cycle. We identify this as Type-II Pomeau-Manneville intermittency by quantifying the statistical distribution of the duration of the aperiodic fluctuations at the onset of intermittency. This study shows that the transition to global instability in low-density jets is not always abrupt but can involve an intermediate state with characteristics of both the initial fixed point and the final limit cycle. This work was supported by the Research Grants Council of Hong Kong (Project No. 16235716 and 26202815).

Metabolite profiling and associated gene expression reveal two metabolic shifts during the seed-to-seedling transition in Arabidopsis thaliana.

PubMed

Silva, Anderson Tadeu; Ligterink, Wilco; Hilhorst, Henk W M

2017-11-01

Metabolic and transcriptomic correlation analysis identified two distinctive profiles involved in the metabolic preparation for seed germination and seedling establishment, respectively. Transcripts were identified that may control metabolic fluxes. The transition from a quiescent metabolic state (dry seed) to the active state of a vigorous seedling is crucial in the plant's life cycle. We analysed this complex physiological trait by measuring the changes in primary metabolism that occur during the transition in order to determine which metabolic networks are operational. The transition involves several developmental stages from seed germination to seedling establishment, i.e. between imbibition of the mature dry seed and opening of the cotyledons, the final stage of seedling establishment. We hypothesized that the advancement of growth is associated with certain signature metabolite profiles. Metabolite-metabolite correlation analysis underlined two specific profiles which appear to be involved in the metabolic preparation for seed germination and efficient seedling establishment, respectively. Metabolite profiles were also compared to transcript profiles and although transcriptional changes did not always equate to a proportional metabolic response, in depth correlation analysis identified several transcripts that may directly influence the flux through metabolic pathways during the seed-to-seedling transition. This correlation analysis also pinpointed metabolic pathways which are significant for the seed-to-seedling transition, and metabolite contents that appeared to be controlled directly by transcript abundance. This global view of the transcriptional and metabolic changes during the seed-to-seedling transition in Arabidopsis opens up new perspectives for understanding the complex regulatory mechanism underlying this transition.

Revealing the halide effect on the kinetics of the aerobic oxidation of Cu(I) to Cu(II)

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

Deng, Yi; Zhang, Guanghui; Qi, Xiaotian

2015-01-01

In situ infrared (IR) and X-ray absorption near-edge structure (XANES) spectroscopic investigations reveal that different halide ligands have distinct effects on the aerobic oxidation of Cu(I) to Cu(II) in the presence of TMEDA (tetramethylethylenediamine). The iodide ligand gives the lowest rate and thus leads to the lowest catalytic reaction rate of aerobic oxidation of hydroquinone to benzoquinone. Further DFT calculations suggest that oxidation of CuI–TMEDA involves a side-on transition state, while oxidation of CuCl–TMEDA involves an end-on transition state which has a lower activation energy.

State-Chart Autocoder

NASA Technical Reports Server (NTRS)

Clark, Kenneth; Watney, Garth; Murray, Alexander; Benowitz, Edward

2007-01-01

A computer program translates Unified Modeling Language (UML) representations of state charts into source code in the C, C++, and Python computing languages. ( State charts signifies graphical descriptions of states and state transitions of a spacecraft or other complex system.) The UML representations constituting the input to this program are generated by using a UML-compliant graphical design program to draw the state charts. The generated source code is consistent with the "quantum programming" approach, which is so named because it involves discrete states and state transitions that have features in common with states and state transitions in quantum mechanics. Quantum programming enables efficient implementation of state charts, suitable for real-time embedded flight software. In addition to source code, the autocoder program generates a graphical-user-interface (GUI) program that, in turn, generates a display of state transitions in response to events triggered by the user. The GUI program is wrapped around, and can be used to exercise the state-chart behavior of, the generated source code. Once the expected state-chart behavior is confirmed, the generated source code can be augmented with a software interface to the rest of the software with which the source code is required to interact.

A uniform transit safety records system for the Commonwealth of Virginia.

DOT National Transportation Integrated Search

1981-01-01

This study was conceived as the first phase of a three-phase program to develop a safety data base for intracity bus transit. It involved reviewing the state of the art of general transportation safety management, examining the current intracity bus ...

The Millimeter- and Submillimeter-Wave Spectrum of Gauche-Ethyl Alcohol

NASA Technical Reports Server (NTRS)

Pearson, J. C.; Sastry, K. V. L. N.; Herbst, Eric; DeLucia, Frank C.

1996-01-01

We report an investigation of the rotational-torsional spectrum of the gauche rotational isomers of ethyl alcohol in the 51-505 GHz frequency region. Over a thousand transitions between rotational levels in the gauche substates of the ground OH torsional state have been measured and assigned. These transitions involve rotational quantum numbers J and K(sub a) up to 30 and 15, respectively, and are of two types: alpha-type transitions between levels in either the gauche+ or the gauche-substate, and c-type transitions between rotational levels in the different substates. The majority of these transitions have been fit satisfactorily using a two-state Hamiltonian based on the Fixed Framework Axis Method (FFAM). The rotation, distortion, and interaction constants have been determined along with the energy difference between the two gauche substates. The derived constants can be used to predict many more transitions accurately for astronomical purposes. The J and K(sub a) region where the two-state analysis can be used has been determined. The basis for a three-state analysis including the trans substate is presented and the applicability of the FFAM approach is discussed.

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

PubMed

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

2011-11-07

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

Mechanism and the origins of stereospecificity in copper-catalyzed ring expansion of vinyl oxiranes: a traceless dual transition-metal-mediated process.

PubMed

Mustard, Thomas J L; Mack, Daniel J; Njardarson, Jon T; Cheong, Paul Ha-Yeon

2013-01-30

Density functional theory computations of the Cu-catalyzed ring expansion of vinyloxiranes is mediated by a traceless dual Cu(I)-catalyst mechanism. Overall, the reaction involves a monomeric Cu(I)-catalyst, but a single key step, the Cu migration, requires two Cu(I)-catalysts for the transformation. This dual-Cu step is found to be a true double Cu(I) transition state rather than a single Cu(I) transition state in the presence of an adventitious, spectator Cu(I). Both Cu(I) catalysts are involved in the bond forming and breaking process. The single Cu(I) transition state is not a stationary point on the potential energy surface. Interestingly, the reductive elimination is rate-determining for the major diastereomeric product, while the Cu(I) migration step is rate-determining for the minor. Thus, while the reaction requires dual Cu(I) activation to proceed, kinetically, the presence of the dual-Cu(I) step is untraceable. The diastereospecificity of this reaction is controlled by the Cu migration step. Suprafacial migration is favored over antarafacial migration due to the distorted Cu π-allyl in the latter.

Origin of Stereodivergence in Cooperative Asymmetric Catalysis with Simultaneous Involvement of Two Chiral Catalysts.

PubMed

Bhaskararao, Bangaru; Sunoj, Raghavan B

2015-12-23

Accomplishing high diastereo- and enantioselectivities simultaneously is a persistent challenge in asymmetric catalysis. The use of two chiral catalysts in one-pot conditions might offer new avenues to this end. Chirality transfer from a catalyst to product gets increasingly complex due to potential chiral match-mismatch issues. The origin of high enantio- and diastereoselectivities in the reaction between a racemic aldehyde and an allyl alcohol, catalyzed by using axially chiral iridium phosphoramidites PR/S-Ir and cinchona amine is established through transition-state modeling. The multipoint contact analysis of the stereocontrolling transition state revealed how the stereodivergence could be achieved by inverting the configuration of the chiral catalysts that are involved in the activation of the reacting partners. While the enantiocontrol is identified as being decided in the generation of PR/S-Ir-π-allyl intermediate from the allyl alcohol, the diastereocontrol arises due to the differential stabilizations in the C-C bond formation transition states. The analysis of the weak interactions in the transition states responsible for chiral induction revealed that the geometric disposition of the quinoline ring at the C8 chiral carbon of cinchona-enamine plays an anchoring role. The quinolone ring is noted as participating in a π-stacking interaction with the phenyl ring of the Ir-π-allyl moiety in the case of PR with the (8R,9R)-cinchona catalyst combination, whereas a series of C-H···π interactions is identified as vital to the relative stabilization of the stereocontrolling transition states when PR is used with (8S,9S)-cinchona.

Integration of kinetic isotope effect analyses to elucidate ribonuclease mechanism.

PubMed

Harris, Michael E; Piccirilli, Joseph A; York, Darrin M

2015-11-01

The well-studied mechanism of ribonuclease A is believed to involve concerted general acid-base catalysis by two histidine residues, His12 and His119. The basic features of this mechanism are often cited to explain rate enhancement by both protein and RNA enzymes that catalyze RNA 2'-O-transphosphorylation. Recent kinetic isotope effect analyses and computational studies are providing a more chemically detailed description of the mechanism of RNase A and the rate limiting transition state. Overall, the results support an asynchronous mechanism for both solution and ribonuclease catalyzed reactions in which breakdown of a transient dianoinic phosphorane intermediate by 5'OP bond cleavage is rate limiting. Relative to non-enzymatic reactions catalyzed by specific base, a smaller KIE on the 5'O leaving group and a less negative βLG are observed for RNase A catalysis. Quantum mechanical calculations consistent with these data support a model in which electrostatic and H-bonding interactions with the non-bridging oxygens and proton transfer from His119 render departure of the 5'O less advanced and stabilize charge buildup in the transition state. Both experiment and computation indicate advanced 2'OP bond formation in the rate limiting transition state. However, this feature makes it difficult to resolve the chemical steps involved in 2'O activation. Thus, modeling the transition state for RNase A catalysis underscores those elements of its chemical mechanism that are well resolved, as well as highlighting those where ambiguity remains. This article is part of a Special Issue entitled: Enzyme Transition States from Theory and Experiment. Published by Elsevier B.V.

Energetic and spatial parameters for gating of the bacterial large conductance mechanosensitive channel, MscL

NASA Technical Reports Server (NTRS)

Sukharev, S. I.; Sigurdson, W. J.; Kung, C.; Sachs, F.

1999-01-01

MscL is multimeric protein that forms a large conductance mechanosensitive channel in the inner membrane of Escherichia coli. Since MscL is gated by tension transmitted through the lipid bilayer, we have been able to measure its gating parameters as a function of absolute tension. Using purified MscL reconstituted in liposomes, we recorded single channel currents and varied the pressure gradient (P) to vary the tension (T). The tension was calculated from P and the radius of curvature was obtained using video microscopy of the patch. The probability of being open (Po) has a steep sigmoidal dependence on T, with a midpoint (T1/2) of 11.8 dyn/cm. The maximal slope sensitivity of Po/Pc was 0.63 dyn/cm per e-fold. Assuming a Boltzmann distribution, the energy difference between the closed and fully open states in the unstressed membrane was DeltaE = 18.6 kBT. If the mechanosensitivity arises from tension acting on a change of in-plane area (DeltaA), the free energy, TDeltaA, would correspond to DeltaA = 6.5 nm2. MscL is not a binary channel, but has four conducting states and a closed state. Most transition rates are independent of tension, but the rate-limiting step to opening is the transition between the closed state and the lowest conductance substate. This transition thus involves the greatest DeltaA. When summed over all transitions, the in-plane area change from closed to fully open was 6 nm2, agreeing with the value obtained in the two-state analysis. Assuming a cylindrical channel, the dimensions of the (fully open) pore were comparable to DeltaA. Thus, the tension dependence of channel gating is primarily one of increasing the external channel area to accommodate the pore of the smallest conducting state. The higher conducting states appear to involve conformational changes internal to the channel that don't involve changes in area.

Involvement of Youth with Disabilities in State-Level Decision Making. inForum

ERIC Educational Resources Information Center

Muller, Eve

2007-01-01

During the National Association of State Directors of Special Education's (NASDSE) 2005 annual meeting, a panel of youth representatives challenged states to do a better job of including youth with disabilities in state-level decision making (e.g., as members of state advisory panels [SAPs] and/or transition councils). State directors of special…

Dynamics of the His79-heme alkaline transition of yeast iso-1-cytochrome c probed by conformationally gated electron transfer with Co(II)bis(terpyridine).

PubMed

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

2013-08-28

Alkaline conformers of cytochrome c may be involved in both its electron transport and apoptotic functions. We use cobalt(II)bis(terpyridine), Co(terpy)2(2+), as a reagent for conformationally gated electron-transfer (gated ET) experiments to study the alkaline conformational transition of K79H variants of yeast iso-1-cytochrome c expressed in Escherichia coli , WT*K79H, with alanine at position 72 and Saccharomyces cerevisiae , yK79H, with trimethyllysine (Tml) at position 72. Co(terpy)2(2+) is well-suited to the 100 ms to 1 s time scale of the His79-mediated alkaline conformational transition of these variants. Reduction of the His79-heme alkaline conformer by Co(terpy)2(2+) occurs primarily by gated ET, which involves conversion to the native state followed by reduction, with a small fraction of the His79-heme alkaline conformer directly reduced by Co(terpy)2(2+). The gated ET experiments show that the mechanism of formation of the His79-heme alkaline conformer involves only two ionizable groups. In previous work, we showed that the mechanism of the His73-mediated alkaline conformational transition requires three ionizable groups. Thus, the mechanism of heme crevice opening depends upon the position of the ligand mediating the process. The microscopic rate constants provided by gated ET studies show that mutation of Tml72 (yK79H variant) in the heme crevice loop to Ala72 (WT*K79H variant) affects the dynamics of heme crevice opening through a small destabilization of both the native conformer and the transition state relative to the His79-heme alkaline conformer. Previous pH jump data had indicated that the Tml72→Ala mutation primarily stabilized the transition state for the His79-mediated alkaline conformational transition.

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

PubMed Central

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

2013-01-01

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

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.

Near 16 micron CO.sub.2 laser system

DOEpatents

Krupke, William F.

1977-01-01

Method and apparatus for inducing laser action in CO.sub.2 at a wavelength of 16 microns involving the transition between the 02.sup.0 0 and 01.sup.1 0 states. The population inversion between these two states is achieved by pumping to the 00.sup.0 1 level, suppressing the usual 10.6 micron transition to the 10.sup.0 0 level and encouraging the 9.6 micron transition, thereby populating the 02.sup.0 0 level, as the principal prerequisite for 16 micron laser action between the 02.sup.0 0 and 01.sup.1 0 levels.

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. PMID:24699246

Amorphous-amorphous transition in a porous coordination polymer.

PubMed

Ohtsu, Hiroyoshi; Bennett, Thomas D; Kojima, Tatsuhiro; Keen, David A; Niwa, Yasuhiro; Kawano, Masaki

2017-07-04

The amorphous state plays a key role in porous coordination polymer and metal-organic framework phase transitions. We investigate a crystalline-to-amorphous-to-amorphous-to-crystalline (CAAC) phase transition in a Zn based coordination polymer, by X-ray absorption fine structure (XAFS) and X-ray pair distribution function (PDF) analysis. We show that the system shows two distinct amorphous phases upon heating. The first involves a reversible transition to a desolvated form of the original network, followed by an irreversible transition to an intermediate phase which has elongated Zn-I bonds.

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.

Fixation times in differentiation and evolution in the presence of bottlenecks, deserts, and oases.

PubMed

Chou, Tom; Wang, Yu

2015-05-07

Cellular differentiation and evolution are stochastic processes that can involve multiple types (or states) of particles moving on a complex, high-dimensional state-space or "fitness" landscape. Cells of each specific type can thus be quantified by their population at a corresponding node within a network of states. Their dynamics across the state-space network involve genotypic or phenotypic transitions that can occur upon cell division, such as during symmetric or asymmetric cell differentiation, or upon spontaneous mutation. Here, we use a general multi-type branching processes to study first passage time statistics for a single cell to appear in a specific state. Our approach readily allows for nonexponentially distributed waiting times between transitions, reflecting, e.g., the cell cycle. For simplicity, we restrict most of our detailed analysis to exponentially distributed waiting times (Poisson processes). We present results for a sequential evolutionary process in which L successive transitions propel a population from a "wild-type" state to a given "terminally differentiated," "resistant," or "cancerous" state. Analytic and numeric results are also found for first passage times across an evolutionary chain containing a node with increased death or proliferation rate, representing a desert/bottleneck or an oasis. Processes involving cell proliferation are shown to be "nonlinear" (even though mean-field equations for the expected particle numbers are linear) resulting in first passage time statistics that depend on the position of the bottleneck or oasis. Our results highlight the sensitivity of stochastic measures to cell division fate and quantify the limitations of using certain approximations (such as the fixed-population and mean-field assumptions) in evaluating fixation times. Published by Elsevier Ltd.

Electronic spectroscopy of diatomic molecules

NASA Technical Reports Server (NTRS)

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

1994-01-01

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

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

Theoretical Study of Energy Levels and Transition Probabilities of Boron Atom

NASA Astrophysics Data System (ADS)

Tian Yi, Zhang; Neng Wu, Zheng

2009-08-01

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

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.

On the vibronic level structure in the NO3 radical. Part III. Observation of intensity borrowing via ground state mixing.

PubMed

Stanton, John F; Okumura, Mitchio

2009-06-21

The A(2)E''<-- X(2)A'(2) absorption spectrum exhibits vibronically allowed transitions from the ground state of NO(3) to upper state levels having a''(1) and e' vibronic symmetries. This paper explores the coupling mechanisms that lend intensities to these features. While transitions to e' vibronic levels borrow intensity from the very strong B(2)E'<-- X(2)A'(2) electronic transition, those to a''(1) levels involve only negligible upper-state borrowing effects. Rather, it is the vibronic mixing of the ground vibronic level of NO(3) with vibrational levels in the B(2)E' electronic state that permit the a''(1) levels to be seen in the spectrum. These ideas are supported by vibronic coupling calculations. The fact that the intensities of features corresponding to the two different vibronic symmetries are comparable is thus accidental.

Laser Induced Optical Pumping Measurements of Cross Sections for Fine and Hyperfine Structure Transitions in Sodium Induced by Collisions with Helium Argon Atoms

NASA Technical Reports Server (NTRS)

Dobson, Chris C.; Sung, C. C.

1998-01-01

Optical pumping of the ground states of sodium can radically alter the shape of the laser induced fluorescence excitation spectrum, complicating measurements of temperature, pressure, etc., which are based on these spectra. Modeling of the fluorescence using rate equations for the eight hyperfine states of the sodium D manifolds can be used to quantify the contribution to the ground state pumping of transitions among the hyperfine excited states induced by collisions with buffer gas atoms. This model is used here to determine, from the shape of experimental spectra, cross sections for (Delta)F transitions of the P(sub 3/2) state induced by collisions with helium and argon atoms, for a range of values assumed for the P(sub 1/2), (Delta)F cross sections. The hyperfine cross sections measured using this method, which is thought to be novel, are compared with cross sections for transitions involving polarized magnetic substates, m(sub F), measured previously using polarization sensitive absorption. Also, fine structure transition ((Delta)J) cross sections were measured in the pumped vapor, giving agreement with previous measurements made in the absence of pumping.

Laser-Induced Optical Pumping Measurements of Cross Section for Fine- and Hyperfine-Structure Transitions in Sodium Induced by Collisions with Helium and Argon Atoms

NASA Technical Reports Server (NTRS)

Dobson, Chris C.; Sung, C. C.

1999-01-01

Optical pumping of the ground states of sodium can radically alter the shape of the laser-induced fluorescence excitation spectrum, complicating measurements of temperature, pressure, etc., which are based on these spectra. Modeling of the fluorescence using rate equations for the eight hyperfine states of the sodium D manifolds can be used to quantify the contribution to the ground state pumping of transitions among the hyperfine excited states induced by collisions with buffer gas atoms. This model is used here to determine, from the shape of experimental spectra, cross sections lor DELTA.F transitions of the P(sub 3/2) state induced by collisions with helium and argon atoms, for a range of values assumed for the P(sub 1/2), DELTA.F cross sections. The hyperfine cross sections measured using this method, which to our knowledge is novel, are compared with cross sections for transitions involving polarized magnetic substates m(sub F) measured previously using polarization sensitive absorption. Also, fine-structure transition cross sections were measured in the pumped vapor, giving agreement with previous measurements made in the absence of pumping.

Band structure dynamics in indium wires

NASA Astrophysics Data System (ADS)

Chávez-Cervantes, M.; Krause, R.; Aeschlimann, S.; Gierz, I.

2018-05-01

One-dimensional indium wires grown on Si(111) substrates, which are metallic at high temperatures, become insulating below ˜100 K due to the formation of a charge density wave (CDW). The physics of this transition is not conventional and involves a multiband Peierls instability with strong interband coupling. This CDW ground state is readily destroyed with femtosecond laser pulses resulting in a light-induced insulator-to-metal phase transition. The current understanding of this transition remains incomplete, requiring measurements of the transient electronic structure to complement previous investigations of the lattice dynamics. Time- and angle-resolved photoemission spectroscopy with extreme ultraviolet radiation is applied to this end. We find that the transition from the insulating to the metallic band structure occurs within ˜660 fs, which is a fraction of the amplitude mode period. The long lifetime of the transient state (>100 ps) is attributed to trapping in a metastable state in accordance with previous work.

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.

Incommensurate Chirality Density Wave Transition in a Hybrid Molecular Framework.

PubMed

Hill, Joshua A; Christensen, Kirsten E; Goodwin, Andrew L

2017-09-15

Using single-crystal x-ray diffraction we characterize the 235 K incommensurate phase transition in the hybrid molecular framework tetraethylammonium silver(I) dicyanoargentate, [NEt_{4}]Ag_{3}(CN)_{4}. We demonstrate the transition to involve spontaneous resolution of chiral [NEt_{4}]^{+} conformations, giving rise to a state in which molecular chirality is incommensurately modulated throughout the crystal lattice. We refer to this state as an incommensurate chirality density wave (XDW) phase, which represents a fundamentally new type of chiral symmetry breaking in the solid state. Drawing on parallels to the incommensurate ferroelectric transition of NaNO_{2}, we suggest the XDW state arises through coupling between acoustic (shear) and molecular rotoinversion modes. Such coupling is symmetry forbidden at the Brillouin zone center but symmetry allowed for small but finite modulation vectors q=[0,0,q_{z}]^{*}. The importance of long-wavelength chirality modulations in the physics of this hybrid framework may have implications for the generation of mesoscale chiral textures, as required for advanced photonic materials.

Incommensurate Chirality Density Wave Transition in a Hybrid Molecular Framework

NASA Astrophysics Data System (ADS)

Hill, Joshua A.; Christensen, Kirsten E.; Goodwin, Andrew L.

2017-09-01

Using single-crystal x-ray diffraction we characterize the 235 K incommensurate phase transition in the hybrid molecular framework tetraethylammonium silver(I) dicyanoargentate, [NEt4]Ag3(CN )4 . We demonstrate the transition to involve spontaneous resolution of chiral [NEt4]+ conformations, giving rise to a state in which molecular chirality is incommensurately modulated throughout the crystal lattice. We refer to this state as an incommensurate chirality density wave (XDW) phase, which represents a fundamentally new type of chiral symmetry breaking in the solid state. Drawing on parallels to the incommensurate ferroelectric transition of NaNO2 , we suggest the XDW state arises through coupling between acoustic (shear) and molecular rotoinversion modes. Such coupling is symmetry forbidden at the Brillouin zone center but symmetry allowed for small but finite modulation vectors q =[0 ,0 ,qz]* . The importance of long-wavelength chirality modulations in the physics of this hybrid framework may have implications for the generation of mesoscale chiral textures, as required for advanced photonic materials.

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

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.

The origin of life is a spatially localized stochastic transition

PubMed Central

2012-01-01

Background Life depends on biopolymer sequences as catalysts and as genetic material. A key step in the Origin of Life is the emergence of an autocatalytic system of biopolymers. Here we study computational models that address the way a living autocatalytic system could have emerged from a non-living chemical system, as envisaged in the RNA World hypothesis. Results We consider (i) a chemical reaction system describing RNA polymerization, and (ii) a simple model of catalytic replicators that we call the Two’s Company model. Both systems have two stable states: a non-living state, characterized by a slow spontaneous rate of RNA synthesis, and a living state, characterized by rapid autocatalytic RNA synthesis. The origin of life is a transition between these two stable states. The transition is driven by stochastic concentration fluctuations involving relatively small numbers of molecules in a localized region of space. These models are simulated on a two-dimensional lattice in which reactions occur locally on single sites and diffusion occurs by hopping of molecules to neighbouring sites. Conclusions If diffusion is very rapid, the system is well-mixed. The transition to life becomes increasingly difficult as the lattice size is increased because the concentration fluctuations that drive the transition become relatively smaller when larger numbers of molecules are involved. In contrast, when diffusion occurs at a finite rate, concentration fluctuations are local. The transition to life occurs in one local region and then spreads across the rest of the surface. The transition becomes easier with larger lattice sizes because there are more independent regions in which it could occur. The key observations that apply to our models and to the real world are that the origin of life is a rare stochastic event that is localized in one region of space due to the limited rate of diffusion of the molecules involved and that the subsequent spread across the surface is deterministic. It is likely that the time required for the deterministic spread is much shorter than the waiting time for the origin, in which case life evolves only once on a planet, and then rapidly occupies the whole surface. Reviewers Reviewed by Omer Markovitch (nominated by Doron Lancet), Claus Wilke, and Nobuto Takeuchi (nominated by Eugene Koonin). PMID:23176307

Enhanced sampling by multiple molecular dynamics trajectories: carbonmonoxy myoglobin 10 micros A0-->A(1-3) transition from ten 400 picosecond simulations.

PubMed

Loccisano, Anne E; Acevedo, Orlando; DeChancie, Jason; Schulze, Brita G; Evanseck, Jeffrey D

2004-05-01

The utility of multiple trajectories to extend the time scale of molecular dynamics simulations is reported for the spectroscopic A-states of carbonmonoxy myoglobin (MbCO). Experimentally, the A0-->A(1-3) transition has been observed to be 10 micros at 300 K, which is beyond the time scale of standard molecular dynamics simulations. To simulate this transition, 10 short (400 ps) and two longer time (1.2 ns) molecular dynamics trajectories, starting from five different crystallographic and solution phase structures with random initial velocities centered in a 37 A radius sphere of water, have been used to sample the native-fold of MbCO. Analysis of the ensemble of structures gathered over the cumulative 5.6 ns reveals two biomolecular motions involving the side chains of His64 and Arg45 to explain the spectroscopic states of MbCO. The 10 micros A0-->A(1-3) transition involves the motion of His64, where distance between His64 and CO is found to vary up to 8.8 +/- 1.0 A during the transition of His64 from the ligand (A(1-3)) to bulk solvent (A0). The His64 motion occurs within a single trajectory only once, however the multiple trajectories populate the spectroscopic A-states fully. Consequently, multiple independent molecular dynamics simulations have been found to extend biomolecular motion from 5 ns of total simulation to experimental phenomena on the microsecond time scale.

Rotationally inelastic collisions of He and Ar with NaK: Experiment and theory

NASA Astrophysics Data System (ADS)

Malenda, R. F.; Jones, J.; Faust, C.; Richter, K.; Wolfe, C. M.; Hickman, A. P.; Huennekens, J.; Talbi, D.; Gatti, F.

2012-06-01

We are investigating collisions of the ground (X^1&+circ;) and first excited (A^1&+circ;) electronic states of NaK using both experimental and theoretical methods. Potential surfaces for HeNaK (fixed NaK bond length) are used for coupled channel calculations of cross sections for rotational energy transfer and also for collisional transfer of orientation and alignment. Additional calculations use the MCTDH wavepacket method. The measurements of the A state collisions involve a pump--probe excitation scheme using polarization labeling and laser-induced fluorescence spectroscopy. The pump excites a particular ro-vibrational level (v,J) of the A state from the X state, and the probe laser is scanned over various transitions to the 3^1π state. In addition to strong direct transitions, weak satellite lines are observed that arise from collisionally-induced transitions from the (v,J) level to (v,J'=J+δJ). This method provides information about the cross sections for transfer of population and orientation for A state levels, and it can be adapted to transitions starting in the X state. For the A state we observe a strong δJ=even propensity for both He and Ar perturbers. Preliminary results for the X state do not show this propensity.

Amyloid Polymorphism in the Protein Folding and Aggregation Energy Landscape.

PubMed

Adamcik, Jozef; Mezzenga, Raffaele

2018-02-15

Protein folding involves a large number of steps and conformations in which the folding protein samples different thermodynamic states characterized by local minima. Kinetically trapped on- or off-pathway intermediates are metastable folding intermediates towards the lowest absolute energy minima, which have been postulated to be the natively folded state where intramolecular interactions dominate, and the amyloid state where intermolecular interactions dominate. However, this view largely neglects the rich polymorphism found within amyloid species. We review the protein folding energy landscape in view of recent findings identifying specific transition routes among different amyloid polymorphs. Observed transitions such as twisted ribbon→crystal or helical ribbon→nanotube, and forbidden transitions such helical ribbon↛crystal, are discussed and positioned within the protein folding and aggregation energy landscape. Finally, amyloid crystals are identified as the ground state of the protein folding and aggregation energy landscape. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Laser Spectroscopy and AB Initio Calculations on the TaF Molecule

NASA Astrophysics Data System (ADS)

Ng, Kiu Fung; Zou, Wenli; Liu, Wenjian; Cheung, Allan S. C.

2016-06-01

Electronic transition spectrum of the tantalum monoflouride (TaF) molecule in the spectral region between 448 and 520 nm has been studied using the technique of laser-ablation/reaction free jet expansion and laser induced fluorescence spectroscopy. TaF molecule was produced by reacting laser-ablated tantalum atoms with sulfur hexafluoride gas seeded in argon. Sixteen vibrational bands with resolved rotational structure have been recorded and analyzed, which were organized into six electronic transition systems and the ground state has been identified to be the X3Σ-(0+) state with bond length, ro, and equilibrium vibrational frequency, ωe, determined to be 1.8209 Å and 700.1 wn respectively. In addition, four vibrational bands belong to another transition system involving lower state with Ω = 2 component has also been analyzed. All observed transitions are with ΔΩ = 0. Least-squares fit of the measured line positions yielded molecular constants for the electronic states involved. The Λ-S and Ω states of TaF were calculated at the state-averaged complete active space self-consistent field (SA-CASSCF) and the subsequent internally contracted multi-reference configuration interaction with singles and doubles and Davidson's cluster correction (MRCISD+Q) levels of theory with the active space of 4 electrons in 6 orbitals, that is, the molecular orbitals corresponding to Ta 5d6s are active. The spin-orbit coupling (SOC) is calculated by the state-interaction approach at the SA-CASSCF level via the relativistic effective core potentials (RECPs) spin-orbit operator, where the diagonal elements of the spin-orbit matrix are replaced by the above MRCISD+Q energies. The spectroscopic properties of the ground and many low-lying electronic states of the TaF molecule will be reported. With respect to the observed electronic states in this work, the calculated results are in good agreement with our experimental determinations. This work represents the first experimental investigation of the molecular structure of the TaF molecule.

Disruption of the ndhF1 gene affects Chl fluorescence through state transition in the Cyanobacterium Synechocystis sp. PCC 6803, resulting in apparent high efficiency of photosynthesis.

PubMed

Ogawa, Takako; Harada, Tetsuyuki; Ozaki, Hiroshi; Sonoike, Kintake

2013-07-01

In Synechocystis sp. PCC 6803, the disruption of the ndhF1 gene (slr0844), which encodes a subunit of one of the NDH-1 complexes (NDH-1L complex) serving for respiratory electron transfer, causes the largest change in Chl fluorescence induction kinetics among the kinetics of 750 disruptants searched in the Fluorome, the cyanobacterial Chl fluorescence database. The cause of the explicit phenotype of the ndhF1 disruptant was examined by measurements of the photosynthetic rate, Chl fluorescence and state transition. The results demonstrate that the defects in respiratory electron transfer obviously have great impact on Chl fluorescence in cyanobacteria. The inactivation of NDH-1L complexes involving electron transfer from NDH-1 to plastoquinone (PQ) would result in the oxidation of the PQ pool, leading to the transition to State 1, where the yield of Chl fluorescence is high. Apparently, respiration, although its rate is far lower than that of photosynthesis, could affect Chl fluorescence through the state transition as leverage. The disruption of the ndhF1 gene caused lower oxygen-evolving activity but the estimated electron transport rate from Chl fluorescence measurements was faster in the mutant than in the wild-type cells. The discrepancy could be ascribed to the decreased level of non-photochemical quenching due to state transition. One must be cautious when using the Chl fluorescence parameter to estimate photosynthesis in mutants defective in state transition.

Theoretical treatment of the processes involving the dipole transitions to the lowest exciton states in hexagonal semiconductors

NASA Astrophysics Data System (ADS)

Semenova, L. E.

2018-04-01

The treatment of the two-photon transitions to the An=1 exciton level and the resonant Raman scattering of light by LO-phonons is given for the hexagonal semiconductors A2B6, taking into account the influence of the complex top valence band and anisotropy of the exciton effective mass.

Description of strong M1 transitions between 4^+ states at N=52 within the sdg-IBM-2

NASA Astrophysics Data System (ADS)

Casperson, R. J.; Werner, V.; Heinze, S.

2009-10-01

The interplay between collective and single-particle degrees of freedom for nuclei near the N=50 shell closure 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. The one-phonon 2^+ mixed-symmetry state was identified from its strong M1 transition to the 2^+1 state. Similar transitions were observed between 4^+ states in ^94Mo and ^92Zr, and shell model calculations indicate that hexadecapole excitations play a role. These phenomena will be investigated within the sdg-Interacting Boson Model-2 in order to gain a better understanding about the structure of the states involved, and to which extent the hexadecapole degree of freedom is important at relatively low energies. First calculations within this model, using an F-spin conserving Hamiltonian to disentangle symmetric and mixed- symmetric structures, will be presented and compared to data.

Molecular dynamics simulation of nanobubble nucleation on rough surfaces

NASA Astrophysics Data System (ADS)

Liu, Yawei; Zhang, Xianren

2017-04-01

Here, we study how nanobubbles nucleate on rough hydrophobic surfaces, using long-time standard simulations to directly observe the kinetic pathways and using constrained simulations combined with the thermodynamic integration approach to quantitatively evaluate the corresponding free energy changes. Both methods demonstrate that a two-step nucleation route involving the formation of an intermediate state is thermodynamically favorable: at first, the system transforms from the Wenzel state (liquid being in full contact with the solid surface) to the Cassie state (liquid being in contact with the peaks of the rough surface) after gas cavities occur in the grooves (i.e., the Wenzel-to-Cassie transition); then, the gas cavities coalesce and form a stable surface nanobubble with pinned contact lines (i.e., the Cassie-to-nanobubble transition). Additionally, the free energy barriers for the two transitions show opposing dependencies on the degree of surface roughness, indicating that the surfaces with moderate roughness are favorable for forming stable surface nanobubbles. Moreover, the simulation results also reveal the coexistence and transition between the Wenzel, Cassie, and nanobubble states on rough surfaces.

Electron transfer by excited benzoquinone anions: slow rates for two-electron transitions.

PubMed

Zamadar, Matibur; Cook, Andrew R; Lewandowska-Andralojc, Anna; Holroyd, Richard; Jiang, Yan; Bikalis, Jin; Miller, John R

2013-09-05

Electron transfer (ET) rate constants from the lowest excited state of the radical anion of benzoquinone, BQ(-•)*, were measured in THF solution. Rate constants for bimolecular electron transfer reactions typically reach the diffusion-controlled limit when the free-energy change, ΔG°, reaches -0.3 eV. The rate constants for ET from BQ(-•)* are one-to-two decades smaller at this energy and do not reach the diffusion-controlled limit until -ΔG° is 1.5-2.0 eV. The rates are so slow probably because a second electron must also undergo a transition to make use of the energy of the excited state. Similarly, ET, from solvated electrons to neutral BQ to form the lowest excited state, is slow, while fast ET is observed at a higher excited state, which can be populated in a transition involving only one electron. A simple picture based on perturbation theory can roughly account for the control of electron transfer by the need for transition of a second electron. The picture also explains how extra driving force (-ΔG°) can restore fast rates of electron transfer.

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.

Jewish Day Schools and Afrocentric Programs as Models for Educating African American Youth.

ERIC Educational Resources Information Center

Gill, Walter

1991-01-01

Examines the success of Jewish Day schools (in terms of curriculum, parent involvement, and societal implications) in the United States and Afrocentric educational programs (in terms of arguments for, focus on male students, transition to adulthood, and community involvement) in developing positive self-concepts and academic success among…

Control of the transition between Ni-C and Ni-SI(a) states by the redox state of the proximal Fe-S cluster in the catalytic cycle of [NiFe] hydrogenase.

PubMed

Tai, Hulin; Nishikawa, Koji; Suzuki, Masayuki; Higuchi, Yoshiki; Hirota, Shun

2014-12-08

[NiFe] hydrogenase catalyzes the reversible cleavage of H2. The electrons produced by the H2 cleavage pass through three Fe-S clusters in [NiFe] hydrogenase to its redox partner. It has been reported that the Ni-SI(a), Ni-C, and Ni-R states of [NiFe] hydrogenase are involved in the catalytic cycle, although the mechanism and regulation of the transition between the Ni-C and Ni-SI(a) states remain unrevealed. In this study, the FT-IR spectra under light irradiation at 138-198 K show that the Ni-L state of [NiFe] hydrogenase is an intermediate between the transition of the Ni-C and Ni-SI(a) states. The transition of the Ni-C state to the Ni-SI(a) state occurred when the proximal [Fe4S4]p(2+/+) cluster was oxidized, but not when it was reduced. These results show that the catalytic cycle of [NiFe] hydrogenase is controlled by the redox state of its [Fe4S4]p(2+/+) cluster, which may function as a gate for the electron flow from the NiFe active site to the redox partner. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Native Hydrophobic Binding Interactions at the Transition State for Association between the TAZ1 Domain of CBP and the Disordered TAD-STAT2 Are Not a Requirement.

PubMed

Lindström, Ida; Dogan, Jakob

2017-08-15

A significant fraction of the eukaryotic proteome consists of proteins that are either partially or completely disordered under native-like conditions. Intrinsically disordered proteins (IDPs) are common in protein-protein interactions and are involved in numerous cellular processes. Although many proteins have been identified as disordered, much less is known about the binding mechanisms of the coupled binding and folding reactions involving IDPs. Here we have analyzed the rate-limiting transition state for binding between the TAZ1 domain of CREB binding protein and the intrinsically disordered transactivation domain of STAT2 (TAD-STAT2) by site-directed mutagenesis and kinetic experiments (Φ-value analysis) and found that the native protein-protein binding interface is not formed at the transition state for binding. Instead, native hydrophobic binding interactions form late, after the rate-limiting barrier has been crossed. The association rate constant in the absence of electrostatic enhancement was determined to be rather high. This is consistent with the Φ-value analysis, which showed that there are few or no obligatory native contacts. Also, linear free energy relationships clearly demonstrate that native interactions are cooperatively formed, a scenario that has usually been observed for proteins that fold according to the so-called nucleation-condensation mechanism. Thus, native hydrophobic binding interactions at the rate-limiting transition state for association between TAD-STAT2 and TAZ1 are not a requirement, which is generally in agreement with previous findings on other IDP systems and might be a common mechanism for IDPs.

At Risk Youth: A Transitory State? Longitudinal Surveys of Australian Youth. Briefing Paper 24

ERIC Educational Resources Information Center

Anlezark, Alison

2011-01-01

By definition, youth transitions involve young people moving between school, post-school study and employment. It is a time of flux, as young people try out different school, post-school work and study options. But are those who don't find work immediately likely to make a poor transition? Given that many may well have a spell out of the labour…

Accurate treatment of total photoabsorption cross sections by an ab initio time-dependent method

NASA Astrophysics Data System (ADS)

Daud, Mohammad Noh

2014-09-01

A detailed discussion of parallel and perpendicular transitions required for the photoabsorption of a molecule is presented within a time-dependent view. Total photoabsorption cross sections for the first two ultraviolet absorption bands of the N2O molecule corresponding to transitions from the X1 A' state to the 21 A' and 11 A'' states are calculated to test the reliability of the method. By fully considering the property of the electric field polarization vector of the incident light, the method treats the coupling of angular momentum and the parity differently for two kinds of transitions depending on the direction of the vector whether it is: (a) situated parallel in a molecular plane for an electronic transition between states with the same symmetry; (b) situated perpendicular to a molecular plane for an electronic transition between states with different symmetry. Through this, for those transitions, we are able to offer an insightful picture of the dynamics involved and to characterize some new aspects in the photoabsorption process of N2O. Our calculations predicted that the parallel transition to the 21 A' state is the major dissociation pathway which is in qualitative agreement with the experimental observations. Most importantly, a significant improvement in the absolute value of the total cross section over previous theoretical results [R. Schinke, J. Chem. Phys. 134, 064313 (2011), M.N. Daud, G.G. Balint-Kurti, A. Brown, J. Chem. Phys. 122, 054305 (2005), S. Nanbu, M.S. Johnson, J. Phys. Chem. A 108, 8905 (2004)] was obtained.

Electronic Transitions of Tungsten Monosulfide

NASA Astrophysics Data System (ADS)

Tsang, L. F.; Chan, Man-Chor; Zou, Wenli; Cheung, Allan S. C.

2017-06-01

Electronic transition spectrum of the tungsten monosulfide (WS) molecule in the near infrared region between 725 nm and 885 nm has been recorded using laser ablation/reaction free-jet expansion and laser induced fluorescence spectroscopy. The WS molecule was produced by reacting laser - ablated tungsten atoms with 1% CS_{2} seeded in argon. Fifteen vibrational bands with resolved rotational structure have been recorded and analyzed, which were organized into seven electronic transition systems. The ground state has been identified to be the X^{3}Σ^{-}(0^{+}) state, and the determined vibrational frequency, ΔG_{1/2} and bond length, r_{0}, are respectively 556.7 cm^{-1} and 2.0676 Å. In addition, vibrational bands belong to another transition system involving lower state with Ω = 1 component have also been analyzed. Least-squares fit of the measured line positions yielded molecular constants for the electronic states involved. The low-lying Λ-S states and Ω sub-states of WS have been calculated using state-averaged complete active space self-consistent field (SA-CASSCF) and followed by MRCISD+Q (internally contracted multi-reference configuration interaction with singles and doubles plus Davidson's cluster correction). The active space consists of 10 electrons in 9 orbitals corresponding to the W 5d6s and S 3p shells. The lower molecular orbitals from W 5s5p and S 3s are inactive but are also correlated, and relativistic effective core potential (RECPs) are adopted to replace the core orbitals with 60 (W) and 10 (S) core electrons, respectively. Spin-orbit coupling (SOC) is calculated via the state-interaction (SI) approach with RECP spin-orbit operators using SA-CASSCF wavefunctions, where the diagonal elements in the SOC matrix are replaced by the corresponding MRCISD+Q energies calculated above. Spectroscopic constants and potential energy curves of the ground and many low-lying Λ-S states and Ω sub-states of the WS molecule are obtained. The calculated spectroscopic constants of the ground and low-lying states are generally in good agreement with our experimental determination. This work represents the first experimental investigation of the electronic and molecular structure of the WS molecule.

Attractor hopping between polarization dynamical states in a vertical-cavity surface-emitting laser subject to parallel optical injection

NASA Astrophysics Data System (ADS)

Denis-le Coarer, Florian; Quirce, Ana; Valle, Angel; Pesquera, Luis; Rodríguez, Miguel A.; Panajotov, Krassimir; Sciamanna, Marc

2018-03-01

We present experimental and theoretical results of noise-induced attractor hopping between dynamical states found in a single transverse mode vertical-cavity surface-emitting laser (VCSEL) subject to parallel optical injection. These transitions involve dynamical states with different polarizations of the light emitted by the VCSEL. We report an experimental map identifying, in the injected power-frequency detuning plane, regions where attractor hopping between two, or even three, different states occur. The transition between these behaviors is characterized by using residence time distributions. We find multistability regions that are characterized by heavy-tailed residence time distributions. These distributions are characterized by a -1.83 ±0.17 power law. Between these regions we find coherence enhancement of noise-induced attractor hopping in which transitions between states occur regularly. Simulation results show that frequency detuning variations and spontaneous emission noise play a role in causing switching between attractors. We also find attractor hopping between chaotic states with different polarization properties. In this case, simulation results show that spontaneous emission noise inherent to the VCSEL is enough to induce this hopping.

Consequences of acid strength for isomerization and elimination catalysis on solid acids.

PubMed

Macht, Josef; Carr, Robert T; Iglesia, Enrique

2009-05-13

We address here the manner in which acid catalysis senses the strength of solid acids. Acid strengths for Keggin polyoxometalate (POM) clusters and zeolites, chosen because of their accurately known structures, are described rigorously by their deprotonation energies (DPE). Mechanistic interpretations of the measured dynamics of alkane isomerization and alkanol dehydration are used to obtain rate and equilibrium constants and energies for intermediates and transition states and to relate them to acid strength. n-Hexane isomerization rates were limited by isomerization of alkoxide intermediates on bifunctional metal-acid mixtures designed to maintain alkane-alkene equilibrium. Isomerization rate constants were normalized by the number of accessible protons, measured by titration with 2,6-di-tert-butylpyridine during catalysis. Equilibrium constants for alkoxides formed by protonation of n-hexene increased slightly with deprotonation energies (DPE), while isomerization rate constants decreased and activation barriers increased with increasing DPE, as also shown for alkanol dehydration reactions. These trends are consistent with thermochemical analyses of the transition states involved in isomerization and elimination steps. For all reactions, barriers increased by less than the concomitant increase in DPE upon changes in composition, because electrostatic stabilization of ion-pairs at the relevant transition states becomes more effective for weaker acids, as a result of their higher charge density at the anionic conjugate base. Alkoxide isomerization barriers were more sensitive to DPE than for elimination from H-bonded alkanols, the step that limits 2-butanol and 1-butanol dehydration rates; the latter two reactions showed similar DPE sensitivities, despite significant differences in their rates and activation barriers, indicating that slower reactions are not necessarily more sensitive to acid strength, but instead reflect the involvement of more unstable organic cations at their transition states. These compensating effects from electrostatic stabilization depend on how similar the charge density in these organic cations is to that in the proton removed. Cations with more localized charge favor strong electrostatic interactions with anions and form more stable ionic structures than do cations with more diffuse charges. Ion-pairs at elimination transition states contain cations with higher local charge density at the sp(2) carbon than for isomerization transition states; as a result, these ion-pairs recover a larger fraction of the deprotonation energy, and, consequently, their reactions become less sensitive to acid strength. These concepts lead us to conclude that the energetic difficulty of a catalytic reaction, imposed by gas-phase reactant proton affinities in transition state analogues, does not determine its sensitivity to the acid strength of solid catalysts.

Fast-timing lifetime measurements of excited states in Cu67

NASA Astrophysics Data System (ADS)

NiÅ£ǎ, C. R.; Bucurescu, D.; Mǎrginean, N.; Avrigeanu, M.; Bocchi, G.; Bottoni, S.; Bracco, A.; Bruce, A. M.; Cǎta-Danil, G.; Coló, G.; Deleanu, D.; Filipescu, D.; GhiÅ£ǎ, D. G.; Glodariu, T.; Leoni, S.; Mihai, C.; Mason, P. J. R.; Mǎrginean, R.; Negret, A.; Pantelicǎ, D.; Podolyak, Z.; Regan, P. H.; Sava, T.; Stroe, L.; Toma, S.; Ur, C. A.; Wilson, E.

2014-06-01

The half-lives of the 9/2+, 13/2+, and 15/2+ yrast states in the neutron-rich Cu67 nucleus were determined by using the in-beam fast-timing technique. The experimentally deduced E3 transition strength for the decay of the 9/2+ level to the 3/2- ground state indicates that the wave function of this level might contain a collective component arising from the coupling of the odd proton p3/2 with the 3- state in Ni66. Theoretical interpretations of the 9/2+ state are presented within the particle-vibration weak-coupling scheme involving the unpaired proton and the 3- state from Ni66 and within shell-model calculations with a Ni56 core using the jj44b residual interaction. The shell model also accounts reasonably well for the other measured electromagnetic transition probabilities.

Identification of Two New Electronic States of NiCl Using Intracavity Laser Spectroscopy and the Correlation Between Theoretical Predictions and Experimental Observations

NASA Astrophysics Data System (ADS)

Harms, Jack C.; Grames, Ethan M.; Han, Shu; O'Brien, Leah C.; O'Brien, James J.

2016-06-01

The near-infrared spectrum of NiCl has been recorded in high resolution in the 13,200-13,500 wn and 13,600-13,750 wn regions using Intracavity Laser Spectroscopy (ILS). The NiCl Molecules were produced in the plasma discharge of a Ni-lined copper hollow cathode with 0.3-0.6 torr of argon as the sputter gas, and a trace amount of CCl_4. The hollow cathode was located within the laser cavity of a Verdi V-10 pumped Ti:sapphire system. A generation of 90 μsec resulted in an effective pathlength of approximately 700 m for the absorption measurements. Several transitions were observed, including 3 transitions involving 2 previously unreported electronic states. The (0,0) and (1,0) bands of the [13.5] 2Φ7/2-[0.16] A 2Δ5/2 transition were observed near 13,709 wn and 13,318 wn, respectively. The (0,0) band of the [13.8] 2Π1/2 - [0.38] X 2Π1/2 transition was observed near 13,480 wn. With the analysis of these transitions, molecular constants have been obtained for 9 of the 12 doublet states of NiCl predicted by Zou and Lou in 2006. Analysis of these transitions and a comparison between the experimentally observed transitions and the theoretically predicted states of NiCl will be presented.

Electronic propensity rules in Li-H+ collisions involving initial and/or final oriented states

NASA Astrophysics Data System (ADS)

Salas, P. J.

2000-12-01

Electronic excitation and capture processes are studied in collisions involving systems with only one active electron such as the alkaline (Li)-proton in the medium-energy region (0.1-15 keV). Using the semiclassical impact parameter method, the probabilities and the orientation parameter are calculated for transitions between initial and/or final oriented states. The results show a strong asymmetry in the probabilities depending on the orientation of the initial and/or final states. An intuitive view of the processes, by means of the concepts of propensity and velocity matching rules, is provided.

Deep donor state of the copper acceptor as a source of green luminescence in ZnO

NASA Astrophysics Data System (ADS)

Lyons, J. L.; Alkauskas, A.; Janotti, A.; Van de Walle, C. G.

2017-07-01

Copper impurities have long been linked with green luminescence (GL) in ZnO. Copper is known to introduce an acceptor level close to the conduction band of ZnO, and the GL has conventionally been attributed to transitions involving an excited state which localizes holes on neighboring oxygen atoms. To date, a theoretical description of the optical properties of such deep centers has been difficult to achieve due to the limitations of functionals in the density functional theory. Here, we employ a screened hybrid density functional to calculate the properties of Cu in ZnO. In agreement with the experiment, we find that CuZn features an acceptor level near the conduction band of ZnO. However, we find that CuZn also gives rise to a deep donor level 0.46 eV above the valence band of ZnO; the calculated optical transitions involving this state agree well with the GL observed in ZnO:Cu.

A stromal region of cytochrome b6f subunit IV is involved in the activation of the Stt7 kinase in Chlamydomonas

PubMed Central

Zito, Francesca; Blangy, Stéphanie; Auroy, Pascaline; Johnson, Xenie; Peltier, Gilles

2017-01-01

The cytochrome (cyt) b6f complex and Stt7 kinase regulate the antenna sizes of photosystems I and II through state transitions, which are mediated by a reversible phosphorylation of light harvesting complexes II, depending on the redox state of the plastoquinone pool. When the pool is reduced, the cyt b6f activates the Stt7 kinase through a mechanism that is still poorly understood. After random mutagenesis of the chloroplast petD gene, coding for subunit IV of the cyt b6f complex, and complementation of a ΔpetD host strain by chloroplast transformation, we screened for impaired state transitions in vivo by chlorophyll fluorescence imaging. We show that residues Asn122, Tyr124, and Arg125 in the stromal loop linking helices F and G of cyt b6f subunit IV are crucial for state transitions. In vitro reconstitution experiments with purified cyt b6f and recombinant Stt7 kinase domain show that cyt b6f enhances Stt7 autophosphorylation and that the Arg125 residue is directly involved in this process. The peripheral stromal structure of the cyt b6f complex had, until now, no reported function. Evidence is now provided of a direct interaction with Stt7 on the stromal side of the membrane. PMID:29078388

Rotator side chains trigger cooperative transition for shape and function memory effect in organic semiconductors.

PubMed

Chung, Hyunjoong; Dudenko, Dmytro; Zhang, Fengjiao; D'Avino, Gabriele; Ruzié, Christian; Richard, Audrey; Schweicher, Guillaume; Cornil, Jérôme; Beljonne, David; Geerts, Yves; Diao, Ying

2018-01-18

Martensitic transition is a solid-state phase transition involving cooperative movement of atoms, mostly studied in metallurgy. The main characteristics are low transition barrier, ultrafast kinetics, and structural reversibility. They are rarely observed in molecular crystals, and hence the origin and mechanism are largely unexplored. Here we report the discovery of martensitic transition in single crystals of two different organic semiconductors. In situ microscopy, single-crystal X-ray diffraction, Raman and nuclear magnetic resonance spectroscopy, and molecular simulations combined indicate that the rotating bulky side chains trigger cooperative transition. Cooperativity enables shape memory effect in single crystals and function memory effect in thin film transistors. We establish a molecular design rule to trigger martensitic transition in organic semiconductors, showing promise for designing next-generation smart multifunctional materials.

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

Density functional tight-binding and infrequent metadynamics can capture entropic effects in intramolecular hydrogen transfer reactions

NASA Astrophysics Data System (ADS)

Oliveira, Luiz F. L.; Fu, Christopher D.; Pfaendtner, Jim

2018-04-01

Infrequent metadynamics uses biased simulations to estimate the unbiased kinetics of a system, facilitating the calculation of rates and barriers. Here the method is applied to study intramolecular hydrogen transfer reactions involving peroxy radicals, a class of reactions that is challenging to model due to the entropic contributions of the formation of ring structures in the transition state. Using the self-consistent charge density-functional based tight-binding (DFTB) method, we applied infrequent metadynamics to the study of four intramolecular H-transfer reactions, demonstrating that the method can qualitatively reproduce these high entropic contributions, as observed in experiments and those predicted by transition state theory modeled by higher levels of theory. We also show that infrequent metadynamics and DFTB are successful in describing the relationship between transition state ring size and kinetic coefficients (e.g., activation energies and the pre-exponential factors).

Taking Ockham's razor to enzyme dynamics and catalysis.

PubMed

Glowacki, David R; Harvey, Jeremy N; Mulholland, Adrian J

2012-01-29

The role of protein dynamics in enzyme catalysis is a matter of intense current debate. Enzyme-catalysed reactions that involve significant quantum tunnelling can give rise to experimental kinetic isotope effects with complex temperature dependences, and it has been suggested that standard statistical rate theories, such as transition-state theory, are inadequate for their explanation. Here we introduce aspects of transition-state theory relevant to the study of enzyme reactivity, taking cues from chemical kinetics and dynamics studies of small molecules in the gas phase and in solution--where breakdowns of statistical theories have received significant attention and their origins are relatively better understood. We discuss recent theoretical approaches to understanding enzyme activity and then show how experimental observations for a number of enzymes may be reproduced using a transition-state-theory framework with physically reasonable parameters. Essential to this simple model is the inclusion of multiple conformations with different reactivity.

Kinetic, Spectroscopic, and Theoretical Assessment of Associative and Dissociative Methanol Dehydration Routes in Zeolites

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

Jones, Andrew J.; Iglesia, Enrique

Mechanistic interpretations of rates and in situ IR spectra combined with density functionals that account for van der Waals interactions of intermediates and transition states within confining voids show that associative routes mediate the formation of dimethyl ether from methanol on zeolitic acids at the temperatures and pressures of practical dehydration catalysis. Methoxy-mediated dissociative routes become prevalent at higher temperatures and lower pressures, because they involve smaller transition states with higher enthalpy, but also higher entropy, than those in associative routes. These enthalpy–entropy trade-offs merely reflect the intervening role of temperature in activation free energies and the prevalence of moremore » complex transition states at low temperatures and high pressures. This work provides a foundation for further inquiry into the contributions of H-bonded methanol and methoxy species in homologation and hydrocarbon synthesis reactions from methanol.« less

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.

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.

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

Park, G. Barratt, E-mail: barratt@mit.edu

Franck-Condon vibrational overlap integrals for the A{sup ~1}A{sub u}—X{sup ~1}Σ{sup +}{sub g} transition in acetylene have been calculated in full dimension in the harmonic normal mode basis. The calculation uses the method of generating functions first developed for polyatomic Franck-Condon factors by Sharp and Rosenstock [J. Chem. Phys. 41(11), 3453–3463 (1964)], and previously applied to acetylene by Watson [J. Mol. Spectrosc. 207(2), 276–284 (2001)] in a reduced-dimension calculation. Because the transition involves a large change in the equilibrium geometry of the electronic states, two different types of corrections to the coordinate transformation are considered to first order: corrections for axis-switchingmore » between the Cartesian molecular frames and corrections for the curvilinear nature of the normal modes at large amplitude. The angular factor in the wave function for the out-of-plane component of the trans bending mode, ν{sub 4}{sup ″}, is treated as a rotation, which results in an Eckart constraint on the polar coordinates of the bending modes. To simplify the calculation, the other degenerate bending mode, ν{sub 5}{sup ″}, is integrated in the Cartesian basis and later transformed to the constrained polar coordinate basis, restoring the conventional v and l quantum numbers. An updated A{sup ~}-state harmonic force field obtained recently in the R. W. Field research group is evaluated. The results for transitions involving the gerade vibrational modes are in qualitative agreement with experiment. Calculated results for transitions involving ungerade modes are presented in Paper II of this series [G. B. Park, J. H. Baraban, and R. W. Field, “Full dimensional Franck–Condon factors for the acetylene A{sup ~1}A{sub u}—X{sup ~1}Σ{sup +}{sub g} transition. II. Vibrational overlap factors for levels involving excitation in ungerade modes,” J. Chem. Phys. 141, 134305 (2014)].« less

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.

Radiative, nonradiative, and mixed-decay transitions of rare-earth ions in dielectric media

NASA Astrophysics Data System (ADS)

Burshtein, Zeev

2010-09-01

We present and discuss in a comprehensive, deductive, and simplified manner, issues of nonradiative transitions involvement in fluorescence of ions embedded in dielectric solid matrices. The semiclassical approach is favored over a full quantum description, and empiric quantities are introduced from the start. One issue is nonradiative single-phonon transitions when the energy gap between the adjacent electronic ion states is smaller than the cutoff matrix phonon energy. Another issue is transitions in a complex energy scheme, where some visible and near-visible transitions are radiative and others are nonradiative. A refined Füchtbauer-Ladenburg recipe for calculation of the stimulated emission spectrum on the basis of measurable absorption and fluorescence emission spectra is worked out. The last issue is multiphonon nonradiative transitions occurring when the energy gap between adjacent electronic ion states is larger than the cutoff matrix phonon energy. Transition probabilities were calculated on the basis of anharmonicity of the effective potential supporting the internal atomic basis vibrations. An expression in a closed form is obtained, similar to the empiric ``energy gap'' law, however, with parameters related to specific host material properties and the actual transition in the ion. Comparison to existing experimental evidence is presented and discussed in detail.

MgH Rydberg series: Transition energies from electron propagator theory and oscillator strengths from the molecular quantum defect orbital method

NASA Astrophysics Data System (ADS)

Corzo, H. H.; Velasco, A. M.; Lavín, C.; Ortiz, J. V.

2018-02-01

Vertical excitation energies belonging to several Rydberg series of MgH have been inferred from 3+ electron-propagator calculations of the electron affinities of MgH+ and are in close agreement with experiment. Many electronically excited states with n > 3 are reported for the first time and new insight is given on the assignment of several Rydberg series. Valence and Rydberg excited states of MgH are distinguished respectively by high and low pole strengths corresponding to Dyson orbitals of electron attachment to the cation. By applying the Molecular Quantum Defect Orbital method, oscillator strengths for electronic transitions involving Rydberg states also have been determined.

The low-energy, charge-transfer excited states of 4-amino-4-prime-nitrodiphenyl sulfide

NASA Technical Reports Server (NTRS)

O'Connor, Donald B.; Scott, Gary W.; Tran, Kim; Coulter, Daniel R.; Miskowski, Vincent M.; Stiegman, Albert E.; Wnek, Gary E.

1992-01-01

Absorption and emission spectra of 4-amino-4-prime-nitrodiphenyl sulfide in polar and nonpolar solvents were used to characterize and assign the low-energy excited states of the molecule. Fluorescence-excitation anisotropy spectra and fluorescence quantum yields were also used to characterize the photophysics of these states. The lowest-energy fluorescent singlet state was determined to be an intramolecular charge transfer (ICT) state involving transfer of a full electron charge from the amino to the nitro group yielding a dipole moment of about 50 D. A low-energy, intense absorption band is assigned as a transition to a different ICT state involving a partial electron charge transfer from sulfur to the nitro group.

State-to-State Internal Energy Relaxation Following the Quantum-Kinetic Model in DSMC

NASA Technical Reports Server (NTRS)

Liechty, Derek S.

2014-01-01

A new model for chemical reactions, the Quantum-Kinetic (Q-K) model of Bird, has recently been introduced that does not depend on macroscopic rate equations or values of local flow field data. Subsequently, the Q-K model has been extended to include reactions involving charged species and electronic energy level transitions. Although this is a phenomenological model, it has been shown to accurately reproduce both equilibrium and non-equilibrium reaction rates. The usefulness of this model becomes clear as local flow conditions either exceed the conditions used to build previous models or when they depart from an equilibrium distribution. Presently, the applicability of the relaxation technique is investigated for the vibrational internal energy mode. The Forced Harmonic Oscillator (FHO) theory for vibrational energy level transitions is combined with the Q-K energy level transition model to accurately reproduce energy level transitions at a reduced computational cost compared to the older FHO models.

Non-equilibrium phase transitions in a driven-dissipative system of interacting bosons

NASA Astrophysics Data System (ADS)

Young, Jeremy T.; Foss-Feig, Michael; Gorshkov, Alexey V.; Maghrebi, Mohammad F.

2017-04-01

Atomic, molecular, and optical systems provide unique opportunities to study simple models of driven-dissipative many-body quantum systems. Typically, one is interested in the resultant steady state, but the non-equilibrium nature of the physics involved presents several problems in understanding its behavior theoretically. Recently, it has been shown that in many of these models, it is possible to map the steady-state phase transitions onto classical equilibrium phase transitions. In the language of Keldysh field theory, this relation typically only becomes apparent after integrating out massive fields near the critical point, leaving behind a single massless field undergoing near-equilibrium dynamics. In this talk, we study a driven-dissipative XXZ bosonic model and discover critical points at which two fields become gapless. Each critical point separates three different possible phases: a uniform phase, an anti-ferromagnetic phase, and a limit cycle phase. Furthermore, a description in terms of an equilibrium phase transition does not seem possible, so the associated phase transitions appear to be inherently non-equilibrium.

Study of diatomic molecules. 2: Intensities. [optical emission spectroscopy of ScO

NASA Technical Reports Server (NTRS)

Femenias, J. L.

1978-01-01

The theory of perturbations, giving the diatomic effective Hamiltonian, is used for calculating actual molecular wave functions and intensity factors involved in transitions between states arising from Hund's coupling cases a,b, intermediate a-b, and c tendency. The Herman and Wallis corrections are derived, without any knowledge of the analytical expressions of the wave functions, and generalized to transitions between electronic states with whatever symmetry and multiplicity. A general method for studying perturbed intensities is presented using primarily modern spectroscopic numerical approaches. The method is used in the study of the ScO optical emission spectrum.

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.

DNA-Binding Kinetics Determines the Mechanism of Noise-Induced Switching in Gene Networks

PubMed Central

Tse, Margaret J.; Chu, Brian K.; Roy, Mahua; Read, Elizabeth L.

2015-01-01

Gene regulatory networks are multistable dynamical systems in which attractor states represent cell phenotypes. Spontaneous, noise-induced transitions between these states are thought to underlie critical cellular processes, including cell developmental fate decisions, phenotypic plasticity in fluctuating environments, and carcinogenesis. As such, there is increasing interest in the development of theoretical and computational approaches that can shed light on the dynamics of these stochastic state transitions in multistable gene networks. We applied a numerical rare-event sampling algorithm to study transition paths of spontaneous noise-induced switching for a ubiquitous gene regulatory network motif, the bistable toggle switch, in which two mutually repressive genes compete for dominant expression. We find that the method can efficiently uncover detailed switching mechanisms that involve fluctuations both in occupancies of DNA regulatory sites and copy numbers of protein products. In addition, we show that the rate parameters governing binding and unbinding of regulatory proteins to DNA strongly influence the switching mechanism. In a regime of slow DNA-binding/unbinding kinetics, spontaneous switching occurs relatively frequently and is driven primarily by fluctuations in DNA-site occupancies. In contrast, in a regime of fast DNA-binding/unbinding kinetics, switching occurs rarely and is driven by fluctuations in levels of expressed protein. Our results demonstrate how spontaneous cell phenotype transitions involve collective behavior of both regulatory proteins and DNA. Computational approaches capable of simulating dynamics over many system variables are thus well suited to exploring dynamic mechanisms in gene networks. PMID:26488666

Spin-forbidden and spin-allowed cyclopropenone (c-H{sub 2}C{sub 3}O) formation in interstellar medium

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

Ahmadvand, Seyedsaeid; Zaari, Ryan R.; Varganov, Sergey A., E-mail: svarganov@unr.edu

2014-11-10

Three proposed mechanisms of cyclopropenone (c-H{sub 2}C{sub 3}O) formation from neutral species are studied using high-level electronic structure methods in combination with nonadiabatic transition state and collision theories to deduce the likelihood of each reaction mechanism under interstellar conditions. The spin-forbidden reaction involving the singlet electronic state of cyclopenylidene (c-C{sub 3}H{sub 2}) and the triplet state of atomic oxygen is studied using nonadiabatic transition state theory to predict the rate constant for c-H{sub 2}C{sub 3}O formation. The spin-allowed reactions of c-C{sub 3}H{sub 2} with molecular oxygen and acetylene with carbon monoxide were also investigated. The reaction involving the ground electronicmore » states of acetylene and carbon monoxide has a very large reaction barrier and is unlikely to contribute to c-H{sub 2}C{sub 3}O formation in interstellar medium. The spin-forbidden reaction of c-C{sub 3}H{sub 2} with atomic oxygen, despite the high probability of nonadiabatic transition between the triplet and singlet states, was found to have a very small rate constant due to the presence of a small (3.8 kcal mol{sup –1}) reaction barrier. In contrast, the spin-allowed reaction between c-C{sub 3}H{sub 2} and molecular oxygen is found to be barrierless, and therefore can be an important path to the formation of c-H{sub 2}C{sub 3}O molecule in interstellar environment.« less

Independent Evaluators of Federal Programs: Approaches, Devices, and Examples

DTIC Science & Technology

2010-08-16

rehabilitation of the disorder; the status of studies and clinical trials involving innovative treatments; a description of each treatment program and a...Transit Administration ( FTA ), a part of the Department of Transportation (DOT), oversees the safety and security of rail transit agencies which...an oversight body for each jurisdiction. The program is designed, according to a GAO summary, “as one in which FTA , other federal agencies, states

Needed: A Twenty-First Century Vision for Economic Assistance

DTIC Science & Technology

1993-04-01

Soviet Union) toward market economies and democratic political systems; and "o Confronting global issues and trends: To address global forces leading...Union, U.S. investment is important for these countries’ successful transitions to market economies. On global issues , U.S. business can offer...to global issues , many of the states involved in active or potential regional conflicts or in democratic transitions need help to avoid general

Stabilizing IkappaBalpha by "consensus" design.

PubMed

Ferreiro, Diego U; Cervantes, Carla F; Truhlar, Stephanie M E; Cho, Samuel S; Wolynes, Peter G; Komives, Elizabeth A

2007-01-26

IkappaBalpha is the major regulator of transcription factor NF-kappaB function. The ankyrin repeat region of IkappaBalpha mediates specific interactions with NF-kappaB dimers, but ankyrin repeats 1, 5 and 6 display a highly dynamic character when not in complex with NF-kappaB. Using chemical denaturation, we show here that IkappaBalpha displays two folding transitions: a non-cooperative conversion under weak perturbation, and a major cooperative folding phase upon stronger insult. Taking advantage of a native Trp residue in ankyrin repeat (AR) 6 and engineered Trp residues in AR2, AR4 and AR5, we show that the cooperative transition involves AR2 and AR3, while the non-cooperative transition involves AR5 and AR6. The major structural transition can be affected by single amino acid substitutions converging to the "consensus" ankyrin repeat sequence, increasing the native state stability significantly. We further characterized the structural and dynamic properties of the native state ensemble of IkappaBalpha and the stabilized mutants by H/(2)H exchange mass spectrometry and NMR. The solution experiments were complemented with molecular dynamics simulations to elucidate the microscopic origins of the stabilizing effect of the consensus substitutions, which can be traced to the fast conformational dynamics of the folded ensemble.

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.

Lack of multiplicative transitivity in person trade-off responses.

PubMed

Schwarzinger, Michaël; Lanoë, Jean-Louis; Nord, Erik; Durand-Zaleski, Isabelle

2004-02-01

The person trade-off (PTO) is a technique for eliciting preferences for resource allocation across patient groups. In principle PTO responses should satisfy a requirement of multiplicative transitivity, i.e. that if people consider treatment of 1 in state A to be equivalent to treating 10 in state B, and 1 in state B to be equivalent to 10 in state C, then they should find 1 in state A equivalent to 100 in state C. Earlier studies addressing labelled diseases (specific diagnoses), have shown multiplicative intransitivity of the PTO responses. Our purpose was to test multiplicative transitivity in the case of health states described with the EuroQol instrument only and to find a possible framing effect such as the number of persons in the reference intervention. Forty-four master degree students were asked to fill in a questionnaire addressing four chronic health states. Their task consisted in (1). ranking the states by severity, (2). valuing each of them by the means of the time trade-off, and (3). doing the PTO for all the 10 possible pairwise combinations of the four chronic states plus a fatal one. In a subsequent questionnaire the number of persons in the reference intervention in the PTO was increased from 10 to 100. Multiplicative transitivity was studied in subjects who demonstrated a willingness to trade off and consistency in ranking individual values. None of the 39 subjects included satisfied a minimum multiplicative transitivity requirement in PTO responses. Internal consistency was not improved when the PTO involved health states close to each other in terms of severity, nor when the prevention of death was not the reference intervention. For the 22 subjects having answered both types of questionnaire, increasing the number of persons in the reference intervention did not improve multiplicative transitivity. The PTO holds promise as a useful method for determining social preferences for priority setting, inasmuch as it captures distributive concerns that individual utility techniques such as the time trade-off do not address. But the lack of multiplicative transitivity in PTO responses is unsatisfactory, and ways to reduce this problem need to be explored. Copyright 2003 John Wiley & Sons, Ltd.

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

Control of atomic transition rates via laser-light shaping

NASA Astrophysics Data System (ADS)

Jáuregui, R.

2015-04-01

A modular systematic analysis of the feasibility of modifying atomic transition rates by tailoring the electromagnetic field of an external coherent light source is presented. The formalism considers both the center of mass and internal degrees of freedom of the atom, and all properties of the field: frequency, angular spectrum, and polarization. General features of recoil effects for internal forbidden transitions are discussed. A comparative analysis of different structured light sources is explicitly worked out. It includes spherical waves, Gaussian beams, Laguerre-Gaussian beams, and propagation invariant beams with closed analytical expressions. It is shown that increments in the order of magnitude of the transition rates for Gaussian and Laguerre-Gaussian beams, with respect to those obtained in the paraxial limit, require waists of the order of the wavelength, while propagation invariant modes may considerably enhance transition rates under more favorable conditions. For transitions that can be naturally described as modifications of the atomic angular momentum, this enhancement is maximal (within propagation invariant beams) for Bessel modes, Mathieu modes can be used to entangle the internal and center-of-mass involved states, and Weber beams suppress this kind of transition unless they have a significant component of odd modes. However, if a recoil effect of the transition with an adequate symmetry is allowed, the global transition rate (center of mass and internal motion) can also be enhanced using Weber modes. The global analysis presented reinforces the idea that a better control of the transitions between internal atomic states requires both a proper control of the available states of the atomic center of mass, and shaping of the background electromagnetic field.

Two-State Reactivity in Low-Valent Iron-Mediated C-H Activation and the Implications for Other First-Row Transition Metals.

PubMed

Sun, Yihua; Tang, Hao; Chen, Kejuan; Hu, Lianrui; Yao, Jiannian; Shaik, Sason; Chen, Hui

2016-03-23

C-H bond activation/functionalization promoted by low-valent iron complexes has recently emerged as a promising approach for the utilization of earth-abundant first-row transition metals to carry out this difficult transformation. Herein we use extensive density functional theory and high-level ab initio coupled cluster calculations to shed light on the mechanism of these intriguing reactions. Our key mechanistic discovery for C-H arylation reactions reveals a two-state reactivity (TSR) scenario in which the low-spin Fe(II) singlet state, which is initially an excited state, crosses over the high-spin ground state and promotes C-H bond cleavage. Subsequently, aryl transmetalation occurs, followed by oxidation of Fe(II) to Fe(III) in a single-electron transfer (SET) step in which dichloroalkane serves as an oxidant, thus promoting the final C-C coupling and finalizing the C-H functionalization. Regeneration of the Fe(II) catalyst for the next round of C-H activation involves SET oxidation of the Fe(I) species generated after the C-C bond coupling. The ligand sphere of iron is found to play a crucial role in the TSR mechanism by stabilization of the reactive low-spin state that mediates the C-H activation. This is the first time that the successful TSR concept conceived for high-valent iron chemistry is shown to successfully rationalize the reactivity for a reaction promoted by low-valent iron complexes. A comparative study involving other divalent middle and late first-row transition metals implicates iron as the optimum metal in this TSR mechanism for C-H activation. It is predicted that stabilization of low-spin Mn(II) using an appropriate ligand sphere should produce another promising candidate for efficient C-H bond activation. This new TSR scenario therefore emerges as a new strategy for using low-valent first-row transition metals for C-H activation reactions.

IMP Dehydrogenase: Structural Schizophrenia and an Unusual Base

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

Hedstrom,L.; Gan, L.

2006-01-01

Textbooks describe enzymes as relatively rigid templates for the transition state of a chemical reaction, and indeed an enzyme such as chymotrypsin, which catalyzes a relatively simple hydrolysis reaction, is reasonably well described by this model. Inosine monophosphate dehydrogenase (IMPDH) undergoes a remarkable array of conformational transitions in the course of a complicated catalytic cycle, offering a dramatic counterexample to this view. IMPDH displays several other unusual mechanistic features, including an Arg residue that may act as a general base catalyst and a dynamic monovalent cation site. Further, IMPDH appears to be involved in 'moon-lighting' functions that may require additionalmore » conformational states. How the balance between conformational states is maintained and how the various conformational states interconvert is only beginning to be understood.« less

Family division in China’s transitional economy

PubMed Central

Chen, Feinian

2009-01-01

Using a longitudinal data-set (the China Health and Nutrition Survey) we explored the effect of various economic factors, including household wealth, employment sector, and involvement in a household business on the division of extended families in China’s transitional economy. Results from event history analyses suggest that these economic factors act as either a dividing or a unifying force on the extended family. Household wealth reduces the risk of family division, but the effect is weaker for families in which parents have upper secondary education. In addition, an extended family is more likely to divide when married children work in the state sector. Further, the probability of family division is higher in families where daughters-in-law work in the state sector than in those with sons in this sector. Finally, involvement in a household business for married children increases family stability. PMID:19184721

A Networks Approach to Modeling Enzymatic Reactions.

PubMed

Imhof, P

2016-01-01

Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is beneficial to obtain a comprehensive picture of possible reaction paths and competing mechanisms. By combining individually generated intermediate states and chemical transition steps a network of such pathways can be constructed. Transition networks are a discretized representation of a potential energy landscape consisting of a multitude of reaction pathways connecting the end states of the reaction. The graph structure of the network allows an easy identification of the energetically most favorable pathways as well as a number of alternative routes. © 2016 Elsevier Inc. All rights reserved.

Estimation of Survival Probabilities for Use in Cost-effectiveness Analyses: A Comparison of a Multi-state Modeling Survival Analysis Approach with Partitioned Survival and Markov Decision-Analytic Modeling

PubMed Central

Williams, Claire; Lewsey, James D.; Mackay, Daniel F.; Briggs, Andrew H.

2016-01-01

Modeling of clinical-effectiveness in a cost-effectiveness analysis typically involves some form of partitioned survival or Markov decision-analytic modeling. The health states progression-free, progression and death and the transitions between them are frequently of interest. With partitioned survival, progression is not modeled directly as a state; instead, time in that state is derived from the difference in area between the overall survival and the progression-free survival curves. With Markov decision-analytic modeling, a priori assumptions are often made with regard to the transitions rather than using the individual patient data directly to model them. This article compares a multi-state modeling survival regression approach to these two common methods. As a case study, we use a trial comparing rituximab in combination with fludarabine and cyclophosphamide v. fludarabine and cyclophosphamide alone for the first-line treatment of chronic lymphocytic leukemia. We calculated mean Life Years and QALYs that involved extrapolation of survival outcomes in the trial. We adapted an existing multi-state modeling approach to incorporate parametric distributions for transition hazards, to allow extrapolation. The comparison showed that, due to the different assumptions used in the different approaches, a discrepancy in results was evident. The partitioned survival and Markov decision-analytic modeling deemed the treatment cost-effective with ICERs of just over £16,000 and £13,000, respectively. However, the results with the multi-state modeling were less conclusive, with an ICER of just over £29,000. This work has illustrated that it is imperative to check whether assumptions are realistic, as different model choices can influence clinical and cost-effectiveness results. PMID:27698003

Estimation of Survival Probabilities for Use in Cost-effectiveness Analyses: A Comparison of a Multi-state Modeling Survival Analysis Approach with Partitioned Survival and Markov Decision-Analytic Modeling.

PubMed

Williams, Claire; Lewsey, James D; Mackay, Daniel F; Briggs, Andrew H

2017-05-01

Modeling of clinical-effectiveness in a cost-effectiveness analysis typically involves some form of partitioned survival or Markov decision-analytic modeling. The health states progression-free, progression and death and the transitions between them are frequently of interest. With partitioned survival, progression is not modeled directly as a state; instead, time in that state is derived from the difference in area between the overall survival and the progression-free survival curves. With Markov decision-analytic modeling, a priori assumptions are often made with regard to the transitions rather than using the individual patient data directly to model them. This article compares a multi-state modeling survival regression approach to these two common methods. As a case study, we use a trial comparing rituximab in combination with fludarabine and cyclophosphamide v. fludarabine and cyclophosphamide alone for the first-line treatment of chronic lymphocytic leukemia. We calculated mean Life Years and QALYs that involved extrapolation of survival outcomes in the trial. We adapted an existing multi-state modeling approach to incorporate parametric distributions for transition hazards, to allow extrapolation. The comparison showed that, due to the different assumptions used in the different approaches, a discrepancy in results was evident. The partitioned survival and Markov decision-analytic modeling deemed the treatment cost-effective with ICERs of just over £16,000 and £13,000, respectively. However, the results with the multi-state modeling were less conclusive, with an ICER of just over £29,000. This work has illustrated that it is imperative to check whether assumptions are realistic, as different model choices can influence clinical and cost-effectiveness results.

Professional Development Experiences of Alternatively Certified Career and Technical Education Teachers in North Carolina

ERIC Educational Resources Information Center

Welfare, Rhonda Marie

2013-01-01

In an effort to increase the quantity and quality of available teachers, states have begun to offer alternate methods of teacher certification. This means that in addition to traditional teacher training, which involves graduation from an accredited teacher-education institution, states provide alternate routes to enable teachers to transition to…

Evolution of Large-Scale Magnetic Fields and State Transitions in Black Hole X-Ray Binaries

NASA Astrophysics Data System (ADS)

Wang, Ding-Xiong; Huang, Chang-Yin; Wang, Jiu-Zhou

2010-04-01

The state transitions of black hole (BH) X-ray binaries are discussed based on the evolution of large-scale magnetic fields, in which the combination of three energy mechanisms are involved: (1) the Blandford-Znajek (BZ) process related to the open field lines connecting a rotating BH with remote astrophysical loads, (2) the magnetic coupling (MC) process related to the closed field lines connecting the BH with its surrounding accretion disk, and (3) the Blandford-Payne (BP) process related to the open field lines connecting the disk with remote astrophysical loads. It turns out that each spectral state of the BH binaries corresponds to each configuration of magnetic field in BH magnetosphere, and the main characteristics of low/hard (LH) state, hard intermediate (HIM) state and steep power law (SPL) state are roughly fitted based on the evolution of large-scale magnetic fields associated with disk accretion.

Applying state diagrams to food processing and development

NASA Technical Reports Server (NTRS)

Roos, Y.; Karel, M.

1991-01-01

The physical state of food components affects their properties during processing, storage, and consumption. Removal of water by evaporation or by freezing often results in formation of an amorphous state (Parks et al., 1928; Troy and Sharp, 1930; Kauzmann, 1948; Bushill et al., 1965; White and Cakebread, 1966; Slade and Levine, 1991). Amorphous foods are also produced from carbohydrate melts by rapid cooling after extrusion or in the manufacturing of hard sugar candies and coatings (Herrington and Branfield, 1984). Formation of the amorphous state and its relation to equilibrium conditions are shown in Fig. 1 [see text]. The most important change, characteristic of the amorphous state, is noticed at the glass transition temperature (Tg), which involves transition from a solid "glassy" to a liquid-like "rubbery" state. The main consequence of glass transition is an increase of molecular mobility and free volume above Tg, which may result in physical and physico-chemical deteriorative changes (White and Cakebread, 1966; Slade and Levine, 1991). We have conducted studies on phase transitions of amorphous food materials and related Tg to composition, viscosity, stickiness, collapse, recrystallization, and ice formation. We have also proposed that some diffusion-limited deteriorative reactions are controlled by the physical state in the vicinity of Tg (Roos and Karel, 1990, 1991a, b, c). The results are summarized in this article, with state diagrams based on experimental and calculated data to characterize the relevant water content, temperature, and time-dependent phenomena of amorphous food components.

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).

Structural basis of urea-induced unfolding: Unraveling the folding pathway of hemochromatosis factor E.

PubMed

Khan, Parvez; Prakash, Amresh; Haque, Md Anzarul; Islam, Asimul; Hassan, Md Imtaiyaz; Ahmad, Faizan

2016-10-01

Hereditary hemochromatosis factor E (HFE) is a type 1 transmembrane protein, and acts as a negative regulator of iron-uptake. The equilibrium unfolding and conformational stability of the HFE protein was examined in the presence of urea. The folding and unfolding transitions were monitored with the help of circular dichroism (CD), intrinsic fluorescence and absorption spectroscopy. Analysis of transition curves revealed that the folding of HFE is not a two-state process. However, it involved stable intermediates. Transition curves (plot of fluorescence (F346) and CD signal at 222nm (θ222) versus [Urea], the molar urea concentration) revealed a biphasic transition with midpoint (Cm) values at 2.88M and 4.95M urea. Whereas, absorption analysis shows one two-state transition centered at 2.96M. To estimate the protein stability, denaturation curves were analyzed for Gibbs free energy change in the absence of urea (ΔGD(0)) associated with the equilibrium of denaturation exist between native state↔denatured state. The intermediate state was further characterized by hydrophobic probe, 1-anilinonaphthalene-8-sulfonic acid (ANS-binding). For seeing the effect of urea on the structure and dynamics of HFE, molecular dynamics simulation for 60ns was also performed. A clear correspondence was established between the in vitro and in silico studies. Copyright © 2016 Elsevier B.V. All rights reserved.

Game Theoretic Approaches to Protect Cyberspace

DTIC Science & Technology

2010-04-20

security problems. 3.1 Definitions Game A description of the strategic interaction between opposing, or co-operating, interests where the con ...that involves probabilistic transitions through several states of the system. The game pro - gresses as a sequence of states. The game begins with a...eventually leads to a discretized model. The reaction functions uniquely minimize the strictly con - vex cost functions. After discretization, this

The Elusive Excited Quintet [superscript 5]D of Tb(III): A Source of Luminescence and Resonance Energy Transfer in Terbium Compounds

ERIC Educational Resources Information Center

Klier, Kamil

2010-01-01

The understanding of electronic structure of atomic and molecular term states involved in spectroscopic transitions is aided by projecting combinations of micro-configurations to multi-electron states with "good" quantum numbers of angular momenta. In rare-earth (RE) compounds, atomic term labels are justifiably carried over to compounds, because…

Exploiting delayed transitions to sustain semiarid ecosystems after catastrophic shifts.

PubMed

Vidiella, Blai; Sardanyés, Josep; Solé, Ricard

2018-06-01

Semiarid ecosystems (including arid, semiarid and dry-subhumid ecosystems) span more than 40% of extant habitats and contain a similar percentage of the human population. Theoretical models and palaeoclimatic data predict a grim future, with rapid shifts towards a desert state, with accelerated diversity losses and ecological collapses. These shifts are a consequence of the special nonlinearities resulting from ecological facilitation. Here, we investigate a simple model of semiarid ecosystems identifying the so-called ghost, which appears after a catastrophic transition from a vegetated to a desert state once a critical rate of soil degradation is overcome. The ghost involves a slowdown of transients towards the desert state, making the ecosystem seem stable even though vegetation extinction is inevitable. We use this model to show how to exploit the ecological ghosts to avoid collapse. Doing so involves the restoration of small fractions of desert areas with vegetation capable of maintaining a stable community once the catastrophic shift condition has been achieved. This intervention method is successfully tested under the presence of demographic stochastic fluctuations. © 2018 The Author(s).

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

Observation of microscopic dynamics of phase transition in ferroelectric crystals using fluorescence spectroscopy

NASA Astrophysics Data System (ADS)

Sedarous, Salah S.

1996-03-01

Despite the large quantity of data on the macroscopic changes in the physical properties of ferroelectric crystals during phase transition, there is a continued need for understanding their microscopic origin. Here we describe a novel method for examining the microscopic dynamics of the ferroelectric phase transition using time-resolved fluorescence spectroscopy. The fluorescence properties of organic chromophores embedded in the ferroelectric crystals triglycine sulfate and potassium dihydrogen phosphate are altered in response to the structural phase transitions. The lifetime and the fractional intensity decay show large changes around Tc and the order of the phase transition is readily recovered (first or second order). To explain the fluorescence lifetime data we present a novel theoretical model based on the concept of polaritons in these crystals. Deactivation of the excited state chromophore involves the participation of the vibrational modes of the chromophore. These modes are coupled to the polarization dispersion of the matrix and facilitate the coupling of the excited state to the collective modes in the crystal. The net result is the flow of energy from the excited state chromophore to the lattice phonon. The data indicate that changes in fluorescence lifetime can be used to examine directly the collective modes in these crystals. Our work provides important insight into the emergence of macroscopic phase transition behavior out of microscopic fluctuations.

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.

Electric control of magnetization reorientation in FeRh /BaTiO3 mediated by a magnetic phase transition

NASA Astrophysics Data System (ADS)

Odkhuu, Dorj

2017-10-01

Employing first-principles calculations we predict magnetization reorientation in FeRh films epitaxially grown on BaTiO3 by reversing the electric polarization or applying the strain effect, which is associated with the recently discovered voltage-induced interfacial magnetic-phase transition by R. O. Cherifi et al. [Nat. Mater. 13, 345 (2014), 10.1038/nmat3870]. We propose that this transition from antiferromagnetic to ferromagnetic phase is the results of the mutual mechanisms of the polarization-reversal-induced volume/strain expansion in the interfacial FeRh layers and the competition between direct and indirect exchange interactions. These mechanisms are mainly driven by the ferroelectrically driven hybridization between Fe and Ti 3 d orbital states at the interface. Such a strong hybridization can further involve Rh 4 d states with large spin-orbit coupling, which, rather than the Fe 3 d orbitals, is responsible for magnetization reorientation at the magnetic-phase transition. These findings point toward the feasibility of electric field control of magnetization switching associated with the magnetic-phase transition in an antiferromagnet structure.

Transition from the diamagnetic insulator to ferromagnetic metal in La1-xSrxCoO3

NASA Astrophysics Data System (ADS)

Knížek, Karel; Jirák, Zdeněk; Hejtmánek, Jiří; Novák, Pavel

2010-05-01

We have analyzed, using the theoretical GGA+U calculations, different configurations of spin states (low-spin, LS; intermediate-spin, IS and high-spin, HS Co) and proposed a model that accounts for magnetic and electric transport properties of perovskite cobaltites upon doping by charge carriers. In particular, it appears that the compositional transition from the diamagnetic LS phase of LaCoO3 to the ferromagnetic metallic IS phase in La1-xSrxCoO3 ( x>0.2) involves the same mechanisms as the high-temperature transition in pure LaCoO3. The process occurs gradually via a phase-separated state, where metallic IS domains stabilized through a charge transfer between Co and Co neighbors coexist with the Co poor regions in the LS ground state (or at higher temperatures, in mixed LS/HS state). This phase separation vanishes when doping in La1-xSrxCoO3 reaches x˜0.2, and a uniform IS phase, analogous to that in pure LaCoO3 in the high-temperature limit, is established.

Amorphous to amorphous transition in particle rafts

NASA Astrophysics Data System (ADS)

Varshney, Atul; Sane, A.; Ghosh, Shankar; Bhattacharya, S.

2012-09-01

Space-filling assemblies of athermal hydrophobic particles floating at an air-water interface, called particle rafts, are shown to undergo an unusual phase transition between two amorphous states, i.e., a low density “less-rigid” state and a high density “more-rigid” state, as a function of particulate number density (Φ). The former is shown to be a capillary bridged solid and the latter is shown to be a frictionally coupled one. Simultaneous studies involving direct imaging as well as measuring its mechanical response to longitudinal and shear stresses show that the transition is marked by a subtle structural anomaly and a weakening of the shear response. The structural anomaly is identified from the variation of the mean coordination number, mean area of the Voronoi cells, and spatial profile of the displacement field with Φ. The weakened shear response is related to local plastic instabilities caused by the depinning of the contact line of the underlying fluid on the rough surfaces of the particles.

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

Ota, S.; Burke, J. T.; Casperson, R. J.

Here, the effect of the production mechanism on the decay of a compound nucleus is investigated. The nucleus 90Zr was produced by three different reactions, namely 90Zr (p,p') 90Zr, 91Zr (p,d) 90Zr, and 92Zr (p,t) 90Zr , which served as surrogate reactions for 89Zr (n,γ). The spin-parity (J π) distributions of the states populated by these reactions were studied to investigate the surrogate reaction approach, which aims at indirectly determining cross sections for compound-nuclear reactions involving unstable targets such as 89Zr. Discrete γ rays, associated with transitions in 90Zr and 89Zr, were measured in coincidence with light ions for scatteringmore » angles of 25°–60° and 90Zr excitation energies extending above the neutron separation energy. The measured transition systematics were used to gain insights into the J π distributions of 90Zr. The 90Zr (p,p') reaction was found to produce fewer γ rays associated with transitions involving high spin states (J = 6–8 ℏ) than the other two reactions, suggesting that inelastic scattering preferentially populates states in 90Zr that have lower spins than those populated in the transfer reactions investigated. The γ-ray production was also observed to vary by factors of 2–3 with the angle at which the outgoing particle was detected. These findings are relevant to the application of the surrogate reaction approach.« less

Tempo: A Toolkit for the Timed Input/Output Automata Formalism

DTIC Science & Technology

2008-01-30

generation of distributed code from specifications. F .4.3 [Formal Languages]: Tempo;, D.3 [Programming Many distributed systems involve a combination of...and require The chek (i) transition is enabled when process i’s program the simulator to check the assertions after every single step counter is set to...output foo (n:Int) The Tempo simulator addresses this issue by putting the states x: Int : = 10;transitions modeler in charge of resolving the non

Niobium-bearing arsenides and germanides from elemental mixtures not involving niobium: a new twist to an old problem in solid-state synthesis.

PubMed

Baranets, Sviatoslav; He, Hua; Bobev, Svilen

2018-05-01

Three isostructural transition-metal arsenides and germanides, namely niobium nickel arsenide, Nb 0.92(1) NiAs, niobium cobalt arsenide, NbCoAs, and niobium nickel germanide, NbNiGe, were obtained as inadvertent side products of high-temperature reactions in sealed niobium containers. In addition to reporting for the very first time the structures of the title compounds, refined from single-crystal X-ray diffraction data, this article also serves as a reminder that niobium containers may not be suitable for the synthesis of ternary arsenides and germanides by traditional high-temperature reactions. Synthetic work involving alkali or alkaline-earth metals, transition or early post-transition metals, and elements from groups 14 or 15 under such conditions may yield Nb-containing products, which at times could be the major products of such reactions.

Long-range interactions between polar bialkali ground-state molecules in arbitrary vibrational levels

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

Vexiau, R.; Lepers, M., E-mail: maxence.lepers@u-psud.fr; Aymar, M.

2015-06-07

We have calculated the isotropic C{sub 6} coefficients characterizing the long-range van der Waals interaction between two identical heteronuclear alkali-metal diatomic molecules in the same arbitrary vibrational level of their ground electronic state X{sup 1}Σ{sup +}. We consider the ten species made up of {sup 7}Li, {sup 23}Na, {sup 39}K, {sup 87}Rb, and {sup 133}Cs. Following our previous work [Lepers et al., Phys. Rev. A 88, 032709 (2013)], we use the sum-over-state formula inherent to the second-order perturbation theory, composed of the contributions from the transitions within the ground state levels, from the transition between ground-state and excited state levels,more » and from a crossed term. These calculations involve a combination of experimental and quantum-chemical data for potential energy curves and transition dipole moments. We also investigate the case where the two molecules are in different vibrational levels and we show that the Moelwyn-Hughes approximation is valid provided that it is applied for each of the three contributions to the sum-over-state formula. Our results are particularly relevant in the context of inelastic and reactive collisions between ultracold bialkali molecules in deeply bound or in Feshbach levels.« less

Force transients and minimum cross-bridge models in muscular contraction

PubMed Central

Halvorson, Herbert R.

2010-01-01

Two- and three-state cross-bridge models are considered and examined with respect to their ability to predict three distinct phases of the force transients that occur in response to step change in muscle fiber length. Particular attention is paid to satisfying the Le Châtelier–Brown Principle. This analysis shows that the two-state model can account for phases 1 and 2 of a force transient, but is barely adequate to account for phase 3 (delayed force) unless a stretch results in a sudden increase in the number of cross-bridges in the detached state. The three-state model (A → B → C → A) makes it possible to account for all three phases if we assume that the A → B transition is fast (corresponding to phase 2), the B → C transition is of intermediate speed (corresponding to phase 3), and the C → A transition is slow; in such a scenario, states A and C can support or generate force (high force states) but state B cannot (detached, or low-force state). This model involves at least one ratchet mechanism. In this model, force can be generated by either of two transitions: B → A or B → C. To determine which of these is the major force-generating step that consumes ATP and transduces energy, we examine the effects of ATP, ADP, and phosphate (Pi) on force transients. In doing so, we demonstrate that the fast transition (phase 2) is associated with the nucleotide-binding step, and that the intermediate-speed transition (phase 3) is associated with the Pi-release step. To account for all the effects of ligands, it is necessary to expand the three-state model into a six-state model that includes three ligand-bound states. The slowest phase of a force transient (phase 4) cannot be explained by any of the models described unless an additional mechanism is introduced. Here we suggest a role of series compliance to account for this phase, and propose a model that correlates the slowest step of the cross-bridge cycle (transition C → A) to: phase 4 of step analysis, the rate constant ktr of the quick-release and restretch experiment, and the rate constant kact for force development time course following Ca2+ activation. PMID:18425593

Force transients and minimum cross-bridge models in muscular contraction.

PubMed

Kawai, Masataka; Halvorson, Herbert R

2007-01-01

Two- and three-state cross-bridge models are considered and examined with respect to their ability to predict three distinct phases of the force transients that occur in response to step change in muscle fiber length. Particular attention is paid to satisfying the Le Châtelier-Brown Principle. This analysis shows that the two-state model can account for phases 1 and 2 of a force transient, but is barely adequate to account for phase 3 (delayed force) unless a stretch results in a sudden increase in the number of cross-bridges in the detached state. The three-state model (A-->B-->C-->A) makes it possible to account for all three phases if we assume that the A-->B transition is fast (corresponding to phase 2), the B-->A transition is of intermediate speed (corresponding to phase 3), and the C-->A transition is slow; in such a scenario, states A and C can support or generate force (high force states) but state B cannot (detached, or low-force state). This model involves at least one ratchet mechanism. In this model, force can be generated by either of two transitions: B-->A or B-->C. To determine which of these is the major force-generating step that consumes ATP and transduces energy, we examine the effects of ATP, ADP, and phosphate (Pi) on force transients. In doing so, we demonstrate that the fast transition (phase 2) is associated with the nucleotide-binding step, and that the intermediate-speed transition (phase 3) is associated with the Pi-release step. To account for all the effects of ligands, it is necessary to expand the three-state model into a six-state model that includes three ligand-bound states. The slowest phase of a force transient (phase 4) cannot be explained by any of the models described unless an additional mechanism is introduced. Here we suggest a role of series compliance to account for this phase, and propose a model that correlates the slowest step of the cross-bridge cycle (transition C-->A) to: phase 4 of step analysis, the rate constant k(tr) of the quick-release and restretch experiment, and the rate constant k(act) for force development time course following Ca(2+) activation.

Geometric structure and information change in phase transitions

NASA Astrophysics Data System (ADS)

Kim, Eun-jin; Hollerbach, Rainer

2017-06-01

We propose a toy model for a cyclic order-disorder transition and introduce a geometric methodology to understand stochastic processes involved in transitions. Specifically, our model consists of a pair of forward and backward processes (FPs and BPs) for the emergence and disappearance of a structure in a stochastic environment. We calculate time-dependent probability density functions (PDFs) and the information length L , which is the total number of different states that a system undergoes during the transition. Time-dependent PDFs during transient relaxation exhibit strikingly different behavior in FPs and BPs. In particular, FPs driven by instability undergo the broadening of the PDF with a large increase in fluctuations before the transition to the ordered state accompanied by narrowing the PDF width. During this stage, we identify an interesting geodesic solution accompanied by the self-regulation between the growth and nonlinear damping where the time scale τ of information change is constant in time, independent of the strength of the stochastic noise. In comparison, BPs are mainly driven by the macroscopic motion due to the movement of the PDF peak. The total information length L between initial and final states is much larger in BPs than in FPs, increasing linearly with the deviation γ of a control parameter from the critical state in BPs while increasing logarithmically with γ in FPs. L scales as |lnD | and D-1 /2 in FPs and BPs, respectively, where D measures the strength of the stochastic forcing. These differing scalings with γ and D suggest a great utility of L in capturing different underlying processes, specifically, diffusion vs advection in phase transition by geometry. We discuss physical origins of these scalings and comment on implications of our results for bistable systems undergoing repeated order-disorder transitions (e.g., fitness).

Geometric structure and information change in phase transitions.

PubMed

Kim, Eun-Jin; Hollerbach, Rainer

2017-06-01

We propose a toy model for a cyclic order-disorder transition and introduce a geometric methodology to understand stochastic processes involved in transitions. Specifically, our model consists of a pair of forward and backward processes (FPs and BPs) for the emergence and disappearance of a structure in a stochastic environment. We calculate time-dependent probability density functions (PDFs) and the information length L, which is the total number of different states that a system undergoes during the transition. Time-dependent PDFs during transient relaxation exhibit strikingly different behavior in FPs and BPs. In particular, FPs driven by instability undergo the broadening of the PDF with a large increase in fluctuations before the transition to the ordered state accompanied by narrowing the PDF width. During this stage, we identify an interesting geodesic solution accompanied by the self-regulation between the growth and nonlinear damping where the time scale τ of information change is constant in time, independent of the strength of the stochastic noise. In comparison, BPs are mainly driven by the macroscopic motion due to the movement of the PDF peak. The total information length L between initial and final states is much larger in BPs than in FPs, increasing linearly with the deviation γ of a control parameter from the critical state in BPs while increasing logarithmically with γ in FPs. L scales as |lnD| and D^{-1/2} in FPs and BPs, respectively, where D measures the strength of the stochastic forcing. These differing scalings with γ and D suggest a great utility of L in capturing different underlying processes, specifically, diffusion vs advection in phase transition by geometry. We discuss physical origins of these scalings and comment on implications of our results for bistable systems undergoing repeated order-disorder transitions (e.g., fitness).

Development of Phased-Array Ultrasonic Testing Acceptability Criteria : (Phase I)

DOT National Transportation Integrated Search

2014-10-01

Phase I of this research effort involved a review of the current state of the art of weld inspection using PAUT, development of the preliminary technical approach to inspecting CJP butt welds with and without transitions, fabrication of suitable test...

Moment of inertia, quadrupole moment, Love number of neutron star and their relations with strange-matter equations of state

NASA Astrophysics Data System (ADS)

Bandyopadhyay, Debades; Bhat, Sajad A.; Char, Prasanta; Chatterjee, Debarati

2018-02-01

We investigate the impact of strange-matter equations of state involving Λ hyperons, Bose-Einstein condensate of K- mesons and first-order hadron-quark phase transition on moment of inertia, quadrupole moment and tidal deformability parameter of slowly rotating neutron stars. All these equations of state are compatible with the 2 M_{solar} constraint. The main findings of this investigation are the universality of the I- Q and I -Love number relations, which are preserved by the EoSs including Λ hyperons and antikaon condensates, but broken in the presence of a first-order hadron-quark phase transition. Furthermore, it is also noted that the quadrupole moment approaches the Kerr value of a black hole for maximum-mass neutron stars.

Vibronic Analysis for widetilde{B} - widetilde{X} Transition of Isopropoxy Radical

NASA Astrophysics Data System (ADS)

Chhantyal-Pun, Rabi; Miller, Terry A.

2013-06-01

Alkoxy radicals are important intermediates in combustion and atmospheric chemistry. Alkoxy radicals are also of significant spectroscopic interest for the study of Jahn Teller and pseudo Jahn Teller effects, involving the widetilde{X} and widetilde{A} states. The Jahn Teller effect has been studied in methoxy. Substitution of one or two hydrogens by methyl groups transforms the interaction to a pseudo Jahn Teller effect in ethoxy and isopropoxy. Previously, moderate resolution scans have been obtained for widetilde{B} - widetilde{X} and widetilde{B} - widetilde{A} transition systems, the latter observable at higher temperature. These measurements have shown that the widetilde{X} and widetilde{A} states of isopropoxy are separated by only 60.7(7) cm^{-1} which indicates a strong pseudo Jahn Teller effect in the widetilde{X} state. Such pseduo Jahn Teller coupling should also introduce additional bands into the widetilde{B} - widetilde{X} spectrum and a number of weaker transitions have been observed which may be caused by such effects. In this talk we present a vibronic analysis for the widetilde{B} - widetilde{X} transition based on the experimental results and also the results from recent quantum chemistry calculations.

National Dance Education Organization: Building a Future for Dance Education in the Arts

ERIC Educational Resources Information Center

Bonbright, Jane; McGreevy-Nichols, Susan

2012-01-01

The field of dance arts education in the United States is in an entirely different place today than it was at the turn of the century. Much of this change is due to a convergence of events that involved: federal and state legislation, policy, and funding that supported dance in arts education; a forty-year transition of dance out of departments of…

Indication of Confirmation of Transition and Formation Boundary from Ordered to Disordered Flux Vortex Chain State in High-Tc Superconductors Y1Ba2Cu3O7- δ and Bi2Sr2Ca2Cu3O10 and New Low-Field Data Delineating Magnetic Transition in Gd1Ba2(Fe0.02Cu0.98)3O7- δ

NASA Astrophysics Data System (ADS)

Vezzoli, G. Christopher; Chen, Michaeline F.; Burke, Terence; Rosen, Carol

1996-08-01

Data are presented herein that support a phase boundary or quasi-phase-boundary delineating in Y1Ba2Cu3O7-δ and in Bi2Sr2Ca2Cu3O10 ceramic materials a transition from a vortex solid lattice to a line-flux disordered state that has been referred to as representing flux lattice melting to a flux liquid, but herein is interpreted not in terms of a liquid but in the form of a less-mobile `polymer'-like or entangled chain species. These data are derived from electrical resistance (r) versus applied magnetic field (H) measurements at various isotherms (T) corresponding to the zero resistance state of yttrium--barium--cuprate, and the mixed state foot regime of bismuth--strontium--calcium--cuprate. We interpret significant slope changes in r versus B at constant T in these materials to be indicative of the H-T conditions for a second-order or weakly first-order phase transition delineating the disordering of a flux lattice vortex solid. We believe that this technique is in ways more direct and at least as accurate as the conventional mechanical oscillator and vibrating magnetometer method to study the flux state. Additional very-low-field studies in Gd1Ba2(Fe0.02Cu0.98)3O7-δ, from 1 to 1000 mT, yield indication for what appears to be a magnetic transition at ca. 77 K at 575 mT, and possibly a second transition at 912 mT (also at ca. 77 K). These data points correspond well with the extrapolated low-field experimental magnetic phase transition boundary curve described at higher field herein (and by others using the mechanical technique), and also correspond well to theoretically predicted work regarding transition involving the vortex state.

0 - π Quantum transition in a carbon nanotube Josephson junction: Universal phase dependence and orbital degeneracy

NASA Astrophysics Data System (ADS)

Delagrange, R.; Weil, R.; Kasumov, A.; Ferrier, M.; Bouchiat, H.; Deblock, R.

2018-05-01

In a quantum dot hybrid superconducting junction, the behavior of the supercurrent is dominated by Coulomb blockade physics, which determines the magnetic state of the dot. In particular, in a single level quantum dot singly occupied, the sign of the supercurrent can be reversed, giving rise to a π-junction. This 0 - π transition, corresponding to a singlet-doublet transition, is then driven by the gate voltage or by the superconducting phase in the case of strong competition between the superconducting proximity effect and Kondo correlations. In a two-level quantum dot, such as a clean carbon nanotube, 0- π transitions exist as well but, because more cotunneling processes are allowed, are not necessarily associated to a magnetic state transition of the dot. In this proceeding, after a review of 0- π transitions in Josephson junctions, we present measurements of current-phase relation in a clean carbon nanotube quantum dot, in the single and two-level regimes. In the single level regime, close to orbital degeneracy and in a regime of strong competition between local electronic correlations and superconducting proximity effect, we find that the phase diagram of the phase-dependent transition is a universal characteristic of a discontinuous level-crossing quantum transition at zero temperature. In the case where the two levels are involved, the nanotube Josephson current exhibits a continuous 0 - π transition, independent of the superconducting phase, revealing a different physical mechanism of the transition.

Enthalpy versus entropy: What drives hard-particle ordering in condensed phases?

DOE PAGES

Anthamatten, Mitchell; Ou, Jane J.; Weinfeld, Jeffrey A.; ...

2016-07-27

In support of mesoscopic-scale materials processing, spontaneous hard-particle ordering has been actively pursued for over a half-century. The generally accepted view that entropy alone can drive hard particle ordering is evaluated. Furthermore, a thermodynamic analysis of hard particle ordering was conducted and shown to agree with existing computations and experiments. Conclusions are that (i) hard particle ordering transitions between states in equilibrium are forbidden at constant volume but are allowed at constant pressure; (ii) spontaneous ordering transitions at constant pressure are driven by enthalpy, and (iii) ordering under constant volume necessarily involves a non-equilibrium initial state which has yet tomore » be rigorously defined.« less

Rate constant calculations in the dimerization of diaminocarbene: a direct dynamics study

NASA Astrophysics Data System (ADS)

Oliva, Josep M.

1999-03-01

Generalized transition state theory calculations are performed on the dimerization of diaminocarbene [(H 2N) 2C:] ( 1) to tetrakis(amino)ethene [(H 2N) 2CC(NH 2) 2] ( 2). This process involves the formation of a double bond from two carbenes and therefore inclusion of correlation energy is vital. The density functionals BPW91, B3LYP and the QCISD(T)//MP2 model are used in the electronic structure calculations of reactants, transition states and products. The goal of this work is to gain insight into the mechanism of dimerization of the diaminocarbenes [(R 2N) 2C:] (R=H, Me), where experimental activation parameters are already available for R=Me.

Amorphous ices explained in terms of nonequilibrium phase transitions in supercooled water

NASA Astrophysics Data System (ADS)

Limmer, David; Chandler, David

2013-03-01

We analyze the phase diagram of supercooled water out-of-equilibrium using concepts from space-time thermodynamics and the dynamic facilitation theory of the glass transition, together with molecular dynamics simulations. We find that when water is driven out-of-equilibrium, it can exist in multiple amorphous states. In contrast, we find that when water is at equilibrium, it can exist in only one liquid state. The amorphous non-equilibrium states are solids, distinguished from the liquid by their lack of mobility, and distinguished from each other by their different densities and local structure. This finding explains the experimentally observed polyamorphism of water as a class of nonequilibrium phenomena involving glasses of different densities. While the amorphous solids can be long lived, they are thermodynamically unstable. When allowed to relax to equilibrium, they crystallize with pathways that pass first through liquid state configurations and then to ordered ice.

High pressure study of acetophenone azine

NASA Astrophysics Data System (ADS)

Tang, X. D.; Ding, Z. J.; Zhang, Z. M.

2009-02-01

High pressure Raman spectra of acetophenone azine (APA) have been measured up to 17.7 GPa with a diamond anvil cell. Two crystalline-to-crystalline phase transformations are found at pressures about 3.6 and 5.8 GPa. A disappearance of external modes and the C-H vibration at pressures higher than 8.7 GPa suggests that the sample undergoes a phase transition to amorphous or orientationally disordered (plastic) state, and the amorphization was completed at about 12.1 GPa. The disordered state is unstable and, then, a polymerization transformation reaction occurs with a further pressure increase. After the pressure has been released, the polymerization state can remain at the ambient condition, indicating that the virgin crystalline state is not recovered. The results show that the phenomenon underlying the pressure induced phase transition of APA may involve profound changes in the coordination environments of the symmetric aromatic azine.

Dipolon Theory of High Temperature Superconductors- Prediction of the Existence of New Very Low Energy Excitations to be Observed in Photoemission Experiments

NASA Astrophysics Data System (ADS)

Sharma, Ram R.

The dipolon theory first discovered two high energy kinks in electron energy. It [1-2] has also predicted two superconducting states, symmetric (''s'') and anti-symmetric (''as''). Here we report the prediction of very low energy excitations due to transition from ''as'' state to ''s'' state (''ass'') (or vice versa) which creates (annihilates) the quantum (''asson'') of energy ℏωa (q-->a) =Es (k' -->) -Eas (k'' -->) ; ''a'' is for ''asson'' and Es (k' -->) and Eas (k'' -->) are electron energies in ''s'' and ''as'' states, respectively (Ei (k -->) =Eri (k -->) [1-4]). Our theory [1-4] finds in BISCCO at M point on Fermi level at T=13 K asson energy about 14 +/- 8 meV . We predict that these assons create a new kink in electron energy at this energy. Also, a single pair transitions are possible which involve two assons.

Density function theoretical study on the complex involved in Th atom-activated C-C bond in C2H6

NASA Astrophysics Data System (ADS)

Qing-Qing, Wang; Peng, Li; Tao, Gao; Hong-Yan, Wang; Bing-Yun, Ao

2016-06-01

Density functional theory (DFT) calculations are performed to investigate the reactivity of Th atom toward ethane C-C bond activation. A comprehensive description of the reaction mechanisms leading to two different reaction products is presented. We report a complete exploration of the potential energy surfaces by taking into consideration different spin states. In addition, the intermediate and transition states along the reaction paths are characterized. Total, partial, and overlap population density of state diagrams and analyses are also presented. Furthermore, the natures of the chemical bonding of intermediate and transition states are studied by using topological method combined with electron localization function (ELF) and Mayer bond order. Infrared spectrum (IR) is obtained and further discussed based on the optimized geometries. Project supported by the National Natural Science Foundation of China (Grant Nos. 21371160, 21401173, and 11364023).

Excitonic linewidth and coherence lifetime in monolayer transition metal dichalcogenides

DOE PAGES

Selig, Malte; Berghäuser, Gunnar; Raja, Archana; ...

2016-11-07

Atomically thin transition metal dichalcogenides are direct-gap semiconductors with strong light–matter and Coulomb interactions. The latter accounts for tightly bound excitons, which dominate their optical properties. Besides the optically accessible bright excitons, these systems exhibit a variety of dark excitonic states. They are not visible in the optical spectra, but can strongly influence the coherence lifetime and the linewidth of the emission from bright exciton states. We investigate the microscopic origin of the excitonic coherence lifetime in two representative materials (WS 2 and MoSe 2) through a study combining microscopic theory with spectroscopic measurements. We also show that the excitonicmore » coherence lifetime is determined by phonon-induced intravalley scattering and intervalley scattering into dark excitonic states. Particularly, we identify exciton relaxation processes involving phonon emission into lower-lying dark states that are operative at all temperatures, in WS 2.« less

A kinetic and thermochemical database for organic sulfur and oxygen compounds.

PubMed

Class, Caleb A; Aguilera-Iparraguirre, Jorge; Green, William H

2015-05-28

Potential energy surfaces and reaction kinetics were calculated for 40 reactions involving sulfur and oxygen. This includes 11 H2O addition, 8 H2S addition, 11 hydrogen abstraction, 7 beta scission, and 3 elementary tautomerization reactions, which are potentially relevant in the combustion and desulfurization of sulfur compounds found in various fuel sources. Geometry optimizations and frequencies were calculated for reactants and transition states using B3LYP/CBSB7, and potential energies were calculated using CBS-QB3 and CCSD(T)-F12a/VTZ-F12. Rate coefficients were calculated using conventional transition state theory, with corrections for internal rotations and tunneling. Additionally, thermochemical parameters were calculated for each of the compounds involved in these reactions. With few exceptions, rate parameters calculated using the two potential energy methods agreed reasonably, with calculated activation energies differing by less than 5 kJ mol(-1). The computed rate coefficients and thermochemical parameters are expected to be useful for kinetic modeling.

Water Dynamics and Dewetting Transitions in the Small Mechanosensitive Channel MscS

PubMed Central

Anishkin, Andriy; Sukharev, Sergei

2004-01-01

The dynamics of confined water in capillaries and nanotubes suggests that gating of ion channels may involve not only changes of the pore geometry, but also transitions between water-filled and empty states in certain locations. The recently solved heptameric structure of the small mechanosensitive channel of Escherichia coli, MscS, has revealed a relatively wide (7–15 Å) yet highly hydrophobic transmembrane pore. Continuum estimations based on the properties of pore surface suggest low conductance and a thermodynamic possibility of dewetting. To test the predictions we performed molecular dynamics simulations of MscS filled with flexible TIP3P water. Irrespective to the initial conditions, several independent 6-ns simulations converged to the same stable state with the pore water-filled in the wider part, but predominantly empty in the narrow hydrophobic part, displaying intermittent vapor-liquid transitions. The polar gain-of-function substitution L109S in the constriction resulted in a stable hydration of the entire pore. Steered passages of Cl− ions through the narrow part of the pore consistently produced partial ion dehydration and required a force of 200–400 pN to overcome an estimated barrier of 10–20 kcal/mole, implying negligibly low conductance. We conclude that the crystal structure of MscS does not represent an open state. We infer that MscS gate, which is similar to that of the nicotinic ACh receptor, involves a vapor-lock mechanism where limited changes of geometry or surface polarity can locally switch the regime between water-filled (conducting) and empty (nonconducting) states. PMID:15111405

Non-equilibrium effects in high temperature chemical reactions

NASA Technical Reports Server (NTRS)

Johnson, Richard E.

1987-01-01

Reaction rate data were collected for chemical reactions occurring at high temperatures during reentry of space vehicles. The principle of detailed balancing is used in modeling kinetics of chemical reactions at high temperatures. Although this principle does not hold for certain transient or incubation times in the initial phase of the reaction, it does seem to be valid for the rates of internal energy transitions that occur within molecules and atoms. That is, for every rate of transition within the internal energy states of atoms or molecules, there is an inverse rate that is related through an equilibrium expression involving the energy difference of the transition.

The Effect of a Helix-Coil Transition on the Extension Elasticity

NASA Astrophysics Data System (ADS)

Buhot, Arnaud; Halperin, Avi

2000-03-01

The secondary structure of a polymer affects its deformation behavior in accordance with the Le Chatelier principle. An important example of such secondary structure is the alpha helix encountered in polypeptides. Similar structure was recently proposed for PEO in aqueous media. Our discussion concerns the coupling of the cooperative helix-coil transition and the extension elasticity. In particular, we analyze the extension of a long single chain by use of optical tweezers or AFM. We consider chains that exist in the coil-state when unperturbed. The transition nevertheless occurs because the extension favors the low entropy helical state. As a result, the corresponding force law exhibits a plateau. The analysis of this situation involves two ingredients: (I) the stretching free energy penalty for a rod-coil mutiblock copolymer (II) the entropy associated with the possible placements of the rod and coil blocks.

Kondo behavior and metamagnetic phase transition in the heavy-fermion compound CeBi2

NASA Astrophysics Data System (ADS)

Zhou, W.; Xu, C. Q.; Li, B.; Sankar, R.; Zhang, F. M.; Qian, B.; Cao, C.; Dai, J. H.; Lu, Jianming; Jiang, W. X.; Qian, Dong; Xu, Xiaofeng

2018-05-01

Heavy fermions represent an archetypal example of strongly correlated electron systems which, due to entanglement among different interactions, often exhibit exotic and fascinating physics involving Kondo screening, magnetism, and unconventional superconductivity. Here we report a comprehensive study on the transport and thermodynamic properties of a cerium-based heavy-fermion compound CeBi2 which undergoes an antiferromagnetic transition at TN˜3.3 K . Its high-temperature paramagnetic state is characterized by an enhanced heat capacity with Sommerfeld coefficient γ over 200 mJ mol-1K-2 . The magnetization in the magnetically ordered state features a metamagnetic transition. Remarkably, a large negative magnetoresistance associated with the magnetism was observed in a wide temperature and field-angle range. Collectively, CeBi2 may serve as an intriguing system to study the interplay between the f electrons and the itinerant Fermi sea.

Total decay and transition rates from LQCD

NASA Astrophysics Data System (ADS)

Hansen, Maxwell T.; Meyer, Harvey B.; Robaina, Daniel

2018-03-01

We present a new technique for extracting total transition rates into final states with any number of hadrons from lattice QCD. The method involves constructing a finite-volume Euclidean four-point function whose corresponding infinite-volume spectral function gives access to the decay and transition rates into all allowed final states. The inverse problem of calculating the spectral function is solved via the Backus-Gilbert method, which automatically includes a smoothing procedure. This smoothing is in fact required so that an infinite-volume limit of the spectral function exists. Using a numerical toy example we find that reasonable precision can be achieved with realistic lattice data. In addition, we discuss possible extensions of our approach and, as an example application, prospects for applying the formalism to study the onset of deep-inelastic scattering. More details are given in the published version of this work, Ref. [1].

High resolution spectral analysis of oxygen. I. Isotopically invariant Dunham fit for the X(3)Σ(g)(-), a(1)Δ(g), b(1)Σ(g)(+) states.

PubMed

Yu, Shanshan; Miller, Charles E; Drouin, Brian J; Müller, Holger S P

2012-07-14

We have developed a simultaneous global fit to the MW, THz, infrared, visible, and UV transitions of all six oxygen isotopologues, (16)O(16)O, (16)O(17)O, (16)O(18)O, (17)O(17)O, (17)O(18)O, (18)O(18)O, with the objective of predicting all transitions below the O((3)P) + O((3)P) dissociation threshold as well as the B(3)Σ(u) (-) state from O((3)P)+O((1)D) within state-of-the-art experimental uncertainty. Here, we report an isotopically invariant Dunham fit for the lowest three electronic states, X(3)Σ(g)(-), a(1)Δ(g), and b(1)Σ(g)(+). Experimental transition frequencies involving these three states of all six O(2) isotopologues were critically reviewed and incorporated into the analysis. For the (16)O(16)O isotopologue, experimental data sample vibrational states v = 0-31 for X(3)Σ(g)(-), v = 0-10 for a(1)Δ(g), and v = 0-12 for b(1)Σ(g)(+). To the best of our knowledge, this is the first analysis that simultaneously fits spectra from all six O(2) isotopologues.

Barriers and facilitators to successful transition from pediatric to adult inflammatory bowel disease care from the perspectives of providers

PubMed Central

Paine, Christine Weirich; Stollon, Natalie B.; Lucas, Matthew S.; Brumley, Lauren D.; Poole, Erika S.; Peyton, Tamara; Grant, Anne W.; Jan, Sophia; Trachtenberg, Symme; Zander, Miriam; Mamula, Petar; Bonafide, Christopher P.; Schwartz, Lisa A.

2014-01-01

Background For adolescents and young adults (AYA) with inflammatory bowel disease (IBD), the transition from pediatric to adult care is often challenging and associated with gaps in care. Our study objectives were to (1) identify outcomes for evaluating transition success and (2) elicit the major barriers and facilitators of successful transition. Methods We interviewed pediatric and adult IBD providers from across the United States with experience caring for AYAs with IBD until thematic saturation was reached after 12 interviews. We elicited the participants' backgrounds, examples of successful and unsuccessful transition of AYAs for whom they cared, and recommendations for improving transition using the Social-ecological Model of Adolescent and Young Adult Readiness to Transition framework. We coded interview transcripts using the constant comparative method and identified major themes. Results Participants reported evaluating transition success and failure using healthcare utilization outcomes (e.g. maintaining continuity with adult providers), health outcomes (e.g. stable symptoms), and quality of life outcomes (e.g. attending school). The patients' level of developmental maturity (i.e. ownership of care) was the most prominent determinant of transition outcomes. The style of parental involvement (i.e. helicopter parent vs. optimally-involved parent) also influenced outcomes as well as the degree of support by providers (e.g. care coordination). Conclusion IBD transition success is influenced by a complex interplay of patient developmental maturity, parenting style, and provider support. Multidisciplinary IBD care teams should aim to optimize these factors for each patient to increase the likelihood of a smooth transfer to adult care. PMID:25137417

Barriers and facilitators to successful transition from pediatric to adult inflammatory bowel disease care from the perspectives of providers.

PubMed

Paine, Christine W; Stollon, Natalie B; Lucas, Matthew S; Brumley, Lauren D; Poole, Erika S; Peyton, Tamara; Grant, Anne W; Jan, Sophia; Trachtenberg, Symme; Zander, Miriam; Mamula, Petar; Bonafide, Christopher P; Schwartz, Lisa A

2014-11-01

For adolescents and young adults (AYA) with inflammatory bowel disease (IBD), the transition from pediatric to adult care is often challenging and associated with gaps in care. Our study objectives were to (1) identify outcomes for evaluating transition success and (2) elicit the major barriers and facilitators of successful transition. We interviewed pediatric and adult IBD providers from across the United States with experience caring for AYAs with IBD until thematic saturation was reached after 12 interviews. We elicited the participants' backgrounds, examples of successful and unsuccessful transition of AYAs for whom they cared, and recommendations for improving transition using the Social-Ecological Model of Adolescent and Young Adult Readiness to Transition framework. We coded interview transcripts using the constant comparative method and identified major themes. Participants reported evaluating transition success and failure using health care utilization outcomes (e.g., maintaining continuity with adult providers), health outcomes (e.g., stable symptoms), and quality of life outcomes (e.g., attending school). The patients' level of developmental maturity (i.e., ownership of care) was the most prominent determinant of transition outcomes. The style of parental involvement (i.e., helicopter parent versus optimally involved parent) and the degree of support by providers (e.g., care coordination) also influenced outcomes. IBD transition success is influenced by a complex interplay of patient developmental maturity, parenting style, and provider support. Multidisciplinary IBD care teams should aim to optimize these factors for each patient to increase the likelihood of a smooth transfer to adult care.

Spin-state transitions and magnetic polaron in lightly doped La1-xSrxCoO3.

NASA Astrophysics Data System (ADS)

Podlesnyak, A.; Haverkort, M. W.; Conder, K.; Pomyakushina, E.; Khomskii, Daniel

2007-03-01

Using the inelastic neutron scattering (INS) technique, we identified the energy levels of the thermally excited states of Co^3+ ions in both LaCoO3 and La0.998Sr0.002CoO3. In LaCoO3 an excitation at ˜0.6 meV appears at T>30K, whose intensity follows the bulk magnetization. Within a model including crystal field interaction and spin-orbit coupling we interpret this excitation as originating from a transition between thermally excited states located about 120 K above the ground state. Since the g-factor obtained from the field dependence of the INS is g˜ 3, we interpret this state as a high-spin state of Co^3+ . The lightly doped material x˜0:002 exhibits paramagnetic properties at low temperatures. An INS peak at energy transfer ˜0.75 meV was observed in it already at T = 1:5 K. We propose that the holes introduced in the LS state of LaCoO3 by doping are extended over the neighboring Co sites, forming thus magnetic polaron and transforming all the involved Co ions (e.g. 6 of them) to the high-spin state. Similarly to LaCoO3, we interpret the INS transition at 0.75 meV as that on these high-spin Co^3+ ions.

Design and Synthesis of Potent “Sulfur-free” Transition State Analogue Inhibitors of 5′-Methylthioadenosine Nucleosidase and 5′-Methylthioadenosine Phosphorylase

PubMed Central

Longshaw, Alistair I.; Adanitsch, Florian; Gutierrez, Jemy A.; Evans, Gary B.; Tyler, Peter C.; Schramm, Vern L.

2013-01-01

5′-Methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is a dual substrate bacterial enzyme involved in S-adenosylmethionine (SAM)-related quorum sensing pathways that regulates virulence in many bacterial species. MTANs from many bacteria are directly involved in the quorum sensing mechanism by regulating the synthesis of autoinducer molecules that are used by bacterial communities to communicate. In humans, 5′-methylthioadenosine phosphorylase (MTAP) is involved in polyamine biosynthesis as well as in purine and SAM salvage pathways and thus has been identified as an anticancer target. Previously we have described the synthesis and biological activity of several aza-C-nucleoside mimics with a sulfur atom at the 5′ position that are potent E. coli MTAN and human MTAP inhibitors. Because of the possibility that the sulfur may affect bioavailability we were interested in synthesizing “sulfur-free” analogues. Herein we describe the preparation of a series of “sulfur-free” transition state analogues inhibitors, of E. coli MTAN and human MTAP that have low nano- to pico-molar dissociation constants and are potentially novel bacterial anti-infective and anti-cancer drug candidates. PMID:20718423

Theoretical study of the reactions of the hydroselenyl radical (HSe●) with the selenenic radical (HSeO●).

PubMed

Vega-Teijido, Mauricio Angel; Kieninger, Martina; Ventura, Oscar N

2017-12-05

The formation of selenium species in some biological processes involves the generation of ionic and radical intermediates such as RSe ● , RSe - , RSeO ● , and RSeO - , among others. We performed a theoretical study of the possible mechanisms for the reaction of the two simplest Se radicals-the hydroselenyl (HSe ● ) and selenenic (HSeO ● ) radicals, in which the possible products, intermediates, and transition-state structures were investigated. Density functional theory (DFT) was applied at the B3LYP/6-311++G(3df,3pd) level and the Ahlrichs Coulomb fitting basis sets were employed with an effective core potential (ECP) for both Se atoms. The same procedure was used to calculate the electronic density. All calculations were also performed using the M06-2X functional, which describes weaker bonds better than B3LYP does. In the reaction of interest, the so-called CR complex (HSe····SeOH) is formed initially. After passing through the transition state TS1, cis-HSeSeOH is obtained as a product. If a low barrier is then overcome (passing through the transition state TS32), the trans-HSeSeOH species is obtained. The CR complex can also rearrange into the intermediate INT after overcoming the barrier presented by the transition state TS2. Additionally, the decomposition of INT to H 2 O and 1 Se 2 is possible through another transition state. This reaction is not included in this study. We also observed a second possible route for the conversion of INT to one of the HSeSeOH species; this route occurs through two pathways (with transition states TS31 and TS32). A comparison of some of the results with those obtained for sulfur analogs along the same pathways is also presented in this work. Graphical abstract Electronic envelopes for HSeO ● and HSe ● radicals.

Determining partial differential cross sections for low-energy electron photodetachment involving conical intersections using the solution of a Lippmann-Schwinger equation constructed with standard electronic structure techniques.

PubMed

Han, Seungsuk; Yarkony, David R

2011-05-07

A method for obtaining partial differential cross sections for low energy electron photodetachment in which the electronic states of the residual molecule are strongly coupled by conical intersections is reported. The method is based on the iterative solution to a Lippmann-Schwinger equation, using a zeroth order Hamiltonian consisting of the bound nonadiabatically coupled residual molecule and a free electron. The solution to the Lippmann-Schwinger equation involves only standard electronic structure techniques and a standard three-dimensional free particle Green's function quadrature for which fast techniques exist. The transition dipole moment for electron photodetachment, is a sum of matrix elements each involving one nonorthogonal orbital obtained from the solution to the Lippmann-Schwinger equation. An expression for the electron photodetachment transition dipole matrix element in terms of Dyson orbitals, which does not make the usual orthogonality assumptions, is derived.

Pressure-decoupled magnetic and structural transitions of the parent compound of iron-based 122 superconductors BaFe2As2

PubMed Central

Wu, J. J.; Lin, Jung-Fu; Wang, X. C.; Liu, Q. Q.; Zhu, J. L.; Xiao, Y. M.; Chow, P.; Jin, Changqing

2013-01-01

The recent discovery of iron ferropnictide superconductors has received intensive concern in connection with magnetically involved superconductors. Prominent features of ferropnictide superconductors are becoming apparent: the parent compounds exhibit an antiferromagnetic ordered spin density wave (SDW) state, the magnetic-phase transition is always accompanied by a crystal structural transition, and superconductivity can be induced by suppressing the SDW phase via either chemical doping or applied external pressure to the parent state. These features generated considerable interest in the interplay between magnetism and structure in chemically doped samples, showing crystal structure transitions always precede or coincide with magnetic transition. Pressure-tuned transition, on the other hand, would be more straightforward to superconducting mechanism studies because there are no disorder effects caused by chemical doping; however, remarkably little is known about the interplay in the parent compounds under controlled pressure due to the experimental challenge of in situ measuring both of magnetic and crystal structure evolution at high pressure and low temperatures. Here we show from combined synchrotron Mössbauer and X-ray diffraction at high pressures that the magnetic ordering surprisingly precedes the structural transition at high pressures in the parent compound BaFe2As2, in sharp contrast to the chemical-doping case. The results can be well understood in terms of the spin fluctuations in the emerging nematic phase before the long-range magnetic order that sheds light on understanding how the parent compound evolves from a SDW state to a superconducting phase, a key scientific inquiry of iron-based superconductors. PMID:24101468

Measurement of a solid-state triple point at the metal-insulator transition in VO2.

PubMed

Park, Jae Hyung; Coy, Jim M; Kasirga, T Serkan; Huang, Chunming; Fei, Zaiyao; Hunter, Scott; Cobden, David H

2013-08-22

First-order phase transitions in solids are notoriously challenging to study. The combination of change in unit cell shape, long range of elastic distortion and flow of latent heat leads to large energy barriers resulting in domain structure, hysteresis and cracking. The situation is worse near a triple point, where more than two phases are involved. The well-known metal-insulator transition in vanadium dioxide, a popular candidate for ultrafast optical and electrical switching applications, is a case in point. Even though VO2 is one of the simplest strongly correlated materials, experimental difficulties posed by the first-order nature of the metal-insulator transition as well as the involvement of at least two competing insulating phases have led to persistent controversy about its nature. Here we show that studying single-crystal VO2 nanobeams in a purpose-built nanomechanical strain apparatus allows investigation of this prototypical phase transition with unprecedented control and precision. Our results include the striking finding that the triple point of the metallic phase and two insulating phases is at the transition temperature, Ttr = Tc, which we determine to be 65.0 ± 0.1 °C. The findings have profound implications for the mechanism of the metal-insulator transition in VO2, but they also demonstrate the importance of this approach for mastering phase transitions in many other strongly correlated materials, such as manganites and iron-based superconductors.

Transitions in Prognostic Awareness Among Terminally Ill Cancer Patients in Their Last 6 Months of Life Examined by Multi-State Markov Modeling.

PubMed

Hsiu Chen, Chen; Wen, Fur-Hsing; Hou, Ming-Mo; Hsieh, Chia-Hsun; Chou, Wen-Chi; Chen, Jen-Shi; Chang, Wen-Cheng; Tang, Siew Tzuh

2017-09-01

Developing accurate prognostic awareness, a cornerstone of preference-based end-of-life (EOL) care decision-making, is a dynamic process involving more prognostic-awareness states than knowing or not knowing. Understanding the transition probabilities and time spent in each prognostic-awareness state can help clinicians identify trigger points for facilitating transitions toward accurate prognostic awareness. We examined transition probabilities in distinct prognostic-awareness states between consecutive time points in 247 cancer patients' last 6 months and estimated the time spent in each state. Prognostic awareness was categorized into four states: (a) unknown and not wanting to know, state 1; (b) unknown but wanting to know, state 2; (c) inaccurate awareness, state 3; and (d) accurate awareness, state 4. Transitional probabilities were examined by multistate Markov modeling. Initially, 59.5% of patients had accurate prognostic awareness, whereas the probabilities of being in states 1-3 were 8.1%, 17.4%, and 15.0%, respectively. Patients' prognostic awareness generally remained unchanged (probabilities of remaining in the same state: 45.5%-92.9%). If prognostic awareness changed, it tended to shift toward higher prognostic-awareness states (probabilities of shifting to state 4 were 23.2%-36.6% for patients initially in states 1-3, followed by probabilities of shifting to state 3 for those in states 1 and 2 [9.8%-10.1%]). Patients were estimated to spend 1.29, 0.42, 0.68, and 3.61 months in states 1-4, respectively, in their last 6 months. Terminally ill cancer patients' prognostic awareness generally remained unchanged, with a tendency to become more aware of their prognosis. Health care professionals should facilitate patients' transitions toward accurate prognostic awareness in a timely manner to promote preference-based EOL decisions. Terminally ill Taiwanese cancer patients' prognostic awareness generally remained stable, with a tendency toward developing higher states of awareness. Health care professionals should appropriately assess patients' readiness for prognostic information and respect patients' reluctance to confront their poor prognosis if they are not ready to know, but sensitively coach them to cultivate their accurate prognostic awareness, provide desired and understandable prognostic information for those who are ready to know, and give direct and honest prognostic information to clarify any misunderstandings for those with inaccurate awareness, thus ensuring that they develop accurate and realistic prognostic knowledge in time to make end-of-life care decisions. © AlphaMed Press 2017.

On the molecular origin of the cooperative coil-to-globule transition of poly(N-isopropylacrylamide) in water.

PubMed

Tavagnacco, L; Zaccarelli, E; Chiessi, E

2018-04-18

By means of atomistic molecular dynamics simulations we investigate the behaviour of poly(N-isopropylacrylamide), PNIPAM, in water at temperatures below and above the lower critical solution temperature (LCST), including the undercooled regime. The transition between water soluble and insoluble states at the LCST is described as a cooperative process involving an intramolecular coil-to-globule transition preceding the aggregation of chains and the polymer precipitation. In this work we investigate the molecular origin of such cooperativity and the evolution of the hydration pattern in the undercooled polymer solution. The solution behaviour of an atactic 30-mer at high dilution is studied in the temperature interval from 243 to 323 K with a favourable comparison to available experimental data. In the water soluble states of PNIPAM we detect a correlation between polymer segmental dynamics and diffusion motion of bound water, occurring with the same activation energy. Simulation results show that below the coil-to-globule transition temperature PNIPAM is surrounded by a network of hydrogen bonded water molecules and that the cooperativity arises from the structuring of water clusters in proximity to hydrophobic groups. Differently, the perturbation of the hydrogen bond pattern involving water and amide groups occurs above the transition temperature. Altogether these findings reveal that even above the LCST PNIPAM remains largely hydrated and that the coil-to-globule transition is related with a significant rearrangement of the solvent in the proximity of the surface of the polymer. The comparison between the hydrogen bonding of water in the surrounding of PNIPAM isopropyl groups and in the bulk displays a decreased structuring of solvent at the hydrophobic polymer-water interface across the transition temperature, as expected because of the topological extension along the chain of such interface. No evidence of an upper critical solution temperature behaviour, postulated in theoretical and thermodynamics studies of PNIPAM aqueous solution, is observed in the low temperature domain.

Nonlinear Optical Fiber Arrays for Limiting Application

DTIC Science & Technology

2006-09-05

Absorption [ RSA ], Two-Photon Absorption [TPA] and Excited State Absorption [ESA] or Nonlinear Scattering properties [NS] (e.g. carbon black suspension...practical implementation: I. "Saturation Effect and Dynamic Range" - In general, RSA materials have low switching threshold (<<pJ), but are (linearly...transition between the molecular levels involved, RSA materials can be easily ’bleached’, i.e. the absorption electronic state is depopulated by the laser. TPA

Electron affinity and excited states of methylglyoxal

NASA Astrophysics Data System (ADS)

Dauletyarov, Yerbolat; Dixon, Andrew R.; Wallace, Adam A.; Sanov, Andrei

2017-07-01

Using photoelectron imaging spectroscopy, we characterized the anion of methylglyoxal (X2A″ electronic state) and three lowest electronic states of the neutral methylglyoxal molecule: the closed-shell singlet ground state (X1A'), the lowest triplet state (a3A″), and the open-shell singlet state (A1A″). The adiabatic electron affinity (EA) of the ground state, EA(X1A') = 0.87(1) eV, spectroscopically determined for the first time, compares to 1.10(2) eV for unsubstituted glyoxal. The EAs (adiabatic attachment energies) of two excited states of methylglyoxal were also determined: EA(a3A″) = 3.27(2) eV and EA(A1A″) = 3.614(9) eV. The photodetachment of the anion to each of these two states produces the neutral species near the respective structural equilibria; hence, the a3A″ ← X2A″ and A1A″ ← X2A″ photodetachment transitions are dominated by intense peaks at their respective origins. The lowest-energy photodetachment transition, on the other hand, involves significant geometry relaxation in the X1A' state, which corresponds to a 60° internal rotation of the methyl group, compared to the anion structure. Accordingly, the X1A' ← X2A″ transition is characterized as a broad, congested band, whose vertical detachment energy, VDE = 1.20(4) eV, significantly exceeds the adiabatic EA. The experimental results are in excellent agreement with the ab initio predictions using several equation-of-motion methodologies, combined with coupled-cluster theory.

Energy landscape of the reactions governing the Na+ deeply occluded state of the Na+/K+-ATPase in the giant axon of the Humboldt squid

PubMed Central

Castillo, Juan P.; De Giorgis, Daniela; Basilio, Daniel; Gadsby, David C.; Rosenthal, Joshua J. C.; Latorre, Ramon; Holmgren, Miguel; Bezanilla, Francisco

2011-01-01

The Na+/K+ pump is a nearly ubiquitous membrane protein in animal cells that uses the free energy of ATP hydrolysis to alternatively export 3Na+ from the cell and import 2K+ per cycle. This exchange of ions produces a steady-state outwardly directed current, which is proportional in magnitude to the turnover rate. Under certain ionic conditions, a sudden voltage jump generates temporally distinct transient currents mediated by the Na+/K+ pump that represent the kinetics of extracellular Na+ binding/release and Na+ occlusion/deocclusion transitions. For many years, these events have escaped a proper thermodynamic treatment due to the relatively small electrical signal. Here, taking the advantages offered by the large diameter of the axons from the squid Dosidicus gigas, we have been able to separate the kinetic components of the transient currents in an extended temperature range and thus characterize the energetic landscape of the pump cycle and those transitions associated with the extracellular release of the first Na+ from the deeply occluded state. Occlusion/deocclusion transition involves large changes in enthalpy and entropy as the ion is exposed to the external milieu for release. Binding/unbinding is substantially less costly, yet larger than predicted for the energetic cost of an ion diffusing through a permeation pathway, which suggests that ion binding/unbinding must involve amino acid side-chain rearrangements at the site. PMID:22143771

Energy landscape of the reactions governing the Na+ deeply occluded state of the Na+/K+-ATPase in the giant axon of the Humboldt squid.

PubMed

Castillo, Juan P; De Giorgis, Daniela; Basilio, Daniel; Gadsby, David C; Rosenthal, Joshua J C; Latorre, Ramon; Holmgren, Miguel; Bezanilla, Francisco

2011-12-20

The Na(+)/K(+) pump is a nearly ubiquitous membrane protein in animal cells that uses the free energy of ATP hydrolysis to alternatively export 3Na(+) from the cell and import 2K(+) per cycle. This exchange of ions produces a steady-state outwardly directed current, which is proportional in magnitude to the turnover rate. Under certain ionic conditions, a sudden voltage jump generates temporally distinct transient currents mediated by the Na(+)/K(+) pump that represent the kinetics of extracellular Na(+) binding/release and Na(+) occlusion/deocclusion transitions. For many years, these events have escaped a proper thermodynamic treatment due to the relatively small electrical signal. Here, taking the advantages offered by the large diameter of the axons from the squid Dosidicus gigas, we have been able to separate the kinetic components of the transient currents in an extended temperature range and thus characterize the energetic landscape of the pump cycle and those transitions associated with the extracellular release of the first Na(+) from the deeply occluded state. Occlusion/deocclusion transition involves large changes in enthalpy and entropy as the ion is exposed to the external milieu for release. Binding/unbinding is substantially less costly, yet larger than predicted for the energetic cost of an ion diffusing through a permeation pathway, which suggests that ion binding/unbinding must involve amino acid side-chain rearrangements at the site.

Sodium ion effect on silk fibroin conformation characterized by solid-state NMR and generalized 2D NMR NMR correlation

NASA Astrophysics Data System (ADS)

Ruan, Qing-Xia; Zhou, Ping

2008-07-01

In the present work, we investigated Na + ion effect on the silk fibroin (SF) conformation. Samples are Na +-involved regenerated silk fibroin films. 13C CP-MAS NMR demonstrates that as added [Na +] increases, partial silk fibroin conformation transit from helix-form to β-form at certain Na + ion concentration which is much higher than that in Bombyx mori silkworm gland. The generalized two-dimensional NMR-NMR correlation analysis reveals that silk fibroin undergoes several intermediate states during its conformation transition process as [Na +] increase. The appearance order of the intermediates is followed as: helix and/or random coil → helix-like → β-sheet-like → β-sheet, which is the same as that produced by pH decrease from 6.8 to 4.8 in the resultant regenerated silk fibroin films. The binding sites of Na + to silk fibroin might involve the carbonyl oxygen atom of certain amino acids sequence which could promote the formation of β-sheet conformation. Since the Na +sbnd O bond is weak, the ability of Na + inducing the secondary structure transition is weaker than those of Ca 2+, Cu 2+ and even K +. It is maybe a reason why the sodium content is much lower than potassium in the silkworm gland.

Weak-field multiphoton femtosecond coherent control in the single-cycle regime.

PubMed

Chuntonov, Lev; Fleischer, Avner; Amitay, Zohar

2011-03-28

Weak-field coherent phase control of atomic non-resonant multiphoton excitation induced by shaped femtosecond pulses is studied theoretically in the single-cycle regime. The carrier-envelope phase (CEP) of the pulse, which in the multi-cycle regime does not play any control role, is shown here to be a new effective control parameter that its effect is highly sensitive to the spectral position of the ultrabroad spectrum. Rationally chosen position of the ultrabroadband spectrum coherently induces several groups of multiphoton transitions from the ground state to the excited state of the system: transitions involving only absorbed photons as well as Raman transitions involving both absorbed and emitted photons. The intra-group interference is controlled by the relative spectral phase of the different frequency components of the pulse, while the inter-group interference is controlled jointly by the CEP and the relative spectral phase. Specifically, non-resonant two- and three-photon excitation is studied in a simple model system within the perturbative frequency-domain framework. The developed intuition is then applied to weak-field multiphoton excitation of atomic cesium (Cs), where the simplified model is verified by non-perturbative numerical solution of the time-dependent Schrödinger equation. We expect this work to serve as a basis for a new line of femtosecond coherent control experiments.

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

High-J rotational spectrum of toluene in |m| ⩽ 3 torsional states

NASA Astrophysics Data System (ADS)

Ilyushin, Vadim V.; Alekseev, Eugene A.; Kisiel, Zbigniew; Pszczółkowski, Lech

2017-09-01

The study of the rotational spectrum of toluene (C6H5CH3) is considerably extended to include transitions in |m| ⩽ 3 torsional states up to the onset of the submillimeter wave region. New data involving torsion-rotation transitions up to 336 GHz were combined with previously published measurements and fitted using the rho-axis-method torsion-rotation Hamiltonian. The final fit used 50 parameters to give an overall weighted root-mean-square deviation of 0.69 for a dataset consisting of 8924 transitions with J up to 94 and Ka up to 50. The new analysis allowed us to resolve all problems encountered previously for m = 0 transitions beyond a certain combination of quantum numbers J and Ka when many lines of appreciable intensity and unambiguous assignment deviated from the distorted asymmetric rotor treatment. Those discrepancies are now identified to result from m = 0 ↔ m = 3 and m = 0 ↔ m = -3 resonances, which have been successfully encompassed by the current fit. At the same time an analogous problem was discovered and fitted for m = 2 transitions, which were found to be affected by many m = 1 ↔ m = 2 resonances.

Magnetic dipole transitions of Bc and Bc* mesons in the relativistic independent quark model

NASA Astrophysics Data System (ADS)

Patnaik, Sonali; Dash, P. C.; Kar, Susmita; Patra, Sweta P.; Barik, N.

2017-12-01

We study M1-transitions involving mesons: Bc(1 s ), Bc*(1 s ), Bc(2 s ), Bc*(2 s ), Bc(3 s ), and Bc*(3 s ) in the relativistic independent quark (RIQ) model based on a flavor independent average potential in the scalar-vector harmonic form. The transition form factor for Bc*→Bcγ is found to have analytical continuation from spacelike to physical timelike region. Our predicted coupling constant gBc*Bc=0.34 GeV-1 and decay width Γ (Bc*→Bcγ )=23 eV agree with other model predictions. In view of possible observation of Bc and Bc* s-wave states at LHC and Z-factory and potential use of theoretical estimate on M1-transitions, we investigate the allowed as well as hindered transitions of orbitally excited Bc-meson states and predict their decay widths in overall agreement with other model predictions. We consider the typical case of Bc*(1 s )→Bc(1 s )γ , where our predicted decay width which is found quite sensitive to the mass difference between Bc* and Bc mesons may help in determining the mass of Bc* experimentally.

Formal Valence, 3 d Occupation, and Charge Ordering Transitions

NASA Astrophysics Data System (ADS)

Pickett, Warren

2014-03-01

The metal-insulator transition (MIT), discovered by Verwey in the late 1930s, has been thought to be one of the best understood of MITs, the other ones being named after Wigner, Peierls, Mott, and Anderson. Continuing work on these transitions finds in some cases less and less charge to order, raising the fundamental question of just where the entropy is coming from, and just what is ordering. To provide insight into the mechanism of charge-ordering transitions, which conventionally are pictured as a disproportionation, I will (1) review and reconsider the charge state (or oxidation number) picture itself, (2) introduce new theoretical results for the rare earth nickelates (viz. YNiO3), the putative charge ordering compound AgNiO2, and the dual charge state insulator AgO, and (3) analyze cationic occupations of actual (not formal) charge, and work to reconcile the conundrums that arise. Several of the clearest cases of charge ordering transitions involve no disproportion; moreover, the experimental data used to support charge ordering can be accounted for within density functional based calculations that contain no charge transfer The challenge of modeling charge ordering transitions with model Hamiltonians will be discussed. Acknowledgment: Y. Quan, V. Pardo. Supported by NSF award DMR-1207622-0.

The ν 1 and ν 3 band system of 15NH3

NASA Astrophysics Data System (ADS)

Fusina, Luciano; Nivellini, Giandomenico; Spezzano, Silvia

2011-09-01

The infrared spectrum of 15NH3 has been investigated by high-resolution Fourier transform infrared spectroscopy in the region of the stretching fundamentals. A large number of ro-vibration transitions in the 3050-3650 cm-1 spectral range has been recorded and assigned to the fundamentals ν 1 and ν 3, and to the 2ν 4 overtone bands. In total, 1606 transitions involving the (s) and (a) inversion-rotation-vibration levels have been identified and assigned. They include 256 perturbation-allowed transitions with selection rules ΔK = ±2, Δl = -1 in ν 3 and Δl = +2 in ? , and ΔK = ±3, Δl = 0 in ν 1 and ? . All assigned transitions were fitted simultaneously to a model Hamiltonian that includes all symmetry-allowed interactions between and within the excited state levels in order to obtain accurate sets of spectroscopic parameters for both inversion states. The standard deviation of the fit, 0.034 cm-1, is about 70 times larger than the estimated measurement precision. This result is similar to that reported for the same band system in 14NH3 by Kleiner et al. [J. Mol. Spectrosc. 193, 46 (1999)] and is a consequence of the neglect of vibration and ro-vibration interactions between the analysed states and vibrationally excited states with close energies.

Widths of atomic 4s and 4p vacancy states, 46 less than or equal to Z less than or equal to 50

NASA Technical Reports Server (NTRS)

Hsiungchen, M.; Crasemann, B.; Yin, L. I.; Tsang, T.; Adler, I.

1975-01-01

Auger and X-ray photoelectron spectra involving N1, N2, and N3 vacancy states of Pd, Ag, Cd, In, and Sn were measured and compared with results of free atom calculations. As previously observed in Cu and Zn Auger spectra that involve 3d-band electrons, free-atom characteristics with regard to widths and structure were found in the Ag and Cd M4-N4,5N4,5 and M5-N4,5N4,5 Auger spectra that arise from transitions of 4d-band electrons. Theoretical N1 widths computed with calculated free-atom Auger energies agree well with measurements. Theory however predicts wider N2 than N3 vacancy states (as observed for Xe), while the measured N2 and N3 widths are nearly equal to each other and to the average of the calculated N2 and N3 widths. The calculations are made difficult by the exceedingly short lifetime of some 4p vacancies and by the extreme sensitivity of super-Coster-Kronig rates, which dominate the deexcitation, to the transition energy and to the fine details of the atomic potential.

Symmetry limit theory for cantilever beam-columns subjected to cyclic reversed bending

NASA Astrophysics Data System (ADS)

Uetani, K.; Nakamura, Tsuneyoshi

THE BEHAVIOR of a linear strain-hardening cantilever beam-column subjected to completely reversed plastic bending of a new idealized program under constant axial compression consists of three stages: a sequence of symmetric steady states, a subsequent sequence of asymmetric steady states and a divergent behavior involving unbounded growth of an anti-symmetric deflection mode. A new concept "symmetry limit" is introduced here as the smallest critical value of the tip-deflection amplitude at which transition from a symmetric steady state to an asymmetric steady state can occur in the response of a beam-column. A new theory is presented for predicting the symmetry limits. Although this transition phenomenon is phenomenologically and conceptually different from the branching phenomenon on an equilibrium path, it is shown that a symmetry limit may theoretically be regarded as a branching point on a "steady-state path" defined anew. The symmetry limit theory and the fundamental hypotheses are verified through numerical analysis of hysteretic responses of discretized beam-column models.

Limiting similarity and niche theory for structured populations.

PubMed

Szilágyi, András; Meszéna, Géza

2009-05-07

We develop the theory of limiting similarity and niche for structured populations with finite number of individual states (i-state). In line with a previously published theory for unstructured populations, the niche of a species is specified by the impact and sensitivity niche vectors. They describe the population's impact on and sensitivity towards the variables involved in the population regulation. Robust coexistence requires sufficient segregation of the impact, as well as of the sensitivity niche vectors. Connection between the population-level impact and sensitivity and the impact/sensitivity of the specific i-states is developed. Each i-state contributes to the impact of the population proportional to its frequency in the population. Sensitivity of the population is composed of the sensitivity of the rates of demographic transitions, weighted by the frequency and by the reproductive value of the initial and final i-states of the transition, respectively. Coexistence in a multi-patch environment is studied. This analysis is interpreted as spatial niche segregation.

Analyzing the equilibrium states of a quasi-neutral spatially inhomogeneous system of charges above a liquid dielectric film based on the first principles of quantum statistics

NASA Astrophysics Data System (ADS)

Lytvynenko, D. M.; Slyusarenko, Yu V.

2017-08-01

A theory of quasi-neutral equilibrium states of charges above a liquid dielectric surface is developed. This theory is based on the first principles of quantum statistics for systems comprising many identical particles. The proposed approach involves applying the variational principle, modified for the considered systems, and the Thomas-Fermi model. In the terms of the developed theory self-consistency equations are obtained. These equations provide the relation between the main parameters describing the system: the potential of the static electric field, the distribution function of charges and the surface profile of the liquid dielectric. The equations are used to study the phase transition in the system to a spatially periodic state. The proposed method can be applied in analyzing the properties of the phase transition in the system in relation to the spatially periodic states of wave type. Using the analytical and numerical methods, we perform a detailed study of the dependence of the critical parameters of such a phase transition on the thickness of the liquid dielectric film. Some stability criteria for the new asymmetric phase of the studied system are discussed.

Electronically non-adiabatic interactions of molecules at metal surfaces

NASA Astrophysics Data System (ADS)

Wodtke, Alec M.; Tully, John C.; Auerbach, Daniel J.

When neutral molecules with low levels of vibrational excitation collide at metal surfaces, vibrational coupling to electron-hole pairs (EHPs) is not thought to be strong unless incidence energies are high. However, there is accumulating evidence that coupling of large-amplitude molecular vibration to metallic electron degrees of freedom can be much stronger even at the lowest accessible incidence energies. As reaching a chemical transition-state also involves large-amplitude vibrational motion, we pose the basic question: are electronically non-adiabatic couplings important at transition states of reactions at metal surfaces? We have indirect evidence in at least one example that the dynamics and rates of chemical reactions at metal surfaces may be strongly influenced by electronically non-adiabatic coupling. This implies that theoretical approaches relying on the Born-Oppenheimer approximation (BOA) may not accurately reflect the nature of transition-state traversal in reactions of catalytic importance. Developing a predictive understanding of surface reactivity beyond the BOA represents one of the most important challenges to current research in physical chemistry. This article reviews the experimental evidence and underlying theoretical framework concerning these and related topics.

Ricin - inhibitor design. Annual report, 15 April 1994-14 April 1995

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

Schramm, V.L.

1995-05-14

Substrates for ricin A-chain include short RNA stem-loop structures which have been synthesized with radioactive labels for ease of catalytic assay and for kinetic isotope effects. Ricin A-chain from several sources is incapable of completing multiple catalytic cycles using these substrates. A family of ricin substrate analogue molecules have been synthesized and tested which are specific for transition states with oxycarbonium character or for enzymatic mechanisms involving protonation of the adenine leaving group. Formycin analogues were incorporated into RNA oligomeric structures and tested for binding to ricin A-chain or as inhibitors of the ricin-inactivation of in vitro translation using rabbitmore » reticulocyte lysates. Ribo-oxycarbonium ion analogues containing iminoribitol analogues of ribose were synthetically incorporated into RNA oligomeric structures. Neither formycin nor ribo-oxycarbonium analogues, either singly or in RNA oligomers caused significant inhibition of ricin A-chain when assayed in reticulocyte lysate translation assays. The results indicate a novel transition state mechanism for ricin A-chain, or a requirement for additional features of 28s rRNA to bind transition state analogues.« less

Spotlight on Transition to Teaching Music

ERIC Educational Resources Information Center

MENC: The National Association for Music Education, 2004

2004-01-01

The latest title in the popular Spotlight series, this timely book focuses on issues involving recruitment and retention of music teachers, a crucial issue in these days of budget constraints. Arranged chronologically, it features a collection of articles from state journals focusing on issues such as mentoring, teacher shortages, burnout, and…

Testing the impact of morphological rate heterogeneity on ancestral state reconstruction of five floral traits in angiosperms.

PubMed

Reyes, Elisabeth; Nadot, Sophie; von Balthazar, Maria; Schönenberger, Jürg; Sauquet, Hervé

2018-06-21

Ancestral state reconstruction is an important tool to study morphological evolution and often involves estimating transition rates among character states. However, various factors, including taxonomic scale and sampling density, may impact transition rate estimation and indirectly also the probability of the state at a given node. Here, we test the influence of rate heterogeneity using maximum likelihood methods on five binary perianth characters, optimized on a phylogenetic tree of angiosperms including 1230 species sampled from all families. We compare the states reconstructed by an equal-rate (Mk1) and a two-rate model (Mk2) fitted either with a single set of rates for the whole tree or as a partitioned model, allowing for different rates on five partitions of the tree. We find strong signal for rate heterogeneity among the five subdivisions for all five characters, but little overall impact of the choice of model on reconstructed ancestral states, which indicates that most of our inferred ancestral states are the same whether heterogeneity is accounted for or not.

Inelastic collision processes in ozone and their relation to atmospheric pressure broadening

NASA Technical Reports Server (NTRS)

Steinfeld, J. I.; Flannery, C.; Klaassen, J.; Mizugai, Y.; Spencer, M.

1990-01-01

The research task employs infrared double-resonance to determine rotational energy transfer rates and pathways, in both the ground and vibrationally excited states of ozone. The resulting data base will then be employed to test inelastic scattering theories and to assess intermolecular potential models, both of which are necessary for the systematization and prediction of infrared pressure-broadening coefficients, which are in turn required by atmospheric ozone monitoring techniques based on infrared remote sensing. In addition, observation of excited-state absorption transitions will permit us to improve the determination of the 2 nu(sub 3), nu(sub 1) + nu(sub 2), and 2 nu(sub 1) rotational constants and to derive band strengths for hot-band transitions involving these levels.

Nonresonant valence-to-core x-ray emission spectroscopy of niobium

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

Ravel, Bruce; Kropf, A. Jeremy; Yang, Dali

The valence-to-core (V2C) portion of x-ray emission spectroscopy (XES) measures the electron states close to the Fermi level. These states are involved in bonding, thus providing a measure of the chemistry of the material. For this paper, we show the V2C XES spectra for several niobium compounds. The Kβ" peak in the V2C XES results from the transition of a ligand 2s electron into the 1s core-hole of the niobium, a transition allowed by hybridization with the niobium 4p . This location in energy of this weak peak shows a strong ligand dependence, thus providing a sensitive probe of themore » ligand environment about the niobium.« less

Nonresonant valence-to-core x-ray emission spectroscopy of niobium

DOE PAGES

Ravel, Bruce; Kropf, A. Jeremy; Yang, Dali; ...

2018-03-23

The valence-to-core (V2C) portion of x-ray emission spectroscopy (XES) measures the electron states close to the Fermi level. These states are involved in bonding, thus providing a measure of the chemistry of the material. For this paper, we show the V2C XES spectra for several niobium compounds. The Kβ" peak in the V2C XES results from the transition of a ligand 2s electron into the 1s core-hole of the niobium, a transition allowed by hybridization with the niobium 4p . This location in energy of this weak peak shows a strong ligand dependence, thus providing a sensitive probe of themore » ligand environment about the niobium.« less

First-principles theoretical assessment of catalysis by confinement: NO-O2 reactions within voids of molecular dimensions in siliceous crystalline frameworks.

PubMed

Maestri, Matteo; Iglesia, Enrique

2018-06-01

Density functional theory methods that include dispersive forces are used to show how voids of molecular dimensions enhance reaction rates by the mere confinement of transition states analogous to those involved in homogeneous routes and without requiring specific binding sites or structural defects within confining voids. These van der Waals interactions account for the observed large rate enhancements for NO oxidation in the presence of purely siliceous crystalline frameworks. The minimum free energy paths for NO oxidation within chabazite (CHA) and silicalite (SIL) frameworks involve intermediates similar in stoichiometry, geometry, and kinetic relevance to those involved in the homogeneous route. The termolecular transition state for the kinetically-relevant cis-NOO2NO isomerization to trans-NOO2NO is strongly stabilized by confinement within CHA (by 36.3 kJ mol-1 in enthalpy) and SIL (by 39.2 kJ mol-1); such enthalpic stabilization is compensated, in part, by concomitant entropy losses brought forth by confinement (CHA: 44.9; SIL: 45.3, J mol-1 K-1 at 298 K). These enthalpy and entropy changes upon confinement agree well with those measured and combine to significantly decrease activation free energies and are consistent with the rate enhancements that become larger as temperature decreases because of the more negative apparent activation energies in confined systems compared with homogeneous routes. Calculated free energies of confinement are in quantitative agreement with measured rate enhancements and with their temperature sensitivity. Such quantitative agreements reflect preeminent effects of geometry in determining the van der Waals contributions from contacts between the transition states (TS) and the confining walls and the weak effects of the level of theory on TS geometries. NO oxidation reactions are chosen here to illustrate these remarkable effects of confinement because detailed kinetic analysis of rate data are available, but also because of their critical role in the treatment of combustion effluents and in the synthesis of nitric acid and nitrates. Similar effects are evident from rate enhancements by confinement observed for Diels-Alder and alkyne oligomerization reactions. These reactions also occur in gaseous media at near ambient temperatures, for which enthalpic stabilization upon confinement of their homogeneous transition states becomes the preeminent component of activation free energies.

Infrared pumping processes for SiO masers. [in interstellar space

NASA Technical Reports Server (NTRS)

Geballe, T. R.; Townes, C. H.

1974-01-01

The J = 2 to 1 transition of the first excited vibrational state (v = 1) Si(28)O(16) has recently been shown to produce maser amplification near 86,245 MHz in Orion A and in several stars. Two possible pumping mechanisms are proposed for such masers. One involves the near coincidence between the frequencies of the 1-0 (RO) and 3-2 (R18) transitions in Si(28)O(16). The other requires emission by SiO and reabsorption without the necessity for an accidental frequency coincidence. Each of these types of mechanisms may occur for other transitions of molecules in a medium illuminated by intense infrared radiation, or with strong temperature gradients.

Assessment of the Sustainability Capacity of a Coordinated Approach to Chronic Disease Prevention.

PubMed

Moreland-Russell, Sarah; Combs, Todd; Polk, LaShaun; Dexter, Sarah

This article outlines some factors that influenced the sustainability capacity of a coordinated approach to chronic disease prevention in state and territory health departments. This study involved a cross-sectional design and mixed-methods approach. Quantitative data were collected using the Program Sustainability Assessment Tool (PSAT), a 40-item multiple-choice instrument that assesses 8 domains of sustainability capacity (environmental support, funding stability, partnerships, organizational capacity, program evaluation, program adaptation, communications, and strategic planning). Qualitative data were collected via phone interviews. The PSAT was administered to staff and stakeholders from public health departments in 50 US states, District of Columbia, and Puerto Rico, who were involved in the implementation of coordinated chronic disease programs. Phone interviews were conducted with program coordinators in each state. Sustainability score patterns and state-level categorical results, as well as strengths and opportunities for improvement across the 8 program sustainability domains, were explored. On average, programs reported the strongest sustainability capacity in the domains of program adaptation, environmental support, and organizational capacity, while funding stability, strategic planning, and communications yielded lowest scores, indicating weakest capacity. Scores varied the most by state in environmental support and strategic planning. The PSAT results highlight the process through which states approached the sustainability of coordinated chronic disease initiatives. This process included an initial focus on program evaluation and partnerships with transfer of priority to long-term strategic planning, communications, and funding stability to further establish coordinated chronic disease efforts. Qualitative interviews provided further context to PSAT results, indicating that leadership, communications, partnerships, funding stability, and policy change were perceived as keys to success of the transition. Integrating these findings into future efforts may help those in transition establish greater sustainability capacity. The PSAT results and interviews provide insight into the capacity for sustainability for programs transitioning from traditional siloed programs to coordinated chronic disease programs.

Improved excitation rate coefficients for the n = 2 and n = 3 levels of Ca XIX and Fe XXV including fine structure

NASA Technical Reports Server (NTRS)

Pradhan, A. K.

1985-01-01

Reently calculated collision strengths, including relativistic and resonance effects, are employed to compute Maxwellian averaged collision strengths for 78 transitions involving states of principal quantum numbers 2-1 and 3-1 in Ca XIX and Fe XXV. These rate parameters are tabulated at temperatures of interest in astrophysical and labortory plasmas with radiation in the hard X-ray wavelength range. For some transitions, significant differences are found with the earlier calculations of Pradhan, Norcross, and Hummer (1981).

Jet-cooled laser-induced fluorescence spectroscopy of cyclohexoxy: rotational and fine structure of molecules in nearly degenerate electronic States.

PubMed

Liu, Jinjun; Miller, Terry A

2014-12-26

The rotational structure of the previously observed B̃(2)A' ← X̃(2)A″ and B̃(2)A' ← Ã(2)A' laser-induced fluorescence spectra of jet-cooled cyclohexoxy radical (c-C6H11O) [ Zu, L.; Liu, J.; Tarczay, G.; Dupré, P; Miller, T. A. Jet-cooled laser spectroscopy of the cyclohexoxy radical. J. Chem. Phys. 2004 , 120 , 10579 ] has been analyzed and simulated using a spectroscopic model that includes the coupling between the nearly degenerate X̃ and à states separated by ΔE. The rotational and fine structure of these two states is reproduced by a 2-fold model using one set of molecular constants including rotational constants, spin-rotation constants (ε's), the Coriolis constant (Aζt), the quenched spin-orbit constant (aζed), and the vibronic energy separation between the two states (ΔE0). The energy level structure of both states can also be reproduced using an isolated-state asymmetric top model with rotational constants and effective spin-rotation constants (ε's) and without involving Coriolis and spin-orbit constants. However, the spin-orbit interaction introduces transitions that have no intensity using the isolated-state model but appear in the observed spectra. The line intensities are well simulated using the 2-fold model with an out-of-plane (b-) transition dipole moment for the B̃ ← X̃ transitions and in-plane (a and c) transition dipole moment for the B̃ ← à transitions, requiring the symmetry for the X̃ (Ã) state to be A″ (A'), which is consistent with a previous determination and opposite to that of isopropoxy, the smallest secondary alkoxy radical. The experimentally determined Ã-X̃ separation and the energy level ordering of these two states with different (A' and A″) symmetries are consistent with quantum chemical calculations. The 2-fold model also enables the independent determination of the two contributions to the Ã-X̃ separation: the relativistic spin-orbit interaction (magnetic effect) and the nonrelativistic vibronic separation between the lowest vibrational energy levels of these two states due to both electrostatic interaction (Coulombic effect) and difference in zero-point energies (kinetic effect).

Conformational heterogeneity in closed and open states of the KcsA potassium channel in lipid bicelles

PubMed Central

Kim, Dorothy M.; Dikiy, Igor; Upadhyay, Vikrant; Posson, David J.

2016-01-01

The process of ion channel gating—opening and closing—involves local and global structural changes in the channel in response to external stimuli. Conformational changes depend on the energetic landscape that underlies the transition between closed and open states, which plays a key role in ion channel gating. For the prokaryotic, pH-gated potassium channel KcsA, closed and open states have been extensively studied using structural and functional methods, but the dynamics within each of these functional states as well as the transition between them is not as well understood. In this study, we used solution nuclear magnetic resonance (NMR) spectroscopy to investigate the conformational transitions within specific functional states of KcsA. We incorporated KcsA channels into lipid bicelles and stabilized them into a closed state by using either phosphatidylcholine lipids, known to favor the closed channel, or mutations designed to trap the channel shut by disulfide cross-linking. A distinct state, consistent with an open channel, was uncovered by the addition of cardiolipin lipids. Using selective amino acid labeling at locations within the channel that are known to move during gating, we observed at least two different slowly interconverting conformational states for both closed and open channels. The pH dependence of these conformations and the predictable disruptions to this dependence observed in mutant channels with altered pH sensing highlight the importance of conformational heterogeneity for KcsA gating. PMID:27432996

The effects of beta-endorphin: state change modification.

PubMed

Veening, Jan G; Barendregt, Henk P

2015-01-29

Beta-endorphin (β-END) is an opioid neuropeptide which has an important role in the development of hypotheses concerning the non-synaptic or paracrine communication of brain messages. This kind of communication between neurons has been designated volume transmission (VT) to differentiate it clearly from synaptic communication. VT occurs over short as well as long distances via the extracellular space in the brain, as well as via the cerebrospinal fluid (CSF) flowing through the ventricular spaces inside the brain and the arachnoid space surrounding the central nervous system (CNS). To understand how β-END can have specific behavioral effects, we use the notion behavioral state, inspired by the concept of machine state, coming from Turing (Proc London Math Soc, Series 2,42:230-265, 1937). In section 1.4 the sequential organization of male rat behavior is explained showing that an animal is not free to switch into another state at any given moment. Funneling-constraints restrict the number of possible behavioral transitions in specific phases while at other moments in the sequence the transition to other behavioral states is almost completely open. The effects of β-END on behaviors like food intake and sexual behavior, and the mechanisms involved in reward, meditation and pain control are discussed in detail. The effects on the sequential organization of behavior and on state transitions dominate the description of these effects.

Public-private partnerships in China's urban water sector.

PubMed

Zhong, Lijin; Mol, Arthur P J; Fu, Tao

2008-06-01

During the past decades, the traditional state monopoly in urban water management has been debated heavily, resulting in different forms and degrees of private sector involvement across the globe. Since the 1990s, China has also started experiments with new modes of urban water service management and governance in which the private sector is involved. It is premature to conclude whether the various forms of private sector involvement will successfully overcome the major problems (capital shortage, inefficient operation, and service quality) in China's water sector. But at the same time, private sector involvement in water provisioning and waste water treatments seems to have become mainstream in transitional China.

Free-energy landscape of ion-channel voltage-sensor–domain activation

PubMed Central

Delemotte, Lucie; Kasimova, Marina A.; Klein, Michael L.; Tarek, Mounir; Carnevale, Vincenzo

2015-01-01

Voltage sensor domains (VSDs) are membrane-bound protein modules that confer voltage sensitivity to membrane proteins. VSDs sense changes in the transmembrane voltage and convert the electrical signal into a conformational change called activation. Activation involves a reorganization of the membrane protein charges that is detected experimentally as transient currents. These so-called gating currents have been investigated extensively within the theoretical framework of so-called discrete-state Markov models (DMMs), whereby activation is conceptualized as a series of transitions across a discrete set of states. Historically, the interpretation of DMM transition rates in terms of transition state theory has been instrumental in shaping our view of the activation process, whose free-energy profile is currently envisioned as composed of a few local minima separated by steep barriers. Here we use atomistic level modeling and well-tempered metadynamics to calculate the configurational free energy along a single transition from first principles. We show that this transition is intrinsically multidimensional and described by a rough free-energy landscape. Remarkably, a coarse-grained description of the system, based on the use of the gating charge as reaction coordinate, reveals a smooth profile with a single barrier, consistent with phenomenological models. Our results bridge the gap between microscopic and macroscopic descriptions of activation dynamics and show that choosing the gating charge as reaction coordinate masks the topological complexity of the network of microstates participating in the transition. Importantly, full characterization of the latter is a prerequisite to rationalize modulation of this process by lipids, toxins, drugs, and genetic mutations. PMID:25535341

Free-energy landscape of ion-channel voltage-sensor-domain activation.

PubMed

Delemotte, Lucie; Kasimova, Marina A; Klein, Michael L; Tarek, Mounir; Carnevale, Vincenzo

2015-01-06

Voltage sensor domains (VSDs) are membrane-bound protein modules that confer voltage sensitivity to membrane proteins. VSDs sense changes in the transmembrane voltage and convert the electrical signal into a conformational change called activation. Activation involves a reorganization of the membrane protein charges that is detected experimentally as transient currents. These so-called gating currents have been investigated extensively within the theoretical framework of so-called discrete-state Markov models (DMMs), whereby activation is conceptualized as a series of transitions across a discrete set of states. Historically, the interpretation of DMM transition rates in terms of transition state theory has been instrumental in shaping our view of the activation process, whose free-energy profile is currently envisioned as composed of a few local minima separated by steep barriers. Here we use atomistic level modeling and well-tempered metadynamics to calculate the configurational free energy along a single transition from first principles. We show that this transition is intrinsically multidimensional and described by a rough free-energy landscape. Remarkably, a coarse-grained description of the system, based on the use of the gating charge as reaction coordinate, reveals a smooth profile with a single barrier, consistent with phenomenological models. Our results bridge the gap between microscopic and macroscopic descriptions of activation dynamics and show that choosing the gating charge as reaction coordinate masks the topological complexity of the network of microstates participating in the transition. Importantly, full characterization of the latter is a prerequisite to rationalize modulation of this process by lipids, toxins, drugs, and genetic mutations.

Prokinetic effects of large-dose lubiprostone on gastrointestinal transit in dogs and its mechanisms.

PubMed

Song, Jun; Yin, Jieyun; Xu, Xiaohong; Chen, Jiande

2015-01-01

To systemically explore effects of large dose of lubiprostone on gastrointestinal (GI) transit and contractions and its safety in dogs. 12 healthy dogs were studied. 6 dogs were operated to receive duodenal cannula and colon cannula and the other 6 dogs received gastric cannula. Lubiprostone was orally administrated at a dose of 24 µg or 48 µg 1 hr prior to the experiments. Gastric emptying (GE) of solids and small bowel transit were evaluated by collecting the effluents from the duodenal cannula and from the colon cannula. Gastric accommodation was measured by barostat. Gastric and intestinal contractions were by manometry. Colon transit was by X-ray pictures. 1) Lubiprostone 48 µg not 24 µg accelerated GE. Atropine could block the effect; 2) Average motility index (MI) of gastric antrum in lubiprostone 48 µg session was significantly higher in both fasting state (P = 0.01) and fed state (P = 0.03). Gastric accommodation was not significantly different; 3) Lubiprostone 48 µg accelerated small bowel and colon transit. Atropine could block the effect on small bowel transit; 4) Lubiprostone 48 µg increased postprandial small bowel MI (P = 0.0008) and colon MI (P = 0.002). 5) No other adverse effects except for diarrhea were observed. Acute administration of lubiprostone at a dose of 48 µg accelerates GI motility and enhances GI contractions in the postprandial state. The findings suggest that lubiprostone may have an indirect prokinetic effects on the GI tract and vagal activity may be involved. Lubiprostone may be safely used.

Prokinetic effects of large-dose lubiprostone on gastrointestinal transit in dogs and its mechanisms

PubMed Central

Song, Jun; Yin, Jieyun; Xu, Xiaohong; Chen, Jiande

2015-01-01

Objective: To systemically explore effects of large dose of lubiprostone on gastrointestinal (GI) transit and contractions and its safety in dogs. Methods: 12 healthy dogs were studied. 6 dogs were operated to receive duodenal cannula and colon cannula and the other 6 dogs received gastric cannula. Lubiprostone was orally administrated at a dose of 24 µg or 48 µg 1 hr prior to the experiments. Gastric emptying (GE) of solids and small bowel transit were evaluated by collecting the effluents from the duodenal cannula and from the colon cannula. Gastric accommodation was measured by barostat. Gastric and intestinal contractions were by manometry. Colon transit was by X-ray pictures. Results: 1) Lubiprostone 48 µg not 24 µg accelerated GE. Atropine could block the effect; 2) Average motility index (MI) of gastric antrum in lubiprostone 48 µg session was significantly higher in both fasting state (P = 0.01) and fed state (P = 0.03). Gastric accommodation was not significantly different; 3) Lubiprostone 48 µg accelerated small bowel and colon transit. Atropine could block the effect on small bowel transit; 4) Lubiprostone 48 µg increased postprandial small bowel MI (P = 0.0008) and colon MI (P = 0.002). 5) No other adverse effects except for diarrhea were observed. Conclusion: Acute administration of lubiprostone at a dose of 48 µg accelerates GI motility and enhances GI contractions in the postprandial state. The findings suggest that lubiprostone may have an indirect prokinetic effects on the GI tract and vagal activity may be involved. Lubiprostone may be safely used. PMID:26045891

Generalised quasiprobability distribution for Hermite polynomial squeezed states

NASA Astrophysics Data System (ADS)

Datta, Sunil; D'Souza, Richard

1996-02-01

Generalized quasiprobability distributions (QPD) for Hermite polynomial states are presented. These states are solutions of an eigenvalue equation which is quadratic in creation and annihilation operators. Analytical expressions for the QPD are presented for some special cases of the eigenvalues. For large squeezing these analytical expressions for the QPD take the form of a finite series in even Hermite functions. These expressions very transparently exhibit the transition between, P, Q and W functions corresponding to the change of the s-parameter of the QPD. Further, they clearly show the two-photon nature of the processes involved in the generation of these states.

Student Preference Rates for Predominately Online, Compressed, or Traditionally Taught University Courses

ERIC Educational Resources Information Center

Krug, Kevin S.; Dickson, Kole W.; Lessiter, Julie A.; Vassar, John S.

2016-01-01

Universities and colleges in the United States are actively searching for new ways to increase student enrollment as one means to offset recent government budget cuts in educational funding. One proposal at a particular institution involves transitioning a commuter university from a traditional semester length calendar to one that offers…

The Metric System: Preparing Your Students for the Big Change

ERIC Educational Resources Information Center

Social Education, 1974

1974-01-01

Information sources to assist teachers and students in making a smooth and efficient transition to the metric system include an annotated bibliography of literature dealing with the history and present state of measurement in the U.S., with the metric system generally, and with problems involved in metric conversion. (Author/KM)

Promoting Positive Family Involvement in Russian Communities through Volunteer Agencies.

ERIC Educational Resources Information Center

Scheer, Scott D.; Safrit, R. Dale

During the state of transition in contemporary Russia from communism to a market economy, nonprofit organizations have been thrust into the forefront to provide to youth and families services formerly rendered by the government. This paper describes Moscow Charity House (MCH) and Nevsky Angel in St. Petersburg, the first nonprofit organizations in…

Using a Crisis to Redefine School Culture

ERIC Educational Resources Information Center

Huddleston, Lisa

2014-01-01

This case involves a small town in the southwestern United States. Background descriptions of the community and school are provided, including historical and demographic information. As the community and school transition from a small ranching town into a bedroom community for the large city nearby, tensions related to race and wealth erupt in a…

(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.

The activation of the [NiFe]-hydrogenase from Allochromatium vinosum. An infrared spectro-electrochemical study.

PubMed

Bleijlevens, Boris; van Broekhuizen, Fleur A; De Lacey, Antonio L; Roseboom, Winfried; Fernandez, Victor M; Albracht, Simon P J

2004-09-01

The membrane-bound [NiFe]-hydrogenase from Allochromatium vinosum can occur in several inactive or active states. This study presents the first systematic infrared characterisation of the A. vinosum enzyme, with emphasis on the spectro-electrochemical properties of the inactive/active transition. This transition involves an energy barrier, which can be overcome at elevated temperatures. The reduced Ready enzyme can exist in two different inactive states, which are in an apparent acid-base equilibrium. It is proposed that a hydroxyl ligand in a bridging position in the Ni-Fe site is protonated and that the formed water molecule is subsequently removed. This enables the active site to bind hydrogen in a bridging position, allowing the formation of the fully active state of the enzyme. It is further shown that the active site in enzyme reduced by 1 bar H(2) can occur in three different electron paramagnetic resonance (EPR)-silent states with a different degree of protonation.

Defect states of complexes involving a vacancy on the boron site in boronitrene

NASA Astrophysics Data System (ADS)

Ngwenya, T. B.; Ukpong, A. M.; Chetty, N.

2011-12-01

First principles calculations have been performed to investigate the ground state properties of freestanding monolayer hexagonal boronitrene (h-BN). We have considered monolayers that contain native point defects and their complexes, which form when the point defects bind with the boron vacancy on the nearest-neighbor position. The changes in the electronic structure are analyzed to show the extent of localization of the defect-induced midgap states. The variations in formation energies suggest that defective h-BN monolayers that contain carbon substitutional impurities are the most stable structures, irrespective of the changes in growth conditions. The high energies of formation of the boron vacancy complexes suggest that they are less stable, and their creation by ion bombardment would require high-energy ions compared to point defects. Using the relative positions of the derived midgap levels for the double vacancy complex, it is shown that the quasi-donor-acceptor pair interpretation of optical transitions is consistent with stimulated transitions between electron and hole states in boronitrene.

Multipole mixing ratios and substate populations in Rn-219

NASA Astrophysics Data System (ADS)

Jones, G. D.

2016-08-01

Historical alpha-gamma angular correlation data for the decay of 223Ra into excited states of 219Rn have been analysed, using the correct spins of the states involved, for the first time. The analyses produced multipole mixing ratios (E2/M1) of δ (144)=-0.11\\+/- 0.03, δ (154)=0, δ (158)=-0.205\\+/- 0.018 and δ (269)=-0.149\\+/- 0.004 where the nominal transition energies, in keV, are given in brackets. These values are consistent with published values obtained from internal conversion electron spectroscopy. It is also found that δ (324)=0 and δ (338)=-0.235\\+/- 0.030 (where both values differ from current tabulations) and that the sign of the multipole mixing ratio for the 122 keV transition is negative. The 158, 269 and 338 keV states are found to be aligned with high population of M=+/- 3/2 substates and the 127 keV state is believed to have undergone spin relaxation.

Loss surface of XOR artificial neural networks

NASA Astrophysics Data System (ADS)

Mehta, Dhagash; Zhao, Xiaojun; Bernal, Edgar A.; Wales, David J.

2018-05-01

Training an artificial neural network involves an optimization process over the landscape defined by the cost (loss) as a function of the network parameters. We explore these landscapes using optimization tools developed for potential energy landscapes in molecular science. The number of local minima and transition states (saddle points of index one), as well as the ratio of transition states to minima, grow rapidly with the number of nodes in the network. There is also a strong dependence on the regularization parameter, with the landscape becoming more convex (fewer minima) as the regularization term increases. We demonstrate that in our formulation, stationary points for networks with Nh hidden nodes, including the minimal network required to fit the XOR data, are also stationary points for networks with Nh+1 hidden nodes when all the weights involving the additional node are zero. Hence, smaller networks trained on XOR data are embedded in the landscapes of larger networks. Our results clarify certain aspects of the classification and sensitivity (to perturbations in the input data) of minima and saddle points for this system, and may provide insight into dropout and network compression.

Parental and Infant Gender Factors in Parent-Infant Interaction: State-Space Dynamic Analysis.

PubMed

Cerezo, M Angeles; Sierra-García, Purificación; Pons-Salvador, Gemma; Trenado, Rosa M

2017-01-01

This study aimed to investigate the influence of parental gender on their interaction with their infants, considering, as well, the role of the infant's gender. The State Space Grid (SSG) method, a graphical tool based on the non-linear dynamic system (NDS) approach was used to analyze the interaction, in Free-Play setting, of 52 infants, aged 6 to 10 months, divided into two groups: half of the infants interacted with their fathers and half with their mothers. There were 50% boys in each group. MANOVA results showed no differential parenting of boys and girls. Additionally, mothers and fathers showed no differences in the Diversity of behavioral dyadic states nor in Predictability. However, differences associated with parent's gender were found in that the paternal dyads were more "active" than the maternal dyads: they were faster in the rates per second of behavioral events and transitions or change of state. In contrast, maternal dyads were more repetitive because, once they visited a certain dyadic state, they tend to be involved in more events. Results showed a significant discriminant function on the parental groups, fathers and mothers. Specifically, the content analyses carried out for the three NDS variables, that previously showed differences between groups, showed particular dyadic behavioral states associated with the rate of Transitions and the Events per Visit ratio. Thus, the transitions involving 'in-out' of 'Child Social Approach neutral - Sensitive Approach neutral' state and the repetitions of events in the dyadic state 'Child Play-Sensitive Approach neutral' distinguished fathers from mothers. The classification of dyads (with fathers and mothers) based on this discriminant function identified 73.10% (19/26) of the father-infant dyads and 88.5% (23/26) of the mother-infant dyads. The study of father-infant interaction using the SSG approach offers interesting possibilities because it characterizes and quantifies the actual moment-to-moment flow of parent-infant interactive dynamics. Our findings showed how observational methods applied to natural contexts offer new facets in father vs. mother interactive behavior with their infants that can inform further developments in this field.

Psychologists and the Transition From Pediatrics to Adult Health Care.

PubMed

Gray, Wendy N; Monaghan, Maureen C; Gilleland Marchak, Jordan; Driscoll, Kimberly A; Hilliard, Marisa E

2015-11-01

Guidelines for optimal transition call for multidisciplinary teams, including psychologists, to address youth and young adults' multifactorial needs. This study aimed to characterize psychologists' roles in and barriers to involvement in transition from pediatric to adult health care. Psychologists were invited via professional listservs to complete an online survey about practice settings, roles in transition programming, barriers to involvement, and funding sources. Participants also responded to open-ended questions about their experiences in transition programs. One hundred participants responded to the survey. Involvement in transition was reported at multiple levels from individual patient care to institutional transition programming, and 65% reported more than one level of involvement. Direct clinical care (88%), transition-related research (50%), and/or leadership (44%) involvement were reported, with 59% reporting more than one role. Respondents often described advocating for their involvement on transition teams. Various sources of funding were reported, yet, 23% reported no funding for their work. Barriers to work in transition were common and included health care systems issues such as poor coordination among providers or lack of a clear transition plan within the clinic/institution. Psychologists assume numerous roles in the transition of adolescents from pediatric to adult health care. With training in health care transition-related issues, psychologists are ideally positioned to partner with other health professionals to develop and implement transition programs in multidisciplinary settings, provided health care system barriers can be overcome. Copyright © 2015 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

First high resolution analysis of the 3ν2 and 3ν2 -ν2 bands of 32S16O2

NASA Astrophysics Data System (ADS)

Ulenikov, O. N.; Bekhtereva, E. S.; Gromova, O. V.; Berezkin, K. B.; Horneman, V.-M.; Sydow, C.; Maul, C.; Bauerecker, S.

2017-11-01

The second bending overtone band 3ν2 of sulfur dioxide has been studied for the first time with high resolution rotation-vibration spectroscopy. The 1530 transitions involving 728 upper state energy levels with Jmax.= 53 and Kamax . = 15 have been assigned to the 3ν2 band. The 746 transitions belonging to the 3ν2 -ν2 "hot" band have been also assigned in the region of 950-1100 cm-1. For the analysis of the assigned transitions, an effective Hamiltonian of an isolated (030) vibrational state (the Watson operator in A-reduction and Ir representation) was used. Set of 9 varied parameters was determined which reproduce the initial experimental data with the drms deviations of 9.0 ×10-4 cm-1 and 9.8 ×10-4 cm-1 for the 3ν2 and 3ν2 -ν2 bands, which are comparable with the experimental uncertainties.

A novel transition pathway of ligand-induced topological conversion from hybrid forms to parallel forms of human telomeric G-quadruplexes

PubMed Central

Wang, Zi-Fu; Li, Ming-Hao; Chen, Wei-Wen; Hsu, Shang-Te Danny; Chang, Ta-Chau

2016-01-01

The folding topology of DNA G-quadruplexes (G4s) depends not only on their nucleotide sequences but also on environmental factors and/or ligand binding. Here, a G4 ligand, 3,6-bis(1-methyl-4-vinylpyridium iodide)-9-(1-(1-methyl-piperidinium iodide)-3,6,9-trioxaundecane) carbazole (BMVC-8C3O), can induce topological conversion of non-parallel to parallel forms in human telomeric DNA G4s. Nuclear magnetic resonance (NMR) spectroscopy with hydrogen-deuterium exchange (HDX) reveals the presence of persistent imino proton signals corresponding to the central G-quartet during topological conversion of Tel23 and Tel25 G4s from hybrid to parallel forms, implying that the transition pathway mainly involves local rearrangements. In contrast, rapid HDX was observed during the transition of 22-CTA G4 from an anti-parallel form to a parallel form, resulting in complete disappearance of all the imino proton signals, suggesting the involvement of substantial unfolding events associated with the topological transition. Site-specific imino proton NMR assignments of Tel23 G4 enable determination of the interconversion rates of individual guanine bases and detection of the presence of intermediate states. Since the rate of ligand binding is much higher than the rate of ligand-induced topological conversion, a three-state kinetic model was evoked to establish the associated energy diagram for the topological conversion of Tel23 G4 induced by BMVC-8C3O. PMID:26975658

Spin differences in the Zr 90 compound nucleus induced by ( p , p ' ) , ( p , d ) , and ( p , t ) surrogate reactions

DOE PAGES

Ota, S.; Burke, J. T.; Casperson, R. J.; ...

2015-11-04

Here, the effect of the production mechanism on the decay of a compound nucleus is investigated. The nucleus 90Zr was produced by three different reactions, namely 90Zr (p,p') 90Zr, 91Zr (p,d) 90Zr, and 92Zr (p,t) 90Zr , which served as surrogate reactions for 89Zr (n,γ). The spin-parity (J π) distributions of the states populated by these reactions were studied to investigate the surrogate reaction approach, which aims at indirectly determining cross sections for compound-nuclear reactions involving unstable targets such as 89Zr. Discrete γ rays, associated with transitions in 90Zr and 89Zr, were measured in coincidence with light ions for scatteringmore » angles of 25°–60° and 90Zr excitation energies extending above the neutron separation energy. The measured transition systematics were used to gain insights into the J π distributions of 90Zr. The 90Zr (p,p') reaction was found to produce fewer γ rays associated with transitions involving high spin states (J = 6–8 ℏ) than the other two reactions, suggesting that inelastic scattering preferentially populates states in 90Zr that have lower spins than those populated in the transfer reactions investigated. The γ-ray production was also observed to vary by factors of 2–3 with the angle at which the outgoing particle was detected. These findings are relevant to the application of the surrogate reaction approach.« less

Structure-guided Protein Transition Modeling with a Probabilistic Roadmap Algorithm.

PubMed

Maximova, Tatiana; Plaku, Erion; Shehu, Amarda

2016-07-07

Proteins are macromolecules in perpetual motion, switching between structural states to modulate their function. A detailed characterization of the precise yet complex relationship between protein structure, dynamics, and function requires elucidating transitions between functionally-relevant states. Doing so challenges both wet and dry laboratories, as protein dynamics involves disparate temporal scales. In this paper we present a novel, sampling-based algorithm to compute transition paths. The algorithm exploits two main ideas. First, it leverages known structures to initialize its search and define a reduced conformation space for rapid sampling. This is key to address the insufficient sampling issue suffered by sampling-based algorithms. Second, the algorithm embeds samples in a nearest-neighbor graph where transition paths can be efficiently computed via queries. The algorithm adapts the probabilistic roadmap framework that is popular in robot motion planning. In addition to efficiently computing lowest-cost paths between any given structures, the algorithm allows investigating hypotheses regarding the order of experimentally-known structures in a transition event. This novel contribution is likely to open up new venues of research. Detailed analysis is presented on multiple-basin proteins of relevance to human disease. Multiscaling and the AMBER ff14SB force field are used to obtain energetically-credible paths at atomistic detail.

An experimental and theoretical study of the A˜ 2A″Π -X˜ 2A' band system of the jet-cooled HBBr/DBBr free radical

NASA Astrophysics Data System (ADS)

Gharaibeh, Mohammed; Clouthier, Dennis J.; Tarroni, Riccardo

2016-06-01

The electronic spectra of the HBBr and DBBr free radicals have been studied in depth. These species were prepared in a pulsed electric discharge jet using a precursor mixture of BBr3 vapor and H2 or D2 in high pressure argon. Transitions to the electronic excited state of the jet-cooled radicals were probed with laser-induced fluorescence and the ground state energy levels were measured from the single vibronic level emission spectra. HBBr has an extensive band system in the red which involves a linear-bent transition between the two Renner-Teller components of what would be a 2Π state at linearity. We have used high level ab initio theory to calculate potential energy surfaces for the bent 2A' ground state and the linear A˜ 2A″Π excited state and we have determined the ro-vibronic energy levels variationally, including spin orbit effects. The correspondence between the computed and experimentally observed transition frequencies, upper state level symmetries, and H and B isotope shifts was used to make reliable assignments. We have shown that the ground state barriers to linearity, which range from 10 000 cm-1 in HBF to 2700 cm-1 in BH2, are inversely related to the energy of the first excited 2Σ (2A') electronic state. This suggests that a vibronic coupling mechanism is responsible for the nonlinear equilibrium geometries of the ground states of the HBX free radicals.

Ionic Salt Effect on the Phase Transition of PS-b-P2VP Copolymers

NASA Astrophysics Data System (ADS)

Kim, Bokyung; An, Hyungju; Ryu, Du Yeol; Kim, Jehan

2009-03-01

Solid-state electrolytes have long been considered as suitable candidates owing to the simple and easy processes for rechargeable battery manufactures, compared to conventional liquid electrolyte counterparts. Especially, polymer/salt systems involving PMMA and PVP complex forms have been studied since they provide stable electrochemical characteristics as well as mechanical properties. We studied the phase behavior of PS-b-P2VP upon the salt addition by small angle x-ray scattering (SAXS) and depolarized light scattering. Transition temperatures of block copolymer were significantly influenced by the salt addition in addition to the changes of d-spacings, which is caused by the effective coordinative interaction between P2VP block and salt. This study suggests a simple approach to solid-state block copolymer electrolytes.

Transient rotordynamic analysis for the space-shuttle main engine high-pressure oxygen turbopump

NASA Technical Reports Server (NTRS)

Childs, D. W.

1974-01-01

A simulation study was conducted to examine the transient rotordynamics of the space shuttle main engine (SSME) high pressure oxygen turbopump (HPOTP) with the objective of identifying, anticipating, and avoiding rotordynamic problem areas. Simulations were performed for steady state operations at emergency power levels and for critical speed transitions. No problems are indicated in steady state operation of the HPOTP emergency power levels, although the results indicated that a rubbing condition will be experienced during critical speed transition at shutdown, particularly involving rotor deceleration rate and imbalance distribution rubbing at the turbine floating-ring seals. The condition is correctable by either reducing the imbalance at the HPOTP hot gas turbine wheels, or by a more rapid deceleration of the rotor through it critical speed.

Near Infrared Emission of Highly Electronically Excited CO: A Sensitive Probe to Study the Interstellar Medium??

NASA Technical Reports Server (NTRS)

Gudipati, Murthy S.

2002-01-01

Among the various spectroscopic features of the second most abundant molecule in the space, CO, "the triplet - triplet transitions involving the lowest triplet state a(sup 3)II and the higher-lying a(sup 1)3 SIGMA (sup +), d(sup 3) (DELTA), e (sup 3) SIGMA (sup -) states spanning near-UV to mid-IR spectral range" have so far not been explored in astrophysical observations. The energies of these transitions are highly sensitive to the surroundings in which CO exists, i.e. gas-phase, polar or non-polar condensed phase. It is proposed here that these triplet-triplet emission/absorption bands can be used as a sensitive probe to investigate the local environments of CO, whether in the planetary atmosphere, stellar atmosphere or interstellar medium.

Full dimensional Franck-Condon factors for the acetylene ˜{A} 1Au—{˜{X}} {^1Σ _g^+} transition. II. Vibrational overlap factors for levels involving excitation in ungerade modes

NASA Astrophysics Data System (ADS)

Park, G. Barratt; Baraban, Joshua H.; Field, Robert W.

2014-10-01

A full-dimensional Franck-Condon calculation has been applied to the tilde{A} 1Au—tilde{X} ^1Σ _g^+ transition in acetylene in the harmonic normal mode basis. Details of the calculation are discussed in Part I of this series. To our knowledge, this is the first full-dimensional Franck-Condon calculation on a tetra-atomic molecule undergoing a linear-to-bent geometry change. In the current work, the vibrational intensity factors for levels involving excitation in ungerade vibrational modes are evaluated. Because the Franck-Condon integral accumulates away from the linear geometry, we have been able to treat the out-of-plane component of trans bend (ν _4^' ' }) in the linear tilde{X} state in the rotational part of the problem, restoring the χ Euler angle and the a-axis Eckart conditions. A consequence of the Eckart conditions is that the out-of-plane component of ν _4^' ' } does not participate in the vibrational overlap integral. This affects the structure of the coordinate transformation and the symmetry of the vibrational wavefunctions used in the overlap integral, and results in propensity rules involving the bending modes of the tilde{X} state that were not previously understood. We explain the origin of some of the unexpected propensities observed in IR-UV laser-induced fluorescence spectra, and we calculate emission intensities from bending levels of the tilde{A} state into bending levels of the tilde{X} state, using normal bending mode and local bending mode basis sets. Our calculations also reveal Franck-Condon propensities for the Cartesian components of the cis bend (ν _5^' ' }), and we predict that the best tilde{A}-state vibrational levels for populating tilde{X}-state levels with large amplitude bending motion localized in a single C-H bond (the acetylene↔vinylidene isomerization coordinate) involve a high degree of excitation in ν _6^' } (cis-bend). Mode ν _4^' } (torsion) populates levels with large amplitude counter-rotational motion of the two hydrogen atoms.

VUV Absorption Spectra of Gas-Phase Quinoline in the 3.5 - 10.7 eV Photon Energy Range.

PubMed

Leach, Sydney; Jones, Nykola C; Hoffmann, Søren Vrønning; Un, Sun

2018-06-16

The absorption spectrum of quinoline was measured in the gas phase between 3.5 and 10.7 eV using a synchrotron photon source. A large number of sharp and broad spectral features were observed, some of which have plasmon-type collective π-electron modes contributing to their intensities. Eight valence electronic transitions were assigned, considerably extending the number of π-π* transitions previously observed mainly in solution. The principal factor in solution red-shifts is found to be the Lorentz-Lorenz polarizability parameter. Rydberg bands, observed for the first time, are analysed into eight different series, converging to the D0 ground and two excited electronic states, D3 and D4, of the quinoline cation. The R1 series limit is 8.628 eV for the first ionization energy of quinoline, a value more precise than previously published. This value, combined with cation electronic transition data provides precise energies, respectively 10.623 eV and 11.355 eV, for the D3 and D4 states. The valence transition assignments are based on DFT calculations as well as on earlier Pariser-Parr-Pople SCF LCAO MO results. The relative quality of the P-P-P and DFT data is discussed. Both are far from spectroscopic accuracy concerning electronic excited states but were nevertheless useful for our assignments. Our time-dependent DFT calculations of quinoline are excellent for its ground state properties such as geometry, rotational constants, dipole moment and vibrational frequencies, which agree well with experimental observations. Vibrational components of the valence and Rydberg transitions mainly involve C-H bend and C=C and C=N stretch modes. Astrophysical applications of the VUV absorption of quinoline are briefly discussed.

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.

Assignment and Analysis of the NO2 In-Plane Rock Band of Nitromethane Recorded by High-Resolution FTIR Synchrotron Spectroscopy

NASA Astrophysics Data System (ADS)

Dawadi, Mahesh B.; Perry, David S.; Twagirayezu, Sylvestre; Billinghurst, Brant E.

2014-06-01

The high-resolution rotationally resolved Fourier Transform Far-infrared spectrum of the NO2 in plane-rock band (440-510 cm-1) of nitromethane (CH3NO2) has been recorded using the Far-Infrared Beamline at the Canadian Light Source, with a resolution of 0.00096 cm-1. More than 1500 transitions lines have been assigned for ' = 0; {_a}' {≤ 7}; ' {≤ 50}; using an automated ground state combination difference program together with the traditional Loomis Wood approach. Transitions involving ' = 0; {_a}' {≤7}; ' {≤ 20}; in the upper vibrational state are fit using the six-fold torsion-rotation program developed by Ilyushin et.al. The torsion-rotation energy pattern in the lowest torsional state ( ' = 0) of the upper vibrational state is similar to that of the vibrational ground state. C. F. Neese., An Interactive Loomis-Wood Package, V2.0, {56th},OSU Interanational Symposium on Molecular Spectroscopy (2001). V. V. Ilyushin, Z. Kisiel, L. Pszczolkowski, H. Mader, and J. T. Hougen, M. Mol. Spectrosc., 259, 26, (2010).

Investigation of Infra-red and Nonequilibrium Air Radiation

NASA Technical Reports Server (NTRS)

Kruger, Charles H.; Laux, Christophe O.

1994-01-01

This report summarizes the results obtained during a research program on the infrared radiation of air plasmas conducted in the High Temperature Gasdynamics Laboratory at Stanford University. This program was intended to investigate the masking of infrared signatures by the air plasma formed behind the bow shock of high velocity missiles. Prior to this work, the radiative emission of air plasmas in the infrared had been the object of few experimental investigations, and although several infrared systems were already modeled in radiation codes such as NEQAIR, measurements were required to validate numerical predictions and indicate whether all transitions of importance were accounted for in the model. The program was further motivated by the fact that 9 excited states (A, B, C, D, B', F, H, and H') of NO radiate in the infrared, especially between 1 and 1.5 microns where at least 9 transitions involving can be observed. Because these IR transitions are relatively well separated from each other, excited NO states concentrations can be easily measured, thus providing essential information on excited-state chemistry for use in optical diagnostics or in electronic excitation model validation. Detailed comparisons between measured and simulated spectra are presented.

A Restricted Open Configuration Interaction with Singles Method To Calculate Valence-to-Core Resonant X-ray Emission Spectra: A Case Study

PubMed Central

2017-01-01

In this work, a new protocol for the calculation of valence-to-core resonant X-ray emission (VtC RXES) spectra is introduced. The approach is based on the previously developed restricted open configuration interaction with singles (ROCIS) method and its parametrized version, based on a ground-state Kohn–Sham determinant (DFT/ROCIS) method. The ROCIS approach has the following features: (1) In the first step approximation, many-particle eigenstates are calculated in which the total spin is retained as a good quantum number. (2) The ground state with total spin S and excited states with spin S′ = S, S ± 1, are obtained. (3) These states have a qualitatively correct multiplet structure. (4) Quasi-degenerate perturbation theory is used to treat the spin–orbit coupling operator variationally at the many-particle level. (5) Transition moments are obtained between the relativistic many-particle states. The method has shown great potential in the field of X-ray spectroscopy, in particular in the field of transition-metal L-edge, which cannot be described correctly with particle–hole theories. In this work, the method is extended to the calculation of resonant VtC RXES [alternatively referred to as 1s-VtC resonant inelastic X-ray scattering (RIXS)] spectra. The complete Kramers–Dirac–Heisenerg equation is taken into account. Thus, state interference effects are treated naturally within this protocol. As a first application of this protocol, a computational study on the previously reported VtC RXES plane on a molecular managanese(V) complex is performed. Starting from conventional X-ray absorption spectra (XAS), we present a systematic study that involves calculations and electronic structure analysis of both the XAS and non-resonant and resonant VtC XES spectra. The very good agreement between theory and experiment, observed in all cases, allows us to unravel the complicated intensity mechanism of these spectroscopic techniques as a synergic function of state polarization and interference effects. In general, intense features in the RIXS spectra originate from absorption and emission processes that involve nonorthogonal transition moments. We also present a graphical method to determine the sign of the interference contributions. PMID:28920680

Effective collision strengths for fine-structure forbidden transitions among the 3s^23p^3 levels of AR IV

NASA Astrophysics Data System (ADS)

Ramsbottom, C. A.; Bell, K. L.; Keenan, F. P.

1997-01-01

The multichannel R-matrix method is used to compute electron impact excitation collision strengths in Ar iv for all fine-structure transitions among the ^4S^o, ^2D^o and ^2P^o levels in the 3s^23p^3 ground configuration. Included in the expansion of the total wavefunction are the lowest 13 LS target eigenstates of Ar iv formed from the 3s^23p^3, 3s3p^4 and 3s^23p^23d configurations. The effective collision strengths, obtained by averaging the electron collision strengths over a Maxwellian distribution of electron velocities, are presented for all 10 fine-structure transitions over a wide range of electron temperatures of astrophysical interest (T_e=2000-100 000K). Comparisons are made with an earlier 7-state close-coupling calculation by Zeippen, Butler & Le Bourlot, and significant differences are found to occur for many of the forbidden transitions considered, in particular those involving the ^4S^o ground state, where discrepancies of up to a factor of 3 are found in the low-temperature region.

Applications of NIR spectroscopy to monitoring and analyzing the solid state during industrial crystallization processes.

PubMed

Févotte, G; Calas, J; Puel, F; Hoff, C

2004-04-01

Fiber-optic near infrared (NIR) spectroscopy was used to investigate several key features of the polymorphic transitions observed during the crystallization and the filtration of SaC, an Active Pharmaceutical Ingredient (API) produced by Sanofi-Synthelabo. Using few samples, the spectroscopic data were calibrated to provide measurements of the polymorphic composition of the solid product which is likely to appear in two crystalline forms or in the amorphous state. Both qualitative and quantitative methods were successfully evaluated to characterize the API. The NIR spectroscopy measurement was then applied to investigate the kinetic behavior of the phase transition phenomena against various operating conditions. From the viewpoint of industrial process development several applications are presented. The effects of temperature and seed crystal habits on the rate of transition of filtration cakes are briefly investigated; and a study of the effect of residual water in the solvent on the transition occurring during filtration is more deeply analyzed. The experimental results demonstrate that highly valuable information can be provided by the NIR spectroscopy measurements, when one aims at understanding more deeply and optimizing the consequences of various and complex phenomena involved during the solid processing chain.

Discontinuous non-equilibrium phase transition in a threshold Schloegl model for autocatalysis: Generic two-phase coexistence and metastability

DOE PAGES

Wang, Chi -Jen; Liu, Da -Jiang; Evans, James W.

2015-04-28

Threshold versions of Schloegl’s model on a lattice, which involve autocatalytic creation and spontaneous annihilation of particles, can provide a simple prototype for discontinuous non-equilibrium phase transitions. These models are equivalent to so-called threshold contact processes. A discontinuous transition between populated and vacuum states can occur selecting a threshold of N ≥ 2 for the minimum number, N, of neighboring particles enabling autocatalytic creation at an empty site. Fundamental open questions remain given the lack of a thermodynamic framework for analysis. For a square lattice with N = 2, we show that phase coexistence occurs not at a unique valuemore » but for a finite range of particle annihilation rate (the natural control parameter). This generic two-phase coexistence also persists when perturbing the model to allow spontaneous particle creation. Such behavior contrasts both the Gibbs phase rule for thermodynamic systems and also previous analysis for this model. We find metastability near the transition corresponding to a non-zero effective line tension, also contrasting previously suggested critical behavior. As a result, mean-field type analysis, extended to treat spatially heterogeneous states, further elucidates model behavior.« less

Local excitation of the 5-bromouracil chromophore in DNA. Computational and UV spectroscopic studies.

PubMed

Storoniak, Piotr; Rak, Janusz; Polska, Katarzyna; Blancafort, Lluís

2011-04-21

The UV electronic transition energies and their oscillator strengths for two stacked dimers having B-DNA geometries and consisting of 5-bromouracil ((Br)U) and a purine base were studied at the MS-CASPT2/6-311G(d) level with an active space of 12 orbitals and 12 electrons. The calculated energy of the first vertical (π,π*) transitions for the studied dimers remain in fair agreement with the maxima in the difference spectra measured for duplexes with the 5'-A(Br)U-3' or 5'-G(Br)U-3' sequences. Our MS-CASPT2 results show that the charge transfer (CT) states in which an electron is transferred from A/G to (Br)U are located at much higher energies than the first (π,π*) transitions, which involve local excitation (LE) of (Br)U. Moreover, CT transitions are characterized by small oscillator strengths, which implies that they could not be excited directly. The results of the current studies suggest that the formation of the reactive uracil-5-yl radical in DNA is preceded by the formation of the highly oxidative LE state of (Br)U, which is followed by electron transfer, presumably from guanine.

Discontinuous non-equilibrium phase transition in a threshold Schloegl model for autocatalysis: Generic two-phase coexistence and metastability

NASA Astrophysics Data System (ADS)

Wang, Chi-Jen; Liu, Da-Jiang; Evans, James W.

2015-04-01

Threshold versions of Schloegl's model on a lattice, which involve autocatalytic creation and spontaneous annihilation of particles, can provide a simple prototype for discontinuous non-equilibrium phase transitions. These models are equivalent to so-called threshold contact processes. A discontinuous transition between populated and vacuum states can occur selecting a threshold of N ≥ 2 for the minimum number, N, of neighboring particles enabling autocatalytic creation at an empty site. Fundamental open questions remain given the lack of a thermodynamic framework for analysis. For a square lattice with N = 2, we show that phase coexistence occurs not at a unique value but for a finite range of particle annihilation rate (the natural control parameter). This generic two-phase coexistence also persists when perturbing the model to allow spontaneous particle creation. Such behavior contrasts both the Gibbs phase rule for thermodynamic systems and also previous analysis for this model. We find metastability near the transition corresponding to a non-zero effective line tension, also contrasting previously suggested critical behavior. Mean-field type analysis, extended to treat spatially heterogeneous states, further elucidates model behavior.

Effective collision strengths for forbidden transitions among the 3s23p3 fine-structure levels of CL IIIIII

NASA Astrophysics Data System (ADS)

Ramsbottom, C. A.; Bell, K. L.; Keenan, F. P.

1999-08-01

Effective collision strengths for the 10 astrophysically important fine-structure forbidden transitions among the ^4S^o, ^2D^o and ^2P^o levels in the 3s^23p^3 configuration of Cliii are presented. The calculation employs the multichannel R-matrix method to compute the electron-impact excitation collision strengths in a close-coupling expansion, which incorporates the lowest 23 LS target eigenstates of Cliii. These states are formed from the 3s^23p^3, 3s3p^4, 3s^23p^23d and 3s^23p^24s configurations. The Maxwellian-averaged effective collision strengths are presented graphically for all 10 fine-structure transitions over a wide range of electron temperatures appropriate for astrophysical applications [logT(K)=3.3-logT(K)=5.9]. Comparisons are made with the earlier seven-state close-coupling calculation of Butler & Zeippen, and in general excellent agreement is found in the low-temperature region where a comparison is possible [logT(K)=3.3-logT(K)=4.7]. However, discrepancies of up to 30 per cent are found to occur for the forbidden transitions which involve the ^4S^o ground state level, particularly for the lowest temperatures considered. At the higher temperatures, the present data are the only reliable results currently available.

Sustainability, polysaccharide science, and bio-economy.

PubMed

ten Bos, René; van Dam, Jan E G

2013-03-01

At the opening of the 2nd EPNOE conference the role and responsibility of polysaccharide scientists was reflected upon and placed in the context of actual global issues like the transition process towards "sustainable bio-economy". Difficulties in the chain of communication between the different parties involved and towards the wider public was addressed. The need for change in the relations between science and the public and to go beyond the horizon of the specialization was discussed. It was stated that polysaccharide science is one of the key sciences in those transitions. Copyright © 2012 Elsevier Ltd. All rights reserved.

Growth of analog Al(x)Ga(1-x)As/GaAs parabolic quantum wells by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Wang, S. M.; Treideris, G.; Chen, W. Q.; Andersson, T. G.

1993-01-01

Parabolic Al(x)Ga(1-x)As/GaAs quantum wells have been grown by molecular beam epitaxy with linear ramping of the Al effusion cell temperature, where the ramping rate was carefully analyzed to avoid a flux lag. The calculated potential profile from the temperature variation was very close to the parabolic one. Low-temperature photoluminescence showed clear interband transitions up to the n = 3 sublevels. The equal energy spacing between adjacent transitions involving heavy-hole states confirmed the parabolic shape of the quantum well.

Public-Private Partnerships in China’s Urban Water Sector

PubMed Central

Mol, Arthur P. J.; Fu, Tao

2008-01-01

During the past decades, the traditional state monopoly in urban water management has been debated heavily, resulting in different forms and degrees of private sector involvement across the globe. Since the 1990s, China has also started experiments with new modes of urban water service management and governance in which the private sector is involved. It is premature to conclude whether the various forms of private sector involvement will successfully overcome the major problems (capital shortage, inefficient operation, and service quality) in China’s water sector. But at the same time, private sector involvement in water provisioning and waste water treatments seems to have become mainstream in transitional China. PMID:18256780

Emirati Women's Higher Educational Leadership Formation under Globalisation: Culture, Religion, Politics, and the Dialectics of Modernisation

ERIC Educational Resources Information Center

Samier, Eugenie

2015-01-01

The United Arab Emirates (UAE) is a small state transitioning from traditional communities into a modern society. This is a complex process: it involves instilling a national identity over tribal structures; modernising and technologising while retaining Islam; ensuring a high level of security while allowing for a liberal and relatively free…

Creating Cartoons as Representation: Visual Narratives of College Students with Learning Disabilities

ERIC Educational Resources Information Center

Connor, David J.

2009-01-01

Students with learning disabilities (LD) are the largest sub-group of all students with disabilities attending college in the United States. However, due to the multiple difficulties involved in transitioning from school to college, many do not succeed during their first year. This article chronicles ways in which three students with LD negotiate…

Improving Middle School Parental Engagement in Transition to Common Core State Standards: An Action Research Study

ERIC Educational Resources Information Center

Harla, Donna K.

2014-01-01

Parental involvement in schools is an important potential contributor to improving American education and making the U.S. more globally competitive. This qualitative and quantitative mixed-methodology action research study probed the viability of engaging parents around issues of educational improvement by inviting them to participate in training…

Lifshitz Transitions, Type-II Dirac and Weyl Fermions, Event Horizon and All That

NASA Astrophysics Data System (ADS)

Volovik, G. E.; Zhang, K.

2017-12-01

The type-II Weyl and type-II Dirac points emerge in semimetals and also in relativistic systems. In particular, the type-II Weyl fermions may emerge behind the event horizon of black holes. In this case the horizon with Painlevé-Gullstrand metric serves as the surface of the Lifshitz transition. This relativistic analogy allows us to simulate the black hole horizon and Hawking radiation using the fermionic superfluid with supercritical velocity, and the Dirac and Weyl semimetals with the interface separating the type-I and type-II states. The difference between such type of the artificial event horizon and that which arises in acoustic metric is discussed. At the Lifshitz transition between type-I and type-II fermions the Dirac lines may also emerge, which are supported by the combined action of topology and symmetry. The type-II Weyl and Dirac points also emerge as the intermediate states of the topological Lifshitz transitions. Different configurations of the Fermi surfaces, involved in such Lifshitz transition, are discussed. In one case the type-II Weyl point connects the Fermi pockets and the Lifshitz transition corresponds to the transfer of the Berry flux between the Fermi pockets. In the other case the type-II Weyl point connects the outer and inner Fermi surfaces. At the Lifshitz transition the Weyl point is released from both Fermi surfaces. They loose their Berry flux, which guarantees the global stability, and without the topological support the inner surface disappears after shrinking to a point at the second Lifshitz transition. These examples reveal the complexity and universality of topological Lifshitz transitions, which originate from the ubiquitous interplay of a variety of topological characters of the momentum-space manifolds. For the interacting electrons, the Lifshitz transitions may lead to the formation of the dispersionless (flat) band with zero energy and singular density of states, which opens the route to room-temperature superconductivity. Originally, the idea of the enhancement of T_c due to flat band has been put forward by the nuclear physics community, and this also demonstrates the close connections between different areas of physics.

Bivariate- distribution for transition matrix elements in Breit-Wigner to Gaussian domains of interacting particle systems.

PubMed

Kota, V K B; Chavda, N D; Sahu, R

2006-04-01

Interacting many-particle systems with a mean-field one-body part plus a chaos generating random two-body interaction having strength lambda exhibit Poisson to Gaussian orthogonal ensemble and Breit-Wigner (BW) to Gaussian transitions in level fluctuations and strength functions with transition points marked by lambda = lambda c and lambda = lambda F, respectively; lambda F > lambda c. For these systems a theory for the matrix elements of one-body transition operators is available, as valid in the Gaussian domain, with lambda > lambda F, in terms of orbital occupation numbers, level densities, and an integral involving a bivariate Gaussian in the initial and final energies. Here we show that, using a bivariate-t distribution, the theory extends below from the Gaussian regime to the BW regime up to lambda = lambda c. This is well tested in numerical calculations for 6 spinless fermions in 12 single-particle states.

Structural changes during a liquid-liquid transition in the deeply undercooled Z r58.5C u15.6N i12.8A l10.3N b2.8 bulk metallic glass forming melt

NASA Astrophysics Data System (ADS)

Stolpe, Moritz; Jonas, Isabell; Wei, Shuai; Evenson, Zach; Hembree, William; Yang, Fan; Meyer, Andreas; Busch, Ralf

2016-01-01

Using high energy synchrotron x-ray radiation combined with electrostatic levitation, in situ structural analysis of a bulk metallic glass forming liquid is performed from above the liquidus temperature down to the glass transition. The data indicate a liquid-liquid transition (LLT) in the deeply undercooled state at T /Tg˜1.2 which manifests as a maximum in the heat capacity and an abrupt shift in the first peak position of the total structure factor in the absence of a pronounced density change. Analysis of the corresponding real-space data shows that the LLT involves changes in short- and medium-range order. The structural changes on the length scale of medium-range order imply a fragile-strong transition in agreement with experimental viscosity data.

Asymmetric shape transitions of epitaxial quantum dots

PubMed Central

2016-01-01

We construct a two-dimensional continuum model to describe the energetics of shape transitions in fully faceted epitaxial quantum dots (strained islands) via minimization of elastic energy and surface energy at fixed volume. The elastic energy of the island is based on a third-order approximation, enabling us to consider shape transitions between pyramids, domes, multifaceted domes and asymmetric intermediate states. The energetics of the shape transitions are determined by numerically calculating the facet lengths that minimize the energy of a given island type of prescribed island volume. By comparing the energy of different island types with the same volume and analysing the energy surface as a function of the island shape parameters, we determine the bifurcation diagram of equilibrium solutions and their stability, as well as the lowest barrier transition pathway for the island shape as a function of increasing volume. The main result is that the shape transition from pyramid to dome to multifaceted dome occurs through sequential nucleation of facets and involves asymmetric metastable transition shapes. We also explicitly determine the effect of corner energy (facet edge energy) on shape transitions and interpret the results in terms of the relative stability of asymmetric island shapes as observed in experiment. PMID:27436989

The Triplet State

NASA Astrophysics Data System (ADS)

Zahlan, A. B.

2010-01-01

Preface; List of participants; Part I. Spin-orbit Coupling and Intersystem Crossing: 1. Spin-orbit interactions in organic molecules; 2. Singlet-triplet transitions in organic molecules; 3. Triplet decay and intersystem crossing in aromatic hydrocarbons; 4. Statistical aspects of resonance energy transfer; Discussion; Part II. Magnetic Resonance and Magnetic Interactions: 5. Magnetic resonance spectra of organic molecules in triplet states in single crystals; 6. Magnetic interactions related to phosphorescence; 7. ESR investigations of naphthalene-d8:Naphthalene-h8 mixed crystals; 8. Biradicals and polyradicals in the nitroxide series; 9. Changes induced in the phosphorescent radiation of aromatic molecules by paramagnetic resonance in their metastable triplet states; 10. Paramagnetic resonance of the triplet state of tetramethylpyrazine; 11. On magnetic dipole contributions to the intrinsic S0 = T1 transition in simple aromatics; Discussion; Part III. Photochemistry: 12. The kinetics of energy transfer from the triplet state in rigid solutions; 13. Triplet states in gas-phase photochemistry; 14. Biphotonic photochemistry, involving the triplet state: polarisation of the effective T-T transition and solvent effects; 15. Direct and sensitised photo-oxidation of aromatic hydrocarbons in boric acid glass; Discussion; Part IV. Radiationless Transitions: 16. Radiationless transitions in gaseous benzene; 17. Low-lying excited triplet states and intersystem crossing in aromatic hydrocarbons; 18. De-excitation rates of triplet states in condensed media; 19. Lifetimes of the triplet state of aromatic hydrocarbons in the vapour phase; Discussion; Part V. Triplet Excitons: 20. Some comments on the properties of triplet excitons in molecular crystals; 21. Exact treatment of coherent and incoherent triplet exciton migration; 22. Magnetic susceptibility of a system of triplet excitons: Würster's Blue Perchlorate; 23. A study of triplet excitons in anthracene crystals under laser excitation; 24. The electronic states in crystaline anthracene; Discussion; Part VI. Delayed Fluorescent and Phosphorescence: 25. Delayed fluorescence of solutions; 26. The kinetics of the excited states of anthracene and phenanthrene vapor; 27. Optical investigations of the triplet states of naphthalene in different crystalline environments; 28. Excitation of the triplet states of organic molecules; 29. The delayed luminescence and triplet quantum yields of pyrene solutions; 30. Triplet state studies of some polyphenyls in rigid glasses; 31. Decay time of delayed fluorescence of anthracene as a function of temperature (2-30ºK); 32. Energy transfer between benzene and biacetyl and the lifetime of triplet benzene in the gas phase; 33. Charge transfer triplet state of molecular complexes. 34. Flash-photolytic detection of triplet acridine formed by energy transfer from biacetyl; 35. Extinction coefficients of triplet-triplet transitions between 3000 and 8800 A in anthracene; 36. Anthracene triplet-triplet annihilation rate constant; Discussion; Part VII. Triplet State Related to Biology: 37. ESR and optical studies of some triplet states of biological interest; 38. The triplet state of DNA; 39. Some characteristics of the triplet states of the nucleic bases; Discussion; Indexes.

Doubly magic 208Pb: High-spin states, isomers, and E 3 collectivity in the yrast decay

NASA Astrophysics Data System (ADS)

Broda, R.; Janssens, R. V. F.; Iskra, Ł. W.; Wrzesinski, J.; Fornal, B.; Carpenter, M. P.; Chiara, C. J.; Cieplicka-Oryńczak, N.; Hoffman, C. R.; Kondev, F. G.; Królas, W.; Lauritsen, T.; Podolyak, Zs.; Seweryniak, D.; Shand, C. M.; Szpak, B.; Walters, W. B.; Zhu, S.; Brown, B. A.

2017-06-01

Yrast and near-yrast levels up to spin values in excess of I =30 ℏ have been delineated in the doubly magic 208Pb nucleus following deep-inelastic reactions involving 208Pb targets and, mostly, 430-MeV 48Ca and 1440-MeV 208Pb beams. The level scheme was established up to an excitation energy of 16.4 MeV, based on multifold γ-ray coincidence relationships measured with the Gammasphere array. Below the well-known, 0.5-μs 10+ isomer, ten new transitions were added to earlier work. The delineation of the higher parts of the level sequence benefited from analyses involving a number of prompt- and delayed-coincidence conditions. Three new isomeric states were established along the yrast line with Iπ=20- (10 342 keV), 23+ (11 361 keV), and 28- (13 675 keV), and respective half-lives of 22(3), 12.7(2), and 60(6) ns. Gamma transitions were also identified preceding in time the 28- isomer; however, only a few could be placed in the level scheme and no firm spin-parity quantum numbers could be proposed. In contrast, for most states below this 28- isomer, firm spin-parity values were assigned, based on total electron-conversion coefficients, deduced for low-energy (<500 keV ) transitions from γ-intensity balances, and on measured γ-ray angular distributions. The latter also enabled the quantitative determination of mixing ratios. The transition probabilities extracted for all isomeric transitions in 208Pb have been reviewed and discussed in terms of the intrinsic structure of the initial and final levels involved. Particular emphasis was placed on the many observed E 3 transitions as they often exhibit significant enhancements in strength [of the order of tens of Weisskopf units (W.u.)] comparable to the one seen for the neutron j15 /2→g9 /2 E 3 transition in 209Pb. In this context, the enhancement of the 725-keV E 3 transition (56 W.u.) associated with the decay of the highest-lying 28- isomer observed in this work remains particularly challenging to explain. Large-scale shell-model calculations were performed with two approaches, a first one where the 1, 2, and 3 particle-hole excitations do not mix with one another, and another more complex one, in which such mixing takes place. The calculated levels were compared with the data and a general agreement is observed for most of the 208Pb level scheme. At the highest spins and energies, however, the correspondence between theory and experiment is less satisfactory and the experimental yrast line appears to be more regular than the calculated one. This regularity is notable when the level energies are plotted versus the I (I +1 ) product and the observed, nearly linear, behavior was considered within a simple "rotational" interpretation. Within this approximate picture, the extracted moment of inertia suggests that only the 76 valence nucleons participate in the "rotation" and that the 132Sn spherical core remains inert.

Tendency to occupy a statistically dominant spatial state of the flow as a driving force for turbulent transition.

PubMed

Chekmarev, Sergei F

2013-03-01

The transition from laminar to turbulent fluid motion occurring at large Reynolds numbers is generally associated with the instability of the laminar flow. On the other hand, since the turbulent flow characteristically appears in the form of spatially localized structures (e.g., eddies) filling the flow field, a tendency to occupy such a structured state of the flow cannot be ruled out as a driving force for turbulent transition. To examine this possibility, we propose a simple analytical model that treats the flow as a collection of localized spatial structures, each of which consists of elementary cells in which the behavior of the particles (atoms or molecules) is uncorrelated. This allows us to introduce the Reynolds number, associating it with the ratio between the total phase volume for the system and that for the elementary cell. Using the principle of maximum entropy to calculate the most probable size distribution of the localized structures, we show that as the Reynolds number increases, the elementary cells group into the localized structures, which successfully explains turbulent transition and some other general properties of turbulent flows. An important feature of the present model is that a bridge between the spatial-statistical description of the flow and hydrodynamic equations is established. We show that the basic assumptions underlying the model, i.e., that the particles are indistinguishable and elementary volumes of phase space exist in which the state of the particles is uncertain, are involved in the derivation of the Navier-Stokes equation. Taking into account that the model captures essential features of turbulent flows, this suggests that the driving force for the turbulent transition is basically the same as in the present model, i.e., the tendency of the system to occupy a statistically dominant state plays a key role. The instability of the flow at high Reynolds numbers can then be a mechanism to initiate structural rearrangement of the flow to find this state.

Quench field sensitivity of two-particle correlation in a Hubbard model

PubMed Central

Zhang, X. Z.; Lin, S.; Song, Z.

2016-01-01

Short-range interaction can give rise to particle pairing with a short-range correlation, which may be destroyed in the presence of an external field. We study the transition between correlated and uncorrelated particle states in the framework of one- dimensional Hubbard model driven by a field. We show that the long time-scale transfer rate from an initial correlated state to final uncorrelated particle states is sensitive to the quench field strength and exhibits a periodic behavior. This process involves an irreversible energy transfer from the field to particles, leading to a quantum electrothermal effect. PMID:27250080

Transition to subthreshold activity with the use of phase shifting in a model thalamic network

NASA Astrophysics Data System (ADS)

Thomas, Elizabeth; Grisar, Thierry

1997-05-01

Absence epilepsy involves a state of low frequency synchronous oscillations by the involved neuronal networks. These oscillations may be either above or subthreshold. In this investigation, we studied the methods which could be utilized to transform the threshold activity of neurons in the network to a subthreshold state. A model thalamic network was constructed using the Hodgkin Huxley framework. Subthreshold activity was achieved by the application of stimuli to the network which caused phase shifts in the oscillatory activity of selected neurons in the network. In some instances the stimulus was a periodic pulse train of low frequency to the reticular thalamic neurons of the network while in others, it was a constant hyperpolarizing current applied to the thalamocortical neurons.

Analysis of energy states in modulation doped multiquantum well heterostructures

NASA Technical Reports Server (NTRS)

Ji, G.; Henderson, T.; Peng, C. K.; Huang, D.; Morkoc, H.

1990-01-01

A precise and effective numerical procedure to model the band diagram of modulation doped multiquantum well heterostructures is presented. This method is based on a self-consistent iterative solution of the Schroedinger equation and the Poisson equation. It can be used rather easily in any arbitrary modulation-doped structure. In addition to confined energy subbands, the unconfined states can be calculated as well. Examples on realistic device structures are given to demonstrate capabilities of this procedure. The numerical results are in good agreement with experiments. With the aid of this method the transitions involving both the confined and unconfined conduction subbands in a modulation doped AlGaAs/GaAs superlattice, and in a strained layer InGaAs/GaAs superlattice are identified. These results represent the first observation of unconfined transitions in modulation doped multiquantum well structures.

Electronic Transitions of Palladium Monoboride and Platinum Monoboride

NASA Astrophysics Data System (ADS)

Ng, Y. W.; Pang, H. F.; Wong, Y. S.; Qian, Yue; Cheung, A. S.-C.

2012-06-01

Electronic transition spectrum of palladium monoboride (PdB) and platinum (PtB) monoboride have been studied using the technique of laser-ablation/reaction free jet expansion and laser induced fluorescence spectroscopy. The metal monoborides were produced by reacting laser ablated metal atoms and diborane ((B_2H_6) seeded in argon. Five and six vibrational bands were observed respectively for the PdB and PtB molecules. Preliminary analysis of the rotationally resolved structure showed that both molecules have X2 Σ+ ground state. Least-squares fit of the measured line positions yielded molecular constants for the electronic states involved. Molecular and electronic structures of PdB and PtB are discussed using a molecular orbital energy level diagram. Financial support from the Research Grants Council of the Hong Kong Special Administrative Region, China (Project No. HKU 701008P) is gratefully acknowledged.

Structure and Inhibition of Quorum Sensing Target from Streptococcus pneumoniae

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

Singh,V.; Shi, W.; Almo, S.

2006-01-01

Streptococcus pneumoniae 5'-methylthioadenosine/S-adenosylhomocysteine hydrolase (MTAN) catalyzes the hydrolytic deadenylation of its substrates to form adenine and 5-methylthioribose or S-ribosylhomocysteine (SRH). MTAN is not found in mammals but is involved in bacterial quorum sensing. MTAN gene disruption affects the growth and pathogenicity of bacteria, making it a target for antibiotic design. Kinetic isotope effects and computational studies have established a dissociative S{sub N}1 transition state for Escherichia coli MTAN, and transition state analogues resembling the transition state are powerful inhibitors of the enzyme [Singh, V., Lee, J. L., Nunez, S., Howell, P. L., and Schramm, V. L. (2005) Biochemistry 44, 11647-11659].more » The sequence of MTAN from S. pneumoniae is 40% identical to that of E. coli MTAN, but S. pneumoniae MTAN exhibits remarkably distinct kinetic and inhibitory properties. 5'-Methylthio-Immucillin-A (MT-ImmA) is a transition state analogue resembling an early S{sub N}1 transition state. It is a weak inhibitor of S. pneumoniae MTAN with a K{sub i} of 1.0 {mu}M. The X-ray structure of S. pneumoniae MTAN with MT-ImmA indicates a dimer with the methylthio group in a flexible hydrophobic pocket. Replacing the methyl group with phenyl (PhT-ImmA), tolyl (p-TolT-ImmA), or ethyl (EtT-ImmA) groups increases the affinity to give K{sub i} values of 335, 60, and 40 nM, respectively. DADMe-Immucillins are geometric and electrostatic mimics of a fully dissociated transition state and bind more tightly than Immucillins. MT-DADMe-Immucillin-A inhibits with a K{sub i} value of 24 nM, and replacing the 5'-methyl group with p-Cl-phenyl (p-Cl-PhT-DADMe-ImmA) gave a K{sub i}* value of 0.36 nM. The inhibitory potential of DADMe-Immucillins relative to the Immucillins supports a fully dissociated transition state structure for S. pneumoniae MTAN. Comparison of active site contacts in the X-ray crystal structures of E. coli and S. pneumoniae MTAN with MT-ImmA would predict equal binding, yet most analogues bind 10{sup 3}-10{sup 4}-fold more tightly to the E. coli enzyme. Catalytic site efficiency is primarily responsible for this difference since k{sub cat}/K{sub m} for S. pneumoniae MTAN is decreased 845-fold relative to that of E. coli MTAN.« less

Selective excitation of exciton transitions in PTCDA crystals and films

NASA Astrophysics Data System (ADS)

Gangilenka, V. R.; Titova, L. V.; Smith, L. M.; Wagner, H. P.; Desilva, L. A. A.; Gisslén, L.; Scholz, R.

2010-04-01

Photoluminescence excitation studies on 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) single crystals and polycrystalline PTCDA films are compared to the calculated excitonic dispersion deduced from an exciton model including the coupling between Frenkel and charge transfer (CT) excitons along the stacking direction. For excitation energies below the 0-0 Frenkel exciton absorption band at 5 K these measurements enable the selective excitation of several CT states. The CT2 state involving stacked PTCDA molecules reveals two excitation resonances originating from different vibronic sublevels. Moreover, the fundamental transition of the CT1 exciton state delocalized over both basis molecules in the crystal unit cell has been identified from the corresponding excitation resonance. From the excitation energy dependence the fundamental transition energies of the CT2 and CT1 excitons have been deduced to occur at 1.95 and 1.98 eV, respectively. When the excitation energy exceeds ˜2.08eV , we observe a strong emission channel which is related to the indirect minimum of the lowest dispersion branch dominated by Frenkel excitons. Photoluminescence excitation spectroscopy measurements on polycrystalline PTCDA films reveal a strong CT2 signal intensity which is attributed to an increased density of defect-related CT2 states that are preferentially formed by slightly deformed or compressed stacked PTCDA molecules in the vicinity of defects or at grain boundaries. Temperature-dependent PL measurements in polycrystalline PTCDA films between 10 and 300 K at an excitation of 1.88 eV further allow a detailed investigation of the CT2 transition and its vibronic subband.

Modeling evolution of hydrogen bonding and stabilization of transition states in the process of cocaine hydrolysis catalyzed by human butyrylcholinesterase.

PubMed

Gao, Daquan; Zhan, Chang-Guo

2006-01-01

Molecular dynamics (MD) simulations and quantum mechanical/molecular mechanical (QM/MM) calculations were performed on the prereactive enzyme-substrate complex, transition states, intermediates, and product involved in the process of human butyrylcholinesterase (BChE)-catalyzed hydrolysis of (-)-cocaine. The computational results consistently reveal a unique role of the oxyanion hole (consisting of G116, G117, and A199) in BChE-catalyzed hydrolysis of cocaine, compared to acetylcholinesterase (AChE)-catalyzed hydrolysis of acetylcholine. During BChE-catalyzed hydrolysis of cocaine, only G117 has a hydrogen bond with the carbonyl oxygen (O31) of the cocaine benzoyl ester in the prereactive BChE-cocaine complex, and the NH groups of G117 and A199 are hydrogen-bonded with O31 of cocaine in all of the transition states and intermediates. Surprisingly, the NH hydrogen of G116 forms an unexpected hydrogen bond with the carboxyl group of E197 side chain and, therefore, is not available to form a hydrogen bond with O31 of cocaine in the acylation. The NH hydrogen of G116 is only partially available to form a weak hydrogen bond with O31 of cocaine in some structures involved in the deacylation. The change of the estimated hydrogen-bonding energy between the oxyanion hole and O31 of cocaine during the reaction process demonstrates how the protein environment can affect the energy barrier for each step of the BChE-catalyzed hydrolysis of cocaine. These insights concerning the effects of the oxyanion hole on the energy barriers provide valuable clues on how to rationally design BChE mutants with a higher catalytic activity for the hydrolysis of (-)-cocaine. 2005 Wiley-Liss, Inc.

Modeling Evolution of Hydrogen Bonding and Stabilization of Transition States in the Process of Cocaine Hydrolysis Catalyzed by Human Butyrylcholinesterase

PubMed Central

Gao, Daquan; Zhan, Chang-Guo

2010-01-01

Molecular dynamics (MD) simulations and quantum mechanical/molecular mechanical (QM/MM) calculations were performed on the prereactive enzyme-substrate complex, transition states, intermediates, and product involved in the process of human butyrylcholinesterase (BChE)-catalyzed hydrolysis of (−)-cocaine. The computational results consistently reveal a unique role of the oxyanion hole (consisting of G116, G117, and A199) in BChE-catalyzed hydrolysis of cocaine, as compared to acetylcholinesterase (AChE)-catalyzed hydrolysis of acetylcholine. During BChE-catalyzed hydrolysis of cocaine, only G117 has a hydrogen bond with the carbonyl oxygen (O31) of the cocaine benzoyl ester in the prereactive BChE-cocaine complex, and the NH groups of G117 and A199 are hydrogen-bonded with O31 of cocaine in all of the transition states and intermediates. Surprisingly, the NH hydrogen of G116 forms an unexpected hydrogen bond with the carboxyl group of E197 side chain and, therefore, is not available to form a hydrogen bond with O31 of cocaine in the acylation. The NH hydrogen of G116 is only partially available to form a weak hydrogen bond with O31 of cocaine in some structures involved in the deacylation. The change of the estimated hydrogen bonding energy between the oxyanion hole and O31 of cocaine during the reaction process demonstrates how the protein environment can affect the energy barrier for each step of the BChE-catalyzed hydrolysis of cocaine. These insights concerning the effects of the oxyanion hole on the energy barriers provide valuable clues on how to rationally design BChE mutants with a higher catalytic activity for the hydrolysis of (−)-cocaine. PMID:16288482

Electronic transitions in quantum dots and rings induced by inhomogeneous off-centered light beams.

PubMed

Quinteiro, G F; Lucero, A O; Tamborenea, P I

2010-12-22

We theoretically investigate the effect of inhomogeneous light beams with (twisted light) and without (plane-wave light) orbital angular momentum on semiconductor-based nanostructures, when the symmetry axes of the beam and the nanostructure are displaced parallel to each other. Exact analytical results are obtained by expanding the off-centered light field in terms of the appropriate light modes centered around the nanostructure. We demonstrate how electronic transitions involving the transfer of different amounts of orbital angular momentum are switched on and off as a function of the separation between the axes of the beam and the system. In particular, we show that even off-centered plane-wave beams induce transitions such that the angular momenta of the initial and final states are different.

Core excitation effects on oscillator strengths for transitions in four electron atomic systems

NASA Astrophysics Data System (ADS)

Chang, T. N.; Luo, Yuxiang

2007-06-01

By including explicitly the electronic configurations with two and three simultaneously excited electronic orbital, we have extended the BSCI (B-spline based configuration interaction) method [1] to estimate directly the effect of inner shell core excitation to oscillator strengths for transitions in four-electron atomic systems. We will present explicitly the change in oscillator strengths due to core excitations, especially for transitions involving doubly excited states and those with very small oscillator strengths. The length and velocity results are typically in agreement better than 1% or less. [1] Tu-nan Chang, in Many-body Theory of Atomic Structure and Photoionization, edited by T. N. Chang (World Scientific, Singapore, 1993), p. 213-47; and T. N. Chang and T. K. Fang, Elsevier Radiation Physics and Chemistry 70, 173-190 (2004).

A Review of Opportunities to Improve the Health of People Involved in the Criminal Justice System in the United States.

PubMed

Freudenberg, Nicholas; Heller, Daliah

2016-01-01

In the past decade, many constituencies have questioned the efficacy, cost, and unintended consequences of mass incarceration in the United States. Although substantial evidence now demonstrates that US incarceration policies have had unintended adverse health consequences, we know less about the strategies and policies that can prevent or reduce these problems for justice-involved individuals and how the criminal justice system (CJS) can contribute to the Healthy People 2020 national goal of eliminating inequities in health. This review examines strategies that have been used to improve the health of people at various stages of CJS involvement, including diversion from jail and prison stays into community settings, improvements to the social and physical environments within correctional facilities, provision of health and other services to inmates, assistance for people leaving correctional facilities to make the transition back to the community, and systems coordination and integration.

Reassessment of fission fragment angular distributions from continuum states in the context of transition-state theory

NASA Astrophysics Data System (ADS)

Vaz, Louis C.; Alexander, John M.

1983-07-01

Fission angular distributions have been studied for years and have been treated as classic examples of trasitions-state theory. Early work involving composite nuclei of relatively low excitation energy E ∗ (⪅35 MeV) and spin I (⪅25ħ) gave support to theory and delimited interesting properties of the transitions-state nuclei. More recent research on fusion fission and sequential fission after deeply inelastic reactions involves composite nuclei of much higher energies (⪅200 MeV) and spins (⪅100ħ). Extension of the basic ideas developed for low-spin nuclei requires detailed consideration of the role of these high spins and, in particular, the “spin window” for fussion. We have made empirical correlations of cross sections for evaporation residues and fission in order to get a description of this spin window. A systematic reanalysis has been made for fusion fission induced by H, He and heavier ions. Empirical correlations of K 20 (K 20 = {IeffT }/{h̷2}) are presented along with comparisons of Ieff to moments of inertia for saddle-point nuclei from the rotating liquid drop model. This model gives an excellent guide for the intermidiate spin zone (30⪅ I ⪅65), while strong shell and/or pairing effects are evident for excitations less than ⪅35 MeV. Observations of strong anisotropies for very high-spin systems signal the demise of certain approximation commonly made in the theory, and suggestions are made toward this end.

Electronic Excitations in Solution: The Interplay between State Specific Approaches and a Time-Dependent Density Functional Theory Description.

PubMed

Guido, Ciro A; Jacquemin, Denis; Adamo, Carlo; Mennucci, Benedetta

2015-12-08

We critically analyze the performances of continuum solvation models when coupled to time-dependent density functional theory (TD-DFT) to predict solvent effects on both absorption and emission energies of chromophores in solution. Different polarization schemes of the polarizable continuum model (PCM), such as linear response (LR) and three different state specific (SS) approaches, are considered and compared. We show the necessity of introducing a SS model in cases where large electron density rearrangements are involved in the excitations, such as charge-transfer transitions in both twisted and quadrupolar compounds, and underline the very delicate interplay between the selected polarization method and the chosen exchange-correlation functional. This interplay originates in the different descriptions of the transition and ground/excited state multipolar moments by the different functionals. As a result, the choice of both the DFT functional and the solvent polarization scheme has to be consistent with the nature of the studied electronic excitation.

Correlation of normal and superconducting properties and unified approach to the description of high Tc oxides

NASA Technical Reports Server (NTRS)

Kresin, V. Z.; Wolf, S. A.

1991-01-01

We present a unified approach based on the Fermi liquid picture which allows us to describe the normal as well as the superconducting properties of the doped cuprates. The theory that is presented is for the doped compounds which are metallic. One can distinguish two interrelated, but nevertheless, different directions in the physics of high T(sub c): one involving the problem of carrier doping and the transition to the metallic state, and the second being the description of the metallic state. It is important that this metallic phase undergoes the transition into the superconducting state; as a result, our analysis is directly related to the origin of high T(sub c). We are using a quasi-2D Fermi liquid model to estimate the fundamental parameters of these very interesting materials. We find that this description is able to describe these materials and also that phonons and plasmons play a major role in the mechanism of high T(sub c).

Optical probing of quantum Hall effect of composite fermions and of the liquid-insulator transition

NASA Astrophysics Data System (ADS)

Rossella, F.; Bellani, V.; Dionigi, F.; Amado, M.; Diez, E.; Kowalik, K.; Biasiol, G.; Sorba, L.

2011-12-01

In the photoluminescence spectra of a two-dimensional electron gas in the fractional quantum Hall regime we observe the states at filling factors ν = 4/5, 5/7, 4/11 and 3/8 as clear minima in the intensity or area emission peak. The first three states are described as interacting composite fermions in fractional quantum Hall regime. The minimum in the intensity at ν = 3/8, which is not explained within this picture, can be an evidence of a suppression of the screening of the Coulomb interaction among the effective quasi-particles involved in this intriguing state. The magnetic field energy dispersion at very low temperatures is also discussed. At low field the emission follows a Landau dispersion with a screened magneto-Coulomb contribution. At intermediate fields the hidden symmetry manifests. At high field above ν = 1/3 the electrons correlate into an insulating phase, and the optical emission behaviour at the liquid-insulator transition is coherent with a charge ordering driven by Coulomb correlations.

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

PubMed

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

2016-12-01

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

Polymorphic phase transitions: Macroscopic theory and molecular simulation.

PubMed

Anwar, Jamshed; Zahn, Dirk

2017-08-01

Transformations in the solid state are of considerable interest, both for fundamental reasons and because they underpin important technological applications. The interest spans a wide spectrum of disciplines and application domains. For pharmaceuticals, a common issue is unexpected polymorphic transformation of the drug or excipient during processing or on storage, which can result in product failure. A more ambitious goal is that of exploiting the advantages of metastable polymorphs (e.g. higher solubility and dissolution rate) while ensuring their stability with respect to solid state transformation. To address these issues and to advance technology, there is an urgent need for significant insights that can only come from a detailed molecular level understanding of the involved processes. Whilst experimental approaches at best yield time- and space-averaged structural information, molecular simulation offers unprecedented, time-resolved molecular-level resolution of the processes taking place. This review aims to provide a comprehensive and critical account of state-of-the-art methods for modelling polymorph stability and transitions between solid phases. This is flanked by revisiting the associated macroscopic theoretical framework for phase transitions, including their classification, proposed molecular mechanisms, and kinetics. The simulation methods are presented in tutorial form, focusing on their application to phase transition phenomena. We describe molecular simulation studies for crystal structure prediction and polymorph screening, phase coexistence and phase diagrams, simulations of crystal-crystal transitions of various types (displacive/martensitic, reconstructive and diffusive), effects of defects, and phase stability and transitions at the nanoscale. Our selection of literature is intended to illustrate significant insights, concepts and understanding, as well as the current scope of using molecular simulations for understanding polymorphic transitions in an accessible way, rather than claiming completeness. With exciting prospects in both simulation methods development and enhancements in computer hardware, we are on the verge of accessing an unprecedented capability for designing and developing dosage forms and drug delivery systems in silico, including tackling challenges in polymorph control on a rational basis. Copyright © 2017 Elsevier B.V. All rights reserved.

Gender and Job Mobility in Postsocialist China: A Longitudinal Study of Job Changes in Six Coastal Cities

ERIC Educational Resources Information Center

Cao, Yang; Hu, Chiung-Yin

2007-01-01

This study examines the gender differences in job mobility in urban China. Conceptualizing China's postsocialist transition as a multi-faceted process, we argue that the emergence of labor markets, gendered role differentiation within the family, and the state's declining involvement in promoting women's rights lead to widened gender gaps in job…

Mesoscopic interactions and species coexistence in evolutionary game dynamics of cyclic competitions.

PubMed

Cheng, Hongyan; Yao, Nan; Huang, Zi-Gang; Park, Junpyo; Do, Younghae; Lai, Ying-Cheng

2014-12-15

Evolutionary dynamical models for cyclic competitions of three species (e.g., rock, paper, and scissors, or RPS) provide a paradigm, at the microscopic level of individual interactions, to address many issues in coexistence and biodiversity. Real ecosystems often involve competitions among more than three species. By extending the RPS game model to five (rock-paper-scissors-lizard-Spock, or RPSLS) mobile species, we uncover a fundamental type of mesoscopic interactions among subgroups of species. In particular, competitions at the microscopic level lead to the emergence of various local groups in different regions of the space, each involving three species. It is the interactions among the groups that fundamentally determine how many species can coexist. In fact, as the mobility is increased from zero, two transitions can occur: one from a five- to a three-species coexistence state and another from the latter to a uniform, single-species state. We develop a mean-field theory to show that, in order to understand the first transition, group interactions at the mesoscopic scale must be taken into account. Our findings suggest, more broadly, the importance of mesoscopic interactions in coexistence of great many species.

Phase transitions in models of human cooperation

NASA Astrophysics Data System (ADS)

Perc, Matjaž

2016-08-01

If only the fittest survive, why should one cooperate? Why should one sacrifice personal benefits for the common good? Recent research indicates that a comprehensive answer to such questions requires that we look beyond the individual and focus on the collective behavior that emerges as a result of the interactions among individuals, groups, and societies. Although undoubtedly driven also by culture and cognition, human cooperation is just as well an emergent, collective phenomenon in a complex system. Nonequilibrium statistical physics, in particular the collective behavior of interacting particles near phase transitions, has already been recognized as very valuable for understanding counterintuitive evolutionary outcomes. However, unlike pairwise interactions among particles that typically govern solid-state physics systems, interactions among humans often involve group interactions, and they also involve a larger number of possible states even for the most simplified description of reality. Here we briefly review research done in the realm of the public goods game, and we outline future research directions with an emphasis on merging the most recent advances in the social sciences with methods of nonequilibrium statistical physics. By having a firm theoretical grip on human cooperation, we can hope to engineer better social systems and develop more efficient policies for a sustainable and better future.

Fast-kick-off monotonically convergent algorithm for searching optimal control fields

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

Liao, Sheng-Lun; Ho, Tak-San; Rabitz, Herschel

2011-09-15

This Rapid Communication presents a fast-kick-off search algorithm for quickly finding optimal control fields in the state-to-state transition probability control problems, especially those with poorly chosen initial control fields. The algorithm is based on a recently formulated monotonically convergent scheme [T.-S. Ho and H. Rabitz, Phys. Rev. E 82, 026703 (2010)]. Specifically, the local temporal refinement of the control field at each iteration is weighted by a fractional inverse power of the instantaneous overlap of the backward-propagating wave function, associated with the target state and the control field from the previous iteration, and the forward-propagating wave function, associated with themore » initial state and the concurrently refining control field. Extensive numerical simulations for controls of vibrational transitions and ultrafast electron tunneling show that the new algorithm not only greatly improves the search efficiency but also is able to attain good monotonic convergence quality when further frequency constraints are required. The algorithm is particularly effective when the corresponding control dynamics involves a large number of energy levels or ultrashort control pulses.« less

State-of-the-art thermochemical and kinetic computations for astrochemical complex organic molecules: formamide formation in cold interstellar clouds as a case study

PubMed Central

Vazart, Fanny; Calderini, Danilo; Puzzarini, Cristina; Skouteris, Dimitrios

2017-01-01

We propose an integrated computational strategy aimed at providing reliable thermochemical and kinetic information on the formation processes of astrochemical complex organic molecules. The approach involves state-of-the-art quantum-mechanical computations, second-order vibrational perturbation theory, and kinetic models based on capture and transition state theory together with the master equation approach. Notably, tunneling, quantum reflection, and leading anharmonic contributions are accounted for in our model. Formamide has been selected as a case study in view of its interest as a precursor in the abiotic amino acid synthesis. After validation of the level of theory chosen for describing the potential energy surface, we have investigated several pathways of the OH+CH2NH and NH2+HCHO reaction channels. Our results indicate that both reaction channels are essentially barrier-less (in the sense that all relevant transition states lie below or only marginally above the reactants) and can, therefore, occur under the low temperature conditions of interstellar objects provided that tunneling is taken into the proper account. PMID:27689448

Transition and mixing in axisymmetric jets and vortex rings

NASA Technical Reports Server (NTRS)

Allen, G. A., Jr.; Cantwell, B. J.

1986-01-01

A class of impulsively started, axisymmetric, laminar jets produced by a time dependent joint source of momentum are considered. These jets are different flows, each initially at rest in an unbounded fluid. The study is conducted at three levels of detail. First, a generalized set of analytic creeping flow solutions are derived with a method of flow classification. Second, from this set, three specific creeping flow solutions are studied in detail: the vortex ring, the round jet, and the ramp jet. This study involves derivation of vorticity, stream function, entrainment diagrams, and evolution of time lines through computer animation. From entrainment diagrams, critical points are derived and analyzed. The flow geometry is dictated by the properties and location of critical points which undergo bifurcation and topological transformation (a form of transition) with changing Reynolds number. Transition Reynolds numbers were calculated. A state space trajectory was derived describing the topological behavior of these critical points. This state space derivation yielded three states of motion which are universal for all axisymmetric jets. Third, the axisymmetric round jet is solved numerically using the unsteady laminar Navier Stokes equations. These equations were shown to be self similar for the round jet. Numerical calculations were performed up to a Reynolds number of 30 for a 60x60 point mesh. Animations generated from numerical solution showed each of the three states of motion for the round jet, including the Re = 30 case.

Change in resonance parameters of a linear molecule as it bends: Evidence in electron-impact vibrational transitions of hot COS and CO2 molecules*

NASA Astrophysics Data System (ADS)

Hoshino, Masamitsu; Ishijima, Yohei; Kato, Hidetoshi; Mogi, Daisuke; Takahashi, Yoshinao; Fukae, Katsuya; Limão-Vieira, Paulo; Tanaka, Hiroshi; Shimamura, Isao

2016-04-01

Inelastic and superelastic electron-impact vibrational excitation functions of hot carbonyl sulphide COS (and hot CO2) are measured for electron energies from 0.5 to 3.0 eV (1.5 to 6.0 eV) and at a scattering angle of 90°. Based on the vibrational populations and the principle of detailed balance, these excitation functions are decomposed into contributions from state-to-state vibrational transitions involving up to the second bending overtone (030) in the electronically ground state. Both the 2Π resonance for COS around 1.2 eV and the 2Πu resonance for CO2 around 3.8 eV are shifted to lower energies as the initial vibrational state is excited in the bending mode. The width of the resonance hump for COS changes only little as the molecule bends, whereas that of the overall boomerang resonance for CO2 becomes narrower. The angular distribution of the electrons resonantly scattered by hot COS and hot CO2 is also measured. The different shapes depending on the vibrational transitions and gas temperatures are discussed in terms of the symmetry of the vibrational wave functions. Contribution to the Topical Issue "Advances in Positron and Electron Scattering", edited by Paulo Limao-Vieira, Gustavo Garcia, E. Krishnakumar, James Sullivan, Hajime Tanuma and Zoran Petrovic.

Nematic order on the surface of a three-dimensional topological insulator

NASA Astrophysics Data System (ADS)

Lundgren, Rex; Yerzhakov, Hennadii; Maciejko, Joseph

2017-12-01

We study the spontaneous breaking of rotational symmetry in the helical surface state of three-dimensional topological insulators due to strong electron-electron interactions, focusing on time-reversal invariant nematic order. Owing to the strongly spin-orbit coupled nature of the surface state, the nematic order parameter is linear in the electron momentum and necessarily involves the electron spin, in contrast with spin-degenerate nematic Fermi liquids. For a chemical potential at the Dirac point (zero doping), we find a first-order phase transition at zero temperature between isotropic and nematic Dirac semimetals. This extends to a thermal phase transition that changes from first to second order at a finite-temperature tricritical point. At finite doping, we find a transition between isotropic and nematic helical Fermi liquids that is second order even at zero temperature. Focusing on finite doping, we discuss various observable consequences of nematic order, such as anisotropies in transport and the spin susceptibility, the partial breakdown of spin-momentum locking, collective modes and induced spin fluctuations, and non-Fermi-liquid behavior at the quantum critical point and in the nematic phase.

Axelrod Model of Social Influence with Cultural Hybridization

NASA Astrophysics Data System (ADS)

Radillo-Díaz, Alejandro; Pérez, Luis A.; Del Castillo-Mussot, Marcelo

2012-10-01

Since cultural interactions between a pair of social agents involve changes in both individuals, we present simulations of a new model based on Axelrod's homogenization mechanism that includes hybridization or mixture of the agents' features. In this new hybridization model, once a cultural feature of a pair of agents has been chosen for the interaction, the average of the values for this feature is reassigned as the new value for both agents after interaction. Moreover, a parameter representing social tolerance is implemented in order to quantify whether agents are similar enough to engage in interaction, as well as to determine whether they belong to the same cluster of similar agents after the system has reached the frozen state. The transitions from a homogeneous state to a fragmented one decrease in abruptness as tolerance is increased. Additionally, the entropy associated to the system presents a maximum within the transition, the width of which increases as tolerance does. Moreover, a plateau was found inside the transition for a low-tolerance system of agents with only two cultural features.

Desynchronization of chaos in coupled logistic maps.

PubMed

Maistrenko, Y L; Maistrenko, V L; Popovych, O; Mosekilde, E

1999-09-01

When identical chaotic oscillators interact, a state of complete or partial synchronization may be attained in which the motion is restricted to an invariant manifold of lower dimension than the full phase space. Riddling of the basin of attraction arises when particular orbits embedded in the synchronized chaotic state become transversely unstable while the state remains attracting on the average. Considering a system of two coupled logistic maps, we show that the transition to riddling will be soft or hard, depending on whether the first orbit to lose its transverse stability undergoes a supercritical or subcritical bifurcation. A subcritical bifurcation can lead directly to global riddling of the basin of attraction for the synchronized chaotic state. A supercritical bifurcation, on the other hand, is associated with the formation of a so-called mixed absorbing area that stretches along the synchronized chaotic state, and from which trajectories cannot escape. This gives rise to locally riddled basins of attraction. We present three different scenarios for the onset of riddling and for the subsequent transformations of the basins of attraction. Each scenario is described by following the type and location of the relevant asynchronous cycles, and determining their stable and unstable invariant manifolds. One scenario involves a contact bifurcation between the boundary of the basin of attraction and the absorbing area. Another scenario involves a long and interesting series of bifurcations starting with the stabilization of the asynchronous cycle produced in the riddling bifurcation and ending in a boundary crisis where the stability of an asynchronous chaotic state is destroyed. Finally, a phase diagram is presented to illustrate the parameter values at which the various transitions occur.

High-resolution infrared studies of the v 10, v 11, v 14, and v 18 levels of [1.1.1]propellane

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

Kirkpatrick, Robynne W.; Masiello, Tony; Martin, Matthew A.

2012-11-15

This paper is a continuation of earlier work for which the high resolution infrared spectrum of [1.1.1]propellane was measured and its k and l structure resolved for the first time. Here we present results from an analysis of more than 16,000 transitions involving three fundamental bands v 10 (E'-A1'), v 11 (E'-A1'), v 14 (A2''-A1') and two difference bands (v 10- v 18) (E'-E'') and (v 11-v 18) (E'-E"). Additional information about v18 was also obtained from the difference band (v 15+v 18)-v 18 (E'-E") and the binary combination band (v 15+v 18) (E'-A1'). Through the use of the groundmore » state constants reported in an earlier paper [1], rovibrational constants have been determined for all the vibrational states involved in these bands. The rovibrational parameters for the v 18(E'') state were obtained from combination-differences and showed no need to include interactions with other states. The v 10(E') state analysis was also straight-forward, with only a weak Coriolis interaction with the levels of the v 14(A2'') state. The latter levels are much more affected by a strong Coriolis interaction with the levels of the nearby v 11(E') state and also by a small but significant interaction with another state, presumably the v16(E'') state, that is not directly observed. Gaussian calculations (B3LYP/cc-pVTZ) computed at the anharmonic level aided the analyses by providing initial values for many of the parameters. These theoretical results generally compare favorably with the final parameter values deduced from the spectral analyses. Finally, evidence was obtained for several level crossings between the rotational levels of the v 11 and v 14 states and, using a weak coupling term corresponding to a Δk = ±5, Δl = ∓1 matrix element, it was possible to find transitions from the ground state that, combined with transitions to the same upper state, give a value of C 0 = 0.1936519(4) cm -1. This result, combined with the value of B 0 = 0.28755833(14) cm-1 reported earlier [1], yields a value of 1.586282(3) Å for the length of the novel axial CC bond in propellane.« less

Modern medical practice: a profession in transition.

PubMed

Merry, M D

1984-05-01

Modern medical practice is in a state of transition. The solo practitioner is slowly giving way to the large organized groups of health care providers. Driving this force of change is a change in payment for health care services from cost plus to preestablished pricing. For the first time, medical practice patterns are having a direct impact on the financial viability of the health care institution. To maintain quality of patient care and contain costs, more and more physicians are becoming involved in the administrative side of running a hospital. This article describes the forces of change, the change itself, and the future of medicine.

Radiative Transitions in Charmonium from Lattice QCD

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

Jozef Dudek; Robert Edwards; David Richards

2006-01-17

Radiative transitions between charmonium states offer an insight into the internal structure of heavy-quark bound states within QCD. We compute, for the first time within lattice QCD, the transition form-factors of various multipolarities between the lightest few charmonium states. In addition, we compute the experimentally unobservable, but physically interesting vector form-factors of the {eta}{sub c}, J/{psi} and {chi}{sub c0}. To this end we apply an ambitious combination of lattice techniques, computing three-point functions with heavy domain wall fermions on an anisotropic lattice within the quenched approximation. With an anisotropy {xi} = 3 at a{sub s} {approx} 0.1 fm we findmore » a reasonable gross spectrum and a hyperfine splitting {approx}90 MeV, which compares favorably with other improved actions. In general, after extrapolation of lattice data at non-zero Q{sup 2} to the photopoint, our results agree within errors with all well measured experimental values. Furthermore, results are compared with the expectations of simple quark models where we find that many features are in agreement; beyond this we propose the possibility of constraining such models using our extracted values of physically unobservable quantities such as the J/{psi} quadrupole moment. We conclude that our methods are successful and propose to apply them to the problem of radiative transitions involving hybrid mesons, with the eventual goal of predicting hybrid meson photoproduction rates at the GlueX experiment.« less

Transient nature of late Pleistocene climate variability.

PubMed

Crowley, Thomas J; Hyde, William T

2008-11-13

Climate in the early Pleistocene varied with a period of 41 kyr and was related to variations in Earth's obliquity. About 900 kyr ago, variability increased and oscillated primarily at a period of approximately 100 kyr, suggesting that the link was then with the eccentricity of Earth's orbit. This transition has often been attributed to a nonlinear response to small changes in external boundary conditions. Here we propose that increasing variablility within the past million years may indicate that the climate system was approaching a second climate bifurcation point, after which it would transition again to a new stable state characterized by permanent mid-latitude Northern Hemisphere glaciation. From this perspective the past million years can be viewed as a transient interval in the evolution of Earth's climate. We support our hypothesis using a coupled energy-balance/ice-sheet model, which furthermore predicts that the future transition would involve a large expansion of the Eurasian ice sheet. The process responsible for the abrupt change seems to be the albedo discontinuity at the snow-ice edge. The best-fit model run, which explains almost 60% of the variance in global ice volume during the past 400 kyr, predicts a rapid transition in the geologically near future to the proposed glacial state. Should it be attained, this state would be more 'symmetric' than the present climate, with comparable areas of ice/sea-ice cover in each hemisphere, and would represent the culmination of 50 million years of evolution from bipolar nonglacial climates to bipolar glacial climates.

Single-molecule studies highlight conformational heterogeneity in the early folding steps of a large ribozyme

PubMed Central

Xie, Zheng; Srividya, Narayanan; Sosnick, Tobin R.; Pan, Tao; Scherer, Norbert F.

2004-01-01

The equilibrium folding of the catalytic domain of Bacillus subtilis RNase P RNA is investigated by single-molecule fluorescence resonance energy transfer (FRET). Previous ensemble studies of this 255-nucleotide ribozyme described the equilibrium folding with two transitions, U-to-Ieq-to-N, and focused on the Ieq-to-N transition. The present study focuses on the U-to-Ieq transition. Comparative ensemble measurements of the ribozyme construct labeled with fluorescein at the 5′ end and Cy3 at the 3′ end show that modifications required for labeling do not interfere with folding and help to define the Mg2+ concentration range for the U-to-Ieq transition. Histogram analysis of the Mg2+-dependent single-molecule FRET efficiency reveals two previously undetermined folding intermediates. The single-molecule FRET trajectories exhibit non-two-state and nonergodic behaviors at intermediate Mg2+ concentrations on the time scale of seconds. The trajectories at intermediate Mg2+ concentrations are classified into five classes based on three FRET levels and their dynamics of interconversion within the measured time range. This heterogeneity, together with the observation of “nonsudden jump” FRET transitions, indicates that the early folding steps of this ribozyme involve a series of intermediates with different degrees of kinetic isolation and that folding occurs under kinetic control and involves many “local” conformational switches. A free energy contour is constructed to illustrate the complex folding surface. PMID:14704266

Design of UV laser pulses for the preparation of matrix isolated homonuclear diatomic molecules in selective vibrational superposition states.

PubMed

Korolkov, M V; Manz, J

2007-05-07

The preparation of matrix isolated homonuclear diatomic molecules in a vibrational superposition state c0Phie=1,v=0+cjPhie=1,v=j, with large (|c0|2 approximately 1) plus small contributions (|cj|2<1) of the ground v=0 and specific v=j low excited vibrational eigenstates, respectively, in the electronic ground (e=1) state, and without any net population transfer to electronic excited (e>1) states, is an important challenge; it serves as a prerequisite for coherent spin control. For this purpose, the authors investigate two scenarios of laser pulse control, involving sequential or intrapulse pump- and dump-type transitions via excited vibronic states Phiex,k with a dominant singlet or triplet character. The mechanisms are demonstrated by means of quantum simulations for representative nuclear wave packets on coupled potential energy surfaces, using as an example a one-dimensional model for Cl2 in an Ar matrix. A simple three-state model (including Phi1,0, Phi1,j and Phiex,k) allows illuminating analyses and efficient determinations of the parameters of the laser pulses based on the values of the transition energies and dipole couplings of the transient state which are derived from the absorption spectra.

Stark effect and dipole moments of the ammonia dimer in different vibration-rotation-tunneling states

NASA Astrophysics Data System (ADS)

Cotti, Gina; Linnartz, Harold; Meerts, W. Leo; van der Avoird, Ad; Olthof, Edgar H. T.

1996-03-01

In this paper we present Stark measurements on the G:K=-1 vibration-rotation-tunneling (VRT) transition, band origin 747.2 GHz, of the ammonia dimer. The observed splitting pattern and selection rules can be explained by considering the G36 and G144 symmetries of the inversion states involved, and almost complete mixing of these states by the applied electric field. The absolute values of the electric dipole moments of the ground and excited state are determined to be 0.763(15) and 0.365(10) D, respectively. From the theoretical analysis and the observed selection rules it is possible to establish that the dipole moments of the two interchange states must have opposite sign. The theoretical calculations are in good agreement with the experimental results: The calculated dipole moments are -0.74 D for the lower and +0.35 D for the higher state. Our results, in combination with the earlier dipole measurements on the G:K=0 ground state and the G:K=1 transition with band origin 486.8 GHz, confirm that the ammonia dimer is highly nonrigid. Its relatively small and strongly K-dependent dipole moment, which changes sign upon far-infrared excitation, originates from the difference in dynamical behavior of ortho and para NH3.

The Ecological Rise of Whales Chronicled by the Fossil Record.

PubMed

Pyenson, Nicholas D

2017-06-05

The evolution of cetaceans is one of the best examples of macroevolution documented from the fossil record. While ecological transitions dominate each phase of cetacean history, this context is rarely stated explicitly. The first major ecological phase involves a transition from riverine and deltaic environments to marine ones, concomitant with dramatic evolutionary transformations documented in their early fossil record. The second major phase involves ecological shifts associated with evolutionary innovations: echolocation (facilitating hunting prey at depth) and filter-feeding (enhancing foraging efficiency on small prey). This latter phase involves body size shifts, attributable to changes in foraging depth and environmental forcing, as well as re-invasions of freshwater systems on continental basins by multiple lineages. Modern phenomena driving cetacean ecology, such as trophic dynamics and arms races, have an evolutionary basis that remains mostly unexamined. The fossil record of cetaceans provides an historical basis for understanding current ecological mechanisms and consequences, especially as global climate change rapidly alters ocean and river ecosystems at rates and scales comparable to those over geologic time. Published by Elsevier Ltd.

Discovering Conformational Sub-States Relevant to Protein Function

PubMed Central

Ramanathan, Arvind; Savol, Andrej J.; Langmead, Christopher J.; Agarwal, Pratul K.; Chennubhotla, Chakra S.

2011-01-01

Background Internal motions enable proteins to explore a range of conformations, even in the vicinity of native state. The role of conformational fluctuations in the designated function of a protein is widely debated. Emerging evidence suggests that sub-groups within the range of conformations (or sub-states) contain properties that may be functionally relevant. However, low populations in these sub-states and the transient nature of conformational transitions between these sub-states present significant challenges for their identification and characterization. Methods and Findings To overcome these challenges we have developed a new computational technique, quasi-anharmonic analysis (QAA). QAA utilizes higher-order statistics of protein motions to identify sub-states in the conformational landscape. Further, the focus on anharmonicity allows identification of conformational fluctuations that enable transitions between sub-states. QAA applied to equilibrium simulations of human ubiquitin and T4 lysozyme reveals functionally relevant sub-states and protein motions involved in molecular recognition. In combination with a reaction pathway sampling method, QAA characterizes conformational sub-states associated with cis/trans peptidyl-prolyl isomerization catalyzed by the enzyme cyclophilin A. In these three proteins, QAA allows identification of conformational sub-states, with critical structural and dynamical features relevant to protein function. Conclusions Overall, QAA provides a novel framework to intuitively understand the biophysical basis of conformational diversity and its relevance to protein function. PMID:21297978

Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis.

PubMed

Yoon, Hanwool; Warshel, Arieh

2017-08-01

Pol η belongs to the important Y family of DNA polymerases that can catalyze translesion synthesis across sites of damaged DNA. This activity involves the reduced fidelity of Pol η for 8-oxo-7,8-dhyedro-2'-deoxoguanosin(8-oxoG). The fundamental interest in Pol η has grown recently with the demonstration of the importance of a 3rd Mg2+ ion. The current work explores both the fidelity of Pol η and the role of the 3rd metal ion, by using empirical valence bond (EVB) simulations. The simulations reproduce the observed trend in fidelity and shed a new light on the role of the 3rd metal ion. It is found that this ion does not lead to a major catalytic effect, but most probably plays an important role in reducing the product release barrier. Furthermore, it is concluded, in contrast to some implications, that the effect of this metal does not violate transition state theory, and the evaluation of the catalytic effect must conserve the molecular composition upon moving from the reactant to the transition state. Proteins 2017; 85:1446-1453. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

State-and-transition models: Conceptual versus simulation perspectives, usefulness and breadth of use, and land management applications

USGS Publications Warehouse

Provencher, Louis; Frid, Leonardo; Czembor, Christina; Morisette, Jeffrey T.

2016-01-01

State-and-Transition Simulation Modeling (STSM) is a quantitative analysis method that can consolidate a wide array of resource management issues under a “what-if” scenario exercise. STSM can be seen as an ensemble of models, such as climate models, ecological models, and economic models that incorporate human dimensions and management options. This chapter presents STSM as a tool to help synthesize information on social–ecological systems and to investigate some of the management issues associated with exotic annual Bromus species, which have been described elsewhere in this book. Definitions, terminology, and perspectives on conceptual and computer-simulated stochastic state-and-transition models are given first, followed by a brief review of past STSM studies relevant to the management of Bromus species. A detailed case study illustrates the usefulness of STSM for land management. As a whole, this chapter is intended to demonstrate how STSM can help both managers and scientists: (a) determine efficient resource allocation for monitoring nonnative grasses; (b) evaluate sources of uncertainty in model simulation results involving expert opinion, and their consequences for management decisions; and (c) provide insight into the consequences of predicted local climate change effects on ecological systems invaded by exotic annual Bromus species.

Cooperative folding of a polytopic α-helical membrane protein involves a compact N-terminal nucleus and nonnative loops

PubMed Central

Paslawski, Wojciech; Lillelund, Ove K.; Kristensen, Julie Veje; Schafer, Nicholas P.; Baker, Rosanna P.; Urban, Sinisa; Otzen, Daniel E.

2015-01-01

Despite the ubiquity of helical membrane proteins in nature and their pharmacological importance, the mechanisms guiding their folding remain unclear. We performed kinetic folding and unfolding experiments on 69 mutants (engineered every 2–3 residues throughout the 178-residue transmembrane domain) of GlpG, a membrane-embedded rhomboid protease from Escherichia coli. The only clustering of significantly positive ϕ-values occurs at the cytosolic termini of transmembrane helices 1 and 2, which we identify as a compact nucleus. The three loops flanking these helices show a preponderance of negative ϕ-values, which are sometimes taken to be indicative of nonnative interactions in the transition state. Mutations in transmembrane helices 3–6 yielded predominantly ϕ-values near zero, indicating that this part of the protein has denatured-state–level structure in the transition state. We propose that loops 1–3 undergo conformational rearrangements to position the folding nucleus correctly, which then drives folding of the rest of the domain. A compact N-terminal nucleus is consistent with the vectorial nature of cotranslational membrane insertion found in vivo. The origin of the interactions in the transition state that lead to a large number of negative ϕ-values remains to be elucidated. PMID:26056273

Dissociation of Calcium Transients and Force Development following a Change in Stimulation Frequency in Isolated Rabbit Myocardium.

PubMed

Haizlip, Kaylan M; Milani-Nejad, Nima; Brunello, Lucia; Varian, Kenneth D; Slabaugh, Jessica L; Walton, Shane D; Gyorke, Sandor; Davis, Jonathan P; Biesiadecki, Brandon J; Janssen, Paul M L

2015-01-01

As the heart transitions from one exercise intensity to another, changes in cardiac output occur, which are modulated by alterations in force development and calcium handling. Although the steady-state force-calcium relationship at various heart rates is well investigated, regulation of these processes during transitions in heart rate is poorly understood. In isolated right ventricular muscle preparations from the rabbit, we investigated the beat-to-beat alterations in force and calcium during the transition from one stimulation frequency to another, using contractile assessments and confocal microscopy. We show that a change in steady-state conditions occurs in multiple phases: a rapid phase, which is characterized by a fast change in force production mirrored by a change in calcium transient amplitude, and a slow phase, which follows the rapid phase and occurs as the muscle proceeds to stabilize at the new frequency. This second/late phase is characterized by a quantitative dissociation between the calcium transient amplitude and developed force. Twitch timing kinetics, such as time to peak tension and 50% relaxation rate, reached steady-state well before force development and calcium transient amplitude. The dynamic relationship between force and calcium upon a switch in stimulation frequency unveils the dynamic involvement of myofilament-based properties in frequency-dependent activation.

Analysis of the A ∼ - X ∼ bands of the ethynyl radical near 1.48 μ m and re-evaluation of X ∼ state energies

NASA Astrophysics Data System (ADS)

Le, A. T.; Gross, Eisen C.; Hall, Gregory E.; Sears, Trevor J.

2018-07-01

We report the observation and analysis of spectra in part of the near-infrared spectrum of C2H, originating in rotational levels in the ground and lowest two excited bending vibrational levels of the ground X ˜ 2Σ+ state. In the analysis, we have combined present and previously reported high resolution spectroscopic data for the lower levels involved in the transitions to determine significantly improved molecular constants to describe the fine and hyperfine split rotational levels of the radical in the zero point, v2 = 1 and the 2Σ+ component of v2 = 2 . Two of the upper state vibronic levels involved had not been observed previously. The data and analysis indicate the electronic wavefunction character changes with bending vibrational excitation in the ground state and provide avenues for future measurements of reactivity of the radical as a function of vibrational excitation.

Analysis of the $$\\tilde{A}$$ - $$\\tilde{X}$$ bands of the Ethynyl Radical near 1.48 μ-m and Re-evaluation of ~X State Energies

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

Le, A T.; Gross, Eisen C.; Hall, Gregory E.

Here, we report the observation and analysis of spectra in part of the near-infrared spectrum of C 2H, originating in rotational levels in the ground and lowest two excited bending vibrational levels of the groundmore » $$\\tilde{X}$$ 2Σ+ state. In the analysis, we have combined present and previously reported high resolution spectroscopic data for the lower levels involved in the transitions to determine significantly improved molecular constants to describe the fine and hyperfine split rotational levels of the radical in the zero point, v 2 = 1 and the 2Σ+ component of v 2 = 2. Two of the upper state vibronic levels involved had not been observed previously. The data and analysis indicate the electronic wavefunction character changes with bending vibrational excitation in the ground state and provide avenues for future measurements of reactivity of the radical as a function of vibrational excitation.« less

Surface hopping with a manifold of electronic states. I. Incorporating surface-leaking to capture lifetimes

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

Ouyang, Wenjun; Dou, Wenjie; Subotnik, Joseph E., E-mail: subotnik@sas.upenn.edu

2015-02-28

We investigate the incorporation of the surface-leaking (SL) algorithm into Tully’s fewest-switches surface hopping (FSSH) algorithm to simulate some electronic relaxation induced by an electronic bath in conjunction with some electronic transitions between discrete states. The resulting SL-FSSH algorithm is benchmarked against exact quantum scattering calculations for three one-dimensional model problems. The results show excellent agreement between SL-FSSH and exact quantum dynamics in the wide band limit, suggesting the potential for a SL-FSSH algorithm. Discrepancies and failures are investigated in detail to understand the factors that will limit the reliability of SL-FSSH, especially the wide band approximation. Considering the easinessmore » of implementation and the low computational cost, we expect this method to be useful in studying processes involving both a continuum of electronic states (where electronic dynamics are probabilistic) and processes involving only a few electronic states (where non-adiabatic processes cannot ignore short-time coherence)« less

Analysis of the $$\\tilde{A}$$ - $$\\tilde{X}$$ bands of the Ethynyl Radical near 1.48 μ-m and Re-evaluation of ~X State Energies

DOE PAGES

Le, A T.; Gross, Eisen C.; Hall, Gregory E.; ...

2018-05-15

Here, we report the observation and analysis of spectra in part of the near-infrared spectrum of C 2H, originating in rotational levels in the ground and lowest two excited bending vibrational levels of the groundmore » $$\\tilde{X}$$ 2Σ+ state. In the analysis, we have combined present and previously reported high resolution spectroscopic data for the lower levels involved in the transitions to determine significantly improved molecular constants to describe the fine and hyperfine split rotational levels of the radical in the zero point, v 2 = 1 and the 2Σ+ component of v 2 = 2. Two of the upper state vibronic levels involved had not been observed previously. The data and analysis indicate the electronic wavefunction character changes with bending vibrational excitation in the ground state and provide avenues for future measurements of reactivity of the radical as a function of vibrational excitation.« less

Investigation of a Structural Phase Transition and Magnetic Structure of Na 2BaFe(VO 4) 2: A Triangular Magnetic Lattice with a Ferromagnetic Ground State

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

Sanjeewa, Liurukara D.; Garlea, Vasile O.; McGuire, Michael A.

The structural and magnetic properties of a glaserite-type Na 2BaFe(VO 4) 2 compound, featuring a triangular magnetic lattice of Fe 2+ (S = 2), are reported. Temperature dependent X-ray single crystal studies indicate that at room temperature the system adopts a trigonal Pmore » $$\\bar{3}$$ m1 structure and undergoes a structural phase transition to a C2/c monoclinic phase slightly below room temperature (T s = 288 K). This structural transition involves a tilting of Fe–O–V bond angles and strongly influences the magnetic correlation within the Fe triangular lattice. The magnetic susceptibility measurements reveal a ferromagnetic transition near 7 K. Single crystal neutron diffraction confirms the structural distortion and the ferromagnetic spin ordering in Na 2BaFe(VO 4) 2. The magnetic structure of the ordered state is modeled in the magnetic space group C2'/c' that implies a ferromagnetic order of the a and c moment components and antiferromagnetic arrangement for the b components. Altogether, the Fe magnetic moments form ferromagnetic layers that are stacked along the c-axis, where the spins point along one of the (111) facets of the FeO 6 octahedron.« less

Investigation of a Structural Phase Transition and Magnetic Structure of Na 2BaFe(VO 4) 2: A Triangular Magnetic Lattice with a Ferromagnetic Ground State

DOE PAGES

Sanjeewa, Liurukara D.; Garlea, Vasile O.; McGuire, Michael A.; ...

2017-12-07

The structural and magnetic properties of a glaserite-type Na 2BaFe(VO 4) 2 compound, featuring a triangular magnetic lattice of Fe 2+ (S = 2), are reported. Temperature dependent X-ray single crystal studies indicate that at room temperature the system adopts a trigonal Pmore » $$\\bar{3}$$ m1 structure and undergoes a structural phase transition to a C2/c monoclinic phase slightly below room temperature (T s = 288 K). This structural transition involves a tilting of Fe–O–V bond angles and strongly influences the magnetic correlation within the Fe triangular lattice. The magnetic susceptibility measurements reveal a ferromagnetic transition near 7 K. Single crystal neutron diffraction confirms the structural distortion and the ferromagnetic spin ordering in Na 2BaFe(VO 4) 2. The magnetic structure of the ordered state is modeled in the magnetic space group C2'/c' that implies a ferromagnetic order of the a and c moment components and antiferromagnetic arrangement for the b components. Altogether, the Fe magnetic moments form ferromagnetic layers that are stacked along the c-axis, where the spins point along one of the (111) facets of the FeO 6 octahedron.« less

Experimental tests of factorization in charmless nonleptonic two-body B decays

NASA Astrophysics Data System (ADS)

Ali, A.; Kramer, G.; Lü, Cai-Dian

1998-11-01

Using a theoretical framework based on the next-to-leading-order QCD-improved effective Hamiltonian and a factorization ansatz for the hadronic matrix elements of the four-quark operators, we reassess branching fractions in two-body nonleptonic decays B-->PP,PV,VV, involving the lowest-lying light pseudoscalar (P) and vector (V) mesons in the standard model. We work out the parametric dependence of the decay rates, making use of the currently available information on the weak mixing matrix elements, form factors, decay constants, and quark masses. Using the sensitivity of the decay rates on the effective number of colors, Nc, as a criterion of theoretical predictivity, we classify all the current-current (tree) and penguin transitions in five different classes. The recently measured charmless two-body B-->PP decays (B+-->K+η', B0-->K0η', B0-->K+π-, B+-->π+K0, and charge conjugates) are dominated by the Nc-stable QCD penguin transitions (class-IV transitions) and their estimates are consistent with the data. The measured charmless B-->PV (B+-->ωK+, B+-->ωh+) and B-->VV transition (B-->φK*), on the other hand, belong to the penguin (class-V) and tree (class-III) transitions. The class-V penguin transitions are Nc sensitive and/or involve large cancellations among competing amplitudes, making their decay rates in general more difficult to predict. Some of these transitions may also receive significant contributions from annihilation and/or final state interactions. We propose a number of tests of the factorization framework in terms of the ratios of branching ratios for some selected B-->h1h2 decays involving light hadrons h1 and h2, which depend only moderately on the form factors. We also propose a set of measurements to determine the effective coefficients of the current-current and QCD penguin operators. The potential impact of B-->h1h2 decays on the CKM phenomenology is emphasized by analyzing a number of decay rates in the factorization framework.

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 significantly for the pathway analysis.

A DFT study of permanganate oxidation of toluene and its ortho-nitroderivatives.

PubMed

Adamczyk, Paweł; Wijker, Reto S; Hofstetter, Thomas B; Paneth, Piotr

2014-02-01

Calculations of alternative oxidation pathways of toluene and its ortho-substituted nitro derivatives by permanganate anion have been performed. The competition between methyl group and ring oxidation has been addressed. Acceptable results have been obtained using IEFPCM/B3LYP/6-31+G(d,p) calculations with zero-point (ZPC) and thermal corrections, as validated by comparison with the experimental data. It has been shown that ring oxidation reactions proceed via relatively early transition states that become quite unsymmetrical for reactions involving ortho-nitrosubstituted derivatives. Transition states for the hydrogen atom abstraction reactions, on the other hand, are late. All favored reactions are characterized by the Gibbs free energy of activation, ΔG(≠), of about 25 kcal mol(-1). Methyl group oxidations are exothermic by about 20 kcal mol(-1) while ring oxidations are around thermoneutrality.

Relativistic, model-independent, multichannel 2 → 2 transition amplitudes in a finite volume

DOE PAGES

Briceno, Raul A.; Hansen, Maxwell T.

2016-07-13

We derive formalism for determining 2 + J → 2 infinite-volume transition amplitudes from finite-volume matrix elements. Specifically, we present a relativistic, model-independent relation between finite-volume matrix elements of external currents and the physically observable infinite-volume matrix elements involving two-particle asymptotic states. The result presented holds for states composed of two scalar bosons. These can be identical or non-identical and, in the latter case, can be either degenerate or non-degenerate. We further accommodate any number of strongly-coupled two-scalar channels. This formalism will, for example, allow future lattice QCD calculations of themore » $$\\rho$$-meson form factor, in which the unstable nature of the $$\\rho$$ is rigorously accommodated. In conclusion, we also discuss how this work will impact future extractions of nuclear parity and hadronic long-range matrix elements from lattice QCD.« less

Identification and properties of molecular systems of potential use in solar-pumped lasers

NASA Technical Reports Server (NTRS)

Micha, D. A.; Oehrn, N. Y.

1985-01-01

The concepts and computational tools of theortical chemistry are used to investigate molecular properties needed in direct solar-pumped lasers. Compounds of the type RR'CXY, with R and R' organic groups, and X and Y halide atoms were identified as likely candidates because of their highly enhanced absorption coefficients over compounds with a single halide atom. The use of a combination of vibrational excitation followed by electronic excitation to enhance quantum yields at certain wavelengths is indicated. A self-consistent eikonal approximation to state-to-state transitions was tested for CH3I and is useful for other problems involving electronic energy and charge transfer. An approach to calculate potential energy surfaces and transition dipoles was developed which is based on the generation of eigenstates of the nonrelativisitc Hamiltonian followed by incorporation of the spin-orbit coupling by configuration interaction.

Active site dynamics of ribonuclease.

PubMed Central

Brünger, A T; Brooks, C L; Karplus, M

1985-01-01

The stochastic boundary molecular dynamics method is used to study the structure, dynamics, and energetics of the solvated active site of bovine pancreatic ribonuclease A. Simulations of the native enzyme and of the enzyme complexed with the dinucleotide substrate CpA and the transition-state analog uridine vanadate are compared. Structural features and dynamical couplings for ribonuclease residues found in the simulation are consistent with experimental data. Water molecules, most of which are not observed in crystallographic studies, are shown to play an important role in the active site. Hydrogen bonding of residues with water molecules in the free enzyme is found to mimic the substrate-enzyme interactions of residues involved in binding. Networks of water stabilize the cluster of positively charged active site residues. Correlated fluctuations between the uridine vanadate complex and the distant lysine residues are mediated through water and may indicate a possible role for these residues in stabilizing the transition state. Images PMID:3866234

Rate processes in gas phase

NASA Technical Reports Server (NTRS)

Hansen, C. F.

1983-01-01

Reaction-rate theory and experiment are given a critical review from the engineers' point of view. Rates of heavy-particle, collision-induced reaction in gas phase are formulated in terms of the cross sections and activation energies for reaction. The effect of cross section function shape and of excited state contributions to reaction both cause the slope of Arrhenius plots to differ from the true activation energy, except at low temperature. The master equations for chemically reacting gases are introduced, and dissociation and ionization reactions are shown to proceed primarily from excited states about kT from the dissociation or ionization limit. Collision-induced vibration, vibration-rotation, and pure rotation transitions are treated, including three-dimensional effects and conservation of energy, which have usually been ignored. The quantum theory of transitions at potential surface crossing is derived, and results are found to be in fair agreement with experiment in spite of some questionable approximations involved.

β-decay half-life of V50 calculated by the shell model

NASA Astrophysics Data System (ADS)

Haaranen, M.; Srivastava, P. C.; Suhonen, J.; Zuber, K.

2014-10-01

In this work we survey the detectability of the β- channel of 2350V leading to the first excited 2+ state in 2450Cr. The electron-capture (EC) half-life corresponding to the transition of 2350V to the first excited 2+ state in 2250Ti had been measured earlier. Both of the mentioned transitions are 4th-forbidden non-unique. We have performed calculations of all the involved wave functions by using the nuclear shell model with the GXPF1A interaction in the full f-p shell. The computed half-life of the EC branch is in good agreement with the measured one. The predicted half-life for the β- branch is in the range ≈2×1019 yr whereas the present experimental lower limit is 1.5×1018 yr. We discuss also the experimental lay-out needed to detect the β--branch decay.

Role of impurities on the optical properties of rectangular graphene flakes

NASA Astrophysics Data System (ADS)

Sadeq, Z. S.; Muniz, Rodrigo A.; Sipe, J. E.

2018-01-01

We study rectangular graphene flakes using mean field states as the basis for a configuration interaction calculation, which allows us to analyze the low lying electronic excited states including electron correlations beyond the mean field level. We find that the lowest energy transition is polarized along the long axis of the flake, but the charge distributions involved in these transitions are invariably localized on the zigzag edges. We also investigate the impact of both short and long range impurity potentials on the optical properties of these systems. We predict that even a weak impurity localized at a zigzag edge of the flake can have a significant—and often dramatic—effect on its optical properties. This is in contrast to impurities localized at armchair edges or central regions of the flake, for which we predict almost no change to the optical properties of the flake even with strong impurity potentials.

Full dimensional Franck-Condon factors for the acetylene A{sup ~} {sup 1}A{sub u}—X{sup ~1}Σ{sub g}{sup +} transition. II. Vibrational overlap factors for levels involving excitation in ungerade modes

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

Park, G. Barratt, E-mail: barratt@mit.edu; Baraban, Joshua H.; Field, Robert W.

2014-10-07

A full-dimensional Franck-Condon calculation has been applied to the A{sup ~} {sup 1}A{sub u}—X{sup ~1}Σ{sub g}{sup +} transition in acetylene in the harmonic normal mode basis. Details of the calculation are discussed in Part I of this series. To our knowledge, this is the first full-dimensional Franck-Condon calculation on a tetra-atomic molecule undergoing a linear-to-bent geometry change. In the current work, the vibrational intensity factors for levels involving excitation in ungerade vibrational modes are evaluated. Because the Franck-Condon integral accumulates away from the linear geometry, we have been able to treat the out-of-plane component of trans bend (ν{sub 4}{sup ′′}) in themore » linear X{sup ~} state in the rotational part of the problem, restoring the χ Euler angle and the a-axis Eckart conditions. A consequence of the Eckart conditions is that the out-of-plane component of ν{sub 4}{sup ′′} does not participate in the vibrational overlap integral. This affects the structure of the coordinate transformation and the symmetry of the vibrational wavefunctions used in the overlap integral, and results in propensity rules involving the bending modes of the X{sup ~} state that were not previously understood. We explain the origin of some of the unexpected propensities observed in IR-UV laser-induced fluorescence spectra, and we calculate emission intensities from bending levels of the A{sup ~} state into bending levels of the X{sup ~} state, using normal bending mode and local bending mode basis sets. Our calculations also reveal Franck-Condon propensities for the Cartesian components of the cis bend (ν{sub 5}{sup ′′}), and we predict that the best A{sup ~}-state vibrational levels for populating X{sup ~}-state levels with large amplitude bending motion localized in a single C–H bond (the acetylene↔vinylidene isomerization coordinate) involve a high degree of excitation in ν{sub 6}{sup ′} (cis-bend). Mode ν{sub 4}{sup ′} (torsion) populates levels with large amplitude counter-rotational motion of the two hydrogen atoms.« less

Transient lattice contraction in the solid-to-plasma transition

PubMed Central

Ferguson, Ken R.; Bucher, Maximilian; Gorkhover, Tais; Boutet, Sébastien; Fukuzawa, Hironobu; Koglin, Jason E.; Kumagai, Yoshiaki; Lutman, Alberto; Marinelli, Agostino; Messerschmidt, Marc; Nagaya, Kiyonobu; Turner, Jim; Ueda, Kiyoshi; Williams, Garth J.; Bucksbaum, Philip H.; Bostedt, Christoph

2016-01-01

In condensed matter systems, strong optical excitations can induce phonon-driven processes that alter their mechanical properties. We report on a new phenomenon where a massive electronic excitation induces a collective change in the bond character that leads to transient lattice contraction. Single large van der Waals clusters were isochorically heated to a nanoplasma state with an intense 10-fs x-ray (pump) pulse. The structural evolution of the nanoplasma was probed with a second intense x-ray (probe) pulse, showing systematic contraction stemming from electron delocalization during the solid-to-plasma transition. These findings are relevant for any material in extreme conditions ranging from the time evolution of warm or hot dense matter to ultrafast imaging with intense x-ray pulses or, more generally, any situation that involves a condensed matter-to-plasma transition. PMID:27152323

Direct Proof of a Defect-Modulated Gap Transition in Semiconducting Nanotubes.

PubMed

Senga, Ryosuke; Pichler, Thomas; Yomogida, Yohei; Tanaka, Takeshi; Kataura, Hiromichi; Suenaga, Kazu

2018-06-13

Measurements of optical properties at a nanometer level are of central importance for the characterization of optoelectronic devices. It is, however, difficult to use conventional light-probe measurements to determine the local optical properties from a single quantum object with nanometrical inhomogeneity. Here, we successfully measured the optical gap transitions of an individual semiconducting carbon nanotube with defects by using a monochromated electron source as a probe. The optical conductivity extracted from an electron energy-loss spectrum for a certain type of defect presents a characteristic modification near the lowest excitation peak ( E 11 ), where excitons and nonradiative transitions, as well as phonon-coupled excitations, are strongly involved. Detailed line-shape analysis of the E 11 peak clearly shows different degrees of exciton lifetime shortening and electronic state modification according to the defect type.

Effect of circulating exosomes from transition cows on Madin-Darby bovine kidney cell function.

PubMed

Crookenden, M A; Walker, C G; Peiris, H; Koh, Y; Almughlliq, F; Vaswani, K; Reed, S; Heiser, A; Loor, J J; Kay, J K; Meier, S; Donkin, S S; Murray, A; Dukkipati, V S R; Roche, J R; Mitchell, M D

2017-07-01

The greatest risk of metabolic and infectious disease in dairy cows is during the transition from pregnancy to lactating (i.e., the transition period). The objective of this experiment was to determine the effects of extracellular vesicles (microvesicles involved in cell-to-cell signaling) isolated from transition cows on target cell function. We previously identified differences in the protein profiles of exosomes isolated from cows divergent in metabolic health status. Therefore, we hypothesized that these exosomes would affect target tissues differently. To investigate this, 2 groups of cows (n = 5/group) were selected based on the concentration of β-hydroxybutyrate and fatty acids in plasma and triacylglycerol concentration in liver at wk 1 and 2 postcalving. Cows with high concentrations of β-hydroxybutyrate, fatty acids, and triacylglycerol were considered at increased risk of clinical disease during the transition period (high-risk group; n = 5) and were compared with cows that had low concentrations of the selected health indicators (low-risk group; n = 5). At 2 time points during the transition period (postcalving at wk 1 and 4), blood was sampled and plasma exosomes were isolated from the high-risk and low-risk cows. The exosomes were applied at concentrations of 10 and 1 µg/mL to 5 × 10 3 Madin-Darby bovine kidney cells grown to 50% confluence in 96-well plates. Results indicate a numerical increase in cell proliferation when exosomes from high-risk cows were applied compared with those from low-risk cows. Consistent with an effect on cell proliferation, quantitative reverse transcriptase PCR indicated a trend for upregulation of 3 proinflammatory genes (granulocyte colony-stimulating factor, ciliary neurotrophic factor, and CD27 ligand) with the application of high-risk exosomes, which are involved in cellular growth and survival. Proteomic analysis indicated 2 proteins in the low-risk group that were not identified in the high-risk group (endoplasmin and catalase), which may also be indicative of the metabolic state of origin. It is likely that the metabolic state of the transition cow affects cellular function through exosomal messaging; however, more in-depth research into cross-talk between exosomes and target cells is required to determine whether exosomes influence Madin-Darby bovine kidney cells in this manner. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Photosynthetic acclimation: state transitions and adjustment of photosystem stoichiometry--functional relationships between short-term and long-term light quality acclimation in plants.

PubMed

Dietzel, Lars; Bräutigam, Katharina; Pfannschmidt, Thomas

2008-03-01

In dense plant populations, individuals shade each other resulting in a low-light habitat that is enriched in far-red light. This light quality gradient decreases the efficiency of the photosynthetic light reaction as a result of imbalanced excitation of the two photosystems. Plants counteract such conditions by performing acclimation reactions. Two major mechanisms are known to assure efficient photosynthesis: state transitions, which act on a short-term timescale; and a long-term response, which enables the plant to re-adjust photosystem stoichiometry in favour of the rate-limiting photosystem. Both processes start with the perception of the imbalanced photosystem excitation via reduction/oxidation (redox) signals from the photosynthetic electron transport chain. Recent data in Arabidopsis indicate that initialization of the molecular processes in both cases involve the activity of the thylakoid membrane-associated kinase, STN7. Thus, redox-controlled phosphorylation events may not only adjust photosystem antenna structure but may also affect plastid, as well as nuclear, gene expression. Both state transitions and the long-term response have been described mainly in molecular terms, while the physiological relevance concerning plant survival and reproduction has been poorly investigated. Recent studies have shed more light on this topic. Here, we give an overview on the long-term response, its physiological effects, possible mechanisms and its relationship to state transitions as well as to nonphotochemical quenching, another important short-term mechanism that mediates high-light acclimation. Special emphasis is given to the functional roles and potential interactions between the different light acclimation strategies. A working model displays the various responses as an integrated molecular system that helps plants to acclimate to the changing light environment.

E2C mechanism of elimination reactions. IX. Secondary deuterium isotope effects on rates of bimolecular reactions in alicyclic systems

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

Cook, D.

1976-06-11

Secondary ..cap alpha..-deuterium isotope effects on the rates of NBu/sub 4/OAc and NBu/sub 4/Cl promoted bimolecular reactions (E2 and SN2) of cyclohexyl tosylate and cyclohexyl bromide have been studied. The E2 reactions, previously categorized as E2C-like, show ..cap alpha..-deuterium isotope effects in the range 1.14--1.22, while the related SN2 reactions give values in the range 1.05--1.08. The discrepancy in the magnitude of the ..cap alpha..-deuterium isotope effect for the E2 and SN2 processes is consistent with the view that E2C-like reactions use ''looser'' transition states than those used in the concurrent SN2 reactions. While the reported ..cap alpha..-d isotope effectsmore » do not provide positive evidence to support the idea that the base interacts with C/sub ..cap alpha../ in the E2 transition states of the reactions studied, neither do they substantiate claims for dismissal of the concept. A comparison of the secondary ..gamma..-deuterium and ..beta..'-deuterium isotope effects arising in the reaction of cyclohexyl tosylate with NBu/sub 4/OAc in acetone indicates the two isotope effects to be of equivalent magnitude (k/sub ..beta..'-d/k/sub ..gamma..-d/ = 0.98). This observation can only be rationalized for this reaction in terms of a transition state structure in which there is extensive double bond development. It provides compelling evidence against the involvement of any transition state structure which accommodates extensive positive charge development at C/sub ..cap alpha../.« less

Theoretical and kinetic study of the hydrogen atom abstraction reactions of esters with H(O.)2 radicals.

PubMed

Mendes, Jorge; Zhou, Chong-Wen; Curran, Henry J

2013-12-27

This work details an ab initio and chemical kinetic study of the hydrogen atom abstraction reactions by the hydroperoxyl radical (HȮ2) on the following esters: methyl ethanoate, methyl propanoate, methyl butanoate, methyl pentanoate, methyl isobutyrate, ethyl ethanoate, propyl ethanoate, and isopropyl ethanoate. Geometry optimizations and frequency calculations of all of the species involved, as well as the hindrance potential descriptions for reactants and transition states, have been performed with the Møller-Plesset (MP2) method using the 6-311G(d,p) basis set. A validation of all of the connections between transition states and local minima was performed by intrinsic reaction coordinate calculations. Electronic energies for all of the species are reported at the CCSD(T)/cc-pVTZ level of theory in kcal mol(-1) with the zero-point energy corrections. The CCSD(T)/CBS (extrapolated from CCSD(T)/cc-pVXZ, in which X = D, T, Q) was used for the reactions of methyl ethanoate + HȮ2 radicals as a benchmark in the electronic energy calculations. High-pressure limit rate constants, in the temperature range 500-2000 K, have been calculated for all of the reaction channels using conventional transition state theory with asymmetric Eckart tunneling corrections. The 1-D hindered rotor approximation has been used for the low frequency torsional modes in both reactants and transition states. The calculated individual and total rate constants are reported for all of the reaction channels in each reaction system. A branching ratio analysis for each reaction site has also been investigated for all of the esters studied in this work.

Revisiting the polytopal rearrangements in penta-coordinate d7-metallocomplexes: modified Berry pseudorotation, octahedral switch, and butterfly isomerization.

PubMed

Asatryan, Rubik; Ruckenstein, Eli; Hachmann, Johannes

2017-08-01

This paper provides a first-principles theoretical investigation of the polytopal rearrangements and fluxional behavior of five-coordinate d 7 -transition metal complexes. Our work is primarily based on a potential energy surface analysis of the iron tetracarbonyl hydride radical HFe˙(CO) 4 . We demonstrate the existence of distorted coordination geometries in this prototypical system and, for the first time, introduce three general rearrangement mechanisms, which account for the non-ideal coordination. The first of these mechanisms constitutes a modified version of the Berry pseudorotation via a square-based pyramidal C 4v transition state that connects two chemically identical edge-bridged tetrahedral stereoisomers of C 2v symmetry. It differs from the classical Berry mechanism, which involves two regular D 3h equilibrium structures and a C 4v transition state. The second mechanism is related to the famous "tetrahedral jump" hypothesis, postulated by Muetterties for a number of d 6 HML 4 and H 2 ML 4 complexes. Here, our study suggests two fluxional rearrangement pathways via distinct types of C 2v transition states. Both pathways of this mechanism can be described as a single-ligand migration to a vacant position of an "octahedron", thus interchanging (switching) the apical and basal ligands of the initial quasi-square pyramidal isomer, which is considered as an idealized octahedron with a vacancy. Accordingly, we call this mechanism "octahedral switch". The third mechanism follows a butterfly-type isomerization featuring a key-angle deformation, and we thus call it "butterfly isomerization". It connects the quasi-square pyramidal and edge-bridged tetrahedral isomers of HFe˙(CO) 4 through a distorted edge-bridged tetrahedral transition state of C s symmetry. Our paper discusses the overall features of the isomers and rearrangement mechanisms as well as their implications. We rationalize the existence of each stationary point through an electronic structure analysis and argue their relevance for isolobal analogues of HFe˙(CO) 4 .

Lifetime measurements in transitional nuclei by fast electronic scintillation timing

NASA Astrophysics Data System (ADS)

Caprio, M. A.; Zamfir, N. V.; Casten, R. F.; Amro, H.; Barton, C. J.; Beausang, C. W.; Cooper, J. R.; Gürdal, G.; Hecht, A. A.; Hutter, C.; Krücken, R.; McCutchan, E. A.; Meyer, D. A.; Novak, J. R.; Pietralla, N.; Ressler, J. J.; Berant, Z.; Brenner, D. S.; Gill, R. L.; Regan, P. H.

2002-10-01

A new generation of experiments studying nuclei in spherical-deformed transition regions has been motivated by the introduction of innovative theoretical approaches to the treatment of these nuclei. The important structural signatures in the transition regions, beyond the basic yrast level properties, involve γ-ray transitions between low-spin, non-yrast levels, and so information on γ-ray branching ratios and absolute matrix elements (or level lifetimes) for these transitions is crucial. A fast electronic scintillation timing (FEST) system [H. Mach, R. L. Gill, and M. Moszyński, Nucl. Instrum. Methods A 280, 49 (1989)], making use of BaF2 and plastic scintillation detectors, has been implemented at the Yale Moving Tape Collector for the measurement of lifetimes of states populated in β^ decay. Experiments in the A100 (Pd, Ru) and A150 (Dy, Yb) regions have been carried out, and a few examples will be presented. Supported by the US DOE under grants and contracts DE-FG02-91ER-40609, DE-FG02-88ER-40417, and DE-AC02-98CH10886 and by the German DFG under grant Pi 393/1.

Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase

PubMed Central

Matsunaga, Yasuhiro; Fujisaki, Hiroshi; Terada, Tohru; Furuta, Tadaomi; Moritsugu, Kei; Kidera, Akinori

2012-01-01

Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space. Such rare events cannot be efficiently captured by conventional molecular dynamics simulations. Here we show that, by combining the on-the-fly string method and the multi-state Bennett acceptance ratio (MBAR) method, the free energy profile of a conformational transition pathway in Escherichia coli adenylate kinase can be characterized in a high-dimensional space. The minimum free energy paths of the conformational transitions in adenylate kinase were explored by the on-the-fly string method in 20-dimensional space spanned by the 20 largest-amplitude principal modes, and the free energy and various kinds of average physical quantities along the pathways were successfully evaluated by the MBAR method. The influence of ligand binding on the pathways was characterized in terms of rigid-body motions of the lid-shaped ATP-binding domain (LID) and the AMP-binding (AMPbd) domains. It was found that the LID domain was able to partially close without the ligand, while the closure of the AMPbd domain required the ligand binding. The transition state ensemble of the ligand bound form was identified as those structures characterized by highly specific binding of the ligand to the AMPbd domain, and was validated by unrestrained MD simulations. It was also found that complete closure of the LID domain required the dehydration of solvents around the P-loop. These findings suggest that the interplay of the two different types of domain motion is an essential feature in the conformational transition of the enzyme. PMID:22685395

Effects of the Self-Directed Individualized Education Program on Self-Determination and Transition of Adolescents with Disabilities

ERIC Educational Resources Information Center

Seong, Youjin; Wehmeyer, Michael L.; Palmer, Susan B.; Little, Todd D.

2015-01-01

The 1990 Individuals with Disabilities Education Act (IDEA) reauthorization introduced transition mandates that included a "student involvement in transition planning" requirement, creating an emphasis on promoting such involvement so as to enhance the self-determination of students with disabilities and positive transition-related…

Parameter optimization on the convergence surface of path simulations

NASA Astrophysics Data System (ADS)

Chandrasekaran, Srinivas Niranj

Computational treatments of protein conformational changes tend to focus on the trajectories themselves, despite the fact that it is the transition state structures that contain information about the barriers that impose multi-state behavior. PATH is an algorithm that computes a transition pathway between two protein crystal structures, along with the transition state structure, by minimizing the Onsager-Machlup action functional. It is rapid but depends on several unknown input parameters whose range of different values can potentially generate different transition-state structures. Transition-state structures arising from different input parameters cannot be uniquely compared with those generated by other methods. I outline modifications that I have made to the PATH algorithm that estimates these input parameters in a manner that circumvents these difficulties, and describe two complementary tests that validate the transition-state structures found by the PATH algorithm. First, I show that although the PATH algorithm and two other approaches to computing transition pathways produce different low-energy structures connecting the initial and final ground-states with the transition state, all three methods agree closely on the configurations of their transition states. Second, I show that the PATH transition states are close to the saddle points of free-energy surfaces connecting initial and final states generated by replica-exchange Discrete Molecular Dynamics simulations. I show that aromatic side-chain rearrangements create similar potential energy barriers in the transition-state structures identified by PATH for a signaling protein, a contractile protein, and an enzyme. Finally, I observed, but cannot account for, the fact that trajectories obtained for all-atom and Calpha-only simulations identify transition state structures in which the Calpha atoms are in essentially the same positions. The consistency between transition-state structures derived by different algorithms for unrelated protein systems argues that although functionally important 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. In the end, I outline the strategies that could enhance the efficiency and applicability of PATH.

A Study of the Spin-State Transition and Phase Transformation in [Fe(bpp)(2)][CF(3)SO(3)](2).H(2)O and [Fe(bpp)(2)][BF(4)](2) Using Mn(2+) Electron Spin Resonance.

PubMed

Sung, Raymond C. W.; McGarvey, Bruce R.

1999-08-09

X-band ESR powder studies have been done on the spin transition in Mn(2+)-doped [Fe(bpp)(2)][CF(3)SO(3)](2).H(2)O and [Fe(bpp)(2)][BF(4)](2) (bpp = 2,6-bis(pyrazol-3-yl) pyridine). The change in D value of Mn(2+) during the thermally induced high-spin (HS) <--> low-spin (LS) transition shows that the spin transition is accompanied by a phase transformation involving a domain mechanism. Irradiation experiments at 77 K have shown that a LS --> HS spin change occurs without a change in the crystalline phase. The rate of the change from the HS phase to the LS phase in the vicinity of 100 K has been measured and is found to be the same as that measured for the corresponding spin change obtained from Mössbauer spectroscopy and magnetic susceptibility studies.

Tunable negative thermal expansion related with the gradual evolution of antiferromagnetic ordering in antiperovskite manganese nitrides Ag{sub 1−x}NMn{sub 3+x} (0 ≤ x ≤ 0.6)

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

Lin, J. C.; Tong, P., E-mail: tongpeng@issp.ac.cn; Lin, S.

2015-02-23

The thermal expansion and magnetic properties of antiperovskite manganese nitrides Ag{sub 1−x}NMn{sub 3+x} were reported. The substitution of Mn for Ag effectively broadens the temperature range of negative thermal expansion and drives it to cryogenic temperatures. As x increases, the paramagnetic (PM) to antiferromagnetic (AFM) phase transition temperature decreases. At x ∼ 0.2, the PM-AFM transition overlaps with the AFM to glass-like state transition. Above x = 0.2, two new distinct magnetic transitions were observed: One occurs above room temperature from PM to ferromagnetic (FM), and the other one evolves at a lower temperature (T{sup *}) below which both AFM and FM orderings aremore » involved. Further, electron spin resonance measurement suggests that the broadened volume change near T{sup *} is closely related with the evolution of Γ{sup 5g} AFM ordering.« less

Continuation of probability density functions using a generalized Lyapunov approach

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

Baars, S., E-mail: s.baars@rug.nl; Viebahn, J.P., E-mail: viebahn@cwi.nl; Mulder, T.E., E-mail: t.e.mulder@uu.nl

Techniques from numerical bifurcation theory are very useful to study transitions between steady fluid flow patterns and the instabilities involved. Here, we provide computational methodology to use parameter continuation in determining probability density functions of systems of stochastic partial differential equations near fixed points, under a small noise approximation. Key innovation is the efficient solution of a generalized Lyapunov equation using an iterative method involving low-rank approximations. We apply and illustrate the capabilities of the method using a problem in physical oceanography, i.e. the occurrence of multiple steady states of the Atlantic Ocean circulation.

The Riemann problem for longitudinal motion in an elastic-plastic bar

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

Trangenstein, J.A.; Pember, R.B.

In this paper the analytical solution to the Riemann problem for the Antman-Szymczak model of longitudinal motion in an elastic-plastic bar is constructed. The model involves two surfaces corresponding to plastic yield in tension and compression, and exhibits the appropriate limiting behavior for total compressions. The solution of the Riemann problem involves discontinuous changes in characteristic speeds due to transitions from elastic to plastic response. Illustrations are presented, in both state-space and self-similar coordinates, of the variety of possible solutions to the Riemann problem for possible use with numerical algorithms.

Hemoglobin redux: combining neutron and X-ray diffraction with mass spectrometry to analyse the quaternary state of oxidized hemoglobins

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

Mueser, Timothy C., E-mail: timothy.mueser@utoledo.edu; Griffith, Wendell P.; Kovalevsky, Andrey Y.

2010-11-01

X-ray and neutron diffraction studies of cyanomethemoglobin are being used to evaluate the structural waters within the dimer–dimer interface involved in quaternary-state transitions. Improvements in neutron diffraction instrumentation are affording the opportunity to re-examine the structures of vertebrate hemoglobins and to interrogate proton and solvent position changes between the different quaternary states of the protein. For hemoglobins of unknown primary sequence, structural studies of cyanomethemoglobin (CNmetHb) are being used to help to resolve sequence ambiguity in the mass spectra. These studies have also provided additional structural evidence for the involvement of oxidized hemoglobin in the process of erythrocyte senescence. X-raymore » crystal studies of Tibetan snow leopard CNmetHb have shown that this protein crystallizes in the B state, a structure with a more open dyad, which possibly has relevance to RBC band 3 protein binding and erythrocyte senescence. R-state equine CNmetHb crystal studies elaborate the solvent differences in the switch and hinge region compared with a human deoxyhemoglobin T-state neutron structure. Lastly, comparison of histidine protonation between the T and R state should enumerate the Bohr-effect protons.« less

Visualizing Active-Site Dynamics in Single Crystals of HePTP: Opening of the WPD Loop Involves Coordinated Movement of the E Loop

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

D Critton; L Tautz; R Page

2011-12-31

Phosphotyrosine hydrolysis by protein tyrosine phosphatases (PTPs) involves substrate binding by the PTP loop and closure over the active site by the WPD loop. The E loop, located immediately adjacent to the PTP and WPD loops, is conserved among human PTPs in both sequence and structure, yet the role of this loop in substrate binding and catalysis is comparatively unexplored. Hematopoietic PTP (HePTP) is a member of the kinase interaction motif (KIM) PTP family. Compared to other PTPs, KIM-PTPs have E loops that are unique in both sequence and structure. In order to understand the role of the E loopmore » in the transition between the closed state and the open state of HePTP, we identified a novel crystal form of HePTP that allowed the closed-state-to-open-state transition to be observed within a single crystal form. These structures, which include the first structure of the HePTP open state, show that the WPD loop adopts an 'atypically open' conformation and, importantly, that ligands can be exchanged at the active site, which is critical for HePTP inhibitor development. These structures also show that tetrahedral oxyanions bind at a novel secondary site and function to coordinate the PTP, WPD, and E loops. Finally, using both structural and kinetic data, we reveal a novel role for E-loop residue Lys182 in enhancing HePTP catalytic activity through its interaction with Asp236 of the WPD loop, providing the first evidence for the coordinated dynamics of the WPD and E loops in the catalytic cycle, which, as we show, is relevant to multiple PTP families.« less

Modifying Operating Cycles to Increase Stability in a LITS

NASA Technical Reports Server (NTRS)

Burt, Eric; Tjoelker, Robert

2009-01-01

The short-term instability in the frequency of a linear-ion-trap frequency standard (LITS) can be reduced by modifying two cycles involved in its operation: (1) the bimodal (bright/dim) cycle of a plasma discharge lamp used for state preparation and detection and (2) a microwave-interrogation cycle. The purpose and effect of the modifications is to enable an increase in the microwave- interrogation cycle time, motivated by the general principle that the short-term uncertainty or instability decreases with increasing microwave-interrogation time. Stated from a slightly different perspective, the effect of modifications is to enable the averaged LITS readings to settle to their longterm stability over a shorter total observation time. The basic principles of a LITS were discussed in several NASA Tech Briefs articles. Here are recapitulated only those items of background information necessary to place the present modifications in context. A LITS includes a microwave local oscillator, the frequency of which is stabilized by comparison with the frequency of a ground-state hyperfine transition of Hg-199(+) ions. In a LITS of the type to which the modifications apply, the comparison involves a combination of optical and micro wave excitation and interrogation of the ions in two collinear ion traps: a quadrupole trap wherein the optical excitation used for state preparation and detection takes place, and a multipole (e.g., 12-pole) trap wherein the microwave interrogation of the clock transition takes place. The ions are initially loaded into the quadrupole trap and are thereafter shuttled between the two traps. This concludes the background information.

The Low Molecular Weight Protein PsaI Stabilizes the Light-Harvesting Complex II Docking Site of Photosystem I.

PubMed

Plöchinger, Magdalena; Torabi, Salar; Rantala, Marjaana; Tikkanen, Mikko; Suorsa, Marjaana; Jensen, Poul-Erik; Aro, Eva Mari; Meurer, Jörg

2016-09-01

PsaI represents one of three low molecular weight peptides of PSI. Targeted inactivation of the plastid PsaI gene in Nicotiana tabacum has no measurable effect on photosynthetic electron transport around PSI or on accumulation of proteins involved in photosynthesis. Instead, the lack of PsaI destabilizes the association of PsaL and PsaH to PSI, both forming the light-harvesting complex (LHC)II docking site of PSI. These alterations at the LHCII binding site surprisingly did not prevent state transition but led to an increased incidence of PSI-LHCII complexes, coinciding with an elevated phosphorylation level of the LHCII under normal growth light conditions. Remarkably, LHCII was rapidly phosphorylated in ΔpsaI in darkness even after illumination with far-red light. We found that this dark phosphorylation also occurs in previously described mutants impaired in PSI function or state transition. A prompt shift of the plastoquinone (PQ) pool into a more reduced redox state in the dark caused an enhanced LHCII phosphorylation in ΔpsaI Since the redox status of the PQ pool is functionally connected to a series of physiological, biochemical, and gene expression reactions, we propose that the shift of mutant plants into state 2 in darkness represents a compensatory and/or protective metabolic mechanism. This involves an increased reduction and/or reduced oxidation of the PQ pool, presumably to sustain a balanced excitation of both photosystems upon the onset of light. © 2016 American Society of Plant Biologists. All rights reserved.

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.

Involving Undergraduates in Aging Research at a University in Transition: An AREA Award

ERIC Educational Resources Information Center

Wood, Stacey

2006-01-01

Involving students in research with older adults at a university in transition has its unique challenges. The goal of this paper is to discuss some of the rewards and lessons learned in undertaking a research program involving undergraduates at the University of Colorado, Colorado Springs (UC-CS). UC-CS is a regional university in transition from…

Hierarchical Modeling of Activation Mechanisms in the ABL and EGFR Kinase Domains: Thermodynamic and Mechanistic Catalysts of Kinase Activation by Cancer Mutations

PubMed Central

Dixit, Anshuman; Verkhivker, Gennady M.

2009-01-01

Structural and functional studies of the ABL and EGFR kinase domains have recently suggested a common mechanism of activation by cancer-causing mutations. However, dynamics and mechanistic aspects of kinase activation by cancer mutations that stimulate conformational transitions and thermodynamic stabilization of the constitutively active kinase form remain elusive. We present a large-scale computational investigation of activation mechanisms in the ABL and EGFR kinase domains by a panel of clinically important cancer mutants ABL-T315I, ABL-L387M, EGFR-T790M, and EGFR-L858R. We have also simulated the activating effect of the gatekeeper mutation on conformational dynamics and allosteric interactions in functional states of the ABL-SH2-SH3 regulatory complexes. A comprehensive analysis was conducted using a hierarchy of computational approaches that included homology modeling, molecular dynamics simulations, protein stability analysis, targeted molecular dynamics, and molecular docking. Collectively, the results of this study have revealed thermodynamic and mechanistic catalysts of kinase activation by major cancer-causing mutations in the ABL and EGFR kinase domains. By using multiple crystallographic states of ABL and EGFR, computer simulations have allowed one to map dynamics of conformational fluctuations and transitions in the normal (wild-type) and oncogenic kinase forms. A proposed multi-stage mechanistic model of activation involves a series of cooperative transitions between different conformational states, including assembly of the hydrophobic spine, the formation of the Src-like intermediate structure, and a cooperative breakage and formation of characteristic salt bridges, which signify transition to the active kinase form. We suggest that molecular mechanisms of activation by cancer mutations could mimic the activation process of the normal kinase, yet exploiting conserved structural catalysts to accelerate a conformational transition and the enhanced stabilization of the active kinase form. The results of this study reconcile current experimental data with insights from theoretical approaches, pointing to general mechanistic aspects of activating transitions in protein kinases. PMID:19714203

Coherent Nuclear Wave Packets in Q States by Ultrafast Internal Conversions in Free Base Tetraphenylporphyrin.

PubMed

Kim, So Young; Joo, Taiha

2015-08-06

Persistence of vibrational coherence in electronic transition has been noted especially in biochemical systems. Here, we report the dynamics between electronic excited states in free base tetraphenylporphyrin (H2TPP) by time-resolved fluorescence with high time resolution. Following the photoexcitation of the B state, ultrafast internal conversion occurs to the Qx state directly as well as via the Qy state. Unique and distinct coherent nuclear wave packet motions in the Qx and Qy states are observed through the modulation of the fluorescence intensity in time. The instant, serial internal conversions from the B to the Qy and Qx states generate the coherent wave packets. Theory and experiment show that the observed vibrational modes involve the out-of-plane vibrations of the porphyrin ring that are strongly coupled to the internal conversion of H2TPP.

Conformational transitions of uracil transporter UraA from Escherichia coli: a molecular simulation study.

PubMed

Yang, Liu; Yang, Lianjuan; Yu, Hui; Liu, Lu; Zhao, Xi; Huang, Xuri

2017-10-26

The Escherichia coli uracil/H + symporter UraA, known as the representative nucleobase/cation symporter 2(NCS2) protein, gets involved in several crucial physiological processes for most living organisms on Earth, such as the uptake of nucleobases and transport of vitamin C. Some experiments proposed a working model to explain proton-coupling and uracil transporting process of UraA on the basis of the crystal structure of NCS2 protein, but the details of conformational changes remained unknown. Thus, in order to make clear conformational changes caused by the protonation and deprotonation process of some conserved proton-coupled residues, the molecular dynamics simulation was used to study the conformation of UraA complexes in different protonation states. The results demonstrated that the protonation of residue Glu241 and Glu290 resulted in the whole conformational transition from the inward-open to the outward-open state. It can be concluded that Glu290 was crucial in a network of hydrogen-bonds in the middle of the core domain involving another essential residue, mainly including tyr288 in TM8, Tyr342, Ser338 in TM12, and the network of hydrogen-bonds was the key to maintain the stability of conformation. Protonation of Glu290 affects the stability of network of H-bond and changed the domains TM3 TM10 TM12. Thus, Glu290 may play a vital role as a 'proton trigger' that affects spatial structural of amino and residues near substrate binding side leading to an outward-open conformation transition.

Regrouping: organized activity involvement and social adjustment across the transition to high school.

PubMed

Bohnert, Amy M; Aikins, Julie Wargo; Arola, Nicole T

2013-01-01

Although organized activities (OAs) have been established as important contexts of development, limited work has examined the role of OAs across the high school transition in buffering adolescents' social adjustment by providing opportunities for visibility and peer affiliation. The transition to high school is characterized by numerous changes and OAs may provide an important setting for establishing and maintaining peer relationships during this tumultuous time. This study included 151 8th grade U.S. students (58% male) who were assessed across the transition to high school (spring of 8th and 9th grade). Continuous involvement in academic activities across the transition and becoming involved (i.e., initiation) in community/service activities following the transition was associated with fewer depressive symptoms in the spring of 9th grade. Continuous involvement in sports and initiation of academic activities was associated with having more friendships. In addition, links between OAs and loneliness were only evident among females. There appear to be significant social benefits for OA involvement. Copyright © 2013 Wiley Periodicals, Inc., A Wiley Company.

On the ambiguity of conformational states: A B&S-LEUS simulation study of the helical conformations of decaalanine in water

NASA Astrophysics Data System (ADS)

Bieler, Noah S.; Hünenberger, Philippe H.

2015-04-01

Estimating the relative stabilities of different conformational states of a (bio-)molecule using molecular dynamics simulations involves two challenging problems: the conceptual problem of how to define the states of interest and the technical problem of how to properly sample these states, along with achieving a sufficient number of interconversion transitions. In this study, the two issues are addressed in the context of a decaalanine peptide in water, by considering the 310-, α-, and π-helical states. The simulations rely on the ball-and-stick local-elevation umbrella-sampling (B&S-LEUS) method. In this scheme, the states are defined as hyperspheres (balls) in a (possibly high dimensional) collective-coordinate space and connected by hypercylinders (sticks) to ensure transitions. A new object, the pipe, is also introduced here to handle curvilinear pathways. Optimal sampling within the so-defined space is ensured by confinement and (one-dimensional) memory-based biasing potentials associated with the three different kinds of objects. The simulation results are then analysed in terms of free energies using reweighting, possibly relying on two distinct sets of collective coordinates for the state definition and analysis. The four possible choices considered for these sets are Cartesian coordinates, hydrogen-bond distances, backbone dihedral angles, or pairwise sums of successive backbone dihedral angles. The results concerning decaalanine underline that the concept of conformational state may be extremely ambiguous, and that its tentative absolute definition as a free-energy basin remains subordinated to the choice of a specific analysis space. For example, within the force-field employed and depending on the analysis coordinates selected, the 310-helical state may refer to weakly overlapping collections of conformations, differing by as much as 25 kJ mol-1 in terms of free energy. As another example, the π-helical state appears to correspond to a free-energy basin for three choices of analysis coordinates, but to be unstable with the fourth one. The problem of conformational-state definition may become even more intricate when comparison with experiment is involved, where the state definition relies on spectroscopic or functional observables.

On the ambiguity of conformational states: A B&S-LEUS simulation study of the helical conformations of decaalanine in water.

PubMed

Bieler, Noah S; Hünenberger, Philippe H

2015-04-28

Estimating the relative stabilities of different conformational states of a (bio-)molecule using molecular dynamics simulations involves two challenging problems: the conceptual problem of how to define the states of interest and the technical problem of how to properly sample these states, along with achieving a sufficient number of interconversion transitions. In this study, the two issues are addressed in the context of a decaalanine peptide in water, by considering the 310-, α-, and π-helical states. The simulations rely on the ball-and-stick local-elevation umbrella-sampling (B&S-LEUS) method. In this scheme, the states are defined as hyperspheres (balls) in a (possibly high dimensional) collective-coordinate space and connected by hypercylinders (sticks) to ensure transitions. A new object, the pipe, is also introduced here to handle curvilinear pathways. Optimal sampling within the so-defined space is ensured by confinement and (one-dimensional) memory-based biasing potentials associated with the three different kinds of objects. The simulation results are then analysed in terms of free energies using reweighting, possibly relying on two distinct sets of collective coordinates for the state definition and analysis. The four possible choices considered for these sets are Cartesian coordinates, hydrogen-bond distances, backbone dihedral angles, or pairwise sums of successive backbone dihedral angles. The results concerning decaalanine underline that the concept of conformational state may be extremely ambiguous, and that its tentative absolute definition as a free-energy basin remains subordinated to the choice of a specific analysis space. For example, within the force-field employed and depending on the analysis coordinates selected, the 310-helical state may refer to weakly overlapping collections of conformations, differing by as much as 25 kJ mol(-1) in terms of free energy. As another example, the π-helical state appears to correspond to a free-energy basin for three choices of analysis coordinates, but to be unstable with the fourth one. The problem of conformational-state definition may become even more intricate when comparison with experiment is involved, where the state definition relies on spectroscopic or functional observables.

On the molecular origin of the cooperative coil-to-globule transition of poly(N-isopropylacrylamide) in water† †Electronic supplementary information (ESI) available: Stereochemistry and initial conformation of PNIPAM 30-mer; pair distribution functions of PNIPAM methyl groups; average time of transitions of dihedral angles; distribution of methyl dihedral angles; temperature dependence of average number of hydration water molecules; correlation between hydrogen bonding of water molecules per repeating unit in the FHS and end to end distance and correlation between PNIPAM–water hydrogen bonding and end to end distance. Time evolution of PNIPAM with the first hydration shell: movie FHSpnipam.avi. See DOI: 10.1039/c8cp00537k

PubMed Central

Zaccarelli, E.

2018-01-01

By means of atomistic molecular dynamics simulations we investigate the behaviour of poly(N-isopropylacrylamide), PNIPAM, in water at temperatures below and above the lower critical solution temperature (LCST), including the undercooled regime. The transition between water soluble and insoluble states at the LCST is described as a cooperative process involving an intramolecular coil-to-globule transition preceding the aggregation of chains and the polymer precipitation. In this work we investigate the molecular origin of such cooperativity and the evolution of the hydration pattern in the undercooled polymer solution. The solution behaviour of an atactic 30-mer at high dilution is studied in the temperature interval from 243 to 323 K with a favourable comparison to available experimental data. In the water soluble states of PNIPAM we detect a correlation between polymer segmental dynamics and diffusion motion of bound water, occurring with the same activation energy. Simulation results show that below the coil-to-globule transition temperature PNIPAM is surrounded by a network of hydrogen bonded water molecules and that the cooperativity arises from the structuring of water clusters in proximity to hydrophobic groups. Differently, the perturbation of the hydrogen bond pattern involving water and amide groups occurs above the transition temperature. Altogether these findings reveal that even above the LCST PNIPAM remains largely hydrated and that the coil-to-globule transition is related with a significant rearrangement of the solvent in the proximity of the surface of the polymer. The comparison between the hydrogen bonding of water in the surrounding of PNIPAM isopropyl groups and in the bulk displays a decreased structuring of solvent at the hydrophobic polymer–water interface across the transition temperature, as expected because of the topological extension along the chain of such interface. No evidence of an upper critical solution temperature behaviour, postulated in theoretical and thermodynamics studies of PNIPAM aqueous solution, is observed in the low temperature domain. PMID:29619464

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

PubMed Central

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

2017-01-01

Neurotransmitter:sodium symporters (NSSs) terminate neurotransmission by the reuptake of released neurotransmitters. This active accumulation of substrate against its concentration gradient is driven by the transmembrane Na+ gradient and requires that the transporter traverses several conformational states. LeuT, a prokaryotic NSS homolog, has been crystallized in outward-open, outward-occluded, and inward-open states. Two crystal structures of another prokaryotic NSS homolog, the multihydrophobic amino acid transporter (MhsT) from Bacillus halodurans, have been resolved in novel inward-occluded states, with the extracellular vestibule closed and the intracellular portion of transmembrane segment 5 (TM5i) in either an unwound or a helical conformation. We have investigated the potential involvement of TM5i in binding and unbinding of Na2, i.e. the Na+ bound in the Na2 site, by carrying out comparative molecular dynamics simulations of the models derived from the two MhsT structures. We find that the helical TM5i conformation is associated with a higher propensity for Na2 release, which leads to the repositioning of the N terminus and transition to an inward-open state. By using comparative interaction network analysis, we also identify allosteric pathways connecting TM5i and the Na2 binding site to the extracellular and intracellular regions. Based on our combined computational and mutagenesis studies of MhsT and LeuT, we propose that TM5i plays a key role in Na2 binding and release associated with the conformational transition toward the inward-open state, a role that is likely to be shared across the NSS family. PMID:28320858

Ultrafast Spectroscopic Studies of Two-Photon States in Third Order Optical Processes of Dye Chromophores.

NASA Astrophysics Data System (ADS)

Yu, Yi-Zhong

1995-01-01

Conjugated organic and polymeric materials usually have large, nonresonant third order optical nonlinearity due to correlations of their delocalized pi -electrons. Most materials studied so far show positive values of third order nonlinear susceptibility when all frequencies that generate the third order effect are below any optical transition. A new class of organic molecules, namely indole squarylium (ISQ) and anilinium squarylium (BSQ), exhibit negative < gamma(-omega_4;omega_1, omega_2,omega_3)> when all three frequencies, omega_1, omega_2 and omega_3, lie below the first electronic transition. Although quantum many-electron calculations based on multiple-excitation configuration interaction have shown that the negative third order coefficient is essentially due to the contribution from high-lying two-photon states, the field of experimental studies exploring the microscopic origins of the negative squaraines remains uncultivated. The work presented in this thesis involves extensive experimental investigation of squaraines using techniques such as time-resolved transit absorption spectroscopy and saturable absorption. Theoretical simulations studying nonlinear absorption behavior of a simplified two-level system with ultrashort pulses are also presented. Part of the thesis is dedicated to the development, fabrication and characterization of our ultrafast laser system which offers tunable femtosecond pulses at wavelengths from UV to IR and served as a major tool in the experimental measurements. The dynamics of the population inversion between the ground state and the first excited state was also investigated through time-resolved experiments. The experiment results agree well with the theoretical predictions. Strong couplings between the gateway state and high-lying two-photon states were observed in BSQ squarylium molecules, which suggested a complete quantum calculation with multiple energy levels is required to correctly describe the negative third order effect.

Scaling Up Family Therapy in Fragile, Conflict-Affected States.

PubMed

Charlés, Laurie L

2015-09-01

This article discusses the design and delivery of two international family therapy-focused mental health and psychosocial support training projects, one in a fragile state and one in a post-conflict state. The training projects took place in Southeast Asia and the Middle East/North Africa. Each was funded, supported, and implemented by local, regional, and international stakeholders, and delivered as part of a broader humanitarian agenda to develop human resource capacity to work with families affected by atrocities. The two examples illustrate how task-shifting/task-sharing and transitional justice approaches were used to inform the scaling-up of professionals involved in each project. They also exemplify how state-citizen phenomena in each location affected the project design and delivery. © 2014 Family Process Institute.

Evolution and cell physiology. 2. The evolution of cell signaling: from mitochondria to Metazoa.

PubMed

Blackstone, Neil W

2013-11-01

The history of life is a history of levels-of-selection transitions. Each transition requires mechanisms that mediate conflict among the lower-level units. In the origins of multicellular eukaryotes, cell signaling is one such mechanism. The roots of cell signaling, however, may extend to the previous major transition, the origin of eukaryotes. Energy-converting protomitochondria within a larger cell allowed eukaryotes to transcend the surface-to-volume constraints inherent in the design of prokaryotes. At the same time, however, protomitochondria can selfishly allocate energy to their own replication. Metabolic signaling may have mediated this principal conflict in several ways. Variation of the protomitochondria was constrained by stoichiometry and strong metabolic demand (state 3) exerted by the protoeukaryote. Variation among protoeukaryotes was increased by the sexual stage of the life cycle, triggered by weak metabolic demand (state 4), resulting in stochastic allocation of protomitochondria to daughter cells. Coupled with selection, many selfish protomitochondria could thus be removed from the population. Hence, regulation of states 3 and 4, as, for instance, provided by the CO2/soluble adenylyl cyclase/cAMP pathway in mitochondria, was critical for conflict mediation. Subsequently, as multicellular eukaryotes evolved, metabolic signaling pathways employed by eukaryotes to mediate conflict within cells could now be co-opted into conflict mediation between cells. For example, in some fungi, the CO2/soluble adenylyl cyclase/cAMP pathway regulates the transition from yeast to forms with hyphae. In animals, this pathway regulates the maturation of sperm. While the particular features (sperm and hyphae) are distinct, both may involve between-cell conflicts that required mediation.

High resolution spectral analysis of oxygen. IV. Energy levels, partition sums, band constants, RKR potentials, Franck-Condon factors involving the X{sup 3}Σ{sub g}{sup −}, a{sup 1}Δ{sub g} and b{sup 1}Σ{sub g}{sup +} states

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

Yu, Shanshan, E-mail: shanshan.yu@jpl.nasa.gov; Drouin, Brian J.; Miller, Charles E.

We have updated the isotopically invariant Dunham fit of O{sub 2} with newly reported literature transitions to derive (1) the energy levels, partition sums, band-by-band molecular constants, and RKR potentials for the X{sup 3}Σ{sub g}{sup −}, a{sup 1}Δ{sub g}, and b{sup 1}Σ{sub g}{sup +} states of the six O{sub 2} isotopologues: {sup 16}O{sup 16}O, {sup 16}O{sup 17}O, {sup 16}O{sup 18}O, {sup 17}O{sup 17}O, {sup 17}O{sup 18}O, and {sup 18}O{sup 18}O; (2) Franck-Condon factors for their a{sup 1}Δ{sub g}−X{sup 3}Σ{sub g}{sup −}, b{sup 1}Σ{sub g}{sup +}−X{sup 3}Σ{sub g}{sup −}, and a{sup 1}Δ{sub g}−b{sup 1}Σ{sub g}{sup +} band systems. This new spectroscopicmore » parameterization characterizes all known transitions within and between the X{sup 3}Σ{sub g}{sup −}, a{sup 1}Δ{sub g}, and b{sup 1}Σ{sub g}{sup +} states within experimental uncertainty and can be used for accurate predictions of as yet unmeasured transitions. All of these results are necessary to provide a consistent linelist of all transitions which will be reported in a followup paper.« less

Variation of parameters using Battin's universal functions

NASA Astrophysics Data System (ADS)

Burton, James R., III; Melton, Robert G.

This paper presents a variation of parameters analysis, suitable for use in situations involving small perturbations to the two-body problem, using Battin's universal functions. Unlike the universal variable formulation, this approach avoids the need to switch among different functional representations if the orbit transitions from elliptical, through parabolic, to hyperbolic state, making it attractive for use in simulating low-thrust trajectories ascending to escape or capturing into orbit.

The discovery of robust magnetism in a technetium oxide: The structure of CaTcO3

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

Avdeev, Maxim; Thorogood, Gordon J.; Carter, Melody L.

The technetium perovskite CaTcO{sub 3} has been synthesized. Combining synchrotron X-ray and neutron diffraction, we found that CaTcO{sub 3} is an antiferromagnetic with a surprisingly high Neel temperature of 800 K. The transition to the magnetic state does not involve a structural change, but there is obvious magnetostriction. Electronic structure calculations confirm the experimental results.

How maltose influences structural changes to bind to maltose-binding protein: results from umbrella sampling simulation.

PubMed

Mascarenhas, Nahren Manuel; Kästner, Johannes

2013-02-01

A well-studied periplasmic-binding protein involved in the abstraction of maltose is maltose-binding protein (MBP), which undergoes a ligand-induced conformational transition from an open (ligand-free) to a closed (ligand-bound) state. Umbrella sampling simulations have been us to estimate the free energy of binding of maltose to MBP and to trace the potential of mean force of the unbinding event using the center-of-mass distance between the protein and ligand as the reaction coordinate. The free energy thus obtained compares nicely with the experimentally measured value justifying our theoretical basis. Measurement of the domain angle (N-terminal-domain - hinge - C-terminal-domain) along the unbinding pathway established the existence of three different states. Starting from a closed state, the protein shifts to an open conformation during the initial unbinding event of the ligand then resides in a semi-open conformation and later resides predominantly in an open-state. These transitions along the ligand unbinding pathway have been captured in greater depth using principal component analysis. It is proposed that in mixed-model, both conformational selection and an induced-fit mechanism combine to the ligand recognition process in MBP. Copyright © 2012 Wiley Periodicals, Inc.

Singlet fission in linear chains of molecules

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

Ambrosio, Francesco, E-mail: F.Ambrosio@warwick.ac.uk, E-mail: A.Troisi@warwick.ac.uk; Troisi, Alessandro, E-mail: F.Ambrosio@warwick.ac.uk, E-mail: A.Troisi@warwick.ac.uk

2014-11-28

We develop a model configuration interaction Hamiltonian to study the electronic structure of a chain of molecules undergoing singlet fission. We first consider models for dimer and trimer and then we use a matrix partitioning technique to build models of arbitrary size able to describe the relevant electronic structure for singlet fission in linear aggregates. We find that the multi-excitonic state (ME) is stabilized at short inter-monomer distance and the extent of this stabilization depends upon the size of orbital coupling between neighboring monomers. We also find that the coupling between ME states located on different molecules is extremely smallmore » leading to bandwidths in the order of ∼10 meV. This observation suggests that multi-exciton states are extremely localized by electron-phonon coupling and that singlet fission involves the transition between a relatively delocalized Frenkel exciton and a strongly localized multi-exciton state. We adopt the methodology commonly used to study non-radiative transitions to describe the singlet fission dynamics in these aggregates and we discuss the limit of validity of the approach. The results indicate that the phenomenology of singlet fission in molecular crystals is different in many important ways from what is observed in isolated dimers.« less

Near-optimal quantum circuit for Grover's unstructured search using a transverse field

NASA Astrophysics Data System (ADS)

Jiang, Zhang; Rieffel, Eleanor G.; Wang, Zhihui

2017-06-01

Inspired by a class of algorithms proposed by Farhi et al. (arXiv:1411.4028), namely, the quantum approximate optimization algorithm (QAOA), we present a circuit-based quantum algorithm to search for a needle in a haystack, obtaining the same quadratic speedup achieved by Grover's original algorithm. In our algorithm, the problem Hamiltonian (oracle) and a transverse field are applied alternately to the system in a periodic manner. We introduce a technique, based on spin-coherent states, to analyze the composite unitary in a single period. This composite unitary drives a closed transition between two states that have high degrees of overlap with the initial state and the target state, respectively. The transition rate in our algorithm is of order Θ (1 /√{N }) , and the overlaps are of order Θ (1 ) , yielding a nearly optimal query complexity of T ≃√{N }(π /2 √{2 }) . Our algorithm is a QAOA circuit that demonstrates a quantum advantage with a large number of iterations that is not derived from Trotterization of an adiabatic quantum optimization (AQO) algorithm. It also suggests that the analysis required to understand QAOA circuits involves a very different process from estimating the energy gap of a Hamiltonian in AQO.

New open conformation of SMYD3 implicates conformational selection and allostery

PubMed Central

Spellmon, Nicholas; Sun, Xiaonan; Xue, Wen; Holcomb, Joshua; Chakravarthy, Srinivas; Shang, Weifeng; Edwards, Brian; Sirinupong, Nualpun; Li, Chunying; Yang, Zhe

2016-01-01

SMYD3 plays a key role in cancer cell viability, adhesion, migration and invasion. SMYD3 promotes formation of inducible regulatory T cells and is involved in reducing autoimmunity. However, the nearly “closed” substrate-binding site and poor in vitro H3K4 methyltransferase activity have obscured further understanding of this oncogenically related protein. Here we reveal that SMYD3 can adopt an “open” conformation using molecular dynamics simulation and small-angle X-ray scattering. This ligand-binding-capable open state is related to the crystal structure-like closed state by a striking clamshell-like inter-lobe dynamics. The two states are characterized by many distinct structural and dynamical differences and the conformational transition pathway is mediated by a reversible twisting motion of the C-terminal domain (CTD). The spontaneous transition from the closed to open states suggests two possible, mutually non-exclusive models for SMYD3 functional regulation and the conformational selection mechanism and allostery may regulate the catalytic or ligand binding competence of SMYD3. This study provides an immediate clue to the puzzling role of SMYD3 in epigenetic gene regulation. PMID:28050603

Band gap states in nanocrystalline WO3 thin films studied by soft x-ray spectroscopy and optical spectrophotometry.

PubMed

Johansson, M B; Kristiansen, P T; Duda, L; Niklasson, G A; Österlund, L

2016-11-30

Nanocrystalline tungsten trioxide (WO3) thin films prepared by DC magnetron sputtering have been studied using soft x-ray spectroscopy and optical spectrophotometry. Resonant inelastic x-ray scattering (RIXS) measurements reveal band gap states in sub-stoichiometric γ-WO3-x with x  =  0.001-0.005. The energy positions of these states are in good agreement with recently reported density functional calculations. The results were compared with optical absorption measurements in the near infrared spectral region. An optical absorption peak at 0.74 eV is assigned to intervalence transfer of polarons between W sites. A less prominent peak at energies between 0.96 and 1.16 eV is assigned to electron excitation of oxygen vacancies. The latter results are supported by RIXS measurements, where an energy loss in this energy range was observed, and this suggests that electron transfer processes involving transitions from oxygen vacancy states can be observed in RIXS. Our results have implications for the interpretation of optical properties of WO3, and the optical transitions close to the band gap, which are important in photocatalytic and photoelectrochemical applications.

Mitochondria Play a Central Role in Nonischemic Cardiomyocyte Necrosis: Common to Acute and Chronic Stressor States

PubMed Central

Khan, M. Usman; Cheema, Yaser; Shahbaz, Atta U.; Ahokas, Robert A.; Sun, Yao; Gerling, Ivan C.; Bhattacharya, Syamal K.; Weber, Karl T.

2012-01-01

The survival of cardiomyocytes must be ensured as the myocardium adjusts to a myriad of competing physiologic and pathophysiologic demands. A significant loss of these contractile cells, together with their replacement by stiff fibrillar collagen in the form of fibrous tissue accounts for a transition from a usually efficient muscular pump into one that is failing. Cellular and subcellular mechanisms involved in the pathogenic origins of cardiomyocyte cell death have long been of interest. This includes programmed molecular pathways to either necrosis or apoptosis which are initiated from ischemic or nonischemic origins. Herein we focus on the central role played by a mitochondriocentric signal-transducer-effector pathway to nonischemic cardiomyocyte necrosis which is common to acute and chronic stressor states. We begin by building upon the hypothesis advanced by Albrecht Fleckenstein and coworkers some 40 years ago based on the importance of calcitropic hormone- mediated intracellular Ca2+ overloading which predominantly involves subsarcolemmal mitochondria and is the signal to pathway activation. Other pathway components, which came to be recognized in subsequent years, include the induction of oxidative stress and opening of the mitochondrial inner membrane permeability transition pore. The ensuing loss of cardiomyocytes and consequent replacement fibrosis, or scarring, represents a disease of adaptation and a classic example of when homeostasis begets dyshomeostasis. PMID:22328074

Case studies from three states: breaking down silos between health care and criminal justice.

PubMed

Bechelli, Matthew J; Caudy, Michael; Gardner, Tracie M; Huber, Alice; Mancuso, David; Samuels, Paul; Shah, Tanya; Venters, Homer D

2014-03-01

The jail-involved population-people with a history of arrest in the previous year-has high rates of illness, which leads to high costs for society. A significant percentage of jail-involved people are estimated to become newly eligible for coverage through the Affordable Care Act's expansion of Medicaid, including coverage of substance abuse treatment and mental health care. In this article we explore the need to break down the current policy silos between health care and criminal justice, to benefit both sectors and reduce unnecessary costs resulting from lack of coordination. To draw attention to the hidden costs of the current system, we review three case studies, from Washington State, Los Angeles County in California, and New York City. Each case study addresses different aspects of care needed by or provided to the jail-involved population, including mental health and substance abuse, emergency care, and coordination of care transitions. Ultimately, bending the cost curve for health care and criminal justice will require greater integration of the two systems.

Mechanistic information from the first volume profile analysis for a reversible intermolecular electron-transfer reaction involving pentaammine(isonicotinamide)ruthenium and cytochrome c

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

Baensch, B.; Meier, M.; Martinez, P.

1994-10-12

The reversible intermolecular electron-transfer reaction between pentaammine(isonicotinamide)ruthenium(II/III) and horse-heart cytochrome c iron(III/II) was subjected to a detailed kinetic and thermodynamic study as a function of temperature and pressure. Theoretical calculations based on the Marcus-Hush theory were employed to predict all rate and equilibrium constants as well as activation parameters. There is an excellent agreement between the kinetically and thermodynamically determined equilibrium constants and associated pressure parameters. These data are used to construct a volume profile for the overall process, from which it follows that the transition state lies halfway between the reactant and product states on a volume basis. Themore » reorganization in the transition state has reached a similar degree in both directions of the electron-transfer process and corresponds to a {lambda}{sup {double_dagger}} value of 0.44 for this reversible reaction. This is the first complete volume profile analysis for a reversible intermolecular electron-transfer reaction.« less

Vibronic Boson Sampling: Generalized Gaussian Boson Sampling for Molecular Vibronic Spectra at Finite Temperature.

PubMed

Huh, Joonsuk; Yung, Man-Hong

2017-08-07

Molecular vibroic spectroscopy, where the transitions involve non-trivial Bosonic correlation due to the Duschinsky Rotation, is strongly believed to be in a similar complexity class as Boson Sampling. At finite temperature, the problem is represented as a Boson Sampling experiment with correlated Gaussian input states. This molecular problem with temperature effect is intimately related to the various versions of Boson Sampling sharing the similar computational complexity. Here we provide a full description to this relation in the context of Gaussian Boson Sampling. We find a hierarchical structure, which illustrates the relationship among various Boson Sampling schemes. Specifically, we show that every instance of Gaussian Boson Sampling with an initial correlation can be simulated by an instance of Gaussian Boson Sampling without initial correlation, with only a polynomial overhead. Since every Gaussian state is associated with a thermal state, our result implies that every sampling problem in molecular vibronic transitions, at any temperature, can be simulated by Gaussian Boson Sampling associated with a product of vacuum modes. We refer such a generalized Gaussian Boson Sampling motivated by the molecular sampling problem as Vibronic Boson Sampling.

General methods for sensitivity analysis of equilibrium dynamics in patch occupancy models

USGS Publications Warehouse

Miller, David A.W.

2012-01-01

Sensitivity analysis is a useful tool for the study of ecological models that has many potential applications for patch occupancy modeling. Drawing from the rich foundation of existing methods for Markov chain models, I demonstrate new methods for sensitivity analysis of the equilibrium state dynamics of occupancy models. Estimates from three previous studies are used to illustrate the utility of the sensitivity calculations: a joint occupancy model for a prey species, its predators, and habitat used by both; occurrence dynamics from a well-known metapopulation study of three butterfly species; and Golden Eagle occupancy and reproductive dynamics. I show how to deal efficiently with multistate models and how to calculate sensitivities involving derived state variables and lower-level parameters. In addition, I extend methods to incorporate environmental variation by allowing for spatial and temporal variability in transition probabilities. The approach used here is concise and general and can fully account for environmental variability in transition parameters. The methods can be used to improve inferences in occupancy studies by quantifying the effects of underlying parameters, aiding prediction of future system states, and identifying priorities for sampling effort.

New insights into the by-product fatigue mechanism of the photo-induced ring-opening in diarylethenes.

PubMed

Mendive-Tapia, David; Perrier, Aurélie; Bearpark, Michael J; Robb, Michael A; Lasorne, Benjamin; Jacquemin, Denis

2014-09-14

The photochromic properties of diarylethenes, some of the most studied class of molecular switches, are known to be controlled by non-adiabatic decay at a conical intersection seam. Nevertheless, as their fatigue-reaction mechanism - leading to non-photochromic products - is yet to be understood, we investigate the photo-chemical formation of the so-called by-product isomer using three complementary computational methods (MMVB, CASSCF and CASPT2) on three model systems of increasing complexity. We show that for the ring-opening reaction a transition state on S1(2A) involving bond breaking of the penta-ring leads to a low energy S1(2A)/S0(1A) conical intersection seam, which lies above one of the transition states leading to the by-product isomer on the ground state. Therefore, radiationless decay and subsequent side-product formation can take place explaining the photo-degradation responsible for the by-product generation in diarylethene-type molecules. The effect of dynamic electron correlation and the possible role of inter-system crossing along the penta-ring opening coordinate are discussed as well.

Theoretical study of photoinduced epoxidation of olefins catalyzed by ruthenium porphyrin.

PubMed

Ishikawa, Atsushi; Sakaki, Shigeyoshi

2011-05-12

Epoxidation of olefin by [Ru(TMP)(CO)(O)](-) (TMP = tetramesitylporphine), which is a key step of the photocatalyzed epoxidation of olefin by [Ru(TMP)(CO)], is studied mainly with the density functional theory (DFT) method, where [Ru(Por)(CO)] is employed as a model complex (Por = unsubstituted porphyrin). The CASSCF method was also used to investigate the electronic structure of important species in the catalytic cycle. In all of the ruthenium porphyrin species involved in the catalytic cycle, the weight of the main configuration of the CASSCF wave function is larger than 85%, suggesting that the static correlation is not very large. Also, unrestricted-DFT-calculated natural orbitals are essentially the same as CASSCF-calculated ones, here. On the basis of these results, we employed the DFT method in this work. Present computational results show characteristic features of this reaction, as follows: (i) The epoxidation reaction occurs via carboradical-type transition state. Neither carbocation-type nor concerted oxene-insertion-type character is observed in the transition state. (ii) Electron and spin populations transfer from the olefin moiety to the porphyrin ring in the step of the C-O bond formation. (iii) Electron and spin populations of the olefin and porphyrin moieties considerably change around the transition state. (iv) The atomic and spin populations of Ru change little in the reaction, indicating that the Ru center keeps the +II oxidation state in the whole catalytic cycle. (v) The stability of the olefin adduct [Ru(Por)(CO)(O)(olefin)](-) considerably depends on the kind of olefin, such as ethylene, n-hexene, and styrene. In particular, styrene forms a stable olefin adduct. And, (vi) interestingly, the difference in the activation barrier among these olefins is small in the quantitative level (within 5 kcal/mol), indicating that this catalyst can be applied to various substrates. This is because the stabilities and electronic structures of both the olefin adduct and the transition state are similarly influenced by the substituent of olefin.

Metal–Ligand Bifunctional Catalysis: The “Accepted” Mechanism, the Issue of Concertedness, and the Function of the Ligand in Catalytic Cycles Involving Hydrogen Atoms

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

Dub, Pavel A.; Gordon, John C.

For years, following the ideas of Shvo and Noyori, the core assumption of metal–ligand bifunctional molecular catalysis has relied on the direct involvement of the chelating ligand in the catalytic reaction via a reversible proton (H +) transfer through cleavage/formation of one of its X–H bonds (X = O, N, C). A recently revised mechanism of the Noyori asymmetric hydrogenation reaction (Dub, P. A. et al. J. Am. Chem. Soc. 2014, 136, 3505) suggests that the ligand is rather involved in the catalytic reaction via the stabilization of determining transition states through N–H···O hydrogen-bonding interactions (HBIs) and not via amore » reversible H + transfer, behaving in a chemically intact manner within the productive cycle or predominantly in a chemically intact manner within productive cycles. By reexamining selected examples of computational mechanistic studies involving bifunctional catalysts from the literature in the years between 2012–2017, the purpose of this paper is to point out common misconceptions in modeling concerted reactions and show that the actual stepwise nature of key transition states unveils a more complicated catalytic reaction pool (all conceivable catalytic pathways and their crossovers). Such a realization can not only potentially result in a reconsideration of the “accepted” mechanism but also lead us to a new conceptual understanding of the role that the ligand plays in the reaction. Finally, the ultimate goal of this paper is, therefore, to encourage the reader to reconsider the function of the ligand in catalytic cycles of hydrogenation/dehydrogenation with bifunctional catalysts, which until recently has relied almost exclusively on a chemically noninnocent ligand.« less

Metal–Ligand Bifunctional Catalysis: The “Accepted” Mechanism, the Issue of Concertedness, and the Function of the Ligand in Catalytic Cycles Involving Hydrogen Atoms

DOE PAGES

Dub, Pavel A.; Gordon, John C.

2017-08-21

For years, following the ideas of Shvo and Noyori, the core assumption of metal–ligand bifunctional molecular catalysis has relied on the direct involvement of the chelating ligand in the catalytic reaction via a reversible proton (H +) transfer through cleavage/formation of one of its X–H bonds (X = O, N, C). A recently revised mechanism of the Noyori asymmetric hydrogenation reaction (Dub, P. A. et al. J. Am. Chem. Soc. 2014, 136, 3505) suggests that the ligand is rather involved in the catalytic reaction via the stabilization of determining transition states through N–H···O hydrogen-bonding interactions (HBIs) and not via amore » reversible H + transfer, behaving in a chemically intact manner within the productive cycle or predominantly in a chemically intact manner within productive cycles. By reexamining selected examples of computational mechanistic studies involving bifunctional catalysts from the literature in the years between 2012–2017, the purpose of this paper is to point out common misconceptions in modeling concerted reactions and show that the actual stepwise nature of key transition states unveils a more complicated catalytic reaction pool (all conceivable catalytic pathways and their crossovers). Such a realization can not only potentially result in a reconsideration of the “accepted” mechanism but also lead us to a new conceptual understanding of the role that the ligand plays in the reaction. Finally, the ultimate goal of this paper is, therefore, to encourage the reader to reconsider the function of the ligand in catalytic cycles of hydrogenation/dehydrogenation with bifunctional catalysts, which until recently has relied almost exclusively on a chemically noninnocent ligand.« less

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

Laser-induced free-free transitions in elastic electron scattering from CO2

NASA Astrophysics Data System (ADS)

Musa, Mohamed; MacDonald, Amy; Tidswell, Lisa; Holmes, Jim; St. Francis Xavier Laser Scattering Lab Team

2011-03-01

This report presents measurements of laser-induced free-free transitions of electrons scattered from CO2 molecules in the ground electronic state at incident electron energies of 3.8 and 5.8 eV under pulsed CO2 laser field. The differential cross section of free-free transitions involving absorption and emission of up to two photons were measured at various scattering angles with the polarization of the laser either parallel with or perpendicular to the the momentum change vector of the scattered electrons. The results of the parallel geometry are found to be in qualitative agreement with the predictions of the Kroll-Watson approximation within the experimental uncertainty whereas those of the perpendicular geometry show marked discrepancy with the Kroll-Watson predictions. This work was supported by the Natural Sciences and Engineering Research Council of Canada and the St. Francis Xavier University Council for Research.

Gravitational decoupling and the Picard-Lefschetz approach

NASA Astrophysics Data System (ADS)

Brown, Jon; Cole, Alex; Shiu, Gary; Cottrell, William

2018-01-01

In this work, we consider tunneling between nonmetastable states in gravitational theories. Such processes arise in various contexts, e.g., in inflationary scenarios where the inflaton potential involves multiple fields or multiple branches. They are also relevant for bubble wall nucleation in some cosmological settings. However, we show that the transition amplitudes computed using the Euclidean method generally do not approach the corresponding field theory limit as Mp→∞ . This implies that in the Euclidean framework, there is no systematic expansion in powers of GN for such processes. Such considerations also carry over directly to no-boundary scenarios involving Hawking-Turok instantons. In this note, we illustrate this failure of decoupling in the Euclidean approach with a simple model of axion monodromy and then argue that the situation can be remedied with a Lorentzian prescription such as the Picard-Lefschetz theory. As a proof of concept, we illustrate with a simple model how tunneling transition amplitudes can be calculated using the Picard-Lefschetz approach.

Multiphoton Rydberg and valence dynamics of CH3Br probed by mass spectrometry and slice imaging.

PubMed

Hafliðason, Arnar; Glodic, Pavle; Koumarianou, Greta; Samartzis, Peter C; Kvaran, Ágúst

2018-06-18

The multiphoton dynamics of CH3Br were probed by Mass Resolved MultiPhoton Ionization (MR-MPI), Slice Imaging and Photoelectron Imaging in the two-photon excitation region of 66 000 to 80 000 cm-1. Slice images of the CH3+ and Br+ photoproducts of ten two-photon resonant transitions to np and nd Rydberg states of the parent molecule were recorded. CH3+ ions dominate the mass spectra. Kinetic energy release spectra (KERs) were derived from slice and photoelectron images and anisotropy parameters were extracted from the angular distributions of the ions to identify the processes and the dynamics involved. At all wavelengths we observe three-photon excitations, via the two-photon resonant transitions to molecular Rydberg states, forming metastable, superexcited (CH3Br#) states which dissociate to form CH3 Rydberg states (CH3**) along with Br/Br*. A correlation between the parent Rydberg states excited and CH3** formed is evident. For the three highest excitation energies used, the CH3Br# metastable states also generate high kinetic energy fragments of CH3(X) and Br/Br*. In addition for two out of these three wavelengths we also measure one-photon photolysis of CH3Br in the A band forming CH3(X) in various vibrational modes and bromine atoms in the ground (Br) and spin-orbit excited (Br*) states.

Juvenile Justice, Mental Health, and the Transition to Adulthood: A Review of Service System Involvement and Unmet Needs in the U.S

PubMed Central

Zajac, Kristyn; Sheidow, Ashli J.; Davis, Maryann

2015-01-01

Although adolescents are the primary focus of juvenile justice, a significant number of young people involved with this system are considered transition age youth (i.e., 16–25 years of age). The aim of this review is to summarize the specific needs of transition age youth with mental health conditions involved with the juvenile justice system, identify the multiple service systems relevant to this group, and offer recommendations for policies and practice. A comprehensive search strategy was used to identify and synthesize the literature. Findings highlight the paucity of research specific to transition age youth. Thus, we also summarized relevant research on justice-involved adolescents, with a focus evaluating its potential relevance in the context of the unique milestones of the transition age, including finishing one’s education, setting and working towards vocational goals, and transitioning from ones’ family of origin to more independent living situations. Existing programs and initiatives relevant to transition age youth with mental health conditions are highlighted, and nine specific recommendations for policy and practice are offered. PMID:26273119

Juvenile Justice, Mental Health, and the Transition to Adulthood: A Review of Service System Involvement and Unmet Needs in the U.S.

PubMed

Zajac, Kristyn; Sheidow, Ashli J; Davis, Maryann

2015-09-01

Although adolescents are the primary focus of juvenile justice, a significant number of young people involved with this system are considered transition age youth (i.e., 16-25 years of age). The aim of this review is to summarize the specific needs of transition age youth with mental health conditions involved with the juvenile justice system, identify the multiple service systems relevant to this group, and offer recommendations for policies and practice. A comprehensive search strategy was used to identify and synthesize the literature. Findings highlight the paucity of research specific to transition age youth. Thus, we also summarized relevant research on justice-involved adolescents, with a focus evaluating its potential relevance in the context of the unique milestones of the transition age, including finishing one's education, setting and working towards vocational goals, and transitioning from ones' family of origin to more independent living situations. Existing programs and initiatives relevant to transition age youth with mental health conditions are highlighted, and nine specific recommendations for policy and practice are offered.

Oxygen sensing with an absolute optical sensor based on biluminescence (Conference Presentation)

NASA Astrophysics Data System (ADS)

Salas Redondo, Caterin; Reineke, Sebastian

2017-06-01

Organic semiconductors are materials having the benefits of semiconductors together with those of organic molecules. That means, on one hand, these are compounds able to absorb and emit light, as well as conduct electricity to a certain extent, which is enough for the functionality of solid state devices. On the other hand, a remarkable characteristic is that the excitations are typically localized on individual molecules, such that the exchange interactions lead to energetically distinct singlet and triplet states. According to the spectroscopic selection rules in quantum mechanics, only transitions from the singlet excited state are allowed, deactivating radiatively while generating fluorescence emission in the process, whereas transitions from the triplet excited state are not allowed, because its decay involves a spin flip, and therefore, it is theoretically forbidden by electric dipole transitions. Nevertheless, there is a small probability of these forbidden transitions to occur at a low rate, resulting in a slow radiative deactivation known as phosphorescence emission. In this context, the property of an organic molecule able to emit light from both their singlet and triplet excited states is called biluminescence. Although this dual state emission, particularly at room temperature, is difficult to achieve by purely organic molecules, it becomes possible if competitive thermal decay is suppressed effectively, allowing emission from the triplet states (i.e. phosphorescence) in addition to the conventional fluorescence. Here, we have identified biluminescence in simple host:guest systems in which a biluminophore (i.e. organic molecule with biluminescence property) is embedded in an optimum rigid matrix, for example, a combination of PMMA [poly(methyl methacrylate)] as host and NPB [N,N'-di(naphtha-1-yl)-N,N'-diphenyl-benzidine] as biluminophore [Reineke and Baldo, Sci. Rep.]. Such system is unique not only because of the dual state emission, but also the large exciton dynamic range extended up to nine orders of magnitude between nanosecond-lifetime fluorescence and millisecond-lifetime phosphorescence. In this presentation, we will report on the oxygen sensing characteristics of this luminescent system compared to a benchmarked single state optical sensor. Such properties can be evaluated because of the sensitivity of the triplet state to oxygen and therefore, we investigate the dependence of the persistent phosphorescence on the oxygen content. Furthermore, we will address our efforts towards the potential integration of novel optical biluminescent sensing into organic electronics.

Shortcuts to adiabaticity for accelerated quantum state transfer

NASA Astrophysics Data System (ADS)

Baksic, Alexandre; Ribeiro, Hugo; Clerk, Aashish A.

Adiabatic transfer protocols are among the most powerful and interesting approaches to move quantum states between two different systems. While having many advantages, those schemes are necessarily slow, and hence can suffer from dissipation and noise in the target and/or source system. In this talk, we present an approach that allows to operate a state transfer much faster, without suffering from non-adiabatic errors. The key idea is to work with a basis of dressed states whose very definition incorporates the matrix elements which give rise to non-adiabatic transitions. By introducing additional control fields, we can ensure that the system ``rides'' these new dressed states during the protocol, thus allowing for a fast high fidelity state transfer. We discuss a recent experimental implementation of these ideas in an NV-center Λ-system, as well as extensions to state transfer problems involving propagating states.

Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

NASA Astrophysics Data System (ADS)

Knott, Michael; Best, Robert B.

2014-05-01

Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an "induced fit" or "conformational selection" mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.

A new Morse-oscillator based Hamiltonian for H 3+: Calculation of line strengths

NASA Astrophysics Data System (ADS)

Jensen, Per; Špirko, V.

1986-07-01

In two recent publications [V. Špirko, P. Jensen, P. R. Bunker, and A. Čejchan, J. Mol. Spectrosc.112, 183-202 (1985); P. Jensen, V. Špirko, and P. R. Bunker, J. Mol. Spectrosc.115, 269-293 (1986)], we have described the development of Morse oscillator adapted rotation-vibration Hamiltonians for equilateral triangular X3 and Y2X molecules, and we have used these Hamiltonians to calculate the rotation-vibration energies for H 3+ and its X3+ and Y2X+ isotopes from ab initio potential energy functions. The present paper presents a method for calculating rotation-vibration line strengths of H 3+ and its isotopes using an ab initio dipole moment function [G. D. Carney and R. N. Porter, J. Chem. Phys.60, 4251-4264 (1974)] together with the energies and wave-functions obtained by diagonalization of the Morse oscillator adapted Hamiltonians. We use this method for calculating the vibrational transition moments involving the lowest vibrational states of H 3+, D 3+, H 2D +, and D 2H +. Further, we calculate the line strengths of the low- J transitions in the rotational spectra of H 3+ in the vibrational ground state and in the ν1 and ν2 states. We hope that the calculations presented will facilitate the search for further rotation-vibration transitions of H 3+ and its isotopes.

Exploring the effectiveness of transit security awareness campaigns in the San Francisco Bay Area.

DOT National Transportation Integrated Search

2010-06-01

Public involvement in alerting officials of suspicious and potentially harmful activity is critical to the overall security of a transit system. As part of an effort to get passengers and the public involved, many transit agencies have security aware...

Theoretical study on the low-lying excited states of the phosphorus monoiodide (PI) including the spin-orbit coupling

NASA Astrophysics Data System (ADS)

Zhang, Xiaomei; Liu, Xiaoting; Liang, Guiying; Li, Rui; Xu, Haifeng; Yan, Bing

2016-01-01

The potential energy curves (PECs) of the 22 Λ-S states of the phosphorus monoiodide (PI) molecule have been calculated at the level of MRCI+Q method with correlation-consistent quadruple-ζ quality basis set. The spectroscopic constants of the bound states are determined, which well reproduce the available measurements. The metastable a1Δ state has been reported for the first time, which lies between the X3Σ- and b1Σ+ states and have much deeper well than the ground state. The R-dependent spin-orbit (SO) matrix elements are calculated with the full-electron Breit-Pauli operator. Based on the SO matrix elements, the perturbations that the 23Π state may suffer from are analyzed in detail. The SOC effect makes the original Λ-S states split into 51 Ω states. In the zero-field splitting of the ground state X3Σ-, the spin-spin coupling contribution (2.23 cm-1) is found to be much smaller compared to the spin-orbit coupling contribution (50 cm-1). The avoided crossings between the Ω states lead to much shallower potential wells and the change of dissociation relationships of the states. The Ω-state wavefunctions are analyzed depending on their Λ-S compositions, showing the strong interactions among several quasidegenerate Λ-S states of the same total SO symmetry. The transition properties including electric dipole (E1), magnetic dipole (M1), and electric quadrupole (E2) transition moments (TMs), the Franck-Condon factors, the transition probabilities and the radiative lifetimes are computed for the transitions between Ω components of a1Δ and b1Σ+ states and ground state. The transition probabilities induced by the E1, E2, and M1 transitions are evaluated. The E2 makes little effect on transition probabilities. In contrast, the E1 transition makes the main contribution to the transition probability and the M1 transition also brings the influence that cannot be neglected. Finally, the radiative lifetimes are determined with the transition moments including E1 and M1. The lifetime of transition (2)0+-X10+ is evaluated at the level of millisecond, much smaller than that of the transition (2)0+-X21.

Non-resonant excitation of rare-earth ions via virtual Auger process

NASA Astrophysics Data System (ADS)

Yassievich, I. N.

2011-05-01

The luminescence of rare-earth ions (REI) is often intensified by defects associated with REIs or excitons bound to these defects. In this paper we show that the presence of such a state opens the possibility of non-resonance optical pumping via the process involving virtual Auger transition. It is the second order perturbation process when an electron arrives in an virtual intermediate state due to the optical transition (the first step) and the Auger transition is the second one. We have calculated the cross-section of such an excitation process when the optical transition is accompanied by creation of the exciton bound to the defect associated with REI and obtained a simple analytical expression for the cross-section. The excess energy of the excitation quanta is taken away by multiphonon emission. The electron-phonon interaction with local phonon vibrations of the bound exciton is assumed to determine the multiphonon process. It is shown that the probability of the process under study exceeds considerably the probability of direct optical 4f-4f absorption even in the case when the energy distance between the excitation quantum energy and the exciton energy is about 0.1 of the exciton energy. The excitation mechanism considered leads to the appearance of a broad unsymmetrical band in the excitation spectrum with the red side much wider and flatter than the blue one.

Non-equilibrium theory of arrested spinodal decomposition

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

Olais-Govea, José Manuel; López-Flores, Leticia; Medina-Noyola, Magdaleno

The non-equilibrium self-consistent generalized Langevin equation theory of irreversible relaxation [P. E. Ramŕez-González and M. Medina-Noyola, Phys. Rev. E 82, 061503 (2010); 82, 061504 (2010)] is applied to the description of the non-equilibrium processes involved in the spinodal decomposition of suddenly and deeply quenched simple liquids. For model liquids with hard-sphere plus attractive (Yukawa or square well) pair potential, the theory predicts that the spinodal curve, besides being the threshold of the thermodynamic stability of homogeneous states, is also the borderline between the regions of ergodic and non-ergodic homogeneous states. It also predicts that the high-density liquid-glass transition line, whosemore » high-temperature limit corresponds to the well-known hard-sphere glass transition, at lower temperature intersects the spinodal curve and continues inside the spinodal region as a glass-glass transition line. Within the region bounded from below by this low-temperature glass-glass transition and from above by the spinodal dynamic arrest line, we can recognize two distinct domains with qualitatively different temperature dependence of various physical properties. We interpret these two domains as corresponding to full gas-liquid phase separation conditions and to the formation of physical gels by arrested spinodal decomposition. The resulting theoretical scenario is consistent with the corresponding experimental observations in a specific colloidal model system.« less

Spectral Assignments and Analysis of the Ground State of Nitromethane in High-Resolution FTIR Synchrotron Spectra

NASA Astrophysics Data System (ADS)

Twagirayezu, Sylvestre; Billinghurst, Brant E.; May, Tim E.; Dawadi, Mahesh B.; Perry, David S.

2014-06-01

The Fourier Transform infrared spectra of CH3NO2, have been recorded, in the 400-950 wn spectral region, at a resolution of 0.00096 wn, using the Far-Infrared Beamline at Canadian Light Source. The observed spectra contain four fundamental vibrations: the NO2 in-plane rock (475.2 wn), the NO2 out-of-plane rock (604.9 wn), the NO2 symmetric bend (657.1 wn), and the CN-stretch (917.2 wn). For the lowest torsional state of CN-stretch and NO2 in-plane rock, transitions involving quantum numbers, " = 0; " {≤ 50} and {_a}" {≤ 10}, have been assigned with the aid of an automated ground state combination difference program together with a traditional Loomis Wood approach Ground state combination differences derived from more than 2100 infrared transitions have been fit with the six-fold torsion-rotation program developed by Ilyushin et al. Additional sextic and octic centrifugal distortion parameters are derived for the ground vibrational state. C. F. Neese., An Interactive Loomis-Wood Package, V2.0, {56th},OSU Interanational Symposium on Molecular Spectroscopy (2001). V. V. Ilyushin, Z. Kisiel, L. Pszczolkowski, H. Mader, and J. T. Hougen, J. Mol. Spectrosc., 259, 26, (2010).

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 layer turbulence are, in many dynamically important respects, similar.

Hidden crossing theory of charge exchange in H+ + He+(1 s) collisions in vicinity of maximum of cross section

NASA Astrophysics Data System (ADS)

Grozdanov, Tasko P.; Solov'ev, Evgeni A.

2018-04-01

Within the framework of dynamical adiabatic approach the hidden crossing theory of inelastic transitions is applied to charge exchange in H+ + He+(1 s) collisions in the wide range of center of mass collision energies E cm = (1.6 -70) keV. The good agreement with experiment and molecular close coupling calculations is obtained. At low energies our 4-state results are closest to the experiment and correctly reproduce the shoulder in energy dependence of the cross section around E cm = 6 keV. The 2-state results correctly predict the position of the maximum of the cross section at E cm ≈ 40 keV, whereas 4-state results fail to correctly describe the region around the maximum. The reason for this is the fact that adiabatic approximation for a given two-state hidden crossing is applicable for values of the Schtueckelberg parameter >1. But with increase of principal quantum number N the Schtueckelberg parameter decreases as N -3. That is why the 4-state approach involving higher excited states fails at smaller collision energies E cm ≈ 15 keV, while the 2-state approximation which involves low lying states can be extended to higher collision energies.

Transition to Kindergarten: Family Experiences and Involvement

ERIC Educational Resources Information Center

McIntyre, Laura Lee; Eckert, Tanya L.; Fiese, Barbara H.; DiGennaro, Florence D.; Wildenger, Leah K.

2007-01-01

The transition to kindergarten is an important developmental milestone for young children, their families, and teachers. Preparing students for successful kindergarten transition has been identified as a national priority, yet the degree to which parents are involved in kindergarten preparation is rarely considered. This study investigated the…

Research in Secondary Special Education and Transitional Employment.

ERIC Educational Resources Information Center

Rusch, Frank R., Comp.

This compilation of eight research papers covers various aspects of secondary-level special education and transitional employment involving individuals with mild to profound disabilities. Titles and authors of the papers are: "Parent Involvement in Transition Programs" (Jeff McNair and Frank R. Rusch); "Using a Cognitive-Process…

Tuning the reactivity of Fe(V)(O) toward C-H bonds at room temperature: effect of water.

PubMed

Singh, Kundan K; Tiwari, Mrityunjay k; Ghosh, Munmun; Panda, Chakadola; Weitz, Andrew; Hendrich, Michael P; Dhar, Basab B; Vanka, Kumar; Sen Gupta, Sayam

2015-02-16

The presence of an Fe(V)(O) species has been postulated as the active intermediate for the oxidation of both C-H and C═C bonds in the Rieske dioxygenase family of enzymes. Understanding the reactivity of these high valent iron-oxo intermediates, especially in an aqueous medium, would provide a better understanding of these enzymatic reaction mechanisms. The formation of an Fe(V)(O) complex at room temperature in an aqueous CH3CN mixture that contains up to 90% water using NaOCl as the oxidant is reported here. The stability of Fe(V)(O) decreases with increasing water concentration. We show that the reactivity of Fe(V)(O) toward the oxidation of C-H bonds, such as those in toluene, can be tuned by varying the amount of water in the H2O/CH3CN mixture. Rate acceleration of up to 60 times is observed for the oxidation of toluene upon increasing the water concentration. The role of water in accelerating the rate of the reaction has been studied using kinetic measurements, isotope labeling experiments, and density functional theory (DFT) calculations. A kinetic isotope effect of ∼13 was observed for the oxidation of toluene and d8-toluene showing that C-H abstraction was involved in the rate-determining step. Activation parameters determined for toluene oxidation in H2O/CH3CN mixtures on the basis of Eyring plots for the rate constants show a gain in enthalpy with a concomitant loss in entropy. This points to the formation of a more-ordered transition state involving water molecules. To further understand the role of water, we performed a careful DFT study, concentrating mostly on the rate-determining hydrogen abstraction step. The DFT-optimized structure of the starting Fe(V)(O) and the transition state indicates that the rate enhancement is due to the transition state's favored stabilization over the reactant due to enhanced hydrogen bonding with water.

Nitric oxide excited under auroral conditions: Excited state densities and band emissions

NASA Astrophysics Data System (ADS)

Cartwright, D. C.; Brunger, M. J.; Campbell, L.; Mojarrabi, B.; Teubner, P. J. O.

2000-09-01

Electron impact excitation of vibrational levels in the ground electronic state and nine excited electronic states in NO has been simulated for an IBC II aurora (i.e., ˜10 kR in 3914 Å radiation) in order to predict NO excited state number densities and band emission intensities. New integral electron impact excitation cross sections for NO were combined with a measured IBC II auroral secondary electron distribution, and the vibrational populations of 10 NO electronic states were determined under conditions of statistical equilibrium. This model predicts an extended vibrational distribution in the NO ground electronic state produced by radiative cascade from the seven higher-lying doublet excited electronic states populated by electron impact. In addition to significant energy storage in vibrational excitation of the ground electronic state, both the a 4Π and L2 Φ excited electronic states are predicted to have relatively high number densities because they are only weakly connected to lower electronic states by radiative decay. Fundamental mode radiative transitions involving the lowest nine excited vibrational levels in the ground electronic state are predicted to produce infrared (IR) radiation from 5.33 to 6.05 μm with greater intensity than any single NO electronic emission band. Fundamental mode radiative transitions within the a 4Π electronic state, in the 10.08-11.37 μm region, are predicted to have IR intensities comparable to individual electronic emission bands in the Heath and ɛ band systems. Results from this model quantitatively predict the vibrational quantum number dependence of the NO IR measurements of Espy et al. [1988].

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.

Chinese Parents' Perceptions and Practices of Parental Involvement during School Transition

ERIC Educational Resources Information Center

Lau, Eva Yi Hung

2014-01-01

Parents' perceptions and practices of parental involvement during the transition from kindergarten to primary school were captured through individual interviews with 18 Chinese parents after their children had entered primary school. The responses revealed that in order to facilitate children's adjustment during school transition, parents tended…

Importance of Teacher Transition Competencies as Rated by Special Educators.

ERIC Educational Resources Information Center

Blanchett, Wanda J.

2001-01-01

Seventy-four special educators who were involved in transition-related activities rated the importance of 30 transition-related teacher competencies. All competencies were identified by the majority of respondents as important. Competencies related to teaching money management skills and involving parents received the highest ratings. (Contains…

Can Chlorine Anion Catalyze the Reaction fo HOCl with HCl?

NASA Technical Reports Server (NTRS)

Richardson, S. L.; Francisco, J. S.; Mebel, A. M.; Morokuma, K.

1997-01-01

The reaction of HOCl + HCl -> Cl2 + H20 in the presence of Cl has been studied using ab initio methods. This reaction has been shown to have a high activation barrier of 46.5 kcal/mol. The chlorine anion, Cl- is found to catalyze the reaction, viz. two mechanisms. The first involves Cl- interacting through the concerted four-center transition state of the neutral reaction. The other mechanism involves the formation of a HCl-HOCl-Cl- intermediate which dissociates into Cl2 + Cl- + H20. The steps are found to have no barriers. The overall exothermicity is 15.5 kcal/mol.

A theoretical study of the molecular mechanism of the GAPDH Trypanosoma cruzi enzyme involving iodoacetate inhibitor

NASA Astrophysics Data System (ADS)

Carneiro, Agnaldo Silva; Lameira, Jerônimo; Alves, Cláudio Nahum

2011-10-01

The glyceraldehyde-3-phosphate dehydrogenase enzyme (GAPDH) is an important biological target for the development of new chemotherapeutic agents against Chagas disease. In this Letter, the inhibition mechanism of GAPDH involving iodoacetate (IAA) inhibitor was studied using the hybrid quantum mechanical/molecular mechanical (QM/MM) approach and molecular dynamic simulations. Analysis of the potential energy surface and potential of mean force show that the covalent attachment of IAA inhibitor to the active site of the enzyme occurs as a concerted process. In addition, the energy terms decomposition shows that NAD+ plays an important role in stabilization of the reagents and transition state.

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

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.

The Role of Epithelial-Mesenchymal Transition in the Formation of Normal and Neoplastic Mammary Epithelial Stem Cells

DTIC Science & Technology

2011-09-01

separating stem cell and non- stem cell populations of normal and breast cancer cells and identified EMT transcription factors most likely involved in... stem cell biology. Preliminary results directly demonstrate that transient induction of EMT increases the number of mammary epithelial stem cells...EMT and entrance into a stem - cell state. The outcome of these experiments holds important implications for the mechanisms controlling the formation of

Resonant recombination and autoionization in electron-ion collisions

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

Mueller, A.

1990-06-01

The occurence of resonances in elastic and inelastic electron-ion collisions is discussed. Resonant processes involve excitation of the ion with simultaneous capture of the initially free electron. The decay mechanism subsequent to the formation of the intermediate multiply excited state determines whether a resonance is found in recombination, excitation, elastic scattering, in single or even in multiple ionization. This review concentrates on resonances in the ionization channel. Correlated two-electron transitions are considered.

Pressure–Temperature Phase Diagram Reveals Spin–Lattice Interactions in Co[N(CN) 2 ] 2

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

Musfeldt, J. L.; O’Neal, K. R.; Brinzari, T. V.

2017-04-07

Diamond anvil cell techniques, synchrotron-based infrared and Raman spectroscopies, and lattice dynamics calculations are combined with prior magnetic property work to reveal the pressure–temperature phase diagram of Co[N(CN)2]2. The second-order structural boundaries converge on key areas of activity involving the spin state exposing how the pressure-induced local lattice distortions trigger the ferromagnetic → antiferromagnetic transition in this quantum material.

Radiation and Laser Potential of Homo and Heteronuclear Rare-Gas Diatomic Molecules.

DTIC Science & Technology

1982-12-01

studied in detail and classified in terms of the transition involved. Molecular constants and H details of the dimer potential curves were determined...identify their origin and determine excited state energies and molecular parameters. Summary of the Research: The rare-gas dimers were studied in the... Molecular Dynamics Symposium, October 1979, by Y. Tanaka. Emission Spectra of Kr 2 in the VUV Region Paper to be presented at AFOSR/ Molecular

Dinuclear Tricyclic Transition State Model for Carbonyl Addition of Organotitanium Reagents: DFT Study on the Activity and Enantioselectivity of BINOLate Titanium Catalysts.

PubMed

Harada, Toshiro

2018-06-08

In the presence of a catalytic amount of chiral BINOL derivatives (or BINOLs), a mixture of various organometallic compounds with Ti(O i Pr) 4 undergoes enantioselective addition to aldehydes and ketones. Although the catalyst and reacting nucleophile of the reaction have been elucidated to be ( BINOLate)Ti 2 (O i Pr) 6 and RTi(O i Pr) 3 , respectively, little is known about the properties of short-lived intermediates and transition structures. In this work, the mechanism of this reaction is investigated with the aid of DFT (M06) calculations. The study provides support for the following mechanistic understandings: (i) The direct racemic reaction proceeds through a pathway involving initial aggregation of RTi(O i Pr) 3 with Ti(O i Pr) 4 followed by carbonyl addition of the resulting dinuclear aggregate. (ii) The enantioselective reaction takes place through a pathway involving initial ligand exchange of RTi(O i Pr) 3 with ( BINOLate)Ti 2 (O i Pr) 6 followed by the addition of the resulting chiral dinuclear titanium species via a chiral BINOLate-chelated, tricyclic transition structure. (iii) The enantioselective pathway is favorable not because BINOLate ligands accelerate the carbonyl addition but because the ligands stabilize the chiral dinuclear species against deaggregation through a chelating bridge. (iv) The chiral transition structure serves as a model accounting for the re-face addition generally observed in the reaction of aldehydes with ( R)- BINOLs.

Empowering Energy Justice.

PubMed

Finley-Brook, Mary; Holloman, Erica L

2016-09-21

The U.S. is experiencing unprecedented movement away from coal and, to a lesser degree, oil. Burdened low-income communities and people of color could experience health benefits from reductions in air and water pollution, yet these same groups could suffer harm if transitions lack broad public input or if policies prioritize elite or corporate interests. This paper highlights how U.S. energy transitions build from, and contribute to, environmental injustices. Energy justice requires not only ending disproportionate harm, it also entails involvement in the design of solutions and fair distribution of benefits, such as green jobs and clean air. To what extent does the confluence of state, civic, and market processes assure "just" transitions to clean, low-carbon energy production involving equitable distribution of costs, benefits, and decision-making power? To explore this question we assess trends with (1) fossil fuel divestment; (2) carbon taxes and social cost of carbon measurements; (3) cap-and-trade; (4) renewable energy; and (5) energy efficiency. Current research demonstrates opportunities and pitfalls in each area with mixed or partial energy justice consequences, leading to our call for greater attention to the specifics of distributive justice , procedural justice , and recognition justice in research, policy, and action. Illustrative energy transition case studies suggest the feasibility and benefit of empowering approaches, but also indicate there can be conflict between "green" and "just", as evident though stark inequities in clean energy initiatives. To identify positive pathways forward, we compile priorities for an energy justice research agenda based on interactive and participatory practices aligning advocacy, activism, and academics.

Evolution of complexity in the volvocine algae: transitions in individuality through Darwin's eye.

PubMed

Herron, Matthew D; Michod, Richard E

2008-02-01

The transition from unicellular to differentiated multicellular organisms constitutes an increase in the level complexity, because previously existing individuals are combined to form a new, higher-level individual. The volvocine algae represent a unique opportunity to study this transition because they diverged relatively recently from unicellular relatives and because extant species display a range of intermediate grades between unicellular and multicellular, with functional specialization of cells. Following the approach Darwin used to understand "organs of extreme perfection" such as the vertebrate eye, this jump in complexity can be reduced to a series of small steps that cumulatively describe a gradual transition between the two levels. We use phylogenetic reconstructions of ancestral character states to trace the evolution of steps involved in this transition in volvocine algae. The history of these characters includes several well-supported instances of multiple origins and reversals. The inferred changes can be understood as components of cooperation-conflict-conflict mediation cycles as predicted by multilevel selection theory. One such cycle may have taken place early in volvocine evolution, leading to the highly integrated colonies seen in extant volvocine algae. A second cycle, in which the defection of somatic cells must be prevented, may still be in progress.

Allylic amination reactivity of Ni, Pd, and Pt heterobimetallic and monometallic complexes.

PubMed

Carlsen, Ryan W; Ess, Daniel H

2016-06-14

Transition metal heterobimetallic complexes with dative metal-metal interactions have the potential for novel fast reactivity. There are few studies that both compare the reactivity of different metal centers in heterobimetallic complexes and compare bimetallic reactivity to monometallic reactivity. Here we report density-functional calculations that show the reactivity of [Cl2Ti(N(t)BuPPh2)2M(II)(η(3)-methallyl)] heterobimetallic complexes for allylic amination follows M = Ni > Pd > Pt. This reactivity trend was not anticipated since the amine addition transition state involves M(II) to M(0) reduction and this could disadvantage Ni. Comparison of heterobimetallic complexes to the corresponding monometallic (CH2)2(N(t)BuPPh2)2M(II)(η(3)-methallyl) complexes reveals that this reactivity trend is due to the bimetallic interaction and that the bimetallic interaction significantly lowers the barrier height for amine addition by >10 kcal mol(-1). The impact of the early transition metal center on the amination addition barrier height depends on the late transition metal center. The lowest barrier heights for this reaction occur when late and early transition metal centers are from the same periodic table row.

Continuous and discontinuous phase transitions in the evolution of a polygenic trait under stabilizing selective pressure

NASA Astrophysics Data System (ADS)

Fierro, Annalisa; Cocozza, Sergio; Monticelli, Antonella; Scala, Giovanni; Miele, Gennaro

2017-06-01

The presence of phenomena analogous to phase transition in Statistical Mechanics has been suggested in the evolution of a polygenic trait under stabilizing selection, mutation and genetic drift. By using numerical simulations of a model system, we analyze the evolution of a population of N diploid hermaphrodites in random mating regime. The population evolves under the effect of drift, selective pressure in form of viability on an additive polygenic trait, and mutation. The analysis allows to determine a phase diagram in the plane of mutation rate and strength of selection. The involved pattern of phase transitions is characterized by a line of critical points for weak selective pressure (smaller than a threshold), whereas discontinuous phase transitions, characterized by metastable hysteresis, are observed for strong selective pressure. A finite-size scaling analysis suggests the analogy between our system and the mean-field Ising model for selective pressure approaching the threshold from weaker values. In this framework, the mutation rate, which allows the system to explore the accessible microscopic states, is the parameter controlling the transition from large heterozygosity ( disordered phase) to small heterozygosity ( ordered one).

Proposal for Laser Cooling of Alkaline Earth Monoalkoxide Free Radicals

NASA Astrophysics Data System (ADS)

Baum, Louis; Kozyryev, Ivan; Matsuda, Kyle; Doyle, John M.

2016-05-01

Cold samples of polyatomic molecules will open new avenues in physics, chemistry, and quantum science. Non-diagonal Franck-Condon factors, technically challenging wavelengths, and the lack of strong electronic transitions inhibit direct laser cooling of nonlinear molecules. We identify a scheme for optical cycling in certain molecules with six or more atoms. Replacing hydrogen in alcohols with an alkaline earth metal (M) leads to alkaline earth monoalkoxide free radicals (MOR), which have favorable properties for laser cooling. M-O bond is very ionic, so the metal orbitals are slightly affected by the nature of R on the ligand. Diagonal Franck-Condon factors, laser accessible transitions, and a small hyperfine structure make MOR molecules suitable for laser cooling. We explore a scheme for optical cycling on the A - X transition of SrOCH3 . Molecules lost to dark vibrational states will be repumped on the B - X transition. Extension to larger species is possible through expansion of the R group since transitions involve the promotion of the metal-centered nonbonding valence electron. We will detail our estimations of the Franck-Condon factors, simulations of the cooling process and describe progress towards the Doppler cooling of MOR polyatomics.

Fourier Transform Emission Spectroscopy of the [7.3] 2Δ- a2Φ and [9.4] 2Φ- a2Φ Systems of ZrCl

NASA Astrophysics Data System (ADS)

Ram, R. S.; Bernath, P. F.

1999-08-01

The emission spectrum of ZrCl has been observed in the 1800-12 000 cm-1 region using a Fourier transform spectrometer. The molecules were excited in a microwave discharge of a mixture of helium and a trace of ZrCl4 vapor. In addition to the C4Δ-X4Φ transition reported previously, numerous new bands observed in the near infrared have been classified into two electronic transitions, [7.3]2Δ-a2Φ and [9.4]2Φ-a2Φ. Five new bands observed in the 6700-7400 cm-1 region have been assigned as 2Δ3/2-2Φ5/2 and 2Δ5/2-2Φ7/2 subbands of a new electronic transition, [7.3]2Δ-a2Φ. The two subbands of the [9.4]2Φ-a2Φ transition were previously observed by G. Phillips, S. P. Davis, and D. C. Galehouse [Astrophys. J. Suppl. 43, 417-434 (1980)], who tentatively labeled them as 2Π1/2-2Π1/2 and 2Π3/2-2Π3/2 subbands. A number of new bands involving higher vibrational levels have been identified for these two subbands. A rotational analysis of a number of bands of both transitions has been obtained and spectroscopic constants have been determined. Global perturbations have been observed in both spin components of the a2Φ state. The assignment of the observed electronic states has been discussed in light of recent theoretical calculations.

Traversing the folding pathway of proteins using temperature-aided cascade molecular dynamics with conformation-dependent charges.

PubMed

Jani, Vinod; Sonavane, Uddhavesh; Joshi, Rajendra

2016-07-01

Protein folding is a multi-micro second time scale event and involves many conformational transitions. Crucial conformational transitions responsible for biological functions of biomolecules are difficult to capture using current state-of-the-art molecular dynamics (MD) simulations. Protein folding, being a stochastic process, witnesses these transitions as rare events. Many new methodologies have been proposed for observing these rare events. In this work, a temperature-aided cascade MD is proposed as a technique for studying the conformational transitions. Folding studies for Engrailed homeodomain and Immunoglobulin domain B of protein A have been carried out. Using this methodology, the unfolded structures with RMSD of 20 Å were folded to a structure with RMSD of 2 Å. Three sets of cascade MD runs were carried out using implicit solvation, explicit solvation, and charge updation scheme. In the charge updation scheme, charges based on the conformation obtained are calculated and are updated in the topology file. In all the simulations, the structure of 2 Å was reached within a few nanoseconds using these methods. Umbrella sampling has been performed using snapshots from the temperature-aided cascade MD simulation trajectory to build an entire conformational transition pathway. The advantage of the method is that the possible pathways for a particular reaction can be explored within a short duration of simulation time and the disadvantage is that the knowledge of the start and end state is required. The charge updation scheme adds the polarization effects in the force fields. This improves the electrostatic interaction among the atoms, which may help the protein to fold faster.

Elucidation of electronic structure by the analysis of hyperfine interactions: The MnH A 7Π-X 7Sigma + (0,0) band

NASA Astrophysics Data System (ADS)

Varberg, Thomas D.; Field, Robert W.; Merer, Anthony J.

1991-08-01

We present a complete analysis of the hyperfine structure of the MnH A 7Π-X 7Σ+ (0,0) band near 5680 Å, studied with sub-Doppler resolution by intermodulated fluorescence spectroscopy. Magnetic hyperfine interactions involving both the 55Mn (I=5/2) and 1H (I=1/2) nuclear spins are observed as well as 55Mn electric quadrupole effects. The manganese Fermi contact interaction in the X 7Σ+ state is the dominant contributor to the observed hyperfine splittings; the ΔF=0, ΔN=0, ΔJ=±1 matrix elements of this interaction mix the electron spin components of the ground state quite strongly at low N, destroying the ``goodness'' of J as a quantum number and inducing rotationally forbidden, ΔJ=±2 and ±3 transitions. The hyperfine splittings of over 50 rotational transitions covering all 7 spin components of both states were analyzed and fitted by least squares, allowing the accurate determination of 14 different hyperfine parameters. Using single electronic configurations to describe the A 7Π and X 7Σ+ states and Herman-Skillman atomic radial wave functions to represent the molecular orbitals, we calculated a priori values for the 55Mn and 1H hyperfine parameters which agree closely with experiment. We show that the five high-spin coupled Mn 3d electrons do not contribute to the manganese hyperfine structure but are responsible for the observed proton magnetic dipolar couplings. Furthermore, the results suggest that the Mn 3d electrons are not significantly involved in bonding and demonstrate that the molecular hyperfine interactions may be quantitatively understood using simple physical interpretations.

Rational Modulation of the Induced-Fit Conformational Change for Slow-Onset Inhibition in Mycobacterium tuberculosis InhA.

PubMed

Lai, Cheng-Tsung; Li, Huei-Jiun; Yu, Weixuan; Shah, Sonam; Bommineni, Gopal R; Perrone, Victoria; Garcia-Diaz, Miguel; Tonge, Peter J; Simmerling, Carlos

2015-08-04

Slow-onset enzyme inhibitors are the subject of considerable interest as an approach to increasing the potency of pharmaceutical compounds by extending the residence time of the inhibitor on the target (the lifetime of the drug-receptor complex). However, rational modulation of residence time presents significant challenges because it requires additional mechanistic insight, such as the nature of the transition state for postbinding isomerization. Our previous work, based on X-ray crystallography, enzyme kinetics, and molecular dynamics simulation, suggested that the slow step in inhibition of the Mycobacterium tuberculosis enoyl-ACP reductase InhA involves a change in the conformation of the substrate binding loop from an open state in the initial enzyme-inhibitor complex to a closed state in the final enzyme-inhibitor complex. Here, we use multidimensional free energy landscapes for loop isomerization to obtain a computational model for the transition state. The results suggest that slow-onset inhibitors crowd key side chains on helices that slide past each other during isomerization, resulting in a steric clash. The landscapes become significantly flatter when residues involved in the steric clash are replaced with alanine. Importantly, this lower barrier can be increased by rational inhibitor redesign to restore the steric clash. Crystallographic studies and enzyme kinetics confirm the predicted effects on loop structure and flexibility, as well as inhibitor residence time. These loss and regain of function studies validate our mechanistic hypothesis for interactions controlling substrate binding loop isomerization, providing a platform for the future design of inhibitors with longer residence times and better in vivo potency. Similar opportunities for slow-onset inhibition via the same mechanism are identified in other pathogens.

Quantum-size-induced phase transitions in quantum dots: Indirect-band gap GaAs nanostructures

NASA Astrophysics Data System (ADS)

Zunger, Alex; Luo, Jun-Wei; Franceschetti, Alberto

2008-03-01

Quantum nanostructures are often advertised as having stronger absorption than the bulk material from which they are made, to the potential benefit of nanotechnology. However, nanostructures made of direct gap materials such as GaAs can convert to indirect-gap, weakly-aborbing systems when the quantum size becomes small. This is the case for spherical GaAs dots of radius 15 å or less (about 1000 atoms) embedded in a wide-gap matrix. The nature of the transition: γ-to-X or γ-to-L is however, controversial. The distinction can not be made on the basis of electronic structure techniques that misrepresent the magnitude of the various competing effective mass tensors (e.g, LDA or GGA) or wavefunction coupling (e.g, tight-binding). Using a carefully fit screened pseudopotential method we show that the transition occurs from γ to X, and, more importantly, that the transition involves a finite V (γ-X) interband coupling, manifested as an ``anti-crossing'' between the confined electron states of GaAs as the dot size crosses 15 å. The physics of this reciprocal-space γ-X transition, as well as the real-space (type II) transition in GaAs/AlGaAs will be briefly discussed.

Measured Boundary Layer Transition and Rotor Hover Performance at Model Scale

NASA Technical Reports Server (NTRS)

Overmeyer, Austin D.; Martin, Preston B.

2017-01-01

An experiment involving a Mach-scaled, 11:08 f t: diameter rotor was performed in hover during the summer of 2016 at NASA Langley Research Center. The experiment investigated the hover performance as a function of the laminar to turbulent transition state of the boundary layer, including both natural and fixed transition cases. The boundary layer transition locations were measured on both the upper and lower aerodynamic surfaces simultaneously. The measurements were enabled by recent advances in infrared sensor sensitivity and stability. The infrared thermography measurement technique was enhanced by a paintable blade surface heater, as well as a new high-sensitivity long wave infrared camera. The measured transition locations showed extensive amounts, x=c>0:90, of laminar flow on the lower surface at moderate to high thrust (CT=s > 0:068) for the full blade radius. The upper surface showed large amounts, x=c > 0:50, of laminar flow at the blade tip for low thrust (CT=s < 0:045). The objective of this paper is to provide an experimental data set for comparisons to newly developed and implemented rotor boundary layer transition models in CFD and rotor design tools. The data is expected to be used as part of the AIAA Rotorcraft SimulationWorking Group

Computational Fluid Dynamics (CFD) Simulation of Hypersonic Turbine-Based Combined-Cycle (TBCC) Inlet Mode Transition

NASA Technical Reports Server (NTRS)

Slater, John W.; Saunders, John D.

2010-01-01

Methods of computational fluid dynamics were applied to simulate the aerodynamics within the turbine flowpath of a turbine-based combined-cycle propulsion system during inlet mode transition at Mach 4. Inlet mode transition involved the rotation of a splitter cowl to close the turbine flowpath to allow the full operation of a parallel dual-mode ramjet/scramjet flowpath. Steady-state simulations were performed at splitter cowl positions of 0deg, -2deg, -4deg, and -5.7deg, at which the turbine flowpath was closed half way. The simulations satisfied one objective of providing a greater understanding of the flow during inlet mode transition. Comparisons of the simulation results with wind-tunnel test data addressed another objective of assessing the applicability of the simulation methods for simulating inlet mode transition. The simulations showed that inlet mode transition could occur in a stable manner and that accurate modeling of the interactions among the shock waves, boundary layers, and porous bleed regions was critical for evaluating the inlet static and total pressures, bleed flow rates, and bleed plenum pressures. The simulations compared well with some of the wind-tunnel data, but uncertainties in both the windtunnel data and simulations prevented a formal evaluation of the accuracy of the simulation methods.

Doubly magic Pb 208 : High-spin states, isomers, and E 3 collectivity in the yrast decay

DOE PAGES

Broda, R.; Janssens, R. V. F.; Iskra, Ł. W.; ...

2017-06-12

Yrast and near-yrast levels up to spin values in excess of I = 30h have been delineated in the doubly-magic 208Pb nucleus following deep-inelastic reactions involving 208Pb targets and, mostly, 430-MeV 48Ca and 1440-MeV 208Pb beams. The level scheme was established up to an excitation energy of 16.4 MeV, based on multi-fold γ-ray coincidence relationships measured with the Gammasphere array. Below the well-known, 0.5-μs 10 + isomer, ten new transitions were added to earlier work. The delineation of the higher parts of the level sequence benefited from analyses involving a number of prompt- and delayed-coincidence conditions. Three new isomeric statesmore » were established along the yrast line with I π = 20 - (10342 keV), 23 + (11361 keV), and 28 - (13675 keV), and respective half-lives of 22(3), 12.7(2), and 60(6) ns. Gamma transitions were also identified preceding in time the 28 - isomer, however, only a few could be placed in the level scheme and no firm spin-parity quantum numbers could be proposed. In contrast, for most states below this 28 - isomer, firm spin-parity values were assigned, based on total electron-conversion coefficients, deduced for low-energy (<500 keV) transitions from γ-intensity balances, and on measured γ-ray angular distributions. The latter also enabled the quantitative determination of mixing ratios. The transition probabilities extracted for all isomeric transitions in 208Pb have been reviewed and discussed in terms of the intrinsic structure of the initial and final levels involved. Particular emphasis was placed on the many observed E3 transitions as they often exhibit significant enhancements in strength (of the order of tens of W.u.) comparable to the one seen for the neutron j 15/2→g 9/2 E3 transition in 209Pb. In this context, the enhancement of the 725-keV E3 transition (56 W.u.) associated with the decay of the highest-lying 28 - isomer observed in this work remains particularly challenging to explain. Large-scale shell-model calculations were performed with two approaches, a first one where the 1, 2, and 3 particle-hole excitations do not mix with one another, and another more complex one, in which such mixing takes place. We compared the calculated levels with the data and a general agreement is observed for most of the 208Pb level scheme. At the highest spins and energies, however, the 2 correspondence between theory and experiment is less satisfactory and the experimental yrast line appears to be more regular than the calculated one. This regularity is notable when the level energies are plotted versus the I(I+1) product and the observed, nearly linear, behavior was considered within a simple “rotational” interpretation. Furthermore, within this approximate picture, the extracted moment of inertia suggests that only the 76 valence nucleons participate in the “rotation” and that the 132Sn spherical core remains inert.« less

How well do services for young people with long term conditions deliver features proposed to improve transition?

PubMed

Colver, A; Pearse, R; Watson, R M; Fay, M; Rapley, T; Mann, K D; Le Couteur, A; Parr, J R; McConachie, H

2018-05-08

For young people with long-term conditions, transition from child to adult-oriented health services is a critical period which, if not managed well, may lead to poor outcomes. There are features of transition services which guidance and research suggest improve outcomes. We studied nine such features, calling them 'proposed beneficial features': age-banded clinic; meet adult team before transfer; promotion of health self-efficacy; written transition plan; appropriate parent involvement; key worker; coordinated team; holistic life-skills training; transition manager for clinical team. We aimed to describe the extent to which service providers offer these nine features, and to compare this with young people's reported experience of them. A longitudinal, mixed methods study followed 374 young people as their care moved from child to adult health services. Participants had type 1 diabetes, cerebral palsy or autism spectrum disorder with additional mental health difficulties. Data are reported from the first two visits, one year apart. Three hundred four (81.3%) of the young people took part in the second visit (128 with diabetes, 91 with autism, 85 with cerebral palsy). Overall, the nine proposed beneficial features of transition services were poorly provided. Fewer than half of services stated they provided an age-banded clinic, written transition plan, transition manager for clinical team, a protocol for promotion of health self-efficacy, or holistic life-skills training. To varying degrees, young people reported that they had not experienced the features which services said they provided. For instance, the agreement for written transition plan, holistic life-skills training and key worker, was 30, 43 and 49% respectively. Agreement was better for appropriate parent involvement, age-banded clinic, promotion of health self-efficacy and coordinated team at 77, 77, 80 and 69% respectively. Variation in the meaning of the features as experienced by young people and families was evident from qualitative interviews and observations. UK services provide only some of the nine proposed beneficial features for supporting healthcare transition of young people with long term conditions. Observational studies or trials which examine the influence of features of transition services on outcomes should ensure that the experiences of young people and families are captured, and not rely on service specifications.

Ionization equilibrium and radiative energy loss rates for C, N, and O ions in low-density plasmas

NASA Technical Reports Server (NTRS)

Jacobs, V. L.; Davis, J.; Rogerson, J. E.; Blaha, M.

1978-01-01

The results of calculations of the ionization equilibrium and radiative energy loss rates for C, N and O ions in low-density plasmas are presented for electron temperatures in the range 10,000-10,000,000 K. The ionization structure is determined by using the steady-state corona model, in which electron impact ionization from the ground states is balanced by direct radiative and dielectronic recombination. With an improved theory, detailed calculations are carried out for the dielectronic recombination rates in which account is taken of all radiative and autoionization processes involving a single-electron electric-dipole transition of the recombining ion. The radiative energy loss processes considered are electron-impact excitation of resonance line emission, direct radiative recombination, dielectronic recombination, and electron-ion bremsstrahlung. For all three elements, resonance line emission resulting from 2s-2p transitions produces a broad maximum in the energy loss rate near 100,000 K.

Quantum Vertex Model for Reversible Classical Computing

NASA Astrophysics Data System (ADS)

Chamon, Claudio; Mucciolo, Eduardo; Ruckenstein, Andrei; Yang, Zhicheng

We present a planar vertex model that encodes the result of a universal reversible classical computation in its ground state. The approach involves Boolean variables (spins) placed on links of a two-dimensional lattice, with vertices representing logic gates. Large short-ranged interactions between at most two spins implement the operation of each gate. The lattice is anisotropic with one direction corresponding to computational time, and with transverse boundaries storing the computation's input and output. The model displays no finite temperature phase transitions, including no glass transitions, independent of circuit. The computational complexity is encoded in the scaling of the relaxation rate into the ground state with the system size. We use thermal annealing and a novel and more efficient heuristic \\x9Dannealing with learning to study various computational problems. To explore faster relaxation routes, we construct an explicit mapping of the vertex model into the Chimera architecture of the D-Wave machine, initiating a novel approach to reversible classical computation based on quantum annealing.

Laser spectroscopy of the 5P3/2 → 6Pj (j = 1/2 and 3/2) electric dipole forbidden transitions in atomic rubidium

NASA Astrophysics Data System (ADS)

Ponciano-Ojeda, F.; Hernández-Gómez, S.; Mojica-Casique, C.; Hoyos, L. M.; Flores-Mijangos, J.; Ramírez-Martínez, F.; Sahagún, D.; Jáuregui, R.; Jiménez-Mier, J.

2018-04-01

Doppler-free optical double-resonance spectroscopy is used to study the 5S1/2 → 5P3/2 → 6Pj (j = 3/2,1/2) excitation sequence in room-temperature rubidium atoms. This involves a 5S1/2 → 5P3/2 electric dipole preparation step followed by the 5P3/2 → 6Pj electric quadrupole excitation. The electric dipole forbidden transitions occur at 911.0 nm (j = 3/2) and 917.5 nm (j = 1/2). Production of atoms in the 6Pj states is detected by observing their direct decay to the ground state through emission of blue photons (λ ≈ 420 nm). A detailed experimental and theoretical study of the dependence on the relative linear polarizations of excitation beams is made. It is shown that specific electric quadrupole selection rules over magnetic quantum numbers are directly related to the relative orientation of the linear polarization of the excitation beams.

Are there dynamical effects in enzyme catalysis? Some thoughts concerning the enzymatic chemical step.

PubMed

Tuñón, Iñaki; Laage, Damien; Hynes, James T

2015-09-15

We offer some thoughts on the much debated issue of dynamical effects in enzyme catalysis, and more specifically on their potential role in the acceleration of the chemical step. Since the term 'dynamics' has been used with different meanings, we find it useful to first return to the Transition State Theory rate constant, its assumptions and the choices it involves, and detail the various sources of deviations from it due to dynamics (or not). We suggest that much can be learned about the key current questions for enzyme catalysis from prior extensive studies of dynamical and other effects in the case of reactions in solution. We analyze dynamical effects both in the neighborhood of the transition state and far from it, together with the situation when quantum nuclear motion is central to the reaction, and we illustrate our discussion with various examples of enzymatic reactions. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Enhanced reactivity in dioxirane C-H oxidations via strain release: a computational and experimental study.

PubMed

Zou, Lufeng; Paton, Robert S; Eschenmoser, Albert; Newhouse, Timothy R; Baran, Phil S; Houk, K N

2013-04-19

The site selectivities and stereoselectivities of C-H oxidations of substituted cyclohexanes and trans-decalins by dimethyldioxirane (DMDO) were investigated computationally with quantum mechanical density functional theory (DFT). The multiconfiguration CASPT2 method was employed on model systems to establish the preferred mechanism and transition state geometry. The reaction pathway involving a rebound step is established to account for the retention of stereochemistry. The oxidation of sclareolide with dioxirane reagents is reported, including the oxidation by the in situ generated tBu-TFDO, a new dioxirane that better discriminates between C-H bonds on the basis of steric effects. The release of 1,3-diaxial strain in the transition state contributes to the site selectivity and enhanced equatorial C-H bond reactivity for tertiary C-H bonds, a result of the lowering of distortion energy. In addition to this strain release factor, steric and inductive effects contribute to the rates of C-H oxidation by dioxiranes.

RICIN-inhibitor design. Final report, 15 April 1993-14 April 1996

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

Schramm, V.L.

1996-05-01

The purpose of this proposal was to provide information which will permit the design of transition state inhibitors for ricin A-chain. The original goals were to solve the transition state structure based on kinetic isotope effects. Substrates were synthesized and the conditions for assays optimized to provide catalytic rates at least 1000 fold greater than those published prior to this work. Reliable assay methods have been established to permit routine assays for ricin A-chain. Substrate analogues for N-ribohydrolase reactions have been designed to establish whether the reaction involves leaving-group activation or oxycarbonium ion formation. Based on these results, leaving groupmore » activation is a major contributor and oxycarbonium-ion formation is a secondary contribution in the mechanism of catalysis by ricin A-chain. Using this information, the first submicromolar inhibitor of ricin A-chain has been synthesized, tested and kinetically characterized. The development of powerful inhibitors will be a direct extrapolation of these results.« less

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

Ensemble of Transition State Structures for the Cis-Trans Isomerization of N-Methylacetamide

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

Mantz, Yves A.; Branduardi, Davide; Bussi, Giovanni

2009-09-17

The cis-trans isomerization of N-methylacetamide (NMA), a model peptidic fragment, is studied theoretically in vacuo and in explicit water solvent at 300 K using the metadynamics technique. The computed cis-trans free energy difference is very similar for NMA(g) and NMA(aq), in agreement with experimental measurements of population ratios and theoretical studies at 0 K. By exploiting the flexibility in the definition of a pair of recently introduced collective variables (Branduardi, D.; Gervasio, F. L.; Parrinello, M. J. Chem. Phys. 2007, 126, 054103), an ensemble of transition state structures is generated at finite temperature for both NMA(g) and NMA(aq), as verifiedmore » by computing committor distribution functions. Ensemble members of NMA(g) are shown to have correlated values of the backbone dihedral angle and a second dihedral angle involving the amide hydrogen atom. The dynamical character of these structures is preserved in the presence of solvent, whose influence on the committor functions can be modeled using effective friction/noise terms.« less

Numerical simulation of a device with two spin crossover complexes: application for temperature and pressure sensors

NASA Astrophysics Data System (ADS)

Linares, Jorge; Eddine Allal, Salah; Dahoo, Pierre Richard; Garcia, Yann

2017-12-01

The spin-crossover (SCO) phenomenon is related to the ability of a transition metal to change its spin state vs. a given perturbation. For an iron(II) SCO complexes the reversible changes involve the diamagnetic low-spin (S = 0) and the paramagnetic high-spin (HS S = 2) states [1,2,3]. In this contribution we simulate the HS Fraction (nHS) for different set values of temperature and pressure for a device using two SCO complexes with weak elastic interactions. We improve the calculation given by Linares et al. [4], taking also into account different volume (VHS, VLS) changes of the SCO. We perform all the calculation in the frame work of an Ising-like model solved in the mean-field approximation. The two SCO show in the case of “weak elastic interactions”, gradual spin transitions such that both temperature and pressure values can be obtained from the optical observation in the light of calculations discussed in this article.

Lessons Learned From Transitioning PEPFAR Track 1.0 Care and Treatment Programs: Case Studies in Financial Management Capacity Building in Zambia and Botswana.

PubMed

Kuehn, Chuck; Tidwell, George; Vhugen, Jann; Sharma, Anjali

2015-01-01

In 2008, the United States government mandated transition of internationally managed HIV care and treatment programs to local country ownership. Three case studies illustrate the US Health Resources Services Administration's fiscal assessment and technical assistance (TA) processes to strengthen local organizations' capabilities to absorb and manage United States government funding. Review of initial, TA and follow-up reports reveal that the 1 Botswanan and 2 Zambian organizations closed 10 of 17 financial capacity gaps, with Health Resources Services Administration assisting on 2. Zambian organizations requested and absorbed targeted TA on the basis of the consultant's desk review, their finance staff revised fiscal policies and procedures, and accordingly trained other staff. In Botswana, delays in integrating recommendations necessitated on-site TA for knowledge building and role modeling. Organizational maturity may explain differences in responsiveness, ownership, and required TA approaches. Clarifying expectations of capacity building, funding agreement, and nonmonetary donor involvement can help new organizations determine and act on intervening actions.

An automated method to find transition states using chemical dynamics simulations.

PubMed

Martínez-Núñez, Emilio

2015-02-05

A procedure to automatically find the transition states (TSs) of a molecular system (MS) is proposed. It has two components: high-energy chemical dynamics simulations (CDS), and an algorithm that analyzes the geometries along the trajectories to find reactive pathways. Two levels of electronic structure calculations are involved: a low level (LL) is used to integrate the trajectories and also to optimize the TSs, and a higher level (HL) is used to reoptimize the structures. The method has been tested in three MSs: formaldehyde, formic acid (FA), and vinyl cyanide (VC), using MOPAC2012 and Gaussian09 to run the LL and HL calculations, respectively. Both the efficacy and efficiency of the method are very good, with around 15 TS structures optimized every 10 trajectories, which gives a total of 7, 12, and 83 TSs for formaldehyde, FA, and VC, respectively. The use of CDS makes it a powerful tool to unveil possible nonstatistical behavior of the system under study. © 2014 Wiley Periodicals, Inc.

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.

Radiative transitions involving the (2p2)(3 Pe) metastable autodetaching of H(-)

NASA Technical Reports Server (NTRS)

Jacobs, V. L.; Bhatia, A. K.; Temkin, A.

1974-01-01

The absorption coefficient for the free-bound transition H (ls) + e(-)+ h omega yields H(-)(2 sq p,(3)P(e)) is calculated (together with the differential emission rate for the inverse process) using ls - 2s - 2p close coupling continuum wave functions and a Hylleraas bound state wave function. A maximum in the absorption and emission spectra is found to occur at a photon wavelength of 1219.5 A, which is 2 A closer to the Lyman alpha line than predicted by the calculations of Drake, and is in closer agreement with the stellar absorption feature identified by Heap and Stecher. The free-bound absorption process appears to be a significant source of continuous ultraviolet opacity.

Tracing iron-carbon redox from surface to core

NASA Astrophysics Data System (ADS)

McCammon, C. A.; Cerantola, V.; Bykova, E.; Kupenko, I.; Bykov, M.; Chumakov, A. I.; Rüffer, R.; Dubrovinsky, L. S.

2017-12-01

Numerous redox reactions separate the Earth's oxidised surface from its reduced core. Many involve iron, the Earth's most abundant element and the mantle's most abundant transition element. Most iron redox reactions (although not all) also involve other elements, including carbon, where iron-carbon interactions drive a number of important processes within the Earth, for example diamond formation. Many of the Earth's redox boundaries are sharp, much like the seismic properties that define them, for example between the lower mantle and the core. Other regions that appear seismically homogeneous, for example the lower mantle, harbour a wealth of reactions between oxidised and reduced phases of iron and carbon. We have undertaken many experiments at high pressure and high temperature on phases containing iron and carbon using synchrotron-based X-rays to probe structures and iron oxidation states. Results demonstrate the dominant role that crystal structures play in determining the stable oxidation states of iron and carbon, even when oxygen fugacity (and common sense) would suggest otherwise. Iron in bridgmanite, for example, occurs predominantly in its oxidised form (ferric iron) throughout the lower mantle, despite the inferred reducing conditions. Newly discovered structures of iron carbonate also stabilise ferric iron, while simultaneously reducing some carbon to diamond to balance charge. Other high-pressure iron carbonates appear to be associated with the emerging zoo of iron oxide phases, involving transitions between ferrous and ferric iron through the exchange of oxygen. The presentation will trace redox relations between iron and carbon from the Earth's surface to its core, with an emphasis on recent experimental results.

A surface hopping algorithm for nonadiabatic minimum energy path calculations.

PubMed

Schapiro, Igor; Roca-Sanjuán, Daniel; Lindh, Roland; Olivucci, Massimo

2015-02-15

The article introduces a robust algorithm for the computation of minimum energy paths transiting along regions of near-to or degeneracy of adiabatic states. The method facilitates studies of excited state reactivity involving weakly avoided crossings and conical intersections. Based on the analysis of the change in the multiconfigurational wave function the algorithm takes the decision whether the optimization should continue following the same electronic state or switch to a different state. This algorithm helps to overcome convergence difficulties near degeneracies. The implementation in the MOLCAS quantum chemistry package is discussed. To demonstrate the utility of the proposed procedure four examples of application are provided: thymine, asulam, 1,2-dioxetane, and a three-double-bond model of the 11-cis-retinal protonated Schiff base. © 2015 Wiley Periodicals, Inc.

Multiple product pathways in photodissociation of nitromethane at 213 nm

NASA Astrophysics Data System (ADS)

Sumida, Masataka; Kohge, Yasunori; Yamasaki, Katsuyoshi; Kohguchi, Hiroshi

2016-02-01

In this paper, we present a photodissociation dynamics study of nitromethane at 213 nm in the π → π* transition. Resonantly enhanced multiphoton ionization spectroscopy and ion-imaging were applied to measure the internal state distributions and state-resolved scattering distributions of the CH3, NO(X 2Π, A 2Σ+), and O(3PJ) photofragments. The rotationally state-resolved scattering distribution of the CH3 fragment showed two velocity components, of which the slower one decreased the relative intensity as the rotational and vibrational excitations. The translational energy distribution of the faster CH3 fragment indicated the production of the NO2 counter-product in the electronic excited state, wherein 1 2B2 was the most probable. The NO(v = 0) fragment exhibited a bimodal translational energy distribution, whereas the NO(v = 1 and 2) fragment exhibited a single translational energy component with a relatively larger internal energy. The translational energy of a portion of the O(3PJ) photofragment was found to be higher than the one-photon dissociation threshold, indicating the two-photon process involved. The NO(A 2Σ+) fragment, which was detected by ionization spectroscopy via the Rydberg ←A 2Σ+ transition, also required two-photon energy. These experimental data corroborate the existence of competing photodissociation product pathways, CH3 + NO2,CH3 + NO + O,CH3O + NO, and CH3NO + O, following the π → π* transition. The origins of the observed photofragments are discussed in this report along with recent theoretical studies and previous dynamics experiments performed at 193 nm.

Multiple product pathways in photodissociation of nitromethane at 213 nm.

PubMed

Sumida, Masataka; Kohge, Yasunori; Yamasaki, Katsuyoshi; Kohguchi, Hiroshi

2016-02-14

In this paper, we present a photodissociation dynamics study of nitromethane at 213 nm in the π → π(*) transition. Resonantly enhanced multiphoton ionization spectroscopy and ion-imaging were applied to measure the internal state distributions and state-resolved scattering distributions of the CH3, NO(X (2)Π, A (2)Σ(+)), and O((3)PJ) photofragments. The rotationally state-resolved scattering distribution of the CH3 fragment showed two velocity components, of which the slower one decreased the relative intensity as the rotational and vibrational excitations. The translational energy distribution of the faster CH3 fragment indicated the production of the NO2 counter-product in the electronic excited state, wherein 1 (2)B2 was the most probable. The NO(v = 0) fragment exhibited a bimodal translational energy distribution, whereas the NO(v = 1 and 2) fragment exhibited a single translational energy component with a relatively larger internal energy. The translational energy of a portion of the O((3)PJ) photofragment was found to be higher than the one-photon dissociation threshold, indicating the two-photon process involved. The NO(A (2)Σ(+)) fragment, which was detected by ionization spectroscopy via the Rydberg ← A (2)Σ(+) transition, also required two-photon energy. These experimental data corroborate the existence of competing photodissociation product pathways, CH3 + NO2,CH3 + NO + O,CH3O + NO, and CH3NO + O, following the π → π(*) transition. The origins of the observed photofragments are discussed in this report along with recent theoretical studies and previous dynamics experiments performed at 193 nm.

The transition of dynamic rupture styles in elastic media under velocity-weakening friction

NASA Astrophysics Data System (ADS)

Gabriel, A.-A.; Ampuero, J.-P.; Dalguer, L. A.; Mai, P. M.

2012-09-01

Although kinematic earthquake source inversions show dominantly pulse-like subshear rupture behavior, seismological observations, laboratory experiments and theoretical models indicate that earthquakes can operate with different rupture styles: either as pulses or cracks, that propagate at subshear or supershear speeds. The determination of rupture style and speed has important implications for ground motions and may inform about the state of stress and strength of active fault zones. We conduct 2D in-plane dynamic rupture simulations with a spectral element method to investigate the diversity of rupture styles on faults governed by velocity-and-state-dependent friction with dramatic velocity-weakening at high slip rate. Our rupture models are governed by uniform initial stresses, and are artificially initiated. We identify the conditions that lead to different rupture styles by investigating the transitions between decaying, steady state and growing pulses, cracks, sub-shear and super-shear ruptures as a function of background stress, nucleation size and characteristic velocity at the onset of severe weakening. Our models show that small changes of background stress or nucleation size may lead to dramatic changes of rupture style. We characterize the asymptotic properties of steady state and self-similar pulses as a function of background stress. We show that an earthquake may not be restricted to a single rupture style, but that complex rupture patterns may emerge that consist of multiple rupture fronts, possibly involving different styles and back-propagating fronts. We also demonstrate the possibility of a super-shear transition for pulse-like ruptures. Finally, we draw connections between our findings and recent seismological observations.

A role for RNA post-transcriptional regulation in satellite cell activation

PubMed Central

2012-01-01

Background Satellite cells are resident skeletal muscle stem cells responsible for muscle maintenance and repair. In resting muscle, satellite cells are maintained in a quiescent state. Satellite cell activation induces the myogenic commitment factor, MyoD, and cell cycle entry to facilitate transition to a population of proliferating myoblasts that eventually exit the cycle and regenerate muscle tissue. The molecular mechanism involved in the transition of a quiescent satellite cell to a transit-amplifying myoblast is poorly understood. Methods Satellite cells isolated by FACS from uninjured skeletal muscle and 12 h post-muscle injury from wild type and Syndecan-4 null mice were probed using Affymetrix 430v2 gene chips and analyzed by Spotfiretm and Ingenuity Pathway analysis to identify gene expression changes and networks associated with satellite cell activation, respectively. Additional analyses of target genes identify miRNAs exhibiting dynamic changes in expression during satellite cell activation. The function of the miRNAs was assessed using miRIDIAN hairpin inhibitors. Results An unbiased gene expression screen identified over 4,000 genes differentially expressed in satellite cells in vivo within 12 h following muscle damage and more than 50% of these decrease dramatically. RNA binding proteins and genes involved in post-transcriptional regulation were significantly over-represented whereas splicing factors were preferentially downregulated and mRNA stability genes preferentially upregulated. Furthermore, six computationally identified miRNAs demonstrated novel expression through muscle regeneration and in satellite cells. Three of the six miRNAs were found to regulate satellite cell fate. Conclusions The quiescent satellite cell is actively maintained in a state poised to activate in response to external signals. Satellite cell activation appears to be regulated by post-transcriptional gene regulation. PMID:23046558

Abnormal sleep/wake dynamics in orexin knockout mice.

PubMed

Diniz Behn, Cecilia G; Klerman, Elizabeth B; Mochizuki, Takatoshi; Lin, Shih-Chieh; Scammell, Thomas E

2010-03-01

Narcolepsy with cataplexy is caused by a loss of orexin (hypocretin) signaling, but the physiologic mechanisms that result in poor maintenance of wakefulness and fragmented sleep remain unknown. Conventional scoring of sleep cannot reveal much about the process of transitioning between states or the variations within states. We developed an EEG spectral analysis technique to determine whether the state instability in a mouse model of narcolepsy reflects abnormal sleep or wake states, faster movements between states, or abnormal transitions between states. We analyzed sleep recordings in orexin knockout (OXKO) mice and wild type (WT) littermates using a state space analysis technique. This non-categorical approach allows quantitative and unbiased examination of sleep/wake states and state transitions. OXKO mice spent less time in deep, delta-rich NREM sleep and in active, theta-rich wake and instead spent more time near the transition zones between states. In addition, while in the midst of what should be stable wake, OXKO mice initiated rapid changes into NREM sleep with high velocities normally seen only in transition regions. Consequently, state transitions were much more frequent and rapid even though the EEG progressions during state transitions were normal. State space analysis enables visualization of the boundaries between sleep and wake and shows that narcoleptic mice have less distinct and more labile states of sleep and wakefulness. These observations provide new perspectives on the abnormal state dynamics resulting from disrupted orexin signaling and highlight the usefulness of state space analysis in understanding narcolepsy and other sleep disorders.

TRANSITIVITY OF ODOR PREFERENCES: CONSTANT AND PARTICULARITIES IN HEDONIC PERCEPTION

PubMed Central

Brand, Gérard; Haaz, Virginie; Jacquot, Laurence

2012-01-01

Transitivity of preferences has been investigated for a long time in decision-making. In the field of perception, the pleasantness of odors raises several questions related to individual versus cultural or universal preferences and the existence of a classification in a delimited hedonic space. The aim of this study was to test transitivity in olfactory hedonicity using a first panel of 10 mixed odors and a second panel of 10 odors from a delimited floral category. Data were collected by paired comparisons in a two-alternative forced choice. Results in both panels showed a strong transitivity for each participant leading to a linear range of 10 odors classified by preference. However, ranges varied from one participant to another and the mean preferences of the group did not allow one to infer individual's hedonic classification of odors. Moreover, the individual classification appeared stable over time and undisturbed by odorant distractors. These findings suggest that humans have considerable ability to classify odors hedonically as a model of individual preferences in a sensory space usually considered to be more involved in affective/emotional states than in cognitive performances. PMID:23008522

The Retirement process: Making the Person and Cultural Meanings malleable

PubMed Central

Luborsky, Mark R.

2012-01-01

In research on life-course transitions, the dynamics of reorganizing meanings and lives were examined in interviews with 32 retiring workers in the United States. New retirees engaged in reorganization of self and social identity by work in special projects involving physical labor to demolish and rebuild backyards and household interiors. Findings indicate that the work in these projects conjoins the reshaping of subjective experience and social life. The projects express a behavioral narrative of the transition in that the spatial sequence of activities (moving from households to the community) parallels the temporal order of reorganization (from self to social identity). Individuals invent and recapitulate partially formed symbols (i.e., dirt, birth, and death) and prior life events to develop new self-images and social lives. These metaphors and processes of separation and death foster creativity and reintegration and must be viewed as integral to transition rather than interpreted as phenomena to be avoided as they are in gerontology and medical practice. Transitions need to be understood as situated within individual histories and cultural contexts. PMID:23308033

Analysis of Optogalvanic Transients at 621.7 nm, 633.4 nm and 640.2 nm of Neon in a Discharge Plasma Fitted with a Monte Carlo Mathematical Model.

NASA Astrophysics Data System (ADS)

Ogungbemi, Kayode; Han, Xianming; Blosser, Micheal; Misra, Prabhakar; LASER Spectroscopy Group Collaboration

2014-03-01

Optogalvanic transitions have been recorded and fitted for 1s5 - 2p7\\ (621.7 nm), 1s5 - 2p8 (633.4 nm) and 1s5 - 2p9 (640.2 nm) transitions of neon in a Fe-Ne hollow cathode plasma discharge as a function of current (2-19 mA) and time evolution (0-50 microsec). The optogalvanic waveforms have been fitted to a Monte carlo mathematical model. The variation in the excited population of neon is governed by the rate of collision of the atoms involving the common metastable state (1s5) for the three transitions investigated. The concomitant changes in amplitudes and intensities of the optogalvanic signal waveforms associated with these transitions have been studied rigorously and the fitted parameters obtained using the Monte Carlo algorithm to help better understand the physics of the hollow cathode discharge. Thanks to Laser Spectroscopy group in Physics and Astronomy Dept. Howard University Washington DC.

Learning from Transitioning to New Technology That Supports Online and Blended Learning: A Case Study

ERIC Educational Resources Information Center

Lock, Jennifer; Johnson, Carol

2017-01-01

Transitioning from one technology to another within educational institutions is complex and multi-faceted, and requires time. Such a transition involves more than making the new technology available for use. It requires knowing the people involved, designing differentiated support structures, and integrating various resources to meet their…

Parental Involvement Protects against Self-Medication Behaviors during the High School Transition

PubMed Central

Gottfredson, Nisha C.; Hussong, Andrea M.

2011-01-01

We examined how drinking patterns change as adolescents transition to high school, particularly as a function of parental involvement. Stress associated with the transition to high school may deplete psychological resources for coping with negative daily emotions in an environment when opportunities to drink are more common. A cohort of elevated-risk middle school students completed daily negative affect (sadness, worry, anger, and stress) and alcohol use assessments before and after the transition to high school, resulting in a measurement burst design. Adolescents who reported less parental involvement were at higher risk for drinking on any given day. After (but not before) the transition to high school, daily within-person fluctuations of sadness predicted an increased probability of same-day alcohol use for adolescents who reported that their parents were minimally involved in their lives. The other negative affect indicators were not predictive of use. Our results suggest that the transition to high school may represent an important intervention leverage point, particularly for adolescents who lack adequate parental support to help them cope with day-to-day changes in sadness. PMID:21880433

Ultrafast photophysics of transition metal complexes.

PubMed

Chergui, Majed

2015-03-17

The properties of transition metal complexes are interesting not only for their potential applications in solar energy conversion, OLEDs, molecular electronics, biology, photochemistry, etc. but also for their fascinating photophysical properties that call for a rethinking of fundamental concepts. With the advent of ultrafast spectroscopy over 25 years ago and, more particularly, with improvements in the past 10-15 years, a new area of study was opened that has led to insightful observations of the intramolecular relaxation processes such as internal conversion (IC), intersystem crossing (ISC), and intramolecular vibrational redistribution (IVR). Indeed, ultrafast optical spectroscopic tools, such as fluorescence up-conversion, show that in many cases, intramolecular relaxation processes can be extremely fast and even shorter than time scales of vibrations. In addition, more and more examples are appearing showing that ultrafast ISC rates do not scale with the magnitude of the metal spin-orbit coupling constant, that is, that there is no heavy-atom effect on ultrafast time scales. It appears that the structural dynamics of the system and the density of states play a crucial role therein. While optical spectroscopy delivers an insightful picture of electronic relaxation processes involving valence orbitals, the photophysics of metal complexes involves excitations that may be centered on the metal (called metal-centered or MC) or the ligand (called ligand-centered or LC) or involve a transition from one to the other or vice versa (called MLCT or LMCT). These excitations call for an element-specific probe of the photophysics, which is achieved by X-ray absorption spectroscopy. In this case, transitions from core orbitals to valence orbitals or higher allow probing the electronic structure changes induced by the optical excitation of the valence orbitals, while also delivering information about the geometrical rearrangement of the neighbor atoms around the atom of interest. With the emergence of new instruments such as X-ray free electron lasers (XFELs), it is now possible to perform ultrafast laser pump/X-ray emission probe experiments. In this case, one probes the density of occupied states. These core-level spectroscopies and other emerging ones, such as photoelectron spectroscopy of solutions, are delivering a hitherto unseen degree of detail into the photophysics of metal-based molecular complexes. In this Account, we will give examples of applications of the various methods listed above to address specific photophysical processes.

State transitions and feedback mechanisms control hydrology in the constructed catchment ´Chicken Creeḱ

NASA Astrophysics Data System (ADS)

Schaaf, Wolfgang; Gerwin, Werner; Hinz, Christoph; Zaplata, Markus

2016-04-01

Landscapes and ecosystems are complex systems with many feedback mechanisms acting between the various abiotic and biotic components. The knowledge about these interacting processes is mainly derived from mature ecosystems. The initial development of ecosystem complexity may involve state transitions following catastrophic shifts, disturbances or transgression of thresholds. The Chicken Creek catchment was constructed in 2005 in the mining area of Lusatia/Germany to study processes and feedback mechanisms during ecosystem evolution. The hillslope-shaped 6 ha site has defined boundary conditions and well-documented inner structures. The dominating substrate above the underlying clay layer is Pleistocene sandy material representing mainly the lower C horizon of the former landscape. Since 2005, the unrestricted, unmanaged development of the catchment was intensively monitored. During the ten years since then, we observed characteristic state transitions in catchment functioning driven by feedbacks between original substrate properties, surface structures, soil development and vegetation succession. Whereas surface runoff induced by surface crusting and infiltration dominated catchment hydrology in the first years, the impact of vegetation on hydrological pathways and groundwater levels became more and more evident during the last years. Discharge from the catchment changed from episodic events driven by precipitation and surface runoff to groundwater driven. This general picture is overlain by spatial patterns and single episodic events of external drivers. The scientific value of the Chicken Creek site with known boundary conditions and structure information could help in disentangling general feedback mechanisms between hydrologic, pedogenic, biological and geomorphological processes as well as a in gaining a more integrative view of succession and its drivers during the transition from initial, less complex systems to more mature ecosystems. Long-term time series of data are a key for a better understanding of these processes and the effects on ecosystem resilience and self-organization.

Liquid-vapor transition on patterned solid surfaces in a shear flow

NASA Astrophysics Data System (ADS)

Yao, Wenqi; Ren, Weiqing

2015-12-01

Liquids on a solid surface patterned with microstructures can exhibit the Cassie-Baxter (Cassie) state and the wetted Wenzel state. The transitions between the two states and the effects of surface topography, surface chemistry as well as the geometry of the microstructures on the transitions have been extensively studied in earlier work. However, most of these work focused on the study of the free energy landscape and the energy barriers. In the current work, we consider the transitions in the presence of a shear flow. We compute the minimum action path between the Wenzel and Cassie states using the minimum action method [W. E, W. Ren, and E. Vanden-Eijnden, Commun. Pure Appl. Math. 57, 637 (2004)]. Numerical results are obtained for transitions on a surface patterned with straight pillars. It is found that the shear flow facilitates the transition from the Wenzel state to the Cassie state, while it inhibits the transition backwards. The Wenzel state becomes unstable when the shear rate reaches a certain critical value. Two different scenarios for the Wenzel-Cassie transition are observed. At low shear rate, the transition happens via nucleation of the vapor phase at the bottom of the groove followed by its growth. At high shear rate, in contrary, the nucleation of the vapor phase occurs at the top corner of a pillar. The vapor phase grows in the direction of the flow, and the system goes through an intermediate metastable state before reaching the Cassie state.

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.

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).

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.

Electronic Rearrangement in Molecular Plasmons: An Electron Density and Electrostatic Potential-Based Study.

PubMed

Paul, Mishu; Balanarayan, P

2018-06-05

Plasmonic modes in single-molecule systems have been previously identified by scaling two-electron interactions in calculating excitation energies. Analysis of transition dipole moments for states of polyacenes based on configuration interaction is another method for characterising molecular plasmons. The principal features in the electronic absorption spectra of polyacenes are a low-intensity, lower-in-energy peak and a high-intensity, higher-in-energy peak. From calculations using time-dependent density functional theory with the B3LYP/cc-pVTZ basis set, both these peaks are found to result from the same set of electronic transitions, that is, HOMO-n to LUMO and HOMO to LUMO+n, where n varies as the number of fused rings increases. In this work, the excited states of polyacenes, naphthalene through pentacene, are analysed using electron densities and molecular electrostatic potential (MESP) topography. Compared to other excited states the bright and dark plasmonic states involve the least electron rearrangement. Quantitatively, the MESP topography indicates that the variance in MESP values and the displacement in MESP minima positions, calculated with respect to the ground state, are lowest for plasmonic states. The excited-state electronic density profiles and electrostatic potential topographies suggest the least electron rearrangement for the plasmonic states. Conversely, high electron rearrangement characterises a single-particle excitation. The molecular plasmon can be called an excited state most similar to the ground state in terms of one-electron properties. This is found to be true for silver (Ag 6 ) and sodium (Na 8 ) linear chains as well. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Point-Defect Nature of the Ultraviolet Absorption Band in AlN

NASA Astrophysics Data System (ADS)

Alden, D.; Harris, J. S.; Bryan, Z.; Baker, J. N.; Reddy, P.; Mita, S.; Callsen, G.; Hoffmann, A.; Irving, D. L.; Collazo, R.; Sitar, Z.

2018-05-01

We present an approach where point defects and defect complexes are identified using power-dependent photoluminescence excitation spectroscopy, impurity data from SIMS, and density-functional-theory (DFT)-based calculations accounting for the total charge balance in the crystal. Employing the capabilities of such an experimental computational approach, in this work, the ultraviolet-C absorption band at 4.7 eV, as well as the 2.7- and 3.9-eV luminescence bands in AlN single crystals grown via physical vapor transport (PVT) are studied in detail. Photoluminescence excitation spectroscopy measurements demonstrate the relationship between the defect luminescent bands centered at 3.9 and 2.7 eV to the commonly observed absorption band centered at 4.7 eV. Accordingly, the thermodynamic transition energy for the absorption band at 4.7 eV and the luminescence band at 3.9 eV is estimated at 4.2 eV, in agreement with the thermodynamic transition energy for the CN- point defect. Finally, the 2.7-eV PL band is the result of a donor-acceptor pair transition between the VN and CN point defects since nitrogen vacancies are predicted to be present in the crystal in concentrations similar to carbon-employing charge-balance-constrained DFT calculations. Power-dependent photoluminescence measurements reveal the presence of the deep donor state with a thermodynamic transition energy of 5.0 eV, which we hypothesize to be nitrogen vacancies in agreement with predictions based on theory. The charge state, concentration, and type of impurities in the crystal are calculated considering a fixed amount of impurities and using a DFT-based defect solver, which considers their respective formation energies and the total charge balance in the crystal. The presented results show that nitrogen vacancies are the most likely candidate for the deep donor state involved in the donor-acceptor pair transition with peak emission at 2.7 eV for the conditions relevant to PVT growth.

XANES, EXAFS and Kbeta spectroscopic studies of the oxygen-evolving complex in Photosystem II

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

Robblee, John Henry

A key question for the understanding of photosynthetic water oxidation is whether the four oxidizing equivalents necessary to oxidize water to dioxygen are accumulated on the four Mn ions of the oxygen evolving complex (OEC), or whether some ligand-centered oxidations take place before the formation and release of dioxygen during the S 3 → [S 4] → S 0 transition. Progress in instrumentation and flash sample preparation allowed us to apply Mn Kβ X-ray emission spectroscopy (Kb XES) to this problem for the first time. The Kβ XES results, in combination with Mn X-ray absorption near-edge structure (XANES) and electronmore » paramagnetic resonance (EPR) data obtained from the same set of samples, show that the S 2 → S 3 transition, in contrast to the S 0 → S 1 and S 1 → S 2 transitions, does not involve a Mn-centered oxidation. This is rationalized by manganese μ-oxo bridge radical formation during the S 2 → S 3 transition. Using extended X-ray absorption fine structure (EXAFS) spectroscopy, the local environment of the Mn atoms in the S 0 state has been structurally characterized. These results show that the Mn-Mn distance in one of the di-μ-oxo-bridged Mn-Mn moieties increases from 2.7 Å in the S 1} state to 2.85 Å in the S 0 state. Furthermore, evidence is presented that shows three di-μ-oxo binuclear Mn 2 clusters may be present in the OEC, which is contrary to the widely held theory that two such clusters are present in the OEC. The EPR properties of the S 0 state have been investigated and a characteristic ''multiline'' signal in the S 0 state has been discovered in the presence of methanol. This provides the first direct confirmation that the native S 0 state is paramagnetic. In addition, this signal was simulated using parameters derived from three possible oxidation states of Mn in the S 0 state. The dichroic nature of X-rays from synchrotron radiation and single-crystal Mn complexes have been exploited to selectively probe Mn-ligand bonds using XANES and EXAFS spectroscopy. The results from single-crystal Mn complexes show that dramatic dichroism exists in these complexes, and are suggestive of a promising future for single-crystal studies of PS II.« less

The multiuniverse transition in superfluid 3He

NASA Astrophysics Data System (ADS)

Bunkov, Yury

2013-10-01

The symmetry-breaking phase transitions of the universe and of superfluid 3He may lead to the formation of different states with different order parameters. In both cases the energy potential below the transition temperature has a complicated multidimensional profile with many local minima and saddle points, which correspond to different states. Consequently, not only topological defects, but also islands of different metastable states can be created. Using 3He we can analyse the properties and experimental consequences of such transitions and, in particular, the first-order phase transition between the two low symmetry states.

The multiuniverse transition in superfluid 3He.

PubMed

Bunkov, Yury

2013-10-09

The symmetry-breaking phase transitions of the universe and of superfluid (3)He may lead to the formation of different states with different order parameters. In both cases the energy potential below the transition temperature has a complicated multidimensional profile with many local minima and saddle points, which correspond to different states. Consequently, not only topological defects, but also islands of different metastable states can be created. Using (3)He we can analyse the properties and experimental consequences of such transitions and, in particular, the first-order phase transition between the two low symmetry states.

Un-catalyzed peptide bond formation between two monomers of glycine, alanine, serine, threonine, and aspartic acid in gas phase: a density functional theory study

NASA Astrophysics Data System (ADS)

Bhunia, Snehasis; Singh, Ajeet; Ojha, Animesh K.

2016-05-01

In the present report, un-catalyzed peptide bond formation between two monomers of glycine (Gly), alanine (Ala), serine (Ser), threonine (Thr), and aspartic acid (Asp) has been investigated in gas phase via two steps reaction mechanism and concerted mechanism at B3LYP/6-31G(d,p) and M062X/6-31G(d,p) level of theories. The peptide bond is formed through a nucleophilic reaction via transition states, TS1 and TS2 in stepwise mechanism. The TS1 reveals formation of a new C-N bond while TS2 illustrate the formation of C=O bond. In case of concerted mechanism, C-N bond is formed by a single four-centre transition state (TS3). The energy barrier is used to explain the involvement of energy at each step of the reaction. The energy barrier (20-48 kcal/mol) is required for the transformation of reactant state R1 to TS1 state and intermediate state I1 to TS2 state. The large value of energy barrier is explained in terms of distortion and interaction energies for stepwise mechanism. The energy barrier of TS3 in concerted mechanism is very close to the energy barrier of the first transition state (TS1) of the stepwise mechanism for the formation of Gly-Gly and Ala-Ala di- peptide. However, in case of Ser-Ser, Thr-Thr and Asp-Asp di-peptide, the energy barrier of TS3 is relatively high than that of the energy barrier of TS1 calculated at B3LYP/6-31G(d,p) and M062X/6-31G(d,p) level of theories. In both the mechanisms, the value of energy barrier calculated at B3LYP/6-31G(d,p) level of theory is greater than that of the value calculated at M062X/6-31G(d,p) level of theory.

Quantum Monte Carlo calculations of electromagnetic transitions in $^8$Be with meson-exchange currents derived from chiral effective field theory

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

Pastore, S.; Wiringa, Robert B.; Pieper, Steven C.

2014-08-01

We report quantum Monte Carlo calculations of electromagnetic transitions inmore » $^8$Be. The realistic Argonne $$v_{18}$$ two-nucleon and Illinois-7 three-nucleon potentials are used to generate the ground state and nine excited states, with energies that are in excellent agreement with experiment. A dozen $M1$ and eight $E2$ transition matrix elements between these states are then evaluated. The $E2$ matrix elements are computed only in impulse approximation, with those transitions from broad resonant states requiring special treatment. The $M1$ matrix elements include two-body meson-exchange currents derived from chiral effective field theory, which typically contribute 20--30\\% of the total expectation value. Many of the transitions are between isospin-mixed states; the calculations are performed for isospin-pure states and then combined with the empirical mixing coefficients to compare to experiment. In general, we find that transitions between states that have the same dominant spatial symmetry are in decent agreement with experiment, but those transitions between different spatial symmetries are often significantly underpredicted.« less

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

SU(1 , 1) and SU(2) approaches to the radial oscillator: Generalized coherent states and squeezing of variances

NASA Astrophysics Data System (ADS)

Rosas-Ortiz, Oscar; Cruz y Cruz, Sara; Enríquez, Marco

2016-10-01

It is shown that each one of the Lie algebras su(1 , 1) and su(2) determine the spectrum of the radial oscillator. States that share the same orbital angular momentum are used to construct the representation spaces of the non-compact Lie group SU(1 , 1) . In addition, three different forms of obtaining the representation spaces of the compact Lie group SU(2) are introduced, they are based on the accidental degeneracies associated with the spherical symmetry of the system as well as on the selection rules that govern the transitions between different energy levels. In all cases the corresponding generalized coherent states are constructed and the conditions to squeeze the involved quadratures are analyzed.

GLC_Exec v. 1.2.1

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

Kilgore, Roger Martin; Soloboda, Alexander Joseph

Launching a rocket involves a controlled transition of the rocket subsystems from a quiescent state to the launch state (i.e., lift-off). In order to launch safely, with confidence that the rocket will successfully complete its mission, the state-of-health for all rocket subsystems and critical ground support equipment must be closely monitored throughout the launch process. This is accomplished by the ground support engineers using mission-specific ground support equipment. A subset of the GSE, the Remote Electrical Ground Interface System (REGIS), is located nearest the rocket to which it's connected via the Umbilical, a wiring harness providing power, sensor, and controlmore » lines. The REGIS also connects via Ethernet to the Ground Launch Computer (GLC).« less

Atomic vapor laser isotope separation of lead-210 isotope

DOEpatents

Scheibner, K.F.; Haynam, C.A.; Johnson, M.A.; Worden, E.F.

1999-08-31

An isotopically selective laser process and apparatus for removal of Pb-210 from natural lead that involves a one-photon near-resonant, two-photon resonant excitation of one or more Rydberg levels, followed by field ionization and then electrostatic extraction. The wavelength to the near-resonant intermediate state is counter propagated with respect to the second wavelength required to populate the final Rydberg state. This scheme takes advantage of the large first excited state cross section, and only modest laser fluences are required. The non-resonant process helps to avoid two problems: first, stimulated Raman Gain due to the nearby F=3/2 hyperfine component of Pb-207 and, second, direct absorption of the first transition process light by Pb-207. 5 figs.

Atomic vapor laser isotope separation of lead-210 isotope

DOEpatents

Scheibner, Karl F.; Haynam, Christopher A.; Johnson, Michael A.; Worden, Earl F.

1999-01-01

An isotopically selective laser process and apparatus for removal of Pb-210 from natural lead that involves a one-photon near-resonant, two-photon resonant excitation of one or more Rydberg levels, followed by field ionization and then electrostatic extraction. The wavelength to the near-resonant intermediate state is counter propagated with respect to the second wavelength required to populate the final Rydberg state. This scheme takes advantage of the large first excited state cross section, and only modest laser fluences are required. The non-resonant process helps to avoid two problems: first, stimulated Raman Gain due to the nearby F=3/2 hyperfine component of Pb-207 and, second, direct absorption of the first transition process light by Pb-207.

Implementation into earthquake sequence simulations of a rate- and state-dependent friction law incorporating pressure solution creep

NASA Astrophysics Data System (ADS)

Noda, H.

2016-05-01

Pressure solution creep (PSC) is an important elementary process in rock friction at high temperatures where solubilities of rock-forming minerals are significantly large. It significantly changes the frictional resistance and enhances time-dependent strengthening. A recent microphysical model for PSC-involved friction of clay-quartz mixtures, which can explain a transition between dilatant and non-dilatant deformation (d-nd transition), was modified here and implemented in dynamic earthquake sequence simulations. The original model resulted in essentially a kind of rate- and state-dependent friction (RSF) law, but assumed a constant friction coefficient for clay resulting in zero instantaneous rate dependency in the dilatant regime. In this study, an instantaneous rate dependency for the clay friction coefficient was introduced, consistent with experiments, resulting in a friction law suitable for earthquake sequence simulations. In addition, a term for time-dependent strengthening due to PSC was added which makes the friction law logarithmically rate-weakening in the dilatant regime. The width of the zone in which clasts overlap or, equivalently, the interface porosity involved in PSC plays a role as the state variable. Such a concrete physical meaning of the state variable is a great advantage in future modelling studies incorporating other physical processes such as hydraulic effects. Earthquake sequence simulations with different pore pressure distributions demonstrated that excess pore pressure at depth causes deeper rupture propagation with smaller slip per event and a shorter recurrence interval. The simulated ruptures were arrested a few kilometres below the point of pre-seismic peak stress at the d-nd transition and did not propagate spontaneously into the region of pre-seismic non-dilatant deformation. PSC weakens the fault against slow deformation and thus such a region cannot produce a dynamic stress drop. Dynamic rupture propagation further down to brittle-plastic transition, evidenced by geological observations, would require even smaller frictional resistance at coseismic slip rate, suggesting the importance of implementation of dynamic weakening activated at coseismic slip rates for more realistic simulation of earthquake sequences. The present models produced much smaller afterslip at deeper parts of arrested ruptures than those with logarithmic RSF laws because of a more significant rate-strengthening effect due to linearly viscous PSC. Detailed investigation of afterslip would give a clue to understand the deformation mechanism which controls shear resistance of the fault in a region of arrest of earthquake ruptures.

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.

Chemical event chain model of coupled genetic oscillators.

PubMed

Jörg, David J; Morelli, Luis G; Jülicher, Frank

2018-03-01

We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their frequency, their quality factor, and their synchrony by the oscillator cross correlation. The steady state is determined by coupling and exhibits stochastic transitions between different modes. The interplay of stochasticity and nonlinearity leads to isolated regions in parameter space in which the coupled system works best as a biological pacemaker. Key features of the stochastic oscillations can be captured by an effective model for phase oscillators that are coupled by signals with distributed delays.

Chemical event chain model of coupled genetic oscillators

NASA Astrophysics Data System (ADS)

Jörg, David J.; Morelli, Luis G.; Jülicher, Frank

2018-03-01

We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their frequency, their quality factor, and their synchrony by the oscillator cross correlation. The steady state is determined by coupling and exhibits stochastic transitions between different modes. The interplay of stochasticity and nonlinearity leads to isolated regions in parameter space in which the coupled system works best as a biological pacemaker. Key features of the stochastic oscillations can be captured by an effective model for phase oscillators that are coupled by signals with distributed delays.

Quadrupole splittings in the near-infrared spectrum of 14NH 3

DOE PAGES

Twagirayezu, Sylvestre; Hall, Gregory E.; Sears, Trevor J.

2016-10-13

Sub-Doppler, saturation dip, spectra of lines in the v 1 + v 3, v 1 + 2v 4 and v 3 + 2v 4 bands of 14NH 3 have been measured by frequency comb-referenced diode laser absorption spectroscopy. The observed spectral line widths are dominated by transit time broadening, and show resolved or partially-resolved hyperfine splittings that are primarily determined by the 14N quadrupole coupling. Modeling of the observed line shapes based on the known hyperfine level structure of the ground state of the molecule shows that, in nearly all cases, the excited state level has hyperfine splittings similar tomore » the same rotational level in the ground state. The data provide accurate frequencies for the line positions and easily separate lines overlapped in Doppler-limited spectra. The observed hyperfine splittings can be used to make and confirm rotational assignments and ground state combination differences obtained from the measured frequencies are comparable in accuracy to those obtained from conventional microwave spectroscopy. Furthermore, several of the measured transitions do not show the quadrupole hyperfine splittings expected based on their existing rotational assignments. Either the assignments are incorrect or the upper levels involved are perturbed in a way that affects the nuclear hyperfine structure.« less

A Comparison of Density Functional Theory with Ab initio Approaches for Systems Involving First Transition Row Metals

NASA Technical Reports Server (NTRS)

Ricca, Alessandra; Bauschlicher, Charles W.; Langhoff, Stephen R. (Technical Monitor)

1994-01-01

Density functional theory (DFT) is found to give a better description of the geometries and vibrational frequencies of FeL and FeL(sup +) systems than second order Moller Plesset perturbation theory (MP2). Namely, the DFT correctly predicts the shift in the CO vibrational frequency between free CO and the Sigma(sup -) state of FeCO and yields a good result for the Fe-C distance in the quartet states of FeCH4(+) 4 These are properties where the MP2 results are unsatisfactory. Thus DFT appears to be an excellent approach for optimizing the geometries and computing the zero-point energies of systems containing first transition row atoms. Because the DFT approach is biased in favor of the 3d(exp 7) occupation, whereas the more traditional approaches are biased in favor of the 3d(exp 6) occupation, differences are found in the relative ordering of states. It is shown that if the dissociation is computed to the most appropriate atomic asymptote and corrected to the ground state asymptote using the experimental separations, the DFT results are in good agreement with high levels of theory. The energetics at the DFT level are much superior to the MP2 and in most cases in good agreement with high levels of theory.

Spin-Forbidden Reactions: Adiabatic Transition States Using Spin-Orbit Coupled Density Functional Theory.

PubMed

Gaggioli, Carlo Alberto; Belpassi, Leonardo; Tarantelli, Francesco; Harvey, Jeremy N; Belanzoni, Paola

2018-04-06

A spin-forbidden chemical reaction involves a change in the total electronic spin state from reactants to products. The mechanistic study is challenging because such a reaction does not occur on a single diabatic potential energy surface (PES), but rather on two (or multiple) spin diabatic PESs. One possible approach is to calculate the so-called "minimum energy crossing point" (MECP) between the diabatic PESs, which however is not a stationary point. Inclusion of spin-orbit coupling between spin states (SOC approach) allows the reaction to occur on a single adiabatic PES, in which a transition state (TS SOC) as well as activation free energy can be calculated. This Concept article summarizes a previously published application in which, for the first time, the SOC effects, using spin-orbit ZORA Hamiltonian within density functional theory (DFT) framework, are included and account for the mechanism of a spin-forbidden reaction in gold chemistry. The merits of the MECP and TS SOC approaches and the accuracy of the results are compared, considering both our recent calculations on molecular oxygen addition to gold(I)-hydride complexes and new calculations for the prototype spin-forbidden N 2 O and N 2 Se dissociation reactions. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

FIR Synchrotron Spectroscopy of High Torsional Levels of CD_3OH: the Tau of Methanol

NASA Astrophysics Data System (ADS)

Lees, Ronald M.; Xu, Li-Hong; Billinghurst, Brant E.

2015-06-01

Sub-bands involving high torsional levels of the CD_3OH isotopologue of methanol have been analyzed in Fourier transform spectra recorded at the Far-Infrared beamline of the Canadian Light Source synchrotron in Saskatoon. Energy term values for A and E torsional species of the third excited torsional state, v_t = 3, are now almost complete up to rotational levels K = 15, and thirteen substates have so far been identified for v_t = 4. The spectra show interesting close groupings of high-v_t sub-bands related by Dennison's torsional symmetry label τ, rather than A and E, that can be understood in terms of a simple and universal free-rotor "spectral predictor" chart. Transitions between states on the same free rotor curve have torsional overlap matrix elements close to unity, so give rise to strong sub-bands providing radiative routes for rapid population transfer through the high torsional manifold. Where the energy curves for the v_t = 3 and 4 ground-state torsional levels pass through the excited vibrational states, strong resonances can occur and a number of anharmonic and Coriolis interactions have been detected through perturbations to the spectra and appearance of forbidden transitions due to strong mixing and intensity borrowing.

Encouraging Democratic Transitions: The Problematic Impact of United States’ Involvement

DTIC Science & Technology

1991-06-20

more abstractly, democracy is consolidated when uncertainty is institutionalized: nobody can control the outcomes of the political process ex post ...for Change in Cuba", Miami Herald, May 27, 1990. See also, Al Kamen, "US Encourages Soviets to Aid Salvadoran Talks". Washington Post , October 18, 1990...Report, September 13, 1990, p. 10, and "Cuba Cuts Fuel Consumption as Soviet Oil Deliveries Fall", Washington Post , August 30, 1990. 20 not even call

Al Qaeda and Affiliates: Historical Perspective, Global Presence, and Implications for U.S. Policy

DTIC Science & Technology

2010-02-05

mountainous tribal belt of northwest Pakistan, where it continues to train operatives, recruit, and disseminate propaganda. But Al Qaeda franchises or...April 2005 to U.S. charges of involvement in the September 11 plot, apparently visited Malaysia and met with cell members in 2000. Additionally, the...Qaeda leader, Malaysia was viewed as an ideal location for transiting and meeting because it allowed visa-free entry to citizens of most Gulf states

PHASE-SHIFT, STIMULI-RESPONSIVE PERFLUOROCARBON NANODROPLETS FOR DRUG DELIVERY TO CANCER

PubMed Central

2012-01-01

This review focuses on phase-shift perfluorocarbon nanoemulsions whose action depends on an ultrasound-triggered phase shift from a liquid to gas state. For drug-loaded perfluorocarbon nanoemulsions, microbubbles are formed under the action of tumor-directed ultrasound and drug is released locally into tumor volume in this process. This review covers in detail mechanisms involved in the droplet-to-bubble transition as well as mechanisms of ultrasound-mediated drug delivery. PMID:22730185

Simulation studies of GST phase change alloys

NASA Astrophysics Data System (ADS)

Martyna, Glenn

2008-03-01

In order to help drive post-Moore's Law technology development, switching processes involving novel materials, in particular, GeSbTe (GST) alloys are being investigated for use in memory and eFuse applications. An anneal/quench thermal process crystallizes/amorphosizes a GST alloy which then has a low/high resistance and thereby forms a readable/writeable bit; for example, a ``one'' might be the low resistance, conducting crystalline state and a ``zero'' might be the high resistance, glassy state. There are many open questions about the precise nature of the structural transitions and the coupling to electronic structure changes. Computational and experimental studies of the effect of pressure on the GST materials were initiated in order to probe the physics behind the thermal switching process. A new pathway to reversible phase change involving pressure-induced structural metal insulator transitions was discovered. In a binary GS system, a room-temperature, direct, pressure-induced transformation from the high resistance amorphous phase to the low resistance crystalline phase was observed experimentally while the reverse process under tensile load was demonstrated via ab initio MD simulations performed on IBM's Blue Gene/L enabled by massively parallel software. Pressure induced transformations of the ternary material GST-225 (Ge2Sb2Te5) were, also, examined In the talk, the behavior of the two systems will be compared and insight into the nature of the phase change given.

QM/MM simulations identify the determinants of catalytic activity differences between type II dehydroquinase enzymes.

PubMed

Lence, Emilio; van der Kamp, Marc W; González-Bello, Concepción; Mulholland, Adrian J

2018-05-16

Type II dehydroquinase enzymes (DHQ2), recognized targets for antibiotic drug discovery, show significantly different activities dependent on the species: DHQ2 from Mycobacterium tuberculosis (MtDHQ2) and Helicobacter pylori (HpDHQ2) show a 50-fold difference in catalytic efficiency. Revealing the determinants of this activity difference is important for our understanding of biological catalysis and further offers the potential to contribute to tailoring specificity in drug design. Molecular dynamics simulations using a quantum mechanics/molecular mechanics potential, with correlated ab initio single point corrections, identify and quantify the subtle determinants of the experimentally observed difference in efficiency. The rate-determining step involves the formation of an enolate intermediate: more efficient stabilization of the enolate and transition state of the key step in MtDHQ2, mainly by the essential residues Tyr24 and Arg19, makes it more efficient than HpDHQ2. Further, a water molecule, which is absent in MtDHQ2 but involved in generation of the catalytic Tyr22 tyrosinate in HpDHQ2, was found to destabilize both the transition state and the enolate intermediate. The quantification of the contribution of key residues and water molecules in the rate-determining step of the mechanism also leads to improved understanding of higher potencies and specificity of known inhibitors, which should aid ongoing inhibitor design.

Quantum phase transitions and local magnetism in Mott insulators: A local probe investigation using muons, neutrons, and photons

NASA Astrophysics Data System (ADS)

Frandsen, Benjamin A.

Mott insulators are materials in which strong correlations among the electrons induce an unconventional insulating state. Rich interplay between the structural, magnetic, and electronic degrees of freedom resulting from the electron correlation can lead to unusual complexity of Mott materials on the atomic scale, such as microscopically heterogeneous phases or local structural correlations that deviate significantly from the average structure. Such behavior must be studied by suitable experimental techniques, i.e. "local probes", that are sensitive to this local behavior rather than just the bulk, average properties. In this thesis, I will present results from our studies of multiple families of Mott insulators using two such local probes: muon spin relaxation (muSR), a probe of local magnetism; and pair distribution function (PDF) analysis of x-ray and neutron total scattering, a probe of local atomic structure. In addition, I will present the development of magnetic pair distribution function analysis, a novel method for studying local magnetic correlations that is highly complementary to the muSR and atomic PDF techniques. We used muSR to study the phase transition from Mott insulator to metal in two archetypal Mott insulating systems: RENiO3 (RE = rare earth element) and V2O3. In both of these systems, the Mott insulating state can be suppressed by tuning a nonthermal parameter, resulting in a "quantum" phase transition at zero temperature from the Mott insulating state to a metallic state. In RENiO3, this occurs through variation of the rare-earth element in the chemical composition; in V 2O3, through the application of hydrostatic pressure. Our results show that the metallic and Mott insulating states unexpectedly coexist in phase-separated regions across a large portion of parameter space near the Mott quantum phase transition and that the magnitude of the ordered antiferromagnetic moment remains constant across the phase diagram until it is abruptly destroyed at the quantum phase transition. Taken together, these findings point unambiguously to a first-order quantum phase transition in these systems. We also conducted x-ray and neutron PDF experiments, which suggest that the distinct atomic structures associated with the insulating and metallic phases similarly coexist near the quantum phase transition. These results have significant implications for our understanding of the Mott metal-insulator quantum phase transition in real materials. The second part of this thesis centers on the derivation and development of the magnetic pair distribution function (mPDF) technique and its application to the antiferromagnetic Mott insulator MnO. The atomic PDF method involves Fourier transforming the x-ray or neutron total scattering intensity from reciprocal space into real space to directly reveal the local atomic correlations in a material, which may deviate significantly from the average crystallographic structure of that material. Likewise, the mPDF method involves Fourier transforming the magnetic neutron total scattering intensity to probe the local correlations of magnetic moments in the material, which may exist on short length scales even when the material has no long-range magnetic order. After deriving the fundamental mPDF equations and providing a proof-of-principle by recovering the known magnetic structure of antiferromagnetic MnO, we used this technique to investigate the short-range magnetic correlations that persist well into the paramagnetic phase of MnO. By combining the mPDF measurements with ab initio calculations of the spin-spin correlation function in paramagnetic MnO, we were able to quantitatively account for the observed mPDF. We also used the mPDF data to evaluate competing ab initio theories, thereby resolving some longstanding questions about the magnetic exchange interactions in MnO.

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.

Localization of electrons and excitations

NASA Astrophysics Data System (ADS)

Larsson, Sven

2006-07-01

Electrons, electron holes, or excitations in finite or infinite 'multimer systems' may be localized or delocalized. In the theory of Hush, localization depends on the ratio Δ/ λ ( Δ/2 = coupling; λ = reorganization energy). The latter theory has been extended to the infinite system [S. Larsson, A. Klimkāns, Mol. Cryst. Liq. Cryst. 355 (2000) 217]. The metal/insulator transition often takes place abruptly as a function of Δ/ λ. It is argued that localization in a system with un-filled bands cannot be determined on the basis of Mott-Hubbard U alone, but depends on the number of accessible valence states, reorganization energy λ and coupling Δ (=2t). In fact U = 0 does not necessarily imply delocalization. The analysis here shows that there are many different situations for an insulator to metal transition. Charge transfer in doped NiO is characterized by Ni 2+ - Ni 3+ exchange while charge transfer in pure NiO is characterized by a disproportionation 2Ni 2+ → Ni + + Ni 3+. In spite of the great differences between these two cases, U has been applied without discrimination to both. The relevant localization parameters appear to be Δ and λ in the first case, with only two oxidation states, and U, Δ and λ in the second case with three oxidation states. The analysis is extended to insulator-metal transitions, giant magnetic resistance (GMR) and high Tc superconductivity (SC). λ and Δ can be determined quite accurately in quantum mechanical calculations involving only one and two monomers, respectively.

Malignant hyperthermia and calcium-induced heat production.

PubMed

Ueda, I; Shinoda, F; Kamaya, H; Krishna, P R

1994-05-01

The abnormal increase in intracellular Ca++ in malignant hyperthermia (MH) is well documented, but the link between the increased Ca++ concentration and high temperature remains speculative. We investigated the possibility that the Ca(++)-induced change in the state of cell membranes may contribute to the temperature elevation. Calcium ion transforms phospholipid membranes from the fluid to solid state. This is analogous to the freezing of water, and liberates latent heat. Differential titration calorimetry (DTC) measures heat production or absorption during ligand binding to macromolecules. When CaCl2 solution was added to anionic dimyristoylphosphatidic acid (DMPA) and dimyristoylphosphatidylglycerol (DMPG) vesicle membranes in incremental doses, DTC showed that the heat production suddenly increased when the Ca++ concentration exceeded about 120 microM. At this Ca++ concentration range, these lipid membranes underwent phase transition. The latent heat of transition was measured by differential scanning calorimetry (DSC). The values were 7.1 +/- 0.7 (SD, n = 4) kcal.mol-1 of DMPA and 6.8 +/- 0.7 (SD, n = 4) kcal.mol-1 of DMPG. The study shows that Ca++ produces heat when bound to lipid membranes. We are not proposing, however, that this is the sole source of heat. We contend that the lipid phase transition is one of the heat sources and it may trigger a hypermetabolic state by elevating the temperature of cell membranes. Because Ca++ is implicated as the second messenger in signal transduction, multiple systems may be involved. More studies are needed to clarify how Ca++ increases body temperature.

Simulation of surface processes

PubMed Central

Jónsson, Hannes

2011-01-01

Computer simulations of surface processes can reveal unexpected insight regarding atomic-scale structure and transitions. Here, the strengths and weaknesses of some commonly used approaches are reviewed as well as promising avenues for improvements. The electronic degrees of freedom are usually described by gradient-dependent functionals within Kohn–Sham density functional theory. Although this level of theory has been remarkably successful in numerous studies, several important problems require a more accurate theoretical description. It is important to develop new tools to make it possible to study, for example, localized defect states and band gaps in large and complex systems. Preliminary results presented here show that orbital density-dependent functionals provide a promising avenue, but they require the development of new numerical methods and substantial changes to codes designed for Kohn–Sham density functional theory. The nuclear degrees of freedom can, in most cases, be described by the classical equations of motion; however, they still pose a significant challenge, because the time scale of interesting transitions, which typically involve substantial free energy barriers, is much longer than the time scale of vibrations—often 10 orders of magnitude. Therefore, simulation of diffusion, structural annealing, and chemical reactions cannot be achieved with direct simulation of the classical dynamics. Alternative approaches are needed. One such approach is transition state theory as implemented in the adaptive kinetic Monte Carlo algorithm, which, thus far, has relied on the harmonic approximation but could be extended and made applicable to systems with rougher energy landscape and transitions through quantum mechanical tunneling. PMID:21199939

Spectroscopy of selected metal-containing diatomic molecules

NASA Astrophysics Data System (ADS)

Gordon, Iouli E.

Fourier transform infrared emission spectra of MnH and MnD were observed in the ground X7Sigma+ electronic state. The vibration-rotation bands from v = 1 → 0 to v = 3 → 2 for MnH, and from v = 1 → 0 to v = 4 → 3 for MnD were recorded at an instrumental resolution of 0.0085 cm-1. Spectroscopic constants were determined for each vibrational level and equilibrium constants were found from a Dunham-type fit. The equilibrium vibrational constant oe for MnH was found to be 1546.84518(65) cm-1, the equilibrium rotational constant Be was found to be 5.6856789(103) cm-1 and the equilibrium bond distance re was determined to be 1.7308601(47) A. New high resolution emission spectra of CoH and CoD molecules have been recorded in the 640 nm to 3.5 mum region using a Fourier transform spectrometer. Many bands were observed for the A'3phi- X3phi electronic transition of CoH and CoD. In addition, a new [13.3]4 electronic state was found by observing the [13.3]4-X3phi3 and [13.3]4- X3phi4 transitions in the spectrum of CoD. Analysis of the transitions with DeltaO = 0, +/-1 provided more accurate values of spin-orbit splittings between O = 4 and O = 3 components. The ground state for both molecules was fitted both to band and Dunham-type constants. The estimated band constants of the perturbed upper states were also obtained. The emission spectrum of gas-phase YbO has been investigated using a Fourier transform spectrometer. A total of 8 red-degraded bands in the range 9 800--11 300 cm-1 were recorded at a resolution of 0.04 cm-1. Because of the multiple isotopomers present in the spectra, only 3 bands were rotationally analyzed. Perturbations were identified in two of these bands and all 3 transitions were found to terminate at the X1Sigma+ ground electronic state. The electronic configurations that give rise to the observed states are discussed and molecular parameters for all of the analyzed bands are reported. Electronic spectra of the previously unobserved EuH and EuD molecules were studied by means of Fourier transform spectroscopy and laser-induced fluorescence. The extreme complexity of these transitions made rotational assignments of EuH bands impossible. However, the spin-spin interaction constant, lambda, and Fermi contact parameter, bF, in the ground X9Sigma- electronic state were estimated for the 151EuH and 153EuH isotopologues. Electronic spectra of SmH, SmCl, TmH and ErF molecules were recorded for the first time using Fourier transform spectrometer. The poor signal to noise ratio of the observed bands coupled with their complexity prevented a rotational analysis. The electronic states that may be involved in the observed transitions are discussed.

Spectroscopy of selected metal-containing diatomic molecules

NASA Astrophysics Data System (ADS)

Gordon, Iouli

Fourier transform infrared emission spectra of MnH and MnD were observed in the ground X7[sigma]+ electronic state. The vibration-rotation bands from v = 1 to 0 to v = 3 to 2 for MnH, and from v = 1 to 0 to v = 4 to 3 for MnD were recorded at an instrumental resolution of 0. 0085 cm-1. Spectroscopic constants were determined for each vibrational level and equilibrium constants were found from a Dunham-type fit. The equilibrium vibrational constant [omega]e for MnH was found to be 1546. 84518(65) cm-1, the equilibrium rotational constant Be was found to be 5. 6856789(103) cm-1 and the equilibrium bond distance re was determined to be 1. 7308601(47) ?. New high resolution emission spectra of CoH and CoD molecules have been recorded in the 640 nm to 3. 5 _m region using a Fourier transform spectrometer. Many bands were observed for the A'3?-X3? electronic transition of CoH and CoD. In addition, a new [13. 3]4 electronic state was found by observing the [13. 3]4- X3?3 and [13. 3]4-X3?4 transitions in the spectrum of CoD. Analysis of the transitions with [delta][omega] = 0, ?1 provided more accurate values of spin-orbit splittings between [omega] = 4 and [omega] = 3 components. The ground state for both molecules was fitted both to band and Dunham-type constants. The estimated band constants of the perturbed upper states were also obtained. The emission spectrum of gas-phase YbO has been investigated using a Fourier transform spectrometer. A total of 8 red-degraded bands in the range 9 800 ? 11 300 cm-1 were recorded at a resolution of 0. 04 cm-1. Because of the multiple isotopomers present in the spectra, only 3 bands were rotationally analyzed. Perturbations were identified in two of these bands and all 3 transitions were found to terminate at the X1[sigma]+ ground electronic state. The electronic configurations that give rise to the observed states are discussed and molecular parameters for all of the analyzed bands are reported. Electronic spectra of the previously unobserved EuH and EuD molecules were studied by means of Fourier transform spectroscopy and laser-induced fluorescence. The extreme complexity of these transitions made rotational assignments of EuH bands impossible. However, the spin-spin interaction constant, [lambda], and Fermi contact parameter, bF, in the ground X9[sigma]- electronic state were estimated for the 151EuH and 153EuH isotopologues. Electronic spectra of SmH, SmCl, TmH and ErF molecules were recorded for the first time using Fourier transform spectrometer. The poor signal to noise ratio of the observed bands coupled with their complexity prevented a rotational analysis. The electronic states that may be involved in the observed transitions are discussed.

A lncRNA fine tunes the dynamics of a cell state transition involving Lin28, let-7 and de novo DNA methylation

PubMed Central

Li, Meng Amy; Amaral, Paulo P; Cheung, Priscilla; Bergmann, Jan H; Kinoshita, Masaki; Kalkan, Tüzer; Ralser, Meryem; Robson, Sam; von Meyenn, Ferdinand; Paramor, Maike; Yang, Fengtang; Chen, Caifu; Nichols, Jennifer; Spector, David L; Kouzarides, Tony; He, Lin; Smith, Austin

2017-01-01

Execution of pluripotency requires progression from the naïve status represented by mouse embryonic stem cells (ESCs) to a state capacitated for lineage specification. This transition is coordinated at multiple levels. Non-coding RNAs may contribute to this regulatory orchestra. We identified a rodent-specific long non-coding RNA (lncRNA) linc1281, hereafter Ephemeron (Eprn), that modulates the dynamics of exit from naïve pluripotency. Eprn deletion delays the extinction of ESC identity, an effect associated with perduring Nanog expression. In the absence of Eprn, Lin28a expression is reduced which results in persistence of let-7 microRNAs, and the up-regulation of de novo methyltransferases Dnmt3a/b is delayed. Dnmt3a/b deletion retards ES cell transition, correlating with delayed Nanog promoter methylation and phenocopying loss of Eprn or Lin28a. The connection from lncRNA to miRNA and DNA methylation facilitates the acute extinction of naïve pluripotency, a pre-requisite for rapid progression from preimplantation epiblast to gastrulation in rodents. Eprn illustrates how lncRNAs may introduce species-specific network modulations. DOI: http://dx.doi.org/10.7554/eLife.23468.001 PMID:28820723

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.

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

Probing the Locality of Excited States with Linear Algebra.

PubMed

Etienne, Thibaud

2015-04-14

This article reports a novel theoretical approach related to the analysis of molecular excited states. The strategy introduced here involves gathering two pieces of physical information, coming from Hilbert and direct space operations, into a general, unique quantum mechanical descriptor of electronic transitions' locality. Moreover, the projection of Hilbert and direct space-derived indices in an Argand plane delivers a straightforward way to visually probe the ability of a dye to undergo a long- or short-range charge-transfer. This information can be applied, for instance, to the analysis of the electronic response of families of dyes to light absorption by unveiling the trend of a given push-pull chromophore to increase the electronic cloud polarization magnitude of its main transition with respect to the size extension of its conjugated spacer. We finally demonstrate that all the quantities reported in this article can be reliably approximated by a linear algebraic derivation, based on the contraction of detachment/attachment density matrices from canonical to atomic space. This alternative derivation has the remarkable advantage of a very low computational cost with respect to the previously used numerical integrations, making fast and accurate characterization of large molecular systems' excited states easily affordable.

Dehydroindigo, the forgotten indigo and its contribution to the color of Maya Blue.

PubMed

Rondão, Raquel; Seixas de Melo, J Sérgio; Bonifácio, Vasco D B; Melo, Maria J

2010-02-04

A comprehensive investigation of the electronic spectral and photophysical properties of the oxidized form of indigo, dehydroindigo (DHI), has been carried out in solution at 293 K. It is shown that dehydroindigo readily converts into its neutral keto form, the blue indigo, in a process which depends on the solvent and water content of the medium. DHI was investigated in toluene, in benzene, and in methanol and it was found that both the oxidized and the keto indigo forms are present in solution. In marked contrast to what has been found for keto-indigo, where the internal conversion channel dominates >99% of the excited state deactivation, or with the fully reduced leuco-indigo, where fluorescence, internal conversion, and singlet-to-triplet intersystem crossing coexist, in the case of DHI in toluene and benzene, the dominant excited state deactivation channel involves the triplet state. Triplet state yields (phi(T)) of 70-80%, with negligible fluorescence (< or = 0.01%) are observed in these solvents. In methanol the phi(T) value decreases to approximately 15%, with an increase of the fluorescence quantum yield to 2%, which makes these processes competitive with the S(1) --> S(0) internal conversion deactivation process. The data are experimentally compatible with the existence of a lowest lying singlet excited state of n,pi* origin in toluene and of pi,pi* origin in methanol. A time-resolved investigation in the picosecond time domain suggests that the emission of DHI involves three interconnected species (involving rotational isomerism), with relative contributions depending on the emission wavelength. DFT calculations (B3LYP 6-31G** level) were performed in order to characterize the electronic ground (S(0)) and excited singlet (S(1)) and triplet (T(1)) states of DHI. The HOMO-LUMO transition was found to accompany an n --> pi* transition of the oxygen nonbonding orbitals to the central CC and adjacent C-N bonds. Calculations also revealed that in S(0) the two indole-like moieties deviate from planarity from ca. 20 degrees, whereas in S(1) and T(1) the predicted structure is basically planar; a gradual decrease of the carbon-carbon central bond distance is seen in the order S(0), S(1), T(1). An additional study on the blue pigment Maya Blue was made, and the comparison between the solid-state spectra of indigo, DHI, and Maya Blue suggests that, in line with recent investigations, DHI is present together with indigo in Maya Blue. These results are relevant to the discussion of the involvement of dehydroindigo in the palette of colors of the ancient Maya Blue pigment.

14 CFR 375.50 - Transit flights; scheduled international air service operations.

Code of Federal Regulations, 2010 CFR

2010-01-01

... WITHIN THE UNITED STATES Transit Flights § 375.50 Transit flights; scheduled international air service operations. (a) Requirement of notice. Scheduled international air services proposed to be operated pursuant to the International Air Services Transit Agreement in transit across the United States may not be...

14 CFR 375.50 - Transit flights; scheduled international air service operations.

Code of Federal Regulations, 2011 CFR

2011-01-01

... WITHIN THE UNITED STATES Transit Flights § 375.50 Transit flights; scheduled international air service operations. (a) Requirement of notice. Scheduled international air services proposed to be operated pursuant to the International Air Services Transit Agreement in transit across the United States may not be...

14 CFR 375.50 - Transit flights; scheduled international air service operations.

Code of Federal Regulations, 2014 CFR

2014-01-01

... WITHIN THE UNITED STATES Transit Flights § 375.50 Transit flights; scheduled international air service operations. (a) Requirement of notice. Scheduled international air services proposed to be operated pursuant to the International Air Services Transit Agreement in transit across the United States may not be...

14 CFR 375.50 - Transit flights; scheduled international air service operations.

Code of Federal Regulations, 2013 CFR

2013-01-01

... WITHIN THE UNITED STATES Transit Flights § 375.50 Transit flights; scheduled international air service operations. (a) Requirement of notice. Scheduled international air services proposed to be operated pursuant to the International Air Services Transit Agreement in transit across the United States may not be...

14 CFR 375.50 - Transit flights; scheduled international air service operations.

Code of Federal Regulations, 2012 CFR

2012-01-01

... WITHIN THE UNITED STATES Transit Flights § 375.50 Transit flights; scheduled international air service operations. (a) Requirement of notice. Scheduled international air services proposed to be operated pursuant to the International Air Services Transit Agreement in transit across the United States may not be...

Reactions of guanine with methyl chloride and methyl bromide: O6-methylation versus charge transfer complex formation

NASA Astrophysics Data System (ADS)

Shukla, P. K.; Mishra, P. C.; Suhai, S.

Density functional theory (DFT) at the B3LYP/6-31+G* and B3LYP/AUG-cc-pVDZ levels was employed to study O6-methylation of guanine due to its reactions with methyl chloride and methyl bromide and to obtain explanation as to why the methyl halides cause genotoxicity and possess mutagenic and carcinogenic properties. Geometries of the various isolated species involved in the reactions, reactant complexes (RCs), and product complexes (PCs) were optimized in gas phase. Transition states connecting the reactant complexes with the product complexes were also optimized in gas phase at the same levels of theory. The reactant complexes, product complexes, and transition states were solvated in aqueous media using the polarizable continuum model (PCM) of the self-consistent reaction field theory. Zero-point energy (ZPE) correction to total energy and the corresponding thermal energy correction to enthalpy were made in each case. The reactant complexes of the keto form of guanine with methyl chloride and methyl bromide in water are appreciably more stable than the corresponding complexes involving the enol form of guanine. The nature of binding in the product complexes was found to be of the charge transfer type (O6mG+ · X-, X dbond Cl, Br). Binding of HCl, HBr, and H2O molecules to the PCs obtained with the keto form of guanine did not alter the positions of the halide anions in the PCs, and the charge transfer character of the PCs was also not modified due to this binding. Further, the complexes obtained due to the binding of HCl, HBr, and H2O molecules to the PCs had greater stability than the isolated PCs. The reaction barriers involved in the formation of PCs were found to be quite high (?50 kcal/mol). Mechanisms of genotoxicity, mutagenesis and carcinogenesis caused by the methyl halides appear to involve charge transfer-type complex formation. Thus the mechanisms of these processes involving the methyl halides appear to be quite different from those that involve the other strongly carcinogenic methylating agents.

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…

Study of spin-dependent transitions and spin coherence at the (111) oriented phosphorous doped crystalline silicon to silicon dioxide interface using pulsed electrically detected magnetic resonance

NASA Astrophysics Data System (ADS)

Paik, Seoyoung

A study of spin-dependent electronic transitions at the (111) oriented phosphorous doped crystalline silicon (c-Si) to silicon dioxide (SiO 2) interface is presented for [31P] = 1015 cm-3 and [31P] = 1016 cm -3 and a temperature range between T ≈ 5K and T ≈ 15K. Using pulsed electrically detected magnetic resonance (pEDMR), spin-dependent transitions involving 31P donor states and two different interface states are observed, namely (i) Pb centers which can be identified by their characteristic anisotropy and (ii) the E' center which is attributed to defects of the near interface SiO 2 bulk. Correlation measurements of the dynamics of spin-dependent recombination confirm that previously proposed transitions between 31P and the interface defects take place. The influence of these near interface transitions on the 31P donor spin coherence time T 2 as well as the donor spin-lattice relaxation time T 1 is then investigated by comparison of spin Hahn echo decay measurements obtained from conventional bulk sensitive pulsed electron paramagnetic resonance and surface sensitive pEDMR measurements, as well as surface sensitive electrically detected inversion recovery experiments. The measurements reveal that the T2 times of both interface states and 31P donor electrons spins in proximity of them are consistently shorter than the T1 times, and both T2 and T1 times of the near interface donors are reduced by several orders of magnitude from those in the bulk, at T ≤ 13 K. The T 2 times of the 31P donor electrons are in agreement with the prediction by De Sousa that they are limited by interface defect-induced field noise. To further investigate the dynamic properties of spin-dependent near interface processes, electrical detection of spin beat oscillation between resonantly induced spin-Rabi nutation is conducted at the phosphorous doped (1016cm-3) Si(111)/SiO2 interface. Predictions of Rabi beat oscillations based on several different spin-pair models are compared with measured Rabi beat nutation data. Due to the g-factor anisotropy of the Pb center (a silicon surface dangling bond), one can tune intra-pair Larmor frequency differences (Larmor separations) by orientation of the crystal with regard to an external magnetic field. Since Larmor separation governs the number of beating spin-pairs, crystal orientation can control the beat current. This is used to identify spin states that are paired by mutual electronic transitions. Based on the agreement between hypothesis and data, the experiments confirm the presence of the previously observed 31P-P b transition and the previously hypothesized P b to near interface SiO2 bulk state (E' center) transition.

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).

Catch and Release: Orbital Symmetry Guided Reaction Dynamics from a Freed “Tension Trapped Transition State”

DOE PAGES

Wang, Junpeng; Ong, Mitchell T.; Kouznetsova, Tatiana B.; ...

2015-08-31

The dynamics of reactions at or in the immediate vicinity of transition states are critical to reaction rates and product distributions, but direct experimental probes of those dynamics are rare. In this paper, s-trans, s-trans 1,3-diradicaloid transition states are trapped by tension along the backbone of purely cis-substituted gem-difluorocyclopropanated polybutadiene using the extensional forces generated by pulsed sonication of dilute polymer solutions. Once released, the branching ratio between symmetry-allowed disrotatory ring closing (of which the trapped diradicaloid structure is the transition state) and symmetry-forbidden conrotatory ring closing (whose transition state is nearby) can be inferred. Finally, net conrotatory ring closingmore » occurred in 5.0 ± 0.5% of the released transition states, in excellent agreement with ab initio molecular dynamics simulations.« less

Remote sensing of rangeland biodiversity

USDA-ARS?s Scientific Manuscript database

Rangelands are managed based on state and transition models for an ecological site. Transitions to alternative ecological states are indicative of degrading rangelands. Three key variables may be remotely sensed to detect transitions between alternative states: amount of bare soil, presence of inva...

Sip1 mediates an E-cadherin-to-N-cadherin switch during cranial neural crest EMT

PubMed Central

Rogers, Crystal D.; Saxena, Ankur

2013-01-01

The neural crest, an embryonic stem cell population, initially resides within the dorsal neural tube but subsequently undergoes an epithelial-to-mesenchymal transition (EMT) to commence migration. Although neural crest and cancer EMTs are morphologically similar, little is known regarding conservation of their underlying molecular mechanisms. We report that Sip1, which is involved in cancer EMT, plays a critical role in promoting the neural crest cell transition to a mesenchymal state. Sip1 transcripts are expressed in premigratory/migrating crest cells. After Sip1 loss, the neural crest specifier gene FoxD3 was abnormally retained in the dorsal neuroepithelium, whereas Sox10, which is normally required for emigration, was diminished. Subsequently, clumps of adherent neural crest cells remained adjacent to the neural tube and aberrantly expressed E-cadherin while lacking N-cadherin. These findings demonstrate two distinct phases of neural crest EMT, detachment and mesenchymalization, with the latter involving a novel requirement for Sip1 in regulation of cadherin expression during completion of neural crest EMT. PMID:24297751

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.

Thermal and fragility studies on microwave synthesized K2O-B2O3-V2O5 glasses

NASA Astrophysics Data System (ADS)

Harikamalasree, Reddy, M. Sudhakara; Viswanatha, R.; Reddy, C. Narayana

2016-05-01

Glasses with composition xK2O-60B2O3-(40-x) V2O5 (15 ≤ x ≤ 39 mol %) was prepared by an energy efficient microwave method. The heat capacity change (ΔCp) at glass transition (Tg), width of glass transition (ΔTg), heat capacities in the glassy (Cpg) and liquid (Cpl) state for the investigated glasses were extracted from Modulated Differential Scanning Calorimetry (MDSC) thermograms. The width of glass transition is less than 30°C, indicating that these glasses belongs to fragile category. Fragility functions [NBO]/(Vm3Tg) and (ΔCp/Cpl)increases with increasing modifier oxide concentration. Increase in fragility is attributed to the increasing coordination of boron. Further, addition of K2O creates NBOs and the flow mechanism involves bond switching between BOs and NBOs. Physical properties exhibit compositional dependence and these properties increase with increasing K2O concentration. The observed variations are qualitatively analyzed.

Experimental Determination of Dynamical Lee-Yang Zeros

NASA Astrophysics Data System (ADS)

Brandner, Kay; Maisi, Ville F.; Pekola, Jukka P.; Garrahan, Juan P.; Flindt, Christian

2017-05-01

Statistical physics provides the concepts and methods to explain the phase behavior of interacting many-body systems. Investigations of Lee-Yang zeros—complex singularities of the free energy in systems of finite size—have led to a unified understanding of equilibrium phase transitions. The ideas of Lee and Yang, however, are not restricted to equilibrium phenomena. Recently, Lee-Yang zeros have been used to characterize nonequilibrium processes such as dynamical phase transitions in quantum systems after a quench or dynamic order-disorder transitions in glasses. Here, we experimentally realize a scheme for determining Lee-Yang zeros in such nonequilibrium settings. We extract the dynamical Lee-Yang zeros of a stochastic process involving Andreev tunneling between a normal-state island and two superconducting leads from measurements of the dynamical activity along a trajectory. From the short-time behavior of the Lee-Yang zeros, we predict the large-deviation statistics of the activity which is typically difficult to measure. Our method paves the way for further experiments on the statistical mechanics of many-body systems out of equilibrium.

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

Videla, Pablo E.; Rossky, Peter J.; Laria, D., E-mail: dhlaria@cnea.gov.ar

We present results of ring polymer molecular dynamics simulations that shed light on the effects of nuclear quantum fluctuations on tunneling motions in cyclic [H{sub 2}O]{sub 3} and [D{sub 2}O]{sub 3}, at the representative temperature of T = 75 K. In particular, we focus attention on free energies associated with two key isomerization processes: The first one corresponds to flipping transitions of dangling OH bonds, between up and down positions with respect to the O–O–O plane of the cluster; the second involves the interchange between connecting and dangling hydrogen bond character of the H-atoms in a tagged water molecule. Zeromore » point energy and tunneling effects lead to sensible reductions of the free energy barriers. Due to the lighter nature of the H nuclei, these modifications are more marked in [H{sub 2}O]{sub 3} than in [D{sub 2}O]{sub 3}. Estimates of the characteristic time scales describing the flipping transitions are consistent with those predicted based on standard transition-state-approximation arguments.« less

Analytical and numerical investigation of bolted steel ring flange connection for offshore wind monopile foundations

NASA Astrophysics Data System (ADS)

Madsen, C. A.; Kragh-Poulsen, J.-C.; Thage, K. J.; Andreassen, M. J.

2017-12-01

The monopile foundation is the dominant solution for support of wind turbines in offshore wind farms. It is normally grouted to the transition piece which connects the foundation to the turbine. Currently, the bolted steel ring flange connection is investigated as an alternative. The monopile--transition piece connection has specific problems, such as out-of-verticality and installation damage from driving the MP into the seabed and it is not fully known how to design for these. This paper presents the status of the ongoing development work and an estimate of what still needs to be covered in order to use the connection in practice. This involves presentation of an analytical and non-linear FE analysis procedure for the monopile-transition piece connection composed of two L flanges connected with preloaded bolts. The connection is verified for ultimate and fatigue limit states based on an integrated load simulation carried out by the turbine manufacturer.

Direct observation of oxygen vacancy-driven structural and resistive phase transitions in La2/3Sr1/3MnO3

NASA Astrophysics Data System (ADS)

Yao, Lide; Inkinen, Sampo; van Dijken, Sebastiaan

2017-02-01

Resistive switching in transition metal oxides involves intricate physical and chemical behaviours with potential for non-volatile memory and memristive devices. Although oxygen vacancy migration is known to play a crucial role in resistive switching of oxides, an in-depth understanding of oxygen vacancy-driven effects requires direct imaging of atomic-scale dynamic processes and their real-time impact on resistance changes. Here we use in situ transmission electron microscopy to demonstrate reversible switching between three resistance states in epitaxial La2/3Sr1/3MnO3 films. Simultaneous high-resolution imaging and resistance probing indicate that the switching events are caused by the formation of uniform structural phases. Reversible horizontal migration of oxygen vacancies within the manganite film, driven by combined effects of Joule heating and bias voltage, predominantly triggers the structural and resistive transitions. Our findings open prospects for ionotronic devices based on dynamic control of physical properties in complex oxide nanostructures.

Communication: Isotopic effects on tunneling motions in the water trimer.

PubMed

Videla, Pablo E; Rossky, Peter J; Laria, D

2016-02-14

We present results of ring polymer molecular dynamics simulations that shed light on the effects of nuclear quantum fluctuations on tunneling motions in cyclic [H2O]3 and [D2O]3, at the representative temperature of T = 75 K. In particular, we focus attention on free energies associated with two key isomerization processes: The first one corresponds to flipping transitions of dangling OH bonds, between up and down positions with respect to the O-O-O plane of the cluster; the second involves the interchange between connecting and dangling hydrogen bond character of the H-atoms in a tagged water molecule. Zero point energy and tunneling effects lead to sensible reductions of the free energy barriers. Due to the lighter nature of the H nuclei, these modifications are more marked in [H2O]3 than in [D2O]3. Estimates of the characteristic time scales describing the flipping transitions are consistent with those predicted based on standard transition-state-approximation arguments.

Fuzzy State Transition and Kalman Filter Applied in Short-Term Traffic Flow Forecasting

PubMed Central

Ming-jun, Deng; Shi-ru, Qu

2015-01-01

Traffic flow is widely recognized as an important parameter for road traffic state forecasting. Fuzzy state transform and Kalman filter (KF) have been applied in this field separately. But the studies show that the former method has good performance on the trend forecasting of traffic state variation but always involves several numerical errors. The latter model is good at numerical forecasting but is deficient in the expression of time hysteretically. This paper proposed an approach that combining fuzzy state transform and KF forecasting model. In considering the advantage of the two models, a weight combination model is proposed. The minimum of the sum forecasting error squared is regarded as a goal in optimizing the combined weight dynamically. Real detection data are used to test the efficiency. Results indicate that the method has a good performance in terms of short-term traffic forecasting. PMID:26779258

Fuzzy State Transition and Kalman Filter Applied in Short-Term Traffic Flow Forecasting.

PubMed

Deng, Ming-jun; Qu, Shi-ru

2015-01-01

Traffic flow is widely recognized as an important parameter for road traffic state forecasting. Fuzzy state transform and Kalman filter (KF) have been applied in this field separately. But the studies show that the former method has good performance on the trend forecasting of traffic state variation but always involves several numerical errors. The latter model is good at numerical forecasting but is deficient in the expression of time hysteretically. This paper proposed an approach that combining fuzzy state transform and KF forecasting model. In considering the advantage of the two models, a weight combination model is proposed. The minimum of the sum forecasting error squared is regarded as a goal in optimizing the combined weight dynamically. Real detection data are used to test the efficiency. Results indicate that the method has a good performance in terms of short-term traffic forecasting.

Investigation of Localized States in GaAsSb Epilayers Grown by Molecular Beam Epitaxy

PubMed Central

Gao, Xian; Wei, Zhipeng; Zhao, Fenghuan; Yang, Yahui; Chen, Rui; Fang, Xuan; Tang, Jilong; Fang, Dan; Wang, Dengkui; Li, Ruixue; Ge, Xiaotian; Ma, Xiaohui; Wang, Xiaohua

2016-01-01

We report the carrier dynamics in GaAsSb ternary alloy grown by molecular beam epitaxy through comprehensive spectroscopic characterization over a wide temperature range. A detailed analysis of the experimental data reveals a complex carrier relaxation process involving both localized and delocalized states. At low temperature, the localized degree shows linear relationship with the increase of Sb component. The existence of localized states is also confirmed by the temperature dependence of peak position and band width of the emission. At temperature higher than 60 K, emissions related to localized states are quenched while the band to band transition dominates the whole spectrum. This study indicates that the localized states are related to the Sb component in the GaAsSb alloy, while it leads to the poor crystal quality of the material, and the application of GaAsSb alloy would be limited by this deterioration. PMID:27381641

A multi-state trajectory method for non-adiabatic dynamics simulations

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

Tao, Guohua, E-mail: taogh@pkusz.edu.cn

2016-03-07

A multi-state trajectory approach is proposed to describe nuclear-electron coupled dynamics in nonadiabatic simulations. In this approach, each electronic state is associated with an individual trajectory, among which electronic transition occurs. The set of these individual trajectories constitutes a multi-state trajectory, and nuclear dynamics is described by one of these individual trajectories as the system is on the corresponding state. The total nuclear-electron coupled dynamics is obtained from the ensemble average of the multi-state trajectories. A variety of benchmark systems such as the spin-boson system have been tested and the results generated using the quasi-classical version of the method showmore » reasonably good agreement with the exact quantum calculations. Featured in a clear multi-state picture, high efficiency, and excellent numerical stability, the proposed method may have advantages in being implemented to realistic complex molecular systems, and it could be straightforwardly applied to general nonadiabatic dynamics involving multiple states.« less

Abnormal Sleep/Wake Dynamics in Orexin Knockout Mice

PubMed Central

Diniz Behn, Cecilia G.; Klerman, Elizabeth B.; Mochizuki, Takatoshi; Lin, Shih-Chieh; Scammell, Thomas E.

2010-01-01

Study Objectives: Narcolepsy with cataplexy is caused by a loss of orexin (hypocretin) signaling, but the physiologic mechanisms that result in poor maintenance of wakefulness and fragmented sleep remain unknown. Conventional scoring of sleep cannot reveal much about the process of transitioning between states or the variations within states. We developed an EEG spectral analysis technique to determine whether the state instability in a mouse model of narcolepsy reflects abnormal sleep or wake states, faster movements between states, or abnormal transitions between states. Design: We analyzed sleep recordings in orexin knockout (OXKO) mice and wild type (WT) littermates using a state space analysis technique. This non-categorical approach allows quantitative and unbiased examination of sleep/wake states and state transitions. Measurements and Results: OXKO mice spent less time in deep, delta-rich NREM sleep and in active, theta-rich wake and instead spent more time near the transition zones between states. In addition, while in the midst of what should be stable wake, OXKO mice initiated rapid changes into NREM sleep with high velocities normally seen only in transition regions. Consequently, state transitions were much more frequent and rapid even though the EEG progressions during state transitions were normal. Conclusions: State space analysis enables visualization of the boundaries between sleep and wake and shows that narcoleptic mice have less distinct and more labile states of sleep and wakefulness. These observations provide new perspectives on the abnormal state dynamics resulting from disrupted orexin signaling and highlight the usefulness of state space analysis in understanding narcolepsy and other sleep disorders. Citation: Diniz Behn CG; Klerman EB; Mochizuki T; Lin S; Scammell TE. Abnormal sleep/wake dynamics in orexin knockout mice. SLEEP 2010;33(3):297-306. PMID:20337187