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Sample records for zundel-like transition state

  1. Variational Transition State Theory

    SciT

    Truhlar, Donald G.

    2016-09-29

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

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

    PubMed

    Schramm, Vern L

    2015-04-21

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

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

    PubMed Central

    Schramm, Vern L.

    2017-01-01

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

  4. Optimal trajectories of brain state transitions

    PubMed Central

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

    2017-01-01

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

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

    PubMed

    Ren, Weiqing

    2014-03-18

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

  6. Typology of State Types: Persistence and Transition

    DTIC Science & Technology

    2015-04-28

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

  7. Operationalizing resilience using state and transition models

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

  8. The Aromaticity of Pericyclic Reaction Transition States

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2007-01-01

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

  9. A hierarchical transition state search algorithm

    NASA Astrophysics Data System (ADS)

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

    2008-07-01

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

  10. Transition state theory for enzyme kinetics

    PubMed Central

    Truhlar, Donald G.

    2015-01-01

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

  11. E1 transitions from octupole vibration states

    NASA Astrophysics Data System (ADS)

    Cottle, P. D.

    1993-04-01

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

  12. A Model of Mental State Transition Network

    NASA Astrophysics Data System (ADS)

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

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

  13. Variational Identification of Markovian Transition States

    NASA Astrophysics Data System (ADS)

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

    2017-07-01

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

  14. State-transition diagrams for biologists.

    PubMed

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

    2012-01-01

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

  15. State-Transition Diagrams for Biologists

    PubMed Central

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

    2012-01-01

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

  16. Mixed state dynamical quantum phase transitions

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Utso; Bandyopadhyay, Souvik; Dutta, Amit

    2017-11-01

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

  17. 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.

  18. 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.

  19. Calibration of state and transition models with FVS

    Melinda Moeur; Don Vandendriesche

    2010-01-01

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

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

    ERIC Educational Resources Information Center

    Weiss, Hilton M.

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2018-05-01

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

  2. Improving Upon String Methods for Transition State Discovery.

    PubMed

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

    2012-02-14

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

  3. An inhibitory gate for state transition in cortex

    PubMed Central

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

    2017-01-01

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

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

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

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

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

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

    ERIC Educational Resources Information Center

    Alamprese, Judith A.

    2012-01-01

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

  7. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2017-06-01

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

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

    PubMed Central

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

    2009-01-01

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

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

    PubMed Central

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

    2010-01-01

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

  11. Densification and state transition across the Missouri Ozarks landscape

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

    2014-01-01

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

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

    DOE PAGES

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

    2015-11-18

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

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

    PubMed

    Zhao, Bin; Sun, Zhigang; Guo, Hua

    2015-12-23

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

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

    NASA Astrophysics Data System (ADS)

    Neilsen, Joseph

    2017-09-01

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

  15. Quantum phase transition between cluster and antiferromagnetic states

    NASA Astrophysics Data System (ADS)

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

    2011-09-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2008-01-01

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

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

    ERIC Educational Resources Information Center

    Sears, Victoria

    2014-01-01

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

  18. States Pave the Way for Smoother Transitions to Kindergarten

    ERIC Educational Resources Information Center

    Loewenberg, Aaron

    2018-01-01

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

  19. 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.

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

    PubMed Central

    Amyes, Tina L.; Richard, John P.

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Cherkaev, Andrej; Kouznetsov, Andrei; Panchenko, Alexander

    2010-09-01

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

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

    NASA Astrophysics Data System (ADS)

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

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

  3. A clock transition in a solid-state system

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

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

    ERIC Educational Resources Information Center

    Xu, Zeyu; Cepa, Kennan

    2018-01-01

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

  5. 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

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

    PubMed

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

    2014-01-15

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

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

    NASA Astrophysics Data System (ADS)

    Jia, Dongming; Manz, Jörn; Yang, Yonggang

    2018-01-01

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

  8. Magnetoelectric Effect in a Spin-State Transition System

    NASA Astrophysics Data System (ADS)

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

    2018-06-01

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

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

    PubMed

    Zimmerman, Paul

    2013-07-09

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

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

    PubMed Central

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

    2016-01-01

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

  11. 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.

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

    PubMed

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

    2017-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2018-01-01

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

  14. A United States regulator's perspective on the ongoing chlorofluorocarbon transition.

    PubMed

    Meyer, R J

    1999-12-01

    The Food and Drug Administration (FDA) put in place a general ban on the use of chlorofluorocarbons for the products it regulates (medical devices, drugs, and foods) in 1978, exempting those products where chlorofluorocarbon use was determined to be essential for the public health. In the intervening years, as the international commitment to a full transition away from all chlorofluorocarbon use took shape under the Montreal Protocol, the FDA has worked with industry to facilitate the development and testing of alternative technologies and products for inhalation drug products. As these alternative products begin to move from testing through the approval process and into marketing, the FDA is working collaboratively with the Environmental Protection Agency, other governmental agencies, and nongovernmental stakeholders to develop a transition policy for the United States. The transition policy for metered dose inhalers must be one that achieves the dual aims of first protecting the patients who rely on these vital medical products, while also achieving the public health need of protecting the ozone layer. As a part of developing such a transition strategy, the FDA published an advance notice of proposed rulemaking (ANPRM) in March 1997. The ANPRM proposed mechanisms by which the FDA could determine when chlorofluorocarbon use in a drug product could no longer be considered essential. The ANPRM resulted in a large amount of valuable public debate and input. The FDA is now working to incorporate the knowledge gained from these public comments as it continues the rule-making process.

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

    PubMed

    Amyes, Tina L; Richard, John P

    2013-03-26

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

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

    ERIC Educational Resources Information Center

    Warren, Paul; Murphy, Patrick

    2014-01-01

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

  17. Mechanical induction of transitions into mesenchymal and amoeboid states

    NASA Astrophysics Data System (ADS)

    Liphardt, Jan

    One of the fundamental mysteries of biology lies in the ability of cells to convert from one phenotype to another in response to external control inputs. We have been studying the Epithelial-to-Mesenchymal Transition (EMT), which allows organized assemblies of epithelial cells to scatter into lone mesenchymal cells. EMT is critical for normal development and wound healing, and may be important for cancer metastasis. I'll present recent data on disorganizing mammary epithelial structures. We have used CRISPR to insert fluorescent tags directly into eight EMT-related genes (such as E-cadherin and Vimentin), which allows us to monitor the dynamics of the transition in real time, subject only to delays imposed by fluorophore folding/maturation times. With this information, we can begin to order events in time (temporal resolution 30 minutes), starting with external signal inputs and proceeding through a secession of intracellular changes of gene expression on the path to the mesenchymal state.

  18. Mechanical properties of 4d transition metals in molten state

    NASA Astrophysics Data System (ADS)

    Singh, Deobrat; Sonvane, Yogesh; Thakor, P. B.

    2016-05-01

    Mechanical properties of 4d transition metals in molten state have been studied in the present study. We have calculated mechanical properties such as isothermal bulk modulus (B), modulus of rigidity (G), Young's modulus (Y) and Hardness have also been calculated from the elastic part of the Phonon dispersion curve (PDC). To describe the structural information, we have used different structure factor S(q) using Percus-Yevick hard sphere (PYHS) reference systems along with our newly constructed parameter free model potential.To see the influence of exchange and correlation effect on the above said properties of 3d liquid transition metals, we have used Sarkar et al (S)local field correction functions. Present results have been found good in agreement with available experimental data.

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

    PubMed Central

    2015-01-01

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

  20. Variational transition state theory: theoretical framework and recent developments.

    PubMed

    Bao, Junwei Lucas; Truhlar, Donald G

    2017-12-11

    This article reviews the fundamentals of variational transition state theory (VTST), its recent theoretical development, and some modern applications. The theoretical methods reviewed here include multidimensional quantum mechanical tunneling, multistructural VTST (MS-VTST), multi-path VTST (MP-VTST), both reaction-path VTST (RP-VTST) and variable reaction coordinate VTST (VRC-VTST), system-specific quantum Rice-Ramsperger-Kassel theory (SS-QRRK) for predicting pressure-dependent rate constants, and VTST in the solid phase, liquid phase, and enzymes. We also provide some perspectives regarding the general applicability of VTST.

  1. 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.

  2. Transition-State Ensembles Navigate the Pathways of Enzyme Catalysis.

    PubMed

    Mickert, Matthias J; Gorris, Hans H

    2018-06-07

    Transition-state theory (TST) provides an important framework for analyzing and explaining the reaction rates of enzymes. TST, however, needs to account for protein dynamic effects and heterogeneities in enzyme catalysis. We have analyzed the reaction rates of β-galactosidase and β-glucuronidase at the single molecule level by using large arrays of femtoliter-sized chambers. Heterogeneities in individual reaction rates yield information on the intrinsic distribution of the free energy of activation (Δ G ‡ ) in an enzyme ensemble. The broader distribution of Δ G ‡ in β-galactosidase compared to β-glucuronidase is attributed to β-galactosidase's multiple catalytic functions as a hydrolase and a transglycosylase. Based on the catalytic mechanism of β-galactosidase, we show that transition-state ensembles do not only contribute to enzyme catalysis but can also channel the catalytic pathway to the formation of different products. We conclude that β-galactosidase is an example of natural evolution, where a new catalytic pathway branches off from an established enzyme function. The functional division of work between enzymatic substates explains why the conformational space represented by the enzyme ensemble is larger than the conformational space that can be sampled by any given enzyme molecule during catalysis.

  3. Physiologic Measures of Animal Stress during Transitional States of Consciousness

    PubMed Central

    Meyer, Robert E.

    2015-01-01

    Simple Summary The humaneness, and therefore suitability, of any particular agent or method used to produce unconsciousness in animals, whether for anesthesia, euthanasia, humane slaughter, or depopulation, depends on the experience of pain or distress prior to loss of consciousness. Commonly reported physiologic measures of animal stress, including physical movement and vocalization, heart rate and ECG, electroencephalographic activity, and plasma and neuronal stress markers are discussed within this context. Abstract Determination of the humaneness of methods used to produce unconsciousness in animals, whether for anesthesia, euthanasia, humane slaughter, or depopulation, relies on our ability to assess stress, pain, and consciousness within the contexts of method and application. Determining the subjective experience of animals during transitional states of consciousness, however, can be quite difficult; further, loss of consciousness with different agents or methods may occur at substantially different rates. Stress and distress may manifest behaviorally (e.g., overt escape behaviors, approach-avoidance preferences [aversion]) or physiologically (e.g., movement, vocalization, changes in electroencephalographic activity, heart rate, sympathetic nervous system [SNS] activity, hypothalamic-pituitary axis [HPA] activity), such that a one-size-fits-all approach cannot be easily applied to evaluate methods or determine specific species applications. The purpose of this review is to discuss methods of evaluating stress in animals using physiologic methods, with emphasis on the transition between the conscious and unconscious states. PMID:26479382

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

    NASA Astrophysics Data System (ADS)

    Lim, Hunhwa

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

  5. Transition of multidiffusive states in a biased periodic potential

    NASA Astrophysics Data System (ADS)

    Zhang, Jia-Ming; Bao, Jing-Dong

    2017-03-01

    We study a frequency-dependent damping model of hyperdiffusion within the generalized Langevin equation. The model allows for the colored noise defined by its spectral density, assumed to be proportional to ωδ -1 at low frequencies with 0 <δ <1 (sub-Ohmic damping) or 1 <δ <2 (super-Ohmic damping), where the frequency-dependent damping is deduced from the noise by means of the fluctuation-dissipation theorem. It is shown that for super-Ohmic damping and certain parameters, the diffusive process of the particle in a titled periodic potential undergos sequentially four time regimes: thermalization, hyperdiffusion, collapse, and asymptotical restoration. For analyzing transition phenomenon of multidiffusive states, we demonstrate that the first exist time of the particle escaping from the locked state into the running state abides by an exponential distribution. The concept of an equivalent velocity trap is introduced in the present model; moreover, reformation of ballistic diffusive system is also considered as a marginal situation but does not exhibit the collapsed state of diffusion.

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

    PubMed

    Nguyen; Mayer; Morton

    2000-11-17

    Gaseous CF(3)(+) interchanges F(+) for O with simple carbonyl compounds. CF(3)(+) reacts with propionaldehyde in the gas phase to produce (CH(3))(2)CF(+) via two competing pathways. Starting with 1-(13)C-propionaldehyde, the major pathway (80%) produces (CH(3))(2)CF(+) with the carbon label in one of the methyl groups. The minor pathway (20%) produces (CH(3))(2)CF(+) with the carbon label in the central position. The relative proportions of these two pathways are measured by (19)F NMR analysis of the neutral CH(3)CF=CH(2) produced by deprotonation of (CH(3))(2)CF(+) at <10(-)(3) Torr in an electron bombardment flow (EBFlow) reactor. Formation of alkene in which carbon is directly bonded to fluorine means that (in the minor product, at least) an F(+) for O transposition occurs via adduct formation followed by 1,3-atom transfer and then isomerization of CH(3)CH(2)CHF(+) to the more stable (CH(3))(2)CF(+). Use of CF(4) as a chemical ionization (CI) reagent gas leads to CF(3)(+) adduct ions for a variety of ketones, in addition to isoelectronic transposition of F(+) for O. Metastable ion decompositions of the adduct ions yield the metathesis products. Decompositions of fluorocycloalkyl cations formed in this manner give evidence for the same kinds of rearrangements as take place in CH(3)CH(2)CHF(+). Density functional calculations confirm that F(+) for O metathesis takes place via addition of CF(3)(+) to the carbonyl oxygen followed by transposition via a four-member cyclic transition state. A computational survey of the effects of different substituents in a series of aldehydes and acyclic ketones reveals no systematic variation of the energy of the transition state as a function of thermochemistry, but the Hammond postulate does appear to be obeyed in terms of progress along the reaction coordinate. Bond lengths corresponding to the central barrier correlate with overall thermochemistry of the F(+) for O interchange, but in a sense opposite to what might have been

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

    DOT National Transportation Integrated Search

    1978-02-01

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

  8. Vibrational states and optical transitions in hydrogen bonds

    NASA Astrophysics Data System (ADS)

    Johannsen, P. G.

    1998-03-01

    Proton energies in hydrogen bonds are mostly calculated using a double Morse potential (the DMP model). This form, however, does not reproduce the experimentally observed correlation between the proton stretching frequency and the bond length in an extended bond-length region sufficiently well. An alternative potential is proposed in the present paper. The quantum states of this non-symmetric double-well potential are calculated numerically using the Numerov (Fox-Goodwin) algorithm. It is shown that the optical spectra of hydrogen bonds in various substances can be well approximated on the basis of the transition frequencies and intensities predicted by the present model. For weakly interacting OH impurities in 0953-8984/10/10/008/img1, the overtone spectrum and line intensities are well reproduced, whereas the line broadenings and the decrease of the fundamental stretching frequencies in intermediate and strong hydrogen bonds are traced back to the influence of the reduced height of the central barrier. The model is also extrapolated to the range of symmetric hydrogen bonds, and the calculated transition frequencies are discussed with respect to most recent infra-red experiments on ice under strong compression. A possible artificial infra-red signal from strained diamond anvils is thereby noted.

  9. 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.

  10. Automated Transition State Theory Calculations for High-Throughput Kinetics.

    PubMed

    Bhoorasingh, Pierre L; Slakman, Belinda L; Seyedzadeh Khanshan, Fariba; Cain, Jason Y; West, Richard H

    2017-09-21

    A scarcity of known chemical kinetic parameters leads to the use of many reaction rate estimates, which are not always sufficiently accurate, in the construction of detailed kinetic models. To reduce the reliance on these estimates and improve the accuracy of predictive kinetic models, we have developed a high-throughput, fully automated, reaction rate calculation method, AutoTST. The algorithm integrates automated saddle-point geometry search methods and a canonical transition state theory kinetics calculator. The automatically calculated reaction rates compare favorably to existing estimated rates. Comparison against high level theoretical calculations show the new automated method performs better than rate estimates when the estimate is made by a poor analogy. The method will improve by accounting for internal rotor contributions and by improving methods to determine molecular symmetry.

  11. Equation of state and QCD transition at finite temperature

    NASA Astrophysics Data System (ADS)

    Bazavov, A.; Bhattacharya, T.; Cheng, M.; Christ, N. H.; Detar, C.; Ejiri, S.; Gottlieb, Steven; Gupta, R.; Heller, U. M.; Huebner, K.; Jung, C.; Karsch, F.; Laermann, E.; Levkova, L.; Miao, C.; Mawhinney, R. D.; Petreczky, P.; Schmidt, C.; Soltz, R. A.; Soeldner, W.; Sugar, R.; Toussaint, D.; Vranas, P.

    2009-07-01

    We calculate the equation of state in 2+1 flavor QCD at finite temperature with physical strange quark mass and almost physical light quark masses using lattices with temporal extent Nτ=8. Calculations have been performed with two different improved staggered fermion actions, the asqtad and p4 actions. Overall, we find good agreement between results obtained with these two O(a2) improved staggered fermion discretization schemes. A comparison with earlier calculations on coarser lattices is performed to quantify systematic errors in current studies of the equation of state. We also present results for observables that are sensitive to deconfining and chiral aspects of the QCD transition on Nτ=6 and 8 lattices. We find that deconfinement and chiral symmetry restoration happen in the same narrow temperature interval. In an appendix we present a simple parametrization of the equation of state that can easily be used in hydrodynamic model calculations. In this parametrization we include an estimate of current uncertainties in the lattice calculations which arise from cutoff and quark mass effects.

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

    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.

  13. 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.

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

    Zweig, Christa L.; Kitchens, Wiley M.

    2009-01-01

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

  15. Light rail transit : state-of-the-art overview

    DOT National Transportation Integrated Search

    1977-05-01

    This document presents an overview of light rail transit, an urban transit alternative which has the potential to help fill the need for flexibility in public transportation. Existing and proposed U.S. and Canadian light rail transit systems are desc...

  16. The Astrophysical Weeds: Rotational Transitions in Excited Vibrational States

    NASA Astrophysics Data System (ADS)

    Alonso, José L.; Kolesniková, Lucie; Alonso, Elena R.; Mata, Santiago

    2017-06-01

    The number of unidentified lines in the millimeter and submillimeter wave surveys of the interstellar medium has grown rapidly. The major contributions are due to rotational transitions in excited vibrational states of a relatively few molecules that are called the astrophysical weeds. necessary data to deal with spectral lines from astrophysical weeds species can be obtained from detailed laboratory rotational measurements in the microwave and millimeter wave region. A general procedure is being used at Valladolid combining different time and/or frequency domain spectroscopic tools of varying importance for providing the precise set of spectroscopic constants that could be used to search for this species in the ISM. This is illustrated in the present contribution through its application to several significant examples. Fortman, S. M., Medvedev, I. R., Neese, C.F., & De Lucia, F.C. 2010, ApJ,725, 1682 Rotational Spectra in 29 Vibrationally Excited States of Interstellar Aminoacetonitrile, L. Kolesniková, E. R. Alonso, S. Mata, and J. L. Alonso, The Astrophysical Journal Supplement Series 2017, (in press).

  17. 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).

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

    NASA Astrophysics Data System (ADS)

    Ramesh, N.; Cane, M. A.

    2017-12-01

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

  19. Methods for finding transition states on reduced potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Burger, Steven K.; Ayers, Paul W.

    2010-06-01

    Three new algorithms are presented for determining transition state (TS) structures on the reduced potential energy surface, that is, for problems in which a few important degrees of freedom can be isolated. All three methods use constrained optimization to rapidly find the TS without an initial Hessian evaluation. The algorithms highlight how efficiently the TS can be located on a reduced surface, where the rest of the degrees of freedom are minimized. The first method uses a nonpositive definite quasi-Newton update for the reduced degrees of freedom. The second uses Shepard interpolation to fit the Hessian and starts from a set of points that bound the TS. The third directly uses a finite difference scheme to calculate the reduced degrees of freedom of the Hessian of the entire system, and searches for the TS on the full potential energy surface. All three methods are tested on an epoxide hydrolase cluster, and the ring formations of cyclohexane and cyclobutenone. The results indicate that all the methods are able to converge quite rapidly to the correct TS, but that the finite difference approach is the most efficient.

  20. Methods for finding transition states on reduced potential energy surfaces.

    PubMed

    Burger, Steven K; Ayers, Paul W

    2010-06-21

    Three new algorithms are presented for determining transition state (TS) structures on the reduced potential energy surface, that is, for problems in which a few important degrees of freedom can be isolated. All three methods use constrained optimization to rapidly find the TS without an initial Hessian evaluation. The algorithms highlight how efficiently the TS can be located on a reduced surface, where the rest of the degrees of freedom are minimized. The first method uses a nonpositive definite quasi-Newton update for the reduced degrees of freedom. The second uses Shepard interpolation to fit the Hessian and starts from a set of points that bound the TS. The third directly uses a finite difference scheme to calculate the reduced degrees of freedom of the Hessian of the entire system, and searches for the TS on the full potential energy surface. All three methods are tested on an epoxide hydrolase cluster, and the ring formations of cyclohexane and cyclobutenone. The results indicate that all the methods are able to converge quite rapidly to the correct TS, but that the finite difference approach is the most efficient.

  1. Transition state theory for activated systems with driven anharmonic barriers.

    PubMed

    Revuelta, F; Craven, Galen T; Bartsch, Thomas; Borondo, F; Benito, R M; Hernandez, Rigoberto

    2017-08-21

    Classical transition state theory has been extended to address chemical reactions across barriers that are driven and anharmonic. This resolves a challenge to the naive theory that necessarily leads to recrossings and approximate rates because it relies on a fixed dividing surface. We develop both perturbative and numerical methods for the computation of a time-dependent recrossing-free dividing surface for a model anharmonic system in a solvated environment that interacts strongly with an oscillatory external field. We extend our previous work, which relied either on a harmonic approximation or on periodic force driving. We demonstrate that the reaction rate, expressed as the long-time flux of reactive trajectories, can be extracted directly from the stability exponents, namely, Lyapunov exponents, of the moving dividing surface. Comparison to numerical results demonstrates the accuracy and robustness of this approach for the computation of optimal (recrossing-free) dividing surfaces and reaction rates in systems with Markovian solvation forces. The resulting reaction rates are in strong agreement with those determined from the long-time flux of reactive trajectories.

  2. Transition-state theory predicts clogging at the microscale

    NASA Astrophysics Data System (ADS)

    Laar, T. Van De; Klooster, S. Ten; Schroën, K.; Sprakel, J.

    2016-06-01

    Clogging is one of the main failure mechanisms encountered in industrial processes such as membrane filtration. Our understanding of the factors that govern the build-up of fouling layers and the emergence of clogs is largely incomplete, so that prevention of clogging remains an immense and costly challenge. In this paper we use a microfluidic model combined with quantitative real-time imaging to explore the influence of pore geometry and particle interactions on suspension clogging in constrictions, two crucial factors which remain relatively unexplored. We find a distinct dependence of the clogging rate on the entrance angle to a membrane pore which we explain quantitatively by deriving a model, based on transition-state theory, which describes the effect of viscous forces on the rate with which particles accumulate at the channel walls. With the same model we can also predict the effect of the particle interaction potential on the clogging rate. In both cases we find excellent agreement between our experimental data and theory. A better understanding of these clogging mechanisms and the influence of design parameters could form a stepping stone to delay or prevent clogging by rational membrane design.

  3. Three equations of state and their application to transition metals

    NASA Astrophysics Data System (ADS)

    Ronggang, Tian; Jiuxun, Sun; Wei, Yang; Fei, Yu

    2010-10-01

    A modified generalized Morse (mGMSE) equation of state (EOS) is proposed that can incorporate the cohesive energy data correctly. It is compared with a four-parameter modified Rose (MR) EOS, which is proposed by following Rose's approach, and the Murnaghan (MNH) EOS. The MR, mGMSE and MNH EOSs are applied to five transition metals and then compared to the available experimental compression data. The results obtained show that for all pressure ranges, the mGMSE EOS fits experimental data most accurately. From a comparison of the variation in pressure and energy versus the compression ratio between MR and mGMSE EOSs, it is clear that the pressure and energy of the MR EOS oscillate both in the neighborhood of (V/V0 ) ≈ 0.005 and in the range (V/V0 )> 1. Generally speaking, the mGMSE EOS has many evident advantages over the other two EOSs, while the practical applications of the MR EOS are seriously limited because of physically incorrect oscillations.

  4. State-Transition Structures in Physics and in Computation

    NASA Astrophysics Data System (ADS)

    Petri, C. A.

    1982-12-01

    In order to establish close connections between physical and computational processes, it is assumed that the concepts of “state” and of “transition” are acceptable both to physicists and to computer scientists, at least in an informal way. The aim of this paper is to propose formal definitions of state and transition elements on the basis of very low level physical concepts in such a way that (1) all physically possible computations can be described as embedded in physical processes; (2) the computational aspects of physical processes can be described on a well-defined level of abstraction; (3) the gulf between the continuous models of physics and the discrete models of computer science can be bridged by simple mathematical constructs which may be given a physical interpretation; (4) a combinatorial, nonstatistical definition of “information” can be given on low levels of abstraction which may serve as a basis to derive higher-level concepts of information, e.g., by a statistical or probabilistic approach. Conceivable practical consequences are discussed.

  5. Fourth-Order Vibrational Transition State Theory and Chemical Kinetics

    NASA Astrophysics Data System (ADS)

    Stanton, John F.; Matthews, Devin A.; Gong, Justin Z.

    2015-06-01

    Second-order vibrational perturbation theory (VPT2) is an enormously successful and well-established theory for treating anharmonic effects on the vibrational levels of semi-rigid molecules. Partially as a consequence of the fact that the theory is exact for the Morse potential (which provides an appropriate qualitative model for stretching anharmonicity), VPT2 calculations for such systems with appropriate ab initio potential functions tend to give fundamental and overtone levels that fall within a handful of wavenumbers of experimentally measured positions. As a consequence, the next non-vanishing level of perturbation theory -- VPT4 -- offers only slight improvements over VPT2 and is not practical for most calculations since it requires information about force constants up through sextic. However, VPT4 (as well as VPT2) can be used for other applications such as the next vibrational correction to rotational constants (the ``gammas'') and other spectroscopic parameters. In addition, the marriage of VPT with the semi-classical transition state theory of Miller (SCTST) has recently proven to be a powerful and accurate treatment for chemical kinetics. In this talk, VPT4-based SCTST tunneling probabilities and cumulative reaction probabilities are give for the first time for selected low-dimensional model systems. The prospects for VPT4, both practical and intrinsic, will also be discussed.

  6. Transition state analogs of 5'-methylthioadenosine nucleosidase disrupt quorum sensing.

    SciT

    Gutierrez, J.; Crowder, T; Rinaldo-Matthis, A

    2009-01-01

    5'-Methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) is a bacterial enzyme involved in S-adenosylmethionine-related quorum sensing pathways that induce bacterial pathogenesis factors. Transition state analogs MT-DADMe-Immucillin-A, EtT-DADMe-Immucillin-A and BuT-DADMe-Immucillin-A are slow-onset, tight-binding inhibitors of Vibrio cholerae MTAN (VcMTAN), with equilibrium dissociation constants of 73, 70 and 208 pM, respectively. Structural analysis of VcMTAN with BuT-DADMe-Immucillin-A revealed interactions contributing to the high affinity. We found that in V. cholerae cells, these compounds are potent MTAN inhibitors with IC50 values of 27, 31 and 6 nM for MT-, EtT- and BuT-DADMe-Immucillin-A, respectively; the compounds disrupt autoinducer production in a dose-dependent manner without affecting growth. MT- andmore » BuT-DADMe-Immucillin-A also inhibited autoinducer-2 production in enterohemorrhagic Escherichia coli O157:H7 with IC{sub 50} values of 600 and 125 nM, respectively. BuT-DADMe-Immucillin-A inhibition of autoinducer-2 production in both strains persisted for several generations and caused reduction in biofilm formation. These results support MTAN's role in quorum sensing and its potential as a target for bacterial anti-infective drug design.« less

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

    ERIC Educational Resources Information Center

    Reid, Carrie

    2007-01-01

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

  8. 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.

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

    NASA Astrophysics Data System (ADS)

    Ma, Suqi; Zhu, Kaiyi; Lei, Jinzhi

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

  10. Streets for Pedestrians and Transit : An Evaluation of Three Transit Malls in the United States

    DOT National Transportation Integrated Search

    1979-02-01

    The report represents the second phase of a two-phase project designed to acquaint the planning community with the concept of transit malls and to provide information about three of the most important and interesting transit mall projects to a wider ...

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

    NASA Astrophysics Data System (ADS)

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

    2017-10-01

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

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

    DOT National Transportation Integrated Search

    1987-11-01

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

  13. Transitions.

    ERIC Educational Resources Information Center

    Nathanson, Jeanne H., Ed.

    1993-01-01

    This theme issue on transitions for individuals with disabilities contains nine papers discussing transition programs and issues. "Transition Issues for the 1990s," by Michael J. Ward and William D. Halloran, discusses self-determination, school responsibility for transition, continued educational engagement of at-risk students, and service…

  14. Migration transition in small Northern and Eastern Caribbean states.

    PubMed

    Mcelroy, J L; De Albuquerque, K

    1988-01-01

    1 area of intra-Caribbean migration that has been overlooked is the "migration transition"--the transformation of rapidly modernizing societies from net labor exporters to net labor importers. This article assembles 8 case studies to 1) briefly present a spectrum of migration experiences in the Caribbean, 2) uncover some transitions under way, 3) pinpoint the forces that underlie the migration transition, and 4) point out some of the more important policy implications of labor migration reversals. The 8 island societies sampled for illustration purposes include 1) the Bahamas and the US Virgin Islands as post-migration transition societies (Zelinsky's advanced society), 2) the British Virgin Islands and the Cayman Islands as undergoing transition (Zelinsky's late transitional society), and 3) Anguilla, St. Kitts-Nevis, Turks and Caicos, and Montserrat as premigration transition societies (Zelinsky's early transitional society). Population data for the islands were derived primarily from the West Indian censuses and government statistics. These 8 historical sketches reveal certain commonalities. All are at various stages in a long-term economic restructuring to displace traditional staple crops with more income elastic, high value export services. In such societies, population growth and progress along the migration transition is an increasing function of this kind of successful export substitution. In addition, along the migration and economic transitions, such insular economies exhibit a relatively large public sector (20-30% of all activity), declining unemployment, increasing fiscal autonomy, and are committed to a development strategy remarkably similar to the "successful" model of the Bahamas and the US Virgin Islands. Cursory evidence suggests that, because of intersectoral competition for land and labor, there is an inverse relationship between farm effort/manufacturing employment and tourism intensity. This review suggests that small islands undergoing

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

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

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

    ERIC Educational Resources Information Center

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

    2018-01-01

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

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

    Colin J. Daniel; Leonardo Frid

    2012-01-01

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

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

    Reuben Weisz; Don Vandendriesche

    2012-01-01

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

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

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

    2015-01-01

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

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

    PubMed Central

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

    2004-01-01

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

  1. 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).

  2. Small Transit Vehicles : State-of-the-Art Overview

    DOT National Transportation Integrated Search

    1981-08-01

    This document presents both an update and expansion of a 1975 Technology Sharing document which profiled small transit vehicles. This document presents information on the vehicles available and on the selection, procurement, and operational considera...

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

    NASA Astrophysics Data System (ADS)

    Zhou, Dan; Wang, Kedong; Li, Xue

    2018-07-01

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

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

    PubMed

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

    2015-10-01

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

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

    DOE PAGES

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

    2014-11-05

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

  6. Lithuanian health care in transitional state: ethical problems.

    PubMed

    Jakusovaite, Irayda; Darulis, Zilvinas; Zekas, Romualdas

    2005-11-09

    Throughout the economic and political reforms in post-communist countries, significant changes have also occurred in public morality. One of the tasks of the Lithuanian health policy is to create mechanisms for strengthening the significance of ethical considerations in the decision-making processes concerning health care of individuals and groups of individuals, as well as considering the positions of physicians and the health care system itself in a general way. Thus, health care ethics could be analyzed at two levels: the micro level (the ethics of doctor-patient relationships) and the macro level (the ethics of health policy-making, which can be realized by applying the principles of equal access, reasonable quality, affordable care and shared responsibilities). To date, the first level remains dominant, but the need arises for our attention to refocus now from the micro level to the patterns of managing and delivering care, managing the health care resources, and conducting business practices. In attempting to increase the efficiency of health services in Lithuania, a common strategy has been in place for the last fifteen years. Decentralization and privatization have been implemented as part of its policy to achieve greater efficiency. Although decentralization in theory is supposed to improve efficiency, in practice the reform of decentralization has still to be completely implemented in Lithuania. Debates on health policy in Lithuania also include the issue of private versus public health care. Although the approach of private health care is changing in a positive way, it is obvious that reduced access to health services is the most vulnerable aspect. In the Lithuanian Health Program adopted in July 1998, the target of equity was stressed, stating that by 2010, differences in health and health care between various socio-economic groups should be reduced by 25%. The restructuring of health care system in Lithuania should be based on a balance between

  7. Lithuanian health care in transitional state: ethical problems

    PubMed Central

    Jakušovaitė, Irayda; Darulis, Žilvinas; Žekas, Romualdas

    2005-01-01

    Background Throughout the economic and political reforms in post-communist countries, significant changes have also occurred in public morality. One of the tasks of the Lithuanian health policy is to create mechanisms for strengthening the significance of ethical considerations in the decision-making processes concerning health care of individuals and groups of individuals, as well as considering the positions of physicians and the health care system itself in a general way. Thus, health care ethics could be analyzed at two levels: the micro level (the ethics of doctor-patient relationships) and the macro level (the ethics of health policy-making, which can be realized by applying the principles of equal access, reasonable quality, affordable care and shared responsibilities). To date, the first level remains dominant, but the need arises for our attention to refocus now from the micro level to the patterns of managing and delivering care, managing the health care resources, and conducting business practices. Discussion In attempting to increase the efficiency of health services in Lithuania, a common strategy has been in place for the last fifteen years. Decentralization and privatization have been implemented as part of its policy to achieve greater efficiency. Although decentralization in theory is supposed to improve efficiency, in practice the reform of decentralization has still to be completely implemented in Lithuania. Debates on health policy in Lithuania also include the issue of private versus public health care. Although the approach of private health care is changing in a positive way, it is obvious that reduced access to health services is the most vulnerable aspect. In the Lithuanian Health Program adopted in July 1998, the target of equity was stressed, stating that by 2010, differences in health and health care between various socio-economic groups should be reduced by 25%. Summary The restructuring of health care system in Lithuania should be

  8. Hybrid phase transition into an absorbing state: Percolation and avalanches

    NASA Astrophysics Data System (ADS)

    Lee, Deokjae; Choi, S.; Stippinger, M.; Kertész, J.; Kahng, B.

    2016-04-01

    Interdependent networks are more fragile under random attacks than simplex networks, because interlayer dependencies lead to cascading failures and finally to a sudden collapse. This is a hybrid phase transition (HPT), meaning that at the transition point the order parameter has a jump but there are also critical phenomena related to it. Here we study these phenomena on the Erdős-Rényi and the two-dimensional interdependent networks and show that the hybrid percolation transition exhibits two kinds of critical behaviors: divergence of the fluctuations of the order parameter and power-law size distribution of finite avalanches at a transition point. At the transition point global or "infinite" avalanches occur, while the finite ones have a power law size distribution; thus the avalanche statistics also has the nature of a HPT. The exponent βm of the order parameter is 1 /2 under general conditions, while the value of the exponent γm characterizing the fluctuations of the order parameter depends on the system. The critical behavior of the finite avalanches can be described by another set of exponents, βa and γa. These two critical behaviors are coupled by a scaling law: 1 -βm=γa .

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

    PubMed

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

    2017-11-14

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

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

    ERIC Educational Resources Information Center

    Burgess, Sloane; Cimera, Robert E.

    2014-01-01

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

  11. 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).

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

    PubMed

    Plessow, Philipp N

    2018-02-13

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

  13. Transitions.

    ERIC Educational Resources Information Center

    Field, David; And Others

    1992-01-01

    Includes four articles: "Career Aspirations" (Field); "Making the Transition to a New Curriculum" (Baker, Householder); "How about a 'Work to School' Transition?" (Glasberg); and "Technological Improvisation: Bringing CNC to Woodworking" (Charles, McDuffie). (SK)

  14. 45 CFR 150.221 - Transition to State enforcement.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... ACCESS CMS ENFORCEMENT IN GROUP AND INDIVIDUAL INSURANCE MARKETS CMS Enforcement Processes for... State enforcement. (a) If CMS determines that a State for which it has assumed enforcement authority has... appropriate to return enforcement authority to the State, CMS will enter into discussions with State officials...

  15. State of the Art of Current Practices for Transit Transfers.

    DOT National Transportation Integrated Search

    1981-07-01

    The major objectives of the study are to: (1) describe and summarize the transfer policies currently in use on U.S. transit properties; (2) identify reasons why properties use or do not use particular transfer policies; (3) determine the consequences...

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

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

    2016-01-01

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

  17. 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.

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

    SciT

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

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

  19. Small City Transit : Summary of State Aid Programs

    DOT National Transportation Integrated Search

    1976-03-01

    The document presents a review of the financial and technical assistance that each state provides to communities of less than 200,000 population. In one section, state capital and operating assistance is examined. A separate section discusses the ava...

  20. Vibrational energy transfer near a dissociative adsorption transition state: State-to-state study of HCl collisions at Au(111).

    PubMed

    Geweke, Jan; Shirhatti, Pranav R; Rahinov, Igor; Bartels, Christof; Wodtke, Alec M

    2016-08-07

    In this work we seek to examine the nature of collisional energy transfer between HCl and Au(111) for nonreactive scattering events that sample geometries near the transition state for dissociative adsorption by varying both the vibrational and translational energy of the incident HCl molecules in the range near the dissociation barrier. Specifically, we report absolute vibrational excitation probabilities for HCl(v = 0 → 1) and HCl(v = 1 → 2) scattering from clean Au(111) as a function of surface temperature and incidence translational energy. The HCl(v = 2 → 3) channel could not be observed-presumably due to the onset of dissociation. The excitation probabilities can be decomposed into adiabatic and nonadiabatic contributions. We find that both contributions strongly increase with incidence vibrational state by a factor of 24 and 9, respectively. This suggests that V-T as well as V-EHP coupling can be enhanced near the transition state for dissociative adsorption at a metal surface. We also show that previously reported HCl(v = 0 → 1) excitation probabilities [Q. Ran et al., Phys. Rev. Lett. 98, 237601 (2007)]-50 times smaller than those reported here-were influenced by erroneous assignment of spectroscopic lines used in the data analysis.

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

    ERIC Educational Resources Information Center

    Ebb, Nancy; And Others

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

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

    ERIC Educational Resources Information Center

    Shimmi, Yukiko

    2014-01-01

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

  3. 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.

  4. 31 CFR 560.406 - Transshipment or transit through United States prohibited.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

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

  5. 31 CFR 560.406 - Transshipment or transit through United States prohibited.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

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

  6. 31 CFR 560.406 - Transshipment or transit through United States prohibited.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

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

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

    ERIC Educational Resources Information Center

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

    2016-01-01

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

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

    ERIC Educational Resources Information Center

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

    2018-01-01

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

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

    PubMed

    Kim, Jandi; Shin, Jong-Shik

    2010-04-27

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

  10. 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.

  11. State and Federal project development procedures for bus rapid transit : managing differences and reducing implementation delays

    DOT National Transportation Integrated Search

    2011-08-01

    This report documents an investigation into the transportation project development process in the : context of the implementation of bus rapid transit systems on the State Highway System as well as such : systems being part of the Federal New Starts ...

  12. 19 CFR 123.42 - Truck shipments transiting the United States.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

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

  13. Review of State Policies and Programs to Support Young People Transitioning Out of Foster Care

    ERIC Educational Resources Information Center

    Dworsky, Amy; Havlicek, Judy

    2009-01-01

    This comprehensive review of policies and programs designed to support youth transitioning out of foster care spans all 50 states and the District of Columbia. As part of the review, Chapin Hall administered a web-based survey of state independent living services coordinators to collect up-to-date information about their state's policies and…

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    SciT

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

    2016-04-21

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

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

    PubMed

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

    2013-03-01

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

  17. Glass Transitions in a Monatomic Liquid with Two Glassy States

    NASA Astrophysics Data System (ADS)

    Gordon, Andrew; Giovambattista, Nicolas

    2014-04-01

    We perform out-of-equilibrium molecular dynamics simulations of a monatomic liquid that exhibits liquid and glass polymorphism, with two distinct glasses, low- (LDA) and high-density (HDA) amorphous solids. By performing isobaric heating simulations of LDA and HDA at different pressures, we determine (a) the glass transition temperature of LDA and HDA, TgLDA(P) and TgHDA(P), as well as (b) the corresponding glass-glass transformation temperatures, TLDA-HDA(P) and THDA-LDA(P). It is found that TgLDA(P) is anomalous; i.e., it decreases with increasing pressure, while TgHDA(P) increases with increasing pressure. Interestingly, the TgLDA(P) and TLDA-HDA(P) loci, as well as the TgHDA(P) and THDA-LDA(P) loci, constitute smooth single lines in the P -T plane, suggesting that heating-induced glass-glass and glass transitions are related. We discuss the present results in the context of water experiments and simulations.

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

    NASA Astrophysics Data System (ADS)

    Iguchi, Kazumoto

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

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

    NASA Astrophysics Data System (ADS)

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

    2005-03-01

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

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

    SciT

    Sinitsyn, Nikolai A.

    2015-04-23

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

  1. 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.

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

    PubMed

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

    2014-06-11

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

  3. 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

  4. Laser-induced transitions between triply excited hollow states

    NASA Astrophysics Data System (ADS)

    Madsen, L. B.; Schlagheck, P.; Lambropoulos, P.

    2000-12-01

    Using complex scaling and a correlated basis constructed in terms of B splines, we calculate the Li+ photoion yield in the presence of a laser-induced coupling between the triply excited 2s22p(2Po) and 2s2p2(2De) resonances in lithium, the first of which is assumed to be excited by synchrotron radiation from the ground state. The laser coupling between the triply excited states is shown to lead to a significant and readily measurable modification of the line profile which provides a unique probe of the dipole strength between highly correlated triply excited states. We also present results for some higher-lying triply excited states of 2Po symmetry.

  5. Limiting Forces on Transit Trucks in Steady-State Curving

    DOT National Transportation Integrated Search

    1981-05-01

    This study develops conservative bounds on wheel/rail forces and flange forces for several types of rigid and flexible trucks in steady-state curving conditions. The approximate analysis presented provides closed-form relations for estimating forces,...

  6. Analyzing Tabular and State-Transition Requirements Specifications in PVS

    NASA Technical Reports Server (NTRS)

    Owre, Sam; Rushby, John; Shankar, Natarajan

    1997-01-01

    We describe PVS's capabilities for representing tabular specifications of the kind advocated by Parnas and others, and show how PVS's Type Correctness Conditions (TCCs) are used to ensure certain well-formedness properties. We then show how these and other capabilities of PVS can be used to represent the AND/OR tables of Leveson and the Decision Tables of Sherry, and we demonstrate how PVS's TCCs can expose and help isolate errors in the latter. We extend this approach to represent the mode transition tables of the Software Cost Reduction (SCR) method in an attractive manner. We show how PVS can check these tables for well-formedness, and how PVS's model checking capabilities can be used to verify invariants and reachability properties of SCR requirements specifications, and inclusion relations between the behaviors of different specifications. These examples demonstrate how several capabilities of the PVS language and verification system can be used in combination to provide customized support for specific methodologies for documenting and analyzing requirements. Because they use only the standard capabilities of PVS, users can adapt and extend these customizations to suit their own needs. Those developing dedicated tools for individual methodologies may find these constructions in PVS helpful for prototyping purposes, or as a useful adjunct to a dedicated tool when the capabilities of a full theorem prover are required. The examples also illustrate the power and utility of an integrated general-purpose system such as PVS. For example, there was no need to adapt or extend the PVS model checker to make it work with SCR specifications described using the PVS TABLE construct: the model checker is applicable to any transition relation, independently of the PVS language constructs used in its definition.

  7. 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.

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

    PubMed

    Burgess, Sloane; Cimera, Robert E

    2014-01-01

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

  9. 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

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

    SciT

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

    2015-07-01

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

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

    SciT

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

    2015-04-30

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

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

    SciT

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

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

  13. State High School Exit Exams: A Policy in Transition

    ERIC Educational Resources Information Center

    McIntosh, Shelby

    2012-01-01

    Since 2002, the Center on Education Policy (CEP) at The George Washington University, a national advocate for public education and improving public schools, has been studying state high school exit examinations--tests students must pass to receive a high school diploma. This year marks the 11th year CEP has reported on exit exams in order to help…

  14. 40 CFR 70.4 - State program submittals and transition.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., administrative regulations, and, where appropriate, judicial decisions that demonstrate adequate authority. State... shield that may be granted pursuant to § 70.6(f) shall remain in effect until the renewal permit has been... regulations a different time frame for emergencies. The source, permitting authority, and EPA shall attach...

  15. 40 CFR 70.4 - State program submittals and transition.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... strategies). (5) A complete description of the State's compliance tracking and enforcement program or... facilitate communications between EPA and the other agencies having program responsibility. (iii) A... Administrator and the permitting authority with written notification as required below in advance of the...

  16. Building and Maintaining Connection: Supporting Transition in a Rural State

    ERIC Educational Resources Information Center

    Flannery, Ann; Mason, Paula; Dunagan, Janna

    2016-01-01

    Deaf and hard of hearing students at Rocky Mountain High School (RMHS), a public school in Meridian, Idaho--and other deaf and hard of hearing students throughout the state, needed skills for the workplace. The demand was critical, and administrators knew change was needed. Co-authors Janna Dunagan, who teaches deaf and hard of hearing students,…

  17. Possible metastable rhombohedral states of the bcc transition metals

    NASA Astrophysics Data System (ADS)

    Mehl, Michael; Finkenstadt, Daniel

    2007-03-01

    The energy E(c/a) for a bcc element stretched along its [001] axis (the Bain path) has a minimum at c/a = 1, a maximum at c/a = √2, and an elastically unstable local minimum at c/a > √2. A rhombohedral strain is an alternative method of connecting the bcc and fcc structures. The primitive lattice keeps R3m symmetry, with the angle α changing from 109.4^o (bcc), to 90^o (simple cubic), to 60^o (fcc). We studied this path for the non-magnetic bcc transition metals (V, Nb, Mo, Ta, and W) using both a full-potential LAPW and PAW VASP. Except for Ta, the energy E(α) has a local maximum at α=60^o, with local minima near 55^o and 70^o, the later having lower energy. We studied the elastic stability of the 70^o minimum structure. Only W is elastically stable in this structure, with the smallest eigenvalue of the elastic tensor at 4 GPa, while the other three elements are unstable. We discuss the possibility that Tungsten is actually metastable in this structure. We also consider the possible epitaxial growth of this structure. M. J. Mehl, A. Aguayo, L. L. Boyer, and R. De Coss, Phys. Rev. B 70, 014105 (2004).

  18. The 10 Hz Frequency: A Fulcrum For Transitional Brain States.

    PubMed

    Garcia-Rill, E; D'Onofrio, S; Luster, B; Mahaffey, S; Urbano, F J; Phillips, C

    A 10 Hz rhythm is present in the occipital cortex when the eyes are closed (alpha waves), in the precentral cortex at rest ( mu rhythm), in the superior and middle temporal lobe ( tau rhythm), in the inferior olive (projection to cerebellar cortex), and in physiological tremor (underlying all voluntary movement). These are all considered resting rhythms in the waking brain which are "replaced" by higher frequency activity with sensorimotor stimulation. That is, the 10 Hz frequency fulcrum is replaced on the one hand by lower frequencies during sleep, or on the other hand by higher frequencies during volition and cognition. The 10 Hz frequency fulcrum is proposed as the natural frequency of the brain during quiet waking, but is replaced by higher frequencies capable of permitting more complex functions, or by lower frequencies during sleep and inactivity. At the center of the transition shifts to and from the resting rhythm is the reticular activating system, a phylogenetically preserved area of the brain essential for preconscious awareness.

  19. The 10 Hz Frequency: A Fulcrum For Transitional Brain States

    PubMed Central

    Garcia-Rill, E.; D’Onofrio, S.; Luster, B.; Mahaffey, S.; Urbano, F. J.; Phillips, C.

    2016-01-01

    A 10 Hz rhythm is present in the occipital cortex when the eyes are closed (alpha waves), in the precentral cortex at rest (mu rhythm), in the superior and middle temporal lobe (tau rhythm), in the inferior olive (projection to cerebellar cortex), and in physiological tremor (underlying all voluntary movement). These are all considered resting rhythms in the waking brain which are “replaced” by higher frequency activity with sensorimotor stimulation. That is, the 10 Hz frequency fulcrum is replaced on the one hand by lower frequencies during sleep, or on the other hand by higher frequencies during volition and cognition. The 10 Hz frequency fulcrum is proposed as the natural frequency of the brain during quiet waking, but is replaced by higher frequencies capable of permitting more complex functions, or by lower frequencies during sleep and inactivity. At the center of the transition shifts to and from the resting rhythm is the reticular activating system, a phylogenetically preserved area of the brain essential for preconscious awareness. PMID:27547831

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2007-01-12

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

  2. P-20 Education Policy: School to College Transition Policy in Washington State

    ERIC Educational Resources Information Center

    Pitre, Paul E.

    2011-01-01

    This study examines Washington State's attempt to move toward an integrated, P-20 system of education that enhances student transitions from high school to college. In analyzing Washington as a single case study, a profile of the state is developed on key access related characteristics. Data for this study were gathered utilizing fundamental case…

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

    ERIC Educational Resources Information Center

    Angelova, Iva

    2016-01-01

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

  4. The Perceived Readiness of the Graduates of Delaware State University to Transition into the Workforce

    ERIC Educational Resources Information Center

    Scott-Cheatham, Lawita Germaine

    2013-01-01

    This study was designed to explore the perceived readiness of the graduating seniors at Delaware State University to transition from the classroom into the workforce. Delaware State University's undergraduate graduating class of 2012, 547 undergraduate seniors, were invited to participate in an online survey comprised of 23 items--derived from the…

  5. 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.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2009-06-28

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

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

    ERIC Educational Resources Information Center

    Achieve, Inc., 2013

    2013-01-01

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

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

    PubMed

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

    2015-04-29

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

  10. Invariant criteria for bound states, degree of ionization, and plasma phase transition

    NASA Technical Reports Server (NTRS)

    Girardeau, M. D.

    1990-01-01

    Basis invariant characterizations of bound states and bound fraction of a partially ionized hydrogen plasma are given in terms of properties of the spectrum of eigenvalues and eigenfunctions of the equilibrium quantum statistical one-proton-one-electron reduced density matrix. It is suggested that these can be used to place theories of a proposed plasma-ionization phase transition on a firm foundation. This general approach may be relevant to cosmological questions such as the quark deconfinement-confinement transition.

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

    PubMed

    Numazawa, Satoshi; Smith, Roger

    2011-10-01

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

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

    PubMed

    Lachapelle, Ugo

    2015-08-01

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

  13. State safety oversight program : audit of the tri-state oversight committee and the Washington metropolitan area transit authority, final audit report, March 4, 2010.

    DOT National Transportation Integrated Search

    2010-03-04

    The Federal Transit Administration (FTA) conducted an on-site audit of the safety program implemented by the Washington Metropolitan Area Transit Authority (WMATA) and overseen by the Tri-State Oversight Committee (TOC) between December 14 and 17, 20...

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

    PubMed

    Yurovsky, Vladimir A

    2017-05-19

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

  15. Quantum transition state dynamics of the cyclooctatetraene unimolecular reaction on ab initio potential energy surfaces

    NASA Astrophysics Data System (ADS)

    Tokizaki, Chihiro; Yoshida, Takahiko; Takayanagi, Toshiyuki

    2016-05-01

    The cyclooctatetraene (COT) anion has a stable D4h structure that is similar to the transition state configurations of the neutral C-C bond-alternation (D4h ↔ D8h ↔ D4h) and ring-inversion (D2d ↔ D4h ↔ D2d) unimolecular reactions. The previously measured photodetachment spectrum of COT- revealed the reaction dynamics in the vicinity of the two transition states on the neutral potential energy surface. In this work, the photodetachment spectrum is calculated quantum mechanically on ab initio-level potential energy surfaces within a three degree-of-freedom reduced-dimensionality model. Very good agreement has been obtained between theory and experiment, providing reliable interpretations for the experimental spectrum. A detailed picture of the reactive molecular dynamics of the COT unimolecular reaction in the transition state region is also discussed.

  16. 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.

  17. Trans-membrane Signaling in Photosynthetic State Transitions

    PubMed Central

    Singh, Sandeep K.; Hasan, S. Saif; Zakharov, Stanislav D.; Naurin, Sejuti; Cohn, Whitaker; Ma, Jia; Whitelegge, Julian P.; Cramer, William A.

    2016-01-01

    Trans-membrane signaling involving a serine/threonine kinase (Stt7 in Chlamydomonas reinhardtii) directs light energy distribution between the two photosystems of oxygenic photosynthesis. Oxidation of plastoquinol mediated by the cytochrome b6f complex on the electrochemically positive side of the thylakoid membrane activates the kinase domain of Stt7 on the trans (negative) side, leading to phosphorylation and redistribution (“state transition”) of the light-harvesting chlorophyll proteins between the two photosystems. The molecular description of the Stt7 kinase and its interaction with the cytochrome b6f complex are unknown or unclear. In this study, Stt7 kinase has been cloned, expressed, and purified in a heterologous host. Stt7 kinase is shown to be active in vitro in the presence of reductant and purified as a tetramer, as determined by analytical ultracentrifugation, electron microscopy, and electrospray ionization mass spectrometry, with a molecular weight of 332 kDa, consisting of an 83.41-kDa monomer. Far-UV circular dichroism spectra show Stt7 to be mostly α-helical and document a physical interaction with the b6f complex through increased thermal stability of Stt7 secondary structure. The activity of wild-type Stt7 and its Cys-Ser mutant at positions 68 and 73 in the presence of a reductant suggest that the enzyme does not require a disulfide bridge for its activity as suggested elsewhere. Kinase activation in vivo could result from direct interaction between Stt7 and the b6f complex or long-range reduction of Stt7 by superoxide, known to be generated in the b6f complex by quinol oxidation. PMID:27539852

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

    NASA Astrophysics Data System (ADS)

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

    2017-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Mueller, A. C.

    1977-01-01

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

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

    SciT

    Soh, Daniel Beom Soo

    We calculated the optical nonlinearities of the atomically thin monolayer transition metal dichalcogenide material (particularly MoS 2), particularly for those linear and nonlinear transition processes that utilize the bound exciton states. We adopted the bound and the unbound exciton states as the basis for the Hilbert space, and derived all the dynamical density matrices that provides the induced current density, from which the nonlinear susceptibilities can be drawn order-by-order via perturbative calculations. We provide the nonlinear susceptibilities for the linear, the second-harmonic, the third-harmonic, and the kerr-type two-photon processes.

  1. 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

  2. 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

  3. Comparison of successive transition states for folding reveals alternative early folding pathways of two homologous proteins

    PubMed Central

    Calosci, Nicoletta; Chi, Celestine N.; Richter, Barbara; Camilloni, Carlo; Engström, Åke; Eklund, Lars; Travaglini-Allocatelli, Carlo; Gianni, Stefano; Vendruscolo, Michele; Jemth, Per

    2008-01-01

    The energy landscape theory provides a general framework for describing protein folding reactions. Because a large number of studies, however, have focused on two-state proteins with single well-defined folding pathways and without detectable intermediates, the extent to which free energy landscapes are shaped up by the native topology at the early stages of the folding process has not been fully characterized experimentally. To this end, we have investigated the folding mechanisms of two homologous three-state proteins, PTP-BL PDZ2 and PSD-95 PDZ3, and compared the early and late transition states on their folding pathways. Through a combination of Φ value analysis and molecular dynamics simulations we obtained atomic-level structures of the transition states of these homologous three-state proteins and found that the late transition states are much more structurally similar than the early ones. Our findings thus reveal that, while the native state topology defines essentially in a unique way the late stages of folding, it leaves significant freedom to the early events, a result that reflects the funneling of the free energy landscape toward the native state. PMID:19033470

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

    PubMed Central

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

    2011-01-01

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

  5. Columbus State University Global Observation and Outreach for the 2012 Transit of Venus

    NASA Astrophysics Data System (ADS)

    Perry, Matthew; McCarty, C.; Bartow, M.; Hood, J. C.; Lodder, K.; Johnson, M.; Cruzen, S. T.; Williams, R. N.

    2013-01-01

    Faculty, staff and students from Columbus State University’s (CSU’s) Coca-Cola Space Science Center presented a webcast of the 2012 Transit of Venus from three continents to a global audience of 1.4 million unique viewers. Team members imaged the transit with telescopes using white-light, hydrogen-alpha, and calcium filters, from Alice Springs, Australia; the Gobi Desert, Mongolia; Bryce Canyon, UT; and Columbus, GA. Images were webcast live during the transit in partnership with NASA’s Sun-Earth Day program, and Science Center staff members were featured on NASA TV. Local members of the public were brought in for a series of outreach initiatives, in both Georgia and Australia, before and during the transit. The data recorded from the various locations have been archived for use in demonstrating principles such as the historical measurement of the astronomical unit.

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

    SciT

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

    2011-01-01

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

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

    PubMed

    Wulff, Günter; Liu, Junqiu

    2012-02-21

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

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

    NASA Astrophysics Data System (ADS)

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

    2018-06-01

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

  9. Facilitating a Major Staffing Transition in a State Psychiatric Hospital With Changes to Nursing Orientation.

    PubMed

    Birnbaum, Shira; Sperber-Weiss, Doreen; Dimitrios, Timothy; Eckel, Donald; Monroy-Miller, Cherry; Monroe, Janet J; Friedman, Ross; Ologbosele, Mathias; Epo, Grace; Sharpe, Debra; Zarski, Yongsuk

    A large state psychiatric hospital experienced a state-mandated Reduction in Force that resulted in the abrupt loss and rapid turnover of more than 40% of its nursing and paraprofessional staff. The change exemplified current national trends toward downsizing and facility closure. This article describes revisions to the nursing orientation program that supported cost containment and fidelity to mission and clinical practices during the transition. An existing nursing orientation program was reconfigured in alignment with principles of rational instructional design and a core-competencies model of curriculum development, evidence-based practices that provided tactical clarity and commonality of purpose during a complex and emotionally charged transition period. Program redesign enabled efficiencies that facilitated the transition, with no evidence of associated negative effects. The process described here offers an example for hospitals facing similar workforce reorganization in an era of public sector downsizing.

  10. Experiences of Nigerian Internationally Educated Nurses Transitioning to United States Health Care Settings.

    PubMed

    Iheduru-Anderson, Kechinyere C; Wahi, Monika M

    2018-04-01

    Successful transition to practice of internationally educated nurses (IENs) can critically affect quality of care. The aim of this study was to characterize the facilitators and barriers to transition of Nigerian IENs (NIENs) to the United States health care setting. Using a descriptive phenomenology approach, 6 NIENs were interviewed about their transitional experiences in the United States. Thematic methods were used for data analysis. The three major themes identified from the participants' stories were "fear/anger and disappointment" (FAD), "road/journey to success/overcoming challenges" (RJO), and "moving forward" (MF). The FAD theme predominated, including experiences of racism, bullying, and inequality. The RJO theme included resilience, and the MF theme encompassed personal growth. NIENs face personal and organizational barriers to adaptation, especially fear, anger and disappointment. Future research should seek to develop a model for optimal adaptation that focuses on improving both personal and organizational facilitators and decreasing barriers.

  11. Reduced probabilities for E2 transitions between excited collective states of triaxial even–even nuclei

    SciT

    Nadyrbekov, M. S., E-mail: nodirbekov@inp.uz; Bozarov, O. A.

    Reduced probabilities for intra- and interband E2 transitions in excited collective states of even–even lanthanide and actinide nuclei are analyzed on the basis of a model that admits an arbitrary triaxiality. They are studied in detail in the energy spectra of {sup 154}Sm, {sup 156}Gd, {sup 158}Dy, {sup 162,164}Er, {sup 230,232}Th, and {sup 232,234,236,238}U even–even nuclei. Theoretical and experimental values of the reduced probabilities for the respective E2 transitions are compared. This comparison shows good agreement for all states, including high-spin ones. The ratios of the reduced probabilities for the E2 transitions in question are compared with results following frommore » the Alaga rules. These comparisons make it possible to assess the sensitivity of the probabilities being considered to the presence of quadrupole deformations.« less

  12. Transition energy measurements in hydrogenlike and heliumlike ions strongly supporting bound-state QED calculations

    NASA Astrophysics Data System (ADS)

    Kubiček, K.; Mokler, P. H.; Mäckel, V.; Ullrich, J.; López-Urrutia, J. R. Crespo

    2014-09-01

    For the hydrogenlike Ar17+ ion, the 1s Lamb shift was absolutely determined with a 1.4% accuracy based on Lyman-α wavelength measurements that have negligible uncertainties from nuclear size effects. The result agrees with state-of-the-art quantum electrodynamics (QED) calculations, and demonstrates the suitability of Lyman-α transitions in highly charged ions as x-ray energy standards, accurate at the five parts-per-million level. For the heliumlike Ar16+ ion the transition energy for the 1s2p1P1→1s21S0 line was also absolutely determined on an even higher level of accuracy. Additionally, we present relative measurements of transitions in S15+,S14+, and Fe24+ ions. The data for the heliumlike S14+,Ar16+, and Fe24+ ions stringently confirm advanced bound-state QED predictions including screened QED terms that had recently been contested.

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

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  15. 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.

  16. Dynamics of harpooning studied by transition state spectroscopy. II. LiṡṡFH

    NASA Astrophysics Data System (ADS)

    Hudson, A. J.; Oh, H. B.; Polanyi, J. C.; Piecuch, P.

    2000-12-01

    The van der Waals complex LiṡṡFH was formed in crossed beams and the transition state of the excited-state reaction, Li*(2p 2P)+HF→LiF+H, was accessed by photoexcitation of this complex. The dynamics of the excited-state reaction were probed by varying the excitation wavelength over the range 570-970 nm while recording the photodepletion of the complex. The findings were interpreted using high-level ab initio calculations of the ground and lowest excited-state potential-energy surfaces.

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

    PubMed

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

    2015-12-04

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

  18. Theory of pure rotational transitions in doubly degenerate torsional states of ethane

    NASA Technical Reports Server (NTRS)

    Rosenberg, A.; Susskind, J.

    1979-01-01

    It is shown that pure rotational transitions in doubly degenerate torsional states of C2H6 (with selection rules Delta K = 0, plus or minus 1) are made allowed by Coriolis interaction between torsion and dipole-allowed vibrations. Expressions are presented for integrated intensities from which strengths of lines in the millimeter region can be calculated.

  19. Development of state and transition model assumptions used in National Forest Plan revision

    Eric B. Henderson

    2008-01-01

    State and transition models are being utilized in forest management analysis processes to evaluate assumptions about disturbances and succession. These models assume valid information about seral class successional pathways and timing. The Forest Vegetation Simulator (FVS) was used to evaluate seral class succession assumptions for the Hiawatha National Forest in...

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

    DOE PAGES

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

    2009-05-01

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

  1. State-and-transition model archetypes: a global taxonomy of rangeland change

    State and transition models (STMs) synthesize science-based and local knowledge to formally represent the dynamics of rangeland and other ecosystems. Mental models or concepts of ecosystem dynamics implicitly underlie all management decisions in rangelands and thus how people influence rangeland sus...

  2. Applying Ecological Site Concepts and State-and-Transition Models to a Grazed Riparian Rangeland

    Ecological site and state-and-transition models are useful tools for generating and testing hypotheses about drivers of vegetation composition in non-equilibrium systems, and have been widely implemented on rangelands. Compared to upland areas, little attention has been given to developing ecologica...

  3. Computer Series 41: Potential-Energy Surfaces and Transition-State Theory.

    ERIC Educational Resources Information Center

    Moss, S. J.; Coady, C. J.

    1983-01-01

    Describes computer programs involving the London-Eyring-Polany-Sato method (LEPS). The programs provide a valuable means of introducing students to potential energy surfaces and to the foundations of transition state theory. Program listings (with copies of student scripts) or programs on DOS 3.3 disc are available from authors. (JN)

  4. Forecasting timber, biomass, and tree carbon pools with the output of state and transition models

    Xiaoping Zhou; Miles A. Hemstrom

    2012-01-01

    The Integrated Landscape Assessment Project (ILAP) uses spatial vegetation data and state and transition models (STM) to forecast future vegetation conditions and the interacting effects of natural disturbances and management activities. Results from ILAP will help land managers, planners, and policymakers evaluate management strategies that reduce fire risk, improve...

  5. Phase transitions in neutron star equation of state induced by the delta resonances matter

    NASA Astrophysics Data System (ADS)

    T, Oliveira J. C.; Rodrigues, H.; Duarte, S. B.

    2016-04-01

    In the present work we determine the equation of state and the population of baryons and leptons, and also we discuss the implication of changes in the baryon-meson coupling constants to the formation of delta matter in the stellar medium. And also in this work the phase transition is explored with respect to the domain of the delta-mesons coupling constants.

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

    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...

  7. Educational Transitions in the United States: Reflections on the American Dream

    ERIC Educational Resources Information Center

    Crawford, Paul T.

    2012-01-01

    Education involves socialization so that individuals become productive members of society. At present, in the United States, educational transitions are primarily viewed in terms of their location in an outcomes-oriented process and framed as helping people achieve the American Dream, but in terms of the status quo national economic interest. But…

  8. A Visualization System for Predicting Learning Activities Using State Transition Graphs

    ERIC Educational Resources Information Center

    Okubo, Fumiya; Shimada, Atsushi; Taniguchi, Yuta

    2017-01-01

    In this paper, we present a system for visualizing learning logs of a course in progress together with predictions of learning activities of the following week and the final grades of students by state transition graphs. Data are collected from 236 students attending the course in progress and from 209 students attending the past course for…

  9. Family Structure States and Transitions: Associations with Children's Well-Being during Middle Childhood

    ERIC Educational Resources Information Center

    Magnuson, Katherine; Berger, Lawrence M.

    2009-01-01

    Using longitudinal data from the Maternal and Child Supplement of the National Longitudinal Survey of Youth (N = 3,862) and Hierarchical Linear Models, we estimated associations of family structure states and transitions with children's achievement and behavior trajectories during middle childhood. Results suggest that residing in a single-mother…

  10. Comparison of 3D Classical Trajectory and Transition-State Theory Reaction Cross Sections

    DOE R&D Accomplishments Database

    Koeppl, G. W.; Karplus, Martin

    1970-10-01

    Although there is excellent agreement for a system such as H+H{sub 2} --> H{sub 2}+H, in which both the potential and the particle masses are symmetric, significant deviations occur for more asymmetric reactions. A detailed analysis show that the calculated differences are from the violation of two assumptions of transition-state theory.

  11. Some properties of asymmetric Hopfield neural networks with finite time of transition between states

    NASA Astrophysics Data System (ADS)

    Suleimenov, Ibragim; Mun, Grigoriy; Panchenko, Sergey; Pak, Ivan

    2016-11-01

    There were implemented samples of asymmetric Hopfield neural networks which have finite time of transition from one state to another. It was shown that in such systems, various oscillation modes could occur. It was revealed that the oscillation of the output signal of certain neuron could be treated as extra logical variable, which describes the state of the neuron. Asymmetric Hopfield neural networks are described in terms of ternary logic. Such logic may be employed in image recognition procedure.

  12. 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

  13. 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.

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

    SciT

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

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

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

    PubMed

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

    2015-03-01

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

  16. Heterogeneous distribution of water in the mantle transition zone beneath United States inferred from seismic observations

    NASA Astrophysics Data System (ADS)

    Wang, Y.; Pavlis, G. L.; Li, M.

    2017-12-01

    The amount of water in the Earth's deep mantle is critical for the evolution of the solid Earth and the atmosphere. Mineral physics studies have revealed that Wadsleyite and Ringwoodite in the mantle transition zone could store several times the volume of water in the ocean. However, the water content and its distribution in the transition zone remain enigmatic due to lack of direct observations. Here we use seismic data from the full deployment of the Earthscope Transportable Array to produce 3D image of P to S scattering of the mantle transition zone beneath the United States. We compute the image volume from 141,080 pairs of high quality receiver functions defined by the Earthscope Automated Receiver Survey, reprocessed by the generalized iterative deconvolution method and imaged by the plane wave migration method. We find that the transition zone is filled with previously unrecognized small-scale heterogeneities that produce pervasive, negative polarity P to S conversions. Seismic synthetic modeling using a point source simulation method suggests two possible structures for these objects: 1) a set of randomly distributed blobs of slight difference in size, and 2) near vertical diapir structures from small scale convections. Combining with geodynamic simulations, we interpret the observation as compositional heterogeneity from small-scale, low-velocity bodies that are water enriched. Our results indicate there is a heterogeneous distribution of water through the entire mantle transition zone beneath the contiguous United States.

  17. Phase transitions of sodium niobate powder and ceramics, prepared by solid state synthesis

    NASA Astrophysics Data System (ADS)

    Koruza, J.; Tellier, J.; Malič, B.; Bobnar, V.; Kosec, M.

    2010-12-01

    Phase transitions of sodium niobate, prepared by the solid state synthesis method, were examined using dielectric measurements, differential scanning calorimetry, and high temperature x-ray diffraction, in order to contribute to the clarification of its structural behavior below 400 °C. Four phase transitions were detected in the ceramic sample using dielectric measurements and differential scanning calorimetry and the obtained temperatures were in a good agreement with previous reports for the transitions of the P polymorph. The anomaly observed by dielectric measurements in the vicinity of 150 °C was frequency dependent and could be related to the dynamics of the ferroelectric nanoregions. The phase transitions of the as-synthesized NaNbO3 powder were investigated using differential scanning calorimetry and high temperature x-ray diffraction. The results show the existence of the Q polymorph at room temperature, not previously reported for the powder, which undergoes a transition to the R polymorph upon heating through a temperature region between 265 and 326.5 °C. This transition is mainly related to the displacement of Na into a more symmetric position and a minor change in the tilting system. The structures at room temperature, 250, 300, and 420 °C were refined by the Rietveld method and the evolution of the tilting system of the octahedral network and cationic displacement are reported.

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

    PubMed

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

    2011-01-01

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

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

    DTIC Science & Technology

    1992-09-01

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

  20. Toward a social justice theory of demographic transition: lessons from India's Kerala State.

    PubMed

    Ratcliffe, J W

    1983-06-01

    Recent research evidence, which suggests that observed demographic trends and patterns are largely consequences of broad structural changes in society, has raised serious doubts about the validity of traditional demographic theory and the framework for action it has generated. This theoretical essay 1st recasts classical demographic transition theory in general systems terms in order to make it consistent with the evidence and to place the processes of fertility and mortality in a larger social context. The demographic transition experience of Kerala State, India is then recounted to provide a concrete example of the demographic response in society to structural reforms based primarily on equity considerations.

  1. Ground state transitions in vertically coupled N-layer single electron quantum dots

    NASA Astrophysics Data System (ADS)

    Xie, Wenfang; Wang, Anmei

    2003-12-01

    A method is proposed to exactly diagonalize the Hamiltonian of a N-layer quantum dot containing a single electron in each dot in arbitrary magnetic fields. For N=4, the energy spectra of the dot are calculated as a function of the applied magnetic field. We find discontinuous ground-state energy transitions induced by an external magnetic field in the case of strong coupling. However, in the case of weak coupling, such a transition does not occur and the angular momentum remains zero.

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

    NASA Astrophysics Data System (ADS)

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

    2018-03-01

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

  3. Efficient dynamical correction of the transition state theory rate estimate for a flat energy barrier.

    PubMed

    Mökkönen, Harri; Ala-Nissila, Tapio; Jónsson, Hannes

    2016-09-07

    The recrossing correction to the transition state theory estimate of a thermal rate can be difficult to calculate when the energy barrier is flat. This problem arises, for example, in polymer escape if the polymer is long enough to stretch between the initial and final state energy wells while the polymer beads undergo diffusive motion back and forth over the barrier. We present an efficient method for evaluating the correction factor by constructing a sequence of hyperplanes starting at the transition state and calculating the probability that the system advances from one hyperplane to another towards the product. This is analogous to what is done in forward flux sampling except that there the hyperplane sequence starts at the initial state. The method is applied to the escape of polymers with up to 64 beads from a potential well. For high temperature, the results are compared with direct Langevin dynamics simulations as well as forward flux sampling and excellent agreement between the three rate estimates is found. The use of a sequence of hyperplanes in the evaluation of the recrossing correction speeds up the calculation by an order of magnitude as compared with the traditional approach. As the temperature is lowered, the direct Langevin dynamics simulations as well as the forward flux simulations become computationally too demanding, while the harmonic transition state theory estimate corrected for recrossings can be calculated without significant increase in the computational effort.

  4. Land management in the American southwest: a state-and-transition approach to ecosystem complexity.

    PubMed

    Bestelmeyer, Brandon T; Herrick, Jeffrey E; Brown, Joel R; Trujillo, David A; Havstad, Kris M

    2004-07-01

    State-and-transition models are increasingly being used to guide rangeland management. These models provide a relatively simple, management-oriented way to classify land condition (state) and to describe the factors that might cause a shift to another state (a transition). There are many formulations of state-and-transition models in the literature. The version we endorse does not adhere to any particular generalities about ecosystem dynamics, but it includes consideration of several kinds of dynamics and management response to them. In contrast to previous uses of state-and-transition models, we propose that models can, at present, be most effectively used to specify and qualitatively compare the relative benefits and potential risks of different management actions (e.g., fire and grazing) and other factors (e.g., invasive species and climate change) on specified areas of land. High spatial and temporal variability and complex interactions preclude the meaningful use of general quantitative models. Forecasts can be made on a case-by-case basis by interpreting qualitative and quantitative indicators, historical data, and spatially structured monitoring data based on conceptual models. We illustrate how science- based conceptual models are created using several rangeland examples that vary in complexity. In doing so, we illustrate the implications of designating plant communities and states in models, accounting for varying scales of pattern in vegetation and soils, interpreting the presence of plant communities on different soils and dealing with our uncertainty about how those communities were assembled and how they will change in the future. We conclude with observations about how models have helped to improve management decision-making.

  5. Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States

    NASA Astrophysics Data System (ADS)

    de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M.

    2018-03-01

    Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

  6. The Role of Leadership in Transitional States: The Cases of Lebanon, Israel-Palestine

    DTIC Science & Technology

    2014-11-01

    Using authoritarian, democratic, and laissez - faire leadership styles as a basis for this work, it was concluded that some leaders were more people...NOV 2014 2. REPORT TYPE 3. DATES COVERED 00-00-2014 to 00-00-2014 4. TITLE AND SUBTITLE The Role of Leadership in Transitional States: The Cases...Prescribed by ANSI Std Z39-18 The United States Army War College U.S. ARMY WAR COLLEGE CENTER for STRATEGIC LEADERSHIP and DEVELOPMENT The United States

  7. Minimum Action Path Theory Reveals the Details of Stochastic Transitions Out of Oscillatory States.

    PubMed

    de la Cruz, Roberto; Perez-Carrasco, Ruben; Guerrero, Pilar; Alarcon, Tomas; Page, Karen M

    2018-03-23

    Cell state determination is the outcome of intrinsically stochastic biochemical reactions. Transitions between such states are studied as noise-driven escape problems in the chemical species space. Escape can occur via multiple possible multidimensional paths, with probabilities depending nonlocally on the noise. Here we characterize the escape from an oscillatory biochemical state by minimizing the Freidlin-Wentzell action, deriving from it the stochastic spiral exit path from the limit cycle. We also use the minimized action to infer the escape time probability density function.

  8. A universal indicator of critical state transitions in noisy complex networked systems

    PubMed Central

    Liang, Junhao; Hu, Yanqing; Chen, Guanrong; Zhou, Tianshou

    2017-01-01

    Critical transition, a phenomenon that a system shifts suddenly from one state to another, occurs in many real-world complex networks. We propose an analytical framework for exactly predicting the critical transition in a complex networked system subjected to noise effects. Our prediction is based on the characteristic return time of a simple one-dimensional system derived from the original higher-dimensional system. This characteristic time, which can be easily calculated using network data, allows us to systematically separate the respective roles of dynamics, noise and topology of the underlying networked system. We find that the noise can either prevent or enhance critical transitions, playing a key role in compensating the network structural defect which suffers from either internal failures or environmental changes, or both. Our analysis of realistic or artificial examples reveals that the characteristic return time is an effective indicator for forecasting the sudden deterioration of complex networks. PMID:28230166

  9. The impact of quantum dot filling on dual-band optical transitions via intermediate quantum states

    SciT

    Wu, Jiang, E-mail: jiang.wu@ucl.ac.uk; Passmore, Brandon; Manasreh, M. O.

    2015-08-28

    InAs/GaAs quantum dot infrared photodetectors with different doping levels were investigated to understand the effect of quantum dot filling on both intraband and interband optical transitions. The electron filling of self-assembled InAs quantum dots was varied by direct doping of quantum dots with different concentrations. Photoresponse in the near infrared and middle wavelength infrared spectral region was observed from samples with low quantum dot filling. Although undoped quantum dots were favored for interband transitions with the absence of a second optical excitation in the near infrared region, doped quantum dots were preferred to improve intraband transitions in the middle wavelengthmore » infrared region. As a result, partial filling of quantum dot was required, to the extent of maintaining a low dark current, to enhance the dual-band photoresponse through the confined electron states.« less

  10. Generic finite size scaling for discontinuous nonequilibrium phase transitions into absorbing states

    NASA Astrophysics Data System (ADS)

    de Oliveira, M. M.; da Luz, M. G. E.; Fiore, C. E.

    2015-12-01

    Based on quasistationary distribution ideas, a general finite size scaling theory is proposed for discontinuous nonequilibrium phase transitions into absorbing states. Analogously to the equilibrium case, we show that quantities such as response functions, cumulants, and equal area probability distributions all scale with the volume, thus allowing proper estimates for the thermodynamic limit. To illustrate these results, five very distinct lattice models displaying nonequilibrium transitions—to single and infinitely many absorbing states—are investigated. The innate difficulties in analyzing absorbing phase transitions are circumvented through quasistationary simulation methods. Our findings (allied to numerical studies in the literature) strongly point to a unifying discontinuous phase transition scaling behavior for equilibrium and this important class of nonequilibrium systems.

  11. 19 CFR 123.64 - Baggage in transit through the United States between ports in Canada or in Mexico.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... between ports in Canada or in Mexico. 123.64 Section 123.64 Customs Duties U.S. CUSTOMS AND BORDER... MEXICO Baggage § 123.64 Baggage in transit through the United States between ports in Canada or in Mexico. (a) Procedure. Baggage in transit from point to point in Canada or Mexico through the United States...

  12. 19 CFR 123.65 - Domestic baggage transiting Canada or Mexico between ports in the United States.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Domestic baggage transiting Canada or Mexico... MEXICO Baggage § 123.65 Domestic baggage transiting Canada or Mexico between ports in the United States... transported from one port in the United States to another through Canada or through Mexico in accord with the...

  13. State transition storyboards: A tool for designing the Goldstone solar system radar data acquisition system user interface software

    NASA Technical Reports Server (NTRS)

    Howard, S. D.

    1987-01-01

    Effective user interface design in software systems is a complex task that takes place without adequate modeling tools. By combining state transition diagrams and the storyboard technique of filmmakers, State Transition Storyboards were developed to provide a detailed modeling technique for the Goldstone Solar System Radar Data Acquisition System human-machine interface. Illustrations are included with a description of the modeling technique.

  14. 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.

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

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

    2018-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Muff, S.; Caflisch, A.

    2009-03-01

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

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

    PubMed Central

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

    2017-01-01

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

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

    PubMed

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

    2017-01-01

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

  19. Characterization of Dynamical Phase Transitions in Quantum Jump Trajectories Beyond the Properties of the Stationary State

    NASA Astrophysics Data System (ADS)

    Lesanovsky, Igor; van Horssen, Merlijn; Guţă, Mădălin; Garrahan, Juan P.

    2013-04-01

    We describe how to characterize dynamical phase transitions in open quantum systems from a purely dynamical perspective, namely, through the statistical behavior of quantum jump trajectories. This approach goes beyond considering only properties of the steady state. While in small quantum systems dynamical transitions can only occur trivially at limiting values of the controlling parameters, in many-body systems they arise as collective phenomena and within this perspective they are reminiscent of thermodynamic phase transitions. We illustrate this in open models of increasing complexity: a three-level system, the micromaser, and a dissipative version of the quantum Ising model. In these examples dynamical transitions are accompanied by clear changes in static behavior. This is however not always the case, and, in general, dynamical phases need to be uncovered by observables which are strictly dynamical, e.g., dynamical counting fields. We demonstrate this via the example of a class of models of dissipative quantum glasses, whose dynamics can vary widely despite having identical (and trivial) stationary states.

  20. Characterization of dynamical phase transitions in quantum jump trajectories beyond the properties of the stationary state.

    PubMed

    Lesanovsky, Igor; van Horssen, Merlijn; Guţă, Mădălin; Garrahan, Juan P

    2013-04-12

    We describe how to characterize dynamical phase transitions in open quantum systems from a purely dynamical perspective, namely, through the statistical behavior of quantum jump trajectories. This approach goes beyond considering only properties of the steady state. While in small quantum systems dynamical transitions can only occur trivially at limiting values of the controlling parameters, in many-body systems they arise as collective phenomena and within this perspective they are reminiscent of thermodynamic phase transitions. We illustrate this in open models of increasing complexity: a three-level system, the micromaser, and a dissipative version of the quantum Ising model. In these examples dynamical transitions are accompanied by clear changes in static behavior. This is however not always the case, and, in general, dynamical phases need to be uncovered by observables which are strictly dynamical, e.g., dynamical counting fields. We demonstrate this via the example of a class of models of dissipative quantum glasses, whose dynamics can vary widely despite having identical (and trivial) stationary states.

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

    NASA Astrophysics Data System (ADS)

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

    2018-05-01

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

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

    PubMed Central

    Afzal, Muhammad Imran; Lee, Yong Tak

    2016-01-01

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

  3. 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

  4. 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

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

    PubMed Central

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

    2012-01-01

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

  6. The failed state transition of the ATOLL source GRS 1724-308

    NASA Astrophysics Data System (ADS)

    Tarana, A.; Capitanio, F.; Cocchi, M.

    2018-07-01

    The 2004-2012 X-ray time history of the NS LMXB GRS 1724-308 shows, along with the episodic brightenings associated with the low-high state transitions typical of the ATOLL sources, a peculiar, long lasting (˜300 d) flaring event, observed in 2008. This rare episode, characterized by a high-flux hard state, has never been observed before for GRS 1724-308, and in any case is not common among ATOLL sources. We discuss here different hypotheses on the origin of this peculiar event that displayed the spectral signatures of a failed transition, similar in shape and duration to those rarely observed in black hole binaries. We also suggest the possibility that the atypical flare occurred in coincidence with a new rising phase of the 12-yr superorbital modulation that has been previously reported by other authors. The analysed data also confirm for GRS 1724-308 the already reported orbital period of ˜90 d.

  7. 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.

  8. Promoting Singlet/triplet Exciton Transformation in Organic Optoelectronic Molecules: Role of Excited State Transition Configuration.

    PubMed

    Chen, Runfeng; Tang, Yuting; Wan, Yifang; Chen, Ting; Zheng, Chao; Qi, Yuanyuan; Cheng, Yuanfang; Huang, Wei

    2017-07-24

    Exciton transformation, a non-radiative process in changing the spin multiplicity of an exciton usually between singlet and triplet forms, has received much attention recently due to its crucial effects in manipulating optoelectronic properties for various applications. However, current understanding of exciton transformation mechanism does not extend far beyond a thermal equilibrium of two states with different multiplicity and it is a significant challenge to probe what exactly control the transformation between the highly active excited states. Here, based on the recent developments of three types of purely organic molecules capable of efficient spin-flipping, we perform ab initio structure/energy optimization and similarity/overlap extent analysis to theoretically explore the critical factors in controlling the transformation process of the excited states. The results suggest that the states having close energy levels and similar exciton characteristics with same transition configurations and high heteroatom participation are prone to facilitating exciton transformation. A basic guideline towards the molecular design of purely organic materials with facile exciton transformation ability is also proposed. Our discovery highlights systematically the critical importance of vertical transition configuration of excited states in promoting the singlet/triplet exciton transformation, making a key step forward in excited state tuning of purely organic optoelectronic materials.

  9. Chapter 5: Application of state-and-transition models to evaluate wildlife habitat

    Anita T. Morzillo; Pamela Comeleo; Blair Csuti; Stephanie Lee

    2014-01-01

    Wildlife habitat analysis often is a central focus of natural resources management and policy. State-and-transition models (STMs) allow for simulation of landscape level ecological processes, and for managers to test “what if” scenarios of how those processes may affect wildlife habitat. This chapter describes the methods used to link STM output to wildlife habitat to...

  10. State-change in the "transition" binary millisecond pulsar J1023+0038

    NASA Astrophysics Data System (ADS)

    Stappers, B. W.; Archibald, A.; Bassa, C.; Hessels, J.; Janssen, G.; Kaspi, V.; Lyne, A.; Patruno, A.; Hill, A. B.

    2013-10-01

    We report a change in the state of PSR J1023+0038, a source which is believed to be transitioning from an X-ray binary to an eclipsing binary radio millisecond pulsar (Archibald et al. 2009, Science, 324, 1411). The system was known to contain an accretion disk in 2001 but has shown no signs of it, or of accretion, since then, rather exhibiting all the properties of an eclipsing binary millisecond radio pulsar (MSP).

  11. Empirical models of transitions between coral reef states: effects of region, protection, and environmental change.

    PubMed

    Lowe, Phillip K; Bruno, John F; Selig, Elizabeth R; Spencer, Matthew

    2011-01-01

    There has been substantial recent change in coral reef communities. To date, most analyses have focussed on static patterns or changes in single variables such as coral cover. However, little is known about how community-level changes occur at large spatial scales. Here, we develop Markov models of annual changes in coral and macroalgal cover in the Caribbean and Great Barrier Reef (GBR) regions. We analyzed reef surveys from the Caribbean and GBR (1996-2006). We defined a set of reef states distinguished by coral and macroalgal cover, and obtained Bayesian estimates of the annual probabilities of transitions between these states. The Caribbean and GBR had different transition probabilities, and therefore different rates of change in reef condition. This could be due to differences in species composition, management or the nature and extent of disturbances between these regions. We then estimated equilibrium probability distributions for reef states, and coral and macroalgal cover under constant environmental conditions. In both regions, the current distributions are close to equilibrium. In the Caribbean, coral cover is much lower and macroalgal cover is higher at equilibrium than in the GBR. We found no evidence for differences in transition probabilities between the first and second halves of our survey period, or between Caribbean reefs inside and outside marine protected areas. However, our power to detect such differences may have been low. We also examined the effects of altering transition probabilities on the community state equilibrium, along a continuum from unfavourable (e.g., increased sea surface temperature) to favourable (e.g., improved management) conditions. Both regions showed similar qualitative responses, but different patterns of uncertainty. In the Caribbean, uncertainty was greatest about effects of favourable changes, while in the GBR, we are most uncertain about effects of unfavourable changes. Our approach could be extended to provide

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

    PubMed Central

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

    2014-01-01

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

  13. Disorder-induced inhomogeneities of the superconducting state close to the superconductor-insulator transition.

    PubMed

    Sacépé, B; Chapelier, C; Baturina, T I; Vinokur, V M; Baklanov, M R; Sanquer, M

    2008-10-10

    Scanning tunneling spectroscopy at very low temperatures on homogeneously disordered superconducting titanium nitride thin films reveals strong spatial inhomogeneities of the superconducting gap Delta in the density of states. Upon increasing disorder, we observe suppression of the superconducting critical temperature Tc towards zero, enhancement of spatial fluctuations in Delta, and growth of the Delta/Tc ratio. These findings suggest that local superconductivity survives across the disorder-driven superconductor-insulator transition.

  14. Synthesis of a new family of acyclic nucleoside phosphonates, analogues of TPases transition states.

    PubMed

    Dayde, Bénédicte; Benzaria, Samira; Pierra, Claire; Gosselin, Gilles; Surleraux, Dominique; Volle, Jean-Noël; Pirat, Jean-Luc; Virieux, David

    2012-05-07

    A 6-step procedure was developed for the synthesis of a new family of acyclic nucleoside phosphonates (ANPs), "PHEEPA" [(2-pyrimidinyl-2-(2-hydroxyethoxy)ethyl)phosphonic acids] in overall yields ranging from 4.5% to 32%. These compounds, which possess on one side a hydroxy function and on the other side a phosphonate group, can be considered either as potential antiviral agents or as transition state analogues of nucleoside phosphorylases such as thymidine phosphorylase.

  15. Regimes of radiative and nonradiative transitions in transport through an electronic system in a photon cavity reaching a steady state

    NASA Astrophysics Data System (ADS)

    Gudmundsson, Vidar; Jonsson, Thorsteinn H.; Bernodusson, Maria Laura; Abdullah, Nzar Rauf; Sitek, Anna; Goan, Hsi-Sheng; Tang, Chi-Shung; Manolescu, Andrei

    2017-01-01

    We analyze how a multilevel many-electron system in a photon cavity approaches the steady state when coupled to external leads. When a plunger gate is used to lower cavity photon dressed one- and two-electron states below the bias window defined by the external leads, we can identify one regime with nonradiative transitions dominating the electron transport, and another regime with radiative transitions. Both transitions trap the electrons in the states below the bias bringing the system into a steady state. The order of the two regimes and their relative strength depends on the location of the bias window in the energy spectrum of the system and the initial conditions.

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

    SciT

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

    2010-01-12

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

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

    NASA Astrophysics Data System (ADS)

    Lee, Timothy J.; Rendell, Alistair P.

    1991-03-01

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

  18. 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

  19. 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

  20. 2009 rail safety statistics report : an analysis of safety data reported by state safety oversight agencies and rail transit agencies for the years 2003-2008

    DOT National Transportation Integrated Search

    2010-01-01

    In calendar year 2008, the rail transit industry provided over 18.5 billion passenger : miles, a 5% increase from 2007 service numbers. Growth in ridership at the rail : transit agencies in the Federal Transit Administrations (FTA) State Safety Ov...

  1. Signatures of the Mott transition in the antiferromagnetic state of the two-dimensional Hubbard model

    DOE PAGES

    Fratino, L.; Sémon, P.; Charlebois, M.; ...

    2017-06-06

    The properties of a phase with large correlation length can be strongly influenced by the underlying normal phase. Here, we illustrate this by studying the half-filled two-dimensional Hubbard model using cellular dynamical mean-field theory with continuous-time quantum Monte Carlo. Sharp crossovers in the mechanism that favors antiferromagnetic correlations and in the corresponding local density of states are observed. We found that these crossovers occur at values of the interaction strength U and temperature T that are controlled by the underlying normal-state Mott transition.

  2. Status in calculating electronic excited states in transition metal oxides from first principles.

    PubMed

    Bendavid, Leah Isseroff; Carter, Emily Ann

    2014-01-01

    Characterization of excitations in transition metal oxides is a crucial step in the development of these materials for photonic and optoelectronic applications. However, many transition metal oxides are considered to be strongly correlated materials, and their complex electronic structure is challenging to model with many established quantum mechanical techniques. We review state-of-the-art first-principles methods to calculate charged and neutral excited states in extended materials, and discuss their application to transition metal oxides. We briefly discuss developments in density functional theory (DFT) to calculate fundamental band gaps, and introduce time-dependent DFT, which can model neutral excitations. Charged excitations can be described within the framework of many-body perturbation theory based on Green's functions techniques, which predominantly employs the GW approximation to the self-energy to facilitate a feasible solution to the quasiparticle equations. We review the various implementations of the GW approximation and evaluate each approach in its calculation of fundamental band gaps of many transition metal oxides. We also briefly review the related Bethe-Salpeter equation (BSE), which introduces an electron-hole interaction between GW-derived quasiparticles to describe accurately neutral excitations. Embedded correlated wavefunction theory is another framework used to model localized neutral or charged excitations in extended materials. Here, the electronic structure of a small cluster is modeled within correlated wavefunction theory, while its coupling to its environment is represented by an embedding potential. We review a number of techniques to represent this background potential, including electrostatic representations and electron density-based methods, and evaluate their application to transition metal oxides.

  3. Interface states, negative differential resistance, and rectification in molecular junctions with transition-metal contacts

    NASA Astrophysics Data System (ADS)

    Dalgleish, Hugh; Kirczenow, George

    2006-06-01

    We present a theory of nonlinear transport phenomena in molecular junctions where single thiolated organic molecules bridge transition metal nanocontacts whose densities of states have strong d orbital components near the Fermi level. At moderate bias, we find electron transmission between the contacts to be mediated by interface states within the molecular highest-occupied-molecular-orbital-lowest-unoccupied-molecular-orbital gap that arise from hybridization between the thiol-terminated ends of the molecules and the d orbitals of the transition metals. Because these interface states are localized mainly within the metal electrodes, we find their energies to accurately track the electrochemical potentials of the contacts when a variable bias is applied across the junction. We predict resonant enhancement and reduction of the interface state transmission as the applied bias is varied, resulting in negative differential resistance (NDR) in molecular junctions with Pd nanocontacts. We show that these nonlinear phenomena can be tailored by suitably choosing the nanocontact materials: If a Rh electrode is substituted for one Pd contact, we predict enhancement of these NDR effects. The same mechanism is also predicted to give rise to rectification in Pd/molecule/Au junctions. The dependences of the interface state resonances on the orientation of the metal interface, the adsorption site of the molecule, and the separation between the thiolated ends of the molecule and the metal contacts are also discussed.

  4. Direct control of transitions between different mode-locking states of a fiber laser

    NASA Astrophysics Data System (ADS)

    Ilday, Fatih; Teamir, Tesfay; Iegorov, Roman; Makey, Ghaith

    Mode-locking corresponds to a far-from-equilibrium steady state of a laser, whereby extremely short pulses can be produced. Capability to directly control mode-locking states can be used to improve laser performance with numerous applications, as well as shed light on their far-from-equilibrium physics using the laser as an experimental platform. Here, we demonstrate direct control of the mode-locking state using spectral pulse shaping by incorporating a spatial light modulator at a Fourier plane inside the cavity of an Yb-doped fiber laser. We show that we can halt and restart mode-locking, suppress instabilities, induce controlled reversible and irreversible transitions between mode-locking states, and perform advanced pulse shaping on pulses as short as 40 fs. This capability can be used to experimentally investigate bifurcations, reversible and irreversible transitions, by selecting, steering, and even competing various mode-locking states. Such studies can explore collective dynamics of dissipative soliton molecules, and ultimately test emerging theories about far-from-equilibrium physics, where there is an acute lack of experimental systems that are sufficiently well controlled. ERC CoG 617521, TUBITAK 113F319.

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

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  6. State-and-transition prototype model of riparian vegetation downstream of Glen Canyon Dam, Arizona

    Ralston, Barbara E.; Starfield, Anthony M.; Black, Ronald S.; Van Lonkhuyzen, Robert A.

    2014-01-01

    Facing an altered riparian plant community dominated by nonnative species, resource managers are increasingly interested in understanding how to manage and promote healthy riparian habitats in which native species dominate. For regulated rivers, managing flows is one tool resource managers consider to achieve these goals. Among many factors that can influence riparian community composition, hydrology is a primary forcing variable. Frame-based models, used successfully in grassland systems, provide an opportunity for stakeholders concerned with riparian systems to evaluate potential riparian vegetation responses to alternative flows. Frame-based, state-and-transition models of riparian vegetation for reattachment bars, separation bars, and the channel margin found on the Colorado River downstream of Glen Canyon Dam were constructed using information from the literature. Frame-based models can be simple spreadsheet models (created in Microsoft® Excel) or developed further with programming languages (for example, C-sharp). The models described here include seven community states and five dam operations that cause transitions between states. Each model divides operations into growing (April–September) and non-growing seasons (October–March) and incorporates upper and lower bar models, using stage elevation as a division. The inputs (operations) can be used by stakeholders to evaluate flows that may promote dynamic riparian vegetation states, or identify those flow options that may promote less desirable states (for example, Tamarisk [Tamarix sp.] temporarily flooded shrubland). This prototype model, although simple, can still elicit discussion about operational options and vegetation response.

  7. Transient transition from free carrier metallic state to exciton insulating state in GaAs by ultrafast photoexcitation

    NASA Astrophysics Data System (ADS)

    Nie, X. C.; Song, Hai-Ying; Zhang, Xiu; Gu, Peng; Liu, Shi-Bing; Li, Fan; Meng, Jian-Qiao; Duan, Yu-Xia; Liu, H. Y.

    2018-03-01

    We present systematic studies of the transient dynamics of GaAs by ultrafast time-resolved reflectivity. In photoexcited non-equilibrium states, we found a sign reverse in reflectivity change ΔR/R, from positive around room temperature to negative at cryogenic temperatures. The former corresponds to a free carrier metallic state, while the latter is attributed to an exciton insulating state, in which the transient electronic properties is mostly dominated by excitons, resulting in a transient metal–insulator transition (MIT). Two transition temperatures (T 1 and T 2) are well identified by analyzing the intensity change of the transient reflectivity. We found that photoexcited MIT starts emerging at T 1 as high as ∼ 230 K, in terms of a dip feature at 0.4 ps, and becomes stabilized below T 2 that is up to ∼ 180 K, associated with a negative constant after 40 ps. Our results address a phase diagram that provides a framework for the inducing of MIT through temperature and photoexcitation, and may shed light on the understanding of light-semiconductor interaction and exciton physics.

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

    PubMed

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

    2011-06-14

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

  9. Dynamics of SARS-coronavirus HR2 domain in the prefusion and transition states

    NASA Astrophysics Data System (ADS)

    McReynolds, Susanna; Jiang, Shaokai; Rong, Lijun; Caffrey, Michael

    2009-12-01

    The envelope glycoproteins S1 and S2 of severe acute respiratory syndrome coronavirus (SARS-CoV) mediate viral entry by conformational change from a prefusion state to a postfusion state that enables fusion of the viral and target membranes. In this work we present the characterization of the dynamic properties of the SARS-CoV S2-HR2 domain (residues 1141-1193 of S) in the prefusion and newly discovered transition states by NMR 15N relaxation studies. The dynamic properties of the different states, which are stabilized under different experimental conditions, extend the current model of viral membrane fusion and give insight into the design of structure-based antagonists of SARS-CoV in particular, as well as other enveloped viruses such as HIV.

  10. Folding mechanism of β-hairpin trpzip2: heterogeneity, transition state and folding pathways.

    PubMed

    Xiao, Yi; Chen, Changjun; He, Yi

    2009-06-22

    We review the studies on the folding mechanism of the beta-hairpin tryptophan zipper 2 (trpzip2) and present some additional computational results to refine the picture of folding heterogeneity and pathways. We show that trpzip2 can have a two-state or a multi-state folding pattern, depending on whether it folds within the native basin or through local state basins on the high-dimensional free energy surface; Trpzip2 can fold along different pathways according to the packing order of tryptophan pairs. We also point out some important problems related to the folding mechanism of trpzip2 that still need clarification, e.g., a wide distribution of the computed conformations for the transition state ensemble.

  11. 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

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

    NASA Astrophysics Data System (ADS)

    Hsu, H.

    2010-12-01

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

  13. GH therapy in transition age: state of the art and future perspectives.

    PubMed

    Cappa, M; Caruso, M; Saggese, G; Salerno, M C; Tonini, G

    2015-03-01

    Growth hormone (GH) has been recently approved by the Italian Health Authorities for use in transition patients with childhood onset-growth hormone deficiency (CO-GHD). GH in addition to promote linear growth influences several key metabolic processes. In particular, in the transition period, from late adolescent to early adulthood, GH plays an important role in the achievement of a complete somatic development including body composition, muscle mass maturation, full skeletal mineralization and reproductive maturation, as well as in the prevention of metabolic and cardiovascular risk. Therefore, GH replacement should be restarted if a GH stimulation test at the re-evaluation fulfills established criteria. Endocrinologists experienced in the care of GHD adolescent patients held a workshop in Rome, Italy in July 2012 to review in detail the literature data and compare experiences of five Italian endocrinological centers on the negative consequences of interrupting GH treatment and the positive effects of continued GH replacement on intermediary metabolism, heart, muscle, pubertal development, and bone. The aim of the meeting was to delineate the state of the art on GH therapy in transition age and provide suggestions to pediatric and adult endocrinologists for a smooth transition care.

  14. Discovering sparse transcription factor codes for cell states and state transitions during development

    PubMed Central

    Furchtgott, Leon A; Melton, Samuel; Menon, Vilas; Ramanathan, Sharad

    2017-01-01

    Computational analysis of gene expression to determine both the sequence of lineage choices made by multipotent cells and to identify the genes influencing these decisions is challenging. Here we discover a pattern in the expression levels of a sparse subset of genes among cell types in B- and T-cell developmental lineages that correlates with developmental topologies. We develop a statistical framework using this pattern to simultaneously infer lineage transitions and the genes that determine these relationships. We use this technique to reconstruct the early hematopoietic and intestinal developmental trees. We extend this framework to analyze single-cell RNA-seq data from early human cortical development, inferring a neocortical-hindbrain split in early progenitor cells and the key genes that could control this lineage decision. Our work allows us to simultaneously infer both the identity and lineage of cell types as well as a small set of key genes whose expression patterns reflect these relationships. DOI: http://dx.doi.org/10.7554/eLife.20488.001 PMID:28296636

  15. Agricultural Drought Transition Periods In the United States Corn Belt Region

    NASA Astrophysics Data System (ADS)

    Schiraldi, Nicholas J.

    Agricultural drought in the U.S. Corn Belt region (CBR) has tremendous global socioeconomic implications. Unfortunately, the weather and climate factors that contribute to transition events toward or away from such droughts, and how well those factors are predicted, are poorly understood. This dissertation focuses on the atmospheric circulation signals associated with agricultural drought transitions periods in the CBR that evolve over 20 and 60 days, and how well those circulation signals are predicted on seasonal to sub-seasonal time scales. Results show that amplification of an intraseasonal Rossby wave train across the Pacific Ocean into North America, which occurs coincident with intraseasonal tropical convection on its equatorward side, triggers these transition events, not shifts in the low frequency base state. This result is confirmed through composite analysis, trajectory analysis and a vertically integrated moisture budget. Trajectory analysis reveals similar source regions for air parcels associated with drought development and breakdown, but with a shift toward more parcels originating over the Gulf of Mexico during transitions away from drought. The primary result from the vertically integrated moisture budget demonstrates that advection and convergence of moisture on intraseasonal time scales dominates during these transitions. The primary conclusion drawn is that weather events are the primary driver of agricultural drought transitions occurring over 20 and 60 days. The seasonal to sub-seasonal hindcast dataset is used to investigate the prediction of the low frequency, intraseasonal and synoptic circulation patterns associated with 20 and 60-day drought transition periods. The forecast models assessed are the European Centre for Medium Range Prediction (ECMWF), National Center for Environment Prediction Climate Forecast System (NCEP) and the Australian Bureau of Meteorology (BoM). Results demonstrate that ECMWF and NCEP are not skillful in

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

    PubMed

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

    2016-10-10

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

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

    NASA Astrophysics Data System (ADS)

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

    2018-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1994-03-01

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

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

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  20. Spectroscopic analysis of transition state energy levels - Bending-rotational spectrum and lifetime analysis of H3 quasibound states

    NASA Technical Reports Server (NTRS)

    Zhao, Meishan; Mladenovic, Mirjana; Truhlar, Donald G.; Schwenke, David W.; Sharafeddin, Omar

    1989-01-01

    Converged quantum mechanical calculations of scattering matrices and transition probabilities are reported for the reaction of H with H2 with total angular momentum 0, 1, and 4 as functions of total energy in the range 0.85-1.15 eV on an accurate potential energy surface. The resonance structure is illustrated with Argand diagrams. State-to-state reactive collision delay times and lifetimes are presented. For J = 0, 1, and 4, the lowest-energy H3 resonance is at total energies of 0.983, 0.985, and 1.01 eV, respectively, with lifetimes of about 16-17 fs. For J = 1 and 4 there is a higher-energy resonance at 1.10-1.11 eV. For J = 1 the lifetime is about 4 fs and for J = 4 it is about 1 fs.

  1. Investigation of transition States in bulk and freestanding film polymer glasses.

    PubMed

    Jain, Tushar S; de Pablo, Juan J

    2004-04-16

    We have performed transition state searches on the potential energy landscape for bulk and freestanding film polymer glasses and identified connected minima. An analysis of the displacements between minima shows that the sites that undergo the greatest displacement are highly localized in space for both the bulk and the thin-film systems studied. In the case of the thin film, the clusters originate at the surface and penetrate into the center of the film thereby coupling the relaxation in the center of the film to the mobile surface layer. Furthermore, the energy barriers between minima are lower in the thin film than in the bulk system. These findings can rationalize the experimentally observed depression of the glass transition temperature in freestanding polymer films.

  2. 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.

  3. Suppression of spin-state transition in epitaxially strained LaCoO3

    NASA Astrophysics Data System (ADS)

    Pinta, C.; Fuchs, D.; Merz, M.; Wissinger, M.; Arac, E.; v. Löhneysen, H.; Samartsev, A.; Nagel, P.; Schuppler, S.

    2008-11-01

    Epitaxial thin films of LaCoO3 (e-LCO) exhibit ferromagnetic order with a transition temperature TC=85K while polycrystalline thin LaCoO3 films (p-LCO) remain paramagnetic. The temperature-dependent spin-state structure for both e-LCO and p-LCO was studied by x-ray absorption spectroscopy at the CoL2,3 and OK edges. Considerable spectral redistributions over temperature are observed for p-LCO . The spectra for e-LCO , on the other hand, do not show any significant changes for temperatures between 30 and 450 K at both edges, indicating that the spin state remains constant and that the epitaxial strain inhibits any population of the low-spin (S=0) state with decreasing temperature. This observation identifies an important prerequisite for ferromagnetism in e-LCO thin films.

  4. Symptoms experienced during menopausal transition: Korean women in South Korea and the United States.

    PubMed

    Im, Eun-Ok

    2003-10-01

    This article reports on cultural influences on symptoms experienced during menopausal transition of Korean women in South Korea and Korean immigrant women in the United States. Data from independent studies of two groups of Korean women were triangulated and analyzed using descriptive and inferential statistics. The analysis indicated that Korean women in South Korea tended to report more symptoms than Korean immigrant women in the United States. Types and severity of prevalent symptoms were also found to be different between the two groups. The findings suggest that recent introduction of menopausal industries in South Korea and contextual influences on Korean women's work and immigration in the United States would be the reason for differences. Based on the findings, implications for future research are proposed.

  5. A method to decompose spectral changes in Synechocystis PCC 6803 during light-induced state transitions.

    PubMed

    Acuña, Alonso M; Kaňa, Radek; Gwizdala, Michal; Snellenburg, Joris J; van Alphen, Pascal; van Oort, Bart; Kirilovsky, Diana; van Grondelle, Rienk; van Stokkum, Ivo H M

    2016-12-01

    Cyanobacteria have developed responses to maintain the balance between the energy absorbed and the energy used in different pigment-protein complexes. One of the relatively rapid (a few minutes) responses is activated when the cells are exposed to high light intensities. This mechanism thermally dissipates excitation energy at the level of the phycobilisome (PB) antenna before it reaches the reaction center. When exposed to low intensities of light that modify the redox state of the plastoquinone pool, the so-called state transitions redistribute energy between photosystem I and II. Experimental techniques to investigate the underlying mechanisms of these responses, such as pulse-amplitude modulated fluorometry, are based on spectrally integrated signals. Previously, a spectrally resolved fluorometry method has been introduced to preserve spectral information. The analysis method introduced in this work allows to interpret SRF data in terms of species-associated spectra of open/closed reaction centers (RCs), (un)quenched PB and state 1 versus state 2. Thus, spectral differences in the time-dependent fluorescence signature of photosynthetic organisms under varying light conditions can be traced and assigned to functional emitting species leading to a number of interpretations of their molecular origins. In particular, we present evidence that state 1 and state 2 correspond to different states of the PB-PSII-PSI megacomplex.

  6. 19 CFR 123.65 - Domestic baggage transiting Canada or Mexico between ports in the United States.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 19 Customs Duties 1 2011-04-01 2011-04-01 false Domestic baggage transiting Canada or Mexico... PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CBP RELATIONS WITH CANADA AND MEXICO Baggage § 123.65 Domestic baggage transiting Canada or Mexico between ports in the United States. (a...

  7. 19 CFR 123.65 - Domestic baggage transiting Canada or Mexico between ports in the United States.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 19 Customs Duties 1 2013-04-01 2013-04-01 false Domestic baggage transiting Canada or Mexico... PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CBP RELATIONS WITH CANADA AND MEXICO Baggage § 123.65 Domestic baggage transiting Canada or Mexico between ports in the United States. (a...

  8. 19 CFR 123.65 - Domestic baggage transiting Canada or Mexico between ports in the United States.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 19 Customs Duties 1 2014-04-01 2014-04-01 false Domestic baggage transiting Canada or Mexico... PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CBP RELATIONS WITH CANADA AND MEXICO Baggage § 123.65 Domestic baggage transiting Canada or Mexico between ports in the United States. (a...

  9. 19 CFR 123.65 - Domestic baggage transiting Canada or Mexico between ports in the United States.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 19 Customs Duties 1 2012-04-01 2012-04-01 false Domestic baggage transiting Canada or Mexico... PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CBP RELATIONS WITH CANADA AND MEXICO Baggage § 123.65 Domestic baggage transiting Canada or Mexico between ports in the United States. (a...

  10. Powder keg divisions in the critical state regime: transition from continuous to explosive percolation

    NASA Astrophysics Data System (ADS)

    Zhou, Zongzheng; Tordesillas, Antoinette

    2017-06-01

    The underlying microstructure and dynamics of a dense granular material as it evolves towards the "critical state", a limit state in which the system deforms with an essentially constant volume and stress ratio, remains widely debated in the micromechanics of granular media community. Strain localization, a common mechanism in the large strain regime, further complicates the characterization of this limit state. Here we revisit the evolution to this limit state within the framework of modern percolation theory. Attention is paid to motion transfer: in this context, percolation translates to the emergence of a large-scale connectivity in graphs that embody information on individual grain displacements. We construct each graph G(r) by connecting nodes, representing the grains, within a distance r in the displacement-state-space. As r increases, we observe a percolation transition on G(r). The size of the jump discontinuity increases in the lead up to failure, indicating that the nature of percolation transition changes from continuous to explosive. We attribute this to the emergence of collective motion, which manifests in increasingly isolated communities in G(r). At the limit state, where the jump discontinuity is highest and invariant across the different unjamming cycles (drops in stress ratio), G(r) encapsulates multiple kinematically distinct communities that are mediated by nodes corresponding to those grains in the shear band. This finding casts light on the dual and opposing roles of the shear band: a mechanism that creates powder keg divisions in the sample, while simultaneously acting as a mechanical link that transfers motion through such subdivisions moving in relative rigid-body motion.

  11. Linking Pattern Formation and Alternative Stable States: Ecohydrologic Thresholds and Critical Transitions in the Everglades Peatlands

    NASA Astrophysics Data System (ADS)

    Heffernan, J. B.; Ross, M. S.; Sah, J. P.; Isherwood, E.; Cohen, M. J.

    2015-12-01

    Spatial patterning occurs in a variety of ecosystems, and is important for the functional properties of landscapes; for testing spatial models of ecological processes; and as an indicator of landscape condition and resilience. Theory suggests that regular patterns arise from coupled local- and landscape-scale feedbacks that can also create multiple stable landscape states. In the Florida Everglades, hydrologic modification has degraded much of the historically-extensive ridge-slough landscape, a patterned peatland mosaic with distinct, flow-parallel patches. However, in the Everglades and in general, the hypothesis that patterned landscapes have homogeneous alternative states has little direct empirical support. Here we use microtopographic and vegetative heterogeneity, and their relation to hydrologic conditions, to infer the existence of multiple landscape equilibria and identify the hydrologic thresholds for critical transitions between these states. Dual relationships between elevation variance and water depth, and bi-modal distributions of both elevation variance and plant community distinctness, are consistent with generic predictions of multiple states, and covariation between these measures suggests that microtopography is the leading indicator of landscape degradation. Furthermore, a simple ecohydrologic multiple-state model correctly predicts the hydrologic thresholds for persistence of distinct ridges and sloughs. Predicted ridge-slough elevation differences and their relation to water depth are much greater than observed in the contemporary Everglades, but correspond closely with historical observations of pre-drainage conditions. These multiple lines of evidence represent the broadest and most direct support for the link between regular spatial pattern and landscape-scale alternative states in any ecosystem, and suggest that other patterned landscapes could undergo sudden collapse in response to changing environmental conditions. Hydrologic thresholds

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

    NASA Astrophysics Data System (ADS)

    Lucarini, Valerio; Bódai, Tamás

    2017-07-01

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

  13. 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

  14. Altered Enthalpy-Entropy Compensation in Picomolar Transition State Analogues of Human Purine Nucleoside Phosphorylase†

    PubMed Central

    Edwards, Achelle A.; Mason, Jennifer M.; Clinch, Keith; Tyler, Peter C.; Evans, Gary B.; Schramm, Vern L.

    2009-01-01

    Human purine nucleoside phosphorylase (PNP) belongs to the trimeric class of PNPs and is essential for catabolism of deoxyguanosine. Genetic deficiency of PNP in humans causes a specific T-cell immune deficiency and transition state analogue inhibitors of PNP are in development for treatment of T-cell cancers and autoimmune disorders. Four generations of Immucillins have been developed, each of which contains inhibitors binding with picomolar affinity to human PNP. Full inhibition of PNP occurs upon binding to the first of three subunits and binding to subsequent sites occurs with negative cooperativity. In contrast, substrate analogue and product bind without cooperativity. Titrations of human PNP using isothermal calorimetery indicate that binding of a structurally rigid first-generation Immucillin (K d = 56 pM) is driven by large negative enthalpy values (ΔH = −21.2 kcal/mol) with a substantial entropic (-TΔS) penalty. The tightest-binding inhibitors (K d = 5 to 9 pM) have increased conformational flexibility. Despite their conformational freedom in solution, flexible inhibitors bind with high affinity because of reduced entropic penalties. Entropic penalties are proposed to arise from conformational freezing of the PNP·inhibitor complex with the entropy term dominated by protein dynamics. The conformationally flexible Immucillins reduce the system entropic penalty. Disrupting the ribosyl 5’-hydroxyl interaction of transition state analogues with PNP causes favorable entropy of binding. Tight binding of the seventeen Immucillins is characterized by large enthalpic contributions, emphasizing their similarity to the transition state. By introducing flexibility into the inhibitor structure, the enthalpy-entropy compensation pattern is altered to permit tighter binding. PMID:19425594

  15. Recycling nicotinamide. The transition-state structure of human nicotinamide phosphoribosyltransferase

    PubMed Central

    Burgos, Emmanuel S.; Vetticatt, Mathew J.; Schramm, Vern L.

    2013-01-01

    Human nicotinamide phosphoribosyltransferase (NAMPT) replenishes the NAD pool and controls the activities of sirtuins (SIRT), mono- and poly-(ADP-ribose) polymerases (PARP) and NAD nucleosidase (CD38). The nature of the enzymatic transition-state (TS) is central to understanding the function of NAMPT. We determined the TS structure for pyrophosphorolysis of nicotinamide mononucleotide (NMN) by kinetic isotope effects (KIEs). With the natural substrates, NMN and pyrophosphate (PPi), the intrinsic KIEs of [1′-14C], [1-15N], [1′-3H] and [2′-3H] are 1.047, 1.029, 1.154 and 1.093, respectively. A unique quantum computational approach was used for TS analysis that included structural elements of the catalytic site. Without constraints (e.g. imposed torsion angles), the theoretical and experimental data are in good agreement. The quantum-mechanical calculations incorporated a crucial catalytic site residue (D313), two magnesium atoms and coordinated water molecules. The transition state model predicts primary 14C, α-secondary 3H, β-secondary 3H and primary 15N KIE close to the experimental values. The analysis reveals significant ribocation character at the TS. The attacking PPi nucleophile is weakly interacting (rC-O = 2.60 Å) and the N-ribosidic C1′-N bond is highly elongated at the TS (rC-N = 2.35 Å), consistent with an ANDN mechanism. Together with the crystal structure of the NMN•PPi•Mg2•enzyme complex, the reaction coordinate is defined. The enzyme holds the nucleophile and leaving group in relatively fixed positions to create a reaction coordinate with C1′-anomeric migration from nicotinamide to the PPi. The transition state is reached by a 0.85 Å migration of C1′. PMID:23373462

  16. Evaluating transition state structures of vanadium-phosphatase protein complexes using shape analysis.

    PubMed

    Sánchez-Lombardo, Irma; Alvarez, Santiago; McLauchlan, Craig C; Crans, Debbie C

    2015-06-01

    Shape analysis of coordination complexes is well-suited to evaluate the subtle distortions in the trigonal bipyramidal (TBPY-5) geometry of vanadium coordinated in the active site of phosphatases and characterized by X-ray crystallography. Recent studies using the tau (τ) analysis support the assertion that vanadium is best described as a trigonal bipyramid, because this geometry is the ideal transition state geometry of the phosphate ester substrate hydrolysis (C.C. McLauchlan, B.J. Peters, G.R. Willsky, D.C. Crans, Coord. Chem. Rev. http://dx.doi.org/10.1016/j.ccr.2014.12.012 ; D.C. Crans, M.L. Tarlton, C.C. McLauchlan, Eur. J. Inorg. Chem. 2014, 4450-4468). Here we use continuous shape measures (CShM) analysis to investigate the structural space of the five-coordinate vanadium-phosphatase complexes associated with mechanistic transformations between the tetrahedral geometry and the five-coordinate high energy TBPY-5 geometry was discussed focusing on the protein tyrosine phosphatase 1B (PTP1B) enzyme. No evidence for square pyramidal geometries was observed in any vanadium-protein complexes. The shape analysis positioned the metal ion and the ligands in the active site reflecting the mechanism of the cleavage of the organic phosphate in a phosphatase. We identified the umbrella distortions to be directly on the reaction path between tetrahedral phosphate and the TBPY-5-types of high-energy species. The umbrella distortions of the trigonal bipyramid are therefore identified as being the most relevant types of transition state structures for the phosphoryl group transfer reactions for phosphatases and this may be related to the possibility that vanadium is an inhibitor for enzymes that support both exploded and five-coordinate transition states. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    NASA Astrophysics Data System (ADS)

    Chakrabarti, Bismayan; Birol, Turan; Haule, Kristjan

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

  18. The Welfare to Work Transition in the United States: Implications for Work-Related Learning

    NASA Astrophysics Data System (ADS)

    Fisher, James C.; Martin, Larry G.

    2000-11-01

    This paper summarizes the legislation upon which the current welfare-to-work transition in the United States is based and describes characteristics of the former welfare population from which various tiers of employment options have emerged: unsubsidized-employed workers, subsidized-employed workers, subsidized-unemployed recipients, and unsubsidized-unemployed individuals. It also discusses current program emphases, and presents a format for directions for future program development which includes academic programs, situated cognition programs, integrated literacy/occupational skills programs, and integrated literacy/soft skills training.

  19. Edge states and topological phase transitions in chains of dielectric nanoparticles

    SciT

    Kruk, Sergey; Slobozhanyuk, Alexey; Denkova, Denitza

    Recently introduced field of topological photonics aims to explore the concepts of topological insulators for novel phenomena in optics. Here polymeric chains of subwavelength silicon nanodisks are studied and it is demonstrated that these chains can support two types of topological edge modes based on magnetic and electric Mie resonances, and their topological properties are fully dictated by the spatial arrangement of the nanoparticles in the chain. Here, it is observed experimentally and described how theoretically topological phase transitions at the nanoscale define a change from trivial to nontrivial topological states when the edge mode is excited.

  20. Spin-State Transition in La1-xSrxCoO3 Single Crystals

    NASA Astrophysics Data System (ADS)

    Bhardwaj, S.; Prabhakaran, D.; Awasthi, A. M.

    2011-07-01

    We present a study of the thermal conductivity (κ), specific heat (Cp) and Raman spectra of La1-xSrxCoO3 (x = 0,0.1) single crystals. Both the specimens have low thermal conductivity and board Raman peaks, arising from strong scattering of phonons by lattice disorder, produced by (and doping-enhanced) spin-states admixture of the Co3+ ions. The thermal conductivity anomalously deviates from ˜1/T behaviour at high (room) temperatures, expected of an insulator. High-temperature specific heat reveals large decrease in the metal-insulator (M-I) transition temperature with Sr-doping.

  1. Highly tunable charge and spin transport in silicene junctions: phase transitions and half-metallic states.

    PubMed

    Mahdavifar, Maryam; Khoeini, Farhad

    2018-08-10

    We report peculiar charge and spin transport properties in S-shaped silicene junctions with the Kane-Mele tight-binding model. In this work, we investigate the effects of electric and exchange fields on the charge and spin transport properties. Our results show that by applying a perpendicular electric field, metal-semiconductor and also semimetal-semiconductor phase transitions occur in our systems. Furthermore, full spin current can be obtained in the structures, so the half-metallic states are observable. Our results enable us to control charge and spin currents and provide new opportunities and applications in silicene-based electronics, optoelectronics, and spintronics.

  2. Variational transition state theory for multidimensional activated rate processes in the presence of anisotropic friction

    NASA Astrophysics Data System (ADS)

    Berezhkovskii, Alexander M.; Frishman, Anatoli M.; Pollak, Eli

    1994-09-01

    Variational transition state theory (VTST) is applied to the study of the activated escape of a particle trapped in a multidimensional potential well and coupled to a heat bath. Special attention is given to the dependence of the rate constant on the friction coefficients in the case of anisotropic friction. It is demonstrated explicitly that both the traditional as well as the nontraditional scenarios for the particle escape are recovered uniformly within the framework of VTST. Effects such as saddle point avoidance and friction dependence of the activation energy are derived from VTST using optimized planar dividing surfaces.

  3. Radiationless Transitions and Excited-State Absorption of Low-Field Chromium Complexes in Solids

    DTIC Science & Technology

    1989-07-20

    host-lattice modes and, in the case of the scandium compound with 5 % chromium concentration, of the a and tIg 2g localized modes. The local-mode...Radiationless transitions and excited-state Final report I/I/86-5/31/89 absorption of low-field chromium complexes 6. PERFORMING ORG. REPORT NUMBER ( 1 in...complexes, chromium ; tunable lasers, high pressure,-photoluminescence 4. 26, AMTVrAC? (Cbm e @CAP N Igemem’ a IdoMit’ by block nambew) The continuation of a

  4. Edge states and topological phase transitions in chains of dielectric nanoparticles

    DOE PAGES

    Kruk, Sergey; Slobozhanyuk, Alexey; Denkova, Denitza; ...

    2017-01-12

    Recently introduced field of topological photonics aims to explore the concepts of topological insulators for novel phenomena in optics. Here polymeric chains of subwavelength silicon nanodisks are studied and it is demonstrated that these chains can support two types of topological edge modes based on magnetic and electric Mie resonances, and their topological properties are fully dictated by the spatial arrangement of the nanoparticles in the chain. Here, it is observed experimentally and described how theoretically topological phase transitions at the nanoscale define a change from trivial to nontrivial topological states when the edge mode is excited.

  5. Surface hopping, transition state theory and decoherence. I. Scattering theory and time-reversibility

    NASA Astrophysics Data System (ADS)

    Jain, Amber; Herman, Michael F.; Ouyang, Wenjun; Subotnik, Joseph E.

    2015-10-01

    We provide an in-depth investigation of transmission coefficients as computed using the augmented-fewest switches surface hopping algorithm in the low energy regime. Empirically, microscopic reversibility is shown to hold approximately. Furthermore, we show that, in some circumstances, including decoherence on top of surface hopping calculations can help recover (as opposed to destroy) oscillations in the transmission coefficient as a function of energy; these oscillations can be studied analytically with semiclassical scattering theory. Finally, in the spirit of transition state theory, we also show that transmission coefficients can be calculated rather accurately starting from the curve crossing point and running trajectories forwards and backwards.

  6. Transition from propagating localized states to spatiotemporal chaos in phase dynamics

    SciT

    Brand, H.R.; Deissler, R.J.; Brand, H.R.

    1998-10-01

    We study the nonlinear phase equation for propagating patterns. We investigate the transition from a propagating localized pattern to a space-filling spatiotemporally disordered pattern and discuss in detail to what extent there are propagating localized states that breathe in time periodically, quasiperiodically, and chaotically. Differences and similarities to the phenomena occurring for the quintic complex Ginzburg-Landau equation are elucidated. We also discuss for which experimentally accessible systems one could observe the phenomena described. {copyright} {ital 1998} {ital The American Physical Society}

  7. Building of Equations of State with Numerous Phase Transitions — Application to Bismuth

    NASA Astrophysics Data System (ADS)

    Heuzé, Olivier

    2006-07-01

    We propose an algorithm to build complete equation of state EOS including several solid/solid or solid/liquid phase transitions. Each phase has its own EOS and independent parameters. The phase diagram is deduced from the thermodynamic equilibrium assumption. Until now, such an approach was used in simple cases and limited to 2 or 3 phases. We have applied it in the general case to bismuth for which up to 13 phases have been identified. This study shows the great influence of binary mixtures and triple points properties in released isentropes after shock waves.

  8. Response to work transitions by United States Army personnel: effects of self-esteem, self-efficacy, and career resilience.

    PubMed

    Gowan, M A; Craft, S L; Zimmermann, R A

    2000-06-01

    This paper examined association of self-esteem, self-efficacy, and career resilience with the responses of 171 United States Army personnel making the transition to civilian jobs. Specifically, the study addresses whether personality traits are related to the appraisal of the transition from Army to civilian life and to how individuals plan to manage the transition to yield employment success. Self-esteem, self-efficacy, and career resilience were the personality variables examined. Only self-esteem and career resilience were related to harm appraisals of the transition. None of the personality variables were related to use of coping strategies. Limitations of the study and suggestions for research are provided.

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

    NASA Astrophysics Data System (ADS)

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

    2018-03-01

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

  10. Coupled superconducting qudit-resonator system: Energy spectrum, state population, and state transition under microwave drive

    NASA Astrophysics Data System (ADS)

    Liu, W. Y.; Xu, H. K.; Su, F. F.; Li, Z. Y.; Tian, Ye; Han, Siyuan; Zhao, S. P.

    2018-03-01

    Superconducting quantum multilevel systems coupled to resonators have recently been considered in some applications such as microwave lasing and high-fidelity quantum logical gates. In this work, using an rf-SQUID type phase qudit coupled to a microwave coplanar waveguide resonator, we study both theoretically and experimentally the energy spectrum of the system when the qudit level spacings are varied around the resonator frequency by changing the magnetic flux applied to the qudit loop. We show that the experimental result can be well described by a theoretical model that extends from the usual two-level Jaynes-Cummings system to the present four-level system. It is also shown that due to the small anharmonicity of the phase device a simplified model capturing the leading state interactions fits the experimental spectra very well. Furthermore we use the Lindblad master equation containing various relaxation and dephasing processes to calculate the level populations in the simpler qutrit-resonator system, which allows a clear understanding of the dynamics of the system under the microwave drive. Our results help to better understand and perform the experiments of coupled multilevel and resonator systems and can be applied in the case of transmon or Xmon qudits having similar anharmonicity to the present phase device.

  11. Large discrete jumps observed in the transition between Chern states in a ferromagnetic topological insulator

    PubMed Central

    Liu, Minhao; Wang, Wudi; Richardella, Anthony R.; Kandala, Abhinav; Li, Jian; Yazdani, Ali; Samarth, Nitin; Ong, N. Phuan

    2016-01-01

    A striking prediction in topological insulators is the appearance of the quantized Hall resistance when the surface states are magnetized. The surface Dirac states become gapped everywhere on the surface, but chiral edge states remain on the edges. In an applied current, the edge states produce a quantized Hall resistance that equals the Chern number C = ±1 (in natural units), even in zero magnetic field. This quantum anomalous Hall effect was observed by Chang et al. With reversal of the magnetic field, the system is trapped in a metastable state because of magnetic anisotropy. We investigate how the system escapes the metastable state at low temperatures (10 to 200 mK). When the dissipation (measured by the longitudinal resistance) is ultralow, we find that the system escapes by making a few very rapid transitions, as detected by large jumps in the Hall and longitudinal resistances. Using the field at which the initial jump occurs to estimate the escape rate, we find that raising the temperature strongly suppresses the rate. From a detailed map of the resistance versus gate voltage and temperature, we show that dissipation strongly affects the escape rate. We compare the observations with dissipative quantum tunneling predictions. In the ultralow dissipation regime, two temperature scales (T1 ~ 70 mK and T2 ~ 145 mK) exist, between which jumps can be observed. The jumps display a spatial correlation that extends over a large fraction of the sample. PMID:27482539

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

    PubMed Central

    Xiong, Ying; Zhan, Chang-Guo

    2010-01-01

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

  13. Proceedings of the First Landscape State-and-Transition Simulation Modeling Conference, June 14–16, 2011, Portland, Oregon

    Becky K. Kerns; Ayn J. Shlisky; Colin J. Daniel

    2012-01-01

    The first ever Landscape State-and-Transition Simulation Modeling Conference was held from June 14–16, 2011, in Portland Oregon. The conference brought together over 70 users of state-and-transition simulation modeling tools—the Vegetation Dynamics Development Tool (VDDT), the Tool for Exploratory Landscape Analysis (TELSA) and the Path Landscape Model. The goal of the...

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

    NASA Astrophysics Data System (ADS)

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

    2017-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2018-05-01

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

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

    PubMed Central

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

    2015-01-01

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

  17. A hyperactive transcriptional state marks genome reactivation at the mitosis–G1 transition

    PubMed Central

    Hsiung, Chris C.-S.; Bartman, Caroline R.; Huang, Peng; Ginart, Paul; Stonestrom, Aaron J.; Keller, Cheryl A.; Face, Carolyne; Jahn, Kristen S.; Evans, Perry; Sankaranarayanan, Laavanya; Giardine, Belinda; Hardison, Ross C.; Raj, Arjun; Blobel, Gerd A.

    2016-01-01

    During mitosis, RNA polymerase II (Pol II) and many transcription factors dissociate from chromatin, and transcription ceases globally. Transcription is known to restart in bulk by telophase, but whether de novo transcription at the mitosis–G1 transition is in any way distinct from later in interphase remains unknown. We tracked Pol II occupancy genome-wide in mammalian cells progressing from mitosis through late G1. Unexpectedly, during the earliest rounds of transcription at the mitosis–G1 transition, ∼50% of active genes and distal enhancers exhibit a spike in transcription, exceeding levels observed later in G1 phase. Enhancer–promoter chromatin contacts are depleted during mitosis and restored rapidly upon G1 entry but do not spike. Of the chromatin-associated features examined, histone H3 Lys27 acetylation levels at individual loci in mitosis best predict the mitosis–G1 transcriptional spike. Single-molecule RNA imaging supports that the mitosis–G1 transcriptional spike can constitute the maximum transcriptional activity per DNA copy throughout the cell division cycle. The transcriptional spike occurs heterogeneously and propagates to cell-to-cell differences in mature mRNA expression. Our results raise the possibility that passage through the mitosis–G1 transition might predispose cells to diverge in gene expression states. PMID:27340175

  18. A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition.

    PubMed

    Hsiung, Chris C-S; Bartman, Caroline R; Huang, Peng; Ginart, Paul; Stonestrom, Aaron J; Keller, Cheryl A; Face, Carolyne; Jahn, Kristen S; Evans, Perry; Sankaranarayanan, Laavanya; Giardine, Belinda; Hardison, Ross C; Raj, Arjun; Blobel, Gerd A

    2016-06-15

    During mitosis, RNA polymerase II (Pol II) and many transcription factors dissociate from chromatin, and transcription ceases globally. Transcription is known to restart in bulk by telophase, but whether de novo transcription at the mitosis-G1 transition is in any way distinct from later in interphase remains unknown. We tracked Pol II occupancy genome-wide in mammalian cells progressing from mitosis through late G1. Unexpectedly, during the earliest rounds of transcription at the mitosis-G1 transition, ∼50% of active genes and distal enhancers exhibit a spike in transcription, exceeding levels observed later in G1 phase. Enhancer-promoter chromatin contacts are depleted during mitosis and restored rapidly upon G1 entry but do not spike. Of the chromatin-associated features examined, histone H3 Lys27 acetylation levels at individual loci in mitosis best predict the mitosis-G1 transcriptional spike. Single-molecule RNA imaging supports that the mitosis-G1 transcriptional spike can constitute the maximum transcriptional activity per DNA copy throughout the cell division cycle. The transcriptional spike occurs heterogeneously and propagates to cell-to-cell differences in mature mRNA expression. Our results raise the possibility that passage through the mitosis-G1 transition might predispose cells to diverge in gene expression states. © 2016 Hsiung et al.; Published by Cold Spring Harbor Laboratory Press.

  19. Study of dipion transitions among Υ(3S), Υ(2S), and Υ(1S) states

    NASA Astrophysics Data System (ADS)

    Cronin-Hennessy, D.; Gao, K. Y.; Hietala, J.; Kubota, Y.; Klein, T.; Lang, B. W.; Poling, R.; Scott, A. W.; Smith, A.; Zweber, P.; Dobbs, S.; Metreveli, Z.; Seth, K. K.; Tomaradze, A.; Ernst, J.; Ecklund, K. M.; Severini, H.; Love, W.; Savinov, V.; Lopez, A.; Mehrabyan, S.; Mendez, H.; Ramirez, J.; Huang, G. S.; Miller, D. H.; Pavlunin, V.; Sanghi, B.; Shipsey, I. P. J.; Xin, B.; Adams, G. S.; Anderson, M.; Cummings, J. P.; Danko, I.; Hu, D.; Moziak, B.; Napolitano, J.; He, Q.; Insler, J.; Muramatsu, H.; Park, C. S.; Thorndike, E. H.; Yang, F.; Artuso, M.; Blusk, S.; Khalil, S.; Li, J.; Menaa, N.; Mountain, R.; Nisar, S.; Randrianarivony, K.; Sia, R.; Skwarnicki, T.; Stone, S.; Wang, J. C.; Bonvicini, G.; Cinabro, D.; Dubrovin, M.; Lincoln, A.; Pappas, S. P.; Weinstein, A. J.; Asner, D. M.; Edwards, K. W.; Naik, P.; Briere, R. A.; Ferguson, T.; Tatishvili, G.; Vogel, H.; Watkins, M. E.; Rosner, J. L.; Adam, N. E.; Alexander, J. P.; Cassel, D. G.; Duboscq, J. E.; Ehrlich, R.; Fields, L.; Galik, R. S.; Gibbons, L.; Gray, R.; Gray, S. W.; Hartill, D. L.; Heltsley, B. K.; Hertz, D.; Jones, C. D.; Kandaswamy, J.; Kreinick, D. L.; Kuznetsov, V. E.; Mahlke-Krüger, H.; Mohapatra, D.; Onyisi, P. U. E.; Patterson, J. R.; Peterson, D.; Pivarski, J.; Riley, D.; Ryd, A.; Sadoff, A. J.; Schwarthoff, H.; Shi, X.; Stroiney, S.; Sun, W. M.; Wilksen, T.; Athar, S. B.; Patel, R.; Yelton, J.; Rubin, P.; Cawlfield, C.; Eisenstein, B. I.; Karliner, I.; Kim, D.; Lowrey, N.; Selen, M.; White, E. J.; Wiss, J.; Mitchell, R. E.; Shepherd, M. R.; Besson, D.; Pedlar, T. K.

    2007-10-01

    We present measurements of decay matrix elements for hadronic transitions of the form Υ(nS)→Υ(mS)ππ, where (n,m)=(3,1),(2,1),(3,2). We reconstruct charged and neutral pion modes with the final state Upsilon decaying to either μ+μ- or e+e-. Dalitz plot distributions for the 12 decay modes are fit individually as well as jointly assuming isospin symmetry, thereby measuring the matrix elements of the decay amplitude. We observe and account for the anomaly previously noted in the dipion invariant mass distribution for the Υ(3S)→Υ(1S)ππ transition and obtain good descriptions of the dynamics of the decay using the most general decay amplitude allowed by partial conservation of the axial-vector current considerations. The fits further indicate that the Υ(2S)→Υ(1S)ππ and Υ(3S)→Υ(2S)ππ transitions also show the presence of terms in the decay amplitude that were previously ignored, although at a relatively suppressed level.

  20. Power law versus exponential state transition dynamics: application to sleep-wake architecture.

    PubMed

    Chu-Shore, Jesse; Westover, M Brandon; Bianchi, Matt T

    2010-12-02

    Despite the common experience that interrupted sleep has a negative impact on waking function, the features of human sleep-wake architecture that best distinguish sleep continuity versus fragmentation remain elusive. In this regard, there is growing interest in characterizing sleep architecture using models of the temporal dynamics of sleep-wake stage transitions. In humans and other mammals, the state transitions defining sleep and wake bout durations have been described with exponential and power law models, respectively. However, sleep-wake stage distributions are often complex, and distinguishing between exponential and power law processes is not always straightforward. Although mono-exponential distributions are distinct from power law distributions, multi-exponential distributions may in fact resemble power laws by appearing linear on a log-log plot. To characterize the parameters that may allow these distributions to mimic one another, we systematically fitted multi-exponential-generated distributions with a power law model, and power law-generated distributions with multi-exponential models. We used the Kolmogorov-Smirnov method to investigate goodness of fit for the "incorrect" model over a range of parameters. The "zone of mimicry" of parameters that increased the risk of mistakenly accepting power law fitting resembled empiric time constants obtained in human sleep and wake bout distributions. Recognizing this uncertainty in model distinction impacts interpretation of transition dynamics (self-organizing versus probabilistic), and the generation of predictive models for clinical classification of normal and pathological sleep architecture.

  1. 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

  2. A model for a transition from a quasicrystalline to a microcrystalline state

    NASA Astrophysics Data System (ADS)

    Coddens, G.; Launois, P.

    1991-07-01

    We propose a monoatomic model for a quasicrystal transition as observed recently in systems with icosahedral [3] and decagonal [5] symmetry. It is developed here for the case of decagonal symmetry and is inspired by the experimental results on the system Al-Cu-Co-Si [5,6]. The model goes beyond the purely geometrical description by an important physical aspect: the transition mediates through a single atomic jump distance such that only one unique double-well potential has to be invoked to describe it; in conformity with the symmetry there are 10 jump vectors. In the framework of the model, the microcrystalline state is energetically more favourable than a monocrystalline approximant phase. Nous proposons un modèle mono-atomique pour une transition quasicristal-microcristal du type de celles observées récemment dans des systèmes à symétrie icosaédrique [3] et décagonale [5]. Il est développé ici pour la symétrie décagonale et est inspiré par des résultats expérimentaux concernant l'alliage Al-Cu-Co-Si [5,6]. Le modèle va au-delà d'une description purement géometrique par un aspect physique important : la transition se fait via une seule distance de saut inter-atomique de telle sorte q'un seul double-puits de potentiel doit être pris en compte ; conformément à la symétrie, il y a 10 directions de saut. Dans le cadre du modèle, la phase microcristalline est énergétiquement favorisée par rapport à une phase approximante monocristalline.

  3. A molecular symmetry analysis of the electronic states and transition dipole moments for molecules with two torsional degrees of freedom

    SciT

    Obaid, R.; Applied Chemistry Department, Palestine Polytechnic University, Hebron, Palestine; Leibscher, M., E-mail: monika.leibscher@itp.uni-hannover.de

    2015-02-14

    We present a molecular symmetry analysis of electronic states and transition dipole moments for molecules which undergo large amplitude intramolecular torsions. The method is based on the correlation between the point group of the molecule at highly symmetric configurations and the molecular symmetry group. As an example, we determine the global irreducible representations of the electronic states and transition dipole moments for the quinodimethane derivative 2-[4-(cyclopenta-2,4-dien-1-ylidene)cyclohexa-2,5-dien-1-ylidene]-2H-1, 3-dioxole for which two torsional degrees of freedom can be activated upon photo-excitation and construct the resulting symmetry adapted transition dipole functions.

  4. An equation-of-state-meter of quantum chromodynamics transition from deep learning

    DOE PAGES

    Pang, Long-Gang; Zhou, Kai; Su, Nan; ...

    2018-01-15

    A primordial state of matter consisting of free quarks and gluons that existed in the early universe a few microseconds after the Big Bang is also expected to form in high-energy heavy-ion collisions. Determining the equation of state (EoS) of such a primordial matter is the ultimate goal of high-energy heavy-ion experiments. Here we use supervised learning with a deep convolutional neural network to identify the EoS employed in the relativistic hydrodynamic simulations of heavy ion collisions. High-level correlations of particle spectra in transverse momentum and azimuthal angle learned by the network act as an effective EoS-meter in deciphering themore » nature of the phase transition in quantum chromodynamics. Finally, such EoS-meter is model-independent and insensitive to other simulation inputs including the initial conditions for hydrodynamic simulations.« less

  5. An equation-of-state-meter of quantum chromodynamics transition from deep learning

    SciT

    Pang, Long-Gang; Zhou, Kai; Su, Nan

    A primordial state of matter consisting of free quarks and gluons that existed in the early universe a few microseconds after the Big Bang is also expected to form in high-energy heavy-ion collisions. Determining the equation of state (EoS) of such a primordial matter is the ultimate goal of high-energy heavy-ion experiments. Here we use supervised learning with a deep convolutional neural network to identify the EoS employed in the relativistic hydrodynamic simulations of heavy ion collisions. High-level correlations of particle spectra in transverse momentum and azimuthal angle learned by the network act as an effective EoS-meter in deciphering themore » nature of the phase transition in quantum chromodynamics. Finally, such EoS-meter is model-independent and insensitive to other simulation inputs including the initial conditions for hydrodynamic simulations.« less

  6. Negative parity states and some electromagnetic transition properties of even-odd erbium isotopes

    SciT

    Yazar, Harun Resit; Uluer, Ihsan

    2007-03-15

    The negative parity states and some electromagnetic transition properties of even-odd erbium isotopes ({sup 159,161,163,165}Er) were studied within the framework of the interacting boson-fermion model. The single fermion is assumed to be in one of the lh{sub 9/2},3p{sub 3/2},2f{sub 5/2}, and 3p{sub 1/2} single-particle orbits. It was found that the calculated negative parity state energy spectra of the even-odd erbium isotopes agree quite well with the experimental data. The B(E2) values were also calculated and compared with the experimental data.

  7. Anisotropy-driven transition from the Moore-Read state to quantum Hall stripes

    NASA Astrophysics Data System (ADS)

    Zhu, Zheng; Sodemann, Inti; Sheng, D. N.; Fu, Liang

    2017-05-01

    We investigate the nature of the quantum Hall liquid in a half-filled second Landau level (n =1 ) as a function of band mass anisotropy using numerical exact diagonalization and density matrix renormalization group methods. We find increasing the mass anisotropy induces a quantum phase transition from the Moore-Read state to a charge density wave state. By analyzing the energy spectrum, guiding center structure factors, and by adding weak pinning potentials, we show that this charge density wave is a unidirectional quantum Hall stripe, which has a periodicity of a few magnetic lengths and survives in the thermodynamic limit. We find smooth profiles for the guiding center occupation function that reveal the strong coupling nature of the array of chiral Luttinger liquids residing at the stripe edges.

  8. An equation-of-state-meter of quantum chromodynamics transition from deep learning.

    PubMed

    Pang, Long-Gang; Zhou, Kai; Su, Nan; Petersen, Hannah; Stöcker, Horst; Wang, Xin-Nian

    2018-01-15

    A primordial state of matter consisting of free quarks and gluons that existed in the early universe a few microseconds after the Big Bang is also expected to form in high-energy heavy-ion collisions. Determining the equation of state (EoS) of such a primordial matter is the ultimate goal of high-energy heavy-ion experiments. Here we use supervised learning with a deep convolutional neural network to identify the EoS employed in the relativistic hydrodynamic simulations of heavy ion collisions. High-level correlations of particle spectra in transverse momentum and azimuthal angle learned by the network act as an effective EoS-meter in deciphering the nature of the phase transition in quantum chromodynamics. Such EoS-meter is model-independent and insensitive to other simulation inputs including the initial conditions for hydrodynamic simulations.

  9. Nudged-elastic band method with two climbing images: Finding transition states in complex energy landscapes

    DOE PAGES

    Zarkevich, Nikolai A.; Johnson, Duane D.

    2015-01-09

    The nudged-elastic band (NEB) method is modified with concomitant two climbing images (C2-NEB) to find a transition state (TS) in complex energy landscapes, such as those with a serpentine minimal energy path (MEP). If a single climbing image (C1-NEB) successfully finds the TS, then C2-NEB finds it too. Improved stability of C2-NEB makes it suitable for more complex cases, where C1-NEB misses the TS because the MEP and NEB directions near the saddle point are different. Generally, C2-NEB not only finds the TS, but guarantees, by construction, that the climbing images approach it from the opposite sides along the MEP.more » In addition, C2-NEB provides an accuracy estimate from the three images: the highest-energy one and its climbing neighbors. C2-NEB is suitable for fixed-cell NEB and the generalized solid-state NEB.« less

  10. Valley-selective photon-dressed states in transition metal dichalcogenides

    NASA Astrophysics Data System (ADS)

    LaMountain, Trevor; Chen, Yen-Jung; Stanev, Teodor K.; Stern, Nathaniel P.

    2018-02-01

    When electronic excitations in a semiconductor interact with light, the relevant quasiparticles are hybrid lightmatter dressed states, or exciton-polaritons. In monolayer transition metal dichalcogenides, a class of 2D direct bandgap semiconductors, optical excitations selectively populate distinct momentum valleys with correlated spin projection. The combination of this spin-valley locking with photon dressed states can lead to new optical phenomena in these materials. We present spectroscopic measurements of valley-specific exciton-polaritons in monolayer 2D materials in distinct regimes. When a monolayer is embedded in a dielectric microcavity, strong coupling exciton-polaritons are achieved. Cavity-modified dynamics of the dressed states are inferred from emission. Polarization persists up to room temperature in monolayer MoS2, in contrast with bare material. We also show that distinct regimes of valley-polarized exciton-polaritons can be accessed with microcavity engineering by tuning system parameters such as cavity decay rate and exciton-photon coupling strength. Further, we report results showing that polarization-sensitive ultrafast spectroscopy can enable sensitive measurements of the valley optical Stark shift, a light-induced dressed state energy shift, in monolayer semiconductors such as WSe2 and MoS2. These findings demonstrate distinct approaches to manipulating the picosecond dynamics of valleysensitive dressed states in monolayer semiconductors.

  11. 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

  12. Post-transition state dynamics and product energy partitioning following thermal excitation of the F⋯HCH2CN transition state: Disagreement with experiment.

    PubMed

    Pratihar, Subha; Ma, Xinyou; Xie, Jing; Scott, Rebecca; Gao, Eric; Ruscic, Branko; Aquino, Adelia J A; Setser, Donald W; Hase, William L

    2017-10-14

    Born-Oppenheimer direct dynamics simulations were performed to study atomistic details of the F + CH 3 CN → HF + CH 2 CN H-atom abstraction reaction. The simulation trajectories were calculated with a combined M06-2X/MP2 algorithm utilizing the 6-311++G** basis set. The experiments were performed at 300 K, and assuming the accuracy of transition state theory (TST), the trajectories were initiated at the F⋯HCH 2 CN abstraction TS with a 300 K Boltzmann distribution of energy and directed towards products. Recrossing of the TS was negligible, confirming the accuracy of TST. HF formation was rapid, occurring within 0.014 ps of the trajectory initiation. The intrinsic reaction coordinate (IRC) for reaction involves rotation of HF about CH 2 CN and then trapping in the CH 2 CN⋯HF post-reaction potential energy well of ∼10 kcal/mol with respect to the HF + CH 2 CN products. In contrast to this IRC, five different trajectory types were observed: the majority proceeded by direct H-atom transfer and only 11% approximately following the IRC. The HF vibrational and rotational quantum numbers, n and J, were calculated when HF was initially formed and they increase as potential energy is released in forming the HF + CH 2 CN products. The population of the HF product vibrational states is only in qualitative agreement with experiment, with the simulations showing depressed and enhanced populations of the n = 1 and 2 states as compared to experiment. Simulations with an anharmonic zero-point energy constraint gave product distributions for relative translation, HF rotation, HF vibration, CH 2 CN rotation, and CH 2 CN vibration as 5%, 11%, 60%, 7%, and 16%, respectively. In contrast, the experimental energy partitioning percentages to HF rotation and vibration are 6% and 41%. Comparisons are made between the current simulation and those for other F + H-atom abstraction reactions. The simulation product energy partitioning and HF vibrational population for F + CH 3 CN

  13. Post-transition state dynamics and product energy partitioning following thermal excitation of the F⋯HCH2CN transition state: Disagreement with experiment

    NASA Astrophysics Data System (ADS)

    Pratihar, Subha; Ma, Xinyou; Xie, Jing; Scott, Rebecca; Gao, Eric; Ruscic, Branko; Aquino, Adelia J. A.; Setser, Donald W.; Hase, William L.

    2017-10-01

    Born-Oppenheimer direct dynamics simulations were performed to study atomistic details of the F + CH3CN → HF + CH2CN H-atom abstraction reaction. The simulation trajectories were calculated with a combined M06-2X/MP2 algorithm utilizing the 6-311++G** basis set. The experiments were performed at 300 K, and assuming the accuracy of transition state theory (TST), the trajectories were initiated at the F⋯HCH2CN abstraction TS with a 300 K Boltzmann distribution of energy and directed towards products. Recrossing of the TS was negligible, confirming the accuracy of TST. HF formation was rapid, occurring within 0.014 ps of the trajectory initiation. The intrinsic reaction coordinate (IRC) for reaction involves rotation of HF about CH2CN and then trapping in the CH2CN⋯HF post-reaction potential energy well of ˜10 kcal/mol with respect to the HF + CH2CN products. In contrast to this IRC, five different trajectory types were observed: the majority proceeded by direct H-atom transfer and only 11% approximately following the IRC. The HF vibrational and rotational quantum numbers, n and J, were calculated when HF was initially formed and they increase as potential energy is released in forming the HF + CH2CN products. The population of the HF product vibrational states is only in qualitative agreement with experiment, with the simulations showing depressed and enhanced populations of the n = 1 and 2 states as compared to experiment. Simulations with an anharmonic zero-point energy constraint gave product distributions for relative translation, HF rotation, HF vibration, CH2CN rotation, and CH2CN vibration as 5%, 11%, 60%, 7%, and 16%, respectively. In contrast, the experimental energy partitioning percentages to HF rotation and vibration are 6% and 41%. Comparisons are made between the current simulation and those for other F + H-atom abstraction reactions. The simulation product energy partitioning and HF vibrational population for F + CH3CN → HF + CH2CN

  14. Thermal isomerization of azobenzenes: on the performance of Eyring transition state theory

    NASA Astrophysics Data System (ADS)

    Rietze, Clemens; Titov, Evgenii; Lindner, Steven; Saalfrank, Peter

    2017-08-01

    The thermal Z\\to E (back-)isomerization of azobenzenes is a prototypical reaction occurring in molecular switches. It has been studied for decades, yet its kinetics is not fully understood. In this paper, quantum chemical calculations are performed to model the kinetics of an experimental benchmark system, where a modified azobenzene (AzoBiPyB) is embedded in a metal-organic framework (MOF). The molecule can be switched thermally from cis to trans, under solvent-free conditions. We critically test the validity of Eyring transition state theory for this reaction. As previously found for other azobenzenes (albeit in solution), good agreement between theory and experiment emerges for activation energies and activation free energies, already at a comparatively simple level of theory, B3LYP/6-31G* including dispersion corrections. However, theoretical Arrhenius prefactors and activation entropies are in qualitiative disagreement with experiment. Several factors are discussed that may have an influence on activation entropies, among them dynamical and geometric constraints (imposed by the MOF). For a simpler model—Z\\to E isomerization in azobenzene—a systematic test of quantum chemical methods from both density functional theory and wavefunction theory is carried out in the context of Eyring theory. Also, the effect of anharmonicities on activation entropies is discussed for this model system. Our work highlights capabilities and shortcomings of Eyring transition state theory and quantum chemical methods, when applied for the Z\\to E (back-)isomerization of azobenzenes under solvent-free conditions.

  15. Steady-state and transitional aerodynamic characteristics of a wing in simulated heavy rain

    NASA Technical Reports Server (NTRS)

    Campbell, Bryan A.; Bezos, Gaudy M.

    1989-01-01

    The steady-state and transient effects of simulated heavy rain on the subsonic aerodynamic characteristics of a wing model were determined in the Langley 14- by 22-Foot Subsonic Tunnel. The 1.29 foot chord wing was comprised of a NACA 23015 airfoil and had an aspect ratio of 6.10. Data were obtained while test variables of liquid water content, angle of attack, and trailing edge flap angle were parametrically varied at dynamic pressures of 10, 30, and 50 psf (i.e., Reynolds numbers of .76x10(6), 1.31x10(6), and 1.69x10(6)). The experimental results showed reductions in lift and increases in drag when in the simulated rain environment. Accompanying this was a reduction of the stall angle of attack by approximately 4 deg. The transient aerodynamic performance during transition from dry to wet steady-state conditions varied between a linear and a nonlinear transition.

  16. The nature of photoinduced phase transition and metastable states in vanadium dioxide

    PubMed Central

    Tao, Zhensheng; Zhou, Faran; Han, Tzong-Ru T.; Torres, David; Wang, Tongyu; Sepulveda, Nelson; Chang, Kiseok; Young, Margaret; Lunt, Richard R.; Ruan, Chong-Yu

    2016-01-01

    Photoinduced threshold switching processes that lead to bistability and the formation of metastable phases in photoinduced phase transition of VO2 are elucidated through ultrafast electron diffraction and diffusive scattering techniques with varying excitation wavelengths. We uncover two distinct regimes of the dynamical phase change: a nearly instantaneous crossover into an intermediate state and its decay led by lattice instabilities over 10 ps timescales. The structure of this intermediate state is identified to be monoclinic, but more akin to M2 rather than M1 based on structure refinements. The extinction of all major monoclinic features within just a few picoseconds at the above-threshold-level (~20%) photoexcitations and the distinct dynamics in diffusive scattering that represents medium-range atomic fluctuations at two photon wavelengths strongly suggest a density-driven and nonthermal pathway for the initial process of the photoinduced phase transition. These results highlight the critical roles of electron correlations and lattice instabilities in driving and controlling phase transformations far from equilibrium. PMID:27982066

  17. In-Situ Phase Transition Control in the Supercooled State for Robust Active Glass Fiber.

    PubMed

    Lv, Shichao; Cao, Maoqing; Li, Chaoyu; Li, Jiang; Qiu, Jianrong; Zhou, Shifeng

    2017-06-21

    The construction of a dopant-activated photonic composite is of great technological importance for various applications, including smart lighting, optical amplification, laser, and optical detection. The bonding arrangement around the introduced dopants largely determines the properties, yet it remains a daunting challenge to manipulate the local state of the matrix (i.e., phase) inside the transparent composite in a controllable manner. Here we demonstrate that the relaxation of the supercooled state enables in-situ phase transition control in glass. Benefiting from the unique local atom arrangement manner, the strategy offers the possibility for simultaneously tuning the chemical environment of the incorporated dopant and engineering the dopant-host interaction. This allows us to effectively activate the dopant with high efficiency (calculated as ∼100%) and profoundly enhance the dopant-host energy-exchange interaction. Our results highlight that the in-situ phase transition control in glass may provide new opportunities for fabrication of unusual photonic materials with intense broadband emission at ∼1100 nm and development of the robust optical detection unit with high compactness and broadband photon-harvesting capability (from X-ray to ultraviolet light).

  18. Engineering electrocatalytic activity in nanosized perovskite cobaltite through surface spin-state transition

    PubMed Central

    Zhou, Shiming; Miao, Xianbing; Zhao, Xu; Ma, Chao; Qiu, Yuhao; Hu, Zhenpeng; Zhao, Jiyin; Shi, Lei; Zeng, Jie

    2016-01-01

    The activity of electrocatalysts exhibits a strongly dependence on their electronic structures. Specifically, for perovskite oxides, Shao-Horn and co-workers have reported a correlation between the oxygen evolution reaction activity and the eg orbital occupation of transition-metal ions, which provides guidelines for the design of highly active catalysts. Here we demonstrate a facile method to engineer the eg filling of perovskite cobaltite LaCoO3 for improving the oxygen evolution reaction activity. By reducing the particle size to ∼80 nm, the eg filling of cobalt ions is successfully increased from unity to near the optimal configuration of 1.2 expected by Shao-Horn's principle. Consequently, the activity is significantly enhanced, comparable to those of recently reported cobalt oxides with eg∼1.2 configurations. This enhancement is ascribed to the emergence of spin-state transition from low-spin to high-spin states for cobalt ions at the surface of the nanoparticles, leading to more active sites with increased reactivity. PMID:27187067

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

    NASA Astrophysics Data System (ADS)

    Kanki, Takashi; Nagata, Masayoshi; Kagei, Yasuhiro

    2008-11-01

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

  20. The nature of photoinduced phase transition and metastable states in vanadium dioxide

    DOE PAGES

    Tao, Zhensheng; Zhou, Faran; Han, Tzong-Ru T.; ...

    2016-12-16

    Photoinduced threshold switching processes that lead to bistability and the formation of metastable phases in photoinduced phase transition of VO 2 are elucidated through ultrafast electron diffraction and diffusive scattering techniques with varying excitation wavelengths. We uncover two distinct regimes of the dynamical phase change: a nearly instantaneous crossover into an intermediate state and its decay led by lattice instabilities over 10 ps timescales. The structure of this intermediate state is identified to be monoclinic, but more akin to M 2 rather than M1 based on structure refinements. The extinction of all major monoclinic features within just a few picosecondsmore » at the above-threshold-level (~20%) photoexcitations and the distinct dynamics in diffusive scattering that represents medium-range atomic fluctuations at two photon wavelengths strongly suggest a density-driven and nonthermal pathway for the initial process of the photoinduced phase transition. These results highlight the critical roles of electron correlations and lattice instabilities in driving and controlling phase transformations far from equilibrium.« less

  1. Thermal isomerization of azobenzenes: on the performance of Eyring transition state theory.

    PubMed

    Rietze, Clemens; Titov, Evgenii; Lindner, Steven; Saalfrank, Peter

    2017-08-09

    The thermal [Formula: see text] (back-)isomerization of azobenzenes is a prototypical reaction occurring in molecular switches. It has been studied for decades, yet its kinetics is not fully understood. In this paper, quantum chemical calculations are performed to model the kinetics of an experimental benchmark system, where a modified azobenzene (AzoBiPyB) is embedded in a metal-organic framework (MOF). The molecule can be switched thermally from cis to trans, under solvent-free conditions. We critically test the validity of Eyring transition state theory for this reaction. As previously found for other azobenzenes (albeit in solution), good agreement between theory and experiment emerges for activation energies and activation free energies, already at a comparatively simple level of theory, B3LYP/6-31G * including dispersion corrections. However, theoretical Arrhenius prefactors and activation entropies are in qualitiative disagreement with experiment. Several factors are discussed that may have an influence on activation entropies, among them dynamical and geometric constraints (imposed by the MOF). For a simpler model-[Formula: see text] isomerization in azobenzene-a systematic test of quantum chemical methods from both density functional theory and wavefunction theory is carried out in the context of Eyring theory. Also, the effect of anharmonicities on activation entropies is discussed for this model system. Our work highlights capabilities and shortcomings of Eyring transition state theory and quantum chemical methods, when applied for the [Formula: see text] (back-)isomerization of azobenzenes under solvent-free conditions.

  2. Transitions between states of labor-force participation among older Israelis.

    PubMed

    Achdut, Leah; Tur-Sinai, Aviad; Troitsky, Rita

    2015-03-01

    The study examines the labor-force behavior of Israelis at older ages, focusing on the determinants of the transitions between states of labor-force participation between 2005 and 2010. The study uses panel data from the first two waves of the SHARE-Israel longitudinal survey. A multinomial logit model is used to examine the impact of sociodemographic characteristics, health state, and economic resources on labor-force transitions of people aged 50-67. The results emphasize the role of age and poor health in "pushing" older people out of the labor force or "keeping" them there. Spouse's participation is found to encourage individuals to leave the labor force or to refrain from joining it. However, living with a participating spouse is negatively associated with staying out of the labor force, consistent with the dominance of the complementarity of leisure effect found in the literature. Wealth as an economic resource available to individuals for retirement is also found to encourage individuals to leave the labor force or to refrain from joining it.

  3. The nature of photoinduced phase transition and metastable states in vanadium dioxide

    NASA Astrophysics Data System (ADS)

    Tao, Zhensheng; Zhou, Faran; Han, Tzong-Ru T.; Torres, David; Wang, Tongyu; Sepulveda, Nelson; Chang, Kiseok; Young, Margaret; Lunt, Richard R.; Ruan, Chong-Yu

    2016-12-01

    Photoinduced threshold switching processes that lead to bistability and the formation of metastable phases in photoinduced phase transition of VO2 are elucidated through ultrafast electron diffraction and diffusive scattering techniques with varying excitation wavelengths. We uncover two distinct regimes of the dynamical phase change: a nearly instantaneous crossover into an intermediate state and its decay led by lattice instabilities over 10 ps timescales. The structure of this intermediate state is identified to be monoclinic, but more akin to M2 rather than M1 based on structure refinements. The extinction of all major monoclinic features within just a few picoseconds at the above-threshold-level (~20%) photoexcitations and the distinct dynamics in diffusive scattering that represents medium-range atomic fluctuations at two photon wavelengths strongly suggest a density-driven and nonthermal pathway for the initial process of the photoinduced phase transition. These results highlight the critical roles of electron correlations and lattice instabilities in driving and controlling phase transformations far from equilibrium.

  4. High Pressure ZZ-Exchange NMR Reveals Key Features of Protein Folding Transition States.

    PubMed

    Zhang, Yi; Kitazawa, Soichiro; Peran, Ivan; Stenzoski, Natalie; McCallum, Scott A; Raleigh, Daniel P; Royer, Catherine A

    2016-11-23

    Understanding protein folding mechanisms and their sequence dependence requires the determination of residue-specific apparent kinetic rate constants for the folding and unfolding reactions. Conventional two-dimensional NMR, such as HSQC experiments, can provide residue-specific information for proteins. However, folding is generally too fast for such experiments. ZZ-exchange NMR spectroscopy allows determination of folding and unfolding rates on much faster time scales, yet even this regime is not fast enough for many protein folding reactions. The application of high hydrostatic pressure slows folding by orders of magnitude due to positive activation volumes for the folding reaction. We combined high pressure perturbation with ZZ-exchange spectroscopy on two autonomously folding protein domains derived from the ribosomal protein, L9. We obtained residue-specific apparent rates at 2500 bar for the N-terminal domain of L9 (NTL9), and rates at atmospheric pressure for a mutant of the C-terminal domain (CTL9) from pressure dependent ZZ-exchange measurements. Our results revealed that NTL9 folding is almost perfectly two-state, while small deviations from two-state behavior were observed for CTL9. Both domains exhibited large positive activation volumes for folding. The volumetric properties of these domains reveal that their transition states contain most of the internal solvent excluded voids that are found in the hydrophobic cores of the respective native states. These results demonstrate that by coupling it with high pressure, ZZ-exchange can be extended to investigate a large number of protein conformational transitions.

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

    PubMed Central

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

    2011-01-01

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

  6. Cosmological implications of the transition from the false vacuum to the true vacuum state

    NASA Astrophysics Data System (ADS)

    Stachowski, Aleksander; Szydłowski, Marek; Urbanowski, Krzysztof

    2017-06-01

    We study cosmology with running dark energy. The energy density of dark energy is obtained from the quantum process of transition from the false vacuum state to the true vacuum state. We use the Breit-Wigner energy distribution function to model the quantum unstable systems and obtain the energy density of the dark energy parametrization ρ _ {de}(t). We also use Krauss and Dent's idea linking properties of the quantum mechanical decay of unstable states with the properties of the observed Universe. In the cosmological model with this parametrization there is an energy transfer between dark matter and dark energy. The intensity of this process, measured by a parameter α , distinguishes two scenarios. As the Universe starts from the false vacuum state, for the small value of α (0<α <0.4) it goes through an intermediate oscillatory (quantum) regime of the density of dark energy, while for α > 0.4 the density of the dark energy jumps down. In both cases the present value of the density of dark energy is reached. From a statistical analysis we find this model to be in good agreement with the astronomical data and practically indistinguishable from the Λ CDM model.

  7. Field-induced magnetic phase transitions and metastable states in Tb3Ni

    NASA Astrophysics Data System (ADS)

    Gubkin, A. F.; Wu, L. S.; Nikitin, S. E.; Suslov, A. V.; Podlesnyak, A.; Prokhnenko, O.; Prokeš, K.; Yokaichiya, F.; Keller, L.; Baranov, N. V.

    2018-04-01

    In this paper we report the detailed study of magnetic phase diagrams, low-temperature magnetic structures, and the magnetic field effect on the electrical resistivity of the binary intermetallic compound Tb3Ni . The incommensurate magnetic structure of the spin-density-wave type described with magnetic superspace group P 1121/a 1'(a b 0 ) 0 s s and propagation vector kIC=[" close="]1/2 ,1/2 ,0 ]">0.506 ,0.299 ,0 was found to emerge just below Néel temperature TN=61 K. Further cooling below 58 K results in the appearance of multicomponent magnetic states: (i) a combination of k1=[1/2 ,0 ,0 ] below 48 K. An external magnetic field suppresses the complex low-temperature antiferromagnetic states and induces metamagnetic transitions towards a forced ferromagnetic state that are accompanied by a substantial magnetoresistance effect due to the magnetic superzone effect. The forced ferromagnetic state induced after application of an external magnetic field along the b and c crystallographic axes was found to be irreversible below 3 and 8 K, respectively.

  8. 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

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

    PubMed

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

    2014-12-09

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

  10. 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.

  11. Thermodynamics and kinetics of protein folding on the ribosome: Alteration in energy landscapes, denatured state, and transition state ensembles

    NASA Astrophysics Data System (ADS)

    O'Brien, Edward; Vendruscolo, Michele; Dobson, Christopher

    2010-03-01

    In vitro experiments examining cotranslational folding utilize ribosome-nascent chain complexes (RNCs) in which the nascent chain is stalled at different points of its biosynthesis on the ribosome. We investigate the thermodynamics, kinetics, and structural properties of RNCs containing five different globular and repeat proteins stalled at ten different nascent chain lengths using coarse grained replica exchange simulations. We find that when the proteins are stalled near the ribosome exit tunnel opening they exhibit altered folding coopserativity, quantified by the van't Hoff enthalpy criterion; a significantly altered denatured state ensemble, in terms of Rg and shape parameters (Rg tensor); and the appearance of partially folded intermediates during cotranslation, evidenced by the appearance of a third basin in the free energy profile. These trends are due in part to excluded volume (crowding) interactions between the ribosome and nascent chain. We perform in silico temperature-jump experiments on the RNCs and examine nascent chain folding kinetics and structural changes in the transition state ensemble at various stall lengths.

  12. Study on the spectroscopic parameters and transition probabilities of 25 low-lying states of the AlC+ cation

    NASA Astrophysics Data System (ADS)

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

    2017-11-01

    This paper investigates the spectroscopic parameters and transition probabilities of 25 low-lying states, which come from the first five dissociation channels of AlC+ cation. The potential energy curves are calculated with the complete active space self-consistent field method, which is followed by the valence internally contracted multireference configuration interaction approach with Davidson correction. Of these 25 states, only the 35Σ-state is repulsive; the c1Σ+, f1Π, and 15Π states have the double well; the first well of c1Σ+ state and the second well of 15Π state are very weakly bound; the first well of c1Σ+ state has no vibrational levels; the 25Π state and the double well of f1Π state have only several vibrational states; the B3Σ-, E3Σ+, D3Π, 15Σ+, 25Σ-, and 15Π states are inverted when the spin-orbit coupling effect is included. The avoided crossings exist between the B3Σ- and 33Σ- states, the c1Σ+ and d1Σ+ states, the f1Π and 31Π states, the 15Π and 25Π states, as well as the 25Π and 35Π states. Core-valence correlation and scalar relativistic corrections are considered. The extrapolation of potential energies to the complete basis set limit is done. The spectroscopic parameters and vibrational levels are determined for all the Λ-S and Ω bound states. The transition dipole moments are calculated. Franck-Condon factors of a great number of electronic transitions are evaluated. On the whole, the spin-orbit coupling effect on the spectroscopic parameters and vibrational levels is small except for very few states. The results determined in this paper could provide some powerful guidelines to observe these states in a spectroscopy experiment.

  13. A Search for Transitions between States in Redbacks and Black Widows Using Seven Years of Fermi-LAT Observations

    DOE PAGES

    Torres, Diego F.; Ji, Long; Li, Jian; ...

    2017-02-08

    Considering about seven years of Fermi-Large Area Telescope (LAT) data, we present a systematic search for variability that is possibly related to transitions between states in redbacks and black widow systems. In addition, the transitions are characterized by sudden and significant changes in the gamma-ray flux that persist on a timescale that is much larger than the orbital period. This phenomenology was already detected in the case of two redback systems, PSR J1023+0038 and PSR J1227-4853, which we present here. We show the existence of only one transition for each of these systems over the past seven years. We determinemore » their spectra, establishing high-energy cutoffs at a few GeV for the high gamma-ray state of PSR J1023+0038, and for both states of PSR J1227-4853. The surveying capability of the Fermi-LAT allows further study of whether similar phenomenology has occurred in other sources. Although we have not found any evidence of a state transition for most of the studied pulsars, we note two black-widow systems, PSR J2234+0944 and PSR J1446-4701, whose apparent variabilities are reminiscent of the transitions in PSR J1023+0038 and PSR J1227-4853. Finally, for the other systems, we set limits on potential transitions in their measured gamma-ray light curves.« less

  14. A Search for Transitions between States in Redbacks and Black Widows Using Seven Years of Fermi-LAT Observations

    SciT

    Torres, Diego F.; Ji, Long; Li, Jian

    Considering about seven years of Fermi-Large Area Telescope (LAT) data, we present a systematic search for variability that is possibly related to transitions between states in redbacks and black widow systems. In addition, the transitions are characterized by sudden and significant changes in the gamma-ray flux that persist on a timescale that is much larger than the orbital period. This phenomenology was already detected in the case of two redback systems, PSR J1023+0038 and PSR J1227-4853, which we present here. We show the existence of only one transition for each of these systems over the past seven years. We determinemore » their spectra, establishing high-energy cutoffs at a few GeV for the high gamma-ray state of PSR J1023+0038, and for both states of PSR J1227-4853. The surveying capability of the Fermi-LAT allows further study of whether similar phenomenology has occurred in other sources. Although we have not found any evidence of a state transition for most of the studied pulsars, we note two black-widow systems, PSR J2234+0944 and PSR J1446-4701, whose apparent variabilities are reminiscent of the transitions in PSR J1023+0038 and PSR J1227-4853. Finally, for the other systems, we set limits on potential transitions in their measured gamma-ray light curves.« less

  15. A Search for Transitions between States in Redbacks and Black Widows Using Seven Years of Fermi -LAT Observations

    SciT

    Torres, Diego F.; Li, Jian; Rea, Nanda

    Considering about seven years of Fermi -Large Area Telescope (LAT) data, we present a systematic search for variability that is possibly related to transitions between states in redbacks and black widow systems. The transitions are characterized by sudden and significant changes in the gamma-ray flux that persist on a timescale that is much larger than the orbital period. This phenomenology was already detected in the case of two redback systems, PSR J1023+0038 and PSR J1227−4853, which we present here. We show the existence of only one transition for each of these systems over the past seven years. We determine theirmore » spectra, establishing high-energy cutoffs at a few GeV for the high gamma-ray state of PSR J1023+0038, and for both states of PSR J1227−4853. The surveying capability of the Fermi -LAT allows further study of whether similar phenomenology has occurred in other sources. Although we have not found any evidence of a state transition for most of the studied pulsars, we note two black-widow systems, PSR J2234+0944 and PSR J1446−4701, whose apparent variabilities are reminiscent of the transitions in PSR J1023+0038 and PSR J1227−4853. For the other systems, we set limits on potential transitions in their measured gamma-ray light curves.« less

  16. Molecular water oxidation mechanisms followed by transition metals: state of the art.

    PubMed

    Sala, Xavier; Maji, Somnath; Bofill, Roger; García-Antón, Jordi; Escriche, Lluís; Llobet, Antoni

    2014-02-18

    One clean alternative to fossil fuels would be to split water using sunlight. However, to achieve this goal, researchers still need to fully understand and control several key chemical reactions. One of them is the catalytic oxidation of water to molecular oxygen, which also occurs at the oxygen evolving center of photosystem II in green plants and algae. Despite its importance for biology and renewable energy, the mechanism of this reaction is not fully understood. Transition metal water oxidation catalysts in homogeneous media offer a superb platform for researchers to investigate and extract the crucial information to describe the different steps involved in this complex reaction accurately. The mechanistic information extracted at a molecular level allows researchers to understand both the factors that govern this reaction and the ones that derail the system to cause decomposition. As a result, rugged and efficient water oxidation catalysts with potential technological applications can be developed. In this Account, we discuss the current mechanistic understanding of the water oxidation reaction catalyzed by transition metals in the homogeneous phase, based on work developed in our laboratories and complemented by research from other groups. Rather than reviewing all of the catalysts described to date, we focus systematically on the several key elements and their rationale from molecules studied in homogeneous media. We organize these catalysts based on how the crucial oxygen-oxygen bond step takes place, whether via a water nucleophilic attack or via the interaction of two M-O units, rather than based on the nuclearity of the water oxidation catalysts. Furthermore we have used DFT methodology to characterize key intermediates and transition states. The combination of both theory and experiments has allowed us to get a complete view of the water oxidation cycle for the different catalysts studied. Finally, we also describe the various deactivation pathways for

  17. Genetic ablation of hypocretin neurons alters behavioral state transitions in zebrafish.

    PubMed

    Elbaz, Idan; Yelin-Bekerman, Laura; Nicenboim, Julian; Vatine, Gad; Appelbaum, Lior

    2012-09-12

    Sleep is an essential biological need of all animals studied to date. The sleep disorder narcolepsy is characterized by excessive daytime sleepiness, fragmentation of nighttime sleep, and cataplexy. Narcolepsy is caused by selective degeneration of hypothalamic hypocretin/orexin (HCRT) neurons. In mammals, HCRT neurons primarily regulate the sleep/wake cycle, feeding, reward-seeking, and addiction. The role of HCRT neurons in zebrafish is implicated in both sleep and wake regulation. We established a transgenic zebrafish model enabling inducible ablation of HCRT neurons and used these animals to understand the function of HCRT neurons and narcolepsy. Loss of HCRT neurons increased the expression of the HCRT receptor (hcrtr). Behavioral assays revealed that HCRT neuron-ablated larvae had normal locomotor activity, but demonstrated an increase in sleep time during the day and an increased number of sleep/wake transitions during both day and night. Mild sleep disturbance reduced sleep and increased c-fos expression in HCRT neuron-ablated larvae. Furthermore, ablation of HCRT neurons altered the behavioral response to external stimuli. Exposure to light during the night decreased locomotor activity of wild-type siblings, but induced an opposite response in HCRT neuron-ablated larvae. Sound stimulus during the day reduced the locomotor activity of wild-type sibling larvae, while HCRT neuron-ablated larvae demonstrated a hyposensitive response. This study establishes zebrafish as a model for narcolepsy, and indicating a role of HCRT neurons in regulation of sleep/wake transitions during both day and night. Our results further suggest a key role of HCRT neurons in mediating behavioral state transitions in response to external stimuli.

  18. Improving the effectiveness of ecological site descriptions: General state-and-transition models and the Ecosystem Dynamics Interpretive Tool (EDIT)

    State-and-transition models (STMs) were conceived as a means to organize and communicate information about ecosystem changes and how to manage them. Information within STMs applies to ecological land classes, such as ecological sites, that possess similar vegetation states. The value of STMs for ran...

  19. State and transition models: Theory, applications, and challenges. In: Briske, D.D. Rangeland Systems: Processes, Management and Challenges

    State and transition models (STMs) are used for communicating about ecosystem change in rangelands and other ecosystems, especially the implications for management. The fundamental premise that rangelands can exhibit multiple states is now widely accepted. The current application of STMs for managem...

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

    PubMed

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

    2015-10-01

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

  1. Calculating Transition Energy Barriers and Characterizing Activation States for Steps of Fusion

    PubMed Central

    Ryham, Rolf J.; Klotz, Thomas S.; Yao, Lihan; Cohen, Fredric S.

    2016-01-01

    We use continuum mechanics to calculate an entire least energy pathway of membrane fusion, from stalk formation, to pore creation, and through fusion pore enlargement. The model assumes that each structure in the pathway is axially symmetric. The static continuum stalk structure agrees quantitatively with experimental stalk architecture. Calculations show that in a stalk, the distal monolayer is stretched and the stored stretching energy is significantly less than the tilt energy of an unstretched distal monolayer. The string method is used to determine the energy of the transition barriers that separate intermediate states and the dynamics of two bilayers as they pass through them. Hemifusion requires a small amount of energy independently of lipid composition, while direct transition from a stalk to a fusion pore without a hemifusion intermediate is highly improbable. Hemifusion diaphragm expansion is spontaneous for distal monolayers containing at least two lipid components, given sufficiently negative diaphragm spontaneous curvature. Conversely, diaphragms formed from single-component distal monolayers do not expand without the continual injection of energy. We identify a diaphragm radius, below which central pore expansion is spontaneous. For larger diaphragms, prior studies have shown that pore expansion is not axisymmetric, and here our calculations supply an upper bound for the energy of the barrier against pore formation. The major energy-requiring deformations in the steps of fusion are: widening of a hydrophobic fissure in bilayers for stalk formation, splay within the expanding hemifusion diaphragm, and fissure widening initiating pore formation in a hemifusion diaphragm. PMID:26958888

  2. Prioritizing bird conservation actions in the Prairie Hardwood transition of the Midwestern United States

    Thogmartin, Wayne E.; Crimmins, Shawn M.; Pearce, Jennie

    2014-01-01

    Large-scale planning for the conservation of species is often hindered by a poor understanding of factors limiting populations. In regions with declining wildlife populations, it is critical that objective metrics of conservation success are developed to ensure that conservation actions achieve desired results. Using spatially explicit estimates of bird abundance, we evaluated several management alternatives for conserving bird populations in the Prairie Hardwood Transition of the United States. We designed landscapes conserving species at 50% of their current predicted abundance as well as landscapes attempting to achieve species population targets (which often required the doubling of current abundance). Conserving species at reduced (half of current) abundance led to few conservation conflicts. However, because of extensive modification of the landscape to suit human use, strategies for achieving regional population targets for forest bird species would be difficult under even ideal circumstances, and even more so if maintenance of grassland bird populations is also desired. Our results indicated that large-scale restoration of agricultural lands to native grassland and forest habitats may be the most productive conservation action for increasing bird population sizes but the level of landscape transition required to approach target bird population sizes may be societally unacceptable.

  3. Theoretical Investigation of the Electronic Structure of Fe(II) Complexes at Spin-State Transitions

    PubMed Central

    2013-01-01

    The electronic structure relevant to low spin (LS)↔high spin (HS) transitions in Fe(II) coordination compounds with a FeN6 core are studied. The selected [Fe(tz)6]2+ (1) (tz = 1H-tetrazole), [Fe(bipy)3]2+ (2) (bipy = 2,2′-bipyridine), and [Fe(terpy)2]2+ (3) (terpy = 2,2′:6′,2″-terpyridine) complexes have been actively studied experimentally, and with their respective mono-, bi-, and tridentate ligands, they constitute a comprehensive set for theoretical case studies. The methods in this work include density functional theory (DFT), time-dependent DFT (TD-DFT), and multiconfigurational second order perturbation theory (CASPT2). We determine the structural parameters as well as the energy splitting of the LS–HS states (ΔEHL) applying the above methods and comparing their performance. We also determine the potential energy curves representing the ground and low-energy excited singlet, triplet, and quintet d6 states along the mode(s) that connect the LS and HS states. The results indicate that while DFT is well suited for the prediction of structural parameters, an accurate multiconfigurational approach is essential for the quantitative determination of ΔEHL. In addition, a good qualitative agreement is found between the TD-DFT and CASPT2 potential energy curves. Although the TD-DFT results might differ in some respect (in our case, we found a discrepancy at the triplet states), our results suggest that this approach, with due care, is very promising as an alternative for the very expensive CASPT2 method. Finally, the two-dimensional (2D) potential energy surfaces above the plane spanned by the two relevant configuration coordinates in [Fe(terpy)2]2+ were computed at both the DFT and CASPT2 levels. These 2D surfaces indicate that the singlet–triplet and triplet–quintet states are separated along different coordinates, i.e., different vibration modes. Our results confirm that in contrast to the case of complexes with mono- and bidentate ligands, the

  4. Post-transition state dynamics and product energy partitioning following thermal excitation of the F∙∙∙HCH 2 CN transition state: Disagreement with experiment

    SciT

    Pratihar, Subha; Ma, Xinyou; Xie, Jing

    Born-Oppenheimer direct dynamics simulations were performed to study atomistic details of the F + CH 3CN → HF + CH 2CN H-atom abstraction reaction. The simulation trajectories were calculated with a combined M06-2X/MP2 algorithm utilizing the 6-311++G** basis set. In accord with experiment and assuming the accuracy of transition state theory (TST), the trajectories were initiated at the F-HCH 2CN abstraction TS with a 300 K Boltzmann distribution of energy and directed towards products. Recrossing of the TS was negligible, confirming the accuracy of TST for the simulation. HF formation was rapid, occurring within 0.014 ps of the trajectory initiation.more » The intrinsic reaction coordinate (IRC) for reaction involves rotation of HF about CH 2CN and then trapping in the CH 2CN-HF post-reaction potential energy well of ~10 kcal/mol with respect to the HF + CH 2CN products. In contrast to this IRC, five different trajectory types were observed, with the majority involving direct dissociation and only 11% approximately following the IRC. The HF vibrational and rotational quantum numbers, n and J, were calculated when HF was initially formed and they increase as potential energy is released in forming the HF + CH 2CN products. The population of the HF product vibrational states is only in qualitative agreement with experiment, with the simulations showing depressed and enhanced populations of the n = 1 and 2 states as compared to experiment. From the simulations and with an anharmonic zero-point energy constraint, the percentage partitioning of the product energy to relative translation, HF rotation, HF vibration, CH 2CN rotation and CH 2CN vibration is 5, 11, 60, 7, and 16%, respectively. In contrast the experimental energy partitioning percentages to HF rotation and vibration are 6 and 41%. Comparisons are made between the current simulation and those for other F + H-atom abstraction reactions. The simulation product energy partitioning and HF vibrational

  5. Test of the Chevallier-Polarski-Linder parametrization for rapid dark energy equation of state transitions

    NASA Astrophysics Data System (ADS)

    Linden, Sebastian; Virey, Jean-Marc

    2008-07-01

    We test the robustness and flexibility of the Chevallier-Polarski-Linder (CPL) parametrization of the dark energy equation of state w(z)=w0+wa(z)/(1+z) in recovering a four-parameter steplike fiducial model. We constrain the parameter space region of the underlying fiducial model where the CPL parametrization offers a reliable reconstruction. It turns out that non-negligible biases leak into the results for recent (z<2.5) rapid transitions, but that CPL yields a good reconstruction in all other cases. The presented analysis is performed with supernova Ia data as forecasted for a space mission like SNAP/JDEM, combined with future expectations for the cosmic microwave background shift parameter R and the baryonic acoustic oscillation parameter A.

  6. Alpha-decay-induced fracturing in zircon - The transition from the crystalline to the metamict state

    NASA Technical Reports Server (NTRS)

    Chakoumakos, Bryan C.; Murakami, Takashi; Lumpkin, Gregory R.; Ewing, Rodney C.

    1987-01-01

    Zonation due to alpha-decay damage in a natural single crystal of zircon from Sri Lanka is discussed. The zones vary in thickness on a scale from one to hundreds of microns. The uranium and thorium concentrations vary from zone to zone such that the alpha decay dose is between 0.2 x 10 to the 16th and 0.8 x 10 to the 16th alpha-events per milligram. The transition from the crystalline to the aperiodic metamict state occurs over this dose range. At doses greater than 0.8 x 10 to the 16th alpha events/mg there is no evidence for long-range order. This type of damage will accumulate in actinide-bearing, ceramic nuclear waste forms. The systematic pattern of fractures would occur in crystalline phases that are zoned with respect to actinide radionuclides.

  7. Surface-Plasmon-Mediated Gradient Force Enhancement and Mechanical State Transitions of Graphene Sheets

    SciT

    Zhang, Peng; Shen, Nian-Hai; Koschny, Thomas

    Graphene, a two-dimensional material possessing extraordinary properties in electronics as well as mechanics, provides a great platform for various optoelectronic and opto-mechanical devices. Here in this article, we theoretically study the optical gradient force arising from the coupling of surface plasmon modes on parallel graphene sheets, which can be several orders stronger than that between regular dielectric waveguides. Furthermore, with an energy functional optimization model, possible force-induced deformation of graphene sheets is calculated. We show that the significantly enhanced optical gradient force may lead to mechanical state transitions of graphene sheets, which are accompanied by abrupt changes in reflection andmore » transmission spectra of the system. Our demonstrations illustrate the potential for a broader graphene-related applications such as force sensors and actuators.« less

  8. Surface-Plasmon-Mediated Gradient Force Enhancement and Mechanical State Transitions of Graphene Sheets

    DOE PAGES

    Zhang, Peng; Shen, Nian-Hai; Koschny, Thomas; ...

    2016-12-16

    Graphene, a two-dimensional material possessing extraordinary properties in electronics as well as mechanics, provides a great platform for various optoelectronic and opto-mechanical devices. Here in this article, we theoretically study the optical gradient force arising from the coupling of surface plasmon modes on parallel graphene sheets, which can be several orders stronger than that between regular dielectric waveguides. Furthermore, with an energy functional optimization model, possible force-induced deformation of graphene sheets is calculated. We show that the significantly enhanced optical gradient force may lead to mechanical state transitions of graphene sheets, which are accompanied by abrupt changes in reflection andmore » transmission spectra of the system. Our demonstrations illustrate the potential for a broader graphene-related applications such as force sensors and actuators.« less

  9. 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

  10. Realizing high-quality ultralarge momentum states and ultrafast topological transitions using semiconductor hyperbolic metamaterials

    DOE PAGES

    Campione, Salvatore; Liu, Sheng; Luk, Ting S.; ...

    2015-08-05

    We employ both the effective medium approximation (EMA) and Bloch theory to compare the dispersion properties of semiconductor hyperbolic metamaterials (SHMs) at mid-infrared frequencies and metallic hyperbolic metamaterials (MHMs) at visible frequencies. This analysis reveals the conditions under which the EMA can be safely applied for both MHMs and SHMs. We find that the combination of precise nanoscale layering and the longer infrared operating wavelengths puts the SHMs well within the effective medium limit and, in contrast to MHMs, allows for the attainment of very high photon momentum states. Additionally, SHMs allow for new phenomena such as ultrafast creation ofmore » the hyperbolic manifold through optical pumping. Furthermore, we examine the possibility of achieving ultrafast topological transitions through optical pumping which can photo-dope appropriately designed quantum wells on the femtosecond time scale.« less

  11. Communication: transition state theory for dissipative systems without a dividing surface.

    PubMed

    Revuelta, F; Bartsch, Thomas; Benito, R M; Borondo, F

    2012-03-07

    Transition state theory is a central cornerstone in reaction dynamics. Its key step is the identification of a dividing surface that is crossed only once by all reactive trajectories. This assumption is often badly violated, especially when the reactive system is coupled to an environment. The calculations made in this way then overestimate the reaction rate and the results depend critically on the choice of the dividing surface. In this Communication, we study the phase space of a stochastically driven system close to an energetic barrier in order to identify the geometric structure unambiguously determining the reactive trajectories, which is then incorporated in a simple rate formula for reactions in condensed phase that is both independent of the dividing surface and exact. © 2012 American Institute of Physics

  12. Laboratory Observation of a Plasma-Flow-State Transition from Diverging to Stretching a Magnetic Nozzle.

    PubMed

    Takahashi, Kazunori; Ando, Akira

    2017-06-02

    An axial magnetic field induced by a plasma flow in a divergent magnetic nozzle is measured when injecting the plasma flow from a radio frequency (rf) plasma source located upstream of the nozzle. The source is operated with a pulsed rf power of 5 kW, and the high density plasma flow is sustained only for the initial ∼100  μsec of the discharge. The measurement shows a decrease in the axial magnetic field near the source exit, whereas an increase in the field is detected at the downstream side of the magnetic nozzle. These results demonstrate a spatial transition of the plasma-flow state from diverging to stretching the magnetic nozzle, where the importance of both the Alfvén and ion Mach numbers is shown.

  13. S-matrix decomposition, natural reaction channels, and the quantum transition state approach to reactive scattering

    SciT

    Manthe, Uwe, E-mail: uwe.manthe@uni-bielefeld.de; Ellerbrock, Roman, E-mail: roman.ellerbrock@uni-bielefeld.de

    2016-05-28

    A new approach for the quantum-state resolved analysis of polyatomic reactions is introduced. Based on the singular value decomposition of the S-matrix, energy-dependent natural reaction channels and natural reaction probabilities are defined. It is shown that the natural reaction probabilities are equal to the eigenvalues of the reaction probability operator [U. Manthe and W. H. Miller, J. Chem. Phys. 99, 3411 (1993)]. Consequently, the natural reaction channels can be interpreted as uniquely defined pathways through the transition state of the reaction. The analysis can efficiently be combined with reactive scattering calculations based on the propagation of thermal flux eigenstates. Inmore » contrast to a decomposition based straightforwardly on thermal flux eigenstates, it does not depend on the choice of the dividing surface separating reactants from products. The new approach is illustrated studying a prototypical example, the H + CH{sub 4} → H{sub 2} + CH{sub 3} reaction. The natural reaction probabilities and the contributions of the different vibrational states of the methyl product to the natural reaction channels are calculated and discussed. The relation between the thermal flux eigenstates and the natural reaction channels is studied in detail.« less

  14. (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.

  15. Ground state and magnetic phase transitions of the spin Lieb nanolattice: Monte Carlo simulations

    NASA Astrophysics Data System (ADS)

    Masrour, R.; Jabar, A.

    2018-02-01

    We study the ground state and magnetic properties of the spin Lieb nanolattice with three lattice sites with spins (S = 2 , σ = 1 / 2 , q = 3 / 2) using Monte Carlo simulations. The ground state phase diagrams of the Lieb nanolattice have been studied. The phase diagrams show some key features: coexistence between regions, points where six, eight and ten states can coexist. The total and partial magnetization of each sublattice is given and the corresponding magnetic susceptibility is also found. The variation of total magnetization with the exchange interaction RSq and Rσq of the Lieb nanolattice with three lattice sites with spins (S , σ , q) has been studied. Moreover, the total magnetization versus the fields Δ /JSσ of the Lieb nanolattice with three lattice sites with spins (S , σ , q) are established for several values of Rσq and Rsq. Magnetic hysteresis cycles of the Lieb nanolattice with three lattice sites with spins (S , σ , q) are found for several values of Rsq and temperature. We show that the superparamagnetism behaviour appears for a weak coupling value between S and q thus around the transition temperature.

  16. 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.

  17. 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.

  18. ACCRETION DISK DYNAMO AS THE TRIGGER FOR X-RAY BINARY STATE TRANSITIONS

    SciT

    Begelman, Mitchell C.; Armitage, Philip J.; Reynolds, Christopher S., E-mail: mitch@jila.colorado.edu

    2015-08-20

    Magnetohydrodynamic accretion disk simulations suggest that much of the energy liberated by the magnetorotational instability (MRI) can be channeled into large-scale toroidal magnetic fields through dynamo action. Under certain conditions, this field can dominate over gas and radiation pressure in providing vertical support against gravity, even close to the midplane. Using a simple model for the creation of this field, its buoyant rise, and its coupling to the gas, we show how disks could be driven into this magnetically dominated state and deduce the resulting vertical pressure and density profiles. Applying an established criterion for MRI to operate in themore » presence of a toroidal field, we show that magnetically supported disks can have two distinct MRI-active regions, separated by a “dead zone” where local MRI is suppressed, but where magnetic energy continues to flow upward from the dynamo region below. We suggest that the relative strengths of the MRI zones, and the local poloidal flux, determine the spectral states of X-ray binaries. Specifically, “intermediate” and “hard” accretion states occur when MRI is triggered in the hot, upper zone of the corona, while disks in “soft” states do not develop the upper MRI zone. We discuss the conditions under which various transitions should take place and speculate on the relationship of dynamo activity to the various types of quasi-periodic oscillations that sometimes appear in the hard spectral components. The model also explains why luminous accretion disks in the “soft” state show no signs of the thermal/viscous instability predicted by standard α-models.« less

  19. Linking state-and-transition simulation and timber supply models for forest biomass production scenarios

    Costanza, Jennifer; Abt, Robert C.; McKerrow, Alexa; Collazo, Jaime

    2015-01-01

    We linked state-and-transition simulation models (STSMs) with an economics-based timber supply model to examine landscape dynamics in North Carolina through 2050 for three scenarios of forest biomass production. Forest biomass could be an important source of renewable energy in the future, but there is currently much uncertainty about how biomass production would impact landscapes. In the southeastern US, if forests become important sources of biomass for bioenergy, we expect increased land-use change and forest management. STSMs are ideal for simulating these landscape changes, but the amounts of change will depend on drivers such as timber prices and demand for forest land, which are best captured with forest economic models. We first developed state-and-transition model pathways in the ST-Sim software platform for 49 vegetation and land-use types that incorporated each expected type of landscape change. Next, for the three biomass production scenarios, the SubRegional Timber Supply Model (SRTS) was used to determine the annual areas of thinning and harvest in five broad forest types, as well as annual areas converted among those forest types, agricultural, and urban lands. The SRTS output was used to define area targets for STSMs in ST-Sim under two scenarios of biomass production and one baseline, business-as-usual scenario. We show that ST-Sim output matched SRTS targets in most cases. Landscape dynamics results indicate that, compared with the baseline scenario, forest biomass production leads to more forest and, specifically, more intensively managed forest on the landscape by 2050. Thus, the STSMs, informed by forest economics models, provide important information about potential landscape effects of bioenergy production.

  20. Crossing the dividing surface of transition state theory. III. Once and only once. Selecting reactive trajectories

    SciT

    Lorquet, J. C., E-mail: jc.lorquet@ulg.ac.be

    2015-09-14

    The purpose of the present work is to determine initial conditions that generate reacting, recrossing-free trajectories that cross the conventional dividing surface of transition state theory (i.e., the plane in configuration space passing through a saddle point of the potential energy surface and perpendicular to the reaction coordinate) without ever returning to it. Local analytical equations of motion valid in the neighborhood of this planar surface have been derived as an expansion in Poisson brackets. We show that the mere presence of a saddle point implies that reactivity criteria can be quite simply formulated in terms of elements of thismore » series, irrespective of the shape of the potential energy function. Some of these elements are demonstrated to be equal to a sum of squares and thus to be necessarily positive, which has a profound impact on the dynamics. The method is then applied to a three-dimensional model describing an atom-diatom interaction. A particular relation between initial conditions is shown to generate a bundle of reactive trajectories that form reactive cylinders (or conduits) in phase space. This relation considerably reduces the phase space volume of initial conditions that generate recrossing-free trajectories. Loci in phase space of reactive initial conditions are presented. Reactivity is influenced by symmetry, as shown by a comparative study of collinear and bent transition states. Finally, it is argued that the rules that have been derived to generate reactive trajectories in classical mechanics are also useful to build up a reactive wave packet.« less

  1. Using state-and-transition modeling to account for imperfect detection in invasive species management

    Frid, Leonardo; Holcombe, Tracy; Morisette, Jeffrey T.; Olsson, Aaryn D.; Brigham, Lindy; Bean, Travis M.; Betancourt, Julio L.; Bryan, Katherine

    2013-01-01

    Buffelgrass, a highly competitive and flammable African bunchgrass, is spreading rapidly across both urban and natural areas in the Sonoran Desert of southern and central Arizona. Damages include increased fire risk, losses in biodiversity, and diminished revenues and quality of life. Feasibility of sustained and successful mitigation will depend heavily on rates of spread, treatment capacity, and cost–benefit analysis. We created a decision support model for the wildland–urban interface north of Tucson, AZ, using a spatial state-and-transition simulation modeling framework, the Tool for Exploratory Landscape Scenario Analyses. We addressed the issues of undetected invasions, identifying potentially suitable habitat and calibrating spread rates, while answering questions about how to allocate resources among inventory, treatment, and maintenance. Inputs to the model include a state-and-transition simulation model to describe the succession and control of buffelgrass, a habitat suitability model, management planning zones, spread vectors, estimated dispersal kernels for buffelgrass, and maps of current distribution. Our spatial simulations showed that without treatment, buffelgrass infestations that started with as little as 80 ha (198 ac) could grow to more than 6,000 ha by the year 2060. In contrast, applying unlimited management resources could limit 2060 infestation levels to approximately 50 ha. The application of sufficient resources toward inventory is important because undetected patches of buffelgrass will tend to grow exponentially. In our simulations, areas affected by buffelgrass may increase substantially over the next 50 yr, but a large, upfront investment in buffelgrass control could reduce the infested area and overall management costs.

  2. Asparagine 285 plays a key role in transition state stabilization in rabbit muscle creatine kinase

    PubMed Central

    Borders, Charles L.; MacGregor, Katherine M.; Edmiston, Paul L.; Gbeddy, Elikem R.K.; Thomenius, Michael J.; Mulligan, Guy B.; Snider, Mark J.

    2003-01-01

    To explore the possibility that asparagine 285 plays a key role in transition state stabilization in phosphagen kinase catalysis, the N285Q, N285D, and N285A site-directed mutants of recombinant rabbit muscle creatine kinase (rmCK) were prepared and characterized. Kinetic analysis of phosphocreatine formation showed that the catalytic efficiency of each N285 mutant was reduced by approximately four orders of magnitude, with the major cause of activity loss being a reduction in kcat in comparison to the recombinant native CK. The data for N285Q still fit a random-order, rapid-equilibrium mechanism, with either MgATP or creatine binding first with affinities very nearly equal to those for native CK. However, the affinity for the binding of the second substrate is reduced approximately 10-fold, suggesting that addition of a single methylene group at position 285 disrupts the symphony of substrate binding. The data for the N285A mutant only fit an ordered binding mechanism, with MgATP binding first. Isosteric replacement to form the N285D mutant has almost no effect on the KM values for either creatine or MgATP, thus the decrease in activity is due almost entirely to a 5000-fold reduction in kcat. Using the quenching of the intrinsic CK tryptophan fluorescence by added MgADP (Borders et al. 2002), it was found that, unlike native CK, none of the mutants have the ability to form a quaternary TSAC. We use these data to propose that asparagine 285 indeed plays a key role in transition state stabilization in the reaction catalyzed by creatine kinase and other phosphagen kinases. PMID:12592023

  3. Asparagine 285 plays a key role in transition state stabilization in rabbit muscle creatine kinase.

    PubMed

    Borders, Charles L; MacGregor, Katherine M; Edmiston, Paul L; Gbeddy, Elikem R K; Thomenius, Michael J; Mulligan, Guy B; Snider, Mark J

    2003-03-01

    To explore the possibility that asparagine 285 plays a key role in transition state stabilization in phosphagen kinase catalysis, the N285Q, N285D, and N285A site-directed mutants of recombinant rabbit muscle creatine kinase (rmCK) were prepared and characterized. Kinetic analysis of phosphocreatine formation showed that the catalytic efficiency of each N285 mutant was reduced by approximately four orders of magnitude, with the major cause of activity loss being a reduction in k(cat) in comparison to the recombinant native CK. The data for N285Q still fit a random-order, rapid-equilibrium mechanism, with either MgATP or creatine binding first with affinities very nearly equal to those for native CK. However, the affinity for the binding of the second substrate is reduced approximately 10-fold, suggesting that addition of a single methylene group at position 285 disrupts the symphony of substrate binding. The data for the N285A mutant only fit an ordered binding mechanism, with MgATP binding first. Isosteric replacement to form the N285D mutant has almost no effect on the K(M) values for either creatine or MgATP, thus the decrease in activity is due almost entirely to a 5000-fold reduction in k(cat). Using the quenching of the intrinsic CK tryptophan fluorescence by added MgADP (Borders et al. 2002), it was found that, unlike native CK, none of the mutants have the ability to form a quaternary TSAC. We use these data to propose that asparagine 285 indeed plays a key role in transition state stabilization in the reaction catalyzed by creatine kinase and other phosphagen kinases.

  4. Downscaling global land-use/land-cover projections for use in region-level state-and-transition simulation modeling

    Sherba, Jason T.; Sleeter, Benjamin M.; Davis, Adam W.; Parker, Owen P.

    2015-01-01

    Global land-use/land-cover (LULC) change projections and historical datasets are typically available at coarse grid resolutions and are often incompatible with modeling applications at local to regional scales. The difficulty of downscaling and reapportioning global gridded LULC change projections to regional boundaries is a barrier to the use of these datasets in a state-and-transition simulation model (STSM) framework. Here we compare three downscaling techniques to transform gridded LULC transitions into spatial scales and thematic LULC classes appropriate for use in a regional STSM. For each downscaling approach, Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathway (RCP) LULC projections, at the 0.5 × 0.5 cell resolution, were downscaled to seven Level III ecoregions in the Pacific Northwest, United States. RCP transition values at each cell were downscaled based on the proportional distribution between ecoregions of (1) cell area, (2) land-cover composition derived from remotely-sensed imagery, and (3) historic LULC transition values from a LULC history database. Resulting downscaled LULC transition values were aggregated according to their bounding ecoregion and “cross-walked” to relevant LULC classes. Ecoregion-level LULC transition values were applied in a STSM projecting LULC change between 2005 and 2100. While each downscaling methods had advantages and disadvantages, downscaling using the historical land-use history dataset consistently apportioned RCP LULC transitions in agreement with historical observations. Regardless of the downscaling method, some LULC projections remain improbable and require further investigation.

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

    PubMed

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

    2012-05-01

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

  6. Comparative Analysis of Light-Harvesting Antennae and State Transition in chlorina and cpSRP Mutants1[OPEN

    PubMed Central

    Wang, Peng

    2016-01-01

    State transitions in photosynthesis provide for the dynamic allocation of a mobile fraction of light-harvesting complex II (LHCII) to photosystem II (PSII) in state I and to photosystem I (PSI) in state II. In the state I-to-state II transition, LHCII is phosphorylated by STN7 and associates with PSI to favor absorption cross-section of PSI. Here, we used Arabidopsis (Arabidopsis thaliana) mutants with defects in chlorophyll (Chl) b biosynthesis or in the chloroplast signal recognition particle (cpSRP) machinery to study the flexible formation of PS-LHC supercomplexes. Intriguingly, we found that impaired Chl b biosynthesis in chlorina1-2 (ch1-2) led to preferentially stabilized LHCI rather than LHCII, while the contents of both LHCI and LHCII were equally depressed in the cpSRP43-deficient mutant (chaos). In view of recent findings on the modified state transitions in LHCI-deficient mutants (Benson et al., 2015), the ch1-2 and chaos mutants were used to assess the influence of varying LHCI/LHCII antenna size on state transitions. Under state II conditions, LHCII-PSI supercomplexes were not formed in both ch1-2 and chaos plants. LHCII phosphorylation was drastically reduced in ch1-2, and the inactivation of STN7 correlates with the lack of state transitions. In contrast, phosphorylated LHCII in chaos was observed to be exclusively associated with PSII complexes, indicating a lack of mobile LHCII in chaos. Thus, the comparative analysis of ch1-2 and chaos mutants provides new evidence for the flexible organization of LHCs and enhances our understanding of the reversible allocation of LHCII to the two photosystems. PMID:27663408

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

    PubMed

    Wang, Peng; Grimm, Bernhard

    2016-11-01

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

  8. T-state inhibitors of E. coli aspartate transcarbamoylase that prevent the allosteric transition.

    PubMed

    Heng, Sabrina; Stieglitz, Kimberly A; Eldo, Joby; Xia, Jiarong; Cardia, James P; Kantrowitz, Evan R

    2006-08-22

    Escherichia coli aspartate transcarbamoylase (ATCase) catalyzes the committed step in pyrimidine nucleotide biosynthesis, the reaction between carbamoyl phosphate (CP) and l-aspartate to form N-carbamoyl-l-aspartate and inorganic phosphate. The enzyme exhibits homotropic cooperativity and is allosterically regulated. Upon binding l-aspartate in the presence of a saturating concentration of CP, the enzyme is converted from the low-activity low-affinity T state to the high-activity high-affinity R state. The potent inhibitor N-phosphonacetyl-l-aspartate (PALA), which combines the binding features of Asp and CP into one molecule, has been shown to induce the allosteric transition to the R state. In the presence of only CP, the enzyme is the T structure with the active site primed for the binding of aspartate. In a structure of the enzyme-CP complex (T(CP)), two CP molecules were observed in the active site approximately 7A apart, one with high occupancy and one with low occupancy. The high occupancy site corresponds to the position for CP observed in the structure of the enzyme with CP and the aspartate analogue succinate bound. The position of the second CP is in a unique site and does not overlap with the aspartate binding site. As a means to generate a new class of inhibitors for ATCase, the domain-open T state of the enzyme was targeted. We designed, synthesized, and characterized three inhibitors that were composed of two phosphonacetamide groups linked together. These two phosphonacetamide groups mimic the positions of the two CP molecules in the T(CP) structure. X-ray crystal structures of ATCase-inhibitor complexes revealed that each of these inhibitors bind to the T state of the enzyme and occupy the active site area. As opposed to the binding of Asp in the presence of CP or PALA, these inhibitors are unable to initiate the global T to R conformational change. Although the best of these T-state inhibitors only has a K(i) value in the micromolar range, the

  9. Transit Marketing : Review of the State-of-the-Art and a Handbook of Current Practice

    DOT National Transportation Integrated Search

    1985-04-01

    Over the past decade, marketing has been given increased emphasis as a way to improve both transit rideship and productivity. While there is near universal agreement among transit managers that some level of marketing is necessary, there is far from ...

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

    PubMed Central

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

    2015-01-01

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

  11. A Conserved Behavioral State Barrier Impedes Transitions between Anesthetic-Induced Unconsciousness and Wakefulness: Evidence for Neural Inertia

    PubMed Central

    Friedman, Eliot B.; Sun, Yi; Moore, Jason T.; Hung, Hsiao-Tung; Meng, Qing Cheng; Perera, Priyan; Joiner, William J.; Thomas, Steven A.; Eckenhoff, Roderic G.; Sehgal, Amita; Kelz, Max B.

    2010-01-01

    One major unanswered question in neuroscience is how the brain transitions between conscious and unconscious states. General anesthetics offer a controllable means to study these transitions. Induction of anesthesia is commonly attributed to drug-induced global modulation of neuronal function, while emergence from anesthesia has been thought to occur passively, paralleling elimination of the anesthetic from its sites in the central nervous system (CNS). If this were true, then CNS anesthetic concentrations on induction and emergence would be indistinguishable. By generating anesthetic dose-response data in both insects and mammals, we demonstrate that the forward and reverse paths through which anesthetic-induced unconsciousness arises and dissipates are not identical. Instead they exhibit hysteresis that is not fully explained by pharmacokinetics as previously thought. Single gene mutations that affect sleep-wake states are shown to collapse or widen anesthetic hysteresis without obvious confounding effects on volatile anesthetic uptake, distribution, or metabolism. We propose a fundamental and biologically conserved concept of neural inertia, a tendency of the CNS to resist behavioral state transitions between conscious and unconscious states. We demonstrate that such a barrier separates wakeful and anesthetized states for multiple anesthetics in both flies and mice, and argue that it contributes to the hysteresis observed when the brain transitions between conscious and unconscious states. PMID:20689589

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

    NASA Astrophysics Data System (ADS)

    Ciszak, Marzena; Bellesi, Michele

    2011-12-01

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

  13. Effects of a Transition to a Hydrogen Economy on Employment in the United States

    SciT

    Tolley, George S.; Jones, Donald W. Mintz, Marianne M.; Smith, Barton A.

    2008-07-01

    The U.S. Department of Energy report, Effects of a Transition to a Hydrogen Economy on Employment in the United States Report to Congress, estimates the effects on employment of a U.S. economy transformation to hydrogen between 2020 and 2050. The report includes study results on employment impacts from hydrogen market expansion in the transportation, stationary, and portable power sectors and highlights possible skill and education needs. This study is in response to Section 1820 of the Energy Policy Act of 2005 (Public Law 109-58) (EPACT). Section 1820, “Overall Employment in a Hydrogen Economy,” requires the Secretary of Energy to carrymore » out a study of the effects of a transition to a hydrogen economy on several employment [types] in the United States. As required by Section 1820, the present report considers: • Replacement effects of new goods and services • International competition • Workforce training requirements • Multiple possible fuel cycles, including usage of raw materials • Rates of market penetration of technologies • Regional variations based on geography • Specific recommendations of the study Both the Administration’s National Energy Policy and the Department’s Strategic Plan call for reducing U.S. reliance on imported oil and reducing greenhouse gas emissions. The National Energy Policy also acknowledges the need to increase energy supplies and use more energy-efficient technologies and practices. President Bush proposed in his January 2003 State of the Union Address to advance research on hydrogen so that it has the potential to play a major role in America’s future energy system. Consistent with these aims, EPACT 2005 authorizes a research, development, and demonstration program for hydrogen and fuel cell technology. Projected results for the national employment impacts, projections of the job creation and job replacement underlying the total employment changes, training implications, regional employment impacts

  14. Transition V & VI in Alabama: A Profile of Commitment. State Conference Proceedings.

    ERIC Educational Resources Information Center

    Browning, Philip; Rabren, Karen

    This publication provides information on the Alabama Transition Initiative for students with disabilities, including papers presented at two statewide transition conferences. Conference papers include: (1) "Pell City School System's Community Transition Team Model" (Deloris Frasier); (2) "Alabama's MH/MR Service Coordinators in…

  15. Spin-valley locking in the normal state of a transition-metal dichalcogenide superconductor.

    PubMed

    Bawden, L; Cooil, S P; Mazzola, F; Riley, J M; Collins-McIntyre, L J; Sunko, V; Hunvik, K W B; Leandersson, M; Polley, C M; Balasubramanian, T; Kim, T K; Hoesch, M; Wells, J W; Balakrishnan, G; Bahramy, M S; King, P D C

    2016-05-23

    Metallic transition-metal dichalcogenides (TMDCs) are benchmark systems for studying and controlling intertwined electronic orders in solids, with superconductivity developing from a charge-density wave state. The interplay between such phases is thought to play a critical role in the unconventional superconductivity of cuprates, Fe-based and heavy-fermion systems, yet even for the more moderately-correlated TMDCs, their nature and origins have proved controversial. Here, we study a prototypical example, 2H-NbSe2, by spin- and angle-resolved photoemission and first-principles theory. We find that the normal state, from which its hallmark collective phases emerge, is characterized by quasiparticles whose spin is locked to their valley pseudospin. This results from a combination of strong spin-orbit interactions and local inversion symmetry breaking, while interlayer coupling further drives a rich three-dimensional momentum dependence of the underlying Fermi-surface spin texture. These findings necessitate a re-investigation of the nature of charge order and superconducting pairing in NbSe2 and related TMDCs.

  16. Evidence That Nucleophile Deprotonation Exceeds Bond Formation in the HDV Ribozyme Transition State.

    PubMed

    Lu, Jun; Koo, Selene C; Weissman, Benjamin P; Harris, Michael E; Li, Nan-Sheng; Piccirilli, Joseph A

    2018-06-26

    Steric constraints imposed by the active sites of protein and RNA enzymes pose major challenges to the investigation of structure-function relationships within these systems. As a strategy to circumvent such constraints in the HDV ribozyme, we have synthesized phosphoramidites from propanediol derivatives and incorporated them at the 5'-termini of RNA and DNA oligonucleotides to generate a series of novel substrates with nucleophiles perturbed electronically through geminal fluorination. In nonenzymatic, hydroxide-catalyzed intramolecular transphosphorylation of the DNA substrates, pH-rate profiles revealed that fluorine substitution reduces the maximal rate and the kinetic p K a , consistent with the expected electron-withdrawing effect. In HDV ribozyme reactions, we observed that the RNA substrates undergo transphosphorylation relatively efficiently, suggesting that the conformational constraints imposed by a ribofuranose ring are not strictly required for ribozyme catalysis. In contrast to the nonenzymatic reactions, however, substrate fluorination modestly increases the ribozyme reaction rate, consistent with a mechanism in which (1) the 2'-hydroxyl nucleophile exists predominantly in its neutral, protonated form in the ground state and (2) the 2'-hydroxyl bears some negative charge in the rate-determining step, consistent with a transition state in which the extent of 2'-OH deprotonation exceeds the extent of P-O bond formation.

  17. Boron monosulfide: Equation of state and pressure-induced phase transition

    NASA Astrophysics Data System (ADS)

    Cherednichenko, K. A.; Kruglov, I. A.; Oganov, A. R.; Le Godec, Y.; Mezouar, M.; Solozhenko, V. L.

    2018-04-01

    Quasi-hydrostatic compression of rhombohedral boron monosulfide (r-BS) has been studied up to 50 GPa at room temperature using diamond-anvil cells and angle-dispersive synchrotron X-ray diffraction. A fit of the experimental P-V data to the Vinet equation of state yields the bulk modulus B0 of 42.2(1.4) GPa and its first pressure derivative B0' of 7.6(2) that are in excellent agreement with our ab initio calculations. Formation of a new high-pressure phase of boron monosulfide (hp-BS) has been observed above 35 GPa. According to ab initio evolutionary crystal structure predictions combined with Rietveld refinement of high-pressure X-ray diffraction data, the structure of hp-BS has trigonal symmetry and belongs to the space group P-3m1. As it follows from the electron density of state calculations, the phase transformation is accompanied by an insulator-metal transition.

  18. Orbit covariance propagation via quadratic-order state transition matrix in curvilinear coordinates

    NASA Astrophysics Data System (ADS)

    Hernando-Ayuso, Javier; Bombardelli, Claudio

    2017-09-01

    In this paper, an analytical second-order state transition matrix (STM) for relative motion in curvilinear coordinates is presented and applied to the problem of orbit uncertainty propagation in nearly circular orbits (eccentricity smaller than 0.1). The matrix is obtained by linearization around a second-order analytical approximation of the relative motion recently proposed by one of the authors and can be seen as a second-order extension of the curvilinear Clohessy-Wiltshire (C-W) solution. The accuracy of the uncertainty propagation is assessed by comparison with numerical results based on Monte Carlo propagation of a high-fidelity model including geopotential and third-body perturbations. Results show that the proposed STM can greatly improve the accuracy of the predicted relative state: the average error is found to be at least one order of magnitude smaller compared to the curvilinear C-W solution. In addition, the effect of environmental perturbations on the uncertainty propagation is shown to be negligible up to several revolutions in the geostationary region and for a few revolutions in low Earth orbit in the worst case.

  19. High P-T phase transitions and P-V-T equation of state of hafnium

    SciT

    Hrubiak, Rostislav; Drozd, Vadym; Karbasi, Ali

    2016-07-29

    We measured the volume of hafnium at several pressures up to 67 GPa and at temperatures between 300 to 780 K using a resistively heated diamond anvil cell with synchrotron x-ray diffraction at the Advanced Photon Source. The measured data allows us to determine the P-V-T equation of state of hafnium. The previously described [Xia et al., Phys. Rev. B 42, 6736-6738 (1990)] phase transition from hcp ({alpha}) to simple hexagonal ({omega}) phase at 38 GPa at room temperature was not observed even up to 51 GPa. The {omega} phase was only observed at elevated temperatures. Our measurements have alsomore » improved the experimental constraint on the high P-T phase boundary between the {omega} phase and high pressure bcc ({beta}) phase of hafnium. Isothermal room temperature bulk modulus and its pressure derivative for the {alpha}-phase of hafnium were measured to be B{sub 0} = 112.9{+-}0.5 GPa and B{sub 0}'=3.29{+-}0.05, respectively. P-V-T data for the {alpha}-phase of hafnium was used to obtain a fit to a thermodynamic P-V-T equation of state based on model by Brosh et al. [CALPHAD 31, 173-185 (2007)].« less

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

    PubMed

    Zhao, Bin; Sun, Zhigang; Guo, Hua

    2015-06-28

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

  1. Phase transition and equation of state of paratellurite (TeO2) under high pressure

    NASA Astrophysics Data System (ADS)

    Liu, Xun; Mashimo, Tsutomu; Kawai, Nobuaki; Sekine, Toshimori; Zeng, Zhaoyi; Zhou, Xianming

    2016-07-01

    The Hugoniot data for TeO2 single crystals were obtained for pressures up to ˜85 GPa along both the <100> (a-axis) and <001> (c-axis) directions using a velocity interferometer system for any reflector and inclined-mirror method combined with a powder gun or two-stage light gas gun. The Hugoniot-elastic limit of TeO2 was determined to be 3.3-4.3 GPa along the c-axes. The shock velocity (U s) versus particle velocity (U p) relation for TeO2 shows a kink around U p = 1.0 km s-1, which suggests a phase transition completes at ˜26 ± 2 GPa. The Hugoniot relations of the low and high pressure phase are given by U s = 3.13(5) + 1.10(6)U p for U p < 1.0 km s-1 and U s = 2.73(9) + 1.49(5)U p for U p > 1.0 km s-1, respectively. First-principles geometry optimizations based on the generalized gradient approximation after Perdew, Burke and Ernzerhof method were also performed on TeO2. It suggested that a continuous structure distortion occurs up to 22 GPa, and the lattice parameters b and c abruptly increase and decrease at 22 GPa, respectively, indicating a first-order phase transition to the cotunnite structure phase. The equation of state of the cotunnite phase TeO2 is discussed based on the experimental and simulation results.

  2. Racial and ethnic differences in the transition to a teenage birth in the United States.

    PubMed

    Manlove, Jennifer; Steward-Streng, Nicole; Peterson, Kristen; Scott, Mindy; Wildsmith, Elizabeth

    2013-06-01

    Rates of teenage childbearing are high in the United States, and they differ substantially by race and ethnicity and nativity status. Data from the National Longitudinal Survey of Youth 1997 cohort were used to link characteristics of white, black, U.S.-born Hispanic and foreign-born Hispanic adolescents to teenage childbearing. Following a sample of 3,294 females aged 12-16 through age 19, discrete-time logistic regression analyses were used to examine which domains of teenagers' lives were associated with the transition to a teenage birth for each racial and ethnic group, and whether these associations help explain racial and ethnic and nativity differences in this transition. In a baseline multivariate analysis controlling for age, compared with whites, foreign-born Hispanics had more than three times the odds of a teenage birth (odds ratio, 3.5), while blacks and native-born Hispanics had about twice the odds (2.1 and 1.9, respectively). Additional controls (for family environments; individual, peer and dating characteristics; characteristics of first sexual relationships; and subsequent sexual experience) reduced the difference between blacks and whites, and between foreign-born Hispanics and whites, and eliminated the difference between U.S.-born Hispanics and whites. Further, if racial or ethnic minority adolescents had the same distribution as did white teenagers across all characteristics, the predicted probability of a teenage birth would be reduced by 40% for blacks and 35% for U.S.-born Hispanics. Differences in the context of adolescence may account for a substantial portion of racial, ethnic and nativity differences in teenage childbearing. Copyright © 2013 by the Guttmacher Institute.

  3. Linking ecosystem services with state-and-transition models to evaluate rangeland management decisions

    NASA Astrophysics Data System (ADS)

    Lohani, S.; Heilman, P.; deSteiguer, J. E.; Guertin, D. P.; Wissler, C.; McClaran, M. P.

    2014-12-01

    Quantifying ecosystem services is a crucial topic for land management decision making. However, market prices are usually not able to capture all the ecosystem services and disservices. Ecosystem services from rangelands, that cover 70% of the world's land area, are even less well-understood since knowledge of rangelands is limited. This study generated a management framework for rangelands that uses remote sensing to generate state and transition models (STMs) for a large area and a linear programming (LP) model that uses ecosystem services to evaluate natural and/or management induced transitions as described in the STM. The LP optimization model determines the best management plan for a plot of semi-arid land in the Empire Ranch in southeastern Arizona. The model allocated land among management activities (do nothing, grazing, fire, and brush removal) to optimize net benefits and determined the impact of monetizing environmental services and disservices on net benefits, acreage allocation and production output. The ecosystem services under study were forage production (AUM/ac/yr), sediment (lbs/ac/yr), water runoff (inches/yr), soil loss (lbs/ac/yr) and recreation (thousands of number of visitors/ac/yr). The optimization model was run for three different scenarios - private rancher, public rancher including environmental services and excluding disservices, and public rancher including both services and disservices. The net benefit was the highest for the public rancher excluding the disservices. A result from the study is a constrained optimization model that incorporates ecosystem services to analyze investments on conservation and management activities. Rangeland managers can use this model to understand and explain, not prescribe, the tradeoffs of management investments.

  4. Calculating Transition Energy Barriers and Characterizing Activation States for Steps of Fusion.

    PubMed

    Ryham, Rolf J; Klotz, Thomas S; Yao, Lihan; Cohen, Fredric S

    2016-03-08

    We use continuum mechanics to calculate an entire least energy pathway of membrane fusion, from stalk formation, to pore creation, and through fusion pore enlargement. The model assumes that each structure in the pathway is axially symmetric. The static continuum stalk structure agrees quantitatively with experimental stalk architecture. Calculations show that in a stalk, the distal monolayer is stretched and the stored stretching energy is significantly less than the tilt energy of an unstretched distal monolayer. The string method is used to determine the energy of the transition barriers that separate intermediate states and the dynamics of two bilayers as they pass through them. Hemifusion requires a small amount of energy independently of lipid composition, while direct transition from a stalk to a fusion pore without a hemifusion intermediate is highly improbable. Hemifusion diaphragm expansion is spontaneous for distal monolayers containing at least two lipid components, given sufficiently negative diaphragm spontaneous curvature. Conversely, diaphragms formed from single-component distal monolayers do not expand without the continual injection of energy. We identify a diaphragm radius, below which central pore expansion is spontaneous. For larger diaphragms, prior studies have shown that pore expansion is not axisymmetric, and here our calculations supply an upper bound for the energy of the barrier against pore formation. The major energy-requiring deformations in the steps of fusion are: widening of a hydrophobic fissure in bilayers for stalk formation, splay within the expanding hemifusion diaphragm, and fissure widening initiating pore formation in a hemifusion diaphragm. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  5. Functional role of a mobile loop of Escherichia coli dihydrofolate reductase in transition-state stabilization.

    PubMed

    Li, L; Falzone, C J; Wright, P E; Benkovic, S J

    1992-09-01

    The function of a highly mobile loop in Escherichia coli dihydrofolate reductase was studied by constructing a mutant (DL1) using cassette mutagenesis that had four residues deleted in the middle section of the loop (Met16-Ala19) and a glycine inserted to seal the gap. This part of the loop involves residues 16-20 and is disordered in the X-ray crystal structures of the apoprotein and the NADP+ binary complex but forms a hairpin turn that folds over the nicotinamide moiety of NADP+ and the pteridine moiety of folate in the ternary complex [Bystroff, C., & Kraut, J. (1991) Biochemistry 30, 2227-2239]. The steady-state and pre-steady-state kinetics and two-dimensional 1H NMR spectra were analyzed and compared to the wild-type protein. The kinetics on the DL1 mutant enzyme show that the KM value for NADPH (5.3 microM), the KM for dihydrofolate (2 microM), the rate constant for the release of the product tetrahydrofolate (10.3 s-1), and the intrinsic pKa value (6.2) are similar to those exhibited by the wild-type enzyme. However, the hydride-transfer rate declines markedly from the wild-type value of 950 s-1 to 1.7 s-1 for the DL1 mutant and when taken with data for substrate binding indicates that the loop contributes to substrate flux by a factor of 3.5 x 10(4). Thus, the mobility of loop I may provide a mechanism of recruiting hydrophobic residues which can properly align the nicotinamide and pteridine rings for the hydride-transfer process (a form of transition-state stabilization).(ABSTRACT TRUNCATED AT 250 WORDS)

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

    PubMed

    Chira, Peter; Ronis, Tova; Ardoin, Stacy; White, Patience

    2014-04-01

    To assess North American pediatric rheumatology providers' perspectives on practices, barriers, and opportunities concerning the transition from pediatric-centered to adult-centered care. Childhood Arthritis and Rheumatology Research Alliance (CARRA) members completed a 25-item survey assessing current transition practices, transition policy awareness, and transitional care barriers and needs. Results were compared to the American Academy of Pediatrics (AAP) 2008 survey on transitional care. Over half (158/288, 55%) of CARRA members completed the survey. Fewer than 10% are very familiar with AAP guidelines about transition care for youth with special healthcare needs. Eight percent have a formal written transition policy, but 42% use an informal approach. Patient request (75%) most frequently initiates transfer to adult care. Two major barriers to transition are fragmented adult medical care and lack of sufficient time to provide services. Compared with AAP survey participants, pediatric rheumatology providers are significantly more likely to help youth find an adult specialist (63% vs 45%) and discuss confidentiality and consent before age 18 (45% vs 33%), but are less likely to help with medical summary creation (16% vs 27%) or find a primary care provider (25% vs 47%). Outcomes ranked as "very important" in defining a successful transition are survival (76%), seeing an adult rheumatologist within 6 months of final pediatric rheumatology visit (66%), and maintaining insurance coverage (57%). This comprehensive survey of North American pediatric rheumatology providers regarding transitional care practices demonstrates deficiencies in education, resources, and a formalized process. Respondents support development of standardized rheumatology-specific transition practices.

  7. Viewing brain processes as Critical State Transitions across levels of organization: Neural events in Cognition and Consciousness, and general principles.

    PubMed

    Werner, Gerhard

    2009-04-01

    In this theoretical and speculative essay, I propose that insights into certain aspects of neural system functions can be gained from viewing brain function in terms of the branch of Statistical Mechanics currently referred to as "Modern Critical Theory" [Stanley, H.E., 1987. Introduction to Phase Transitions and Critical Phenomena. Oxford University Press; Marro, J., Dickman, R., 1999. Nonequilibrium Phase Transitions in Lattice Models. Cambridge University Press, Cambridge, UK]. The application of this framework is here explored in two stages: in the first place, its principles are applied to state transitions in global brain dynamics, with benchmarks of Cognitive Neuroscience providing the relevant empirical reference points. The second stage generalizes to suggest in more detail how the same principles could also apply to the relation between other levels of the structural-functional hierarchy of the nervous system and between neural assemblies. In this view, state transitions resulting from the processing at one level are the input to the next, in the image of a 'bucket brigade', with the content of each bucket being passed on along the chain, after having undergone a state transition. The unique features of a process of this kind will be discussed and illustrated.

  8. Field-induced magnetic phase transitions and metastable states in Tb 3 Ni

    SciT

    Gubkin, A. F.; Wu, L. S.; Nikitin, S. E.

    In this study we report the detailed study of magnetic phase diagrams, low-temperature magnetic structures, and the magnetic field effect on the electrical resistivity of the binary intermetallic compoundmore » $${\\mathrm{Tb}}_{3}\\mathrm{Ni}$$. The incommensurate magnetic structure of the spin-density-wave type described with magnetic superspace group $$P{112}_{1}/a{1}^{{'}}(ab0)0ss$$ and propagation vector $${\\mathbf{k}}_{\\mathrm{IC}}=\\left[0.506,0.299,0\\right]$$ was found to emerge just below Néel temperature $${T}_{\\mathrm{N}}=61$$ K. Further cooling below 58 K results in the appearance of multicomponent magnetic states: (i) a combination of $${\\mathbf{k}}_{1}=\\left[\\frac{1}{2},\\frac{1}{2},0\\right]$$ and $${\\mathbf{k}}_{\\mathrm{IC}}$$ in the temperature range 51 < T < 58 K; (ii) a mixed magnetic state of $${\\mathbf{k}}_{\\mathrm{IC}}, {\\mathbf{k}}_{1}$$, and $${\\mathbf{k}}_{2}=\\left[\\frac{1}{2},\\frac{1}{4},0\\right]$$ with the partially locked-in incommensurate component in the temperature range 48 < T < 51 K; and (iii) a low-temperature magnetic structure that is described by the intersection of two isotropy subgroups associated with the irreducible representations of two coupled primary order parameters (OPs) $${\\mathbf{k}}_{2}=\\left[\\frac{1}{2},\\frac{1}{4},0\\right]$$ and $${\\mathbf{k}}_{3}=\\left[\\frac{1}{2},\\frac{1}{3},0\\right]$$ and involves irreducible representations of the secondary OPs $${\\mathbf{k}}_{1}=\\left[\\frac{1}{2},\\frac{1}{2},0\\right]$$ and $${\\mathbf{k}}_{4}=\\left[\\frac{1}{2},0,0\\right]$$ below 48 K. An external magnetic field suppresses the complex low-temperature antiferromagnetic states and induces metamagnetic transitions towards a forced ferromagnetic state that are accompanied by a substantial magnetoresistance effect due to the magnetic superzone effect. Finally, the forced ferromagnetic state induced after application of an external magnetic field along the $b$ and $c$ crystallographic axes was

  9. Field-induced magnetic phase transitions and metastable states in Tb 3 Ni

    DOE PAGES

    Gubkin, A. F.; Wu, L. S.; Nikitin, S. E.; ...

    2018-04-26

    In this study we report the detailed study of magnetic phase diagrams, low-temperature magnetic structures, and the magnetic field effect on the electrical resistivity of the binary intermetallic compoundmore » $${\\mathrm{Tb}}_{3}\\mathrm{Ni}$$. The incommensurate magnetic structure of the spin-density-wave type described with magnetic superspace group $$P{112}_{1}/a{1}^{{'}}(ab0)0ss$$ and propagation vector $${\\mathbf{k}}_{\\mathrm{IC}}=\\left[0.506,0.299,0\\right]$$ was found to emerge just below Néel temperature $${T}_{\\mathrm{N}}=61$$ K. Further cooling below 58 K results in the appearance of multicomponent magnetic states: (i) a combination of $${\\mathbf{k}}_{1}=\\left[\\frac{1}{2},\\frac{1}{2},0\\right]$$ and $${\\mathbf{k}}_{\\mathrm{IC}}$$ in the temperature range 51 < T < 58 K; (ii) a mixed magnetic state of $${\\mathbf{k}}_{\\mathrm{IC}}, {\\mathbf{k}}_{1}$$, and $${\\mathbf{k}}_{2}=\\left[\\frac{1}{2},\\frac{1}{4},0\\right]$$ with the partially locked-in incommensurate component in the temperature range 48 < T < 51 K; and (iii) a low-temperature magnetic structure that is described by the intersection of two isotropy subgroups associated with the irreducible representations of two coupled primary order parameters (OPs) $${\\mathbf{k}}_{2}=\\left[\\frac{1}{2},\\frac{1}{4},0\\right]$$ and $${\\mathbf{k}}_{3}=\\left[\\frac{1}{2},\\frac{1}{3},0\\right]$$ and involves irreducible representations of the secondary OPs $${\\mathbf{k}}_{1}=\\left[\\frac{1}{2},\\frac{1}{2},0\\right]$$ and $${\\mathbf{k}}_{4}=\\left[\\frac{1}{2},0,0\\right]$$ below 48 K. An external magnetic field suppresses the complex low-temperature antiferromagnetic states and induces metamagnetic transitions towards a forced ferromagnetic state that are accompanied by a substantial magnetoresistance effect due to the magnetic superzone effect. Finally, the forced ferromagnetic state induced after application of an external magnetic field along the $b$ and $c$ crystallographic axes was

  10. Are rapid transitions between invasive and native species caused by alternative stable states, and does it matter?

    PubMed

    Hansen, Gretchen J A; Ives, Anthony R; Vander Zanden, M Jake; Carpenter, Stephen R

    2013-10-01

    Rapid transitions in ecosystem structure, or regime shifts, are a hallmark of alternative stable states (ASS). However, regime shifts can occur even when feedbacks are not strong enough to cause ASS. We investigated the potential for ASS to explain transitions between dominance of an invasive species, rusty crayfish (Orconectes rusticus), and native sunfishes (Lepomis spp.) in northern Wisconsin (USA) lakes. A rapid transition from Lepomis to rusty crayfish dominance occurred as rusty crayfish invaded Trout Lake, and the reverse transition resulted from an eight-year experimental removal of rusty crayfish from Sparkling Lake. We fit a stage-structured population model of species interactions to 31 years of time-series data from each lake. The model identified water level as an important driver, with drought conditions reducing rusty crayfish recruitment and allowing Lepomis dominance. The maximum-likelihood parameter estimates of the negative interaction between rusty crayfish and Lepomis led to ASS in the model, where each species was capable of excluding the other within a narrow range of environmental conditions. However, uncertainty in parameter estimates made it impossible to exclude the potential that rapid transitions were caused by a simpler threshold response lacking alternative equilibria. Simulated forward and backward transitions between species dominance occurred at different environmental conditions (i.e., hysteresis), even when the parameters used for simulation did not predict ASS as a result of slow species responses to environmental drivers. Thus, ASS are possible, but by no means certain, explanations for rapid transitions in this system, and our results highlight the difficulties associated with distinguishing ASS from other types of threshold responses. However, whether regime shifts are caused by ASS may be relatively unimportant in this system, as the range of conditions over which transitions occur is narrow, and under most conditions, the

  11. Can quantum transition state theory be defined as an exact t = 0+ limit?

    NASA Astrophysics Data System (ADS)

    Jang, Seogjoo; Voth, Gregory A.

    2016-02-01

    The definition of the classical transition state theory (TST) as a t → 0+ limit of the flux-side time correlation function relies on the assumption that simultaneous measurement of population and flux is a well defined physical process. However, the noncommutativity of the two measurements in quantum mechanics makes the extension of such a concept to the quantum regime impossible. For this reason, quantum TST (QTST) has been generally accepted as any kind of quantum rate theory reproducing the TST in the classical limit, and there has been a broad consensus that no unique QTST retaining all the properties of TST can be defined. Contrary to this widely held view, Hele and Althorpe (HA) [J. Chem. Phys. 138, 084108 (2013)] recently suggested that a true QTST can be defined as the exact t → 0+ limit of a certain kind of quantum flux-side time correlation function and that it is equivalent to the ring polymer molecular dynamics (RPMD) TST. This work seeks to question and clarify certain assumptions underlying these suggestions and their implications. First, the time correlation function used by HA as a starting expression is not related to the kinetic rate constant by virtue of linear response theory, which is the first important step in relating a t = 0+ limit to a physically measurable rate. Second, a theoretical analysis calls into question a key step in HA's proof which appears not to rely on an exact quantum mechanical identity. The correction of this makes the true t = 0+ limit of HA's QTST different from the RPMD-TST rate expression, but rather equal to the well-known path integral quantum transition state theory rate expression for the case of centroid dividing surface. An alternative quantum rate expression is then formulated starting from the linear response theory and by applying a recently developed formalism of real time dynamics of imaginary time path integrals [S. Jang, A. V. Sinitskiy, and G. A. Voth, J. Chem. Phys. 140, 154103 (2014)]. It is shown

  12. Identification of predictive biomarkers of disease state in transition dairy cows.

    PubMed

    Hailemariam, D; Mandal, R; Saleem, F; Dunn, S M; Wishart, D S; Ametaj, B N

    2014-05-01

    In dairy cows, periparturient disease states, such as metritis, mastitis, and laminitis, are leading to increasingly significant economic losses for the dairy industry. Treatments for these pathologies are often expensive, ineffective, or not cost-efficient, leading to production losses, high veterinary bills, or early culling of the cows. Early diagnosis or detection of these conditions before they manifest themselves could lower their incidence, level of morbidity, and the associated economic losses. In an effort to identify predictive biomarkers for postpartum or periparturient disease states in dairy cows, we undertook a cross-sectional and longitudinal metabolomics study to look at plasma metabolite levels of dairy cows during the transition period, before and after becoming ill with postpartum diseases. Specifically we employed a targeted quantitative metabolomics approach that uses direct flow injection mass spectrometry to track the metabolite changes in 120 different plasma metabolites. Blood plasma samples were collected from 12 dairy cows at 4 time points during the transition period (-4 and -1 wk before and 1 and 4 wk after parturition). Out of the 12 cows studied, 6 developed multiple periparturient disorders in the postcalving period, whereas the other 6 remained healthy during the entire experimental period. Multivariate data analysis (principal component analysis and partial least squares discriminant analysis) revealed a clear separation between healthy controls and diseased cows at all 4 time points. This analysis allowed us to identify several metabolites most responsible for separating the 2 groups, especially before parturition and the start of any postpartum disease. Three metabolites, carnitine, propionyl carnitine, and lysophosphatidylcholine acyl C14:0, were significantly elevated in diseased cows as compared with healthy controls as early as 4 wk before parturition, whereas 2 metabolites, phosphatidylcholine acyl-alkyl C42:4 and

  13. 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.

  14. MHD Simulation for Investigating the Dynamic State Transition Responsible for a Solar Eruption in Active Region 12158

    NASA Astrophysics Data System (ADS)

    Lee, Hwanhee; Magara, Tetsuya

    2018-06-01

    We present a magnetohydrodynamic model of solar eruption based on the dynamic state transition from the quasi-static state to the eruptive state of an active region (AR) magnetic field. For the quasi-static state before an eruption, we consider the existence of a slow solar wind originating from an AR, which may continuously make the AR magnetic field deviate from mechanical equilibrium. In this model, we perform a three-dimensional magnetohydrodynamic simulation of AR 12158 producing a coronal mass ejection, where the initial magnetic structure of the simulation is given by a nonlinear force-free field derived from an observed photospheric vector magnetic field. We then apply a pressure-driven outflow to the upper part of the magnetic structure to achieve a quasi-static pre-eruptive state. The simulation shows that the eruptive process observed in this AR may be caused by the dynamic state transition of an AR magnetic field, which is essentially different from the destabilization of a static magnetic field. The dynamic state transition is determined from the shape evolution of the magnetic field line according to the κH-mechanism. This work demonstrates how the mechanism works to produce a solar eruption in the dynamic solar corona governed by the gravitational field and the continuous outflows of solar wind.

  15. Hydrogen-bonded intermediates and transition states during spontaneous and acid-catalyzed hydrolysis of the carcinogen (+)-anti-BPDE.

    PubMed

    Palenik, Mark C; Rodriguez, Jorge H

    2014-07-07

    Understanding mechanisms of (+)-anti-BPDE detoxification is crucial for combating its mutagenic and potent carcinogenic action. However, energetic-structural correlations of reaction intermediates and transition states during detoxification via hydrolysis are poorly understood. To gain mechanistic insight we have computationally characterized intermediate and transition species associated with spontaneous and general-acid catalyzed hydrolysis of (+)-anti-BPDE. We studied the role of cacodylic acid as a proton donor in the rate limiting step. The computed activation energy (ΔG‡) is in agreement with the experimental value for hydrolysis in a sodium cacodylate buffer. Both types of, spontaneous and acid catalyzed, BPDE hydrolysis can proceed through low-entropy hydrogen bonded intermediates prior to formation of transition states whose energies determine reaction activation barriers and rates.

  16. Different secondary structure elements as scaffolds for protein folding transition states of two homologous four-helix bundles.

    PubMed

    Teilum, Kaare; Thormann, Thorsten; Caterer, Nigel R; Poulsen, Heidi I; Jensen, Peter H; Knudsen, Jens; Kragelund, Birthe B; Poulsen, Flemming M

    2005-04-01

    Comparison of the folding processes for homologue proteins can provide valuable information about details in the interactions leading to the formation of the folding transition state. Here the folding kinetics of 18 variants of yACBP and 3 variants of bACBP have been studied by Phi-value analysis. In combination with Phi-values from previous work, detailed insight into the transition states for folding of both yACBP and bACBP has been obtained. Of the 16 sequence positions that have been studied in both yACBP and bACBP, 5 (V12, I/L27, Y73, V77, and L80) have high Phi-values and appear to be important for the transition state formation in both homologues. Y31, A34, and A69 have high Phi-values only in yACBP, while F5, A9, and I74 have high Phi-values only in bACBP. Thus, additional interactions between helices A2 and A4 appear to be important for the transition state of yACBP, whereas additional interactions between helices A1 and A4 appear to be important for the transition state of bACBP. To examine whether these differences could be assigned to different packing of the residues in the native state, a solution structure of yACBP was determined by NMR. Small changes in the packing of the hydrophobic side-chains, which strengthen the interactions between helices A2 and A4, are observed in yACBP relative to bACBP. It is suggested that different structure elements serve as scaffolds for the folding of the 2 ACBP homologues. (c) 2005 Wiley-Liss, Inc.

  17. Interface and phase transition between Moore-Read and Halperin 331 fractional quantum Hall states: Realization of chiral Majorana fermion

    NASA Astrophysics Data System (ADS)

    Yang, Kun

    2017-12-01

    We consider an interface separating the Moore-Read state and Halperin 331 state in a half-filled Landau level, which can be realized in a double quantum well system with varying interwell tunneling and/or interaction strengths. In the presence of electron tunneling and strong Coulomb interactions across the interface, we find that all charge modes localize and the only propagating mode left is a chiral Majorana fermion mode. Methods to probe this neutral mode are proposed. A quantum phase transition between the Moore-Read and Halperin 331 states is described by a network of such Majorana fermion modes. In addition to a direct transition, they may also be separated by a phase in which the Majorana fermions are delocalized, realizing an incompressible state which exhibits quantum Hall charge transport and bulk heat conduction.

  18. Identification of ground-state spin ordering in antiferromagnetic transition metal oxides using the Ising model and a genetic algorithm

    PubMed Central

    Lee, Kyuhyun; Youn, Yong; Han, Seungwu

    2017-01-01

    Abstract We identify ground-state collinear spin ordering in various antiferromagnetic transition metal oxides by constructing the Ising model from first-principles results and applying a genetic algorithm to find its minimum energy state. The present method can correctly reproduce the ground state of well-known antiferromagnetic oxides such as NiO, Fe2O3, Cr2O3 and MnO2. Furthermore, we identify the ground-state spin ordering in more complicated materials such as Mn3O4 and CoCr2O4. PMID:28458746

  19. 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.

  20. Evaluating Systemic Change in the National Head Start-Public School Transition Project: Perspectives from Five States.

    ERIC Educational Resources Information Center

    Greene, Andrea; And Others

    In 1991 the Department of Health and Human Services funded 32 sites throughout the United States to develop and implement Head Start-Public School Early Childhood Transition Demonstration Projects. The purpose of 31 projects, which are in their fourth year of operation, is to stimulate partnerships among Head Start agencies, public schools, and…

  1. Developing ecological site and state-and-transition models for grazed riparian pastures at Tejon Ranch, California

    Felix P. Ratcliff; James Bartolome; Michele Hammond; Sheri Spiegal; Michael White

    2015-01-01

    Ecological site descriptions and associated state-and-transition models are useful tools for understanding the variable effects of management and environment on range resources. Models for woody riparian sites have yet to be fully developed. At Tejon Ranch, in the southern San Joaquin Valley of California, we are using ecological site theory to investigate the role of...

  2. Use of state-and-transition simulation modeling in National Forest planning in the Pacific Northwest, U.S.A

    Ayn J. Shlisky; Don Vandendriesche

    2012-01-01

    Effective national forest planning depends on scientifically sound analyses of land management alternatives relative to desired future conditions and environmental effects. The USDA Forest Service Pacific Northwest Region is currently using state-and-transition simulation models (STMs) to simulate changes in forest composition and structure for the revisions of five...

  3. Stated Briefly: Participation and Pass Rates for College Preparatory Transition Courses in Kentucky. REL 2015-060

    ERIC Educational Resources Information Center

    Cramer, Eric; Mokher, Christine

    2015-01-01

    This study examines Kentucky high school students' participation and pass rates in college preparatory transition courses, voluntary remedial courses in math and reading offered to grade 12 students. These courses are targeted to students scoring just below the state's college readiness benchmarks on the ACT in grade 11. The study found that:…

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

    PubMed

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

    2010-06-03

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

  5. 19 CFR 123.64 - Baggage in transit through the United States between ports in Canada or in Mexico.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... between ports in Canada or in Mexico. 123.64 Section 123.64 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CBP RELATIONS WITH CANADA AND MEXICO Baggage § 123.64 Baggage in transit through the United States between ports in Canada or in Mexico. (a...

  6. 19 CFR 123.64 - Baggage in transit through the United States between ports in Canada or in Mexico.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... between ports in Canada or in Mexico. 123.64 Section 123.64 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CBP RELATIONS WITH CANADA AND MEXICO Baggage § 123.64 Baggage in transit through the United States between ports in Canada or in Mexico. (a...

  7. 19 CFR 123.64 - Baggage in transit through the United States between ports in Canada or in Mexico.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... between ports in Canada or in Mexico. 123.64 Section 123.64 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CBP RELATIONS WITH CANADA AND MEXICO Baggage § 123.64 Baggage in transit through the United States between ports in Canada or in Mexico. (a...

  8. 19 CFR 123.64 - Baggage in transit through the United States between ports in Canada or in Mexico.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... between ports in Canada or in Mexico. 123.64 Section 123.64 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY CBP RELATIONS WITH CANADA AND MEXICO Baggage § 123.64 Baggage in transit through the United States between ports in Canada or in Mexico. (a...

  9. Effects of a transition to a hydrogen economy on employment in the United States Report to Congress

    SciT

    None, None

    2008-07-01

    DOE's Effects of a Transition to a Hydrogen Economy on Employment in the United States Report to Congress estimates the employment effects of a transformation of the U.S. economy to the use of hydrogen in the 2020 to 2050 timeframe. This report fulfills requirements of section 1820 of the Energy Policy Act of 2005.

  10. Fire rehabilitation decisions at landscape scales: utilizing state-and-transition models developed through disturbance response grouping of ecological sites

    Recognizing the utility of ecological sites and the associated state-and-transition model (STM) for decision support, the Bureau of Land Management in Nevada partnered with Nevada NRCS and the University of Nevada, Reno (UNR) in 2009 with the goal of creating a team that could (1) expedite developme...

  11. State-of-the-Art Review Prediction and Control of Groundborne Noise and Vibration from Rail Transit Trains : Annotated Bibliography

    DOT National Transportation Integrated Search

    1982-02-01

    This interim report presents an annotated bibliography that has been compiled as part of a comprehensive review of the state-of-the-art in the prediction and control of groundborne noise and vibration created by rail transit operations. Included in t...

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

    PubMed Central

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

    2010-01-01

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

  13. Rupture and Adaptation: British Technical Expertise to the Singapore Polytechnic and the Transition to a Nation-State

    ERIC Educational Resources Information Center

    Seng, Loh Kah

    2015-01-01

    The Singapore Polytechnic underwent a period of both rupture and adaptation as British advisers worked with the post-colonial government to facilitate technical education reform and Singapore's transition to a nation-state. Established in 1958 and based on the metropolitan model, the Singapore Polytechnic constituted an imperial project for…

  14. Dynamical transitions in large systems of mean field-coupled Landau-Stuart oscillators: Extensive chaos and cluster states.

    PubMed

    Ku, Wai Lim; Girvan, Michelle; Ott, Edward

    2015-12-01

    In this paper, we study dynamical systems in which a large number N of identical Landau-Stuart oscillators are globally coupled via a mean-field. Previously, it has been observed that this type of system can exhibit a variety of different dynamical behaviors. These behaviors include time periodic cluster states in which each oscillator is in one of a small number of groups for which all oscillators in each group have the same state which is different from group to group, as well as a behavior in which all oscillators have different states and the macroscopic dynamics of the mean field is chaotic. We argue that this second type of behavior is "extensive" in the sense that the chaotic attractor in the full phase space of the system has a fractal dimension that scales linearly with N and that the number of positive Lyapunov exponents of the attractor also scales linearly with N. An important focus of this paper is the transition between cluster states and extensive chaos as the system is subjected to slow adiabatic parameter change. We observe discontinuous transitions between the cluster states (which correspond to low dimensional dynamics) and the extensively chaotic states. Furthermore, examining the cluster state, as the system approaches the discontinuous transition to extensive chaos, we find that the oscillator population distribution between the clusters continually evolves so that the cluster state is always marginally stable. This behavior is used to reveal the mechanism of the discontinuous transition. We also apply the Kaplan-Yorke formula to study the fractal structure of the extensively chaotic attractors.

  15. Dynamical transitions in large systems of mean field-coupled Landau-Stuart oscillators: Extensive chaos and cluster states

    SciT

    Ku, Wai Lim; Girvan, Michelle; Ott, Edward

    In this paper, we study dynamical systems in which a large number N of identical Landau-Stuart oscillators are globally coupled via a mean-field. Previously, it has been observed that this type of system can exhibit a variety of different dynamical behaviors. These behaviors include time periodic cluster states in which each oscillator is in one of a small number of groups for which all oscillators in each group have the same state which is different from group to group, as well as a behavior in which all oscillators have different states and the macroscopic dynamics of the mean field ismore » chaotic. We argue that this second type of behavior is “extensive” in the sense that the chaotic attractor in the full phase space of the system has a fractal dimension that scales linearly with N and that the number of positive Lyapunov exponents of the attractor also scales linearly with N. An important focus of this paper is the transition between cluster states and extensive chaos as the system is subjected to slow adiabatic parameter change. We observe discontinuous transitions between the cluster states (which correspond to low dimensional dynamics) and the extensively chaotic states. Furthermore, examining the cluster state, as the system approaches the discontinuous transition to extensive chaos, we find that the oscillator population distribution between the clusters continually evolves so that the cluster state is always marginally stable. This behavior is used to reveal the mechanism of the discontinuous transition. We also apply the Kaplan-Yorke formula to study the fractal structure of the extensively chaotic attractors.« less

  16. Dynamical transitions in large systems of mean field-coupled Landau-Stuart oscillators: Extensive chaos and cluster states

    NASA Astrophysics Data System (ADS)

    Ku, Wai Lim; Girvan, Michelle; Ott, Edward

    2015-12-01

    In this paper, we study dynamical systems in which a large number N of identical Landau-Stuart oscillators are globally coupled via a mean-field. Previously, it has been observed that this type of system can exhibit a variety of different dynamical behaviors. These behaviors include time periodic cluster states in which each oscillator is in one of a small number of groups for which all oscillators in each group have the same state which is different from group to group, as well as a behavior in which all oscillators have different states and the macroscopic dynamics of the mean field is chaotic. We argue that this second type of behavior is "extensive" in the sense that the chaotic attractor in the full phase space of the system has a fractal dimension that scales linearly with N and that the number of positive Lyapunov exponents of the attractor also scales linearly with N. An important focus of this paper is the transition between cluster states and extensive chaos as the system is subjected to slow adiabatic parameter change. We observe discontinuous transitions between the cluster states (which correspond to low dimensional dynamics) and the extensively chaotic states. Furthermore, examining the cluster state, as the system approaches the discontinuous transition to extensive chaos, we find that the oscillator population distribution between the clusters continually evolves so that the cluster state is always marginally stable. This behavior is used to reveal the mechanism of the discontinuous transition. We also apply the Kaplan-Yorke formula to study the fractal structure of the extensively chaotic attractors.

  17. Ground state of underdoped cuprates in vicinity of superconductor-to-insulator transition

    DOE PAGES

    Wu, Jie; Bollinger, Anthony T.; Sun, Yujie; ...

    2016-08-15

    When an insulating underdoped cuprate is doped beyond a critical concentration (x c), high-temperature superconductivity emerges. We have synthesized a series of La 2–xSr xCuO 4 (LSCO) samples using the combinatorial spread technique that allows us to traverse the superconductor-to-insulator transition (SIT) in extremely fine doping steps, Δx≈0.00008. We have measured the Hall resistivity (ρ H) as a function of temperature down to 300 mK in magnetic fields up to 9 T. At very low temperatures, ρ H shows an erratic behavior, jumps and fluctuations exceeding 100%, hysteresis, and memory effects, indicating that the insulating ground state is a charge-clustermore » glass (CCG). Furthermore, based on the phase diagram depicted in our experiment, we propose a unified picture to account for the anomalous electric transport in the vicinity of the SIT, suggesting that the CCG is in fact a disordered and glassy version of the charge density wave.« less

  18. Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site.

    PubMed

    Roston, Daniel; Demapan, Darren; Cui, Qiang

    2016-06-15

    A reaction's transition state (TS) structure plays a critical role in determining reactivity and has important implications for the design of catalysts, drugs, and other applications. Here, we explore TS structure in the enzyme alkaline phosphatase using hybrid Quantum Mechanics/Molecular Mechanics simulations. We find that minor perturbations to the substrate have major effects on TS structure and the way the enzyme stabilizes the TS. Substrates with good leaving groups (LGs) have little cleavage of the phosphorus-LG bond at the TS, while substrates with poor LGs have substantial cleavage of that bond. The results predict nonlinear free energy relationships for a single rate-determining step, and substantial differences in kinetic isotope effects for different substrates; both trends were observed in previous experimental studies, although the original interpretations differed from the present model. Moreover, due to different degrees of phosphorus-LG bond cleavage at the TS for different substrates, the LG is stabilized by different interactions at the TS: while a poor LG is directly stabilized by an active site zinc ion, a good LG is mainly stabilized by active site water molecules. Our results demonstrate the considerable plasticity of TS structure and stabilization in enzymes. Furthermore, perturbations to reactivity that probe TS structure experimentally (i.e., substituent effects) may substantially perturb the TS they aim to probe, and thus classical experimental approaches such as free energy relations should be interpreted with care.

  19. Rate constants of chemical reactions from semiclassical transition state theory in full and one dimension.

    PubMed

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

    2016-06-28

    Semiclassical Transition State Theory (SCTST), a method for calculating rate constants of chemical reactions, offers gains in computational efficiency relative to more accurate quantum scattering methods. In full-dimensional (FD) SCTST, reaction probabilities are calculated from third and fourth potential derivatives along all vibrational degrees of freedom. However, the computational cost of FD SCTST scales unfavorably with system size, which prohibits its application to larger systems. In this study, the accuracy and efficiency of 1-D SCTST, in which only third and fourth derivatives along the reaction mode are used, are investigated in comparison to those of FD SCTST. Potential derivatives are obtained from numerical ab initio Hessian matrix calculations at the MP2/cc-pVTZ level of theory, and Richardson extrapolation is applied to improve the accuracy of these derivatives. Reaction barriers are calculated at the CCSD(T)/cc-pVTZ level. Results from FD SCTST agree with results from previous theoretical and experimental studies when Richardson extrapolation is applied. Results from our implementation of 1-D SCTST, which uses only 4 single-point MP2/cc-pVTZ energy calculations in addition to those for conventional TST, agree with FD results to within a factor of 5 at 250 K. This degree of agreement and the efficiency of the 1-D method suggest its potential as a means of approximating rate constants for systems too large for existing quantum scattering methods.

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

    NASA Astrophysics Data System (ADS)

    Zopf, Michael; Keil, Robert; Chen, Yan; HöFer, Bianca; Zhang, Jiaxiang; Ding, Fei; Schmidt, Oliver G.

    Semiconductor InAs/GaAs quantum dots grown by the Stranski-Krastanov method are among the leading candidates for the deterministic generation of polarization entangled photon pairs. Despite remarkable progress in the last twenty years, many challenges still remain for this material, such as the extremely low yield (< 1% quantum dots can emit entangled photons), the low degree of entanglement, and the large wavelength distribution. Here we show that, with an emerging family of GaAs/AlGaAs quantum dots grown by droplet etching and nanohole infilling, it is possible to obtain a large ensemble (close to 100%) of polarization-entangled photon emitters on a wafer without any post-growth tuning. Under pulsed resonant two-photon excitation, all measured quantum dots emit single pairs of entangled photons with ultra-high purity, high degree of entanglement (fidelity up to F=0.91, with a record high concurrence C=0.90), and ultra-narrow wavelength distribution at rubidium transitions. Therefore, a solid-state quantum repeater - among many other key enabling quantum photonic elements - can be practically implemented with this new material. Financially supported by BMBF Q.Com-H (16KIS0106) and the Euro- pean Union Seventh Framework Programme 209 (FP7/2007-2013) under Grant Agreement No. 601126 210 (HANAS).

  1. Characterisation of transition state structures for protein folding using 'high', 'medium' and 'low' {Phi}-values.

    PubMed

    Geierhaas, Christian D; Salvatella, Xavier; Clarke, Jane; Vendruscolo, Michele

    2008-03-01

    It has been suggested that Phi-values, which allow structural information about transition states (TSs) for protein folding to be obtained, are most reliably interpreted when divided into three classes (high, medium and low). High Phi-values indicate almost completely folded regions in the TS, intermediate Phi-values regions with a detectable amount of structure and low Phi-values indicate mostly unstructured regions. To explore the extent to which this classification can be used to characterise in detail the structure of TSs for protein folding, we used Phi-values divided into these classes as restraints in molecular dynamics simulations. This type of procedure is related to that used in NMR spectroscopy to define the structure of native proteins from the measurement of inter-proton distances derived from nuclear Overhauser effects. We illustrate this approach by determining the TS ensembles of five proteins and by showing that the results are similar to those obtained by using as restraints the actual numerical Phi-values measured experimentally. Our results indicate that the simultaneous consideration of a set of low-resolution Phi-values can provide sufficient information for characterising the architecture of a TS for folding of a protein.

  2. State Transition Matrix for Perturbed Orbital Motion Using Modified Chebyshev Picard Iteration

    NASA Astrophysics Data System (ADS)

    Read, Julie L.; Younes, Ahmad Bani; Macomber, Brent; Turner, James; Junkins, John L.

    2015-06-01

    The Modified Chebyshev Picard Iteration (MCPI) method has recently proven to be highly efficient for a given accuracy compared to several commonly adopted numerical integration methods, as a means to solve for perturbed orbital motion. This method utilizes Picard iteration, which generates a sequence of path approximations, and Chebyshev Polynomials, which are orthogonal and also enable both efficient and accurate function approximation. The nodes consistent with discrete Chebyshev orthogonality are generated using cosine sampling; this strategy also reduces the Runge effect and as a consequence of orthogonality, there is no matrix inversion required to find the basis function coefficients. The MCPI algorithms considered herein are parallel-structured so that they are immediately well-suited for massively parallel implementation with additional speedup. MCPI has a wide range of applications beyond ephemeris propagation, including the propagation of the State Transition Matrix (STM) for perturbed two-body motion. A solution is achieved for a spherical harmonic series representation of earth gravity (EGM2008), although the methodology is suitable for application to any gravity model. Included in this representation the normalized, Associated Legendre Functions are given and verified numerically. Modifications of the classical algorithm techniques, such as rewriting the STM equations in a second-order cascade formulation, gives rise to additional speedup. Timing results for the baseline formulation and this second-order formulation are given.

  3. 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.

  4. The mechanism and high-free-energy transition state of lac repressor–lac operator interaction

    PubMed Central

    Sengupta, Rituparna; Capp, Michael W.; Shkel, Irina A.

    2017-01-01

    Abstract Significant, otherwise-unavailable information about mechanisms and transition states (TS) of protein folding and binding is obtained from solute effects on rate constants. Here we characterize TS for lac repressor(R)–lac operator(O) binding by analyzing effects of RO-stabilizing and RO-destabilizing solutes on association (ka) and dissociation (kd) rate constants. RO-destabilizing solutes (urea, KCl) reduce ka comparably (urea) or more than (KCl) they increase kd, demonstrating that they destabilize TS relative to reactants and RO, and that TS exhibits most of the Coulombic interactions between R and O. Strikingly, three solutes which stabilize RO by favoring burial/dehydration of amide oxygens and anionic phosphate oxygens all reduce kd without affecting ka significantly. The lack of stabilization of TS by these solutes indicates that O phosphates remain hydrated in TS and that TS preferentially buries aromatic carbons and amide nitrogens while leaving amide oxygens exposed. In our proposed mechanism, DNA-binding-domains (DBD) of R insert in major grooves of O pre-TS, forming most Coulombic interactions of RO and burying aromatic carbons. Nucleation of hinge helices creates TS, burying sidechain amide nitrogens. Post-TS, hinge helices assemble and the DBD-hinge helix-O-DNA module docks on core repressor, partially dehydrating phosphate oxygens and tightening all interfaces to form RO. PMID:29036376

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

    PubMed

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

    2015-01-01

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

  6. The anatomy of microbial cell state transitions in response to oxygen.

    PubMed

    Schmid, Amy K; Reiss, David J; Kaur, Amardeep; Pan, Min; King, Nichole; Van, Phu T; Hohmann, Laura; Martin, Daniel B; Baliga, Nitin S

    2007-10-01

    Adjustment of physiology in response to changes in oxygen availability is critical for the survival of all organisms. However, the chronology of events and the regulatory processes that determine how and when changes in environmental oxygen tension result in an appropriate cellular response is not well understood at a systems level. Therefore, transcriptome, proteome, ATP, and growth changes were analyzed in a halophilic archaeon to generate a temporal model that describes the cellular events that drive the transition between the organism's two opposing cell states of anoxic quiescence and aerobic growth. According to this model, upon oxygen influx, an initial burst of protein synthesis precedes ATP and transcription induction, rapidly driving the cell out of anoxic quiescence, culminating in the resumption of growth. This model also suggests that quiescent cells appear to remain actively poised for energy production from a variety of different sources. Dynamic temporal analysis of relationships between transcription and translation of key genes suggests several important mechanisms for cellular sustenance under anoxia as well as specific instances of post-transcriptional regulation.

  7. The anatomy of microbial cell state transitions in response to oxygen

    PubMed Central

    Schmid, Amy K.; Reiss, David J.; Kaur, Amardeep; Pan, Min; King, Nichole; Van, Phu T.; Hohmann, Laura; Martin, Daniel B.; Baliga, Nitin S.

    2007-01-01

    Adjustment of physiology in response to changes in oxygen availability is critical for the survival of all organisms. However, the chronology of events and the regulatory processes that determine how and when changes in environmental oxygen tension result in an appropriate cellular response is not well understood at a systems level. Therefore, transcriptome, proteome, ATP, and growth changes were analyzed in a halophilic archaeon to generate a temporal model that describes the cellular events that drive the transition between the organism’s two opposing cell states of anoxic quiescence and aerobic growth. According to this model, upon oxygen influx, an initial burst of protein synthesis precedes ATP and transcription induction, rapidly driving the cell out of anoxic quiescence, culminating in the resumption of growth. This model also suggests that quiescent cells appear to remain actively poised for energy production from a variety of different sources. Dynamic temporal analysis of relationships between transcription and translation of key genes suggests several important mechanisms for cellular sustenance under anoxia as well as specific instances of post-transcriptional regulation. PMID:17785531

  8. Transition-state charge transfer reveals electrophilic, ambiphilic, and nucleophilic carbon-hydrogen bond activation.

    PubMed

    Ess, Daniel H; Nielsen, Robert J; Goddard, William A; Periana, Roy A

    2009-08-26

    Absolutely localized molecular orbital energy decomposition analysis of C-H activation transition states (TSs), including Pt, Au, Ir, Ru, W, Sc, and Re metal centers, shows an electrophilic, ambiphilic, and nucleophilic charge transfer (CT) continuum irrespective of the bonding paradigm (oxidative addition, sigma-bond metathesis, oxidative hydrogen migration, 1,2-substitution). Pt(II) insertion and Au(III) substitution TSs are highly electrophilic and dominated by C-H bond to metal/ligand orbital stabilization, while Ir-X and Ru-X (X = R, NH(2), OR, or BOR(2)) substitution TSs are ambiphilic in nature. In this ambiphilic activation regime, an increase in one direction of CT typically leads to a decrease in the reverse direction. Comparison of Tp(CO)Ru-OH and Tp(CO)Ru-NH(2) complexes showed no evidence for the classic d(pi)-p(pi) repulsion model. Complexes such as and Cp(CO)(2)W-B(OR)(2), (PNP)Ir(I), Cp(2)ScMe, and (acac-kappaO,kappaO)(2)Re(III)-OH were found to mediate nucleophilic C-H activation, where the CT is dominated by the metal/ligand orbital to C-H antibonding orbital interaction. This CT continuum ultimately affects the metal-alkyl intermediate polarization and possible functionalization reactions. This analysis will impact the design of new activation reactions and stimulate the discovery of more nucleophilic activation complexes.

  9. Ensemble of Transition State Structures for the Cis-Trans Isomerization of N-Methylacetamide

    SciT

    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

  10. Rapid solid-state metathesis route to transition-metal doped titanias

    SciT

    Coleman, Nathaniel; Perera, Sujith; Gillan, Edward G., E-mail: edward-gillan@uiowa.edu

    2015-12-15

    Rapid solid-state metathesis (SSM) reactions are often short-lived highly exothermic reactions that yield a molten alkali halide salt that aids in product growth and crystallization. SSM reactions may also produce kinetically stabilized structures due to the short (seconds) reaction times. This report describes the investigation of rapid SSM reactions in the synthesis of transition-metal doped titanias (M–TiO{sub 2}). The dopant targeted compositions were ten mol percent and based on elemental analysis, many of the M–TiO{sub 2} samples were close to this targeted level. Based on surface analysis, some samples showed large enrichment in surface dopant content, particularly chromium and manganesemore » doped samples. Due to the highly exothermic nature of these reactions, rutile structured TiO{sub 2} was observed in all cases. The M–TiO{sub 2} samples are visible colored and show magnetic and optical properties consistent with the dopant in an oxide environment. UV and visible photocatalytic experiments with these visibly colored rutile M–TiO{sub 2} powders showed that many of them are strongly absorbent for methylene blue dye and degrade the dye under both UV and visible light illumination. This work may open up SSM reactions as an alternate non-thermodynamic reaction strategy for dopant incorporation into a wide range of oxide and non-oxides.« less

  11. Transition-state characterization: a new approach combining inhibitor analogues and variation in enzyme structure.

    PubMed

    Phillips, M A; Kaplan, A P; Rutter, W J; Bartlett, P A

    1992-02-04

    A new strategy of potentially broad application for probing transition-state (TS) analogy in enzymatic systems is described in this paper. The degree to which a series of phosphonate inhibitors act as TS analogues of rat carboxypeptidase A1 has been determined for the wild-type enzyme, for the R127K, R127M, and R127A mutants, and for the R127A mutant in the presence of 0.5 M guanidine hydrochloride. The impact that the mutations have on the inverse second-order rate constants (Km/kcat) for substrate hydrolysis is mirrored by the effect on the inhibition constants (Ki) for the corresponding phosphonate inhibitors. These results demonstrate that the phosphonate moiety mimics some of the electronic as well as the geometric characteristics of the TS. A similar but distinctly separate correlation is observed for tripeptide analogues in comparison to analogues of the dipeptide Cbz-Gly-Phe, reflecting an anomalous mode of binding for the latter system. The selective rate increases and corresponding enhancement in inhibitor binding observed on addition of 0.5 M guanidine hydrochloride to the R127A mutant indicate that the exogenous cation can assume the role played by Arg-127 in stabilizing the TS and in providing substrate selectivity at the P2 position.

  12. Quantifying the structural requirements of the folding transition state of Protein A and other systems

    PubMed Central

    Baxa, Michael C.; Freed, Karl F.; Sosnick, Tobin R.

    2009-01-01

    The B-domain of protein A (BdpA) is a small 3-helix bundle that has been the subject of considerable experimental and theoretical investigation. Nevertheless, a unified view of the structure of the transition state ensemble (TSE) is still lacking. To characterize the TSE of this surprisingly challenging protein, we apply a combination of ψ-analysis (which probes the role of specific side chain to side chain contacts) and kinetic H/D amide isotope effects (which measures of hydrogen bond content), building upon previous studies using mutational φ-analysis (which probes the energetic influence of side chain substitutions). The second helix (H2) is folded in the TSE, while helix formation appears just at the carboxy and amino termini of the first and third helices, respectively. The experimental data suggest a homogenous, yet plastic TS with a native-like topology. This study generalizes our earlier conclusion, based on two larger α/β proteins, that the TSEs of most small proteins achieve ~70% of their native state’s relative contact order. This high percentage limits the degree of possible TS heterogeneity and requires a re-evaluation of the structural content of the TSE of other proteins, especially when they are characterized as small or polarized. PMID:18625237

  13. Time course of myosin heavy chain transitions in neonatal rats: importance of innervation and thyroid state

    NASA Technical Reports Server (NTRS)

    Adams, G. R.; McCue, S. A.; Zeng, M.; Baldwin, K. M.

    1999-01-01

    During the postnatal period, rat limb muscles adapt to weight bearing via the replacement of embryonic (Emb) and neonatal (Neo) myosin heavy chains (MHCs) by the adult isoforms. Our aim was to characterize this transition in terms of the six MHC isoforms expressed in skeletal muscle and to determine the importance of innervation and thyroid hormone status on the attainment of the adult MHC phenotype. Neonatal rats were made hypothyroid via propylthiouracil (PTU) injection. In normal and PTU subgroups, leg muscles were unilaterally denervated at 15 days of age. The MHC profiles of plantaris (PLN) and soleus (Sol) muscles were determined at 7, 14, 23, and 30 days postpartum. At day 7, the Sol MHC profile was 55% type I, 30% Emb, and 10% Neo; in the PLN, the pattern was 60% Neo and 25% Emb. By day 30 the Sol and PLN had essentially attained an adult MHC profile in the controls. PTU augmented slow MHC expression in the Sol, whereas in the PLN it markedly repressed IIb MHC by retaining neonatal MHC expression. Denervation blunted the upregulation of IIb in the PLN and of Type I in the Sol and shifted the pattern to greater expression of IIa and IIx MHCs in both muscles. In contrast to previous observations, these findings collectively suggest that both an intact thyroid and innervation state are obligatory for the attainment of the adult MHC phenotype, particularly in fast-twitch muscles.

  14. Numerical Computation of a Continuous-thrust State Transition Matrix Incorporating Accurate Hardware and Ephemeris Models

    NASA Technical Reports Server (NTRS)

    Ellison, Donald; Conway, Bruce; Englander, Jacob

    2015-01-01

    A significant body of work exists showing that providing a nonlinear programming (NLP) solver with expressions for the problem constraint gradient substantially increases the speed of program execution and can also improve the robustness of convergence, especially for local optimizers. Calculation of these derivatives is often accomplished through the computation of spacecraft's state transition matrix (STM). If the two-body gravitational model is employed as is often done in the context of preliminary design, closed form expressions for these derivatives may be provided. If a high fidelity dynamics model, that might include perturbing forces such as the gravitational effect from multiple third bodies and solar radiation pressure is used then these STM's must be computed numerically. We present a method for the power hardward model and a full ephemeris model. An adaptive-step embedded eight order Dormand-Prince numerical integrator is discussed and a method for the computation of the time of flight derivatives in this framework is presented. The use of these numerically calculated derivatieves offer a substantial improvement over finite differencing in the context of a global optimizer. Specifically the inclusion of these STM's into the low thrust missiondesign tool chain in use at NASA Goddard Spaceflight Center allows for an increased preliminary mission design cadence.

  15. Interfacial states and far-from-equilibrium transitions in the epitaxial growth and erosion on (110) crystal surfaces

    NASA Astrophysics Data System (ADS)

    Levandovsky, Artem; Golubović, Leonardo; Moldovan, Dorel

    2006-12-01

    We discuss the far-from-equilibrium interfacial phenomena occurring in the multilayer homoepitaxial growth and erosion on (110) crystal surfaces. Experimentally, these rectangular symmetry surfaces exhibit a multitude of interesting nonequilibrium interfacial structures, such as the rippled one-dimensional periodic states that are not present in the homoepitaxial growth and erosion on the high symmetry (100) and (111) crystal surfaces. Within a unified phenomenological model, we reveal and elucidate this multitude of states on (110) surfaces as well as the transitions between them. By analytic arguments and numerical simulations, we address experimentally observed transitions between two types of rippled states on (110) surfaces. We discuss several intermediary interface states intervening, via consecutive transitions, between the two rippled states. One of them is the rhomboidal pyramid state, theoretically predicted by Golubovic [Phys. Rev. Lett. 89, 266104 (2002)] and subsequently seen, by de Mongeot and co-workers, in the epitaxial erosion of Cu(110) and Rh(110) surfaces [A. Molle , Phys. Rev. Lett. 93, 256103 (2004), and A. Molle , Phys. Rev. B 73, 155418 (2006)]. In addition, we find a number of interesting intermediary states having structural properties somewhere between those of rippled and pyramidal states. Prominent among them are the rectangular rippled states of long rooflike objects (huts) recently seen on Ag(110) surface. We also predict the existence of a striking interfacial structure that carries nonzero, persistent surface currents. Periodic surface currents vortex lattice formed in this so-called buckled rippled interface state is a far-from-equilibrium relative of the self-organized convective flow patterns in hydrodynamic systems. We discuss the coarsening growth of the multitude of the interfacial states on (110) crystal surfaces.

  16. From Crisis to Transition: The State of Russian Science Based on Focus Groups with Nuclear Physicists

    SciT

    Gerber, T P; Ball, D Y

    and fuel renewed economic progress in Russia. Russian scientists could also be an important source of support for democratic norms: sociologists of science have long argued that scientists tend to support democracy because it provides them with the freedom in which their research can flourish. At the same time, a more recent study suggests that funding shortages may override the researcher's need for freedom and drive scientists to align themselves with the economic policies espoused by Nationalists and Communists in order to survive. Therefore, much turns on the question: ''What is the state of science in Russia today?'' The good news is that focus group interviews with Russian nuclear physicists conducted in October 2001 suggest that the ''science in crisis'' image is one-sided and misleading. Though scientists still complained about low salaries, lack of respect in society, and other similar issues, the participants in the focus groups also expressed positive sentiments about recent changes in the field of science. To be sure, the financing of science remains at a considerably lower level than during the heyday of Soviet times. Yet, it is now possible to earn a decent living as a scientist because of the greater availability of foreign and domestic grants and contracts. In addition, state funding has stabilized over the past few years. Thus, it is more accurate to say that Russian science is in a state of transition rather than in a state of crisis.« less

  17. Manganese Deficiency Leads to Genotype-Specific Changes in Fluorescence Induction Kinetics and State Transitions1[C][OA

    PubMed Central

    Husted, Søren; Laursen, Kristian H.; Hebbern, Christopher A.; Schmidt, Sidsel B.; Pedas, Pai; Haldrup, Anna; Jensen, Poul E.

    2009-01-01

    Barley (Hordeum vulgare) genotypes display a marked difference in their ability to tolerate growth at low manganese (Mn) concentrations, a phenomenon designated as differential Mn efficiency. Induction of Mn deficiency in two genotypes differing in Mn efficiency led to a decline in the quantum yield efficiency for both, although faster in the Mn-inefficient genotype. Leaf tissue and thylakoid Mn concentrations were reduced under Mn deficiency, but no difference between genotypes was observed and no visual Mn deficiency symptoms were developed. Analysis of the fluorescence induction kinetics revealed that in addition to the usual O-J-I-P steps, clear K and D steps were developed in the Mn-inefficient genotype under Mn deficiency. These marked changes indicated damages to photosystem II (PSII). This was further substantiated by state transition measurements, indicating that the ability of plants to redistribute excitation energy was reduced. The percentage change in state transitions for control plants with normal Mn supply of both genotypes was 9% to 11%. However, in Mn-deficient leaves of the Mn-inefficient genotypes, state transitions were reduced to less than 1%, whereas no change was observed for the Mn-efficient genotypes. Immunoblotting and the chlorophyll a/b ratio confirmed that Mn deficiency in general resulted in a significant reduction in abundance of PSII reaction centers relative to the peripheral antenna. In addition, PSII appeared to be significantly more affected by Mn limitation than PSI. However, the striking genotypic differences observed in Mn-deficient plants, when analyzing state transitions and fluorescence induction kinetics, could not be correlated with specific changes in photosystem proteins. Thus, there is no simple linkage between protein expression and the differential reduction in state transition and fluorescence induction kinetics observed for the genotypes under Mn deficiency. PMID:19369593

  18. Efficiently reducing transition curvature in heat-assisted magnetic recording with state-of-the-art write heads

    NASA Astrophysics Data System (ADS)

    Vogler, Christoph; Abert, Claas; Bruckner, Florian; Suess, Dieter

    2017-05-01

    Curvatures of bit transitions on granular media are a serious problem for the read-back process. We address this fundamental issue and propose a possibility to efficiently reduce transition curvatures with state-of-the-art heat-assisted magnetic recording heads. We compare footprints of conventional with those of the proposed head design on different media, consisting of exchange coupled and single phase grains. Additionally, we investigate the impact of various recording parameters, such as the full width at half maximum (FWHM) of the applied heat pulse and the coercivity gradient near the write temperature of the recording grains. The footprints are calculated with a coarse grained model, based on the Landau-Lifshitz-Bloch equation. The presented simulations show a transition curvature reduction of up to 40%, in the case of a medium with exchange coupled grains and a heat pulse with a FWHM of 40 nm. We further give the reason for the straightening of the bit transitions, by means of basic considerations with regard to the effective recording time window of the write process. Besides the transition curvature reduction, the proposed head design yields an improvement of the transition jitter in both down-track and off-track directions.

  19. Integrating Ecosystem Carbon Dynamics into State-and-Transition Simulation Models of Land Use/Land Cover Change

    NASA Astrophysics Data System (ADS)

    Sleeter, B. M.; Daniel, C.; Frid, L.; Fortin, M. J.

    2016-12-01

    State-and-transition simulation models (STSMs) provide a general approach for incorporating uncertainty into forecasts of landscape change. Using a Monte Carlo approach, STSMs generate spatially-explicit projections of the state of a landscape based upon probabilistic transitions defined between states. While STSMs are based on the basic principles of Markov chains, they have additional properties that make them applicable to a wide range of questions and types of landscapes. A current limitation of STSMs is that they are only able to track the fate of discrete state variables, such as land use/land cover (LULC) classes. There are some landscape modelling questions, however, for which continuous state variables - for example carbon biomass - are also required. Here we present a new approach for integrating continuous state variables into spatially-explicit STSMs. Specifically we allow any number of continuous state variables to be defined for each spatial cell in our simulations; the value of each continuous variable is then simulated forward in discrete time as a stochastic process based upon defined rates of change between variables. These rates can be defined as a function of the realized states and transitions of each cell in the STSM, thus providing a connection between the continuous variables and the dynamics of the landscape. We demonstrate this new approach by (1) developing a simple IPCC Tier 3 compliant model of ecosystem carbon biomass, where the continuous state variables are defined as terrestrial carbon biomass pools and the rates of change as carbon fluxes between pools, and (2) integrating this carbon model with an existing LULC change model for the state of Hawaii, USA.

  20. Disability and Transition from State Education to Community Life: Next Steps for Parents

    ERIC Educational Resources Information Center

    Wills, Rod; Chenoweth, Lesley; Ellem, Kathleen

    2016-01-01

    In this paper we explore the experiences of mothers of young adults with Down syndrome as their daughters and sons transition from schooling to adult life. These transitions occurred in a society shaped by neo-liberal political reform that commenced in the mid-1980s. The hallmarks of education are now expressed in terms of national achievement…

  1. Transition for Students with Learning Disabilities in Four Rocky Mountain States.

    ERIC Educational Resources Information Center

    McCuller, Glen L.; And Others

    Recent research indicates that problems in the transition from school to employment are frequent among students with learning disabilities, particularly those in rural areas. While a systematic approach to transition appears to be beneficial, the best method for implementing such an approach is still in question. One hundred seventeen special…

  2. Iowa in motion : transit system plan : implementing Iowa's state transportation plan

    DOT National Transportation Integrated Search

    1999-09-14

    The Iowa Transit System Plan was developed as a result of the on-going long-range transportation planning process known as Iowa In Motion This planning document, the 1999 Iowa Transit System Plan, is the result of this continuing planning process and...

  3. The reduced transition probabilities for excited states of rare-earths and actinide even-even nuclei

    SciT

    Ghumman, S. S.

    The theoretical B(E2) ratios have been calculated on DF, DR and Krutov models. A simple method based on the work of Arima and Iachello is used to calculate the reduced transition probabilities within SU(3) limit of IBA-I framework. The reduced E2 transition probabilities from second excited states of rare-earths and actinide even–even nuclei calculated from experimental energies and intensities from recent data, have been found to compare better with those calculated on the Krutov model and the SU(3) limit of IBA than the DR and DF models.

  4. Transitions between strongly correlated and random steady-states for catalytic CO-oxidation on surfaces at high-pressure

    DOE PAGES

    Liu, Da -Jiang; Evans, James W.

    2015-04-02

    We explore simple lattice-gas reaction models for CO-oxidation on 1D and 2D periodic arrays of surface adsorption sites. The models are motivated by studies of CO-oxidation on RuO 2(110) at high-pressures. Although adspecies interactions are neglected, the effective absence of adspecies diffusion results in kinetically-induced spatial correlations. A transition occurs from a random mainly CO-populated steady-state at high CO-partial pressure p CO, to a strongly-correlated near-O-covered steady-state for low p CO as noted. In addition, we identify a second transition to a random near-O-covered steady-state at very low p CO.

  5. Trends in Ground-State Entropies for Transition Metal Based Hydrogen Atom Transfer Reactions

    PubMed Central

    Mader, Elizabeth A.; Manner, Virginia W.; Markle, Todd F.; Wu, Adam; Franz, James A.; Mayer, James M.

    2009-01-01

    Reported herein are thermochemical studies of hydrogen atom transfer (HAT) reactions involving transition metal H-atom donors MIILH and oxyl radicals. [FeII(H2bip)3]2+, [FeII(H2bim)3]2+, [CoII(H2bim)3]2+ and RuII(acac)2(py-imH) [H2bip = 2,2’-bi-1,4,5,6-tetrahydropyrimidine, H2bim = 2,2’-bi-imidazoline, acac = 2,4-pentandionato, py-imH = 2-(2’-pyridyl)-imidazole)] each react with TEMPO (2,2,6,6-tetramethyl-1-piperidinoxyl) or tBu3PhO• (2,4,6-tri-tert-butylphenoxyl) to give the deprotonated, oxidized metal complex MIIIL, and TEMPOH or tBu3PhOH. Solution equilibrium measurements for the reaction of [CoII(H2bim)3]2+ with TEMPO show a large, negative ground-state entropy for hydrogen atom transfer, −41 ± 2 cal mol−1 K−1. This is even more negative than the ΔSoHAT = −30 ± 2 cal mol−1 K−1 for the two iron complexes and the ΔSoHAT for RuII(acac)2(py-imH) + TEMPO, 4.9 ± 1.1 cal mol−1 K−1, as reported earlier. Calorimetric measurements quantitatively confirm the enthalpy of reaction for [FeII(H2bip)3]2+ + TEMPO, thus also confirming ΔSoHAT. Calorimetry on TEMPOH + tBu3PhO• gives ΔHoHAT = −11.2 ± 0.5 kcal mol−1 which matches the enthalpy predicted from the difference in literature solution BDEs. A brief evaluation of the literature thermochemistry of TEMPOH and tBu3PhOH supports the common assumption that ΔSoHAT ≈ 0 for HAT reactions of organic and small gas-phase molecules. However, this assumption does not hold for transition metal based HAT reactions. The trend in magnitude of |ΔSoHAT| for reactions with TEMPO, RuII(acac)2(py-imH) << [FeII(H2bip)3]2+ = [FeII(H2bim)3]2+ < [CoII(H2bim)3]2+, is surprisingly well predicted by the trends for electron transfer half-reaction entropies, ΔSoET, in aprotic solvents. This is because both ΔSoET and ΔSoHAT have substantial contributions from vibrational entropy, which varies significantly with the metal center involved. The close connection between ΔSoHAT and ΔSoET provides an important

  6. Quantum-to-classical transition and entanglement sudden death in Gaussian states under local-heat-bath dynamics

    SciT

    Goyal, Sandeep K.; Ghosh, Sibasish

    2010-10-15

    Entanglement sudden death (ESD) in spatially separated two-mode Gaussian states coupled to local thermal and squeezed thermal baths is studied by mapping the problem to that of the quantum-to-classical transition. Using Simon's criterion concerning the characterization of classicality in Gaussian states, the time to ESD is calculated by analyzing the covariance matrices of the system. The results for the two-mode system at T=0 and T>0 for the two types of bath states are generalized to n modes, and are shown to be similar in nature to the results for the general discrete n-qubit system.

  7. Transition state region in the A-Band photodissociation of allyl iodide—A femtosecond extreme ultraviolet transient absorption study

    SciT

    Bhattacherjee, Aditi, E-mail: abhattacherjee@berkeley.edu, E-mail: andrewattar@berkeley.edu; Attar, Andrew R., E-mail: abhattacherjee@berkeley.edu, E-mail: andrewattar@berkeley.edu; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720

    2016-03-28

    Femtosecond extreme ultraviolet (XUV) transient absorption spectroscopy based on a high-harmonic generation source is used to study the 266 nm induced A-band photodissociation dynamics of allyl iodide (CH{sub 2} =CHCH{sub 2}I). The photolysis of the C—I bond at this wavelength produces iodine atoms both in the ground ({sup 2}P{sub 3/2}, I) and spin-orbit excited ({sup 2}P{sub 1/2}, I*) states, with the latter as the predominant channel. Using XUV absorption at the iodine N{sub 4/5} edge (45–60 eV), the experiments constitute a direct probe of not only the long-lived atomic iodine reaction products but also the fleeting transition state region ofmore » the repulsive n{sub I}σ{sup ∗}{sub C—I} excited states. Specifically, three distinct features are identified in the XUV transient absorption spectrum at 45.3 eV, 47.4 eV, and 48.4 eV (denoted transients A, B, and C, respectively), which arise from the repulsive valence-excited nσ{sup ∗} states and project onto the high-lying core-excited states of the dissociating molecule via excitation of 4d(I) core electrons. Transients A and B originate from 4d(I) → n(I) core-to-valence transitions, whereas transient C is best assigned to a 4d(I) →σ{sup ∗}(C—I) transition. The measured differential absorbance of these new features along with the I/I* branching ratios known from the literature is used to suggest a more definitive assignment, albeit provisional, of the transients to specific dissociative states within the A-band manifold. The transients are found to peak around 55 fs–65 fs and decay completely by 145 fs–185 fs, demonstrating the ability of XUV spectroscopy to map the evolution of reactants into products in real time. The similarity in the energies of transients A and B with analogous features observed in methyl iodide [Attar et al. J. Phys. Chem. Lett. 6, 5072, (2015)] together with the new observation of transient C in the present work provides a more complete picture of the valence

  8. Contribution of cutinase serine 42 side chain to the stabilization of the oxyanion transition state.

    PubMed

    Nicolas, A; Egmond, M; Verrips, C T; de Vlieg, J; Longhi, S; Cambillau, C; Martinez, C

    1996-01-16

    Cutinase from the fungus Fusarium solani pisi is a lipolytic enzyme able to hydrolyze both aggregated and soluble substrates. It therefore provides a powerful tool for probing the mechanisms underlying lipid hydrolysis. Lipolytic enzymes have a catalytic machinery similar to those present in serine proteinases. It is characterized by the triad Ser, His, and Asp (Glu) residues, by an oxyanion binding site that stabilizes the transition state via hydrogen bonds with two main chain amide groups, and possibly by other determinants. It has been suggested on the basis of a covalently bond inhibitor that the cutinase oxyanion hole may consist not only of two main chain amide groups but also of the Ser42 O gamma side chain. Among the esterases and the serine and the cysteine proteases, only Streptomyces scabies esterase, subtilisin, and papain, respectively, have a side chain residue which is involved in the oxyanion hole formation. The position of the cutinase Ser42 side chain is structurally conserved in Rhizomucor miehei lipase with Ser82 O gamma, in Rhizopus delemar lipase with Thr83 O gamma 1, and in Candida antartica B lipase with Thr40 O gamma 1. To evaluate the increase in the tetrahedral intermediate stability provided by Ser42 O gamma, we mutated Ser42 into Ala. Furthermore, since the proper orientation of Ser42 O gamma is directed by Asn84, we mutated Asn84 into Ala, Leu, Asp, and Trp, respectively, to investigate the contribution of this indirect interaction to the stabilization of the oxyanion hole. The S42A mutation resulted in a drastic decrease in the activity (450-fold) without significantly perturbing the three-dimensional structure. The N84A and N84L mutations had milder kinetic effects and did not disrupt the structure of the active site, whereas the N84W and N84D mutations abolished the enzymatic activity due to drastic steric and electrostatic effects, respectively.

  9. The transition state for formation of the peptide bond in the ribosome

    PubMed Central

    Gindulyte, Asta; Bashan, Anat; Agmon, Ilana; Massa, Lou; Yonath, Ada; Karle, Jerome

    2006-01-01

    Using quantum mechanics and exploiting known crystallographic coordinates of tRNA substrate located in the ribosome peptidyl transferase center around the 2-fold axis, we have investigated the mechanism for peptide-bond formation. The calculation is based on a choice of 50 atoms assumed to be important in the mechanism. We used density functional theory to optimize the geometry and energy of the transition state (TS) for peptide-bond formation. The TS is formed simultaneously with the rotatory motion enabling the translocation of the A-site tRNA 3′ end into the P site, and we estimated the magnitude of rotation angle between the A-site starting position and the place at which the TS occurs. The calculated TS activation energy, Ea, is 35.5 kcal (1 kcal = 4.18 kJ)/mol, and the increase in hydrogen bonding between the rotating A-site tRNA and ribosome nucleotides as the TS forms appears to stabilize it to a value qualitatively estimated to be ≈18 kcal/mol. The optimized geometry corresponds to a structure in which the peptide bond is being formed as other bonds are being broken, in such a manner as to release the P-site tRNA so that it may exit as a free molecule and be replaced by the translocating A-site tRNA. At TS formation the 2′ OH group of the P-site tRNA A76 forms a hydrogen bond with the oxygen atom of the carboxyl group of the amino acid attached to the A-site tRNA, which may be indicative of its catalytic role, consistent with recent biochemical experiments. PMID:16938893

  10. Resilience and resistance of sagebrush ecosystems: implications for state and transition models and management treatments

    Chambers, Jeanne C.; Miller, Richard F.; Board, David I.; Pyke, David A.; Roundy, Bruce A.; Grace, James B.; Schupp, Eugene W.; Tausch, Robin J.

    2014-01-01

    In sagebrush ecosystems invasion of annual exotics and expansion of piñon (Pinus monophylla Torr. and Frem.) and juniper (Juniperus occidentalis Hook., J. osteosperma [Torr.] Little) are altering fire regimes and resulting in large-scale ecosystem transformations. Management treatments aim to increase resilience to disturbance and enhance resistance to invasive species by reducing woody fuels and increasing native perennial herbaceous species. We used Sagebrush Steppe Treatment Evaluation Project data to test predictions on effects of fire vs. mechanical treatments on resilience and resistance for three site types exhibiting cheatgrass (Bromus tectorum L.) invasion and/or piñon and juniper expansion: 1) warm and dry Wyoming big sagebrush (WY shrub); 2) warm and moist Wyoming big sagebrush (WY PJ); and 3) cool and moist mountain big sagebrush (Mtn PJ). Warm and dry (mesic/aridic) WY shrub sites had lower resilience to fire (less shrub recruitment and native perennial herbaceous response) than cooler and moister (frigid/xeric) WY PJ and Mtn PJ sites. Warm (mesic) WY Shrub and WY PJ sites had lower resistance to annual exotics than cool (frigid to cool frigid) Mtn PJ sites. In WY shrub, fire and sagebrush mowing had similar effects on shrub cover and, thus, on perennial native herbaceous and exotic cover. In WY PJ and Mtn PJ, effects were greater for fire than cut-and-leave treatments and with high tree cover in general because most woody vegetation was removed increasing resources for other functional groups. In WY shrub, about 20% pretreatment perennial native herb cover was necessary to prevent increases in exotics after treatment. Cooler and moister WY PJ and especially Mtn PJ were more resistant to annual exotics, but perennial native herb cover was still required for site recovery. We use our results to develop state and transition models that illustrate how resilience and resistance influence vegetation dynamics and management options.

  11. Force-dependent switch in protein unfolding pathways and transition-state movements

    PubMed Central

    Zhuravlev, Pavel I.; Hinczewski, Michael; Chakrabarti, Shaon; Marqusee, Susan; Thirumalai, D.

    2016-01-01

    Although it is known that single-domain proteins fold and unfold by parallel pathways, demonstration of this expectation has been difficult to establish in experiments. Unfolding rate, ku(f), as a function of force f, obtained in single-molecule pulling experiments on src SH3 domain, exhibits upward curvature on a log⁡ku(f) plot. Similar observations were reported for other proteins for the unfolding rate ku([C]). These findings imply unfolding in these single-domain proteins involves a switch in the pathway as f or [C] is increased from a low to a high value. We provide a unified theory demonstrating that if log⁡ku as a function of a perturbation (f or [C]) exhibits upward curvature then the underlying energy landscape must be strongly multidimensional. Using molecular simulations we provide a structural basis for the switch in the pathways and dramatic shifts in the transition-state ensemble (TSE) in src SH3 domain as f is increased. We show that a single-point mutation shifts the upward curvature in log⁡ku(f) to a lower force, thus establishing the malleability of the underlying folding landscape. Our theory, applicable to any perturbation that affects the free energy of the protein linearly, readily explains movement in the TSE in a β-sandwich (I27) protein and single-chain monellin as the denaturant concentration is varied. We predict that in the force range accessible in laser optical tweezer experiments there should be a switch in the unfolding pathways in I27 or its mutants. PMID:26818842

  12. Force-dependent switch in protein unfolding pathways and transition-state movements.

    PubMed

    Zhuravlev, Pavel I; Hinczewski, Michael; Chakrabarti, Shaon; Marqusee, Susan; Thirumalai, D

    2016-02-09

    Although it is known that single-domain proteins fold and unfold by parallel pathways, demonstration of this expectation has been difficult to establish in experiments. Unfolding rate, [Formula: see text], as a function of force f, obtained in single-molecule pulling experiments on src SH3 domain, exhibits upward curvature on a [Formula: see text] plot. Similar observations were reported for other proteins for the unfolding rate [Formula: see text]. These findings imply unfolding in these single-domain proteins involves a switch in the pathway as f or [Formula: see text] is increased from a low to a high value. We provide a unified theory demonstrating that if [Formula: see text] as a function of a perturbation (f or [Formula: see text]) exhibits upward curvature then the underlying energy landscape must be strongly multidimensional. Using molecular simulations we provide a structural basis for the switch in the pathways and dramatic shifts in the transition-state ensemble (TSE) in src SH3 domain as f is increased. We show that a single-point mutation shifts the upward curvature in [Formula: see text] to a lower force, thus establishing the malleability of the underlying folding landscape. Our theory, applicable to any perturbation that affects the free energy of the protein linearly, readily explains movement in the TSE in a β-sandwich (I27) protein and single-chain monellin as the denaturant concentration is varied. We predict that in the force range accessible in laser optical tweezer experiments there should be a switch in the unfolding pathways in I27 or its mutants.

  13. Gendered transitions to adulthood by college field of study in the United States.

    PubMed

    Han, Siqi; Tumin, Dmitry; Qian, Zhenchao

    2016-01-01

    Field of study may influence the timing of transitions to the labor market, marriage, and parenthood among college graduates. Research to date has yet to study how field of study is associated with the interweaving of these transitions in the USA. The current study examines gendered influences of college field of study on transitions to a series of adult roles, including full-time work, marriage, and parenthood. We use Cox proportional hazards models and multinomial logistic regression to examine gendered associations between field of study and the three transitions among college graduates of the NLSY97 (National Longitudinal Survey of Youth) cohort. Men majoring in STEM achieve early transitions to full-time work, marriage, and parenthood; women majoring in STEM show no significant advantage in finding full-time work and delayed marriage and childbearing; women in business have earlier transitions to full-time work and marriage than women in other fields, demonstrating an advantage similar to that of men in STEM. The contrast between men and women in STEM shows that transition to adulthood remains gendered; the contrast between women in STEM and women in business illustrates that a prestigious career may not necessarily delay family formation.

  14. Gendered transitions to adulthood by college field of study in the United States

    PubMed Central

    Han, Siqi; Tumin, Dmitry; Qian, Zhenchao

    2017-01-01

    BACKGROUND Field of study may influence the timing of transitions to the labor market, marriage, and parenthood among college graduates. Research to date has yet to study how field of study is associated with the interweaving of these transitions in the USA. OBJECTIVE The current study examines gendered influences of college field of study on transitions to a series of adult roles, including full-time work, marriage, and parenthood. METHODS We use Cox proportional hazards models and multinomial logistic regression to examine gendered associations between field of study and the three transitions among college graduates of the NLSY97 (National Longitudinal Survey of Youth) cohort. RESULTS Men majoring in STEM achieve early transitions to full-time work, marriage, and parenthood; women majoring in STEM show no significant advantage in finding full-time work and delayed marriage and childbearing; women in business have earlier transitions to full-time work and marriage than women in other fields, demonstrating an advantage similar to that of men in STEM. CONCLUSIONS The contrast between men and women in STEM shows that transition to adulthood remains gendered; the contrast between women in STEM and women in business illustrates that a prestigious career may not necessarily delay family formation. PMID:29075146

  15. Nature of hardness evolution in nanocrystalline NiTi shape memory alloys during solid-state phase transition

    PubMed Central

    Amini, Abbas; Cheng, Chun

    2013-01-01

    Due to a distinct nature of thermomechanical smart materials' reaction to applied loads, a revolutionary approach is needed to measure the hardness and to understand its size effect for pseudoelastic NiTi shape memory alloys (SMAs) during the solid-state phase transition. Spherical hardness is increased with depths during the phase transition in NiTi SMAs. This behaviour is contrary to the decrease in the hardness of NiTi SMAs with depths using sharp tips and the depth-insensitive hardness of traditional metallic alloys using spherical tips. In contrast with the common dislocation theory for the hardness measurement, the nature of NiTi SMAs' hardness is explained by the balance between the interface and the bulk energy of phase transformed SMAs. Contrary to the energy balance in the indentation zone using sharp tips, the interface energy was numerically shown to be less dominant than the bulk energy of the phase transition zone using spherical tips. PMID:23963305

  16. Quantum phase transitions in a two-dimensional quantum XYX model: ground-state fidelity and entanglement.

    PubMed

    Li, Bo; Li, Sheng-Hao; Zhou, Huan-Qiang

    2009-06-01

    A systematic analysis is performed for quantum phase transitions in a two-dimensional anisotropic spin-1/2 antiferromagnetic XYX model in an external magnetic field. With the help of an innovative tensor network algorithm, we compute the fidelity per lattice site to demonstrate that the field-induced quantum phase transition is unambiguously characterized by a pinch point on the fidelity surface, marking a continuous phase transition. We also compute an entanglement estimator, defined as a ratio between the one-tangle and the sum of squared concurrences, to identify both the factorizing field and the critical point, resulting in a quantitative agreement with quantum Monte Carlo simulation. In addition, the local order parameter is "derived" from the tensor network representation of the system's ground-state wave functions.

  17. 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.

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

    PubMed

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

    2007-04-01

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

  19. Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble

    PubMed Central

    Fisher, Kaitlin M.; Haglund, Ellinor; Noel, Jeffrey K.; Hailey, Kendra L.; Onuchic, José N.; Jennings, Patricia A.

    2015-01-01

    Interleukin-33 (IL-33) is currently the focus of multiple investigations into targeting pernicious inflammatory disorders. This mediator of inflammation plays a prevalent role in chronic disorders such as asthma, rheumatoid arthritis, and progressive heart disease. In order to better understand the possible link between the folding free energy landscape and functional regions in IL-33, a combined experimental and theoretical approach was applied. IL-33 is a pseudo- symmetrical protein composed of three distinct structural elements that complicate the folding mechanism due to competition for nucleation on the dominant folding route. Trefoil 1 constitutes the majority of the binding interface with the receptor whereas Trefoils 2 and 3 provide the stable scaffold to anchor Trefoil 1. We identified that IL-33 folds with a three-state mechanism, leading to a rollover in the refolding arm of its chevron plots in strongly native conditions. In addition, there is a second slower refolding phase that exhibits the same rollover suggesting similar limitations in folding along parallel routes. Characterization of the intermediate state and the rate limiting steps required for folding suggests that the rollover is attributable to a moving transition state, shifting from a post- to pre-intermediate transition state as you move from strongly native conditions to the midpoint of the transition. On a structural level, we found that initially, all independent Trefoil units fold equally well until a QCA of 0.35 when Trefoil 1 will backtrack in order to allow Trefoils 2 and 3 to fold in the intermediate state, creating a stable scaffold for Trefoil 1 to fold onto during the final folding transition. The formation of this intermediate state and subsequent moving transition state is a result of balancing the difficulty in folding the functionally important Trefoil 1 onto the remainder of the protein. Taken together our results indicate that the functional element of the protein is

  20. A multi-state model examining patterns of transitioning among states of engagement in care in HIV-positive individuals initiating combination antiretroviral therapy

    PubMed Central

    Gillis, Jennifer; Loutfy, Mona; Bayoumi, Ahmed M; Antoniou, Tony; Burchell, Ann N; Walmsley, Sharon; Cooper, Curtis; Klein, Marina B.; Machouf, Nima; Montaner, Julio SG; Rourke, Sean B.; Tsoukas, Christos; Hogg, Robert; Raboud, Janet

    2016-01-01

    Background Common measures of engagement in care fail to acknowledge that infrequent follow-up may occur either intentionally among patients with sustained virologic suppression or unintentionally among patients with poor clinical outcomes. Methods Five states of HIV care were defined within the Canadian Observational Cohort (CANOC) Collaboration following combination antiretroviral therapy (cART) initiation: (1) guidelines HIV care (suppressed viral load (VL) and CD4 >200 cells/mm3, no gaps in cART >3 months, no gaps in CD4 or VL measurement >6 months), (2) successful care with decreased frequency of follow-up (as above except no gaps in CD4 or VL measurement >12 months), (3) suboptimal care (unsuppressed VL, CD4<200 cells/mm3 on 2 consecutive visits, ≥1 gap in cART >3 months, or ≥1 gap in CD4 or VL measurement >12 months), (4) loss to follow-up (no contact for 18 months), and (5) death. Multi-state models were used to determine factors associated with transitioning among states. Results 7810 participants were included. Younger age, female gender, Indigenous ethnicity and people who have injected drugs (PWID) were associated with increased likelihoods of transitioning from guidelines to suboptimal care and decreased likelihoods of transitioning from suboptimal to guidelines care. One-fifth of individuals in successful, decreased follow-up after cART initiation (mean sojourn time 0.72 years) were in suboptimal care in subsequent years. Conclusions Using routinely collected data, we have developed a flexible framework that characterizes patient transitions among states of HIV clinical care. We have demonstrated that multi-state models provide a useful approach to supplement ‘cascade of care’ work. PMID:27851713

  1. Use of Neuroanatomical Pattern Classification to Identify Subjects in At-Risk Mental States of Psychosis and Predict Disease Transition

    PubMed Central

    Koutsouleris, Nikolaos; Meisenzahl, Eva M.; Davatzikos, Christos; Bottlender, Ronald; Frodl, Thomas; Scheuerecker, Johanna; Schmitt, Gisela; Zetzsche, Thomas; Decker, Petra; Reiser, Maximilian; Möller, Hans-Jürgen; Gaser, Christian

    2014-01-01

    Context Identification of individuals at high risk of developing psychosis has relied on prodromal symptomatology. Recently, machine learning algorithms have been successfully used for magnetic resonance imaging–based diagnostic classification of neuropsychiatric patient populations. Objective To determine whether multivariate neuroanatomical pattern classification facilitates identification of individuals in different at-risk mental states (ARMS) of psychosis and enables the prediction of disease transition at the individual level. Design Multivariate neuroanatomical pattern classification was performed on the structural magnetic resonance imaging data of individuals in early or late ARMS vs healthy controls (HCs). The predictive power of the method was then evaluated by categorizing the baseline imaging data of individuals with transition to psychosis vs those without transition vs HCs after 4 years of clinical follow-up. Classification generalizability was estimated by cross-validation and by categorizing an independent cohort of 45 new HCs. Setting Departments of Psychiatry and Psychotherapy, Ludwig-Maximilians-University, Munich, Germany. Participants The first classification analysis included 20 early and 25 late at-risk individuals and 25 matched HCs. The second analysis consisted of 15 individuals with transition, 18 without transition, and 17 matched HCs. Main Outcome Measures Specificity, sensitivity, and accuracy of classification. Results The 3-group, cross-validated classification accuracies of the first analysis were 86% (HCs vs the rest), 91% (early at-risk individuals vs the rest), and 86% (late at-risk individuals vs the rest). The accuracies in the second analysis were 90% (HCs vs the rest), 88% (individuals with transition vs the rest), and 86% (individuals without transition vs the rest). Independent HCs were correctly classified in 96% (first analysis) and 93% (second analysis) of cases. Conclusions Different ARMSs and their clinical outcomes

  2. Memo Clarifying Requirements and State Reporting Guidance to Transition to the Revised Total Coliform Rule

    EPA Pesticide Factsheets

    This memorandum provides guidance to primacy agencies with enforcement responsibility under the Safe Drinking Water Act (SDWA) concerning the requirements to transition public water systems (PWSs) from the Total Coliform Rule (TCR) to the RTCR

  3. Prediction and Control of Rail Transit Noise and Vibration - A State-of-the-Art Assessment

    DOT National Transportation Integrated Search

    1974-04-01

    As systems manager for the Urban Mass Transportation Administration's Rail Supporting Technology Program, the Transportation Systems Center has undertaken research in rail transit noise abatement. As part of this effort, this report contains the resu...

  4. Assessing the efficiency of mass transit systems in the United States.

    DOT National Transportation Integrated Search

    2017-04-01

    Frustrated with increased parking problems, unstable gasoline prices, and stifling traffic congestion, a growing number of : metropolitan city dwellers consider utilizing the mass transit system. Reflecting this sentiment, a ridership of the mass tra...

  5. Determining effective roadway design treatments for transitioning from rural areas to urban areas on state highways.

    DOT National Transportation Integrated Search

    2008-09-01

    This report reviews an Oregon research effort to identify ways to calm operating speeds as the vehicles transition into developed suburban/urban areas from rural roads. Drivers of vehicles approaching the urban environment have few visual cues to red...

  6. Atmospheric conditions during the spring and fall transitions in the coastal ocean off western United States

    NASA Technical Reports Server (NTRS)

    Strub, P. Ted; James, Corinne

    1988-01-01

    Atmospheric events which force the spring and fall oceanic transitions in the coastal ocean off the west coast of North America were examined by analyzing the records of adjusted sea level (ASL), coastal wind stress, sea level atmospheric pressure (SLP), and 500-mbar heights for the years 1971-1975 and 1980-1983. The records cover periods of 91 days, centered on the dates of the spring and fall transitions as determined from coastal ASL data. It was found that the dominant mode of the ASL and coastal wind stress are similar around the times of both the spring and fall transitions, and that the time series for these modes are highly correlated with one another. Principal estimator patterns show the spatial patterns of SLP which force the ASL and coastal wind stress during the transitions.

  7. Nationwide examples of state and local funds for mass transit : final report, December 2008.

    DOT National Transportation Integrated Search

    2008-12-04

    One of the transportation challenges facing Texas is the identification of adequate funding for : mobility projects. During the 80th Texas Legislature, several proposals were made to address : mass transit funding for the metropolitan areas of the st...

  8. 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.

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

    PubMed

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

    1987-11-17

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

  10. Anaerobiosis Induced State Transition: A Non Photochemical Reduction of PQ Pool Mediated by NDH in Arabidopsis thaliana

    PubMed Central

    Tirupathi, Malavath; Subramanyam, Rajagopal

    2012-01-01

    Background Non photochemical reduction of PQ pool and mobilization of LHCII between PSII and PSI are found to be linked under abiotic stress conditions. The interaction of non photochemical reduction of PQ pool and state transitions associated physiological changes are critically important under anaerobic condition in higher plants. Methodology/Findings The present study focused on the effect of anaerobiosis on non-photochemical reduction of PQ pool which trigger state II transition in Arabidopsis thaliana. Upon exposure to dark-anaerobic condition the shape of the OJIP transient rise is completely altered where as in aerobic treated leaves the rise is unaltered. Rise in F o and F J was due to the loss of oxidized PQ pool as the PQ pool becomes more reduced. The increase in Fo′ was due to the non photochemical reduction of PQ pool which activated STN7 kinase and induced LHCII phosphorylation under anaerobic condition. Further, it was observed that the phosphorylated LHCII is migrated and associated with PSI supercomplex increasing its absorption cross-section. Furthermore, evidences from crr2-2 (NDH mutant) and pgr5 mutants (deficient in non NDH pathway of cyclic electron transport) have indicated that NDH is responsible for non photochemical reduction of the PQ pool. We propose that dark anaerobic condition accelerates production of reducing equivalents (such as NADPH by various metabolic pathways) which reduce PQ pool and is mediated by NDH leading to state II transition. Conclusions/Significance Anaerobic condition triggers non photochemical reduction of PQ pool mediated by NDH complex. The reduced PQ pool activates STN7 kinase leading to state II transition in A. thaliana. PMID:23185453

  11. Methods used to parameterize the spatially-explicit components of a state-and-transition simulation model

    Sleeter, Rachel; Acevedo, William; Soulard, Christopher E.; Sleeter, Benjamin M.

    2015-01-01

    Spatially-explicit state-and-transition simulation models of land use and land cover (LULC) increase our ability to assess regional landscape characteristics and associated carbon dynamics across multiple scenarios. By characterizing appropriate spatial attributes such as forest age and land-use distribution, a state-and-transition model can more effectively simulate the pattern and spread of LULC changes. This manuscript describes the methods and input parameters of the Land Use and Carbon Scenario Simulator (LUCAS), a customized state-and-transition simulation model utilized to assess the relative impacts of LULC on carbon stocks for the conterminous U.S. The methods and input parameters are spatially explicit and describe initial conditions (strata, state classes and forest age), spatial multipliers, and carbon stock density. Initial conditions were derived from harmonization of multi-temporal data characterizing changes in land use as well as land cover. Harmonization combines numerous national-level datasets through a cell-based data fusion process to generate maps of primary LULC categories. Forest age was parameterized using data from the North American Carbon Program and spatially-explicit maps showing the locations of past disturbances (i.e. wildfire and harvest). Spatial multipliers were developed to spatially constrain the location of future LULC transitions. Based on distance-decay theory, maps were generated to guide the placement of changes related to forest harvest, agricultural intensification/extensification, and urbanization. We analyze the spatially-explicit input parameters with a sensitivity analysis, by showing how LUCAS responds to variations in the model input. This manuscript uses Mediterranean California as a regional subset to highlight local to regional aspects of land change, which demonstrates the utility of LUCAS at many scales and applications.

  12. 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

  13. Origin of the Hawaiian rainforest and its transition states in long-term primary succession

    NASA Astrophysics Data System (ADS)

    Mueller-Dombois, D.; Boehmer, H. J.

    2013-07-01

    This paper addresses the question of transition states in the Hawaiian rainforest ecosystem with emphasis on their initial developments. Born among volcanoes in the north central Pacific about 4 million years ago, the Hawaiian rainforest became assembled from spores of algae, fungi, lichens, bryophytes, ferns and from seeds of about 275 flowering plants that over the millennia evolved into ca. 1000 endemic species. Outstanding among the forest builders were the tree ferns (Cibotium spp.) and the 'ōhi'a lehua trees (Metrosideros spp.), which still dominate the Hawaiian rainforest ecosystem today. The structure of this forest is simple. The canopy in closed mature rainforests is dominated by cohorts of Metrosideros polymorpha and the undergrowth by tree fern species of Cibotium. When a new lava flow cuts through this forest, kipuka are formed, i.e., islands of remnant vegetation. On the new volcanic substrate, the assemblage of plant life forms is similar to the assemblage during the evolution of this system. In open juvenile forests, a mat-forming fern, the uluhe fern (Dicranopteris linearis), becomes established. It inhibits further regeneration of the dominant 'ōhi'a tree, thereby reinforcing the cohort structure of the canopy guild. In the later part of its life cycle, the canopy guild breaks down often in synchrony. The trigger is hypothesized to be a climatic perturbation. After the disturbance, the forest becomes reestablished in about 30-40 yr. As the volcanic surfaces age, they go from a mesotrophic to a eutrophic phase, reaching a biophilic nutrient climax by about 1-25 K yr. Thereafter, a regressive oligotrophic phase follows; the soils become exhausted of nutrients. The shield volcanoes break down. Marginally, forest habitats change into bogs and stream ecosystems. The broader 'ōhi'a rainforest redeveloping in the more dissected landscapes of the older islands loses stature, often forming large gaps that are invaded by the aluminum tolerant uluhe fern

  14. Hydrogen-related excitons and their excited-state transitions in ZnO

    NASA Astrophysics Data System (ADS)

    Heinhold, R.; Neiman, A.; Kennedy, J. V.; Markwitz, A.; Reeves, R. J.; Allen, M. W.

    2017-02-01

    The role of hydrogen in the photoluminescence (PL) of ZnO was investigated using four different types of bulk ZnO single crystal, with varying concentrations of unintentional hydrogen donor and Group I acceptor impurities. Photoluminescence spectra were measured at 3 K, with emission energies determined to ±50 μeV, before and after separate annealing in O2, N2, and H2 atmospheres. Using this approach, several new hydrogen-related neutral-donor-bound excitons, and their corresponding B exciton, ionized donor, and two electron satellite (TES) excited state transitions were identified and their properties further investigated using hydrogen and deuterium ion implantation. The commonly observed I4 (3.36272 eV) emission due to excitons bound to multicoordinated hydrogen inside an oxygen vacancy (HO), that is present in most ZnO material, was noticeably absent in hydrothermally grown (HT) ZnO and instead was replaced by a doublet of two closely lying recombination lines I4 b ,c (3.36219, 3.36237 eV) due to a hydrogen-related donor with a binding energy (ED) of 47.7 meV. A new and usually dominant recombination line I6 -H (3.36085 eV) due to a different hydrogen-related defect complex with an ED of 49.5 meV was also identified in HT ZnO. Here, I4 b ,c and I6 -H were stable up to approximately 400 and 600 °C, respectively, indicating that they are likely to contribute to the unintentional n -type conductivity of ZnO. Another doublet I5 (3.36137, 3.36148 eV) was identified in hydrogenated HT ZnO single crystals with low Li concentrations, and this was associated with a defect complex with an ED of 49.1 meV. A broad near band edge (NBE) emission centered at 3.366 eV was associated with excitons bound to subsurface hydrogen. We further demonstrate that hydrogen incorporates on different lattice sites for different annealing conditions and show that the new features I4 b ,c, I6 -H, and I5 most likely originate from the lithium-hydrogen defect complexes L iZn-HO , A l

  15. Kinetic restriction of simple gases in porous carbons: transition-state theory study.

    PubMed

    Nguyen, Thanh X; Bhatia, Suresh K

    2008-01-01

    The separation of simple gases such as N2, Ar, CO2, and CH4 is an industrially important problem, particularly for the mitigation of greenhouse emissions. Furthermore, these gases are widely accepted as standard probing gases for the characterization of the microstructure of porous solids. However, a consistent set of microstructural parameters of a microporous solid determined from the use of adsorption measurements of these different gases is not always achieved because of differences in their pore accessibility. This is a long-standing and poorly understood problem. Here, we present the calculated results of the crossing time of N2, Ar, CO2, and CH4 between two neighboring cages through a constricted window in a realistic structural model of saccharose char, generated from hybrid reverse Monte Carlo (HRMC) simulation (Nguyen, T. X.; Bhatia, S. K.; Jain, S. K.; Gubbins, K. E. Mol. Simul. 2006, 32, 567-577) using transition state theory (TST), as described in our recent work (Nguyen, T. X.; Bhatia, S. K. J. Phys. Chem. 2007, 111, 2212-2222). The striking feature in these results is that whereas very fast diffusion of carbon dioxide within the temperature range of 273-343 K, with crossing time on the molecular dynamics scale (10-4-10-6 s), leads to instantaneous equilibrium and no hysteresis on the experimental time scale, slower diffusion of Ar and N2 at the low temperature of analysis indicates an accessibility problem. These results rationalize the experimental results of hysteresis for N2 at 77 K and Ar at 87 K but not for CO2 at 273 K in Takeda 3 A carbon molecular sieves. Furthermore, it is shown that CH4 diffusion through narrow pore mouths can be hindered even at ambient temperature. Finally, we show that the use of pore size and wall thickness distributions extracted from the adsorption of Ar at 87 K using the finite wall thickness (FWT) model (Nguyen, T. X.; Bhatia, S. K. Langmuir 2004, 20, 3532-3535 and Nguyen, T. X.; Bhatia, S. K. J. Phys. Chem. B 2004

  16. Characterization of pH-sensitive molecular switches that trigger the structural transition of vesicular stomatitis virus glycoprotein from the postfusion state toward the prefusion state.

    PubMed

    Ferlin, Anna; Raux, Hélène; Baquero, Eduard; Lepault, Jean; Gaudin, Yves

    2014-11-01

    Vesicular stomatitis virus (VSV; the prototype rhabdovirus) fusion is triggered at low pH and mediated by glycoprotein G, which undergoes a low-pH-induced structural transition. A unique feature of rhabdovirus G is that its conformational change is reversible. This allows G to recover its native prefusion state at the viral surface after its transport through the acidic Golgi compartments. The crystal structures of G pre- and postfusion states have been elucidated, leading to the identification of several acidic amino acid residues, clustered in the postfusion trimer, as potential pH-sensitive switches controlling the transition back toward the prefusion state. We mutated these residues and produced a panel of single and double mutants whose fusion properties, conformational change characteristics, and ability to pseudotype a virus lacking the glycoprotein gene were assayed. Some of these mutations were also introduced in the genome of recombinant viruses which were further characterized. We show that D268, located in the segment consisting of residues 264 to 273, which refolds into postfusion helix F during G structural transition, is the major pH sensor while D274, D395, and D393 have additional contributions. Furthermore, a single passage of recombinant virus bearing the mutation D268L (which was demonstrated to stabilize the G postfusion state) resulted in a pseudorevertant with a compensatory second mutation, L271P. This revealed that the propensity of the segment of residues 264 to 273 to refold into helix F has to be finely tuned since either an increase (mutation D268L alone) or a decrease (mutation L271P alone) of this propensity is detrimental to the virus. Vesicular stomatitis virus enters cells via endocytosis. Endosome acidification induces a structural transition of its unique glycoprotein (G), which mediates fusion between viral and endosomal membranes. G conformational change is reversible upon increases in pH. This allows G to recover its native

  17. Pressure-induced magneto-structural transition in iron via a modified solid-state nudged elastic band method

    NASA Astrophysics Data System (ADS)

    Zarkevich, Nikolai A.; Johnson, Duane D.

    2015-03-01

    Materials under pressure may exhibit critical electronic and structural transitions that affect equation of states, as known for superconductors and the magneto-structural transformations of iron with both geophysical and planetary implications. While experiments often use constant-pressure (diamond-anvil cell, DAC) measurements, many theoretical results address a constant-volume transitions, which avoid issues with magnetic collapse but cannot be directly compared to experiment. We establish a modified solid-state nudge elastic band (MSS-NEB) method to handle magnetic systems that may exhibit moment (and volume) collapse during transformation. We apply it to the pressure-induced transformation in iron between the low-pressure body-centered cubic (bcc) and the high-pressure hexagonal close-packed (hcp) phases, find the bcc-hcp equilibrium coexistence pressure and a transitional pathway, and compare to shock and DAC experiments. We use methods developed with support by the U.S. Department of Energy (DE-FG02-03ER46026 and DE-AC02-07CH11358). Ames Laboratory is operated for the DOE by Iowa State University under contract DE-AC02-07CH11358.

  18. Large enhancement of second harmonic generation from transition-metal dichalcogenide monolayer on grating near bound states in the continuum.

    PubMed

    Wang, Tiecheng; Zhang, Shihao

    2018-01-08

    Second harmonic generation from the two-layer structure where a transition-metal dichalcogenide monolayer is put on a one-dimensional grating has been studied. This grating supports bound states in the continuum which have no leakage lying within the continuum of radiation modes, we can enhance the second harmonic generation from the transition-metal dichalcogenide monolayer by more than four orders of magnitude based on the critical field enhancement near the bound states in the continuum. In order to complete this calculation, the scattering matrix theory has been extended to include the nonlinear effect and the scattering matrix of a two-dimensional material including nonlinear terms; furthermore, two methods to observe the bound states in the continuum are considered, where one is tuning the thickness of the grating and the other is changing the incident angle of the electromagnetic wave. We have also discussed various modulation of the second harmonic generation enhancement by adjusting the azimuthal angle of the transition-metal dichalcogenide monolayer.

  19. Free-end adaptive nudged elastic band method for locating transition states in minimum energy path calculation.

    PubMed

    Zhang, Jiayong; Zhang, Hongwu; Ye, Hongfei; Zheng, Yonggang

    2016-09-07

    A free-end adaptive nudged elastic band (FEA-NEB) method is presented for finding transition states on minimum energy paths, where the energy barrier is very narrow compared to the whole paths. The previously proposed free-end nudged elastic band method may suffer from convergence problems because of the kinks arising on the elastic band if the initial elastic band is far from the minimum energy path and weak springs are adopted. We analyze the origin of the formation of kinks and present an improved free-end algorithm to avoid the convergence problem. Moreover, by coupling the improved free-end algorithm and an adaptive strategy, we develop a FEA-NEB method to accurately locate the transition state with the elastic band cut off repeatedly and the density of images near the transition state increased. Several representative numerical examples, including the dislocation nucleation in a penta-twinned nanowire, the twin boundary migration under a shear stress, and the cross-slip of screw dislocation in face-centered cubic metals, are investigated by using the FEA-NEB method. Numerical results demonstrate both the stability and efficiency of the proposed method.

  20. Health Changes in Low Income Men Transitioning from a State Funded Prostate Cancer Program to Comprehensive Insurance.

    PubMed

    Nabhani, Jamal A; Kuang, Ruby; Liu, Hui; Kwan, Lorna; Litwin, Mark S

    2018-07-01

    We evaluated the effect of transitioning from a prostate cancer specific treatment program to comprehensive insurance under the ACA (Patient Protection and Affordable Care Act) on the physical, mental and prostate cancer related health of poor, previously uninsured men. We assessed general and prostate cancer specific health related quality of life using the RAND SF-12v2™ (12-Item Short Form Survey, version 2) and the UCLA PCI (Prostate Cancer Index) at 3 time points in 24 men who transitioned to comprehensive insurance as the insured group relative to 39 who remained in the prostate cancer program as the control group. We used mixed effects models controlling for treatment and patient factors to measure health differences between the groups during the transition period. Demographics, prostate cancer treatment patterns, and mental, physical and general health were similar before transition in the control and insured groups. After transition men who gained insurance coverage reported significantly worse physical health than men who remained in the prostate cancer program (p = 0.0038). After adjustment in the mixed effects model physical health remained worse in men who gained insurance (p = 0.0036). Mental health and prostate cancer related quality of life did not differ with time between the groups. Compared to controls who remained in the state funded prostate cancer treatment program for poor, uninsured men, newly insured men reported worse physical health after transitioning to ACA coverage. Providers and policy makers may draw important lessons from understanding the mechanisms of this paradoxical worsening in physical health after gaining insurance. These results inform the development of disease specific models of care in the broader health insurance context. Copyright © 2018 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.