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Sample records for active state transition

  1. Slow State Transitions of Sustained Neural Oscillations by Activity-Dependent Modulation of Intrinsic Excitability

    Science.gov (United States)

    Fröhlich, Flavio; Bazhenov, Maxim; Timofeev, Igor; Steriade, Mircea; Sejnowski, Terrence J.

    2010-01-01

    Little is known about the dynamics and mechanisms of transitions between tonic firing and bursting in cortical networks. Here, we use a computational model of a neocortical circuit with extracellular potassium dynamics to show that activity-dependent modulation of intrinsic excitability can lead to sustained oscillations with slow transitions between two distinct firing modes: fast run (tonic spiking or fast bursts with few spikes) and slow bursting. These transitions are caused by a bistability with hysteresis in a pyramidal cell model. Balanced excitation and inhibition stabilizes a network of pyramidal cells and inhibitory interneurons in the bistable region and causes sustained periodic alternations between distinct oscillatory states. During spike-wave seizures, neocortical paroxysmal activity exhibits qualitatively similar slow transitions between fast run and bursting. We therefore predict that extracellular potassium dynamics can cause alternating episodes of fast and slow oscillatory states in both normal and epileptic neocortical networks. PMID:16763023

  2. Visualization of the Differential Transition State Stabilization within the Active Site Environment

    Directory of Open Access Journals (Sweden)

    Jerzy Leszczynski

    2004-05-01

    Full Text Available Abstract: Increasing interest in the enzymatic reaction mechanisms and in the nature of catalytic effects in enzymes causes the need of appropriate visualization methods. A new interactive method to investigate catalytic effects using differential transition state stabilization approach (DTSS [1, 2] is presented. The catalytic properties of the active site of cytidine deaminase (E.C. 3.5.4.5 is visualized in the form of differential electrostatic properties. The visualization was implemented using scripting interface of VMD [3]. Cumulative Atomic Multipole Moments (CAMM [4,5,6] were utilized for efficient yet accurate evaluation of the electrostatic properties. The implementation is efficient enough for interactive presentation of catalytic effects in the active site of the enzyme due to transition state or substrate movement. This system of visualization of DTTS approach can be potentially used to validate hypotheses regarding the catalytic mechanism or to study binding properties of transition state analogues.

  3. A Semi-Continuous State-Transition Probability HMM-Based Voice Activity Detector

    Directory of Open Access Journals (Sweden)

    H. Othman

    2007-02-01

    Full Text Available We introduce an efficient hidden Markov model-based voice activity detection (VAD algorithm with time-variant state-transition probabilities in the underlying Markov chain. The transition probabilities vary in an exponential charge/discharge scheme and are softly merged with state conditional likelihood into a final VAD decision. Working in the domain of ITU-T G.729 parameters, with no additional cost for feature extraction, the proposed algorithm significantly outperforms G.729 Annex B VAD while providing a balanced tradeoff between clipping and false detection errors. The performance compares very favorably with the adaptive multirate VAD, option 2 (AMR2.

  4. A Semi-Continuous State-Transition Probability HMM-Based Voice Activity Detector

    Directory of Open Access Journals (Sweden)

    Othman H

    2007-01-01

    Full Text Available We introduce an efficient hidden Markov model-based voice activity detection (VAD algorithm with time-variant state-transition probabilities in the underlying Markov chain. The transition probabilities vary in an exponential charge/discharge scheme and are softly merged with state conditional likelihood into a final VAD decision. Working in the domain of ITU-T G.729 parameters, with no additional cost for feature extraction, the proposed algorithm significantly outperforms G.729 Annex B VAD while providing a balanced tradeoff between clipping and false detection errors. The performance compares very favorably with the adaptive multirate VAD, option 2 (AMR2.

  5. Spin state transition in the active center of the hemoglobin molecule: DFT + DMFT study

    Science.gov (United States)

    Novoselov, D.; Korotin, Dm. M.; Anisimov, V. I.

    2016-05-01

    An ab initio study of electronic and spin configurations of the iron ion in the active center of the human hemoglobin molecule is presented. With a combination of the Density Functional Theory (DFT) method and the Dynamical Mean Field Theory (DMFT) approach, the spin state transition description in the iron ion during the oxidation process is significantly improved in comparison with previous attempts. It was found that the origin of the iron ion local moment behavior both for the high-spin and for the low-spin states in the hemoglobin molecule is caused by the presence of a mixture of several atomic states with comparable statistical probability.

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

    Science.gov (United States)

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

    2016-05-01

    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.

  7. Transition of arrestin into the active receptor-binding state requires an extended interdomain hinge.

    Science.gov (United States)

    Vishnivetskiy, Sergey A; Hirsch, Joel A; Velez, Maria-Gabriela; Gurevich, Yulia V; Gurevich, Vsevolod V

    2002-11-15

    Arrestins selectively bind to the phosphorylated activated form of G protein-coupled receptors, thereby blocking further G protein activation. Structurally, arrestins consist of two domains topologically connected by a 12-residue long loop, which we term the "hinge" region. Both domains contain receptor-binding elements. The relative size and shape of arrestin and rhodopsin suggest that dramatic changes in arrestin conformation are required to bring all of its receptor-binding elements in contact with the cytoplasmic surface of the receptor. Here we use the visual arrestin/rhodopsin system to test the hypothesis that the transition of arrestin into its active receptor-binding state involves a movement of the two domains relative to each other that might be limited by the length of the hinge. We have introduced three insertions and 24 deletions in the hinge region and measured the binding of all of these mutants to light-activated phosphorylated (P-Rh*), dark phosphorylated (P-Rh), dark unphosphorylated (Rh), and light-activated unphosphorylated rhodopsin (Rh*). The addition of 1-3 extra residues to the hinge has no effect on arrestin function. In contrast, sequential elimination of 1-8 residues results in a progressive decrease in P-Rh* binding without changing arrestin selectivity for P-Rh*. These results suggest that there is a minimum length of the hinge region necessary for high affinity binding, consistent with the idea that the two domains move relative to each other in the process of arrestin transition into its active receptor-binding state. The same length of the hinge is also necessary for the binding of "constitutively active" arrestin mutants to P-Rh*, dark P-Rh, and Rh*, suggesting that the active (receptor-bound) arrestin conformation is essentially the same in both wild type and mutant forms.

  8. Variational Transition State Theory

    Energy Technology Data Exchange (ETDEWEB)

    Truhlar, Donald G. [Univ. of Minnesota, Minneapolis, MN (United States)

    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.

  9. Evolution of a transition state: role of Lys100 in the active site of isocitrate dehydrogenase.

    Science.gov (United States)

    Miller, Stephen P; Gonçalves, Susana; Matias, Pedro M; Dean, Antony M

    2014-05-26

    An active site lysine essential to catalysis in isocitrate dehydrogenase (IDH) is absent from related enzymes. As all family members catalyze the same oxidative β-decarboxylation at the (2R)-malate core common to their substrates, it seems odd that an amino acid essential to one is not found in all. Ordinarily, hydride transfer to a nicotinamide C4 neutralizes the positive charge at N1 directly. In IDH, the negatively charged C4-carboxylate of isocitrate stabilizes the ground state positive charge on the adjacent nicotinamide N1, opposing hydride transfer. The critical lysine is poised to stabilize-and perhaps even protonate-an oxyanion formed on the nicotinamide 3-carboxamide, thereby enabling the hydride to be transferred while the positive charge at N1 is maintained. IDH might catalyze the same overall reaction as other family members, but dehydrogenation proceeds through a distinct, though related, transition state. Partial activation of lysine mutants by K(+) and NH4 (+) represents a throwback to the primordial state of the first promiscuous substrate family member.

  10. Nonstationary Stochastic Dynamics Underlie Spontaneous Transitions between Active and Inactive Behavioral States.

    Science.gov (United States)

    Melanson, Alexandre; Mejias, Jorge F; Jun, James J; Maler, Leonard; Longtin, André

    2017-01-01

    The neural basis of spontaneous movement generation is a fascinating open question. Long-term monitoring of fish, swimming freely in a constant sensory environment, has revealed a sequence of behavioral states that alternate randomly and spontaneously between periods of activity and inactivity. We show that key dynamical features of this sequence are captured by a 1-D diffusion process evolving in a nonlinear double well energy landscape, in which a slow variable modulates the relative depth of the wells. This combination of stochasticity, nonlinearity, and nonstationary forcing correctly captures the vastly different timescales of fluctuations observed in the data (∼1 to ∼1000 s), and yields long-tailed residence time distributions (RTDs) also consistent with the data. In fact, our model provides a simple mechanism for the emergence of long-tailed distributions in spontaneous animal behavior. We interpret the stochastic variable of this dynamical model as a decision-like variable that, upon reaching a threshold, triggers the transition between states. Our main finding is thus the identification of a threshold crossing process as the mechanism governing spontaneous movement initiation and termination, and to infer the presence of underlying nonstationary agents. Another important outcome of our work is a dimensionality reduction scheme that allows similar segments of data to be grouped together. This is done by first extracting geometrical features in the dataset and then applying principal component analysis over the feature space. Our study is novel in its ability to model nonstationary behavioral data over a wide range of timescales.

  11. Variational transition state theory

    Energy Technology Data Exchange (ETDEWEB)

    Truhlar, D.G. [Univ. of Minnesota, Minneapolis (United States)

    1993-12-01

    This research program involves the development of variational transition state theory (VTST) and semiclassical tunneling methods for the calculation of gas-phase reaction rates and selected applications. The applications are selected for their fundamental interest and/or their relevance to combustion.

  12. Nonstationary Stochastic Dynamics Underlie Spontaneous Transitions between Active and Inactive Behavioral States

    Science.gov (United States)

    Jun, James J.; Longtin, André

    2017-01-01

    Abstract The neural basis of spontaneous movement generation is a fascinating open question. Long-term monitoring of fish, swimming freely in a constant sensory environment, has revealed a sequence of behavioral states that alternate randomly and spontaneously between periods of activity and inactivity. We show that key dynamical features of this sequence are captured by a 1-D diffusion process evolving in a nonlinear double well energy landscape, in which a slow variable modulates the relative depth of the wells. This combination of stochasticity, nonlinearity, and nonstationary forcing correctly captures the vastly different timescales of fluctuations observed in the data (∼1 to ∼1000 s), and yields long-tailed residence time distributions (RTDs) also consistent with the data. In fact, our model provides a simple mechanism for the emergence of long-tailed distributions in spontaneous animal behavior. We interpret the stochastic variable of this dynamical model as a decision-like variable that, upon reaching a threshold, triggers the transition between states. Our main finding is thus the identification of a threshold crossing process as the mechanism governing spontaneous movement initiation and termination, and to infer the presence of underlying nonstationary agents. Another important outcome of our work is a dimensionality reduction scheme that allows similar segments of data to be grouped together. This is done by first extracting geometrical features in the dataset and then applying principal component analysis over the feature space. Our study is novel in its ability to model nonstationary behavioral data over a wide range of timescales. PMID:28374017

  13. The Differential Gibbs Free Energy of Activation and its Implications in the Transition-State of Enzymatic Reactions

    Science.gov (United States)

    Maggi, F.; Riley, W. J.

    2016-12-01

    We propose a mathematical framework to introduce the concept of differential free energy of activation in enzymatically catalyzed reactions, and apply it to N uptake by microalgae and bacteria. This framework extends the thermodynamic capabilities of the classical transition-state theory in and harmonizes the consolidated definitions of kinetic parameters with their thermodynamic and physical meaning. Here, the activation energy is assumed to be a necessary energetic level for equilibrium complexation between reactants and activated complex; however, an additional energy contribution is required for the equilibrium activated complex to release reaction products. We call this "differential free energy of activation"; it can be described by a Boltzmann distribution, and corresponds to a free energy level different from that of complexation. Whether this level is above or below the free energy of activation depends on the reaction, and defines energy domains that correspond to "superactivated", "activated", and "subactivated" complexes. The activated complex reaching one of those states will eventually release the products from an energy level different than that of activation. The concept of differential free energy of activation was tested on 57 independent experiments of NH­4+ and NO3- uptake by various microalgae and bacteria at temperatures ranging between 1 and 45oC. Results showed that the complexation equilibrium always favored the activated complex, but the differential energy of activation led to an apparent energy barrier consistent with observations. Temperature affected all energy levels within this framework but did not alter substantially these thermodynamic features. Overall the approach: (1) provides a thermodynamic and mathematical link between Michaelis-Menten and rate constants; (2) shows that both kinetic parameters can be described or approximated by Arrhenius' like equations; (3) describes the likelihood of formation of sub-, super-, and

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

    Science.gov (United States)

    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.

  15. Post-Transition State Dynamics in Gas Phase Reactivity: Importance of Bifurcations and Rotational Activation.

    Science.gov (United States)

    Martín-Sómer, Ana; Yáñez, Manuel; Hase, William L; Gaigeot, Marie-Pierre; Spezia, Riccardo

    2016-03-01

    Beyond the established use of thermodynamic vs kinetic control to explain chemical reaction selectivity, the concept of bifurcations on a potential energy surface (PES) is proving to be of pivotal importance with regard to selectivity. In this article, we studied by means of post-transition state (TS) direct dynamics simulations the effect that vibrational and rotational excitation at the TS may have on selectivity on a bifurcating PES. With this aim, we studied the post-TS unimolecular reactivity of the [Ca(formamide)](2+) ion, for which Coulomb explosion and neutral loss reactions compete. The PES exhibits different kinds of nonintrinsic reaction coordinate (IRC) dynamics, among them PES bifurcations, which direct the trajectories to multiple reaction paths after passing the TS. Direct dynamics simulations were used to distinguish between the bifurcation non-IRC dynamics and non-IRC dynamics arising from atomistic motions directing the trajectories away from the IRC. Overall, we corroborated the idea that kinetic selectivity often does not reduce to a simple choice between paths with different barrier heights and instead dynamical behavior after passing the TS may be crucial. Importantly, rotational excitation may play a pivotal role on the reaction selectivity favoring nonthermodynamic products.

  16. Virtual screening of mandelate racemase mutants with enhanced activity based on binding energy in the transition state.

    Science.gov (United States)

    Gu, Jiali; Liu, Min; Guo, Fei; Xie, Wenping; Lu, Wenqiang; Ye, Lidan; Chen, Zhirong; Yuan, Shenfeng; Yu, Hongwei

    2014-02-05

    Mandelate racemase (MR) is a promising candidate for the dynamic kinetic resolution of racemates. However, the poor activity of MR towards most of its non-natural substrates limits its widespread application. In this work, a virtual screening method based on the binding energy in the transition state was established to assist in the screening of MR mutants with enhanced catalytic efficiency. Using R-3-chloromandelic acid as a model substrate, a total of 53 mutants were constructed based on rational design in the two rounds of screening. The number of mutants for experimental validation was brought down to 17 by the virtual screening method, among which 14 variants turned out to possess improved catalytic efficiency. The variant V26I/Y54V showed 5.2-fold higher catalytic efficiency (k(cat)/K(m)) towards R-3-chloromandelic acid than that observed for the wild-type enzyme. Using this strategy, mutants were successfully obtained for two other substrates, R-mandelamide and R-2-naphthylglycolate (V26I and V29L, respectively), both with a 2-fold improvement in catalytic efficiency. These results demonstrated that this method could effectively predict the trend of mutational effects on catalysis. Analysis from the energetic and structural assays indicated that the enhanced interactions between the active sites and the substrate in the transition state led to improved catalytic efficiency. It was concluded that this virtual screening method based on the binding energy in the transition state was beneficial in enzyme rational redesign and helped to better understand the catalytic properties of the enzyme.

  17. Effect of Pair Interactions on Transition Probabilities between Inactive and Active States — Achieving Collective Behaviour via Pair Interactions in Social Insects —

    Science.gov (United States)

    Hayashi, Yoshikatsu; Yuki, Mai; Kikuchi, Tomonori; Tsuji, Kazuki; Sugawara, Ken

    2015-10-01

    To understand the evolution of well-organized social behaviour, we must first understand the mechanism by which collective behaviour is established. In this study, the mechanisms of collective behaviour in a colony of social insects were studied in terms of the transition probability between active and inactive states, which is linked to mutual interactions. The active and inactive states of the social insects were statistically extracted from the velocity profiles. From the duration distributions of the two states, we found that (1) the durations of active and inactive states follow an exponential law, and (2) pair interactions increase the transition probability from inactive to active states. The regulation of the transition probability by pair interactions suggests that such interactions control the populations of active and inactive workers in the colony.

  18. Exploring the Cross-sectional Association between Transit-Oriented Development Zoning and Active Travel and Transit Usage in the United States, 2010-2014

    Directory of Open Access Journals (Sweden)

    Emily eThrun

    2016-06-01

    Full Text Available Background: In response to traditional zoning codes that contribute to car-dependent, sprawling, and disconnected neighborhoods, communities are reforming their land use laws to create pedestrian-friendly areas that promote physical activity. One such reform is the adoption of transit-oriented developments or districts (TODs. TODs are higher-density, compact, mixed use areas located around transit stops that are designed to encourage walking.Purpose: To identify the characteristics of communities that have adopted TODs in their land use laws and examine if communities that have included TODs in their zoning codes are more likely to have adults that commute by any form of active transportation (i.e., walking, biking, or public transportation or by using public transportation specifically.Methods: Zoning codes effective as of 2010 were obtained for a purposeful sample of the largest 3,914 municipal jurisdictions located in 473 of the most populous US counties and consolidated cities within 48 states and the District of Columbia. They were evaluated to determine whether they included TOD districts or regulations using a coding tool developed by the study team. Descriptive statistics together with t-tests and Pearson’s chi-squared independence test were used to compare characteristics of jurisdictions with and without TOD zoning. Multivariate linear regressions were used to compute the adjusted association between TOD zoning and taking public or active transportation to work.Results: Jurisdictions with TOD zoning were located more in the South and West than non-TOD jurisdictions and were more populous, higher income, more racially diverse, and younger. Jurisdictions with TOD zoning had significantly higher percentages of occupied housing with no vehicle than those without TOD zoning. TOD zoning was associated with significantly higher rates of public transportation to work (β=2.10, 95% CI=0.88, 3.32 and active transportation to work (β=2.48, 95

  19. Quantum Transition-State Theory

    CERN Document Server

    Hele, Timothy J H

    2014-01-01

    This dissertation unifies one of the central methods of classical rate calculation, `Transition-State Theory' (TST), with quantum mechanics, thereby deriving a rigorous `Quantum Transition-State Theory' (QTST). The resulting QTST is identical to ring polymer molecular dynamics transition-state theory (RPMD-TST), which was previously considered a heuristic method, and whose results we thereby validate. The key step in deriving a QTST is alignment of the flux and side dividing surfaces in path-integral space to obtain a quantum flux-side time-correlation function with a non-zero $t\\to 0_+$ limit. We then prove that this produces the exact quantum rate in the absence of recrossing by the exact quantum dynamics, fulfilling the requirements of a QTST. Furthermore, strong evidence is presented that this is the only QTST with positive-definite Boltzmann statistics and therefore the pre-eminent method for computation of thermal quantum rates in direct reactions.

  20. Transition-state theory and dynamical corrections

    DEFF Research Database (Denmark)

    Henriksen, Niels Engholm; Hansen, Flemming Yssing

    2002-01-01

    . The correction factor due to non-adiabatic dynamics is considered in relation to the non-activated dissociative sticking of N-2 on Fe(111). For this process, conventional transition-state theory gives a sticking probability which is about 10 times too large (at T = 300 K). We estimate that the sticking......We consider conventional transition-state theory, and show how quantum dynamical correction factors can be incorporated in a simple fashion, as a natural extension of the fundamental formulation. Corrections due to tunneling and non-adiabatic dynamics are discussed, with emphasis on the latter...

  1. Modified Transition State Theory for Evaporation and Condensation

    Institute of Scientific and Technical Information of China (English)

    王遵敬; 陈民; 过增元

    2002-01-01

    A modification of the transition state theory for evaporation and condensation is presented by analysing the kinetic characteristics of liquid-vapour interphase transport. In the modified transition state theory, the moving orientation of molecules is introduced into the calculation of the free volume of the activated complex. The condensation coefficients of argon at different temperatures are calculated with the modified transition state theory. The results agree well with those from molecular dynamics simulations.

  2. Dependency in State Transitions of Wind Turbines

    DEFF Research Database (Denmark)

    Herp, Jürgen; Ramezani, Mohammad Hossein; S. Nadimi, Esmaeil

    2017-01-01

    the state transitions are based on a hidden variable relevant for the predictor, namely the information of the current state. Given an underlying predictive model based on a Student's t-distribution for the samples and a conditional prior on the state transition, it is shown that state transitions can...... configurations. Comparing to heuristic interpretations of the residuals both models can qualitatively inform about the time when a state transition occurs.......Abstracting turbine states and predicting the transition into failure states ahead of time is important in operation and maintenance of wind turbines. This study presents a method to monitor state transitions of a wind turbine based on the online inference on residuals. In a Bayesian framework...

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

    Science.gov (United States)

    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.

  4. Multiferroic behavior at a spin state transition

    Science.gov (United States)

    Zapf, Vivien; Chikara, Shalinee; Singleton, John; Lin, Shizeng; Batista, Cristian; Scott, Brian; Smythe, Nathan

    Traditionally, multiferroic behavior is studied in materials with coexisting long-range orders, such as ferromagnetism and ferroelectricity. Here we present multiferroic behavior at a spin-state transition (SST). SSTs, for example, the S = 1 to S = 2 transition in Mn3+ can become cooperative magneto-structural phase transitions due to structural coupling between ions. SSTs are accompanied by change in the orbital occupation and hence, strongly coupled to the lattice and charge degrees of freedom. They are a dominant functionality in metal-organic materials, persisting up to room temperature in some compounds. We demonstrate that a magnetic SST can induce ferroelectricity. We study a Mn-based metal-organic system in which a three-fold degenerate dynamic Jahn-Teller effect at high temperatures vanishes when the temperature is lowered, and the system drops into a lower spin state. Application of a magnetic field restores the high spin Jahn-Teller-active state and allows the Jahn Teller distortions to order cooperatively, creating a dielectric constant change and a net electric polarization. We use high magnetic fields at the NHMFL to study the magnetic and electric behavior of this system across a significant fraction of its T-H phase space, and compare to theoretical modeling.

  5. Structural analysis of the transitional state of Arp2/3 complex activation by two actin-bound WCAs.

    Science.gov (United States)

    Boczkowska, Malgorzata; Rebowski, Grzegorz; Kast, David J; Dominguez, Roberto

    2014-01-01

    Actin filament nucleation and branching by Arp2/3 complex is activated by nucleation-promoting factors (NPFs), whose C-terminal WCA region contains binding sites for actin (W) and Arp2/3 complex (CA). It is debated whether one or two NPFs are required for activation. Here we present evidence in support of the two-NPF model and show that actin plays a crucial role in the interactions of two mammalian NPFs, N-WASP and WAVE2, with Arp2/3 complex. Competition between actin-WCA and glia maturation factor (GMF) for binding to Arp2/3 complex suggests that during activation the first actin monomer binds at the barbed end of Arp2. Based on distance constraints obtained by time-resolved fluorescence resonance energy transfer, we define the relative position of the two actin-WCAs on Arp2/3 complex and propose an atomic model of the 11-subunit transitional complex.

  6. Boronic Acid Transition State Inhibitors Active against KPC and Other Class A β-Lactamases: Structure-Activity Relationships as a Guide to Inhibitor Design.

    Science.gov (United States)

    Rojas, Laura J; Taracila, Magdalena A; Papp-Wallace, Krisztina M; Bethel, Christopher R; Caselli, Emilia; Romagnoli, Chiara; Winkler, Marisa L; Spellberg, Brad; Prati, Fabio; Bonomo, Robert A

    2016-01-04

    Boronic acid transition state inhibitors (BATSIs) are competitive, reversible β-lactamase inhibitors (BLIs). In this study, a series of BATSIs with selectively modified regions (R1, R2, and amide group) were strategically designed and tested against representative class A β-lactamases of Klebsiella pneumoniae, KPC-2 and SHV-1. Firstly, the R1 group of compounds 1a to 1c and 2a to 2e mimicked the side chain of cephalothin, whereas for compounds 3a to 3c, 4a, and 4b, the thiophene ring was replaced by a phenyl, typical of benzylpenicillin. Secondly, variations in the R2 groups which included substituted aryl side chains (compounds 1a, 1b, 1c, 3a, 3b, and 3c) and triazole groups (compounds 2a to 2e) were chosen to mimic the thiazolidine and dihydrothiazine ring of penicillins and cephalosporins, respectively. Thirdly, the amide backbone of the BATSI, which corresponds to the amide at C-6 or C-7 of β-lactams, was also changed to the following bioisosteric groups: urea (compound 3b), thiourea (compound 3c), and sulfonamide (compounds 4a and 4b). Among the compounds that inhibited KPC-2 and SHV-1 β-lactamases, nine possessed 50% inhibitory concentrations (IC50s) of ≤ 600 nM. The most active compounds contained the thiopheneacetyl group at R1 and for the chiral BATSIs, a carboxy- or hydroxy-substituted aryl group at R2. The most active sulfonamido derivative, compound 4b, lacked an R2 group. Compound 2b (S02030) was the most active, with acylation rates (k2/K) of 1.2 ± 0.2 × 10(4) M(-1) s(-1) for KPC-2 and 4.7 ± 0.6 × 10(3) M(-1) s(-1) for SHV-1, and demonstrated antimicrobial activity against Escherichia coli DH10B carrying blaSHV variants and blaKPC-2 or blaKPC-3 and against clinical strains of Klebsiella pneumoniae and E. coli producing different class A β-lactamase genes. At most, MICs decreased from 16 to 0.5 mg/liter.

  7. Final Technical Report: Variational Transition State Theory

    Energy Technology Data Exchange (ETDEWEB)

    Truhlar, Donald G. [University of Minnesota; Truhlar, Donald G. [University of Minnesota

    2016-09-15

    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 coupledmode 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 multidimensional 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 MPVTST 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 (EAVTST), 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.

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

    Science.gov (United States)

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

    2016-03-23

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

  9. Kinetics of Hydrogen Radical Reactions with Toluene Including Chemical Activation Theory Employing System-Specific Quantum RRK Theory Calibrated by Variational Transition State Theory.

    Science.gov (United States)

    Bao, Junwei Lucas; Zheng, Jingjing; Truhlar, Donald G

    2016-03-02

    Pressure-dependent reactions are ubiquitous in combustion and atmospheric chemistry. We employ a new calibration procedure for quantum Rice-Ramsperger-Kassel (QRRK) unimolecular rate theory within a chemical activation mechanism to calculate the pressure-falloff effect of a radical association with an aromatic ring. The new theoretical framework is applied to the reaction of H with toluene, which is a prototypical reaction in the combustion chemistry of aromatic hydrocarbons present in most fuels. Both the hydrogen abstraction reactions and the hydrogen addition reactions are calculated. Our system-specific (SS) QRRK approach is adjusted with SS parameters to agree with multistructural canonical variational transition state theory with multidimensional tunneling (MS-CVT/SCT) at the high-pressure limit. The new method avoids the need for the usual empirical estimations of the QRRK parameters, and it eliminates the need for variational transition state theory calculations as a function of energy, although in this first application we do validate the falloff curves by comparing SS-QRRK results without tunneling to multistructural microcanonical variational transition state theory (MS-μVT) rate constants without tunneling. At low temperatures, the two approaches agree well with each other, but at high temperatures, SS-QRRK tends to overestimate falloff slightly. We also show that the variational effect is important in computing the energy-resolved rate constants. Multiple-structure anharmonicity, torsional-potential anharmonicity, and high-frequency-mode vibrational anharmonicity are all included in the rate computations, and torsional anharmonicity effects on the density of states are investigated. Branching fractions, which are both temperature- and pressure-dependent (and for which only limited data is available from experiment), are predicted as a function of pressure.

  10. Combining active-space coupled-cluster methods with moment energy corrections via the CC(P;Q) methodology, with benchmark calculations for biradical transition states

    Science.gov (United States)

    Shen, Jun; Piecuch, Piotr

    2012-04-01

    We have recently suggested the CC(P;Q) methodology that can correct energies obtained in the active-space coupled-cluster (CC) or equation-of-motion (EOM) CC calculations, which recover much of the nondynamical and some dynamical electron correlation effects, for the higher-order, mostly dynamical, correlations missing in the active-space CC/EOMCC considerations. It is shown that one can greatly improve the description of biradical transition states, both in terms of the resulting energy barriers and total energies, by combining the CC approach with singles, doubles, and active-space triples, termed CCSDt, with the CC(P;Q)-style correction due to missing triple excitations defining the CC(t;3) approximation.

  11. Transition States of Telecommunication Network

    Directory of Open Access Journals (Sweden)

    Gustav Cepciansky

    2004-01-01

    Full Text Available The dimensioning and performance of the telecommunication network take place according to the theory of teletrafficalways taking into account the stable state. But the utterance of the network being in an unstable state is less known. In this paper, wewould like to remind the network performance in the unstable state and to draw attention to the practical consequences of transitionstates.

  12. An inhibitory gate for state transition in cortex

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2003-06-27

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

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

    Science.gov (United States)

    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.

  15. On primordial equation of state transitions

    CERN Document Server

    Aravind, Aditya; Paban, Sonia

    2016-01-01

    We revisit the physics of transitions from a general equation of state parameter to the final stage of slow-roll inflation. We show that it is unlikely for the modes comprising the cosmic microwave background to contain imprints from a pre-inflationary equation of state transition and still be consistent with observations. We accomplish this by considering observational consistency bounds on the amplitude of excitations resulting from such a transition. As a result, the physics which initially led to inflation likely cannot be probed with observations of the cosmic microwave background. Furthermore, we show that it is unlikely that equation of state transitions may explain the observed low multipole power suppression anomaly.

  16. Transition of polymers from rubbery elastic state to fluid state

    Institute of Scientific and Technical Information of China (English)

    Renyuan QIAN; Yansheng YU

    2009-01-01

    On increasing the temperature of a polymer,the transition of the polymer from a rubbery elastic state to a fluid state could occur. The transition temperature is termed the fluid temperature of the polymer, Tf, which has a direct relationship with the polymer molecular weight.As one of polymer parameters, Tf is as important as the glass transition temperature of a polymer, Tg. Moreover,special attention to Tf should be paid for polymer processing. In research on the transition of a polymer from a rubbery elastic state to a fluid state, the concept of Tfwould be more reasonable and more effective than the concept of T1,1 because it is neglected in the concept of T1,1in that the molecular weight of a polymer may affect the transition of the polymer. In this paper the discussion on the fluid temperature involves the characters of polymers,such as the deformation-temperature curve, the tempera-ture range of the rubbery state and the shear viscosity of polymer melt. From the viewpoint of the cohesional state of polymers, the transition of a polymer from a rubbery elastic state to a fluid state responds to destruction and construction of the cohesional entanglement network in the polymer. The relaxing network of polymer melt would be worthy to be considered as an object of study.

  17. State Transitions of Black Hole Accretion Flows

    Institute of Scientific and Technical Information of China (English)

    卢炬甫; 潘刘彬

    2001-01-01

    We show that the thermal instability-triggered transition from the state of the Shakura-Sunyaev disc to the state of the advection-dominated accretion flow is possible for black hole accretion flows composed of two-temperature plasma with bremsstrahlung and synchrotron radiation and Comptonization.

  18. Operationalizing resilience using state and transition models

    Science.gov (United States)

    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...

  19. State transition algorithm for traveling salesman problem

    CERN Document Server

    Chunhua, Yang; Xiaojun, Zhou; Weihua, Gui

    2012-01-01

    Discrete version of state transition algorithm is proposed in order to solve the traveling salesman problem. Three special operators for discrete optimization problem named swap, shift and symmetry transformations are presented. Convergence analysis and time complexity of the algorithm are also considered. To make the algorithm simple and efficient, no parameter adjusting is suggested in current version. Experiments are carried out to test the performance of the strategy, and comparisons with simulated annealing and ant colony optimization have demonstrated the effectiveness of the proposed algorithm. The results also show that the discrete state transition algorithm consumes much less time and has better search ability than its counterparts, which indicates that state transition algorithm is with strong adaptability.

  20. Cassini State Transitions with a Fossil Figure

    Science.gov (United States)

    Matsuyama, Isamu; Tuttle Keane, James

    2016-10-01

    The Moon has experienced large obliquity variations during Cassini state transitions which greatly impact tidal heating, and the long-term stability of polar volatiles. It has been known for centuries that the lunar rotational and tidal bulges are much larger than expected. The South Pole-Aitken basin can explain a large fraction of the excess deformation. Accounting for the contribution of this basin (and other large basins), the remaining excess deformation arises due to a fossil figure established when the Moon orbited much closer to Earth than it does today. Previous studies assume that the present, excess deformation is entirely preserved throughout Cassini state transitions. This ignores basin contributions to the excess deformation, and requires an interior with infinite rigidity. We consider Cassini state transition models that take into account basin contributions to the excess deformation, and the effect of finite rigidity on the fossil figure.

  1. Visualizing Cell State Transition Using Raman Spectroscopy

    Science.gov (United States)

    Ichimura, Taro; Chiu, Liang-da; Fujita, Katsumasa; Kawata, Satoshi; Watanabe, Tomonobu M.; Yanagida, Toshio; Fujita, Hideaki

    2014-01-01

    System level understanding of the cell requires detailed description of the cell state, which is often characterized by the expression levels of proteins. However, understanding the cell state requires comprehensive information of the cell, which is usually obtained from a large number of cells and their disruption. In this study, we used Raman spectroscopy, which can report changes in the cell state without introducing any label, as a non-invasive method with single cell capability. Significant differences in Raman spectra were observed at the levels of both the cytosol and nucleus in different cell-lines from mouse, indicating that Raman spectra reflect differences in the cell state. Difference in cell state was observed before and after the induction of differentiation in neuroblastoma and adipocytes, showing that Raman spectra can detect subtle changes in the cell state. Cell state transitions during embryonic stem cell (ESC) differentiation were visualized when Raman spectroscopy was coupled with principal component analysis (PCA), which showed gradual transition in the cell states during differentiation. Detailed analysis showed that the diversity between cells are large in undifferentiated ESC and in mesenchymal stem cells compared with terminally differentiated cells, implying that the cell state in stem cells stochastically fluctuates during the self-renewal process. The present study strongly indicates that Raman spectral morphology, in combination with PCA, can be used to establish cells' fingerprints, which can be useful for distinguishing and identifying different cellular states. PMID:24409302

  2. A New Approach toward Transition State Spectroscopy

    CERN Document Server

    Prozument, Kirill; Ciuba, Monika A; Muenter, John S; Park, G Barratt; Stanton, John F; Guo, Hua; Wong, Bryan M; Perry, David S; Field, Robert W

    2013-01-01

    Chirped-Pulse millimetre-Wave (CPmmW) rotational spectroscopy provides a new class of information about photolysis transition state(s). Measured intensities in rotational spectra determine species-isomer-vibrational populations, provided that rotational populations can be thermalized. The formation and detection of S0 vinylidene is discussed in the limits of low and high initial rotational excitation. CPmmW spectra of 193 nm photolysis of Vinyl Cyanide (Acrylonitrile) contain J=0-1 transitions in more than 20 vibrational levels of HCN, HNC, but no transitions in vinylidene or highly excited local-bender vibrational levels of acetylene. Reasons for the non-observation of the vinylidene co-product of HCN are discussed.

  3. Variational Identification of Markovian Transition States

    Directory of Open Access Journals (Sweden)

    Linda Martini

    2017-09-01

    Full Text Available 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 Ala_{5}, and of larger, biomedically important systems: the 15-lipoxygenase-2 enzyme (15-LOX-2, the epidermal growth factor receptor (EGFR protein, and the Mga2 fungal transcription factor. The analysis of 15-LOX-2 uses data generated exclusively from biased umbrella sampling simulations carried out at the hybrid ab initio density functional theory (DFT quantum mechanics/molecular mechanics (QM/MM level of theory. In all cases, our method automatically identifies the corresponding transition states and metastable conformations in a variationally optimal way, with the input of a set of relevant coordinates, by accurately reproducing the intrinsic slowest relaxation rate of each system. Our approach offers a general yet easy-to-implement analysis method that provides unique insight into the molecular mechanism and the rare but crucial (i.e., rate-limiting transition states occurring along conformational transition paths in complex dynamical systems such as molecular trajectories.

  4. Perimenopause as a neurological transition state.

    Science.gov (United States)

    Brinton, Roberta D; Yao, Jia; Yin, Fei; Mack, Wendy J; Cadenas, Enrique

    2015-07-01

    Perimenopause is a midlife transition state experienced by women that occurs in the context of a fully functioning neurological system and results in reproductive senescence. Although primarily viewed as a reproductive transition, the symptoms of perimenopause are largely neurological in nature. Neurological symptoms that emerge during perimenopause are indicative of disruption in multiple estrogen-regulated systems (including thermoregulation, sleep, circadian rhythms and sensory processing) and affect multiple domains of cognitive function. Estrogen is a master regulator that functions through a network of estrogen receptors to ensure that the brain effectively responds at rapid, intermediate and long timescales to regulate energy metabolism in the brain via coordinated signalling and transcriptional pathways. The estrogen receptor network becomes uncoupled from the bioenergetic system during the perimenopausal transition and, as a corollary, a hypometabolic state associated with neurological dysfunction can develop. For some women, this hypometabolic state might increase the risk of developing neurodegenerative diseases later in life. The perimenopausal transition might also represent a window of opportunity to prevent age-related neurological diseases. This Review considers the importance of neurological symptoms in perimenopause in the context of their relationship to the network of estrogen receptors that control metabolism in the brain.

  5. A Model of Mental State Transition Network

    Science.gov (United States)

    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.

  6. State-transition diagrams for biologists.

    Science.gov (United States)

    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.

  7. Transition problems and play as transitory activity

    DEFF Research Database (Denmark)

    Broström, Stig

    2005-01-01

    Because too many children experience the transition to school as a culture shock, during the past decade teachers have implemented so-called transition activities in order to bridge the gap betwen pre-school and schoo. However, transition to school also calls for a development of higher mental fu...

  8. Transition problems and play as transitory activity

    DEFF Research Database (Denmark)

    Broström, Stig

    2005-01-01

    Because too many children experience the transition to school as a culture shock, during the past decade teachers have implemented so-called transition activities in order to bridge the gap betwen pre-school and schoo. However, transition to school also calls for a development of higher mental fu...

  9. State-to-state reaction probabilities within the quantum transition state framework.

    Science.gov (United States)

    Welsch, Ralph; Huarte-Larrañaga, Fermín; Manthe, Uwe

    2012-02-14

    Rigorous quantum dynamics calculations of reaction rates and initial state-selected reaction probabilities of polyatomic reactions can be efficiently performed within the quantum transition state concept employing flux correlation functions and wave packet propagation utilizing the multi-configurational time-dependent Hartree approach. Here, analytical formulas and a numerical scheme extending this approach to the calculation of state-to-state reaction probabilities are presented. The formulas derived facilitate the use of three different dividing surfaces: two dividing surfaces located in the product and reactant asymptotic region facilitate full state resolution while a third dividing surface placed in the transition state region can be used to define an additional flux operator. The eigenstates of the corresponding thermal flux operator then correspond to vibrational states of the activated complex. Transforming these states to reactant and product coordinates and propagating them into the respective asymptotic region, the full scattering matrix can be obtained. To illustrate the new approach, test calculations study the D + H(2)(ν, j) → HD(ν', j') + H reaction for J = 0. © 2012 American Institute of Physics

  10. Serine 83 in DosR, a response regulator from Mycobacterium tuberculosis, promotes its transition from an activated, phosphorylated state to an inactive, unphosphorylated state.

    Science.gov (United States)

    Cho, Ha Yeon; Kang, Beom Sik

    2014-02-21

    A sensor kinase, DosS, and its corresponding response regulator, DosR, constitute a two component system for regulating gene expression under hypoxic conditions in Mycobacterium tuberculosis. Among response regulators in M. tuberculosis, NarL has high sequence similarity to DosR, and autophosphorylated DosS transfers its phosphate group not only to DosR but also to NarL. Phosphorylated DosR is more rapidly dephosphorylated than phosphorylated NarL. DosR and NarL differ with respect to the amino acids at positions T+1 and T+2 around the phosphorylation sites in the N-terminal phosphoacceptor domain; NarL has S83 and Y84, whereas DosR has A90 and H91. A DosR S83A mutant shows prolonged phosphorylation. Structural comparison with a histidinol phosphate phosphatase suggests that the hydroxyl group of DosR S83 could play a role in activating the water molecule involved in the triggering of autodephosphorylation.

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

    Directory of Open Access Journals (Sweden)

    Robert E. Meyer

    2015-08-01

    Full Text Available 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.

  12. CDENPROP: Transition matrix elements involving continuum states

    CERN Document Server

    Harvey, Alex G; Morales, Felipe; Smirnova, Olga

    2014-01-01

    Transition matrix elements between electronic states where one electron can be in the continuum are required for a wide range of applications of the molecular R-matrix method. These include photoionization, photorecombination and photodetachment; electron-molecule scattering and photon-induced processes in the presence of an external D.C. field, and time-dependent R-matrix approaches to study the effect of the exposure of molecules to strong laser fields. We present a new algorithm, implemented as a module (CDENPROP) in the UKRmol electron-molecule scattering code suite.

  13. Immigration Control in Transit States: The Case of Turkey

    Directory of Open Access Journals (Sweden)

    Zeynep Sahin Mencutek

    2016-02-01

    Full Text Available Transit countries exhibit many similarities with respect to state-led anti-transit and more restrictive actions toward contemporary transit migration flows. This paper examines the changes after 1990s in state concerns, behaviors, and policies regarding transit migration by taking Turkey as a case study. Which factors led to Turkey's increased attention to immigration, specifically transit migration in spite of its long history of immigration, emigration and the transit migration. Why has Turkey employed restrictive policies and projects to regularize immigration since 1993? How can we explain the anti-transit immigration projects in Turkey? I argue that two driving forces can explain the restrictive policies of Turkey as a transit state. First, Turkey attempts to reconfigure its state authority in different forms to respond to the challenges of irregular migration through immigration control. Second, the Turkish state`s concern is based upon the externalization/adoption of European Union's immigration control policies.

  14. Immigration Control in Transit States: The Case of Turkey

    Directory of Open Access Journals (Sweden)

    Zeynep Sahin-Mencütek

    2012-05-01

    Full Text Available Transit countries exhibit many similarities with respect to state-led anti-transit and more restrictive actions toward contemporary transit migration flows. This paper examines the changes after 1990s in state concerns, behaviors, and policies regarding transit migration by taking Turkey as a case study. Which factors led to Turkey’s increased attention to immigration, specifically transit migration in spite of its long history of immigration, emigration and the transit migration. Why has Turkey employed restrictive policies and projects to regularize immigration since 1993? How can we explain the anti-transit immigration projects in Turkey? I argue that two driving forces can explain the restrictive policies of Turkey as a transit state. First, Turkey attempts to reconfigure its state authority in different forms to respond to the challenges of irregular migration through immigration control. Second, the Turkish state`s concern is based upon the externalization/adoption of European Union’s immigration control policies.

  15. Information content in cortical spike trains during brain state transitions.

    Science.gov (United States)

    Arnold, Maria M; Szczepanski, Janusz; Montejo, Noelia; Amigó, José M; Wajnryb, Eligiusz; Sanchez-Vives, Maria V

    2013-02-01

    Even in the absence of external stimuli there is ongoing activity in the cerebral cortex as a result of recurrent connectivity. This paper attempts to characterize one aspect of this ongoing activity by examining how the information content carried by specific neurons varies as a function of brain state. We recorded from rats chronically implanted with tetrodes in the primary visual cortex during awake and sleep periods. Electro-encephalogram and spike trains were recorded during 30-min periods, and 2-4 neuronal spikes were isolated per tetrode off-line. All the activity included in the analysis was spontaneous, being recorded from the visual cortex in the absence of visual stimuli. The brain state was determined through a combination of behavior evaluation, electroencephalogram and electromyogram analysis. Information in the spike trains was determined by using Lempel-Ziv Complexity. Complexity was used to estimate the entropy of neural discharges and thus the information content (Amigóet al. Neural Comput., 2004, 16: 717-736). The information content in spike trains (range 4-70 bits s(-1) ) was evaluated during different brain states and particularly during the transition periods. Transitions toward states of deeper sleep coincided with a decrease of information, while transitions to the awake state resulted in an increase in information. Changes in both directions were of the same magnitude, about 30%. Information in spike trains showed a high temporal correlation between neurons, reinforcing the idea of the impact of the brain state in the information content of spike trains.

  16. Quantum Transition State Theory for proton transfer reactions in enzymes

    CERN Document Server

    Bothma, Jacques P; McKenzie, Ross H

    2009-01-01

    We consider the role of quantum effects in the transfer of hyrogen-like species in enzyme-catalysed reactions. This study is stimulated by claims that the observed magnitude and temperature dependence of kinetic isotope effects imply that quantum tunneling below the energy barrier associated with the transition state significantly enhances the reaction rate in many enzymes. We use a path integral approach which provides a general framework to understand tunneling in a quantum system which interacts with an environment at non-zero temperature. Here the quantum system is the active site of the enzyme and the environment is the surrounding protein and water. Tunneling well below the barrier only occurs for temperatures less than a temperature $T_0$ which is determined by the curvature of potential energy surface near the top of the barrier. We argue that for most enzymes this temperature is less than room temperature. For physically reasonable parameters quantum transition state theory gives a quantitative descr...

  17. An absorbing phase transition from a structured active particle phase

    Energy Technology Data Exchange (ETDEWEB)

    Lopez, Cristobal [Instituto Mediterraneo de Estudios Avanzados IMEDEA (CSIC-UIB), Campus de la Universidad de las Islas Baleares, E-07122 Palma de Mallorca (Spain); Ramos, Francisco [Departamento de Electromagnetismo y Fisica de la Materia and Instituto de Fisica Teorica y Computacional Carlos I, Facultad de Ciencias, Universidad de Granada, 18071 Granada (Spain); Hernandez-GarcIa, Emilio [Instituto Mediterraneo de Estudios Avanzados IMEDEA (CSIC-UIB), Campus de la Universidad de las Islas Baleares, E-07122 Palma de Mallorca (Spain)

    2007-02-14

    In this work we study the absorbing state phase transition of a recently introduced model for interacting particles with neighbourhood-dependent reproduction rates. The novelty of the transition is that as soon as the active phase is reached by increasing a control parameter a periodically arranged structure of particle clusters appears. A numerical study in one and two dimensions shows that the system falls into the directed percolation universality class.

  18. Critical Transitions in Social Network Activity

    DEFF Research Database (Denmark)

    Kuehn, Christian; Martens, Erik Andreas; Romero, Daniel M

    2014-01-01

    A large variety of complex systems in ecology, climate science, biomedicine and engineering have been observed to exhibit tipping points, where the dynamical state of the system abruptly changes. For example, such critical transitions may result in the sudden change of ecological environments...... a priori known events are preceded by variance and autocorrelation growth. Our findings thus clearly establish the necessary starting point to further investigate the relationship between abstract mathematical theory and various classes of critical transitions in social networks....

  19. A P-loop Mutation in G[alpha] Subunits Prevents Transition to the Active State: Implications for G-protein Signaling in Fungal Pathogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Bosch, Dustin E.; Willard, Francis S.; Ramanujam, Ravikrishna; Kimple, Adam J.; Willard, Melinda D.; Naqvi, Naweed I.; Siderovski, David P. (UNC); (Singapore)

    2012-10-23

    Heterotrimeric G-proteins are molecular switches integral to a panoply of different physiological responses that many organisms make to environmental cues. The switch from inactive to active G{alpha}{beta}{gamma} heterotrimer relies on nucleotide cycling by the G{alpha} subunit: exchange of GTP for GDP activates G{alpha}, whereas its intrinsic enzymatic activity catalyzes GTP hydrolysis to GDP and inorganic phosphate, thereby reverting G{alpha} to its inactive state. In several genetic studies of filamentous fungi, such as the rice blast fungus Magnaporthe oryzae, a G42R mutation in the phosphate-binding loop of G{alpha} subunits is assumed to be GTPase-deficient and thus constitutively active. Here, we demonstrate that G{alpha}(G42R) mutants are not GTPase deficient, but rather incapable of achieving the activated conformation. Two crystal structure models suggest that Arg-42 prevents a typical switch region conformational change upon G{alpha}{sub i1}(G42R) binding to GDP {center_dot} AlF{sub 4}{sup -} or GTP, but rotameric flexibility at this locus allows for unperturbed GTP hydrolysis. G{alpha}(G42R) mutants do not engage the active state-selective peptide KB-1753 nor RGS domains with high affinity, but instead favor interaction with G{beta}{gamma} and GoLoco motifs in any nucleotide state. The corresponding G{alpha}{sub q}(G48R) mutant is not constitutively active in cells and responds poorly to aluminum tetrafluoride activation. Comparative analyses of M. oryzae strains harboring either G42R or GTPase-deficient Q/L mutations in the G{alpha} subunits MagA or MagB illustrate functional differences in environmental cue processing and intracellular signaling outcomes between these two G{alpha} mutants, thus demonstrating the in vivo functional divergence of G42R and activating G-protein mutants.

  20. Magneto-thermally activated spin-state transition in La0.95Ca0.05CoO3: magnetically-tunable dipolar glass and giant magneto-electricity.

    Science.gov (United States)

    Pandey, Suchita; Kumar, Jitender; Awasthi, A M

    2016-03-01

    The magneto-dielectric spectroscopy of La0.95Ca0.05CoO3 covering the crossover of spin states reveals the strong coupling of its spin and dipolar degrees of freedom. The signature of the spin-state transition at 30 K clearly manifests in the magnetization data at a 1 Tesla optimal field. Our Co L3,2-edge X-ray absorption spectrum on the doped specimen is consistent with its suppressed low-to-intermediate spin-state transition temperature at ∼30 K compared to ∼150 K, documented for pure LaCoO3. The dispersive activation step in the dielectric constant with the associated relaxation peak in imaginary permittivity characterize the allied influence of coexistent spin-states on the dielectric character. Dipolar relaxation in the low-spin regime below the transition temperature is partly segmental (Vogel-Fulcher-Tamman (VFT) kinetics) and features magnetic-field tunability, whereas in the low/intermediate-spin disordered state above ∼30 K, it is uncorrelated (Arrhenic kinetics) and almost impervious to the magnetic field H. Kinetics-switchover defines the dipolar-glass transition temperature Tg(H) (=27 K|0T), below which their magneto-thermally-activated cooperative relaxations freeze out by the VFT temperature T0(H) (=15 K|0T). An applied magnetic field facilitates thermal activation in toggling the low spins up into the intermediate states. Consequently, the downsized dipolar-glass segments in the low-spin state and the independent dipoles in the intermediate state exhibit accelerated dynamics. A critical 5 Tesla field collapses the entire relaxation kinetics into a single Arrhenic behaviour, signaling that the dipolar glass is completely devitrified under all higher fields. The magneto-electricity (ME) spanning sizeable thermo-spectral range registers diverse signatures here in kinetic, spectral, and field behaviors, in contrast to the static/perturbative ME observed close to the spin-ordering in typical multiferroics. Intrinsic magneto-dielectricity (50%) along

  1. Activating Welfare States

    DEFF Research Database (Denmark)

    Kvist, Jon

    This paper investigates how welfare states may actively contribute to promote employment opportunities, i.e. participation in the labour market through various operations and policies. The principal operations concern in particular the de-familiarisation of caring tasks through social services...

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

    Science.gov (United States)

    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

  3. Stacking transition in bilayer graphene caused by thermally activated rotation

    Science.gov (United States)

    Zhu, Mengjian; Ghazaryan, Davit; Son, Seok-Kyun; Woods, Colin R.; Misra, Abhishek; He, Lin; Taniguchi, Takashi; Watanabe, Kenji; Novoselov, Kostya S.; Cao, Yang; Mishchenko, Artem

    2017-03-01

    Crystallographic alignment between two-dimensional crystals in van der Waals heterostructures brought a number of profound physical phenomena, including observation of Hofstadter butterfly and topological currents, and promising novel applications, such as resonant tunnelling transistors. Here, by probing the electronic density of states in graphene using graphene-hexagonal boron nitride-graphene tunnelling transistors, we demonstrate a structural transition of bilayer graphene from incommensurate twisted stacking state into a commensurate AB stacking due to a macroscopic graphene self-rotation. This structural transition is accompanied by a topological transition in the reciprocal space and by pseudospin texturing. The stacking transition is driven by van der Waals interaction energy of the two graphene layers and is thermally activated by unpinning the microscopic chemical adsorbents which are then removed by the self-cleaning of graphene.

  4. Savannah River Site prioritization of transition activities

    Energy Technology Data Exchange (ETDEWEB)

    Finley, R.H.

    1993-11-01

    Effective management of SRS conversion from primarily a production facility to other missions (or Decontamination and Decommissioning (D&D)) requires a systematic and consistent method of prioritizing the transition activities. This report discusses the design of a prioritizing method developed to achieve systematic and consistent methods of prioritizing these activities.

  5. Fluctuating States: What is the Probability of a Thermodynamical Transition?

    Science.gov (United States)

    Alhambra, Álvaro M.; Oppenheim, Jonathan; Perry, Christopher

    2016-10-01

    If the second law of thermodynamics forbids a transition from one state to another, then it is still possible to make the transition happen by using a sufficient amount of work. But if we do not have access to this amount of work, can the transition happen probabilistically? In the thermodynamic limit, this probability tends to zero, but here we find that for finite-sized and quantum systems it can be finite. We compute the maximum probability of a transition or a thermodynamical fluctuation from any initial state to any final state and show that this maximum can be achieved for any final state that is block diagonal in the energy eigenbasis. We also find upper and lower bounds on this transition probability, in terms of the work of transition. As a by-product, we introduce a finite set of thermodynamical monotones related to the thermomajorization criteria which governs state transitions and compute the work of transition in terms of them. The trade-off between the probability of a transition and any partial work added to aid in that transition is also considered. Our results have applications in entanglement theory, and we find the amount of entanglement required (or gained) when transforming one pure entangled state into any other.

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

    Science.gov (United States)

    McMinis, Jeremy; Morales, Miguel A; Ceperley, David M; Kim, Jeongnim

    2015-11-21

    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 paramagnetic and anti-ferromagnetic body centered cubic atomic hydrogen in its ground state. We locate the density of the transition by computing the equation of state for these two phases and identify the phase transition 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 rs = 2.27(3) a0. We compare our results to previously reported density functional theory, Hedin's GW approximation, and dynamical mean field theory results.

  7. Carbonyl Activation by Borane Lewis Acid Complexation: Transition States of H2 Splitting at the Activated Carbonyl Carbon Atom in a Lewis Basic Solvent and the Proton-Transfer Dynamics of the Boroalkoxide Intermediate.

    Science.gov (United States)

    Heshmat, Mojgan; Privalov, Timofei

    2017-07-06

    By using transition-state (TS) calculations, we examined how Lewis acid (LA) complexation activates carbonyl compounds in the context of hydrogenation of carbonyl compounds by H2 in Lewis basic (ethereal) solvents containing borane LAs of the type (C6 F5 )3 B. According to our calculations, LA complexation does not activate a ketone sufficiently enough for the direct addition of H2 to the O=C unsaturated bond; but, calculations indicate a possibly facile heterolytic cleavage of H2 at the activated and thus sufficiently Lewis acidic carbonyl carbon atom with the assistance of the Lewis basic solvent (i.e., 1,4-dioxane or THF). For the solvent-assisted H2 splitting at the carbonyl carbon atom of (C6 F5 )3 B adducts with different ketones, a number of TSs are computed and the obtained results are related to insights from experiment. By using the Born-Oppenheimer molecular dynamics with the DFT for electronic structure calculations, the evolution of the (C6 F5 )3 B-alkoxide ionic intermediate and the proton transfer to the alkoxide oxygen atom were investigated. The results indicate a plausible hydrogenation mechanism with a LA, that is, (C6 F5 )3 B, as a catalyst, namely, 1) the step of H2 cleavage that involves a Lewis basic solvent molecule plus the carbonyl carbon atom of thermodynamically stable and experimentally identifiable (C6 F5 )3 B-ketone adducts in which (C6 F5 )3 B is the "Lewis acid promoter", 2) the transfer of the solvent-bound proton to the oxygen atom of the (C6 F5 )3 B-alkoxide intermediate giving the (C6 F5 )3 B-alcohol adduct, and 3) the SN 2-style displacement of the alcohol by a ketone or a Lewis basic solvent molecule. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. A Quantum Version of Wigner's Transition State Theory

    NARCIS (Netherlands)

    Schubert, R.; Waalkens, H.; Wiggins, S.

    2009-01-01

    A quantum version of a recent realization of Wigner's transition state theory in phase space is presented. The theory developed builds on a quantum normal form which locally decouples the quantum dynamics near the transition state to any desired order in (h) over bar. This leads to an explicit algor

  9. A Quantum Version of Wigner’s Transition State Theory

    NARCIS (Netherlands)

    Schubert, R.; Waalkens, H.; Wiggins, S.

    2009-01-01

    A quantum version of a recent realization of Wigner’s transition state theory in phase space is presented. The theory developed builds on a quantum normal form which locally decouples the quantum dynamics near the transition state to any desired order in ħ. This leads to an explicit algorithm to com

  10. Periodic-orbit formula for quantum reactions through transition states

    NARCIS (Netherlands)

    Schubert, Roman; Waalkens, Holger; Goussev, Arseni; Wiggins, Stephen

    2010-01-01

    Transition state theory forms the basis of computing reaction rates in chemical and other systems. Recently, it has been shown how transition state theory can rigorously be realized in phase space by using an explicit algorithm. The quantization has been demonstrated to lead to an efficient procedur

  11. Locating transition states using double-ended classical trajectories

    CERN Document Server

    Matro, A; Doll, J D

    1994-01-01

    In this paper we present a method for locating transition states and higher-order saddles on potential energy surfaces using double-ended classical trajectories. We then apply this method to 7- and 8-atom Lennard-Jones clusters, finding one previously unreported transition state for the 7-atom cluster and two for the 8-atom cluster.

  12. Systematics of α -decay transitions to excited states

    Science.gov (United States)

    Delion, D. S.; Dumitrescu, A.

    2015-08-01

    We systematize the available experimental material concerning α -decay transitions to low-lying excited states in even-even and odd-mass emitters. We generalize our previous theoretical prediction concerning the linear dependence between hindrance factors and the excitation energy for transitions in even-even α emitters. Thus, we show that α intensities for transitions to excited states depend linearly upon the excitation energy for all known even-even and odd-mass α emitters. It turns out that the well-known Viola-Seaborg law for α -decay transitions between ground states can be generalized for transitions to excited states. This rule can be used to predict any α -decay half-life to a low-lying excited state.

  13. Markov chain evaluation of acute postoperative pain transition states.

    Science.gov (United States)

    Tighe, Patrick J; Bzdega, Matthew; Fillingim, Roger B; Rashidi, Parisa; Aytug, Haldun

    2016-03-01

    Previous investigations on acute postoperative pain dynamicity have focused on daily pain assessments, and so were unable to examine intraday variations in acute pain intensity. We analyzed 476,108 postoperative acute pain intensity ratings, which were clinically documented on postoperative days 1 to 7 from 8346 surgical patients using Markov chain modeling to describe how patients are likely to transition from one pain state to another in a probabilistic fashion. The Markov chain was found to be irreducible and positive recurrent, with no absorbing states. Transition probabilities ranged from 0.0031, for the transition from state 10 to state 1, to 0.69 for the transition from state 0 to state 0. The greatest density of transitions was noted in the diagonal region of the transition matrix, suggesting that patients were generally most likely to transition to the same pain state as their current state. There were also slightly increased probability densities in transitioning to a state of asleep or 0 from the current state. An examination of the number of steps required to traverse from a particular first pain score to a target state suggested that overall, fewer steps were required to reach a state of 0 (range 6.1-8.8 steps) or asleep (range 9.1-11) than were required to reach a mild pain intensity state. Our results suggest that using Markov chains is a feasible method for describing probabilistic postoperative pain trajectories, pointing toward the possibility of using Markov decision processes to model sequential interactions between pain intensity ratings, and postoperative analgesic interventions.

  14. Improving Upon String Methods for Transition State Discovery.

    Science.gov (United States)

    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.

  15. Transition State Structure of RNA Depurination by Saporin L3.

    Science.gov (United States)

    Yuan, Hongling; Stratton, Christopher F; Schramm, Vern L

    2016-05-20

    Saporin L3 from the leaves of the common soapwort is a catalyst for hydrolytic depurination of adenine from RNA. Saporin L3 is a type 1 ribosome inactivating protein (RIP) composed only of a catalytic domain. Other RIPs have been used in immunotoxin cancer therapy, but off-target effects have limited their development. In the current study, we use transition state theory to understand the chemical mechanism and transition state structure of saporin L3. In favorable cases, transition state structures guide the design of transition state analogues as inhibitors. Kinetic isotope effects (KIEs) were determined for an A14C mutant of saporin L3. To permit KIE measurements, small stem-loop RNAs that contain an AGGG tetraloop structure were enzymatically synthesized with the single adenylate bearing specific isotopic substitutions. KIEs were measured and corrected for forward commitment to obtain intrinsic values. A model of the transition state structure for depurination of stem-loop RNA (5'-GGGAGGGCCC-3') by saporin L3 was determined by matching KIE values predicted via quantum chemical calculations to a family of intrinsic KIEs. This model indicates saporin L3 displays a late transition state with the N-ribosidic bond to the adenine nearly cleaved, and the attacking water nucleophile weakly bonded to the ribosyl anomeric carbon. The transition state retains partial ribocation character, a feature common to most N-ribosyl transferases. However, the transition state geometry for saporin L3 is distinct from ricin A-chain, the only other RIP whose transition state is known.

  16. Dependency in State Transitions of Wind Turbines - Inference on model Residuals for State Abstractions

    DEFF Research Database (Denmark)

    Herp, Jürgen; Ramezani, Mohammad Hossein; S. Nadimi, Esmaeil

    2017-01-01

    the state transitions are based on a hidden variable relevant for the predictor, namely the information of the current state. Given an underlying predictive model based on a Student's t-distribution for the samples and a conditional prior on the state transition, it is shown that state transitions can...... configurations. Comparing to heuristic interpretations of the residuals both models can qualitatively inform about the time when a state transition occurs.......Abstracting turbine states and predicting the transition into failure states ahead of time is important in operation and maintenance of wind turbines. This study presents a method to monitor state transitions of a wind turbine based on the online inference on residuals. In a Bayesian framework...

  17. A periodic orbit formula for quantum reactions through transition states

    CERN Document Server

    Schubert, Roman; Goussev, Arseni; Wiggins, Stephen

    2010-01-01

    Transition State Theory forms the basis of computing reaction rates in chemical and other systems. Recently it has been shown how transition state theory can rigorously be realized in phase space using an explicit algorithm. The quantization has been demonstrated to lead to an efficient procedure to compute cumulative reaction probabilities and the associated Gamov-Siegert resonances. In this letter these results are used to express the cumulative reaction probability as an absolutely convergent sum over periodic orbits contained in the transition state.

  18. Control wetting state transition by micro-rod geometry

    Science.gov (United States)

    He, Yang; Jiang, Chengyu; Wang, Shengkun; Yin, Hengxu; Yuan, Weizheng

    2013-11-01

    Understanding the effect of micro-structure geometry on wetting state transition is important to design and control surface wettability. Micro-rod model was proposed and the relationship between micro-rod geometry and wetting state was investigated in the paper taking into account only the surface roughness and neglecting the chemistry interaction. Micro-rods with different geometric parameters were fabricated using micro-fabrication technology. Their contact angles were measured and compared with theoretical ones. The experimental results indicated that increasing the height and decreasing the space of micro-rod may result in Cassie wetting state, while decreasing the height and increasing the space may result in Wenzel wetting state. A suspended wetting state model due to scallops was proposed. The wetting state transition was interpreted by intruding height, de-pinning and sag mechanism. It may offer a facile way to control the surface wetting state transition by changing the geometry of micro-rod.

  19. Observation of Hyperfine Transitions in Trapped Ground-State Antihydrogen

    CERN Document Server

    Olin, Arthur

    2015-01-01

    This paper discusses the first observation of stimulated magnetic resonance transitions between the hyperfine levels of trapped ground state atomic antihydrogen, confirming its presence in the ALPHA apparatus. Our observations show that these transitions are consistent with the values in hydrogen to within 4~parts~in~$10^3$. Simulations of the trapped antiatoms in a microwave field are consistent with our measurements.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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

  2. Identifying transition rates of ionic channels via observations at a single state

    CERN Document Server

    Deng Ying Chun; Qian Min Ping; Feng Jian Feng

    2003-01-01

    We consider how to determine all transition rates of an ion channel when it can be described by a birth-death chain or a Markov chain on a star-graph with continuous time. It is found that all transition rates are uniquely determined by the distribution of its lifetime and death-time histograms at a single state. An algorithm to calculate the transition rates exactly, based on the statistics of the lifetime and death-time of the Markov chain at the state, is provided. Examples to illustrate how an ion channel activity is fully determined by the observation of a single state of the ion channel are included.

  3. Religion, state, society and identity in transition: Ukraine

    NARCIS (Netherlands)

    van der Laarse, R.; Cherenkov, M.N.; Proshak, V.V.; Mykhalchuk, T.

    2015-01-01

    State-society-identity relations could be defined as interaction(s) between state institutions, societal groups and individuals living within the borders of a (political) community/ state. These relations are never static, but vibrant, being in constant transition under the influence of cultural, re

  4. Critical Transitions in Social Network Activity

    DEFF Research Database (Denmark)

    Kuehn, Christian; Martens, Erik Andreas; Romero, Daniel M

    2014-01-01

    a priori known events are preceded by variance and autocorrelation growth. Our findings thus clearly establish the necessary starting point to further investigate the relationship between abstract mathematical theory and various classes of critical transitions in social networks.......A large variety of complex systems in ecology, climate science, biomedicine and engineering have been observed to exhibit tipping points, where the dynamical state of the system abruptly changes. For example, such critical transitions may result in the sudden change of ecological environments...... and climate conditions. Data and models suggest that detectable warning signs may precede some of these drastic events. This view is also corroborated by abstract mathematical theory for generic bifurcations in stochastic multi-scale systems. Whether such stochastic scaling laws used as warning signs...

  5. 2014 Report: Wetland State-and-transition Model Project

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Report from the 2014 field season of the Wetland State-and-Transition Project. Many National Wildlife Refuges in the Intermountain West and Prairie Pothole regions...

  6. Formalization of Abstract State Transition Systems for SAT

    CERN Document Server

    Marić, Filip

    2011-01-01

    We present a formalization of modern SAT solvers and their properties in a form of abstract state transition systems. SAT solving procedures are described as transition relations over states that represent the values of the solver's global variables. Several different SAT solvers are formalized, including both the classical DPLL procedure and its state-of-the-art successors. The formalization is made within the Isabelle/HOL system and the total correctness (soundness, termination, completeness) is shown for each presented system (with respect to a simple notion of satisfiability that can be manually checked). The systems are defined in a general way and cover procedures used in a wide range of modern SAT solvers. Our formalization builds up on the previous work on state transition systems for SAT, but it gives machine-verifiable proofs, somewhat more general specifications, and weaker assumptions that ensure the key correctness properties. The presented proofs of formal correctness of the transition systems c...

  7. Relating transition-state spectroscopy to standard chemical spectroscopic processes

    Science.gov (United States)

    Reimers, Jeffrey R.; Hush, Noel S.

    2017-09-01

    Transition-state spectra are mapped out using generalized adiabatic electron-transfer theory. This simple model depicts diverse chemical properties, from aromaticity, through bound reactions such as isomerizations and atom-transfer processes with classic transition states, to processes often described as being ;non-adiabatic;, to those in the ;inverted; region that become slower as they are made more exothermic. Predictably, the Born-Oppenheimer approximation is found inadequate for modelling transition-state spectra in the weak-coupling limit. In this limit, the adiabatic Born-Huang approximation is found to perform much better than non-adiabatic surface-hopping approaches. Transition-state spectroscopy is shown to involve significant quantum entanglement between electronic and nuclear motion.

  8. Transition state theory and the dynamics of hard disks.

    Science.gov (United States)

    Barnett-Jones, M; Dickinson, P A; Godfrey, M J; Grundy, T; Moore, M A

    2013-11-01

    The dynamics of two- and five-disk systems confined in a square has been studied using molecular dynamics simulations and compared with the predictions of transition state theory. We determine the partition functions Z and Z(‡) of transition state theory using a procedure first used by Salsburg and Wood for the pressure. Our simulations show this procedure and transition state theory are in excellent agreement with the simulations. A generalization of the transition state theory to the case of a large number of disks N is made and shown to be in full agreement with simulations of disks moving in a narrow channel. The same procedure for hard spheres in three dimensions leads to the Vogel-Fulcher-Tammann formula for their alpha relaxation time.

  9. The Immucillins: Design, Synthesis and Application of Transition- State Analogues.

    Science.gov (United States)

    Evans, Gary B; Schramm, Vern L; Tyler, Peter C

    2015-01-01

    Transition-state analysis based on kinetic isotope effects and computational chemistry provides electrostatic potential maps to serve as blueprints for the design and chemical synthesis of transition-state analogues. The utility of these molecules is exemplified by potential clinical applications toward leukemia, autoimmune disorders, gout, solid tumors, bacterial quorum sensing and bacterial antibiotics. In some cases, transition-state analogues have chemical features that have allowed them to be repurposed for new indications, including potential antiviral use. Three compounds from this family have entered clinical trials. The transition-state analogues bind to their target proteins with high affinity and specificity. The physical and structural properties of binding teach valuable and often surprising lessons about the nature of tight-binding inhibitors.

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

    Science.gov (United States)

    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.

  11. CSTEA: a webserver for the Cell State Transition Expression Atlas.

    Science.gov (United States)

    Zhu, Guanghui; Yang, Hui; Chen, Xiao; Wu, Jun; Zhang, Yong; Zhao, Xing-Ming

    2017-05-09

    Cell state transition is one of the fundamental events in the development of multicellular organisms, and the transition trajectory path has recently attracted much attention. With the accumulation of large amounts of "-omics" data, it is becoming possible to get insights into the molecule mechanisms underlying the transitions between cell states. Here, we present CSTEA (Cell State Transition Expression Atlas), a webserver that organizes, analyzes and visualizes the time-course gene expression data during cell differentiation, cellular reprogramming and trans-differentiation in human and mouse. In particular, CSTEA defines gene signatures for uncharacterized stages during cell state transitions, thereby enabling both experimental and computational biologists to better understand the mechanisms of cell fate determination in mammals. To our best knowledge, CSTEA is the first webserver dedicated to the analysis of time-series gene expression data during cell state transitions. CSTEA is freely available at http://comp-sysbio.org/cstea/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  12. Mixed ligand complexation of some transition metal ions in solution and solid state: Spectral characterization, antimicrobial, antioxidant, DNA cleavage activities and molecular modeling

    Science.gov (United States)

    Shobana, Sutha; Dharmaraja, Jeyaprakash; Selvaraj, Shanmugaperumal

    2013-04-01

    Equilibrium studies of Ni(II), Cu(II) and Zn(II) mixed ligand complexes involving a primary ligand 5-fluorouracil (5-FU; A) and imidazoles viz., imidazole (him), benzimidazole (bim), histamine (hist) and L-histidine (his) as co-ligands(B) were carried out pH-metrically in aqueous medium at 310 ± 0.1 K with I = 0.15 M (NaClO4). In solution state, the stoichiometry of MABH, MAB and MAB2 species have been detected. The primary ligand(A) binds the central M(II) ions in a monodentate manner whereas him, bim, hist and his co-ligands(B) bind in mono, mono, bi and tridentate modes respectively. The calculated Δ log K, log X and log X' values indicate higher stability of the mixed ligand complexes in comparison to binary species. Stability of the mixed ligand complex equilibria follows the Irving-Williams order of stability. In vitro biological evaluations of the free ligand(A) and their metal complexes by well diffusion technique show moderate activities against common bacterial and fungal strains. Oxidative cleavage interaction of ligand(A) and their copper complexes with CT DNA is also studied by gel electrophoresis method in the presence of oxidant. In vitro antioxidant evaluations of the primary ligand(A), CuA and CuAB complexes by DPPH free radical scavenging model were carried out. In solid, the MAB type of M(II)sbnd 5-FU(A)sbnd his(B) complexes were isolated and characterized by various physico-chemical and spectral techniques. Both the magnetic susceptibility and electronic spectral analysis suggest distorted octahedral geometry. Thermal studies on the synthesized mixed ligand complexes show loss of coordinated water molecule in the first step followed by decomposition of the organic residues subsequently. XRD and SEM analysis suggest that the microcrystalline nature and homogeneous morphology of MAB complexes. Further, the 3D molecular modeling and analysis for the mixed ligand MAB complexes have also been carried out.

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

    Energy Technology Data Exchange (ETDEWEB)

    McMinis, Jeremy; Morales, Miguel A. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States); Ceperley, David M. [Department of Physics, University of Illinois, Urbana, Illinois 61801 (United States); Kim, Jeongnim [Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States)

    2015-11-21

    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 paramagnetic and anti-ferromagnetic body centered cubic atomic hydrogen in its ground state. We locate the density of the transition by computing the equation of state for these two phases and identify the phase transition 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{sub s} = 2.27(3) a{sub 0}. We compare our results to previously reported density functional theory, Hedin’s GW approximation, and dynamical mean field theory results.

  14. Reaction dynamics: The view from a transition state

    Science.gov (United States)

    Continetti, Robert E.

    2017-10-01

    Ejecting electrons from negative ions using light can create structures that very closely resemble the transition states of bimolecular reactions. Now, using this technique, trapped quantum states, or 'resonances', have been observed in a seven-atom reaction, and theory has been shown to be up to the task of capturing such complex phenomena.

  15. Transition State Analog Inhibitors for Esterases.

    Science.gov (United States)

    1983-06-02

    Propanones." SCIENTIFIC PERSONNEL SUPPORTED BY THIS PROJECT AND DEGREES AWARDED DURING THIS REPORTING PERIOD Dr. Alan Dafforn Dr. Antoon Brouwer Dr. John P...294, Raven Press, New York. 11. Hansch, C. and Leo , A., (1979) "Substituent Constants for Correlation Analysis in Chemistry and Biology," pp. 69-70...BORONIC ACIDS AS 1INSITION STATE ANALOG INHIBITORS OF ACTYLCHOLINESTERASE by Alan Dafforn and Antoon C. Brouwer Department of Chemistry Bowling Green

  16. A Comparison of Vanadate to a 2'-5' Linkage at the Active Site of a Small Ribozyme Suggests a Role for Water in Transition-State Stabilization

    Energy Technology Data Exchange (ETDEWEB)

    Torelli, A.T.; Krucinska, J.; Wedekind, J.E.

    2009-06-04

    The potential for water to participate in RNA catalyzed reactions has been the topic of several recent studies. Here, we report crystals of a minimal, hinged hairpin ribozyme in complex with the transition-state analog vanadate at 2.05 A resolution. Waters are present in the active site and are discussed in light of existing views of catalytic strategies employed by the hairpin ribozyme. A second structure harboring a 2',5'-phosphodiester linkage at the site of cleavage was also solved at 2.35 A resolution and corroborates the assignment of active site waters in the structure containing vanadate. A comparison of the two structures reveals that the 2',5' structure adopts a conformation that resembles the reaction intermediate in terms of (1) the positioning of its nonbridging oxygens and (2) the covalent attachment of the 2'-O nucleophile with the scissile G+1 phosphorus. The 2',5'-linked structure was then overlaid with scissile bonds of other small ribozymes including the glmS metabolite-sensing riboswitch and the hammerhead ribozyme, and suggests the potential of the 2',5' linkage to elicit a reaction-intermediate conformation without the need to form metalloenzyme complexes. The hairpin ribozyme structures presented here also suggest how water molecules bound at each of the nonbridging oxygens of G+1 may electrostatically stabilize the transition state in a manner that supplements nucleobase functional groups. Such coordination has not been reported for small ribozymes, but is consistent with the structures of protein enzymes. Overall, this work establishes significant parallels between the RNA and protein enzyme worlds.

  17. Fractal complexity in spontaneous EEG metastable-state transitions: new vistas on integrated neural dynamics

    Directory of Open Access Journals (Sweden)

    Paolo Allegrini

    2010-09-01

    Full Text Available Resting-state EEG signals undergo Rapid Transition Processes (RTPs that glue otherwise stationary epochs. We study the fractal properties of RTPs in space and time, supporting the hypothesis that the brain works at a critical state. We discuss how the global intermittent dynamics of collective excitations is linked to mentation, namely non-constrained non-task-oriented mental activity.

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

    Science.gov (United States)

    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.

  19. Variation in Event-Related Potentials by State Transitions.

    Science.gov (United States)

    Higashi, Hiroshi; Minami, Tetsuto; Nakauchi, Shigeki

    2017-01-01

    The probability of an event's occurrence affects event-related potentials (ERPs) on electroencephalograms. The relation between probability and potentials has been discussed by using a quantity called surprise that represents the self-information that humans receive from the event. Previous studies have estimated surprise based on the probability distribution in a stationary state. Our hypothesis is that state transitions also play an important role in the estimation of surprise. In this study, we compare the effects of surprise on the ERPs based on two models that generate an event sequence: a model of a stationary state and a model with state transitions. To compare these effects, we generate the event sequences with Markov chains to avoid a situation that the state transition probability converges with the stationary probability by the accumulation of the event observations. Our trial-by-trial model-based analysis showed that the stationary probability better explains the P3b component and the state transition probability better explains the P3a component. The effect on P3a suggests that the internal model, which is constantly and automatically generated by the human brain to estimate the probability distribution of the events, approximates the model with state transitions because Bayesian surprise, which represents the degree of updating of the internal model, is highly reflected in P3a. The global effect reflected in P3b, however, may not be related to the internal model because P3b depends on the stationary probability distribution. The results suggest that an internal model can represent state transitions and the global effect is generated by a different mechanism than the one for forming the internal model.

  20. Activation of Wnt/β-Catenin in Ewing Sarcoma Cells Antagonizes EWS/ETS Function and Promotes Phenotypic Transition to More Metastatic Cell States.

    Science.gov (United States)

    Pedersen, Elisabeth A; Menon, Rajasree; Bailey, Kelly M; Thomas, Dafydd G; Van Noord, Raelene A; Tran, Jenny; Wang, Hongwei; Qu, Ping Ping; Hoering, Antje; Fearon, Eric R; Chugh, Rashmi; Lawlor, Elizabeth R

    2016-09-01

    Ewing sarcomas are characterized by the presence of EWS/ETS fusion genes in the absence of other recurrent genetic alterations and mechanisms of tumor heterogeneity that contribute to disease progression remain unclear. Mutations in the Wnt/β-catenin pathway are rare in Ewing sarcoma but the Wnt pathway modulator LGR5 is often highly expressed, suggesting a potential role for the axis in tumor pathogenesis. We evaluated β-catenin and LGR5 expression in Ewing sarcoma cell lines and tumors and noted marked intra- and inter-tumor heterogeneity. Tumors with evidence of active Wnt/β-catenin signaling were associated with increased incidence of tumor relapse and worse overall survival. Paradoxically, RNA sequencing revealed a marked antagonism of EWS/ETS transcriptional activity in Wnt/β-catenin-activated tumor cells. Consistent with this, Wnt/β-catenin-activated cells displayed a phenotype that was reminiscent of Ewing sarcoma cells with partial EWS/ETS loss of function. Specifically, activation of Wnt/β-catenin induced alterations to the actin cytoskeleton, acquisition of a migratory phenotype, and upregulation of EWS/ETS-repressed genes. Notably, activation of Wnt/β-catenin signaling led to marked induction of tenascin C (TNC), an established promoter of cancer metastasis, and an EWS/ETS-repressed target gene. Loss of TNC function in Ewing sarcoma cells profoundly inhibited their migratory and metastatic potential. Our studies reveal that heterogeneous activation of Wnt/β-catenin signaling in subpopulations of tumor cells contributes to phenotypic heterogeneity and disease progression in Ewing sarcoma. Significantly, this is mediated, at least in part, by inhibition of EWS/ETS fusion protein function that results in derepression of metastasis-associated gene programs. Cancer Res; 76(17); 5040-53. ©2016 AACR. ©2016 American Association for Cancer Research.

  1. Analysis of slow transitions between nonequilibrium steady states

    Science.gov (United States)

    Mandal, Dibyendu; Jarzynski, Christopher

    2016-06-01

    Transitions between nonequilibrium steady states obey a generalized Clausius inequality, which becomes an equality in the quasistatic limit. For slow but finite transitions, we show that the behavior of the system is described by a response matrix whose elements are given by a far-from-equilibrium Green-Kubo formula, involving the decay of correlations evaluated in the nonequilibrium steady state. This result leads to a fluctuation-dissipation relation between the mean and variance of the nonadiabatic entropy production, Δ {{s}\\text{na}} . Furthermore, our results extend—to nonequilibrium steady states—the thermodynamic metric structure introduced by Sivak and Crooks for analyzing minimal-dissipation protocols for transitions between equilibrium states.

  2. Morse bifurcations of transition states in bimolecular reactions

    CERN Document Server

    MacKay, Robert S

    2015-01-01

    The transition states and dividing surfaces used to find rate constants for bimolecular reactions are shown to undergo qualitative changes, known as Morse bifurcations, and to exist for a large range of energies, not just immediately above the critical energy for first connection between reactants and products. Specifically, we consider capture between two molecules and the associated transition states for the case of non-zero angular momentum and general attitudes. The capture between an atom and a diatom, and then a general molecule are presented, providing concrete examples of Morse bifurcations of transition states and dividing surfaces. The reduction of the $n$-body systems representing the reactions is discussed and reviewed with comments on the difficulties associated with choosing appropriate charts and the global geometry of the reduced spaces.

  3. Complexity and state-transitions in social dependence networks

    Directory of Open Access Journals (Sweden)

    Giuliano Pistolesi

    2001-01-01

    Full Text Available Computation of complexity in Social Dependence Networks is an interesting research domain to understand evolution processes and group exchange dynamics in natural and artificial intelligent Multi-Agent Systems. We perform an agent-based simulation by NET-PLEX (Conte and Pistolesi, 2000, a new software system able both to build interdependence networks tipically emerging in Multi-Agent System scenarios and to investigate complexity phenomena, i.e., unstability and state-transitions like Hopf bifurcation (Nowak and Lewenstein, 1994, and to describe social self organization phenomena emerging in these artificial social systems by means of complexity measures similar to those introduced by Hubermann and Hogg (1986. By performing analysis of complexity in these kind of artificial societies we observed interesting phenomena in emerging organizations that suggest state-transitions induced by critical configurations of parameters describing the social system similar to those observed in many studies on state-transitions in bifurcation chaos (Schuster, 1988; Ruelle, 1989.

  4. Transition state ensemble optimization for reactions of arbitrary complexity

    Science.gov (United States)

    Zinovjev, Kirill; Tuñón, Iñaki

    2015-10-01

    In the present work, we use Variational Transition State Theory (VTST) to develop a practical method for transition state ensemble optimization by looking for an optimal hyperplanar dividing surface in a space of meaningful trial collective variables. These might be interatomic distances, angles, electrostatic potentials, etc. Restrained molecular dynamics simulations are used to obtain on-the-fly estimates of ensemble averages that guide the variations of the hyperplane maximizing the transmission coefficient. A central result of our work is an expression that quantitatively estimates the importance of the coordinates used for the localization of the transition state ensemble. Starting from an arbitrarily large set of trial coordinates, one can distinguish those that are indeed essential for the advance of the reaction. This facilitates the use of VTST as a practical theory to study reaction mechanisms of complex processes. The technique was applied to the reaction catalyzed by an isochorismate pyruvate lyase. This reaction involves two simultaneous chemical steps and has a shallow transition state region, making it challenging to define a good reaction coordinate. Nevertheless, the hyperplanar transition state optimized in the space of 18 geometrical coordinates provides a transmission coefficient of 0.8 and a committor histogram well-peaked about 0.5, proving the strength of the method. We have also tested the approach with the study of the NaCl dissociation in aqueous solution, a stringest test for a method based on transition state theory. We were able to find essential degrees of freedom consistent with the previous studies and to improve the transmission coefficient with respect to the value obtained using solely the NaCl distance as the reaction coordinate.

  5. Quantum phase transition between cluster and antiferromagnetic states

    CERN Document Server

    Son, Wonmin; Fazio, Rosario; Hamma, Alioscia; Pascazio, Saverio; Vedral, Vlatko

    2011-01-01

    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. 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.

  6. Factorised steady states and condensation transitions in nonequilibrium systems

    Indian Academy of Sciences (India)

    M R Evans

    2005-06-01

    Systems driven out of equilibrium can often exhibit behaviour not seen in systems in thermal equilibrium – for example phase transitions in one-dimensional systems. In this talk I will review a simple model of a nonequilibrium system known as the `zero-range process' and its recent developments. The nonequilibrium stationary state of this model factorises and this property allows a detailed analysis of several `condensation' transitions wherein a finite fraction of the constituent particles condenses onto a single lattice site. I will then consider a more general class of mass transport models, encompassing continuous mass variables and discrete time updating, and present a necessary and sufficient condition for the steady state to factorise. The property of factorisation again allows an analysis of the condensation transitions which may occur.

  7. Nonequilibrium Markov state modeling of the globule-stretch transition

    Science.gov (United States)

    Knoch, Fabian; Speck, Thomas

    2017-01-01

    We describe a systematic approach to construct coarse-grained Markov state models from molecular dynamics data of systems driven into a nonequilibrium steady state. We apply this method to study the globule-stretch transition of a single tethered model polymer in shear flow. The folding and unfolding rates of the coarse-grained model agree with the original detailed model. We demonstrate that the folding and unfolding proceeds through the same narrow region of configuration space but along different cycles.

  8. Planar Homotropenylium Cation : A Transition State with Reversed Aromaticity

    NARCIS (Netherlands)

    Gibson, Christopher M.; Havenith, Remco W. A.; Fowler, Patrick W.; Jenneskens, Leonardus W.

    2015-01-01

    In contrast to the equilibrium structure of the homoaromatic C-s homotropenylium cation, C8H9+ (1), which supports a pinched diatropic ring current, the C(2)v transition state (2) for inversion of the methylene bridge of 1 is antiaromatic and supports a two-lobe paratropic pi current, as detected by

  9. Green's function approach to edge states in transition metal dichalcogenides

    NARCIS (Netherlands)

    Farmanbar Gelepordsari, M.; Amlaki, T.; Brocks, G.

    2016-01-01

    The semiconducting two-dimensional transition metal dichalcogenides MX 2 show an abundance of one-dimensional metallic edges and grain boundaries. Standard techniques for calculating edge states typically model nanoribbons, and require the use of supercells. In this paper, we formulate a Green's fun

  10. Self-organized two-state membrane potential transitions in a network of realistically modeled cortical neurons.

    Science.gov (United States)

    Kang, Siu; Kitano, Katsunori; Fukai, Tomoki

    2004-04-01

    Recent studies have revealed that in vivo cortical neurons show spontaneous transitions between two subthreshold levels of the membrane potentials, 'up' and 'down' states. The neural mechanism of generating those spontaneous states transitions, however, remains unclear. Recent electrophysiological studies have suggested that those state transitions may occur through activation of a hyperpolarization-activated cation current (H-current), possibly by inhibitory synaptic inputs. Here, we demonstrate that two-state membrane potential fluctuations similar to those exhibited by in vivo neurons can be generated through a spike-timing-dependent self-organizing process in a network of inhibitory neurons and excitatory neurons expressing the H-current.

  11. Dynamics of a first-order transition to an absorbing state

    Science.gov (United States)

    Néel, Baptiste; Rondini, Ignacio; Turzillo, Alex; Mujica, Nicolás; Soto, Rodrigo

    2014-04-01

    A granular system confined in a quasi-two-dimensional box that is vertically vibrated can transit to an absorbing state in which all particles bounce vertically in phase with the box, with no horizontal motion. In principle, this state can be reached for any density lower than the one corresponding to one complete monolayer, which is then the critical density. Below this critical value, the transition to the absorbing state is of first order, with long metastable periods, followed by rapid transitions driven by homogeneous nucleation. Molecular dynamics simulations and experiments show that there is a dramatic increase on the metastable times far below the critical density; in practice, it is impossible to observe spontaneous transitions close to the critical density. This peculiar feature is a consequence of the nonequilibrium nature of this first-order transition to the absorbing state. A Ginzburg-Landau model, with multiplicative noise, describes qualitatively the observed phenomena and explains the macroscopic size of the critical nuclei. The nuclei become of small size only close to a second critical point where the active phase becomes unstable via a saddle node bifurcation. It is only close to this second critical point that experiments and simulations can evidence spontaneous transitions to the absorbing state while the metastable times grow dramatically moving away from it.

  12. Theoretical analysis of droplet transition from Cassie to Wenzel state

    Institute of Scientific and Technical Information of China (English)

    刘天庆; 李艳杰; 李香琴; 孙玮

    2015-01-01

    Whether droplets transit from the Cassie to the Wenzel state (C–W) on a textured surface is the touchstone that the superhydrophobicity of the surface is still maintained. However, the C–W transition mechanism, especially the spontaneous transition of small droplets, is still not very clear to date. The interface free energy gradient of a small droplet is firstly proposed and derived as the driving force for its C–W evolution in this study based on the energy and gradient analysis. Then the physical and mathematical model of the C–W transition is found after the C–W driving force or transition pressure, the resistance, and the parameters of the meniscus beneath the droplet are formulated. The results show that the micro/nano structural parameters significantly affect the C–W driving force and resistance. The smaller the pillar diameter and pitch, the minor the C–W transition pressure, and the larger the resistance. Consequently, the C–W transition is difficult to be completed for the droplets on nano-textured surfaces. Meanwhile if the posts are too short, the front of the curved liquid–air interface below the droplet will touch the structural substrate easily even though the three phase contact line (TPCL) has not depinned. When the posts are high enough, the TPCL beneath the drop must move firstly before the meniscus can reach the substrate. As a result, the droplet on a textured surface with short pillars is easy to complete its C–W evolution. On the other hand, the smaller the droplet, the easier the C–W shift, since the transition pressure becomes larger, which well explains why an evaporating drop will collapse spontaneously from composite to Wenzel state. Besides, both intrinsic and advancing contact angles affect the C–W transition as well. The greater the two angles, the harder the C–W transition. In the end, the C–W transition parameters and the critical conditions measured in literatures are calculated and compared, and the

  13. Background field functional renormalization group for absorbing state phase transitions.

    Science.gov (United States)

    Buchhold, Michael; Diehl, Sebastian

    2016-07-01

    We present a functional renormalization group approach for the active to inactive phase transition in directed percolation-type systems, in which the transition is approached from the active, finite density phase. By expanding the effective potential for the density field around its minimum, we obtain a background field action functional, which serves as a starting point for the functional renormalization group approach. Due to the presence of the background field, the corresponding nonperturbative flow equations yield remarkably good estimates for the critical exponents of the directed percolation universality class, even in low dimensions.

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

    Science.gov (United States)

    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

  15. Critical Transitions in Social Network Activity

    CERN Document Server

    Kuehn, Christian; Romero, Daniel

    2013-01-01

    A large variety of complex systems in ecology, climate science, biomedicine and engineering have been observed to exhibit tipping points, where the internal dynamical state of the system abruptly changes. For example, such critical transitions may result in the sudden change of ecological environments and climate conditions. Data and models suggest that some of these drastic events may be preceded by detectable early-warning signs. This view is also corroborated by abstract mathematical theory for generic bifurcations in stochastic multi-scale systems. Whether early-warnings are also present in social networks that anticipate \\textit{a-priori unknown} events in society is an open problem to which only highly speculative answers can be given at present. Here, we focus on \\textit{a-priori known} events and analyze a social network data set with a focus on classical variance and autocorrelation warning signs. We find that several a-priori known events are preceded by variance and autocorrelation growth as predic...

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

    Science.gov (United States)

    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.

  17. Nonlinear system identification and control using state transition algorithm

    CERN Document Server

    Yang, Chunhua; Gui, Weihua

    2012-01-01

    This paper presents a novel optimization method named state transition algorithm (STA) to solve the problem of identification and control for nonlinear system. In the proposed algorithm, a solution to optimization problem is considered as a state, and the updating of a solution equates to the process of state transition, which makes the STA easy to understand and convenient to be implemented. First, the STA is applied to identify the optimal parameters of the estimated system with previously known structure. With the accurate estimated model, an off-line PID controller is then designed optimally by using the STA as well. Experimental results demonstrate the validity of the methodology, and comparison to STA with other optimization algorithms confirms that STA is a promising alternative method for system identification and control due to its stronger search ability, faster convergence speed and more stable performance.

  18. Raman transitions between hyperfine clock states in a magnetic trap

    CERN Document Server

    Naber, J B; Hubert, T; Spreeuw, R J C

    2016-01-01

    We present our experimental investigation of an optical Raman transition between the magnetic clock states of $^{87}$Rb in an atom chip magnetic trap. The transfer of atomic population is induced by a pair of diode lasers which couple the two clock states off-resonantly to an intermediate state manifold. This transition is subject to destructive interference of two excitation paths, which leads to a reduction of the effective two-photon Rabi-frequency. Furthermore, we find that the transition frequency is highly sensitive to the intensity ratio of the diode lasers. Our results are well described in terms of light shifts in the multi-level structure of $^{87}$Rb. The differential light shifts vanish at an optimal intensity ratio, which we observe as a narrowing of the transition linewidth. We also observe the temporal dynamics of the population transfer and find good agreement with a model based on the system's master equation and a Gaussian laser beam profile. Finally, we identify several sources of decoheren...

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

    Science.gov (United States)

    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.

  20. Transition Strategies to Ensure Active Student Engagement

    Science.gov (United States)

    Korbel, Donna M.; McGuire, Joan M.; Banerjee, Manju; Saunders, Sue A.

    2011-01-01

    Transition into college for students with disabilities has been written about extensively over the past decade, due in part to legislative mandates implemented at the secondary level. With significant increases in the number of these students in the college population, a focus on their transition through college is imperative to improve retention…

  1. Transition Strategies to Ensure Active Student Engagement

    Science.gov (United States)

    Korbel, Donna M.; McGuire, Joan M.; Banerjee, Manju; Saunders, Sue A.

    2011-01-01

    Transition into college for students with disabilities has been written about extensively over the past decade, due in part to legislative mandates implemented at the secondary level. With significant increases in the number of these students in the college population, a focus on their transition through college is imperative to improve retention…

  2. Kinetic study on Michael-type reactions of β-nitrostyrenes with cyclic secondary amines in acetonitrile: transition-state structures and reaction mechanism deduced from negative enthalpy of activation and analyses of LFERs.

    Science.gov (United States)

    Um, Ik-Hwan; Kang, Ji-Sun; Park, Jong-Yoon

    2013-06-07

    A kinetic study is reported for the Michael-type reactions of X-substituted β-nitrostyrenes (1a-j) with a series of cyclic secondary amines in MeCN. The plots of pseudo-first-order rate constant k(obsd) vs [amine] curve upward, indicating that the reactions proceed through catalyzed and uncatalyzed routes. The dissection of k(obsd) into Kk2 and Kk3 (i.e., the rate constants for the uncatalyzed and catalyzed routes, respectively) revealed that Kk3 is much larger than Kk2, implying that the reactions proceed mainly through the catalyzed route when [amine] > 0.01 M. Strikingly, the reactivity of β-nitrostyrene (1g) toward piperidine decreases as the reaction temperature increases. Consequently, a negative enthalpy of activation is obtained, indicating that the reaction proceeds through a relatively stable intermediate. The Brønsted-type plots for the reactions of 1g are linear with β(nuc) = 0.51 and 0.61, and the Hammett plots for the reactions of 1a-j are also linear with ρX = 0.84 and 2.10 for the uncatalyzed and catalyzed routes, respectively. The reactions are concluded to proceed through six-membered cyclic transition states for both the catalyzed and uncatalyzed routes. The effects of the substituent X on reactivity and factors influencing β(nuc) and ρX obtained in this study are discussed.

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

    Science.gov (United States)

    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...

  4. Evolutionary transitions in enzyme activity of ant fungus gardens.

    Science.gov (United States)

    De Fine Licht, Henrik H; Schiøtt, Morten; Mueller, Ulrich G; Boomsma, Jacobus J

    2010-07-01

    Fungus-growing (attine) ants and their fungal symbionts passed through several evolutionary transitions during their 50 million year old evolutionary history. The basal attine lineages often shifted between two main cultivar clades, whereas the derived higher-attine lineages maintained an association with a monophyletic clade of specialized symbionts. In conjunction with the transition to specialized symbionts, the ants advanced in colony size and social complexity. Here we provide a comparative study of the functional specialization in extracellular enzyme activities in fungus gardens across the attine phylogeny. We show that, relative to sister clades, gardens of higher-attine ants have enhanced activity of protein-digesting enzymes, whereas gardens of leaf-cutting ants also have increased activity of starch-digesting enzymes. However, the enzyme activities of lower-attine fungus gardens are targeted primarily toward partial degradation of plant cell walls, reflecting a plesiomorphic state of nondomesticated fungi. The enzyme profiles of the higher-attine and leaf-cutting gardens appear particularly suited to digest fresh plant materials and to access nutrients from live cells without major breakdown of cell walls. The adaptive significance of the lower-attine symbiont shifts remains unclear. One of these shifts was obligate, but digestive advantages remained ambiguous, whereas the other remained facultative despite providing greater digestive efficiency.

  5. Critical behavior of the absorbing state transition in the contact process with relaxing immunization

    Science.gov (United States)

    Cruz, Claudia P. T.; Lyra, M. L.; Fulco, U. L.; Corso, Gilberto

    2012-11-01

    We introduce a model for the Contact Process with relaxing immunization CPRI. In this model, local memory is introduced by a time and space dependence of the contamination probability. The model has two parameters: a typical immunization time τ and a maximum contamination probability a. The system presents an absorbing state phase transition whenever the contamination probability a is above a minimum threshold. For short immunization times, the system evolves to a statistically stationary active state. Above τc(a), immunization predominates and the system evolves to the absorbing vacuum state. We employ a finite-size scaling analysis to show that the transition belongs to the standard directed percolation universality class. The critical immunization time diverges in the limit of a→1. In this regime, the density of active sites decays exponentially as τ increases, but never reaches the vacuum state in the thermodynamic limit.

  6. Absorbing State Phase Transition with Competing Quantum and Classical Fluctuations

    Science.gov (United States)

    Marcuzzi, Matteo; Buchhold, Michael; Diehl, Sebastian; Lesanovsky, Igor

    2016-06-01

    Stochastic processes with absorbing states feature examples of nonequilibrium universal phenomena. While the classical regime has been thoroughly investigated in the past, relatively little is known about the behavior of these nonequilibrium systems in the presence of quantum fluctuations. Here, we theoretically address such a scenario in an open quantum spin model which, in its classical limit, undergoes a directed percolation phase transition. By mapping the problem to a nonequilibrium field theory, we show that the introduction of quantum fluctuations stemming from coherent, rather than statistical, spin flips alters the nature of the transition such that it becomes first order. In the intermediate regime, where classical and quantum dynamics compete on equal terms, we highlight the presence of a bicritical point with universal features different from the directed percolation class in a low dimension. We finally propose how this physics could be explored within gases of interacting atoms excited to Rydberg states.

  7. Inequivalent models of irreversible dimer filling: ``Transition state'' dependence

    Science.gov (United States)

    Nord, R. S.; Evans, J. W.

    1990-12-01

    Irreversible adsorption of diatomics on crystalline surfaces is sometimes modeled as random dimer filling of adjacent pairs of sites on a lattice. We note that this process can be implemented in two distinct ways: (i) randomly pick adjacent pairs of sites, jj', and fill jj' only if both are empty (horizontal transition state); or (ii) randomly pick a single site, j, and if j and at least one neighbor are empty, then fill j and a randomly chosen empty neighbor (vertical transition state). Here it is instructive to consider processes which also include competitive random monomer filling of single sites. We find that although saturation (partial) coverages differ little between the models for pure dimer filling, there is a significant difference for comparable monomer and dimer filling rates. We present exact results for saturation coverage behavior for a linear lattice, and estimates for a square lattice. Ramifications for simple models of CO oxidation on surfaces are indicated.

  8. Identification and Analysis of Transition and Metastable Markov States

    CERN Document Server

    Martini, Linda; Hummer, Gerhard; Buchete, Nicolae-Viorel; Rosta, Edina

    2016-01-01

    We present a new method that enables the identification and analysis of both transition and metastable conformational states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented and studied by using both analytical and actual examples from MD simulations of the helix-forming peptide Ala5, and of a larger system, the epidermal growth factor receptor (EGFR) protein. In all cases, our method identifies automatically the corresponding transition states and metastable conformations in an optimal way, with the input of a set of relevant coordinates, by capturing accurately the intrinsic slowest relaxation rate. Our approach provides a general and easy to implement analysis method that provides unique insight into the molecular mechanism and the rare but crucial rate limiting conformational pathways occurring in complex dynamical systems such as molecular trajectories.

  9. Heat Capacity Changes for Transition-State Analogue Binding and Catalysis with Human 5'-Methylthioadenosine Phosphorylase.

    Science.gov (United States)

    Firestone, Ross S; Cameron, Scott A; Karp, Jerome M; Arcus, Vickery L; Schramm, Vern L

    2017-02-17

    Human 5'-methylthioadenosine phosphorylase (MTAP) catalyzes the phosphorolysis of 5'-methylthioadenosine (MTA). Its action regulates cellular MTA and links polyamine synthesis to S-adenosylmethionine (AdoMet) salvage. Transition state analogues with picomolar dissociation constants bind to MTAP in an entropically driven process at physiological temperatures, suggesting increased hydrophobic character or dynamic structure for the complexes. Inhibitor binding exhibits a negative heat capacity change (-ΔCp), and thus the changes in enthalpy and entropy upon binding are strongly temperature-dependent. The ΔCp of inhibitor binding by isothermal titration calorimetry does not follow conventional trends and is contrary to that expected from the hydrophobic effect. Thus, ligands of increasing hydrophobicity bind with increasing values of ΔCp. Crystal structures of MTAP complexed to transition-state analogues MT-DADMe-ImmA, BT-DADMe-ImmA, PrT-ImmA, and a substrate analogue, MT-tubercidin, reveal similar active site contacts and overall protein structural parameters, despite large differences in ΔCp for binding. In addition, ΔCp values are not correlated with Kd values. Temperature dependence of presteady state kinetics revealed the chemical step for the MTAP reaction to have a negative heat capacity for transition state formation (-ΔCp(‡)). A comparison of the ΔCp(‡) for MTAP presteady state chemistry and ΔCp for inhibitor binding revealed those transition-state analogues most structurally and thermodynamically similar to the transition state. Molecular dynamics simulations of MTAP apoenzyme and complexes with MT-DADMe-ImmA and MT-tubercidin show small, but increased dynamic motion in the inhibited complexes. Variable temperature CD spectroscopy studies for MTAP-inhibitor complexes indicate remarkable protein thermal stability (to Tm = 99 °C) in complexes with transition-state analogues.

  10. The generation of animated sequences from state transition systems.

    OpenAIRE

    Clark, Tony; Palmer, I. J.

    1995-01-01

    We address the issue of the construction of a computer animation system by composing together a collection of behaviours for the individual objects which are to be animated. The behaviours are developed using a formal notation for state transition systems. The notation is particularly flexible, allowing both a constructive and constraining aproach to behaviour representation. The behaviour necessary for animating Newton's Cradle for an arbitrary number of spheres is developed as an example of...

  11. Modeling Enzymatic Transition States by Force Field Methods

    DEFF Research Database (Denmark)

    Hansen, Mikkel Bo; Jensen, Hans Jørgen Aagaard; Jensen, Frank

    2009-01-01

    The SEAM method, which models a transition structure as a minimum on the seam of two diabatic surfaces represented by force field functions, has been used to generate 20 transition structures for the decarboxylation of orotidine by the orotidine-5'-monophosphate decarboxylase enzyme. The dependence...... by various electronic structure methods, where part of the enzyme is represented by a force field description and the effects of the solvent are represented by a continuum model. The relative energies vary by several hundreds of kJ/mol between the transition structures, and tests showed that a large part...... of this variation is due to changes in the enzyme structure at distances more than 5 Å from the active site. There are significant differences between the results obtained by pure quantum methods and those from mixed quantum and molecular mechanics methods....

  12. Transition State Theory: Variational Formulation, Dynamical Corrections, and Error Estimates

    Science.gov (United States)

    vanden-Eijnden, Eric

    2009-03-01

    Transition state theory (TST) is discussed from an original viewpoint: it is shown how to compute exactly the mean frequency of transition between two predefined sets which either partition phase space (as in TST) or are taken to be well separate metastable sets corresponding to long-lived conformation states (as necessary to obtain the actual transition rate constants between these states). Exact and approximate criterions for the optimal TST dividing surface with minimum recrossing rate are derived. Some issues about the definition and meaning of the free energy in the context of TST are also discussed. Finally precise error estimates for the numerical procedure to evaluate the transmission coefficient κS of the TST dividing surface are given, and it shown that the relative error on κS scales as 1/√κS when κS is small. This implies that dynamical corrections to the TST rate constant can be computed efficiently if and only if the TST dividing surface has a transmission coefficient κS which is not too small. In particular the TST dividing surface must be optimized upon (for otherwise κS is generally very small), but this may not be sufficient to make the procedure numerically efficient (because the optimal dividing surface has maximum κS, but this coefficient may still be very small).

  13. Biosynthetic consequences of multiple sequential post-transition-state bifurcations

    Science.gov (United States)

    Hong, Young Joo; Tantillo, Dean J.

    2014-02-01

    Selectivity in chemical reactions that form complex molecular architectures from simpler precursors is usually rationalized by comparing competing transition-state structures that lead to different possible products. Herein we describe a system for which a single transition-state structure leads to the formation of many isomeric products via pathways that feature multiple sequential bifurcations. The reaction network described connects the pimar-15-en-8-yl cation to miltiradiene, a tricyclic diterpene natural product, and isomers via cyclizations and/or rearrangements. The results suggest that the selectivity of the reaction is controlled by (post-transition-state) dynamic effects, that is, how the carbocation structure changes in response to the distribution of energy in its vibrational modes. The inherent dynamical effects revealed herein (characterized through quasiclassical direct dynamics calculations using density functional theory) have implications not only for the general principles of selectivity prediction in systems with complex potential energy surfaces, but also for the mechanisms of terpene synthase enzymes and their evolution. These findings redefine the challenges faced by nature in controlling the biosynthesis of complex natural products.

  14. Excited-state quantum phase transition in the Rabi model

    Science.gov (United States)

    Puebla, Ricardo; Hwang, Myung-Joong; Plenio, Martin B.

    2016-08-01

    The Rabi model, a two-level atom coupled to a harmonic oscillator, can undergo a second-order quantum phase transition (QPT) [M.-J. Hwang et al., Phys. Rev. Lett. 115, 180404 (2015), 10.1103/PhysRevLett.115.180404]. Here we show that the Rabi QPT accompanies critical behavior in the higher-energy excited states, i.e., the excited-state QPT (ESQPT). We derive analytic expressions for the semiclassical density of states, which show a logarithmic divergence at a critical energy eigenvalue in the broken symmetry (superradiant) phase. Moreover, we find that the logarithmic singularities in the density of states lead to singularities in the relevant observables in the system such as photon number and atomic polarization. We corroborate our analytical semiclassical prediction of the ESQPT in the Rabi model with its numerically exact quantum mechanical solution.

  15. Modeling of Cancer Stem Cell State Transitions Predicts Therapeutic Response.

    Directory of Open Access Journals (Sweden)

    Mary E Sehl

    Full Text Available Cancer stem cells (CSCs possess capacity to both self-renew and generate all cells within a tumor, and are thought to drive tumor recurrence. Targeting the stem cell niche to eradicate CSCs represents an important area of therapeutic development. The complex nature of many interacting elements of the stem cell niche, including both intracellular signals and microenvironmental growth factors and cytokines, creates a challenge in choosing which elements to target, alone or in combination. Stochastic stimulation techniques allow for the careful study of complex systems in biology and medicine and are ideal for the investigation of strategies aimed at CSC eradication. We present a mathematical model of the breast cancer stem cell (BCSC niche to predict population dynamics during carcinogenesis and in response to treatment. Using data from cell line and mouse xenograft experiments, we estimate rates of interconversion between mesenchymal and epithelial states in BCSCs and find that EMT/MET transitions occur frequently. We examine bulk tumor growth dynamics in response to alterations in the rate of symmetric self-renewal of BCSCs and find that small changes in BCSC behavior can give rise to the Gompertzian growth pattern observed in breast tumors. Finally, we examine stochastic reaction kinetic simulations in which elements of the breast cancer stem cell niche are inhibited individually and in combination. We find that slowing self-renewal and disrupting the positive feedback loop between IL-6, Stat3 activation, and NF-κB signaling by simultaneous inhibition of IL-6 and HER2 is the most effective combination to eliminate both mesenchymal and epithelial populations of BCSCs. Predictions from our model and simulations show excellent agreement with experimental data showing the efficacy of combined HER2 and Il-6 blockade in reducing BCSC populations. Our findings will be directly examined in a planned clinical trial of combined HER2 and IL-6 targeted

  16. Evidence for a catalytic six-membered cyclic transition state in aminolysis of 4-nitrophenyl 3,5-dinitrobenzoate in acetonitrile: comparative brønsted-type plot, entropy of activation, and deuterium kinetic isotope effects.

    Science.gov (United States)

    Um, Ik-Hwan; Kim, Min-Young; Bae, Ae-Ri; Dust, Julian M; Buncel, Erwin

    2015-01-02

    A kinetic study for reactions of 4-nitrophenyl 3,5-dinitrobenzoate (1a) with a series of cyclic secondary amines in acetonitrile is reported. Plots of the pseudo-first-order rate constant (kobsd) vs [amine] curve upward, while those of kobsd /[amine] vs [amine] exhibit excellent linear correlations with positive intercepts, indicating that the reaction proceeds through both uncatalyzed and catalyzed routes. Brønsted-type plots for uncatalyzed and catalyzed reactions are linear with βnuc = 1.03 and 0.69, respectively. The ΔH(⧧) and ΔS(⧧) values measured for the catalytic reaction with morpholine are -0.80 kcal/mol and -61.7 cal/(mol K), respectively. The negative ΔH(⧧) with a large negative ΔS(⧧) suggests that the reaction proceeds through a highly ordered transition state (i.e., a six-membered cyclic transition state, which includes a second amine molecule that accepts a proton from the aminium moiety of the zwitterionic tetrahedral intermediate and simultaneously donates a proton to the aryloxyl oxygen of the nucleofuge with concomitant C-OAr bond scission). This proposal is consistent with the smaller βnuc value for the catalyzed reaction as compared to the uncatalyzed reaction. An inverse deuterium kinetic isotope effect (DKIE) value of 0.93 and a contrasting normal primary DKIE value of 3.23 for the uncatalyzed and catalyzed routes, respectively, also support the proposed cyclic transition state.

  17. The Role of the State in Economic Transformation: Comparing the Transition Experiences of Russia and China

    OpenAIRE

    David M. Kotz

    2005-01-01

    This paper compares two radically different approaches to transforming an economic system based on central planning and state property into a capitalist system, the neoliberal transition strategy and the state directed transition strategy. Russia’s transition since 1992 is examined as an example of the neoliberal approach, while China’s transition since 1978 is analyzed as an example of the state directed approach. The primary explanation for China’s economically superior transition performan...

  18. Nonequilibrium stationary states and phase transitions in directed Ising models

    Science.gov (United States)

    Godrèche, Claude; Bray, Alan J.

    2009-12-01

    We study the nonequilibrium properties of directed Ising models with non-conserved dynamics, in which each spin is influenced by only a subset of its nearest neighbours. We treat the following models: (i) the one-dimensional chain; (ii) the two-dimensional square lattice; (iii) the two-dimensional triangular lattice and (iv) the three-dimensional cubic lattice. We raise and answer the question: (a) under what conditions is the stationary state described by the equilibrium Boltzmann-Gibbs distribution? We show that, for models (i), (ii) and (iii), in which each spin 'sees' only half of its neighbours, there is a unique set of transition rates, namely with exponential dependence in the local field, for which this is the case. For model (iv), we find that any rates satisfying the constraints required for the stationary measure to be Gibbsian should satisfy detailed balance, ruling out the possibility of directed dynamics. We finally show that directed models on lattices of coordination number z>=8 with exponential rates cannot accommodate a Gibbsian stationary state. We conjecture that this property extends to any form of the rates. We are thus led to the conclusion that directed models with Gibbsian stationary states only exist in dimensions one and two. We then raise the question: (b) do directed Ising models, augmented by Glauber dynamics, exhibit a phase transition to a ferromagnetic state? For the models considered above, the answers are open problems, with the exception of the simple cases (i) and (ii). For Cayley trees, where each spin sees only the spins further from the root, we show that there is a phase transition provided the branching ratio, q, satisfies q>=3.

  19. Fate of Extended States and Localization Transition at Weak Fields

    Science.gov (United States)

    Yang, Kun

    1997-03-01

    The reconciliation between the nonexistence of extended states in two dimensions in zero magnetic field, and the existence of critical energies in the high field limit, first addressed qualitatively (D. E. Khmelnitskii, Phys. Lett. A 106), 182 (1984); R. B. Laughlin, Phys. Rev. Lett. 52, 2304 (1984). a decade ago, has reemerged as a subject of considerable interest and debate, following experimental investigations in the two dimensional electron gas at low fields. We have addressed the problem on two fronts. For strong magnetic fields, where Landau level mixing effects are weak, we have developed a systematic analytic expansion in powers of 1\\over B. (F. D. M. Haldane and Kun Yang, Phys. Rev. Lett. 78), to appear. We find the dominant level repulsion effect (of order 1\\over B^2), lowers the energies of typical states in a Landau band. The critical energies, however, are not affected at this order. In contrast, we find that, the extended state energies levitates to order 1\\over B^3, thus reconciling levitation of extended states with level repulsion due to Landau level mixing. In the regime of weak magnetic field and strong Landau level mixing, where the perturbative approach is not applicable, we have performed a numerical study on lattice models, (Kun Yang and R. N. Bhatt, Phys. Rev. Lett. 76), 1316 (1996). which provides evidence for this levitation at weak magnetic field. Furthermore, we obtain a localization transition to an insulating phase at weak field, and a finite size scaling analysis shows that the localization length diverges at this transition with an exponent that is the same as that of the plateau transitions in the strong field regime, ν≈ 2.3. Relations between our theoretical results and experimental findings will be discussed.

  20. Transition state for the NSD2-catalyzed methylation of histone H3 lysine 36.

    Science.gov (United States)

    Poulin, Myles B; Schneck, Jessica L; Matico, Rosalie E; McDevitt, Patrick J; Huddleston, Michael J; Hou, Wangfang; Johnson, Neil W; Thrall, Sara H; Meek, Thomas D; Schramm, Vern L

    2016-02-02

    Nuclear receptor SET domain containing protein 2 (NSD2) catalyzes the methylation of histone H3 lysine 36 (H3K36). It is a determinant in Wolf-Hirschhorn syndrome and is overexpressed in human multiple myeloma. Despite the relevance of NSD2 to cancer, there are no potent, selective inhibitors of this enzyme reported. Here, a combination of kinetic isotope effect measurements and quantum chemical modeling was used to provide subangstrom details of the transition state structure for NSD2 enzymatic activity. Kinetic isotope effects were measured for the methylation of isolated HeLa cell nucleosomes by NSD2. NSD2 preferentially catalyzes the dimethylation of H3K36 along with a reduced preference for H3K36 monomethylation. Primary Me-(14)C and (36)S and secondary Me-(3)H3, Me-(2)H3, 5'-(14)C, and 5'-(3)H2 kinetic isotope effects were measured for the methylation of H3K36 using specifically labeled S-adenosyl-l-methionine. The intrinsic kinetic isotope effects were used as boundary constraints for quantum mechanical calculations for the NSD2 transition state. The experimental and calculated kinetic isotope effects are consistent with an SN2 chemical mechanism with methyl transfer as the first irreversible chemical step in the reaction mechanism. The transition state is a late, asymmetric nucleophilic displacement with bond separation from the leaving group at (2.53 Å) and bond making to the attacking nucleophile (2.10 Å) advanced at the transition state. The transition state structure can be represented in a molecular electrostatic potential map to guide the design of inhibitors that mimic the transition state geometry and charge.

  1. Wetting reversal at gelation transition freezes thermodynamically unstable states.

    Science.gov (United States)

    Hirayama, Shinya; Sano, Masahito

    2013-07-23

    The contact angle of a drop of gelling solution on a flat, solid surface was monitored as the hot solution was allowed to cool. When a solvent with a high cohesive energy and a wettable solid surface was used, a wetting solution turned into a dewetting solid at the gelation transition. The density profiles in gel as probed by confocal Raman microscopy reveal that the adsorption of both gelator and solvent shifts at the transition and the solvent is severely depleted from the interfacial region. Thus, the wetting reversal is accompanied by the interfacial desolvation. As a result of the adsorption shift during the gelation process in progress, a locally concentrated region of the gelator is frozen in space far away from the surface. This is a thermodynamically unstable state but can be realized reproducibly. The profile analysis also shows that the effect of the surface extends out to a few hundred micrometers, 2 orders of magnitude larger than the bulk correlation length.

  2. Mechanical induction of transitions into mesenchymal and amoeboid states

    Science.gov (United States)

    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.

  3. Equation of state and QCD transition at finite temperature

    CERN Document Server

    Bazavov, A; 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; Söldner, W; Sugar, R; Toussaint, D; Vranas, P

    2009-01-01

    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 Nt=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(a^2) 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 Nt=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 also incorporated an estimate of c...

  4. Control of State Transitions in Complex and Biophysical Networks

    Science.gov (United States)

    Motter, Adilson; Wells, Daniel; Kath, William

    Noise is a fundamental part of intracellular processes. While the response of biological systems to noise has been studied extensively, there has been limited understanding of how to exploit it to induce a desired cell state. Here I will present a scalable, quantitative method based on the Freidlin-Wentzell action to predict and control noise-induced switching between different states in genetic networks that, conveniently, can also control transitions between stable states in the absence of noise. I will discuss applications of this methodology to predict control interventions that can induce lineage changes and to identify new candidate strategies for cancer therapy. This framework offers a systems approach to identifying the key factors for rationally manipulating network dynamics, and should also find use in controlling other classes of complex networks exhibiting multi-stability. Reference: D. K. Wells, W. L. Kath, and A. E. Motter, Phys. Rev. X 5, 031036 (2015). Work funded by CBC, NCI, NIGMS, and NSF.

  5. Heat storage by phase transition, equation of state

    Energy Technology Data Exchange (ETDEWEB)

    Stunic, Z.

    1984-01-01

    Incongruent phase transitions accompanied by phase separation frequently cause a deterioration of heat-of-fusion storing systems. This kind of deterioration progresses, cycle after cycle, and is especially damaging in technical devices in which hydrated salts, e.g. CaCl/sub 2/ x 6H/sub 2/O, Na/sub 2/SO/sub 4/ x 10H/sub 2/O, Na/sub 2/S/sub 2/O/sub 3/ x 5H/sub 2/O, etc., are used as heat storing materials. Processes contributing to deterioration of hydrated-salt systems are analyzed, novel thermodynamic characteristics are proposed to enable unambiguous descriptions, and these are related in an equation of state for triads of characteristics so that any one of them can be calculated if the other two are known. State equations fo the three salts mentioned above are represented graphically in three-dimensional diagrams. Predictions deduced from state equations are tested experimentally with systems undergoing rapid (or purely incongruent) and slow (or pseudocongruent) phase transitions (CaCl/sub 2/ x 6H/sub 2/O and Na/sub 2/SO/sub 4/ 10H/sub 2/O, respectively). Good accordance between prognosis and experiment is shown.

  6. Approximate State Transition Matrix and Secular Orbit Model

    Directory of Open Access Journals (Sweden)

    M. P. Ramachandran

    2015-01-01

    Full Text Available The state transition matrix (STM is a part of the onboard orbit determination system. It is used to control the satellite’s orbital motion to a predefined reference orbit. Firstly in this paper a simple orbit model that captures the secular behavior of the orbital motion in the presence of all perturbation forces is derived. Next, an approximate STM to match the secular effects in the orbit due to oblate earth effect and later in the presence of all perturbation forces is derived. Numerical experiments are provided for illustration.

  7. E2 transitions between excited single-phonon states: Role of ground-state correlations

    Energy Technology Data Exchange (ETDEWEB)

    Kamerdzhiev, S. P. [National Research Centre Kurchatov Institute (Russian Federation); Voitenkov, D. A., E-mail: dvoytenkov@ippe.ru [Institute for Physics and Power Engineering (Russian Federation)

    2016-11-15

    The probabilities for E2 transitions between low-lying excited 3{sup −} and 5{sup −} single-phonon states in the {sup 208}Pb and {sup 132}Sn magic nuclei are estimated on the basis of the theory of finite Fermi systems. The approach used involves a new type of ground-state correlations, that which originates from integration of three (rather than two, as in the random-phase approximation) single-particle Green’s functions. These correlations are shown to make a significant contribution to the probabilities for the aforementioned transitions.

  8. TRANSITING THE SUN. II. THE IMPACT OF STELLAR ACTIVITY ON Lyα TRANSITS

    Energy Technology Data Exchange (ETDEWEB)

    Llama, J.; Shkolnik, E. L., E-mail: joe.llama@lowell.edu [Lowell Observatory, 1400 W Mars Hill Road, Flagstaff, AZ 86001 (United States)

    2016-01-20

    High-energy observations of the Sun provide an opportunity to test the limits of our ability to accurately measure the properties of transiting exoplanets in the presence of stellar activity. Here we insert the transit of a hot Jupiter into continuous disk integrated data of the Sun in Lyα from NASA’s Solar Dynamics Observatory/EVE instrument to assess the impact of stellar activity on the measured planet-to-star radius ratio (R{sub p}/R{sub ⋆}). In 75% of our simulated light curves, we measure the correct radius ratio; however, incorrect values can be measured if there is significant short-term variability in the light curve. The maximum measured value of R{sub p}/R{sub ⋆} is 50% larger than the input value, which is much smaller than the large Lyα transit depths that have been reported in the literature, suggesting that for stars with activity levels comparable to the Sun, stellar activity alone cannot account for these deep transits. We ran simulations without a transit and found that stellar activity cannot mimic the Lyα transit of 55 Cancari b, strengthening the conclusion that this planet has a partially transiting exopshere. We were able to compare our simulations to more active stars by artificially increasing the variability in the Solar Lyα light curve. In the higher variability data, the largest value of R{sub p}/R{sub ⋆} we measured is <3× the input value, which again is not large enough to reproduce the Lyα transit depth reported for the more active stars HD 189733 and GJ 436, supporting the interpretation that these planets have extended atmospheres and possible cometary tails.

  9. Discovering Unique, Low-Energy Transition States Using Evolutionary Molecular Memetic Computing

    DEFF Research Database (Denmark)

    Ellabaan, Mostafa M Hashim; Ong, Y.S.; Handoko, S.D.

    2013-01-01

    be accurately identified through the transition states. Transition states describe the paths of molecular systems in transiting across stable states. In this article, we present the discovery of unique, low-energy transition states and showcase the efficacy of their identification using the memetic computing......In the last few decades, identification of transition states has experienced significant growth in research interests from various scientific communities. As per the transition states theory, reaction paths and landscape analysis as well as many thermodynamic properties of biochemical systems can...... of several state-of-the-art algorithms. Not only did the MMC uncover the largest number of transition states, but it also incurred the least amount of computational costs....

  10. Large-Scale Density Functional Theory Transition State Searching in Enzymes.

    Science.gov (United States)

    Lever, Greg; Cole, Daniel J; Lonsdale, Richard; Ranaghan, Kara E; Wales, David J; Mulholland, Adrian J; Skylaris, Chris-Kriton; Payne, Mike C

    2014-11-06

    Linear-scaling quantum mechanical density functional theory calculations have been applied to study the rearrangement of chorismate to prephenate in large-scale models of the Bacillus subtilis chorismate mutase enzyme. By treating up to 2000 atoms at a consistent quantum mechanical level of theory, we obtain an unbiased, almost parameter-free description of the transition state geometry and energetics. The activation energy barrier is calculated to be lowered by 10.5 kcal mol(-1) in the enzyme, compared with the equivalent reaction in water, which is in good agreement with experiment. Natural bond orbital analysis identifies a number of active site residues that are important for transition state stabilization in chorismate mutase. This benchmark study demonstrates that linear-scaling density functional theory techniques are capable of simulating entire enzymes at the ab initio quantum mechanical level of accuracy.

  11. Transition state theory demonstrated at the micron scale with out-of-equilibrium transport in a confined environment

    DEFF Research Database (Denmark)

    Vestergaard, Christian L.; Mikkelsen, Morten Bo Lindholm; Reisner, Walter

    2016-01-01

    and polymers crossing entropic barriers. Here we apply TST to out-of-equilibrium transport through confined environments: the thermally activated translocation of single DNA molecules over an entropic barrier helped by an external force field. Reaction pathways are effectively one dimensional and so long...... that they are observable in a microscope. Reaction rates are so slow that transitions are recorded on video. We find sharp transition states that are independent of the applied force, similar to chemical bond rupture, as well as transition states that change location on the reaction pathway with the strength...

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

    Science.gov (United States)

    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.

  13. A Stochastic Description of Transition Between Granular Flow States

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Two-dimensional granular flow in a channel with small exit is studied by molecular dynamics simulations. We Erstly define a key area near the exit, which is considered to be the choke area of the system. Then we observe the time variation of the local packing fraction and flow rate in this area for several fixed inflow rate, and find that these quantities change abruptly when the transition from dilute How state to dense Bow state happens. A relationship between the local flow rate and the local packing fraction in the key area is also given. The relationship is a continuous function under the fixed particle number condition, and has the characteristic that the flow rate has a maximum at a moderate packing fraction and the packing fraction is terminated at a high value with negative slope. By use of the relationship, the properties of the How states under the fixed inflow rate condition are discussed in detail, and the discontinuities and the complex time variation behavior observed in the preexisting works are naturally explained by a stochastic process.

  14. Co-operativity in a nanocrystalline solid-state transition

    Science.gov (United States)

    White, Sarah L.; Smith, Jeremy G.; Behl, Mayank; Jain, Prashant K.

    2013-12-01

    Co-operativity is a remarkable phenomenon mostly seen in biology, where initial reaction events significantly alter the propensity of subsequent reaction events, giving rise to a nonlinear tightly regulated synergistic response. Here we have found unique evidence of atomic level co-operativity in an inorganic material. A thousand-atom nanocrystal (NC) of the inorganic solid cadmium selenide exhibits strong positive co-operativity in its reaction with copper ions. A NC doped with a few copper impurities becomes highly prone to be doped even further, driving an abrupt transition of the entire NC to the copper selenide phase, as manifested by a strongly sigmoidal response in optical spectroscopy and electron diffraction measurements. The examples presented here suggest that cooperative phenomena may have an important role in the solid state, especially in the nucleation of new chemical phases, crystal growth, and other materials’ transformations.

  15. Co-operativity in a nanocrystalline solid-state transition.

    Science.gov (United States)

    White, Sarah L; Smith, Jeremy G; Behl, Mayank; Jain, Prashant K

    2013-01-01

    Co-operativity is a remarkable phenomenon mostly seen in biology, where initial reaction events significantly alter the propensity of subsequent reaction events, giving rise to a nonlinear tightly regulated synergistic response. Here we have found unique evidence of atomic level co-operativity in an inorganic material. A thousand-atom nanocrystal (NC) of the inorganic solid cadmium selenide exhibits strong positive co-operativity in its reaction with copper ions. A NC doped with a few copper impurities becomes highly prone to be doped even further, driving an abrupt transition of the entire NC to the copper selenide phase, as manifested by a strongly sigmoidal response in optical spectroscopy and electron diffraction measurements. The examples presented here suggest that cooperative phenomena may have an important role in the solid state, especially in the nucleation of new chemical phases, crystal growth, and other materials' transformations.

  16. Transition State Theory for dissipative systems without a dividing surface

    CERN Document Server

    Revuelta, F; Benito, R M; Borondo, F

    2015-01-01

    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 Letter, 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.

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

    Science.gov (United States)

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

    2017-08-18

    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.

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

    Science.gov (United States)

    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.

  19. 34 CFR 300.704 - State-level activities.

    Science.gov (United States)

    2010-07-01

    ... certify to the Secretary that the arrangements to establish responsibility for services pursuant to... transition of students with disabilities to postsecondary activities; (vii) To assist LEAs in meeting... State Medicaid program under Title XIX of the Social Security Act. (9) Funds reserved under paragraph...

  20. Transition state structure of arginine kinase: implications for catalysis of bimolecular reactions.

    Science.gov (United States)

    Zhou, G; Somasundaram, T; Blanc, E; Parthasarathy, G; Ellington, W R; Chapman, M S

    1998-07-21

    Arginine kinase belongs to the family of enzymes, including creatine kinase, that catalyze the buffering of ATP in cells with fluctuating energy requirements and that has been a paradigm for classical enzymological studies. The 1.86-A resolution structure of its transition-state analog complex, reported here, reveals its active site and offers direct evidence for the importance of precise substrate alignment in the catalysis of bimolecular reactions, in contrast to the unimolecular reactions studied previously. In the transition-state analog complex studied here, a nitrate mimics the planar gamma-phosphoryl during associative in-line transfer between ATP and arginine. The active site is unperturbed, and the reactants are not constrained covalently as in a bisubstrate complex, so it is possible to measure how precisely they are pre-aligned by the enzyme. Alignment is exquisite. Entropic effects may contribute to catalysis, but the lone-pair orbitals are also aligned close enough to their optimal trajectories for orbital steering to be a factor during nucleophilic attack. The structure suggests that polarization, strain toward the transition state, and acid-base catalysis also contribute, but, in contrast to unimolecular enzyme reactions, their role appears to be secondary to substrate alignment in this bimolecular reaction.

  1. Virtual Screening for Transition State Analogue Inhibitors of IRAP Based on Quantum Mechanically Derived Reaction Coordinates.

    Science.gov (United States)

    Svensson, Fredrik; Engen, Karin; Lundbäck, Thomas; Larhed, Mats; Sköld, Christian

    2015-09-28

    Transition state and high energy intermediate mimetics have the potential to be very potent enzyme inhibitors. In this study, a model of peptide hydrolysis in the active site of insulin-regulated aminopeptidase (IRAP) was developed using density functional theory calculations and the cluster approach. The 3D structure models of the reaction coordinates were used for virtual screening to obtain new chemical starting points for IRAP inhibitors. This mechanism-based virtual screening process managed to identify several known peptidase inhibitors from a library of over 5 million compounds, and biological testing identified one compound not previously reported as an IRAP inhibitor. This novel methodology for virtual screening is a promising approach to identify new inhibitors mimicking key transition states or intermediates of an enzymatic reaction.

  2. From 3-geometry transition amplitudes to graviton states

    CERN Document Server

    Mattei, F; Speziale, S; Testa, M; Mattei, Federico; Rovelli, Carlo; Speziale, Simone; Testa, Massimo

    2006-01-01

    In various background independent approaches, quantum gravity is defined in terms of a field propagation kernel: a sum over paths interpreted as a transition amplitude between 3-geometries, expected to project quantum states of the geometry on the solutions of the Wheeler-DeWitt equation. We study the relation between this formalism and conventional quantum field theory methods. We consider the propagation kernel of 4d Lorentzian general relativity in the temporal gauge, defined by a conventional formal Feynman path integral, gauge fixed a' la Fadeev--Popov. If space is compact, this turns out to depend only on the initial and final 3--geometries, while in the asymptotically flat case it depends also on the asymptotic proper time. We compute the explicit form of this kernel at first order around flat space, and show that it projects on the solutions of all quantum constraints, including the Wheeler-DeWitt equation, and yields the correct vacuum and n-graviton states. We also illustrate how the Newtonian inter...

  3. From 3-geometry transition amplitudes to graviton states

    Science.gov (United States)

    Mattei, Federico; Rovelli, Carlo; Speziale, Simone; Testa, Massimo

    2006-04-01

    In various background independent approaches, quantum gravity is defined in terms of a field propagation kernel: a sum over paths interpreted as a transition amplitude between 3-geometries, expected to project quantum states of the geometry on the solutions of the Wheeler-deWitt equation. We study the relation between this formalism and conventional quantum field theory methods. We consider the propagation kernel of 4d Lorentzian general relativity in the temporal gauge, defined by a conventional formal Feynman path integral, gauge fixed à la Faddeev-Popov. If space is compact, this turns out to depend only on the initial and final 3-geometries, while in the asymptotically flat case it depends also on the asymptotic proper time. We compute the explicit form of this kernel at first order around flat space, and show that it projects on the solutions of all quantum constraints, including the Wheeler-DeWitt equation, and yields the correct vacuum and n-graviton states. We also illustrate how the Newtonian interaction is coded into the propagation kernel, a key open issue in the spinfoam approach.

  4. Equation of State and the Finite Temperature Transition in QCD

    CERN Document Server

    Gupta, Rajan

    2009-01-01

    This talk provides a summary of the results obtained by the HotQCD collaboration on the equation of state and the crossover transition in 2+1 flavor QCD. We investigate bulk thermodynamic quantities - energy density, pressure, entropy density, and the speed of sound over the temperature range 140 < T < 540 MeV. These results have been obtained on lattices of temporal size N_tau = 6 and 8 and with two improved staggered fermion actions, asqtad and p4. Our most extensive results are with masses of the two degenerate light quarks set at m_l = 0.1 m_s corresponding to the Goldstone pion mass m_pi between 220-260 MeV. In these simulations, the strange quark mass is tuned to its physical value and constant values of m_l/m_s define lines of constant physics. We also summarize the current state of results on observables sensitive to the chiral and deconfining physics -- the light and strange quark number susceptibilities, the chiral condensate and its susceptibility, and the renormalized Polyakov loop. Our resu...

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

    Science.gov (United States)

    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).

  6. Analysis of the chloroplast protein kinase Stt7 during state transitions.

    Directory of Open Access Journals (Sweden)

    Sylvain Lemeille

    2009-03-01

    Full Text Available State transitions allow for the balancing of the light excitation energy between photosystem I and photosystem II and for optimal photosynthetic activity when photosynthetic organisms are subjected to changing light conditions. This process is regulated by the redox state of the plastoquinone pool through the Stt7/STN7 protein kinase required for phosphorylation of the light-harvesting complex LHCII and for the reversible displacement of the mobile LHCII between the photosystems. We show that Stt7 is associated with photosynthetic complexes including LHCII, photosystem I, and the cytochrome b6f complex. Our data reveal that Stt7 acts in catalytic amounts. We also provide evidence that Stt7 contains a transmembrane region that separates its catalytic kinase domain on the stromal side from its N-terminal end in the thylakoid lumen with two conserved Cys that are critical for its activity and state transitions. On the basis of these data, we propose that the activity of Stt7 is regulated through its transmembrane domain and that a disulfide bond between the two lumen Cys is essential for its activity. The high-light-induced reduction of this bond may occur through a transthylakoid thiol-reducing pathway driven by the ferredoxin-thioredoxin system which is also required for cytochrome b6f assembly and heme biogenesis.

  7. Transition states and modeling for Co9S8/MoS 2 catalysis

    Science.gov (United States)

    Gonzalez, Gabriel Angel

    Transition state computational studies of the sulfur removal from dibenzothiophene (DBT) molecule have herein been performed considering the Co9S8/MoS2 interface existing on unsupported Co/MoS2 catalysts. The linear synchronous transit (LST) and quadratic synchronous transit (QST) methods integrated in a density functional theory (DFT) program such as Dmol3 were used for the calculations of energy barriers of the transition states. Three different configurations present on the Co9S8/MoS2 interface have been envisaged as possible catalytic sites: sulfur-sulfur (S, S) sites, and molybdenum-sulfur (Mo, S) and molybdenum-molybdenum (Mo, Mo) edge sites. This study revealed that the (Mo, Mo) edge site is the most catalytically active site for the hydrodesulfurization (HDS) reaction followed by the (Mo, S) edge site while the (S, S) site shows almost inertness for the HDS reaction. This information allows us to propose clues to design new catalysts based on bulk Co9S8/MoS2 phases with higher efficiency by increasing the proportion of (Mo, Mo) edge sites.

  8. Increased firing irregularity as an emergent property of neural-state transition in monkey prefrontal cortex.

    Science.gov (United States)

    Sakamoto, Kazuhiro; Katori, Yuichi; Saito, Naohiro; Yoshida, Shun; Aihara, Kazuyuki; Mushiake, Hajime

    2013-01-01

    Flexible behaviors are organized by complex neural networks in the prefrontal cortex. Recent studies have suggested that such networks exhibit multiple dynamical states, and can switch rapidly from one state to another. In many complex systems such as the brain, the early-warning signals that may predict whether a critical threshold for state transitions is approaching are extremely difficult to detect. We hypothesized that increases in firing irregularity are a crucial measure for predicting state transitions in the underlying neuronal circuits of the prefrontal cortex. We used both experimental and theoretical approaches to test this hypothesis. Experimentally, we analyzed activities of neurons in the prefrontal cortex while monkeys performed a maze task that required them to perform actions to reach a goal. We observed increased firing irregularity before the activity changed to encode goal-to-action information. Theoretically, we constructed theoretical generic neural networks and demonstrated that changes in neuronal gain on functional connectivity resulted in a loss of stability and an altered state of the networks, accompanied by increased firing irregularity. These results suggest that assessing the temporal pattern of neuronal fluctuations provides important clues regarding the state stability of the prefrontal network. We also introduce a novel scheme that the prefrontal cortex functions in a metastable state near the critical point of bifurcation. According to this scheme, firing irregularity in the prefrontal cortex indicates that the system is about to change its state and the flow of information in a flexible manner, which is essential for executive functions. This metastable and/or critical dynamical state of the prefrontal cortex may account for distractibility and loss of flexibility in the prefrontal cortex in major mental illnesses such as schizophrenia.

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

    Institute of Scientific and Technical Information of China (English)

    SUN YouMin; WU JunSen; LIU ChengBu

    2007-01-01

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

  10. Studies of transition states and radicals by negative ion photodetachment

    Energy Technology Data Exchange (ETDEWEB)

    Metz, R.B.

    1991-12-01

    Negative ion photodetachment is a versatile tool for the production and study of transient neutral species such as reaction intermediates and free radicals. Photodetachment of the stable XHY{sup {minus}} anion provides a direct spectroscopic probe of the transition state region of the potential energy surface for the neutral hydrogen transfer reaction X + HY {yields} XH + Y, where X and Y are halogen atoms. The technique is especially sensitive to resonances, which occur at a specific energy, but the spectra also show features due to direct scattering. We have used collinear adiabatic simulations of the photoelectron spectra to evaluate trail potential energy surfaces for the biomolecular reactions and have extended the adiabatic approach to three dimensions and used it to evaluate empirical potential energy surfaces for the I + Hl and Br + HI reactions. In addition, we have derived an empirical, collinear potential energy surface for the Br + HBr reaction that reproduces our experimental results and have extended this surface to three dimensions. Photodetachment of a negative ion can be also used to study neutral free radicals. We have studied the vibrational and electronic spectroscopy of CH{sub 2}NO{sub 2} by photoelectron spectroscopy of CH{sub 2}NO{sub 2}{sup {minus}}, determining the electron affinity of CH{sub 2}NO{sub 2}, gaining insight on the bonding of the {sup 2}B{sub 1} ground state and observing the {sup 2}A{sub 2} excited state for the first time. Negative ion photodetachment also provides a novel and versatile source of mass-selected, jet-cooled free radicals. We have studied the photodissociation of CH{sub 2}NO{sub 2} at 270, 235, and 208 nm, obtaining information on the dissociation products by measuring the kinetic energy release in the photodissociation.

  11. Studies of transition states and radicals by negative ion photodetachment

    Energy Technology Data Exchange (ETDEWEB)

    Metz, R.B.

    1991-12-01

    Negative ion photodetachment is a versatile tool for the production and study of transient neutral species such as reaction intermediates and free radicals. Photodetachment of the stable XHY{sup {minus}} anion provides a direct spectroscopic probe of the transition state region of the potential energy surface for the neutral hydrogen transfer reaction X + HY {yields} XH + Y, where X and Y are halogen atoms. The technique is especially sensitive to resonances, which occur at a specific energy, but the spectra also show features due to direct scattering. We have used collinear adiabatic simulations of the photoelectron spectra to evaluate trail potential energy surfaces for the biomolecular reactions and have extended the adiabatic approach to three dimensions and used it to evaluate empirical potential energy surfaces for the I + Hl and Br + HI reactions. In addition, we have derived an empirical, collinear potential energy surface for the Br + HBr reaction that reproduces our experimental results and have extended this surface to three dimensions. Photodetachment of a negative ion can be also used to study neutral free radicals. We have studied the vibrational and electronic spectroscopy of CH{sub 2}NO{sub 2} by photoelectron spectroscopy of CH{sub 2}NO{sub 2}{sup {minus}}, determining the electron affinity of CH{sub 2}NO{sub 2}, gaining insight on the bonding of the {sup 2}B{sub 1} ground state and observing the {sup 2}A{sub 2} excited state for the first time. Negative ion photodetachment also provides a novel and versatile source of mass-selected, jet-cooled free radicals. We have studied the photodissociation of CH{sub 2}NO{sub 2} at 270, 235, and 208 nm, obtaining information on the dissociation products by measuring the kinetic energy release in the photodissociation.

  12. Long-Lived Intermediates in a Cooperative Two-State Folding Transition.

    Science.gov (United States)

    El-Baba, Tarick J; Kim, Doyong; Rogers, Dylan B; Khan, Faizan A; Hales, David A; Russell, David H; Clemmer, David E

    2016-12-01

    Biomolecular folding often occurs through a cooperative two-state reactant ↔ product transition; the term cooperative does not convey that intermediate structures are nonexistent but rather that these states are not observable by existing experimental techniques. Because of this, few intermediates have been studied and characterized. Recently, ion mobility spectrometry (IMS) measurements revealed that the oligomer polyproline-13 (Pro13, which in propanol (PrOH) favors the right-handed helical PPI structure having adjacent pyrrolidine rings in a cis configuration) folds through six sequential long-lived intermediates as it converts to the all-trans-configured PPII structure that is favored in aqueous solutions. Here, we examine the PPIPrOH → PPIIaq folding transition for a HisPro13 sequence, i.e., Pro13 having a single histidine residue added to the N-terminus. Remarkably, the IMS measurements show that, upon addition of histidine, all of the IMS peaks associated with intermediate structures disappear. Instead, HisPro13 folds via a cooperative two-state transition, delayed by a significant induction period. The induction period is temperature dependent-shifting the transition to longer times at lower temperatures. Equilibrium studies show that the HisPro13 PPIPrOH → PPIIaq transition is endothermic but favored entropically. From these clues, we propose a sequential folding mechanism and develop a model that suggests that ∼13-17 long-lived intermediates are likely responsible for the induction period. In this model, intermediates are separated by average individual activation barriers of ∼90 kJ·mol(-1), and are entropically favorable.

  13. Transiting the Sun: The impact of stellar activity on X-ray and ultraviolet transits

    CERN Document Server

    Llama, J

    2015-01-01

    Transits of hot Jupiters in X-rays and the ultraviolet have been shown to be both deeper and more variable than the corresponding optical transits. This variability has been attributed to hot Jupiters having extended atmospheres at these wavelengths. Using resolved images of the Sun from NASA's Solar Dynamics Observatory spanning 3.5 years of Solar Cycle 24 we simulate transit light curves of a hot Jupiter to investigate the impact of Solar like activity on our ability to reliably recover properties of the planet's atmosphere in soft X-rays (94 {\\AA}), the UV (131-1700 {\\AA}), and the optical (4500 {\\AA}). We find that for stars with similar activity levels to the Sun, the impact of stellar activity results in the derived radius of the planet in soft X-ray/EUV to be underestimated by up-to 25% or overestimated by up-to 50% depending on whether the planet occults active regions. We also find that in up-to 70% of the X-ray light curves the planet transits over bright star spots. In the far ultraviolet (1600 &am...

  14. Transiting the Sun II: The impact of stellar activity on Lyman-$\\alpha$ transits

    CERN Document Server

    Llama, J

    2015-01-01

    High-energy observations of the Sun provide an opportunity to test the limits of our ability to accurately measure properties of transiting exoplanets in the presence of stellar activity. Here we insert transits of a hot Jupiter into continuous disk integrated data of the Sun in Lyman-alpha (Ly$\\alpha$) from NASA's SDO/EVE instrument to assess the impact of stellar activity on the measured planet-to-star radius ratio $(\\textrm{R}_\\textrm{p}/\\textrm{R}_\\star)$. In 75% of our simulated light curves we measure the correct radius ratio; however, incorrect values can be measured if there is significant short term variability in the light curve. The maximum measured value of $(\\textrm{R}_\\textrm{p}/\\textrm{R}_\\star)$ is $50\\%$ larger than the input value, which is much smaller than the large Ly$\\alpha$ transit depths that have been reported in the literature, suggesting that for stars with activity levels comparable to the Sun, stellar activity alone cannot account for these deep transits. We ran simulations withou...

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

    Science.gov (United States)

    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.

  16. Active Life Expectancy and Functional Health Transition among Filipino Older People

    Directory of Open Access Journals (Sweden)

    Grace T. Cruz

    2007-12-01

    Full Text Available The study provides a baseline information on the functional health transition patterns of older people and computes for the Active Life Expectancy (ALE using a multistate life table method. Findings on ALE demonstrate that females and urban residents live longer and have a greater proportion of their remaining life in active state compared to their counterparts. Health transition analysis indicates a significant proportion experiencing recovery. Age, sex, place of residence and health status/behavior indicators (self-assessed health, drinking and exercise display a significant influence on future health and mortality trajectories although surprisingly, education did not show any significant effect.

  17. Modelling transition states of a small once-through boiler

    Energy Technology Data Exchange (ETDEWEB)

    Talonpoika, T. [Lappeenranta Univ. of Technology (Finland). Dept. of Energy Technology

    1997-12-31

    This article presents a model for the unsteady dynamic behaviour of a once-through counter flow boiler that uses an organic working fluid. The boiler is a compact waste-heat boiler without a furnace and it has a preheater, a vaporiser and a superheater. The relative lengths of the boiler parts vary with the operating conditions since they are all parts of a single tube. The boiler model is presented using a selected example case that uses toluene as the process fluid and flue gas from natural gas combustion as the heat source. The dynamic behaviour of the boiler means transition from the steady initial state towards another steady state that corresponds to the changed process conditions. The solution method chosen is to find such a pressure of the process fluid that the mass of the process fluid in the boiler equals the mass calculated using the mass flows into and out of the boiler during a time step, using the finite difference method. A special method of fast calculation of the thermal properties is used, because most of the calculation time is spent in calculating the fluid properties. The boiler is divided into elements. The values of the thermodynamic properties and mass flows are calculated in the nodes that connect the elements. Dynamic behaviour is limited to the process fluid and tube wall, and the heat source is regarded as to be steady. The elements that connect the preheater to the vaporiser and the vaporiser to the superheater are treated in a special way that takes into account a flexible change from one part to the other. The initial state of the boiler is received from a steady process model that is not a part of the boiler model. The known boundary values that may vary during the dynamic calculation were the inlet temperature and mass flow rates of both the heat source fluid and the process fluid. The dynamic boiler model is analysed for linear and step charges of the entering fluid temperatures and flow rates. The heat source side tests show that

  18. Traffic model with an absorbing-state phase transition

    Science.gov (United States)

    Iannini, M. L. L.; Dickman, Ronald

    2017-02-01

    We consider a modified Nagel-Schreckenberg (NS) model in which drivers do not decelerate if their speed is smaller than the headway (number of empty sites to the car ahead). (In the original NS model, such a reduction in speed occurs with probability p , independent of the headway, as long as the current speed is greater than zero.) In the modified model the free-flow state (with all vehicles traveling at the maximum speed, vmax) is absorbing for densities ρ smaller than a critical value ρc=1 /(vmax+2 ) . The phase diagram in the ρ -p plane is reentrant: for densities in the range ρc ,<<ρ <ρc , both small and large values of p favor free flow, while for intermediate values, a nonzero fraction of vehicles have speeds transition in the original model. Our results suggest an unexpected connection between traffic models and stochastic sandpiles.

  19. A traffic model with an absorbing-state phase transition

    CERN Document Server

    Iannini, M L L

    2016-01-01

    We consider a modified Nagel-Schreckenberg (NS) model in which drivers do not decelerate if their speed is smaller than the headway (number of empty sites to the car ahead). (In the original NS model, such a reduction in speed occurs with probability $p$, independent of the headway, as long as the current speed is greater than zero.) In the modified model the free-flow state (with all vehicles traveling at the maximum speed, $v_{max}$) is {\\it absorbing} for densities $\\rho$ smaller than a critical value $\\rho_c = 1/(v_{max} + 2)$. The phase diagram in the $\\rho - p$ plane is reentrant: for densities in the range $\\rho_{c,<} < \\rho < \\rho_c$, both small and large values of $p$ favor free flow, while for intermediate values, a nonzero fraction of vehicles have speeds $< v_{max}$. In addition to representing a more realistic description of driving behavior, this change leads to a better understanding of the phase transition in the original model. Our results suggest an unexpected connection between ...

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

    Science.gov (United States)

    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.

  1. Iterative minimization algorithm for efficient calculations of transition states

    Science.gov (United States)

    Gao, Weiguo; Leng, Jing; Zhou, Xiang

    2016-03-01

    This paper presents an efficient algorithmic implementation of the iterative minimization formulation (IMF) for fast local search of transition state on potential energy surface. The IMF is a second order iterative scheme providing a general and rigorous description for the eigenvector-following (min-mode following) methodology. We offer a unified interpretation in numerics via the IMF for existing eigenvector-following methods, such as the gentlest ascent dynamics, the dimer method and many other variants. We then propose our new algorithm based on the IMF. The main feature of our algorithm is that the translation step is replaced by solving an optimization subproblem associated with an auxiliary objective function which is constructed from the min-mode information. We show that using an efficient scheme for the inexact solver and enforcing an adaptive stopping criterion for this subproblem, the overall computational cost will be effectively reduced and a super-linear rate between the accuracy and the computational cost can be achieved. A series of numerical tests demonstrate the significant improvement in the computational efficiency for the new algorithm.

  2. Classical trajectory simulations of post-transition state dynamics

    Science.gov (United States)

    Lourderaj, Upakarasamy; Park, Kyoyeon; Hase, William L.

    Classical chemical dynamics simulations of post-transition state dynamics are reviewed. Most of the simulations involve direct dynamics for which the potential energy and gradient are obtained directly from an electronic structure theory. The chemical reaction attributes and chemical systems presented are product energy partitioning for Cl- ··· CH3Br → ClCH3 + Br- and C2H5F → C2H4 + HF dissociation, non-RRKM dynamics for cyclopropane stereomutation and the Cl- ··· CH3Cl complexes mediating the Cl- + CH3Cl SN2 nucleophilic substitution reaction, and non-IRC dynamics for the OH- + CH3F and F- + CH3OOH chemical reactions. These studies illustrate the important role of chemical dynamics simulations in understanding atomic-level reaction dynamics and interpreting experiments. They also show that widely used paradigms and model theories for interpreting reaction kinetics and dynamics are often inaccurate and are not applicable.

  3. Transition-state theory predicts clogging at the microscale

    Science.gov (United States)

    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.

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

    CERN Document Server

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

    2014-01-01

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

  5. Time delay between cardiac and brain activity during sleep transitions

    Science.gov (United States)

    Long, Xi; Arends, Johan B.; Aarts, Ronald M.; Haakma, Reinder; Fonseca, Pedro; Rolink, Jérôme

    2015-04-01

    Human sleep consists of wake, rapid-eye-movement (REM) sleep, and non-REM (NREM) sleep that includes light and deep sleep stages. This work investigated the time delay between changes of cardiac and brain activity for sleep transitions. Here, the brain activity was quantified by electroencephalographic (EEG) mean frequency and the cardiac parameters included heart rate, standard deviation of heartbeat intervals, and their low- and high-frequency spectral powers. Using a cross-correlation analysis, we found that the cardiac variations during wake-sleep and NREM sleep transitions preceded the EEG changes by 1-3 min but this was not the case for REM sleep transitions. These important findings can be further used to predict the onset and ending of some sleep stages in an early manner.

  6. Dynamics of transitions between capillary stable states under weightlessness

    Science.gov (United States)

    Srikanth, Praveen

    The study of two phase systems with one of the phases obstructing the other is of importance in a lot of fields. Liquid droplets in airways and air bubbles in the blood stream both fall under this category of problems. Helium bubbles in hydrazine fuel lines of satellites also have been found to cause frequent thruster shutdown and also seriously affect spacecraft control. Studies have been carried out until now to look at static equilibrium topologies and stability of such two phase systems in straight, bent and laterally compressed capillaries. In this investigation we look at the dynamics of the transitions between the stable topologies identified for a straight cylindrical capillary. The break up of the interface could adversely affect system performance. OpenFOAM is used to compute transitions from a stable droplet to a plug or the reverse by suitably adding or removing the obstructing phase through inlet patches on the wall of the cylinder. The main parameters presented are the non-dimensional energy, non-dimensional transition times, non-dimensional transition volumes and the general dynamics of the transitions itself. Before computing transitions the static equilibrium topologies computed by OpenFOAM are compared with those predicted by Surface Evolver and are found to be within acceptable deviations. The grid dependence of these transitions has also been studied. Transitions are computed for contact angles in the range of 10° to 170°. Different modes of transitions are observed depending on the contact angle of the case for both the types of transitions. The transition volumes are compared to the volume of existence limits for the corresponding initial topology at a particular contact angle for both the transitions.

  7. Liquid-Gas Phase Transition in Nuclear Equation of State

    CERN Document Server

    Lee, S J

    1997-01-01

    A canonical ensemble model is used to describe a caloric curve of nuclear liquid-gas phase transition. Allowing a discontinuity in the freeze out density from one spinodal density to another for a given initial temperature, the nuclear liquid-gas phase transition can be described as first order. Averaging over various freeze out densities of all the possible initial temperatures for a given total reaction energy, the first order characteristics of liquid-gas phase transition is smeared out to a smooth transition. Two experiments, one at low beam energy and one at high beam energy show different caloric behaviors and are discussed.

  8. Modeling Enzymatic Transition States by Force Field Methods

    DEFF Research Database (Denmark)

    Hansen, Mikkel Bo; Jensen, Hans Jørgen Aagaard; Jensen, Frank

    2009-01-01

    The SEAM method, which models a transition structure as a minimum on the seam of two diabatic surfaces represented by force field functions, has been used to generate 20 transition structures for the decarboxylation of orotidine by the orotidine-5'-monophosphate decarboxylase enzyme. The dependence...

  9. Innovation Activities of Industrial Enterprises in Market and Transition Economies

    OpenAIRE

    Zhuravskaya, E.G.; Gracheva, M.V.

    1994-01-01

    The purpose of this paper is to make an overview of the recent economic tendency surveys as the source of information on enterprises' innovation activities in market and transition economies. The introductory section focuses on innovation theory as the basis of currently conducted innovation tests. The second and third sections are devoted to the analysis of changes in innovation activities of West and East German enterprises reflected in the results of regular surveys. The fourth section exa...

  10. Influence of transitional states on the microbial ecology of anaerobic digesters treating solid wastes.

    Science.gov (United States)

    Regueiro, Leticia; Veiga, Patricia; Figueroa, Mónica; Lema, Juan M; Carballa, Marta

    2014-03-01

    A better understanding of the microbial ecology of anaerobic processes during transitional states is important to achieve a long-term efficient reactor operation. Five wastes (pig manure, biodiesel residues, ethanol stillage, molasses residues, and fish canning waste) were treated in five anaerobic reactors under the same operational conditions. The influence of the type of substrate and the effect of modifying feeding composition on the microbial community structure was evaluated. The highest biomethanation efficiency was observed in reactors fed with fish canning waste, which also presented the highest active archaeal population and the most diverse microbial communities. Only two Bacteria populations could be directly related to a particular substrate: Ilyobacter with biodiesel residues and Trichococcus with molasses residues. Results showed that the time to achieve steady-state performance after these transitional states was not dependent on the substrate treated. But reactors needed more time to handle the stress conditions derived from the start-up compared to the adaptation to a new feeding. Cluster analyses showed that the type of substrate had a clear influence on the microbiology of the reactors, and that segregation was related to the reactors performance. Finally, we conclude that the previous inoculum history treating solid waste and higher values of active Archaea population are important factors to face a successful change in substrate not entailing stability failure.

  11. A transition-state interaction shifts nucleobase ionization toward neutrality to facilitate small ribozyme catalysis.

    Science.gov (United States)

    Liberman, Joseph A; Guo, Man; Jenkins, Jermaine L; Krucinska, Jolanta; Chen, Yuanyuan; Carey, Paul R; Wedekind, Joseph E

    2012-10-17

    One mechanism by which ribozymes can accelerate biological reactions is by adopting folds that favorably perturb nucleobase ionization. Herein we used Raman crystallography to directly measure pK(a) values for the Ade38 N1 imino group of a hairpin ribozyme in distinct conformational states. A transition-state analogue gave a pK(a) value of 6.27 ± 0.05, which agrees strikingly well with values measured by pH-rate analyses. To identify the chemical attributes that contribute to the shifted pK(a), we determined crystal structures of hairpin ribozyme variants containing single-atom substitutions at the active site and measured their respective Ade38 N1 pK(a) values. This approach led to the identification of a single interaction in the transition-state conformation that elevates the base pK(a) > 0.8 log unit relative to the precatalytic state. The agreement of the microscopic and macroscopic pK(a) values and the accompanying structural analysis supports a mechanism in which Ade38 N1(H)+ functions as a general acid in phosphodiester bond cleavage. Overall the results quantify the contribution of a single electrostatic interaction to base ionization, which has broad relevance for understanding how RNA structure can control chemical reactivity.

  12. Maximizing power saving with state transition overhead for multiple mobile subscriber stations in WiMAX

    Institute of Scientific and Technical Information of China (English)

    Bo LI; Sung-kwon PARK

    2016-01-01

    In the IEEE 802.16e/m standard, three power saving classes (PSCs) are defined to save the energy of a mobile sub-scriber station (MSS). However, how to set the parameters of PSCs to maximize the power saving and guarantee the quality of service is not specified in the standard. Thus, many algorithms were proposed to set the PSCs in IEEE 802.16 networks. However, most of the proposed algorithms consider only the power saving for a single MSS. In the algorithms designed for multiple MSSs, the sleep state, which is set for activation of state transition overhead power, is not considered. The PSC setting for real-time connections in multiple MSSs with consideration of the state transition overhead is studied. The problem is non-deterministic polynomial time hard (NP-hard), and a suboptimal algorithm for the problem is proposed. Simulation results demonstrate that the energy saving of the proposed algorithm is higher than that of state-of-the-art algorithms and approaches the optimum limit.

  13. Microalloying of transition metal silicides by mechanical activation and field-activated reaction

    Energy Technology Data Exchange (ETDEWEB)

    Munir, Zuhair A. (Davis, CA); Woolman, Joseph N. (Davis, CA); Petrovic, John J. (Los Alamos, NM)

    2003-09-02

    Alloys of transition metal suicides that contain one or more alloying elements are fabricated by a two-stage process involving mechanical activation as the first stage and densification and field-activated reaction as the second stage. Mechanical activation, preferably performed by high-energy planetary milling, results in the incorporation of atoms of the alloying element(s) into the crystal lattice of the transition metal, while the densification and field-activated reaction, preferably performed by spark plasma sintering, result in the formation of the alloyed transition metal silicide. Among the many advantages of the process are its ability to accommodate materials that are incompatible in other alloying methods.

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

    Science.gov (United States)

    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...

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

    Science.gov (United States)

    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.

  16. On the way of classifying new states of active matter

    Science.gov (United States)

    Menzel, Andreas M.

    2016-07-01

    With ongoing research into the collective behavior of self-propelled particles, new states of active matter are revealed. Some of them are entirely based on the non-equilibrium character and do not have an immediate equilibrium counterpart. In their recent work, Romanczuk et al (2016 New J. Phys. 18 063015) concentrate on the characterization of smectic-like states of active matter. A new type, referred to by the authors as smectic P, is described. In this state, the active particles form stacked layers and self-propel along them. Identifying and classifying states and phases of non-equilibrium matter, including the transitions between them, is an up-to-date effort that will certainly extend for a longer period into the future.

  17. Ab initio transition dipole moments and potential energy curves for the low-lying electronic states of CaH

    Science.gov (United States)

    Shayesteh, Alireza; Alavi, S. Fatemeh; Rahman, Moloud; Gharib-Nezhad, Ehsan

    2017-01-01

    Ab initio potential energy curves have been calculated for the X2Σ+, A2Π, B2Σ+, 12Δ, E2Π and D2Σ+ states of CaH using the multi-reference configuration interaction method with large active space and basis sets. Transition dipole moments were calculated at Ca-H distances from 2.0 a0 to 14.0 a0, and excited state lifetimes were obtained. Our theoretical transition dipole moments can be combined with the available experimental data on the X2Σ+, A2Π and B2Σ+ states to calculate Einstein A coefficients for all rovibronic transitions of CaH appearing in solar and stellar spectra.

  18. EVOLUTIONARY TRANSITIONS IN ENZYME ACTIVITY OF ANT FUNGUS GARDENS

    DEFF Research Database (Denmark)

    De Fine Licht, Henrik H; Schiøtt, Morten; Mueller, Ulrich G

    2010-01-01

    Fungus-growing (attine) ants and their fungal symbionts passed through several evolutionary transitions during their 50 million year old evolutionary history. The basal attine lineages often shifted between two main cultivar clades, whereas the derived higher-attine lineages maintained an associa......Fungus-growing (attine) ants and their fungal symbionts passed through several evolutionary transitions during their 50 million year old evolutionary history. The basal attine lineages often shifted between two main cultivar clades, whereas the derived higher-attine lineages maintained...... an association with a monophyletic clade of specialized symbionts. In conjunction with the transition to specialized symbionts, the ants advanced in colony size and social complexity. Here we provide a comparative study of the functional specialization in extracellular enzyme activities in fungus gardens across...... the attine phylogeny. We show that, relative to sister clades, gardens of higher-attine ants have enhanced activity of protein-digesting enzymes, whereas gardens of leaf-cutting ants also have increased activity of starch-digesting enzymes. However, the enzyme activities of lower-attine fungus gardens...

  19. Antimycobacterial, antimicrobial activity, experimental (FT-IR, FT-Raman, NMR, UV-Vis, DSC) and DFT (transition state, chemical reactivity, NBO, NLO) studies on pyrrole-isonicotinyl hydrazine.

    Science.gov (United States)

    Rawat, Poonam; Singh, R N; Ranjan, Alok; Ahmad, Sartaj; Saxena, Rajat

    2017-05-15

    As part of a study of pyrrole hydrazone, we have investigated quantum chemical calculations, molecular geometry, relative energy, vibrational properties and antimycobacterial/antimicrobial activity of pyrrole-2-carboxaldehyde isonicotinyl hydrazone (PCINH), by applying the density functional theory (DFT) and Hartree Fock (HF). Good reproduction of experimental values is obtained and with small percentage error in majority of the cases in comparison to theoretical result (DFT). The experimental FT-IR and Raman wavenumbers were compared with the respective theoretical values obtained from DFT calculations and found to agree well. In crystal structure studies the hydrated PCINH (syn-syn conformer) shows different conformation than from anhydrous form (syn-anti conformer). The rotational barrier between syn-syn and syn-anti conformers of PCINH is 12.7kcal/mol in the gas phase. In this work, use of FT-IR, FT-Raman, (1)H NMR, (13)C NMR and UV-Vis spectroscopies has been made for full characterization of PCINH. A detailed interpretation of the vibrational spectrum was carried out with the aid of normal coordinate analysis using single scaling factor. Our results support the hydrogen bonding pattern proposed by reported crystalline structure. The calculated nature of electronic transitions within molecule found to be π→π*. The electronic descriptors study indicates that PCINH can be used as robust synthon for synthesis of new heterocyclic compounds. The first static hyperpolarizability (β0) of PCINH is calculated as 33.89×10(-30)esu, (gas phase); 68.79×10(-30) (CHCl3), esu; 76.76×10(-30)esu (CH2Cl2), 85.16×10(-30)esu (DMSO). The solvent induced effects on the first static hyperpolarizability were studied and found to increase as dielectric constants of the solvents increases. Investigated molecule shows better NLO value than Para nitroaniline (PNA). The compound PCINH shows good antifungal and antibacterial activity against Aspergillus niger and gram

  20. Lithuanian health care in transitional state: ethical problems

    Directory of Open Access Journals (Sweden)

    Žekas Romualdas

    2005-11-01

    Full Text Available Abstract 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

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

    Science.gov (United States)

    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

  2. Gene networks of fully connected triads with complete auto-activation enable multistability and stepwise stochastic transitions.

    Directory of Open Access Journals (Sweden)

    Philippe C Faucon

    Full Text Available Fully-connected triads (FCTs, such as the Oct4-Sox2-Nanog triad, have been implicated as recurring transcriptional motifs embedded within the regulatory networks that specify and maintain cellular states. To explore the possible connections between FCT topologies and cell fate determinations, we employed computational network screening to search all possible FCT topologies for multistability, a dynamic property that allows the rise of alternate regulatory states from the same transcriptional network. The search yielded a hierarchy of FCTs with various potentials for multistability, including several topologies capable of reaching eight distinct stable states. Our analyses suggested that complete auto-activation is an effective indicator for multistability, and, when gene expression noise was incorporated into the model, the networks were able to transit multiple states spontaneously. Different levels of stochasticity were found to either induce or disrupt random state transitioning with some transitions requiring layovers at one or more intermediate states. Using this framework we simulated a simplified model of induced pluripotency by including constitutive overexpression terms. The corresponding FCT showed random state transitioning from a terminal state to the pluripotent state, with the temporal distribution of this transition matching published experimental data. This work establishes a potential theoretical framework for understanding cell fate determinations by connecting conserved regulatory modules with network dynamics. Our results could also be employed experimentally, using established developmental transcription factors as seeds, to locate cell lineage specification networks by using auto-activation as a cipher.

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

    Directory of Open Access Journals (Sweden)

    Chaoqun Li

    2014-03-01

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

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

    Science.gov (United States)

    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 β_{m} of the order parameter is 1/2 under general conditions, while the value of the exponent γ_{m} 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, β_{a} and γ_{a}. These two critical behaviors are coupled by a scaling law: 1-β_{m}=γ_{a}.

  5. The transition from fracton to phonon states in a Sierpinski triangle lattice

    Energy Technology Data Exchange (ETDEWEB)

    Rocha, E.L. da, E-mail: edroaldo@gmail.co [Departamento de Engenharia Eletrica, Universidade Federal de Santa Catarina, Florianopolis-SC 88040-900 (Brazil); Cunha, C.R. da, E-mail: creq@eel.ufsc.b [Departamento de Engenharia Eletrica, Universidade Federal de Santa Catarina, Florianopolis-SC 88040-900 (Brazil)

    2011-04-15

    Research highlights: A Sierpinski triangle was studied with different self-similarity levels and disorder. A transition from fracton to phonon states was observed for low disorder. A second transition was observed from extended to localized phonon states. The transitions correspond to a change in topology in the average density of states. - Abstract: Lattice dynamics of a Sierpinski triangle submitted to different levels of disorder was studied via atomistic Green's functions. It was found that there is a critical level of disorder that separates two regions of thermal transport. The first is characterized by a fast destruction of fracton states and the formation of spatially extended phonon states. The second region is characterized by a transition from extended to localized phonon states as predicted by the Anderson model.

  6. Transition Strength Sums and Quantum Chaos in Shell Model States

    CERN Document Server

    Kota, V K B; Kar, K; Gómez, J M G; Retamosa, J

    2000-01-01

    For the embedded Gaussian orthogonal ensemble (EGOE) of random matrices, the strength sums generated by a transition operator acting on an eigenstate vary with the excitation energy as the ratio of two Gaussians. This general result is compared to exact shell model calculations, with realistic interactions, of spherical orbit occupancies and Gamow-Teller strength sums in some $(ds)$ and $(fp)$ shell examples. In order to confirm that EGOE operates in the chaotic domain of the shell model spectrum, calculations are carried out using two different interpolating hamiltonians generating order-chaos transitions. Good agreement is obtained in the chaotic domain of the spectrum, and strong deviations are observed as nuclear motion approaches a regular regime (transition strength sums appear to follow the Dyson's $\\Delta_3$ statistic). More importantly, they shed new light on the newly emerging understanding that in the chaotic domain of isolated finite interacting many particle systems smoothed densities (they inclu...

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

    Science.gov (United States)

    Holbrook, Joseph D.; Pilliod, David; 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

  8. Model of EF4-induced ribosomal state transitions and mRNA translocation

    Science.gov (United States)

    Xie, Ping

    2014-08-01

    EF4, a highly conserved protein present in bacteria, mitochondria and chloroplasts, can bind to both the posttranslocation and pretranslocation ribosomal complexes. When binding to the posttranslocation state, it catalyzes backward translocation to a pretranslocation state. When binding to the pretranslocation state, it catalyzes transition to another pretranslocation state that is similar and possibly identical to that resulting from the posttranslocation state bound by EF4, and competes with EF-G to regulate the elongation cycle. However, the molecular mechanism on how EF4 induces state transitions and mRNA translocation remains unclear. Here, we present both the model for state transitions induced by EF4 binding to the posttranslocation state and that by EF4 binding to the pretranslocation state, based on which we study the kinetics of EF4-induced state transitions and mRNA translocation, giving quantitative explanations of the available experimental data. Moreover, we present some predicted results on state transitions and mRNA translocation induced by EF4 binding to the pretranslocation state complexed with the mRNA containing a duplex region.

  9. Universality classes of the absorbing state transition in a system with interacting static and diffusive populations.

    Science.gov (United States)

    Argolo, C; Quintino, Yan; Siqueira, Y; Gleria, Iram; Lyra, M L

    2009-12-01

    In this work, we study the critical behavior of a one-dimensional model that mimics the propagation of an epidemic process mediated by a density of diffusive individuals which can infect a static population upon contact. We simulate the above model on linear chains to determine the critical density of the diffusive population, above which the system achieves a statistically stationary active state, as a function of two relevant parameters related to the average lifetimes of the diffusive and nondiffusive populations. A finite-size scaling analysis is employed to determine the order parameter and correlation length critical exponents. For high-recovery rates, the critical exponents are compatible with the usual directed percolation universality class. However, in the opposite regime of low-recovery rates, the diffusion is a relevant mechanism responsible for the propagation of the disease and the absorbing state phase transition is governed by a distinct set of critical exponents.

  10. Decreased replication origin activity in temporal transition regions.

    Science.gov (United States)

    Guan, Zeqiang; Hughes, Christina M; Kosiyatrakul, Settapong; Norio, Paolo; Sen, Ranjan; Fiering, Steven; Allis, C David; Bouhassira, Eric E; Schildkraut, Carl L

    2009-11-30

    In the mammalian genome, early- and late-replicating domains are often separated by temporal transition regions (TTRs) with novel properties and unknown functions. We identified a TTR in the mouse immunoglobulin heavy chain (Igh) locus, which contains replication origins that are silent in embryonic stem cells but activated during B cell development. To investigate which factors contribute to origin activation during B cell development, we systematically modified the genetic and epigenetic status of the endogenous Igh TTR and used a single-molecule approach to analyze DNA replication. Introduction of a transcription unit into the Igh TTR, activation of gene transcription, and enhancement of local histone modifications characteristic of active chromatin did not lead to origin activation. Moreover, very few replication initiation events were observed when two ectopic replication origin sequences were inserted into the TTR. These findings indicate that the Igh TTR represents a repressive compartment that inhibits replication initiation, thus maintaining the boundaries between early and late replication domains.

  11. The activation energy for the FCC rolling texture transition and the activation energy for cross slip

    DEFF Research Database (Denmark)

    Leffers, T.; Pedersen, O.B.

    2002-01-01

    Already in 1968 one of the present authors determined the activation energy for the rolling-texture transition in Cu-5%Zn as a spin off of an investigation of the strain-rate dependence of the rolling texture. In the present work this determination of theactivation energy is explained and discussed...... (whereas very few details were given in the original work), and an error in the original work is corrected. The activation energy for the texture transition is compared with recent values for the activationenergy for cross slip derived from atomic-scale modelling. After adjustment to a stress level...... corresponding to the stress in Cu-5%Zn during heavy rolling the theoretical activation energy for cross slip is pretty close to the activation energy for thetexture transition. It is concluded that the texture transition is governed by cross slip, and the detailed mechanism is discussed....

  12. The Mercury Transit 2016: educational activities from CESAR

    Science.gov (United States)

    Pérez-Ayúcar, Miguel; Breitfelner, Michel

    2017-04-01

    A transit of Mercury in front of the solar disk as seen from Earth is a rare astronomical event which occurs only about every 13-14 times per century. Although its historic scientific importance, e.g. to measure the distances in the solar system, has diminished since humanity roams our solar system with robotic spacecrafts, a Mercury Transit remains a spectacular astronomical event that is used very effectively to engage general public and students to Science and Space in general. The educational project CESAR (Cooperation through Education in Science and Astronomy Research) , working upon previous experience (Venus transit 2012, live Sun transmissions ..), prepared a dual observation of the transit from two separate locations: the CESAR Solar Observatory at ESAC (European Space Astronomy Center), Madrid, Spain, and a twin portable telescope set-up in Cerro Paranal, Chile, achieving a ground baseline parallax of 10.000km. CESAR organized an educational and outreach event in collaboration with several Spanish schools/universities, the ESA Education and Communications offices, the Teide observatory and the ESA projects Bepi Colombo and Solar Orbiter. The driving activity was a continuous 10h interactive Google hangout that connected students in Spain (Ciudad de las Artes y las Ciencias, CAC in Valencia), students in observatories in Chile, the remote observing teams, and scientists at ESAC. Live images were transmitted via a specific web in two bands (h-alpha and visible). Experts in the fields of Solar and Planetary Physics gave presentations related to the Sun and Mercury. Questions and answers sessions were performed so that world-wide audience could interact with the scientists and engineers. In this paper we explain how this public educational and outreach event was created, what activities it comprised, and the follow up activities.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2016-08-01

    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.

  15. Behavior of transition state regulator AbrB in batch cultures of Bacillus thuringiensis.

    Science.gov (United States)

    Lozano Goné, Astrid Magdalena; Dinorín Téllez Girón, Jabel; Jiménez Montejo, Fabiola Eloisa; Hidalgo-Lara, María Eugenia; López Y López, Víctor Eric

    2014-11-01

    The transition state regulator AbrB is involved in the regulation of various cellular functions such as exponential growth, transition state and sporulation onset, due to its ability to activate, suppress or prevent the inappropriate expression of various genes in Bacillus subtilis. In order to understand combined behavior in batch cultures of AbrB in Bacillus thuringiensis, we cloned and expressed the abrB gene of B. thuringiensis in Escherichia coli. The deduced sequence of abrB gene coded for a protein consisting of 94 amino acids with ~10.5 kDa protein that shares 100 and 85 % identity with those from Bacillus cereus and Bacillus subtilis. The recombinant AbrB protein was used as antigen for the production of rabbit polyclonal antibodies anti-AbrB. Two media cultures with carbon: nitrogen ratios of 7.0, but varying access to nutrients were tested in batch cultures. In the case of both media, AbrB accumulation occurred from the beginning of the process and was maximal during early exponential growth. Thereafter, the level of AbrB decreased when there were no nutrient limitations and coincided with a decreased value in specific growth rate, although growth continued exponentially. Nonetheless, sporulation onset was determined 3 h and 4 h later, in media with highly metabolizable nutrients clean medium and Farrera medium, respectively. Hence, the maximal level of AbrB accumulation in batch cultures of B. thuringiensis is not influenced by limiting nutrients; however, nutrient availability affects the required time lapse for transition state regulator accumulation.

  16. Fiscal Federalism in Transition Countries: The Three Baltic States Compared

    NARCIS (Netherlands)

    Groenendijk, Nico; Jaansoo, Annika

    2016-01-01

    This paper analyzes three transition countries (Estonia, Latvia and Lithuania) regarding four essential features of fiscal federalism: (a) the administrative set-up, (b) the tasks and functions allocated to sub-national governments, (c) revenue structure and fiscal autonomy, and (d) fiscal disciplin

  17. Quantum manifestation of systems on the macro-scale – the concept of transition state and transition amplitude wave

    Indian Academy of Sciences (India)

    Ram K Varma

    2007-06-01

    Quantum effects which have usually been associated with micro-scale phenomena can also arise on the macro-scale in situations other than the well-known macro-quantum phenomena of superconductivity and superfluidity. Such situations have been shown here to arise in processes involving inelastic scattering with bound or partially bound systems (not bound in all degrees of freedom), and the macro-quantum behaviour is associated with the state of the total system in transition in the process of scattering. Such a state is designated as a `transition-state'. It is pointed out that we have already observed such manifestations for a particular system, the charged particles in a magnetic field where interference effects involving macro-scale matter waves along the magnetic field have been reported [R K Varma et al, Phys. Rev. E65, 026503 (2002)].

  18. Frozen steady states in active systems

    CERN Document Server

    Schaller, Volker; Hammerich, Benjamin; Frey, Erwin; Bausch, Andreas R

    2011-01-01

    Even simple active systems can show a plethora of intriguing phenomena and often we find complexity were we would have expected simplicity. One striking example is the occurrence of a quiescent or absorbing state with frozen fluctuations that at first sight seems to be impossible for active matter driven by the incessant input of energy. While such states were reported for externally driven systems through macroscopic shear or agitation, the investigation of frozen active states in inherently active systems like cytoskeletal suspensions or active gels is still at large. Using high density motility assay experiments, we demonstrate that frozen steady states can arise in active systems if active transport is coupled to growth processes. The experiments are complemented by agent-based simulations which identify the coupling between self-organization, growth and mechanical properties to be responsible for the pattern formation process.

  19. Spin-state transition in LaCoO3: direct neutron spectroscopic evidence of excited magnetic states.

    Science.gov (United States)

    Podlesnyak, A; Streule, S; Mesot, J; Medarde, M; Pomjakushina, E; Conder, K; Tanaka, A; Haverkort, M W; Khomskii, D I

    2006-12-15

    A gradual spin-state transition occurs in LaCoO3 around T approximately 80-120 K, whose detailed nature remains controversial. We studied this transition by means of inelastic neutron scattering and found that with increasing temperature an excitation at approximately 0.6 meV appears, whose intensity increases with temperature, following 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. We further discuss the nature of the magnetic excited state in terms of intermediate-spin (t(2g)(5)e(g)(1), S=1) versus high-spin (t(2g)(4)e(g)(2), S=2) states. Since the g factor obtained from the field dependence of the inelastic neutron scattering is g approximately 3, the second interpretation is definitely favored.

  20. Study on State Transition Method Applied to Motion Planning for a Humanoid Robot

    Directory of Open Access Journals (Sweden)

    Xuyang Wang

    2008-11-01

    Full Text Available This paper presents an approach of motion planning for a humanoid robot using a state transition method. In this method, motion planning is simplified by introducing a state-space to describe the whole motion series. And each state in the state-space corresponds to a contact state specified during the motion. The continuous motion is represented by a sequence of discrete states. The concept of the transition between two neighboring states, that is the state transition, can be realized by using some traditional path planning methods. Considering the dynamical stability of the robot, a state transition method based on search strategy is proposed. Different sets of trajectories are generated by using a variable 5th-order polynomial interpolation method. After quantifying the stabilities of these trajectories, the trajectories with the largest stability margin are selected as the final state transition trajectories. Rising motion process is exemplified to validate the method and the simulation results show the proposed method to be feasible and effective.

  1. Confinement-deconfinement transition in the algebraic RVB states

    Science.gov (United States)

    Pei, Ji-Quan; Jian, Shao-Kai; Yao, Hong

    2015-03-01

    Deconfined algebraic spin liquids are usually expected when Gutzwiller projecting the non-interacting wave function of half-filled electrons on the square lattice with staggered flux ϕ. However, our large-scale variational Monte Carlo simulations show that there is the confinement-deconfinement transition at ϕ =ϕc where ϕc ~ 0 . 2 is the critical flux. When 0 Gutzwiller projected wave function might be due to the large anisotropy of Fermi velocity of Dirac fermions.

  2. Estimation and asymptotic theory for transition probabilities in Markov Renewal Multi–state models

    NARCIS (Netherlands)

    Spitoni, C.; Verduijn, M.; Putter, H.

    2012-01-01

    In this paper we discuss estimation of transition probabilities for semi–Markov multi–state models. Non–parametric and semi–parametric estimators of the transition probabilities for a large class of models (forward going models) are proposed. Large sample theory is derived using the functional delta

  3. Human P-glycoprotein exhibits reduced affinity for substrates during a catalytic transition state.

    Science.gov (United States)

    Ramachandra, M; Ambudkar, S V; Chen, D; Hrycyna, C A; Dey, S; Gottesman, M M; Pastan, I

    1998-04-01

    Human P-glycoprotein (Pgp), a plasma membrane protein that confers multidrug resistance, functions as an ATP-dependent drug efflux pump. Pgp contains two ATP binding/utilization sites and exhibits ATPase activity that is stimulated in the presence of substrates and modulating agents. The mechanism of coupling of ATP hydrolysis to drug transport is not known. To understand the role of ATP hydrolysis in drug binding, it is necessary to develop methods for purifying and reconstituting Pgp that retains properties including stimulation of ATPase activity by known substrates to an extent similar to that in the native membrane. In this study, (His)6-tagged Pgp was expressed in Trichoplusia ni (High Five) cells using the recombinant baculovirus system and purified by metal affinity chromatography. Upon reconstitution into phospholipid vesicles, purified Pgp exhibited specific binding to analogues of substrates and ATP in affinity labeling experiments and displayed a high level of drug-stimulated ATPase activity (specific activity ranging from 4.5 to 6.5 micromol min-1 mg-1). The ATPase activity was inhibited by ADP in a competitive manner, and by vanadate and N-ethylmaleimide at low concentrations. Vanadate which is known to inhibit ATPase activity by trapping MgADP at the catalytic site inhibited photoaffinity labeling of Pgp with substrate analogues, [125I]iodoarylazidoprazosin and [3H]azidopine, only under ATP hydrolysis conditions. Because vanadate-trapped Pgp is known to resemble the ADP and phosphate-bound catalytic transition state, our findings indicate that ATP hydrolysis results in a conformation with reduced affinity for substrates. A catalytic transition conformation with reduced affinity would essentially result in substrate dissociation and supports a model for drug transport in which an ATP hydrolysis-induced conformational change leads to drug release toward the extracellular medium.

  4. Computer simulation of reactions in beta-cyclodextrin molecular reactors: transition state recognition.

    Science.gov (United States)

    Yeguas, Violeta; López, Ramón; Lambert, Alexandrine; Monard, Gérald; Ruiz-López, Manuel F

    2010-10-07

    Cyclodextrins have attracted much interest in recent years because of their potential use as molecular reactors allowing organic reactions in aqueous solution. To better understand their effect on reaction mechanisms, we have carried out a computational study of a prototypical process (neutral ester hydrolysis) in a beta-cyclodextrin (beta-CD). Two models have been used for the reactor. The first and simpler one assumes that the medium can be described by a polarizable dielectric continuum. The second one takes into account the discrete nature of the beta-CD and water molecules thanks to a computational approach that combines the use of Quantum Mechanics, Molecular Mechanics and Molecular Dynamics techniques. We focus on neutral pH processes for which either acceleration or inhibition has experimentally been observed depending on ester derivatives. Our calculations rationalize such observations by showing that the two reaction mechanisms usually invoked for hydrolysis, stepwise (involving two transitions states with formation of a -C(OH)(2)OR tetrahedral intermediate) and concerted, undergo opposite effects in the beta-CD environment. The results highlight the role played by molecular shape recognition. Thus, in spite of a higher polarity exhibited by the three transition states with respect to the reactants, the interactions with the beta-CD cavity may either increase or decrease the activation barrier due to different 3D-arrangements of the chemical structures.

  5. Shape transition of state density for bosonic systems

    Indian Academy of Sciences (India)

    Harshal N Deota; N D Chavda; V Potbhare

    2013-12-01

    For a finite boson system, the ensemble-averaged state density has been computed with respect to the body interaction rank . The shape of such a state density changes from Gaussian to semicircle as the body rank of the interaction increases. This state density is expressed as a linear superposition of Gaussian and semicircular states. The nearest-neighbour spacing distribution (NNSD), which is one of the most important spectral properties of a system, is studied. The NNSDs are rather independent of body rank and show a Wigner distribution throughout.

  6. Thermoelectric signals of state transition in polycrystalline SmB6

    Science.gov (United States)

    Yue, Z. J.; Chen, Q. J.; Wang, X. L.

    2016-09-01

    Topological Kondo insulator SmB6 has attracted quite a lot of attention from the condensed matter physics community. A number of unique electronic properties, including low-temperature resistivity anomaly, 1D electronic transport and 2D Fermi surfaces have been observed in SmB6. Here, we report on thermoelectric transport properties of polycrystalline SmB6 over a broad temperature from 300 to 2 K. An anomalous transition in the temperature-dependent Seebeck coefficient S from S(T) \\propto T -1 to S(T) \\propto T was observed around 12 K. Such a transition demonstrates a transition of conductivity from 3D metallic bulk states to 2D metallic surface states with insulating bulk states. Our results suggest that the thermotransport measurements could be used for the characterization of state transition in topological insulators.

  7. Discontinuous phase transition in a multi-state majority-vote model

    CERN Document Server

    Li, Guofeng; Huang, Feng; Shen, Chuansheng

    2016-01-01

    In this paper, we generalize the original majority-vote (MV) model with noise from two states to arbitrary $q$ states, where $q$ is an integer no less than two. The main emphasis is paid to the comparison on the nature of phase transitions between the two-state MV (MV2) model and the three-state MV (MV3) model. By extensive Monte Carlo simulation and mean-field analysis, we find that the MV3 model undergoes a discontinuous order-disorder phase transition, in contrast to a continuous phase transition in the MV2 model. A central feature of such a discontinuous transition is a strong hysteresis behavior as noise intensity goes forward and backward. Within the hysteresis region, the disordered phase and ordered phase are coexisting.

  8. Determining Transition State Geometries in Liquids Using 2D-IR

    Energy Technology Data Exchange (ETDEWEB)

    Harris, Charles; Cahoon, James F.; Sawyer, Karma R.; Schlegel, Jacob P.; Harris, Charles B.

    2007-12-11

    Many properties of chemical reactions are determined by the transition state connecting reactant and product, yet it is difficult to directly obtain any information about these short-lived structures in liquids. We show that two-dimensional infrared (2D-IR) spectroscopy can provide direct information about transition states by tracking the transformation of vibrational modes as a molecule crossed a transition state. We successfully monitored a simple chemical reaction, the fluxional rearrangement of Fe(CO)5, in which the exchange of axial and equatorial CO ligands causes an exchange of vibrational energy between the normal modes of the molecule. This energy transfer provides direct evidence regarding the time scale, transition state, and mechanism of the reaction.

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

    Energy Technology Data Exchange (ETDEWEB)

    Golosova, N. O. [Joint Institute for Nuclear Research, Dubna, Russia; Kozlenko, D. P. [Joint Institute for Nuclear Research, Dubna, Russia; Kolesnikov, Alexander I [ORNL; Kazimirov, V. Yu. [Joint Institute for Nuclear Research, Dubna, Russia; Smirnov, M. B. [St. Petersburg State University, St. Petersburg, Russia; Jirak, Z. [Institute of Physics, Czech Republic; Savenko, B. N. [Joint Institute for Nuclear Research, Dubna, Russia

    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 spin state transition and relevant orbital-phonon coupling.

  10. Electronic transition dipole moment and radiative lifetime calculations of sodium dimer ion-pair states.

    Science.gov (United States)

    Sanli, Aydin; Beser, Bediha; Edwardson, John R; Magnier, Sylvie; Ahmed, Ergin H; Marjatta Lyyra, A

    2015-09-14

    We report here ab initio calculated electronic transition dipole moments for the sodium dimer ion pair states of (1)Σg (+) symmetry. They vary strongly as a function of internuclear distance because of the effect of the Na(+) + Na(-) ion pair potential, which also causes the formation of additional wells and shoulders in the molecular potential energy curves. We also present a computational study of the transition dipole moment matrix elements and lifetimes for these ion-pair states.

  11. Evidence for a transition state model compound of in-plane vinylic SN2 reaction.

    Science.gov (United States)

    Yamaguchi, Torahiko; Yamamoto, Yohsuke; Fujiwara, Yoshihisa; Tanimoto, Yoshifumi

    2005-06-23

    [reaction: see text] To isolate a transition state model compound of an in-plane vinylic S(N)2 reaction, vinyl bromide 6 bearing a newly synthesized tridentate ligand derived from 1,8-dimethoxythioxanthen-9-one (5) was prepared as a precursor. Although irradiation of 6 gave demethylated benzofuran 12, a transient broad peak which indicates formation of the desired transition state model compound was observed in the laser flash photolytic study.

  12. The Interfacial Transition Zone in Alkali-Activated Slag Mortars

    Directory of Open Access Journals (Sweden)

    Rackel eSan Nicolas

    2015-12-01

    Full Text Available The interfacial transition zone (ITZ is known to strongly influence the mechanical and transport properties of mortars and concretes. This paper studies the ITZ between siliceous (quartz aggregates and alkali activated slag binders in the context of mortar specimens. Backscattered electron images (BSE generated in an environmental scanning electron microscope (ESEM are used to identify unreacted binder components, reaction products and porosity in the zone surrounding aggregate particles, by composition and density contrast. X-ray mapping is used to exclude the regions corresponding to the aggregates from the BSE image of the ITZ, thus enabling analysis of only the binder phases, which are segmented into binary images by grey level discrimination. A distinct yet dense ITZ region is present in the alkali-activated slag mortars, containing a reduced content of unreacted slag particles compared to the bulk binder. The elemental analysis of this region shows that it contains a (C,N-A-S-H gel which seems to have a higher content of Na (potentially deposited through desiccation of the pore solution and a lower content of Ca than the bulk inner and outer products forming in the main binding region. These differences are potentially important in terms of long-term concrete performance, as the absence of a highly porous interfacial transition zone region is expected to provide a positive influence on the mechanical and transport properties of alkali-activated slag concretes.

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

    Science.gov (United States)

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

    2013-02-25

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

  14. TRANSITION STATE FOR THE GAS-PHASE REACTION OF URANIUM HEXAFLUORIDE WITH WATER

    Energy Technology Data Exchange (ETDEWEB)

    Garrison, S; James Becnel, J

    2008-03-18

    Density Functional Theory and small-core, relativistic pseudopotentials were used to look for symmetric and asymmetric transitions states of the gas-phase hydrolysis reaction of uranium hexafluoride, UF{sub 6}, with water. At the B3LYP/6-31G(d,p)/SDD level, an asymmetric transition state leading to the formation of a uranium hydroxyl fluoride, U(OH)F{sub 5}, and hydrogen fluoride was found with an energy barrier of +77.3 kJ/mol and an enthalpy of reaction of +63.0 kJ/mol (both including zero-point energy corrections). Addition of diffuse functions to all atoms except uranium led to only minor changes in the structure and relative energies of the reacting complex and transition state. However, a significant change in the product complex structure was found, significantly reducing the enthalpy of reaction to +31.9 kJ/mol. Similar structures and values were found for PBE0 and MP2 calculations with this larger basis set, supporting the B3LYP results. No symmetric transition state leading to the direct formation of uranium oxide tetrafluoride, UOF{sub 4}, was found, indicating that the reaction under ambient conditions likely includes several more steps than the mechanisms commonly mentioned. The transition state presented here appears to be the first published transition state for the important gas-phase reaction of UF{sub 6} with water.

  15. Analytical expressions for partial wave two-body Coulomb transition matrices at ground-state energy

    Science.gov (United States)

    Kharchenko, V. F.

    2016-11-01

    Leaning upon the Fock method of the stereographic projection of the three-dimensional momentum space onto the four-dimensional unit sphere the possibility of the analytical solving of the Lippmann-Schwinger integral equation for the partial wave two-body Coulomb transition matrix at the ground bound state energy has been studied. In this case new expressions for the partial p-, d- and f-wave two-body Coulomb transition matrices have been obtained in the simple analytical form. The developed approach can also be extended to determine analytically the partial wave Coulomb transition matrices at the energies of excited bound states.

  16. Diversity of Active States in TMT Opsins.

    Directory of Open Access Journals (Sweden)

    Kazumi Sakai

    Full Text Available Opn3/TMT opsins belong to one of the opsin groups with vertebrate visual and non-visual opsins, and are widely distributed in eyes, brains and other internal organs in various vertebrates and invertebrates. Vertebrate Opn3/TMT opsins are further classified into four groups on the basis of their amino acid identities. However, there is limited information about molecular properties of these groups, due to the difficulty in preparing the recombinant proteins. Here, we successfully expressed recombinant proteins of TMT1 and TMT2 opsins of medaka fish (Oryzias latipes in cultured cells and characterized their molecular properties. Spectroscopic and biochemical studies demonstrated that TMT1 and TMT2 opsins functioned as blue light-sensitive Gi/Go-coupled receptors, but exhibited spectral properties and photo-convertibility of the active state different from each other. TMT1 opsin forms a visible light-absorbing active state containing all-trans-retinal, which can be photo-converted to 7-cis- and 9-cis-retinal states in addition to the original 11-cis-retinal state. In contrast, the active state of TMT2 opsin is a UV light-absorbing state having all-trans-retinal and does not photo-convert to any other state, including the original 11-cis-retinal state. Thus, TMT opsins are diversified so as to form a different type of active state, which may be responsible for their different functions.

  17. Active dry granular flows: Rheology and rigidity transitions

    Science.gov (United States)

    Peshkov, Anton; Claudin, Philippe; Clément, Eric; Andreotti, Bruno

    2016-10-01

    The constitutive relations of a dense granular flow composed of self-propelling frictional hard particles are investigated by means of DEM numerical simulations. We show that the rheology, which relates the dynamical friction μ and the volume fraction ϕ to the inertial number I, depends on a dimensionless number A , which compares the active force to the confining pressure. Two liquid/solid transitions —in the Maxwell rigidity sense— are observed. As soon as the activity is turned on, the packing becomes an “active solid” with a mean number of particle contacts larger than the isostatic value. The quasi-static values of μ and ϕ decrease with A . At a finite value of the activity At , corresponding to the isostatic condition, a second “active rigidity transition” is observed beyond which the quasi-static values of the friction vanishes and the rheology becomes Newtonian. For A>At , we provide evidence for a highly intermittent dynamics of this “active fluid”.

  18. Seizure in People with Newly Diagnosed Active or Transitional Neurocysticercosis

    Science.gov (United States)

    Kelvin, Elizabeth A.; Carpio, Arturo; Bagiella, Emilia; Leslie, Denise; Leon, Pietro; Andrews, Howard; Hauser, W. Allen

    2011-01-01

    Purpose The aim of this study is to describe seizure as a presenting symptom in individuals with recently diagnosed neurocysticercosis (NCC). Methods Using logistic regression, we examined the probability of having seizures as a presenting symptom among those with active or transitional NCC by host age and gender, and by number of cysts, location of the cysts in the brain, and phase of evolution of the encysted parasite. Results We found that the odds of having seizures as presenting symptom for those in the youngest age group (3–24 years old) were 12.9 times that of the oldest participants (age 55–82 years) (p=0.006). People with cysts in parenchymal locations had a significantly higher odds of seizures compared to those with all their cysts elsewhere (ventricles or subarachnoid) (OR=6.2, p=0.028); and the number of cysts was significantly associated with having seizures (OR=1.1, p=0.026). Host gender and cyst phase were not significantly associated with having seizures after adjusting for confounders and covariates. Conclusion Children, those with cysts in parenchymal locations, and those with a higher number of cysts appear to be more likely to experience seizure when they have NCC cysts in the active or transitional stage. PMID:21145263

  19. Transitional discharge based on therapeutic relationships: state of the art.

    Science.gov (United States)

    Forchuk, Cheryl; Reynolds, William; Sharkey, Siobhan; Martin, Mary-Lou; Jensen, Elsabeth

    2007-04-01

    The Transitional Discharge Model (TDM) has been used to facilitate effective discharge from psychiatric hospital to community. A summary of the research to date on TDM is given. The model is based on the provision of therapeutic relationships to provide a safety net throughout the discharge and community reintegration processes. These relationships include both staff and peer involvement; hospital inpatient staff continue to remain involved with the client until a therapeutic relationship is established with a community care provider, and peer support is offered from a former consumer of mental health services who is currently living in the community. Studies found that the TDM facilitates increased discharge rates, lower readmission rates, and cost savings--making it a collaborative, cost-effective method of providing quality patient care and positive health care outcomes. The TDM Plan of Research is presented and reflects the collaboration between stakeholders and the integration of consumer advocacy, clinical practice, education, policy, and research in various countries.

  20. Design, Synthesis, and Evaluation of Novel Prodrugs of Transition State Inhibitors of Norovirus 3CL Protease.

    Science.gov (United States)

    Galasiti Kankanamalage, Anushka C; Kim, Yunjeong; Rathnayake, Athri D; Alliston, Kevin R; Butler, Michelle M; Cardinale, Steven C; Bowlin, Terry L; Groutas, William C; Chang, Kyeong-Ok

    2017-07-27

    Ester and carbamate prodrugs of aldehyde bisulfite adduct inhibitors were synthesized in order to improve their pharmacokinetic and pharmacodynamic properties. The inhibitory activity of the compounds against norovirus 3C-like protease in enzyme and cell-based assays was determined. The ester and carbamate prodrugs displayed equivalent potency to those of the precursor aldehyde bisulfite adducts and precursor aldehydes. Furthermore, the rate of ester cleavage was found to be dependent on alkyl chain length. The generated prodrugs exhibited low cytotoxicity and satisfactory liver microsomes stability and plasma protein binding. The methodology described herein has wide applicability and can be extended to the bisulfite adducts of common warheads employed in the design of transition state inhibitors of serine and cysteine proteases of medical relevance.

  1. Importance of hydrophobic cluster formation through long-range contacts in the folding transition state of two-state proteins.

    Science.gov (United States)

    Selvaraj, S; Gromiha, M Michael

    2004-06-01

    Understanding the folding pathways of proteins is a challenging task. The Phi value approach provides a detailed understanding of transition-state structures of folded proteins. In this work, we have computed the hydrophobicity associated with each residue in the folded state of 16 two-state proteins and compared the Phi values of each mutant residue. We found that most of the residues with high Phi value coincide with local maximum in surrounding hydrophobicity, or have nearby residues that show such maximum in hydrophobicity, indicating the importance of hydrophobic interactions in the transition state. We have tested our approach to different structural classes of proteins, such as alpha-helical, SH3 domains of all-beta proteins, beta-sandwich, and alpha/beta proteins, and we observed a good agreement with experimental results. Further, we have proposed a hydrophobic contact network pattern to relate the Phi values with long-range contacts, which will be helpful to understand the transition-state structures of folded proteins. The present approach could be used to identify potential hydrophobic clusters that may form through long-range contacts during the transition state.

  2. 40 CFR 70.4 - State program submittals and transition.

    Science.gov (United States)

    2010-07-01

    ... of the employees. The State need not submit complete job descriptions for every employee carrying out... program submission. The submission shall contain the following: (1) A complete program description... for monitoring source compliance (e.g., inspection strategies). (5) A complete description of...

  3. Localized Electronic States near Dislocations in Transition Metals

    NARCIS (Netherlands)

    Hosson, J.Th.M. De

    1978-01-01

    This article outlines a model for calculating the localized states of a <100> edge dislocation in Mo. The model used for the calculations is based on the multiple-scattering model (SCF-Xα-SW). The purpose of this investigation is (1) to determine changes in the electronic structure of the lattice ne

  4. Tuned Transition from Quantum to Classical for Macroscopic Quantum States

    NARCIS (Netherlands)

    Fedorov, A.; Macha, P.; Feofanov, A.K.; Harmans, C.J.P.M.; Mooij, J.E.

    2011-01-01

    The boundary between the classical and quantum worlds has been intensely studied. It remains fascinating to explore how far the quantum concept can reach with use of specially fabricated elements. Here we employ a tunable flux qubit with basis states having persistent currents of 1  μA carried by a

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

    Energy Technology Data Exchange (ETDEWEB)

    Tsui, Lokman; Jiang, Hong-Chen; Lu, Yuan-Ming; Lee, Dung-Hai

    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 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.

  6. State Isomorphism in the Post-Socialist Transition

    Directory of Open Access Journals (Sweden)

    Ioannis Kyvelidis

    2000-02-01

    Full Text Available With the collapse of the communist regimes, the post-socialist countries are facing the problem of building new legal and institutional systems which will adequately address the needs of the markets. They also try to implement new reforms. But the transition towards economic and market reforms across the bloc has been very uneven, producing the countries-winners, countries-laggards, and countries-losers. There have been some attempts to explain that unevenness from the temporal path dependency perspective and from geographic proximity perspective. Can we explain this unevenness better drawing upon the theory of institutional isomorphism? This paper is not ambitious and built exclusively on literature review. It attempts to borrow from some middle-range social theories of institution building and, especially, the theory of institutional isomorphism by DiMaggio and Powell. It shows that some parts of the bloc seem to be surprisingly isomorphic. The paper suggests an explanation of the possible causes and applicability of the phenomenon of isomorphism in the post-Soviet bloc. In particular, it: 1 contrasts the facts of the transformation with the theory of institutional and organizational isomorphism, 2 makes a fair causal comparison with other explanations, 3 claims the adequate causal depth for the explanation, 4 points at an adequate causal mechanism of the transformation.

  7. Youth in Transition: From Incarceration to Reintegration. A National Survey of State Juvenile Correctional Services.

    Science.gov (United States)

    Eastern Kentucky Univ., Richmond. Dept. of Correctional Services.

    A national phone survey was conducted by the Eastern Kentucky University Training Resource Center to determine how states were addressing the problems associated with the transition of youth from correctional facilities to their home communities. The survey, which was conducted during March-May 1987, asked chief state juvenile correctional…

  8. The role of the transition state in polyatomic reactions: Initial state-selected reaction probabilities of the H + CH4 → H2 + CH3 reaction

    Science.gov (United States)

    Welsch, Ralph; Manthe, Uwe

    2014-11-01

    Full-dimensional calculations of initial state-selected reaction probabilities on an accurate ab initio potential energy surface (PES) have been communicated recently [R. Welsch and U. Manthe, J. Chem. Phys. 141, 051102 (2014)]. These calculations use the quantum transition state concept, the multi-layer multi-configurational time-dependent Hartree approach, and graphics processing units to speed up the potential evaluation. Here further results of these calculations and an extended analysis are presented. State-selected reaction probabilities are given for many initial ro-vibrational states. The role of the vibrational states of the activated complex is analyzed in detail. It is found that rotationally cold methane mainly reacts via the ground state of the activated complex while rotationally excited methane mostly reacts via H-H-CH3-bending excited states of the activated complex. Analyzing the different contributions to the reactivity of the vibrationally states of methane, a complex pattern is found. Comparison with initial state-selected reaction probabilities computed on the semi-empirical Jordan-Gilbert PES reveals the dependence of the results on the specific PES.

  9. The role of the transition state in polyatomic reactions: initial state-selected reaction probabilities of the H + CH₄ → H₂ + CH₃ reaction.

    Science.gov (United States)

    Welsch, Ralph; Manthe, Uwe

    2014-11-07

    Full-dimensional calculations of initial state-selected reaction probabilities on an accurate ab initio potential energy surface (PES) have been communicated recently [R. Welsch and U. Manthe, J. Chem. Phys. 141, 051102 (2014)]. These calculations use the quantum transition state concept, the multi-layer multi-configurational time-dependent Hartree approach, and graphics processing units to speed up the potential evaluation. Here further results of these calculations and an extended analysis are presented. State-selected reaction probabilities are given for many initial ro-vibrational states. The role of the vibrational states of the activated complex is analyzed in detail. It is found that rotationally cold methane mainly reacts via the ground state of the activated complex while rotationally excited methane mostly reacts via H-H-CH3-bending excited states of the activated complex. Analyzing the different contributions to the reactivity of the vibrationally states of methane, a complex pattern is found. Comparison with initial state-selected reaction probabilities computed on the semi-empirical Jordan-Gilbert PES reveals the dependence of the results on the specific PES.

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

    Science.gov (United States)

    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.

  11. Ground State Transitions in Vertically Coupled Four-Layer Single Electron Quantum Dots

    Institute of Scientific and Technical Information of China (English)

    WANGAn-Mei; XIEWen-Fang

    2005-01-01

    We study a four-electron system in a vertically coupled four-layer quantum dot under a magnetic field by the exact diagonalization of the Hamiltonian matr/x. We find that discontinuous ground-state energy transitions are induced by an external magnetic field. We find that dot-dot distance and electron-electron interaction strongly affect the low-lying states of the coupled quantum dots. The inter-dot correlation leads to some sequences of possible disappearances of ground state transitions, which are present for uncoupled dots.

  12. Cygnus X-3 transition from the ultrasoft to the hard state

    DEFF Research Database (Denmark)

    Beckmann, V.; Soldi, S.; Belanger, G.

    2007-01-01

    Aims. The nature of Cygnus X-3 is still not understood well. This binary system might host a black hole or a neutron star. Recent observations by INTEGRAL have shown that Cygnus X- 3 was again in an extremely ultrasoft state. Here we present our analysis of the transition from the ultrasoft state......, dominated by blackbody radiation at soft X- rays plus non-thermal emission in the hard X- rays, to the low hard state. Methods. INTEGRAL observed Cyg X-3 six times during three weeks in late May and early June 2007. Data from IBIS/ISGRI and JEM-X1 were analysed to show the spectral transition. Results...

  13. Ground State Transitions in Vertically Coupled Four-Layer Single Electron Quantum Dots

    Institute of Scientific and Technical Information of China (English)

    WANG An-Mei; XIE Wen-Fang

    2005-01-01

    We study a four-electron system in a vertically coupled four-layer quantum dot under a magnetic field by the exact diagonalization of the Hamiltonian matrix. We find that discontinuous ground-state energy transitions are induced by an external magnetic field. We find that dot-dot distance and electron-electron interaction strongly affect the low-lying states of the coupled quantum dots. The inter-dot correlation leads to some sequences of possible disappearances of ground state transitions, which are present for uncoupled dots.

  14. A state-and-transition simulation modeling approach for estimating the historical range of variability

    Directory of Open Access Journals (Sweden)

    Kori Blankenship

    2015-04-01

    Full Text Available Reference ecological conditions offer important context for land managers as they assess the condition of their landscapes and provide benchmarks for desired future conditions. State-and-transition simulation models (STSMs are commonly used to estimate reference conditions that can be used to evaluate current ecosystem conditions and to guide land management decisions and activities. The LANDFIRE program created more than 1,000 STSMs and used them to assess departure from a mean reference value for ecosystems in the United States. While the mean provides a useful benchmark, land managers and researchers are often interested in the range of variability around the mean. This range, frequently referred to as the historical range of variability (HRV, offers model users improved understanding of ecosystem function, more information with which to evaluate ecosystem change and potentially greater flexibility in management options. We developed a method for using LANDFIRE STSMs to estimate the HRV around the mean reference condition for each model state in ecosystems by varying the fire probabilities. The approach is flexible and can be adapted for use in a variety of ecosystems. HRV analysis can be combined with other information to help guide complex land management decisions.

  15. Chaos control applied to coherent states in transitional flows

    Energy Technology Data Exchange (ETDEWEB)

    Pausch, Marina; Eckhardt, Bruno, E-mail: bruno.eckhardt@physik.uni-marburg.de [Fachbereich Physik, Philipps-Universitaet Marburg, Renthof 6, 35032 Marburg (Germany)

    2011-12-22

    Chaos control refers to a group of techniques by which an otherwise unstable dynamical state of a system can be maintained by small control forces. We here discuss their application to stabilizing the fixed points in a low dimensional model for shear flows. The simulations demonstrate a prototypical application of chaos control, show that control is almost always possible, and give insights into optimizing the control matrix from a design point of view.

  16. 5-Thio-D-glycopyranosylamines and their amidinium salts as potential transition-state mimics of glycosyl hydrolases: synthesis, enzyme inhibitory activities, X-ray crystallography, and molecular modeling

    DEFF Research Database (Denmark)

    Kavlekar, Lizie M.; Kuntz, Douglas A.; Wen, Xin

    2005-01-01

    in the enzyme active site of Golgi alpha-mannosidase II (GM II). Compounds 1 and 2 have been found to be inhibitors with IC50 values of 0.07 and 0.9 mM, respectively. We also report the docked structures of 5-thin-D-glucopyranosylamine 3 and 5-thio-D-glucopyranosylamidinium bromide 4 in the active site...

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

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Ho-Ling [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Wilson, Daniel W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Reuscher, Tim [Macrosys, Arlington, VA (United States); Chin, Shih-Miao [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Taylor, Rob D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2015-12-01

    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, 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 transit

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

    Energy Technology Data Exchange (ETDEWEB)

    Hwang, Ho-Ling [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Wilson, Daniel W. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Reuscher, Tim [Macrosys, Arlington, VA (United States); Chin, Shih-Miao [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Taylor, Rob D. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2015-12-01

    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, 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 transit

  19. High-energy observations of the state transition of the X-ray nova and black hole candidate XTE J1720-318

    DEFF Research Database (Denmark)

    Bel, M.C.; Rodriguez, J.; Sizun, P.

    2004-01-01

    , typical of a black-hole binary in the so-called High/Soft State. We then followed the evolution of the source outburst over several months using the INTEGRAL Galactic Centre survey observations. The source became active again at the end of March: it showed a clear transition towards a much harder state...

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

    CERN Document Server

    Chestnov, I Yu

    2013-01-01

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

  1. The Transition States for CO2 Capture by Substituted Ethanolamines

    NARCIS (Netherlands)

    Gangarapu, S.; Marcelis, A.T.M.; Alhamed, Y.A.; Zuilhof, H.

    2015-01-01

    Quantum chemical studies are used to understand the electronic and steric effects on the mechanisms of the reaction of substituted ethanolamines with CO2. SCS-MP2/6-311+G(2d,2p) calculations are used to obtain the activation energy barriers and reaction energies for both the carbamate and bicarbonat

  2. The Transition States for CO2 Capture by Substituted Ethanolamines

    NARCIS (Netherlands)

    Gangarapu, S.; Marcelis, A.T.M.; Alhamed, Y.A.; Zuilhof, H.

    2015-01-01

    Quantum chemical studies are used to understand the electronic and steric effects on the mechanisms of the reaction of substituted ethanolamines with CO2. SCS-MP2/6-311+G(2d,2p) calculations are used to obtain the activation energy barriers and reaction energies for both the carbamate and

  3. Transition-state-guided drug design for treatment of parasitic neglected tropical diseases.

    Science.gov (United States)

    Murkin, A S; Moynihan, M M

    2014-01-01

    Many of the deadliest neglected tropical diseases are caused by protozoan and helminthic parasites. These organisms have evolved several enzymes to exploit their host's metabolic resources and evade immune responses. Because these essential proteins are absent in humans, they are targets for antiparasitic drug development. Despite decades of investigation, no therapy has been successful in the eradication of these diseases, so new approaches are desired. Chemically stable analogues of the transition states of enzymatic reactions are often potent inhibitors, and several examples of clinically effective compounds are known for other diseases. The design of transition-state analogues is aided by structural models of the transition state, which are obtained by complementing experimental measurement of kinetic isotope effects with theoretical calculations. Such transition-state-guided inhibitor design has been demonstrated for human, bovine, malarial, and trypanosomal enzymes of the purine salvage pathway, including purine nucleoside phosphorylase, nucleoside hydrolases, and adenosine deaminase. Cysteine proteases, trans-sialidase, 1-deoxy-d-xylulose-5-phosphate reductoisomerase, and trypanothione synthetase are presented as additional candidates for application of transition-state analysis with the goal of identifying new leads for the treatment of parasitic neglected tropical diseases.

  4. A physical scenario for the high and low X-ray luminosity states in the transitional pulsar PSR J1023+0038

    Science.gov (United States)

    Campana, S.; Coti Zelati, F.; Papitto, A.; Rea, N.; Torres, D. F.; Baglio, M. C.; D'Avanzo, P.

    2016-10-01

    The binary system PSR J1023+0038 (J1023) hosts a neutron star and a low-mass companion. J1023 is the best studied transitional pulsar, alternating a faint eclipsing millisecond radio pulsar state to a brighter X-ray active state. At variance with other low-mass X-ray binaries, this active state reaches luminosities of only ~1034 erg s-1, showing strong, fast variability. In the active state, J1023 displays: i) a high state (LX ~ 7 × 1033 erg s-1, 0.3-80 keV) occurring ~80% of the time and during which X-ray pulsations at the neutron star spin period are detected (pulsed fraction ~ 8%); ii) a low state (LX ~ 1033 erg s-1) during which pulsations are not detected (≲ 3%); and iii) a flaring state during which sporadic flares occur in excess of ~ 1034 erg s-1, with no pulsation too. The transition between the high and the low states is very rapid, on a ~10 s timescale. Here we propose a plausible physical interpretation of the high and low states based on the (fast) transition among the propeller state and the radio pulsar state. We modelled the XMM-Newton spectra of the high, low and radio pulsar states, and found a good agreement with this physical picture.

  5. Probing the NO2 --> NO+O transition state via time resolved unimolecular decomposition

    Science.gov (United States)

    Ionov, S. I.; Brucker, G. A.; Jaques, C.; Chen, Y.; Wittig, C.

    1993-09-01

    Time resolved, subpicosecond resolution measurements of photoinitiated NO2 unimolecular decomposition rates are reported for expansion cooled and room temperature samples. The molecules are excited by 375-402 nm tunable subpicosecond pulses having bandwidths ≥20 cm-1 to levels which are known to be thorough admixtures of the 2B2 electronically excited state and the 2A1 ground electronic state. Subsequent decomposition is probed by a 226 nm subpicosecond pulse that excites laser-induced fluorescence (LIF) in the NO product. When increasing the amount of excitation over the dissociation threshold, an uneven, ``step-like'' increase of the decomposition rate vs energy is observed for expansion cooled samples. The steps are spaced by ˜100 cm-1 and can be assigned ad hoc to bending at the transition state. Relying on experimental estimates for the near threshold density of states, we point out that simple transition state theory predictions give rates that are consistent with these measured values. The rates are sufficiently rapid to question the assumption of rapid intramolecular vibrational redistribution, which is implicit in transition state theories. In contrast to expansion cooled samples, room temperature samples exhibit a smooth variation of the reaction rate vs photon energy. By comparing rates for rotationally cold and room temperature NO2, the ON-O bond is estimated to be ˜40% longer in the transition state than in the parent molecule.

  6. GBM Monitoring of Cyg X-1 During the Recent State Transition

    CERN Document Server

    Case, G L; Cherry, M L; Camero-Arranz, A; Finger, M; Jenke, P; Wilson-Hodge, C A; Chaplin, V

    2011-01-01

    Cygnus X-1 is a high-mass x-ray binary with a black hole compact object. It is normally extremely bright in hard x-rays and low energy gamma rays and resides in the canonical hard spectral state. Recently, however, Cyg X-1 made a transition to the canonical soft state, with a rise in the soft x-ray flux and a decrease in the flux in the hard x-ray and low energy gamma-ray energy bands. We have been using the Gamma-Ray Burst Monitor on Fermi to monitor the fluxes of a number of sources in the 8--1000 keV energy range, including Cyg X-1. We present light curves of Cyg X-1 showing the flux decrease in hard x-ray and low energy gamma-ray energy bands during the state transition as well as the several long flares observed in these higher energies during the soft state. We also present preliminary spectra from GBM for the pre-transition state, showing the spectral evolution to the soft state, and the post-transition state.

  7. DNA nuclease activity of Rev-coupled transition metal chelates.

    Science.gov (United States)

    Joyner, Jeff C; Keuper, Kevin D; Cowan, J A

    2012-06-07

    Artificial nucleases containing Rev-coupled metal chelates based on combinations of the transition metals Fe(2+), Co(2+), Ni(2+), and Cu(2+) and the chelators DOTA, DTPA, EDTA, NTA, tripeptide GGH, and tetrapeptide KGHK have been tested for DNA nuclease activity. Originally designed to target reactive transition metal chelates (M-chelates) to the HIV-1 Rev response element mRNA, attachment to the arginine-rich Rev peptide also increases DNA-binding affinity for the attached M-chelates. Apparent K(D) values ranging from 1.7 to 3.6 µM base pairs for binding of supercoiled pUC19 plasmid DNA by Ni-chelate-Rev complexes were observed, as a result of electrostatic attraction between the positively-charged Rev peptide and negatively-charged DNA. Attachment of M-chelates to the Rev peptide resulted in enhancements of DNA nuclease activity ranging from 1-fold (no enhancement) to at least 13-fold (for Cu-DTPA-Rev), for the rate of DNA nicking, with second order rate constants for conversion of DNA(supercoiled) to DNA(nicked) up to 6 × 10(6) M(-1) min(-1), and for conversion of DNA(nicked) to DNA(linear) up to 1 × 10(5) M(-1) min(-1). Freifelder-Trumbo analysis and the ratios of linearization and nicking rate constants (k(lin)/k(nick)) revealed concerted mechanisms for nicking and subsequent linearization of plasmid DNA for all of the Rev-coupled M-chelates, consistent with higher DNA residency times for the Rev-coupled M-chelates. Observed rates for Rev-coupled M-chelates were less skewed by differing DNA-binding affinities than for M-chelates lacking Rev, as a result of the narrow range of DNA-binding affinities observed, and therefore relationships between DNA nuclease activity and other catalyst properties, such as coordination unsaturation, the ability to consume ascorbic acid and generate diffusible radicals, and the identity of the metal center, are now clearly illustrated in light of the similar DNA-binding affinities of all M-chelate-Rev complexes. This work

  8. Active states and structure transformations in accreting white dwarfs

    Science.gov (United States)

    Boneva, Daniela; Kaygorodov, Pavel

    2016-07-01

    Active states in white dwarfs are usually associated with light curve's effects that concern to the bursts, flickering or flare-up occurrences. It is common that a gas-dynamics source exists for each of these processes there. We consider the white dwarf binary stars with accretion disc around the primary. We suggest a flow transformation modeling of the mechanisms that are responsible for ability to cause some flow instability and bring the white dwarfs system to the outburst's development. The processes that cause the accretion rate to sufficiently increase are discussed. Then the transition from a quiescent to an active state is realized. We analyze a quasi-periodic variability in the luminosity of white dwarf binary stars systems. The results are supported with an observational data.

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

    CERN Document Server

    Parniak, Michał; Wasilewski, Wojciech

    2015-01-01

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

  10. Forbidden Electronic Transitions between the Singlet Ground State and the Triplet Excited State of Pt(II) Complexes.

    Science.gov (United States)

    Zheng, Greg Y.; Rillema, D. Paul; DePriest, Jeff; Woods, Clifton

    1998-07-13

    Direct access to the triplet emitting state from the ground state is observed for Pt(II) complexes containing heterocyclic (CwedgeC', CwedgeN, NwedgeN') and bis(diphenylphosphino)alkane (PwedgeP') ligands. Extinction coefficients for such transitions are in the range 4-25 M(-)(1) cm(-)(1). Emission quantum yields resulting from singlet-to-triplet excitation are as high as 61-77 times the emission quantum yields resulting from singlet-to-singlet excitation at 296 K. The intersystem crossing quantum yield from the singlet excited state to triplet emitting state is lower than 2% at 296 K but is greatly enhanced at 77 K. The forbidden electronic transition observed for Pt(II) complexes is attributed to result from spin-orbit coupling due to the presence of Pt(II) in the skeleton structure. The importance of excitation spectra on the computation of emission quantum yields is discussed.

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

    OpenAIRE

    Junhao Liang; Yanqing Hu; Guanrong Chen; Tianshou Zhou

    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,...

  12. 1 and 2 transitions in the ground-state configuration of atomic manganese

    Indian Academy of Sciences (India)

    S Kabakçi; B Karaçoban Usta; L Özdemir

    2015-10-01

    Using the multiconfiguration Hartree–Fock approximation within the framework of the Breit–Pauli Hamiltonian (MCHF+BP) and the relativistic Hartree–Fock (HFR) approximation, we have calculated the forbidden transition (1 and 2) parameters such as transition energies, logarithmic weighted oscillator strengths and transition probabilities between the fine-structure levels in the ground-state configuration of 3d5 4s2 for atomic manganese (Mn I, Z =25). A discussion of these calculations for manganese using MCHF+BP and HFR methods is given here.

  13. Prediction of monomer reactivity in radical copolymerizations from transition state quantum chemical descriptors

    Directory of Open Access Journals (Sweden)

    Zhengde Tan

    2013-01-01

    Full Text Available In comparison with the Q-e scheme, the Revised Patterns Scheme: the U, V Version (the U-V scheme has greatly improved both its accessibility and its accuracy in interpreting and predicting the reactivity of a monomer in free-radical copolymerizations. Quantitative structure-activity relationship (QSAR models were developed to predict the reactivity parameters u and v of the U-V scheme, by applying genetic algorithm (GA and support vector machine (SVM techniques. Quantum chemical descriptors used for QSAR models were calculated from transition state species with structures C¹H3 - C²HR³• or •C¹H2 - C²H2R³ (formed from vinyl monomers C¹H²=C²HR³ + H•, using density functional theory (DFT, at the UB3LYP level of theory with 6-31G(d basis set. The optimum support vector regression (SVR model of the reactivity parameter u based on Gaussian radial basis function (RBF kernel (C = 10, ε = 10- 5 and γ = 1.0 produced root-mean-square (rms errors for the training, validation and prediction sets being 0.220, 0.326 and 0.345, respectively. The optimal SVR model for v with the RBF kernel (C = 20, ε = 10- 4 and γ = 1.2 produced rms errors for the training set of 0.123, the validation set of 0.206 and the prediction set of 0.238. The feasibility of applying the transition state quantum chemical descriptors to develop SVM models for reactivity parameters u and v in the U-V scheme has been demonstrated.

  14. Examining the Link Between Public Transit Use and Active Commuting

    Directory of Open Access Journals (Sweden)

    Melissa Bopp

    2015-04-01

    Full Text Available Background: An established relationship exists between public transportation (PT use and physical activity. However, there is limited literature that examines the link between PT use and active commuting (AC behavior. This study examines this link to determine if PT users commute more by active modes. Methods: A volunteer, convenience sample of adults (n = 748 completed an online survey about AC/PT patterns, demographic, psychosocial, community and environmental factors. t-test compared differences between PT riders and non-PT riders. Binary logistic regression analyses examined the effect of multiple factors on AC and a full logistic regression model was conducted to examine AC. Results: Non-PT riders (n = 596 reported less AC than PT riders. There were several significant relationships with AC for demographic, interpersonal, worksite, community and environmental factors when considering PT use. The logistic multivariate analysis for included age, number of children and perceived distance to work as negative predictors and PT use, feelings of bad weather and lack of on-street bike lanes as a barrier to AC, perceived behavioral control and spouse AC were positive predictors. Conclusions: This study revealed the complex relationship between AC and PT use. Further research should investigate how AC and public transit use are related.

  15. Satellites of Xe transitions induced by infrared active vibrational modes of CF4 and C2F6 molecules.

    Science.gov (United States)

    Alekseev, Vadim A; Schwentner, Nikolaus

    2011-07-28

    Absorption and luminescence excitation spectra of Xe/CF(4) mixtures were studied in the vacuum UV region at high resolution using tunable synchrotron radiation. Pressure-broadened resonance bands and bands associated with dipole-forbidden states of the Xe atom due to collision-induced breakdown of the optical selection rules are reported. The spectra display in addition numerous satellite bands corresponding to transitions to vibrationally excited states of a Xe-CF(4) collisional complex. These satellites are located at energies of Xe atom transition increased by one quantum energy in the IR active v(3) vibrational mode of CF(4) (v(3) = 1281 cm(-1)). Satellites of both resonance and dipole-forbidden transitions were observed. Satellites of low lying resonance states are spectrally broad bands closely resembling in shape their parent pressure-broadened resonance bands. In contrast, satellites of dipole-forbidden states and of high lying resonance states are spectrally narrow bands (FWHM ∼10 cm(-1)). The satellites of dipole-forbidden states are orders of magnitude stronger than transitions to their parent states due to collision-induced breakdown of the optical selection rules. These satellites are attributed to a coupling of dipole-forbidden and resonance states induced by the electric field of the transient CF(4) (v(3) = 0 ↔ v(3) = 1) dipole. Similar satellites are present in spectra of Xe/C(2)F(6) mixtures where these bands are induced by the IR active v(10) mode of C(2)F(6). Transitions to vibrationally excited states of Xe-CF(4)(C(2)F(6)) collision pairs were also observed in two-photon LIF spectra.

  16. Dynamic State Transitions in the Nervous System: From Ion Channels to Neurons to Networks

    Science.gov (United States)

    Århem, Peter; Braun, Hans A.; Huber, Martin T.; Liljenström, Hans

    The following sections are included: * Introduction * Ion channels: The microscopic scale * The variety of ion channels * Channel kinetics * Neurons: The mesoscopic scale * The feedback loops between membrane potential and ion currents * Neuron models: Concepts and examples * Impulse pattern modulation by ion channel densities * Oscillatory patterns * Irregular patterns * Impulse pattern modulation by subthreshold oscillations * The cold receptor model * Deterministic patterns and noise induced state-transitions on temperature scaling * Neuronal networks: The oscopic scale * Random channel events cause network state transitions * A hippocampal neural network model * Simulating noise-induced state transitions * Functional significance of oscopic neurodynamics * Conclusions * Appendix A: Computation of the neuron models * Hippocampal neuron model * The cold receptor model * Appendix B: Neural network model * References

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

    Science.gov (United States)

    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.

  18. The roles of entropy and enthalpy in stabilizing ion-pairs at transition states in zeolite acid catalysis.

    Science.gov (United States)

    Gounder, Rajamani; Iglesia, Enrique

    2012-02-21

    Acidic zeolites are indispensable catalysts in the petrochemical industry because they select reactants and their chemical pathways based on size and shape. Voids of molecular dimensions confine reactive intermediates and transition states that mediate chemical reactions, stabilizing them by van der Waals interactions. This behavior is reminiscent of the solvation effects prevalent within enzyme pockets and has analogous consequences for catalytic specificity. Voids provide the "right fit" for certain transition states, reflected in their lower free energies, thus extending the catalytic diversity of zeolites well beyond simple size discrimination. This catalytic diversity is even more remarkable because acid strength is essentially unaffected by confinement among known crystalline aluminosilicates. In this Account, we discuss factors that determine the "right fit" for a specific chemical reaction, exploring predictive criteria that extend the prevailing discourse based on size and shape. We link the structures of reactants, transition states, and confining voids to chemical reactivity and selectivity. Confinement mediates enthalpy-entropy compromises that determine the Gibbs free energies of transition states and relevant reactants; these activation free energies determine turnover rates via transition state theory. At low temperatures (400-500 K), dimethyl ether carbonylation occurs with high specificity within small eight-membered ring (8-MR) voids in FER and MOR zeolite structures, but at undetectable rates within larger voids (MFI, BEA, FAU, and SiO(2)-Al(2)O(3)). More effective van der Waals stabilization within 8-MR voids leads to lower ion-pair enthalpies but also lower entropies; taken together, carbonylation activation free energies are lower within 8-MR voids. The "right fit" is a "tight fit" at low temperatures, a consequence of how temperature appears in the defining equation for Gibbs free energy. In contrast, entropy effects dominate in high

  19. Where are Children Active and Does it Matter for Physical Activity? A Latent Transition Analysis.

    Science.gov (United States)

    Colabianchi, Natalie; Griffin, Jamie L; McIver, Kerry L; Dowda, Marsha; Pate, Russell R

    2016-12-01

    Numerous studies have focused on the role of environments in promoting physical activity, but few studies have examined the specific locations where children are active and whether being active in these locations is associated with physical activity levels over time. Self-reported locations of where physical activity occurred and physical activity measured via accelerometry were obtained for a cohort of 520 children in 5th and 6th grades. Latent class analysis was used to generate classes of children defined by the variety of locations where they were active (ie, home, school grounds, gyms, recreational centers, parks or playgrounds, neighborhood, and church). Latent transition analyses were used to characterize how these latent classes change over time and to determine whether the latent transitions were associated with changes in physical activity levels. Two latent classes were identified at baseline with the majority of children in the class labeled as 'limited variety.' Most children maintained their latent status over time. Physical activity levels declined for all groups, but significantly less so for children who maintained their membership in the 'greater variety' latent status. Supporting and encouraging physical activity in a variety of locations may improve physical activity levels in children.

  20. Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails.

    Directory of Open Access Journals (Sweden)

    Peter M Kasson

    2010-06-01

    Full Text Available Membrane fusion is essential to both cellular vesicle trafficking and infection by enveloped viruses. While the fusion protein assemblies that catalyze fusion are readily identifiable, the specific activities of the proteins involved and nature of the membrane changes they induce remain unknown. Here, we use many atomic-resolution simulations of vesicle fusion to examine the molecular mechanisms for fusion in detail. We employ committor analysis for these million-atom vesicle fusion simulations to identify a transition state for fusion stalk formation. In our simulations, this transition state occurs when the bulk properties of each lipid bilayer remain in a lamellar state but a few hydrophobic tails bulge into the hydrophilic interface layer and make contact to nucleate a stalk. Additional simulations of influenza fusion peptides in lipid bilayers show that the peptides promote similar local protrusion of lipid tails. Comparing these two sets of simulations, we obtain a common set of structural changes between the transition state for stalk formation and the local environment of peptides known to catalyze fusion. Our results thus suggest that the specific molecular properties of individual lipids are highly important to vesicle fusion and yield an explicit structural model that could help explain the mechanism of catalysis by fusion proteins.

  1. Jump Markov models and transition state theory: the quasi-stationary distribution approach.

    Science.gov (United States)

    Di Gesù, Giacomo; Lelièvre, Tony; Le Peutrec, Dorian; Nectoux, Boris

    2016-12-22

    We are interested in the connection between a metastable continuous state space Markov process (satisfying e.g. the Langevin or overdamped Langevin equation) and a jump Markov process in a discrete state space. More precisely, we use the notion of quasi-stationary distribution within a metastable state for the continuous state space Markov process to parametrize the exit event from the state. This approach is useful to analyze and justify methods which use the jump Markov process underlying a metastable dynamics as a support to efficiently sample the state-to-state dynamics (accelerated dynamics techniques). Moreover, it is possible by this approach to quantify the error on the exit event when the parametrization of the jump Markov model is based on the Eyring-Kramers formula. This therefore provides a mathematical framework to justify the use of transition state theory and the Eyring-Kramers formula to build kinetic Monte Carlo or Markov state models.

  2. Jump Markov models and transition state theory: the Quasi-Stationary Distribution approach

    CERN Document Server

    Di Gesù, Giacomo; Peutrec, Dorian Le; Nectoux, Boris

    2016-01-01

    We are interested in the connection between a metastable continuous state space Markov process (satisfying e.g. the Langevin or overdamped Langevin equation) and a jump Markov process in a discrete state space. More precisely, we use the notion of quasi-stationary distribution within a metastable state for the continuous state space Markov process to parametrize the exit event from the state. This approach is useful to analyze and justify methods which use the jump Markov process underlying a metastable dynamics as a support to efficiently sample the state-to-state dynamics (accelerated dynamics techniques). Moreover, it is possible by this approach to quantify the error on the exit event when the parametrization of the jump Markov model is based on the Eyring-Kramers formula. This therefore provides a mathematical framework to justify the use of transition state theory and the Eyring-Kramers formula to build kinetic Monte Carlo or Markov state models.

  3. Anaerobiosis induced state transition: a non photochemical reduction of PQ pool mediated by NDH in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Sreedhar Nellaepalli

    Full Text Available 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 F(o' 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.

  4. Traffic states and jamming transitions induced by a bus in two-lane traffic flow

    Science.gov (United States)

    Nagai, Ryoichi; Nagatani, Takashi; Taniguchi, Naoki

    2005-05-01

    We study the traffic states and jamming transitions induced by a bus (slow car) in a two-lane traffic of cars. We use the dynamic model which is an extended one of the optimal velocity model to take into account the lane changing. The fundamental (flow-density) diagram is presented. The fundamental diagram changes highly by introducing a bus on a two-lane roadway. It is found that there are the six distinct states for the two-lane traffic flow including a bus. The spatio-temporal patterns are presented for the distinct traffic states. The dynamical state of traffic changes with density of cars. It is shown that the dynamical transitions among the distinct traffic states occur at some values of density. The phase diagram (region map) is shown for the two-lane traffic flow including a bus.

  5. Irreversible transitions in the exchange-striction model of spin-glass state

    Science.gov (United States)

    Valkov, V. I.; Golovchan, A. V.

    2014-08-01

    Based on the assumption of a negative volume dependence of random exchange integrals, it is possible to switch to a compressible Sherrington-Kirkpatrick spin-glass model. Within the proposed model, temperature-pressure phase diagrams were calculated and pressure- and magnetic-field-induced first-order phase transitions from the initial paramagnetic and spin-glass states to the ferromagnetic state were predicted. It was shown that the application of pressure in the spin-glass state not only increases and shifts magnetic susceptibility, but also reduces the critical magnetic fields of irreversible induced phase transitions from the spin-glass to the ferromagnetic state. The obtained results are used to describe the spin-glass state in (Sm1-xGdx)0.55Sr0.45MnO3.

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

    Directory of Open Access Journals (Sweden)

    Vicente Martí-Centelles

    2012-01-01

    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.

  7. Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects.

    Science.gov (United States)

    Roston, Daniel; Cui, Qiang

    2016-09-14

    Enzymes are powerful catalysts, and a thorough understanding of the sources of their catalytic power will facilitate many medical and industrial applications. Here we have studied the catalytic mechanism of alkaline phosphatase (AP), which is one of the most catalytically proficient enzymes known. We have used quantum mechanics calculations and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to model a variety of isotope effects relevant to the reaction of AP. We have calculated equilibrium isotope effects (EIEs), binding isotope effects (BIEs), and kinetic isotope effects (KIEs) for a range of phosphate mono- and diester substrates. The results agree well with experimental values, but the model for the reaction's transition state (TS) differs from the original interpretation of those experiments. Our model indicates that isotope effects on binding make important contributions to measured KIEs on V/K, which complicated interpretation of the measured values. Our results provide a detailed interpretation of the measured isotope effects and make predictions that can test the proposed model. The model indicates that the substrate is deformed in the ground state (GS) of the reaction and partially resembles the TS. The highly preorganized active site preferentially binds conformations that resemble the TS and not the GS, which induces the substrate to adapt to the enzyme, rather than the other way around-as with classic "induced fit" models. The preferential stabilization of the TS over the GS is what lowers the barrier to the chemical step.

  8. SUMOylation inhibits FOXM1 activity and delays mitotic transition.

    Science.gov (United States)

    Myatt, S S; Kongsema, M; Man, C W-Y; Kelly, D J; Gomes, A R; Khongkow, P; Karunarathna, U; Zona, S; Langer, J K; Dunsby, C W; Coombes, R C; French, P M; Brosens, J J; Lam, E W-F

    2014-08-21

    The forkhead box transcription factor FOXM1 is an essential effector of G2/M-phase transition, mitosis and the DNA damage response. As such, it is frequently deregulated during tumorigenesis. Here we report that FOXM1 is dynamically modified by SUMO1 but not by SUMO2/3 at multiple sites. We show that FOXM1 SUMOylation is enhanced in MCF-7 breast cancer cells in response to treatment with epirubicin and mitotic inhibitors. Mutation of five consensus conjugation motifs yielded a SUMOylation-deficient mutant FOXM1. Conversely, fusion of the E2 ligase Ubc9 to FOXM1 generated an auto-SUMOylating mutant (FOXM1-Ubc9). Analysis of wild-type FOXM1 and mutants revealed that SUMOylation inhibits FOXM1 activity, promotes translocation to the cytoplasm and enhances APC/Cdh1-mediated ubiquitination and degradation. Further, expression of the SUMOylation-deficient mutant enhanced cell proliferation compared with wild-type FOXM1, whereas the FOXM1-Ubc9 fusion protein resulted in persistent cyclin B1 expression and slowed the time from mitotic entry to exit. In summary, our findings suggest that SUMOylation attenuates FOXM1 activity and causes mitotic delay in cytotoxic drug response.

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Bin [Center for Theoretical and Computational Chemistry, and State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States); Sun, Zhigang, E-mail: zsun@dicp.ac.cn, E-mail: hguo@unm.edu [Center for Theoretical and Computational Chemistry, and State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023 (China); Guo, Hua, E-mail: zsun@dicp.ac.cn, E-mail: hguo@unm.edu [Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131 (United States)

    2014-06-21

    A recently proposed transition-state wave packet method [R. Welsch, F. Huarte-Larrañaga, and U. Manthe, J. Chem. Phys. 136, 064117 (2012)] provides an efficient and intuitive framework to study reactive quantum scattering at the state-to-state level. It propagates a few transition-state wave packets, defined by the eigenfunctions of the low-rank thermal flux operator located near the transition state, into the asymptotic regions of the reactant and product arrangement channels separately using the corresponding Jacobi coordinates. The entire S-matrix can then be assembled from the corresponding flux-flux cross-correlation functions for all arrangement channels. Since the transition-state wave packets can be defined in a relatively small region, its transformation into either the reactant or product Jacobi coordinates is accurate and efficient. Furthermore, the grid/basis for the propagation, including the maximum helicity quantum number K, is much smaller than that required in conventional wave packet treatments of state-to-state reactive scattering. This approach is implemented for atom-diatom reactions using a time-dependent wave packet method and applied to the H + D{sub 2} reaction with all partial waves. Excellent agreement with benchmark integral and differential cross sections is achieved.

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

    Science.gov (United States)

    Zhao, Bin; Sun, Zhigang; Guo, Hua

    2014-06-01

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

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

    Institute of Scientific and Technical Information of China (English)

    WANG Hai; CHANG Hong; WU Haibin; XIE Chande

    2004-01-01

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

  12. Possible ground states and parallel magnetic-field-driven phase transitions of collinear antiferromagnets

    Science.gov (United States)

    Li, Hai-Feng

    2016-10-01

    Understanding the nature of all possible ground states and especially magnetic-field-driven phase transitions of antiferromagnets represents a major step towards unravelling the real nature of interesting phenomena such as superconductivity, multiferroicity or magnetoresistance in condensed-matter science. Here a consistent mean-field calculation endowed with antiferromagnetic (AFM) exchange interaction (J), easy axis anisotropy (γ), uniaxial single-ion anisotropy (D) and Zeeman coupling to a magnetic field parallel to the AFM easy axis consistently unifies the AFM state, spin-flop (SFO) and spin-flip transitions. We reveal some mathematically allowed exotic spin states and fluctuations depending on the relative coupling strength of (J, γ and D). We build the three-dimensional (J, γ and D) and two-dimensional (γ and D) phase diagrams clearly displaying the equilibrium phase conditions and discuss the origins of various magnetic states as well as their transitions in different couplings. Besides the traditional first-order type one, we unambiguously confirm an existence of a second-order type SFO transition. This study provides an integrated theoretical model for the magnetic states of collinear antiferromagnets with two interpenetrating sublattices and offers a practical approach as an alternative to the estimation of magnetic exchange parameters (J, γ and D), and the results may shed light on nontrivial magnetism-related properties of bulks, thin films and nanostructures of correlated electron systems.

  13. Characterizing metastable states beyond energies and lifetimes: Dyson orbitals and transition dipole moments.

    Science.gov (United States)

    Jagau, Thomas-C; Krylov, Anna I

    2016-02-07

    The theoretical description of electronic resonances is extended beyond calculations of energies and lifetimes. We present the formalism for calculating Dyson orbitals and transition dipole moments within the equation-of-motion coupled-cluster singles and doubles method for electron-attached states augmented by a complex absorbing potential (CAP-EOM-EA-CCSD). The capabilities of the new methodology are illustrated by calculations of Dyson orbitals of various transient anions. We also present calculations of transition dipole moments between transient and stable anionic states as well as between different transient states. Dyson orbitals characterize the differences between the initial neutral and final electron-attached states without invoking the mean-field approximation. By extending the molecular-orbital description to correlated many-electron wave functions, they deliver qualitative insights into the character of resonance states. Dyson orbitals and transition moments are also needed for calculating experimental observables such as spectra and cross sections. Physically meaningful results for those quantities are obtained only in the framework of non-Hermitian quantum mechanics, e.g., in the presence of a complex absorbing potential (CAP), when studying resonances. We investigate the dependence of Dyson orbitals and transition moments on the CAP strength and illustrate how Dyson orbitals help understand the properties of metastable species and how they are affected by replacing the usual scalar product by the so-called c-product.

  14. Characterizing metastable states beyond energies and lifetimes: Dyson orbitals and transition dipole moments

    Energy Technology Data Exchange (ETDEWEB)

    Jagau, Thomas-C.; Krylov, Anna I. [Department of Chemistry, University of Southern California, Los Angeles, California 90089 (United States)

    2016-02-07

    The theoretical description of electronic resonances is extended beyond calculations of energies and lifetimes. We present the formalism for calculating Dyson orbitals and transition dipole moments within the equation-of-motion coupled-cluster singles and doubles method for electron-attached states augmented by a complex absorbing potential (CAP-EOM-EA-CCSD). The capabilities of the new methodology are illustrated by calculations of Dyson orbitals of various transient anions. We also present calculations of transition dipole moments between transient and stable anionic states as well as between different transient states. Dyson orbitals characterize the differences between the initial neutral and final electron-attached states without invoking the mean-field approximation. By extending the molecular-orbital description to correlated many-electron wave functions, they deliver qualitative insights into the character of resonance states. Dyson orbitals and transition moments are also needed for calculating experimental observables such as spectra and cross sections. Physically meaningful results for those quantities are obtained only in the framework of non-Hermitian quantum mechanics, e.g., in the presence of a complex absorbing potential (CAP), when studying resonances. We investigate the dependence of Dyson orbitals and transition moments on the CAP strength and illustrate how Dyson orbitals help understand the properties of metastable species and how they are affected by replacing the usual scalar product by the so-called c-product.

  15. Laboratory rotational ground state transitions of NH$_3$D$^+$ and CF$^+$

    CERN Document Server

    Stoffels, Alexander; Schlemmer, Stephan; Brünken, Sandra

    2016-01-01

    Aims. This paper reports accurate laboratory frequencies of the rotational ground state transitions of two astronomically relevant molecular ions, NH3D+ and CF+. Methods. Spectra in the millimeter-wave band were recorded by the method of rotational state-selective attachment of He-atoms to the molecular ions stored and cooled in a cryogenic ion trap held at 4 K. The lowest rotational transition in the A state (ortho state) of NH$_3$D$^+$ ($J_K = 1_0 - 0_0$), and the two hyperfine components of the ground state transition of CF$^+$($J = 1 - 0$) were measured with a relative precision better than $10^{-7}$. Results. For both target ions the experimental transition frequencies agree with recent observations of the same lines in different astronomical environments. In the case of NH$_3$D$^+$ the high-accuracy laboratory measurements lend support to its tentative identification in the interstellar medium. For CF$^+$ the experimentally determined hyperfine splitting confirms previous quantum-chemical calculations a...

  16. Ejection of the corona at State transitions: a common behaviour in microquasars?

    CERN Document Server

    Prat, Lionel

    2009-01-01

    The onset of most microquasar outbursts is characterized by a state transition between a Low/Hard State (LHS) and a High/Soft State (HSS). Besides drastic spectral and timing changes, this transition often shows a discrete ejection event detectable in the radio range. However, the exact nature of the ejected material and the mechanisms that give birth to these phenomena are yet to be unraveled. Recent simultaneous radio and X-ray observations on several sources point to a coronal nature of the ejected material. In the cases of GRS 1915+105, XTE J1550-564, and the 2002 outburst of GX 339-4, the flux of the Compton component decreases sharply just before an ejection is detected in the radio range. Finally, in the case of H1743-322, drastic physical changes occurred in the corona just before the state transition, compatible with the disappearance of part of this medium. Thus, the behaviour of at least 4 microquasars points in the direction of an ejection of the corona at the state transition, feature that is yet...

  17. The charge percolation mechanism and simulation of Ziegler–Natta polymerizations Part III. Oxidation states of transition metals

    Directory of Open Access Journals (Sweden)

    BRANKA PILIC

    2006-04-01

    Full Text Available The oxidation state of the transition metal (Mt active centre is the most disputable question in the polymerization of olefins by Ziegler–Natta (ZN and metallocene complexes. In this paper the importance and the changes of the Mt active centres are presented and discussed on the basis of a charge percolation mechanism (CPM of olefin polymerization. Mt atoms can exist in different oxidation states and can be easily transformed from one to another state during activation. In all cases, the Mt atoms are present in several oxidation states, i.e., Mt+(n-1, Mt+(n to Mt+(n+1, producing an irregular charge distribution over the support surface. There is a tendency to equalize the oxidation states by a charge transfer from Mt+(n–1 (donor toMt+(n+1 (acceptor. This cannot occur since the different oxidation states are highly separated on the support. However, monomer molecules are adsorbed on the support producing clusters with stacked p-bonds, making a p-bond bridge between a donor and an acceptor. Once a bridge is formed (percolation moment, charge transfer occurs. The donor and acceptor equalize their oxidation states simultaneously with the polymerization of the monomer. The polymer chain is desorbed from the support, freeing the surface for subsequent monomer adsorption. The whole process is repeated with the oxidation-reduction of other donor-acceptor ensembles.

  18. Transit apps for people with brain injury and other cognitive disabilities: the state of the art.

    Science.gov (United States)

    Livingstone-Lee, Sharon A; Skelton, Ronald W; Livingston, Nigel

    2014-01-01

    Individuals with cognitive disability have difficulty using public transit, but little research is directed toward this issue. Recent studies suggest that smartphones may be useful assistive devices in this context. Current objectives were to (1) survey research into difficulties people with cognitive disabilities experience when using public transit, (2) survey the current state of the art of transit and personal navigation applications (apps) and features, (3) recommend best existing transit apps for people with cognitive disability, and (4) recommend the best designs and features of these apps to developers of future transit apps. Potentially useful features were found in four categories: Transit apps for (1) individuals with cognitive disabilities and (2) healthy individuals, and personal navigation apps for (3) individuals with cognitive disabilities and (4) healthy individuals. A total of 159 apps were examined, but only seven were found specific to public transit for cognitive disability. By comparing research recommendations and currently available features, we identified several unmet needs. We note that there appears to be a shortage of apps for this population-function but that there is good research in the area and it is well suited to inform app development.

  19. Dynamical transition in a jammed state of a quasi-two-dimensional foam

    Science.gov (United States)

    Kurita, Rei; Furuta, Yujiro; Yanagisawa, Naoya; Oikawa, Noriko

    2017-06-01

    The states of foam are empirically classified into dry foam and wet foam by the volume fraction of the liquid. Recently, a transition between the dry foam state and the wet foam state has been found by characterizing the bubble shapes [Furuta et al., Sci. Rep. 6, 37506 (2016), 10.1038/srep37506]. In the literature, it is indirectly ascertained that the transition from the dry to the wet form is related to the onset of the rearrangement of the bubbles, namely, the liquid fraction at which the bubbles become able to move to replace their positions. The bubble shape is a static property, and the rearrangement of the bubbles is a dynamic property. Thus, we investigate the relation between the bubble shape transition and the rearrangement event occurring in a collapsing process of the bubbles in a quasi-two-dimensional foam system. The current setup brings a good advantage to observe the above transitions, since the liquid fraction of the foam continuously changes in the system. It is revealed that the rearrangement of the bubbles takes place at the dry-wet transition point where the characteristics of the bubble shape change.

  20. Electronic states and spin-forbidden cooling transitions of AlH and AlF.

    Science.gov (United States)

    Wells, Nathan; Lane, Ian C

    2011-11-14

    The feasibility of laser cooling AlH and AlF is investigated using ab initio quantum chemistry. All the electronic states corresponding to the ground and lowest two excited states of the Al atom are calculated using multi-reference configuration interaction (MRCI) and the large AV6Z basis set for AlH. The smaller AVQZ basis set is used to calculate the valence electronic states of AlF. Theoretical Franck-Condon factors are determined for the A(1)Π→ X(1)Σ(+) transitions in both radicals and found to agree with the highly diagonal factors found experimentally, suggesting computational chemistry is an effective method for screening suitable laser cooling candidates. AlH does not appear to have a transition quite as diagonal as that in SrF (which has been laser cooled) but the A(1)Π→ X(1)Σ(+) transition transition of AlF is a strong candidate for cooling with just a single laser, though the cooling frequency is deep in the UV. Furthermore, the a(3)Π→ X(1)Σ(+) transitions are also strongly diagonal and in AlF is a practical method for obtaining very low final temperatures around 3 μK.

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

    Science.gov (United States)

    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.

  2. Outbursts and State Transitions in Black Hole Candidates observed by MAXI

    Science.gov (United States)

    Negoro, H.; Maxi Team

    2010-12-01

    MAXI continuously observes several black hole candidates in our Galaxy and LMC. MAXI already detected various state transitions in Cyg X-1, GX 339-4, Swift J1752.5-127, and black hole transients, H 1743-332, 4U 1630, XTE J1752-223, and MAXI J1659-125. From these observations, we try to clarify what happens during the transitions, and what triggers the transitions. In any case, fast alerts just before the transitions and soon after the outbursts are crucial to detect, for instance, radio and high energy gamma-ray jets or emission. We also present some successful examples of alerts from our MAXI transient alert system.

  3. Application of active disturbance rejection control method in aeroengines afterburning transition state control%自抗扰控制算法在发动机加力过渡态控制中的应用

    Institute of Scientific and Technical Information of China (English)

    张海波; 孙健国

    2010-01-01

    主要研究了航空发动机加力过渡态控制的新方法.在不改变原有发动机控制结构的基础上,提出了一种增广LQR法(Augmented Linear Quadratic regulator-ALQR)综合ADRC(Active Disturbance Rejection Control)干扰补偿控制的算法(简称ALQR+ADRC),该算法除了有原ALQR控制所具备的强的消除静差能力之外,还兼具ADRC优良的干扰补偿能力.通过模拟快速进入/退出发动机加力过渡态过程,验证了该算法具有理想的控制效果,能够较好地协调加力燃油供给和喷口开张,在整个过渡态过程中对核心机工作有较小的影响.

  4. Self-organization of stress patterns drives state transitions in actin cortices

    CERN Document Server

    Tan, Tzer Han; Abu-Shah, Enas; Li, Junang; Sharma, Abhinav; MacKintosh, Fred C; Keren, Kinneret; Schmidt, Christoph F; Fakhri, Nikta

    2016-01-01

    Biological functions rely on ordered structures and intricately controlled collective dynamics. In contrast to systems in thermodynamic equilibrium, order is typically established and sustained in stationary states by continuous dissipation of energy. Non-equilibrium dynamics is a necessary condition to make the systems highly susceptible to signals that cause transitions between different states. How cellular processes self-organize under this general principle is not fully understood. Here, we find that model actomyosin cortices, in the presence of rapid turnover, display distinct steady states, each distinguished by characteristic order and dynamics as a function of network connectivity. The different states arise from a subtle interaction between mechanical percolation of the actin network and myosin-generated stresses. Remarkably, myosin motors generate actin architectures, which in turn, force the emergence of ordered stress patterns. Reminiscent of second order phase transitions, the emergence of order...

  5. Non-equilibrium Phase Transitions: Activated Random Walks at Criticality

    Science.gov (United States)

    Cabezas, M.; Rolla, L. T.; Sidoravicius, V.

    2014-06-01

    In this paper we present rigorous results on the critical behavior of the Activated Random Walk model. We conjecture that on a general class of graphs, including , and under general initial conditions, the system at the critical point does not reach an absorbing state. We prove this for the case where the sleep rate is infinite. Moreover, for the one-dimensional asymmetric system, we identify the scaling limit of the flow through the origin at criticality. The case remains largely open, with the exception of the one-dimensional totally-asymmetric case, for which it is known that there is no fixation at criticality.

  6. Dimer-tetramer transition controls RUNX1/ETO leukemogenic activity.

    Science.gov (United States)

    Wichmann, Christian; Becker, Yvonne; Chen-Wichmann, Linping; Vogel, Vitali; Vojtkova, Anna; Herglotz, Julia; Moore, Sandra; Koch, Joachim; Lausen, Jörn; Mäntele, Werner; Gohlke, Holger; Grez, Manuel

    2010-07-29

    RUNX1/ETO, the fusion protein resulting from the chromosomal translocation t(8;21), is one of the most frequent translocation products in acute myeloid leukemia. Several in vitro and in vivo studies have shown that the homo-tetramerization domain of ETO, the nervy homology region 2 (NHR2), is essential for RUNX1/ETO oncogenic activity. We analyzed the energetic contribution of individual amino acids within the NHR2 to RUNX1/ETO dimer-tetramer transition and found a clustered area of 5 distinct amino acids with strong contribution to the stability of tetramers. Substitution of these amino acids abolishes tetramer formation without affecting dimer formation. Similar to RUNX1/ETO monomers, dimers failed to bind efficiently to DNA and to alter expression of RUNX1-dependent genes. RUNX1/ETO dimers do not block myeloid differentiation, are unable to enhance the self-renewal capacity of hematopoietic progenitors, and fail to induce leukemia in a murine transplantation model. Our data reveal the existence of an essential structural motif (hot spot) at the NHR2 dimer-tetramer interface, suitable for a molecular intervention in t(8;21) leukemias.

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

    Science.gov (United States)

    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.

  8. Efficient Computation of Transition State Resonances and Reaction Rates from a Quantum Normal Form

    NARCIS (Netherlands)

    Schubert, Roman; Waalkens, Holger; Wiggins, Stephen

    2006-01-01

    A quantum version of a recent formulation of transition state theory in phase space is presented. The theory developed provides an algorithm to compute quantum reaction rates and the associated Gamov-Siegert resonances with very high accuracy. The algorithm is especially efficient for multi-degree-o

  9. Wigner's dynamical transition state theory in phase space : classical and quantum

    NARCIS (Netherlands)

    Waalkens, Holger; Schubert, Roman; Wiggins, Stephen

    2008-01-01

    We develop Wigner's approach to a dynamical transition state theory in phase space in both the classical and quantum mechanical settings. The key to our development is the construction of a normal form for describing the dynamics in the neighbourhood of a specific type of saddle point that governs t

  10. Demonstration of the DSST State Transition Matrix Time-Update Properties Using the Linux GTDS Program

    Science.gov (United States)

    2011-09-01

    semigroup property of the state transition matrix. In Section 4 we describe the DSST orbit determination test cases. The test cases demonstrate the...via the semigroup property and its corollary (Test 3 and Test 3B) Closure Test with Mean Elements Only (Test Case 1 and 1B) This test starts with a 10

  11. Transition Operators Entering Neutrinoles Double Electron Capture to Excited Nuclear States

    CERN Document Server

    Vergados, J D

    2011-01-01

    We construct the effective transition operators relevant for neutrinoless double electron capture leading to final nuclear states different than $0^{+}$. From the structure of these operators we see that, if such a process is observed experimentally, it will be very helpful in singling out the very important light neutrino mass contribution from the other lepton violating mechanisms

  12. Molecular dynamics simulations from putative transition states of alpha-spectrin SH3 domain

    NARCIS (Netherlands)

    Periole, Xavier; Vendruscolo, Michele; Mark, Alan E.

    2007-01-01

    A series of molecular dynamics simulations in explicit solvent were started from nine structural models of the transition state of the SH3 domain of alpha-spectrin, which were generated by Lindorff Larsen et al. (Nat Struct Mol Biol 2004;11:443-449) using molecular dynamics simulations in which expe

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

    Science.gov (United States)

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

  14. A Cbx8-containing polycomb complex facilitates the transition to gene activation during ES cell differentiation.

    Directory of Open Access Journals (Sweden)

    Catherine Creppe

    2014-12-01

    Full Text Available Polycomb proteins play an essential role in maintaining the repression of developmental genes in self-renewing embryonic stem cells. The exact mechanism allowing the derepression of polycomb target genes during cell differentiation remains unclear. Our project aimed to identify Cbx8 binding sites in differentiating mouse embryonic stem cells. Therefore, we used a genome-wide chromatin immunoprecipitation of endogenous Cbx8 coupled to direct massive parallel sequencing (ChIP-Seq. Our analysis identified 171 high confidence peaks. By crossing our data with previously published microarray analysis, we show that several differentiation genes transiently recruit Cbx8 during their early activation. Depletion of Cbx8 partially impairs the transcriptional activation of these genes. Both interaction analysis, as well as chromatin immunoprecipitation experiments support the idea that activating Cbx8 acts in the context of an intact PRC1 complex. Prolonged gene activation results in eviction of PRC1 despite persisting H3K27me3 and H2A ubiquitination. The composition of PRC1 is highly modular and changes when embryonic stem cells commit to differentiation. We further demonstrate that the exchange of Cbx7 for Cbx8 is required for the effective activation of differentiation genes. Taken together, our results establish a function for a Cbx8-containing complex in facilitating the transition from a Polycomb-repressed chromatin state to an active state. As this affects several key regulatory differentiation genes this mechanism is likely to contribute to the robust execution of differentiation programs.

  15. High transition frequencies of dynamic functional connectivity states in the creative brain

    Science.gov (United States)

    Li, Junchao; Zhang, Delong; Liang, Aiying; Liang, Bishan; Wang, Zengjian; Cai, Yuxuan; Gao, Mengxia; Gao, Zhenni; Chang, Song; Jiao, Bingqing; Huang, Ruiwang; Liu, Ming

    2017-01-01

    Creativity is thought to require the flexible reconfiguration of multiple brain regions that interact in transient and complex communication patterns. In contrast to prior emphases on searching for specific regions or networks associated with creative performance, we focused on exploring the association between the reconfiguration of dynamic functional connectivity states and creative ability. We hypothesized that a high frequency of dynamic functional connectivity state transitions will be associated with creative ability. To test this hypothesis, we recruited a high-creative group (HCG) and a low-creative group (LCG) of participants and collected resting-state fMRI (R-fMRI) data and Torrance Tests of Creative Thinking (TTCT) scores from each participant. By combining an independent component analysis with a dynamic network analysis approach, we discovered the HCG had more frequent transitions between dynamic functional connectivity (dFC) states than the LCG. Moreover, a confirmatory analysis using multiplication of temporal derivatives also indicated that there were more frequent dFC state transitions in the HCG. Taken together, these results provided empirical evidence for a linkage between the flexible reconfiguration of dynamic functional connectivity states and creative ability. These findings have the potential to provide new insights into the neural basis of creativity. PMID:28383052

  16. High transition frequencies of dynamic functional connectivity states in the creative brain.

    Science.gov (United States)

    Li, Junchao; Zhang, Delong; Liang, Aiying; Liang, Bishan; Wang, Zengjian; Cai, Yuxuan; Gao, Mengxia; Gao, Zhenni; Chang, Song; Jiao, Bingqing; Huang, Ruiwang; Liu, Ming

    2017-04-06

    Creativity is thought to require the flexible reconfiguration of multiple brain regions that interact in transient and complex communication patterns. In contrast to prior emphases on searching for specific regions or networks associated with creative performance, we focused on exploring the association between the reconfiguration of dynamic functional connectivity states and creative ability. We hypothesized that a high frequency of dynamic functional connectivity state transitions will be associated with creative ability. To test this hypothesis, we recruited a high-creative group (HCG) and a low-creative group (LCG) of participants and collected resting-state fMRI (R-fMRI) data and Torrance Tests of Creative Thinking (TTCT) scores from each participant. By combining an independent component analysis with a dynamic network analysis approach, we discovered the HCG had more frequent transitions between dynamic functional connectivity (dFC) states than the LCG. Moreover, a confirmatory analysis using multiplication of temporal derivatives also indicated that there were more frequent dFC state transitions in the HCG. Taken together, these results provided empirical evidence for a linkage between the flexible reconfiguration of dynamic functional connectivity states and creative ability. These findings have the potential to provide new insights into the neural basis of creativity.

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

    Science.gov (United States)

    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.

  18. Energy use, efficiency gains and emission abatement in transitional industrialised economies. Poland and the Baltic states

    Energy Technology Data Exchange (ETDEWEB)

    Salay, Juergen

    1999-05-01

    This thesis is a study of how energy use and air pollution in Poland, Estonia, Latvia and Lithuania have been affected by the economic transition after 1989. It consists of six articles, which examine three different aspects of these changes. The first group of articles analyses the structure of energy use in the Baltic states (Article 1) and Poland (Articles 2 and 3) at the outset of transition. The results show that these countries had a primary energy consumption per GDP which was two to three times higher than in developed market economics because of a more energy intensive structure of the economy and higher specific energy intensities in many sectors of the economy. They also had significantly higher levels of air pollution per primary energy consumption and GDP because of a heavy reliance on fossil fuels, an energy intensive economy and an ineffective control of emissions. The deep fall in energy consumption during the first phase of transition was due to a sharp drop in industrial output and higher fuel prices. In the Baltic states, part of the fall in energy consumption was the result of shortfalls in the supply of oil and gas from Russia. The second group of articles (Articles 4 and 5) examines changes in electricity production, fuel consumption, generation efficiency and sulphur dioxide (SO{sub 2}) emissions in the Polish power industry between 1988 and 1997. The results show that SO{sub 2} emissions dropped by 45 per cent between 1988 and 1997. The drop in emissions was partly the result of a fall in economic activity and electricity production in the early 1990s. Other reasons were more important. One reason was the restructuring of the power industry, during which hard budget constraints were introduced and the price of coal was raised. Another reason for the fall in emissions was the reorganisation and stricter enforcement of environmental protection. Together, these reforms created strong incentives for power plants to switch to high-quality coal

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-10-29

    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 POM 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.

  20. Ionic and covalent stabilization of intermediates and transition states in catalysis by solid acids.

    Science.gov (United States)

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

    2014-10-29

    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 POM 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.

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

    Science.gov (United States)

    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.

  2. Bona fide interaction-driven topological phase transition in correlated symmetry-protected topological states

    Science.gov (United States)

    He, Yuan-Yao; Wu, Han-Qing; You, Yi-Zhuang; Xu, Cenke; Meng, Zi Yang; Lu, Zhong-Yi

    2016-03-01

    It is expected that the interplay between nontrivial band topology and strong electron correlation will lead to very rich physics. Thus a controlled study of the competition between topology and correlation is of great interest. Here, employing large-scale quantum Monte Carlo simulations, we provide a concrete example of the Kane-Mele-Hubbard model on an AA-stacking bilayer honeycomb lattice with interlayer antiferromagnetic interaction. Our simulation identified several different phases: a quantum spin Hall insulator (QSH), an x y -plane antiferromagnetic Mott insulator, and an interlayer dimer-singlet insulator. Most importantly, a bona fide topological phase transition between the QSH and the dimer-singlet insulators, purely driven by the interlayer antiferromagnetic interaction, is found. At the transition, the spin and charge gap of the system close while the single-particle excitations remain gapped, which means that this transition has no mean-field analog and it can be viewed as a transition between bosonic symmetry-protected topological (SPT) states. At one special point, this transition is described by a (2 +1 )d O (4 ) nonlinear sigma model with exact S O (4 ) symmetry and a topological term at exactly Θ =π . The relevance of this work towards more general interacting SPT states is discussed.

  3. Bona fide interaction-driven topological phase transition in correlated SPT states

    Science.gov (United States)

    Meng, Zi Yang; He, Yuan-Yao; Wu, Han-Qing; You, Yi-Zhuang; Xu, Cenke; Lu, Zhong-Yi

    It is expected the interplay between non-trivial band topology and strong electron correlation will lead to very rich physics. Thus a controlled study of the competition between topology and correlation is of great interest. Here, employing large-scale quantum Monte Carlo simulations, we provide a concrete example of the Kane-Mele-Hubbard model on an AA stacking bilayer honeycomb lattice with inter-layer antiferromagnetic interaction. Our simulation identified several different phases: a quantum spin-Hall insulator (QSH), a xy-plane antiferromagnetic Mott insulator (xy-AFM) and an inter-layer dimer-singlet insulator (dimer-singlet). Most importantly, a bona fide topological phase transition between the QSH and the dimer-singlet insulators, purely driven by the inter-layer antiferromagnetic interaction is found. At the transition, the spin and charge gap of the system close while the single-particle excitations remain gapped, which means that this transition has no mean field analogue and it can be viewed as a transition between bosonic SPT states. At one special point, this transition is described by a (2+1)d O(4) nonlinear sigma model with exact SO(4) symmetry, and a topological term at theta=p. Relevance of this work towards more general interacting SPT states is discussed.

  4. SEMICONDUCTOR DEVICES Physical effect on transition from blocking to conducting state of barrier-type thyristor

    Science.gov (United States)

    Hairong, Li; Siyuan, Li

    2010-12-01

    The transition of the barrier-type thyristor (BTH) from blocking to conducting-state occurs between two entirely contrary physical states with great disparity in nature. The physical effects and mechanisms of the transition are studied in depth. The features of the transition snapback point are analyzed in detail. The transition snapback point has duality and is just the position where the barrier is flattened. It has a significant influence on the capture cross-section of the hole and high-level hole lifetime, resulting in the device entering into deep base conductance modulation. The physical nature of the negative differential resistance segment I-V characteristics is studied. It is testified by using experimental data that the deep conductance modulation is the basic feature and the linchpin of the transition process. The conditions and physical mechanisms of conductance modulation are investigated. The related physical subjects, including the flattening of the channel barrier, the buildup of the double injection, the formation of the plasma, the realization of the high-level injection, the elimination of the gate junction depletion region, the deep conductance modulation, and the increase in the hole's lifetime are all discussed in this paper.

  5. Collapse of the normal-state pseudogap at a Lifshitz transition in the Bi(2)Sr(2)CaCu(2)O(8+δ) cuprate superconductor.

    Science.gov (United States)

    Benhabib, S; Sacuto, A; Civelli, M; Paul, I; Cazayous, M; Gallais, Y; Méasson, M-A; Zhong, R D; Schneeloch, J; Gu, G D; Colson, D; Forget, A

    2015-04-10

    We report a fine tuned doping study of strongly overdoped Bi_{2}Sr_{2}CaCu_{2}O_{8+δ} single crystals using electronic Raman scattering. Combined with theoretical calculations, we show that the doping, at which the normal-state pseudogap closes, coincides with a Lifshitz quantum phase transition where the active holelike Fermi surface becomes electronlike. This conclusion suggests that the microscopic cause of the pseudogap is sensitive to the Fermi surface topology. Furthermore, we find that the superconducting transition temperature is unaffected by this transition, demonstrating that their origins are different on the overdoped side.

  6. Visualizing the Contributions of Virtual States to Two-Photon Absorption Cross Sections by Natural Transition Orbitals of Response Transition Density Matrices.

    Science.gov (United States)

    Nanda, Kaushik D; Krylov, Anna I

    2017-07-20

    Observables such as two-photon absorption cross sections cannot be computed from the wave functions of initial and final states alone because of their nonlinear nature. Rather, they depend on the entire manifold of the excited states, which follows from the familiar sum-over-states expressions of second- and higher-order properties. Consequently, the interpretation of the computed nonlinear optical properties in terms of molecular orbitals is not straightforward and usually relies on approximate few-states models. Here, we show that the two-photon absorption (2PA) transitions can be visualized using response one-particle transition density matrices, which are defined as transition density matrices between the zero-order and first-order perturbed states. We also extend the concept of natural transition orbitals to 2PA transitions. We illustrate the utility of this new tool, which provides a rigorous black box alternative to traditional qualitative few-states analysis, by considering 2PA transitions in ethylene, trans-stilbene, and para-nitroaniline.

  7. Transition from vibrational to rotational character in low-lying states of hypernuclei

    Science.gov (United States)

    Mei, H.; Hagino, K.; Yao, J. M.; Motoba, T.

    2017-07-01

    In order to clarify the nature of hypernuclear low-lying states, we carry out a comprehensive study of the structure of Λ 145-155Sm hypernuclei, which exhibit a transition from vibrational to rotational character as the neutron number increases. To this end, we employ a microscopic particle-core coupling scheme based on a covariant density functional theory. We find that the positive-parity ground-state band in the hypernuclei shares a similar structure to that of the corresponding core nucleus. That is, regardless of whether the core nucleus is spherical or deformed, each hypernuclear state is dominated by the single configuration of the Λ particle in the s1 /2 state (Λ s1 /2 ) coupled to one core state of the ground band. In contrast, the low-lying negative-parity states mainly consist of Λ p1 /2 and Λ p3 /2 configurations coupled to plural nuclear core states. We show that, while the mixing amplitude between these configurations is negligibly small in spherical and weakly deformed nuclei, it strongly increases as the core nucleus undergoes a transition to a well deformed shape, which is consistent with the Nilsson wave functions. We demonstrate that the structure of these negative-parity states with spin I can be well understood based on a naive L S coupling scheme, with total orbital angular momentum L =[I ⊗1 ] and spin angular momentum S =1 /2 .

  8. Chaotic state to self-organized critical state transition of serrated flow dynamics during brittle-to-ductile transition in metallic glass

    Energy Technology Data Exchange (ETDEWEB)

    Wang, C.; Wang, W. H.; Bai, H. Y., E-mail: hybai@aphy.iphy.ac.cn [Institute of Physics, Chinese Academy of Sciences, Beijing 100190 (China); Sun, B. A. [Centre for Advanced Structural Materials, Department of Mechanical and Biomedical Engineering, City University of Hong Kong, Kowloon Tong, Kowloon (Hong Kong)

    2016-02-07

    We study serrated flow dynamics during brittle-to-ductile transition induced by tuning the sample aspect ratio in a Zr-based metallic glass. The statistical analysis reveals that the serrated flow dynamics transforms from a chaotic state characterized by Gaussian-distribution serrations corresponding to stick-slip motion of randomly generated and uncorrelated single shear band and brittle behavior, into a self-organized critical state featured by intermittent scale-free distribution of shear avalanches corresponding to a collective motion of multiple shear bands and ductile behavior. The correlation found between serrated flow dynamics and plastic deformation might shed light on the plastic deformation dynamic and mechanism in metallic glasses.

  9. Topological phase transition and quantum spin Hall edge states of antimony few layers

    Science.gov (United States)

    Kim, Sung Hwan; Jin, Kyung-Hwan; Park, Joonbum; Kim, Jun Sung; Jhi, Seung-Hoon; Yeom, Han Woong

    2016-09-01

    While two-dimensional (2D) topological insulators (TI’s) initiated the field of topological materials, only very few materials were discovered to date and the direct access to their quantum spin Hall edge states has been challenging due to material issues. Here, we introduce a new 2D TI material, Sb few layer films. Electronic structures of ultrathin Sb islands grown on Bi2Te2Se are investigated by scanning tunneling microscopy. The maps of local density of states clearly identify robust edge electronic states over the thickness of three bilayers in clear contrast to thinner islands. This indicates that topological edge states emerge through a 2D topological phase transition predicted between three and four bilayer films in recent theory. The non-trivial phase transition and edge states are confirmed for epitaxial films by extensive density-functional-theory calculations. This work provides an important material platform to exploit microscopic aspects of the quantum spin Hall phase and its quantum phase transition.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

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

    2016-09-01

    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.

  12. Equation of state and transition temperatures in the quark-hadron hybrid model

    Science.gov (United States)

    Miyahara, Akihisa; Torigoe, Yuhei; Kouno, Hiroaki; Yahiro, Masanobu

    2016-07-01

    We analyze the equation of state of 2 +1 flavor lattice QCD at zero baryon density by constructing a simple quark-hadron hybrid model that has both quark and hadron components simultaneously. We calculate the hadron and quark contributions separately and parameterize those to match with lattice QCD data. Lattice data on the equation of state are decomposed into hadron and quark components by using the model. The transition temperature is defined by the temperature at which the hadron component is equal to the quark one in the equation of state. The transition temperature thus obtained is about 215 MeV; this is somewhat higher than the chiral and the deconfinement pseudocritical temperatures defined by the temperature at which the susceptibility or the absolute value of the derivative of the order parameter with respect to temperature becomes maximum.

  13. Existence of topological nontrivial surface states in strained transition metals: W, Ta, Mo, and Nb

    Science.gov (United States)

    Thonig, Danny; Rauch, Tomáš; Mirhosseini, Hossein; Henk, Jürgen; Mertig, Ingrid; Wortelen, Henry; Engelkamp, Bernd; Schmidt, Anke B.; Donath, Markus

    2016-10-01

    We show that a series of transition metals with strained body-centered cubic lattice—W, Ta, Nb, and Mo—hosts surface states that are topologically protected by mirror symmetry and, thus, exhibits nonzero topological invariants. These findings extend the class of topologically nontrivial systems by topological crystalline transition metals. The investigation is based on calculations of the electronic structures and of topological invariants. The signatures of a Dirac-type surface state in W(110), e.g., the linear dispersion and the spin texture, are verified. To further support our prediction, we investigate Ta(110) both theoretically and experimentally by spin-resolved inverse photoemission: unoccupied topologically nontrivial surface states are observed.

  14. Ferroelasticity and spin-state transitions of LaCoO3

    Science.gov (United States)

    Araki, Wakako; Abe, Takehiro; Arai, Yoshio

    2014-07-01

    A uniaxial compression test of polycrystalline lanthanum cobaltite (LCO) was performed to investigate mechanical behavior of LCO in the temperature range of 83-553 K. Prepared by solid-state reaction, the electrical resistivity and the linear expansion coefficient of polycrystalline LCO, measured between 80 and 1273 K, exhibit distinct changes attributed to spin-state transitions of cobalt ions around 100-200 K and 400-600 K, but are relatively constant between 200 and 400 K. The stress-strain curve obtained under uniaxial compression shows strong nonlinearity due to ferroelastic domain switching process between 83 and 553 K. Initial Young's moduli, critical stress, and dissipated energy evaluated from the stress-strain curves decrease by about a half with increasing the temperature, whereas there was no drastic changes even around the spin-state transition temperatures. The initial modulus agrees with the temperature dependence of the apparent Young's modulus measured under low-stress cyclic loading.

  15. Forbidden Transition Probabilities of Astrophysical Interest among Low-lying States of V III

    Indian Academy of Sciences (India)

    Andrei Irimia

    2007-06-01

    Electric and magnetic multipole transitions among low-lying states of doubly ionized vanadium were computed using the multi-configuration Hartree–Fock (MCHF) method with Breit–Pauli (BP) corrections to a non-relativistic Hamiltonian. Energy levels were determined up to and including 32(1)4 b 27/2 and computed energies were found to be in good agreement with experiment and other theories. In addition to Einstein coefficients for some E2 and M1 transitions, lifetime data and selected weighted oscillator strengths are also reported.

  16. Immigration transition and depressive symptoms: four major ethnic groups of midlife women in the United States.

    Science.gov (United States)

    Im, Eun-Ok; Chang, Sun Ju; Chee, Wonshik; Chee, Eunice; Mao, Jun James

    2015-01-01

    The purpose of this study was to explore the relationships between immigration transition and depressive symptoms among 1,054 midlife women in the United States. This was a secondary analysis of the data from two national Internet survey studies. Questions on background characteristics and immigration transition and the Depression Index for Midlife Women were used to collect the data. The data were analyzed using inferential statistics including multiple regressions. Immigrants reported lower numbers of symptoms and less severe symptoms than nonimmigrants (p immigration status were significant predictors of depressive symptoms (R(2) =.01, p <.05).

  17. High-pressure resistance and equation-of-state anomalies in Zn: a possible Lifshitz transition

    Energy Technology Data Exchange (ETDEWEB)

    Garg, Alka B.; Vijayakumar, V.; Modak, P.; Gaitonde, D.M.; Rao, R.S.; Godwal, B.K.; Sikka, S.K. [High Pressure Physics Division, Bhabha Atomic Research Centre, Mumbai (India)

    2002-09-30

    Experimental results on electrical resistance variation with pressure up to 25 GPa are presented for zinc; they reveal the signature of an electronic topological transition. Theoretical estimates based on the results of first-principles band structure calculations corroborate the observed variation of the resistance. The Lifshitz transition, which is hardly observable in experimental P-V data, becomes discernible via the equation of state, in the universal as well as in Holzapfel's form. Another anomaly in the measured resistance is also observed around 20 GPa pressure. The resistance variation with pressure exhibits considerable hysteresis. (author)

  18. Catalytic Efficiency Is a Function of How Rhodium(I) (5 + 2) Catalysts Accommodate a Conserved Substrate Transition State Geometry: Induced Fit Model for Explaining Transition Metal Catalysis.

    Science.gov (United States)

    Mustard, Thomas J L; Wender, Paul A; Cheong, Paul Ha-Yeon

    2015-03-06

    The origins of differential catalytic reactivities of four Rh(I) catalysts and their derivatives in the (5 + 2) cycloaddition reaction were elucidated using density functional theory. Computed free energy spans are in excellent agreement with known experimental rates. For every catalyst, the substrate geometries in the transition state remained constant (Catalytic efficiency is shown to be a function of how well the catalyst accommodates the substrate transition state geometry and electronics. This shows that the induced fit model for explaining biological catalysis may be relevant to transition metal catalysis. This could serve as a general model for understanding the origins of efficiencies of catalytic reactions.

  19. Within-state availability of transition-to-adulthood services for youths with serious mental health conditions.

    Science.gov (United States)

    Davis, Maryann; Geller, Jeffrey L; Hunt, Bethany

    2006-11-01

    This study describes the existence and nature of services within state child and adult mental health systems that support the transition from adolescence to adulthood. State child and adult mental health administrators from all but one state were interviewed by telephone with a semistructured questionnaire regarding transition services in their state mental health system, such as supported housing, vocational support, preparation for independent living, and dual diagnosis treatment. Eight states were deemed sufficiently decentralized to render state-level administrator reports invalid. Specific service data from the remaining 41 states and the District of Columbia were analyzed with descriptive statistics. One-quarter of child state mental health systems and one-half of adult state mental health systems offered no transition services, and few provided any kind of transition service at more than one site. Most types of transition services were available at all in less than 20 percent of the states. Across the United States transition support services are lacking. The adult system in particular will require major transformation to provide the service capacity that is needed to meet the current standards of transition service accessibility for young Americans with serious mental health conditions.

  20. Transition state models for probing stereoinduction in Evans chiral auxiliary-based asymmetric aldol reactions.

    Science.gov (United States)

    Shinisha, C B; Sunoj, Raghavan B

    2010-09-08

    The use of chiral auxiliaries is one of the most fundamental protocols employed in asymmetric synthesis. In the present study, stereoselectivity-determining factors in a chiral auxiliary-based asymmetric aldol reaction promoted by TiCl(4) are investigated by using density functional theory methods. The aldol reaction between chiral titanium enolate [derived from Evans propionyl oxazolidinone (1a) and its variants oxazolidinethione (1b) and thiazolidinethione (1c)] and benzaldehyde is examined by using transition-state modeling. Different stereochemical possibilities for the addition of titanium enolates to aldehyde are compared. On the basis of the coordination of the carbonyl/thiocarbonyl group of the chiral auxiliary with titanium, both pathways involving nonchelated and chelated transition states (TSs) are considered. The computed relative energies of the stereoselectivity-determining C-C bond formation TSs in the nonchelated pathway, for both 1a and 1c, indicate a preference toward Evans syn aldol product. The presence of a ring carbonyl or thiocarbonyl group in the chiral auxiliary renders the formation of neutral TiCl(3)-enolate, which otherwise is energetically less favored as compared to the anionic TiCl(4)-enolate. Hence, under suitable conditions, the reaction between titanium enolate and aldehyde is expected to be viable through chelated TSs leading to the selective formation of non-Evans syn aldol product. Experimentally known high stereoselectivity toward Evans syn aldol product is effectively rationalized by using the larger energy differences between the corresponding diastereomeric TSs. In both chelated and nonchelated pathways, the attack by the less hindered face of the enolate on aldehyde through a chair-like TS with an equatorial disposition of the aldehydic substituent is identified as the preferred mode. The steric hindrance offered by the isopropyl group and the possible chelation are identified as the key reasons behind the interesting

  1. Ground-State Transition in a Two-Dimensional Frenkel-Kontorova Model

    Institute of Scientific and Technical Information of China (English)

    YUAN Xiao-Ping; ZHENG Zhi-Gang

    2011-01-01

    The ground state of a generalized Frenkel-Kontorova model with a transversaJ degree of freedom is studied. When the coupling strength, K, and the frequency of & single-Atom vibration in the transversaJ direction, ωou are increased, the ground state of the model undergoes a transition from a two-dimensional configuration to a one-dimensional one. This transition can manifest in different ways. Furthermore, we find that the prerequisite of a two-dimensionai ground state is θ≠1//q.%The ground state of a generalized Frenkel-Kontorova model with a transversal degree of freedom is studied.When the coupling strength,K,and the frequency of a single-atom vibration in the transversal direction,ωoy,are increased,the ground state of the model undergoes a transition from a two-dimensional configuration to a one-dimensional one.This transition can manifest in different ways.Furthermore,we find that the prerequisite of a two-dimensional ground state is θ ≠ 1/q.In recent years,the Frenkel-Kontorova (FK) model has been applied to a variety of physical systems,such as adsorbed monolayers,[1,2] Josephsonjunction arrays,[3-5] tribology[6-8] and charge-density waves.[9,10] Experimental and large-scale simulation data at the nanoscale have become available,and more complicated FK-type models have been investigated using simulations of molecular dynamics.[11

  2. NuSTAR Observations of the State Transition of Millisecond Pulsar Binary PSR J1023+0038

    DEFF Research Database (Denmark)

    Tendulkar, Shriharsh P.; Yang, Chengwei; An, Hongjun

    2014-01-01

    disappearance of the pulsar, the 3-79 keV X-ray spectrum was well fit by a simple power law with a photon index of Gamma = 1.17(-0.07)(+0.08) (at 90% confidence) with a 3-79 keV luminosity of 7.4 +/- 0.4 x 10(32) erg s(-1). Significant orbital modulation was observed with a modulation fraction of 36% +/- 10......-60 s. No change in hardness ratio was observed during the dips. Consecutive dip separations are log-normal in distribution with a typical separation of approximately 400 s. These dips are distinct from dipping activity observed in LMXBs. We compare and contrast these dips to observations of dips...... and state changes in the similar transition systems PSR J1824-2452I and XSS J1227.0-4859 and discuss possible interpretations based on the transitions in the inner disk....

  3. NuSTAR Observations of the State Transition of Millisecond Pulsar Binary PSR J1023+0038

    DEFF Research Database (Denmark)

    Tendulkar, Shriharsh P.; Yang, Chengwei; An, Hongjun

    2014-01-01

    of the pulsar, the 3-79 keV X-ray spectrum was well fit by a simple power law with a photon index of Gamma=1.17 +/-0.08 (at 90% confidence) with a 3-79 keV luminosity of 7.4+/-0.4 x 10^32 erg/s. Significant orbital modulation was observed with a modulation fraction of 36+/-10%. During the October 19....... Consecutive dip separations are log-normal in distribution with a typical separation of approximately 400 s. These dips are distinct from dipping activity observed in LMXBs. We compare and contrast these dips to observations of dips and state changes in the similar transition systems PSR J1824-2452I and XSS J......1227.0-4859 and discuss possible interpretations based on the transitions in the inner disk....

  4. Possible Realization of Cluster States and Quantum Information Transfer in Cavity QED via Raman Transition

    Institute of Scientific and Technical Information of China (English)

    ZHAN Zhi-Ming; LI Wei-Bin

    2007-01-01

    We present a scheme to generate cluster states with many atoms in cavity QED via Raman transition. In this scheme, no transfer of quantum information between the atoms and cavities is required, the cavity fields are only virtually excited and thus the cavity decay is suppressed during the generation of cluster states. The atoms are always populated in the two ground states. Therefore, the scheme is insensitive to the atomic spontaneous emission and cavity decay. We also show how to transfer quantum information from one atom to another.

  5. Crossover of high and low spin states in transition metal complexes

    CERN Document Server

    Raebiger, Hannes; Yasuhara, Hiroshi

    2012-01-01

    The stability of high vs. low spin states of transition metal complexes has been interpreted by ligand field theory, which is a perturbation theory of the electron-electron interaction. The present first principles calculation of a series of five cobalt complexes shows that the electron-electron interaction energy difference between the two states (i) exhibits the opposite trend to the total energy difference as the ligand nuclear charge varies, and (ii) is three or four orders of magnitude greater than the total energy difference. A new interpretation of the crossover of high and low spin states is given in terms of the chemical bonding.

  6. On matrix stabilisation of d- and f-transition metal ions in unstable oxidation states

    Energy Technology Data Exchange (ETDEWEB)

    Kiselev, Yurii M [Department of Chemistry, M.V. Lomonosov Moscow State University, Moscow (Russian Federation)

    2009-01-31

    The state-of-the-art in matrix stabilisation of d- and f-transition metal ions in unstable oxidation states is analysed. Main aspects of this problem concerning the genealogy of appropriate matrix systems are classified. Relevant examples are given and the data that contradict the scheme proposed are discussed. The thermodynamics of the matrix stabilisation effect is considered using the concept of isomorphic miscibility. The influence of defects and non-equilibrium on the matrix stabilisation effect is discussed. The problem of identification of the oxidation states in matrix systems is examined and various types of matrix systems are considered.

  7. Atomic clock with a nuclear transition: solid state approach at TU Wien

    CERN Document Server

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

    2011-01-01

    The nucleus of 229Thorium presents a unique isomer state of very low energy and long lifetime, current estimates are around 7.8 eV and seconds to hours respectively. This nuclear transitions therefore is a promising candidate for a novel type of frequency standard and several groups worldwide have set out to investigate this system. Our aim is to construct a "solid state nuclear clock", i.e. a frequency standard where Thorium ions are implanted into Calciumfluoride crystals transparent in vacuum ultraviolet range. As a first step towards an accurate determination of the exact energy and lifetime of this isomer state we perform low-resolution fluorescent spectroscopic measurements.

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

    Science.gov (United States)

    Fajer, Mikolai; Meng, Yilin; Roux, Benoît

    2016-10-28

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

  9. Simulation study on dynamics transition in neuronal activity during sleep cycle by using asynchronous and symmetry neural network model.

    Science.gov (United States)

    Nakao, M; Takahashi, T; Mizutani, Y; Yamamoto, M

    1990-01-01

    We have found that single neuronal activities in different regions in the brain commonly exhibit the distinct dynamics transition during sleep-waking cycle in cats. Especially, power spectral densities of single neuronal activities change their profiles from the white to the 1/f along with sleep cycle from slow wave sleep (SWS) to paradoxical sleep (PS). Each region has different neural network structure and physiological function. This suggests a globally working mechanism may be underlying the dynamics transition we concern. Pharmacological studies have shown that a change in a wide-spread serotonergic input to these regions possibly causes the neuronal dynamics transition during sleep cycle. In this paper, based on these experimental results, an asynchronous and symmetry neural network model including inhibitory input, which represents the role of the serotonergic system, is utilized to examine the reality of our idea that the inhibitory input level varying during sleep cycle induce that transition. Simulation results show that the globally applied inhibitory input can control the dynamics of single neuronal state evolution in the artificial neural network: 1/f-like power spectral density profiles result under weak inhibition, which possibly corresponds to PS, and white profiles under strong inhibition, which possibly corresponds to SWS. An asynchronous neural network is known to change its state according to its energy function. The geometrical structure of network energy function is thought to vary along with the change in inhibitory level, which is expected to cause the dynamics transition of neuronal state evolution in the network model. These simulation results support the possibility that the serotonergic system is essential for the dynamics transition of single neuronal activities during sleep cycle.

  10. Alternation of up and down states at a dynamical phase-transition of a neural networkwith spatiotemporal attractors

    Directory of Open Access Journals (Sweden)

    Silvia eScarpetta

    2014-05-01

    Full Text Available Complex collective activity emerges spontaneously in cortical circuits in-vivo and in-vitro, such as alternation of up and down states, precise spatiotemporal patterns replay, and power law scaling of neural avalanches. We focus on such critical features observed in cortical slices.We study spontaneous dynamics emerging in noisy recurrent networks of spiking neurons with sparse structured connectivity.The emerging spontaneous dynamics is studied, in presence of noise, with fixed connections. Note that no short-term synaptic depression is used. Two different regimes of spontaneous activity emerge changing the connection strength or noise intensity: a low activity regime, characterized by a nearly exponential distribution of firing rates with a maximum at rate zero, and a high activity regime, characterized by a nearly Gaussian distribution peaked at a high rate for high activity, with long-lasting replay of stored patterns. Between this two regimes, a transition region is observed, where firing rates show a bimodal distribution, with alternation of up and down states. In this region, one observes neuronal avalanches exhibiting power laws in size and duration, and a waiting time distribution between successive avalanches which shows a non-monotonic behaviour. During periods of high activity (up states consecutive avalanches are correlated, since they are part of a short transient replay initiated by noise focusing, and waiting times show a power law distribution. One can think at this critical dynamics as a reservoire of dynamical patterns for memory functions.

  11. Universal dynamics of density correlations at the transition to the many-body localized state

    Science.gov (United States)

    Mierzejewski, M.; Herbrych, J.; Prelovšek, P.

    2016-12-01

    Within one-dimensional disordered models of interacting fermions, we perform a numerical study of several dynamical density correlations, which can serve as hallmarks of the transition to the many-body localized state. The results confirm that density-wave correlations exhibit quite an abrupt change with increasing disorder, with a nonvanishing long-time value characteristic for the nonergodic phase. In addition, our results reveal a logarithmic variation of correlations in time in a wide time window, which we can bring in connection with the anomalous behavior of the dynamical conductivity near the transition. Our results support the view that the transition to many-body localization can be characterized by universal dynamical exponents.

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

    Science.gov (United States)

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

    2017-02-23

    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.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  15. Transition State Models for Understanding the Origin of Chiral Induction in Asymmetric Catalysis.

    Science.gov (United States)

    Sunoj, Raghavan B

    2016-05-17

    In asymmetric catalysis, a chiral catalyst bearing chiral center(s) is employed to impart chirality to developing stereogenic center(s). A rich and diverse set of chiral catalysts is now available in the repertoire of synthetic organic chemistry. The most recent trends point to the emergence of axially chiral catalysts based on binaphthyl motifs, in particular, BINOL-derived phosphoric acids and phosphoramidites. More fascinating ideas took shape in the form of cooperative multicatalysis wherein organo- and transition-metal catalysts are made to work in concert. At the heart of all such manifestations of asymmetric catalysis, classical or contemporary, is the stereodetermining transition state, which holds a perennial control over the stereochemical outcome of the catalytic process. Delving one step deeper, one would find that the origin of the stereoselectivity is delicately dependent on the relative stabilization of one transition state, responsible for the formation of the predominant stereoisomer, over the other transition state for the minor stereoisomer. The most frequently used working hypothesis to rationalize the experimentally observed stereoselectivity places an undue emphasis on steric factors and tends to regard the same as the origin of facial discrimination between the prochiral faces of the reacting partners. In light of the increasing number of asymmetric catalysts that rely on hydrogen bonding as well as other weak non-covalent interactions, it is important to take cognizance of the involvement of such interactions in the sterocontrolling transition states. Modern density functional theories offer a pragmatic and effective way to capture non-covalent interactions in transition states. Aided by the availability of such improved computational tools, it is quite timely that the molecular origin of stereoselectivity is subjected to more intelligible analysis. In this Account, we describe interesting molecular insights into the stereocontrolling

  16. Trends in oxygen reduction and methanol activation on transition metal chalcogenides

    DEFF Research Database (Denmark)

    Tritsaris, Georgios; Nørskov, Jens Kehlet; Rossmeisl, Jan

    2011-01-01

    We use density functional theory calculations to study the oxygen reduction reaction and methanol activation on selenium and sulfur-containing transition metal surfaces. With ruthenium selenium as a starting point, we study the effect of the chalcogen on the activity, selectivity and stability...... of the catalyst. Ruthenium surfaces with moderate content of selenium are calculated active for the oxygen reduction reaction, and insensitive to methanol. A significant upper limit for the activity of transition metal chalcogenides is estimated....

  17. Cygnus X-3 transition from the ultrasoft to the hard state

    CERN Document Server

    Beckmann, V; Bélanger, G; Brandt, S; Caballero-Garcia, M D; De Cesare, G; Gehrels, N; Grebenev, S; Vilhu, O; Von Kienlin, A; Courvoisier, T J -L

    2007-01-01

    Aims: The nature of Cygnus X-3 is still not understood well. This binary system might host a black hole or a neutron star. Recent observations by INTEGRAL have shown that Cygnus X-3 was again in an extremely ultrasoft state. Here we present our analysis of the transition from the ultrasoft state, dominated by blackbody radiation at soft X-rays plus non-thermal emission in the hard X-rays, to the low hard state. Methods: INTEGRAL observed Cyg X-3 six times during three weeks in late May and early June 2007. Data from IBIS/ISGRI and JEM-X1 were analysed to show the spectral transition. Results: During the ultrasoft state, the soft X-ray spectrum is well-described by an absorbed (NH = 1.5E22 1/cm**2) black body model, whereas the X-ray spectrum above 20 keV appears to be extremely low and hard (Gamma = 1.7). During the transition, the radio flux rises to a level of >1 Jy, and the soft X-ray emission drops by a factor of 3, while the hard X-ray emission rises by a factor of 14 and becomes steeper (up to Gamma = 4...

  18. Temperature induced structural transitions from native to unfolded aggregated states of tobacco etch virus protease

    Science.gov (United States)

    Zhu, Guo-Fei; Ren, Si-Yan; Xi, Lei; Du, Lin-Fang; Zhu, Xiao-Feng

    2015-02-01

    Tobacco etch virus protease (TEVp) is widely used to remove fusion tags from recombinant proteins because of its high and unique specificity. This work describes the conformational and the thermodynamic properties in the unfolding/refolding process of TEVp3M (three-point mutant: L56V/S135G/S219V) induced by temperature. With temperature increasing from 20 to 100 °C, the CD spectra showed a transition trend from α-helix to β-sheet, and the fluorescence emission, synchronous fluorescence, ANS and RLS spectroscopy consistently revealed that the temperature-induced unfolding process behaved in a three-state manner, for there was a relatively stable intermediate state observed around 50 °C. The reversibility of thermal unfolding of TEVp3M further showed that the transition from the native to the intermediate state was reversible (below 50 °C), however the transition from the intermediate to the unfolded state was irreversible (above 60 °C). Moreover, aggregates were observed above 60 °C as revealed by SDS-PAGE, Thioflavin-T fluorescence and Congo red absorbance.

  19. Spectral hardening as a viable alternative to disc truncation in black hole state transitions

    CERN Document Server

    Salvesen, Greg; Reis, Rubens C; Begelman, Mitchell C

    2013-01-01

    Constraining the accretion flow geometry of black hole binaries in outburst is complicated by the inability of simplified multi-colour disc models to distinguish between changes in the inner disc radius and alterations to the emergent spectrum, parameterised by the phenomenological colour correction factor, f_col. We analyse Rossi X-ray Timing Explorer observations of the low mass Galactic black hole X-ray binary, GX 339-4, taken over seven epochs when the source was experiencing a state transition. The accretion disc component is isolated using a pipeline resulting in robust detections for disc luminosities, 0.001 < L_disc / L_Edd < 0.5. Assuming that the inner disc remains situated at the innermost stable circular orbit over the course of a state transition, we measure the relative degree of change in f_col required to explain the spectral evolution of the disc component. A variable f_col that increases by a factor of ~ 2.0 - 3.5 as the source transitions from the high/soft state to the low/hard state...

  20. Hot accretion flow with radiative cooling: state transitions in black hole X-ray binaries

    Science.gov (United States)

    Wu, Mao-Chun; Xie, Fu-Guo; Yuan, Ye-Fei; Gan, Zhaoming

    2016-06-01

    We investigate state transitions in black hole X-ray binaries through different parameters by using two-dimensional axisymmetric hydrodynamical simulation method. For radiative cooling in hot accretion flow, we take into account the bremsstrahlung, synchrotron and synchrotron self-Comptonization self-consistently in the dynamics. Our main result is that the state transitions occur when the accretion rate reaches a critical value dot{M} ˜ 3α dot{M}_Edd, above which cold and dense clumpy/filamentary structures are formed, embedded within the hot gas. We argued this mode likely corresponds to the proposed two-phase accretion model, which may be responsible for the intermediate state of black hole X-ray binaries. When the accretion rate becomes sufficiently high, the clumpy/filamentary structures gradually merge and settle down on to the mid-plane. Eventually the accretion geometry transforms to a disc-corona configuration. In summary, our results are consistent with the truncated accretion scenario for the state transition.

  1. C-H Bond Activation by Early Transition Metal Carbide Cluster Anion MoC3 (-).

    Science.gov (United States)

    Li, Zi-Yu; Hu, Lianrui; Liu, Qing-Yu; Ning, Chuan-Gang; Chen, Hui; He, Sheng-Gui; Yao, Jiannian

    2015-12-01

    Although early transition metal (ETM) carbides can activate CH bonds in condensed-phase systems, the electronic-level mechanism is unclear. Atomic clusters are ideal model systems for understanding the mechanisms of bond activation. For the first time, CH activation of a simple alkane (ethane) by an ETM carbide cluster anion (MoC3 (-) ) under thermal-collision conditions has been identified by using high-resolution mass spectrometry, photoelectron imaging spectroscopy, and high-level quantum chemical calculations. Dehydrogenation and ethene elimination were observed in the reaction of MoC3 (-) with C2 H6 . The CH activation follows a mechanism of oxidative addition that is much more favorable in the carbon-stabilized low-spin ground electronic state than in the high-spin excited state. The reaction efficiency between the MoC3 (-) anion and C2 H6 is low (0.23±0.05) %. A comparison between the anionic and a highly efficient cationic reaction system (Pt(+) +C2 H6 ) was made. It turned out that the potential-energy surfaces for the entrance channels of the anionic and cationic reaction systems can be very different. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

    Science.gov (United States)

    Afzal, Muhammad Imran; Lee, Yong Tak

    2016-12-01

    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.

  3. Study of radicals, clusters and transition state species by anion photoelectron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, D.W.

    1994-08-01

    Free radicals, elemental and van der Waals clusters and transition state species for bimolecular chemical reactions are investigated using anion photoelectron spectroscopy. Several low-lying electronic states of ozone have been identified via photoelectron spectroscopy of O{sub 3}{sup {minus}}. A characterization of these states is important to models for atmospheric ozone reaction kinetics. The fluoroformyloxyl radical, FCO{sub 2}, has been investigated, providing vibrational frequencies and energies for two electronic states. The technique has also been employed to make the first direct observation and characterization of the NNO{sub 2} molecule. Several electronic states are observed for this species which is believed to play a role as a reactive intermediate in the N + NO{sub 2} reaction. The experimental results for all three of these radicals are supplemented by ab initio investigations of their molecular properties. The clusters investigations include studies of elemental carbon clusters (C{sub 2}{sup {minus}} {minus} C{sub 11}{sup {minus}}), and van der Waals clusters (X{sup {minus}}(CO{sub 2}){sub n}, X = I, Br, Cl; n {le} 13 and I{sup {minus}} (N{sub 2}O){sub n=1--11}). Primarily linear clusters are observed for the smaller carbon clusters, while the spectra of the larger clusters contain contribution from cyclic anion photodetachment. Very interesting ion-solvent interactions are observed in the X{sup {minus}}(CO{sub 2})n clusters. The transition state regions for several bimolecular chemical reactions have also been investigated by photodetachment of a negative ion precursor possessing a geometry similar to that of the transition state species. These spectra show features which are assigned to motions of the unstable neutral complex existing between reactants and products.

  4. Study of radicals, clusters and transition state species by anion photoelectron spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Arnold, Don Wesley [Univ. of California, Berkeley, CA (United States)

    1994-08-01

    Free radicals, elemental and van der Waals clusters and transition state species for bimolecular chemical reactions are investigated using anion photoelectron spectroscopy. Several low-lying electronic states of ozone have been identified via photoelectron spectroscopy of O3-. A characterization of these states is important to models for atmospheric ozone reaction kinetics. The fluoroformyloxyl radical, FCO2, has been investigated, providing vibrational frequencies and energies for two electronic states. The technique has also been employed to make the first direct observation and characterization of the NNO2 molecule. Several electronic states are observed for this species which is believed to play a role as a reactive intermediate in the N + NO2 reaction. The experimental results for all three of these radicals are supplemented by ab initio investigations of their molecular properties. The clusters investigations include studies of elemental carbon clusters (C2- - C11-), and van der Waals clusters (X-(CO2)n, X = I, Br, Cl; n {le} 13 and I- (N2O)n=1--11). Primarily linear clusters are observed for the smaller carbon clusters, while the spectra of the larger clusters contain contribution from cyclic anion photodetachment. Very interesting ion-solvent interactions are observed in the X-(CO2)n clusters. The transition state regions for several bimolecular chemical reactions have also been investigated by photodetachment of a negative ion precursor possessing a geometry similar to that of the transition state species. These spectra show features which are assigned to motions of the unstable neutral complex existing between reactants and products.

  5. Nonequilibrium effective field theory for absorbing state phase transitions in driven open quantum spin systems

    Science.gov (United States)

    Buchhold, Michael; Everest, Benjamin; Marcuzzi, Matteo; Lesanovsky, Igor; Diehl, Sebastian

    2017-01-01

    Phase transitions to absorbing states are among the simplest examples of critical phenomena out of equilibrium. The characteristic feature of these models is the presence of a fluctuationless configuration which the dynamics cannot leave, which has proved a rather stringent requirement in experiments. Recently, a proposal to seek such transitions in highly tunable systems of cold-atomic gases offers to probe this physics and, at the same time, to investigate the robustness of these transitions to quantum coherent effects. Here, we specifically focus on the interplay between classical and quantum fluctuations in a simple driven open quantum model which, in the classical limit, reproduces a contact process, which is known to undergo a continuous transition in the "directed percolation" universality class. We derive an effective long-wavelength field theory for the present class of open spin systems and show that, due to quantum fluctuations, the nature of the transition changes from second to first order, passing through a bicritical point which appears to belong instead to the "tricritical directed percolation" class.

  6. Pressure controlled transition into a self-induced topological superconducting surface state

    KAUST Repository

    Zhu, Zhiyong

    2014-02-07

    Ab-initio calculations show a pressure induced trivial-nontrivial-trivial topological phase transition in the normal state of 1T-TiSe2. The pressure range in which the nontrivial phase emerges overlaps with that of the superconducting ground state. Thus, topological superconductivity can be induced in protected surface states by the proximity effect of superconducting bulk states. This kind of self-induced topological surface superconductivity is promising for a realization of Majorana fermions due to the absence of lattice and chemical potential mismatches. For appropriate electron doping, the formation of the topological superconducting surface state in 1T-TiSe 2 becomes accessible to experiments as it can be controlled by pressure.

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

    Science.gov (United States)

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

    2013-07-01

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

  8. State-dependent cellular activity patterns of the cat paraventricular hypothalamus measured by reflectance imaging

    DEFF Research Database (Denmark)

    Kristensen, Morten Pilgaard; Rector, D M; Poe, G R

    1996-01-01

    Activity within the cat paraventricular hypothalamus (PVH) during sleep and waking states was measured by quantifying intrinsic tissue reflectivity. A fiber optic probe consisting of a 1.0 mm coherent image conduit, surrounded by plastic fibers which conducted 660 nm source light, was attached...... to a charge-coupled device camera, and positioned over the PVH in five cats. Electrodes for assessing state variables, including electroencephalographic activity, eye movement, and somatic muscle tone were also placed. After surgical recovery, reflected light intensity was measured continuously at 2.5 Hz...... during spontaneously varying sleep/waking states. Sequential state transitions from active waking to quiet waking, quiet sleep and active sleep were accompanied by progressively increased levels of PVH activity. Overall activity was highest during active sleep, and decreased markedly upon awakening...

  9. Single-step linking transition from superdeformed to spherical states in {sup 143}Eu

    Energy Technology Data Exchange (ETDEWEB)

    Atac, A.; Axelsson, A.; Persson, J. [Uppsala Univ. (Sweden)] [and others

    1996-12-31

    A discrete {gamma}-ray transition which connects the second lowest SD state with a normally deformed one in {sup 143}Eu has been discovered. It has an energy of 3360.6 keV and carries 3.2 % of the full intensity of the SD band. It feeds into a nearly spherical state which is above the I = 35/2{sup +}, E=4947 keV level. The exact placement of the single-step link could, however, not be established due to the especially complicated level scheme in the region of interest. The angular correlation study favours a stretched dipole character for the 3360.6 keV transition. The single-step link agrees well with the previously determined two-step links, both with respect to energy and spin.

  10. Theory of edge-state optical absorption in two-dimensional transition metal dichalcogenide flakes

    Science.gov (United States)

    Trushin, Maxim; Kelleher, Edmund J. R.; Hasan, Tawfique

    2016-10-01

    We develop an analytical model to describe sub-band-gap optical absorption in two-dimensional semiconducting transition metal dichalcogenide (s-TMD) nanoflakes. The material system represents an array of few-layer molybdenum disulfide crystals, randomly orientated in a polymer matrix. We propose that optical absorption involves direct transitions between electronic edge states and bulk bands, depends strongly on the carrier population, and is saturable with sufficient fluence. For excitation energies above half the band gap, the excess energy is absorbed by the edge-state electrons, elevating their effective temperature. Our analytical expressions for the linear and nonlinear absorption could prove useful tools in the design of practical photonic devices based on s-TMDs.

  11. An alternative derivation of ring-polymer molecular dynamics transition-state theory

    CERN Document Server

    Hele, Timothy J H

    2016-01-01

    In a previous article [J. Chem. Phys. 138, 084108 (2013)], we showed that the transition-state-theory ($t\\rightarrow 0_+$) limit of ring-polymer molecular dynamics rate-theory (RPMD-TST) is also the $t\\rightarrow 0_+$ limit of a new type of quantum flux-side time-correlation function, in which the dividing surfaces are invariant to imaginary-time translation; in other words, that RPMD-TST is a $t\\rightarrow 0_+$ quantum transition-state theory (QTST). Recently, Jang and Voth [J. Chem. Phys. 144, 084110 (2016)] rederived this quantum $t\\rightarrow 0_+$ limit, and claimed that it gives instead the centroid-density approximation. Here we show that the $t\\rightarrow 0_+$ limit derived by Jang and Voth is in fact RPMD-TST.

  12. A mesoscopic approach on stability and phase transition between different traffic flow states

    CERN Document Server

    Qian, Wei-Liang; Lin, Kai; Machado, Romuel F; Hama, Yogiro

    2015-01-01

    It is understood that congestion in traffic can be interpreted in terms of the instability of the equation of dynamic motion. The evoltuion of a traffic system from an unstable or metastable state to a globally stable state bears a strong resemblance to the phase transition in thermodynamics. In this work, we explore the underlying physics of the traffic system, by examing closely the physical properties and mathematical constraints of the phase transitons therein. By using a mesoscopic approach, one entitles the catastrophe model the same physical content as in the Landau's theory, and uncovers its close connection to the instability and phase transitions. In addition to the one-dimensional configuration space, we generalize our discussion to the higher-dimensional case, where the observed temporal oscillation in traffic flow data is attributed to the curl of a vector field. We exhibit that our model can reproduce main features of the observed fundamental diagram including the inverse-$\\lambda$ shape and the...

  13. Quantum anomalous Hall effect and tunable topological states in 3d transition metals doped silicene.

    Science.gov (United States)

    Zhang, Xiao-Long; Liu, Lan-Feng; Liu, Wu-Ming

    2013-10-09

    Silicene is an intriguing 2D topological material which is closely analogous to graphene but with stronger spin orbit coupling effect and natural compatibility with current silicon-based electronics industry. Here we demonstrate that silicene decorated with certain 3d transition metals (Vanadium) can sustain a stable quantum anomalous Hall effect using both analytical model and first-principles Wannier interpolation. We also predict the quantum valley Hall effect and electrically tunable topological states could be realized in certain transition metal doped silicene where the energy band inversion occurs. Our findings provide new scheme for the realization of quantum anomalous Hall effect and platform for electrically controllable topological states which are highly desirable for future nanoelectronics and spintronics application.

  14. Photon-assisted Landau-Zener transition: Role of coherent superposition states

    CERN Document Server

    Sun, Zhe; Wang, Xiaoguang; Nori, Franco

    2012-01-01

    We investigate a Landau-Zener (LZ) transition process modelled by a quantum two-level system (TLS) coupled to a photon mode when the bias energy is varied linearly in time. The initial state of the photon field is assumed to be a superposition of coherent states, leading to a more intricate LZ transition. Applying the rotating-wave approximation (RWA), analytical results are obtained revealing the enhancement of the LZ probability by increasing the average photon number. We also consider the creation of entanglement and the change of photon statistics during the LZ process. When without the RWA, we find some qualitative differences of the LZ dynamics from the RWA results, e.g., the average photon number no longer monotonically enhances the LZ probability.

  15. Instantaneous Formulation for Transitions Between Two Instantaneous Bound States and Its Gauge Invariance

    Institute of Scientific and Technical Information of China (English)

    CHANG Chao-Hsi; CHEN Jiao-Kai; WANG Guo-Li

    2006-01-01

    We have precisely derived a "rigorous instantaneous formulation" for transitions between two bound states when the bound states are well-described by instantaneous Bethe-Salpeter (BS) equation (i.e. the kernel of the equation is instantaneous"occasionally"). The obtained rigorous instantaneous formulation, in fact, is expressed as an operator sandwiched by two "reduced BS wave functions" properly, while the reduced BS wave functions appearing in the formulation are the rigorous solutions of the instantaneous BS equation, and they may relate to Schr(o)dinger wave functions straightforwardly. We also show that the rigorous instantaneous formulation is gauge-invariant with respect to the Uem(1) transformation precisely, if the concerned transitions are radiative. Some applications of the formulation are outlined.

  16. Double excitations and state-to-state transition dipoles in π-π∗ excited singlet states of linear polyenes: Time-dependent density-functional theory versus multiconfigurational methods

    Science.gov (United States)

    Mikhailov, Ivan A.; Tafur, Sergio; Masunov, Artëm E.

    2008-01-01

    The effect of static and dynamic electron correlation on the nature of excited states and state-to-state transition dipole moments is studied with a multideterminant wave function approach on the example of all-trans linear polyenes ( C4H6 , C6H8 , and C8H10 ). Symmetry-forbidden singlet nAg states were found to separate into three groups: purely single, mostly single, and mostly double excitations. The excited-state absorption spectrum is dominated by two bright transitions: 1Bu-2Ag and 1Bu-mAg , where mAg is the state, corresponding to two-electron excitation from the highest occupied to lowest unoccupied molecular orbital. The richness of the excited-state absorption spectra and strong mixing of the doubly excited determinants into lower- nAg states, reported previously at the complete active space self-consistent field level of theory, were found to be an artifact of the smaller active space, limited to π orbitals. When dynamic σ-π correlation is taken into account, single- and double-excited states become relatively well separated at least at the equilibrium geometry of the ground state. This electronic structure is closely reproduced within time-dependent density-functional theory (TD DFT), where double excitations appear in a second-order coupled electronic oscillator formalism and do not mix with the single excitations obtained within the linear response. An extension of TD DFT is proposed, where the Tamm-Dancoff approximation (TDA) is invoked after the linear response equations are solved (a posteriori TDA). The numerical performance of this extension is validated against multideterminant-wave-function and quadratic-response TD DFT results. It is recommended for use with a sum-over-states approach to predict the nonlinear optical properties of conjugated molecules.

  17. Supersymmetrically bounding of asymmetric states and quantum phase transitions by anti-crossing of symmetric states

    CERN Document Server

    Afzal, Muhammad Imran; Lee, Yong Tak

    2016-01-01

    Von Neumann and Wigner theorized bounding of asymmetric eigenstates and anti-crossing of symmetric eigenstates. Experiments have shown that owing to anti-crossing and similar radiation rates, graphene-like resonance of inhomogeneously strained photonic eigenstates can generate pseudomagnetic field, bandgaps and Landau levels, while dissimilar rates induce non-Hermicity. Here, we showed experimentally higher-order supersymmetry and quantum phase transitions by resonance between similar one dimensional lattices. The lattices consisted of inhomgeneously strain-like phases of triangular solitons. The resonance created two dimensional inhomogeneously deformed photonic graphene. All parent eigenstates are annihilated. Where eigenstates of mildly strained solitons are annihilated with similar (power law) rates through one tail only and generated Hermitianally bounded eigenstates. The strongly strained solitons, positive defects are annihilated exponentially through both tails with dissimilar rates. Which bounded eig...

  18. Wind Lidar Activities in the United States

    Energy Technology Data Exchange (ETDEWEB)

    Clifton, Andrew; Newman, Jennifer; St. Pe, Alexandra; Iungo, G. Valerio; Wharton, Sonia; Herges, Tommy; Filippelli, Matthew; Pontbriand, Philippe; Osler, Evan

    2017-06-28

    IEA Wind Task 32 seeks to identify and mitigate the barriers to the adoption of lidar for wind energy applications. This work is partly achieved by sharing experience across researchers and practitioners in the United States and worldwide. This presentation is a short summary of some wind lidar-related activities taking place in the country, and was presented by Andrew Clifton at the Task 32 meeting in December 2016 in his role as the U.S. Department of Energy-nominated country representative to the task.

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

    Science.gov (United States)

    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.

  20. Heat capacity for systems with excited-state quantum phase transitions

    Science.gov (United States)

    Cejnar, Pavel; Stránský, Pavel

    2017-03-01

    Heat capacities of model systems with finite numbers of effective degrees of freedom are evaluated using canonical and microcanonical thermodynamics. Discrepancies between both approaches, which are observed even in the infinite-size limit, are particularly large in systems that exhibit an excited-state quantum phase transition. The corresponding irregularity of the spectrum generates a singularity in the microcanonical heat capacity and affects smoothly the canonical heat capacity.

  1. Multiple Transition States and Roaming in Ion-Molecule Reactions: a Phase Space Perspective

    CERN Document Server

    Mauguiere, Frederic A L; Ezra, Gregory S; Farantos, Stavros C; Wiggins, Stephen

    2013-01-01

    We provide a dynamical interpretation of the recently identified `roaming' mechanism for molecular dissociation reactions in terms of geometrical structures in phase space. These are NHIMs (Normally Hyperbolic Invariant Manifolds) and their stable/unstable manifolds that define transition states for ion-molecule association or dissociation reactions. The associated dividing surfaces rigorously define a roaming region of phase space, in which both reactive and nonreactive trajectories can be trapped for arbitrarily long times.

  2. Political education in post-transition states: the case of (East-)Germany

    OpenAIRE

    Bruen, Jennifer

    2012-01-01

    This paper investigates whether states, which are post transition from dictatorship to democracy, engage in a narrower form of political education in schools, focussing on the transmission of declarative knowledge, with the result that they produce citizens more likely to accept the status quo than to critically analyse and attempt to transform it. Attitudinal and behavioural data from the European/World Values Surveys is used to test this hypothesis with regard to the five new eastern ...

  3. A comparative DFT study of the catalytic activity of the 3d transition metal sulphides surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Gomez-Balderas, R. (Depto de F& amp; #237; s. y Qu& amp; #237; m. Te& amp; #243; rica. Edif. B, Fac. de Qu& amp; #237; mica, UNAM ); Oviedo-Roa, R (Instituto Mexicano del Petroleo); Martinez-Magadan, J M.(Instituto Mexicano del Petroleo); Amador, C. (Depto de F& amp; #237; s. y Qu& amp; #237; m. Te& amp; #243; rica. Edif. B, Fac. de Qu& amp; #237; mica, UNAM ); Dixon, David A.(BATTELLE (PACIFIC NW LAB))

    2002-10-10

    The catalytic activity of the first transition metal series sulphides for hydrodesulfurization (HDS) reactions exhibits a particular behaviour when analysed as a function of the metal position in the Periodic Table. This work reports a comparative study of the electronic structure of the bulk and of the (0 0 1) metal surface (assumed to be the reactive surface) for the Sc-Zn monosulphides. The systems were modeled using the NiAs prototype crystal structure for the bulk and by applying the supercell model with seven atomic layers for (0 0 1) surfaces. The electronic structure of closed-packed solids code based on the density-functional theory and adopting the muffin-tin approximation to the potential was employed in the calculations of the electronic properties. For the Co and Ni sulphides, the density of states (DOS) variations between the metal atom present in the bulk and the ones exposed at the surface show that at the surface, there exists a higher DOS in the occupied states region just below the Fermi level. This feature might indicate a good performance of these two metal sulphides substrates in the HDS reactions favouring a donation, back-donation mechanism. In contrast, the DOS at the surface of Mn is increased in the unoccupied states region, just above the Fermi level. This suggests the possibility of a strong interaction with charge dontating sulphur adsorbate atoms poisoning the active substrate surface.

  4. Muon-Substituted Malonaldehyde: Transforming a Transition State into a Stable Structure by Isotope Substitution.

    Science.gov (United States)

    Goli, Mohammad; Shahbazian, Shant

    2016-02-12

    Isotope substitutions are usually conceived to play a marginal role on the structure and bonding pattern of molecules. However, a recent study [Angew. Chem. Int. Ed. 2014, 53, 13706-13709; Angew. Chem. 2014, 126, 13925-13929] further demonstrates that upon replacing a proton with a positively charged muon, as the lightest radioisotope of hydrogen, radical changes in the nature of the structure and bonding of certain species may take place. The present report is a primary attempt to introduce another example of structural transformation on the basis of the malonaldehyde system. Accordingly, upon replacing the proton between the two oxygen atoms of malonaldehyde with the positively charged muon a serious structural transformation is observed. By using the ab initio nuclear-electronic orbital non-Born-Oppenheimer procedure, the nuclear configuration of the muon-substituted species is derived. The resulting nuclear configuration is much more similar to the transition state of the proton transfer in malonaldehyde rather than to the stable configuration of malonaldehyde. The comparison of the "atoms in molecules" (AIM) structure of the muon-substituted malonaldehyde and the AIM structure of the stable and the transition-state configurations of malonaldehyde also unequivocally demonstrates substantial similarities of the muon-substituted malonaldehyde to the transition state.

  5. Bending crystals. Solid state photomechanical properties of transition metal complexes containing semiquinonate ligands

    Indian Academy of Sciences (India)

    Cortlandt G Pierpont

    2002-08-01

    The properties of transition metal complexes containing catecholate and radical semiquinonate ligands have often been found to be unusual and unexpected. Crystals of Rh(CO)2(3,6-DBSQ), containing the 3,6-di-tert-butyl-1,2-semiquinonate ligand, form as long thin needles that are observed to bend reversibly upon irradiation with NIR light. Crystallographic characterization reveals a stacked solid state lattice with planar molecules aligned with metal atoms atop one another. Electronic spectra recorded in the solid state and in solution show an intense band at 1600 nm that maps the energy dependence of crystal bend angle. The transition is a property of the stacked assembly, rather than of an individual complex molecule, and appears associated with an MLCT process that transfers charge from an antibonding band formed by interacting Rh $d_{z}^{2}$ orbitals to the vacant quinone * orbital. Related observations have been made on the [Co(-pyz)(3,6-DBSQ)(3,6-DBCat)] polymer. Photomechanical properties appear associated with electronic transitions that lead to a physical change in axial length of a linear polymer, coupled with a soft solid state lattice that permits axial contraction/expansion without crystal fracture.

  6. A complex state transition from the black hole candidate Swift J1753.5-0127

    CERN Document Server

    Soleri, P; Motta, S; Belloni, T; Casella, P; Méndez, M; Altamirano, D; Linares, M; Wijnands, R; Fender, R; van der Klis, M

    2012-01-01

    We present our monitoring campaign of the outburst of the black-hole candidate Swift J1753.5-0127, observed with the Rossi X-ray Timing Explorer and the Swift satellites. After ~4.5 years since its discovery, the source had a transition to the hard intermediate state. We performed spectral and timing studies of the transition showing that, unlike the majority of the transient black holes, the system did not go to the soft states but it returned to the hard state after a few months. During this transition Swift J1753.5-0127 features properties which are similar to those displayed by the black hole Cygnus X-1. We compared Swift J1753.5-0127 to one dynamically confirmed black hole and two neutron stars showing that its power spectra are in agreement with the binary hosting a black hole. We also suggest that the prolonged period at low flux that followed the initial flare is reminiscent of that observed in other X-ray binaries, as well as in cataclysmic variables.

  7. Rational design of catalysts for asymmetric diamination reaction using transition state modeling.

    Science.gov (United States)

    Jindal, Garima; Sunoj, Raghavan B

    2014-05-07

    The stereoselective synthesis of 1,2-diamines has remained a formidable challenge. A recent palladium-catalyzed asymmetric diamination of conjugated double bonds using di-tert-butyldiaziridinone appears promising. The axially chiral binol phosphoramidite ligands are successful in offering high enantioselectivity. The density functional theory investigations revealed that the energies of the stereocontrolling transition states for the C-N bond formation depend on a number of weak non-covalent interactions such as C-H···π, C-H···O and anagostic interactions. We envisaged that the modulation in these interactions in the transition states, through subtle changes in chiral phosphoramidite substituents, could be exploited toward steering the stereoselectivity. The effect of systematic modifications on both 3,3' positions of the binol as well as on the amido nitrogen on the stereochemical outcome is predicted. It is identified that high enantioselectivity requires a balance between the nature of the substituents on binol and amido groups. The reduced size of the amido substituents demands increased bulk on the binol whereas lowering the size on the binol demands increased bulk on the amido for higher stereoselectivity. The substituent at the α-position of the amido group is found to be vital and appears to be a hot spot for modifications. These insights derived from studies on the stereocontrolling transition states could help improve the catalytic efficacies in palladium-catalyzed asymmetric diamination reactions.

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

    Science.gov (United States)

    Naumov, Ivan I.; Hemley, Russell J.

    2015-04-01

    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. 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 multicenter chemical bonding 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 reentrant (i.e., metal-insulator-metal) transition sequences are detailed, resulting in predictions of behavior such as phases having band-contact lines. The general principles developed are tested and applied to the alkali and alkaline earth metals, including elements where high-pressure insulating phases have been reported (e.g., Li, Na, and Ca).

  9. Exciton states in a circular graphene quantum dot: Magnetic field induced intravalley to intervalley transition

    Science.gov (United States)

    Li, L. L.; Zarenia, M.; Xu, W.; Dong, H. M.; Peeters, F. M.

    2017-01-01

    The magnetic-field dependence of the energy spectrum, wave function, binding energy, and oscillator strength of exciton states confined in a circular graphene quantum dot (CGQD) is obtained within the configuration interaction method. We predict that (i) excitonic effects are very significant in the CGQD as a consequence of a combination of geometric confinement, magnetic confinement, and reduced screening; (ii) two types of excitons (intravalley and intervalley) are present in the CGQD because of the valley degree of freedom in graphene; (iii) the intravalley and intervalley exciton states display different magnetic-field dependencies due to the different electron-hole symmetries of the single-particle energy spectra; (iv) with increasing magnetic field, the exciton ground state in the CGQD undergoes an intravalley to intervalley transition accompanied by a change of angular momentum; (v) the exciton binding energy does not increase monotonically with the magnetic field due to the competition between geometric and magnetic confinements; and (vi) the optical transitions of the intervalley and intravalley excitons can be tuned by the magnetic field, and valley-dependent excitonic transitions can be realized in a CGQD.

  10. Ground State Transitions of Four-Electron Quantum Dots in Zero Magnetic Field

    Institute of Scientific and Technical Information of China (English)

    KANG Shuai; XIE Wen-Fang; LIU Yi-Ming; SHI Ting-Yun

    2008-01-01

    In this paper, we study four electrons confined in a parabolic quantum dot in the absence of magnetic field, by the exact diagonalization method. The ground-state electronic structures and orbital and spin angular momenta transitions as a function of the confined strength are investigated. We find that the confinement may cause accidental degeneracies between levels with different low-lying states and the inversion of the energy values. The present results are useful to understand the optical properties and internal electron-electron correlations of quantum dot materials.

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

    Energy Technology Data Exchange (ETDEWEB)

    Soh, Daniel Beom Soo

    2017-09-01

    We calculated the optical nonlinearities of the atomically thin monolayer transition metal dichalcogenide material (particularly MoS 2 ), particularly for those linear and nonlinear tran- sition 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 matri- ces that provides the induced current density, from which the nonlinear susceptibilities can be drawn order-by-order via perturbative calculations. We provide the nonlinear susceptibil- ities for the linear, the second-harmonic, the third-harmonic, and the kerr-type two-photon processes.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  14. Bias stress instability involving subgap state transitions in a-IGZO Schottky barrier diodes

    Science.gov (United States)

    Qian, Huimin; Wu, Chenfei; Lu, Hai; Xu, Weizong; Zhou, Dong; Ren, Fangfang; Chen, Dunjun; Zhang, Rong; Zheng, Youdou

    2016-10-01

    Vertical Schottky barrier diodes (SBDs) based on amorphous indium-gallium-zinc-oxide (a-IGZO) with either a top or bottom Schottky contact are fabricated by controlling the oxygen partial pressure during a-IGZO deposition. Although Au electrodes are employed for both Schottky and Ohmic contacts, it is found that Schottky contacts are preferentially formed on a-IGZO film in lower oxygen vacancy concentrations. The effect of negative bias stress on device performance is studied. The Schottky barrier height and series resistance of the a-IGZO SBD are found to increase upon negative bias stress, which is correlated with a reduction of the trap state and background carrier concentration within the a-IGZO film. A physical model based on subgap state transitions from ionized V\\text{O}2+ states to neutralized V O states is proposed to explain the observed electrical instability behavior.

  15. Laminar-Turbulent Transition: The change of the flow state temperature with the Reynolds number

    CERN Document Server

    Chekmarev, Sergei F

    2014-01-01

    Using the previously developed model to describe laminar/turbulent states of a viscous fluid flow, which treats the flow as a collection of coherent structures of various size (Chekmarev, Chaos, 2013, 013144), the statistical temperature of the flow state is determined as a function of the Reynolds number. It is shown that at small Reynolds numbers, associated with laminar states, the temperature is positive, while at large Reynolds numbers, associated with turbulent states, it is negative. At intermediate Reynolds numbers, the temperature changes from positive to negative as the size of the coherent structures increases, similar to what was predicted by Onsager for a system of parallel point-vortices in an inviscid fluid. It is also shown that in the range of intermediate Reynolds numbers the temperature exhibits a power-law divergence characteristic of second-order phase transitions.

  16. Study of thermally induced spin state transition in NdCoO3 single crystal

    Science.gov (United States)

    Janaki, J.; Nithya, R.; Ganesamoorthy, S.; Sairam, T. N.; Ravindran, T. R.; Vinod, K.; Bharathi, A.

    2013-02-01

    We have carried out Magnetization, Raman spectroscopy and IR spectroscopy studies as a function of temperature to investigate the spin state transition in NdCoO3 single crystal. The crystal has been grown by Optical Float Zone technique and characterized by Synchrotron X-ray Diffraction. Our results indicate that the spin crossover from low spin state (LS) to intermediate spin state (IS) occurs continuously over a wide range of temperature above 200K. The wide temperature range of the spin crossover reflects possible electronic or magnetic in-homogeneity at the microscopic level, which is a common feature of some cobalt perovskites. The magnetization studies indicate a spin gap which is higher than that of LaCoO3 (180 K) and Raman spectroscopy studies reveal a Jahn Teller vibration mode characteristic of the intermediate spin state similar to that reported for LaCoO3 in literature.

  17. State governance evolution in resource-rich transition economies: An application to Russia and Kazakhstan

    Energy Technology Data Exchange (ETDEWEB)

    Kalyuzhnova, Yelena; Nygaard, Christian [The Centre for Euro-Asian Studies, The University of Reading, Whiteknights, PO Box, Reading RG6 6AA (United Kingdom)

    2008-06-15

    Following a decade of transition in the Former Soviet Union (FSU), governance of the oil and gas sectors has evolved to economic nationalism. In the newly independent states this has manifested itself through greater (direct) state ownership or participation in oil and gas production, at the expense of both domestic (in the case of Russia) and international oil companies, as well as legislative developments that increase the flow of oil and gas value to the state. Here we analyse some of the dynamics giving rise to economic nationalism within a model of a state capacity and the ability to implement policy and extract value. Our analysis is based on the institutional and economic functioning of the oil and gas sector. We analyse a vector of institutions and examine Production Sharing Agreements and National Oil Companies. (author)

  18. A physical scenario for the high and low X-ray luminosity states in the transitional pulsar PSR J1023+0038

    CERN Document Server

    Campana, S; Papitto, A; Rea, N; Torres, D F; Baglio, M C; D'Avanzo, P

    2016-01-01

    PSR J1023+0038 (J1023) is a binary system hosting a neutron star and a low mass companion. J1023 is the best studied transitional pulsar, alternating a faint eclipsing millisecond radio pulsar state to a brighter X-ray active state. At variance with other Low Mass X-ray binaries, this active state reaches luminosities of only ~$10^{34}$ erg s$^{-1}$, showing strong, fast variability. In the active state, J1023 displays: i) a high state ($L_X\\sim7\\times10^{33}$ erg s$^{-1}$, 0.3-80 keV) occurring ~80% of the time and during which X-ray pulsations at the neutron star spin period are detected (pulsed fraction ~8%); ii) a low state ($L_X~10^{33}$ erg s$^{-1}$) during which pulsations are not detected (~<3%); and iii) a flaring state during which sporadic flares occur in excess of ~$10^{34}$ erg s$^{-1}$, with no pulsation too. The transition between the high and the low states is very rapid, on a ~10 s timescale. Here we put forward a plausible physical interpretation of the high and low states based on the (f...

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

    Science.gov (United States)

    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

  20. Analytic model for low energy excitation states and phase transitions in spin-ice systems

    Science.gov (United States)

    López-Bara, F. I.; López-Aguilar, F.

    2017-04-01

    Low energy excitation states in magnetic structures of the so-called spin-ices are produced via spin flips among contiguous tetrahedra of their crystal structure. These spin flips generate entities which mimic magnetic dipoles in every two tetrahedra according to the dumbbell model. When the temperature increases, the spin-flip processes are transmitted in the lattice, generating so-called Dirac strings, which constitute structural entities that can present mimetic behavior similar to that of magnetic monopoles. In recent studies of both specific heat and ac magnetic susceptibility, two (even possibly three) phases have been shown to vary the temperature. The first of these phases presents a sharp peak in the specific heat and another phase transition occurs for increasing temperature whose peak is broader than that of the former phase. The sharp peak occurs when there are no free individual magnetic charges and temperature of the second phase transition coincides with the maximum proliferation of free deconfined magnetic charges. In the present paper, we propose a model for analyzing the low energy excitation many-body states of these spin-ice systems. We give analytical formulas for the internal energy, specific heat, entropy and their temperature evolution. We study the description of the possible global states via the nature and structure of their one-body components by means of the thermodynamic functions. Below 0.37 K, the Coulomb-like magnetic charge interaction can generate a phase transition to a condensation of pole–antipole pairs, possibly having Bose–Einstein structure which is responsible for the sharp peak of the first phase transition. When there are sufficient free positive and negative charges, the system tends to behave as a magnetic plasma, which implies the broader peak in the specific heat appearing at higher temperature than the sharper experimental peak.

  1. Does Global Astrocytic Calcium Signaling Participate in Awake Brain State Transitions and Neuronal Circuit Function?

    DEFF Research Database (Denmark)

    Kjaerby, Celia; Rasmussen, Rune; Andersen, Mie

    2017-01-01

    We continuously need to adapt to changing conditions within our surrounding environment, and our brain needs to quickly shift between resting and working activity states in order to allow appropriate behaviors. These global state shifts are intimately linked to the brain-wide release...... of the neuromodulators, noradrenaline and acetylcholine. Astrocytes have emerged as a new player participating in the regulation of brain activity, and have recently been implicated in brain state shifts. Astrocytes display global Ca2+ signaling in response to activation of the noradrenergic system, but whether...... astrocytic Ca2+ signaling is causative or correlative for shifts in brain state and neural activity patterns is not known. Here we review the current available literature on astrocytic Ca2+ signaling in awake animals in order to explore the role of astrocytic signaling in brain state shifts. Furthermore, we...

  2. Enhanced photocatalytic activity induced by sp 3 to sp 2 transition of carbon dopants in BiOCl crystals

    KAUST Repository

    Sun, Jianguo

    2017-09-19

    The insufficient light absorption and low quantum efficiency limit the photocatalytic performance of wide bandgap semiconductors. Here, we report a facile strategy to engineer the surface disordered defects of BiOCl nanosheets via carbon doping. The surface defects boost the light absorption and also the quantum yields, as the doped carbon atoms exhibit a transition from sp3 to sp2 hybridization at elevated temperature, corresponding to a change of assembly state from 3D cluster to 2D graphite-like structure. This transition results in an effective charge separation and thus one order of enhancement in photocatalytic activity toward phenol degradation under visible light. The current study opens an avenue to introduce sp3 to sp2 transition of carbon dopants for simultaneous increment of light absorption and quantum efficiency for application in photocatalysis and energy conversion.

  3. Optical fingerprint of dark 2p-states in transition metal dichalcogenides

    Science.gov (United States)

    Berghäuser, Gunnar; Knorr, Andreas; Malic, Ermin

    2017-03-01

    Atomically thin transition metal dichalcogenides exhibit a remarkably strong Coulomb interaction. This results in a fascinating many-particle physics including a variety of bright and dark excitonic states that determine optical and electronic properties of these materials. So far, the impact of dark states has remained literally in the dark to a large extent, since a measurement of these optically forbidden states is very challenging. Here we demonstrate a strategy to measure a direct fingerprint of dark states even in standard linear absorption spectroscopy. We present a microscopic study on bright and dark higher excitonic states in the presence of disorder for the exemplary material of tungsten disulfide (WS2). We show that the geometric phase cancels the degeneration of 2s and 2p states and that a significant disorder-induced coupling of these bright and dark states offers a strategy to circumvent optical selection rules. As a proof, we show a clear fingerprint of dark 2p states in the absorption spectrum of WS2. The predicted softening of optical selection rules through exciton-disorder coupling is of general nature and therefore applicable to related two-dimensional semiconductors.

  4. Change of proton motive force across thylakoid membrane in soybean leaf during state transitions

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    Change of proton gradient across thylakoid membrane in soybean leaves was studied with millisecond delayed light emission (ms-DLE) during the course of state transitions which were indicated by the chlorophyll fluorescence at room temperature and 77 K. When dark-adapted leaves were induced to stateⅠ with far-red light, Fm/Fo, F685/F735 and the intensity of fast phase of ms-DLE were affected slightly. However, during the induction to stateⅡ with red light, both Fm/Fo and F685/F735 decreased immediately and the former were quicker than the latter. In this interval, the intensity of fast phase of ms-DLE increased to a maximum and then decreased to a lower value during the transition to stateⅡ. Nigericin, an uncoupler which eliminates the proton gradient across thylakoid membrane, inhibited the increase in the intensity of fast phase of ms-DLE during the transition to stateⅡ. Another uncoupler, valinomycin, which eliminates the membrane potential, did not affect the changes of the intensity of fast phase. These results suggest that the prompt increase in the intensity of fast phase of ms-DLE at the beginning of transitions to stateⅡ is correlated mainly with the proton gradient released from water oxidation in photosystemⅡ.

  5. The Catalytic Scaffold fo the Haloalkanoic Acid Dehalogenase Enzyme Superfamily Acts as a Mold for the Trigonal Bipyramidal Transition State

    Energy Technology Data Exchange (ETDEWEB)

    Lu,Z.; Dunaway-Mariano, D.; Allen, K.

    2008-01-01

    The evolution of new catalytic activities and specificities within an enzyme superfamily requires the exploration of sequence space for adaptation to a new substrate with retention of those elements required to stabilize key intermediates/transition states. Here, we propose that core residues in the large enzyme family, the haloalkanoic acid dehalogenase enzyme superfamily (HADSF) form a 'mold' in which the trigonal bipyramidal transition states formed during phosphoryl transfer are stabilized by electrostatic forces. The vanadate complex of the hexose phosphate phosphatase BT4131 from Bacteroides thetaiotaomicron VPI-5482 (HPP) determined at 1.00 Angstroms resolution via X-ray crystallography assumes a trigonal bipyramidal coordination geometry with the nucleophilic Asp-8 and one oxygen ligand at the apical position. Remarkably, the tungstate in the complex determined to 1.03 Angstroms resolution assumes the same coordination geometry. The contribution of the general acid/base residue Asp-10 in the stabilization of the trigonal bipyramidal species via hydrogen-bond formation with the apical oxygen atom is evidenced by the 1.52 Angstroms structure of the D10A mutant bound to vanadate. This structure shows a collapse of the trigonal bipyramidal geometry with displacement of the water molecule formerly occupying the apical position. Furthermore, the 1.07 Angstroms resolution structure of the D10A mutant complexed with tungstate shows the tungstate to be in a typical 'phosphate-like' tetrahedral configuration. The analysis of 12 liganded HADSF structures deposited in the protein data bank (PDB) identified stringently conserved elements that stabilize the trigonal bipyramidal transition states by engaging in favorable electrostatic interactions with the axial and equatorial atoms of the transferring phosphoryl group.

  6. Transition states for the dimerization of 1,3-cyclohexadiene: a DFT, CASPT2, and CBS-QB3 quantum mechanical investigation.

    Science.gov (United States)

    Ess, Daniel H; Hayden, Amy E; Klärner, Frank-Gerrit; Houk, K N

    2008-10-03

    Quantum mechanical calculations using restricted and unrestricted B3LYP density functional theory, CASPT2, and CBS-QB3 methods for the dimerization of 1,3-cyclohexadiene (1) reveal several highly competitive concerted and stepwise reaction pathways leading to [4 + 2] and [2 + 2] cycloadducts, as well as a novel [6 + 4] ene product. The transition state for endo-[4 + 2] cycloaddition (endo-2TS, DeltaH(double dagger)(B3LYP(0K)) = 28.7 kcal/mol and DeltaH(double dagger)(CBS-QB3(0K)) = 19.0 kcal/mol) is not bis-pericyclic, leading to nondegenerate primary and secondary orbital interactions. However, the C(s) symmetric second-order saddle point on the B3LYP energy surface is only 0.3 kcal/mol above endo-2TS. The activation enthalpy for the concerted exo-[4 + 2] cycloaddition (exo-2TS, DeltaH(double dagger)(B3LYP(0K)) = 30.1 kcal/mol and DeltaH(double dagger)(CBS-QB3(0K)) = 21.1 kcal/mol) is 1.4 kcal/mol higher than that of the endo transition state. Stepwise pathways involving diallyl radicals are formed via two different C-C forming transition states (rac-5TS and meso-5TS) and are predicted to be competitive with the concerted cycloaddition. Transition states were located for cyclization from intermediate rac-5 leading to the endo-[4 + 2] (endo-2) and exo-[2 + 2] (anti-3) cycloadducts. Only the endo-[2 + 2] (syn-3) transition state was located for cyclization of intermediate meso-5. The novel [6 + 4] "concerted" ene transition state (threo-4TS, DeltaH(double dagger)(UB3LYP(0K)) = 28.3 kcal/mol) is found to be unstable with respect to an unrestricted calculation. This diradicaloid transition state closely resembles the cyclohexadiallyl radical rather than the linked cyclohexadienyl radical. Several [3,3] sigmatropic rearrangement transition states were also located and have activation enthalpies between 27 and 31 kcal/mol.

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

    Science.gov (United States)

    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.

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

    CERN Document Server

    Mökkönen, Harri; Jónsson, Hannes

    2016-01-01

    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 i...

  9. Symmetry of electron states and optical transitions in GaN/AlN hexagonal quantum dots

    Science.gov (United States)

    Tronc, P.; Smirnov, V. P.; Zhuravlev, K. S.

    2004-11-01

    The exact symmetry of hexagonal quantum dots (QDs) made of materials with the wurtzite structure such as GaN/AlN QDs for example, is described by the C3v point group and does not depend on the existence of a wetting layer. We have determined the possible exact symmetries of electron states and vibration modes in the dots and derived the optical selection rules. The vibration modes involved in the Frölich interaction are totally symmetric with respect to the C3v group and can induce transitions only between states with the same symmetry. The not totally symmetric modes provide other channels for lowering the energy of excited carriers and excitons by connecting states with symmetries different one from another. The rapid decay of created polarons, due to the short lifetime of vibration modes, releases the carriers and excitons into ground levels. In the envelope function approximation (EFA), the symmetry of the dots is represented by the C6v point group. Interband transitions are allowed only between states whose envelope functions have the same symmetry. EFA artificially increases the number of dark exciton symmetries.

  10. Mott insulating states and quantum phase transitions of correlated SU(2 N ) Dirac fermions

    Science.gov (United States)

    Zhou, Zhichao; Wang, Da; Meng, Zi Yang; Wang, Yu; Wu, Congjun

    2016-06-01

    The interplay between charge and spin degrees of freedom in strongly correlated fermionic systems, in particular of Dirac fermions, is a long-standing problem in condensed matter physics. We investigate the competing orders in the half-filled SU (2 N ) Hubbard model on a honeycomb lattice, which can be accurately realized in optical lattices with ultracold large-spin alkaline-earth fermions. Employing large-scale projector determinant quantum Monte Carlo simulations, we have explored quantum phase transitions from the gapless Dirac semimetals to the gapped Mott insulating phases in the SU(4) and SU(6) cases. Both of these Mott insulating states are found to be columnar valence bond solid (cVBS) and to be absent of the antiferromagnetic Néel ordering and the loop current ordering. Inside the cVBS phases, the dimer ordering is enhanced by increasing fermion components and behaves nonmonotonically as the interaction strength increases. Although the transitions generally should be of first order due to a cubic invariance possessed by the cVBS order, the coupling to gapless Dirac fermions can soften the transitions to second order through a nonanalytic term in the free energy. Our simulations provide important guidance for the experimental explorations of novel states of matter with ultracold alkaline-earth fermions.

  11. Estimation of Time-Varying Channel State Transition Probabilities for Cognitive Radio Systems by means of Particle Swarm Optimization

    Directory of Open Access Journals (Sweden)

    A. Akbulut

    2012-04-01

    Full Text Available In this study, Particle Swarm Optimization is applied for the estimation of the channel state transition probabilities. Unlike most other studies, where the channel state transition probabilities are assumed to be known and/or constant, in this study, these values are realistically considered to be time-varying parameters, which are unknown to the secondary users of the cognitive radio systems. The results of this study demonstrate the following: without any a priori information about the channel characteristics, even in a very transient environment, it is quite possible to achieve reasonable estimates of channel state transition probabilities with a practical and simple implementation.

  12. Genome-wide diel growth state transitions in the diatom Thalassiosira pseudonana.

    Science.gov (United States)

    Ashworth, Justin; Coesel, Sacha; Lee, Allison; Armbrust, E Virginia; Orellana, Mónica V; Baliga, Nitin S

    2013-04-30

    Marine diatoms are important primary producers that thrive in diverse and dynamic environments. They do so, in theory, by sensing changing conditions and adapting their physiology accordingly. Using the model species Thalassiosira pseudonana, we conducted a detailed physiological and transcriptomic survey to measure the recurrent transcriptional changes that characterize typical diatom growth in batch culture. Roughly 40% of the transcriptome varied significantly and recurrently, reflecting large, reproducible cell-state transitions between four principal states: (i) "dawn," following 12 h of darkness; (ii) "dusk," following 12 h of light; (iii) exponential growth and nutrient repletion; and (iv) stationary phase and nutrient depletion. Increases in expression of thousands of genes at the end of the reoccurring dark periods (dawn), including those involved in photosynthesis (e.g., ribulose-1,5-bisphosphate carboxylase oxygenase genes rbcS and rbcL), imply large-scale anticipatory circadian mechanisms at the level of gene regulation. Repeated shifts in the transcript levels of hundreds of genes encoding sensory, signaling, and regulatory functions accompanied the four cell-state transitions, providing a preliminary map of the highly coordinated gene regulatory program under varying conditions. Several putative light sensing and signaling proteins were associated with recurrent diel transitions, suggesting that these genes may be involved in light-sensitive and circadian regulation of cell state. These results begin to explain, in comprehensive detail, how the diatom gene regulatory program operates under varying environmental conditions. Detailed knowledge of this dynamic molecular process will be invaluable for new hypothesis generation and the interpretation of genetic, environmental, and metatranscriptomic data from field studies.

  13. Transition from Cassie to impaled state during drop impact on groove-textured solid surfaces.

    Science.gov (United States)

    Vaikuntanathan, V; Sivakumar, D

    2014-05-07

    Liquid drops impacted on textured surfaces undergo a transition from the Cassie state characterized by the presence of air pockets inside the roughness valleys below the drop to an impaled state with at least one of the roughness valleys filled with drop liquid. This occurs when the drop impact velocity exceeds a particular value referred to as the critical impact velocity. The present study investigates such a transition process during water drop impact on surfaces textured with unidirectional parallel grooves referred to as groove-textured surfaces. The process of liquid impalement into a groove in the vicinity of drop impact through de-pinning of the three-phase contact line (TPCL) beneath the drop as well as the critical impact velocity were identified experimentally from high speed video recordings of water drop impact on six different groove-textured surfaces made from intrinsically hydrophilic (stainless steel) as well as intrinsically hydrophobic (PDMS and rough aluminum) materials. The surface energy of various 2-D configurations of liquid-vapor interface beneath the drop near the drop impact point was theoretically investigated to identify the locally stable configurations and establish a pathway for the liquid impalement process. A force balance analysis performed on the liquid-vapor interface configuration just prior to TPCL de-pinning provided an expression for the critical drop impact velocity, Uo,cr, beyond which the drop state transitions from the Cassie to an impaled state. The theoretical model predicts that Uo,cr increases with the increase in pillar side angle, α, and intrinsic hydrophobicity whereas it decreases with the increase in groove top width, w, of the groove-textured surface. The quantitative predictions of the theoretical model were found to show good agreement with the experimental measurements of Uo,cr plotted against the surface texture geometry factor in our model, {tan(α/2)/w}(0.5).

  14. Transition-metal-doped ZnO nanoparticles: synthesis, characterization and photocatalytic activity under UV light.

    Science.gov (United States)

    Saleh, Rosari; Djaja, Nadia Febiana

    2014-09-15

    ZnO nanoparticles doped with transition metals (Mn and Co) were prepared by a co-precipitation method. The synthesized nanoparticles were characterized using X-ray diffraction, scanning electron microscopy, energy dispersive X-rays, Fourier transform infrared spectroscopy, electron spin resonance spectroscopy and diffuse reflectance spectroscopy. The photocatalytic activities of the transition-metal-doped ZnO nanoparticles were evaluated in the degradation of methyl orange under UV irradiation. ZnO nanoparticles doped with 12 at.% of Mn and Co ions exhibited the maximum photodegradation efficiency. The experiment also demonstrated that the photodegradation efficiency of Mn-doped ZnO nanoparticles was higher than that of Co-doped ZnO nanoparticles. These results indicate that charge trapping states due to the doping were the decisive factor rather than the average particle size and energy gap. Moreover the effect of pH values on the degradation efficiency was discussed in the photocatalytic experiments using 12 at.% Mn- and Co-doped ZnO nanoparticles.

  15. Theory of activated dynamics and glass transition of hard colloids in two dimensions.

    Science.gov (United States)

    Zhang, Bo-kai; Li, Hui-shu; Tian, Wen-de; Chen, Kang; Ma, Yu-qiang

    2014-03-07

    The microscopic nonlinear Langevin equation theory is applied to study the localization and activated hopping of two-dimensional hard disks in the deeply supercooled and glass states. Quantitative comparisons of dynamic characteristic length scales, barrier, and their dependence on the reduced packing fraction are presented between hard-disk and hard-sphere suspensions. The dynamic barrier of hard disks emerges at higher absolute and reduced packing fractions and correspondingly, the crossover size of the dynamic cage which correlates to the Lindemann length for melting is smaller. The localization lengths of both hard disks and spheres decrease exponentially with packing fraction. Larger localization length of hard disks than that of hard spheres is found at the same reduced packing fraction. The relaxation time of hard disks rises dramatically above the reduced packing fraction of 0.88, which leads to lower reduced packing fraction at the kinetic glass transition than that of hard spheres. The present work provides a foundation for the subsequent study of the glass transition of binary or polydisperse mixtures of hard disks, normally adopted in experiments and simulations to avoid crystallization, and further, the rheology and mechanical response of the two-dimensional glassy colloidal systems.

  16. Controlling the transition of bright and dark states via scanning dressing field

    Science.gov (United States)

    Li, Peiying; Zheng, Huaibin; Zhang, Yiqi; Sun, Jia; Li, Changbiao; Huang, Gaoping; Zhang, Zhaoyang; Li, Yuanyuan; Zhang, Yanpeng

    2013-03-01

    We report the transitions between the bright and dark states of singly-dressed four-wave mixing (FWM) and doubly-dressed FWMs, and the corresponding probe transmissions by scanning the dressing field frequency detuning in a five-level atomic system. Moreover, doubly-dressed six-wave mixing with avoided-crossing plots and triple-dressed eight-wave mixing with the comparison of scanning probe field and dressing field are studied. Such controlled transitions of the nonlinear optical signals can be realizable not only in atomic vapors but also in solid medium. The investigations maybe have potential applications in optical communication, quantum information processing and optoelectronic devices, and maybe also provide a sensitive probe method to study the dressing effect.

  17. Transitions to Care in the Community for Prison Releasees with HIV: a Qualitative Study of Facilitators and Challenges in Two States.

    Science.gov (United States)

    Hammett, Theodore M; Donahue, Sara; LeRoy, Lisa; Montague, Brian T; Rosen, David L; Solomon, Liza; Costa, Michael; Wohl, David; Rich, Josiah D

    2015-08-01

    One in seven people living with HIV in the USA passes through a prison or jail each year, and almost all will return to the community. Discharge planning and transitional programs are critical but challenging elements in ensuring continuity of care, maintaining treatment outcomes achieved in prison, and preventing further viral transmission. This paper describes facilitators and challenges of in-prison care, transitional interventions, and access to and continuity of care in the community in Rhode Island and North Carolina based on qualitative data gathered as part of the mixed-methods Link Into Care Study of prisoners and releasees with HIV. We conducted 65 interviews with correctional and community-based providers and administrators and analyzed the transcripts using NVivo 10 to identify major themes. Facilitators of effective transitional systems in both states included the following: health providers affiliated with academic institutions or other entities independent of the corrections department; organizational philosophy emphasizing a patient-centered, personal, and holistic approach; strong leadership with effective "champions"; a team approach with coordination, collaboration and integration throughout the system, mutual respect and learning between corrections and health providers, staff dedicated to transitional services, and effective communication and information sharing among providers; comprehensive transitional activities and services including HIV, mental health and substance use services in prisons, timely and comprehensive discharge planning with specific linkages/appointments, supplies of medications on release, access to benefits and entitlements, case management and proactive follow-up on missed appointments; and releasees' commitment to transitional plans. These elements were generally present in both study states but their absence, which also sometimes occurred, represent ongoing challenges to success. The qualitative findings on the

  18. Phase transitions in definite total spin states of two-component Fermi gases

    CERN Document Server

    Yurovsky, Vladimir A

    2016-01-01

    Symmetry under permutations of indistinguishable particles, contained in each medium, is one of the fundamental symmetries. Generally, a change in symmetry affects the medium's thermodynamic properties, leading to phase transitions. Permutation symmetry can be changed since, in addition to the conventional symmetric and anti-symmetric 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. However, the thermodynamic effects of non-Abelian symmetry are unknown. 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, saturated and unsaturated phases appear associated with fermionic and non-Abelian symmetry under permutations of particle states, respe...

  19. Transition state theory: a generalization to nonequilibrium systems with power-law distributions

    CERN Document Server

    Jiulin, Du

    2011-01-01

    Transition state theory (TST) is generalized for the nonequilibrium system with power-law distributions. The stochastic dynamics that gives rise to the power-law distributions for the reaction coordinate and momentum is modeled by the Langevin equations and corresponding Fokker-Planck equations. It is assumed that the system far away from equilibrium has not to relax to a thermal equilibrium state with Boltzmann-Gibbs distribution, but asymptotically approaches to a nonequilibrium stationary-state with power-law distributions. Thus, we obtain a generalization of TST rates to nonequilibrium systems with power-law distributions. Furthermore, we derive the generalized TST rate constants for one-dimension and n-dimension Hamiltonian systems away from equilibrium, and receive a generalized Arrhenius rate for the system with power-law distributions.

  20. An Accurate Calculation of Potential Energy Curves and Transition Dipole Moment for Low-Lying Electronic States of CO

    Institute of Scientific and Technical Information of China (English)

    LU Peng-Fei; YAN Lei; YU Zhong-Yuan; GAO Yu-Feng; GAO Tao

    2013-01-01

    In this paper,potential energy curves for the X1∑+,a3∏,a'3∑+,d3△,A1∏ and I1∑-states of CO have been calculated using complete active space self-consistent field and multi-reference configuration interaction methods.The calculations have been performed at 108 nuclear separations from 0.7 to 4.0 (A) by the aug-cc-PV5Z basis set.Spectroscopic constants for the six low-lying electronic states are found in good agreement with experimental data.The vibrational states of the X1∑+ and A1∏ states are also calculated,which are reliable and accurate by comparison with the experimental data and the other theoretical values.The transition dipole moment (TDM) shows that the TDM of the two states (X1∑+ → A1∏) are reduced strongly with increase of bond length.

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

    Science.gov (United States)

    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

  2. Folding of a LysM domain: entropy-enthalpy compensation in the transition state of an ideal two-state folder.

    Science.gov (United States)

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

    2008-07-11

    Protein-engineering methods (Phi-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 betaalphaalphabeta arrangement and is the smallest alphabeta 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 Phi-values denotes a highly polarised transition state, with significant formation of the helices but no structure within the beta-sheet. Remarkably, this transition state remains polarised after circularisation of the domain, and exhibits an identical Phi-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.

  3. 19 CFR 123.64 - Baggage in transit through the United States between ports in Canada or in Mexico.

    Science.gov (United States)

    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...

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

    Science.gov (United States)

    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

  5. Salmonella enterica MTAN at 1.36 Å resolution: a structure-based design of tailored transition state analogs.

    Science.gov (United States)

    Haapalainen, Antti M; Thomas, Keisha; Tyler, Peter C; Evans, Gary B; Almo, Steven C; Schramm, Vern L

    2013-06-04

    Accumulation of 5'-methylthioadenosine (MTA) and S-adenosylhomocysteine (SAH) in bacteria disrupts the S-adenosylmethionine pool to alter biological methylations, synthesis of polyamines, and production of quorum-sensing molecules. Bacterial metabolism of MTA and SAH depends on MTA/SAH nucleosidase (MTAN), an enzyme not present in humans and a target for quorum sensing because MTAN activity is essential for synthesis of autoinducer-2 molecules. Crystals of Salmonella enterica MTAN with product and transition state analogs of MTA and SAH explain the structural contacts causing pM binding affinity for the inhibitor and reveal a "water-wire" channel for the catalytic nucleophile. The crystal structure shows an extension of the binding pocket filled with polyethylene glycol. We exploited this discovery by the design and synthesis of tailored modifications of the currently existing transition state analogs to fill this site. This site was not anticipated in MTAN structures. Tailored inhibitors with dissociation constants of 5 to 15 pM are characterized.

  6. Edge states and quantum phase transition in graphene under in-plane effective exchange fields

    Science.gov (United States)

    Liu, Zheng-Fang; Wu, Qing-Ping; Chen, Ai-Xi; Xiao, Xian-Bo; Liu, Nian-Hua; Miao, Guo-Xing

    2017-02-01

    We investigated the edge states and quantum phase transition in graphene under an in-plane effective exchange field. The result shows that the combined effects of the in-plane effective exchange field and a staggered sublattice potential can induce zero-energy flat bands of edge states. Such flat-band edge states can evolve into helical-like ones in the presence of intrinsic spin-orbit coupling, with a unique spin texture. We also find that the bulk energy gap induced by the spin-orbit coupling and staggered sublattice potential can be closed and reopened with the in-plane effective exchange field, and the reopened bulk gap can be even larger than that induced by only the spin-orbit coupling and staggered sublattice potential, which is different from the case of an out-of-plane effective exchange field. The calculated spin-dependent Chern numbers suggest that the bulk gap closing and reopening is accompanied by a quantum phase transition from a trivial insulator phase across a metal phase into a spin-dependent quantum Hall phase.

  7. Transition from spin accumulation into interface states to spin injection in silicon and germanium conduction bands

    Science.gov (United States)

    Jain, Abhinav; Rojas-Sanchez, Juan-Carlos; Cubukcu, Murat; Peiro, Julian; Le Breton, Jean-Christophe; Vergnaud, Céline; Augendre, Emmanuel; Vila, Laurent; Attané, Jean-Philippe; Gambarelli, Serge; Jaffrès, Henri; George, Jean-Marie; Jamet, Matthieu

    2013-04-01

    Electrical spin injection into semiconductors paves the way for exploring new phenomena in the area of spin physics and new generations of spintronic devices. However the exact role of interface states in the electrical spin injection mechanism from a magnetic tunnel junction into a semiconductor is still under debate. Here we demonstrate a clear transition from spin accumulation into interface states to spin injection in the conduction band of n-Si and n-Ge using a CoFeB/MgO tunnel contact. We observe spin signal amplification at low temperature due to spin accumulation into interface states followed by a clear transition towards spin injection in the conduction band from approximately 150 K up to room temperature. In this regime, the spin signal is reduced down to a value compatible with the standard spin diffusion model. More interestingly, in the case of germanium, we demonstrate a significant modulation of the spin signal by applying a back-gate voltage to the conduction channel. We also observe the inverse spin Hall effect in Ge by spin pumping from the CoFeB electrode. Both observations are consistent with spin accumulation in the Ge conduction band.

  8. Hot accretion flow with radiative cooling: state transitions in black hole X-ray binaries

    CERN Document Server

    Wu, Mao-Chun; Yuan, Ye-Fei; Gan, Zhao-Ming

    2016-01-01

    We investigate state transitions in black hole X-ray binaries through different parameters by using two-dimensional axisymmetric hydrodynamical simulation method. For radiative cooling in hot accretion flow, we take into account the bremsstrahlung, synchrotron and synchrotron-self Comptonization self-consistently in the dynamics. Our main result is that the state transitions occur when the accretion rate reaches a critical value $\\dot M \\sim 3\\alpha\\ \\dot M_{\\rm Edd}$, above which cold and dense clumpy/filamentary structures are formed, embedded within the hot gas. We argued this mode likely corresponds to the proposed two-phase accretion model, which may be responsible for the intermediate state of black hole X-ray binaries. When the accretion rate becomes sufficiently high, the clumpy/filamentary structures gradually merge and settle down onto the mid-plane. Eventually the accretion geometry transforms to a disc-corona configuration. In summary our results are consistent with the truncated accretion scenari...

  9. Transition-state structure for the hydronium-ion-promoted hydrolysis of α-d-glucopyranosyl fluoride

    National Research Council Canada - National Science Library

    Tang, Ariel; Chan, Jefferson; Bennet, Andrew J

    2015-01-01

    The transition state for the hydronium-ion-promoted hydrolysis of α- d -glucopyranosyl fluoride in water has been characterized by combining multiple kinetic isotope effect measurements with theoretical modelling...

  10. Transition-state structure for the hydronium-ion-promoted hydrolysis of [alpha]-D-glucopyranosyl fluoride

    National Research Council Canada - National Science Library

    Chan, Jefferson; Tang, Ariel; Bennet, Andrew J

    2015-01-01

    The transition state for the hydronium-ion-promoted hydrolysis of [alpha]-D-glucopyranosyl fluoride in water has been characterized by combining multiple kinetic isotope effect measurements with theoretical modelling...

  11. Transition state trajectory stability determines barrier crossing rates in chemical reactions induced by time-dependent oscillating fields

    CERN Document Server

    Craven, Galen T; Hernandez, Rigoberto

    2015-01-01

    When a chemical reaction is driven by an external field, the transition state that the system must pass through as it changes from reactant to product -for example, an energy barrier- becomes time-dependent. We show that for periodic forcing the rate of barrier crossing can be determined through stability analysis of the non-autonomous transition state. Specifically, strong agreement is observed between the difference in the Floquet exponents describing stability of the transition state trajectory, which defines a recrossing-free dividing surface [G. T. Craven, T. Bartsch, and R. Hernandez, Phys. Rev. E 89, 040801(R) (2014)], and the rates calculated by simulation of ensembles of trajectories. This result opens the possibility to extract rates directly from the intrinsic stability of the transition state, even when it is time-dependent, without requiring a numerically-expensive simulation of the long-time dynamics of a large ensemble of trajectories.

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

    Science.gov (United States)

    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.

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

    Science.gov (United States)

    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.

  14. Temperature-Dependent Surface States and Transitions of Si(111)-7x7.

    Science.gov (United States)

    1984-09-01

    TRANSTONS OF Si(Il1)-7x7 by J. E. Demuth, B. N. J. Persson and A. J. Scheil-Sorokin Prepared for Publication in Physical Review Letters IBM T. J. Watson...NUMBER 24 PHYSICAL REVIEW LETTERS 12 DEiEMiER 1983 Temperature-Dependent Surface States and Transitions of Si(11l)-7x7 J. E. Demuth, B. N. J. Persson...8217 ’ " " " .. . .; " ’ " ’ " " " " "h " - -’ ; - ’ . . ": - - VOLUME 51, NUMBER 24 PHYSICAL REVIEW LETTERS 12

  15. Degree of Rate Control: How Much the Energies of Intermediates and Transition States Control Rates

    DEFF Research Database (Denmark)

    Stegelmann, Carsten; Andreasen, Anders; Campbell, Charles T.

    2009-01-01

    For many decades, the concept of a “rate-determining step” has been of central importance in understanding chemical kinetics in multistep reaction mechanisms and using that understanding to advantage. Yet a rigorous method for identifying the rate-determining step in a reaction mechanism was only...... model for any reaction mechanism. Thus, it is very important to identify these rate-controlling transition states and rate-controlling intermediates for both applied and basic research. Here, we present a method for doing that....

  16. Inequalities generalizing the second law of thermodynamics for transitions between nonstationary states.

    Science.gov (United States)

    Verley, Gatien; Chétrite, Raphaël; Lacoste, David

    2012-03-23

    We discuss the consequences of a variant of the Hatano-Sasa relation in which a nonstationary distribution is used in place of the usual stationary one. We first show that this nonstationary distribution is related to a difference of traffic between the direct and dual dynamics. With this formalism, we extend the definition of the adiabatic and nonadiabatic entropies introduced by M. Esposito and C. Van den Broeck in Phys. Rev. Lett. 104, 090601 (2010) for the stationary case. We also obtain interesting second-law-like inequalities for transitions between nonstationary states.

  17. Density induced phase transitions in QED$_\\mathrm{2}$ - A study with matrix product states

    CERN Document Server

    Bañuls, Mari Carmen; Cirac, J Ignacio; Jansen, Karl; Kühn, Stefan

    2016-01-01

    We numerically study the zero temperature phase structure of the multi-flavor Schwinger model at non-zero chemical potential. Using matrix product states, we reproduce analytical results for the phase structure for two flavors in the massless case and extend the computation to the massive case, where no analytical predictions are available. Our calculations allow us to locate phase transitions in the mass-chemical potential plane with great precision, and provide a concrete example of tensor networks overcoming the sign problem in a lattice gauge theory calculation.

  18. Density induced phase transitions in the Schwinger model. A study with matrix product states

    Energy Technology Data Exchange (ETDEWEB)

    Banuls, Mari Carmen; Cirac, J. Ignacio; Kuehn, Stefan [Max-Planck-Institut fuer Quantenoptik (MPQ), Garching (Germany); Cichy, Krzysztof [Frankfurt Univ. (Germany). Inst. fuer Theoretische Physik; Adam Mickiewicz Univ., Poznan (Poland). Faculty of Physics; Jansen, Karl [Deutsches Elektronen-Synchrotron (DESY), Zeuthen (Germany). John von Neumann-Inst. fuer Computing NIC

    2017-02-15

    We numerically study the zero temperature phase structure of the multiflavor Schwinger model at nonzero chemical potential. Using matrix product states, we reproduce analytical results for the phase structure for two flavors in the massless case and extend the computation to the massive case, where no analytical predictions are available. Our calculations allow us to locate phase transitions in the mass-chemical potential plane with great precision and provide a concrete example of tensor networks overcoming the sign problem in a lattice gauge theory calculation.

  19. Transition and Excited States of 1,1'-azo-bis-1,2,3-triazole

    Science.gov (United States)

    Goncharov, Vladimir; Goncharova, Olga; Varga, Kalman

    2011-03-01

    A novel photochromic molecule has been recently synthesized. The photo-isomerization of this nitrogen-rich small molecule is efficiently controlled by a xenon flash lamp suggesting a potential in photonic and molecular mechanics applications. We perform a synergistic quantum molecular dynamics (QMD), real-time time dependent density functional theory (TDDFT) and TDDFT- perturbation theory study to capture and elucidate the transition state, excitation energies and optical properties of the molecule. We also use it to test performance of recently developed real-time TDDFT method to calculate hyperpolarizabilities and compare results with the Sternheimer method. Yu-Chuan Li et al. J. Am. Chem. Soc., 2010, 132, 12172

  20. Phase transition in PT symmetric active plasmonic systems

    CERN Document Server

    Mattheakis, M; Molina, M I; Tsironis, G P

    2015-01-01

    Surface plasmon polaritons (SPPs) are coherent electromagnetic surface waves trapped on an insulator-conductor interface. The SPPs decay exponentially along the propagation due to conductor losses, restricting the SPPs propagation length to few microns. Gain materials can be used to counterbalance the aforementioned losses. We provide an exact expression for the gain, in terms of the optical properties of the interface, for which the losses are eliminated. In addition, we show that systems characterized by lossless SPP propagation are related to PT symmetric systems. Furthermore, we derive an analytical critical value of the gain describing a phase transition between lossless and prohibited SPPs propagation. The regime of the aforementioned propagation can be directed by the optical properties of the system under scrutiny. Finally, we perform COMSOL simulations verifying the theoretical findings.

  1. Hypothesis: could the signalling function of membrane microdomains involve a localized transition of lipids from liquid to solid state?

    Directory of Open Access Journals (Sweden)

    Joly Etienne

    2004-01-01

    Full Text Available Abstract Background Over the past decade, it has become apparent that specialised membrane microdomains, commonly called rafts, where lipids like sphingolipids and cholesterol are arranged compactly in a liquid ordered phase are involved in cell signalling. Hypothesis The core of the hypothesis presented here is that resting cells may actively maintain their plasma membrane in liquid phase, corresponding to a metastable thermodynamic state. Following a physiological stimulus such as ligands binding to their membrane receptors, the tendency of membrane components to undergo a localised transition towards a gel state would increase, resulting in initial minute solid structures. These few membrane components having undergone a liquid to solid state transition, would then act as seeds for the specific recruitment of additional membrane components whose properties are compatible with the crystalline growth of these initial docks. Cells could therefore be using the propensity of lipids to assemble selectively to generate stable platforms of particular cellular components either for intra-cellular transport or for signal transduction. Testing the hypothesis could presumably be done via biophysical approaches such as EPR spin labelling, X-ray diffraction or FRET coupled to direct microscopic observation of cells to which very localized stimuli would be delivered. Implications Such a model of selective growth of membrane docks would provide an explanation for the existence of different types of microdomains, and for the fact that, depending on the state of the cells and on the procedures used to isolate them, membrane microdomains can vary greatly in their properties and composition. Ultimately, a thorough understanding of how and why lipid domains are assembled in biological membranes will be essential for many aspects of cell biology and medicine.

  2. Derivation of a true (t → 0+) quantum transition-state theory. I. Uniqueness and equivalence to ring-polymer molecular dynamics transition-state-theory.

    Science.gov (United States)

    Hele, Timothy J H; Althorpe, Stuart C

    2013-02-28

    Surprisingly, there exists a quantum flux-side time-correlation function which has a non-zero t → 0+ limit and thus yields a rigorous quantum generalization of classical transition-state theory (TST). In this Part I of two articles, we introduce the new time-correlation function and derive its t → 0+ limit. The new ingredient is a generalized Kubo transform which allows the flux and side dividing surfaces to be the same function of path-integral space. Choosing this function to be a single point gives a t → 0+ limit which is identical to an expression introduced on heuristic grounds by Wigner in 1932; however, this expression does not give positive-definite quantum statistics, causing it to fail while still in the shallow-tunnelling regime. Positive-definite quantum statistics is obtained only if the dividing surface is invariant to imaginary-time translation, in which case the t → 0+ limit is identical to ring-polymer molecular dynamics (RPMD) TST. The RPMD-TST rate is not a strict upper bound to the exact quantum rate, but is a good approximation to one if real-time coherence effects are small. Part II will show that the RPMD-TST rate is equal to the exact quantum rate in the absence of recrossing.

  3. Activation of PKA leads to mesenchymal-to-epithelial transition and loss of tumor-initiating ability.

    Science.gov (United States)

    Pattabiraman, Diwakar R; Bierie, Brian; Kober, Katharina Isabelle; Thiru, Prathapan; Krall, Jordan A; Zill, Christina; Reinhardt, Ferenc; Tam, Wai Leong; Weinberg, Robert A

    2016-03-04

    The epithelial-to-mesenchymal transition enables carcinoma cells to acquire malignancy-associated traits and the properties of tumor-initiating cells (TICs). TICs have emerged in recent years as important targets for cancer therapy, owing to their ability to drive clinical relapse and enable metastasis. Here, we propose a strategy to eliminate mesenchymal TICs by inducing their conversion to more epithelial counterparts that have lost tumor-initiating ability. We report that increases in intracellular levels of the second messenger, adenosine 3',5'-monophosphate, and the subsequent activation of protein kinase A (PKA) induce a mesenchymal-to-epithelial transition (MET) in mesenchymal human mammary epithelial cells. PKA activation triggers epigenetic reprogramming of TICs by the histone demethylase PHF2, which promotes their differentiation and loss of tumor-initiating ability. This study provides proof-of-principle for inducing an MET as differentiation therapy for TICs and uncovers a role for PKA in enforcing and maintaining the epithelial state.

  4. Metallocarbene Artificial Enzymes : Extending Transition Metal Selectivity and Protein Activity

    NARCIS (Netherlands)

    Basauri Molina, M.

    2015-01-01

    A series of new semi-synthetic metalloprotein hybrids were created via the covalent binding of organometallic species in the active site of lipases, accordingly resulting in the first active site-directed (ASD) homogeneous artificial metalloenzymes. The use of this method promises the generation of

  5. Oxidation-reduction signalling components in regulatory pathways of state transitions and photosystem stoichiometry adjustment in chloroplasts.

    Science.gov (United States)

    Puthiyaveetil, Sujith; Ibrahim, Iskander M; Allen, John F

    2012-02-01

    State transitions and photosystem stoichiometry adjustment are two oxidation-reduction (redox)-regulated acclimatory responses in photosynthesis. State transitions are short-term adaptations that, in chloroplasts, involve reversible post-translational modification by phosphorylation of light-harvesting complex II (LHC II). Photosystem stoichiometry adjustments are long-term responses involving transcriptional regulation of reaction centre genes. Both responses are initiated by changes in light quality and are regulated by the redox state of plastoquinone (PQ). The LHC II kinase involved in the state 2 transition is a serine/threonine kinase known as STT7 in Chlamydomonas, and as STN7 in Arabidopsis. The phospho-LHC II phosphatase that produces the state 1 transition is a PP2C-type protein phosphatase currently termed both TAP38 and PPH1. In plants and algae, photosystem stoichiometry adjustment is governed by a modified two-component sensor kinase of cyanobacterial origin - chloroplast sensor kinase (CSK). CSK is a sensor of the PQ redox state. Chloroplast sigma factor 1 (SIG1) and plastid transcription kinase (PTK) are the functional partners of CSK in chloroplast gene regulation. We suggest a signalling pathway for photosystem stoichiometry adjustment. The signalling pathways of state transitions and photosystem stoichiometry adjustments are proposed to be distinct, with the two pathways sensing PQ redox state independently of each other.

  6. Rapid increases in ventilation accompany the transition from passive to active movement.

    Science.gov (United States)

    Bell, Harold J; Duffin, James

    2006-06-01

    We used a novel movement transition technique to look for evidence of a rapid onset drive to breathe related to the active component of exercise in humans. Ten volunteers performed the following transitions in a specially designed tandem exercise chair apparatus: rest to passive movement, passive to active movement, and rest to active movement. The transition from rest to active exercise was accompanied by an immediate increase in ventilation, as was the transition from rest to passive leg movement (Delta = 6.06 +/- 1.09 l min(-1), p ventilation again increased immediately and significantly (Delta = 2.55 +/- 0.52 l min(-1), p = 0.032). Ventilation at the first point of active exercise was the same when started either from rest or from a background of passive leg movement (p = 1.00). We conclude that the use of a transition from passive to active leg movements in humans recruits a ventilatory drive related to the active component of exercise, and this can be discerned as a rapid increase in breathing.

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

    Science.gov (United States)

    Fried, Eliot; Gurtin, Morton E.

    1999-06-01

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

  8. The highly synergistic, broad spectrum, antibacterial activity of organic acids and transition metals

    Science.gov (United States)

    Zhitnitsky, Daniel; Rose, Jessica; Lewinson, Oded

    2017-01-01

    For millennia, transition metals have been exploited to inhibit bacterial growth. We report here the potentiation of the anti-bacterial activity of transition metals by organic acids. Strong synergy between low, non-toxic concentrations of transition metals and organic acids was observed with up to ~1000-fold higher inhibitory effect on bacterial growth. We show that organic acids shuttle transition metals through the permeability barrier of the bacterial membrane, leading to increased influx of transition metals into bacterial cells. We demonstrate that this synergy can be effectively used to inhibit the growth of a broad range of plant and human bacterial pathogens, and suggest that a revision of food preservation and crop protection strategies may be in order. These findings bear significant biomedical, agricultural, financial and environmental opportunities. PMID:28294164

  9. Transitions between hyperfine-structure states of the 2s metastable muonic hydrogen in collision processes

    Energy Technology Data Exchange (ETDEWEB)

    Czaplinski, W.

    1992-12-31

    Hyperfine effects in the symmetric collisions of the 2s metastable muonic hydrogen with hydrogen atoms: (p{mu}){sub 2s} + H, (d{mu}){sub 2s} + D, (t{mu}){sub 2s} + t are presented. Elastic and spin-flip cross sections for the scattering of The 2s muonic atoms are calculated in the two-level approximation as a function of collision energy. The corresponding formulae are derived with inclusion of electron screening and Lamb-shift between 2s and 2p energy levels of the muonic atom. The obtained spin-flip cross sections are about two orders of magnitude higher than their ground state counterparts and are much more influenced by electron screening. The rates of the spin-flip transitions are also calculated and are found to be about three orders of magnitude higher than the decay rate of the 2s state. (author). 65 refs, 15 figs, 4 tabs.

  10. Probing the transition state region in catalytic CO oxidation on Ru

    Energy Technology Data Exchange (ETDEWEB)

    Ostrom, H. [Stockholm Univ. (Sweden); Oberg, H. [Stockholm Univ. (Sweden); Xin, H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); LaRue, J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); Beye, M. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Dell' Angela, M. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Gladh, J. [Stockholm Univ. (Sweden); Ng, M. L. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Sellberg, J. A. [Stockholm Univ. (Sweden); SLAC National Accelerator Lab., Menlo Park, CA (United States); Kaya, S. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Mercurio, G. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Nordlund, D. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Hantschmann, M. [Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Hieke, F. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); Kuhn, D. [Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Schlotter, W. F. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Dakovski, G. L. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Turner, J. J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Minitti, M. P. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Mitra, A. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Moeller, S. P. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Fohlisch, A. [Helmholtz Zentrum Berlin fur Materialien und Energie GmbH, Berlin (Germany); Univ. Potsdam, Potsdam (Germany); Wolf, M. [Fritz-Haber Institute of the Max-Planck-Society, Berlin (Germany); Wurth, W. [Univ. of Hamburg and Center for Free Electron Laser Science, Hamburg (Germany); DESY Photon Science, Hamburg (Germany); Persson, M. [The Univ. of Liverpool, Liverpool (United Kingdom); Norskov, J. K. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Stanford Univ., Stanford, CA (United States); Abild-Pedersen, F. [Stanford Univ., Stanford, CA (United States); Ogasawara, H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Pettersson, L. G. M. [Stockholm Univ. (Sweden); Nilsson, A. [Stockholm Univ. (Sweden); SLAC National Accelerator Lab., Menlo Park, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2015-02-12

    Femtosecond x-ray laser pulses are used to probe the CO oxidation reaction on ruthenium (Ru) initiated by an optical laser pulse. On a time scale of a few hundred femtoseconds, the optical laser pulse excites motions of CO and O on the surface, allowing the reactants to collide, and, with a transient close to a picosecond (ps), new electronic states appear in the O K-edge x-ray absorption spectrum. Density functional theory calculations indicate that these result from changes in the adsorption site and bond formation between CO and O with a distribution of OC–O bond lengths close to the transition state (TS). After 1 ps, 10% of the CO populate the TS region, which is consistent with predictions based on a quantum oscillator model.

  11. Floquet topological phase transitions and chiral edge states in a kagome lattice

    Energy Technology Data Exchange (ETDEWEB)

    He, Chaocheng; Zhang, Zhiyong, E-mail: zyzhang@nju.edu.cn

    2014-09-05

    The Floquet topological phases and chiral edge states in a kagome lattice under a circularly-polarized driving field are studied. In the off-resonant case, the system exhibits the similar character as the kagome lattice model with staggered magnetic fluxes, but the total band width is damped in oscillation. In the on-resonant case, the degeneracy splitting at the Γ point does not always result in a gap. The positions of the other two gaps are influenced by the flat band. With the field intensity increased, these two gaps undergo closing-then-reopening processes, accompanied with the changing of the winding numbers. - Highlights: • A kagome lattice under a circularly-polarized driving field is studied. • The band structures and chiral edge states are studied via exact Floquet method. • Various modifications of the Floquet band structure are found. • Floquet topological phase transitions appear in both off- and on-resonant cases.

  12. Molecular wave-packet dynamics on laser-controlled transition states

    CERN Document Server

    Fischer, Andreas; Cörlin, Philipp; Sperl, Alexander; Schönwald, Michael; Mizuno, Tomoya; Sansone, Giuseppe; Senftleben, Arne; Ullrich, Joachim; Feuerstein, Bernold; Pfeifer, Thomas; Moshammer, Robert

    2016-01-01

    Understanding and controlling the electronic as well as ro-vibrational motion and, thus, the entire chemical dynamics in molecules is the ultimate goal of ultrafast laser and imaging science. In photochemistry, laser-induced dissociation has become a valuable tool for modification and control of reaction pathways and kinetics. Here, we present a pump-probe study of the dissociation dynamics of H$_2^+$ using ultrashort extreme-ultraviolet (XUV) and near-infrared (IR) laser pulses. The reaction kinematics can be controlled by varying the pump-probe delay. We demonstrate that the nuclear motion through the transition state can be reduced to isolated pairs of initial vibrational states. The dynamics is well reproduced by intuitive semi-classical trajectories on a time-dependent potential curve. From this most fundamental scenario we gain insight in the underlying mechanisms which can be applied as design principles for molecular quantum control, particularly for ultrafast reactions involving protons.

  13. Topological phase transition and interface states in hybrid plasmonic-photonic systems

    Science.gov (United States)

    Ge, Lixin; Liu, Liang; Xiao, Meng; Du, Guiqiang; Shi, Lei; Han, Dezhuan; Chan, C. T.; Zi, Jian

    2017-06-01

    The geometric phase and topological property for one-dimensional hybrid plasmonic-photonic crystals consisting of a simple lattice of graphene sheets are investigated systematically. For transverse magnetic waves, both plasmonic and photonic modes exist in the momentum space. The accidental degeneracy point of these two kinds of modes is identified to be a diabolic point accompanied with a topological phase transition. For a closed loop around this degeneracy point, the Berry phase is π as a consequence of the discontinuous jump of the geometric Zak phase. The wave impedance is calculated analytically for the semi-infinite system, and the corresponding topological interface states either start from or terminate at the degeneracy point. This type of localized interface state may find potential applications in manipulation of photon emission of quantum dots, optical sensing and enhancement of nonlinear effects, etc.

  14. Chaotic-to-ordered state transition of cathode-sheath instabilities in DC glow discharge plasmas

    Indian Academy of Sciences (India)

    Md Nurujjaman; A N Sekar Iyengar

    2006-08-01

    Transition from chaotic to ordered state has been observed during the initial stage of a discharge in a cylindrical DC glow discharge plasma. Initially it shows a chaotic behavior but increasing the discharge voltage changes the characteristics of the discharge glow and shows a period subtraction of order 7 period → 5 period → 3 period → 1 period, i.e. the system goes to single mode through odd cycle subtraction. On further increasing the discharge voltage, the system goes through period doubling, like 1 period → 2 period → 4 period. On further increasing the voltage, the system goes to stable state through two period subtraction, like 4 period → 2 period → stable.

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

    CERN Document Server

    Zarkevich, Nikolai A

    2014-01-01

    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 serpentine minimal energy path (MEP). If a single climbing image (C1-NEB) successfully finds the TS, C2-NEB finds it with higher stability and accuracy. However, C2-NEB is 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 that the climbing images approach it from the opposite sides along the MEP, and it estimates accuracy 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 (SS-NEB).

  16. Hydroxyl radical reactions with adenine: reactant complexes, transition states, and product complexes.

    Science.gov (United States)

    Cheng, Qianyi; Gu, Jiande; Compaan, Katherine R; Schaefer, Henry F

    2010-10-18

    In order to address problems such as aging, cell death, and cancer, it is important to understand the mechanisms behind reactions causing DNA damage. One specific reaction implicated in DNA oxidative damage is hydroxyl free-radical attack on adenine (A) and other nucleic acid bases. The adenine reaction has been studied experimentally, but there are few theoretical results. In the present study, adenine dehydrogenation at various sites, and the potential-energy surfaces for these reactions, are investigated theoretically. Four reactant complexes [A···OH]* have been found, with binding energies relative to A+OH* of 32.8, 11.4, 10.7, and 10.1 kcal mol(-1). These four reactant complexes lead to six transition states, which in turn lie +4.3, -5.4, (-3.7 and +0.8), and (-2.3 and +0.8) kcal mol(-1) below A+OH*, respectively. Thus the lowest lying [A···OH]* complex faces the highest local barrier to formation of the product (A-H)*+H(2)O. Between the transition states and the products lie six product complexes. Adopting the same order as the reactant complexes, the product complexes [(A-H)···H(2)O]* lie at -10.9, -22.4, (-24.2 and -18.7), and (-20.5 and -17.5) kcal mol(-1), respectively, again relative to separated A+OH*. All six A+OH* → (A-H)*+H(2)O pathways are exothermic, by -0.3, -14.7, (-17.4 and -7.8), and (-13.7 and -7.8) kcal mol(-1), respectively. The transition state for dehydrogenation at N(6) lies at the lowest energy (-5.4 kcal mol(-1) relative to A+OH*), and thus reaction is likely to occur at this site. This theoretical prediction dovetails with the observed high reactivity of OH radicals with the NH(2) group of aromatic amines. However, the high barrier (37.1 kcal mol(-1)) for reaction at the C(8) site makes C(8) dehydrogenation unlikely. This last result is consistent with experimental observation of the imidazole ring opening upon OH radical addition to C(8). In addition, TD-DFT computed electronic transitions of the N(6) product around 420 nm

  17. Xanthine oxidase activity during transition period and its association ...

    African Journals Online (AJOL)

    Dr BC Mili

    2013-08-07

    Aug 7, 2013 ... 3Division of Dairy Cattle Nutrition, National Dairy Research Institute, Karnal, Haryana, India. Accepted 3 .... day of calving in relation to the pre-partum day 21 value ... by activated immune cells includes inflammatory media-.

  18. Superfluid phase transition with activated velocity fluctuations: Renormalization group approach.

    Science.gov (United States)

    Dančo, Michal; Hnatič, Michal; Komarova, Marina V; Lučivjanský, Tomáš; Nalimov, Mikhail Yu

    2016-01-01

    A quantum field model that incorporates Bose-condensed systems near their phase transition into a superfluid phase and velocity fluctuations is proposed. The stochastic Navier-Stokes equation is used for a generation of the velocity fluctuations. As such this model generalizes model F of critical dynamics. The field-theoretic action is derived using the Martin-Siggia-Rose formalism and path integral approach. The regime of equilibrium fluctuations is analyzed within the perturbative renormalization group method. The double (ε,δ)-expansion scheme is employed, where ε is a deviation from space dimension 4 and δ describes scaling of velocity fluctuations. The renormalization procedure is performed to the leading order. The main corollary gained from the analysis of the thermal equilibrium regime suggests that one-loop calculations of the presented models are not sufficient to make a definite conclusion about the stability of fixed points. We also show that critical exponents are drastically changed as a result of the turbulent background and critical fluctuations are in fact destroyed by the developed turbulence fluctuations. The scaling exponent of effective viscosity is calculated and agrees with expected value 4/3.

  19. State transitions and feedback mechanisms control hydrology in the constructed catchment ´Chicken Creeḱ

    Science.gov (United States)

    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

  20. Entanglement generation in periodically driven integrable systems: Dynamical phase transitions and steady state

    Science.gov (United States)

    Sen, Arnab; Nandy, Sourav; Sengupta, K.

    2016-12-01

    We study a class of periodically driven d -dimensional integrable models and show that after n drive cycles with frequency ω , pure states with non-area-law entanglement entropy Sn(l ) ˜lα (n ,ω ) are generated, where l is the linear dimension of the subsystem, and d -1 ≤α (n ,ω )≤d . The exponent α (n ,ω ) eventually approaches d (volume law) for large enough l when n →∞ . We identify and analyze the crossover phenomenon from an area (S ˜ld -1 for d ≥1 ) to a volume (S ˜ld ) law and provide a criterion for their occurrence which constitutes a generalization of Hastings's theorem to driven integrable systems in one dimension. We also find that Sn generically decays to S∞ as (ω/n ) (d +2 )/2 for fast and (ω/n ) d /2 for slow periodic drives; these two dynamical phases are separated by a topological transition in the eigenspectrum of the Floquet Hamiltonian. This dynamical transition manifests itself in the temporal behavior of all local correlation functions and does not require a critical point crossing during the drive. We find that these dynamical phases show a rich re-entrant behavior as a function of ω for d =1 models and also discuss the dynamical transition for d >1 models. Finally, we study entanglement properties of the steady state and show that singular features (cusps and kinks in d =1 ) appear in S∞ as a function of ω whenever there is a crossing of the Floquet bands. We discuss experiments which can test our theory.

  1. A structural analysis of the A5/1 state transition graph

    Directory of Open Access Journals (Sweden)

    Andreas Beckmann

    2012-10-01

    Full Text Available We describe efficient algorithms to analyze the cycle structure of the graph induced by the state transition function of the A5/1 stream cipher used in GSM mobile phones and report on the results of the implementation. The analysis is performed in five steps utilizing HPC clusters, GPGPU and external memory computation. A great reduction of this huge state transition graph of 2^64 nodes is achieved by focusing on special nodes in the first step and removing leaf nodes that can be detected with limited effort in the second step. This step does not break the overall structure of the graph and keeps at least one node on every cycle. In the third step the nodes of the reduced graph are connected by weighted edges. Since the number of nodes is still huge an efficient bitslice approach is presented that is implemented with NVIDIA's CUDA framework and executed on several GPUs concurrently. An external memory algorithm based on the STXXL library and its parallel pipelining feature further reduces the graph in the fourth step. The result is a graph containing only cycles that can be further analyzed in internal memory to count the number and size of the cycles. This full analysis which previously would take months can now be completed within a few days and allows to present structural results for the full graph for the first time. The structure of the A5/1 graph deviates notably from the theoretical results for random mappings.

  2. The argument expression of change-of-state verbs and pseudo-transitive verbs

    Directory of Open Access Journals (Sweden)

    Eva Kardos

    2010-12-01

    Full Text Available Normal 0 21 MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Normál táblázat"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman";} In this paper, I aim to explore the argument realization properties of change-of-state verbs and those of pseudo-transitives. I pursue this by (1 providing an overview of two approaches towards the representation of argument structure and event structure information and (2 applying them to English and Hungarian change-of-state verbs and pseudo-transitives. In the end, although I acknowledge the merits of both models, I would like to emphasize the descriptive power of the second model with regard to my Hungarian data.

  3. Inequivalent models of irreversible dimer filling: Transition state'' dependence

    Energy Technology Data Exchange (ETDEWEB)

    Nord, R.S. (Department of Chemistry, Eastern Michigan University, Ypsilanti, MI (USA)); Evans, J.W. (Ames Laboratory, Ames IA (USA) Department of Physics, Iowa State Univ., Ames, IA (USA) Department of Mathematics, Iowa State Univ., Ames, IA (USA))

    1990-12-01

    Irreversible adsorption of diatomics on crystalline surfaces is sometimes modeled as random dimer filling of adjacent pairs of sites on a lattice. We note that this process can be implemented in two distinct ways: (i) randomly pick adjacent pairs of sites, {ital jj}{prime}, and fill {ital jj}{prime} only if both are empty (horizontal transition state); or (ii) randomly pick a single site, {ital j}, and if {ital j} and at least one neighbor are empty, then fill {ital j} and a randomly chosen empty neighbor (vertical transition state). Here it is instructive to consider processes which also include competitive random monomer filling of single sites. We find that although saturation (partial) coverages differ little between the models for pure dimer filling, there is a significant difference for comparable monomer and dimer filling rates. We present exact results for saturation coverage behavior for a linear lattice, and estimates for a square lattice. Ramifications for simple models of CO oxidation on surfaces are indicated.

  4. Equation of State and Phase Transitions in the Nuclear and Hadronic Systems

    CERN Document Server

    Bugaev, Kyrill A

    2010-01-01

    An investigation of strongly interacting matter equation of state remains one of the major tasks of modern high energy nuclear physics for almost a quarter of century. The present work is my doctor of science thesis which contains my contribution (42 works) to this field made between 1993 and 2008. Inhere I mainly discuss the common physical and mathematical features of several exactly solvable statistical models which describe the nuclear liquid-gas phase transition and the deconfinement phase transition. Luckily, in some cases it was possible to rigorously extend the solutions found in thermodynamic limit to finite volumes and to formulate the finite volume analogs of phases directly from the grand canonical partition. It turns out that finite volume (surface) of a system generates also the temporal constraints, i.e. the finite formation/decay time of possible states in this finite system. Among other results I would like to mention the calculation of upper and lower bounds for the surface entropy of physic...

  5. D-state effects in the electromagnetic N-Delta transition

    CERN Document Server

    Ramalho, G; Gross, Franz

    2008-01-01

    We consider here a manifestly covariant quark model of the nucleon and the Delta, where one quark is off-shell and the other two quarks form an on-shell diquark pair. Using this model, we have shown previously that the nucleon form factors and the dominant form factor for the gamma N -> Delta transition (the magnetic dipole (M1) form factor) can be well described by nucleon and Delta wave functions with S-state components only. In this paper we show that non-vanishing results for the small electric (E2) and Coulomb (C2) quadrupole form factors can be obtained if D-state components are added to the Delta valence quark wave function. We present a covariant definition of these components and compute their contributions to the form factors. We find that these components cannot, by themselves, describe the data. Explicit pion cloud contributions must also be added and these contributions dominate both the E2 and the C2 form factors. By parametrizing the pion cloud contribution for the transition electric and Coulo...

  6. Topological states and phase transitions in Sb2Te3-GeTe multilayers

    Science.gov (United States)

    Nguyen, Thuy-Anh; Backes, Dirk; Singh, Angadjit; Mansell, Rhodri; Barnes, Crispin; Ritchie, David A.; Mussler, Gregor; Lanius, Martin; Grützmacher, Detlev; Narayan, Vijay

    2016-06-01

    Topological insulators (TIs) are bulk insulators with exotic ‘topologically protected’ surface conducting modes. It has recently been pointed out that when stacked together, interactions between surface modes can induce diverse phases including the TI, Dirac semimetal, and Weyl semimetal. However, currently a full experimental understanding of the conditions under which topological modes interact is lacking. Here, working with multilayers of the TI Sb2Te3 and the band insulator GeTe, we provide experimental evidence of multiple topological modes in a single Sb2Te3-GeTe-Sb2Te3 structure. Furthermore, we show that reducing the thickness of the GeTe layer induces a phase transition from a Dirac-like phase to a gapped phase. By comparing different multilayer structures we demonstrate that this transition occurs due to the hybridisation of states associated with different TI films. Our results demonstrate that the Sb2Te3-GeTe system offers strong potential towards manipulating topological states as well as towards controlledly inducing various topological phases.

  7. Stimulated Raman transitions from the metastable 2s state of hydrogen

    Science.gov (United States)

    Bachau, Henri; Dondera, Mihai; Florescu, Viorica; Marian, Tudor A.

    2017-09-01

    We consider the hydrogen atom H(2s) exposed to a short laser pulse with a central frequency {ω }0 ranging from 136 eV to 1.5 keV ({ω }0≈ 5{--}55 au) at the intensity of 3.51× {10}16 W cm-2. We study stimulated Raman scattering transitions to the 1s ground state (anti-Stokes) and to the upper ns, np and nd states (with n> 2) (Stokes). Nondipole (retardation) effects are included up to { O }(1/c) (c is the speed of light in a vacuum). The calculation of the transition probabilities, based on the integration of the time-dependent Schrödinger equation, is confronted with results obtained by applying perturbation theory. The two methods are in very good agreement. We show that retardation effects play an important role for frequencies {ω }0 larger than a few hundred eV and pulse durations of the order of the femtosecond. In this regime, as the frequency {ω }0 increases, the contribution of the {{A}}2 term dominates over {A}\\cdot {P} (where {A} and {P} denote the vector potential of the field and the momentum operator, respectively). Results are presented for various values of the pulse frequency and duration.

  8. Crossing the dividing surface of transition state theory. III. Once and only once. Selecting reactive trajectories

    Energy Technology Data Exchange (ETDEWEB)

    Lorquet, J. C., E-mail: jc.lorquet@ulg.ac.be [Department of Chemistry, University of Liège, Sart-Tilman (Bâtiment B6), B-4000 Liège 1 (Belgium)

    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 this 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.

  9. Direct measurement of the low-temperature spin-state transition in LaCoO3.

    Science.gov (United States)

    Klie, R F; Zheng, J C; Zhu, Y; Varela, M; Wu, J; Leighton, C

    2007-07-27

    LaCoO3 exhibits an anomaly in its magnetic susceptibility around 80 K associated with a thermally excited transition of the Co3+-ion spin. We show that electron energy-loss spectroscopy is sensitive to this Co3+-ion spin-state transition, and that the O K edge prepeak provides a direct measure of the Co3+ spin state in LaCoO3 as a function of temperature. Our experimental results are confirmed by first-principles calculations, and we conclude that the thermally excited spin-state transition occurs from a low to an intermediate spin state, which can be distinguished from the high-spin state.

  10. Does Global Astrocytic Calcium Signaling Participate in Awake Brain State Transitions and Neuronal Circuit Function?

    Science.gov (United States)

    Kjaerby, Celia; Rasmussen, Rune; Andersen, Mie; Nedergaard, Maiken

    2017-02-16

    We continuously need to adapt to changing conditions within our surrounding environment, and our brain needs to quickly shift between resting and working activity states in order to allow appropriate behaviors. These global state shifts are intimately linked to the brain-wide release of the neuromodulators, noradrenaline and acetylcholine. Astrocytes have emerged as a new player participating in the regulation of brain activity, and have recently been implicated in brain state shifts. Astrocytes display global Ca(2+) signaling in response to activation of the noradrenergic system, but whether astrocytic Ca(2+) signaling is causative or correlative for shifts in brain state and neural activity patterns is not known. Here we review the current available literature on astrocytic Ca(2+) signaling in awake animals in order to explore the role of astrocytic signaling in brain state shifts. Furthermore, we look at the development and availability of innovative new methodological tools that are opening up for new ways of visualizing and perturbing astrocyte activity in awake behaving animals. With these new tools at hand, the field of astrocyte research will likely be able to elucidate the causal and mechanistic roles of astrocytes in complex behaviors within a very near future.

  11. From magma-poor Ocean Continent Transitions to steady state oceanic spreading: the balance between tectonic and magmatic processes

    Science.gov (United States)

    Gillard, Morgane; Manatschal, Gianreto; Autin, Julia; Decarlis, Alessandro; Sauter, Daniel

    2016-04-01

    The evolution of magma-poor rifted margins is linked to the development of a transition zone whose basement is neither clearly continental nor oceanic. The development of this Ocean-Continent Transition (OCT) is generally associated to the exhumation of serpentinized mantle along one or several detachment faults. That model is supported by numerous observations (IODP wells, dredges, fossil margins) and by numerical modelling. However, if the initiation of detachment faults in a magma-poor setting tends to be better understood by numerous studies in various area, the transition with the first steady state oceanic crust and the associated processes remain enigmatic and poorly studied. Indeed, this latest stage of evolution appears to be extremely gradual and involves strong interactions between tectonic processes and magmatism. Contrary to the proximal part of the exhumed domain where we can observe magmatic activity linked to the exhumation process (exhumation of gabbros, small amount of basalts above the exhumed mantle), in the most distal part the magmatic system appears to be independent and more active. In particular, we can observe large amounts of extrusive material above a previously exhumed and faulted basement (e.g. Alps, Australia-Antarctica margins). It seems that some faults can play the role of feeder systems for the magma in this area. Magmatic underplating is also important, as suggested by basement uplift and anomalously thick crust (e.g. East Indian margin). It results that the transition with the first steady state oceanic crust is marked by the presence of a hybrid basement, composed by exhumed mantle and magmatic material, whose formation is linked to several tectonic and magmatic events. One could argue that this basement is not clearly different from an oceanic basement. However, we consider that true, steady state oceanic crust only exists, if the entire rock association forming the crust is created during a single event, at a localized

  12. Effect of stellar activity on the high precision transit light curve

    Directory of Open Access Journals (Sweden)

    Oshagh, M.

    2015-01-01

    Full Text Available Stellar activity features such as spots and plages can create difficulties in determining planetary parameters through spectroscopic and photometric observations. The overlap of a transiting planet and a stellar spot, for instance, can produce anomalies in the transit light curve that may lead to inaccurate estimation of the transit duration, depth, and timing. Such inaccuracies can affect the precise derivation of the planet’s radius. In this talk we will present the results of a quantitative study on the effects of stellar spots on high precision transit light curves. We show that spot anomalies can lead to the estimate of a planet radius that is 4% smaller than the real value. The effects on the transit duration can also be of the order of 4%, longer or shorter. Depending on the size and distribution of spots, anomalies can also produce transit timing variations with significant amplitudes. For instance, TTVs with signal amplitudes of 200 seconds can be produced by spots as large as the largest sunspot. Finally, we examine the impact of active regions on the transit depth measurements in different wavelengths, in order to probe the impact of this effect on transmission spectroscopy measurements. We show that significant (up to 10% underestimation/overestimation of the planet-to-star radius ratio can be measured, especially in the short wavelength regime.

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

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

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

  14. Helping Children Make Transitions between Activities. What Works Briefs.

    Science.gov (United States)

    Ostrosky, M. M.; Jung, E. Y.; Hemmeter, M. L.

    This brief discusses the confusion some young children feel in moving from one activity to another (e.g., bus to classroom, cubbies to book reading, art time to lunch) that often results in frustration and challenging behaviors. The paper provides practical information on a variety of strategies to help preschool children make smooth, independent…

  15. Recycling CO 2 ? Computational Considerations of the Activation of CO 2 with Homogeneous Transition Metal Catalysts

    KAUST Repository

    Drees, Markus

    2012-08-10

    Faced with depleting fossil carbon sources, the search for alternative energy carriers and energy storage possibilities has become an important issue. Nature utilizes carbon dioxide as starting material for storing sun energy in plant hydrocarbons. A similar approach, storing energy from renewable sources in chemical bonds with CO 2 as starting material, may lead to partial recycling of CO 2 created by human industrial activities. Unfortunately, currently available routes for the transformation of CO 2 involve high temperatures and are often not selective. With the development of more sophisticated methods and better software, theoretical studies have become both increasingly widespread and useful. This concept article summarizes theoretical investigations of the current state of the feasibility of CO 2 activation with molecular transition metal catalysts, highlighting the most promising reactions of CO 2 with olefins to industrially relevant acrylic acid/acrylates, and the insertion of CO 2 into metal-element bonds, particularly for the synthesis of cyclic carbonates and polymers. Rapidly improving computational power and methods help to increase the importance and accuracy of calculations continuously and make computational chemistry a useful tool helping to solve some of the most important questions for the future. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. GRHL3 binding and enhancers rearrange as epidermal keratinocytes transition between functional states.

    Directory of Open Access Journals (Sweden)

    Rachel Herndon Klein

    2017-04-01

    Full Text Available Transcription factor binding, chromatin modifications and large scale chromatin re-organization underlie progressive, irreversible cell lineage commitments and differentiation. We know little, however, about chromatin changes as cells enter transient, reversible states such as migration. Here we demonstrate that when human progenitor keratinocytes either differentiate or migrate they form complements of typical enhancers and super-enhancers that are unique for each state. Unique super-enhancers for each cellular state link to gene expression that confers functions associated with the respective cell state. These super-enhancers are also enriched for skin disease sequence variants. GRHL3, a transcription factor that promotes both differentiation and migration, binds preferentially to super-enhancers in differentiating keratinocytes, while during migration, it binds preferentially to promoters along with REST, repressing the expression of migration inhibitors. Key epidermal differentiation transcription factor genes, including GRHL3, are located within super-enhancers, and many of these transcription factors in turn bind to and regulate super-enhancers. Furthermore, GRHL3 represses the formation of a number of progenitor and non-keratinocyte super-enhancers in differentiating keratinocytes. Hence, chromatin relocates GRHL3 binding and enhancers to regulate both the irreversible commitment of progenitor keratinocytes to differentiation and their reversible transition to migration.

  17. Transitions between turbulent and laminar superfluid vorticity states in the outer core of a neutron star

    CERN Document Server

    Peralta, C; Giacobello, M; Ooi, A

    2006-01-01

    We investigate the global transition from a turbulent state of superfluid vorticity to a laminar state, and vice versa, in the outer core of a neutron star. By solving numerically the hydrodynamic Hall-Vinen-Bekarevich-Khalatnikov equations for a rotating superfluid in a differentially rotating spherical shell, we find that the meridional counterflow driven by Ekman pumping exceeds the Donnelly-Glaberson threshold throughout most of the outer core, exciting unstable Kelvin waves which disrupt the rectilinear vortex array, creating a vortex tangle. In the turbulent state, the torque exerted on the crust oscillates, and the crust-core coupling is weaker than in the laminar state. This leads to a new scenario for the rotational glitches observed in radio pulsars: a vortex tangle is sustained in the differentially rotating outer core by the meridional counterflow, a sudden spin-up event brings the crust and core into corotation, the vortex tangle relaxes back to a rectilinear vortex array, then the crust spins do...

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

    Energy Technology Data Exchange (ETDEWEB)

    Stachowski, Aleksander [Jagiellonian University, Astronomical Observatory, Krakow (Poland); Szydlowski, Marek [Jagiellonian University, Astronomical Observatory, Krakow (Poland); Jagiellonian University, Mark Kac Complex Systems Research Centre, Krakow (Poland); Urbanowski, Krzysztof [University of Zielona Gora, Institute of Physics, Zielona Gora (Poland)

    2017-06-15

    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{sub 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 ΛCDM model. (orig.)

  19. Inhibition and Structure of Trichomonas vaginalis Purine Nucleoside Phosphorylase with Picomolar Transition State Analogues

    Energy Technology Data Exchange (ETDEWEB)

    Rinaldo-Matthis,A.; Wing, C.; Ghanem, M.; Deng, H.; Wu, P.; Gupta, A.; Tyler, P.; Evans, G.; Furneaux, R.; et al.

    2007-01-01

    Trichomonas vaginalis is a parasitic protozoan purine auxotroph possessing a unique purine salvage pathway consisting of a bacterial type purine nucleoside phosphorylase (PNP) and a purine nucleoside kinase. Thus, T. vaginalis PNP (TvPNP) functions in the reverse direction relative to the PNPs in other organisms. Immucillin-A (ImmA) and DADMe-Immucillin-A (DADMe-ImmA) are transition stte mimics of adenosine with geometric and electrostatic features that resemble early and late transition states of adenosine at the transition state stabilized by TvPNP. ImmA demonstrates slow-onset tight-binding inhibition with TvPNP, to give an equilibrium dissociation constant of 87 pM, an inhibitor release half-time of 17.2 min, and a K{sub m}/K{sub d} ratio of 70,100. DADMe-ImmA resembles a late ribooxacarbenium ion transition state for TvPNP to give a dissociation constant of 30 pM, an inhibitor release half-time of 64 min, and a K{sub m}/K{sub d} ratio of 203,300. The tight binding of DADMe-ImmA supports a late S{sub N}1 transition state. Despite their tight binding to TvPNP, ImmA and DADMe-ImmA are weak inhibitors of human and P. falciparum PNPs. The crystal structures of the TvPNP-ImmA{center_dot}PO{sub 4} and TvPNP{center_dot}DADMe-ImmA{center_dot}PO{sub 4} ternary complexes differ from previous structures with substrate anologues. The tight binding with DADMe-ImmA is in part due to a 2.7 {angstrom} ionic interaction between a PO{sub 4} oxygen and the N1 cation of the hydroxypyrrolidine and is weaker in the TvPNP{center_dot}ImmA{center_dot}PO{sub 4} structure at 3.5 {angstrom}. However, the TvPNP{center_dot}ImmA{center_dot}PO{sub 4} structure includes hydrogen bonds between the 2'-hydroxyl and the protein that are not present in TvPNP{center_dot}DADMe-ImmA{center_dot}PO{sub 4}. These structures explain why DADMe-ImmA binds tighter than ImmA. Immucillin-H is a 12 nM inhibitor of TvPNP but a 56 pM inhibitor of human PNP. And this difference is explained by isotope

  20. Metastability of the Nonlinear Wave Equation: Insights from Transition State Theory

    Science.gov (United States)

    Newhall, Katherine A.; Vanden-Eijnden, Eric

    2017-06-01

    This paper is concerned with the longtime dynamics of the nonlinear wave equation in one-space dimension, u_{tt} - κ ^2 u_{xx} +V'(u) =0 \\quad x\\in [0,1] where κ >0 is a parameter and V( u) is a potential bounded from below and growing at least like u^2 as |u|→ ∞. Infinite energy solutions of this equation preserve a natural Gibbsian invariant measure, and when the potential is double-welled, for example when V(u) = 1/4 (1-u^2)^2, there is a regime such that two small disjoint sets in the system's phase-space concentrate most of the mass of this measure. This suggests that the solutions to the nonlinear wave equation can be metastable over these sets, in the sense that they spend long periods of time in these sets and only rarely transition between them. Here, we quantify this phenomenon by calculating exactly via transition state theory (TST) the mean frequency at which the solutions of the nonlinear wave equation with initial conditions drawn from its invariant measure cross a dividing surface lying in between the metastable sets. We also investigate numerically how the mean TST frequency compares to the rate at which a typical solution crosses this dividing surface. These numerical results suggest that the dynamics of the nonlinear wave equation is ergodic and rapidly mixing with respect to the Gibbs invariant measure when the parameter κ in small enough. In this case, successive transitions between the two regions are roughly uncorrelated and their dynamics can be coarse-grained to jumps in a two-state Markov chain whose rate can be deduced from the mean TST frequency. This is a regime in which the dynamics of the nonlinear wave equation displays a metastable behavior that is not fundamentally different from that observed in its stochastic counterpart in which random noise and damping terms are added to the equation. For larger κ , however, the dynamics either stops being ergodic, or its mixing time becomes larger than the inverse of the TST frequency

  1. Metastability of the Nonlinear Wave Equation: Insights from Transition State Theory

    Science.gov (United States)

    Newhall, Katherine A.; Vanden-Eijnden, Eric

    2017-01-01

    This paper is concerned with the longtime dynamics of the nonlinear wave equation in one-space dimension, u_{tt} - κ^2 u_{xx} +V'(u) =0 quad xin [0,1] where κ >0 is a parameter and V(u) is a potential bounded from below and growing at least like u^2 as |u|→ ∞. Infinite energy solutions of this equation preserve a natural Gibbsian invariant measure, and when the potential is double-welled, for example when V(u) = 1/4 (1-u^2)^2 , there is a regime such that two small disjoint sets in the system's phase-space concentrate most of the mass of this measure. This suggests that the solutions to the nonlinear wave equation can be metastable over these sets, in the sense that they spend long periods of time in these sets and only rarely transition between them. Here, we quantify this phenomenon by calculating exactly via transition state theory (TST) the mean frequency at which the solutions of the nonlinear wave equation with initial conditions drawn from its invariant measure cross a dividing surface lying in between the metastable sets. We also investigate numerically how the mean TST frequency compares to the rate at which a typical solution crosses this dividing surface. These numerical results suggest that the dynamics of the nonlinear wave equation is ergodic and rapidly mixing with respect to the Gibbs invariant measure when the parameter κ in small enough. In this case, successive transitions between the two regions are roughly uncorrelated and their dynamics can be coarse-grained to jumps in a two-state Markov chain whose rate can be deduced from the mean TST frequency. This is a regime in which the dynamics of the nonlinear wave equation displays a metastable behavior that is not fundamentally different from that observed in its stochastic counterpart in which random noise and damping terms are added to the equation. For larger κ, however, the dynamics either stops being ergodic, or its mixing time becomes larger than the inverse of the TST frequency

  2. Peak activation of lower limb musculature during high flexion kneeling and transitional movements.

    Science.gov (United States)

    Kingston, David C; Tennant, Liana M; Chong, Helen C; Acker, Stacey M

    2016-09-01

    Few studies have measured lower limb muscle activation during high knee flexion or investigated the effects of occupational safety footwear. Therefore, our understanding of injury and disease mechanisms, such as knee osteoarthritis, is limited for these high-risk postures. Peak activation was assessed in eight bilateral lower limb muscles for twelve male participants, while shod or barefoot. Transitions between standing and kneeling had peak quadriceps and tibialis anterior (TA) activations above 50% MVC. Static kneeling and simulated tasks performed when kneeling had peak TA activity above 15% MVC but below 10% MVC for remaining muscles. In three cases, peak muscle activity was significantly higher (mean 8.9% MVC) when shod. However, net compressive knee joint forces may not be significantly increased when shod. EMG should be used as a modelling input when estimating joint contact forces for these postures, considering the activation levels in the hamstrings and quadriceps muscles during transitions. Practitioner Summary: Kneeling transitional movements are used in activities of daily living and work but are linked to increased knee osteoarthritis risk. We found peak EMG activity of some lower limb muscles to be over 70% MVC during transitions and minimal influence of wearing safety footwear.

  3. Effects of a Transition to a Hydrogen Economy on Employment in the United States

    Energy Technology Data Exchange (ETDEWEB)

    Tolley, George S.; Jones, Donald W. Mintz, Marianne M.; Smith, Barton A.; Carlson, Eric; Unnasch, Stefan; Lawrence, Michael; Chmelynski, Harry

    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 carry 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 and the

  4. Association between body weight, physical activity and food choices among metropolitan transit workers

    Directory of Open Access Journals (Sweden)

    Hannan Peter J

    2007-11-01

    Full Text Available Abstract Background Associations between body weight, physical activity and dietary intake among a population of metropolitan transit workers are described. Methods Data were collected during October through December, 2005, as part of the baseline measures for a worksite weight gain prevention intervention in four metro transit bus garages. All garage employees were invited to complete behavioral surveys that assessed food choices and physical activity, and weight and height were directly measured. Seventy-eight percent (N = 1092 of all employees participated. Results The prevalence of obesity (BMI >= 30 kg/m2 was 56%. Over half of the transit workers reported consuming fruit (55% and vegetables (59% ≥ 3/week. Reported fast food restaurant frequency was low (13% visited ≥ 3/week. Drivers reported high levels of physical activity (eg. walking 93 minutes/day. However, an objective measure of physical activity measured only 16 minutes moderate/vigorous per day. Compared to other drivers, obese drivers reported significantly less vigorous physical activity, more time sitting, and more time watching television. Healthy eating, physical activity and weight management were perceived to be difficult at the worksite, particularly among obese transit workers, and perceived social support for these behaviors was modest. However, most workers perceived weight management and increased physical activity to be personally important for their health. Conclusion Although transit workers' self-report of fruit and vegetable intake, and physical activity was high, perceived access to physical activity and healthful eating opportunities at the worksite was low. Obese workers were significantly less physically active and were more likely to report work environmental barriers to physical activity.

  5. Accurate spectroscopic calculations of 21 electronic states of ClO radical including transition properties

    Science.gov (United States)

    Wang, Xinxin; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue

    2016-08-01

    The potential energy curves were calculated for the 21 states (X2Π, A2Π, 32Π, 42Π, 52Π, 12Σ+, 22Σ+, 32Σ+, 12Σ-, 22Σ-, 32Σ-, 12Δ, 22Δ, 32Δ, 12Φ, 14Σ+, a4Σ-, 24Σ-, 14Π, 24Π and 14Δ), which originated from the two lowest dissociation channels of ClO radical. The calculations were done for internuclear separations approximately from 0.08 to 1.10 nm using the CASSCF method, which was followed by the icMRCI approach with the aug-cc-pV5Z basis set. Of these 21 states, the 14Π, 24Π, 32Δ, 42Π, 52Π, 12Φ, 32Σ+, 14Δ and 24Σ- states are repulsive. The 12Δ, 12Σ-, 14Σ+, 22Σ-, 12Σ+, 22Σ+, 22Δ and 32Σ- states are very weakly bound. Only the A2Π state has one barrier. The avoided crossing exists between the A2Π and the 32Π state. However, the avoided crossing does not generate any double wells. Core- valence correlation correction was accounted for at the level of an aug-cc-pCVQZ basis set. Scalar relativistic correction was included by the third-order Douglas-Kroll Hamiltonian approximation at the level of an aug-cc-pVQZ basis set. All the potential energy curves were extrapolated to the complete basis set limit. The spectroscopic parameters were determined. The 12Σ-, 22Σ-, 32Σ- and 14Σ+ states may be very difficult to be detected in an experiment, since each of these Λ-S states has only one or two vibrational states. The Franck-Condon factors and radiative lifetimes were calculated for several low vibrational levels of the A2Π - X2Π, 32Π - a4Σ-, 22Δ - a4Σ- and 32Σ- - 12Σ- transitions. The spin-orbit coupling effect on the spectroscopic parameters of the X2Π, A2Π, 32Π, a4Σ- and 22Σ+ states were discussed. The spectroscopic properties reported here can be expected to be reliably predicted ones.

  6. Validity Evidence for the State Mindfulness Scale for Physical Activity

    Science.gov (United States)

    Cox, Anne E.; Ullrich-French, Sarah; French, Brian F.

    2016-01-01

    Being attentive to and aware of one's experiences in the present moment with qualities of acceptance and openness reflects the state of mindfulness. Positive associations exist between state mindfulness and state autonomous motivation for everyday activities. Though this suggests that state mindfulness links with adaptive motivational experiences,…

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

    Science.gov (United States)

    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...

  8. Transition state to mode locking in a passively mode-locked erbium-doped fibre ring laser

    Institute of Scientific and Technical Information of China (English)

    Liu Jia-Rui; Xu Wen-Cheng; Luo Zhi-Chao; Luo Ai-Ping; Yin Hai-Sen

    2011-01-01

    The transition state between the continuous wave region and the mode-locked region in a passively mode-locked erbium-doped fibre ring laser has been experimentally observed by utilizing the nonlinear polarization rotation technique. When the pump power reaches the mode-locked threshold, the metastable pulse train with a tunable repetition rate is obtained in the transition from the continuous wave state to the passive mode-locked state via proper adjustment of the polarization controller. A simple model has been established to explain the experimental observation.

  9. On apparent quantized transition-state thresholds in the photofragmentation of acetaldehyde

    Energy Technology Data Exchange (ETDEWEB)

    King, Rollin A. [Center for Computational Quantum Chemistry, Department of Chemistry, The University of Georgia, Athens, Georgia 30602-2525 (United States); Allen, Wesley D. [Center for Computational Quantum Chemistry, Department of Chemistry, The University of Georgia, Athens, Georgia 30602-2525 (United States); Schaefer, Henry F. III [Center for Computational Quantum Chemistry, Department of Chemistry, The University of Georgia, Athens, Georgia 30602-2525 (United States)

    2000-04-01

    Recent photofragmentation experiments have observed stepwise increases in the dissociation rate for CH{sub 3}CHO (T{sub 1}){yields}CH{sub 3} (X(tilde sign) {sup 2}A{sub 2}{sup ''})+HCO (X(tilde sign) {sup 2}A{sup '}) as a function of excitation energy. In accord with the Rice-Ramsperger-Kassel-Marcus (RRKM) form of transition-state theory, these steps were interpreted as corresponding to vibrational levels of the fragmentation transition state on the triplet surface. We have investigated this acetaldehyde dissociation using coupled cluster (CC) and density functional (DFT) methods with [C,O/H] atomic-orbital basis sets ranging in quality from [4s2p1d/2s1p] to [6s5p4d3f2g1h/5s4p3d2 f1g]. A high-level focal point analysis, along with harmonic force field computations, results in predictions of the dissociation energy, D{sub 0}=1583 cm{sup -1}, and the association barrier height, V{sub 0}{sup *}=3149 cm{sup -1}. With a basis set of triple-{zeta} plus double-polarization plus f(TZ2Pf ) quality, the DFT method UB3LYP and the CC method RCCSD predict barrier frequencies of 355i cm{sup -1} and 516i cm{sup -1}, respectively, while the empirical value inferred from RRKM models is only 60i cm{sup -1}. The RRKM-derived frequencies for the degrees of freedom orthogonal to the reaction path are more reasonable but still not in convincing agreement with electronic structure theory. Thus, while the experimental steps in the dissociation rate of acetaldehyde (as well as ketene) have yet to be satisfactorily explained, proven ab initio methods provide strong evidence that simple RRKM fits to the k(E) profile provide misleading vibrational frequencies of the transition state on the corresponding triplet potential energy surface. (c) 2000 American Institute of Physics.

  10. Intra-urban human mobility and activity transition: evidence from social media check-in data.

    Science.gov (United States)

    Wu, Lun; Zhi, Ye; Sui, Zhengwei; Liu, Yu

    2014-01-01

    Most existing human mobility literature focuses on exterior characteristics of movements but neglects activities, the driving force that underlies human movements. In this research, we combine activity-based analysis with a movement-based approach to model the intra-urban human mobility observed from about 15 million check-in records during a yearlong period in Shanghai, China. The proposed model is activity-based and includes two parts: the transition of travel demands during a specific time period and the movement between locations. For the first part, we find the transition probability between activities varies over time, and then we construct a temporal transition probability matrix to represent the transition probability of travel demands during a time interval. For the second part, we suggest that the travel demands can be divided into two classes, locationally mandatory activity (LMA) and locationally stochastic activity (LSA), according to whether the demand is associated with fixed location or not. By judging the combination of predecessor activity type and successor activity type we determine three trip patterns, each associated with a different decay parameter. To validate the model, we adopt the mechanism of an agent-based model and compare the simulated results with the observed pattern from the displacement distance distribution, the spatio-temporal distribution of activities, and the temporal distribution of travel demand transitions. The results show that the simulated patterns fit the observed data well, indicating that these findings open new directions for combining activity-based analysis with a movement-based approach using social media check-in data.

  11. Intra-urban human mobility and activity transition: evidence from social media check-in data.

    Directory of Open Access Journals (Sweden)

    Lun Wu

    Full Text Available Most existing human mobility literature focuses on exterior characteristics of movements but neglects activities, the driving force that underlies human movements. In this research, we combine activity-based analysis with a movement-based approach to model the intra-urban human mobility observed from about 15 million check-in records during a yearlong period in Shanghai, China. The proposed model is activity-based and includes two parts: the transition of travel demands during a specific time period and the movement between locations. For the first part, we find the transition probability between activities varies over time, and then we construct a temporal transition probability matrix to represent the transition probability of travel demands during a time interval. For the second part, we suggest that the travel demands can be divided into two classes, locationally mandatory activity (LMA and locationally stochastic activity (LSA, according to whether the demand is associated with fixed location or not. By judging the combination of predecessor activity type and successor activity type we determine three trip patterns, each associated with a different decay parameter. To validate the model, we adopt the mechanism of an agent-based model and compare the simulated results with the observed pattern from the displacement distance distribution, the spatio-temporal distribution of activities, and the temporal distribution of travel demand transitions. The results show that the simulated patterns fit the observed data well, indicating that these findings open new directions for combining activity-based analysis with a movement-based approach using social media check-in data.

  12. Asymmetric photoredox transition-metal catalysis activated by visible light

    Science.gov (United States)

    Huo, Haohua; Shen, Xiaodong; Wang, Chuanyong; Zhang, Lilu; Röse, Philipp; Chen, Liang-An; Harms, Klaus; Marsch, Michael; Hilt, Gerhard; Meggers, Eric

    2014-11-01

    Asymmetric catalysis is seen as one of the most economical strategies to satisfy the growing demand for enantiomerically pure small molecules in the fine chemical and pharmaceutical industries. And visible light has been recognized as an environmentally friendly and sustainable form of energy for triggering chemical transformations and catalytic chemical processes. For these reasons, visible-light-driven catalytic asymmetric chemistry is a subject of enormous current interest. Photoredox catalysis provides the opportunity to generate highly reactive radical ion intermediates with often unusual or unconventional reactivities under surprisingly mild reaction conditions. In such systems, photoactivated sensitizers initiate a single electron transfer from (or to) a closed-shell organic molecule to produce radical cations or radical anions whose reactivities are then exploited for interesting or unusual chemical transformations. However, the high reactivity of photoexcited substrates, intermediate radical ions or radicals, and the low activation barriers for follow-up reactions provide significant hurdles for the development of efficient catalytic photochemical processes that work under stereochemical control and provide chiral molecules in an asymmetric fashion. Here we report a highly efficient asymmetric catalyst that uses visible light for the necessary molecular activation, thereby combining asymmetric catalysis and photocatalysis. We show that a chiral iridium complex can serve as a sensitizer for photoredox catalysis and at the same time provide very effective asymmetric induction for the enantioselective alkylation of 2-acyl imidazoles. This new asymmetric photoredox catalyst, in which the metal centre simultaneously serves as the exclusive source of chirality, the catalytically active Lewis acid centre, and the photoredox centre, offers new opportunities for the `green' synthesis of non-racemic chiral molecules.

  13. New avenues for redox-active ligands: Non-classical reactivity with late transition metals facilitated by o-aminophenol derived architectures

    NARCIS (Netherlands)

    D.L.J. Broere

    2016-01-01

    Many homogeneous and heterogeneous catalyst systems contain one or more transition metals. The widespread employment of these metals as catalysts is ascribed to their accessible d-orbitals to activate chemical bonds, and the ability to undergo metal-based oxidation state changes to facilitate desira

  14. A method to measure the resonance transitions between the gravitationally bound quantum states of neutrons in the GRANIT spectrometer

    Energy Technology Data Exchange (ETDEWEB)

    Kreuz, M. [ILL, 6 rue Jules Horowitz, Grenoble F-38042 (France); Nesvizhevsky, V.V., E-mail: nesvizhevsky@ill.f [ILL, 6 rue Jules Horowitz, Grenoble F-38042 (France); Schmidt-Wellenburg, P.; Soldner, T.; Thomas, M. [ILL, 6 rue Jules Horowitz, Grenoble F-38042 (France); Boerner, H.G. [ILL (France); Naraghi, F.; Pignol, G.; Protasov, K.V.; Rebreyend, D.; Vezzu, F. [LPSC/UJF-IN2P3-INPG, 53, rue des Martyrs, Grenoble F-38026 (France); Flaminio, R.; Michel, C.; Morgado, N.; Pinard, L. [LMA, 7 avenue Pierre de Coubertin, Villeurbanne F-69622 (France); Baessler, S. [Virginia University, 1101 Millmont Street, Charlottesville 22904 (United States); Gagarski, A.M.; Grigorieva, L.A. [PNPI, Orlova Roscha, Gatchina, Leningrad Reg. 188350 (Russian Federation); Kuzmina, T.M. [Khlopin Institute, 28 Vtoroi Murinsky Per., St. Peterburg 194021 (Russian Federation); Meyerovich, A.E. [University of Rhode Island, Kingston RI-02881 (United States)

    2009-12-11

    We present a method to measure the resonance transitions between the gravitationally bound quantum states of neutrons in the GRANIT spectrometer. The purpose of GRANIT is to improve the accuracy of measurement of the quantum states parameters by several orders of magnitude, taking advantage of long storage of ultracold neutrons at specular trajectories. The transitions could be excited using a periodic spatial variation of a magnetic field gradient. If the frequency of such a perturbation (in the frame of a moving neutron) coincides with a resonance frequency defined by the energy difference of two quantum states, the transition probability will sharply increase. The GRANIT experiment is motivated by searches for short-range interactions (in particular spin-dependent interactions), by studying the interaction of a quantum system with a gravitational field, by searches for extensions of the Standard model, by the unique possibility to check the equivalence principle for an object in a quantum state and by studying various quantum optics phenomena.

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

    Directory of Open Access Journals (Sweden)

    Jesse Chu-Shore

    Full Text Available BACKGROUND: 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. METHODOLOGY/PRINCIPAL FINDINGS: 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. CONCLUSIONS/SIGNIFICANCE: 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.

  16. Active Affordance Learning in Continuous State and Action Spaces

    NARCIS (Netherlands)

    Wang, C.; Hindriks, K.V.; Babuska, R.

    2014-01-01

    Learning object affordances and manipulation skills is essential for developing cognitive service robots. We propose an active affordance learning approach in continuous state and action spaces without manual discretization of states or exploratory motor primitives. During exploration in the action

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

    Science.gov (United States)

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

    2013-01-01

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

  18. Generation of vertical convective vortex in the transition from anomalous to normal steady-state convection

    Science.gov (United States)

    Sharifulin, Albert; Poludnitsin, Anatoly

    2010-11-01

    This phenomenon was discovered in the framework of experimental attempt[1] to define form of bifurcation curve in enclosed cavity with boulders temperature state of which could slowly deviate from condition of directly from bottom heating. In order to verify the discovered regularity experiment with slow cubic cell inclination form direct form bottom heat position was performed. The transition process from abnormal convection flow(When heated, and therefore more light, fluid moves down) to normal one during bifurcation curve crossing appeared to be completely unexpected and in radical contrast to served one in our 2D calculations and of other authors. The transition process appears as a fast, for 1-2 seconds, the rotation around the vertical axis of the entire mass of fluid filling the cavity. In the presentation the effect theoretical investigations results are discussed. Series of new problems concerned with the effect of existence borders definition and with possibility to control the effect through fluid properties and heat conditions is formulated Possibility of spontaneous vertical convective vortex generation application to atmospheric behavior explanation and to Earth's mantle one is discussed. [1] A.N. Sharifulin, A.N. Poludnitsin A.N., A.S. Kravchuk Laboratory Scale Simulation of Nonlocal Generation of a Tropical Cyclone. Journal of Experimental and Theoretical Physics, 2008, Vol.107, No.6, pp.1090-1093.

  19. Line Strengths of Rovibrational and Rotational Transitions in the X$^2\\Pi$ Ground State of OH

    CERN Document Server

    Brooke, James S A; Western, Colin M; Sneden, Christopher; Afşar, Melike; Li, Gang; Gordon, Iouli E

    2015-01-01

    A new line list including positions and absolute intensities (in the form of Einstein $A$ values and oscillator strengths) has been produced for the OH ground X\\DP\\ state rovibrational (Meinel system) and pure rotational transitions. All possible transitions are included with v$\\primed$ and v$\\Dprimed$ up to 13, and $J$ up to between 9.5 and 59.5, depending on the band. An updated fit to determine molecular constants has been performed, which includes some new rotational data and a simultaneous fitting of all molecular constants. The absolute line intensities are based on a new dipole moment function, which is a combination of two high level ab initio calculations. The calculations show good agreement with an experimental v=1 lifetime, experimental $\\mu_\\mathrm{v}$ values, and $\\Delta$v=2 line intensity ratios from an observed spectrum. To achieve this good agreement, an alteration in the method of converting matrix elements from Hund's case (b) to (a) was made. Partitions sums have been calculated using the ...

  20. Lifespan method as a tool to study criticality in absorbing-state phase transitions

    Science.gov (United States)

    Mata, Angélica S.; Boguñá, Marian; Castellano, Claudio; Pastor-Satorras, Romualdo

    2015-05-01

    In a recent work, a new numerical method (the lifespan method) has been introduced to study the critical properties of epidemic processes on complex networks [M. Boguñá, C. Castellano, and R. Pastor-Satorras, Phys. Rev. Lett. 111, 068701 (2013), 10.1103/PhysRevLett.111.068701]. Here, we present a detailed analysis of the viability of this method for the study of the critical properties of generic absorbing-state phase transitions in lattices. Focusing on the well-understood case of the contact process, we develop a finite-size scaling theory to measure the critical point and its associated critical exponents. We show the validity of the method by studying numerically the contact process on a one-dimensional lattice and comparing the findings of the lifespan method with the standard quasistationary method. We find that the lifespan method gives results that are perfectly compatible with those of quasistationary simulations and with analytical results. Our observations confirm that the lifespan method is a fully legitimate tool for the study of the critical properties of absorbing phase transitions in regular lattices.