Uniting statistical and individual-based approaches for animal movement modelling.

PubMed

Latombe, Guillaume; Parrott, Lael; Basille, Mathieu; Fortin, Daniel

2014-01-01

The dynamic nature of their internal states and the environment directly shape animals' spatial behaviours and give rise to emergent properties at broader scales in natural systems. However, integrating these dynamic features into habitat selection studies remains challenging, due to practically impossible field work to access internal states and the inability of current statistical models to produce dynamic outputs. To address these issues, we developed a robust method, which combines statistical and individual-based modelling. Using a statistical technique for forward modelling of the IBM has the advantage of being faster for parameterization than a pure inverse modelling technique and allows for robust selection of parameters. Using GPS locations from caribou monitored in Québec, caribou movements were modelled based on generative mechanisms accounting for dynamic variables at a low level of emergence. These variables were accessed by replicating real individuals' movements in parallel sub-models, and movement parameters were then empirically parameterized using Step Selection Functions. The final IBM model was validated using both k-fold cross-validation and emergent patterns validation and was tested for two different scenarios, with varying hardwood encroachment. Our results highlighted a functional response in habitat selection, which suggests that our method was able to capture the complexity of the natural system, and adequately provided projections on future possible states of the system in response to different management plans. This is especially relevant for testing the long-term impact of scenarios corresponding to environmental configurations that have yet to be observed in real systems.

Uniting Statistical and Individual-Based Approaches for Animal Movement Modelling

PubMed Central

Latombe, Guillaume; Parrott, Lael; Basille, Mathieu; Fortin, Daniel

2014-01-01

The dynamic nature of their internal states and the environment directly shape animals' spatial behaviours and give rise to emergent properties at broader scales in natural systems. However, integrating these dynamic features into habitat selection studies remains challenging, due to practically impossible field work to access internal states and the inability of current statistical models to produce dynamic outputs. To address these issues, we developed a robust method, which combines statistical and individual-based modelling. Using a statistical technique for forward modelling of the IBM has the advantage of being faster for parameterization than a pure inverse modelling technique and allows for robust selection of parameters. Using GPS locations from caribou monitored in Québec, caribou movements were modelled based on generative mechanisms accounting for dynamic variables at a low level of emergence. These variables were accessed by replicating real individuals' movements in parallel sub-models, and movement parameters were then empirically parameterized using Step Selection Functions. The final IBM model was validated using both k-fold cross-validation and emergent patterns validation and was tested for two different scenarios, with varying hardwood encroachment. Our results highlighted a functional response in habitat selection, which suggests that our method was able to capture the complexity of the natural system, and adequately provided projections on future possible states of the system in response to different management plans. This is especially relevant for testing the long-term impact of scenarios corresponding to environmental configurations that have yet to be observed in real systems. PMID:24979047

Dynamic properties in the four-state haploid coupled discrete-time mutation-selection model with an infinite population limit

NASA Astrophysics Data System (ADS)

Lee, Kyu Sang; Gill, Wonpyong

2017-11-01

The dynamic properties, such as the crossing time and time-dependence of the relative density of the four-state haploid coupled discrete-time mutation-selection model, were calculated with the assumption that μ ij = μ ji , where μ ij denotes the mutation rate between the sequence elements, i and j. The crossing time for s = 0 and r 23 = r 42 = 1 in the four-state model became saturated at a large fitness parameter when r 12 > 1, was scaled as a power law in the fitness parameter when r 12 = 1, and diverged when the fitness parameter approached the critical fitness parameter when r 12 < 1, where r ij = μ ij / μ 14.

From ab Initio Potential Energy Surfaces to State-Resolved Reactivities: X + H 2O ↔ HX + OH [X = F, Cl, and O( 3P)] Reactions

DOE PAGES

Li, Jun; Jiang, Bin; Song, Hongwei; ...

2015-04-17

Here, we survey the recent advances in theoretical understanding of quantum state resolved dynamics, using the title reactions as examples. It is shown that the progress was made possible by major developments in two areas. First, an accurate analytical representation of many high-level ab initio points over a large configuration space can now be made with high fidelity and the necessary permutation symmetry. The resulting full-dimensional global potential energy surfaces enable dynamical calculations using either quasi-classical trajectory or more importantly quantum mechanical methods. The second advance is the development of accurate and efficient quantum dynamical methods, which are necessary formore » providing a reliable treatment of quantum effects in reaction dynamics such as tunneling, resonances, and zero-point energy. The powerful combination of the two advances has allowed us to achieve a quantitatively accurate characterization of the reaction dynamics, which unveiled rich dynamical features such as steric steering, strong mode specificity, and bond selectivity. The dependence of reactivity on reactant modes can be rationalized by the recently proposed sudden vector projection model, which attributes the mode specificity and bond selectivity to the coupling of reactant modes with the reaction coordinate at the relevant transition state. The deeper insights provided by these theoretical studies have advanced our understanding of reaction dynamics to a new level.« less

Reversible adaptation to photoinduced shape switching by oligomer-macrocycle interconversion with component selection in a three-state constitutional dynamic system.

PubMed

Vantomme, Ghislaine; Lehn, Jean-Marie

2014-12-01

Light irradiation of the molecular photoswitch 1-E causes isomerization into the 1-Z configuration stabilized by an internal hydrogen bond. 1-E bears aldehyde groups allowing for dynamic covalent reaction with linear diamines. On photoinduced E/Z shape switching of 1 in presence of diamines, the system undergoes interconversion between two states, a non-cyclic oligomeric one and a macrocyclic one, corresponding respectively to the E and Z configurations of 1. With a mixture of linear α,ω-diamines, 1-E yields non-selective dynamic oligomers by random incorporation of diamine components. Photoswitching to the 1-Z form leads to constitutional adaptation with preferential formation of the macrocycle incorporating the best suited diamine, H2 N(CH2 )7 NH2 . In presence of metal cations, the E form switches from its unbound W shape to its coordinated U shape and yields the macrocycle resulting from the selective incorporation of the diamine H2 NCH2 CH2 OCH2 CH2 NH2 that contains an additional O coordination site. Taken together, the results obtained describe constitutional adaptation in a triple state system: an oligomeric one and two different macrocyclic ones generated in response to two orthogonal agents, a physical stimulus, light, or a chemical effector, metal cations. These three states present, towards the incorporation of diamine components, respectively no selection, photoselection and metalloselection. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Probing Ultrafast Electron Dynamics at Surfaces Using Soft X-Ray Transient Reflectivity Spectroscopy

NASA Astrophysics Data System (ADS)

Baker, L. Robert; Husek, Jakub; Biswas, Somnath; Cirri, Anthony

The ability to probe electron dynamics with surface sensitivity on the ultrafast time scale is critical for understanding processes such as charge separation, injection, and surface trapping that mediate efficiency in catalytic and energy conversion materials. Toward this goal, we have developed a high harmonic generation (HHG) light source for femtosecond soft x-ray reflectivity. Using this light source we investigated the ultrafast carrier dynamics at the surface of single crystalline α-Fe2O3, polycrystalline α-Fe2O3, and the mixed metal oxide, CuFeO2. We have recently demonstrated that CuFeO2 in particular is a selective catalyst for photo-electrochemical CO2 reduction to acetate; however, the role of electronic structure and charge carrier dynamics in mediating catalytic selectivity has not been well understood. Soft x-ray reflectivity measurements probe the M2,3, edges of the 3d transition metals, which provide oxidation and spin state resolution with element specificity. In addition to chemical state specificity, these measurements are also surface sensitive, and by independently simulating the contributions of the real and imaginary components of the complex refractive index, we can differentiate between surface and sub-surface contributions to the excited state spectrum. Accordingly, this work demonstrates the ability to probe ultrafast carrier dynamics in catalytic materials with element and chemical state specificity and with surface sensitivity.

Dynamical differences of hemoglobin and the ionotropic glutamate receptor in different states revealed by a new dynamics alignment method.

PubMed

Tobi, Dror

2017-08-01

A new algorithm for comparison of protein dynamics is presented. Compared protein structures are superposed and their modes of motions are calculated using the anisotropic network model. The obtained modes are aligned using the dynamic programming algorithm of Needleman and Wunsch, commonly used for sequence alignment. Dynamical comparison of hemoglobin in the T and R2 states reveals that the dynamics of the allosteric effector 2,3-bisphosphoglycerate binding site is different in the two states. These differences can contribute to the selectivity of the effector to the T state. Similar comparison of the ionotropic glutamate receptor in the kainate+(R,R)-2b and ZK bound states reveals that the kainate+(R,R)-2b bound states slow modes describe upward motions of ligand binding domain and the transmembrane domain regions. Such motions may lead to the opening of the receptor. The upper lobes of the LBDs of the ZK bound state have a smaller interface with the amino terminal domains above them and have a better ability to move together. The present study exemplifies the use of dynamics comparison as a tool to study protein function. Proteins 2017; 85:1507-1517. © 2014 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Rare beneficial mutations can halt Muller's ratchet

NASA Astrophysics Data System (ADS)

Balick, Daniel; Goyal, Sidhartha; Jerison, Elizabeth; Neher, Richard; Shraiman, Boris; Desai, Michael

2012-02-01

In viral, bacterial, and other asexual populations, the vast majority of non-neutral mutations are deleterious. This motivates the application of models without beneficial mutations. Here we show that the presence of surprisingly few compensatory mutations halts fitness decay in these models. Production of deleterious mutations is balanced by purifying selection, stabilizing the fitness distribution. However, stochastic vanishing of fitness classes can lead to slow fitness decay (i.e. Muller's ratchet). For weakly deleterious mutations, production overwhelms purification, rapidly decreasing population fitness. We show that when beneficial mutations are introduced, a stable steady state emerges in the form of a dynamic mutation-selection balance. We argue this state is generic for all mutation rates and population sizes, and is reached as an end state as genomes become saturated by either beneficial or deleterious mutations. Assuming all mutations have the same magnitude selective effect, we calculate the fraction of beneficial mutations necessary to maintain the dynamic balance. This may explain the unexpected maintenance of asexual genomes, as in mitochondria, in the presence of selection. This will affect in the statistics of genetic diversity in these populations.

Coevolution of dynamical states and interactions in dynamic networks

NASA Astrophysics Data System (ADS)

Zimmermann, Martín G.; Eguíluz, Víctor M.; San Miguel, Maxi

2004-06-01

We explore the coupled dynamics of the internal states of a set of interacting elements and the network of interactions among them. Interactions are modeled by a spatial game and the network of interaction links evolves adapting to the outcome of the game. As an example, we consider a model of cooperation in which the adaptation is shown to facilitate the formation of a hierarchical interaction network that sustains a highly cooperative stationary state. The resulting network has the characteristics of a small world network when a mechanism of local neighbor selection is introduced in the adaptive network dynamics. The highly connected nodes in the hierarchical structure of the network play a leading role in the stability of the network. Perturbations acting on the state of these special nodes trigger global avalanches leading to complete network reorganization.

Resonance dynamics of DCO (X ˜ '2A ) simulated with the dynamically pruned discrete variable representation (DP-DVR)

NASA Astrophysics Data System (ADS)

Larsson, Henrik R.; Riedel, Jens; Wei, Jie; Temps, Friedrich; Hartke, Bernd

2018-05-01

Selected resonance states of the deuterated formyl radical in the electronic ground state X ˜ '2A are computed using our recently introduced dynamically pruned discrete variable representation [H. R. Larsson, B. Hartke, and D. J. Tannor, J. Chem. Phys. 145, 204108 (2016)]. Their decay and asymptotic distributions are analyzed and, for selected resonances, compared to experimental results obtained by a combination of stimulated emission pumping and velocity-map imaging of the product D atoms. The theoretical results show good agreement with the experimental kinetic energy distributions. The intramolecular vibrational energy redistribution is analyzed and compared with previous results from an effective polyad Hamiltonian. Specifically, we analyzed the part of the wavefunction that remains in the interaction region during the decay. The results from the polyad Hamiltonian could mainly be confirmed. The C=O stretch quantum number is typically conserved, while the D—C=O bend quantum number decreases. Differences are due to strong anharmonic coupling such that all resonances have major contributions from several zero-order states. For some of the resonances, the coupling is so strong that no further zero-order states appear during the dynamics in the interaction region, even after propagating for 300 ps.

Selected Aspects of Markovian and Non-Markovian Quantum Master Equations

NASA Astrophysics Data System (ADS)

Lendi, K.

A few particular marked properties of quantum dynamical equations accounting for general relaxation and dissipation are selected and summarized in brief. Most results derive from the universal concept of complete positivity. The considerations mainly regard genuinely irreversible processes as characterized by a unique asymptotically stationary final state for arbitrary initial conditions. From ordinary Markovian master equations and associated quantum dynamical semigroup time-evolution, derivations of higher order Onsager coefficients and related entropy production are discussed. For general processes including non-faithful states a regularized version of quantum relative entropy is introduced. Further considerations extend to time-dependent infinitesimal generators of time-evolution and to a possible description of propagation of initial states entangled between open system and environment. In the coherence-vector representation of the full non-Markovian equations including entangled initial states, first results are outlined towards identifying mathematical properties of a restricted class of trial integral-kernel functions suited to phenomenological applications.

Dynamic refractometer

NASA Technical Reports Server (NTRS)

Curley, Michael J. (Inventor); Sarkisov, Sergey S. (Inventor)

2008-01-01

A refractometer computer controls the rotation of a rotary plate upon which are mounted a prism optically coupled via an optical window to a spectroscopic cell holding a resin exhibiting a dynamic refractive index during photocuring. The computer system positions the prism and spectroscopic cell relative to a visible light laser which illuminates the prism-resin interface at selected incidence angles. A photodetector mounted on the plate generates a signal to the computer proportional to intensity of an internally reflected light beam. A curing light is selectively transmitted through the prism and into the photocurable resin. The refractometer determines the intensity of the internally reflected beam a selected incidence angles and determines the effective refractive index curve of the resin at an uncured state and, optionally, at a completely cured state. Next, an amount of uncured resin and selected optical components to be joined by the resin is placed in the spectroscopic cell and irradiated with the UV light. The refractometer is fixed at a selected incidence angle and measures the intensity of an internally reflected light beam of light throughout the cure cycle. The refractometer determines the resin's refractive index of the polymeric mixture by means of extrapolation of a horizontal shift in the effective refractive index curve of the resin from an uncured state to a selected point in the cure cycle.

Hybrid Cascading Outage Analysis of Extreme Events with Optimized Corrective Actions

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

Vallem, Mallikarjuna R.; Vyakaranam, Bharat GNVSR; Holzer, Jesse T.

2017-10-19

Power system are vulnerable to extreme contingencies (like an outage of a major generating substation) that can cause significant generation and load loss and can lead to further cascading outages of other transmission facilities and generators in the system. Some cascading outages are seen within minutes following a major contingency, which may not be captured exclusively using the dynamic simulation of the power system. The utilities plan for contingencies either based on dynamic or steady state analysis separately which may not accurately capture the impact of one process on the other. We address this gap in cascading outage analysis bymore » developing Dynamic Contingency Analysis Tool (DCAT) that can analyze hybrid dynamic and steady state behavior of the power system, including protection system models in dynamic simulations, and simulating corrective actions in post-transient steady state conditions. One of the important implemented steady state processes is to mimic operator corrective actions to mitigate aggravated states caused by dynamic cascading. This paper presents an Optimal Power Flow (OPF) based formulation for selecting corrective actions that utility operators can take during major contingency and thus automate the hybrid dynamic-steady state cascading outage process. The improved DCAT framework with OPF based corrective actions is demonstrated on IEEE 300 bus test system.« less

Engineering dynamical control of cell fate switching using synthetic phospho-regulons

PubMed Central

Gordley, Russell M.; Williams, Reid E.; Bashor, Caleb J.; Toettcher, Jared E.; Yan, Shude; Lim, Wendell A.

2016-01-01

Many cells can sense and respond to time-varying stimuli, selectively triggering changes in cell fate only in response to inputs of a particular duration or frequency. A common motif in dynamically controlled cells is a dual-timescale regulatory network: although long-term fate decisions are ultimately controlled by a slow-timescale switch (e.g., gene expression), input signals are first processed by a fast-timescale signaling layer, which is hypothesized to filter what dynamic information is efficiently relayed downstream. Directly testing the design principles of how dual-timescale circuits control dynamic sensing, however, has been challenging, because most synthetic biology methods have focused solely on rewiring transcriptional circuits, which operate at a single slow timescale. Here, we report the development of a modular approach for flexibly engineering phosphorylation circuits using designed phospho-regulon motifs. By then linking rapid phospho-feedback with slower downstream transcription-based bistable switches, we can construct synthetic dual-timescale circuits in yeast in which the triggering dynamics and the end-state properties of the ON state can be selectively tuned. These phospho-regulon tools thus open up the possibility to engineer cells with customized dynamical control. PMID:27821768

State-selected chemical reaction dynamics at the S matrix level - Final-state specificities of near-threshold processes at low and high energies

NASA Technical Reports Server (NTRS)

Chatfield, David C.; Truhlar, Donald G.; Schwenke, David W.

1992-01-01

State-to-state reaction probabilities are found to be highly final-state specific at state-selected threshold energies for the reactions O + H2 yield OH + H and H + H2 yield H2 + H. The study includes initial rotational states with quantum numbers 0-15, and the specificity is especially dramatic for the more highly rotationally excited reactants. The analysis is based on accurate quantum mechanical reactive scattering calculations. Final-state specificity is shown in general to increase with the rotational quantum number of the reactant diatom, and the trends are confirmed for both zero and nonzero values of the total angular momentum.

Force-Manipulation Single-Molecule Spectroscopy Studies of Enzymatic Dynamics

NASA Astrophysics Data System (ADS)

Lu, H. Peter; He, Yufan; Lu, Maolin; Cao, Jin; Guo, Qing

2014-03-01

Subtle conformational changes play a crucial role in protein functions, especially in enzymatic reactions involving complex substrate-enzyme interactions and chemical reactions. We applied AFM-enhanced and magnetic tweezers-correlated single-molecule spectroscopy to study the mechanisms and dynamics of enzymatic reactions involved with kinase and lysozyme proteins. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time by single-molecule FRET detections. Our single-molecule spectroscopy measurements of enzymatic conformational dynamics have revealed time bunching effect and intermittent coherence in conformational state change dynamics involving in enzymatic reaction cycles. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing. Our results support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation.

The sequence relay selection strategy based on stochastic dynamic programming

NASA Astrophysics Data System (ADS)

Zhu, Rui; Chen, Xihao; Huang, Yangchao

2017-07-01

Relay-assisted (RA) network with relay node selection is a kind of effective method to improve the channel capacity and convergence performance. However, most of the existing researches about the relay selection did not consider the statically channel state information and the selection cost. This shortage limited the performance and application of RA network in practical scenarios. In order to overcome this drawback, a sequence relay selection strategy (SRSS) was proposed. And the performance upper bound of SRSS was also analyzed in this paper. Furthermore, in order to make SRSS more practical, a novel threshold determination algorithm based on the stochastic dynamic program (SDP) was given to work with SRSS. Numerical results are also presented to exhibit the performance of SRSS with SDP.

New open conformation of SMYD3 implicates conformational selection and allostery

PubMed Central

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

2016-01-01

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

Exponential Sensitivity and its Cost in Quantum Physics

PubMed Central

Gilyén, András; Kiss, Tamás; Jex, Igor

2016-01-01

State selective protocols, like entanglement purification, lead to an essentially non-linear quantum evolution, unusual in naturally occurring quantum processes. Sensitivity to initial states in quantum systems, stemming from such non-linear dynamics, is a promising perspective for applications. Here we demonstrate that chaotic behaviour is a rather generic feature in state selective protocols: exponential sensitivity can exist for all initial states in an experimentally realisable optical scheme. Moreover, any complex rational polynomial map, including the example of the Mandelbrot set, can be directly realised. In state selective protocols, one needs an ensemble of initial states, the size of which decreases with each iteration. We prove that exponential sensitivity to initial states in any quantum system has to be related to downsizing the initial ensemble also exponentially. Our results show that magnifying initial differences of quantum states (a Schrödinger microscope) is possible; however, there is a strict bound on the number of copies needed. PMID:26861076

Exponential Sensitivity and its Cost in Quantum Physics.

PubMed

Gilyén, András; Kiss, Tamás; Jex, Igor

2016-02-10

State selective protocols, like entanglement purification, lead to an essentially non-linear quantum evolution, unusual in naturally occurring quantum processes. Sensitivity to initial states in quantum systems, stemming from such non-linear dynamics, is a promising perspective for applications. Here we demonstrate that chaotic behaviour is a rather generic feature in state selective protocols: exponential sensitivity can exist for all initial states in an experimentally realisable optical scheme. Moreover, any complex rational polynomial map, including the example of the Mandelbrot set, can be directly realised. In state selective protocols, one needs an ensemble of initial states, the size of which decreases with each iteration. We prove that exponential sensitivity to initial states in any quantum system has to be related to downsizing the initial ensemble also exponentially. Our results show that magnifying initial differences of quantum states (a Schrödinger microscope) is possible; however, there is a strict bound on the number of copies needed.

Nonlinear Wavelength Selection in Surface Faceting under Electromigration

NASA Astrophysics Data System (ADS)

Barakat, Fatima; Martens, Kirsten; Pierre-Louis, Olivier

2012-08-01

We report on the control of the faceting of crystal surfaces by means of surface electromigration. When electromigration reinforces the faceting instability, we find perpetual coarsening with a wavelength increasing as t1/2. For strongly stabilizing electromigration, the surface is stable. For weakly stabilizing electromigration, a cellular pattern is obtained, with a nonlinearly selected wavelength. The selection mechanism is not caused by an instability of steady states, as suggested by previous works in the literature. Instead, the dynamics is found to exhibit coarsening before reaching a continuous family of stable nonequilibrium steady states.

Relaxation processes in a low-order three-dimensional magnetohydrodynamics model

NASA Technical Reports Server (NTRS)

Stribling, Troy; Matthaeus, William H.

1991-01-01

The time asymptotic behavior of a Galerkin model of 3D magnetohydrodynamics (MHD) has been interpreted using the selective decay and dynamic alignment relaxation theories. A large number of simulations has been performed that scan a parameter space defined by the rugged ideal invariants, including energy, cross helicity, and magnetic helicity. It is concluded that time asymptotic state can be interpreted as a relaxation to minimum energy. A simple decay model, based on absolute equilibrium theory, is found to predict a mapping of initial onto time asymptotic states, and to accurately describe the long time behavior of the runs when magnetic helicity is present. Attention is also given to two processes, operating on time scales shorter than selective decay and dynamic alignment, in which the ratio of kinetic to magnetic energy relaxes to values 0(1). The faster of the two processes takes states initially dominant in magnetic energy to a state of near-equipartition between kinetic and magnetic energy through power law growth of kinetic energy. The other process takes states initially dominant in kinetic energy to the near-equipartitioned state through exponential growth of magnetic energy.

Set selection dynamical system neural networks with partial memories, with applications to Sudoku and KenKen puzzles.

PubMed

Boreland, B; Clement, G; Kunze, H

2015-08-01

After reviewing set selection and memory model dynamical system neural networks, we introduce a neural network model that combines set selection with partial memories (stored memories on subsets of states in the network). We establish that feasible equilibria with all states equal to ± 1 correspond to answers to a particular set theoretic problem. We show that KenKen puzzles can be formulated as a particular case of this set theoretic problem and use the neural network model to solve them; in addition, we use a similar approach to solve Sudoku. We illustrate the approach in examples. As a heuristic experiment, we use online or print resources to identify the difficulty of the puzzles and compare these difficulties to the number of iterations used by the appropriate neural network solver, finding a strong relationship. Copyright © 2015 Elsevier Ltd. All rights reserved.

Nonparametric variational optimization of reaction coordinates

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

Banushkina, Polina V.; Krivov, Sergei V., E-mail: s.krivov@leeds.ac.uk

State of the art realistic simulations of complex atomic processes commonly produce trajectories of large size, making the development of automated analysis tools very important. A popular approach aimed at extracting dynamical information consists of projecting these trajectories into optimally selected reaction coordinates or collective variables. For equilibrium dynamics between any two boundary states, the committor function also known as the folding probability in protein folding studies is often considered as the optimal coordinate. To determine it, one selects a functional form with many parameters and trains it on the trajectories using various criteria. A major problem with such anmore » approach is that a poor initial choice of the functional form may lead to sub-optimal results. Here, we describe an approach which allows one to optimize the reaction coordinate without selecting its functional form and thus avoiding this source of error.« less

Selective Hydrogen Isotope Separation via Breathing Transition in MIL-53(Al).

PubMed

Kim, Jin Yeong; Zhang, Linda; Balderas-Xicohténcatl, Rafael; Park, Jaewoo; Hirscher, Michael; Moon, Hoi Ri; Oh, Hyunchul

2017-12-13

Breathing of MIL-53(Al), a flexible metal-organic framework (MOF), leads to dynamic changes as narrow pore (np) transitions to large pore (lp). During the flexible and reversible transition, the pore apertures are continuously adjusted, thus providing the tremendous opportunity to separate mixtures of similar-sized and similar-shaped molecules that require precise pore tuning. Herein, for the first time, we report a strategy for effectively separating hydrogen isotopes through the dynamic pore change during the breathing of MIL-53(Al), a representative of flexible MOFs. The experiment shows that the selectivity for D 2 over H 2 is strongly related to the state of the pore structure of MIL-53(Al). The highest selectivity (S D 2 /H 2 = 13.6 at 40 K) was obtained by optimizing the exposure temperature, pressure, and time to systematically tune the pore state of MIL-53(Al).

Spinfoam cosmology with the proper vertex amplitude

NASA Astrophysics Data System (ADS)

Vilensky, Ilya

2017-11-01

The proper vertex amplitude is derived from the Engle-Pereira-Rovelli-Livine vertex by restricting to a single gravitational sector in order to achieve the correct semi-classical behaviour. We apply the proper vertex to calculate a cosmological transition amplitude that can be viewed as the Hartle-Hawking wavefunction. To perform this calculation we deduce the integral form of the proper vertex and use extended stationary phase methods to estimate the large-volume limit. We show that the resulting amplitude satisfies an operator constraint whose classical analogue is the Hamiltonian constraint of the Friedmann-Robertson-Walker cosmology. We find that the constraint dynamically selects the relevant family of coherent states and demonstrate a similar dynamic selection in standard quantum mechanics. We investigate the effects of dynamical selection on long-range correlations.

Selectivity of Electronic Coherence and Attosecond Ionization Delays in Strong-Field Double Ionization

NASA Astrophysics Data System (ADS)

Kobayashi, Yuki; Reduzzi, Maurizio; Chang, Kristina F.; Timmers, Henry; Neumark, Daniel M.; Leone, Stephen R.

2018-06-01

Experiments are presented on real-time probing of coherent electron dynamics in xenon initiated by strong-field double ionization. Attosecond transient absorption measurements allow for characterization of electronic coherences as well as relative ionization timings in multiple electronic states of Xe+ and Xe2 + . A high degree of coherence g =0.4 is observed between P3 2 0-P3 0 0 of Xe2 + , whereas for other possible pairs of states the coherences are below the detection limits of the experiments. A comparison of the experimental results with numerical simulations based on an uncorrelated electron-emission model shows that the coherences produced by strong-field double ionization are more selective than predicted. Surprisingly short ionization time delays, 0.85 fs, 0.64 fs, and 0.75 fs relative to Xe+ formation, are also measured for the P2 3 , P0 3 , and P1 3 states of Xe2 + , respectively. Both the unpredicted selectivity in the formation of coherence and the subfemtosecond time delays of specific states provide new insight into correlated electron dynamics in strong-field double ionization.

Dynamic modulation of corticospinal excitability and short-latency afferent inhibition during onset and maintenance phase of selective finger movement.

PubMed

Cho, Hyun Joo; Panyakaew, Pattamon; Thirugnanasambandam, Nivethida; Wu, Tianxia; Hallett, Mark

2016-06-01

During highly selective finger movement, corticospinal excitability is reduced in surrounding muscles at the onset of movement but this phenomenon has not been demonstrated during maintenance of movement. Sensorimotor integration may play an important role in selective movement. We sought to investigate how corticospinal excitability and short-latency afferent inhibition changes in active and surrounding muscles during onset and maintenance of selective finger movement. Using transcranial magnetic stimulation (TMS) and paired peripheral stimulation, input-output recruitment curve and short-latency afferent inhibition (SAI) were measured in the first dorsal interosseus and abductor digiti minimi muscles during selective index finger flexion. Motor surround inhibition was present only at the onset phase, but not at the maintenance phase of movement. SAI was reduced at onset but not at the maintenance phase of movement in both active and surrounding muscles. Our study showed dynamic changes in corticospinal excitability and sensorimotor modulation for active and surrounding muscles in different movement states. SAI does not appear to contribute to motor surround inhibition at the movement onset phase. Also, there seems to be different inhibitory circuit(s) other than SAI for the movement maintenance phase in order to delineate the motor output selectively when corticospinal excitability is increased in both active and surrounding muscles. This study enhances our knowledge of dynamic changes in corticospinal excitability and sensorimotor interaction in different movement states to understand normal and disordered movements. Published by Elsevier Ireland Ltd.

Selective ultrafast probing of transient hot chemisorbed and precursor states of CO on Ru(0001).

PubMed

Beye, M; Anniyev, T; Coffee, R; Dell'Angela, M; Föhlisch, A; Gladh, J; Katayama, T; Kaya, S; Krupin, O; Møgelhøj, A; Nilsson, A; Nordlund, D; Nørskov, J K; Öberg, H; Ogasawara, H; Pettersson, L G M; Schlotter, W F; Sellberg, J A; Sorgenfrei, F; Turner, J J; Wolf, M; Wurth, W; Oström, H

2013-05-03

We have studied the femtosecond dynamics following optical laser excitation of CO adsorbed on a Ru surface by monitoring changes in the occupied and unoccupied electronic structure using ultrafast soft x-ray absorption and emission. We recently reported [M. Dell'Angela et al. Science 339, 1302 (2013)] a phonon-mediated transition into a weakly adsorbed precursor state occurring on a time scale of >2 ps prior to desorption. Here we focus on processes within the first picosecond after laser excitation and show that the metal-adsorbate coordination is initially increased due to hot-electron-driven vibrational excitations. This process is faster than, but occurs in parallel with, the transition into the precursor state. With resonant x-ray emission spectroscopy, we probe each of these states selectively and determine the respective transient populations depending on optical laser fluence. Ab initio molecular dynamics simulations of CO adsorbed on Ru(0001) were performed at 1500 and 3000 K providing insight into the desorption process.

A fast chaos-based image encryption scheme with a dynamic state variables selection mechanism

NASA Astrophysics Data System (ADS)

Chen, Jun-xin; Zhu, Zhi-liang; Fu, Chong; Yu, Hai; Zhang, Li-bo

2015-03-01

In recent years, a variety of chaos-based image cryptosystems have been investigated to meet the increasing demand for real-time secure image transmission. Most of them are based on permutation-diffusion architecture, in which permutation and diffusion are two independent procedures with fixed control parameters. This property results in two flaws. (1) At least two chaotic state variables are required for encrypting one plain pixel, in permutation and diffusion stages respectively. Chaotic state variables produced with high computation complexity are not sufficiently used. (2) The key stream solely depends on the secret key, and hence the cryptosystem is vulnerable against known/chosen-plaintext attacks. In this paper, a fast chaos-based image encryption scheme with a dynamic state variables selection mechanism is proposed to enhance the security and promote the efficiency of chaos-based image cryptosystems. Experimental simulations and extensive cryptanalysis have been carried out and the results prove the superior security and high efficiency of the scheme.

Achieving Optimal Self-Adaptivity for Dynamic Tuning of Organic Semiconductors through Resonance Engineering.

PubMed

Tao, Ye; Xu, Lijia; Zhang, Zhen; Chen, Runfeng; Li, Huanhuan; Xu, Hui; Zheng, Chao; Huang, Wei

2016-08-03

Current static-state explorations of organic semiconductors for optimal material properties and device performance are hindered by limited insights into the dynamically changed molecular states and charge transport and energy transfer processes upon device operation. Here, we propose a simple yet successful strategy, resonance variation-based dynamic adaptation (RVDA), to realize optimized self-adaptive properties in donor-resonance-acceptor molecules by engineering the resonance variation for dynamic tuning of organic semiconductors. Organic light-emitting diodes hosted by these RVDA materials exhibit remarkably high performance, with external quantum efficiencies up to 21.7% and favorable device stability. Our approach, which supports simultaneous realization of dynamically adapted and selectively enhanced properties via resonance engineering, illustrates a feasible design map for the preparation of smart organic semiconductors capable of dynamic structure and property modulations, promoting the studies of organic electronics from static to dynamic.

Coriolis-coupled wave packet dynamics of H + HLi reaction.

PubMed

Padmanaban, R; Mahapatra, S

2006-05-11

We investigated the effect of Coriolis coupling (CC) on the initial state-selected dynamics of H+HLi reaction by a time-dependent wave packet (WP) approach. Exact quantum scattering calculations were obtained by a WP propagation method based on the Chebyshev polynomial scheme and ab initio potential energy surface of the reacting system. Partial wave contributions up to the total angular momentum J=30 were found to be necessary for the scattering of HLi in its vibrational and rotational ground state up to a collision energy approximately 0.75 eV. For each J value, the projection quantum number K was varied from 0 to min (J, K(max)), with K(max)=8 until J=20 and K(max)=4 for further higher J values. This is because further higher values of K do not have much effect on the dynamics and also because one wishes to maintain the large computational overhead for each calculation within the affordable limit. The initial state-selected integral reaction cross sections and thermal rate constants were calculated by summing up the contributions from all partial waves. These were compared with our previous results on the title system, obtained within the centrifugal sudden and J-shifting approximations, to demonstrate the impact of CC on the dynamics of this system.

Hardware-efficient Bell state preparation using Quantum Zeno Dynamics in superconducting circuits

NASA Astrophysics Data System (ADS)

Flurin, Emmanuel; Blok, Machiel; Hacohen-Gourgy, Shay; Martin, Leigh S.; Livingston, William P.; Dove, Allison; Siddiqi, Irfan

By preforming a continuous joint measurement on a two qubit system, we restrict the qubit evolution to a chosen subspace of the total Hilbert space. This extension of the quantum Zeno effect, called Quantum Zeno Dynamics, has already been explored in various physical systems such as superconducting cavities, single rydberg atoms, atomic ensembles and Bose Einstein condensates. In this experiment, two superconducting qubits are strongly dispersively coupled to a high-Q cavity (χ >> κ) allowing for the doubly excited state | 11 〉 to be selectively monitored. The Quantum Zeno Dynamics in the complementary subspace enables us to coherently prepare a Bell state. As opposed to dissipation engineering schemes, we emphasize that our protocol is deterministic, does not rely direct coupling between qubits and functions only using single qubit controls and cavity readout. Such Quantum Zeno Dynamics can be generalized to larger Hilbert space enabling deterministic generation of many-body entangled states, and thus realizes a decoherence-free subspace allowing alternative noise-protection schemes.

Ultrafast quantum control of ionization dynamics in krypton.

PubMed

Hütten, Konrad; Mittermair, Michael; Stock, Sebastian O; Beerwerth, Randolf; Shirvanyan, Vahe; Riemensberger, Johann; Duensing, Andreas; Heider, Rupert; Wagner, Martin S; Guggenmos, Alexander; Fritzsche, Stephan; Kabachnik, Nikolay M; Kienberger, Reinhard; Bernhardt, Birgitta

2018-02-19

Ultrafast spectroscopy with attosecond resolution has enabled the real time observation of ultrafast electron dynamics in atoms, molecules and solids. These experiments employ attosecond pulses or pulse trains and explore dynamical processes in a pump-probe scheme that is selectively sensitive to electronic state of matter via photoelectron or XUV absorption spectroscopy or that includes changes of the ionic state detected via photo-ion mass spectrometry. Here, we demonstrate how the implementation of combined photo-ion and absorption spectroscopy with attosecond resolution enables tracking the complex multidimensional excitation and decay cascade of an Auger auto-ionization process of a few femtoseconds in highly excited krypton. In tandem with theory, our study reveals the role of intermediate electronic states in the formation of multiply charged ions. Amplitude tuning of a dressing laser field addresses different groups of decay channels and allows exerting temporal and quantitative control over the ionization dynamics in rare gas atoms.

A self-cognizant dynamic system approach for prognostics and health management

NASA Astrophysics Data System (ADS)

Bai, Guangxing; Wang, Pingfeng; Hu, Chao

2015-03-01

Prognostics and health management (PHM) is an emerging engineering discipline that diagnoses and predicts how and when a system will degrade its performance and lose its partial or whole functionality. Due to the complexity and invisibility of rules and states of most dynamic systems, developing an effective approach to track evolving system states becomes a major challenge. This paper presents a new self-cognizant dynamic system (SCDS) approach that incorporates artificial intelligence into dynamic system modeling for PHM. A feed-forward neural network (FFNN) is selected to approximate a complex system response which is challenging task in general due to inaccessible system physics. The trained FFNN model is then embedded into a dual extended Kalman filter algorithm to track down system dynamics. A recursive computation technique used to update the FFNN model using online measurements is also derived. To validate the proposed SCDS approach, a battery dynamic system is considered as an experimental application. After modeling the battery system by a FFNN model and a state-space model, the state-of-charge (SoC) and state-of-health (SoH) are estimated by updating the FFNN model using the proposed approach. Experimental results suggest that the proposed approach improves the efficiency and accuracy for battery health management.

Sampling-based real-time motion planning under state uncertainty for autonomous micro-aerial vehicles in GPS-denied environments.

PubMed

Li, Dachuan; Li, Qing; Cheng, Nong; Song, Jingyan

2014-11-18

This paper presents a real-time motion planning approach for autonomous vehicles with complex dynamics and state uncertainty. The approach is motivated by the motion planning problem for autonomous vehicles navigating in GPS-denied dynamic environments, which involves non-linear and/or non-holonomic vehicle dynamics, incomplete state estimates, and constraints imposed by uncertain and cluttered environments. To address the above motion planning problem, we propose an extension of the closed-loop rapid belief trees, the closed-loop random belief trees (CL-RBT), which incorporates predictions of the position estimation uncertainty, using a factored form of the covariance provided by the Kalman filter-based estimator. The proposed motion planner operates by incrementally constructing a tree of dynamically feasible trajectories using the closed-loop prediction, while selecting candidate paths with low uncertainty using efficient covariance update and propagation. The algorithm can operate in real-time, continuously providing the controller with feasible paths for execution, enabling the vehicle to account for dynamic and uncertain environments. Simulation results demonstrate that the proposed approach can generate feasible trajectories that reduce the state estimation uncertainty, while handling complex vehicle dynamics and environment constraints.

Sampling-Based Real-Time Motion Planning under State Uncertainty for Autonomous Micro-Aerial Vehicles in GPS-Denied Environments

PubMed Central

Li, Dachuan; Li, Qing; Cheng, Nong; Song, Jingyan

2014-01-01

This paper presents a real-time motion planning approach for autonomous vehicles with complex dynamics and state uncertainty. The approach is motivated by the motion planning problem for autonomous vehicles navigating in GPS-denied dynamic environments, which involves non-linear and/or non-holonomic vehicle dynamics, incomplete state estimates, and constraints imposed by uncertain and cluttered environments. To address the above motion planning problem, we propose an extension of the closed-loop rapid belief trees, the closed-loop random belief trees (CL-RBT), which incorporates predictions of the position estimation uncertainty, using a factored form of the covariance provided by the Kalman filter-based estimator. The proposed motion planner operates by incrementally constructing a tree of dynamically feasible trajectories using the closed-loop prediction, while selecting candidate paths with low uncertainty using efficient covariance update and propagation. The algorithm can operate in real-time, continuously providing the controller with feasible paths for execution, enabling the vehicle to account for dynamic and uncertain environments. Simulation results demonstrate that the proposed approach can generate feasible trajectories that reduce the state estimation uncertainty, while handling complex vehicle dynamics and environment constraints. PMID:25412217

Laser sculpting of atomic sp, sp(2) , and sp(3) hybrid orbitals.

PubMed

Liu, Chunmei; Manz, Jörn; Yang, Yonggang

2015-01-12

Atomic sp, sp(2) , and sp(3) hybrid orbitals were introduced by Linus Pauling to explain the nature of the chemical bond. Quantum dynamics simulations show that they can be sculpted by means of a selective series of coherent laser pulses, starting from the 1s orbital of the hydrogen atom. Laser hybridization generates atoms with state-selective electric dipoles, opening up new possibilities for the study of chemical reaction dynamics and heterogeneous catalysis. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Maximum entropy principle for stationary states underpinned by stochastic thermodynamics.

PubMed

Ford, Ian J

2015-11-01

The selection of an equilibrium state by maximizing the entropy of a system, subject to certain constraints, is often powerfully motivated as an exercise in logical inference, a procedure where conclusions are reached on the basis of incomplete information. But such a framework can be more compelling if it is underpinned by dynamical arguments, and we show how this can be provided by stochastic thermodynamics, where an explicit link is made between the production of entropy and the stochastic dynamics of a system coupled to an environment. The separation of entropy production into three components allows us to select a stationary state by maximizing the change, averaged over all realizations of the motion, in the principal relaxational or nonadiabatic component, equivalent to requiring that this contribution to the entropy production should become time independent for all realizations. We show that this recovers the usual equilibrium probability density function (pdf) for a conservative system in an isothermal environment, as well as the stationary nonequilibrium pdf for a particle confined to a potential under nonisothermal conditions, and a particle subject to a constant nonconservative force under isothermal conditions. The two remaining components of entropy production account for a recently discussed thermodynamic anomaly between over- and underdamped treatments of the dynamics in the nonisothermal stationary state.

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

Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use inmore » combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.« less

Dynamic proteomics emphasizes the importance of selective mRNA translation and protein turnover during Arabidopsis seed germination.

PubMed

Galland, Marc; Huguet, Romain; Arc, Erwann; Cueff, Gwendal; Job, Dominique; Rajjou, Loïc

2014-01-01

During seed germination, the transition from a quiescent metabolic state in a dry mature seed to a proliferative metabolic state in a vigorous seedling is crucial for plant propagation as well as for optimizing crop yield. This work provides a detailed description of the dynamics of protein synthesis during the time course of germination, demonstrating that mRNA translation is both sequential and selective during this process. The complete inhibition of the germination process in the presence of the translation inhibitor cycloheximide established that mRNA translation is critical for Arabidopsis seed germination. However, the dynamics of protein turnover and the selectivity of protein synthesis (mRNA translation) during Arabidopsis seed germination have not been addressed yet. Based on our detailed knowledge of the Arabidopsis seed proteome, we have deepened our understanding of seed mRNA translation during germination by combining two-dimensional gel-based proteomics with dynamic radiolabeled proteomics using a radiolabeled amino acid precursor, namely [(35)S]-methionine, in order to highlight de novo protein synthesis, stability, and turnover. Our data confirm that during early imbibition, the Arabidopsis translatome keeps reflecting an embryonic maturation program until a certain developmental checkpoint. Furthermore, by dividing the seed germination time lapse into discrete time windows, we highlight precise and specific patterns of protein synthesis. These data refine and deepen our knowledge of the three classical phases of seed germination based on seed water uptake during imbibition and reveal that selective mRNA translation is a key feature of seed germination. Beyond the quantitative control of translational activity, both the selectivity of mRNA translation and protein turnover appear as specific regulatory systems, critical for timing the molecular events leading to successful germination and seedling establishment.

Dynamic Proteomics Emphasizes the Importance of Selective mRNA Translation and Protein Turnover during Arabidopsis Seed Germination*

PubMed Central

Galland, Marc; Huguet, Romain; Arc, Erwann; Cueff, Gwendal; Job, Dominique; Rajjou, Loïc

2014-01-01

During seed germination, the transition from a quiescent metabolic state in a dry mature seed to a proliferative metabolic state in a vigorous seedling is crucial for plant propagation as well as for optimizing crop yield. This work provides a detailed description of the dynamics of protein synthesis during the time course of germination, demonstrating that mRNA translation is both sequential and selective during this process. The complete inhibition of the germination process in the presence of the translation inhibitor cycloheximide established that mRNA translation is critical for Arabidopsis seed germination. However, the dynamics of protein turnover and the selectivity of protein synthesis (mRNA translation) during Arabidopsis seed germination have not been addressed yet. Based on our detailed knowledge of the Arabidopsis seed proteome, we have deepened our understanding of seed mRNA translation during germination by combining two-dimensional gel-based proteomics with dynamic radiolabeled proteomics using a radiolabeled amino acid precursor, namely [35S]-methionine, in order to highlight de novo protein synthesis, stability, and turnover. Our data confirm that during early imbibition, the Arabidopsis translatome keeps reflecting an embryonic maturation program until a certain developmental checkpoint. Furthermore, by dividing the seed germination time lapse into discrete time windows, we highlight precise and specific patterns of protein synthesis. These data refine and deepen our knowledge of the three classical phases of seed germination based on seed water uptake during imbibition and reveal that selective mRNA translation is a key feature of seed germination. Beyond the quantitative control of translational activity, both the selectivity of mRNA translation and protein turnover appear as specific regulatory systems, critical for timing the molecular events leading to successful germination and seedling establishment. PMID:24198433

Observing single quantum trajectories of a superconducting qubit: ensemble properties and driven dynamics

NASA Astrophysics Data System (ADS)

Weber, Steven; Murch, K. W.; Chantasri, A.; Dressel, J.; Jordan, A. N.; Siddiqi, I.

2014-03-01

We use weak measurements to track individual quantum trajectories of a superconducting qubit embedded in a microwave cavity. Using a near-quantum-limited parametric amplifier, we selectively measure either the phase or amplitude of the cavity field, and thereby confine trajectories to either the equator or a meridian of the Bloch sphere. We analyze ensembles of trajectories to determine statistical properties such as the most likely path and most likely time connecting pre and post-selected quantum states. We compare our results with theoretical predictions derived from an action principle for continuous quantum measurement. Furthermore, by introducing a qubit drive, we investigate the interplay between unitary state evolution and non-unitary measurement dynamics. This work was supported by the IARPA CSQ program and the ONR.

Future Directions in Personality, Occupational and Medical Selection: Myths, Misunderstandings, Measurement, and Suggestions

ERIC Educational Resources Information Center

Ferguson, Eamonn; Lievens, Filip

2017-01-01

This paper has two objectives: (1) presenting recent advances in personality theory whereby personality traits are conceptualized within a framework that focuses on the dynamic interactions of behaviour, biology, context, and states, and (2) discussing the implications of these developments for measurement and medical selection. We start by…

Flight control synthesis for flexible aircraft using Eigenspace assignment

NASA Technical Reports Server (NTRS)

Davidson, J. B.; Schmidt, D. K.

1986-01-01

The use of eigenspace assignment techniques to synthesize flight control systems for flexible aircraft is explored. Eigenspace assignment techniques are used to achieve a specified desired eigenspace, chosen to yield desirable system impulse residue magnitudes for selected system responses. Two of these are investigated. The first directly determines constant measurement feedback gains that will yield a close-loop system eigenspace close to a desired eigenspace. The second technique selects quadratic weighting matrices in a linear quadratic control synthesis that will asymptotically yield the close-loop achievable eigenspace. Finally, the possibility of using either of these techniques with state estimation is explored. Application of the methods to synthesize integrated flight-control and structural-mode-control laws for a large flexible aircraft is demonstrated and results discussed. Eigenspace selection criteria based on design goals are discussed, and for the study case it would appear that a desirable eigenspace can be obtained. In addition, the importance of state-space selection is noted along with problems with reduced-order measurement feedback. Since the full-state control laws may be implemented with dynamic compensation (state estimation), the use of reduced-order measurement feedback is less desirable. This is especially true since no change in the transient response from the pilot's input results if state estimation is used appropriately. The potential is also noted for high actuator bandwidth requirements if the linear quadratic synthesis approach is utilized. Even with the actuator pole location selected, a problem with unmodeled modes is noted due to high bandwidth. Some suggestions for future research include investigating how to choose an eigenspace that will achieve certain desired dynamics and stability robustness, determining how the choice of measurements effects synthesis results, and exploring how the phase relationships between desired eigenvector elements effects the synthesis results.

Hamilton's missing link.

PubMed

van Veelen, Matthijs

2007-06-07

Hamilton's famous rule was presented in 1964 in a paper called "The genetical theory of social behaviour (I and II)", Journal of Theoretical Biology 7, 1-16, 17-32. The paper contains a mathematical genetical model from which the rule supposedly follows, but it does not provide a link between the paper's central result, which states that selection dynamics take the population to a state where mean inclusive fitness is maximized, and the rule, which states that selection will lead to maximization of individual inclusive fitness. This note provides a condition under which Hamilton's rule does follow from his central result.

Folding and stability of helical bundle proteins from coarse-grained models.

PubMed

Kapoor, Abhijeet; Travesset, Alex

2013-07-01

We develop a coarse-grained model where solvent is considered implicitly, electrostatics are included as short-range interactions, and side-chains are coarse-grained to a single bead. The model depends on three main parameters: hydrophobic, electrostatic, and side-chain hydrogen bond strength. The parameters are determined by considering three level of approximations and characterizing the folding for three selected proteins (training set). Nine additional proteins (containing up to 126 residues) as well as mutated versions (test set) are folded with the given parameters. In all folding simulations, the initial state is a random coil configuration. Besides the native state, some proteins fold into an additional state differing in the topology (structure of the helical bundle). We discuss the stability of the native states, and compare the dynamics of our model to all atom molecular dynamics simulations as well as some general properties on the interactions governing folding dynamics. Copyright © 2013 Wiley Periodicals, Inc.

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein.

PubMed

Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Roitberg, Adrian E; Fernandez-Alberti, Sebastian

2015-06-28

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

On the analysis and comparison of conformer-specific essential dynamics upon ligand binding to a protein

NASA Astrophysics Data System (ADS)

Grosso, Marcos; Kalstein, Adrian; Parisi, Gustavo; Roitberg, Adrian E.; Fernandez-Alberti, Sebastian

2015-06-01

The native state of a protein consists of an equilibrium of conformational states on an energy landscape rather than existing as a single static state. The co-existence of conformers with different ligand-affinities in a dynamical equilibrium is the basis for the conformational selection model for ligand binding. In this context, the development of theoretical methods that allow us to analyze not only the structural changes but also changes in the fluctuation patterns between conformers will contribute to elucidate the differential properties acquired upon ligand binding. Molecular dynamics simulations can provide the required information to explore these features. Its use in combination with subsequent essential dynamics analysis allows separating large concerted conformational rearrangements from irrelevant fluctuations. We present a novel procedure to define the size and composition of essential dynamics subspaces associated with ligand-bound and ligand-free conformations. These definitions allow us to compare essential dynamics subspaces between different conformers. Our procedure attempts to emphasize the main similarities and differences between the different essential dynamics in an unbiased way. Essential dynamics subspaces associated to conformational transitions can also be analyzed. As a test case, we study the glutaminase interacting protein (GIP), composed of a single PDZ domain. Both GIP ligand-free state and glutaminase L peptide-bound states are analyzed. Our findings concerning the relative changes in the flexibility pattern upon binding are in good agreement with experimental Nuclear Magnetic Resonance data.

Individual-based models for adaptive diversification in high-dimensional phenotype spaces.

PubMed

Ispolatov, Iaroslav; Madhok, Vaibhav; Doebeli, Michael

2016-02-07

Most theories of evolutionary diversification are based on equilibrium assumptions: they are either based on optimality arguments involving static fitness landscapes, or they assume that populations first evolve to an equilibrium state before diversification occurs, as exemplified by the concept of evolutionary branching points in adaptive dynamics theory. Recent results indicate that adaptive dynamics may often not converge to equilibrium points and instead generate complicated trajectories if evolution takes place in high-dimensional phenotype spaces. Even though some analytical results on diversification in complex phenotype spaces are available, to study this problem in general we need to reconstruct individual-based models from the adaptive dynamics generating the non-equilibrium dynamics. Here we first provide a method to construct individual-based models such that they faithfully reproduce the given adaptive dynamics attractor without diversification. We then show that a propensity to diversify can be introduced by adding Gaussian competition terms that generate frequency dependence while still preserving the same adaptive dynamics. For sufficiently strong competition, the disruptive selection generated by frequency-dependence overcomes the directional evolution along the selection gradient and leads to diversification in phenotypic directions that are orthogonal to the selection gradient. Copyright © 2015 Elsevier Ltd. All rights reserved.

A dynamical mean-field study of orbital-selective Mott phase enhanced by next-nearest neighbor hopping

NASA Astrophysics Data System (ADS)

Niu, Yuekun; Sun, Jian; Ni, Yu; Song, Yun

2018-06-01

The dynamical mean-field theory is employed to study the orbital-selective Mott transition (OSMT) of the two-orbital Hubbard model with nearest neighbor hopping and next-nearest neighbor (NNN) hopping. The NNN hopping breaks the particle-hole symmetry at half filling and gives rise to an asymmetric density of states (DOS). Our calculations show that the broken symmetry of DOS benefits the OSMT, where the region of the orbital-selective Mott phase significantly extends with the increasing NNN hopping integral. We also find that Hund's rule coupling promotes OSMT by blocking the orbital fluctuations, but the influence of NNN hopping is more remarkable.

Residue solvent accessibilities in the unfolded polypeptide chain.

PubMed Central

Zielenkiewicz, P; Saenger, W

1992-01-01

The difference of solvent accessibilities in the native and unfolded states of the protein is used as a measure of the hydrophobic contribution to the free energy of folding. We present a new approximation of amino acids solvent accessibilities in the unfolded state based on the 1-ns molecular dynamics simulation of Ala-X-Ala tripeptides at a temperature of 368 K. The standard accessibility values averaged from the molecular dynamics study are significantly lower from those previously obtained by considering only selected conformations of Ala-X-Ala tripeptides. PMID:1489908

Selectivity of the gas sensor based on the 50%In2O3-50%Ga2O3 thin film in dynamic mode of operation

NASA Astrophysics Data System (ADS)

Demin, I. E.; Kozlov, A. G.

2018-01-01

The article considers the gas sensor with the sensitive layer based on the 50%In2O3 -50%Ga2O3 thin film. The temperature and concentration dependencies of gas-induced resistance response of this sensor and the dynamical dependencies of its resistance response on the test gases in air are investigated. The test gases were ethanol, acetone, ammonia and liquefied petroleum gas. The information parameters of the sensor in the dynamical mode of operation were considered to improve its selectivity. The presented results show that the selectivity of the sensor in this mode may be improved by using the following information parameters: gas-induced resistance response in steady state, activation energy of the response and pre-exponential factor of the temperature dependence of the response time constant.

The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp.

PubMed

Duchi, Diego; Mazumder, Abhishek; Malinen, Anssi M; Ebright, Richard H; Kapanidis, Achillefs N

2018-06-06

RNA polymerase (RNAP) contains a mobile structural module, the 'clamp,' that forms one wall of the RNAP active-center cleft and that has been linked to crucial aspects of the transcription cycle, including promoter melting, transcription elongation complex stability, transcription pausing, and transcription termination. Using single-molecule FRET on surface-immobilized RNAP molecules, we show that the clamp in RNAP holoenzyme populates three distinct conformational states and interconvert between these states on the 0.1-1 s time-scale. Similar studies confirm that the RNAP clamp is closed in open complex (RPO) and in initial transcribing complexes (RPITC), including paused initial transcribing complexes, and show that, in these complexes, the clamp does not exhibit dynamic behaviour. We also show that, the stringent-response alarmone ppGpp, which reprograms transcription during amino acid starvation stress, selectively stabilizes the partly-closed-clamp state and prevents clamp opening; these results raise the possibility that ppGpp controls promoter opening by modulating clamp dynamics.

The brain as a dynamic physical system.

PubMed

McKenna, T M; McMullen, T A; Shlesinger, M F

1994-06-01

The brain is a dynamic system that is non-linear at multiple levels of analysis. Characterization of its non-linear dynamics is fundamental to our understanding of brain function. Identifying families of attractors in phase space analysis, an approach which has proven valuable in describing non-linear mechanical and electrical systems, can prove valuable in describing a range of behaviors and associated neural activity including sensory and motor repertoires. Additionally, transitions between attractors may serve as useful descriptors for analysing state changes in neurons and neural ensembles. Recent observations of synchronous neural activity, and the emerging capability to record the spatiotemporal dynamics of neural activity by voltage-sensitive dyes and electrode arrays, provide opportunities for observing the population dynamics of neural ensembles within a dynamic systems context. New developments in the experimental physics of complex systems, such as the control of chaotic systems, selection of attractors, attractor switching and transient states, can be a source of powerful new analytical tools and insights into the dynamics of neural systems.

On Selective Harvesting of an Inshore-Offshore Fishery: A Bioeconomic Model

ERIC Educational Resources Information Center

Purohit, D.; Chaudhuri, K. S.

2004-01-01

A bioeconomic model is developed for the selective harvesting of a single species, inshore-offshore fishery, assuming that the growth of the species is governed by the Gompertz law. The dynamical system governing the fishery is studied in depth; the local and global stability of its non-trivial steady state are examined. Existence of a bionomic…

Evolution and selection of river networks: Statics, dynamics, and complexity

PubMed Central

Rinaldo, Andrea; Rigon, Riccardo; Banavar, Jayanth R.; Maritan, Amos; Rodriguez-Iturbe, Ignacio

2014-01-01

Moving from the exact result that drainage network configurations minimizing total energy dissipation are stationary solutions of the general equation describing landscape evolution, we review the static properties and the dynamic origins of the scale-invariant structure of optimal river patterns. Optimal channel networks (OCNs) are feasible optimal configurations of a spanning network mimicking landscape evolution and network selection through imperfect searches for dynamically accessible states. OCNs are spanning loopless configurations, however, only under precise physical requirements that arise under the constraints imposed by river dynamics—every spanning tree is exactly a local minimum of total energy dissipation. It is remarkable that dynamically accessible configurations, the local optima, stabilize into diverse metastable forms that are nevertheless characterized by universal statistical features. Such universal features explain very well the statistics of, and the linkages among, the scaling features measured for fluvial landforms across a broad range of scales regardless of geology, exposed lithology, vegetation, or climate, and differ significantly from those of the ground state, known exactly. Results are provided on the emergence of criticality through adaptative evolution and on the yet-unexplored range of applications of the OCN concept. PMID:24550264

Use of non-adiabatic geometric phase for quantum computing by NMR.

PubMed

Das, Ranabir; Kumar, S K Karthick; Kumar, Anil

2005-12-01

Geometric phases have stimulated researchers for its potential applications in many areas of science. One of them is fault-tolerant quantum computation. A preliminary requisite of quantum computation is the implementation of controlled dynamics of qubits. In controlled dynamics, one qubit undergoes coherent evolution and acquires appropriate phase, depending on the state of other qubits. If the evolution is geometric, then the phase acquired depend only on the geometry of the path executed, and is robust against certain types of error. This phenomenon leads to an inherently fault-tolerant quantum computation. Here we suggest a technique of using non-adiabatic geometric phase for quantum computation, using selective excitation. In a two-qubit system, we selectively evolve a suitable subsystem where the control qubit is in state |1, through a closed circuit. By this evolution, the target qubit gains a phase controlled by the state of the control qubit. Using the non-adiabatic geometric phase we demonstrate implementation of Deutsch-Jozsa algorithm and Grover's search algorithm in a two-qubit system.

Real time unsupervised learning of visual stimuli in neuromorphic VLSI systems

NASA Astrophysics Data System (ADS)

Giulioni, Massimiliano; Corradi, Federico; Dante, Vittorio; Del Giudice, Paolo

2015-10-01

Neuromorphic chips embody computational principles operating in the nervous system, into microelectronic devices. In this domain it is important to identify computational primitives that theory and experiments suggest as generic and reusable cognitive elements. One such element is provided by attractor dynamics in recurrent networks. Point attractors are equilibrium states of the dynamics (up to fluctuations), determined by the synaptic structure of the network; a ‘basin’ of attraction comprises all initial states leading to a given attractor upon relaxation, hence making attractor dynamics suitable to implement robust associative memory. The initial network state is dictated by the stimulus, and relaxation to the attractor state implements the retrieval of the corresponding memorized prototypical pattern. In a previous work we demonstrated that a neuromorphic recurrent network of spiking neurons and suitably chosen, fixed synapses supports attractor dynamics. Here we focus on learning: activating on-chip synaptic plasticity and using a theory-driven strategy for choosing network parameters, we show that autonomous learning, following repeated presentation of simple visual stimuli, shapes a synaptic connectivity supporting stimulus-selective attractors. Associative memory develops on chip as the result of the coupled stimulus-driven neural activity and ensuing synaptic dynamics, with no artificial separation between learning and retrieval phases.

Real time unsupervised learning of visual stimuli in neuromorphic VLSI systems.

PubMed

Giulioni, Massimiliano; Corradi, Federico; Dante, Vittorio; del Giudice, Paolo

2015-10-14

Neuromorphic chips embody computational principles operating in the nervous system, into microelectronic devices. In this domain it is important to identify computational primitives that theory and experiments suggest as generic and reusable cognitive elements. One such element is provided by attractor dynamics in recurrent networks. Point attractors are equilibrium states of the dynamics (up to fluctuations), determined by the synaptic structure of the network; a 'basin' of attraction comprises all initial states leading to a given attractor upon relaxation, hence making attractor dynamics suitable to implement robust associative memory. The initial network state is dictated by the stimulus, and relaxation to the attractor state implements the retrieval of the corresponding memorized prototypical pattern. In a previous work we demonstrated that a neuromorphic recurrent network of spiking neurons and suitably chosen, fixed synapses supports attractor dynamics. Here we focus on learning: activating on-chip synaptic plasticity and using a theory-driven strategy for choosing network parameters, we show that autonomous learning, following repeated presentation of simple visual stimuli, shapes a synaptic connectivity supporting stimulus-selective attractors. Associative memory develops on chip as the result of the coupled stimulus-driven neural activity and ensuing synaptic dynamics, with no artificial separation between learning and retrieval phases.

Conformational exchange of aromatic side chains characterized by L-optimized TROSY-selected ¹³C CPMG relaxation dispersion.

PubMed

Weininger, Ulrich; Respondek, Michal; Akke, Mikael

2012-09-01

Protein dynamics on the millisecond time scale commonly reflect conformational transitions between distinct functional states. NMR relaxation dispersion experiments have provided important insights into biologically relevant dynamics with site-specific resolution, primarily targeting the protein backbone and methyl-bearing side chains. Aromatic side chains represent attractive probes of protein dynamics because they are over-represented in protein binding interfaces, play critical roles in enzyme catalysis, and form an important part of the core. Here we introduce a method to characterize millisecond conformational exchange of aromatic side chains in selectively (13)C labeled proteins by means of longitudinal- and transverse-relaxation optimized CPMG relaxation dispersion. By monitoring (13)C relaxation in a spin-state selective manner, significant sensitivity enhancement can be achieved in terms of both signal intensity and the relative exchange contribution to transverse relaxation. Further signal enhancement results from optimizing the longitudinal relaxation recovery of the covalently attached (1)H spins. We validated the L-TROSY-CPMG experiment by measuring fast folding-unfolding kinetics of the small protein CspB under native conditions. The determined unfolding rate matches perfectly with previous results from stopped-flow kinetics. The CPMG-derived chemical shift differences between the folded and unfolded states are in excellent agreement with those obtained by urea-dependent chemical shift analysis. The present method enables characterization of conformational exchange involving aromatic side chains and should serve as a valuable complement to methods developed for other types of protein side chains.

An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks.

PubMed

Salis, Howard; Kaznessis, Yiannis N

2005-12-01

Stochastic chemical kinetics more accurately describes the dynamics of "small" chemical systems, such as biological cells. Many real systems contain dynamical stiffness, which causes the exact stochastic simulation algorithm or other kinetic Monte Carlo methods to spend the majority of their time executing frequently occurring reaction events. Previous methods have successfully applied a type of probabilistic steady-state approximation by deriving an evolution equation, such as the chemical master equation, for the relaxed fast dynamics and using the solution of that equation to determine the slow dynamics. However, because the solution of the chemical master equation is limited to small, carefully selected, or linear reaction networks, an alternate equation-free method would be highly useful. We present a probabilistic steady-state approximation that separates the time scales of an arbitrary reaction network, detects the convergence of a marginal distribution to a quasi-steady-state, directly samples the underlying distribution, and uses those samples to accurately predict the state of the system, including the effects of the slow dynamics, at future times. The numerical method produces an accurate solution of both the fast and slow reaction dynamics while, for stiff systems, reducing the computational time by orders of magnitude. The developed theory makes no approximations on the shape or form of the underlying steady-state distribution and only assumes that it is ergodic. We demonstrate the accuracy and efficiency of the method using multiple interesting examples, including a highly nonlinear protein-protein interaction network. The developed theory may be applied to any type of kinetic Monte Carlo simulation to more efficiently simulate dynamically stiff systems, including existing exact, approximate, or hybrid stochastic simulation techniques.

Single-Molecule Spectroscopy and Imaging Studies of Protein Dynamics

NASA Astrophysics Data System (ADS)

Lu, H. Peter

2012-04-01

Enzymatic reactions and protein-protein interactions are traditionally studied at the ensemble level, despite significant static and dynamic inhomogeneities. Subtle conformational changes play a crucial role in protein functions, and these protein conformations are highly dynamic rather than being static. We applied AFM-enhanced single-molecule spectroscopy to study the mechanisms and dynamics of enzymatic reactions involved with kinase and lysozyme proteins. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time by single-molecule FRET detections. Our single-molecule spectroscopy measurements of T4 lysozyme and HPPK enzymatic conformational dynamics have revealed time bunching effect and intermittent coherence in conformational state change dynamics involving in enzymatic reaction cycles. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing, presenting as an extreme dynamic behavior intrinsically related to the time bunching effect that we have reported previously. Our results of HPPK interaction with substrate support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation. Our new approach is applicable to a wide range of single-molecule FRET measurements for protein conformational changes under enzymatic reactions.

A Time-Dependent Quantum Dynamics Study of the H2 + CH3 yields H + CH4 Reaction

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Kwak, Dochan (Technical Monitor)

2002-01-01

We present a time-dependent wave-packet propagation calculation for the H2 + CH3 yields H + CH4 reaction in six degrees of freedom and for zero total angular momentum. Initial state selected reaction probability for different initial rotational-vibrational states are presented in this study. The cumulative reaction probability (CRP) is obtained by summing over initial-state-selected reaction probability. The energy-shift approximation to account for the contribution of degrees of freedom missing in the 6D calculation is employed to obtain an approximate full-dimensional CRP. Thermal rate constant is compared with different experiment results.

Excited State Structural Dynamics of Carotenoids and ChargeTransfer Systems

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

Van Tassle, Aaron Justin

This dissertation describes the development andimplementation of a visible/near infrared pump/mid-infrared probeapparatus. Chapter 1 describes the background and motivation ofinvestigating optically induced structural dynamics, paying specificattention to solvation and the excitation selection rules of highlysymmetric molecules such as carotenoids. Chapter 2 describes thedevelopment and construction of the experimental apparatus usedthroughout the remainder of this dissertation. Chapter 3 will discuss theinvestigation of DCM, a laser dye with a fluorescence signal resultingfrom a charge transfer state. By studying the dynamics of DCM and of itsmethyl deuterated isotopomer (an otherwise identical molecule), we areable to investigate the origins of the charge transfer statemore » and provideevidence that it is of the controversial twisted intramolecular (TICT)type. Chapter 4 introduces the use of two-photon excitation to the S1state, combined with one-photon excitation to the S2 state of thecarotenoid beta-apo-8'-carotenal. These 2 investigations show evidencefor the formation of solitons, previously unobserved in molecular systemsand found only in conducting polymers Chapter 5 presents an investigationof the excited state dynamics of peridinin, the carotenoid responsiblefor the light harvesting of dinoflagellates. This investigation allowsfor a more detailed understanding of the importance of structuraldynamics of carotenoids in light harvesting.« less

Filming nuclear dynamics of iodine using x-ray diffraction at the LCLS

NASA Astrophysics Data System (ADS)

Ware, Matthew; Natan, Adi; Glownia, James; Cryan, James; Bucksbaum, Phil

2017-04-01

We will provide an overview of our analysis of the nuclear dynamics of iodine. At the LCLS, we pumped a gas cell of iodine with a weak 520nm, 50 fs pulse, and the nuclear dynamics are then probed with 9 keV, 40 fs x-rays with variable time delay. This allows us to simultaneously image nuclear wavepackets on the dissociating A state, on the bound B state, and even Raman wavepackets in the ground electronic state. We will explain at length how we isolate each of these signals using a Legendre decomposition of our x-ray data and the selection rules for each of the transitions. Likewise, we will discuss how we convert the x-ray diffraction patterns into real-space movies of the nuclear dynamics. Research supported by the U.S. Department of Energy, Office of Basic Energy Sciences, Atomic, Molecular, and Optical Science Program. Use of LCLS supported under DOE Contract No. DE-AC02-76F00515.

Kinetic or Dynamic Control on a Bifurcating Potential Energy Surface? An Experimental and DFT Study of Gold-Catalyzed Ring Expansion and Spirocyclization of 2-Propargyl-β-tetrahydrocarbolines.

PubMed

Zhang, Lei; Wang, Yi; Yao, Zhu-Jun; Wang, Shaozhong; Yu, Zhi-Xiang

2015-10-21

In classical transition state theory, a transition state is connected to its reactant(s) and product(s). Recently, chemists found that reaction pathways may bifurcate after a transition state, leading to two or more sets of products. The product distribution for such a reaction containing a bifurcating potential energy surface (bPES) is usually determined by the shape of the bPES and dynamic factors. However, if the bPES leads to two intermediates (other than two products), which then undergo further transformations to give different final products, what factors control the selectivity is still not fully examined. This missing link in transition state theory is founded in the present study. Aiming to develop new methods for the synthesis of azocinoindole derivatives, we found that 2-propargyl-β-tetrahydrocarbolines can undergo ring expansion and spirocyclization under gold catalysis. DFT study revealed that the reaction starts with the intramolecular cyclization of the gold-activated 2-propargyl-β-tetrahydrocarboline with a bPES. The cyclization intermediates can not only interconvert into each other via a [1,5]-alkenyl shift, but also undergo ring expansion (through fragmentation/protodeauration mechanism) or spirocyclization (through deprotonation/protodeauration mechanism). Detailed analysis of the complex PESs for substrates with different substituents indicated that the reaction selectivity is under dynamic control if the interconversion of the intermediates is slower than the ring expansion and spirocyclization processes. Otherwise, the chemical outcome is under typical kinetic control and determined by the relative preference of ring expansion versus spirocyclization pathways. The present study may enrich chemist's understanding of the determinants for selectivities on bPESs.

Near-microsecond human aquaporin 4 gating dynamics in static and alternating external electric fields: Non-equilibrium molecular dynamics

NASA Astrophysics Data System (ADS)

English, Niall J.; Garate, José-A.

2016-08-01

An extensive suite of non-equilibrium molecular-dynamics simulation has been performed for ˜0.85-0.9 μs of human aquaporin 4 in the absence and presence of externally applied static and alternating electric fields applied along the channels (in both axial directions in the static case, taken as the laboratory z-axis). These external fields were of 0.0065 V/Å (r.m.s.) intensity (of the same order as physiological electrical potentials); alternating fields ranged in frequency from 2.45 to 500 GHz. In-pore gating dynamics was studied, particularly of the relative propensities for "open" and "closed" states of the conserved arginines in the arginine/aromatic area (itself governed in no small part by external-field response of the dipolar alignment of the histidine-201 residue in the selectivity filter). In such a manner, the intimate connection of field-response governing "two-state" histidine states was established statistically and mechanistically. Given the appreciable size of the energy barriers for histidine-201 alignment, we have also performed non-equilibrium metadynamics/local-elevation of static fields applied along both directions to construct the free-energy landscape thereof in terms of external-field direction, elucidating the importance of field direction on energetics. We conclude from direct measurement of deterministic molecular dynamics in conjunction with applied-field metadynamics that the intrinsic electric field within the channel points along the +z-axis, such that externally applied static fields in this direction serve to "open" the channel in the selectivity-filter and the asparagine-proline-alanine region.

Near-microsecond human aquaporin 4 gating dynamics in static and alternating external electric fields: Non-equilibrium molecular dynamics.

PubMed

English, Niall J; Garate, José-A

2016-08-28

An extensive suite of non-equilibrium molecular-dynamics simulation has been performed for ∼0.85-0.9 μs of human aquaporin 4 in the absence and presence of externally applied static and alternating electric fields applied along the channels (in both axial directions in the static case, taken as the laboratory z-axis). These external fields were of 0.0065 V/Å (r.m.s.) intensity (of the same order as physiological electrical potentials); alternating fields ranged in frequency from 2.45 to 500 GHz. In-pore gating dynamics was studied, particularly of the relative propensities for "open" and "closed" states of the conserved arginines in the arginine/aromatic area (itself governed in no small part by external-field response of the dipolar alignment of the histidine-201 residue in the selectivity filter). In such a manner, the intimate connection of field-response governing "two-state" histidine states was established statistically and mechanistically. Given the appreciable size of the energy barriers for histidine-201 alignment, we have also performed non-equilibrium metadynamics/local-elevation of static fields applied along both directions to construct the free-energy landscape thereof in terms of external-field direction, elucidating the importance of field direction on energetics. We conclude from direct measurement of deterministic molecular dynamics in conjunction with applied-field metadynamics that the intrinsic electric field within the channel points along the +z-axis, such that externally applied static fields in this direction serve to "open" the channel in the selectivity-filter and the asparagine-proline-alanine region.

Pore Helices Play a Dynamic Role as Integrators of Domain Motion during Kv11.1 Channel Inactivation Gating*

PubMed Central

Perry, Matthew D.; Ng, Chai Ann; Vandenberg, Jamie I.

2013-01-01

Proteins that form ion-selective pores in the membrane of cells are integral to many rapid signaling processes, including regulating the rhythm of the heartbeat. In potassium channels, the selectivity filter is critical for both endowing an exquisite selectivity for potassium ions, as well as for controlling the flow of ions through the pore. Subtle rearrangements in the complex hydrogen-bond network that link the selectivity filter to the surrounding pore helices differentiate conducting (open) from nonconducting (inactivated) conformations of the channel. Recent studies suggest that beyond the selectivity filter, inactivation involves widespread rearrangements of the channel protein. Here, we use rate equilibrium free energy relationship analysis to probe the structural changes that occur during selectivity filter gating in Kv11.1 channels, at near atomic resolution. We show that the pore helix plays a crucial dynamic role as a bidirectional interface during selectivity filter gating. We also define the molecular bases of the energetic coupling between the pore helix and outer helix of the pore domain that occurs early in the transition from open to inactivated states, as well as the coupling between the pore helix and inner helix late in the transition. Our data demonstrate that the pore helices are more than just static structural elements supporting the integrity of the selectivity filter; instead they play a crucial dynamic role during selectivity filter gating. PMID:23471968

Reduced size first-order subsonic and supersonic aeroelastic modeling

NASA Technical Reports Server (NTRS)

Karpel, Mordechay

1990-01-01

Various aeroelastic, aeroservoelastic, dynamic-response, and sensitivity analyses are based on a time-domain first-order (state-space) formulation of the equations of motion. The formulation of this paper is based on the minimum-state (MS) aerodynamic approximation method, which yields a low number of aerodynamic augmenting states. Modifications of the MS and the physical weighting procedures make the modeling method even more attractive. The flexibility of constraint selection is increased without increasing the approximation problem size; the accuracy of dynamic residualization of high-frequency modes is improved; and the resulting model is less sensitive to parametric changes in subsequent analyses. Applications to subsonic and supersonic cases demonstrate the generality, flexibility, accuracy, and efficiency of the method.

Corticostriatal circuit mechanisms of value-based action selection: Implementation of reinforcement learning algorithms and beyond.

PubMed

Morita, Kenji; Jitsev, Jenia; Morrison, Abigail

2016-09-15

Value-based action selection has been suggested to be realized in the corticostriatal local circuits through competition among neural populations. In this article, we review theoretical and experimental studies that have constructed and verified this notion, and provide new perspectives on how the local-circuit selection mechanisms implement reinforcement learning (RL) algorithms and computations beyond them. The striatal neurons are mostly inhibitory, and lateral inhibition among them has been classically proposed to realize "Winner-Take-All (WTA)" selection of the maximum-valued action (i.e., 'max' operation). Although this view has been challenged by the revealed weakness, sparseness, and asymmetry of lateral inhibition, which suggest more complex dynamics, WTA-like competition could still occur on short time scales. Unlike the striatal circuit, the cortical circuit contains recurrent excitation, which may enable retention or temporal integration of information and probabilistic "soft-max" selection. The striatal "max" circuit and the cortical "soft-max" circuit might co-implement an RL algorithm called Q-learning; the cortical circuit might also similarly serve for other algorithms such as SARSA. In these implementations, the cortical circuit presumably sustains activity representing the executed action, which negatively impacts dopamine neurons so that they can calculate reward-prediction-error. Regarding the suggested more complex dynamics of striatal, as well as cortical, circuits on long time scales, which could be viewed as a sequence of short WTA fragments, computational roles remain open: such a sequence might represent (1) sequential state-action-state transitions, constituting replay or simulation of the internal model, (2) a single state/action by the whole trajectory, or (3) probabilistic sampling of state/action. Copyright © 2016. Published by Elsevier B.V.

Valley-selective photon-dressed states in transition metal dichalcogenides

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Discrete Time McKean–Vlasov Control Problem: A Dynamic Programming Approach

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

Pham, Huyên, E-mail: pham@math.univ-paris-diderot.fr; Wei, Xiaoli, E-mail: tyswxl@gmail.com

We consider the stochastic optimal control problem of nonlinear mean-field systems in discrete time. We reformulate the problem into a deterministic control problem with marginal distribution as controlled state variable, and prove that dynamic programming principle holds in its general form. We apply our method for solving explicitly the mean-variance portfolio selection and the multivariate linear-quadratic McKean–Vlasov control problem.

Selective predation and productivity jointly drive complex behavior in host-parasite systems.

PubMed

Hall, Spencer R; Duffy, Meghan A; Cáceres, Carla E

2005-01-01

Successful invasion of a parasite into a host population and resulting host-parasite dynamics can depend crucially on other members of a host's community such as predators. We do not fully understand how predation intensity and selectivity shape host-parasite dynamics because the interplay between predator density, predator foraging behavior, and ecosystem productivity remains incompletely explored. By modifying a standard susceptible-infected model, we show how productivity can modulate complex behavior induced by saturating and selective foraging behavior of predators in an otherwise stable host-parasite system. When predators strongly prefer parasitized hosts, the host-parasite system can oscillate, but predators can also create alternative stable states, Allee effects, and catastrophic extinction of parasites. In the latter three cases, parasites have difficulty invading and/or persisting in ecosystems. When predators are intermediately selective, these more complex behaviors become less important, but the host-parasite system can switch from stable to oscillating and then back to stable states along a gradient of predator control. Surprisingly, at higher productivity, predators that neutrally select or avoid parasitized hosts can catalyze extinction of both hosts and parasites. Thus, synergy between two enemies can end disastrously for the host. Such diverse outcomes underscore the crucial importance of the community and ecosystem context in which host-parasite interactions occur.

Cultural-based particle swarm for dynamic optimisation problems

NASA Astrophysics Data System (ADS)

Daneshyari, Moayed; Yen, Gary G.

2012-07-01

Many practical optimisation problems are with the existence of uncertainties, among which a significant number belong to the dynamic optimisation problem (DOP) category in which the fitness function changes through time. In this study, we propose the cultural-based particle swarm optimisation (PSO) to solve DOP problems. A cultural framework is adopted incorporating the required information from the PSO into five sections of the belief space, namely situational, temporal, domain, normative and spatial knowledge. The stored information will be adopted to detect the changes in the environment and assists response to the change through a diversity-based repulsion among particles and migration among swarms in the population space, and also helps in selecting the leading particles in three different levels, personal, swarm and global levels. Comparison of the proposed heuristics over several difficult dynamic benchmark problems demonstrates the better or equal performance with respect to most of other selected state-of-the-art dynamic PSO heuristics.

Carbon nanorings with inserted acenes: Breaking symmetry in excited state dynamics

DOE PAGES

Franklin-Mergarejo, R.; Alvarez, D. Ondarse; Tretiak, S.; ...

2016-08-10

Conjugated cycloparaphenylene rings have unique electronic properties being the smallest segments of carbon nanotubes. Their conjugated backbones support delocalized electronic excitations, which dynamics is strongly influenced by cyclic geometry. Here we present a comparative theoretical study of the electronic and vibrational energy relaxation and redistribution in photoexcited cycloparaphenylene carbon nanorings with inserted naphthalene, anthracene, and tetracene units using non-adiabatic excited-state molecular dynamics simulations. Calculated excited state structures reflect modifications of optical selection rules and appearance of low-energy electronic states localized on the acenes due to gradual departure from a perfect circular symmetry. After photoexcitation, an ultrafast electronic energy relaxation tomore » the lowest excited state is observed on the time scale of hundreds of femtoseconds in all molecules studied. Concomitantly, the efficiency of the exciton trapping in the acene raises when moving from naphthalene to anthracene and to tetracene, being negligible in naphthalene, and ~60% and 70% in anthracene and tetracene within the first 500 fs after photoexcitation. Observed photoinduced dynamics is further analyzed in details using induced molecular distortions, delocatization properties of participating electronic states and non-adiabatic coupling strengths. Lastly, our results provide a number of insights into design of cyclic molecular systems for electronic and light-harvesting applications.« less

Toward the Darwinian transition: Switching between distributed and speciated states in a simple model of early life.

PubMed

Arnoldt, Hinrich; Strogatz, Steven H; Timme, Marc

2015-01-01

It has been hypothesized that in the era just before the last universal common ancestor emerged, life on earth was fundamentally collective. Ancient life forms shared their genetic material freely through massive horizontal gene transfer (HGT). At a certain point, however, life made a transition to the modern era of individuality and vertical descent. Here we present a minimal model for stochastic processes potentially contributing to this hypothesized "Darwinian transition." The model suggests that HGT-dominated dynamics may have been intermittently interrupted by selection-driven processes during which genotypes became fitter and decreased their inclination toward HGT. Stochastic switching in the population dynamics with three-point (hypernetwork) interactions may have destabilized the HGT-dominated collective state and essentially contributed to the emergence of vertical descent and the first well-defined species in early evolution. A systematic nonlinear analysis of the stochastic model dynamics covering key features of evolutionary processes (such as selection, mutation, drift and HGT) supports this view. Our findings thus suggest a viable direction out of early collective evolution, potentially enabling the start of individuality and vertical Darwinian evolution.

Nanocluster building blocks of artificial square spin ice: Stray-field studies of thermal dynamics

NASA Astrophysics Data System (ADS)

Pohlit, Merlin; Porrati, Fabrizio; Huth, Michael; Ohno, Yuzo; Ohno, Hideo; Müller, Jens

2015-05-01

We present measurements of the thermal dynamics of a Co-based single building block of an artificial square spin ice fabricated by focused electron-beam-induced deposition. We employ micro-Hall magnetometry, an ultra-sensitive tool to study the stray field emanating from magnetic nanostructures, as a new technique to access the dynamical properties during the magnetization reversal of the spin-ice nanocluster. The obtained hysteresis loop exhibits distinct steps, displaying a reduction of their "coercive field" with increasing temperature. Therefore, thermally unstable states could be repetitively prepared by relatively simple temperature and field protocols allowing one to investigate the statistics of their switching behavior within experimentally accessible timescales. For a selected switching event, we find a strong reduction of the so-prepared states' "survival time" with increasing temperature and magnetic field. Besides the possibility to control the lifetime of selected switching events at will, we find evidence for a more complex behavior caused by the special spin ice arrangement of the macrospins, i.e., that the magnetic reversal statistically follows distinct "paths" most likely driven by thermal perturbation.

The "Rust" Challenge: On the Correlations between Electronic Structure, Excited State Dynamics, and Photoelectrochemical Performance of Hematite Photoanodes for Solar Water Splitting.

PubMed

Grave, Daniel A; Yatom, Natav; Ellis, David S; Toroker, Maytal Caspary; Rothschild, Avner

2018-03-05

In recent years, hematite's potential as a photoanode material for solar hydrogen production has ignited a renewed interest in its physical and interfacial properties, which continues to be an active field of research. Research on hematite photoanodes provides new insights on the correlations between electronic structure, transport properties, excited state dynamics, and charge transfer phenomena, and expands our knowledge on solar cell materials into correlated electron systems. This research news article presents a snapshot of selected theoretical and experimental developments linking the electronic structure to the photoelectrochemical performance, with particular focus on optoelectronic properties and charge carrier dynamics. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of a tunable femtosecond stimulated raman apparatus and its application to beta-carotene.

PubMed

Shim, Sangdeok; Mathies, Richard A

2008-04-17

We have developed a tunable femtosecond stimulated Raman spectroscopy (FSRS) apparatus and used it to perform time-resolved resonance Raman experiments with <100 fs temporal and <35 cm(-1) spectral resolution. The key technical change that facilitates this advance is the use of a tunable narrow-bandwidth optical parametric amplifier (NB-OPA) presented recently by Shim et al. (Shim, S.; Mathies, R. A. Appl. Phys. Lett. 2006, 89, 121124). The practicality of tunable FSRS is demonstrated by examining the photophysical dynamics of beta-carotene. Using 560 nm Raman excitation, the resonant S1 state modes are enhanced by a factor of approximately 200 compared with 800 nm FSRS experiments. The improved signal-to-noise ratios facilitate the measurement of definitive time constants for beta-carotene dynamics including the 180 fs appearance of the S1 vibrational features due to direct internal conversion from S2 and their characteristic 9 ps decay to S0. By tuning the FSRS system to 590 nm Raman excitation, we are able to selectively enhance vibrational features of the hot ground state S hot 0 and monitor its approximately 5 ps cooling dynamics. This tunable FSRS system is valuable because it facilitates the direct observation of structural changes of selected resonantly enhanced states and intermediates during photochemical and photobiological reactions.

Parallel cascade selection molecular dynamics for efficient conformational sampling and free energy calculation of proteins

NASA Astrophysics Data System (ADS)

Kitao, Akio; Harada, Ryuhei; Nishihara, Yasutaka; Tran, Duy Phuoc

2016-12-01

Parallel Cascade Selection Molecular Dynamics (PaCS-MD) was proposed as an efficient conformational sampling method to investigate conformational transition pathway of proteins. In PaCS-MD, cycles of (i) selection of initial structures for multiple independent MD simulations and (ii) conformational sampling by independent MD simulations are repeated until the convergence of the sampling. The selection is conducted so that protein conformation gradually approaches a target. The selection of snapshots is a key to enhance conformational changes by increasing the probability of rare event occurrence. Since the procedure of PaCS-MD is simple, no modification of MD programs is required; the selections of initial structures and the restart of the next cycle in the MD simulations can be handled with relatively simple scripts with straightforward implementation. Trajectories generated by PaCS-MD were further analyzed by the Markov state model (MSM), which enables calculation of free energy landscape. The combination of PaCS-MD and MSM is reported in this work.

Optimal Linear Responses for Markov Chains and Stochastically Perturbed Dynamical Systems

NASA Astrophysics Data System (ADS)

Antown, Fadi; Dragičević, Davor; Froyland, Gary

2018-03-01

The linear response of a dynamical system refers to changes to properties of the system when small external perturbations are applied. We consider the little-studied question of selecting an optimal perturbation so as to (i) maximise the linear response of the equilibrium distribution of the system, (ii) maximise the linear response of the expectation of a specified observable, and (iii) maximise the linear response of the rate of convergence of the system to the equilibrium distribution. We also consider the inhomogeneous, sequential, or time-dependent situation where the governing dynamics is not stationary and one wishes to select a sequence of small perturbations so as to maximise the overall linear response at some terminal time. We develop the theory for finite-state Markov chains, provide explicit solutions for some illustrative examples, and numerically apply our theory to stochastically perturbed dynamical systems, where the Markov chain is replaced by a matrix representation of an approximate annealed transfer operator for the random dynamical system.

Crystal nucleation and metastable bcc phase in charged colloids: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Ji, Xinqiang; Sun, Zhiwei; Ouyang, Wenze; Xu, Shenghua

2018-05-01

The dynamic process of homogenous nucleation in charged colloids is investigated by brute-force molecular dynamics simulation. To check if the liquid-solid transition will pass through metastable bcc, simulations are performed at the state points that definitely lie in the phase region of thermodynamically stable fcc. The simulation results confirm that, in all of these cases, the preordered precursors, acting as the seeds of nucleation, always have predominant bcc symmetry consistent with Ostwald's step rule and the Alexander-McTague mechanism. However, the polymorph selection is not straightforward because the crystal structures formed are not often determined by the symmetry of intermediate precursors but have different characters under different state points. The region of the state point where bcc crystal structures of large enough size are formed during crystallization is narrow, which gives a reasonable explanation as to why the metastable bcc phase in charged colloidal suspensions is rarely detected in macroscopic experiments.

Inference of Spatio-Temporal Functions Over Graphs via Multikernel Kriged Kalman Filtering

NASA Astrophysics Data System (ADS)

Ioannidis, Vassilis N.; Romero, Daniel; Giannakis, Georgios B.

2018-06-01

Inference of space-time varying signals on graphs emerges naturally in a plethora of network science related applications. A frequently encountered challenge pertains to reconstructing such dynamic processes, given their values over a subset of vertices and time instants. The present paper develops a graph-aware kernel-based kriged Kalman filter that accounts for the spatio-temporal variations, and offers efficient online reconstruction, even for dynamically evolving network topologies. The kernel-based learning framework bypasses the need for statistical information by capitalizing on the smoothness that graph signals exhibit with respect to the underlying graph. To address the challenge of selecting the appropriate kernel, the proposed filter is combined with a multi-kernel selection module. Such a data-driven method selects a kernel attuned to the signal dynamics on-the-fly within the linear span of a pre-selected dictionary. The novel multi-kernel learning algorithm exploits the eigenstructure of Laplacian kernel matrices to reduce computational complexity. Numerical tests with synthetic and real data demonstrate the superior reconstruction performance of the novel approach relative to state-of-the-art alternatives.

Dynamic generation of light states with discrete symmetries

NASA Astrophysics Data System (ADS)

Cordero, S.; Nahmad-Achar, E.; Castaños, O.; López-Peña, R.

2018-01-01

A dynamic procedure is established within the generalized Tavis-Cummings model to generate light states with discrete point symmetries, given by the cyclic group Cn. We consider arbitrary dipolar coupling strengths of the atoms with a one-mode electromagnetic field in a cavity. The method uses mainly the matter-field entanglement properties of the system, which can be extended to any number of three-level atoms. An initial state constituted by the superposition of two states with definite total excitation numbers, |ψ〉 M1,and |ψ〉 M 2, is considered. It can be generated by the proper selection of the time of flight of an atom passing through the cavity. We demonstrate that the resulting Husimi function of the light is invariant under cyclic point transformations of order n =| M1-M2| .

Selectivity in the inelastic rotational scattering of D2 and HD molecules from graphite: Similarities and differences respect to the H2 case

NASA Astrophysics Data System (ADS)

Rutigliano, Maria; Pirani, Fernando

2018-03-01

The inelastic scattering of D2 and HD molecules impinging on a graphite surface in well-defined initial roto-vibrational states has been studied by using the computational setup recently developed to characterize important selectivities in the molecular dynamics occurring at the gas-surface interface. In order to make an immediate comparison of determined elastic and inelastic scattering probabilities, we considered for D2 and HD molecules the same initial states, as well as the same collision energy range, previously selected for the investigation of H2 behaviour. The analysis of the back-scattered molecules shows that, while low-lying initial vibrational states are preserved, the medium-high initial ones give rise to final states covering the complete ladder of vibrational levels, although with different probability for the various cases investigated. Moreover, propensities in the formation of the final rotational states are found to depend strongly on the initial ones, on the collision energy, and on the isotopologue species.

Simulating Molecular Mechanisms of the MDM2-Mediated Regulatory Interactions: A Conformational Selection Model of the MDM2 Lid Dynamics

PubMed Central

Verkhivker, Gennady M.

2012-01-01

Diversity and complexity of MDM2 mechanisms govern its principal function as the cellular antagonist of the p53 tumor suppressor. Structural and biophysical studies have demonstrated that MDM2 binding could be regulated by the dynamics of a pseudo-substrate lid motif. However, these experiments and subsequent computational studies have produced conflicting mechanistic models of MDM2 function and dynamics. We propose a unifying conformational selection model that can reconcile experimental findings and reveal a fundamental role of the lid as a dynamic regulator of MDM2-mediated binding. In this work, structure, dynamics and energetics of apo-MDM2 are studied as a function of posttranslational modifications and length of the lid. We found that the dynamic equilibrium between “closed” and “semi-closed” lid forms may be a fundamental characteristic of MDM2 regulatory interactions, which can be modulated by phosphorylation, phosphomimetic mutation as well as by the lid size. Our results revealed that these factors may regulate p53-MDM2 binding by fine-tuning the thermodynamic equilibrium between preexisting conformational states of apo-MDM2. In agreement with NMR studies, the effect of phosphorylation on MDM2 interactions was more pronounced with the truncated lid variant that favored the thermodynamically dominant closed form. The phosphomimetic mutation S17D may alter the lid dynamics by shifting the thermodynamic equilibrium towards the ensemble of “semi-closed” conformations. The dominant “semi-closed” lid form and weakened dependence on the phosphorylation seen in simulations with the complete lid can provide a rationale for binding of small p53-based mimetics and inhibitors without a direct competition with the lid dynamics. The results suggested that a conformational selection model of preexisting MDM2 states may provide a robust theoretical framework for understanding MDM2 dynamics. Probing biological functions and mechanisms of MDM2 regulation would require further integration of computational and experimental studies and may help to guide drug design of novel anti-cancer therapeutics. PMID:22815859

Utilizing multiple state variables to improve the dynamic range of analog switching in a memristor

NASA Astrophysics Data System (ADS)

Jeong, YeonJoo; Kim, Sungho; Lu, Wei D.

2015-10-01

Memristors and memristive systems have been extensively studied for data storage and computing applications such as neuromorphic systems. To act as synapses in neuromorphic systems, the memristor needs to exhibit analog resistive switching (RS) behavior with incremental conductance change. In this study, we show that the dynamic range of the analog RS behavior can be significantly enhanced in a tantalum-oxide-based memristor. By controlling different state variables enabled by different physical effects during the RS process, the gradual filament expansion stage can be selectively enhanced without strongly affecting the abrupt filament length growth stage. Detailed physics-based modeling further verified the observed experimental effects and revealed the roles of oxygen vacancy drift and diffusion processes, and how the diffusion process can be selectively enhanced during the filament expansion stage. These findings lead to more desirable and reliable memristor behaviors for analog computing applications. Additionally, the ability to selectively control different internal physical processes demonstrated in the current study provides guidance for continued device optimization of memristor devices in general.

Selective Population of Edge States in a 2D Topological Band System.

PubMed

Galilo, Bogdan; Lee, Derek K K; Barnett, Ryan

2015-12-11

We consider a system of interacting spin-one atoms in a hexagonal lattice under the presence of a synthetic gauge field. Quenching the quadratic Zeeman field is shown to lead to a dynamical instability of the edge modes. This, in turn, leads to a spin current along the boundary of the system which grows exponentially fast in time following the quench. Tuning the magnitude of the quench can be used to selectively populate edge modes of different momenta. Implications of the intrinsic symmetries of the Hamiltonian on the dynamics are discussed. The results hold for atoms with both antiferromagnetic and ferromagnetic interactions.

Sum frequency generation and solid-state NMR study of the structure, orientation, and dynamics of polystyrene-adsorbed peptides

PubMed Central

Weidner, Tobias; Breen, Nicholas F.; Li, Kun; Drobny, Gary P.; Castner, David G.

2010-01-01

The power of combining sum frequency generation (SFG) vibrational spectroscopy and solid-state nuclear magnetic resonance (ssNMR) spectroscopy to quantify, with site specificity and atomic resolution, the orientation and dynamics of side chains in synthetic model peptides adsorbed onto polystyrene (PS) surfaces is demonstrated in this study. Although isotopic labeling has long been used in ssNMR studies to site-specifically probe the structure and dynamics of biomolecules, the potential of SFG to probe side chain orientation in isotopically labeled surface-adsorbed peptides and proteins remains largely unexplored. The 14 amino acid leucine-lysine peptide studied in this work is known to form an α-helical secondary structure at liquid-solid interfaces. Selective, individual deuteration of the isopropyl group in each leucine residue was used to probe the orientation and dynamics of each individual leucine side chain of LKα14 adsorbed onto PS. The selective isotopic labeling methods allowed SFG analysis to determine the orientations of individual side chains in adsorbed peptides. Side chain dynamics were obtained by fitting the deuterium ssNMR line shape to specific motional models. Through the combined use of SFG and ssNMR, the dynamic trends observed for individual side chains by ssNMR have been correlated with side chain orientation relative to the PS surface as determined by SFG. This combination provides a more complete and quantitative picture of the structure, orientation, and dynamics of these surface-adsorbed peptides than could be obtained if either technique were used separately. PMID:20628016

Real time unsupervised learning of visual stimuli in neuromorphic VLSI systems

PubMed Central

Giulioni, Massimiliano; Corradi, Federico; Dante, Vittorio; del Giudice, Paolo

2015-01-01

Neuromorphic chips embody computational principles operating in the nervous system, into microelectronic devices. In this domain it is important to identify computational primitives that theory and experiments suggest as generic and reusable cognitive elements. One such element is provided by attractor dynamics in recurrent networks. Point attractors are equilibrium states of the dynamics (up to fluctuations), determined by the synaptic structure of the network; a ‘basin’ of attraction comprises all initial states leading to a given attractor upon relaxation, hence making attractor dynamics suitable to implement robust associative memory. The initial network state is dictated by the stimulus, and relaxation to the attractor state implements the retrieval of the corresponding memorized prototypical pattern. In a previous work we demonstrated that a neuromorphic recurrent network of spiking neurons and suitably chosen, fixed synapses supports attractor dynamics. Here we focus on learning: activating on-chip synaptic plasticity and using a theory-driven strategy for choosing network parameters, we show that autonomous learning, following repeated presentation of simple visual stimuli, shapes a synaptic connectivity supporting stimulus-selective attractors. Associative memory develops on chip as the result of the coupled stimulus-driven neural activity and ensuing synaptic dynamics, with no artificial separation between learning and retrieval phases. PMID:26463272

Fitness Trade-Offs in Competence Differentiation of Bacillus subtilis

PubMed Central

Yüksel, Melih; Power, Jeffrey J.; Ribbe, Jan; Volkmann, Thorsten; Maier, Berenike

2016-01-01

In the stationary phase, Bacillus subtilis differentiates stochastically and transiently into the state of competence for transformation (K-state). The latter is associated with growth arrest, and it is unclear how the ability to develop competence is stably maintained, despite its cost. To quantify the effect differentiation has on the competitive fitness of B. subtilis, we characterized the competition dynamics between strains with different probabilities of entering the K-state. The relative fitness decreased with increasing differentiation probability both during the stationary phase and during outgrowth. When exposed to antibiotics inhibiting cell wall synthesis, transcription, and translation, cells that differentiated into the K-state showed a selective advantage compared to differentiation-deficient bacteria; this benefit did not require transformation. Although beneficial, the K-state was not induced by sub-MIC concentrations of antibiotics. Increasing the differentiation probability beyond the wt level did not significantly affect the competition dynamics with transient antibiotic exposure. We conclude that the competition dynamics are very sensitive to the fraction of competent cells under benign conditions but less sensitive during antibiotic exposure, supporting the picture of stochastic differentiation as a fitness trade-off. PMID:27375604

Fitness Trade-Offs in Competence Differentiation of Bacillus subtilis.

PubMed

Yüksel, Melih; Power, Jeffrey J; Ribbe, Jan; Volkmann, Thorsten; Maier, Berenike

2016-01-01

In the stationary phase, Bacillus subtilis differentiates stochastically and transiently into the state of competence for transformation (K-state). The latter is associated with growth arrest, and it is unclear how the ability to develop competence is stably maintained, despite its cost. To quantify the effect differentiation has on the competitive fitness of B. subtilis, we characterized the competition dynamics between strains with different probabilities of entering the K-state. The relative fitness decreased with increasing differentiation probability both during the stationary phase and during outgrowth. When exposed to antibiotics inhibiting cell wall synthesis, transcription, and translation, cells that differentiated into the K-state showed a selective advantage compared to differentiation-deficient bacteria; this benefit did not require transformation. Although beneficial, the K-state was not induced by sub-MIC concentrations of antibiotics. Increasing the differentiation probability beyond the wt level did not significantly affect the competition dynamics with transient antibiotic exposure. We conclude that the competition dynamics are very sensitive to the fraction of competent cells under benign conditions but less sensitive during antibiotic exposure, supporting the picture of stochastic differentiation as a fitness trade-off.

Microscopic description of orbital-selective spin ordering in BaMn2As2

NASA Astrophysics Data System (ADS)

Craco, L.; Carara, S. S.

2018-05-01

Using generalized gradient approximation+dynamical mean-field theory, we provide a microscopic description of orbital-selective spin ordering in the tetragonal manganese pnictide BaMn2As2 . We demonstrate the coexistence of local moments and small band-gap electronic states in the parent compound. We also explore the role played by electron/hole doping, showing that the Mott insulating state is rather robust to small removal of electron charge carriers similar to cuprate oxide superconductors. Good qualitative accord between theory and angle-resolved photoemission as well as electrical transport provides support to our view of orbital-selective spin ordering in BaMn2As2 . Our proposal is expected to be an important step to understanding the emergent correlated electronic structure of materials with persisting ordered localized moments coexisting with Coulomb reconstructed nonmagnetic electronic states.

Bifurcations on Potential Energy Surfaces of Organic Reactions

PubMed Central

Ess, Daniel H.; Wheeler, Steven E.; Iafe, Robert G.; Xu, Lai; Çelebi-Ölçüm, Nihan; Houk, K. N.

2009-01-01

A single transition state may lead to multiple intermediates or products if there is a post-transition state reaction path bifurcation. These bifurcations arise when there are sequential transition states with no intervening energy minimum. For such systems, the shape of the potential energy surface and dynamic effects control selectivity rather than transition state energetics. This minireview covers recent investigations of organic reactions exhibiting reaction pathway bifurcations. Such phenomena are surprisingly general and affect experimental observables such as kinetic isotope effects and product distributions. PMID:18767086

Reservoir Computing Properties of Neural Dynamics in Prefrontal Cortex

PubMed Central

Procyk, Emmanuel; Dominey, Peter Ford

2016-01-01

Primates display a remarkable ability to adapt to novel situations. Determining what is most pertinent in these situations is not always possible based only on the current sensory inputs, and often also depends on recent inputs and behavioral outputs that contribute to internal states. Thus, one can ask how cortical dynamics generate representations of these complex situations. It has been observed that mixed selectivity in cortical neurons contributes to represent diverse situations defined by a combination of the current stimuli, and that mixed selectivity is readily obtained in randomly connected recurrent networks. In this context, these reservoir networks reproduce the highly recurrent nature of local cortical connectivity. Recombining present and past inputs, random recurrent networks from the reservoir computing framework generate mixed selectivity which provides pre-coded representations of an essentially universal set of contexts. These representations can then be selectively amplified through learning to solve the task at hand. We thus explored their representational power and dynamical properties after training a reservoir to perform a complex cognitive task initially developed for monkeys. The reservoir model inherently displayed a dynamic form of mixed selectivity, key to the representation of the behavioral context over time. The pre-coded representation of context was amplified by training a feedback neuron to explicitly represent this context, thereby reproducing the effect of learning and allowing the model to perform more robustly. This second version of the model demonstrates how a hybrid dynamical regime combining spatio-temporal processing of reservoirs, and input driven attracting dynamics generated by the feedback neuron, can be used to solve a complex cognitive task. We compared reservoir activity to neural activity of dorsal anterior cingulate cortex of monkeys which revealed similar network dynamics. We argue that reservoir computing is a pertinent framework to model local cortical dynamics and their contribution to higher cognitive function. PMID:27286251

Conformational selection in a protein-protein interaction revealed by dynamic pathway analysis

DOE PAGES

Chakrabarti, Kalyan S.; Agafonov, Roman V.; Pontiggia, Francesco; ...

2015-12-24

Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsinmore » kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using NMR spectroscopy, stopped-flow kinetics and isothermal titration calorimetry we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Lastly, protein dynamics in free recoverin limits the overall rate of binding.« less

Oscillatory dynamics and place field maps reflect hippocampal ensemble processing of sequence and place memory under NMDA receptor control.

PubMed

Cabral, Henrique O; Vinck, Martin; Fouquet, Celine; Pennartz, Cyriel M A; Rondi-Reig, Laure; Battaglia, Francesco P

2014-01-22

Place coding in the hippocampus requires flexible combination of sensory inputs (e.g., environmental and self-motion information) with memory of past events. We show that mouse CA1 hippocampal spatial representations may either be anchored to external landmarks (place memory) or reflect memorized sequences of cell assemblies depending on the behavioral strategy spontaneously selected. These computational modalities correspond to different CA1 dynamical states, as expressed by theta and low- and high-frequency gamma oscillations, when switching from place to sequence memory-based processing. These changes are consistent with a shift from entorhinal to CA3 input dominance on CA1. In mice with a deletion of forebrain NMDA receptors, the ability of place cells to maintain a map based on sequence memory is selectively impaired and oscillatory dynamics are correspondingly altered, suggesting that oscillations contribute to selecting behaviorally appropriate computations in the hippocampus and that NMDA receptors are crucial for this function. Copyright © 2014 Elsevier Inc. All rights reserved.

Conformational selection in a protein-protein interaction revealed by dynamic pathway analysis

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

Chakrabarti, Kalyan S.; Agafonov, Roman V.; Pontiggia, Francesco

Molecular recognition plays a central role in biology, and protein dynamics has been acknowledged to be important in this process. However, it is highly debated whether conformational changes happen before ligand binding to produce a binding-competent state (conformational selection) or are caused in response to ligand binding (induced fit). Proposals for both mechanisms in protein/protein recognition have been primarily based on structural arguments. However, the distinction between them is a question of the probabilities of going via these two opposing pathways. Here we present a direct demonstration of exclusive conformational selection in protein/protein recognition by measuring the flux for rhodopsinmore » kinase binding to its regulator recoverin, an important molecular recognition in the vision system. Using NMR spectroscopy, stopped-flow kinetics and isothermal titration calorimetry we show that recoverin populates a minor conformation in solution that exposes a hydrophobic binding pocket responsible for binding rhodopsin kinase. Lastly, protein dynamics in free recoverin limits the overall rate of binding.« less

Controlling Flexible Manipulators, an Experimental Investigation. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Hastings, Gordon Greene

1986-01-01

Lightweight, slender manipulators offer faster response and/or greater workspace range for the same size actuators than tradional manipulators. Lightweight construction of manipulator links results in increased structural flexibility. The increase flexibility must be considered in the design of control systems to properly account for the dynamic flexible vibrations and static deflections. Real time control of the flexible manipulator vibrations are experimentally investigated. Models intended for real-time control of distributed parameter system such as flexible manipulators rely on model approximation schemes. An linear model based on the application of Lagrangian dynamics to a rigid body mode and a series of separable flexible modes is examined with respect to model order requirements, and modal candidate selection. Balanced realizations are applied to the linear flexible model to obtain an estimate of appropriate order for a selected model. Describing the flexible deflections as a linear combination of modes results in measurements of beam state, which yield information about several modes. To realize the potential of linear systems theory, knowledge of each state must be available. State estimation is also accomplished by implementation of a Kalman Filter. State feedback control laws are implemented based upon linear quadratic regulator design.

Role of Dynamics in the Autoinhibition and Activation of the Exchange Protein Directly Activated by Cyclic AMP (EPAC)*

PubMed Central

VanSchouwen, Bryan; Selvaratnam, Rajeevan; Fogolari, Federico; Melacini, Giuseppe

2011-01-01

The exchange protein directly activated by cAMP (EPAC) is a key receptor of cAMP in eukaryotes and controls critical signaling pathways. Currently, no residue resolution information is available on the full-length EPAC dynamics, which are known to be pivotal determinants of allostery. In addition, no information is presently available on the intermediates for the classical induced fit and conformational selection activation pathways. Here these questions are addressed through molecular dynamics simulations on five key states along the thermodynamic cycle for the cAMP-dependent activation of a fully functional construct of EPAC2, which includes the cAMP-binding domain and the integral catalytic region. The simulations are not only validated by the agreement with the experimental trends in cAMP-binding domain dynamics determined by NMR, but they also reveal unanticipated dynamic attributes, rationalizing previously unexplained aspects of EPAC activation and autoinhibition. Specifically, the simulations show that cAMP binding causes an extensive perturbation of dynamics in the distal catalytic region, assisting the recognition of the Rap1b substrate. In addition, analysis of the activation intermediates points to a possible hybrid mechanism of EPAC allostery incorporating elements of both the induced fit and conformational selection models. In this mechanism an entropy compensation strategy results in a low free-energy pathway of activation. Furthermore, the simulations indicate that the autoinhibitory interactions of EPAC are more dynamic than previously anticipated, leading to a revised model of autoinhibition in which dynamics fine tune the stability of the autoinhibited state, optimally sensitizing it to cAMP while avoiding constitutive activation. PMID:21873431

Effects of reactant rotation on the dynamics of the OH + CH4 → H2O + CH3 reaction: a six-dimensional study.

PubMed

Song, Hongwei; Li, Jun; Jiang, Bin; Yang, Minghui; Lu, Yunpeng; Guo, Hua

2014-02-28

The dynamics of the hydrogen abstraction reaction between methane and hydroxyl radical is investigated using an initial state selected time-dependent wave packet method within a six-dimensional model. The ab initio calibrated global potential energy surface of Espinosa-García and Corchado was used. Integral cross sections from several low-lying rotational states of both reactants have been obtained using the centrifugal sudden and J-shifting approximations. On the empirical potential energy surface, the rotational excitation of methane has little effect on the reaction cross section, but excited rotational states of OH inhibit the reactivity slightly. These results are rationalized with the newly proposed sudden vector projection model.

Effect of bioaugmented inoculation on microbiota dynamics during solid-state fermentation of Daqu starter using autochthonous of Bacillus, Pediococcus, Wickerhamomyces and Saccharomycopsis.

PubMed

Li, Pan; Lin, Weifeng; Liu, Xiong; Wang, Xiaowen; Gan, Xing; Luo, Lixin; Lin, Wei-Tie

2017-02-01

Daqu, a traditional fermentation starter that is used for Chinese liquor and vinegar production, is still manufactured through a traditional spontaneous solid-state fermentation process with no selected microorganisms are intentionally inoculated. The aim of this work was to analyze the microbiota dynamics during the solid-state fermentation process of Daqu using a traditional and bioaugmented inoculation with autochthonous of Bacillus, Pediococcus, Saccharomycopsis and Wickerhamomyces at an industrial scale. Highly similar dynamics of physicochemical parameters, enzymatic activities and microbial communities were observed during the traditional and bioaugmented solid-state fermentation processes. Both in the two cases, groups of Streptophyta, Rickettsiales and Xanthomonadales only dominated the first two days, but Bacillales and Eurotiales became predominant members after 2 and 10 days fermentation, respectively. Phylotypes of Enterobacteriales, Lactobacillales, Saccharomycetales and Mucorales dominated the whole fermentation process. No significant difference (P > 0.05) in microbial structure was observed between the traditional and bioaugmented fermentation processes. However, slightly higher microbial richness was found during the bioaugmented fermentation process after 10 days fermentation. Our results reinforced the microbiota dynamic stability during the solid-state fermentation process of Daqu, and might aid in controlling the traditional Daqu manufacturing process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Evolutionary dynamics on graphs: Efficient method for weak selection

NASA Astrophysics Data System (ADS)

Fu, Feng; Wang, Long; Nowak, Martin A.; Hauert, Christoph

2009-04-01

Investigating the evolutionary dynamics of game theoretical interactions in populations where individuals are arranged on a graph can be challenging in terms of computation time. Here, we propose an efficient method to study any type of game on arbitrary graph structures for weak selection. In this limit, evolutionary game dynamics represents a first-order correction to neutral evolution. Spatial correlations can be empirically determined under neutral evolution and provide the basis for formulating the game dynamics as a discrete Markov process by incorporating a detailed description of the microscopic dynamics based on the neutral correlations. This framework is then applied to one of the most intriguing questions in evolutionary biology: the evolution of cooperation. We demonstrate that the degree heterogeneity of a graph impedes cooperation and that the success of tit for tat depends not only on the number of rounds but also on the degree of the graph. Moreover, considering the mutation-selection equilibrium shows that the symmetry of the stationary distribution of states under weak selection is skewed in favor of defectors for larger selection strengths. In particular, degree heterogeneity—a prominent feature of scale-free networks—generally results in a more pronounced increase in the critical benefit-to-cost ratio required for evolution to favor cooperation as compared to regular graphs. This conclusion is corroborated by an analysis of the effects of population structures on the fixation probabilities of strategies in general 2×2 games for different types of graphs. Computer simulations confirm the predictive power of our method and illustrate the improved accuracy as compared to previous studies.

An alternative mechanism for spin-forbidden photo-ionization of diatomic molecules and its rotation-electronic selection rules

NASA Astrophysics Data System (ADS)

Chiu, Ying-Nan; Chiu, Lue-Yung Chow

1990-02-01

The spin-forbidden photo-ionization of diatomic molecules is proposed. Spin orbit interaction is invoked, resulting in the correction and mixing of the wave functions of different multiplicities. The rotation-electronic selection rules given by Dixit and McKoy (1986) for Hund's case a based on the conventional mechanism of electric dipole transition are rederived and expressed in a different format. This new format permits the generalization of the selection rules to other photoionization transitions caused by the magnetic dipole, the electric quadrupole, and the two- and three-photon operators. These selection rules, which are for transitions from one specific rotational level of a given Kronig reflection symmetry to another, will help understand rotational branching and the dynamics of interaction in the excited state. They will also help in the selective preparation of well-defined rovibronic states in resonant-enhanced multi-photon ionization processes.

Diversity in times of adversity: probabilistic strategies in microbial survival games.

PubMed

Wolf, Denise M; Vazirani, Vijay V; Arkin, Adam P

2005-05-21

Population diversification strategies are ubiquitous among microbes, encompassing random phase-variation (RPV) of pathogenic bacteria, viral latency as observed in some bacteriophage and HIV, and the non-genetic diversity of bacterial stress responses. Precise conditions under which these diversification strategies confer an advantage have not been well defined. We develop a model of population growth conditioned on dynamical environmental and cellular states. Transitions among cellular states, in turn, may be biased by possibly noisy readings of the environment from cellular sensors. For various types of environmental dynamics and cellular sensor capability, we apply game-theoretic analysis to derive the evolutionarily stable strategy (ESS) for an organism and determine when that strategy is diversification. We find that: (1) RPV, effecting a sort of Parrondo paradox wherein random alternations between losing strategies produce a winning strategy, is selected when transitions between different selective environments cannot be sensed, (2) optimal RPV cell switching rates are a function of environmental lifecycle asymmetries and environmental autocorrelation, (3) probabilistic diversification upon entering a new environment is selected when sensors can detect environmental transitions but have poor precision in identifying new environments, and (4) in the presence of excess additive noise, low-pass filtering is required for evolutionary stability. We show that even when RPV is not the ESS, it may minimize growth rate variance and the risk of extinction due to 'unlucky' environmental dynamics.

Model reduction in a subset of the original states

NASA Technical Reports Server (NTRS)

Yae, K. H.; Inman, D. J.

1992-01-01

A model reduction method is investigated to provide a smaller structural dynamic model for subsequent structural control design. A structural dynamic model is assumed to be derived from finite element analysis. It is first converted into the state space form, and is further reduced by the internal balancing method. Through the co-ordinate transformation derived from the states that are deleted during reduction, the reduced model is finally expressed with the states that are members of the original states. Therefore, the states in the final reduced model represent the degrees of freedom of the nodes that are selected by the designer. The procedure provides a more practical implementation of model reduction for applications in which specific nodes, such as sensor and/or actuator attachment points, are to be retained in the reduced model. Thus, it ensures that the reduced model is under the same input and output condition as the original physical model. The procedure is applied to two simple examples and comparisons are made between the full and reduced order models. The method can be applied to a linear, continuous and time-invariant model of structural dynamics with nonproportional viscous damping.

Invisible Electronic States and Their Dynamics Revealed by Perturbations

NASA Astrophysics Data System (ADS)

Merer, Anthony J.

2011-06-01

Sooner or later everyone working in the field of spectroscopy encounters perturbations. These can range in size from a small shift of a single rotational level to total destruction of the vibrational and rotational patterns of an electronic state. To some workers perturbations are a source of terror, but to others they are the most fascinating features of molecular spectra, because they give information about molecular dynamics, and about states that would otherwise be invisible as a result of unfavorable selection rules. An example of the latter is the essentially complete characterization of the tilde{b}^3A_2 state of SO_2 from the vibronic perturbations it causes in the tilde{a}^3B_1 state. The S_1-trans state of acetylene is a beautiful example of dynamics in action. The level patterns of the three bending vibrations change dramatically with increasing vibrational excitation as a result of the vibrational angular momentum and the approach to the isomerization barrier. Several vibrational levels of the S_1-cis isomer, previously thought to be unobservable, can now be assigned. They obtain their intensity through interactions with nearby levels of the trans isomer.

A visualization method for teaching the geometric design of highways

DOT National Transportation Integrated Search

2000-04-11

In this project the authors employed state-of-the-art technology for developing visualization tools for teaching highway design. Specifically, the authors used photolog images as the basis for developing dynamic 3-D models of selected geometric eleme...

Dynamic optimization approach for integrated supplier selection and tracking control of single product inventory system with product discount

NASA Astrophysics Data System (ADS)

Sutrisno; Widowati; Heru Tjahjana, R.

2017-01-01

In this paper, we propose a mathematical model in the form of dynamic/multi-stage optimization to solve an integrated supplier selection problem and tracking control problem of single product inventory system with product discount. The product discount will be stated as a piece-wise linear function. We use dynamic programming to solve this proposed optimization to determine the optimal supplier and the optimal product volume that will be purchased from the optimal supplier for each time period so that the inventory level tracks a reference trajectory given by decision maker with minimal total cost. We give a numerical experiment to evaluate the proposed model. From the result, the optimal supplier was determined for each time period and the inventory level follows the given reference well.

Molecular Dynamics Simulations Reveal the Mechanisms of Allosteric Activation of Hsp90 by Designed Ligands

NASA Astrophysics Data System (ADS)

Vettoretti, Gerolamo; Moroni, Elisabetta; Sattin, Sara; Tao, Jiahui; Agard, David A.; Bernardi, Anna; Colombo, Giorgio

2016-04-01

Controlling biochemical pathways through chemically designed modulators may provide novel opportunities to develop therapeutic drugs and chemical tools. The underlying challenge is to design new molecular entities able to act as allosteric chemical switches that selectively turn on/off functions by modulating the conformational dynamics of their target protein. We examine the origins of the stimulation of ATPase and closure kinetics in the molecular chaperone Hsp90 by allosteric modulators through atomistic molecular dynamics (MD) simulations and analysis of protein-ligand interactions. In particular, we focus on the cross-talk between allosteric ligands and protein conformations and its effect on the dynamic properties of the chaperone’s active state. We examine the impact of different allosteric modulators on the stability, structural and internal dynamics properties of Hsp90 closed state. A critical aspect of this study is the development of a quantitative model that correlates Hsp90 activation to the presence of a certain compound, making use of information on the dynamic adaptation of protein conformations to the presence of the ligand, which allows to capture conformational states relevant in the activation process. We discuss the implications of considering the conformational dialogue between allosteric ligands and protein conformations for the design of new functional modulators.

New insights into photodissociation dynamics of cyclobutanone from the AIMS dynamic simulation

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

Liu, Lihong; Fang, Wei-Hai, E-mail: fangwh@bnu.edu.cn

2016-04-14

In this work, the combined electronic structure calculations and non-adiabatic dynamics simulations were performed for understanding mechanistic photodissociation of cyclobutanone at ∼248 nm. Besides the stationary and intersection structures reported before, two new conical intersections between the ground (S{sub 0}) and the first excited singlet (S{sub 1}) states were determined in the present study, which were confirmed to be the new S{sub 1} → S{sub 0} funnels by the ab initio multiple spawning dynamic simulation, giving rise to products in the S{sub 0} state selectively. The time evolution of the S{sub 1} electronic population was fitted with the pure exponentialmore » formulae, from which the S{sub 1} lifetime was estimated to be 484.0 fs. The time constant for the S{sub 1} α-cleavage is calculated to be 176.6 fs, which is based on the present dynamics simulation. As a result of the ultrafast S{sub 1} processes, the statistical distribution of the excess energies is prevented in the S{sub 1} state. The S{sub 1} dynamic effect (the nonergodic behavior) was predicted to be an important factor that is responsible for the wavelength dependence of the branching ratio of photodissociation products, which will be discussed in detail.« less

Large scale exact quantum dynamics calculations: Ten thousand quantum states of acetonitrile

NASA Astrophysics Data System (ADS)

Halverson, Thomas; Poirier, Bill

2015-03-01

'Exact' quantum dynamics (EQD) calculations of the vibrational spectrum of acetonitrile (CH3CN) are performed, using two different methods: (1) phase-space-truncated momentum-symmetrized Gaussian basis and (2) correlated truncated harmonic oscillator basis. In both cases, a simple classical phase space picture is used to optimize the selection of individual basis functions-leading to drastic reductions in basis size, in comparison with existing methods. Massive parallelization is also employed. Together, these tools-implemented into a single, easy-to-use computer code-enable a calculation of tens of thousands of vibrational states of CH3CN to an accuracy of 0.001-10 cm-1.

Variationally optimal selection of slow coordinates and reaction coordinates in macromolecular systems

NASA Astrophysics Data System (ADS)

Noe, Frank

To efficiently simulate and generate understanding from simulations of complex macromolecular systems, the concept of slow collective coordinates or reaction coordinates is of fundamental importance. Here we will introduce variational approaches to approximate the slow coordinates and the reaction coordinates between selected end-states given MD simulations of the macromolecular system and a (possibly large) basis set of candidate coordinates. We will then discuss how to select physically intuitive order paremeters that are good surrogates of this variationally optimal result. These result can be used in order to construct Markov state models or other models of the stationary and kinetics properties, in order to parametrize low-dimensional / coarse-grained model of the dynamics. Deutsche Forschungsgemeinschaft, European Research Council.

Manipulating the motion of large molecules: Information from the molecular frame

NASA Astrophysics Data System (ADS)

Küpper, Jochen

2011-05-01

Large molecules have complex potential-energy surfaces with many local minima. They exhibit multiple stereoisomers, even at the low temperatures (~1 K) in a molecular beam, with rich intra- and intermolecular dynamics. Over the last years, we have developed methods to manipulate the motion of large, complex molecules and to select their quantum states. We have exploited this state-selectivity, for example, to spatially separate individual structural isomers of complex molecules and to demonstrate unprecedented degrees of laser alignment and mixed-field orientation of these molecules. Such clean, well-defined samples strongly benefit, or simply allow, novel experiments on the dynamics of complex molecules, for instance, femtosecond pump-probe measurements, X-ray or electron diffraction of molecular ensembles (including diffraction-from-within experiments), or tomographic reconstructions of molecular orbitals. These samples could also be very advantageous for metrology applications, such as, for example, matter-wave interferometry or the search for electroweak interactions in chiral molecules. Moreover, they provide an extreme level of control for stereo-dynamically controlled reaction dynamics. We have recently exploited these state-selected and oriented samples to measure photoelectron angular distributions in the molecular frame (MFPADs) from non-resonant femtosecond-laser photoionization and using the X-ray Free-Electron-Laser LCLS. We have also investigated X-ray diffraction imaging and, using ion momentum imaging, the induced radiation damage of these samples using the LCLS. This work was carried out within a collaboration for which J. Küpper, H. Chapman, and D. Rolles are spokespersons. The collaboration consists of CFEL (DESY, MPG, University Hamburg), Fritz-Haber-Institute Berlin, MPI Nuclear Physics Heidelberg, MPG Semi-conductor Lab, Aarhus University, FOM AMOLF Amsterdam, Lund University, MPI Medical Research Heidelberg, TU Berlin, Max Born Institute Berlin, and SLAC Menlo Park, CA, USA. The experiments were carried out using CAMP (designed and built by the MPG-ASG at CFEL) at the LCLS (operated by Stanford University on behalf of the US DOE).

Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex.

PubMed

Raveh, Barak; Karp, Jerome M; Sparks, Samuel; Dutta, Kaushik; Rout, Michael P; Sali, Andrej; Cowburn, David

2016-05-03

Nucleocytoplasmic transport is mediated by the interaction of transport factors (TFs) with disordered phenylalanine-glycine (FG) repeats that fill the central channel of the nuclear pore complex (NPC). However, the mechanism by which TFs rapidly diffuse through multiple FG repeats without compromising NPC selectivity is not yet fully understood. In this study, we build on our recent NMR investigations showing that FG repeats are highly dynamic, flexible, and rapidly exchanging among TF interaction sites. We use unbiased long timescale all-atom simulations on the Anton supercomputer, combined with extensive enhanced sampling simulations and NMR experiments, to characterize the thermodynamic and kinetic properties of FG repeats and their interaction with a model transport factor. Both the simulations and experimental data indicate that FG repeats are highly dynamic random coils, lack intrachain interactions, and exhibit significant entropically driven resistance to spatial confinement. We show that the FG motifs reversibly slide in and out of multiple TF interaction sites, transitioning rapidly between a strongly interacting state and a weakly interacting state, rather than undergoing a much slower transition between strongly interacting and completely noninteracting (unbound) states. In the weakly interacting state, FG motifs can be more easily displaced by other competing FG motifs, providing a simple mechanism for rapid exchange of TF/FG motif contacts during transport. This slide-and-exchange mechanism highlights the direct role of the disorder within FG repeats in nucleocytoplasmic transport, and resolves the apparent conflict between the selectivity and speed of transport.

The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations.

PubMed

Wang, Moye; Hu, Jie; Zhang, Zhuqing

2016-04-26

As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD) simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD) simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5-10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design.

The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations

PubMed Central

Wang, Moye; Hu, Jie; Zhang, Zhuqing

2016-01-01

As they are not subjected to natural selection process, de novo designed proteins usually fold in a manner different from natural proteins. Recently, a de novo designed mini-protein DS119, with a βαβ motif and 36 amino acids, has folded unusually slowly in experiments, and transient dimers have been detected in the folding process. Here, by means of all-atom replica exchange molecular dynamics (REMD) simulations, several comparably stable intermediate states were observed on the folding free-energy landscape of DS119. Conventional molecular dynamics (CMD) simulations showed that when two unfolded DS119 proteins bound together, most binding sites of dimeric aggregates were located at the N-terminal segment, especially residues 5–10, which were supposed to form β-sheet with its own C-terminal segment. Furthermore, a large percentage of individual proteins in the dimeric aggregates adopted conformations similar to those in the intermediate states observed in REMD simulations. These results indicate that, during the folding process, DS119 can easily become trapped in intermediate states. Then, with diffusion, a transient dimer would be formed and stabilized with the binding interface located at N-terminals. This means that it could not quickly fold to the native structure. The complicated folding manner of DS119 implies the important influence of natural selection on protein-folding kinetics, and more improvement should be achieved in rational protein design. PMID:27128902

The growth of selected leisure industries

Treesearch

Elizabeth R. Owen

1980-01-01

Rapidly rising sales of sporting equipment, as well as the phenomenal growth of receipts from a variety of recreation-oriented service industries, have contributed in establishing the recreation market as one of the most dynamic and fastest expanding sectors of the United States economy.

A technique for pole-zero placement for dual-input control systems. [computer simulation of CH-47 helicopter longitudinal dynamics

NASA Technical Reports Server (NTRS)

Reid, G. F.

1976-01-01

A technique is presented for determining state variable feedback gains that will place both the poles and zeros of a selected transfer function of a dual-input control system at pre-determined locations in the s-plane. Leverrier's algorithm is used to determine the numerator and denominator coefficients of the closed-loop transfer function as functions of the feedback gains. The values of gain that match these coefficients to those of a pre-selected model are found by solving two systems of linear simultaneous equations. The algorithm has been used in a computer simulation of the CH-47 helicopter to control longitudinal dynamics.

Nanocluster building blocks of artificial square spin ice: Stray-field studies of thermal dynamics

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

Pohlit, Merlin, E-mail: pohlit@physik.uni-frankfurt.de; Porrati, Fabrizio; Huth, Michael

We present measurements of the thermal dynamics of a Co-based single building block of an artificial square spin ice fabricated by focused electron-beam-induced deposition. We employ micro-Hall magnetometry, an ultra-sensitive tool to study the stray field emanating from magnetic nanostructures, as a new technique to access the dynamical properties during the magnetization reversal of the spin-ice nanocluster. The obtained hysteresis loop exhibits distinct steps, displaying a reduction of their “coercive field” with increasing temperature. Therefore, thermally unstable states could be repetitively prepared by relatively simple temperature and field protocols allowing one to investigate the statistics of their switching behavior withinmore » experimentally accessible timescales. For a selected switching event, we find a strong reduction of the so-prepared states' “survival time” with increasing temperature and magnetic field. Besides the possibility to control the lifetime of selected switching events at will, we find evidence for a more complex behavior caused by the special spin ice arrangement of the macrospins, i.e., that the magnetic reversal statistically follows distinct “paths” most likely driven by thermal perturbation.« less

Cortical and thalamic contributions to response dynamics across layers of the primary somatosensory cortex during tactile discrimination

PubMed Central

Pais-Vieira, Miguel; Kunicki, Carolina; Tseng, Po-He; Martin, Joel; Lebedev, Mikhail

2015-01-01

Tactile information processing in the rodent primary somatosensory cortex (S1) is layer specific and involves modulations from both thalamocortical and cortico-cortical loops. However, the extent to which these loops influence the dynamics of the primary somatosensory cortex while animals execute tactile discrimination remains largely unknown. Here, we describe neural dynamics of S1 layers across the multiple epochs defining a tactile discrimination task. We observed that neuronal ensembles within different layers of the S1 cortex exhibited significantly distinct neurophysiological properties, which constantly changed across the behavioral states that defined a tactile discrimination. Neural dynamics present in supragranular and granular layers generally matched the patterns observed in the ventral posterior medial nucleus of the thalamus (VPM), whereas the neural dynamics recorded from infragranular layers generally matched the patterns from the posterior nucleus of the thalamus (POM). Selective inactivation of contralateral S1 specifically switched infragranular neural dynamics from POM-like to those resembling VPM neurons. Meanwhile, ipsilateral M1 inactivation profoundly modulated the firing suppression observed in infragranular layers. This latter effect was counterbalanced by contralateral S1 block. Tactile stimulus encoding was layer specific and selectively affected by M1 or contralateral S1 inactivation. Lastly, causal information transfer occurred between all neurons in all S1 layers but was maximal from infragranular to the granular layer. These results suggest that tactile information processing in the S1 of awake behaving rodents is layer specific and state dependent and that its dynamics depend on the asynchronous convergence of modulations originating from ipsilateral M1 and contralateral S1. PMID:26180115

Imaging of Myocardial Fatty Acid Oxidation

PubMed Central

Mather, Kieren J; DeGrado, Tim

2016-01-01

Myocardial fuel selection is a key feature of the health and function of the heart, with clear links between myocardial function and fuel selection and important impacts of fuel selection on ischemia tolerance. Radiopharmaceuticals provide uniquely valuable tools for in vivo, non-invasive assessment of these aspects of cardiac function and metabolism. Here we review the landscape of imaging probes developed to provide noninvasive assessment of myocardial fatty acid oxidation (MFAO). Also, we review the state of current knowledge that myocardial fatty acid imaging has helped establish of static and dynamic fuel selection that characterizes cardiac and cardiometabolic disease and the interplay between fuel selection and various aspects of cardiac function. PMID:26923433

Global attractors and extinction dynamics of cyclically competing species.

PubMed

Rulands, Steffen; Zielinski, Alejandro; Frey, Erwin

2013-05-01

Transitions to absorbing states are of fundamental importance in nonequilibrium physics as well as ecology. In ecology, absorbing states correspond to the extinction of species. We here study the spatial population dynamics of three cyclically interacting species. The interaction scheme comprises both direct competition between species as in the cyclic Lotka-Volterra model, and separated selection and reproduction processes as in the May-Leonard model. We show that the dynamic processes leading to the transient maintenance of biodiversity are closely linked to attractors of the nonlinear dynamics for the overall species' concentrations. The characteristics of these global attractors change qualitatively at certain threshold values of the mobility and depend on the relative strength of the different types of competition between species. They give information about the scaling of extinction times with the system size and thereby the stability of biodiversity. We define an effective free energy as the negative logarithm of the probability to find the system in a specific global state before reaching one of the absorbing states. The global attractors then correspond to minima of this effective energy landscape and determine the most probable values for the species' global concentrations. As in equilibrium thermodynamics, qualitative changes in the effective free energy landscape indicate and characterize the underlying nonequilibrium phase transitions. We provide the complete phase diagrams for the population dynamics and give a comprehensive analysis of the spatio-temporal dynamics and routes to extinction in the respective phases.

Adaptive neural network output feedback control for stochastic nonlinear systems with unknown dead-zone and unmodeled dynamics.

PubMed

Tong, Shaocheng; Wang, Tong; Li, Yongming; Zhang, Huaguang

2014-06-01

This paper discusses the problem of adaptive neural network output feedback control for a class of stochastic nonlinear strict-feedback systems. The concerned systems have certain characteristics, such as unknown nonlinear uncertainties, unknown dead-zones, unmodeled dynamics and without the direct measurements of state variables. In this paper, the neural networks (NNs) are employed to approximate the unknown nonlinear uncertainties, and then by representing the dead-zone as a time-varying system with a bounded disturbance. An NN state observer is designed to estimate the unmeasured states. Based on both backstepping design technique and a stochastic small-gain theorem, a robust adaptive NN output feedback control scheme is developed. It is proved that all the variables involved in the closed-loop system are input-state-practically stable in probability, and also have robustness to the unmodeled dynamics. Meanwhile, the observer errors and the output of the system can be regulated to a small neighborhood of the origin by selecting appropriate design parameters. Simulation examples are also provided to illustrate the effectiveness of the proposed approach.

Chaos in Dirac Electron Optics: Emergence of a Relativistic Quantum Chimera.

PubMed

Xu, Hong-Ya; Wang, Guang-Lei; Huang, Liang; Lai, Ying-Cheng

2018-03-23

We uncover a remarkable quantum scattering phenomenon in two-dimensional Dirac material systems where the manifestations of both classically integrable and chaotic dynamics emerge simultaneously and are electrically controllable. The distinct relativistic quantum fingerprints associated with different electron spin states are due to a physical mechanism analogous to a chiroptical effect in the presence of degeneracy breaking. The phenomenon mimics a chimera state in classical complex dynamical systems but here in a relativistic quantum setting-henceforth the term "Dirac quantum chimera," associated with which are physical phenomena with potentially significant applications such as enhancement of spin polarization, unusual coexisting quasibound states for distinct spin configurations, and spin selective caustics. Experimental observations of these phenomena are possible through, e.g., optical realizations of ballistic Dirac fermion systems.

Chaos in Dirac Electron Optics: Emergence of a Relativistic Quantum Chimera

NASA Astrophysics Data System (ADS)

Xu, Hong-Ya; Wang, Guang-Lei; Huang, Liang; Lai, Ying-Cheng

2018-03-01

We uncover a remarkable quantum scattering phenomenon in two-dimensional Dirac material systems where the manifestations of both classically integrable and chaotic dynamics emerge simultaneously and are electrically controllable. The distinct relativistic quantum fingerprints associated with different electron spin states are due to a physical mechanism analogous to a chiroptical effect in the presence of degeneracy breaking. The phenomenon mimics a chimera state in classical complex dynamical systems but here in a relativistic quantum setting—henceforth the term "Dirac quantum chimera," associated with which are physical phenomena with potentially significant applications such as enhancement of spin polarization, unusual coexisting quasibound states for distinct spin configurations, and spin selective caustics. Experimental observations of these phenomena are possible through, e.g., optical realizations of ballistic Dirac fermion systems.

Collisional quenching at ultralow energies: controlling efficiency with internal state selection.

PubMed

Bovino, S; Bodo, E; Gianturco, F A

2007-12-14

Calculations have been carried out for the vibrational quenching of excited H(2) molecules which collide with Li(+) ions at ultralow energies. The dynamics has been treated exactly using the well-known quantum coupled-channel expansions over different initial vibrational levels. The overall interaction potential has been obtained from the calculations carried out earlier by our group using highly correlated ab initio methods. The results indicate that specific features of the scattering observables, e.g., the appearance of Ramsauer-Townsend minima in elastic channel cross sections and the marked increase of the cooling rates from specific initial states, can be linked to potential properties at vanishing energies (sign and size of scattering lengths) and to the presence of either virtual states or bound states. The suggestion is made such that by selecting the initial state preparation of the molecular partners, the ionic interactions would be amenable to controlling quenching efficiency at ultralow energies.

Communication: Reactivity borrowing in the mode selective chemistry of H + CHD3 → H2 + CD3

NASA Astrophysics Data System (ADS)

Ellerbrock, Roman; Manthe, Uwe

2017-12-01

Quantum state-resolved reaction probabilities for the H + CHD3 → H2 + CD3 reaction are calculated by accurate full-dimensional quantum dynamics calculations using the multi-layer multi-configurational time-dependent Hartree approach and the quantum transition state concept. Reaction probabilities of various ro-vibrational states of the CHD3 reactant are investigated for vanishing total angular momentum. While the reactivity of the different vibrational states of CHD3 mostly follows intuitive patterns, an unusually large reaction probability is found for CHD3 molecules triply excited in the CD3 umbrella-bending vibration. This surprising reactivity can be explained by a Fermi resonance-type mixing of the single CH-stretch excited and the triple CD3 umbrella-bend excited vibrational states of CHD3. These findings show that resonant energy transfer can significantly affect the mode-selective chemistry of CHD3 and result in counter-intuitive reactivity patterns.

Highly Selective Relaxation of the OH Stretching Overtones in Isolated HDO Molecules Observed by Infrared Pump-Repump-Probe Spectroscopy.

PubMed

Hutzler, Daniel; Werhahn, Jasper C; Heider, Rupert; Bradler, Maximilian; Kienberger, Reinhard; Riedle, Eberhard; Iglev, Hristo

2015-07-02

A quantitative investigation of the relaxation dynamics of higher-lying vibrational states is afforded by a novel method of infrared pump-repump-probe spectroscopy. The technique is used to study the dynamics of OH stretching overtones in NaClO4·HDO monohydrate. We observe a continuous decrease of the energy separation for the first four states, i.e. v01 = 3575 cm(-1), v12 = 3370 cm(-1), and v23 = 3170 cm(-1), respectively. The population lifetime of the first excited state is 7.2 ps, while the one of the second excited state is largely reduced to 1.4 ps. The relaxation of the v = 2 state proceeds nearly quantitatively to the v = 1 state. The new information on the OH stretching overtones demands improved theoretical potentials and modeling of the H bond interactions. This work shows the potential of the new technique for the precise study of complex vibrational relaxation pathways.

Zombie states for description of structure and dynamics of multi-electron systems

NASA Astrophysics Data System (ADS)

Shalashilin, Dmitrii V.

2018-05-01

Canonical Coherent States (CSs) of Harmonic Oscillator have been extensively used as a basis in a number of computational methods of quantum dynamics. However, generalising such techniques for fermionic systems is difficult because Fermionic Coherent States (FCSs) require complicated algebra of Grassmann numbers not well suited for numerical calculations. This paper introduces a coherent antisymmetrised superposition of "dead" and "alive" electronic states called here Zombie State (ZS), which can be used in a manner of FCSs but without Grassmann algebra. Instead, for Zombie States, a very simple sign-changing rule is used in the definition of creation and annihilation operators. Then, calculation of electronic structure Hamiltonian matrix elements between two ZSs becomes very simple and a straightforward technique for time propagation of fermionic wave functions can be developed. By analogy with the existing methods based on Canonical Coherent States of Harmonic Oscillator, fermionic wave functions can be propagated using a set of randomly selected Zombie States as a basis. As a proof of principles, the proposed Coupled Zombie States approach is tested on a simple example showing that the technique is exact.

Predicting Mood Changes in Bipolar Disorder through Heartbeat Nonlinear Dynamics.

PubMed

Valenza, Gaetano; Nardelli, Mimma; Lanata', Antonio; Gentili, Claudio; Bertschy, Gilles; Kosel, Markus; Scilingo, Enzo Pasquale

2016-04-20

Bipolar Disorder (BD) is characterized by an alternation of mood states from depression to (hypo)mania. Mixed states, i.e., a combination of depression and mania symptoms at the same time, can also be present. The diagnosis of this disorder in the current clinical practice is based only on subjective interviews and questionnaires, while no reliable objective psychophysiological markers are available. Furthermore, there are no biological markers predicting BD outcomes, or providing information about the future clinical course of the phenomenon. To overcome this limitation, here we propose a methodology predicting mood changes in BD using heartbeat nonlinear dynamics exclusively, derived from the ECG. Mood changes are here intended as transitioning between two mental states: euthymic state (EUT), i.e., the good affective balance, and non-euthymic (non-EUT) states. Heart Rate Variability (HRV) series from 14 bipolar spectrum patients (age: 33.439.76, age range: 23-54; 6 females) involved in the European project PSYCHE, undergoing whole night ECG monitoring were analyzed. Data were gathered from a wearable system comprised of a comfortable t-shirt with integrated fabric electrodes and sensors able to acquire ECGs. Each patient was monitored twice a week, for 14 weeks, being able to perform normal (unstructured) activities. From each acquisition, the longest artifact-free segment of heartbeat dynamics was selected for further analyses. Sub-segments of 5 minutes of this segment were used to estimate trends of HRV linear and nonlinear dynamics. Considering data from a current observation at day t0, and past observations at days (t1, t2,...,), personalized prediction accuracies in forecasting a mood state (EUT/non-EUT) at day t+1 were 69% on average, reaching values as high as 83.3%. This approach opens to the possibility of predicting mood states in bipolar patients through heartbeat nonlinear dynamics exclusively.

MIMO model of an interacting series process for Robust MPC via System Identification.

PubMed

Wibowo, Tri Chandra S; Saad, Nordin

2010-07-01

This paper discusses the empirical modeling using system identification technique with a focus on an interacting series process. The study is carried out experimentally using a gaseous pilot plant as the process, in which the dynamic of such a plant exhibits the typical dynamic of an interacting series process. Three practical approaches are investigated and their performances are evaluated. The models developed are also examined in real-time implementation of a linear model predictive control. The selected model is able to reproduce the main dynamic characteristics of the plant in open-loop and produces zero steady-state errors in closed-loop control system. Several issues concerning the identification process and the construction of a MIMO state space model for a series interacting process are deliberated. 2010 ISA. Published by Elsevier Ltd. All rights reserved.

Theoretical investigation into the possibility of multiorbital magnetically ordered states in isotropically superstrained graphene

NASA Astrophysics Data System (ADS)

Craco, L.

2017-10-01

Using density functional dynamical mean-field theory (DFDMFT) we address the problem of antiferromagnetic spin ordering in isotropically superstrained graphene. It is shown that the interplay between strain-induced one-particle band narrowing and sizable on-site electron-electron interactions naturally stabilizes a magnetic phase with orbital-selective spin-polarized p -band electronic states. While an antiferromagnetic phase with strong local moments arises in the pz orbitals, the px ,y bands reveal a metallic state with quenched sublattice magnetization. We next investigate the possibility of superconductivity to emerge in this selective magnetoelectronic state. Our theory is expected to be an important step to understanding the next generation of flexible electronics made of Mott localized carbon-based materials as well as the ability of superstrained graphene to host coexisting superconductivity and magnetism at low temperatures.

Capturing Guest Dynamics in Metal-Organic Framework CPO-27-M (M = Mg, Zn) by (2)H Solid-State NMR Spectroscopy.

PubMed

Xu, Jun; Sinelnikov, Regina; Huang, Yining

2016-06-07

Metal-organic frameworks (MOFs) are promising porous materials for gas separation and storage as well as sensing. In particular, a series of isostructural MOFs with coordinately unsaturated metal centers, namely, CPO-27-M or M-MOF-74 (M = Mg, Zn, Mn, Fe, Ni, Co, Cu), have shown exceptional adsorption capacity and selectivity compared to those of classical MOFs that contain only fully coordinated metal sites. Although it is widely accepted that the interaction between guest molecules and exposed metal centers is responsible for good selectivity and large maximum uptake, the investigation of such guest-metal interaction is very challenging because adsorbed molecules are usually disordered in the pores and undergo rapid thermal motions. (2)H solid-state NMR (SSNMR) spectroscopy is one of the most extensively used techniques for capturing guest dynamics in porous materials. In this work, variable-temperature (2)H wide-line SSNMR experiments were performed on CPO-27-M (M = Mg, Zn) loaded with four prototypical guest molecules: D2O, CD3CN, acetone-d6, and C6D6. The results indicate that different guest molecules possess distinct dynamic behaviors inside the channel of CPO-27-M. For a given guest molecule, its dynamic behavior also depends on the nature of the metal centers. The binding strength of guest molecules is discussed on the basis of the (2)H SSNMR data.

Spectroscopy of exotic hadrons formed from dynamical diquarks

NASA Astrophysics Data System (ADS)

Lebed, Richard F.

2017-12-01

The dynamical diquark picture asserts that exotic hadrons can be formed from widely separated colored diquark or triquark components. We use the Born-Oppenheimer (BO) approximation to study the spectrum of states thus constructed, both in the basis of diquark spins and in the basis of heavy quark-antiquark spins. We develop a compact notation for naming these states, and use the results of lattice simulations for hybrid mesons to predict the lowest expected BO potentials for both tetraquarks and pentaquarks. We then compare to the set of exotic candidates with experimentally determined quantum numbers, and find that all of them can be accommodated. Once decay modes are also considered, one can develop selection rules of both exact (JP C conservation) and approximate (within the context of the BO approximation) types and test their effectiveness. We find that the most appealing way to satisfy both sets of selection rules requires including additional low-lying BO potentials, a hypothesis that can be checked on the lattice.

Ultrafast nuclear dynamics in halomethanes studied with time-resolved Coulomb explosion imaging and channel-selective Fourier spectroscopy

NASA Astrophysics Data System (ADS)

Malakar, Y.; Kaderiya, B.; Pearson, W. L.; Ziaee, F.; Kanaka Raju, P.; Zohrabi, M.; Jensen, K.; Rajput, J.; Ben-Itzhak, I.; Rolles, D.; Rudenko, A.

2016-05-01

Halomethanes have recently attracted considerable attention since they often serve as prototype systems for laser-controlled chemistry (e.g., selective bond breaking or concerted elimination reactions), and are important molecules in atmospheric chemistry. Here we combine a femtosecond laser pump-probe setup with coincident 3D ion momentum imaging apparatus to study strong-field induced nuclear dynamics in methane and several of its halogenated derivatives (CH3 I, CH2 I2, CH2 ICl). We apply a time-resolved Coulomb explosion imaging technique to map the nuclear motion on both, bound and continuum potential surfaces, disentangle different fragmentation pathways and, for halogenated molecules, observe clear signatures of vibrational wave packets in neutral or ionized states. Channel-selective and kinetic-energy resolved Fourier analysis of these data allows for unique identification of different electronic states and vibrational modes responsible for a particular structure. Supported by the Chemical Sciences, Geosciences, and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U. S. DOE. K. R. P. and W. L. P. supported by NSF Award No. IIA-143049. K.J. supported by the NSF-REU Grant No. PHYS-1461251.

Femtochemistry in the electronic ground state: Dynamic Stark control of vibrational dynamics

NASA Astrophysics Data System (ADS)

Shu, Chuan-Cun; Thomas, Esben F.; Henriksen, Niels E.

2017-09-01

We study the interplay of vibrational and rotational excitation in a diatomic molecule due to the non-resonant dynamic Stark effect. With a fixed peak intensity, optimal Gaussian pulse durations for maximizing vibrational or rotational transitions are obtained analytically and confirmed numerically for the H2 and Cl2 molecules. In general, pulse trains or more advanced pulse shaping techniques are required in order to obtain significant vibrational excitation. To that end, we demonstrate that a high degree of selectivity between vibrational and rotational excitation is possible with a suitably phase-modulated Gaussian pulse.

Phase-selective entrainment of nonlinear oscillator ensembles

DOE PAGES

Zlotnik, Anatoly V.; Nagao, Raphael; Kiss, Istvan Z.; ...

2016-03-18

The ability to organize and finely manipulate the hierarchy and timing of dynamic processes is important for understanding and influencing brain functions, sleep and metabolic cycles, and many other natural phenomena. However, establishing spatiotemporal structures in biological oscillator ensembles is a challenging task that requires controlling large collections of complex nonlinear dynamical units. In this report, we present a method to design entrainment signals that create stable phase patterns in ensembles of heterogeneous nonlinear oscillators without using state feedback information. We demonstrate the approach using experiments with electrochemical reactions on multielectrode arrays, in which we selectively assign ensemble subgroups intomore » spatiotemporal patterns with multiple phase clusters. As a result, the experimentally confirmed mechanism elucidates the connection between the phases and natural frequencies of a collection of dynamical elements, the spatial and temporal information that is encoded within this ensemble, and how external signals can be used to retrieve this information.« less

Phase-selective entrainment of nonlinear oscillator ensembles

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

Zlotnik, Anatoly V.; Nagao, Raphael; Kiss, Istvan Z.

The ability to organize and finely manipulate the hierarchy and timing of dynamic processes is important for understanding and influencing brain functions, sleep and metabolic cycles, and many other natural phenomena. However, establishing spatiotemporal structures in biological oscillator ensembles is a challenging task that requires controlling large collections of complex nonlinear dynamical units. In this report, we present a method to design entrainment signals that create stable phase patterns in ensembles of heterogeneous nonlinear oscillators without using state feedback information. We demonstrate the approach using experiments with electrochemical reactions on multielectrode arrays, in which we selectively assign ensemble subgroups intomore » spatiotemporal patterns with multiple phase clusters. As a result, the experimentally confirmed mechanism elucidates the connection between the phases and natural frequencies of a collection of dynamical elements, the spatial and temporal information that is encoded within this ensemble, and how external signals can be used to retrieve this information.« less

Phase-selective entrainment of nonlinear oscillator ensembles

NASA Astrophysics Data System (ADS)

Zlotnik, Anatoly; Nagao, Raphael; Kiss, István Z.; Li-Shin, Jr.

2016-03-01

The ability to organize and finely manipulate the hierarchy and timing of dynamic processes is important for understanding and influencing brain functions, sleep and metabolic cycles, and many other natural phenomena. However, establishing spatiotemporal structures in biological oscillator ensembles is a challenging task that requires controlling large collections of complex nonlinear dynamical units. In this report, we present a method to design entrainment signals that create stable phase patterns in ensembles of heterogeneous nonlinear oscillators without using state feedback information. We demonstrate the approach using experiments with electrochemical reactions on multielectrode arrays, in which we selectively assign ensemble subgroups into spatiotemporal patterns with multiple phase clusters. The experimentally confirmed mechanism elucidates the connection between the phases and natural frequencies of a collection of dynamical elements, the spatial and temporal information that is encoded within this ensemble, and how external signals can be used to retrieve this information.

The one-third law of evolutionary dynamics.

PubMed

Ohtsuki, Hisashi; Bordalo, Pedro; Nowak, Martin A

2007-11-21

Evolutionary game dynamics in finite populations provide a new framework for studying selection of traits with frequency-dependent fitness. Recently, a "one-third law" of evolutionary dynamics has been described, which states that strategy A fixates in a B-population with selective advantage if the fitness of A is greater than that of B when A has a frequency 13. This relationship holds for all evolutionary processes examined so far, from the Moran process to games on graphs. However, the origin of the "number"13 is not understood. In this paper we provide an intuitive explanation by studying the underlying stochastic processes. We find that in one invasion attempt, an individual interacts on average with B-players twice as often as with A-players, which yields the one-third law. We also show that the one-third law implies that the average Malthusian fitness of A is positive.

Cyberspace: A Selected Bibliography

DTIC Science & Technology

2013-05-01

Implications of the Private Sector’s Role in Cyber Conflict." Texas International Law Journal 47, no. 3 (Summer 2012): 617-640. ProQuest Lucas, George R...Cyberspace." Proceedings: United States Naval Institute 137, no. 2 (February 2011): 32-37. ProQuest Lin, Herbert . "Escalation Dynamics and Conflict...Harold Hongju. "International Law in Cyberspace." USCYBERCOM [United States Cyber Command] Inter-Agency Legal Conference, Ft. Meade , MD, September 18

Solid-state NMR on bacterial cells: selective cell wall signal enhancement and resolution improvement using dynamic nuclear polarization.

PubMed

Takahashi, Hiroki; Ayala, Isabel; Bardet, Michel; De Paëpe, Gaël; Simorre, Jean-Pierre; Hediger, Sabine

2013-04-03

Dynamic nuclear polarization (DNP) enhanced solid-state nuclear magnetic resonance (NMR) has recently emerged as a powerful technique for the study of material surfaces. In this study, we demonstrate its potential to investigate cell surface in intact cells. Using Bacillus subtilis bacterial cells as an example, it is shown that the polarizing agent 1-(TEMPO-4-oxy)-3-(TEMPO-4-amino)propan-2-ol (TOTAPOL) has a strong binding affinity to cell wall polymers (peptidoglycan). This particular interaction is thoroughly investigated with a systematic study on extracted cell wall materials, disrupted cells, and entire cells, which proved that TOTAPOL is mainly accumulating in the cell wall. This property is used on one hand to selectively enhance or suppress cell wall signals by controlling radical concentrations and on the other hand to improve spectral resolution by means of a difference spectrum. Comparing DNP-enhanced and conventional solid-state NMR, an absolute sensitivity ratio of 24 was obtained on the entire cell sample. This important increase in sensitivity together with the possibility of enhancing specifically cell wall signals and improving resolution really opens new avenues for the use of DNP-enhanced solid-state NMR as an on-cell investigation tool.

Elimination of spiral waves in a locally connected chaotic neural network by a dynamic phase space constraint.

PubMed

Li, Yang; Oku, Makito; He, Guoguang; Aihara, Kazuyuki

2017-04-01

In this study, a method is proposed that eliminates spiral waves in a locally connected chaotic neural network (CNN) under some simplified conditions, using a dynamic phase space constraint (DPSC) as a control method. In this method, a control signal is constructed from the feedback internal states of the neurons to detect phase singularities based on their amplitude reduction, before modulating a threshold value to truncate the refractory internal states of the neurons and terminate the spirals. Simulations showed that with appropriate parameter settings, the network was directed from a spiral wave state into either a plane wave (PW) state or a synchronized oscillation (SO) state, where the control vanished automatically and left the original CNN model unaltered. Each type of state had a characteristic oscillation frequency, where spiral wave states had the highest, and the intra-control dynamics was dominated by low-frequency components, thereby indicating slow adjustments to the state variables. In addition, the PW-inducing and SO-inducing control processes were distinct, where the former generally had longer durations but smaller average proportions of affected neurons in the network. Furthermore, variations in the control parameter allowed partial selectivity of the control results, which were accompanied by modulation of the control processes. The results of this study broaden the applicability of DPSC to chaos control and they may also facilitate the utilization of locally connected CNNs in memory retrieval and the exploration of traveling wave dynamics in biological neural networks. Copyright © 2017 Elsevier Ltd. All rights reserved.

Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways

PubMed Central

Chu, Wen-Ting; Chu, Xiakun; Wang, Jin

2017-01-01

The catalytic subunit of PKA (PKAc) exhibits three major conformational states (open, intermediate, and closed) during the biocatalysis process. Both ATP and substrate/inhibitor can effectively induce the conformational changes of PKAc from open to closed states. Aiming to explore the mechanism of this allosteric regulation, we developed a coarse-grained model and analyzed the dynamics of conformational changes of PKAc during binding by performing molecular dynamics simulations for apo PKAc, binary PKAc (PKAc with ATP, PKAc with PKI), and ternary PKAc (PKAc with ATP and PKI). Our results suggest a mixed binding mechanism of induced fit and conformational selection, with the induced fit dominant. The ligands can drive the movements of Gly-rich loop as well as some regions distal to the active site in PKAc and stabilize them at complex state. In addition, there are two parallel pathways (pathway with PKAc-ATP as an intermediate and pathway PKAc-PKI as an intermediate) during the transition from open to closed states. By molecular dynamics simulations and rate constant analyses, we find that the pathway through PKAc-ATP intermediate is the main binding route from open to closed state because of the fact that the bound PKI will hamper ATP from successful binding and significantly increase the barrier for the second binding subprocess. These findings will provide fundamental insights of the mechanisms of PKAc conformational change upon binding. PMID:28855336

Binding mechanism and dynamic conformational change of C subunit of PKA with different pathways.

PubMed

Chu, Wen-Ting; Chu, Xiakun; Wang, Jin

2017-09-19

The catalytic subunit of PKA (PKAc) exhibits three major conformational states (open, intermediate, and closed) during the biocatalysis process. Both ATP and substrate/inhibitor can effectively induce the conformational changes of PKAc from open to closed states. Aiming to explore the mechanism of this allosteric regulation, we developed a coarse-grained model and analyzed the dynamics of conformational changes of PKAc during binding by performing molecular dynamics simulations for apo PKAc, binary PKAc (PKAc with ATP, PKAc with PKI), and ternary PKAc (PKAc with ATP and PKI). Our results suggest a mixed binding mechanism of induced fit and conformational selection, with the induced fit dominant. The ligands can drive the movements of Gly-rich loop as well as some regions distal to the active site in PKAc and stabilize them at complex state. In addition, there are two parallel pathways (pathway with PKAc-ATP as an intermediate and pathway PKAc-PKI as an intermediate) during the transition from open to closed states. By molecular dynamics simulations and rate constant analyses, we find that the pathway through PKAc-ATP intermediate is the main binding route from open to closed state because of the fact that the bound PKI will hamper ATP from successful binding and significantly increase the barrier for the second binding subprocess. These findings will provide fundamental insights of the mechanisms of PKAc conformational change upon binding.

Information-theoretic model selection for optimal prediction of stochastic dynamical systems from data

NASA Astrophysics Data System (ADS)

Darmon, David

2018-03-01

In the absence of mechanistic or phenomenological models of real-world systems, data-driven models become necessary. The discovery of various embedding theorems in the 1980s and 1990s motivated a powerful set of tools for analyzing deterministic dynamical systems via delay-coordinate embeddings of observations of their component states. However, in many branches of science, the condition of operational determinism is not satisfied, and stochastic models must be brought to bear. For such stochastic models, the tool set developed for delay-coordinate embedding is no longer appropriate, and a new toolkit must be developed. We present an information-theoretic criterion, the negative log-predictive likelihood, for selecting the embedding dimension for a predictively optimal data-driven model of a stochastic dynamical system. We develop a nonparametric estimator for the negative log-predictive likelihood and compare its performance to a recently proposed criterion based on active information storage. Finally, we show how the output of the model selection procedure can be used to compare candidate predictors for a stochastic system to an information-theoretic lower bound.

Application of Spaceborne Scatterometer for Mapping Freeze-Thaw State in Northern Landscapes as a Measure of Ecological and Hydrological Processes

NASA Technical Reports Server (NTRS)

McDonald, Kyle; Kimball, John; Zimmermann, Reiner; Way, JoBea; Frolking, Steve; Running, Steve

1999-01-01

Landscape freeze/thaw transitions coincide with marked shifts in albedo, surface energy and mass exchange, and associated snow dynamics. Monitoring landscape freeze/thaw dynamics would improve our ability to quantify the interannual variability of boreal hydrology and river runoff/flood dynamics. The annual duration of frost-free period also bounds the period of photosynthetic activity in boreal and arctic regions thus affecting the annual carbon budget and the interannual variability of regional carbon fluxes. In this study, we use the NASA scatterometer (NSCAT) to monitor the temporal change in the radar backscatter signature across selected ecoregions of the boreal zone. We have measured vegetation tissue temperatures, soil temperature profiles, and micrometeorological parameters in situ at selected sites along a north-south transect extending across Alaska from Prudhoe Bay to the Kenai Peninsula and in Siberia near the Yenisey River. Data from these stations have been used to quantify the scatterometer's sensitivity to freeze/thaw state under a variety of terrain and landcover conditions. Analysis of the NSCAT temporal response over the 1997 spring thaw cycle shows a 3 to 5 dB change in measured backscatter that is well correlated with the landscape springtime thaw process. Having verified the instrument's capability to monitor freeze/thaw transitions, regional scale mosaicked data are applied to derive temporal series of freeze/thaw transition maps for selected circumpolar high latitude regions. These maps are applied to derive areal extent of frozen and thawed landscape and demonstrate the utility of spaceborne radar for operational monitoring of seasonal freeze-thaw dynamics and associated biophysical processes for the circumpolar high latitudes.

Model of a Frame of Dynamic Routing and Its Equilibrium

NASA Astrophysics Data System (ADS)

Zhang, Shu; Yuan, Yuan; Xu, Jian

Dynamic routing algorithm based on the shortest path principle is criticized due to the oscillation induced by such routing scheme. In the present work, we propose the model of TCP/RED algorithm by a new frame of dynamic routing, based on the measurement of occupation ratio of router buffer for different links, which only requires the information of the queue size at the buffer of the router, to stabilize the system. We classify several types of equilibrium and employ the numerical method to study the stability of the steady state. Our numerical results show that the careful selection of the parameters characterizing the dynamic routing algorithm can stabilize the system in some cases.

Selected Gravity Models in Terms of the fit to the GOCE Kinematic Orbit in the Dynamic Orbit Determination Process

NASA Astrophysics Data System (ADS)

Bobojć, Andrzej; Drożyner, Andrzej; Rzepecka, Zofia

2017-04-01

The work includes the comparison of performance of selected geopotential models in the dynamic orbit estimation of the satellite of the Gravity Field and Steady-State Ocean Circulation Explorer (GOCE) mission. This was realized by fitting estimated orbital arcs to the official centimeter-accuracy GOCE kinematic orbit which is provided by the European Space Agency. The Cartesian coordinates of kinematic orbit were treated as observations in the orbit estimation. The initial satellite state vector components were corrected in an iterative process with respect to the J2000.0 inertial reference frame using the given geopotential model, the models describing the remaining gravitational perturbations and the solar radiation pressure. Taking the obtained solutions into account, the RMS values of orbital residuals were computed. These residuals result from the difference between the determined orbit and the reference one - the GOCE kinematic orbit. The performance of selected gravity models was also determined using various orbital arc lengths. Additionally, the RMS fit values were obtained for some gravity models truncated at given degree and order of spherical harmonic coefficients. The advantage of using the kinematic orbit is its independence from any a priori dynamical models. For the research such GOCE-independent gravity models as HUST-Grace2016s, ITU_GRACE16, ITSG-Grace2014s, ITSG-Grace2014k, GGM05S, Tongji-GRACE01, ULUX_CHAMP2013S, ITG-GRACE2010S, EIGEN-51C, EIGEN5S, EGM2008 and EGM96 were adopted.

Isotopic and quantum-rovibrational-state effects for the ion-molecule reaction in the collision energy range of 0.03-10.00 eV.

PubMed

Xu, Yuntao; Xiong, Bo; Chang, Yih Chung; Ng, C Y

2017-03-29

We report detailed quantum-rovibrational-state-selected integral cross sections for the formation of H 3 O + via H-transfer (σ HT ) and H 2 DO + via D-transfer (σ DT ) from the reaction in the center-of-mass collision energy (E cm ) range of 0.03-10.00 eV, where (vvv) = (000), (100), and (020) and . The E cm inhibition and rotational enhancement observed for these reactions at E cm < 0.5 eV are generally consistent with those reported previously for H 2 O + + H 2 (D 2 ) reactions. However, in contrast to the vibrational inhibition observed for the latter reactions at low E cm < 0.5 eV, both the σ HT and σ DT for the H 2 O + + HD reaction are found to be enhanced by (100) vibrational excitation, which is not predicted by the current state-of-the-art theoretical dynamics calculations. Furthermore, the (100) vibrational enhancement for the H 2 O + + HD reaction is observed in the full E cm range of 0.03-10.00 eV. The fact that vibrational enhancement is only observed for the reaction of H 2 O + + HD, and not for H 2 O + + H 2 (D 2 ) reactions suggests that the asymmetry of HD may play a role in the reaction dynamics. In addition to the strong isotopic effect favoring the σ HT channel of the H 2 O + + HD reaction at low E cm < 0.5 eV, competition between the σ HT and σ DT of the H 2 O + + HD reaction is also observed at E cm = 0.3-10.0 eV. The present state-selected study of the H 2 O + + HD reaction, along with the previous studies of the H 2 O + + H 2 (D 2 ) reactions, clearly shows that the chemical reactivity of H 2 O + toward H 2 (HD, D 2 ) depends not only on E cm , but also on the rotational and vibrational states of H 2 O + (X 2 B 1 ). The detailed σ HT and σ DT values obtained here with single rovibrational-state selections of the reactant H 2 O + are expected to be valuable benchmarks for state-of-the-art theoretical calculations on the chemical dynamics of the title reaction.

Early Visual Cortex Dynamics during Top-Down Modulated Shifts of Feature-Selective Attention.

PubMed

Müller, Matthias M; Trautmann, Mireille; Keitel, Christian

2016-04-01

Shifting attention from one color to another color or from color to another feature dimension such as shape or orientation is imperative when searching for a certain object in a cluttered scene. Most attention models that emphasize feature-based selection implicitly assume that all shifts in feature-selective attention underlie identical temporal dynamics. Here, we recorded time courses of behavioral data and steady-state visual evoked potentials (SSVEPs), an objective electrophysiological measure of neural dynamics in early visual cortex to investigate temporal dynamics when participants shifted attention from color or orientation toward color or orientation, respectively. SSVEPs were elicited by four random dot kinematograms that flickered at different frequencies. Each random dot kinematogram was composed of dashes that uniquely combined two features from the dimensions color (red or blue) and orientation (slash or backslash). Participants were cued to attend to one feature (such as color or orientation) and respond to coherent motion targets of the to-be-attended feature. We found that shifts toward color occurred earlier after the shifting cue compared with shifts toward orientation, regardless of the original feature (i.e., color or orientation). This was paralleled in SSVEP amplitude modulations as well as in the time course of behavioral data. Overall, our results suggest different neural dynamics during shifts of attention from color and orientation and the respective shifting destinations, namely, either toward color or toward orientation.

International Education at Community Colleges: Themes, Practices, and Case Studies

ERIC Educational Resources Information Center

Latiner Raby, Rosalind, Ed.; Valeau, Edward J., Ed.

2016-01-01

This book brings together distinguished scholars, community college practitioners, and emerging leaders to expand upon existing theories, provide reflection on practice, and demonstrate the dynamic nature of community college internationalization. There is a special challenge for United States community colleges to move from selected international…

Fingerprints of electronic, spin and structural dynamics from resonant inelastic soft X-ray scattering in transient photo-chemical species

DOE PAGES

Norell, Jesper; Jay, Raphael M.; Hantschmann, Markus; ...

2018-02-20

Here, we describe how inversion symmetry separation of electronic state manifolds in resonant inelastic soft X-ray scattering (RIXS) can be applied to probe excited-state dynamics with compelling selectivity. In a case study of Fe L 3-edge RIXS in the ferricyanide complex Fe(CN) 6 3-, we demonstrate with multi-configurational restricted active space spectrum simulations how the information content of RIXS spectral fingerprints can be used to unambiguously separate species of different electronic configurations, spin multiplicities, and structures, with possible involvement in the decay dynamics of photo-excited ligand-to-metal charge-transfer. Specifically, we propose that this could be applied to confirm or reject themore » presence of a hitherto elusive transient Quartet species. Thus, RIXS offers a particular possibility to settle a recent controversy regarding the decay pathway, and we expect the technique to be similarly applicable in other model systems of photo-induced dynamics.« less

Fingerprints of electronic, spin and structural dynamics from resonant inelastic soft X-ray scattering in transient photo-chemical species

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

Norell, Jesper; Jay, Raphael M.; Hantschmann, Markus

Here, we describe how inversion symmetry separation of electronic state manifolds in resonant inelastic soft X-ray scattering (RIXS) can be applied to probe excited-state dynamics with compelling selectivity. In a case study of Fe L 3-edge RIXS in the ferricyanide complex Fe(CN) 6 3-, we demonstrate with multi-configurational restricted active space spectrum simulations how the information content of RIXS spectral fingerprints can be used to unambiguously separate species of different electronic configurations, spin multiplicities, and structures, with possible involvement in the decay dynamics of photo-excited ligand-to-metal charge-transfer. Specifically, we propose that this could be applied to confirm or reject themore » presence of a hitherto elusive transient Quartet species. Thus, RIXS offers a particular possibility to settle a recent controversy regarding the decay pathway, and we expect the technique to be similarly applicable in other model systems of photo-induced dynamics.« less

Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

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

Fischer, Sean A.; Aprà, Edoardo; Govind, Niranjan

2017-02-03

Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting withmore » a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.« less

Dynamic differentiation of GABAA-sensitive influences on orientation selectivity of complex cells in the cat striate cortex.

PubMed

Pfleger, B; Bonds, A B

1995-01-01

The influence of GABAA receptors on orientation selectivity of cat complex cells was tested by iontophoresis of the GABAA receptor blockers bicuculline and N-methyl-bicuculline while stimulating with drifting sinusoidal gratings. Reduction of orientation tuning was markedly less than reported in previous studies that used drifting bars as visual stimuli. Only 3/31 cells lost orientation selectivity, with an average increase in bandwidth of 33%, as opposed to half the cells losing selectivity and a bandwidth increase for the remainder of 47% as reported previously. Infusion of GABAA blockers revealed a prominent stimulus onset transient response, lasting about 120 ms, that showed a broadening of orientation selectivity comparable to that found using drifting bars under similar circumstances. We believe that drifting gratings emphasize a steady-state response component that retains, in the presence of GABAA blockers, significant orientation selectivity. Because the onset transient is initially unselective for orientation, we suggest that the steady-state, orientation-selective response component develops from an alternate inhibitory mechanism, possibly mediated by GABAB receptors.

A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2

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

Perez-Aguilar, Jose Manuel; Shan, Jufang; LeVine, Michael V.

With recent progress in determination of G protein-coupled receptor (GPCR) structure with crystallography, a variety of other experimental approaches (e.g., NMR spectroscopy, fluorescent-based assays, mass spectrometry techniques) are also being used to characterize state-specific and ligand-specific conformational states. MD simulations offer a powerful complementary approach to elucidate the dynamic features associated with ligand-specific GPCR conformations. To shed light on the conformational elements and dynamics of the important aspect of GPCR functional selectivity, we carried out unbiased microsecond-length MD simulations of the human serotonin 2A receptor (5-HT 2AR) in the absence of ligand and bound to four distinct serotonergic agonists. Themore » 5-HT 2AR is a suitable system to study the structural features involved in the ligand-dependent conformational heterogeneity of GPCRs because it is well-characterized experimentally and exhibits a strong agonist-specific phenotype in that some 5-HT 2AR agonists induce LSD-like hallucinations, while others lack this psychoactive property entirely. Here we report evidence for structural and dynamic differences in 5-HT 2AR interacting with such pharmacologically distinct ligands, hallucinogens, and nonhallucinogens obtained from all-atom MD simulations. Differential ligand binding contacts were identified for structurally similar hallucinogens and nonhallucinogens and found to correspond to different conformations in the intracellular loop 2 (ICL2). From the different ICL2 conformations, functional selective phenotypes are suggested through effects on dimerization and/or distinct direct interaction with effector proteins. Lastly, the findings are presented in the context of currently proposed hallucinogenesis mechanisms, and ICL2 is proposed as a fine-tuning selective switch that can differentiates modes of 5-HT 2AR activation.« less

A functional selectivity mechanism at the serotonin-2A GPCR involves ligand-dependent conformations of intracellular loop 2

DOE PAGES

Perez-Aguilar, Jose Manuel; Shan, Jufang; LeVine, Michael V.; ...

2014-10-14

With recent progress in determination of G protein-coupled receptor (GPCR) structure with crystallography, a variety of other experimental approaches (e.g., NMR spectroscopy, fluorescent-based assays, mass spectrometry techniques) are also being used to characterize state-specific and ligand-specific conformational states. MD simulations offer a powerful complementary approach to elucidate the dynamic features associated with ligand-specific GPCR conformations. To shed light on the conformational elements and dynamics of the important aspect of GPCR functional selectivity, we carried out unbiased microsecond-length MD simulations of the human serotonin 2A receptor (5-HT 2AR) in the absence of ligand and bound to four distinct serotonergic agonists. Themore » 5-HT 2AR is a suitable system to study the structural features involved in the ligand-dependent conformational heterogeneity of GPCRs because it is well-characterized experimentally and exhibits a strong agonist-specific phenotype in that some 5-HT 2AR agonists induce LSD-like hallucinations, while others lack this psychoactive property entirely. Here we report evidence for structural and dynamic differences in 5-HT 2AR interacting with such pharmacologically distinct ligands, hallucinogens, and nonhallucinogens obtained from all-atom MD simulations. Differential ligand binding contacts were identified for structurally similar hallucinogens and nonhallucinogens and found to correspond to different conformations in the intracellular loop 2 (ICL2). From the different ICL2 conformations, functional selective phenotypes are suggested through effects on dimerization and/or distinct direct interaction with effector proteins. Lastly, the findings are presented in the context of currently proposed hallucinogenesis mechanisms, and ICL2 is proposed as a fine-tuning selective switch that can differentiates modes of 5-HT 2AR activation.« less

A state space approach for piecewise-linear recurrent neural networks for identifying computational dynamics from neural measurements.

PubMed

Durstewitz, Daniel

2017-06-01

The computational and cognitive properties of neural systems are often thought to be implemented in terms of their (stochastic) network dynamics. Hence, recovering the system dynamics from experimentally observed neuronal time series, like multiple single-unit recordings or neuroimaging data, is an important step toward understanding its computations. Ideally, one would not only seek a (lower-dimensional) state space representation of the dynamics, but would wish to have access to its statistical properties and their generative equations for in-depth analysis. Recurrent neural networks (RNNs) are a computationally powerful and dynamically universal formal framework which has been extensively studied from both the computational and the dynamical systems perspective. Here we develop a semi-analytical maximum-likelihood estimation scheme for piecewise-linear RNNs (PLRNNs) within the statistical framework of state space models, which accounts for noise in both the underlying latent dynamics and the observation process. The Expectation-Maximization algorithm is used to infer the latent state distribution, through a global Laplace approximation, and the PLRNN parameters iteratively. After validating the procedure on toy examples, and using inference through particle filters for comparison, the approach is applied to multiple single-unit recordings from the rodent anterior cingulate cortex (ACC) obtained during performance of a classical working memory task, delayed alternation. Models estimated from kernel-smoothed spike time data were able to capture the essential computational dynamics underlying task performance, including stimulus-selective delay activity. The estimated models were rarely multi-stable, however, but rather were tuned to exhibit slow dynamics in the vicinity of a bifurcation point. In summary, the present work advances a semi-analytical (thus reasonably fast) maximum-likelihood estimation framework for PLRNNs that may enable to recover relevant aspects of the nonlinear dynamics underlying observed neuronal time series, and directly link these to computational properties.

Ecosystems and the Biosphere as Complex Adaptive Systems

NASA Technical Reports Server (NTRS)

Levin, Simon A.

1998-01-01

Ecosystems are prototypical examples of complex adaptive systems, in which patterns at higher levels emerge from localized interactions and selection processes acting at lower levels. An essential aspect of such systems is nonlinearity, leading to historical dependency and multiple possible outcomes of dynamics. Given this, it is essential to determine the degree to which system features are determined by environmental conditions, and the degree to which they are the result of self-organization. Furthermore, given the multiple levels at which dynamics become apparent and at which selection can act, central issues relate to how evolution shapes ecosystems properties, and whether ecosystems become buffered to changes (more resilient) over their ecological and evolutionary development or proceed to critical states and the edge of chaos.

Collective translational and rotational Monte Carlo cluster move for general pairwise interaction

NASA Astrophysics Data System (ADS)

Růžička, Štěpán; Allen, Michael P.

2014-09-01

Virtual move Monte Carlo is a cluster algorithm which was originally developed for strongly attractive colloidal, molecular, or atomistic systems in order to both approximate the collective dynamics and avoid sampling of unphysical kinetic traps. In this paper, we present the algorithm in the form, which selects the moving cluster through a wider class of virtual states and which is applicable to general pairwise interactions, including hard-core repulsion. The newly proposed way of selecting the cluster increases the acceptance probability by up to several orders of magnitude, especially for rotational moves. The results have their applications in simulations of systems interacting via anisotropic potentials both to enhance the sampling of the phase space and to approximate the dynamics.

Direct Visualization of Exciton Reequilibration in the LH1 and LH2 Complexes of Rhodobacter sphaeroides by Multipulse Spectroscopy

PubMed Central

Cohen Stuart, Thomas A.; Vengris, Mikas; Novoderezhkin, Vladimir I.; Cogdell, Richard J.; Hunter, C. Neil; van Grondelle, Rienk

2011-01-01

The dynamics of the excited states of the light-harvesting complexes LH1 and LH2 of Rhodobacter sphaeroides are governed, mainly, by the excitonic nature of these ring-systems. In a pump-dump-probe experiment, the first pulse promotes LH1 or LH2 to its excited state and the second pulse dumps a portion of the excited state. By selective dumping, we can disentangle the dynamics normally hidden in the excited-state manifold. We find that by using this multiple-excitation technique we can visualize a 400-fs reequilibration reflecting relaxation between the two lowest exciton states that cannot be directly explored by conventional pump-probe. An oscillatory feature is observed within the exciton reequilibration, which is attributed to a coherent motion of a vibrational wavepacket with a period of ∼150 fs. Our disordered exciton model allows a quantitative interpretation of the observed reequilibration processes occurring in these antennas. PMID:21539791

Direct visualization of exciton reequilibration in the LH1 and LH2 complexes of Rhodobacter sphaeroides by multipulse spectroscopy.

PubMed

Cohen Stuart, Thomas A; Vengris, Mikas; Novoderezhkin, Vladimir I; Cogdell, Richard J; Hunter, C Neil; van Grondelle, Rienk

2011-05-04

The dynamics of the excited states of the light-harvesting complexes LH1 and LH2 of Rhodobacter sphaeroides are governed, mainly, by the excitonic nature of these ring-systems. In a pump-dump-probe experiment, the first pulse promotes LH1 or LH2 to its excited state and the second pulse dumps a portion of the excited state. By selective dumping, we can disentangle the dynamics normally hidden in the excited-state manifold. We find that by using this multiple-excitation technique we can visualize a 400-fs reequilibration reflecting relaxation between the two lowest exciton states that cannot be directly explored by conventional pump-probe. An oscillatory feature is observed within the exciton reequilibration, which is attributed to a coherent motion of a vibrational wavepacket with a period of ∼150 fs. Our disordered exciton model allows a quantitative interpretation of the observed reequilibration processes occurring in these antennas. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Understanding the role of ecohydrological feedbacks in ecosystem state change in drylands

USGS Publications Warehouse

Turnbull, L.; Wilcox, B.P.; Belnap, J.; Ravi, S.; D'Odorico, P.; Childers, D.; Gwenzi, W.; Okin, G.; Wainwright, J.; Caylor, K.K.; Sankey, T.

2012-01-01

Ecohydrological feedbacks are likely to be critical for understanding the mechanisms by which changes in exogenous forces result in ecosystem state change. We propose that in drylands, the dynamics of ecosystem state change are determined by changes in the type (stabilizing vs amplifying) and strength of ecohydrological feedbacks following a change in exogenous forces. Using a selection of five case studies from drylands, we explore the characteristics of ecohydrological feedbacks and resulting dynamics of ecosystem state change. We surmise that stabilizing feedbacks are critical for the provision of plant-essential resources in drylands. Exogenous forces that break these stabilizing feedbacks can alter the state of the system, although such changes are potentially reversible if strong amplifying ecohydrological feedbacks do not develop. The case studies indicate that if amplifying ecohydrological feedbacks do develop, they are typically associated with abiotic processes such as runoff, erosion (by wind and water), and fire. These amplifying ecohydrological feedbacks progressively modify the system in ways that are long-lasting and possibly irreversible on human timescales.

Intelligent control of non-linear dynamical system based on the adaptive neurocontroller

NASA Astrophysics Data System (ADS)

Engel, E.; Kovalev, I. V.; Kobezhicov, V.

2015-10-01

This paper presents an adaptive neuro-controller for intelligent control of non-linear dynamical system. The formed as the fuzzy selective neural net the adaptive neuro-controller on the base of system's state, creates the effective control signal under random perturbations. The validity and advantages of the proposed adaptive neuro-controller are demonstrated by numerical simulations. The simulation results show that the proposed controller scheme achieves real-time control speed and the competitive performance, as compared to PID, fuzzy logic controllers.

Protonation of key acidic residues is critical for the K+-selectivity of the Na/K pump

PubMed Central

Yu, Haibo; Ratheal, Ian; Artigas, Pablo; Roux, Benoît

2011-01-01

The sodium-potassium (Na/K) pump is a P-type ATPase that generates Na+ and K+ concentration gradients across the cell membrane. For each ATP molecule, the pump extrudes three Na+ and imports two K+ by alternating between outward- and inward-facing conformations that preferentially bind K+ or Na+, respectively. Remarkably, the selective K+ and Na+ binding sites share several residues, and how the pump is able to achieve the selectivity required for the functional cycle is unclear. Here, free energy perturbation molecular dynamics (FEP/MD) simulations based on the crystal structures of the Na/K pump in a K+-loaded state (E2·Pi) reveal that protonation of the high-field acidic side-chains involved in the binding sites is critical to achieve the proper K+ selectivity. This prediction is tested with electrophysiological experiments showing that the selectivity of the E2P state for K+ over Na+ is affected by extracellular pH. PMID:21909093

Dissociative chemisorption of methane on metal surfaces: Tests of dynamical assumptions using quantum models and ab initio molecular dynamics

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

Jackson, Bret, E-mail: jackson@chem.umass.edu; Nattino, Francesco; Kroes, Geert-Jan

The dissociative chemisorption of methane on metal surfaces is of great practical and fundamental importance. Not only is it the rate-limiting step in the steam reforming of natural gas, the reaction exhibits interesting mode-selective behavior and a strong dependence on the temperature of the metal. We present a quantum model for this reaction on Ni(100) and Ni(111) surfaces based on the reaction path Hamiltonian. The dissociative sticking probabilities computed using this model agree well with available experimental data with regard to variation with incident energy, substrate temperature, and the vibrational state of the incident molecule. We significantly expand the vibrationalmore » basis set relative to earlier studies, which allows reaction probabilities to be calculated for doubly excited initial vibrational states, though it does not lead to appreciable changes in the reaction probabilities for singly excited initial states. Sudden models used to treat the center of mass motion parallel to the surface are compared with results from ab initio molecular dynamics and found to be reasonable. Similar comparisons for molecular rotation suggest that our rotationally adiabatic model is incorrect, and that sudden behavior is closer to reality. Such a model is proposed and tested. A model for predicting mode-selective behavior is tested, with mixed results, though we find it is consistent with experimental studies of normal vs. total (kinetic) energy scaling. Models for energy transfer into lattice vibrations are also examined.« less

Time series analyses of breathing patterns of lung cancer patients using nonlinear dynamical system theory.

PubMed

Tewatia, D K; Tolakanahalli, R P; Paliwal, B R; Tomé, W A

2011-04-07

The underlying requirements for successful implementation of any efficient tumour motion management strategy are regularity and reproducibility of a patient's breathing pattern. The physiological act of breathing is controlled by multiple nonlinear feedback and feed-forward couplings. It would therefore be appropriate to analyse the breathing pattern of lung cancer patients in the light of nonlinear dynamical system theory. The purpose of this paper is to analyse the one-dimensional respiratory time series of lung cancer patients based on nonlinear dynamics and delay coordinate state space embedding. It is very important to select a suitable pair of embedding dimension 'm' and time delay 'τ' when performing a state space reconstruction. Appropriate time delay and embedding dimension were obtained using well-established methods, namely mutual information and the false nearest neighbour method, respectively. Establishing stationarity and determinism in a given scalar time series is a prerequisite to demonstrating that the nonlinear dynamical system that gave rise to the scalar time series exhibits a sensitive dependence on initial conditions, i.e. is chaotic. Hence, once an appropriate state space embedding of the dynamical system has been reconstructed, we show that the time series of the nonlinear dynamical systems under study are both stationary and deterministic in nature. Once both criteria are established, we proceed to calculate the largest Lyapunov exponent (LLE), which is an invariant quantity under time delay embedding. The LLE for all 16 patients is positive, which along with stationarity and determinism establishes the fact that the time series of a lung cancer patient's breathing pattern is not random or irregular, but rather it is deterministic in nature albeit chaotic. These results indicate that chaotic characteristics exist in the respiratory waveform and techniques based on state space dynamics should be employed for tumour motion management.

A waved journal bearing concept with improved steady-state and dynamic performance

NASA Technical Reports Server (NTRS)

Dimofte, Florin

1994-01-01

Analysis of the waved journal bearing concept featuring a waved inner bearing diameter for use with a compressible lubricant (gas) is presented. A three wave, waved journal bearing geometry is used to show the geometry of this concept. The performance of generic waved bearings having either three, four, six, or eight waves is predicted for air lubricated bearings. Steady-state performance is discussed in terms of bearing load capacity, while the dynamic performance is discussed in terms of dynamic coefficients and fluid film stability. It was found that the bearing wave amplitude has an important influence on both steady-state and dynamic performance of the waved journal bearing. For a fixed eccentricity ratio, the bearing steady-state load capacity and direct dynamic stiffness coefficient increase as the wave amplitude increases. Also, the waved bearing becomes more stable as the wave amplitude increases. In addition, increasing the number of waves reduces the waved bearing's sensitivity to the direction of the applied load relative to the wave. However, the range in which the bearing performance can be varied decreases as the number of waves increases. Therefore, both the number and the amplitude of the waves must be properly selected to optimize the waved bearing design for a specific application. It is concluded that the stiffness of an air bearing, due to the hydrodynamic effect, could be doubled and made to run stably by using a six or eight wave geometry with a wave amplitude approximately half of the bearing radial clearance.

Quantum Dynamics Study of the Isotopic Effect on Capture Reactions: HD, D2 + CH3

NASA Technical Reports Server (NTRS)

Wang, Dunyou; Kwak, Dochan (Technical Monitor)

2002-01-01

Time-dependent wave-packet-propagation calculations are reported for the isotopic reactions, HD + CH3 and D2 + CH3, in six degrees of freedom and for zero total angular momentum. Initial state selected reaction probabilities for different initial rotational-vibrational states are presented in this study. This study shows that excitations of the HD(D2) enhances the reactivities; whereas the excitations of the CH3 umbrella mode have the opposite effects. This is consistent with the reaction of H2 + CH3. The comparison of these three isotopic reactions also shows the isotopic effects in the initial-state-selected reaction probabilities. The cumulative reaction probabilities (CRP) are obtained by summing over initial-state-selected reaction probabilities. The energy-shift approximation to account for the contribution of degrees of freedom missing in the six dimensionality calculation is employed to obtain approximate full-dimensional CRPs. The rate constant comparison shows H2 + CH3 reaction has the biggest reactivity, then HD + CH3, and D2 + CH3 has the smallest.

THE ROLE OF DEFAMILIALIZATION IN THE RELATIONSHIP BETWEEN PARTNERSHIP AND SELF-RATED HEALTH: A CROSS-NATIONAL COMPARISON OF CANADA AND THE UNITED STATES

PubMed Central

Quesnel-Vallée, Amélie; Clouston, Sean

2013-01-01

Partnered individuals live longer, healthier lives. It has been hypothesized that both social causation (partnership benefits) and health selection may explain this association. Since much of this literature is focused in the U.S., comparative studies of the potential impact of policy on the causation and selection components of this association have been scant. Using comparable data from the U.S. Panel Study of Income Dynamics and the Canadian Survey of Labour and Income Dynamics, we test the selective and causal relationships evident during entrance into partnership. We use fixed change-point analysis with multilevel models (MLM) to fit trajectories of change in both Canada and the U.S. to understand the role of both health selection and partnership benefits. In Canada, partnership benefits were evident, while health selection was only marginally significant. In the US, health selection was prominent in both men and women, but partnership benefits were not significant. We argue that the differences in the extent of defamilialization of social policy between the two countries may impact the way and extent to which people choose partners and benefit from those partnerships. PMID:22800920

Models of life: epigenetics, diversity and cycles.

PubMed

Sneppen, Kim

2017-04-01

This review emphasizes aspects of biology that can be understood through repeated applications of simple causal rules. The selected topics include perspectives on gene regulation, phage lambda development, epigenetics, microbial ecology, as well as model approaches to diversity and to punctuated equilibrium in evolution. Two outstanding features are repeatedly described. One is the minimal number of rules to sustain specific states of complex systems for a long time. The other is the collapse of such states and the subsequent dynamical cycle of situations that restitute the system to a potentially new metastable state.

Models of life: epigenetics, diversity and cycles

NASA Astrophysics Data System (ADS)

Sneppen, Kim

2017-04-01

This review emphasizes aspects of biology that can be understood through repeated applications of simple causal rules. The selected topics include perspectives on gene regulation, phage lambda development, epigenetics, microbial ecology, as well as model approaches to diversity and to punctuated equilibrium in evolution. Two outstanding features are repeatedly described. One is the minimal number of rules to sustain specific states of complex systems for a long time. The other is the collapse of such states and the subsequent dynamical cycle of situations that restitute the system to a potentially new metastable state.

Statistical State Dynamics Based Study of the Role of Nonlinearity in the Maintenance of Turbulence in Couette Flow

NASA Astrophysics Data System (ADS)

Farrell, Brian; Ioannou, Petros; Nikolaidis, Marios-Andreas

2017-11-01

While linear non-normality underlies the mechanism of energy transfer from the externally driven flow to the perturbation field, nonlinearity is also known to play an essential role in sustaining turbulence. We report a study based on the statistical state dynamics of Couette flow turbulence with the goal of better understanding the role of nonlinearity in sustaining turbulence. The statistical state dynamics implementations used are ensemble closures at second order in a cumulant expansion of the Navier-Stokes equations in which the averaging operator is the streamwise mean. Two fundamentally non-normal mechanisms potentially contributing to maintaining the second cumulant are identified. These are essentially parametric perturbation growth arising from interaction of the perturbations with the fluctuating mean flow and transient growth of perturbations arising from nonlinear interaction between components of the perturbation field. By the method of selectively including these mechanisms parametric growth is found to maintain the perturbation field in the turbulent state while the more commonly invoked mechanism associated with transient growth of perturbations arising from scattering by nonlinear interaction is found to suppress perturbation variance. Funded by ERC Coturb Madrid Summer Program and NSF AGS-1246929.

Exploring warm dense matter using quantum molecular dynamics

NASA Astrophysics Data System (ADS)

Clérouin, J.; Mazevet, S.

2006-06-01

For dense plasmas produced in shock experiments, the influence of the media on the isolated atomic properties can no longer be treated as a perturbation and conventional atomic physics approaches usually fail. Recently, quantum molecular dynamics (QMD) has been used to successfully predict static, dynamical and optical properties in this regime within the framework of a first principle method. In this short report, we illustrate the usefulness of the method for dense plasmas with a few selected examples: the equation of state of liquid deuterium, the electrical properties of expanded metals, the optical properties of shocked insulators, and the interaction of femto-second lasers with gold thin films.

Does social selection explain the association between state-level racial animus and racial disparities in self-rated health in the United States?

PubMed

McKetta, Sarah; Hatzenbuehler, Mark L; Pratt, Charissa; Bates, Lisa; Link, Bruce G; Keyes, Katherine M

2017-08-01

Racism, whether defined at individual, interpersonal, or structural levels, is associated with poor health among Blacks. This association may arise because exposure to racism causes poor health, but geographic mobility patterns pose an alternative explanation-namely, Black individuals with better health and resources can move away from racist environments. We examine the evidence for selection effects using nationally representative, longitudinal data (1990-2009) from the Panel Study on Income Dynamics (n = 33,852). We conceptualized state-level racial animus as an ecologic measure of racism and operationalized it as the percent of racially-charged Google search terms in each state. Among those who move out of state, Blacks reporting good self-rated health (SRH) are more likely to move to a state with less racial animus than Blacks reporting poor SRH (P = .01), providing evidence for at least some selection into environments with less racial animus. However, among Blacks who moved states, over 80% moved to a state within the same quartile of racial animus, and fewer than 5% resided in states with the lowest level of racial animus. Geographic mobility patterns are therefore likely to explain only a small part of the relationship between racial animus and SRH. These results require replication with alternative measures of racist attitudes and health outcomes. Copyright © 2017 Elsevier Inc. All rights reserved.

Bayesian switching factor analysis for estimating time-varying functional connectivity in fMRI.

PubMed

Taghia, Jalil; Ryali, Srikanth; Chen, Tianwen; Supekar, Kaustubh; Cai, Weidong; Menon, Vinod

2017-07-15

There is growing interest in understanding the dynamical properties of functional interactions between distributed brain regions. However, robust estimation of temporal dynamics from functional magnetic resonance imaging (fMRI) data remains challenging due to limitations in extant multivariate methods for modeling time-varying functional interactions between multiple brain areas. Here, we develop a Bayesian generative model for fMRI time-series within the framework of hidden Markov models (HMMs). The model is a dynamic variant of the static factor analysis model (Ghahramani and Beal, 2000). We refer to this model as Bayesian switching factor analysis (BSFA) as it integrates factor analysis into a generative HMM in a unified Bayesian framework. In BSFA, brain dynamic functional networks are represented by latent states which are learnt from the data. Crucially, BSFA is a generative model which estimates the temporal evolution of brain states and transition probabilities between states as a function of time. An attractive feature of BSFA is the automatic determination of the number of latent states via Bayesian model selection arising from penalization of excessively complex models. Key features of BSFA are validated using extensive simulations on carefully designed synthetic data. We further validate BSFA using fingerprint analysis of multisession resting-state fMRI data from the Human Connectome Project (HCP). Our results show that modeling temporal dependencies in the generative model of BSFA results in improved fingerprinting of individual participants. Finally, we apply BSFA to elucidate the dynamic functional organization of the salience, central-executive, and default mode networks-three core neurocognitive systems with central role in cognitive and affective information processing (Menon, 2011). Across two HCP sessions, we demonstrate a high level of dynamic interactions between these networks and determine that the salience network has the highest temporal flexibility among the three networks. Our proposed methods provide a novel and powerful generative model for investigating dynamic brain connectivity. Copyright © 2017 Elsevier Inc. All rights reserved.

Dynamic Data-Driven Reduced-Order Models of Macroscale Quantities for the Prediction of Equilibrium System State for Multiphase Porous Medium Systems

NASA Astrophysics Data System (ADS)

Talbot, C.; McClure, J. E.; Armstrong, R. T.; Mostaghimi, P.; Hu, Y.; Miller, C. T.

2017-12-01

Microscale simulation of multiphase flow in realistic, highly-resolved porous medium systems of a sufficient size to support macroscale evaluation is computationally demanding. Such approaches can, however, reveal the dynamic, steady, and equilibrium states of a system. We evaluate methods to utilize dynamic data to reduce the cost associated with modeling a steady or equilibrium state. We construct data-driven models using extensions to dynamic mode decomposition (DMD) and its connections to Koopman Operator Theory. DMD and its variants comprise a class of equation-free methods for dimensionality reduction of time-dependent nonlinear dynamical systems. DMD furnishes an explicit reduced representation of system states in terms of spatiotemporally varying modes with time-dependent oscillation frequencies and amplitudes. We use DMD to predict the steady and equilibrium macroscale state of a realistic two-fluid porous medium system imaged using micro-computed tomography (µCT) and simulated using the lattice Boltzmann method (LBM). We apply Koopman DMD to direct numerical simulation data resulting from simulations of multiphase fluid flow through a 1440x1440x4320 section of a full 1600x1600x5280 realization of imaged sandstone. We determine a representative set of system observables via dimensionality reduction techniques including linear and kernel principal component analysis. We demonstrate how this subset of macroscale quantities furnishes a representation of the time-evolution of the system in terms of dynamic modes, and discuss the selection of a subset of DMD modes yielding the optimal reduced model, as well as the time-dependence of the error in the predicted equilibrium value of each macroscale quantity. Finally, we describe how the above procedure, modified to incorporate methods from compressed sensing and random projection techniques, may be used in an online fashion to facilitate adaptive time-stepping and parsimonious storage of system states over time.

Brownian dynamics of self-regulated particles with additional degrees of freedom: Symmetry breaking and homochirality

NASA Astrophysics Data System (ADS)

Bhattacharyya, Debankur; Paul, Shibashis; Ghosh, Shyamolina; Ray, Deb Shankar

2018-04-01

We consider the Brownian motion of a collection of particles each with an additional degree of freedom. The degree of freedom of a particle (or, in general, a molecule) can assume distinct values corresponding to certain states or conformations. The time evolution of the additional degree of freedom of a particle is guided by those of its neighbors as well as the temperature of the system. We show that the local averaging over these degrees of freedom results in emergence of a collective order in the dynamics in the form of selection or dominance of one of the isomers leading to a symmetry-broken state. Our statistical model captures the basic features of homochirality, e.g., autocatalysis and chiral inhibition.

Are genetically robust regulatory networks dynamically different from random ones?

NASA Astrophysics Data System (ADS)

Sevim, Volkan; Rikvold, Per Arne

We study a genetic regulatory network model developed to demonstrate that genetic robustness can evolve through stabilizing selection for optimal phenotypes. We report preliminary results on whether such selection could result in a reorganization of the state space of the system. For the chosen parameters, the evolution moves the system slightly toward the more ordered part of the phase diagram. We also find that strong memory effects cause the Derrida annealed approximation to give erroneous predictions about the model's phase diagram.

Nonadiabatic dynamics of O(1D) + N2(X1Σg+) → O(3P) + N2(X1Σg+) on three coupled potential surfaces: symmetry, Coriolis, spin-orbit, and Renner-Teller effects.

PubMed

Defazio, Paolo; Gamallo, Pablo; Petrongolo, Carlo

2012-02-07

We present the spin-orbit (SO) and Renner-Teller (RT) quantum dynamics of the spin-forbidden quenching O((1)D) + N(2)(X(1)Σ(g)(+)) → O((3)P) + N(2)(X(1)Σ(g)(+)) on the N(2)O X(1)A', ã(3)A", and b(3)A' coupled PESs. We use the permutation-inversion symmetry, propagate coupled-channel (CC) real wavepackets, and compute initial-state-resolved probabilities and cross sections σ(j(0)) for the ground vibrational and the first two rotational states of N(2), j(0) = 0 and 1. Labeling symmetry angular states by j and K, we report selection rules for j and for the minimum K value associated with any electronic state, showing that ã(3)A" is uncoupled in the centrifugal-sudden (CS) approximation at j(0) = 0. The dynamics is resonance-dominated, the probabilities are larger at low K, σ(j(0)) decrease with the collision energy and increase with j(0), and the CS σ(0) is lower than the CC one. The nonadiabatic interactions play different roles on the quenching dynamics, because the X(1)A'-b(3)A' SO effects are those most important while the ã(3)A"-b(3)A' RT ones are negligible.

Understanding the Differential Selectivity of Arrestins toward the Phosphorylation State of the Receptor.

PubMed

Sensoy, Ozge; Moreira, Irina S; Morra, Giulia

2016-09-21

Proteins in the arrestin family exhibit a conserved structural fold that nevertheless allows for significant differences in their selectivity for G-protein coupled receptors (GPCRs) and their phosphorylation states. To reveal the mechanism of activation that prepares arrestin for selective interaction with GPCRs, and to understand the basis for these differences, we used unbiased molecular dynamics simulations to compare the structural and dynamic properties of wild type Arr1 (Arr1-WT), Arr3 (Arr3-WT), and a constitutively active Arr1 mutant, Arr1-R175E, characterized by a perturbation of the phosphate recognition region called "polar core". We find that in our simulations the mutant evolves toward a conformation that resembles the known preactivated structures of an Arr1 splice-variant, and the structurally similar phosphopeptide-bound Arr2-WT, while this does not happen for Arr1-WT. Hence, we propose an activation allosteric mechanism connecting the perturbation of the polar core to a global conformational change, including the relative reorientation of N- and C-domains, and the emergence of electrostatic properties of putative binding surfaces. The underlying local structural changes are interpreted as markers of the evolution of an arrestin structure toward an active-like conformation. Similar activation related changes occur in Arr3-WT in the absence of any perturbation of the polar core, suggesting that this system could spontaneously visit preactivated states in solution. This hypothesis is proposed to explain the lower selectivity of Arr3 toward nonphosphorylated receptors. Moreover, by elucidating the allosteric mechanism underlying activation, we identify functionally critical regions on arrestin structure that can be targeted with drugs or chemical tools for functional modulation.

Dynamic State Estimation of Terrestrial and Solar Plasmas

NASA Astrophysics Data System (ADS)

Kamalabadi, Farzad

A pervasive problem in virtually all branches of space science is the estimation of multi-dimensional state parameters of a dynamical system from a collection of indirect, often incomplete, and imprecise measurements. Subsequent scientific inference is predicated on rigorous analysis, interpretation, and understanding of physical observations and on the reliability of the associated quantitative statistical bounds and performance characteristics of the algorithms used. In this work, we focus on these dynamic state estimation problems and illustrate their importance in the context of two timely activities in space remote sensing. First, we discuss the estimation of multi-dimensional ionospheric state parameters from UV spectral imaging measurements anticipated to be acquired the recently selected NASA Heliophysics mission, Ionospheric Connection Explorer (ICON). Next, we illustrate that similar state-space formulations provide the means for the estimation of 3D, time-dependent densities and temperatures in the solar corona from a series of white-light and EUV measurements. We demonstrate that, while a general framework for the stochastic formulation of the state estimation problem is suited for systematic inference of the parameters of a hidden Markov process, several challenges must be addressed in the assimilation of an increasing volume and diversity of space observations. These challenges are: (1) the computational tractability when faced with voluminous and multimodal data, (2) the inherent limitations of the underlying models which assume, often incorrectly, linear dynamics and Gaussian noise, and (3) the unavailability or inaccuracy of transition probabilities and noise statistics. We argue that pursuing answers to these questions necessitates cross-disciplinary research that enables progress toward systematically reconciling observational and theoretical understanding of the space environment.

Experimental Insights into Ground-State Selection of Quantum XY Pyrochlores

NASA Astrophysics Data System (ADS)

Hallas, Alannah M.; Gaudet, Jonathan; Gaulin, Bruce D.

2018-03-01

Extensive experimental investigations of the magnetic structures and excitations in the XY pyrochlores have been carried out over the past decade. Three families of XY pyrochlores have emerged: Yb2B2O7, Er2B2O7, and, most recently, [Formula: see text]Co2F7. In each case, the magnetic cation (either Yb, Er, or Co) exhibits XY anisotropy within the local pyrochlore coordinates, a consequence of crystal field effects. Materials in these families display rich phase behavior and are candidates for exotic ground states, such as quantum spin ice, and exotic ground-state selection via order-by-disorder mechanisms. In this review, we present an experimental summary of the ground-state properties of the XY pyrochlores, including evidence that they are strongly influenced by phase competition. We empirically demonstrate the signatures for phase competition in a frustrated magnet: multiple heat capacity anomalies, suppressed TN or TC, sample- and pressure-dependent ground states, and unconventional spin dynamics.

Brain State Is a Major Factor in Preseizure Hippocampal Network Activity and Influences Success of Seizure Intervention

PubMed Central

Ewell, Laura A.; Liang, Liang; Armstrong, Caren; Soltész, Ivan; Leutgeb, Stefan

2015-01-01

Neural dynamics preceding seizures are of interest because they may shed light on mechanisms of seizure generation and could be predictive. In healthy animals, hippocampal network activity is shaped by behavioral brain state and, in epilepsy, seizures selectively emerge during specific brain states. To determine the degree to which changes in network dynamics before seizure are pathological or reflect ongoing fluctuations in brain state, dorsal hippocampal neurons were recorded during spontaneous seizures in a rat model of temporal lobe epilepsy. Seizures emerged from all brain states, but with a greater likelihood after REM sleep, potentially due to an observed increase in baseline excitability during periods of REM compared with other brains states also characterized by sustained theta oscillations. When comparing the firing patterns of the same neurons across brain states associated with and without seizures, activity dynamics before seizures followed patterns typical of the ongoing brain state, or brain state transitions, and did not differ until the onset of the electrographic seizure. Next, we tested whether disparate activity patterns during distinct brain states would influence the effectiveness of optogenetic curtailment of hippocampal seizures in a mouse model of temporal lobe epilepsy. Optogenetic curtailment was significantly more effective for seizures preceded by non-theta states compared with seizures that emerged from theta states. Our results indicate that consideration of behavioral brain state preceding a seizure is important for the appropriate interpretation of network dynamics leading up to a seizure and for designing effective seizure intervention. SIGNIFICANCE STATEMENT Hippocampal single-unit activity is strongly shaped by behavioral brain state, yet this relationship has been largely ignored when studying activity dynamics before spontaneous seizures in medial temporal lobe epilepsy. In light of the increased attention on using single-unit activity for the prediction of seizure onset and closed-loop seizure intervention, we show a need for monitoring brain state to interpret correctly whether changes in neural activity before seizure onset is pathological or normal. Moreover, we also find that the brain state preceding a seizure determines the success of therapeutic interventions to curtail seizure duration. Together, these findings suggest that seizure prediction and intervention will be more successful if tailored for the specific brain states from which seizures emerge. PMID:26609157

Opinion formation models in static and dynamic social networks

NASA Astrophysics Data System (ADS)

Singh, Pramesh

We study models of opinion formation on static as well as dynamic networks where interaction among individuals is governed by widely accepted social theories. In particular, three models of competing opinions based on distinct interaction mechanisms are studied. A common feature in all of these models is the existence of a tipping point in terms of a model parameter beyond which a rapid consensus is reached. In the first model that we study on a static network, a node adopts a particular state (opinion) if a threshold fraction of its neighbors are already in that state. We introduce a few initiator nodes which are in state '1' in a population where every node is in state '0'. Thus, opinion '1' spreads through the population until no further influence is possible. Size of the spread is greatly affected by how these initiator nodes are selected. We find that there exists a critical fraction of initiators pc that is needed to trigger global cascades for a given threshold phi. We also study heuristic strategies for selecting a set of initiator nodes in order to maximize the cascade size. The structural properties of networks also play an important role in the spreading process. We study how the dynamics is affected by changing the clustering in a network. It turns out that local clustering is helpful in spreading. Next, we studied a model where the network is dynamic and interactions are homophilic. We find that homophily-driven rewiring impedes the reaching of consensus and in the absence of committed nodes (nodes that are not influenceable on their opinion), consensus time Tc diverges exponentially with network size N . As we introduce a fraction of committed nodes, beyond a critical value, the scaling of Tc becomes logarithmic in N. We also find that slight change in the interaction rule can produce strikingly different scaling behaviors of T c . However, introducing committed agents in the system drastically improves the scaling of the consensus time regardless of the interaction rules considered. Finally, a three-state (leftist, rightist, centrist) model that couples the dynamics of social balance with an external deradicalizing field is studied. The mean-field analysis shows that for a weak external field, the system exhibits a metastable fixed point and a saddle point in addition to a stable fixed point. However, if the strength of the external field is sufficiently large (larger than a critical value), there is only one (stable) fixed point which corresponds to an all-centrist consensus state (absorbing state). In the weak-field regime, the convergence time to the absorbing state is evaluated using the quasi-stationary(QS) distribution and is found to be in good agreement with the results obtained by numerical simulations.

Female mating preferences determine system-level evolution in a gene network model.

PubMed

Fierst, Janna L

2013-06-01

Environmental patterns of directional, stabilizing and fluctuating selection can influence the evolution of system-level properties like evolvability and mutational robustness. Intersexual selection produces strong phenotypic selection and these dynamics may also affect the response to mutation and the potential for future adaptation. In order to to assess the influence of mating preferences on these evolutionary properties, I modeled a male trait and female preference determined by separate gene regulatory networks. I studied three sexual selection scenarios: sexual conflict, a Gaussian model of the Fisher process described in Lande (in Proc Natl Acad Sci 78(6):3721-3725, 1981) and a good genes model in which the male trait signalled his mutational condition. I measured the effects these mating preferences had on the potential for traits and preferences to evolve towards new states, and mutational robustness of both the phenotype and the individual's overall viability. All types of sexual selection increased male phenotypic robustness relative to a randomly mating population. The Fisher model also reduced male evolvability and mutational robustness for viability. Under good genes sexual selection, males evolved an increased mutational robustness for viability. Females choosing their mates is a scenario that is sufficient to create selective forces that impact genetic evolution and shape the evolutionary response to mutation and environmental selection. These dynamics will inevitably develop in any population where sexual selection is operating, and affect the potential for future adaptation.

Rural and Small School Principal Candidates: Perspectives of Hiring Superintendents

ERIC Educational Resources Information Center

Cruzeiro, Patricia A.; Boone, Mike

2009-01-01

This article reports the results of an inquiry into the dynamics of principal selection in rural school districts in two mid-American states with high numbers of rural schools. The study focuses on two questions: (1) are rural school districts experiencing a shortage of qualified applicants for vacant principal's positions; and (2) what…

Selecting, Preparing and Developing the School District Superintendent.

ERIC Educational Resources Information Center

Carter, David S. G.; And Others

Although there are about 15,000 school districts in the United States, each headed by a superintendent, research on the superintendency has not been systematic and dynamic. This book presents a synthesis of research on the superintendency. Chapters include the following: (1) "Smoke, Mirrors, or Reality: Another Instructional Leader" (Shirley M.…

Convergence analysis of sliding mode trajectories in multi-objective neural networks learning.

PubMed

Costa, Marcelo Azevedo; Braga, Antonio Padua; de Menezes, Benjamin Rodrigues

2012-09-01

The Pareto-optimality concept is used in this paper in order to represent a constrained set of solutions that are able to trade-off the two main objective functions involved in neural networks supervised learning: data-set error and network complexity. The neural network is described as a dynamic system having error and complexity as its state variables and learning is presented as a process of controlling a learning trajectory in the resulting state space. In order to control the trajectories, sliding mode dynamics is imposed to the network. It is shown that arbitrary learning trajectories can be achieved by maintaining the sliding mode gains within their convergence intervals. Formal proofs of convergence conditions are therefore presented. The concept of trajectory learning presented in this paper goes further beyond the selection of a final state in the Pareto set, since it can be reached through different trajectories and states in the trajectory can be assessed individually against an additional objective function. Copyright © 2012 Elsevier Ltd. All rights reserved.

Quantum Dynamics Scattering Study of AB+CDE Reactions: A Seven Dimensional Treatment for the H2+C2H Reaction

NASA Technical Reports Server (NTRS)

Wang, Dunyou

2003-01-01

A time-dependent wave-packet approach is presented for the quantum dynamics study of the AB+CDE reaction system for zero total angular momentum. A seven-degree-of-freedom calculation is employed to study the chemical reaction of H2+C2H yields H + C2H2 by treating C2H as a linear molecule. Initial state selected reaction probabilities are presented for various initial ro-vibrational states. This study shows that vibrational excitation of H2 enhances the reaction probability, whereas the excitation of C2H has only a small effect on the reactivity. An integral cross section is also reported for the initial ground states of H2 and C2H. The theoretical and experimental results agree with each other very well when the calculated seven dimensional results are adjusted to account for the lower transition state barrier heights found in recent ab initio calculations.

Non-radiative relaxation of photoexcited chlorophylls: Theoretical and experimental study

DOE PAGES

Bricker, William P.; Shenai, Prathamesh M.; Ghosh, Avishek; ...

2015-09-08

Nonradiative relaxation of high-energy excited states to the lowest excited state in chlorophylls marks the first step in the process of photosynthesis. We perform ultrafast transient absorption spectroscopy measurements, that reveal this internal conversion dynamics to be slightly slower in chlorophyll B than in chlorophyll A. With modeling this process, non-adiabatic excited state molecular dynamics simulations uncovers a critical role played by the different side groups in the two molecules in governing the intramolecular redistribution of excited state wavefunction, leading, in turn, to different time-scales. Even given smaller electron-vibrational couplings compared to common organic conjugated chromophores, these molecules are ablemore » to efficiently dissipate about 1 eV of electronic energy into heat on the timescale of around 200 fs. This is achieved via selective participation of specific atomic groups and complex global migration of the wavefunction from the outer to inner ring, which may have important implications for biological light-harvesting function.« less

Optically modulated fluorescence bioimaging: visualizing obscured fluorophores in high background.

PubMed

Hsiang, Jung-Cheng; Jablonski, Amy E; Dickson, Robert M

2014-05-20

Fluorescence microscopy and detection have become indispensible for understanding organization and dynamics in biological systems. Novel fluorophores with improved brightness, photostability, and biocompatibility continue to fuel further advances but often rely on having minimal background. The visualization of interactions in very high biological background, especially for proteins or bound complexes at very low copy numbers, remains a primary challenge. Instead of focusing on molecular brightness of fluorophores, we have adapted the principles of high-sensitivity absorption spectroscopy to improve the sensitivity and signal discrimination in fluorescence bioimaging. Utilizing very long wavelength transient absorptions of kinetically trapped dark states, we employ molecular modulation schemes that do not simultaneously modulate the background fluorescence. This improves the sensitivity and ease of implementation over high-energy photoswitch-based recovery schemes, as no internal dye reference or nanoparticle-based fluorophores are needed to separate the desired signals from background. In this Account, we describe the selection process for and identification of fluorophores that enable optically modulated fluorescence to decrease obscuring background. Differing from thermally stable photoswitches using higher-energy secondary lasers, coillumination at very low energies depopulates transient dark states, dynamically altering the fluorescence and giving characteristic modulation time scales for each modulatable emitter. This process is termed synchronously amplified fluorescence image recovery (SAFIRe) microscopy. By understanding and optically controlling the dye photophysics, we selectively modulate desired fluorophore signals independent of all autofluorescent background. This shifts the fluorescence of interest to unique detection frequencies with nearly shot-noise-limited detection, as no background signals are collected. Although the fluorescence brightness is improved slightly, SAFIRe yields up to 100-fold improved signal visibility by essentially removing obscuring, unmodulated background (Richards, C. I.; J. Am. Chem. Soc. 2009, 131, 4619). While SAFIRe exhibits a wide, linear dynamic range, we have demonstrated single-molecule signal recovery buried within 200 nM obscuring dye. In addition to enabling signal recovery through background reduction, each dye exhibits a characteristic modulation frequency indicative of its photophysical dynamics. Thus, these characteristic time scales offer opportunities not only to expand the dimensionality of fluorescence imaging by using dark-state lifetimes but also to distinguish the dynamics of subpopulations on the basis of photophysical versus diffusional time scales, even within modulatable populations. The continued development of modulation for signal recovery and observation of biological dynamics holds great promise for studying a range of transient biological phenomena in natural environments. Through the development of a wide range of fluorescent proteins, organic dyes, and inorganic emitters that exhibit significant dark-state populations under steady-state illumination, we can drastically expand the applicability of fluorescence imaging to probe lower-abundance complexes and their dynamics.

The molecular and mathematical basis of Waddington's epigenetic landscape: a framework for post-Darwinian biology?

PubMed

Huang, Sui

2012-02-01

The Neo-Darwinian concept of natural selection is plausible when one assumes a straightforward causation of phenotype by genotype. However, such simple 1:1 mapping must now give place to the modern concepts of gene regulatory networks and gene expression noise. Both can, in the absence of genetic mutations, jointly generate a diversity of inheritable randomly occupied phenotypic states that could also serve as a substrate for natural selection. This form of epigenetic dynamics challenges Neo-Darwinism. It needs to incorporate the non-linear, stochastic dynamics of gene networks. A first step is to consider the mathematical correspondence between gene regulatory networks and Waddington's metaphoric 'epigenetic landscape', which actually represents the quasi-potential function of global network dynamics. It explains the coexistence of multiple stable phenotypes within one genotype. The landscape's topography with its attractors is shaped by evolution through mutational re-wiring of regulatory interactions - offering a link between genetic mutation and sudden, broad evolutionary changes. Copyright © 2012 WILEY Periodicals, Inc.

Stable and Dynamic Coding for Working Memory in Primate Prefrontal Cortex

PubMed Central

Watanabe, Kei; Funahashi, Shintaro; Stokes, Mark G.

2017-01-01

Working memory (WM) provides the stability necessary for high-level cognition. Influential theories typically assume that WM depends on the persistence of stable neural representations, yet increasing evidence suggests that neural states are highly dynamic. Here we apply multivariate pattern analysis to explore the population dynamics in primate lateral prefrontal cortex (PFC) during three variants of the classic memory-guided saccade task (recorded in four animals). We observed the hallmark of dynamic population coding across key phases of a working memory task: sensory processing, memory encoding, and response execution. Throughout both these dynamic epochs and the memory delay period, however, the neural representational geometry remained stable. We identified two characteristics that jointly explain these dynamics: (1) time-varying changes in the subpopulation of neurons coding for task variables (i.e., dynamic subpopulations); and (2) time-varying selectivity within neurons (i.e., dynamic selectivity). These results indicate that even in a very simple memory-guided saccade task, PFC neurons display complex dynamics to support stable representations for WM. SIGNIFICANCE STATEMENT Flexible, intelligent behavior requires the maintenance and manipulation of incoming information over various time spans. For short time spans, this faculty is labeled “working memory” (WM). Dominant models propose that WM is maintained by stable, persistent patterns of neural activity in prefrontal cortex (PFC). However, recent evidence suggests that neural activity in PFC is dynamic, even while the contents of WM remain stably represented. Here, we explored the neural dynamics in PFC during a memory-guided saccade task. We found evidence for dynamic population coding in various task epochs, despite striking stability in the neural representational geometry of WM. Furthermore, we identified two distinct cellular mechanisms that contribute to dynamic population coding. PMID:28559375

Dynamics at Conical Intersections

NASA Astrophysics Data System (ADS)

Schuurman, Michael S.; Stolow, Albert

2018-04-01

The nonadiabatic coupling of electronic and vibrational degrees of freedom is the defining feature of electronically excited states of polyatomic molecules. Once considered a theoretical curiosity, conical intersections (CIs) are now generally accepted as being the dominant source of coupled charge and vibrational energy flow in molecular excited states. Passage through CIs leads to the conversion of electronic to vibrational energy, which drives the ensuing photochemistry, isomerization being a canonical example. It has often been remarked that the CI may be thought of as a transition state in the excited state. As such, we expect that both the direction and the velocity of approach to the CI will matter. We explore this suggestion by looking for dynamical aspects of passage through CIs and for analogies with well-known concepts from ground-state reaction dynamics. Great progress has been made in the development of both experimental techniques and ab initio dynamics simulations, to a degree that direct comparisons may now be made. Here we compare time-resolved photoelectron spectroscopy results with on-the-fly ab initio multiple spawning calculations of the experimental observables, thereby validating each. We adopt a phenomenological approach and specifically concentrate on the excited-state dynamics of the C=C bond in unsaturated hydrocarbons. In particular, we make use of selective chemical substitution (such as replacing an H atom by a methyl group) so as to alter the inertia of certain vibrations relative to others, thus systematically varying (mass-weighted) directions and velocities of approach to a CI. Chemical substituents, however, may affect both the nuclear and electronic components of the total wave function. The former, which we call an inertial effect, influences the direction and velocity of approach. The latter, which we call a potential effect, modifies the electronic structure and therefore the energetic location and topography of the potential energy surfaces involved. Using a series of examples, we discuss both types of effects. We argue that there is a need for dynamical pictures and simple models of nonadiabatic dynamics at CIs and hope that the phenomenology presented here will help inspire such developments.

Bayesian Inference of High-Dimensional Dynamical Ocean Models

NASA Astrophysics Data System (ADS)

Lin, J.; Lermusiaux, P. F. J.; Lolla, S. V. T.; Gupta, A.; Haley, P. J., Jr.

2015-12-01

This presentation addresses a holistic set of challenges in high-dimension ocean Bayesian nonlinear estimation: i) predict the probability distribution functions (pdfs) of large nonlinear dynamical systems using stochastic partial differential equations (PDEs); ii) assimilate data using Bayes' law with these pdfs; iii) predict the future data that optimally reduce uncertainties; and (iv) rank the known and learn the new model formulations themselves. Overall, we allow the joint inference of the state, equations, geometry, boundary conditions and initial conditions of dynamical models. Examples are provided for time-dependent fluid and ocean flows, including cavity, double-gyre and Strait flows with jets and eddies. The Bayesian model inference, based on limited observations, is illustrated first by the estimation of obstacle shapes and positions in fluid flows. Next, the Bayesian inference of biogeochemical reaction equations and of their states and parameters is presented, illustrating how PDE-based machine learning can rigorously guide the selection and discovery of complex ecosystem models. Finally, the inference of multiscale bottom gravity current dynamics is illustrated, motivated in part by classic overflows and dense water formation sites and their relevance to climate monitoring and dynamics. This is joint work with our MSEAS group at MIT.

The dynamics of surface-catalyzed reactions studied by infrared chemiluminescence of the CO and CO{sub 2} products

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

Watanabe, K.; Uetsuka, H.; Ohnuma, H.

The infrared chemiluminescence technique has been applied to the selective formation of syngas (CO + H{sub 2}) from the oxidation of small alkanes on Pt, the decomposition and oxidation of CH{sub 3}OH and HCOOH on Pt and Ni, and CO oxidation on Pd(111) and Pd(110). The different internal (vibrational and rotational) energy states of the CO and CO{sub 2} products have been observed, which reflect the difference in the dynamics of these reactions.

Ultrafast Independent N-H and N-C Bond Deformation Investigated with Resonant Inelastic X-Ray Scattering

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

Eckert, Sebastian; Norell, Jesper; Miedema, Piter S.

Here, the femtosecond excited-state dynamics following resonant photoexcitation enable the selective deformation of N-H and N-C chemical bonds in 2-thiopyridone in aqueous solution with optical or X-ray pulses. In combination with multiconfigurational quantum-chemical calculations, the orbital-specific electronic structure and its ultrafast dynamics accessed with resonant inelastic X-ray scattering at the N 1s level using synchrotron radiation and the soft X-ray free-electron laser LCLS provide direct evidence for this controlled photoinduced molecular deformation and its ultrashort timescale.

Ultrafast Independent N-H and N-C Bond Deformation Investigated with Resonant Inelastic X-Ray Scattering

DOE PAGES

Eckert, Sebastian; Norell, Jesper; Miedema, Piter S.; ...

2017-04-04

Here, the femtosecond excited-state dynamics following resonant photoexcitation enable the selective deformation of N-H and N-C chemical bonds in 2-thiopyridone in aqueous solution with optical or X-ray pulses. In combination with multiconfigurational quantum-chemical calculations, the orbital-specific electronic structure and its ultrafast dynamics accessed with resonant inelastic X-ray scattering at the N 1s level using synchrotron radiation and the soft X-ray free-electron laser LCLS provide direct evidence for this controlled photoinduced molecular deformation and its ultrashort timescale.

Representing and selecting vibrational angular momentum states for quasiclassical trajectory chemical dynamics simulations.

PubMed

Lourderaj, Upakarasamy; Martínez-Núñez, Emilio; Hase, William L

2007-10-18

Linear molecules with degenerate bending modes have states, which may be represented by the quantum numbers N and L. The former gives the total energy for these modes and the latter identifies their vibrational angular momentum jz. In this work, the classical mechanical analog of the N,L-quantum states is reviewed, and an algorithm is presented for selecting initial conditions for these states in quasiclassical trajectory chemical dynamics simulations. The algorithm is illustrated by choosing initial conditions for the N = 3 and L = 3 and 1 states of CO2. Applications of this algorithm are considered for initial conditions without and with zero-point energy (zpe) included in the vibrational angular momentum states and the C-O stretching modes. The O-atom motions in the x,y-plane are determined for these states from classical trajectories in Cartesian coordinates and are compared with the motion predicted by the normal-mode model. They are only in agreement for the N = L = 3 state without vibrational angular momentum zpe. For the remaining states, the Cartesian O-atom motions are considerably different from the elliptical motion predicted by the normal-mode model. This arises from bend-stretch coupling, including centrifugal distortion, in the Cartesian trajectories, which results in tubular instead of elliptical motion. Including zpe in the C-O stretch modes introduces considerable complexity into the O-atom motions for the vibrational angular momentum states. The short-time O-atom motions for these trajectories are highly irregular and do not appear to have any identifiable characteristics. However, the O-atom motions for trajectories integrated for substantially longer period of times acquire unique properties. With C-O stretch zpe included, the long-time O-atom motion becomes tubular for trajectories integrated to approximately 14 ps for the L = 3 states and to approximately 44 ps for the L = 1 states.

A quantum dynamics study of the benzopyran ring opening guided by laser pulses

NASA Astrophysics Data System (ADS)

Saab, Mohamad; Doriol, Loïc Joubert; Lasorne, Benjamin; Guérin, Stéphane; Gatti, Fabien

2014-10-01

The ring-opening photoisomerization of benzopyran, which occurs via a photochemical route involving a conical intersection, has been studied with quantum dynamics calculations using the multi-configuration time-dependent Hartree method (MCTDH). We introduce a mechanistic strategy to control the conversion of benzopyran to merocyanine with laser pulses. We use a six-dimensional model developed in a previous work for the potential energy surfaces (PES) based on an extension of the vibronic-coupling Hamiltonian model (diabatization method by ansatz), which depends on the most active degrees of freedom. The main objective of these quantum dynamics simulations is to provide a set of strategies that could help experimentalists to control the photoreactivity vs. photostability ratio (selectivity). In this work we present: (i) a pump-dump technique used to control the photostability, (ii) a two-step strategy to enhance the reactivity of the system: first, a pure vibrational excitation in the electronic ground state that prepares the system and, second, an ultraviolet excitation that brings the system to the first adiabatic electronic state; (iii) finally the effect of a non-resonant pulse (Stark effect) on the dynamics.

Theorems and application of local activity of CNN with five state variables and one port.

PubMed

Xiong, Gang; Dong, Xisong; Xie, Li; Yang, Thomas

2012-01-01

Coupled nonlinear dynamical systems have been widely studied recently. However, the dynamical properties of these systems are difficult to deal with. The local activity of cellular neural network (CNN) has provided a powerful tool for studying the emergence of complex patterns in a homogeneous lattice, which is composed of coupled cells. In this paper, the analytical criteria for the local activity in reaction-diffusion CNN with five state variables and one port are presented, which consists of four theorems, including a serial of inequalities involving CNN parameters. These theorems can be used for calculating the bifurcation diagram to determine or analyze the emergence of complex dynamic patterns, such as chaos. As a case study, a reaction-diffusion CNN of hepatitis B Virus (HBV) mutation-selection model is analyzed and simulated, the bifurcation diagram is calculated. Using the diagram, numerical simulations of this CNN model provide reasonable explanations of complex mutant phenomena during therapy. Therefore, it is demonstrated that the local activity of CNN provides a practical tool for the complex dynamics study of some coupled nonlinear systems.

Non-Equilibrium Dynamics Contribute to Ion Selectivity in the KcsA Channel

PubMed Central

Haas, Stephan; Farley, Robert A.

2014-01-01

The ability of biological ion channels to conduct selected ions across cell membranes is critical for the survival of both animal and bacterial cells. Numerous investigations of ion selectivity have been conducted over more than 50 years, yet the mechanisms whereby the channels select certain ions and reject others are not well understood. Here we report a new application of Jarzynski’s Equality to investigate the mechanism of ion selectivity using non-equilibrium molecular dynamics simulations of Na+ and K+ ions moving through the KcsA channel. The simulations show that the selectivity filter of KcsA adapts and responds to the presence of the ions with structural rearrangements that are different for Na+ and K+. These structural rearrangements facilitate entry of K+ ions into the selectivity filter and permeation through the channel, and rejection of Na+ ions. A mechanistic model of ion selectivity by this channel based on the results of the simulations relates the structural rearrangement of the selectivity filter to the differential dehydration of ions and multiple-ion occupancy and describes a mechanism to efficiently select and conduct K+. Estimates of the K+/Na+ selectivity ratio and steady state ion conductance for KcsA from the simulations are in good quantitative agreement with experimental measurements. This model also accurately describes experimental observations of channel block by cytoplasmic Na+ ions, the “punch through” relief of channel block by cytoplasmic positive voltages, and is consistent with the knock-on mechanism of ion permeation. PMID:24465882

Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards.

PubMed

Hagey, Travis J; Uyeda, Josef C; Crandell, Kristen E; Cheney, Jorn A; Autumn, Kellar; Harmon, Luke J

2017-10-01

Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics. Here, we ask whether convergent evolution of pad-bearing lizards has followed similar evolutionary dynamics, or whether independent origins are accompanied by unique constraints and selective pressures over macroevolutionary time. We hypothesized that geckos and anoles each have unique evolutionary tempos and modes. Using performance data from 59 species, we modified Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to account for repeated origins estimated using Bayesian ancestral state reconstructions. We discovered that adhesive performance in geckos evolved in a fashion consistent with Brownian motion with a trend, whereas anoles evolved in bounded performance space consistent with more constrained evolution (an Ornstein-Uhlenbeck model). Our results suggest that convergent phenotypes can have quite distinctive evolutionary patterns, likely as a result of idiosyncratic constraints or ecological opportunities. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Identifying and Modeling Dynamic Preference Evolution in Multipurpose Water Resources Systems

NASA Astrophysics Data System (ADS)

Mason, E.; Giuliani, M.; Castelletti, A.; Amigoni, F.

2018-04-01

Multipurpose water systems are usually operated on a tradeoff of conflicting operating objectives. Under steady state climatic and socioeconomic conditions, such tradeoff is supposed to represent a fair and/or efficient preference. Extreme variability in external forcing might affect water operators' risk aversion and force a change in her/his preference. Properly accounting for these shifts is key to any rigorous retrospective assessment of the operator's behaviors, and to build descriptive models for projecting the future system evolution. In this study, we explore how the selection of different preferences is linked to variations in the external forcing. We argue that preference selection evolves according to recent, extreme variations in system performance: underperforming in one of the objectives pushes the preference toward the harmed objective. To test this assumption, we developed a rational procedure to simulate the operator's preference selection. We map this selection onto a multilateral negotiation, where multiple virtual agents independently optimize different objectives. The agents periodically negotiate a compromise policy for the operation of the system. Agents' attitudes in each negotiation step are determined by the recent system performance measured by the specific objective they maximize. We then propose a numerical model of preference dynamics that implements a concept from cognitive psychology, the availability bias. We test our modeling framework on a synthetic lake operated for flood control and water supply. Results show that our model successfully captures the operator's preference selection and dynamic evolution driven by extreme wet and dry situations.

The effect of synaptic plasticity on orientation selectivity in a balanced model of primary visual cortex

PubMed Central

Gonzalo Cogno, Soledad; Mato, Germán

2015-01-01

Orientation selectivity is ubiquitous in the primary visual cortex (V1) of mammals. In cats and monkeys, V1 displays spatially ordered maps of orientation preference. Instead, in mice, squirrels, and rats, orientation selective neurons in V1 are not spatially organized, giving rise to a seemingly random pattern usually referred to as a salt-and-pepper layout. The fact that such different organizations can sharpen orientation tuning leads to question the structural role of the intracortical connections; specifically the influence of plasticity and the generation of functional connectivity. In this work, we analyze the effect of plasticity processes on orientation selectivity for both scenarios. We study a computational model of layer 2/3 and a reduced one-dimensional model of orientation selective neurons, both in the balanced state. We analyze two plasticity mechanisms. The first one involves spike-timing dependent plasticity (STDP), while the second one considers the reconnection of the interactions according to the preferred orientations of the neurons. We find that under certain conditions STDP can indeed improve selectivity but it works in a somehow unexpected way, that is, effectively decreasing the modulated part of the intracortical connectivity as compared to the non-modulated part of it. For the reconnection mechanism we find that increasing functional connectivity leads, in fact, to a decrease in orientation selectivity if the network is in a stable balanced state. Both counterintuitive results are a consequence of the dynamics of the balanced state. We also find that selectivity can increase due to a reconnection process if the resulting connections give rise to an unstable balanced state. We compare these findings with recent experimental results. PMID:26347615

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

Choi, Jeong

The research program reported here is focused on critical issues that represent conspicuous gaps in current understanding of rapid solidification, limiting our ability to predict and control microstructural evolution (i.e. morphological dynamics and microsegregation) at high undercooling, where conditions depart significantly from local equilibrium. More specifically, through careful application of phase-field modeling, using appropriate thin-interface and anti-trapping corrections and addressing important details such as transient effects and a velocity-dependent (i.e. adaptive) numerics, the current analysis provides a reasonable simulation-based picture of non-equilibrium solute partitioning and the corresponding oscillatory dynamics associated with single-phase rapid solidification and show that this method ismore » a suitable means for a self-consistent simulation of transient behavior and operating point selection under rapid growth conditions. Moving beyond the limitations of conventional theoretical/analytical treatments of non-equilibrium solute partitioning, these results serve to substantiate recent experimental findings and analytical treatments for single-phase rapid solidification. The departure from the equilibrium solid concentration at the solid-liquid interface was often observed during rapid solidification, and the energetic associated non-equilibrium solute partitioning has been treated in detail, providing possible ranges of interface concentrations for a given growth condition. Use of these treatments for analytical description of specific single-phase dendritic and cellular operating point selection, however, requires a model for solute partitioning under a given set of growth conditions. Therefore, analytical solute trapping models which describe the chemical partitioning as a function of steady state interface velocities have been developed and widely utilized in most of the theoretical investigations of rapid solidification. However, these solute trapping models are not rigorously verified due to the difficulty in experimentally measuring under rapid growth conditions. Moreover, since these solute trapping models include kinetic parameters which are difficult to directly measure from experiments, application of the solute trapping models or the associated analytic rapid solidification model is limited. These theoretical models for steady state rapid solidification which incorporate the solute trapping models do not describe the interdependency of solute diffusion, interface kinetics, and alloy thermodynamics. The phase-field approach allows calculating, spontaneously, the non-equilibrium growth effects of alloys and the associated time-dependent growth dynamics, without making the assumptions that solute partitioning is an explicit function of velocity, as is the current convention. In the research described here, by utilizing the phase-field model in the thin-interface limit, incorporating the anti-trapping current term, more quantitatively valid interface kinetics and solute diffusion across the interface are calculated. In order to sufficiently resolve the physical length scales (i.e. interface thickness and diffusion boundary length), grid spacings are continually adjusted in calculations. The full trajectories of transient planar growth dynamics under rapid directional solidification conditions with different pulling velocities are described. As a validation of a model, the predicted steady state conditions are consistent with the analytic approach for rapid growth. It was confirmed that rapid interface dynamics exhibits the abrupt acceleration of the planar front when the effect of the non-equilibrium solute partitioning at the interface becomes signi ficant. This is consistent with the previous linear stability analysis for the non-equilibrium interface dynamics. With an appropriate growth condition, the continuous oscillation dynamics was able to be simulated using continually adjusting grid spacings. This oscillatory dynamics including instantaneous jump of interface velocities are consistent with a previous phenomenological model by and a numerical investigation, which may cause the formation of banded structures. Additionally, the selection of the steady state growth dynamics in the highly undercooled melt is demonstrated. The transition of the growth morphology, interface velocity selection, and solute trapping phenomenon with increasing melt supersaturations was described by the phase-field simulation. The tip selection for the dendritic growth was consistent with Ivantsov's function, and the non-equilibrium chemical partitioning behavior shows good qualitative agreement with the Aziz's solute trapping model even though the model parameter(V D) remains as an arbitrary constant. This work is able to show the possibility of comprehensive description of rapid alloy growth over the entire time-dependent non-equilibrium phenomenon.« less

Multiple quantum coherence spectroscopy.

PubMed

Mathew, Nathan A; Yurs, Lena A; Block, Stephen B; Pakoulev, Andrei V; Kornau, Kathryn M; Wright, John C

2009-08-20

Multiple quantum coherences provide a powerful approach for studies of complex systems because increasing the number of quantum states in a quantum mechanical superposition state increases the selectivity of a spectroscopic measurement. We show that frequency domain multiple quantum coherence multidimensional spectroscopy can create these superposition states using different frequency excitation pulses. The superposition state is created using two excitation frequencies to excite the symmetric and asymmetric stretch modes in a rhodium dicarbonyl chelate and the dynamic Stark effect to climb the vibrational ladders involving different overtone and combination band states. A monochromator resolves the free induction decay of different coherences comprising the superposition state. The three spectral dimensions provide the selectivity required to observe 19 different spectral features associated with fully coherent nonlinear processes involving up to 11 interactions with the excitation fields. The different features act as spectroscopic probes of the diagonal and off-diagonal parts of the molecular potential energy hypersurface. This approach can be considered as a coherent pump-probe spectroscopy where the pump is a series of excitation pulses that prepares a multiple quantum coherence and the probe is another series of pulses that creates the output coherence.

Thirst and the state-dependent representation of incentive stimulus value in human motive circuitry.

PubMed

Becker, Christoph A; Schmälzle, Ralf; Flaisch, Tobias; Renner, Britta; Schupp, Harald T

2015-12-01

Depletion imposes both need and desire to drink, and potentiates the response to need-relevant cues in the environment. The present fMRI study aimed to determine which neural structures selectively increase the incentive value of need-relevant stimuli in a thirst state. Towards this end, participants were scanned twice--either in a thirst or no-thirst state--while viewing pictures of beverages and chairs. As expected, thirst led to a selective increase in self-reported pleasantness and arousal by beverages. Increased responses to beverage when compared with chair stimuli were observed in the cingulate cortex, insular cortex and the amygdala in the thirst state, which were absent in the no-thirst condition. Enhancing the incentive value of need-relevant cues in a thirst state is a key mechanism for motivating drinking behavior. Overall, distributed regions of the motive circuitry, which are also implicated in salience processing, craving and interoception, provide a dynamic body-state dependent representation of stimulus value. © The Author (2015). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

A Network of Conformational Transitions in the Apo Form of NDM-1 Enzyme Revealed by MD Simulation and a Markov State Model.

PubMed

Gao, Kaifu; Zhao, Yunjie

2017-04-13

New Delhi metallo-β-lactamase-1 (NDM-1) is a novel β-lactamase enzyme that confers enteric bacteria with nearly complete resistance to all β-lactam antibiotics, so it raises a formidable and global threat to human health. However, the binding mechanism between apo-NDM-1 and antibiotics as well as related conformational changes remains poorly understood, which largely hinders the overcoming of its antibiotic resistance. In our study, long-time conventional molecular dynamics simulation and Markov state models were applied to reveal both the dynamical and conformational landscape of apo-NDM-1: the MD simulation demonstrates that loop L3, which is responsible for antibiotic binding, is the most flexible and undergoes dramatic conformational changes; moreover, the Markov state model built from the simulation maps four metastable states including open, semiopen, and closed conformations of loop L3 as well as frequent transitions between the states. Our findings propose a possible conformational selection model for the binding mechanism between apo-NDM-1 and antibiotics, which facilitates the design of novel inhibitors and antibiotics.

State selectivity and dynamics in dissociative electron attachment to CF₃I revealed through velocity slice imaging.

PubMed

Ómarsson, Frímann H; Mason, Nigel J; Krishnakumar, E; Ingólfsson, Oddur

2014-11-03

In light of its substantially more environmentally friendly nature, CF3I is currently being considered as a replacement for the highly potent global-warming gas CF4, which is used extensively in plasma processing. In this context, we have studied the electron-driven dissociation of CF3I to form CF3(-) and I, and we compare this process to the corresponding photolysis channel. By using the velocity slice imaging (VSI) technique we can visualize the complete dynamics of this process and show that electron-driven dissociation proceeds from the same initial parent state as the corresponding photolysis process. However, in contrast to photolysis, which leads nearly exclusively to the (2)P(1/2) excited state of iodine, electron-induced dissociation leads predominantly to the (2)P(3/2) ground state. We believe that the changed spin state of the negative ion allows an adiabatic dissociation through a conical intersection, whereas this path is efficiently repressed by a required spin flip in the photolysis process. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations.

PubMed

Lin, Yao-Cheng; Boone, Morgane; Meuris, Leander; Lemmens, Irma; Van Roy, Nadine; Soete, Arne; Reumers, Joke; Moisse, Matthieu; Plaisance, Stéphane; Drmanac, Radoje; Chen, Jason; Speleman, Frank; Lambrechts, Diether; Van de Peer, Yves; Tavernier, Jan; Callewaert, Nico

2014-09-03

The HEK293 human cell lineage is widely used in cell biology and biotechnology. Here we use whole-genome resequencing of six 293 cell lines to study the dynamics of this aneuploid genome in response to the manipulations used to generate common 293 cell derivatives, such as transformation and stable clone generation (293T); suspension growth adaptation (293S); and cytotoxic lectin selection (293SG). Remarkably, we observe that copy number alteration detection could identify the genomic region that enabled cell survival under selective conditions (i.c. ricin selection). Furthermore, we present methods to detect human/vector genome breakpoints and a user-friendly visualization tool for the 293 genome data. We also establish that the genome structure composition is in steady state for most of these cell lines when standard cell culturing conditions are used. This resource enables novel and more informed studies with 293 cells, and we will distribute the sequenced cell lines to this effect.

Marangoni-induced symmetry-breaking pattern selection on viscous fluids

NASA Astrophysics Data System (ADS)

Shen, Li; Denner, Fabian; Morgan, Neal; van Wachem, Berend; Dini, Daniele

2016-11-01

Symmetry breaking transitions on curved surfaces are found in a wide range of dissipative systems, ranging from asymmetric cell divisions to structure formation in thin films. Inherent within the nonlinearities are the associated curvilinear geometry, the elastic stretching, bending and the various fluid dynamical processes. We present a generalised Swift-Hohenberg pattern selection theory on a thin, curved and viscous films in the presence of non-trivial Marangoni effect. Testing the theory with experiments on soap bubbles, we observe the film pattern selection to mimic that of the elastic wrinkling morphology on a curved elastic bilayer in regions of slow viscous flow. By examining the local state of damping of surface capillary waves we attempt to establish an equivalence between the Marangoni fluid dynamics and the nonlinear elastic shell theory above the critical wavenumber of the instabilities and propose a possible explanation for the perceived elastic-fluidic duality. The authors acknowledge the financial support of the Shell University Technology Centre for fuels and lubricants.

Population size effects in evolutionary dynamics on neutral networks and toy landscapes

NASA Astrophysics Data System (ADS)

Sumedha; Martin, Olivier C.; Peliti, Luca

2007-05-01

We study the dynamics of a population subject to selective pressures, evolving either on RNA neutral networks or on toy fitness landscapes. We discuss the spread and the neutrality of the population in the steady state. Different limits arise depending on whether selection or random drift is dominant. In the presence of strong drift we show that the observables depend mainly on Mμ, M being the population size and μ the mutation rate, while corrections to this scaling go as 1/M: such corrections can be quite large in the presence of selection if there are barriers in the fitness landscape. Also we find that the convergence to the large-Mμ limit is linear in 1/Mμ. Finally we introduce a protocol that minimizes drift; then observables scale like 1/M rather than 1/(Mμ), allowing one to determine the large-M limit more quickly when μ is small; furthermore the genotypic diversity increases from O(lnM) to O(M).

Dynamic resource allocation in conservation planning

USGS Publications Warehouse

Golovin, D.; Krause, A.; Gardner, B.; Converse, S.J.; Morey, S.

2011-01-01

Consider the problem of protecting endangered species by selecting patches of land to be used for conservation purposes. Typically, the availability of patches changes over time, and recommendations must be made dynamically. This is a challenging prototypical example of a sequential optimization problem under uncertainty in computational sustainability. Existing techniques do not scale to problems of realistic size. In this paper, we develop an efficient algorithm for adaptively making recommendations for dynamic conservation planning, and prove that it obtains near-optimal performance. We further evaluate our approach on a detailed reserve design case study of conservation planning for three rare species in the Pacific Northwest of the United States. Copyright ?? 2011, Association for the Advancement of Artificial Intelligence. All rights reserved.

Photodissociation dynamics and spectroscopy of free radical combustion intermediates

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

Osborn, David Lewis

1996-12-01

The photodissociation spectroscopy and dynamics of free radicals is studied by the technique of fast beam photofragment translational spectroscopy. Photodetachment of internally cold, mass-selected negative ions produces a clean source of radicals, which are subsequently dissociated and detected. The photofragment yield as a function of photon energy is obtained, mapping out the dissociative and predissociative electronic states of the radical. In addition, the photodissociation dynamics, product branching ratios, and bond energies are probed at fixed photon energies by measuring the translational energy, P(E T), and angular distribution of the recoiling fragments using a time- and position-sensitive detector. Ab initio calculationsmore » are combined with dynamical and statistical models to interpret the observed data. The photodissociation of three prototypical hydrocarbon combustion intermediates forms the core of this work.« less

LabVIEW Task Manager v. 1.10.0

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

Vargo, Timothy D.

LabVIEW Task Manager is a debugging tool for use during code development in the National Instruments (NI) LabVIEW® IDE. While providing a dynamic & big-picture view of running code, an expandable/collapsible tree diagram displays detailed information (both static and dynamic) on all VIs in memory, belonging to a selected project/target. It allows for interacting with single or multiple selected VIs at a time, providing significant benefits while troubleshooting, and has the following features: Look & Feel similar to Windows® Task Manager; Selection of project/target; Lists all VIs in memory, grouped by class/library; Searches for and enumerates clones in memory; DropInmore » VI for including dynamically referenced clones (Clone Beacon); 'Refresh Now' (F5) re-reads all VIs in memory and adds new ones to the tree; Displays VI name, owning class/library, state, path, data size & code size; Displays VI FP Behavior, Reentrant?, Reentrancy Type, Paused? & Highlight?; Sort by any column, including by library name; Filter by item types vi, ctl, and vit/ctt; Filter out vi.lib and global VIs; Tracking of, and ability to toggle, execution highlighting on multiple selected VIs; Tracking of paused VIs with ability to Pause/Resume/TogglePause multiple selected VIs; DropIn VI for pausing on a condition; If a clone initiates a pause, a different pause symbol is used for all clones of that same reentrant original VI; Select multiple VIs and open or close their FPs or BDs; Double Click a VI from the tree to bring the BD (first choice) or FP to front, if already open; and Select multiple top-level VIs and Abort them.« less

Large-Scale Conformational Dynamics Control H5N1 Influenza Polymerase PB2 Binding to Importin α.

PubMed

Delaforge, Elise; Milles, Sigrid; Bouvignies, Guillaume; Bouvier, Denis; Boivin, Stephane; Salvi, Nicola; Maurin, Damien; Martel, Anne; Round, Adam; Lemke, Edward A; Jensen, Malene Ringkjøbing; Hart, Darren J; Blackledge, Martin

2015-12-09

Influenza A RNA polymerase complex is formed from three components, PA, PB1, and PB2. PB2 is independently imported into the nucleus prior to polymerase reconstitution. All crystallographic structures of the PB2 C-terminus (residues 536-759) reveal two globular domains, 627 and NLS, that form a tightly packed heterodimer. The molecular basis of the affinity of 627-NLS for importins remained unclear from these structures, apparently requiring large-scale conformational changes prior to importin binding. Using a combination of solution-state NMR, small-angle neutron scattering, small-angle X-ray scattering (SAXS), and Förster resonance energy transfer (FRET), we show that 627-NLS populates a temperature-dependent dynamic equilibrium between closed and open states. The closed state is stabilized by a tripartite salt bridge involving the 627-NLS interface and the linker, that becomes flexible in the open state, with 627 and NLS dislocating into a highly dynamic ensemble. Activation enthalpies and entropies associated with the rupture of this interface were derived from simultaneous analysis of temperature-dependent chemical exchange saturation transfer measurements, revealing a strong temperature dependence of both open-state population and exchange rate. Single-molecule FRET and SAXS demonstrate that only the open-form is capable of binding to importin α and that, upon binding, the 627 domain samples a dynamic conformational equilibrium in the vicinity of the C-terminus of importin α. This intrinsic large-scale conformational flexibility therefore enables 627-NLS to bind importin through conformational selection from a temperature-dependent equilibrium comprising both functional forms of the protein.

Characterizing highly dynamic conformational states: The transcription bubble in RNAP-promoter open complex as an example

NASA Astrophysics Data System (ADS)

Lerner, Eitan; Ingargiola, Antonino; Weiss, Shimon

2018-03-01

Bio-macromolecules carry out complicated functions through structural changes. To understand their mechanism of action, the structure of each step has to be characterized. While classical structural biology techniques allow the characterization of a few "structural snapshots" along the enzymatic cycle (usually of stable conformations), they do not cover all (and often fast interconverting) structures in the ensemble, where each may play an important functional role. Recently, several groups have demonstrated that structures of different conformations in solution could be solved by measuring multiple distances between different pairs of residues using single-molecule Förster resonance energy transfer (smFRET) and using them as constrains for hybrid/integrative structural modeling. However, this approach is limited in cases where the conformational dynamics is faster than the technique's temporal resolution. In this study, we combine existing tools that elucidate sub-millisecond conformational dynamics together with hybrid/integrative structural modeling to study the conformational states of the transcription bubble in the bacterial RNA polymerase-promoter open complex (RPo). We measured microsecond alternating laser excitation-smFRET of differently labeled lacCONS promoter dsDNA constructs. We used a combination of burst variance analysis, photon-by-photon hidden Markov modeling, and the FRET-restrained positioning and screening approach to identify two conformational states for RPo. The experimentally derived distances of one conformational state match the known crystal structure of bacterial RPo. The experimentally derived distances of the other conformational state have characteristics of a scrunched RPo. These findings support the hypothesis that sub-millisecond dynamics in the transcription bubble are responsible for transcription start site selection.

Management of California Oak Woodlands: Uncertainties and Modeling

Treesearch

Jay E. Noel; Richard P. Thompson

1995-01-01

A mathematical policy model of oak woodlands is presented. The model illustrates the policy uncertainties that exist in the management of oak woodlands. These uncertainties include: (1) selection of a policy criterion function, (2) woodland dynamics, (3) initial and final state of the woodland stock. The paper provides a review of each of the uncertainty issues. The...

Dynamic membrane interactions of antibacterial and antifungal biomolecules, and amyloid peptides, revealed by solid-state NMR spectroscopy.

PubMed

Naito, Akira; Matsumori, Nobuaki; Ramamoorthy, Ayyalusamy

2018-02-01

A variety of biomolecules acting on the cell membrane folds into a biologically active structure in the membrane environment. It is, therefore, important to determine the structures and dynamics of such biomolecules in a membrane environment. While several biophysical techniques are used to obtain low-resolution information, solid-state NMR spectroscopy is one of the most powerful means for determining the structure and dynamics of membrane bound biomolecules such as antibacterial biomolecules and amyloidogenic proteins; unlike X-ray crystallography and solution NMR spectroscopy, applications of solid-state NMR spectroscopy are not limited by non-crystalline, non-soluble nature or molecular size of membrane-associated biomolecules. This review article focuses on the applications of solid-state NMR techniques to study a few selected antibacterial and amyloid peptides. Solid-state NMR studies revealing the membrane inserted bent α-helical structure associated with the hemolytic activity of bee venom melittin and the chemical shift oscillation analysis used to determine the transmembrane structure (with α-helix and 3 10 -helix in the N- and C-termini, respectively) of antibiotic peptide alamethicin are discussed in detail. Oligomerization of an amyloidogenic islet amyloid polypeptide (IAPP, or also known as amylin) resulting from its aggregation in a membrane environment, molecular interactions of the antifungal natural product amphotericin B with ergosterol in lipid bilayers, and the mechanism of lipid raft formation by sphingomyelin studied using solid state NMR methods are also discussed in this review article. This article is part of a Special Issue entitled "Biophysical Exploration of Dynamical Ordering of Biomolecular Systems" edited by Dr. Koichi Kato. Copyright © 2017 Elsevier B.V. All rights reserved.

Markov State Models Reveal a Two-Step Mechanism of miRNA Loading into the Human Argonaute Protein: Selective Binding followed by Structural Re-arrangement.

PubMed

Jiang, Hanlun; Sheong, Fu Kit; Zhu, Lizhe; Gao, Xin; Bernauer, Julie; Huang, Xuhui

2015-07-01

Argonaute (Ago) proteins and microRNAs (miRNAs) are central components in RNA interference, which is a key cellular mechanism for sequence-specific gene silencing. Despite intensive studies, molecular mechanisms of how Ago recognizes miRNA remain largely elusive. In this study, we propose a two-step mechanism for this molecular recognition: selective binding followed by structural re-arrangement. Our model is based on the results of a combination of Markov State Models (MSMs), large-scale protein-RNA docking, and molecular dynamics (MD) simulations. Using MSMs, we identify an open state of apo human Ago-2 in fast equilibrium with partially open and closed states. Conformations in this open state are distinguished by their largely exposed binding grooves that can geometrically accommodate miRNA as indicated in our protein-RNA docking studies. miRNA may then selectively bind to these open conformations. Upon the initial binding, the complex may perform further structural re-arrangement as shown in our MD simulations and eventually reach the stable binary complex structure. Our results provide novel insights in Ago-miRNA recognition mechanisms and our methodology holds great potential to be widely applied in the studies of other important molecular recognition systems.

Emergence of unusual coexistence states in cyclic game systems.

PubMed

Park, Junpyo; Do, Younghae; Jang, Bongsoo; Lai, Ying-Cheng

2017-08-07

Evolutionary games of cyclic competitions have been extensively studied to gain insights into one of the most fundamental phenomena in nature: biodiversity that seems to be excluded by the principle of natural selection. The Rock-Paper-Scissors (RPS) game of three species and its extensions [e.g., the Rock-Paper-Scissors-Lizard-Spock (RPSLS) game] are paradigmatic models in this field. In all previous studies, the intrinsic symmetry associated with cyclic competitions imposes a limitation on the resulting coexistence states, leading to only selective types of such states. We investigate the effect of nonuniform intraspecific competitions on coexistence and find that a wider spectrum of coexistence states can emerge and persist. This surprising finding is substantiated using three classes of cyclic game models through stability analysis, Monte Carlo simulations and continuous spatiotemporal dynamical evolution from partial differential equations. Our finding indicates that intraspecific competitions or alternative symmetry-breaking mechanisms can promote biodiversity to a broader extent than previously thought.

A global reaction route mapping-based kinetic Monte Carlo algorithm

NASA Astrophysics Data System (ADS)

Mitchell, Izaac; Irle, Stephan; Page, Alister J.

2016-07-01

We propose a new on-the-fly kinetic Monte Carlo (KMC) method that is based on exhaustive potential energy surface searching carried out with the global reaction route mapping (GRRM) algorithm. Starting from any given equilibrium state, this GRRM-KMC algorithm performs a one-step GRRM search to identify all surrounding transition states. Intrinsic reaction coordinate pathways are then calculated to identify potential subsequent equilibrium states. Harmonic transition state theory is used to calculate rate constants for all potential pathways, before a standard KMC accept/reject selection is performed. The selected pathway is then used to propagate the system forward in time, which is calculated on the basis of 1st order kinetics. The GRRM-KMC algorithm is validated here in two challenging contexts: intramolecular proton transfer in malonaldehyde and surface carbon diffusion on an iron nanoparticle. We demonstrate that in both cases the GRRM-KMC method is capable of reproducing the 1st order kinetics observed during independent quantum chemical molecular dynamics simulations using the density-functional tight-binding potential.

A global reaction route mapping-based kinetic Monte Carlo algorithm.

PubMed

Mitchell, Izaac; Irle, Stephan; Page, Alister J

2016-07-14

We propose a new on-the-fly kinetic Monte Carlo (KMC) method that is based on exhaustive potential energy surface searching carried out with the global reaction route mapping (GRRM) algorithm. Starting from any given equilibrium state, this GRRM-KMC algorithm performs a one-step GRRM search to identify all surrounding transition states. Intrinsic reaction coordinate pathways are then calculated to identify potential subsequent equilibrium states. Harmonic transition state theory is used to calculate rate constants for all potential pathways, before a standard KMC accept/reject selection is performed. The selected pathway is then used to propagate the system forward in time, which is calculated on the basis of 1st order kinetics. The GRRM-KMC algorithm is validated here in two challenging contexts: intramolecular proton transfer in malonaldehyde and surface carbon diffusion on an iron nanoparticle. We demonstrate that in both cases the GRRM-KMC method is capable of reproducing the 1st order kinetics observed during independent quantum chemical molecular dynamics simulations using the density-functional tight-binding potential.

Solid-state NMR characterization of cross-linking in EPDM/PP blends from 1H-13C polarization transfer dynamics.

PubMed

Aluas, Mihaela; Filip, Claudiu

2005-05-01

A novel approach for solid-state NMR characterization of cross-linking in polymer blends from the analysis of (1)H-(13)C polarization transfer dynamics is introduced. It extends the model of residual dipolar couplings under permanent cross-linking, typically used to describe (1)H transverse relaxation techniques, by considering a more realistic distribution of the order parameter along a polymer chain in rubbers. Based on a systematic numerical analysis, the extended model was shown to accurately reproduce all the characteristic features of the cross-polarization curves measured on such materials. This is particularly important for investigating blends of great technological potential, like thermoplastic elastomers, where (13)C high-resolution techniques, such as CP-MAS, are indispensable to selectively investigate structural and dynamical properties of the desired component. The validity of the new approach was demonstrated using the example of the CP build-up curves measured on a well resolved EPDM resonance line in a series of EPDM/PP blends.

Mathematical modeling of control subsystems for CELSS: Application to diet

NASA Technical Reports Server (NTRS)

Waleh, Ahmad; Nguyen, Thoi K.; Kanevsky, Valery

1991-01-01

The dynamic control of a Closed Ecological Life Support System (CELSS) in a closed space habitat is of critical importance. The development of a practical method of control is also a necessary step for the selection and design of realistic subsystems and processors for a CELSS. Diet is one of the dynamic factors that strongly influences, and is influenced, by the operational states of all major CELSS subsystems. The problems of design and maintenance of a stable diet must be obtained from well characterized expert subsystems. The general description of a mathematical model that forms the basis of an expert control program for a CELSS is described. The formulation is expressed in terms of a complete set of time dependent canonical variables. System representation is dynamic and includes time dependent storage buffers. The details of the algorithm are described. The steady state results of the application of the method for representative diets made from wheat, potato, and soybean are presented.

Can Internal Conversion BE Controlled by Mode-Specific Vibrational Excitation in Polyatomic Molecules

NASA Astrophysics Data System (ADS)

Portnov, Alexander; Epshtein, Michael; Bar, Ilana

2017-06-01

Nonadiabatic processes, dominated by dynamic passage of reactive fluxes through conical intersections (CIs) are considered to be appealing means for manipulating reaction paths. One approach that is considered to be effective in controlling the course of dissociation processes is the selective excitation of vibrational modes containing a considerable component of motion. Here, we have chosen to study the predissociation of the model test molecule, methylamine and its deuterated isotopologues, excited to well-characterized quantum states on the first excited electronic state, S_{1}, by following the N-H(D) bond fission dynamics through sensitive H(D) photofragment probing. The branching ratios between slow and fast H(D) photofragments, the internal energies of their counter radical photofragments and the anisotropy parameters for fast H photofragments, confirm correlated anomalies for predissociation initiated from specific rovibronic states, reflecting the existence of a dynamic resonance in each molecule. This resonance strongly depends on the energy of the initially excited rovibronic states, the evolving vibrational mode on the repulsive S_{1} part during N-H(D) bond elongation, and the manipulated passage through the CI that leads to radicals excited with C-N-H(D) bending and preferential perpendicular bond breaking, relative to the photolyzing laser polarization, in molecules containing the NH_{2} group. The indicated resonance plays an important role in the bifurcation dynamics at the CI and can be foreseen to exist in other photoinitiated processes and to control their outcome.

Correlation-induced superconductivity dynamically stabilized and enhanced by laser irradiation.

PubMed

Ido, Kota; Ohgoe, Takahiro; Imada, Masatoshi

2017-08-01

Studies on out-of-equilibrium dynamics have paved a way to realize a new state of matter. Superconductor-like properties above room temperatures recently suggested to be in copper oxides achieved by selectively exciting vibrational phonon modes by laser have inspired studies on an alternative and general strategy to be pursued for high-temperature superconductivity. We show that the superconductivity can be enhanced by irradiating laser to correlated electron systems owing to two mechanisms: First, the effective attractive interaction of carriers is enhanced by the dynamical localization mechanism, which drives the system into strong coupling regions. Second, the irradiation allows reaching uniform and enhanced superconductivity dynamically stabilized without deteriorating into equilibrium inhomogeneities that suppress superconductivity. The dynamical superconductivity is subject to the Higgs oscillations during and after the irradiation. Our finding sheds light on a way to enhance superconductivity that is inaccessible in equilibrium in strongly correlated electron systems.

Microscopic Chain Motion in Polymer Nanocomposites with Dynamically Asymmetric Interphases

PubMed Central

Senses, Erkan; Faraone, Antonio; Akcora, Pinar

2016-01-01

Dynamics of the interphase region between matrix and bound polymers on nanoparticles is important to understand the macroscopic rheological properties of nanocomposites. Here, we present neutron scattering investigations on nanocomposites with dynamically asymmetric interphases formed by a high-glass transition temperature polymer, poly(methyl methacrylate), adsorbed on nanoparticles and a low-glass transition temperature miscible matrix, poly(ethylene oxide). By taking advantage of selective isotope labeling of the chains, we studied the role of interfacial polymer on segmental and collective dynamics of the matrix chains from subnanoseconds to 100 nanoseconds. Our results show that the Rouse relaxation remains unchanged in a weakly attractive composite system while the dynamics significantly slows down in a strongly attractive composite. More importantly, the chains disentangle with a remarkable increase of the reptation tube size when the bound polymer is vitreous. The glassy and rubbery states of the bound polymer as temperature changes underpin the macroscopic stiffening of nanocomposites. PMID:27457056

Modelling the formation of working memory with networks of integrate-and-fire neurons connected by plastic synapses.

PubMed

Del Giudice, Paolo; Fusi, Stefano; Mattia, Maurizio

2003-01-01

In this paper we review a series of works concerning models of spiking neurons interacting via spike-driven, plastic, Hebbian synapses, meant to implement stimulus driven, unsupervised formation of working memory (WM) states. Starting from a summary of the experimental evidence emerging from delayed matching to sample (DMS) experiments, we briefly review the attractor picture proposed to underlie WM states. We then describe a general framework for a theoretical approach to learning with synapses subject to realistic constraints and outline some general requirements to be met by a mechanism of Hebbian synaptic structuring. We argue that a stochastic selection of the synapses to be updated allows for optimal memory storage, even if the number of stable synaptic states is reduced to the extreme (bistable synapses). A description follows of models of spike-driven synapses that implement the stochastic selection by exploiting the high irregularity in the pre- and post-synaptic activity. Reasons are listed why dynamic learning, that is the process by which the synaptic structure develops under the only guidance of neural activities, driven in turn by stimuli, is hard to accomplish. We provide a 'feasibility proof' of dynamic formation of WM states in this context the beneficial role of short-term depression (STD) is illustrated. by showing how an initially unstructured network autonomously develops a synaptic structure supporting simultaneously stable spontaneous and WM states in this context the beneficial role of short-term depression (STD) is illustrated. After summarizing heuristic indications emerging from the study performed, we conclude by briefly discussing open problems and critical issues still to be clarified.

Adaptive transmission based on multi-relay selection and rate-compatible LDPC codes

NASA Astrophysics Data System (ADS)

Su, Hualing; He, Yucheng; Zhou, Lin

2017-08-01

In order to adapt to the dynamical changeable channel condition and improve the transmissive reliability of the system, a cooperation system of rate-compatible low density parity check (RC-LDPC) codes combining with multi-relay selection protocol is proposed. In traditional relay selection protocol, only the channel state information (CSI) of source-relay and the CSI of relay-destination has been considered. The multi-relay selection protocol proposed by this paper takes the CSI between relays into extra account in order to obtain more chances of collabration. Additionally, the idea of hybrid automatic request retransmission (HARQ) and rate-compatible are introduced. Simulation results show that the transmissive reliability of the system can be significantly improved by the proposed protocol.

Different conformational dynamics of β-arrestin1 and β-arrestin2 analyzed by hydrogen/deuterium exchange mass spectrometry

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

Yun, Youngjoo; Kim, Dong Kyun; Seo, Min-Duk

2015-01-30

Highlights: • The conformational dynamics of β-arrestin1 or β-arrestin2 were analyzed by HDX-MS. • β-Strands II through IV were more dynamic in β-arrestin2 than in β-arrestin1. • The middle loop was less dynamic in β-arrestin2 than in β-arrestin1. • Upon pre-activation by the R169E mutation, β-arrestins became more dynamic. • Pre-activation affected a wider region of β-arrestin1 compared to β-arrestin2. - Abstract: Arrestins have important roles in G protein-coupled receptor (GPCR) signaling including desensitization of GPCRs and G protein-independent signaling. There have been four arrestins identified: arrestin1, arrestin2 (e.g. β-arrestin1), arrestin3 (e.g. β-arrestin2), and arrestin4. β-Arrestin1 and β-arrestin2 are ubiquitouslymore » expressed and regulate a broad range of GPCRs, while arrestin1 and arrestin4 are expressed in the visual system. Although the functions of β-arrestin1 and β-arrestin2 widely overlap, β-arrestin2 has broader receptor selectivity, and a few studies have suggested that β-arrestin1 and β-arrestin2 have distinct cellular functions. Here, we compared the conformational dynamics of β-arrestin1 and β-arrestin2 by hydrogen/deuterium exchange mass spectrometry (HDX-MS). We also used the R169E mutant as a pre-activation model system. HDX-MS data revealed that β-strands II through IV were more dynamic in β-arrestin2 in the basal state, while the middle loop was more dynamic in β-arrestin1. With pre-activation, both β-arrestin1 and β-arrestin2 became more flexible, but broader regions of β-arrestin1 became flexible compared to β-arrestin2. The conformational differences between β-arrestin1 and β-arrestin2 in both the basal and pre-activated states might determine their different receptor selectivities and different cellular functions.« less

Conformational Plasticity of an Enzyme during Catalysis: Intricate Coupling between Cyclophilin A Dynamics and Substrate Turnover

PubMed Central

McGowan, Lauren C.; Hamelberg, Donald

2013-01-01

Enzyme catalysis is central to almost all biochemical processes, speeding up rates of reactions to biological relevant timescales. Enzymes make use of a large ensemble of conformations in recognizing their substrates and stabilizing the transition states, due to the inherent dynamical nature of biomolecules. The exact role of these diverse enzyme conformations and the interplay between enzyme conformational dynamics and catalysis is, according to the literature, not well understood. Here, we use molecular dynamics simulations to study human cyclophilin A (CypA), in order to understand the role of enzyme motions in the catalytic mechanism and recognition. Cyclophilin A is a tractable model system to study using classical simulation methods, because catalysis does not involve bond formation or breakage. We show that the conformational dynamics of active site residues of substrate-bound CypA is inherent in the substrate-free enzyme. CypA interacts with its substrate via conformational selection as the configurations of the substrate changes during catalysis. We also show that, in addition to tight intermolecular hydrophobic interactions between CypA and the substrate, an intricate enzyme-substrate intermolecular hydrogen-bonding network is extremely sensitive to the configuration of the substrate. These enzyme-substrate intermolecular interactions are loosely formed when the substrate is in the reactant and product states and become well formed and reluctant to break when the substrate is in the transition state. Our results clearly suggest coupling among enzyme-substrate intermolecular interactions, the dynamics of the enzyme, and the chemical step. This study provides further insights into the mechanism of peptidyl-prolyl cis/trans isomerases and the general interplay between enzyme conformational dynamics and catalysis. PMID:23332074

Conformational plasticity of an enzyme during catalysis: intricate coupling between cyclophilin A dynamics and substrate turnover.

PubMed

McGowan, Lauren C; Hamelberg, Donald

2013-01-08

Enzyme catalysis is central to almost all biochemical processes, speeding up rates of reactions to biological relevant timescales. Enzymes make use of a large ensemble of conformations in recognizing their substrates and stabilizing the transition states, due to the inherent dynamical nature of biomolecules. The exact role of these diverse enzyme conformations and the interplay between enzyme conformational dynamics and catalysis is, according to the literature, not well understood. Here, we use molecular dynamics simulations to study human cyclophilin A (CypA), in order to understand the role of enzyme motions in the catalytic mechanism and recognition. Cyclophilin A is a tractable model system to study using classical simulation methods, because catalysis does not involve bond formation or breakage. We show that the conformational dynamics of active site residues of substrate-bound CypA is inherent in the substrate-free enzyme. CypA interacts with its substrate via conformational selection as the configurations of the substrate changes during catalysis. We also show that, in addition to tight intermolecular hydrophobic interactions between CypA and the substrate, an intricate enzyme-substrate intermolecular hydrogen-bonding network is extremely sensitive to the configuration of the substrate. These enzyme-substrate intermolecular interactions are loosely formed when the substrate is in the reactant and product states and become well formed and reluctant to break when the substrate is in the transition state. Our results clearly suggest coupling among enzyme-substrate intermolecular interactions, the dynamics of the enzyme, and the chemical step. This study provides further insights into the mechanism of peptidyl-prolyl cis/trans isomerases and the general interplay between enzyme conformational dynamics and catalysis. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Vortex-Core Reversal Dynamics: Towards Vortex Random Access Memory

NASA Astrophysics Data System (ADS)

Kim, Sang-Koog

2011-03-01

An energy-efficient, ultrahigh-density, ultrafast, and nonvolatile solid-state universal memory is a long-held dream in the field of information-storage technology. The magnetic random access memory (MRAM) along with a spin-transfer-torque switching mechanism is a strong candidate-means of realizing that dream, given its nonvolatility, infinite endurance, and fast random access. Magnetic vortices in patterned soft magnetic dots promise ground-breaking applications in information-storage devices, owing to the very stable twofold ground states of either their upward or downward core magnetization orientation and plausible core switching by in-plane alternating magnetic fields or spin-polarized currents. However, two technologically most important but very challenging issues --- low-power recording and reliable selection of each memory cell with already existing cross-point architectures --- have not yet been resolved for the basic operations in information storage, that is, writing (recording) and readout. Here, we experimentally demonstrate a magnetic vortex random access memory (VRAM) in the basic cross-point architecture. This unique VRAM offers reliable cell selection and low-power-consumption control of switching of out-of-plane core magnetizations using specially designed rotating magnetic fields generated by two orthogonal and unipolar Gaussian-pulse currents along with optimized pulse width and time delay. Our achievement of a new device based on a new material, that is, a medium composed of patterned vortex-state disks, together with the new physics on ultrafast vortex-core switching dynamics, can stimulate further fruitful research on MRAMs that are based on vortex-state dot arrays.

Stability analysis of BWR nuclear-coupled thermal-hyraulics using a simple model

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

Karve, A.A.; Rizwan-uddin; Dorning, J.J.

1995-09-01

A simple mathematical model is developed to describe the dynamics of the nuclear-coupled thermal-hydraulics in a boiling water reactor (BWR) core. The model, which incorporates the essential features of neutron kinetics, and single-phase and two-phase thermal-hydraulics, leads to simple dynamical system comprised of a set of nonlinear ordinary differential equations (ODEs). The stability boundary is determined and plotted in the inlet-subcooling-number (enthalpy)/external-reactivity operating parameter plane. The eigenvalues of the Jacobian matrix of the dynamical system also are calculated at various steady-states (fixed points); the results are consistent with those of the direct stability analysis and indicate that a Hopf bifurcationmore » occurs as the stability boundary in the operating parameter plane is crossed. Numerical simulations of the time-dependent, nonlinear ODEs are carried out for selected points in the operating parameter plane to obtain the actual damped and growing oscillations in the neutron number density, the channel inlet flow velocity, and the other phase variables. These indicate that the Hopf bifurcation is subcritical, hence, density wave oscillations with growing amplitude could result from a finite perturbation of the system even where the steady-state is stable. The power-flow map, frequently used by reactor operators during start-up and shut-down operation of a BWR, is mapped to the inlet-subcooling-number/neutron-density (operating-parameter/phase-variable) plane, and then related to the stability boundaries for different fixed inlet velocities corresponding to selected points on the flow-control line. The stability boundaries for different fixed inlet subcooling numbers corresponding to those selected points, are plotted in the neutron-density/inlet-velocity phase variable plane and then the points on the flow-control line are related to their respective stability boundaries in this plane.« less

Selective Efficacy of Static and Dynamic Imagery in Different States of Physical Fatigue.

PubMed

Kanthack, Thiago Ferreira Dias; Guillot, Aymeric; Altimari, Leandro Ricardo; Nunez Nagy, Susana; Collet, Christian; Di Rienzo, Franck

2016-01-01

There is compelling evidence that motor imagery contributes to improved motor performance, and recent work showed that dynamic motor imagery (dMI) might provide additional benefits by comparison with traditional MI practice. However, the efficacy of motor imagery in different states of physical fatigue remains largely unknown, especially as imagery accuracy may be hampered by the physical fatigue states elicited by training. We investigated the effect of static motor imagery (sMI) and dMI on free-throw accuracy in 10 high-level basketball athletes, both in a non-fatigued state (Experiment 1) and immediately after an incremental running test completed until exhaustion (20 m shuttle run-test-Experiment 2). We collected perceived exhaustion and heart rate to quantify the subjective experience of fatigue and energy expenditure. We found that dMI brought better shooting performance than sMI, except when athletes were physically exhausted. These findings shed light on the conditions eliciting optimal use of sMI and dMI. In particular, considering that the current physical state affects body representation, performing dMI under fatigue may result in mismatches between actual and predicted body states.

Real-Space Mapping of Surface Trap States in CIGSe Nanocrystals Using 4D Electron Microscopy.

PubMed

Bose, Riya; Bera, Ashok; Parida, Manas R; Adhikari, Aniruddha; Shaheen, Basamat S; Alarousu, Erkki; Sun, Jingya; Wu, Tom; Bakr, Osman M; Mohammed, Omar F

2016-07-13

Surface trap states in copper indium gallium selenide semiconductor nanocrystals (NCs), which serve as undesirable channels for nonradiative carrier recombination, remain a great challenge impeding the development of solar and optoelectronics devices based on these NCs. In order to design efficient passivation techniques to minimize these trap states, a precise knowledge about the charge carrier dynamics on the NCs surface is essential. However, selective mapping of surface traps requires capabilities beyond the reach of conventional laser spectroscopy and static electron microscopy; it can only be accessed by using a one-of-a-kind, second-generation four-dimensional scanning ultrafast electron microscope (4D S-UEM) with subpicosecond temporal and nanometer spatial resolutions. Here, we precisely map the collective surface charge carrier dynamics of copper indium gallium selenide NCs as a function of the surface trap states before and after surface passivation in real space and time using S-UEM. The time-resolved snapshots clearly demonstrate that the density of the trap states is significantly reduced after zinc sulfide (ZnS) shelling. Furthermore, the removal of trap states and elongation of carrier lifetime are confirmed by the increased photocurrent of the self-biased photodetector fabricated using the shelled NCs.

Contributions of pocket depth and electrostatic interactions to affinity and selectivity of receptors for methylated lysine in water.

PubMed

Beaver, Joshua E; Peacor, Brendan C; Bain, Julianne V; James, Lindsey I; Waters, Marcey L

2015-03-21

Dynamic combinatorial chemistry was used to generate a set of receptors for peptides containing methylated lysine (KMen, n = 0-3) and study the contribution of electrostatic effects and pocket depth to binding affinity and selectivity. We found that changing the location of a carboxylate resulted in an increase in preference for KMe2, presumably based on ability to form a salt bridge with KMe2. The number of charged groups on either the receptor or peptide guest systematically varied the binding affinities to all guests by approximately 1-1.5 kcal mol(-1), with little influence on selectivity. Lastly, formation of a deeper pocket led to both increased affinity and selectivity for KMe3 over the lower methylation states. From these studies, we identified that the tightest binder was a receptor with greater net charge, with a Kd of 0.2 μM, and the receptor with the highest selectivity was the one with the deepest pocket, providing 14-fold selectivity between KMe3 and KMe2 and a Kd for KMe3 of 0.3 μM. This work provides key insights into approaches to improve binding affinity and selectivity in water, while also demonstrating the versatility of dynamic combinatorial chemistry for rapidly exploring the impact of subtle changes in receptor functionality on molecular recognition in water.

Nuclear spin/parity dependent spectroscopy and predissociation dynamics in vOH = 2 ← 0 overtone excited Ne-H2O clusters: Theory and experiment

NASA Astrophysics Data System (ADS)

Ziemkiewicz, Michael P.; Pluetzer, Christian; Loreau, Jérôme; van der Avoird, Ad; Nesbitt, David J.

2017-12-01

Vibrationally state selective overtone spectroscopy and state- and nuclear spin-dependent predissociation dynamics of weakly bound ortho- and para-Ne-H2O complexes (D0(ortho) = 34.66 cm-1 and D0(para) = 31.67 cm-1) are reported, based on near-infrared excitation of van der Waals cluster bands correlating with vOH = 2 ← 0 overtone transitions (|02-〉 and |02+〉) out of the ortho (101) and para (000) internal rotor states of the H2O moiety. Quantum theoretical calculations for nuclear motion on a high level potential energy surface [CCSD(T)/VnZf12 (n = 3, 4)], corrected for basis set superposition error and extrapolated to the complete basis set (CBS) limit, are employed to successfully predict and assign Π-Σ, Σ-Σ, and Σ-Π infrared bands in the spectra, where Σ or Π represent approximate projections of the body-fixed H2O angular momentum along the Ne-H2O internuclear axis. IR-UV pump-probe experimental capabilities permit real-time measurements of the vibrational predissociation dynamics, which indicate facile intramolecular vibrational energy transfer from the H2O vOH = 2 overtone vibrations into the VdWs (van der Waals) dissociation coordinate on the τprediss = 15-25 ns time scale. Whereas all predicted strong transitions in the ortho-Ne-H2O complexes are readily detected and assigned, vibrationally mediated photolysis spectra for the corresponding para-Ne-H2O bands are surprisingly absent despite ab initio predictions of Q-branch intensities with S/N > 20-40. Such behavior signals the presence of highly selective nuclear spin ortho-para predissociation dynamics in the upper state, for which we offer a simple mechanism based on Ne-atom mediated intramolecular vibrational relaxation in the H2O subunit (i.e., |02±〉 → {|01±〉; v2 = 2}), which is confirmed by the ab initio energy level predictions and the nascent OH rotational (N), spin orbit (Π1/2,3/2), and lambda doublet product distributions.

Dynamic Changes in the Structure, Chemical State and Catalytic Selectivity of Cu Nanocubes during CO2 Electroreduction: Size and Support Effects.

PubMed

Grosse, Philipp; Gao, Dunfeng; Scholten, Fabian; Sinev, Ilya; Mistry, Hemma; Roldan Cuenya, Beatriz

2018-05-22

In situ and operando spectroscopic and microscopic methods were used to gain insight into the correlation between the structure, chemical state, and reactivity of size- and shape-controlled ligand-free Cu nanocubes during CO 2 electroreduction (CO 2 RR). Dynamic changes in the morphology and composition of Cu cubes supported on carbon were monitored under potential control through electrochemical atomic force microscopy, X-ray absorption fine-structure spectroscopy and X-ray photoelectron spectroscopy. Under reaction conditions, the roughening of the nanocube surface, disappearance of the (100) facets, formation of pores, loss of Cu and reduction of CuO x species observed were found to lead to a suppression of the selectivity for multi-carbon products (i.e. C 2 H 4 and ethanol) versus CH 4 . A comparison with Cu cubes supported on Cu foils revealed an enhanced morphological stability and persistence of Cu I species under CO 2 RR in the former samples. Both factors are held responsible for the higher C 2 /C 1 product ratio observed for the Cu cubes/Cu as compared to Cu cubes/C. Our findings highlight the importance of the structure of the active nanocatalyst but also its interaction with the underlying substrate in CO 2 RR selectivity. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enhanced inter-subject brain computer interface with associative sensorimotor oscillations.

PubMed

Saha, Simanto; Ahmed, Khawza I; Mostafa, Raqibul; Khandoker, Ahsan H; Hadjileontiadis, Leontios

2017-02-01

Electroencephalography (EEG) captures electrophysiological signatures of cortical events from the scalp with high-dimensional electrode montages. Usually, excessive sources produce outliers and potentially affect the actual event related sources. Besides, EEG manifests inherent inter-subject variability of the brain dynamics, at the resting state and/or under the performance of task(s), caused probably due to the instantaneous fluctuation of psychophysiological states. A wavelet coherence (WC) analysis for optimally selecting associative inter-subject channels is proposed here and is being used to boost performances of motor imagery (MI)-based inter-subject brain computer interface (BCI). The underlying hypothesis is that optimally associative inter-subject channels can reduce the effects of outliers and, thus, eliminate dissimilar cortical patterns. The proposed approach has been tested on the dataset IVa from BCI competition III, including EEG data acquired from five healthy subjects who were given visual cues to perform 280 trials of MI for the right hand and right foot. Experimental results have shown increased classification accuracy (81.79%) using the WC-based selected 16 channels compared to the one (56.79%) achieved using all the available 118 channels. The associative channels lie mostly around the sensorimotor regions of the brain, reinforced by the previous literature, describing spatial brain dynamics during sensorimotor oscillations. Apparently, the proposed approach paves the way for optimised EEG channel selection that could boost further the efficiency and real-time performance of BCI systems.

Developing a molecular dynamics force field for both folded and disordered protein states.

PubMed

Robustelli, Paul; Piana, Stefano; Shaw, David E

2018-05-07

Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural dynamics of folded proteins and should be similarly applicable to disordered proteins and proteins with both folded and disordered regions. It has been unclear, however, whether any physical model (force field) used in MD simulations accurately describes both folded and disordered proteins. Here, we select a benchmark set of 21 systems, including folded and disordered proteins, simulate these systems with six state-of-the-art force fields, and compare the results to over 9,000 available experimental data points. We find that none of the tested force fields simultaneously provided accurate descriptions of folded proteins, of the dimensions of disordered proteins, and of the secondary structure propensities of disordered proteins. Guided by simulation results on a subset of our benchmark, however, we modified parameters of one force field, achieving excellent agreement with experiment for disordered proteins, while maintaining state-of-the-art accuracy for folded proteins. The resulting force field, a99SB- disp , should thus greatly expand the range of biological systems amenable to MD simulation. A similar approach could be taken to improve other force fields. Copyright © 2018 the Author(s). Published by PNAS.

Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics.

PubMed

Higo, Junichi; Umezawa, Koji

2014-01-01

We introduce computational studies on intrinsically disordered proteins (IDPs). Especially, we present our multicanonical molecular dynamics (McMD) simulations of two IDP-partner systems: NRSF-mSin3 and pKID-KIX. McMD is one of enhanced conformational sampling methods useful for conformational sampling of biomolecular systems. IDP adopts a specific tertiary structure upon binding to its partner molecule, although it is unstructured in the unbound state (i.e. the free state). This IDP-specific property is called "coupled folding and binding". The McMD simulation treats the biomolecules with an all-atom model immersed in an explicit solvent. In the initial configuration of simulation, IDP and its partner molecules are set to be distant from each other, and the IDP conformation is disordered. The computationally obtained free-energy landscape for coupled folding and binding has shown that native- and non-native-complex clusters distribute complicatedly in the conformational space. The all-atom simulation suggests that both of induced-folding and population-selection are coupled complicatedly in the coupled folding and binding. Further analyses have exemplified that the conformational fluctuations (dynamical flexibility) in the bound and unbound states are essentially important to characterize IDP functioning.

Prediction of movement intention using connectivity within motor-related network: An electrocorticography study.

PubMed

Kang, Byeong Keun; Kim, June Sic; Ryun, Seokyun; Chung, Chun Kee

2018-01-01

Most brain-machine interface (BMI) studies have focused only on the active state of which a BMI user performs specific movement tasks. Therefore, models developed for predicting movements were optimized only for the active state. The models may not be suitable in the idle state during resting. This potential maladaptation could lead to a sudden accident or unintended movement resulting from prediction error. Prediction of movement intention is important to develop a more efficient and reasonable BMI system which could be selectively operated depending on the user's intention. Physical movement is performed through the serial change of brain states: idle, planning, execution, and recovery. The motor networks in the primary motor cortex and the dorsolateral prefrontal cortex are involved in these movement states. Neuronal communication differs between the states. Therefore, connectivity may change depending on the states. In this study, we investigated the temporal dynamics of connectivity in dorsolateral prefrontal cortex and primary motor cortex to predict movement intention. Movement intention was successfully predicted by connectivity dynamics which may reflect changes in movement states. Furthermore, dorsolateral prefrontal cortex is crucial in predicting movement intention to which primary motor cortex contributes. These results suggest that brain connectivity is an excellent approach in predicting movement intention.

Dynamic functional-structural coupling within acute functional state change phases: Evidence from a depression recognition study.

PubMed

Bi, Kun; Hua, Lingling; Wei, Maobin; Qin, Jiaolong; Lu, Qing; Yao, Zhijian

2016-02-01

Dynamic functional-structural connectivity (FC-SC) coupling might reflect the flexibility by which SC relates to functional connectivity (FC). However, during the dynamic acute state change phases of FC, the relationship between FC and SC may be distinctive and embody the abnormality inherent in depression. This study investigated the depression-related inter-network FC-SC coupling within particular dynamic acute state change phases of FC. Magnetoencephalography (MEG) and diffusion tensor imaging (DTI) data were collected from 26 depressive patients (13 women) and 26 age-matched controls (13 women). We constructed functional brain networks based on MEG data and structural networks from DTI data. The dynamic connectivity regression algorithm was used to identify the state change points of a time series of inter-network FC. The time period of FC that contained change points were partitioned into types of dynamic phases (acute rising phase, acute falling phase,acute rising and falling phase and abrupt FC variation phase) to explore the inter-network FC-SC coupling. The selected FC-SC couplings were then fed into the support vector machine (SVM) for depression recognition. The best discrimination accuracy was 82.7% (P=0.0069) with FC-SC couplings, particularly in the acute rising phase of FC. Within the FC phases of interest, the significant discriminative network pair was related to the salience network vs ventral attention network (SN-VAN) (P=0.0126) during the early rising phase (70-170ms). This study suffers from a small sample size, and the individual acute length of the state change phases was not considered. The increased values of significant discriminative vectors of FC-SC coupling in depression suggested that the capacity to process negative emotion might be more directly related to the SC abnormally and be indicative of more stringent and less dynamic brain function in SN-VAN, especially in the acute rising phase of FC. We demonstrated that depressive brain dysfunctions could be better characterized by reduced FC-SC coupling flexibility in this particular phase. Copyright © 2015 Elsevier B.V. All rights reserved.

Attractor concretion as a mechanism for the formation of context representations

PubMed Central

Rigotti, Mattia; Ben Dayan Rubin, Daniel; Morrison, Sara E.; Salzman, C. Daniel; Fusi, Stefano

2010-01-01

Complex tasks often require the memory of recent events, the knowledge about the context in which they occur, and the goals we intend to reach. All this information is stored in our mental states. Given a set of mental states, reinforcement learning (RL) algorithms predict the optimal policy that maximizes future reward. RL algorithms assign a value to each already-known state so that discovering the optimal policy reduces to selecting the action leading to the state with the highest value. But how does the brain create representations of these mental states in the first place? We propose a mechanism for the creation of mental states that contain information about the temporal statistics of the events in a particular context. We suggest that the mental states are represented by stable patterns of reverberating activity, which are attractors of the neural dynamics. These representations are built from neurons that are selective to specific combinations of external events (e.g. sensory stimuli) and pre-existent mental states. Consistent with this notion, we find that neurons in the amygdala and in orbito-frontal cortex (OFC) often exhibit this form of mixed selectivity. We propose that activating different mixed selectivity neurons in a fixed temporal order modifies synaptic connections so that conjunctions of events and mental states merge into a single pattern of reverberating activity. This process corresponds to the birth of a new different mental state that encodes a different temporal context. The concretion process depends on temporal contiguity, i.e. on the probability that a combination of an event and mental states follows or precedes the events and states that define a certain context. The information contained in the context thereby allows an animal to assign unambiguously a value to the events that initially appeared in different situations with different meanings. PMID:20100580

Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms

PubMed Central

Yang, Li-Quan; Sang, Peng; Tao, Yan; Fu, Yun-Xin; Zhang, Ke-Qin; Xie, Yue-Hui; Liu, Shu-Qun

2013-01-01

Proteins are dynamic entities in cellular solution with functions governed essentially by their dynamic personalities. We review several dynamics studies on serine protease proteinase K and HIV-1 gp120 envelope glycoprotein to demonstrate the importance of investigating the dynamic behaviors and molecular motions for a complete understanding of their structure–function relationships. Using computer simulations and essential dynamic (ED) analysis approaches, the dynamics data obtained revealed that: (i) proteinase K has highly flexible substrate-binding site, thus supporting the induced-fit or conformational selection mechanism of substrate binding; (ii) Ca2+ removal from proteinase K increases the global conformational flexibility, decreases the local flexibility of substrate-binding region, and does not influence the thermal motion of catalytic triad, thus explaining the experimentally determined decreased thermal stability, reduced substrate affinity, and almost unchanged catalytic activity upon Ca2+ removal; (iii) substrate binding affects the large concerted motions of proteinase K, and the resulting dynamic pocket can be connected to substrate binding, orientation, and product release; (iv) amino acid mutations 375 S/W and 423 I/P of HIV-1 gp120 have distinct effects on molecular motions of gp120, facilitating 375 S/W mutant to assume the CD4-bound conformation, while 423 I/P mutant to prefer for CD4-unliganded state. The mechanisms underlying protein dynamics and protein–ligand binding, including the concept of the free energy landscape (FEL) of the protein–solvent system, how the ruggedness and variability of FEL determine protein's dynamics, and how the three ligand-binding models, the lock-and-key, induced-fit, and conformational selection are rationalized based on the FEL theory are discussed in depth. PMID:23527883

Protein dynamics and motions in relation to their functions: several case studies and the underlying mechanisms.

PubMed

Yang, Li-Quan; Sang, Peng; Tao, Yan; Fu, Yun-Xin; Zhang, Ke-Qin; Xie, Yue-Hui; Liu, Shu-Qun

2014-01-01

Proteins are dynamic entities in cellular solution with functions governed essentially by their dynamic personalities. We review several dynamics studies on serine protease proteinase K and HIV-1 gp120 envelope glycoprotein to demonstrate the importance of investigating the dynamic behaviors and molecular motions for a complete understanding of their structure-function relationships. Using computer simulations and essential dynamic (ED) analysis approaches, the dynamics data obtained revealed that: (i) proteinase K has highly flexible substrate-binding site, thus supporting the induced-fit or conformational selection mechanism of substrate binding; (ii) Ca(2+) removal from proteinase K increases the global conformational flexibility, decreases the local flexibility of substrate-binding region, and does not influence the thermal motion of catalytic triad, thus explaining the experimentally determined decreased thermal stability, reduced substrate affinity, and almost unchanged catalytic activity upon Ca(2+) removal; (iii) substrate binding affects the large concerted motions of proteinase K, and the resulting dynamic pocket can be connected to substrate binding, orientation, and product release; (iv) amino acid mutations 375 S/W and 423 I/P of HIV-1 gp120 have distinct effects on molecular motions of gp120, facilitating 375 S/W mutant to assume the CD4-bound conformation, while 423 I/P mutant to prefer for CD4-unliganded state. The mechanisms underlying protein dynamics and protein-ligand binding, including the concept of the free energy landscape (FEL) of the protein-solvent system, how the ruggedness and variability of FEL determine protein's dynamics, and how the three ligand-binding models, the lock-and-key, induced-fit, and conformational selection are rationalized based on the FEL theory are discussed in depth.

Mining Time-Resolved Functional Brain Graphs to an EEG-Based Chronnectomic Brain Aged Index (CBAI).

PubMed

Dimitriadis, Stavros I; Salis, Christos I

2017-01-01

The brain at rest consists of spatially and temporal distributed but functionally connected regions that called intrinsic connectivity networks (ICNs). Resting state electroencephalography (rs-EEG) is a way to characterize brain networks without confounds associated with task EEG such as task difficulty and performance. A novel framework of how to study dynamic functional connectivity under the notion of functional connectivity microstates (FCμstates) and symbolic dynamics is further discussed. Furthermore, we introduced a way to construct a single integrated dynamic functional connectivity graph (IDFCG) that preserves both the strength of the connections between every pair of sensors but also the type of dominant intrinsic coupling modes (DICM). The whole methodology is demonstrated in a significant and unexplored task for EEG which is the definition of an objective Chronnectomic Brain Aged index (CBAI) extracted from resting-state data ( N = 94 subjects) with both eyes-open and eyes-closed conditions. Novel features have been defined based on symbolic dynamics and the notion of DICM and FCμstates. The transition rate of FCμstates, the symbolic dynamics based on the evolution of FCμstates (the Markovian Entropy, the complexity index), the probability distribution of DICM, the novel Flexibility Index that captures the dynamic reconfiguration of DICM per pair of EEG sensors and the relative signal power constitute a valuable pool of features that can build the proposed CBAI. Here we applied a feature selection technique and Extreme Learning Machine (ELM) classifier to discriminate young adults from middle-aged and a Support Vector Regressor to build a linear model of the actual age based on EEG-based spatio-temporal features. The most significant type of features for both prediction of age and discrimination of young vs. adults age groups was the dynamic reconfiguration of dominant coupling modes derived from a subset of EEG sensor pairs. Specifically, our results revealed a very high prediction of age for eyes-open ( R 2 = 0.60; y = 0.79x + 8.03) and lower for eyes-closed ( R 2 = 0.48; y = 0.71x + 10.91) while we succeeded to correctly classify young vs. middle-age group with 97.8% accuracy in eyes-open and 87.2% for eyes-closed. Our results were reproduced also in a second dataset for further external validation of the whole analysis. The proposed methodology proved valuable for the characterization of the intrinsic properties of dynamic functional connectivity through the age untangling developmental differences using EEG resting-state recordings.

Line Narrowing of Excited-State Transitions in Nonlinear Polarization Spectroscopy: Application to Water-Soluble Chlorophyll-Binding Protein

NASA Astrophysics Data System (ADS)

Schoth, Mario; Richter, Marten; Knorr, Andreas; Renger, Thomas

2012-04-01

The homogeneous linewidth of dye aggregates like photosynthetic light-harvesting complexes contains important information about energy transfer and relaxation times that is, however, masked by inhomogeneous broadening caused by static disorder. Whereas there exist line narrowing techniques for the study of low-energy exciton states, the homogeneous linewidth of the high-energy states is not so easy to decipher. Here we present a microscopic theory for nonlinear polarization spectroscopy in the frequency domain that contains a dynamic aggregate selection revealing the homogeneous linewidth of these states. The theory is applied to the water-soluble chlorophyll-binding protein for which the high-energy exciton state was predicted to exhibit a sub-100-fs lifetime.

Gelation-driven selection in dynamic covalent C 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 C/CN exchange.

PubMed

Liang, Chunshuang; Kulchat, Sirinan; Jiang, Shimei; Lehn, Jean-Marie

2017-10-01

Knoevenagel barbiturate derivatives bearing long alkyl chains were proven to form organogels in suitable solvents based on supramolecular interactions. Their reaction with imines allows for component exchange through CC/CN recombination. The effect of various parameters (solvents, chain length, and temperature) on the CC/CN exchange reaction has been studied. Mixing Knoevenagel compound K and imine I-16 in a 1 : 1 ratio generated a constitutional dynamic library containing the four constituents K , I-16 , K'-16 , and I' . The reversible exchange reaction was monitored by 1 H-NMR, showing marked changes in the fractions of the four constituents on sol-gel interconversion as a function of temperature. The library composition changed from statistical distribution of the four constituents in the sol state to selective amplification of the gel forming K'-16 constituent together with that of its agonist I' . The process amounts to self-organization driven component selection in a constitutional dynamic organogel system undergoing gelation. This process displays up-regulation of the gel-forming constituent by component redistribution through reversible covalent connections.

Dynamic load simulator

NASA Technical Reports Server (NTRS)

Joncas, K. P.

1972-01-01

Concepts and techniques for identifying and simulating both the steady state and dynamic characteristics of electrical loads for use during integrated system test and evaluation are discussed. The investigations showed that it is feasible to design and develop interrogation and simulation equipment to perform the desired functions. During the evaluation, actual spacecraft loads were interrogated by stimulating the loads with their normal input voltage and measuring the resultant voltage and current time histories. Elements of the circuits were optimized by an iterative process of selecting element values and comparing the time-domain response of the model with those obtained from the real equipment during interrogation.

Stimulated Raman Spectroscopy with Entangled Light: Enhanced Resolution and Pathway Selection

PubMed Central

2015-01-01

We propose a novel femtosecond stimulated Raman spectroscopy (FSRS) technique that combines entangled photons with interference detection to select matter pathways and enhance the resolution. Following photoexcitation by an actinic pump, the measurement uses a pair of broad-band entangled photons; one (signal) interacts with the molecule and together with a third narrow-band pulse induces the Raman process. The other (idler) photon provides a reference for the coincidence measurement. This interferometric photon coincidence counting detection allows one to separately measure the Raman gain and loss signals, which is not possible with conventional probe transmission detection. Entangled photons further provide a unique temporal and spectral detection window that can better resolve fast excited-state dynamics compared to classical and correlated disentangled states of light. PMID:25177427

Development and application of a new grey dynamic hierarchy analysis system (GDHAS) for evaluating urban ecological security.

PubMed

Shao, Chaofeng; Tian, Xiaogang; Guan, Yang; Ju, Meiting; Xie, Qiang

2013-05-21

Selecting indicators based on the characteristics and development trends of a given study area is essential for building a framework for assessing urban ecological security. However, few studies have focused on how to select the representative indicators systematically, and quantitative research is lacking. We developed an innovative quantitative modeling approach called the grey dynamic hierarchy analytic system (GDHAS) for both the procedures of indicator selection and quantitative assessment of urban ecological security. Next, a systematic methodology based on the GDHAS is developed to assess urban ecological security comprehensively and dynamically. This assessment includes indicator selection, driving force-pressure-state-impact-response (DPSIR) framework building, and quantitative evaluation. We applied this systematic methodology to assess the urban ecological security of Tianjin, which is a typical coastal super megalopolis and the industry base in China. This case study highlights the key features of our approach. First, 39 representative indicators are selected for the evaluation index system from 62 alternative ones available through the GDHAS. Second, the DPSIR framework is established based on the indicators selected, and the quantitative assessment of the eco-security of Tianjin is conducted. The results illustrate the following: urban ecological security of Tianjin in 2008 was in alert level but not very stable; the driving force and pressure subsystems were in good condition, but the eco-security levels of the remainder of the subsystems were relatively low; the pressure subsystem was the key to urban ecological security; and 10 indicators are defined as the key indicators for five subsystems. These results can be used as the basis for urban eco-environmental management.

Development and Application of a New Grey Dynamic Hierarchy Analysis System (GDHAS) for Evaluating Urban Ecological Security

PubMed Central

Shao, Chaofeng; Tian, Xiaogang; Guan, Yang; Ju, Meiting; Xie, Qiang

2013-01-01

Selecting indicators based on the characteristics and development trends of a given study area is essential for building a framework for assessing urban ecological security. However, few studies have focused on how to select the representative indicators systematically, and quantitative research is lacking. We developed an innovative quantitative modeling approach called the grey dynamic hierarchy analytic system (GDHAS) for both the procedures of indicator selection and quantitative assessment of urban ecological security. Next, a systematic methodology based on the GDHAS is developed to assess urban ecological security comprehensively and dynamically. This assessment includes indicator selection, driving force-pressure-state-impact-response (DPSIR) framework building, and quantitative evaluation. We applied this systematic methodology to assess the urban ecological security of Tianjin, which is a typical coastal super megalopolis and the industry base in China. This case study highlights the key features of our approach. First, 39 representative indicators are selected for the evaluation index system from 62 alternative ones available through the GDHAS. Second, the DPSIR framework is established based on the indicators selected, and the quantitative assessment of the eco-security of Tianjin is conducted. The results illustrate the following: urban ecological security of Tianjin in 2008 was in alert level but not very stable; the driving force and pressure subsystems were in good condition, but the eco-security levels of the remainder of the subsystems were relatively low; the pressure subsystem was the key to urban ecological security; and 10 indicators are defined as the key indicators for five subsystems. These results can be used as the basis for urban eco-environmental management. PMID:23698700

Agent-Based Modeling of Mitochondria Links Sub-Cellular Dynamics to Cellular Homeostasis and Heterogeneity.

PubMed

Dalmasso, Giovanni; Marin Zapata, Paula Andrea; Brady, Nathan Ryan; Hamacher-Brady, Anne

2017-01-01

Mitochondria are semi-autonomous organelles that supply energy for cellular biochemistry through oxidative phosphorylation. Within a cell, hundreds of mobile mitochondria undergo fusion and fission events to form a dynamic network. These morphological and mobility dynamics are essential for maintaining mitochondrial functional homeostasis, and alterations both impact and reflect cellular stress states. Mitochondrial homeostasis is further dependent on production (biogenesis) and the removal of damaged mitochondria by selective autophagy (mitophagy). While mitochondrial function, dynamics, biogenesis and mitophagy are highly-integrated processes, it is not fully understood how systemic control in the cell is established to maintain homeostasis, or respond to bioenergetic demands. Here we used agent-based modeling (ABM) to integrate molecular and imaging knowledge sets, and simulate population dynamics of mitochondria and their response to environmental energy demand. Using high-dimensional parameter searches we integrated experimentally-measured rates of mitochondrial biogenesis and mitophagy, and using sensitivity analysis we identified parameter influences on population homeostasis. By studying the dynamics of cellular subpopulations with distinct mitochondrial masses, our approach uncovered system properties of mitochondrial populations: (1) mitochondrial fusion and fission activities rapidly establish mitochondrial sub-population homeostasis, and total cellular levels of mitochondria alter fusion and fission activities and subpopulation distributions; (2) restricting the directionality of mitochondrial mobility does not alter morphology subpopulation distributions, but increases network transmission dynamics; and (3) maintaining mitochondrial mass homeostasis and responding to bioenergetic stress requires the integration of mitochondrial dynamics with the cellular bioenergetic state. Finally, (4) our model suggests sources of, and stress conditions amplifying, cell-to-cell variability of mitochondrial morphology and energetic stress states. Overall, our modeling approach integrates biochemical and imaging knowledge, and presents a novel open-modeling approach to investigate how spatial and temporal mitochondrial dynamics contribute to functional homeostasis, and how subcellular organelle heterogeneity contributes to the emergence of cell heterogeneity.

Modelling and simulation of biased agonism dynamics at a G protein-coupled receptor.

PubMed

Bridge, L J; Mead, J; Frattini, E; Winfield, I; Ladds, G

2018-04-07

Theoretical models of G protein-coupled receptor (GPCR) concentration-response relationships often assume an agonist producing a single functional response via a single active state of the receptor. These models have largely been analysed assuming steady-state conditions. There is now much experimental evidence to suggest that many GPCRs can exist in multiple receptor conformations and elicit numerous functional responses, with ligands having the potential to activate different signalling pathways to varying extents-a concept referred to as biased agonism, functional selectivity or pluri-dimensional efficacy. Moreover, recent experimental results indicate a clear possibility for time-dependent bias, whereby an agonist's bias with respect to different pathways may vary dynamically. Efforts towards understanding the implications of temporal bias by characterising and quantifying ligand effects on multiple pathways will clearly be aided by extending current equilibrium binding and biased activation models to include G protein activation dynamics. Here, we present a new model of time-dependent biased agonism, based on ordinary differential equations for multiple cubic ternary complex activation models with G protein cycle dynamics. This model allows simulation and analysis of multi-pathway activation bias dynamics at a single receptor for the first time, at the level of active G protein (α GTP ), towards the analysis of dynamic functional responses. The model is generally applicable to systems with N G G proteins and N* active receptor states. Numerical simulations for N G =N * =2 reveal new insights into the effects of system parameters (including cooperativities, and ligand and receptor concentrations) on bias dynamics, highlighting new phenomena including the dynamic inter-conversion of bias direction. Further, we fit this model to 'wet' experimental data for two competing G proteins (G i and G s ) that become activated upon stimulation of the adenosine A 1 receptor with adenosine derivative compounds. Finally, we show that our model can qualitatively describe the temporal dynamics of this competing G protein activation. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Agent-Based Modeling of Mitochondria Links Sub-Cellular Dynamics to Cellular Homeostasis and Heterogeneity

PubMed Central

Dalmasso, Giovanni; Marin Zapata, Paula Andrea; Brady, Nathan Ryan; Hamacher-Brady, Anne

2017-01-01

Mitochondria are semi-autonomous organelles that supply energy for cellular biochemistry through oxidative phosphorylation. Within a cell, hundreds of mobile mitochondria undergo fusion and fission events to form a dynamic network. These morphological and mobility dynamics are essential for maintaining mitochondrial functional homeostasis, and alterations both impact and reflect cellular stress states. Mitochondrial homeostasis is further dependent on production (biogenesis) and the removal of damaged mitochondria by selective autophagy (mitophagy). While mitochondrial function, dynamics, biogenesis and mitophagy are highly-integrated processes, it is not fully understood how systemic control in the cell is established to maintain homeostasis, or respond to bioenergetic demands. Here we used agent-based modeling (ABM) to integrate molecular and imaging knowledge sets, and simulate population dynamics of mitochondria and their response to environmental energy demand. Using high-dimensional parameter searches we integrated experimentally-measured rates of mitochondrial biogenesis and mitophagy, and using sensitivity analysis we identified parameter influences on population homeostasis. By studying the dynamics of cellular subpopulations with distinct mitochondrial masses, our approach uncovered system properties of mitochondrial populations: (1) mitochondrial fusion and fission activities rapidly establish mitochondrial sub-population homeostasis, and total cellular levels of mitochondria alter fusion and fission activities and subpopulation distributions; (2) restricting the directionality of mitochondrial mobility does not alter morphology subpopulation distributions, but increases network transmission dynamics; and (3) maintaining mitochondrial mass homeostasis and responding to bioenergetic stress requires the integration of mitochondrial dynamics with the cellular bioenergetic state. Finally, (4) our model suggests sources of, and stress conditions amplifying, cell-to-cell variability of mitochondrial morphology and energetic stress states. Overall, our modeling approach integrates biochemical and imaging knowledge, and presents a novel open-modeling approach to investigate how spatial and temporal mitochondrial dynamics contribute to functional homeostasis, and how subcellular organelle heterogeneity contributes to the emergence of cell heterogeneity. PMID:28060865

Orbital-selective Mott phase in multiorbital models for iron pnictides and chalcogenides

NASA Astrophysics Data System (ADS)

Yu, Rong; Si, Qimiao

2017-09-01

There is increasing recognition that the multiorbital nature of the 3 d electrons is important to the proper description of the electronic states in the normal state of the iron-based superconductors. Earlier studies of the pertinent multiorbital Hubbard models identified an orbital-selective Mott phase, which anchors the orbital-selective behavior seen in the overall phase diagram. An important characteristics of the models is that the orbitals are kinetically coupled, i.e., hybridized, to each other, which makes the orbital-selective Mott phase especially nontrivial. A U (1 ) slave-spin method was used to analyze the model with nonzero orbital-level splittings. Here we develop a Landau free-energy functional to shed further light on this issue. We put the microscopic analysis from the U (1 ) slave-spin approach in this perspective, and show that the intersite spin correlations are crucial to the renormalization of the bare hybridization amplitude towards zero and the concomitant realization of the orbital-selective Mott transition. Based on this insight, we discuss additional ways to study the orbital-selective Mott physics from a dynamical competition between the interorbital hybridization and collective spin correlations. Our results demonstrate the robustness of the orbital-selective Mott phase in the multiorbital models appropriate for the iron-based superconductors.

Hamiltonian flow over saddles for exploring molecular phase space structures

NASA Astrophysics Data System (ADS)

Farantos, Stavros C.

2018-03-01

Despite using potential energy surfaces, multivariable functions on molecular configuration space, to comprehend chemical dynamics for decades, the real happenings in molecules occur in phase space, in which the states of a classical dynamical system are completely determined by the coordinates and their conjugate momenta. Theoretical and numerical results are presented, employing alanine dipeptide as a model system, to support the view that geometrical structures in phase space dictate the dynamics of molecules, the fingerprints of which are traced by following the Hamiltonian flow above saddles. By properly selecting initial conditions in alanine dipeptide, we have found internally free rotor trajectories the existence of which can only be justified in a phase space perspective. This article is part of the theme issue `Modern theoretical chemistry'.

The Behavior of Matter under Nonequilibrium Conditions: Fundamental Aspects and Applications in Energy-oriented Problems: Progress Report for Period September 1984--November 1987

DOE R&D Accomplishments Database

Prigogine, I.

1987-10-07

This report briefly discusses progress on the following topics: state selection dynamics; polymerization under nonequilibrium conditions; inhomogeneous fluctuations in hydrodynamics and in completely mixed reactors; homoclinic bifurcations and mixed-mode oscillations; intrinsic randomness and spontaneous symmetry breaking in explosive systems; and microscopic means of irreversibility.

Temperature modulation and quadrature detection for selective titration of two-state exchanging reactants.

PubMed

Zrelli, K; Barilero, T; Cavatore, E; Berthoumieux, H; Le Saux, T; Croquette, V; Lemarchand, A; Gosse, C; Jullien, L

2011-04-01

Biological samples exhibit huge molecular diversity over large concentration ranges. Titrating a given compound in such mixtures is often difficult, and innovative strategies emphasizing selectivity are thus demanded. To overcome limitations inherent to thermodynamics, we here present a generic technique where discrimination relies on the dynamics of interaction between the target of interest and a probe introduced in excess. Considering an ensemble of two-state exchanging reactants submitted to temperature modulation, we first demonstrate that the amplitude of the out-of-phase concentration oscillations is maximum for every compound involved in a reaction whose equilibrium constant is equal to unity and whose relaxation time is equal to the inverse of the excitation angular frequency. Taking advantage of this feature, we next devise a highly specific detection protocol and validate it using a microfabricated resistive heater and an epifluorescence microscope, as well as labeled oligonucleotides to model species displaying various dynamic properties. As expected, quantification of a sought for strand is obtained even if interfering reagents are present in similar amounts. Moreover, our approach does not require any separation and is compatible with imaging. It could then benefit some of the numerous binding assays performed every day in life sciences.

Probing Silica-Biomolecule Interactions by Solid-State NMR and Molecular Dynamics Simulations.

PubMed

Brückner, Stephan Ingmar; Donets, Sergii; Dianat, Arezoo; Bobeth, Manfred; Gutiérrez, Rafael; Cuniberti, Gianaurelio; Brunner, Eike

2016-11-08

Understanding the molecular interactions between inorganic phases such as silica and organic material is fundamental for chromatographic applications, for tailoring silica-enzyme interactions, and for elucidating the mechanisms of biomineralization. The formation, structure, and properties of the organic/inorganic interface is crucial in this context. Here, we investigate the interaction of selectively 13 C-labeled choline with 29 Si-labeled monosilicic acid/silica at the molecular level. Silica/choline nanocomposites were analyzed by solid-state NMR spectroscopy in combination with extended molecular dynamics (MD) simulations to understand the silica/organic interface. Cross-polarization magic angle spinning (CP MAS)-based NMR experiments like 1 H- 13 C CP-REDOR (rotational-echo double resonance), 1 H- 13 C HETCOR (heteronuclear correlation), and 1 H- 29 Si- 1 H double CP are employed to determine spatial parameters. The measurement of 29 Si- 13 C internuclear distances for selectively 13 C-labeled choline provides an experimental parameter that allows the direct verification of MD simulations. Atomistic modeling using classical MD methodologies is performed using the INTERFACE force field. The modeling results are in excellent agreement with the experimental data and reveal the relevant molecular conformations as well as the nature and interplay of the interactions between the choline cation and the silica surface. Electrostatic interactions and hydrogen bonding are both important and depend strongly on the hydration level as well as the charge state of the silica surface.

Non-steady state mass action dynamics without rate constants: dynamics of coupled reactions using chemical potentials

NASA Astrophysics Data System (ADS)

Cannon, William R.; Baker, Scott E.

2017-10-01

Comprehensive and predictive simulation of coupled reaction networks has long been a goal of biology and other fields. Currently, metabolic network models that utilize enzyme mass action kinetics have predictive power but are limited in scope and application by the fact that the determination of enzyme rate constants is laborious and low throughput. We present a statistical thermodynamic formulation of the law of mass action for coupled reactions at both steady states and non-stationary states. The formulation uses chemical potentials instead of rate constants. When used to model deterministic systems, the method corresponds to a rescaling of the time dependent reactions in such a way that steady states can be reached on the same time scale but with significantly fewer computational steps. The relationships between reaction affinities, free energy changes and generalized detailed balance are central to the discussion. The significance for applications in systems biology are discussed as is the concept and assumption of maximum entropy production rate as a biological principle that links thermodynamics to natural selection.

Component-Level Selection and Qualification for the Global Ecosystem Dynamics Investigation (GEDI) Laser Altimeter Transmitter

NASA Technical Reports Server (NTRS)

Frese, Erich A.; Chiragh, Furqan L.; Switzer, Robert; Vasilyev, Aleksey A.; Thomes, Joe; Coyle, D. Barry; Stysley, Paul R.

2018-01-01

Flight quality solid-state lasers require a unique and extensive set of testing and qualification processes, both at the system and component levels to insure the laser's promised performance. As important as the overall laser transmitter design is, the quality and performance of individual subassemblies, optics, and electro-optics dictate the final laser unit's quality. The Global Ecosystem Dynamics Investigation (GEDI) laser transmitters employ all the usual components typical for a diode-pumped, solid-state laser, yet must each go through their own individual process of specification, modeling, performance demonstration, inspection, and destructive testing. These qualification processes and results for the laser crystals, laser diode arrays, electro-optics, and optics, will be reviewed as well as the relevant critical issues encountered, prior to their installation in the GEDI flight laser units.

Methods for Modeling Brassinosteroid-Mediated Signaling in Plant Development.

PubMed

Frigola, David; Caño-Delgado, Ana I; Ibañes, Marta

2017-01-01

Mathematical modeling of biological processes is a useful tool to draw conclusions that are contained in the data, but not directly reachable, as well as to make predictions and select the most efficient follow-up experiments. Here we outline a method to model systems of a few proteins that interact transcriptionally and/or posttranscriptionally, by representing the system as Ordinary Differential Equations and to study the model dynamics and stationary states. We exemplify this method by focusing on the regulation by the brassinosteroid (BR) signaling component BRASSINOSTEROID INSENSITIVE1 ETHYL METHYL SULFONATE SUPPRESSOR1 (BES1) of BRAVO, a quiescence-regulating transcription factor expressed in the quiescent cells of Arabidopsis thaliana roots. The method to extract the stationary states and the dynamics is provided as a Mathematica code and requires basic knowledge of the Mathematica software to be executed.

Dynamic Stall Suppression Using Combustion-Powered Actuation (COMPACT)

NASA Technical Reports Server (NTRS)

Matalanis, Claude G.; Bowles, Patrick O.; Jee, Solkeun; Min, Byung-Young; Kuczek, Andrzej E.; Croteau, Paul F.; Wake, Brian E.; Crittenden, Thomas; Glezer, Ari; Lorber, Peter F.

2016-01-01

Retreating blade stall is a well-known phenomenon that limits rotorcraft speed, maneuverability, and efficiency. Airfoil dynamic stall is a simpler problem, which demonstrates many of the same flow phenomena. Combustion Powered Actuation (COMPACT) is an active flow control technology, which at the outset of this work, had been shown to mitigate static and dynamic stall at low Mach numbers. The attributes of this technology suggested strong potential for success at higher Mach numbers, but such experiments had never been conducted. The work detailed in this report documents a 3-year effort focused on assessing the effectiveness of COMPACT for dynamic stall suppression at freestream conditions up to Mach 0.5. The work done has focused on implementing COMPACT on a high-lift rotorcraft airfoil: the VR-12. This selection was made in order to ensure that any measured benefits are over and above the capabilities of state-of-the-art high-lift rotorcraft airfoils. The detailed Computational Fluid Dynamics (CFD) simulations, wind-tunnel experiments, and system-level modeling conducted have shown the following: (1) COMPACT, in its current state of development, is capable of reducing the adverse effects of deep dynamic stall at Mach numbers up to 0.4; (2) The two-dimensional (2D) CFD results trend well compared to the experiments; and (3) Implementation of the CFD results into a system-level model suggest that significant rotor-level benefits are possible.

Structure-Functional Basis of Ion Transport in Sodium–Calcium Exchanger (NCX) Proteins

PubMed Central

Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

2016-01-01

The membrane-bound sodium–calcium exchanger (NCX) proteins shape Ca2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen–deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α1 and α2 repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na+ or Ca2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca2+/cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins. PMID:27879668

Structure-Functional Basis of Ion Transport in Sodium-Calcium Exchanger (NCX) Proteins.

PubMed

Giladi, Moshe; Shor, Reut; Lisnyansky, Michal; Khananshvili, Daniel

2016-11-22

The membrane-bound sodium-calcium exchanger (NCX) proteins shape Ca 2+ homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen-deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants. Strikingly, the apo NCX_Mj protein exhibits characteristic patterns in the local backbone dynamics at particular helix segments, thereby possessing characteristic HDX profiles, suggesting structure-dynamic preorganization (geometric arrangements of catalytic residues before the transition state) of conserved α₁ and α₂ repeats at ion-coordinating residues involved in transport activities. Moreover, dynamic preorganization of local structural entities in the apo protein predefines the status of ion-occlusion and transition states, even though Na⁺ or Ca 2+ binding modifies the preceding backbone dynamics nearby functionally important residues. Future challenges include resolving the structural-dynamic determinants governing the ion selectivity, functional asymmetry and ion-induced alternating access. Taking into account the structural similarities of NCX_Mj with the other proteins belonging to the Ca 2+ /cation exchanger superfamily, the recent findings can significantly improve our understanding of ion transport mechanisms in NCX and similar proteins.

Optimizing Experimental Design for Comparing Models of Brain Function

PubMed Central

Daunizeau, Jean; Preuschoff, Kerstin; Friston, Karl; Stephan, Klaas

2011-01-01

This article presents the first attempt to formalize the optimization of experimental design with the aim of comparing models of brain function based on neuroimaging data. We demonstrate our approach in the context of Dynamic Causal Modelling (DCM), which relates experimental manipulations to observed network dynamics (via hidden neuronal states) and provides an inference framework for selecting among candidate models. Here, we show how to optimize the sensitivity of model selection by choosing among experimental designs according to their respective model selection accuracy. Using Bayesian decision theory, we (i) derive the Laplace-Chernoff risk for model selection, (ii) disclose its relationship with classical design optimality criteria and (iii) assess its sensitivity to basic modelling assumptions. We then evaluate the approach when identifying brain networks using DCM. Monte-Carlo simulations and empirical analyses of fMRI data from a simple bimanual motor task in humans serve to demonstrate the relationship between network identification and the optimal experimental design. For example, we show that deciding whether there is a feedback connection requires shorter epoch durations, relative to asking whether there is experimentally induced change in a connection that is known to be present. Finally, we discuss limitations and potential extensions of this work. PMID:22125485

Identifying highly connected counties compensates for resource limitations when evaluating national spread of an invasive pathogen.

PubMed

Sutrave, Sweta; Scoglio, Caterina; Isard, Scott A; Hutchinson, J M Shawn; Garrett, Karen A

2012-01-01

Surveying invasive species can be highly resource intensive, yet near-real-time evaluations of invasion progress are important resources for management planning. In the case of the soybean rust invasion of the United States, a linked monitoring, prediction, and communication network saved U.S. soybean growers approximately $200 M/yr. Modeling of future movement of the pathogen (Phakopsora pachyrhizi) was based on data about current disease locations from an extensive network of sentinel plots. We developed a dynamic network model for U.S. soybean rust epidemics, with counties as nodes and link weights a function of host hectarage and wind speed and direction. We used the network model to compare four strategies for selecting an optimal subset of sentinel plots, listed here in order of increasing performance: random selection, zonal selection (based on more heavily weighting regions nearer the south, where the pathogen overwinters), frequency-based selection (based on how frequently the county had been infected in the past), and frequency-based selection weighted by the node strength of the sentinel plot in the network model. When dynamic network properties such as node strength are characterized for invasive species, this information can be used to reduce the resources necessary to survey and predict invasion progress.

Iowa State University – Final Report for SciDAC3/NUCLEI

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

Vary, James P

The Iowa State University (ISU) contributions to the NUCLEI project are focused on developing, implementing and running an efficient and scalable configuration interaction code (Many-Fermion Dynamics – nuclear or MFDn) for leadership class supercomputers addressing forefront research problems in low-energy nuclear physics. We investigate nuclear structure and reactions with realistic nucleon-nucleon (NN) and three-nucleon (3N) interactions. We select a few highlights from our work that has produced a total of more than 82 refereed publications and more than 109 invited talks under SciDAC3/NUCLEI.

Inner-shell excitation and ionic fragmentation of molecules

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

Hitchcock, A.P.; Tyliszczak, T.; Cavell, R.G.

1997-04-01

Inner-shell excitation and associated decay spectroscopies are site specific probes of electronic and geometrical structure and photoionization dynamics. X-ray absorption probes the geometric and electronic structure, while time-of-flight mass spectrometry with multi-coincidence detection provides information on the photofragmentation dynamics of the initially produced inner-shell state. Auger decay of inner-shell excited and ionised states is an efficient source of multiply charged ions. The charge separation and fragmentation of these species, studied by photoelectron-photoion-photoion coincidence (also called charge separation mass spectrometry) gives insights into bonding and electronic structure. In molecules, the dependence of the fragmentation process on the X-ray energy can revealmore » cases of site and/or state selective fragmentation. At the ALS the authors have examined the soft X-ray spectroscopy and ionic fragmentation of a number of molecules, including carboranes, silylenes, phosphorus halides, SF{sub 6} and CO{sub 2}. Their work is illustrated using results from the carborane and PF{sub 3} studies.« less

Excited-state absorption and fluorescence dynamics of Er3+:KY3F10

NASA Astrophysics Data System (ADS)

Labbé, C.; Doualan, J. L.; Moncorgé, R.; Braud, A.; Camy, P.

2018-05-01

We report here on a complete investigation of the excited-state absorption and fluorescence dynamics of Er3+ doped KY3F10 single crystals versus dopant concentrations and optical excitation conditions. Radiative and effective (including non-radiative relaxations) emission lifetimes and branching ratios are determined from a Judd-Ofelt analysis of the absorption spectra and via specific fluorescence experiments using wavelength selective laser excitations. Excited-state absorption and emission spectra are registered within seven spectral domains, i.e. 560 nm, 650 nm, 710 nm, 810 nm, 970 nm, 1550 nm and 2750 nm. A maximum gain cross-section of 0.93 × 10-21 cm2 is determined at the potential laser wavelength of 2.801 μm for a population ratio of 0.48. Saturation of fluorescence intensities and variations of population ratios versus pumping rates are registered and confronted with a rate equation model to derive the rates of the most important up-conversion and cross-relaxation energy transfers occurring at high dopant concentrations.

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

Williamson, David L.; Olson, Jerry G.; Hannay, Cécile

An error in the energy formulation in the Community Atmosphere Model (CAM) is identified and corrected. Ten year AMIP simulations are compared using the correct and incorrect energy formulations. Statistics of selected primary variables all indicate physically insignificant differences between the simulations, comparable to differences with simulations initialized with rounding sized perturbations. The two simulations are so similar mainly because of an inconsistency in the application of the incorrect energy formulation in the original CAM. CAM used the erroneous energy form to determine the states passed between the parameterizations, but used a form related to the correct formulation for themore » state passed from the parameterizations to the dynamical core. If the incorrect form is also used to determine the state passed to the dynamical core the simulations are significantly different. In addition, CAM uses the incorrect form for the global energy fixer, but that seems to be less important. The difference of the magnitude of the fixers using the correct and incorrect energy definitions is very small.« less

Ultrafast X-ray Auger probing of photoexcited molecular dynamics

DOE PAGES

McFarland, B. K.; Farrell, J. P.; Miyabe, S.; ...

2014-06-23

Here, molecules can efficiently and selectively convert light energy into other degrees of freedom. Disentangling the underlying ultrafast motion of electrons and nuclei of the photoexcited molecule presents a challenge to current spectroscopic approaches. Here we explore the photoexcited dynamics of molecules by an interaction with an ultrafast X-ray pulse creating a highly localized core hole that decays via Auger emission. We discover that the Auger spectrum as a function of photoexcitation—X-ray-probe delay contains valuable information about the nuclear and electronic degrees of freedom from an element-specific point of view. For the nucleobase thymine, the oxygen Auger spectrum shifts towardsmore » high kinetic energies, resulting from a particular C–O bond stretch in the ππ* photoexcited state. A subsequent shift of the Auger spectrum towards lower kinetic energies displays the electronic relaxation of the initial photoexcited state within 200 fs. Ab-initio simulations reinforce our interpretation and indicate an electronic decay to the nπ* state.« less

Energy considerations in the Community Atmosphere Model (CAM)

DOE PAGES

Williamson, David L.; Olson, Jerry G.; Hannay, Cécile; ...

2015-06-30

An error in the energy formulation in the Community Atmosphere Model (CAM) is identified and corrected. Ten year AMIP simulations are compared using the correct and incorrect energy formulations. Statistics of selected primary variables all indicate physically insignificant differences between the simulations, comparable to differences with simulations initialized with rounding sized perturbations. The two simulations are so similar mainly because of an inconsistency in the application of the incorrect energy formulation in the original CAM. CAM used the erroneous energy form to determine the states passed between the parameterizations, but used a form related to the correct formulation for themore » state passed from the parameterizations to the dynamical core. If the incorrect form is also used to determine the state passed to the dynamical core the simulations are significantly different. In addition, CAM uses the incorrect form for the global energy fixer, but that seems to be less important. The difference of the magnitude of the fixers using the correct and incorrect energy definitions is very small.« less

Bound States and Field-Polarized Haldane Modes in a Quantum Spin Ladder.

PubMed

Ward, S; Mena, M; Bouillot, P; Kollath, C; Giamarchi, T; Schmidt, K P; Normand, B; Krämer, K W; Biner, D; Bewley, R; Guidi, T; Boehm, M; McMorrow, D F; Rüegg, Ch

2017-04-28

The challenge of one-dimensional systems is to understand their physics beyond the level of known elementary excitations. By high-resolution neutron spectroscopy in a quantum spin-ladder material, we probe the leading multiparticle excitation by characterizing the two-magnon bound state at zero field. By applying high magnetic fields, we create and select the singlet (longitudinal) and triplet (transverse) excitations of the fully spin-polarized ladder, which have not been observed previously and are close analogs of the modes anticipated in a polarized Haldane chain. Theoretical modeling of the dynamical response demonstrates our complete quantitative understanding of these states.

Using Dynamic Multi-Task Non-Negative Matrix Factorization to Detect the Evolution of User Preferences in Collaborative Filtering

PubMed Central

Ju, Bin; Qian, Yuntao; Ye, Minchao; Ni, Rong; Zhu, Chenxi

2015-01-01

Predicting what items will be selected by a target user in the future is an important function for recommendation systems. Matrix factorization techniques have been shown to achieve good performance on temporal rating-type data, but little is known about temporal item selection data. In this paper, we developed a unified model that combines Multi-task Non-negative Matrix Factorization and Linear Dynamical Systems to capture the evolution of user preferences. Specifically, user and item features are projected into latent factor space by factoring co-occurrence matrices into a common basis item-factor matrix and multiple factor-user matrices. Moreover, we represented both within and between relationships of multiple factor-user matrices using a state transition matrix to capture the changes in user preferences over time. The experiments show that our proposed algorithm outperforms the other algorithms on two real datasets, which were extracted from Netflix movies and Last.fm music. Furthermore, our model provides a novel dynamic topic model for tracking the evolution of the behavior of a user over time. PMID:26270539

Using Dynamic Multi-Task Non-Negative Matrix Factorization to Detect the Evolution of User Preferences in Collaborative Filtering.

PubMed

Ju, Bin; Qian, Yuntao; Ye, Minchao; Ni, Rong; Zhu, Chenxi

2015-01-01

Predicting what items will be selected by a target user in the future is an important function for recommendation systems. Matrix factorization techniques have been shown to achieve good performance on temporal rating-type data, but little is known about temporal item selection data. In this paper, we developed a unified model that combines Multi-task Non-negative Matrix Factorization and Linear Dynamical Systems to capture the evolution of user preferences. Specifically, user and item features are projected into latent factor space by factoring co-occurrence matrices into a common basis item-factor matrix and multiple factor-user matrices. Moreover, we represented both within and between relationships of multiple factor-user matrices using a state transition matrix to capture the changes in user preferences over time. The experiments show that our proposed algorithm outperforms the other algorithms on two real datasets, which were extracted from Netflix movies and Last.fm music. Furthermore, our model provides a novel dynamic topic model for tracking the evolution of the behavior of a user over time.

Femtosecond excitation tuning and site energy memory of population transfer in poly(p-phenylenevinylene): Gated luminescence experiments and simulation

NASA Astrophysics Data System (ADS)

Sperling, J.; Milota, F.; Tortschanoff, A.; Warmuth, Ch.; Mollay, B.; Bässler, H.; Kauffmann, H. F.

2002-12-01

We present a comprehensive experimental and computational study on fs-relaxational dynamics of optical excitations in the conjugated polymer poly(p-phenylenevinylene) (PPV) under selective excitation tuning conditions into the long-wavelength, low-vibrational S1ν=0-density-of-states (DOS). The dependence of single-wavelength luminescence kinetics and time-windowed spectral transients on distinct, initial excitation boundaries at 1.4 K and at room temperature was measured applying the luminescence up-conversion technique. The typical energy-dispersive intra-DOS energy transfer was simulated by a combination of static Monte Carlo method with a dynamical algorithm for solving the energy-space transport Master-Equation in population-space. For various, selective excitations that give rise to specific S1-population distributions in distinct spatial and energetic subspaces inside the DOS, simulations confirm the experimental results and show that the subsequent, energy-dissipative, multilevel relaxation is hierarchically constrained, and reveals a pronounced site-energy memory effect with a migration-threshold, characteristic of the (dressed) excitation dynamics in the disordered PPV many-body system.

Elucidating Peptide and Protein Structure and Dynamics: UV Resonance Raman Spectroscopy

PubMed Central

Oladepo, Sulayman A.; Xiong, Kan; Hong, Zhenmin; Asher, Sanford A.

2011-01-01

UV resonance Raman spectroscopy (UVRR) is a powerful method that has the requisite selectivity and sensitivity to incisively monitor biomolecular structure and dynamics in solution. In this perspective, we highlight applications of UVRR for studying peptide and protein structure and the dynamics of protein and peptide folding. UVRR spectral monitors of protein secondary structure, such as the Amide III3 band and the Cα-H band frequencies and intensities can be used to determine Ramachandran Ψ angle distributions for peptide bonds. These incisive, quantitative glimpses into conformation can be combined with kinetic T-jump methodologies to monitor the dynamics of biomolecular conformational transitions. The resulting UVRR structural insight is impressive in that it allows differentiation of, for example, different α-helix-like states that enable differentiating π- and 310- states from pure α-helices. These approaches can be used to determine the Gibbs free energy landscape of individual peptide bonds along the most important protein (un)folding coordinate. Future work will find spectral monitors that probe peptide bond activation barriers that control protein (un)folding mechanisms. In addition, UVRR studies of sidechain vibrations will probe the role of side chains in determining protein secondary, tertiary and quaternary structures. PMID:21379371

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

PubMed

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

2018-05-24

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

SO(4) algebraic approach to the three-body bound state problem in two dimensions

NASA Astrophysics Data System (ADS)

Dmitrašinović, V.; Salom, Igor

2014-08-01

We use the permutation symmetric hyperspherical three-body variables to cast the non-relativistic three-body Schrödinger equation in two dimensions into a set of (possibly decoupled) differential equations that define an eigenvalue problem for the hyper-radial wave function depending on an SO(4) hyper-angular matrix element. We express this hyper-angular matrix element in terms of SO(3) group Clebsch-Gordan coefficients and use the latter's properties to derive selection rules for potentials with different dynamical/permutation symmetries. Three-body potentials acting on three identical particles may have different dynamical symmetries, in order of increasing symmetry, as follows: (1) S3 ⊗ OL(2), the permutation times rotational symmetry, that holds in sums of pairwise potentials, (2) O(2) ⊗ OL(2), the so-called "kinematic rotations" or "democracy symmetry" times rotational symmetry, that holds in area-dependent potentials, and (3) O(4) dynamical hyper-angular symmetry, that holds in hyper-radial three-body potentials. We show how the different residual dynamical symmetries of the non-relativistic three-body Hamiltonian lead to different degeneracies of certain states within O(4) multiplets.

Langevin approach to a chemical wave front: Selection of the propagation velocity in the presence of internal noise

NASA Astrophysics Data System (ADS)

Lemarchand, A.; Lesne, A.; Mareschal, M.

1995-05-01

The reaction-diffusion equation associated with the Fisher chemical model A+B-->2A admits wave-front solutions by replacing an unstable stationary state with a stable one. The deterministic analysis concludes that their propagation velocity is not prescribed by the dynamics. For a large class of initial conditions the velocity which is spontaneously selected is equal to the minimum allowed velocity vmin, as predicted by the marginal stability criterion. In order to test the relevance of this deterministic description we investigate the macroscopic consequences, on the velocity and the width of the front, of the intrinsic stochasticity due to the underlying microscopic dynamics. We solve numerically the Langevin equations, deduced analytically from the master equation within a system size expansion procedure. We show that the mean profile associated with the stochastic solution propagates faster than the deterministic solution at a velocity up to 25% greater than vmin.

Global dynamics of selective attention and its lapses in primary auditory cortex.

PubMed

Lakatos, Peter; Barczak, Annamaria; Neymotin, Samuel A; McGinnis, Tammy; Ross, Deborah; Javitt, Daniel C; O'Connell, Monica Noelle

2016-12-01

Previous research demonstrated that while selectively attending to relevant aspects of the external world, the brain extracts pertinent information by aligning its neuronal oscillations to key time points of stimuli or their sampling by sensory organs. This alignment mechanism is termed oscillatory entrainment. We investigated the global, long-timescale dynamics of this mechanism in the primary auditory cortex of nonhuman primates, and hypothesized that lapses of entrainment would correspond to lapses of attention. By examining electrophysiological and behavioral measures, we observed that besides the lack of entrainment by external stimuli, attentional lapses were also characterized by high-amplitude alpha oscillations, with alpha frequency structuring of neuronal ensemble and single-unit operations. Entrainment and alpha-oscillation-dominated periods were strongly anticorrelated and fluctuated rhythmically at an ultra-slow rate. Our results indicate that these two distinct brain states represent externally versus internally oriented computational resources engaged by large-scale task-positive and task-negative functional networks.

Coevolutionary dynamics in large, but finite populations

NASA Astrophysics Data System (ADS)

Traulsen, Arne; Claussen, Jens Christian; Hauert, Christoph

2006-07-01

Coevolving and competing species or game-theoretic strategies exhibit rich and complex dynamics for which a general theoretical framework based on finite populations is still lacking. Recently, an explicit mean-field description in the form of a Fokker-Planck equation was derived for frequency-dependent selection with two strategies in finite populations based on microscopic processes [A. Traulsen, J. C. Claussen, and C. Hauert, Phys. Rev. Lett. 95, 238701 (2005)]. Here we generalize this approach in a twofold way: First, we extend the framework to an arbitrary number of strategies and second, we allow for mutations in the evolutionary process. The deterministic limit of infinite population size of the frequency-dependent Moran process yields the adjusted replicator-mutator equation, which describes the combined effect of selection and mutation. For finite populations, we provide an extension taking random drift into account. In the limit of neutral selection, i.e., whenever the process is determined by random drift and mutations, the stationary strategy distribution is derived. This distribution forms the background for the coevolutionary process. In particular, a critical mutation rate uc is obtained separating two scenarios: above uc the population predominantly consists of a mixture of strategies whereas below uc the population tends to be in homogeneous states. For one of the fundamental problems in evolutionary biology, the evolution of cooperation under Darwinian selection, we demonstrate that the analytical framework provides excellent approximations to individual based simulations even for rather small population sizes. This approach complements simulation results and provides a deeper, systematic understanding of coevolutionary dynamics.

Optimal control of the population dynamics of the ground vibrational state of a polyatomic molecule

NASA Astrophysics Data System (ADS)

de Clercq, Ludwig E.; Botha, Lourens R.; Rohwer, Erich G.; Uys, Hermann; Du Plessis, Anton

2011-03-01

Simulating coherent control with femtosecond pulses on a polyatomic molecule with anharmonic splitting was demonstrated. The simulation mimicked pulse shaping of a Spatial Light Modulator (SLM) and the interaction was described with the Von Neumann equation. A transform limited pulse with a fluence of 600 J/m2 produced 18% of the population in an arbitrarily chosen upper vibrational state, n =2. Phase only and amplitude only shaped pulse produced optimum values of 60% and 40% respectively, of the population in the vibrational state, n=2, after interaction with the ultra short pulse. The combination of phase and amplitude shaping produced the best results, 80% of the population was in the targeted vibrational state, n=2, after interaction. These simulations were carried out with all the population initially in the ground vibrational level. It was found that even at room temperatures (300 Kelvin) that the population in the selected level is comparable with the case where all population is initially in the ground vibrational state. With a 10% noise added to the amplitude and phase masks, selective excitation of the targeted vibrational state is still possible.

The Birth and Death of Redundancy in Decoherence and Quantum Darwinism

NASA Astrophysics Data System (ADS)

Riedel, Charles; Zurek, Wojciech; Zwolak, Michael

2012-02-01

Understanding the quantum-classical transition and the identification of a preferred classical domain through quantum Darwinism is based on recognizing high-redundancy states as both ubiquitous and exceptional. They are produced ubiquitously during decoherence, as has been demonstrated by the recent identification of very general conditions under which high-redundancy states develop. They are exceptional in that high-redundancy states occupy a very narrow corner of the global Hilbert space; states selected at random are overwelming likely to exhibit zero redundancy. In this letter, we examine the conditions and time scales for the transition from high-redundancy states to zero-redundancy states in many-body dynamics. We identify sufficient condition for the development of redundancy from product states and show that the destruction of redundancy can be accomplished even with highly constrained interactions.

Learning to read and write in evolution: from static pseudoenzymes and pseudosignalers to dynamic gear shifters.

PubMed

Abudukelimu, Abulikemu; Mondeel, Thierry D G A; Barberis, Matteo; Westerhoff, Hans V

2017-06-15

We present a systems biology view on pseudoenzymes that acknowledges that genes are not selfish: the genome is. With network function as the selectable unit, there has been an evolutionary bonus for recombination of functions of and within proteins. Many proteins house a functionality by which they 'read' the cell's state, and one by which they 'write' and thereby change that state. Should the writer domain lose its cognate function, a 'pseudoenzyme' or 'pseudosignaler' arises. GlnK involved in Escherichia coli ammonia assimilation may well be a pseudosignaler, associating 'reading' the nitrogen state of the cell to 'writing' the ammonium uptake activity. We identify functional pseudosignalers in the cyclin-dependent kinase complexes regulating cell-cycle progression. For the mitogen-activated protein kinase pathway, we illustrate how a 'dead' pseudosignaler could produce potentially selectable functionalities. Four billion years ago, bioenergetics may have shuffled 'electron-writers', producing various networks that all served the same function of anaerobic ATP synthesis and carbon assimilation from hydrogen and carbon dioxide, but at different ATP/acetate ratios. This would have enabled organisms to deal with variable challenges of energy need and substrate supply. The same principle might enable 'gear-shifting' in real time, by dynamically generating different pseudo-redox enzymes, reshuffling their coenzymes, and rerouting network fluxes. Non-stationary pH gradients in thermal vents together with similar such shuffling mechanisms may have produced a first selectable proton-motivated pyrophosphate synthase and subsequent ATP synthase. A combination of functionalities into enzymes, signalers, and the pseudo-versions thereof may offer fitness in terms of plasticity, both in real time and in evolution. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

Full-dimensional quantum dynamics study of the H{sub 2} + C{sub 2}H → H + C{sub 2}H{sub 2} reaction on an ab initio potential energy surface

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

Chen, Liuyang; University of Chinese Academy of Sciences, Beijing 100049; Shao, Kejie

2016-05-21

This work performs a time-dependent wavepacket study of the H{sub 2} + C{sub 2}H → H + C{sub 2}H{sub 2} reaction on a new ab initio potential energy surface (PES). The PES is constructed using neural network method based on 68 478 geometries with energies calculated at UCCSD(T)-F12a/aug-cc-pVTZ level and covers H{sub 2} + C{sub 2}H↔H + C{sub 2}H{sub 2}, H + C{sub 2}H{sub 2} → HCCH{sub 2}, and HCCH{sub 2} radial isomerization reaction regions. The reaction dynamics of H{sub 2} + C{sub 2}H → H + C{sub 2}H{sub 2} are investigated using full-dimensional quantum dynamics method. The initial-state selected reactionmore » probabilities are calculated for reactants in eight vibrational states. The calculated results showed that the H{sub 2} vibrational excitation predominantly enhances the reactivity while the excitation of bending mode of C{sub 2}H slightly inhibits the reaction. The excitations of two stretching modes of C{sub 2}H molecule have negligible effect on the reactivity. The integral cross section is calculated with J-shift approximation and the mode selectivity in this reaction is discussed. The rate constants over 200-2000 K are calculated and agree well with the experimental measured values.« less

Time Scale Hierarchies in the Functional Organization of Complex Behaviors

PubMed Central

Perdikis, Dionysios; Huys, Raoul; Jirsa, Viktor K.

2011-01-01

Traditional approaches to cognitive modelling generally portray cognitive events in terms of ‘discrete’ states (point attractor dynamics) rather than in terms of processes, thereby neglecting the time structure of cognition. In contrast, more recent approaches explicitly address this temporal dimension, but typically provide no entry points into cognitive categorization of events and experiences. With the aim to incorporate both these aspects, we propose a framework for functional architectures. Our approach is grounded in the notion that arbitrary complex (human) behaviour is decomposable into functional modes (elementary units), which we conceptualize as low-dimensional dynamical objects (structured flows on manifolds). The ensemble of modes at an agent’s disposal constitutes his/her functional repertoire. The modes may be subjected to additional dynamics (termed operational signals), in particular, instantaneous inputs, and a mechanism that sequentially selects a mode so that it temporarily dominates the functional dynamics. The inputs and selection mechanisms act on faster and slower time scales then that inherent to the modes, respectively. The dynamics across the three time scales are coupled via feedback, rendering the entire architecture autonomous. We illustrate the functional architecture in the context of serial behaviour, namely cursive handwriting. Subsequently, we investigate the possibility of recovering the contributions of functional modes and operational signals from the output, which appears to be possible only when examining the output phase flow (i.e., not from trajectories in phase space or time). PMID:21980278

Validity of the site-averaging approximation for modeling the dissociative chemisorption of H{sub 2} on Cu(111) surface: A quantum dynamics study on two potential energy surfaces

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

Liu, Tianhui; Fu, Bina, E-mail: bina@dicp.ac.cn, E-mail: zhangdh@dicp.ac.cn; Zhang, Dong H., E-mail: bina@dicp.ac.cn, E-mail: zhangdh@dicp.ac.cn

A new finding of the site-averaging approximation was recently reported on the dissociative chemisorption of the HCl/DCl+Au(111) surface reaction [T. Liu, B. Fu, and D. H. Zhang, J. Chem. Phys. 139, 184705 (2013); T. Liu, B. Fu, and D. H. Zhang, J. Chem. Phys. 140, 144701 (2014)]. Here, in order to investigate the dependence of new site-averaging approximation on the initial vibrational state of H{sub 2} as well as the PES for the dissociative chemisorption of H{sub 2} on Cu(111) surface at normal incidence, we carried out six-dimensional quantum dynamics calculations using the initial state-selected time-dependent wave packet approach, withmore » H{sub 2} initially in its ground vibrational state and the first vibrational excited state. The corresponding four-dimensional site-specific dissociation probabilities are also calculated with H{sub 2} fixed at bridge, center, and top sites. These calculations are all performed based on two different potential energy surfaces (PESs). It is found that the site-averaging dissociation probability over 15 fixed sites obtained from four-dimensional quantum dynamics calculations can accurately reproduce the six-dimensional dissociation probability for H{sub 2} (v = 0) and (v = 1) on the two PESs.« less

Mixed strategy and coevolution dynamics in social networks

NASA Astrophysics Data System (ADS)

Zhong, Weicai; Abbass, Hussein A.; Bender, Axel; Liu, Jing

2011-01-01

We investigate coevolution dynamics of both individual strategies and social ties as they adapt within the snowdrift game with mixed strategies. We propose a partner selection mechanism based on the concept of trust. Here trust is considered an instrument for an individual both selecting the right partners and being selected amongst other potential partners. Based on her local views of the system, the focal individual dismisses the link from the partner with the lowest trust and rewires to the partner’s partner with the highest trust. It is shown that such a trust-based partner switching mechanism favors the emergence of cooperators. Furthermore, when the number of an individual’s partners is restricted (which is a metaphor of limited capacities and capabilities of an individual in real environments), surprising assortative mixing patterns are formed in the emerging network and change the network’s degree distribution from a power-law distribution to an asymmetrically U-shaped distribution. This plays a leading role in preventing global avalanches triggered by perturbations acting on the state of the highly connected individuals.

Cloud Service Selection Using Multicriteria Decision Analysis

PubMed Central

Anuar, Nor Badrul; Shiraz, Muhammad; Haque, Israat Tanzeena

2014-01-01

Cloud computing (CC) has recently been receiving tremendous attention from the IT industry and academic researchers. CC leverages its unique services to cloud customers in a pay-as-you-go, anytime, anywhere manner. Cloud services provide dynamically scalable services through the Internet on demand. Therefore, service provisioning plays a key role in CC. The cloud customer must be able to select appropriate services according to his or her needs. Several approaches have been proposed to solve the service selection problem, including multicriteria decision analysis (MCDA). MCDA enables the user to choose from among a number of available choices. In this paper, we analyze the application of MCDA to service selection in CC. We identify and synthesize several MCDA techniques and provide a comprehensive analysis of this technology for general readers. In addition, we present a taxonomy derived from a survey of the current literature. Finally, we highlight several state-of-the-art practical aspects of MCDA implementation in cloud computing service selection. The contributions of this study are four-fold: (a) focusing on the state-of-the-art MCDA techniques, (b) highlighting the comparative analysis and suitability of several MCDA methods, (c) presenting a taxonomy through extensive literature review, and (d) analyzing and summarizing the cloud computing service selections in different scenarios. PMID:24696645

Cloud service selection using multicriteria decision analysis.

PubMed

Whaiduzzaman, Md; Gani, Abdullah; Anuar, Nor Badrul; Shiraz, Muhammad; Haque, Mohammad Nazmul; Haque, Israat Tanzeena

2014-01-01

Cloud computing (CC) has recently been receiving tremendous attention from the IT industry and academic researchers. CC leverages its unique services to cloud customers in a pay-as-you-go, anytime, anywhere manner. Cloud services provide dynamically scalable services through the Internet on demand. Therefore, service provisioning plays a key role in CC. The cloud customer must be able to select appropriate services according to his or her needs. Several approaches have been proposed to solve the service selection problem, including multicriteria decision analysis (MCDA). MCDA enables the user to choose from among a number of available choices. In this paper, we analyze the application of MCDA to service selection in CC. We identify and synthesize several MCDA techniques and provide a comprehensive analysis of this technology for general readers. In addition, we present a taxonomy derived from a survey of the current literature. Finally, we highlight several state-of-the-art practical aspects of MCDA implementation in cloud computing service selection. The contributions of this study are four-fold: (a) focusing on the state-of-the-art MCDA techniques, (b) highlighting the comparative analysis and suitability of several MCDA methods, (c) presenting a taxonomy through extensive literature review, and (d) analyzing and summarizing the cloud computing service selections in different scenarios.

Advanced coal cleaning meets acid rain emission limits

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

Boron, D.J.; Matoney, J.P.; Albrecht, M.C.

1987-03-01

The following processes were selected for study: fine-coal, heavy-medium cyclone separation/flotation, advanced flotation, Dow true heavy liquid separation, Advanced Energy Dynamics (AED) electrostatic separation, and National Research Council of Canada oil agglomeration. Advanced coal cleaning technology was done for the state of New York to investigate methods to use high sulfur coal in view of anticipated lower SO/sub 2/ emission limits.

Small Scale Burner Review

DTIC Science & Technology

2009-07-01

dopants in the semiconductor components of the devices (5). Venkatasubramanian (46) reviewed some state- of-the-art TE materials such as quantum-dot...conversion efficiency of a GaSb micro TPV system incorporating broadband silicon carbide (SiC) and selective emitted materials ( cobalt [Co]/nickel...carbon CFD computational fluid dynamics Co cobalt CO carbon monoxide CO2 carbon dioxide Cu copper GaSb gallium antimonide InGaAs indium gallium

The classical and quantum dynamics of molecular spins on graphene.

PubMed

Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

2016-02-01

Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain's threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.

The classical and quantum dynamics of molecular spins on graphene

NASA Astrophysics Data System (ADS)

Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

2016-02-01

Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic and quantum computing devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics and electrical spin manipulation. However, the influence of the graphene environment on the spin systems has yet to be unravelled. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets on graphene. Whereas the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly developed model. Coupling to Dirac electrons introduces a dominant quantum relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully coherent, resonant spin tunnelling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin manipulation in graphene nanodevices.

Diffusive and Arrestedlike Dynamics in Currency Exchange Markets

NASA Astrophysics Data System (ADS)

Clara-Rahola, J.; Puertas, A. M.; Sánchez-Granero, M. A.; Trinidad-Segovia, J. E.; de las Nieves, F. J.

2017-02-01

This work studies the symmetry between colloidal dynamics and the dynamics of the Euro-U.S. dollar currency exchange market (EURUSD). We consider the EURUSD price in the time range between 2001 and 2015, where we find significant qualitative symmetry between fluctuation distributions from this market and the ones belonging to colloidal particles in supercooled or arrested states. In particular, we find that models used for arrested physical systems are suitable for describing the EURUSD fluctuation distributions. Whereas the corresponding mean-squared price displacement (MSPD) to the EURUSD is diffusive for all years, when focusing in selected time frames within a day, we find a two-step MSPD when the New York Stock Exchange market closes, comparable to the dynamics in supercooled systems. This is corroborated by looking at the price correlation functions and non-Gaussian parameters and can be described by the theoretical model. We discuss the origin and implications of this analogy.

Effect of Ca2+ on the promiscuous target-protein binding of calmodulin

PubMed Central

Westerlund, Annie M.

2018-01-01

Calmodulin (CaM) is a calcium sensing protein that regulates the function of a large number of proteins, thus playing a crucial part in many cell signaling pathways. CaM has the ability to bind more than 300 different target peptides in a Ca2+-dependent manner, mainly through the exposure of hydrophobic residues. How CaM can bind a large number of targets while retaining some selectivity is a fascinating open question. Here, we explore the mechanism of CaM selective promiscuity for selected target proteins. Analyzing enhanced sampling molecular dynamics simulations of Ca2+-bound and Ca2+-free CaM via spectral clustering has allowed us to identify distinct conformational states, characterized by interhelical angles, secondary structure determinants and the solvent exposure of specific residues. We searched for indicators of conformational selection by mapping solvent exposure of residues in these conformational states to contacts in structures of CaM/target peptide complexes. We thereby identified CaM states involved in various binding classes arranged along a depth binding gradient. Binding Ca2+ modifies the accessible hydrophobic surface of the two lobes and allows for deeper binding. Apo CaM indeed shows shallow binding involving predominantly polar and charged residues. Furthermore, binding to the C-terminal lobe of CaM appears selective and involves specific conformational states that can facilitate deep binding to target proteins, while binding to the N-terminal lobe appears to happen through a more flexible mechanism. Thus the long-ranged electrostatic interactions of the charged residues of the N-terminal lobe of CaM may initiate binding, while the short-ranged interactions of hydrophobic residues in the C-terminal lobe of CaM may account for selectivity. This work furthers our understanding of the mechanism of CaM binding and selectivity to different target proteins and paves the way towards a comprehensive model of CaM selectivity. PMID:29614072

Effect of Ca2+ on the promiscuous target-protein binding of calmodulin.

PubMed

Westerlund, Annie M; Delemotte, Lucie

2018-04-01

Calmodulin (CaM) is a calcium sensing protein that regulates the function of a large number of proteins, thus playing a crucial part in many cell signaling pathways. CaM has the ability to bind more than 300 different target peptides in a Ca2+-dependent manner, mainly through the exposure of hydrophobic residues. How CaM can bind a large number of targets while retaining some selectivity is a fascinating open question. Here, we explore the mechanism of CaM selective promiscuity for selected target proteins. Analyzing enhanced sampling molecular dynamics simulations of Ca2+-bound and Ca2+-free CaM via spectral clustering has allowed us to identify distinct conformational states, characterized by interhelical angles, secondary structure determinants and the solvent exposure of specific residues. We searched for indicators of conformational selection by mapping solvent exposure of residues in these conformational states to contacts in structures of CaM/target peptide complexes. We thereby identified CaM states involved in various binding classes arranged along a depth binding gradient. Binding Ca2+ modifies the accessible hydrophobic surface of the two lobes and allows for deeper binding. Apo CaM indeed shows shallow binding involving predominantly polar and charged residues. Furthermore, binding to the C-terminal lobe of CaM appears selective and involves specific conformational states that can facilitate deep binding to target proteins, while binding to the N-terminal lobe appears to happen through a more flexible mechanism. Thus the long-ranged electrostatic interactions of the charged residues of the N-terminal lobe of CaM may initiate binding, while the short-ranged interactions of hydrophobic residues in the C-terminal lobe of CaM may account for selectivity. This work furthers our understanding of the mechanism of CaM binding and selectivity to different target proteins and paves the way towards a comprehensive model of CaM selectivity.

A controls engineering approach for analyzing airplane input-output characteristics

NASA Technical Reports Server (NTRS)

Arbuckle, P. Douglas

1991-01-01

An engineering approach for analyzing airplane control and output characteristics is presented. State-space matrix equations describing the linear perturbation dynamics are transformed from physical coordinates into scaled coordinates. The scaling is accomplished by applying various transformations to the system to employ prior engineering knowledge of the airplane physics. Two different analysis techniques are then explained. Modal analysis techniques calculate the influence of each system input on each fundamental mode of motion and the distribution of each mode among the system outputs. The optimal steady state response technique computes the blending of steady state control inputs that optimize the steady state response of selected system outputs. Analysis of an example airplane model is presented to demonstrate the described engineering approach.

Two-colour dip spectroscopy of jet-cooled molecules

NASA Astrophysics Data System (ADS)

Ito, Mitsuo

In optical-optical double resonance spectroscopy, the resonance transition from an intermediate state to a final state can be detected by a dip of the signal (fluorescence or ion) associated with the intermediate state. This method probing the signal of the intermediate state may be called `two-colour dip spectroscopy'. Various kinds of two-colour dip spectroscopy such as two-colour fluorescence/ion dip spectroscopy, two-colour ionization dip spectroscopy employing stimulated emission, population labelling spectroscopy and mass-selected ion dip spectroscopy with dissociation were briefly described, paying special attention to their characteristics in excitation, detection and application. They were extensively and successfully applied to jet-cooled large molecules and provided us with new useful information on the energy and dynamics of excited molecules.

Electron-Phonon Coupling and Resonant Relaxation from 1D and 1P States in PbS Quantum Dots.

PubMed

Kennehan, Eric R; Doucette, Grayson S; Marshall, Ashley R; Grieco, Christopher; Munson, Kyle T; Beard, Matthew C; Asbury, John B

2018-05-31

Observations of the hot-phonon bottleneck, which is predicted to slow the rate of hot carrier cooling in quantum confined nanocrystals, have been limited to date for reasons that are not fully understood. We used time-resolved infrared spectroscopy to directly measure higher energy intraband transitions in PbS colloidal quantum dots. Direct measurements of these intraband transitions permitted detailed analysis of the electronic overlap of the quantum confined states that may influence their relaxation processes. In smaller PbS nanocrystals, where the hot-phonon bottleneck is expected to be most pronounced, we found that relaxation of parity selection rules combined with stronger electron-phonon coupling led to greater spectral overlap of transitions among the quantum confined states. This created pathways for fast energy transfer and relaxation that may bypass the predicted hot-phonon bottleneck. In contrast, larger, but still quantum confined nanocrystals did not exhibit such relaxation of the parity selection rules and possessed narrower intraband states. These observations were consistent with slower relaxation dynamics that have been measured in larger quantum confined systems. These findings indicated that, at small radii, electron-phonon interactions overcome the advantageous increase in energetic separation of the electronic states for PbS quantum dots. Selection of appropriately sized quantum dots, which minimize spectral broadening due to electron-phonon interactions while maximizing electronic state separation, is necessary to observe the hot-phonon bottleneck. Such optimization may provide a framework for achieving efficient hot carrier collection and multiple exciton generation.

A global reaction route mapping-based kinetic Monte Carlo algorithm

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

Mitchell, Izaac; Page, Alister J., E-mail: sirle@chem.nagoya-u.ac.jp, E-mail: alister.page@newcastle.edu.au; Irle, Stephan, E-mail: sirle@chem.nagoya-u.ac.jp, E-mail: alister.page@newcastle.edu.au

2016-07-14

We propose a new on-the-fly kinetic Monte Carlo (KMC) method that is based on exhaustive potential energy surface searching carried out with the global reaction route mapping (GRRM) algorithm. Starting from any given equilibrium state, this GRRM-KMC algorithm performs a one-step GRRM search to identify all surrounding transition states. Intrinsic reaction coordinate pathways are then calculated to identify potential subsequent equilibrium states. Harmonic transition state theory is used to calculate rate constants for all potential pathways, before a standard KMC accept/reject selection is performed. The selected pathway is then used to propagate the system forward in time, which is calculatedmore » on the basis of 1st order kinetics. The GRRM-KMC algorithm is validated here in two challenging contexts: intramolecular proton transfer in malonaldehyde and surface carbon diffusion on an iron nanoparticle. We demonstrate that in both cases the GRRM-KMC method is capable of reproducing the 1st order kinetics observed during independent quantum chemical molecular dynamics simulations using the density-functional tight-binding potential.« less

Two-dimensional spectra of electron collisions with acrylonitrile and methacrylonitrile reveal nuclear dynamics

NASA Astrophysics Data System (ADS)

Regeta, K.; Allan, M.

2015-05-01

Detailed experimental information on the motion of a nuclear packet on a complex (resonant) anion potential surface is obtained by measuring 2-dimensional (2D) electron energy loss spectra. The cross section is plotted as a function of incident electron energy, which determines which resonant anion state is populated, i.e., along which normal coordinate the wave packet is launched, and of the electron energy loss, which reveals into which final states each specific resonant state decays. The 2D spectra are presented for acrylonitrile and methacrylonitrile, at the incident energy range 0.095-1.0 eV, where the incoming electron is temporarily captured in the lowest π∗ orbital. The 2D spectra reveal selectivity patterns with respect to which vibrations are excited in the attachment and de-excited in the detachment. Further insight is gained by recording 1D spectra measured along horizontal, vertical, and diagonal cuts of the 2D spectrum. The methyl group in methacrylonitrile increases the resonance width 7 times. This converts the sharp resonances of acrylonitrile into boomerang structures but preserves the essence of the selectivity patterns. Selectivity of vibrational excitation by higher-lying shape resonances up to 8 eV is also reported.

Evolution Models with Conditional Mutation Rates: Strange Plateaus in Population Distribution

NASA Astrophysics Data System (ADS)

Saakian, David B.

2017-08-01

Cancer is related to clonal evolution with a strongly nonlinear, collective behavior. Here we investigate a slightly advanced version of the popular Crow-Kimura evolution model, suggested recently, by simply assuming a conditional mutation rate. We investigated the steady-state solution and found a highly intriguing plateau in the distribution. There are selective and nonselective phases, with a rather narrow plateau in the distribution at the peak in the first phase, and a wide plateau for many Hamming classes (a collection of genomes with the same number of mutations from the reference genome) in the second phase. We analytically solved the steady state distribution in the selective and nonselective phases, calculating the widths of the plateaus. Numerically, we also found an intermediate phase with several plateaus in the steady-state distribution, related to large finite-genome-length corrections. We assume that the newly observed phenomena should exist in other versions of evolution dynamics when the parameters of the model are conditioned to the population distribution.

X-ray Scattering Combined with Coordinate-Based Analyses for Applications in Natural and Artificial Photosynthesis

PubMed Central

Tiede, David M.; Mardis, Kristy L.; Zuo, Xiaobing

2009-01-01

Advances in x-ray light sources and detectors have created opportunities for advancing our understanding of structure and structural dynamics for supramolecular assemblies in solution by combining x-ray scattering measurement with coordinate-based modeling methods. In this review the foundations for x-ray scattering are discussed and illustrated with selected examples demonstrating the ability to correlate solution x-ray scattering measurements to molecular structure, conformation, and dynamics. These approaches are anticipated to have a broad range of applications in natural and artificial photosynthesis by offering possibilities for structure resolution for dynamic supramolecular assemblies in solution that can not be fully addressed with crystallographic techniques, and for resolving fundamental mechanisms for solar energy conversion by mapping out structure in light-excited reaction states. PMID:19636808

Prediction-based Dynamic Energy Management in Wireless Sensor Networks

PubMed Central

Wang, Xue; Ma, Jun-Jie; Wang, Sheng; Bi, Dao-Wei

2007-01-01

Energy consumption is a critical constraint in wireless sensor networks. Focusing on the energy efficiency problem of wireless sensor networks, this paper proposes a method of prediction-based dynamic energy management. A particle filter was introduced to predict a target state, which was adopted to awaken wireless sensor nodes so that their sleep time was prolonged. With the distributed computing capability of nodes, an optimization approach of distributed genetic algorithm and simulated annealing was proposed to minimize the energy consumption of measurement. Considering the application of target tracking, we implemented target position prediction, node sleep scheduling and optimal sensing node selection. Moreover, a routing scheme of forwarding nodes was presented to achieve extra energy conservation. Experimental results of target tracking verified that energy-efficiency is enhanced by prediction-based dynamic energy management.

Dynamics of Galaxies

NASA Astrophysics Data System (ADS)

Bertin, Giuseppe

2000-08-01

Part I. Basic Phenomenology: 1. Scales; 2. Observational windows; 3. Classifications; 4. Photometry, kinematics, dark matter; 5. Basic questions, semi-empirical approach, dynamical window; Part II. Physical Models: 6. Self-gravity and relation with plasma physics; 7. Relaxation times, absence of thermodynamical equilibrium; 8. Models; 9. Equilibrium and stability: symmetry and symmetry breaking; 10. Classical ellipsoids; 11. Introduction to dispersive waves; 12. Jeans instability; Part III. Spiral Galaxies: 13. Orbits; 14. The basic state: vertical and horizontal equilibrium in the disk; 15. Density waves; 16. Role of gas; 17. Global spiral modes; 18. Spiral structure in galaxies; 19. Bending waves; 20. Dark matter in spiral galaxies; Part IV. Elliptical Galaxies: 21. Orbits; 22. Stellar dynamical approach; 23. Stability; 24. Dark matter in elliptical galaxies; Part V. In Perspective: 25. Selected aspects of formation and evolution; Notes; Index.

Static and dynamic light scattering of healthy and malaria-parasite invaded red blood cells

NASA Astrophysics Data System (ADS)

Park, Yongkeun; Diez-Silva, Monica; Fu, Dan; Popescu, Gabriel; Choi, Wonshik; Barman, Ishan; Suresh, Subra; Feld, Michael S.

2010-03-01

We present the light scattering of individual Plasmodium falciparum-parasitized human red blood cells (Pf-RBCs), and demonstrate progressive alterations to the scattering signal arising from the development of malaria-inducing parasites. By selectively imaging the electric fields using quantitative phase microscopy and a Fourier transform light scattering technique, we calculate the light scattering maps of individual Pf-RBCs. We show that the onset and progression of pathological states of the Pf-RBCs can be clearly identified by the static scattering maps. Progressive changes to the biophysical properties of the Pf-RBC membrane are captured from dynamic light scattering.

Spontaneous emergence of cataclysmic networks in spatially extended systems

NASA Astrophysics Data System (ADS)

Manrubia, Susanna C.; Poyatos, Juan F.; Pérez-Mercader, Juan

2002-11-01

A system of interacting chemical species able to catalyse each others' production is studied. We consider a two-dimensional surface where single molecules attach, diffuse, catalytically interact, and decay. The population of species molecules and the network of interactions among them are dynamical entities. After a short transient time, robust catalytic cycles emerge and a "stationary" state of high diversity and large population numbers settles down. Population dynamics and physical space select among possible graphs of catalytic interactions. The organization of the system is robust: parasitic invaders are short-lived, their populations are kept at low levels, and are unable to sweep away the emerging catalytic cycles.

Intercomparison of four regional climate models for the German State of Saxonia

NASA Astrophysics Data System (ADS)

Kreienkamp, F.; Spekat, A.; Enke, W.

2009-09-01

Results from four regional climate models which focus on Central Europe are presented: CCLM, the climate version of the German Weather Service's Local Model - REMO, the regional dynamic model from the Max Planck Institute for Meteorology in Hamburg - STAR, the statistical model developed at the PIK Potsdam Institute and WETTREG, the statistic-dynamic model developed by the company CEC Potsdam. For the area of the German State of Saxonia a host of properties and indicators were analyzed aiming to show the models' abilities to reconstruct the current climate and compare climate model scenarios. These include a group of thermal indicators, such as the number of ice, frost, summer and hot days, the number of tropical nights; then there are hydrometeorological indicators such as the exceedance of low and high precipitation thresholds; humidity, cloudiness and wind indicators complement the array. A selection of them showing similarities and differences of the models investigated will be presented.

Dynamic properties of ceramic materials

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

Grady, D.E.

1995-02-01

The present study offers new data and analysis on the transient shock strength and equation-of-state properties of ceramics. Various dynamic data on nine high strength ceramics are provided with wave profile measurements, through velocity interferometry techniques, the principal observable. Compressive failure in the shock wave front, with emphasis on brittle versus ductile mechanisms of deformation, is examined in some detail. Extensive spall strength data are provided and related to the theoretical spall strength, and to energy-based theories of the spall process. Failure waves, as a mechanism of deformation in the transient shock process, are examined. Strength and equation-of-state analysis ofmore » shock data on silicon carbide, boron carbide, tungsten carbide, silicon dioxide and aluminum nitride is presented with particular emphasis on phase transition properties for the latter two. Wave profile measurements on selected ceramics are investigated for evidence of rate sensitive elastic precursor decay in the shock front failure process.« less

Pattern Selection and Super-Patterns in Opinion Dynamics

NASA Astrophysics Data System (ADS)

Ben-Naim, Eli; Scheel, Arnd

We study pattern formation in the bounded confidence model of opinion dynamics. In this random process, opinion is quantified by a single variable. Two agents may interact and reach a fair compromise, but only if their difference of opinion falls below a fixed threshold. Starting from a uniform distribution of opinions with compact support, a traveling wave forms and it propagates from the domain boundary into the unstable uniform state. Consequently, the system reaches a steady state with isolated clusters that are separated by distance larger than the interaction range. These clusters form a quasi-periodic pattern where the sizes of the clusters and the separations between them are nearly constant. We obtain analytically the average separation between clusters L. Interestingly, there are also very small quasi-periodic modulations in the size of the clusters. The spatial periods of these modulations are a series of integers that follow from the continued-fraction representation of the irrational average separation L.

Theoretical description of the mixed-field orientation of asymmetric-top molecules: A time-dependent study

NASA Astrophysics Data System (ADS)

Omiste, Juan J.; González-Férez, Rosario

2016-12-01

We present a theoretical study of the mixed-field-orientation of asymmetric-top molecules in tilted static electric field and nonresonant linearly polarized laser pulse by solving the time-dependent Schrödinger equation. Within this framework, we compute the mixed-field orientation of a state-selected molecular beam of benzonitrile (C7H5N ) and compare with the experimental observations [J. L. Hansen et al., Phys. Rev. A 83, 023406 (2011), 10.1103/PhysRevA.83.023406] and with our previous time-independent descriptions [J. J. Omiste et al., Phys. Chem. Chem. Phys. 13, 18815 (2011), 10.1039/c1cp21195a]. For an excited rotational state, we investigate the field-dressed dynamics for several field configurations as those used in the mixed-field experiments. The nonadiabatic phenomena and their consequences on the rotational dynamics are analyzed in detail.

A model of two-way selection system for human behavior.

PubMed

Zhou, Bin; Qin, Shujia; Han, Xiao-Pu; He, Zhe; Xie, Jia-Rong; Wang, Bing-Hong

2014-01-01

Two-way selection is a common phenomenon in nature and society. It appears in the processes like choosing a mate between men and women, making contracts between job hunters and recruiters, and trading between buyers and sellers. In this paper, we propose a model of two-way selection system, and present its analytical solution for the expectation of successful matching total and the regular pattern that the matching rate trends toward an inverse proportion to either the ratio between the two sides or the ratio of the state total to the smaller group's people number. The proposed model is verified by empirical data of the matchmaking fairs. Results indicate that the model well predicts this typical real-world two-way selection behavior to the bounded error extent, thus it is helpful for understanding the dynamics mechanism of the real-world two-way selection system.

Exploiting Fast-Variables to Understand Population Dynamics and Evolution

NASA Astrophysics Data System (ADS)

Constable, George W. A.; McKane, Alan J.

2018-07-01

We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are caused by individual events while the dynamics are described in terms of the time-evolution of a probability density function. In general, the application of the diffusion approximation still leaves a description that is quite complex. However, in many biological applications one or more of the processes happen slowly relative to the system's other processes, and the dynamics can be approximated as occurring within a slow low-dimensional subspace. We review these time-scale separation arguments and analyse the more simple stochastic dynamics that result in a number of cases. We stress that it is important to retain the demographic noise derived in this way, and emphasise this point by showing that it can alter the direction of selection compared to the prediction made from an analysis of the corresponding deterministic model.

Exploiting Fast-Variables to Understand Population Dynamics and Evolution

NASA Astrophysics Data System (ADS)

Constable, George W. A.; McKane, Alan J.

2017-11-01

We describe a continuous-time modelling framework for biological population dynamics that accounts for demographic noise. In the spirit of the methodology used by statistical physicists, transitions between the states of the system are caused by individual events while the dynamics are described in terms of the time-evolution of a probability density function. In general, the application of the diffusion approximation still leaves a description that is quite complex. However, in many biological applications one or more of the processes happen slowly relative to the system's other processes, and the dynamics can be approximated as occurring within a slow low-dimensional subspace. We review these time-scale separation arguments and analyse the more simple stochastic dynamics that result in a number of cases. We stress that it is important to retain the demographic noise derived in this way, and emphasise this point by showing that it can alter the direction of selection compared to the prediction made from an analysis of the corresponding deterministic model.

Optimal estimation of recurrence structures from time series

NASA Astrophysics Data System (ADS)

beim Graben, Peter; Sellers, Kristin K.; Fröhlich, Flavio; Hutt, Axel

2016-05-01

Recurrent temporal dynamics is a phenomenon observed frequently in high-dimensional complex systems and its detection is a challenging task. Recurrence quantification analysis utilizing recurrence plots may extract such dynamics, however it still encounters an unsolved pertinent problem: the optimal selection of distance thresholds for estimating the recurrence structure of dynamical systems. The present work proposes a stochastic Markov model for the recurrent dynamics that allows for the analytical derivation of a criterion for the optimal distance threshold. The goodness of fit is assessed by a utility function which assumes a local maximum for that threshold reflecting the optimal estimate of the system's recurrence structure. We validate our approach by means of the nonlinear Lorenz system and its linearized stochastic surrogates. The final application to neurophysiological time series obtained from anesthetized animals illustrates the method and reveals novel dynamic features of the underlying system. We propose the number of optimal recurrence domains as a statistic for classifying an animals' state of consciousness.

Reaction dynamics of Al + O₂ → AlO + O studied by a crossed-beam velocity map imaging technique: vib-rotational state selected angular-kinetic energy distribution.

PubMed

Honma, Kenji; Miyashita, Kazuki; Matsumoto, Yoshiteru

2014-06-07

Oxidation reaction of a gas-phase aluminum atom by a molecular oxygen was studied by a crossed-beam condition at 12.4 kJ/mol of collision energy. A (1+1) resonance-enhanced multiphoton ionization (REMPI) via the D(2)Σ(+)-X(2)Σ(+) transition of AlO was applied to ionize the product. The REMPI spectrum was analyzed to determine rotational state distributions for v = 0-2 of AlO. For several vib-rotational states of AlO, state selected angular and kinetic energy distributions were determined by a time-sliced ion imaging technique for the first time. Kinetic energy distributions were well represented by that taken into account initial energy spreads of collision energy and the population of the spin-orbit levels of the counter product O((3)P(J)) determined previously. All angular distributions showed forward and backward peaks, and the forward peaks were more pronounced than the backward one for the states of low internal energy. The backward peak intensity became comparable to the forward one for the states of high internal energy. These results and the rotational state distributions suggested that the reaction proceeds via an intermediate which has a lifetime comparable to or shorter than its rotational period.

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

NASA Astrophysics Data System (ADS)

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

1996-03-01

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

Competition between dynamic and structural disorder in a doped triangular antiferromagnet RbFe(MoO4)2

NASA Astrophysics Data System (ADS)

Smirnov, A. I.; Soldatov, T. A.; Petrenko, O. A.; Takata, A.; Kida, T.; Hagiwara, M.; Zhitomirsky, M. E.; Shapiro, A. Ya

2018-03-01

Magnetisation measurements and electron spin resonance (ESR) spectra of a doped quasi two dimensional (2D) antiferromagnet on a triangular lattice Rb1 ‑ x K x Fe(MoO4)2 reveal a crucial change of the ground state spin configuration and a disappearance of a characteristic 1/3-magnetisation plateau at x = 0.15. According to theory for triangular antiferromagnets with a weak random modulation of the exchange bonds, this is a result of the competition between the structural and dynamic disorders. The dynamic zero-point or thermal fluctuations are known to lift the degeneracy of the mean field ground state of a triangular antiferromagnet and cause the spin configuration to be the most collinear, while the static disorder provides another selection of the ground state, with the least collinear structure. Low-level doping (x ≤ 0.15) was found to decrease the Néel temperature and saturation field by only few percent, while the magnetisation plateau disappears completely and the spin configuration is drastically changed. ESR spectra confirm an impurity-induced change of the so-called Y-type structure to an inverted Y-structure for x = 0.15. For x = 0.075 the intermediate regime with the decrease of width and weakening of flattening of 1/3-plateau was found.

Sequential selection of economic good and action in medial frontal cortex of macaques during value-based decisions

PubMed Central

Chen, Xiaomo; Stuphorn, Veit

2015-01-01

Value-based decisions could rely either on the selection of desired economic goods or on the selection of the actions that will obtain the goods. We investigated this question by recording from the supplementary eye field (SEF) of monkeys during a gambling task that allowed us to distinguish chosen good from chosen action signals. Analysis of the individual neuron activity, as well as of the population state-space dynamic, showed that SEF encodes first the chosen gamble option (the desired economic good) and only ~100 ms later the saccade that will obtain it (the chosen action). The action selection is likely driven by inhibitory interactions between different SEF neurons. Our results suggest that during value-based decisions, the selection of economic goods precedes and guides the selection of actions. The two selection steps serve different functions and can therefore not compensate for each other, even when information guiding both processes is given simultaneously. DOI: http://dx.doi.org/10.7554/eLife.09418.001 PMID:26613409

Thermodynamic coupling between activation and inactivation gating in potassium channels revealed by free energy molecular dynamics simulations.

PubMed

Pan, Albert C; Cuello, Luis G; Perozo, Eduardo; Roux, Benoît

2011-12-01

The amount of ionic current flowing through K(+) channels is determined by the interplay between two separate time-dependent processes: activation and inactivation gating. Activation is concerned with the stimulus-dependent opening of the main intracellular gate, whereas inactivation is a spontaneous conformational transition of the selectivity filter toward a nonconductive state occurring on a variety of timescales. A recent analysis of multiple x-ray structures of open and partially open KcsA channels revealed the mechanism by which movements of the inner activation gate, formed by the inner helices from the four subunits of the pore domain, bias the conformational changes at the selectivity filter toward a nonconductive inactivated state. This analysis highlighted the important role of Phe103, a residue located along the inner helix, near the hinge position associated with the opening of the intracellular gate. In the present study, we use free energy perturbation molecular dynamics simulations (FEP/MD) to quantitatively elucidate the thermodynamic basis for the coupling between the intracellular gate and the selectivity filter. The results of the FEP/MD calculations are in good agreement with experiments, and further analysis of the repulsive, van der Waals dispersive, and electrostatic free energy contributions reveals that the energetic basis underlying the absence of inactivation in the F103A mutation in KcsA is the absence of the unfavorable steric interaction occurring with the large Ile100 side chain in a neighboring subunit when the intracellular gate is open and the selectivity filter is in a conductive conformation. Macroscopic current analysis shows that the I100A mutant indeed relieves inactivation in KcsA, but to a lesser extent than the F103A mutant.

Dynamical characterization of inactivation path in voltage-gated Na+ ion channel by non-equilibrium response spectroscopy

PubMed Central

Pal, Krishnendu; Gangopadhyay, Gautam

2016-01-01

ABSTRACT Inactivation path of voltage gated sodium channel has been studied here under various voltage protocols as it is the main governing factor for the periodic occurrence and shape of the action potential. These voltage protocols actually serve as non-equilibrium response spectroscopic tools to study the ion channel in non-equilibrium environment. In contrast to a lot of effort in finding the crystal structure based molecular mechanism of closed-state(CSI) and open-state inactivation(OSI); here our approach is to understand the dynamical characterization of inactivation. The kinetic flux as well as energetic contribution of the closed and open- state inactivation path is compared here for voltage protocols, namely constant, pulsed and oscillating. The non-equilibrium thermodynamic quantities used in response to these voltage protocols serve as improved characterization tools for theoretical understanding which not only agrees with the previously known kinetic measurements but also predict the energetically optimum processes to sustain the auto-regulatory mechanism of action potential and the consequent inactivation steps needed. The time dependent voltage pattern governs the population of the conformational states which when couple with characteristic rate parameters, the CSI and OSI selectivity arise dynamically to control the inactivation path. Using constant, pulsed and continuous oscillating voltage protocols we have shown that during depolarization the OSI path is more favored path of inactivation however, in the hyper-polarized situation the CSI is favored. It is also shown that the re-factorisation of inactivated sodium channel to resting state occurs via CSI path. Here we have shown how the subtle energetic and entropic cost due to the change in the depolarization magnitude determines the optimum path of inactivation. It is shown that an efficient CSI and OSI dynamical profile in principle can characterize the open-state drug blocking phenomena. PMID:27367642

Hyperspectral imaging polarimeter in the infrared

NASA Astrophysics Data System (ADS)

Jensen, Gary L.; Peterson, James Q.

1998-11-01

The Space Dynamics Laboratory at Utah State University is building an infrared Hyperspectral Imaging Polarimeter (HIP). Designed for high spatial and spectral resolution polarimetry of backscattered sunlight from cloud tops in the 2.7 micrometer water band, it will fly aboard the Flying Infrared Signatures Technology Aircraft (FISTA), an Air Force KC-135. It is a proof-of-concept sensor, combining hyperspectral pushbroom imaging with high speed, solid state polarimetry, using as many off-the-shelf components as possible, and utilizing an optical breadboard design for rapid prototyping. It is based around a 256 X 320 window selectable InSb camera, a solid-state Ferro-electric Liquid Crystal (FLC) polarimeter, and a transmissive diffraction grating.

The rise and fall of redundancy in decoherence and quantum Darwinism

NASA Astrophysics Data System (ADS)

Jess Riedel, C.; Zurek, Wojciech H.; Zwolak, Michael

2012-08-01

A state selected at random from the Hilbert space of a many-body system is overwhelmingly likely to exhibit highly non-classical correlations. For these typical states, half of the environment must be measured by an observer to determine the state of a given subsystem. The objectivity of classical reality—the fact that multiple observers can agree on the state of a subsystem after measuring just a small fraction of its environment—implies that the correlations found in nature between macroscopic systems and their environments are exceptional. Building on previous studies of quantum Darwinism showing that highly redundant branching states are produced ubiquitously during pure decoherence, we examine the conditions needed for the creation of branching states and study their demise through many-body interactions. We show that even constrained dynamics can suppress redundancy to the values typical of random states on relaxation timescales, and prove that these results hold exactly in the thermodynamic limit.

Method and system for detecting a failure or performance degradation in a dynamic system such as a flight vehicle

NASA Technical Reports Server (NTRS)

Miller, Robert H. (Inventor); Ribbens, William B. (Inventor)

2003-01-01

A method and system for detecting a failure or performance degradation in a dynamic system having sensors for measuring state variables and providing corresponding output signals in response to one or more system input signals are provided. The method includes calculating estimated gains of a filter and selecting an appropriate linear model for processing the output signals based on the input signals. The step of calculating utilizes one or more models of the dynamic system to obtain estimated signals. The method further includes calculating output error residuals based on the output signals and the estimated signals. The method also includes detecting one or more hypothesized failures or performance degradations of a component or subsystem of the dynamic system based on the error residuals. The step of calculating the estimated values is performed optimally with respect to one or more of: noise, uncertainty of parameters of the models and un-modeled dynamics of the dynamic system which may be a flight vehicle or financial market or modeled financial system.

Resting state cerebral blood flow with arterial spin labeling MRI in developing human brains.

PubMed

Liu, Feng; Duan, Yunsuo; Peterson, Bradley S; Asllani, Iris; Zelaya, Fernando; Lythgoe, David; Kangarlu, Alayar

2018-07-01

The development of brain circuits is coupled with changes in neurovascular coupling, which refers to the close relationship between neural activity and cerebral blood flow (CBF). Studying the characteristics of CBF during resting state in developing brain can be a complementary way to understand the functional connectivity of the developing brain. Arterial spin labeling (ASL), as a noninvasive MR technique, is particularly attractive for studying cerebral perfusion in children and even newborns. We have collected pulsed ASL data in resting state for 47 healthy subjects from young children to adolescence (aged from 6 to 20 years old). In addition to studying the developmental change of static CBF maps during resting state, we also analyzed the CBF time series to reveal the dynamic characteristics of CBF in differing age groups. We used the seed-based correlation analysis to examine the temporal relationship of CBF time series between the selected ROIs and other brain regions. We have shown the developmental patterns in both static CBF maps and dynamic characteristics of CBF. While higher CBF of default mode network (DMN) in all age groups supports that DMN is the prominent active network during the resting state, the CBF connectivity patterns of some typical resting state networks show distinct patterns of metabolic activity during the resting state in the developing brains. Copyright © 2018 European Paediatric Neurology Society. All rights reserved.

Assessing the Utility of Temporally Dynamic Terrain Indices in Alaskan Moose Resource Selection

NASA Astrophysics Data System (ADS)

Jennewein, J. S.; Hebblewhite, M.; Meddens, A. J.; Gilbert, S.; Vierling, L. A.; Boelman, N.; Eitel, J.

2017-12-01

The accelerated warming in arctic and boreal regions impacts ecosystem structure and plant species distribution, which have secondary effects on wildlife. In summer months, moose (Alces alces) are especially vulnerable to changes in the availability and quality of forage and foliage cover due to their thermoregulatory needs and high energetic demands post calving. Resource selection functions (RSFs) have been used with great success to model such tradeoffs in habitat selection. Recently, RSFs have expanded to include more dynamic representations of habitat selection through the use of time-varying covariates such as dynamic habitat indices. However, to date few studies have investigated dynamic terrain indices, which incorporate long-term, highly-dynamic meteorological data (e.g., albedo, air temperature) and their utility in modeling habitat selection. The purpose of this study is to compare two dynamic terrain indices (i.e., solar insolation and topographic wetness) to their static counterparts in Alaskan moose resource selection over a ten-year period (2008-2017). Additionally, the utility of a dynamic wind-shelter index is assessed. Three moose datasets (n=130 total), spanning a north-to-south gradient in Alaska, are analyzed independently to assess location-specific resource selection. The newly-released, high-resolution Arctic Digital Elevation Model (5m2) is used as the terrain input into both dynamic and static indices. Dynamic indices are programmed with meteorological data from the North American Regional Analysis (NARR) and NASA's Goddard Earth Sciences Data and Information Services Center (GES-DISC) databases. Static wetness and solar insolation indices are estimated using only topographic parameters (e.g., slope, aspect). Preliminary results from pilot analyses suggest that dynamic terrain indices may provide novel insights into resource selection of moose that could not be gained when using static counterparts. Future applications of such dynamic terrain indices that incorporate time-varying meteorological data may be increasingly important in modelling habitat selection under continued climate change scenarios.

Smoking-based selection and influence in gender-segregated friendship networks: a social network analysis of adolescent smoking.

PubMed

Mercken, Liesbeth; Snijders, Tom A B; Steglich, Christian; Vertiainen, Erkki; de Vries, Hein

2010-07-01

The main goal of this study was to examine differences between adolescent male and female friendship networks regarding smoking-based selection and influence processes using newly developed social network analysis methods that allow the current state of continuously changing friendship networks to act as a dynamic constraint for changes in smoking behaviour, while allowing current smoking behaviour to be simultaneously a dynamic constraint for changes in friendship networks. Longitudinal design with four measurements. Nine junior high schools in Finland. A total of 1163 adolescents (mean age = 13.6 years) who participated in the control group of the ESFA (European Smoking prevention Framework Approach) study, including 605 males and 558 females. Smoking behaviour of adolescents, parents, siblings and friendship ties. Smoking-based selection of friends was found in male as well as female networks. However, support for influence among friends was found only in female networks. Furthermore, females and males were both influenced by parental smoking behaviour. In Finnish adolescents, both male and female smokers tend to select other smokers as friends but it appears that only females are influenced to smoke by their peer group. This suggests that prevention campaigns targeting resisting peer pressure may be more effective in adolescent girls than boys.

Computational analysis for selectivity of histone deacetylase inhibitor by replica-exchange umbrella sampling molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Tsukamoto, Shuichiro; Sakae, Yoshitake; Itoh, Yukihiro; Suzuki, Takayoshi; Okamoto, Yuko

2018-03-01

We performed protein-ligand docking simulations with a ligand T247, which has been reported as a selective inhibitor of a histone deacetylase HDAC3, by the replica-exchange umbrella sampling method in order to estimate the free energy profiles along ligand docking pathways of HDAC3-T247 and HDAC2-T247 systems. The simulation results showed that the docked state of the HDAC3-T247 system is more stable than that of the HDAC2-T247 system although the amino-acid sequences and structures of HDAC3 and HDAC2 are very similar. By comparing structures obtained from the simulations of both systems, we found the difference between structures of hydrophobic residues at the entrance of the catalytic site. Moreover, we performed conventional molecular dynamics simulations of HDAC3 and HDAC2 systems without T247, and the results also showed the same difference of the hydrophobic structures. Therefore, we consider that this hydrophobic structure contributes to the stabilization of the docked state of the HDAC3-T247 system. Furthermore, we show that Tyr209, which is one of the hydrophobic residues in HDAC2, plays a key role in the instability from the simulation results of a mutated-HDAC2 system.

A System-Oriented Approach for the Optimal Control of Process Chains under Stochastic Influences

NASA Astrophysics Data System (ADS)

Senn, Melanie; Schäfer, Julian; Pollak, Jürgen; Link, Norbert

2011-09-01

Process chains in manufacturing consist of multiple connected processes in terms of dynamic systems. The properties of a product passing through such a process chain are influenced by the transformation of each single process. There exist various methods for the control of individual processes, such as classical state controllers from cybernetics or function mapping approaches realized by statistical learning. These controllers ensure that a desired state is obtained at process end despite of variations in the input and disturbances. The interactions between the single processes are thereby neglected, but play an important role in the optimization of the entire process chain. We divide the overall optimization into two phases: (1) the solution of the optimization problem by Dynamic Programming to find the optimal control variable values for each process for any encountered end state of its predecessor and (2) the application of the optimal control variables at runtime for the detected initial process state. The optimization problem is solved by selecting adequate control variables for each process in the chain backwards based on predefined quality requirements for the final product. For the demonstration of the proposed concept, we have chosen a process chain from sheet metal manufacturing with simplified transformation functions.

Probing the Energy Landscape of Activation Gating of the Bacterial Potassium Channel KcsA

PubMed Central

Linder, Tobias; de Groot, Bert L.; Stary-Weinzinger, Anna

2013-01-01

The bacterial potassium channel KcsA, which has been crystallized in several conformations, offers an ideal model to investigate activation gating of ion channels. In this study, essential dynamics simulations are applied to obtain insights into the transition pathways and the energy profile of KcsA pore gating. In agreement with previous hypotheses, our simulations reveal a two phasic activation gating process. In the first phase, local structural rearrangements in TM2 are observed leading to an intermediate channel conformation, followed by large structural rearrangements leading to full opening of KcsA. Conformational changes of a highly conserved phenylalanine, F114, at the bundle crossing region are crucial for the transition from a closed to an intermediate state. 3.9 µs umbrella sampling calculations reveal that there are two well-defined energy barriers dividing closed, intermediate, and open channel states. In agreement with mutational studies, the closed state was found to be energetically more favorable compared to the open state. Further, the simulations provide new insights into the dynamical coupling effects of F103 between the activation gate and the selectivity filter. Investigations on individual subunits support cooperativity of subunits during activation gating. PMID:23658510

HiMoP: A three-component architecture to create more human-acceptable social-assistive robots : Motivational architecture for assistive robots.

PubMed

Rodríguez-Lera, Francisco J; Matellán-Olivera, Vicente; Conde-González, Miguel Á; Martín-Rico, Francisco

2018-05-01

Generation of autonomous behavior for robots is a general unsolved problem. Users perceive robots as repetitive tools that do not respond to dynamic situations. This research deals with the generation of natural behaviors in assistive service robots for dynamic domestic environments, particularly, a motivational-oriented cognitive architecture to generate more natural behaviors in autonomous robots. The proposed architecture, called HiMoP, is based on three elements: a Hierarchy of needs to define robot drives; a set of Motivational variables connected to robot needs; and a Pool of finite-state machines to run robot behaviors. The first element is inspired in Alderfer's hierarchy of needs, which specifies the variables defined in the motivational component. The pool of finite-state machine implements the available robot actions, and those actions are dynamically selected taking into account the motivational variables and the external stimuli. Thus, the robot is able to exhibit different behaviors even under similar conditions. A customized version of the "Speech Recognition and Audio Detection Test," proposed by the RoboCup Federation, has been used to illustrate how the architecture works and how it dynamically adapts and activates robots behaviors taking into account internal variables and external stimuli.

Nonadiabatic dynamics of O({sup 1}D) + N{sub 2}(X{sup 1}{Sigma}{sub g}{sup +}){yields}O({sup 3}P) + N{sub 2}(X{sup 1}{Sigma}{sub g}{sup +}) on three coupled potential surfaces: Symmetry, Coriolis, spin-orbit, and Renner-Teller effects

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

Defazio, Paolo; Gamallo, Pablo; Petrongolo, Carlo

2012-02-07

We present the spin-orbit (SO) and Renner-Teller (RT) quantum dynamics of the spin-forbidden quenching O({sup 1}D) + N{sub 2}(X{sup 1}{Sigma}{sub g}{sup +}){yields}O({sup 3}P) + N{sub 2}(X{sup 1}{Sigma}{sub g}{sup +}) on the N{sub 2}O X-tilde{sup 1}A{sup '}, a-tilde{sup 3}A', and b-tilde{sup 3}A{sup '} coupled PESs. We use the permutation-inversion symmetry, propagate coupled-channel (CC) real wavepackets, and compute initial-state-resolved probabilities and cross sections {sigma}{sub j0} for the ground vibrational and the first two rotational states of N{sub 2}, j{sub 0}= 0 and 1. Labeling symmetry angular states by j and K, we report selection rules for j and for the minimum Kmore » value associated with any electronic state, showing that a-tilde{sup 3}A' is uncoupled in the centrifugal-sudden (CS) approximation at j{sub 0}= 0. The dynamics is resonance-dominated, the probabilities are larger at low K, {sigma}{sub j0} decrease with the collision energy and increase with j{sub 0}, and the CS {sigma}{sub 0} is lower than the CC one. The nonadiabatic interactions play different roles on the quenching dynamics, because the X-tilde{sup 1}A{sup '}-b-tilde{sup 3}A{sup '} SO effects are those most important while the a-tilde{sup 3}A'-b-tilde{sup 3}A{sup '} RT ones are negligible.« less

From cognitive networks to seizures: Stimulus evoked dynamics in a coupled cortical network

NASA Astrophysics Data System (ADS)

Lee, Jaejin; Ermentrout, Bard; Bodner, Mark

2013-12-01

Epilepsy is one of the most common neuropathologies worldwide. Seizures arising in epilepsy or in seizure disorders are characterized generally by uncontrolled spread of excitation and electrical activity to a limited region or even over the entire cortex. While it is generally accepted that abnormal excessive firing and synchronization of neuron populations lead to seizures, little is known about the precise mechanisms underlying human epileptic seizures, the mechanisms of transitions from normal to paroxysmal activity, or about how seizures spread. Further complication arises in that seizures do not occur with a single type of dynamics but as many different phenotypes and genotypes with a range of patterns, synchronous oscillations, and time courses. The concept of preventing, terminating, or modulating seizures and/or paroxysmal activity through stimulation of brain has also received considerable attention. The ability of such stimulation to prevent or modulate such pathological activity may depend on identifiable parameters. In this work, firing rate networks with inhibitory and excitatory populations were modeled. Network parameters were chosen to model normal working memory behaviors. Two different models of cognitive activity were developed. The first model consists of a single network corresponding to a local area of the brain. The second incorporates two networks connected through sparser recurrent excitatory connectivity with transmission delays ranging from approximately 3 ms within local populations to 15 ms between populations residing in different cortical areas. The effect of excitatory stimulation to activate working memory behavior through selective persistent activation of populations is examined in the models, and the conditions and transition mechanisms through which that selective activation breaks down producing spreading paroxysmal activity and seizure states are characterized. Specifically, we determine critical parameters and architectural changes that produce the different seizure dynamics in the networks. This provides possible mechanisms for seizure generation. Because seizures arise as attractors in a multi-state system, the system may possibly be returned to its baseline state through some particular stimulation. The ability of stimulation to terminate seizure dynamics in the local and distributed models is studied. We systematically examine when this may occur and the form of the stimulation necessary for the range of seizure dynamics. In both the local and distributed network models, termination is possible for all seizure types observed by stimulation possessing some particular configuration of spatial and temporal characteristics.

Trees wanted--dead or alive! Host selection and population dynamics in tree-killing bark beetles.

PubMed

Kausrud, Kyrre L; Grégoire, Jean-Claude; Skarpaas, Olav; Erbilgin, Nadir; Gilbert, Marius; Økland, Bjørn; Stenseth, Nils Chr

2011-01-01

Bark beetles (Coleoptera: Curculionidae, Scolytinae) feed and breed in dead or severely weakened host trees. When their population densities are high, some species aggregate on healthy host trees so that their defences may be exhausted and the inner bark successfully colonized, killing the tree in the process. Here we investigate under what conditions participating with unrelated conspecifics in risky mass attacks on living trees is an adaptive strategy, and what this can tell us about bark beetle outbreak dynamics. We find that the outcome of individual host selection may deviate from the ideal free distribution in a way that facilitates the emergence of tree-killing (aggressive) behavior, and that any heritability on traits governing aggressiveness seems likely to exist in a state of flux or cycles consistent with variability observed in natural populations. This may have implications for how economically and ecologically important species respond to environmental changes in climate and landscape (forest) structure. The population dynamics emerging from individual behavior are complex, capable of switching between "endemic" and "epidemic" regimes spontaneously or following changes in host availability or resistance. Model predictions are compared to empirical observations, and we identify some factors determining the occurrence and self-limitation of epidemics.

Population Dynamics of Genetic Regulatory Networks

NASA Astrophysics Data System (ADS)

Braun, Erez

2005-03-01

Unlike common objects in physics, a biological cell processes information. The cell interprets its genome and transforms the genomic information content, through the action of genetic regulatory networks, into proteins which in turn dictate its metabolism, functionality and morphology. Understanding the dynamics of a population of biological cells presents a unique challenge. It requires to link the intracellular dynamics of gene regulation, through the mechanism of cell division, to the level of the population. We present experiments studying adaptive dynamics of populations of genetically homogeneous microorganisms (yeast), grown for long durations under steady conditions. We focus on population dynamics that do not involve random genetic mutations. Our experiments follow the long-term dynamics of the population distributions and allow to quantify the correlations among generations. We focus on three interconnected issues: adaptation of genetically homogeneous populations following environmental changes, selection processes on the population and population variability and expression distributions. We show that while the population exhibits specific short-term responses to environmental inputs, it eventually adapts to a robust steady-state, largely independent of external conditions. Cycles of medium-switch show that the adapted state is imprinted in the population and that this memory is maintained for many generations. To further study population adaptation, we utilize the process of gene recruitment whereby a gene naturally regulated by a specific promoter is placed under a different regulatory system. This naturally occurring process has been recognized as a major driving force in evolution. We have recruited an essential gene to a foreign regulatory network and followed the population long-term dynamics. Rewiring of the regulatory network allows us to expose their complex dynamics and phase space structure.

What Can Be Learned from Nuclear Resonance Vibrational Spectroscopy: Vibrational Dynamics and Hemes

PubMed Central

2017-01-01

Nuclear resonance vibrational spectroscopy (NRVS; also known as nuclear inelastic scattering, NIS) is a synchrotron-based method that reveals the full spectrum of vibrational dynamics for Mössbauer nuclei. Another major advantage, in addition to its completeness (no arbitrary optical selection rules), is the unique selectivity of NRVS. The basics of this recently developed technique are first introduced with descriptions of the experimental requirements and data analysis including the details of mode assignments. We discuss the use of NRVS to probe 57Fe at the center of heme and heme protein derivatives yielding the vibrational density of states for the iron. The application to derivatives with diatomic ligands (O2, NO, CO, CN–) shows the strong capabilities of identifying mode character. The availability of the complete vibrational spectrum of iron allows the identification of modes not available by other techniques. This permits the correlation of frequency with other physical properties. A significant example is the correlation we find between the Fe–Im stretch in six-coordinate Fe(XO) hemes and the trans Fe–N(Im) bond distance, not possible previously. NRVS also provides uniquely quantitative insight into the dynamics of the iron. For example, it provides a model-independent means of characterizing the strength of iron coordination. Prediction of the temperature-dependent mean-squared displacement from NRVS measurements yields a vibrational “baseline” for Fe dynamics that can be compared with results from techniques that probe longer time scales to yield quantitative insights into additional dynamical processes. PMID:28921972

Gossip and Distributed Kalman Filtering: Weak Consensus Under Weak Detectability

NASA Astrophysics Data System (ADS)

Kar, Soummya; Moura, José M. F.

2011-04-01

The paper presents the gossip interactive Kalman filter (GIKF) for distributed Kalman filtering for networked systems and sensor networks, where inter-sensor communication and observations occur at the same time-scale. The communication among sensors is random; each sensor occasionally exchanges its filtering state information with a neighbor depending on the availability of the appropriate network link. We show that under a weak distributed detectability condition: 1. the GIKF error process remains stochastically bounded, irrespective of the instability properties of the random process dynamics; and 2. the network achieves \\emph{weak consensus}, i.e., the conditional estimation error covariance at a (uniformly) randomly selected sensor converges in distribution to a unique invariant measure on the space of positive semi-definite matrices (independent of the initial state.) To prove these results, we interpret the filtered states (estimates and error covariances) at each node in the GIKF as stochastic particles with local interactions. We analyze the asymptotic properties of the error process by studying as a random dynamical system the associated switched (random) Riccati equation, the switching being dictated by a non-stationary Markov chain on the network graph.

Subdiffractional tracking of internalized molecules reveals heterogeneous motion states of synaptic vesicles

PubMed Central

Morrow, Isabel C.; Harper, Callista B.

2016-01-01

Our understanding of endocytic pathway dynamics is severely restricted by the diffraction limit of light microscopy. To address this, we implemented a novel technique based on the subdiffractional tracking of internalized molecules (sdTIM). This allowed us to image anti–green fluorescent protein Atto647N-tagged nanobodies trapped in synaptic vesicles (SVs) from live hippocampal nerve terminals expressing vesicle-associated membrane protein 2 (VAMP2)–pHluorin with 36-nm localization precision. Our results showed that, once internalized, VAMP2–pHluorin/Atto647N–tagged nanobodies exhibited a markedly lower mobility than on the plasma membrane, an effect that was reversed upon restimulation in presynapses but not in neighboring axons. Using Bayesian model selection applied to hidden Markov modeling, we found that SVs oscillated between diffusive states or a combination of diffusive and transport states with opposite directionality. Importantly, SVs exhibiting diffusive motion were relatively less likely to switch to the transport motion. These results highlight the potential of the sdTIM technique to provide new insights into the dynamics of endocytic pathways in a wide variety of cellular settings. PMID:27810917

A Dynamic View of Molecular Switch Behavior at Serotonin Receptors: Implications for Functional Selectivity

PubMed Central

Martí-Solano, Maria; Sanz, Ferran; Pastor, Manuel; Selent, Jana

2014-01-01

Functional selectivity is a property of G protein-coupled receptors that allows them to preferentially couple to particular signaling partners upon binding of biased agonists. Publication of the X-ray crystal structure of serotonergic 5-HT1B and 5-HT2B receptors in complex with ergotamine, a drug capable of activating G protein coupling and β-arrestin signaling at the 5-HT1B receptor but clearly favoring β-arrestin over G protein coupling at the 5-HT2B subtype, has recently provided structural insight into this phenomenon. In particular, these structures highlight the importance of specific residues, also called micro-switches, for differential receptor activation. In our work, we apply classical molecular dynamics simulations and enhanced sampling approaches to analyze the behavior of these micro-switches and their impact on the stabilization of particular receptor conformational states. Our analysis shows that differences in the conformational freedom of helix 6 between both receptors could explain their different G protein-coupling capacity. In particular, as compared to the 5-HT1B receptor, helix 6 movement in the 5-HT2B receptor can be constrained by two different mechanisms. On the one hand, an anchoring effect of ergotamine, which shows an increased capacity to interact with the extracellular part of helices 5 and 6 and stabilize them, hinders activation of a hydrophobic connector region at the center of the receptor. On the other hand, this connector region in an inactive conformation is further stabilized by unconserved contacts extending to the intracellular part of the 5-HT2B receptor, which hamper opening of the G protein binding site. This work highlights the importance of considering receptor capacity to adopt different conformational states from a dynamic perspective in order to underpin the structural basis of functional selectivity. PMID:25313636

A dynamic view of molecular switch behavior at serotonin receptors: implications for functional selectivity.

PubMed

Martí-Solano, Maria; Sanz, Ferran; Pastor, Manuel; Selent, Jana

2014-01-01

Functional selectivity is a property of G protein-coupled receptors that allows them to preferentially couple to particular signaling partners upon binding of biased agonists. Publication of the X-ray crystal structure of serotonergic 5-HT1B and 5-HT2B receptors in complex with ergotamine, a drug capable of activating G protein coupling and β-arrestin signaling at the 5-HT1B receptor but clearly favoring β-arrestin over G protein coupling at the 5-HT2B subtype, has recently provided structural insight into this phenomenon. In particular, these structures highlight the importance of specific residues, also called micro-switches, for differential receptor activation. In our work, we apply classical molecular dynamics simulations and enhanced sampling approaches to analyze the behavior of these micro-switches and their impact on the stabilization of particular receptor conformational states. Our analysis shows that differences in the conformational freedom of helix 6 between both receptors could explain their different G protein-coupling capacity. In particular, as compared to the 5-HT1B receptor, helix 6 movement in the 5-HT2B receptor can be constrained by two different mechanisms. On the one hand, an anchoring effect of ergotamine, which shows an increased capacity to interact with the extracellular part of helices 5 and 6 and stabilize them, hinders activation of a hydrophobic connector region at the center of the receptor. On the other hand, this connector region in an inactive conformation is further stabilized by unconserved contacts extending to the intracellular part of the 5-HT2B receptor, which hamper opening of the G protein binding site. This work highlights the importance of considering receptor capacity to adopt different conformational states from a dynamic perspective in order to underpin the structural basis of functional selectivity.

Spatial structure of disordered proteins dictates conductance and selectivity in nuclear pore complex mimics

PubMed Central

Frey, Steffen; Dwarkasing, Arvind; Versloot, Roderick; van der Giessen, Erik

2018-01-01

Nuclear pore complexes (NPCs) lined with intrinsically disordered FG-domains act as selective gatekeepers for molecular transport between the nucleus and the cytoplasm in eukaryotic cells. The underlying physical mechanism of the intriguing selectivity is still under debate. Here, we probe the transport of ions and transport receptors through biomimetic NPCs consisting of Nsp1 domains attached to the inner surface of solid-state nanopores. We examine both wildtype FG-domains and hydrophilic SG-mutants. FG-nanopores showed a clear selectivity as transport receptors can translocate across the pore whereas other proteins cannot. SG mutant pores lack such selectivity. To unravel this striking difference, we present coarse-grained molecular dynamics simulations that reveal that FG-pores exhibit a high-density, nonuniform protein distribution, in contrast to a uniform and significantly less-dense protein distribution in the SG-mutant. We conclude that the sequence-dependent density distribution of disordered proteins inside the NPC plays a key role for its conductivity and selective permeability. PMID:29442997

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

Huang, Li; Wang, Yilin; Werner, Philipp

Understanding the electronic properties of actinide oxides under pressure poses a great challenge for experimental and theoretical studies. Here, we investigate the electronic structure of cubic phase uranium dioxide at different volumes using a combination of density functional theory and dynamical mean-field theory. The ab initio calculations predict an orbital-selective insulator-metal transition at a moderate pressure of ~45 GPa. At this pressure the uranium's 5f 5/2 state becomes metallic, while the 5f 7/2 state remains insulating up to about 60 GPa. In the metallic state, we observe a rapid decrease of the 5f occupation and total angular momentum with pressure.more » Simultaneously, the so-called "Zhang-Rice state", which is of predominantly 5f 5/2 character, quickly disappears after the transition into the metallic phase.« less

Mapping the Dynamics Landscape of Conformational Transitions in Enzyme: The Adenylate Kinase Case

PubMed Central

Li, Dechang; Liu, Ming S.; Ji, Baohua

2015-01-01

Conformational transition describes the essential dynamics and mechanism of enzymes in pursuing their various functions. The fundamental and practical challenge to researchers is to quantitatively describe the roles of large-scale dynamic transitions for regulating the catalytic processes. In this study, we tackled this challenge by exploring the pathways and free energy landscape of conformational changes in adenylate kinase (AdK), a key ubiquitous enzyme for cellular energy homeostasis. Using explicit long-timescale (up to microseconds) molecular dynamics and bias-exchange metadynamics simulations, we determined at the atomistic level the intermediate conformational states and mapped the transition pathways of AdK in the presence and absence of ligands. There is clearly chronological operation of the functional domains of AdK. Specifically in the ligand-free AdK, there is no significant energy barrier in the free energy landscape separating the open and closed states. Instead there are multiple intermediate conformational states, which facilitate the rapid transitions of AdK. In the ligand-bound AdK, the closed conformation is energetically most favored with a large energy barrier to open it up, and the conformational population prefers to shift to the closed form coupled with transitions. The results suggest a perspective for a hybrid of conformational selection and induced fit operations of ligand binding to AdK. These observations, depicted in the most comprehensive and quantitative way to date, to our knowledge, emphasize the underlying intrinsic dynamics of AdK and reveal the sophisticated conformational transitions of AdK in fulfilling its enzymatic functions. The developed methodology can also apply to other proteins and biomolecular systems. PMID:26244746

Real-time ab initio simulations of excited-state dynamics in nanostructures

NASA Astrophysics Data System (ADS)

Tomanek, David

2007-03-01

Combining time-dependent ab initio density functional calculations for electrons with molecular dynamics simulations for ions, we investigate the effect of excited-state dynamics in nanostructures. In carbon nanotubes, we find electronic excitations to last for a large fraction of a picosecond. The de-excitation process is dominated by coupling to other electronic degrees of freedom during the first few hundred femtoseconds. Later, the de-excitation process becomes dominated by coupling to ionic motion. The onset point and damping rate in that regime change with initial ion velocities, a manifestation of temperature dependent electron-phonon coupling. Considering the fact that the force field in the electronically excited state differs significantly from the ground state, as reflected in the Franck-Condon effect, atomic bonds can easily be broken or restored during the relatively long lifetime of electronic excitations. This effect can be utilized in a ``photo-surgery" of nanotubes, causing structural self-healing at vacancy sites or selective de-oxidation processes induced by photo-absorption. Also, electronic excitations are a key ingredient for the understanding of sputtering processes in nanostructures, induced by energetic collisions with ions. Yoshiyuki Miyamoto, Angel Rubio, and David Tomanek, Phys. Rev. Lett. 97, 126104 (2006). Yoshiyuki Miyamoto, Savas Berber, Mina Yoon, Angel Rubio, and David Tomanek, Chem. Phys. Lett. 392, 209 (2004). Yoshiyuki Miyamoto, Noboru Jinbo, Hisashi Nakamura, Angel Rubio, and David Tomanek, Phys. Rev. B 70, 233408 (2004). Yoshiyuki Miyamoto, Arkady Krasheninnikov, and David Tomanek (in preparation).

Nonenzymatic all-solid-state coated wire electrode for acetylcholine determination in vitro.

PubMed

He, Cheng; Wang, Zhan; Wang, You; Hu, Ruifen; Li, Guang

2016-11-15

A nonenzymatic all-solid-state coated wire acetylcholine electrode was investigated. Poly(3,4-ethylenedioxythiophene) doped with poly(styrenesulfonate) (PEDOT/PSS) as conducting polymer was coated on one end of a gold wire (0.5mm in diameter). The acetylcholine selective membrane containing heptakis(2,3,6-tri-Ο-methyl)-β-cyclodextrin as an ionophore covered the conducting polymer layer. The electrode could work stably in a pH range of 6.5-8.5 and a temperature range of 15-40°C. It covered an acetylcholine concentration range of 10(-5)-10(-1)M with a slope of 54.04±1.70mV/decade, while detection limit was 5.69±1.06µM. The selectivity, dynamic response, reproducibility and stability were evaluated. The electrode could work properly in the rat brain homogenate to detect different concentrations of acetylcholine. Copyright © 2016 Elsevier B.V. All rights reserved.

Estimating Power System Dynamic States Using Extended Kalman Filter

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

Huang, Zhenyu; Schneider, Kevin P.; Nieplocha, Jaroslaw

2014-10-31

Abstract—The state estimation tools which are currently deployed in power system control rooms are based on a steady state assumption. As a result, the suite of operational tools that rely on state estimation results as inputs do not have dynamic information available and their accuracy is compromised. This paper investigates the application of Extended Kalman Filtering techniques for estimating dynamic states in the state estimation process. The new formulated “dynamic state estimation” includes true system dynamics reflected in differential equations, not like previously proposed “dynamic state estimation” which only considers the time-variant snapshots based on steady state modeling. This newmore » dynamic state estimation using Extended Kalman Filter has been successfully tested on a multi-machine system. Sensitivity studies with respect to noise levels, sampling rates, model errors, and parameter errors are presented as well to illustrate the robust performance of the developed dynamic state estimation process.« less

Effect of fluid compressibility on journal bearing performance

NASA Technical Reports Server (NTRS)

Dimofte, Florin

1993-01-01

An analysis was undertaken to determine the effect of fluid film compressibility on the performance of fluid film bearings. A new version of the Reynolds equation was developed, using a polytropic expansion, for both steady-state and dynamic conditions. Polytropic exponents from 1 (isothermal) to 1000 (approaching an incompressible liquid) were evaluated for two bearing numbers, selected from a range of practical interest for cryogenic application, and without cavitation. Bearing loads were insensitive to fluid compressibility for low bearing numbers, as was expected. The effect of compressibility on attitude angle was significant, even when the bearing number was low. A small amount of fluid compressibility was enough to obtain stable running conditions. Incompressible liquid lacked stability at all conditions. Fluid compressibility can be used to control the bearing dynamic coefficients, thereby influencing the dynamic behavior of the rotor-bearing system.

Temporal-spatial distribution of American bison (Bison bison) in a tallgrass prairie fire mosaic

USGS Publications Warehouse

Schuler, K.L.; Leslie, David M.; Shaw, J.H.; Maichak, E.J.

2006-01-01

Fire and bison (Bison bison) are thought to be historically responsible for shaping prairie vegetation in North America. Interactions between temporal-spatial distributions of bison and prescribed burning protocols are important in current restoration of tallgrass prairies. We examined dynamics of bison distribution in a patch-burned tallgrass prairie in the south-central United States relative to bison group size and composition, and burn age and temporal distribution. Bison formed larger mixed groups during summer and smaller sexually segregated groups the rest of the year, and bison selected dormant-season burn patches in the 1st posture growing season most often during spring and summer. Large bison herds selecting recently burned areas resulted in seasonally variable and concentrated grazing pressure that may substantially alter site-specific vegetation. These dynamics must be considered when reintroducing bison and fire into tallgrass prairie because variable outcomes of floral richness and structural complexity are likely depending on temporal-spatial distribution of bison. ?? 2006 American Society of Mammalogists.

Computing by robust transience: How the fronto-parietal network performs sequential category-based decisions

PubMed Central

Chaisangmongkon, Warasinee; Swaminathan, Sruthi K.; Freedman, David J.; Wang, Xiao-Jing

2017-01-01

Summary Decision making involves dynamic interplay between internal judgements and external perception, which has been investigated in delayed match-to-category (DMC) experiments. Our analysis of neural recordings shows that, during DMC tasks, LIP and PFC neurons demonstrate mixed, time-varying, and heterogeneous selectivity, but previous theoretical work has not established the link between these neural characteristics and population-level computations. We trained a recurrent network model to perform DMC tasks and found that the model can remarkably reproduce key features of neuronal selectivity at the single-neuron and population levels. Analysis of the trained networks elucidates that robust transient trajectories of the neural population are the key driver of sequential categorical decisions. The directions of trajectories are governed by network self-organized connectivity, defining a ‘neural landscape’, consisting of a task-tailored arrangement of slow states and dynamical tunnels. With this model, we can identify functionally-relevant circuit motifs and generalize the framework to solve other categorization tasks. PMID:28334612

Multiple equilibria, bifurcations and selection scenarios in cosymmetric problem of thermal convection in porous medium

NASA Astrophysics Data System (ADS)

Govorukhin, Vasily N.; Shevchenko, Igor V.

2017-12-01

We study convection in a two-dimensional container of porous material saturated with fluid and heated from below. This problem belongs to the class of dynamical systems with nontrivial cosymmetry. The cosymmetry gives rise to a hidden parameter in the system and continuous families of infinitely many equilibria, and leads to non-trivial bifurcations. In this article we present our numerical studies that demonstrate nonlinear phenomena resulting from the existence of cosymmetry. We give a comprehensive picture of different bifurcations which occur in cosymmetric dynamical systems and in the convection problem. It includes internal and external (as an invariant set) bifurcations of one-parameter families of equilibria, as well as bifurcations leading to periodic, quasiperiodic and chaotic behaviour. The existence of infinite number of stable steady-state regimes begs the important question as to which of them can realize in physical experiments. In this paper, this question (known as the selection problem) is studied in detail. In particular, we show that the selection scenarios strongly depend on the initial temperature distribution of the fluid. The calculations are carried out by the global cosymmetry-preserving Galerkin method, and numerical methods used to analyse cosymmetric systems are also described.

Model-independent plot of dynamic PET data facilitates data interpretation and model selection.

PubMed

Munk, Ole Lajord

2012-02-21

When testing new PET radiotracers or new applications of existing tracers, the blood-tissue exchange and the metabolism need to be examined. However, conventional plots of measured time-activity curves from dynamic PET do not reveal the inherent kinetic information. A novel model-independent volume-influx plot (vi-plot) was developed and validated. The new vi-plot shows the time course of the instantaneous distribution volume and the instantaneous influx rate. The vi-plot visualises physiological information that facilitates model selection and it reveals when a quasi-steady state is reached, which is a prerequisite for the use of the graphical analyses by Logan and Gjedde-Patlak. Both axes of the vi-plot have direct physiological interpretation, and the plot shows kinetic parameter in close agreement with estimates obtained by non-linear kinetic modelling. The vi-plot is equally useful for analyses of PET data based on a plasma input function or a reference region input function. The vi-plot is a model-independent and informative plot for data exploration that facilitates the selection of an appropriate method for data analysis. Copyright © 2011 Elsevier Ltd. All rights reserved.

Conceptual design of a Moving Belt Radiator (MBR) shuttle-attached experiment

NASA Technical Reports Server (NTRS)

Aguilar, Jerry L.

1990-01-01

The conceptual design of a shuttle-attached Moving Belt Radiator (MBR) experiment is presented. The MBR is an advanced radiator concept in which a rotating belt is used to radiate thermal energy to space. The experiment is developed with the primary focus being the verification of the dynamic characteristics of a rotating belt with a secondary objective of proving the thermal and sealing aspects in a reduced gravity, vacuum environment. The mechanical design, selection of the belt material and working fluid, a preliminary test plan, and program plan are presented. The strategy used for selecting the basic sizes and materials of the components are discussed. Shuttle and crew member requirements are presented with some options for increasing or decreasing the demands on the STS. An STS carrier and the criteria used in the selection process are presented. The proposed carrier for the Moving Belt Radiator experiment is the Hitchhiker-M. Safety issues are also listed with possible results. This experiment is designed so that a belt can be deployed, run at steady state conditions, run with dynamic perturbations imposed, verify the operation of the interface heat exchanger and seals, and finally be retracted into a stowed position for transport back to earth.

Comparative study of crystallization process in metallic melts using ab initio molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Debela, Tekalign T.; Wang, X. D.; Cao, Q. P.; Zhang, D. X.; Jiang, J. Z.

2017-05-01

The crystallization process of liquid metals is studied using ab initio molecular dynamics simulations. The evolution of short-range order during quenching in Pb and Zn liquids is compared with body-centered cubic (bcc) Nb and V, and hexagonal closed-packed (hcp) Mg. We found that the fraction and type of the short-range order depends on the system under consideration, in which the icosahedral symmetry seems to dominate in the body-centered cubic metals. Although the local atomic structures in stable liquids are similar, liquid hcp-like Zn, bcc-like Nb and V can be deeply supercooled far below its melting point before crystallization while the supercooled temperature range in liquid Pb is limited. Further investigations into the nucleation process reveal the process of polymorph selection. In the body-centered cubic systems, the polymorph selection occurs in the supercooled state before the nucleation is initiated, while in the closed-packed systems it starts at the time of onset of crystallization. Atoms with bcc-like lattices in all studied supercooled liquids are always detected before the polymorph selection. It is also found that the bond orientational ordering is strongly correlated with the crystallization process in supercooled Zn and Pb liquids.

Evidence for ProTα-TLR4/MD-2 binding: molecular dynamics and gravimetric assay studies.

PubMed

Omotuyi, Olaposi; Matsunaga, Hayato; Ueda, Hiroshi

2015-01-01

During preconditioning, lipopolysaccharide (LPS) selectively activates TLR4/MD-2/Toll/IL-1 receptor-domain-containing adaptor inducing IFN-β (TRIF) pathway instead of pro-inflammatory myeloid differentiation protein-88 (MyD88)/MyD88-adaptor-like protein (MAL) pathway. Extracellular prothymosin alpha (ProTα) is also known to selectively activate the TLR4/MD2/TRIF-IRF3 pathway in certain diseased conditions. In the current study, biophysical evidence for ProTα/TLR4/MD-2 complex formation and its interaction dynamics have been studied. Gravimetric assay was used to investigate ProTα/TLR4/MD-2 complex formation while molecular dynamics (MD) simulation was used to study its interaction dynamics. Through electrostatic interaction, full-length ProTα (F-ProTα) C-terminal peptide (aa 91 - 111) superficially interacts with similar TLR4/MD-2 (KD = 273.36 nm vs 16.07 μg/ml [LPS]) conformation with LPS at an overlapping three-dimensional space while F-ProTα is hinged to the TLR4 scaffold by one-amino acid shift-Mosoian domain (aa-51 - 90). Comparatively, F-ProTα better stabilizes MD-2 metastable states transition and mediates higher TLR4/MD-2 interaction than LPS. ProTα via its C-terminal peptide (aa 91 - 111) exhibits in vitro biophysical contact with TLR4/MD-2 complex conformation recognized by LPS at overlapping LPS-binding positions.

Dynamic Seascapes Predict the Marine Occurrence of an Endangered Species

NASA Astrophysics Data System (ADS)

Breece, M.; Fox, D. A.; Dunton, K. J.; Frisk, M. G.; Jordaan, A.; Oliver, M. J.

2016-02-01

Landscapes are powerful environmental partitions that index complex biogeochemical processes that drive terrestrial species distributions. However, translating landscapes into seascapes requires that the dynamic nature of the fluid environment be reflected in spatial and temporal boundaries such that seascapes can be used in marine species distribution models and conservation decisions. A seascape product derived from satellite ocean color and sea surface temperature partitioned mid-Atlantic coastal waters on scales commensurate with the Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus coastal migration. The seascapes were then matched with acoustic telemetry records of Atlantic Sturgeon to determine seascape selectivity. To test our model, we used real-time satellite seascape maps to normalize the sampling of an autonomous underwater vehicle that resampled similar geographic regions with time varying seascape classifications. We found that Atlantic Sturgeon exhibited preference for one seascape class over those available in the coastal ocean, indicating selection for environmental properties that co-varied with the dynamic seascape class rather than geographical location. The recent listing of Atlantic Sturgeon as Endangered throughout much of their United States range has highlighted the need for improved understanding of their occurrence in marine waters to reduce interactions with various anthropogenic stressors. Narrow dynamic migration corridors may enable seascapes to be used as a daily decision tool by industry and managers to reduce interactions with this Endangered Species during coastal migrations.

Dynamic Seascapes Predict the Marine Occurrence of an Endangered Species

NASA Astrophysics Data System (ADS)

Breece, M.; Fox, D. A.; Dunton, K. J.; Frisk, M. G.; Jordaan, A.; Oliver, M. J.

2016-12-01

Landscapes are powerful environmental partitions that index complex biogeochemical processes that drive terrestrial species distributions. However, translating landscapes into seascapes requires that the dynamic nature of the fluid environment be reflected in spatial and temporal boundaries such that seascapes can be used in marine species distribution models and conservation decisions. A seascape product derived from satellite ocean color and sea surface temperature partitioned mid-Atlantic coastal waters on scales commensurate with the Atlantic Sturgeon Acipenser oxyrinchus oxyrinchus coastal migration. The seascapes were then matched with acoustic telemetry records of Atlantic Sturgeon to determine seascape selectivity. To test our model, we used real-time satellite seascape maps to normalize the sampling of an autonomous underwater vehicle that resampled similar geographic regions with time varying seascape classifications. We found that Atlantic Sturgeon exhibited preference for one seascape class over those available in the coastal ocean, indicating selection for environmental properties that co-varied with the dynamic seascape class rather than geographical location. The recent listing of Atlantic Sturgeon as Endangered throughout much of their United States range has highlighted the need for improved understanding of their occurrence in marine waters to reduce interactions with various anthropogenic stressors. Narrow dynamic migration corridors may enable seascapes to be used as a daily decision tool by industry and managers to reduce interactions with this Endangered Species during coastal migrations.

A DMFT+CTQMC Investigation of Strange Metallicity in Local Quantum Critical Scenario

NASA Astrophysics Data System (ADS)

Acharya, Swagata; Laad, M. S.; Taraphder, A.

2016-10-01

“Strange” metallicity is now a pseudonym for a novel metallic state exhibiting anomalous infra-red (branch-cut) continuum features in one- and two-particle responses. Here, we employ dynamical mean-field theory (DMFT) using low-temperature continuous-time- quantum Monte-Carlo (CTQMC) solver for an extended periodic Anderson model (EPAM) model to investigate unusual magnetic fluctuations in the strange metal. We show how extinction of Landau quasiparticles in the orbital selective Mott phase (OSMP) leads to (i) qualitative explication of strange transport features and (ii) anomalous quantum critical magnetic fluctuations due to critical liquid-like features in dynamical spin fluctuations, in excellent accord with data in some f-electron systems.

Mapping the Free Energy Landscape of PKA Inhibition and Activation: A Double-Conformational Selection Model for the Tandem cAMP-Binding Domains of PKA RIα

PubMed Central

Akimoto, Madoka; McNicholl, Eric Tyler; Ramkissoon, Avinash; Moleschi, Kody; Taylor, Susan S.; Melacini, Giuseppe

2015-01-01

Protein Kinase A (PKA) is the major receptor for the cyclic adenosine monophosphate (cAMP) secondary messenger in eukaryotes. cAMP binds to two tandem cAMP-binding domains (CBD-A and -B) within the regulatory subunit of PKA (R), unleashing the activity of the catalytic subunit (C). While CBD-A in RIα is required for PKA inhibition and activation, CBD-B functions as a “gatekeeper” domain that modulates the control exerted by CBD-A. Preliminary evidence suggests that CBD-B dynamics are critical for its gatekeeper function. To test this hypothesis, here we investigate by Nuclear Magnetic Resonance (NMR) the two-domain construct RIα (91–379) in its apo, cAMP2, and C-bound forms. Our comparative NMR analyses lead to a double conformational selection model in which each apo CBD dynamically samples both active and inactive states independently of the adjacent CBD within a nearly degenerate free energy landscape. Such degeneracy is critical to explain the sensitivity of CBD-B to weak interactions with C and its high affinity for cAMP. Binding of cAMP eliminates this degeneracy, as it selectively stabilizes the active conformation within each CBD and inter-CBD contacts, which require both cAMP and W260. The latter is contributed by CBD-B and mediates capping of the cAMP bound to CBD-A. The inter-CBD interface is dispensable for intra-CBD conformational selection, but is indispensable for full activation of PKA as it occludes C-subunit recognition sites within CBD-A. In addition, the two structurally homologous cAMP-bound CBDs exhibit marked differences in their residual dynamics profiles, supporting the notion that conservation of structure does not necessarily imply conservation of dynamics. PMID:26618408

The selectivity of the Na+/K+-pump is controlled by binding site protonation and self-correcting occlusion

PubMed Central

Rui, Huan; Artigas, Pablo; Roux, Benoît

2016-01-01

The Na+/K+-pump maintains the physiological K+ and Na+ electrochemical gradients across the cell membrane. It operates via an 'alternating-access' mechanism, making iterative transitions between inward-facing (E1) and outward-facing (E2) conformations. Although the general features of the transport cycle are known, the detailed physicochemical factors governing the binding site selectivity remain mysterious. Free energy molecular dynamics simulations show that the ion binding sites switch their binding specificity in E1 and E2. This is accompanied by small structural arrangements and changes in protonation states of the coordinating residues. Additional computations on structural models of the intermediate states along the conformational transition pathway reveal that the free energy barrier toward the occlusion step is considerably increased when the wrong type of ion is loaded into the binding pocket, prohibiting the pump cycle from proceeding forward. This self-correcting mechanism strengthens the overall transport selectivity and protects the stoichiometry of the pump cycle. DOI: http://dx.doi.org/10.7554/eLife.16616.001 PMID:27490484

Development of Multi-physics (Multiphase CFD + MCNP) simulation for generic solution vessel power calculation

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

Kim, Seung Jun; Buechler, Cynthia Eileen

The current study aims to predict the steady state power of a generic solution vessel and to develop a corresponding heat transfer coefficient correlation for a Moly99 production facility by conducting a fully coupled multi-physics simulation. A prediction of steady state power for the current application is inherently interconnected between thermal hydraulic characteristics (i.e. Multiphase computational fluid dynamics solved by ANSYS-Fluent 17.2) and the corresponding neutronic behavior (i.e. particle transport solved by MCNP6.2) in the solution vessel. Thus, the development of a coupling methodology is vital to understand the system behavior at a variety of system design and postulated operatingmore » scenarios. In this study, we report on the k-effective (keff) calculation for the baseline solution vessel configuration with a selected solution concentration using MCNP K-code modeling. The associated correlation of thermal properties (e.g. density, viscosity, thermal conductivity, specific heat) at the selected solution concentration are developed based on existing experimental measurements in the open literature. The numerical coupling methodology between multiphase CFD and MCNP is successfully demonstrated, and the detailed coupling procedure is documented. In addition, improved coupling methods capturing realistic physics in the solution vessel thermal-neutronic dynamics are proposed and tested further (i.e. dynamic height adjustment, mull-cell approach). As a key outcome of the current study, a multi-physics coupling methodology between MCFD and MCNP is demonstrated and tested for four different operating conditions. Those different operating conditions are determined based on the neutron source strength at a fixed geometry condition. The steady state powers for the generic solution vessel at various operating conditions are reported, and a generalized correlation of the heat transfer coefficient for the current application is discussed. The assessment of multi-physics methodology and preliminary results from various coupled calculations (power prediction and heat transfer coefficient) can be further utilized for the system code validation and generic solution vessel design improvement.« less

Quasispecies in population of compositional assemblies.

PubMed

Gross, Renan; Fouxon, Itzhak; Lancet, Doron; Markovitch, Omer

2014-12-30

The quasispecies model refers to information carriers that undergo self-replication with errors. A quasispecies is a steady-state population of biopolymer sequence variants generated by mutations from a master sequence. A quasispecies error threshold is a minimal replication accuracy below which the population structure breaks down. Theory and experimentation of this model often refer to biopolymers, e.g. RNA molecules or viral genomes, while its prebiotic context is often associated with an RNA world scenario. Here, we study the possibility that compositional entities which code for compositional information, intrinsically different from biopolymers coding for sequential information, could show quasispecies dynamics. We employed a chemistry-based model, graded autocatalysis replication domain (GARD), which simulates the network dynamics within compositional molecular assemblies. In GARD, a compotype represents a population of similar assemblies that constitute a quasi-stationary state in compositional space. A compotype's center-of-mass is found to be analogous to a master sequence for a sequential quasispecies. Using single-cycle GARD dynamics, we measured the quasispecies transition matrix (Q) for the probabilities of transition from one center-of-mass Euclidean distance to another. Similarly, the quasispecies' growth rate vector (A) was obtained. This allowed computing a steady state distribution of distances to the center of mass, as derived from the quasispecies equation. In parallel, a steady state distribution was obtained via the GARD equation kinetics. Rewardingly, a significant correlation was observed between the distributions obtained by these two methods. This was only seen for distances to the compotype center-of-mass, and not to randomly selected compositions. A similar correspondence was found when comparing the quasispecies time dependent dynamics towards steady state. Further, changing the error rate by modifying basal assembly joining rate of GARD kinetics was found to display an error catastrophe, similar to the standard quasispecies model. Additional augmentation of compositional mutations leads to the complete disappearance of the master-like composition. Our results show that compositional assemblies, as simulated by the GARD formalism, portray significant attributes of quasispecies dynamics. This expands the applicability of the quasispecies model beyond sequence-based entities, and potentially enhances validity of GARD as a model for prebiotic evolution.

A dynamic multiarmed bandit-gene expression programming hyper-heuristic for combinatorial optimization problems.

PubMed

Sabar, Nasser R; Ayob, Masri; Kendall, Graham; Qu, Rong

2015-02-01

Hyper-heuristics are search methodologies that aim to provide high-quality solutions across a wide variety of problem domains, rather than developing tailor-made methodologies for each problem instance/domain. A traditional hyper-heuristic framework has two levels, namely, the high level strategy (heuristic selection mechanism and the acceptance criterion) and low level heuristics (a set of problem specific heuristics). Due to the different landscape structures of different problem instances, the high level strategy plays an important role in the design of a hyper-heuristic framework. In this paper, we propose a new high level strategy for a hyper-heuristic framework. The proposed high-level strategy utilizes a dynamic multiarmed bandit-extreme value-based reward as an online heuristic selection mechanism to select the appropriate heuristic to be applied at each iteration. In addition, we propose a gene expression programming framework to automatically generate the acceptance criterion for each problem instance, instead of using human-designed criteria. Two well-known, and very different, combinatorial optimization problems, one static (exam timetabling) and one dynamic (dynamic vehicle routing) are used to demonstrate the generality of the proposed framework. Compared with state-of-the-art hyper-heuristics and other bespoke methods, empirical results demonstrate that the proposed framework is able to generalize well across both domains. We obtain competitive, if not better results, when compared to the best known results obtained from other methods that have been presented in the scientific literature. We also compare our approach against the recently released hyper-heuristic competition test suite. We again demonstrate the generality of our approach when we compare against other methods that have utilized the same six benchmark datasets from this test suite.

Photodissociation dynamics of allyl chloride at 200 and 266 nm studied by time-resolved mass spectrometry and photoelectron imaging.

PubMed

Shen, Huan; Chen, Jianjun; Hua, Linqiang; Zhang, Bing

2014-06-26

The photodissociation dynamics of allyl chloride at 200 and 266 nm has been studied by femtosecond time-resolved mass spectrometry coupled with photoelectron imaging. The molecule was prepared to different excited states by selectively pumping with 400 or 266 nm pulse. The dissociated products were then probed by multiphoton ionization with 800 nm pulse. After absorbing two photons at 400 nm, several dissociation channels were directly observed from the mass spectrum. The two important channels, C-Cl fission and HCl elimination, were found to decay with multiexponential functions. For C-Cl fission, two time constants, 48 ± 1 fs and 85 ± 40 ps, were observed. The first one was due to the fast predissociation process on the repulsive nσ*/πσ* state. The second one could be ascribed to dissociation on the vibrationally excited ground state which is generated after internal conversion from the initially prepared ππ* state. HCl elimination, which is a typical example of a molecular elimination reaction, was found to proceed with two time constants, 600 ± 135 fs and 14 ± 2 ps. We assigned the first one to dissociation on the excited state and the second one to the internal conversion from the ππ* state to the ground state and then dissociation on the ground state. As we excited the molecule with 266 nm light, the transient signals decayed exponentially with a time constant of ∼48 fs, which is coincident with the time scale of C-halogen direct dissociation. Photoelectron images, which provided translational and angular distributions of the generated electron, were also recorded. Detailed analysis of the kinetic energy distribution strongly suggested that C3H4(+) and C3H5(+) were generated from ionization of the neutral radical. The present study reveals the dissociation dynamics of allyl chloride in a time-resolved way.

A dynamic model of soil salinity and drainage generation in irrigated agriculture: A framework for policy analysis

NASA Astrophysics Data System (ADS)

Dinar, Ariel; Aillery, Marcel P.; Moore, Michael R.

1993-06-01

This paper presents a dynamic model of irrigated agriculture that accounts for drainage generation and salinity accumulation. Critical model relationships involving crop production, soil salinity, and irrigation drainage are based on newly estimated functions derived from lysimeter field tests. The model allocates land and water inputs over time based on an intertemporal profit maximization objective function and soil salinity accumulation process. The model is applied to conditions in the San Joaquin Valley of California, where environmental degradation from irrigation drainage has become a policy issue. Findings indicate that in the absence of regulation, drainage volumes increase over time before reaching a steady state as increased quantities of water are allocated to leaching soil salts. The model is used to evaluate alternative drainage abatement scenarios involving drainage quotas and taxes, water supply quotas and taxes, and irrigation technology subsidies. In our example, direct drainage policies are more cost-effective in reducing drainage than policies operating indirectly through surface water use, although differences in cost efficiency are relatively small. In some cases, efforts to control drainage may result in increased soil salinity accumulation, with implications for long-term cropland productivity. While policy adjustments may alter the direction and duration of convergence to a steady state, findings suggest that a dynamic model specification may not be necessary due to rapid convergence to a comon steady state under selected scenarios.

A new structural framework for integrating replication protein A into DNA processing machinery

PubMed Central

Brosey, Chris A.; Yan, Chunli; Tsutakawa, Susan E.; Heller, William T.; Rambo, Robert P.; Tainer, John A.; Ivanov, Ivaylo; Chazin, Walter J.

2013-01-01

By coupling the protection and organization of single-stranded DNA (ssDNA) with recruitment and alignment of DNA processing factors, replication protein A (RPA) lies at the heart of dynamic multi-protein DNA processing machinery. Nevertheless, how RPA coordinates biochemical functions of its eight domains remains unknown. We examined the structural biochemistry of RPA’s DNA-binding activity, combining small-angle X-ray and neutron scattering with all-atom molecular dynamics simulations to investigate the architecture of RPA’s DNA-binding core. The scattering data reveal compaction promoted by DNA binding; DNA-free RPA exists in an ensemble of states with inter-domain mobility and becomes progressively more condensed and less dynamic on binding ssDNA. Our results contrast with previous models proposing RPA initially binds ssDNA in a condensed state and becomes more extended as it fully engages the substrate. Moreover, the consensus view that RPA engages ssDNA in initial, intermediate and final stages conflicts with our data revealing that RPA undergoes two (not three) transitions as it binds ssDNA with no evidence for a discrete intermediate state. These results form a framework for understanding how RPA integrates the ssDNA substrate into DNA processing machinery, provides substrate access to its binding partners and promotes the progression and selection of DNA processing pathways. PMID:23303776

New approaches to the analysis of complex samples using fluorescence lifetime techniques and organized media

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

Hertz, P.R.

Fluorescence spectroscopy is a highly sensitive and selective tool for the analysis of complex systems. In order to investigate the efficacy of several steady state and dynamic techniques for the analysis of complex systems, this work focuses on two types of complex, multicomponent samples: petrolatums and coal liquids. It is shown in these studies dynamic, fluorescence lifetime-based measurements provide enhanced discrimination between complex petrolatum samples. Additionally, improved quantitative analysis of multicomponent systems is demonstrated via incorporation of organized media in coal liquid samples. This research provides the first systematic studies of (1) multifrequency phase-resolved fluorescence spectroscopy for dynamic fluorescence spectralmore » fingerprinting of complex samples, and (2) the incorporation of bile salt micellar media to improve accuracy and sensitivity for characterization of complex systems. In the petroleum studies, phase-resolved fluorescence spectroscopy is used to combine spectral and lifetime information through the measurement of phase-resolved fluorescence intensity. The intensity is collected as a function of excitation and emission wavelengths, angular modulation frequency, and detector phase angle. This multidimensional information enhances the ability to distinguish between complex samples with similar spectral characteristics. Examination of the eigenvalues and eigenvectors from factor analysis of phase-resolved and steady state excitation-emission matrices, using chemometric methods of data analysis, confirms that phase-resolved fluorescence techniques offer improved discrimination between complex samples as compared with conventional steady state methods.« less

Stochastic opinion formation in scale-free networks

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

M. Bartolozzi; D. B. Leinweber; A. W. Thomas

2005-10-01

The dynamics of opinion formation in large groups of people is a complex nonlinear phenomenon whose investigation is just beginning. Both collective behavior and personal views play an important role in this mechanism. In the present work we mimic the dynamics of opinion formation of a group of agents, represented by two states 1, as a stochastic response of each agent to the opinion of his/her neighbors in the social network and to feedback from the average opinion of the whole. In the light of recent studies, a scale-free Barabsi-Albert network has been selected to simulate the topology of themore » interactions. A turbulent-like dynamics, characterized by an intermittent behavior, is observed for a certain range of the model parameters. The problem of uncertainty in decision taking is also addressed both from a topological point of view, using random and targeted removal of agents from the network, and by implementing a three-state model, where the third state, zero, is related to the information available to each agent. Finally, the results of the model are tested against the best known network of social interactions: the stock market. A time series of daily closures of the Dow-Jones index has been used as an indicator of the possible applicability of our model in the financial context. Good qualitative agreement is found.« less

Role of the plurality rule in multiple choices

NASA Astrophysics Data System (ADS)

Calvão, A. M.; Ramos, M.; Anteneodo, C.

2016-02-01

People are often challenged to select one among several alternatives. This situation is present not only in decisions about complex issues, e.g. political or academic choices, but also about trivial ones, such as in daily purchases at a supermarket. We tackle this scenario by means of the tools of statistical mechanics. Following this approach, we introduce and analyse a model of opinion dynamics, using a Potts-like state variable to represent the multiple choices, including the ‘undecided state’, which represents the individuals who do not make a choice. We investigate the dynamics over Erdös-Rényi and Barabási-Albert networks, two paradigmatic classes with the small-world property, and we show the impact of the type of network on the opinion dynamics. Depending on the number of available options q and on the degree distribution of the network of contacts, different final steady states are accessible: from a wide distribution of choices to a state where a given option largely dominates. The abrupt transition between them is consistent with the sudden viral dominance of a given option over many similar ones. Moreover, the probability distributions produced by the model are validated by real data. Finally, we show that the model also contemplates the real situation of overchoice, where a large number of similar alternatives makes the choice process harder and indecision prevail.

Chemical substitutions in the selectivity filter of potassium channels do not rule out constricted-like conformations for C-type inactivation

PubMed Central

Li, Jing; Boulanger, Eliot; Rui, Huan; Perozo, Eduardo; Roux, Benoît

2017-01-01

In many K+ channels, prolonged activating stimuli lead to a time-dependent reduction in ion conduction, a phenomenon known as C-type inactivation. X-ray structures of the KcsA channel suggest that this inactivated state corresponds to a “constricted” conformation of the selectivity filter. However, the functional significance of the constricted conformation has become a matter of debate. Functional and structural studies based on chemically modified semisynthetic KcsA channels along the selectivity filter led to the conclusion that the constricted conformation does not correspond to the C-type inactivated state. The main results supporting this view include the observation that C-type inactivation is not suppressed by a substitution of D-alanine at Gly77, even though this modification is believed to lock the selectivity filter into its conductive conformation, whereas it is suppressed following amide-to-ester backbone substitutions at Gly77 and Tyr78, even though these structure-conserving modifications are not believed to prevent the selectivity filter from adopting the constricted conformation. However, several untested assumptions about the structural and functional impact of these chemical modifications underlie these arguments. To make progress, molecular dynamics simulations based on atomic models of the KcsA channel were performed. The computational results support the notion that the constricted conformation of the selectivity filter corresponds to the functional C-type inactivated state of the KcsA. Importantly, MD simulations reveal that the semisynthetic KcsAD-ala77 channel can adopt an asymmetrical constricted-like nonconductive conformation and that the amide-to-ester backbone substitutions at Gly77 and Tyr78 perturb the hydrogen bonding involving the buried water molecules stabilizing the constricted conformation. PMID:28973956

Application of system identification to analytic rotor modeling from simulated and wind tunnel dynamic test data, part 2

NASA Technical Reports Server (NTRS)

Hohenemser, K. H.; Banerjee, D.

1977-01-01

An introduction to aircraft state and parameter identification methods is presented. A simplified form of the maximum likelihood method is selected to extract analytical aeroelastic rotor models from simulated and dynamic wind tunnel test results for accelerated cyclic pitch stirring excitation. The dynamic inflow characteristics for forward flight conditions from the blade flapping responses without direct inflow measurements were examined. The rotor blades are essentially rigid for inplane bending and for torsion within the frequency range of study, but flexible in out-of-plane bending. Reverse flow effects are considered for high rotor advance ratios. Two inflow models are studied; the first is based on an equivalent blade Lock number, the second is based on a time delayed momentum inflow. In addition to the inflow parameters, basic rotor parameters like the blade natural frequency and the actual blade Lock number are identified together with measurement bias values. The effect of the theoretical dynamic inflow on the rotor eigenvalues is evaluated.

Window Glasses: State and Prospects

NASA Astrophysics Data System (ADS)

Maiorov, V. A.

2018-04-01

Analysis and generalization of the results of investigations devoted to the improvement of optical properties have been carried out, and descriptions of a structure and a reaction mechanism of available and promising window glasses with solar radiation are presented. All devices are divided into groups with static constant and dynamic regulated spectral characteristics. The group of static glasses includes heat-protective and spectrally selective glasses with low-emissivity coatings and infrared filters with dispersed plasmonic nanoparticles. Electrochromic glasses, nanostructured dynamic infrared filters, and glasses with separated regulation of the transmission of visible-light and near-infrared radiation are dynamic devices. It is noted that the use of mesoporous films made of plasmonic nanoparticles open up especially wide possibilities. Their application allows one to realize a dynamic separated regulation of the transmission of visible light and nearinfrared radiation in which, under the gradual increase in the electric potential on the glass, mechanisms of plasmon and polaron reduction of solar radiation gradually change the glass' condition from light warm to light cold and then to dark cold consecutively.

The classical and quantum dynamics of molecular spins on graphene

PubMed Central

Cervetti, Christian; Rettori, Angelo; Pini, Maria Gloria; Cornia, Andrea; Repollés, Ana; Luis, Fernando; Dressel, Martin; Rauschenbach, Stephan; Kern, Klaus; Burghard, Marko; Bogani, Lapo

2015-01-01

Controlling the dynamics of spins on surfaces is pivotal to the design of spintronic1 and quantum computing2 devices. Proposed schemes involve the interaction of spins with graphene to enable surface-state spintronics3,4, and electrical spin-manipulation4-11. However, the influence of the graphene environment on the spin systems has yet to be unraveled12. Here we explore the spin-graphene interaction by studying the classical and quantum dynamics of molecular magnets13 on graphene. While the static spin response remains unaltered, the quantum spin dynamics and associated selection rules are profoundly modulated. The couplings to graphene phonons, to other spins, and to Dirac fermions are quantified using a newly-developed model. Coupling to Dirac electrons introduces a dominant quantum-relaxation channel that, by driving the spins over Villain’s threshold, gives rise to fully-coherent, resonant spin tunneling. Our findings provide fundamental insight into the interaction between spins and graphene, establishing the basis for electrical spin-manipulation in graphene nanodevices. PMID:26641019

Incremental Dynamic Analysis of Koyna Dam under Repeated Ground Motions

NASA Astrophysics Data System (ADS)

Zainab Nik Azizan, Nik; Majid, Taksiah A.; Nazri, Fadzli Mohamed; Maity, Damodar; Abdullah, Junaidah

2018-03-01

This paper discovers the incremental dynamic analysis (IDA) of concrete gravity dam under single and repeated earthquake loadings to identify the limit state of the dam. Seven ground motions with horizontal and vertical direction as seismic input considered in the nonlinear dynamic analysis based on the real repeated earthquake in the worldwide. All the ground motions convert to respond spectrum and scaled according to the developed elastic respond spectrum in order to match the characteristic of the ground motion to the soil type. The scaled was depends on the fundamental period, T1 of the dam. The Koyna dam has been selected as a case study for the purpose of the analysis by assuming that no sliding and rigid foundation, has been estimated. IDA curves for Koyna dam developed for single and repeated ground motions and the performance level of the dam identifies. The IDA curve of repeated ground motion shown stiffer rather than single ground motion. The ultimate state displacement for a single event is 45.59mm and decreased to 39.33mm under repeated events which are decreased about 14%. This showed that the performance level of the dam based on seismic loadings depend on ground motion pattern.

Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain.

PubMed

Selwa, Edithe; Huynh, Tru; Ciccotti, Giovanni; Maragliano, Luca; Malliavin, Thérèse E

2014-10-01

The catalytic domain of the adenyl cyclase (AC) toxin from Bordetella pertussis is activated by interaction with calmodulin (CaM), resulting in cAMP overproduction in the infected cell. In the X-ray crystallographic structure of the complex between AC and the C terminal lobe of CaM, the toxin displays a markedly elongated shape. As for the structure of the isolated protein, experimental results support the hypothesis that more globular conformations are sampled, but information at atomic resolution is still lacking. Here, we use temperature-accelerated molecular dynamics (TAMD) simulations to generate putative all-atom models of globular conformations sampled by CaM-free AC. As collective variables, we use centers of mass coordinates of groups of residues selected from the analysis of standard molecular dynamics (MD) simulations. Results show that TAMD allows extended conformational sampling and generates AC conformations that are more globular than in the complexed state. These structures are then refined via energy minimization and further unrestrained MD simulations to optimize inter-domain packing interactions, thus resulting in the identification of a set of hydrogen bonds present in the globular conformations. © 2014 Wiley Periodicals, Inc.

Dynamic stability and bifurcation analysis in fractional thermodynamics

NASA Astrophysics Data System (ADS)

Béda, Péter B.

2018-02-01

In mechanics, viscoelasticity was the first field of applications in studying geomaterials. Further possibilities arise in spatial non-locality. Non-local materials were already studied in the 1960s by several authors as a part of continuum mechanics and are still in focus of interest because of the rising importance of materials with internal micro- and nano-structure. When material instability gained more interest, non-local behavior appeared in a different aspect. The problem was concerned to numerical analysis, because then instability zones exhibited singular properties for local constitutive equations. In dynamic stability analysis, mathematical aspects of non-locality were studied by using the theory of dynamic systems. There the basic set of equations describing the behavior of continua was transformed to an abstract dynamic system consisting of differential operators acting on the perturbation field variables. Such functions should satisfy homogeneous boundary conditions and act as indicators of stability of a selected state of the body under consideration. Dynamic systems approach results in conditions for cases, when the differential operators have critical eigenvalues of zero real parts (dynamic stability or instability conditions). When the critical eigenvalues have non-trivial eigenspace, the way of loss of stability is classified as a typical (or generic) bifurcation. Our experiences show that material non-locality and the generic nature of bifurcation at instability are connected, and the basic functions of the non-trivial eigenspace can be used to determine internal length quantities of non-local mechanics. Fractional calculus is already successfully used in thermo-elasticity. In the paper, non-locality is introduced via fractional strain into the constitutive relations of various conventional types. Then, by defining dynamic systems, stability and bifurcation are studied for states of thermo-mechanical solids. Stability conditions and genericity conditions are presented for constitutive relations under consideration.

A Pipeline To Enhance Ligand Virtual Screening: Integrating Molecular Dynamics and Fingerprints for Ligand and Proteins.

PubMed

Spyrakis, Francesca; Benedetti, Paolo; Decherchi, Sergio; Rocchia, Walter; Cavalli, Andrea; Alcaro, Stefano; Ortuso, Francesco; Baroni, Massimo; Cruciani, Gabriele

2015-10-26

The importance of taking into account protein flexibility in drug design and virtual ligand screening (VS) has been widely debated in the literature, and molecular dynamics (MD) has been recognized as one of the most powerful tools for investigating intrinsic protein dynamics. Nevertheless, deciphering the amount of information hidden in MD simulations and recognizing a significant minimal set of states to be used in virtual screening experiments can be quite complicated. Here we present an integrated MD-FLAP (molecular dynamics-fingerprints for ligand and proteins) approach, comprising a pipeline of molecular dynamics, clustering and linear discriminant analysis, for enhancing accuracy and efficacy in VS campaigns. We first extracted a limited number of representative structures from tens of nanoseconds of MD trajectories by means of the k-medoids clustering algorithm as implemented in the BiKi Life Science Suite ( http://www.bikitech.com [accessed July 21, 2015]). Then, instead of applying arbitrary selection criteria, that is, RMSD, pharmacophore properties, or enrichment performances, we allowed the linear discriminant analysis algorithm implemented in FLAP ( http://www.moldiscovery.com [accessed July 21, 2015]) to automatically choose the best performing conformational states among medoids and X-ray structures. Retrospective virtual screenings confirmed that ensemble receptor protocols outperform single rigid receptor approaches, proved that computationally generated conformations comprise the same quantity/quality of information included in X-ray structures, and pointed to the MD-FLAP approach as a valuable tool for improving VS performances.

Effects of state contraceptive insurance mandates.

PubMed

Dills, Angela K; Grecu, Anca M

2017-02-01

Using U.S. Natality data for 1996 through 2009 and an event analysis specification, we investigate the dynamics of the effects of state insurance contraceptive mandates on births and measures of parental investment: prenatal visits, non-marital childbearing, and risky behaviors during pregnancy. We analyze outcomes separately by age, race, and ethnicity. Among young Hispanic women, we find a 4% decline in the birth rate. There is evidence of a decrease in births to single mothers, consistent with increased wantedness. We also find evidence of selection into motherhood, which could explain the lack of a significant effect on birth outcomes. Copyright © 2016 Elsevier B.V. All rights reserved.

Unexpectedly Fast Phonon-Assisted Exciton Hopping between Carbon Nanotubes

DOE PAGES

Davoody, A. H.; Karimi, F.; Arnold, M. S.; ...

2017-06-05

Carbon-nanotube (CNT) aggregates are promising light-absorbing materials for photovoltaics. The hopping rate of excitons between CNTs directly affects the efficiency of these devices. We theoretically investigate phonon-assisted exciton hopping, where excitons scatter with phonons into a same-tube transition state, followed by intertube Coulomb scattering into the final state. Second-order hopping between bright excitonic states is as fast as the first-order process (~1 ps). For perpendicular CNTs, the high rate stems from the high density of phononic states; for parallel CNTs, the reason lies in relaxed selection rules. Moreover, second-order exciton transfer between dark and bright states, facilitated by phonons withmore » large angular momentum, has rates comparable to bright-to-bright transfer, so dark excitons provide an additional pathway for energy transfer in CNT composites. Furthermore, as dark excitons are difficult to probe in experiment, predictive theory is critical for understanding exciton dynamics in CNT composites.« less

Unexpectedly Fast Phonon-Assisted Exciton Hopping between Carbon Nanotubes

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

Davoody, A. H.; Karimi, F.; Arnold, M. S.

Carbon-nanotube (CNT) aggregates are promising light-absorbing materials for photovoltaics. The hopping rate of excitons between CNTs directly affects the efficiency of these devices. We theoretically investigate phonon-assisted exciton hopping, where excitons scatter with phonons into a same-tube transition state, followed by intertube Coulomb scattering into the final state. Second-order hopping between bright excitonic states is as fast as the first-order process (~1 ps). For perpendicular CNTs, the high rate stems from the high density of phononic states; for parallel CNTs, the reason lies in relaxed selection rules. Moreover, second-order exciton transfer between dark and bright states, facilitated by phonons withmore » large angular momentum, has rates comparable to bright-to-bright transfer, so dark excitons provide an additional pathway for energy transfer in CNT composites. Furthermore, as dark excitons are difficult to probe in experiment, predictive theory is critical for understanding exciton dynamics in CNT composites.« less

Interference in acetylene intersystem crossing acts as the molecular analog of Young's double-slit experiment

PubMed Central

de Groot, Mattijs; Field, Robert W.; Buma, Wybren J.

2009-01-01

We report on an experimental approach that reveals crucial details of the composition of singlet-triplet mixed eigenstates in acetylene. Intersystem crossing in this prototypical polyatomic molecule embodies the mixing of the lowest excited singlet state (S1) with 3 triplet states (T1, T2, and T3). Using high-energy (157-nm) photons from an F2 laser to record excited-state photoelectron spectra, we have decomposed the mixed eigenstates into their S1, T3, T2, and T1 constituent parts. One example of the interpretive power that ensues from the selective sensitivity of the experiment to the individual electronic state characters is the discovery and examination of destructive interference between two doorway-mediated intersystem crossing pathways. This observation of an interference effect in nonradiative decay opens up possibilities for rational coherent control over molecular excited state dynamics. PMID:19179288

PHYSICAL EFFECTS OCCURRING DURING GENERATION AND AMPLIFICATION OF LASER RADIATION: Self-induced resonance under conditions of radiative equilibrium of quasienergy states in a three-level system

NASA Astrophysics Data System (ADS)

Sarkisyan, M. A.

1989-02-01

An analysis is made of the interaction of a three-level "cascade" atomic system with a resonant laser field. An investigation is made of the dynamics of the populations of the quasienergy states and of the atomic levels over times greater than the spontaneous transition times. In the steady-state regime the distribution of atoms over various quasienergy states is obtained under two-photon resonance conditions and for the case when all the resonances are strong. It is found that a suitable selection of the interaction parameters can establish an inversion between the quasienergy states and also due to atomic transitions. The total probability of spontaneous scattering is calculated. It is shown that, under two-photon resonance conditions, the scattering intensity increases sharply due to a self-induced resonance.

Warfarin traps human vitamin K epoxide reductase in an intermediate state during electron transfer

PubMed Central

Shen, Guomin; Cui, Weidong; Zhang, Hao; Zhou, Fengbo; Huang, Wei; Liu, Qian; Yang, Yihu; Li, Shuang; Bowman, Gregory R.; Sadler, J. Evan; Gross, Michael L.; Li, Weikai

2017-01-01

Although warfarin is the most widely used anticoagulant worldwide, the mechanism by which warfarin inhibits its target, human vitamin K epoxide reductase (hVKOR), remains unclear. Here we show that warfarin blocks a dynamic electron-transfer process in hVKOR. A major fraction of cellular hVKOR is at an intermediate redox state of this process containing a Cys51-Cys132 disulfide, a characteristic accommodated by a four-transmembrane-helix structure of hVKOR. Warfarin selectively inhibits this major cellular form of hVKOR, whereas disruption of the Cys51-Cys132 disulfide impairs warfarin binding and causes warfarin resistance. Relying on binding interactions identified by cysteine alkylation footprinting and mass spectrometry coupled with mutagenesis analysis, we are able to conduct structure simulations to reveal a closed warfarin-binding pocket stabilized by the Cys51-Cys132 linkage. Understanding the selective warfarin inhibition of a specific redox state of hVKOR should enable the rational design of drugs that exploit the redox chemistry and associated conformational changes in hVKOR. PMID:27918545

Wave packet interferometry and quantum state reconstruction by acousto-optic phase modulation

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

Tekavec, Patrick F.; Dyke, Thomas R.; Marcus, Andrew H.

2006-11-21

Studies of wave packet dynamics often involve phase-selective measurements of coherent optical signals generated from sequences of ultrashort laser pulses. In wave packet interferometry (WPI), the separation between the temporal envelopes of the pulses must be precisely monitored or maintained. Here we introduce a new (and easy to implement) experimental scheme for phase-selective measurements that combines acousto-optic phase modulation with ultrashort laser excitation to produce an intensity-modulated fluorescence signal. Synchronous detection, with respect to an appropriately constructed reference, allows the signal to be simultaneously measured at two phases differing by 90 deg. Our method effectively decouples the relative temporal phasemore » from the pulse envelopes of a collinear train of optical pulse pairs. We thus achieve a robust and high signal-to-noise scheme for WPI applications, such as quantum state reconstruction and electronic spectroscopy. The validity of the method is demonstrated, and state reconstruction is performed, on a model quantum system - atomic Rb vapor. Moreover, we show that our measurements recover the correct separation between the absorptive and dispersive contributions to the system susceptibility.« less

Modelling tropical forests response to logging

NASA Astrophysics Data System (ADS)

Cazzolla Gatti, Roberto; Di Paola, Arianna; Valentini, Riccardo; Paparella, Francesco

2013-04-01

Tropical rainforests are among the most threatened ecosystems by large-scale fragmentation due to human activity such as heavy logging and agricultural clearance. Although, they provide crucial ecosystem goods and services, such as sequestering carbon from the atmosphere, protecting watersheds and conserving biodiversity. In several countries forest resource extraction has experienced a shift from clearcutting to selective logging to maintain a significant forest cover and understock of living biomass. However the knowledge on the short and long-term effects of removing selected species in tropical rainforest are scarce and need to be further investigated. One of the main effects of selective logging on forest dynamics seems to be the local disturbance which involve the invasion of open space by weed, vines and climbers at the expense of the late-successional state cenosis. We present a simple deterministic model that describes the dynamics of tropical rainforest subject to selective logging to understand how and why weeds displace native species. We argue that the selective removal of tallest tropical trees carries out gaps of light that allow weeds, vines and climbers to prevail on native species, inhibiting the possibility of recovery of the original vegetation. Our results show that different regime shifts may occur depending on the type of forest management adopted. This hypothesis is supported by a dataset of trees height and weed/vines cover that we collected from 9 plots located in Central and West Africa both in untouched and managed areas.

Rapid Glucose Depletion Immobilizes Active Myosin-V on Stabilized Actin Cables

PubMed Central

Xu, Li; Bretscher, Anthony

2014-01-01

Summary Polarization of eukaryotic cells requires organelles and protein complexes to be transported to their proper destinations along the cytoskeleton [1]. When nutrients are abundant, budding yeast grows rapidly transporting secretory vesicles for localized growth and actively segregating organelles [2, 3]. This is mediated by myosin-Vs transporting cargos along F-actin bundles known as actin cables [4]. Actin cables are dynamic structures regulated by assembly, stabilization and disassembly [5]. Polarized growth and actin filament dynamics consume energy. For most organisms, glucose is the preferred energy source and generally represses alternative carbon source usage [6]. Thus upon abrupt glucose depletion, yeast shuts down pathways consuming large amounts of energy, including the vacuolar-ATPase [7, 8], translation [9] and phosphoinositide metabolism [10]. Here we show that glucose withdrawal rapidly (<1 min) depletes ATP levels and the yeast myosin V, Myo2, responds by relocalizing to actin cables, making it the fastest response documented. Myo2 immobilized on cables releases its secretory cargo, defining a new rigor-like state of a myosin-V in vivo. Only actively transporting Myo2 can be converted to the rigor-like state. Glucose depletion has differential effects on the actin cytoskeleton resulting in disassembly of actin patches with concomitant inhibition of endocytosis, and strong stabilization of actin cables, thereby revealing a selective and previously unappreciated ATP requirement for actin cable disassembly. A similar response is seen in HeLa cells to ATP depletion. These findings reveal a new fast-acting energy conservation strategy halting growth by immobilizing myosin-V in a newly described state on selectively stabilized actin cables. PMID:25308080

Physical and Emotional Benefits of Different Exercise Environments Designed for Treadmill Running

PubMed Central

Churchill, Sarah M.; Brymer, Eric; Davids, Keith

2017-01-01

(1) Background: Green physical activity promotes physical health and mental wellbeing and interesting questions concern effects of this information on designing indoor exercise environments. This study examined the physical and emotional effects of different nature-based environments designed for indoor treadmill running; (2) Methods: In a counterbalanced experimental design, 30 participants performed three, twenty-minute treadmill runs at a self-selected pace while viewing either a static nature image, a dynamic nature image or self-selected entertainment. Distance ran, heart rate (HR) and five pre-and post-exercise emotional states were measured; (3) Results: Participants ran farther, and with higher HRs, with self-selected entertainment compared to the two nature-based environment designs. Participants attained lowered anger, dejection, anxiety and increased excitement post exercise in all of the designed environments. Happiness increased during the two nature-based environment designs compared with self-selected entertainment; (4) Conclusions: Self-selected entertainment encouraged greater physical performances whereas running in nature-based exercise environments elicited greater happiness immediately after running. PMID:28696384

Physical and Emotional Benefits of Different Exercise Environments Designed for Treadmill Running.

PubMed

Yeh, Hsiao-Pu; Stone, Joseph A; Churchill, Sarah M; Brymer, Eric; Davids, Keith

2017-07-11

(1) Background: Green physical activity promotes physical health and mental wellbeing and interesting questions concern effects of this information on designing indoor exercise environments. This study examined the physical and emotional effects of different nature-based environments designed for indoor treadmill running; (2) Methods: In a counterbalanced experimental design, 30 participants performed three, twenty-minute treadmill runs at a self-selected pace while viewing either a static nature image, a dynamic nature image or self-selected entertainment. Distance ran, heart rate (HR) and five pre-and post-exercise emotional states were measured; (3) Results: Participants ran farther, and with higher HRs, with self-selected entertainment compared to the two nature-based environment designs. Participants attained lowered anger, dejection, anxiety and increased excitement post exercise in all of the designed environments. Happiness increased during the two nature-based environment designs compared with self-selected entertainment; (4) Conclusions: Self-selected entertainment encouraged greater physical performances whereas running in nature-based exercise environments elicited greater happiness immediately after running.

Conserved conformational selection mechanism of Hsp70 chaperone-substrate interactions

PubMed Central

Velyvis, Algirdas; Zoltsman, Guy; Rosenzweig, Rina; Bouvignies, Guillaume

2018-01-01

Molecular recognition is integral to biological function and frequently involves preferred binding of a molecule to one of several exchanging ligand conformations in solution. In such a process the bound structure can be selected from the ensemble of interconverting ligands a priori (conformational selection, CS) or may form once the ligand is bound (induced fit, IF). Here we focus on the ubiquitous and conserved Hsp70 chaperone which oversees the integrity of the cellular proteome through its ATP-dependent interaction with client proteins. We directly quantify the flux along CS and IF pathways using solution NMR spectroscopy that exploits a methyl TROSY effect and selective isotope-labeling methodologies. Our measurements establish that both bacterial and human Hsp70 chaperones interact with clients by selecting the unfolded state from a pre-existing array of interconverting structures, suggesting a conserved mode of client recognition among Hsp70s and highlighting the importance of molecular dynamics in this recognition event. PMID:29460778

Ab initio theory of spin-orbit coupling for quantum bits in diamond exhibiting dynamic Jahn-Teller effect

NASA Astrophysics Data System (ADS)

Gali, Adam; Thiering, Gergő

Dopants in solids are promising candidates for implementations of quantum bits for quantum computing. In particular, the high-spin negatively charged nitrogen-vacancy defect (NV) in diamond has become a leading contender in solid-state quantum information processing. The initialization and readout of the spin is based on the spin-selective decay of the photo-excited electron to the ground state which is mediated by spin-orbit coupling between excited states states and phonons. Generally, the spin-orbit coupling plays a crucial role in the optical spinpolarization and readout of NV quantum bit (qubit) and alike. Strong electron-phonon coupling in dynamic Jahn-Teller (DJT) systems can substantially influence the effective strength of spin-orbit coupling. Here we show by ab initio supercell density functional theory (DFT) calculations that the intrinsic spin-orbit coupling is strongly damped by DJT effect in the triplet excited state that has a consequence on the rate of non-radiative decay. This theory is applied to the ground state of silicon-vacancy (SiV) and germanium-vacancy (GeV) centers in their negatively charged state that can also act like qubits. We show that the intrinsic spin-orbit coupling in SiV and GeV centers is in the 100 GHz region, in contrast to the NV center of 10 GHz region. Our results provide deep insight in the nature of SiV and GeV qubits in diamond. EU FP7 DIADEMS project (Contract No. 611143).

Pressure-driven insulator-metal transition in cubic phase UO 2

DOE PAGES

Huang, Li; Wang, Yilin; Werner, Philipp

2017-09-21

Understanding the electronic properties of actinide oxides under pressure poses a great challenge for experimental and theoretical studies. Here, we investigate the electronic structure of cubic phase uranium dioxide at different volumes using a combination of density functional theory and dynamical mean-field theory. The ab initio calculations predict an orbital-selective insulator-metal transition at a moderate pressure of ~45 GPa. At this pressure the uranium's 5f 5/2 state becomes metallic, while the 5f 7/2 state remains insulating up to about 60 GPa. In the metallic state, we observe a rapid decrease of the 5f occupation and total angular momentum with pressure.more » Simultaneously, the so-called "Zhang-Rice state", which is of predominantly 5f 5/2 character, quickly disappears after the transition into the metallic phase.« less

Dense and dynamic 3D selection for game-based virtual environments.

PubMed

Cashion, Jeffrey; Wingrave, Chadwick; LaViola, Joseph J

2012-04-01

3D object selection is more demanding when, 1) objects densly surround the target object, 2) the target object is significantly occluded, and 3) when the target object is dynamically changing location. Most 3D selection techniques and guidelines were developed and tested on static or mostly sparse environments. In contrast, games tend to incorporate densly packed and dynamic objects as part of their typical interaction. With the increasing popularity of 3D selection in games using hand gestures or motion controllers, our current understanding of 3D selection needs revision. We present a study that compared four different selection techniques under five different scenarios based on varying object density and motion dynamics. We utilized two existing techniques, Raycasting and SQUAD, and developed two variations of them, Zoom and Expand, using iterative design. Our results indicate that while Raycasting and SQUAD both have weaknesses in terms of speed and accuracy in dense and dynamic environments, by making small modifications to them (i.e., flavoring), we can achieve significant performance increases.

Elastic Multi-scale Mechanisms: Computation and Biological Evolution.

PubMed

Diaz Ochoa, Juan G

2018-01-01

Explanations based on low-level interacting elements are valuable and powerful since they contribute to identify the key mechanisms of biological functions. However, many dynamic systems based on low-level interacting elements with unambiguous, finite, and complete information of initial states generate future states that cannot be predicted, implying an increase of complexity and open-ended evolution. Such systems are like Turing machines, that overlap with dynamical systems that cannot halt. We argue that organisms find halting conditions by distorting these mechanisms, creating conditions for a constant creativity that drives evolution. We introduce a modulus of elasticity to measure the changes in these mechanisms in response to changes in the computed environment. We test this concept in a population of predators and predated cells with chemotactic mechanisms and demonstrate how the selection of a given mechanism depends on the entire population. We finally explore this concept in different frameworks and postulate that the identification of predictive mechanisms is only successful with small elasticity modulus.

On-Demand Generation of Neutral and Negatively Charged Silicon-Vacancy Centers in Diamond

NASA Astrophysics Data System (ADS)

Dhomkar, Siddharth; Zangara, Pablo R.; Henshaw, Jacob; Meriles, Carlos A.

2018-03-01

Point defects in wide-band-gap semiconductors are emerging as versatile resources for nanoscale sensing and quantum information science, but our understanding of the photoionization dynamics is presently incomplete. Here, we use two-color confocal microscopy to investigate the dynamics of charge in type 1b diamond hosting nitrogen-vacancy (NV) and silicon-vacancy (SiV) centers. By examining the nonlocal fluorescence patterns emerging from local laser excitation, we show that, in the simultaneous presence of photogenerated electrons and holes, SiV (NV) centers selectively transform into the negative (neutral) charge state. Unlike NVs, 532 nm illumination ionizes SiV- via a single-photon process, thus hinting at a comparatively shallower ground state. In particular, slower ionization rates at longer wavelengths suggest the latter lies approximately ˜1.9 eV below the conduction band minimum. Building on the above observations, we demonstrate on-demand SiV and NV charge initialization over large areas via green laser illumination of variable intensity.

Bioinspired design of a polymer gel sensor for the realization of extracellular Ca2+ imaging

NASA Astrophysics Data System (ADS)

Ishiwari, Fumitaka; Hasebe, Hanako; Matsumura, Satoko; Hajjaj, Fatin; Horii-Hayashi, Noriko; Nishi, Mayumi; Someya, Takao; Fukushima, Takanori

2016-04-01

Although the role of extracellular Ca2+ draws increasing attention as a messenger in intercellular communications, there is currently no tool available for imaging Ca2+ dynamics in extracellular regions. Here we report the first solid-state fluorescent Ca2+ sensor that fulfills the essential requirements for realizing extracellular Ca2+ imaging. Inspired by natural extracellular Ca2+-sensing receptors, we designed a particular type of chemically-crosslinked polyacrylic acid gel, which can undergo single-chain aggregation in the presence of Ca2+. By attaching aggregation-induced emission luminogen to the polyacrylic acid as a pendant, the conformational state of the main chain at a given Ca2+ concentration is successfully translated into fluorescence property. The Ca2+ sensor has a millimolar-order apparent dissociation constant compatible with extracellular Ca2+ concentrations, and exhibits sufficient dynamic range and excellent selectivity in the presence of physiological concentrations of biologically relevant ions, thus enabling monitoring of submillimolar fluctuations of Ca2+ in flowing analytes containing millimolar Ca2+ concentrations.

Materials Properties and Solvated Electron Dynamics of Isolated Nanoparticles and Nanodroplets Probed with Ultrafast Extreme Ultraviolet Beams.

PubMed

Ellis, Jennifer L; Hickstein, Daniel D; Xiong, Wei; Dollar, Franklin; Palm, Brett B; Keister, K Ellen; Dorney, Kevin M; Ding, Chengyuan; Fan, Tingting; Wilker, Molly B; Schnitzenbaumer, Kyle J; Dukovic, Gordana; Jimenez, Jose L; Kapteyn, Henry C; Murnane, Margaret M

2016-02-18

We present ultrafast photoemission measurements of isolated nanoparticles in vacuum using extreme ultraviolet (EUV) light produced through high harmonic generation. Surface-selective static EUV photoemission measurements were performed on nanoparticles with a wide array of compositions, ranging from ionic crystals to nanodroplets of organic material. We find that the total photoelectron yield varies greatly with nanoparticle composition and provides insight into material properties such as the electron mean free path and effective mass. Additionally, we conduct time-resolved photoelectron yield measurements of isolated oleylamine nanodroplets, observing that EUV photons can create solvated electrons in liquid nanodroplets. Using photoemission from a time-delayed 790 nm pulse, we observe that a solvated electron is produced in an excited state and subsequently relaxes to its ground state with a lifetime of 151 ± 31 fs. This work demonstrates that femotosecond EUV photoemission is a versatile surface-sensitive probe of the properties and ultrafast dynamics of isolated nanoparticles.

X-ray morphological study of the ESZ sample

NASA Astrophysics Data System (ADS)

Lovisari, L.; Forman, W.; Jones, C.; Andrade-Santos, F.; Democles, J.; Pratt, G.; Ettori, S.; Arnaud, M.; Randall, S.; Kraft, R.

2017-10-01

An accurate knowledge of the scaling relations between X-ray observables and cluster mass is a crucial step for studies that aim to constrain cosmological parameters using galaxy clusters. The measure of the dynamical state of the systems offers important information to obtain precise scaling relations and understand their scatter. Unfortunately, characterize the dynamical state of a galaxy cluster requires to access a large set of information in different wavelength which are available only for a few individual systems. An alternative is to compute well defined morphological parameters making use of the relatively cheap X-ray images and profiles. Due to different projection effects none of the methods is good in all the cases and a combination of them is more effective to quantify the level of substructures. I will present the cluster morphologies that we derived for the ESZ sample. I will show their dependence on different cluster properties like total mass, redshift, and luminosity and how they differ from the ones obtained for X-ray selected clusters.

Extrinsic effects on the disorder dynamics of Bénard-Marangoni patterns

NASA Astrophysics Data System (ADS)

Cerisier, P.; Rahal, S.; Billia, B.

1996-10-01

The influence of the vessel shape, the initial conditions, and the vertical temperature gradient on dynamics and amount of disorder in convective patterns evolving in Bénard-Marangoni instability have been analyzed by using statistical tools, namely the density of defects, a disorder function, the order-disorder (m,σ) diagram introduced from the minimal spanning tree approach by Dussert et al., [Phys. Rev. B 34, 3528 (1986)] and the entropy function recently defined by Loeffler (unpublished). Pattern disorder is studied for transient and steady states. Experimental results show that the disorder in the hexagonal patterns of Bénard-Marangoni convection (i) is minimized in a hexagonal vessel and (ii) can be described as a Gaussian noise superimposed on a perfect array of hexagonal cells. Starting from imposed arrays, both hexagonal and nonhexagonal, with a wavelength different from the one that is naturally selected, the final state is independent of initial conditions. Disorder increases with the distance from the threshold. Depending on the Prandtl number, different behaviors of the patterns are observed.

Molecular dynamics simulations of polyelectrolyte brushes under poor solvent conditions: origins of bundle formation.

PubMed

He, Gui-Li; Merlitz, Holger; Sommer, Jens-Uwe

2014-03-14

Molecular dynamics simulations are applied to investigate salt-free planar polyelectrolyte brushes under poor solvent conditions. Starting above the Θ-point with a homogeneous brush and then gradually reducing the temperature, the polymers initially display a lateral structure formation, forming vertical bundles of chains. A further reduction of the temperature (or solvent quality) leads to a vertical collapse of the brush. By varying the size and selectivity of the counterions, we show that lateral structure formation persists and therefore demonstrate that the entropy of counterions being the dominant factor for the formation of the bundle phase. By applying an external compression force on the brush we calculate the minimal work done on the polymer phase only and prove that the entropy gain of counterions in the bundle state, as compared to the homogeneously collapsed state at the same temperature, is responsible for the lateral microphase segregation. As a consequence, the observed lateral structure formation has to be regarded universal for osmotic polymer brushes below the Θ-point.

Noise focusing and the emergence of coherent activity in neuronal cultures

NASA Astrophysics Data System (ADS)

Orlandi, Javier G.; Soriano, Jordi; Alvarez-Lacalle, Enrique; Teller, Sara; Casademunt, Jaume

2013-09-01

At early stages of development, neuronal cultures in vitro spontaneously reach a coherent state of collective firing in a pattern of nearly periodic global bursts. Although understanding the spontaneous activity of neuronal networks is of chief importance in neuroscience, the origin and nature of that pulsation has remained elusive. By combining high-resolution calcium imaging with modelling in silico, we show that this behaviour is controlled by the propagation of waves that nucleate randomly in a set of points that is specific to each culture and is selected by a non-trivial interplay between dynamics and topology. The phenomenon is explained by the noise focusing effect--a strong spatio-temporal localization of the noise dynamics that originates in the complex structure of avalanches of spontaneous activity. Results are relevant to neuronal tissues and to complex networks with integrate-and-fire dynamics and metric correlations, for instance, in rumour spreading on social networks.

Computational Analysis of the Transonic Dynamics Tunnel Using FUN3D

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

Chwalowski, Pawel; Quon, Eliot; Brynildsen, Scott E.

This paper presents results from an explanatory two-year effort of applying Computational Fluid Dynamics (CFD) to analyze the empty-tunnel flow in the NASA Langley Research Center Transonic Dynamics Tunnel (TDT). The TDT is a continuous-flow, closed circuit, 16- x 16-foot slotted-test-section wind tunnel, with capabilities to use air or heavy gas as a working fluid. In this study, experimental data acquired in the empty tunnel using the R-134a test medium was used to calibrate the computational data. The experimental calibration data includes wall pressures, boundary-layer profiles, and the tunnel centerline Mach number profiles. Subsonic and supersonic flow regimes were considered,more » focusing on Mach 0.5, 0.7 and Mach 1.1 in the TDT test section. This study discusses the computational domain, boundary conditions, and initial conditions selected in the resulting steady-state analyses using NASA's FUN3D CFD software.« less

Computational Analysis of the Transonic Dynamics Tunnel Using FUN3D

NASA Technical Reports Server (NTRS)

Chwalowski, Pawel; Quon, Eliot; Brynildsen, Scott E.

2016-01-01

This paper presents results from an exploratory two-year effort of applying Computational Fluid Dynamics (CFD) to analyze the empty-tunnel flow in the NASA Langley Research Center Transonic Dynamics Tunnel (TDT). The TDT is a continuous-flow, closed circuit, 16- x 16-foot slotted-test-section wind tunnel, with capabilities to use air or heavy gas as a working fluid. In this study, experimental data acquired in the empty tunnel using the R-134a test medium was used to calibrate the computational data. The experimental calibration data includes wall pressures, boundary-layer profiles, and the tunnel centerline Mach number profiles. Subsonic and supersonic flow regimes were considered, focusing on Mach 0.5, 0.7 and Mach 1.1 in the TDT test section. This study discusses the computational domain, boundary conditions, and initial conditions selected and the resulting steady-state analyses using NASA's FUN3D CFD software.

Four-time 7Li stimulated-echo spectroscopy for the study of dynamic heterogeneities: Application to lithium borate glass.

PubMed

Storek, M; Tilly, J F; Jeffrey, K R; Böhmer, R

2017-09-01

To study the nature of the nonexponential ionic hopping in solids a pulse sequence was developed that yields four-time stimulated-echo functions of previously inaccessible spin-3/2-nuclei such as 7 Li. It exploits combined Zeeman and octupolar order as longitudinal carrier state. Higher-order correlation functions were successfully generated for natural-abundance and isotopically-enriched lithium diborate glasses. Four-time 7 Li measurements are presented and compared with two-time correlation functions. The results are discussed with reference to approaches devised to quantify the degree of nonexponentiality in glass forming systems and evidence for the occurrence of dynamic heterogeneities and dynamic exchange were found. Additional experiments using the 6 Li species illustrate the challenge posed by subensemble selection when the dipolar interactions are not very much smaller than the quadrupolar ones. Copyright © 2017 Elsevier Inc. All rights reserved.

Vegetation cover dynamics of the Mongolian semiarid zone according to multi-temporal LANDSAT imagery (the case of Darkhan test range)

NASA Astrophysics Data System (ADS)

Zharnikova, M. A.; Alymbaeva, ZH B.; Ayurzhanaev, A. A.; Garmaev, E. ZH

2016-11-01

At present much attention is given to the spatio-temporal dynamics of plant communities of steppes to assess their response to the current climate changes. In this study, a mapping of a selected modeling polygon was carried out on the basis of data decoding and field surveys of vegetation cover in the semi-arid zone. The resulting large-scale map of actual vegetation reflects the current state of the vegetation cover and its horizontal structure. It is a valuable material for monitoring of changes in the chosen area. With multi-temporal satellite Landsat imagery we consider the vegetation cover dynamics of the test range. To analyze the transformation of the environment by the climatic factors, we compared series of NDVI versus the precipitation and of NDVI versus the temperatures. Then we calculated the degree of correlation between them.

The motion and control of a complex three-body space tethered system

NASA Astrophysics Data System (ADS)

Shi, Gefei; Zhu, Zhanxia; Chen, Shiyu; Yuan, Jianping; Tang, Biwei

2017-11-01

This paper is mainly devoted to investigating the dynamics and stability control of a three body-tethered satellite system which contains a main satellite and two subsatellites connected by two straight, massless and inextensible tethers. Firstly, a detailed mathematical model is established in the central gravitational field. Then, the dynamic characteristics of the established system are investigated and analyzed. Based on the dynamic analysis, a novel sliding mode prediction model (SMPM) control strategy is proposed to suppress the motion of the built tethered system. The numerical results show that the proposed underactuated control law is highly effective in suppressing the attitude/libration motion of the underactuated three-body tethered system. Furthermore, cases of different target angles are also examined and analyzed. The simulation results reveal that even if the final equilibrium states differ from different selections of the target angles, the whole system can still be maintained in acceptable areas.

Inter-Fullerene Electronic Coupling Controls the Efficiency of Photoinduced Charge Generation in Organic Bulk Heterojunctions

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

Larson, Bryon W.; Reid, Obadiah G.; Coffey, David C.

2016-09-26

Photoinduced charge generation (PCG) dynamics are notoriously difficult to correlate with specific molecular properties in device relevant polymer:fullerene organic photovoltaic blend films due to the highly complex nature of the solid state blend morphology. Here, this study uses six judiciously selected trifluoromethylfullerenes blended with the prototypical polymer poly(3-hexylthiophene) and measure the PCG dynamics in 50 fs-500 ns time scales with time-resolved microwave conductivity and femtosecond transient absorption spectroscopy. The isomeric purity and thorough chemical characterization of the fullerenes used in this study allow for a detailed correlation between molecular properties, driving force, local intermolecular electronic coupling and, ultimately, the efficiencymore » of PCG yield. The findings show that the molecular design of the fullerene not only determines inter-fullerene electronic coupling, but also influences the decay dynamics of free holes in the donor phase even when the polymer microstructure remains unchanged.« less

Random walks on activity-driven networks with attractiveness

NASA Astrophysics Data System (ADS)

Alessandretti, Laura; Sun, Kaiyuan; Baronchelli, Andrea; Perra, Nicola

2017-05-01

Virtually all real-world networks are dynamical entities. In social networks, the propensity of nodes to engage in social interactions (activity) and their chances to be selected by active nodes (attractiveness) are heterogeneously distributed. Here, we present a time-varying network model where each node and the dynamical formation of ties are characterized by these two features. We study how these properties affect random-walk processes unfolding on the network when the time scales describing the process and the network evolution are comparable. We derive analytical solutions for the stationary state and the mean first-passage time of the process, and we study cases informed by empirical observations of social networks. Our work shows that previously disregarded properties of real social systems, such as heterogeneous distributions of activity and attractiveness as well as the correlations between them, substantially affect the dynamical process unfolding on the network.

Analysis of tuning methods in semiconductor frequency-selective surfaces

NASA Astrophysics Data System (ADS)

Shemelya, Corey; Palm, Dominic; Fip, Tassilo; Rahm, Marco

2017-02-01

Advanced technology, such as sensing and communication equipment, has recently begun to combine optically sensitive nano-scale structures with customizable semiconductor material systems. Included within this broad field of study is the aptly named frequency-selective surface; which is unique in that it can be artificially designed to produce a specific electromagnetic or optical response. With the inherent utility of a frequency-selective surface, there has been an increased interest in the area of dynamic frequency-selective surfaces, which can be altered through optical or electrical tuning. This area has had exciting break throughs as tuning methods have evolved; however, these methods are typically energy intensive (optical tuning) or have met with limited success (electrical tuning). As such, this work investigates multiple structures and processes which implement semiconductor electrical biasing and/or optical tuning. Within this study are surfaces ranging from transmission meta-structures to metamaterial surface-waves and the associated coupling schemes. This work shows the utility of each design, while highlighting potential methods for optimizing dynamic meta-surfaces. As an added constraint, the structures were also designed to operate in unison with a state-of-the-art Ti:Sapphire Spitfire Ace and Spitfire Ace PA dual system (12 Watt) with pulse front matching THz generation and an EOS detection system. Additionally, the Ti:Sapphire laser system would provide the means for optical tunablity, while electrical tuning can be obtained through external power supplies.

Molecular Dynamics Simulations of Orai Reveal How the Third Transmembrane Segment Contributes to Hydration and Ca2+ Selectivity in Calcium Release-Activated Calcium Channels.

PubMed

Alavizargar, Azadeh; Berti, Claudio; Ejtehadi, Mohammad Reza; Furini, Simone

2018-04-26

Calcium release-activated calcium (CRAC) channels open upon depletion of Ca 2+ from the endoplasmic reticulum, and when open, they are permeable to a selective flux of calcium ions. The atomic structure of Orai, the pore domain of CRAC channels, from Drosophila melanogaster has revealed many details about conduction and selectivity in this family of ion channels. However, it is still unclear how residues on the third transmembrane helix can affect the conduction properties of the channel. Here, molecular dynamics and Brownian dynamics simulations were employed to analyze how a conserved glutamate residue on the third transmembrane helix (E262) contributes to selectivity. The comparison between the wild-type and mutated channels revealed a severe impact of the mutation on the hydration pattern of the pore domain and on the dynamics of residues K270, and Brownian dynamics simulations proved that the altered configuration of residues K270 in the mutated channel impairs selectivity to Ca 2+ over Na + . The crevices of water molecules, revealed by molecular dynamics simulations, are perfectly located to contribute to the dynamics of the hydrophobic gate and the basic gate, suggesting a possible role in channel opening and in selectivity function.

Designed amyloid fibers as materials for selective carbon dioxide capture

PubMed Central

Li, Dan; Furukawa, Hiroyasu; Deng, Hexiang; Liu, Cong; Yaghi, Omar M.; Eisenberg, David S.

2014-01-01

New materials capable of binding carbon dioxide are essential for addressing climate change. Here, we demonstrate that amyloids, self-assembling protein fibers, are effective for selective carbon dioxide capture. Solid-state NMR proves that amyloid fibers containing alkylamine groups reversibly bind carbon dioxide via carbamate formation. Thermodynamic and kinetic capture-and-release tests show the carbamate formation rate is fast enough to capture carbon dioxide by dynamic separation, undiminished by the presence of water, in both a natural amyloid and designed amyloids having increased carbon dioxide capacity. Heating to 100 °C regenerates the material. These results demonstrate the potential of amyloid fibers for environmental carbon dioxide capture. PMID:24367077

Mitigating Insider Sabotage and Espionage: A Review of the United States Air Force’s Current Posture

DTIC Science & Technology

2009-03-01

published on ins ider threat, to include the variables that come into play and historical case studies. Existing insider threat models are discussed ...problem, including the initial development of a logical da ta mod el and a system dynamics model. This chapter also discusses the selection of the...Finally, Chapter V provides a summary of the research along with a discussion of its conclusions and impact. Recommendations for future research

NMR crystallography: structure and properties of materials from solid-state nuclear magnetic resonance observables

PubMed Central

Bryce, David L.

2017-01-01

This topical review provides a brief overview of recent developments in NMR crystallography and related NMR approaches to studying the properties of molecular and ionic solids. Areas of complementarity with diffraction-based methods are underscored. These include the study of disordered systems, of dynamic systems, and other selected examples where NMR can provide unique insights. Highlights from the literature as well as recent work from my own group are discussed. PMID:28875022

Ultrafast Mid-Infrared Dynamics in Quantum Cascade Lasers

DTIC Science & Technology

2010-01-07

pump and probe were tuned to be resonant with the gain transition at each bias . In Fig. 2(a), selected bias - dependent DT results at 30 K are displayed...emission just below threshold. Well below threshold, the phonon-assisted lifetime is weakly bias - dependent . Just below threshold, the photon density in...corresponds to the decay of the lower lasing state via tunneling . The second component, on the time scale of 2 ps, shows a characteristic inverse dependence

Differentially Coexpressed Disease Gene Identification Based on Gene Coexpression Network.

PubMed

Jiang, Xue; Zhang, Han; Quan, Xiongwen

2016-01-01

Screening disease-related genes by analyzing gene expression data has become a popular theme. Traditional disease-related gene selection methods always focus on identifying differentially expressed gene between case samples and a control group. These traditional methods may not fully consider the changes of interactions between genes at different cell states and the dynamic processes of gene expression levels during the disease progression. However, in order to understand the mechanism of disease, it is important to explore the dynamic changes of interactions between genes in biological networks at different cell states. In this study, we designed a novel framework to identify disease-related genes and developed a differentially coexpressed disease-related gene identification method based on gene coexpression network (DCGN) to screen differentially coexpressed genes. We firstly constructed phase-specific gene coexpression network using time-series gene expression data and defined the conception of differential coexpression of genes in coexpression network. Then, we designed two metrics to measure the value of gene differential coexpression according to the change of local topological structures between different phase-specific networks. Finally, we conducted meta-analysis of gene differential coexpression based on the rank-product method. Experimental results demonstrated the feasibility and effectiveness of DCGN and the superior performance of DCGN over other popular disease-related gene selection methods through real-world gene expression data sets.

Modelling gene expression profiles related to prostate tumor progression using binary states

PubMed Central

2013-01-01

Background Cancer is a complex disease commonly characterized by the disrupted activity of several cancer-related genes such as oncogenes and tumor-suppressor genes. Previous studies suggest that the process of tumor progression to malignancy is dynamic and can be traced by changes in gene expression. Despite the enormous efforts made for differential expression detection and biomarker discovery, few methods have been designed to model the gene expression level to tumor stage during malignancy progression. Such models could help us understand the dynamics and simplify or reveal the complexity of tumor progression. Methods We have modeled an on-off state of gene activation per sample then per stage to select gene expression profiles associated to tumor progression. The selection is guided by statistical significance of profiles based on random permutated datasets. Results We show that our method identifies expected profiles corresponding to oncogenes and tumor suppressor genes in a prostate tumor progression dataset. Comparisons with other methods support our findings and indicate that a considerable proportion of significant profiles is not found by other statistical tests commonly used to detect differential expression between tumor stages nor found by other tailored methods. Ontology and pathway analysis concurred with these findings. Conclusions Results suggest that our methodology may be a valuable tool to study tumor malignancy progression, which might reveal novel cancer therapies. PMID:23721350

Saccade selection when reward probability is dynamically manipulated using Markov chains

PubMed Central

Lovejoy, Lee P.; Krauzlis, Richard J.

2012-01-01

Markov chains (stochastic processes where probabilities are assigned based on the previous outcome) are commonly used to examine the transitions between behavioral states, such as those that occur during foraging or social interactions. However, relatively little is known about how well primates can incorporate knowledge about Markov chains into their behavior. Saccadic eye movements are an example of a simple behavior influenced by information about probability, and thus are good candidates for testing whether subjects can learn Markov chains. In addition, when investigating the influence of probability on saccade target selection, the use of Markov chains could provide an alternative method that avoids confounds present in other task designs. To investigate these possibilities, we evaluated human behavior on a task in which stimulus reward probabilities were assigned using a Markov chain. On each trial, the subject selected one of four identical stimuli by saccade; after selection, feedback indicated the rewarded stimulus. Each session consisted of 200–600 trials, and on some sessions, the reward magnitude varied. On sessions with a uniform reward, subjects (n = 6) learned to select stimuli at a frequency close to reward probability, which is similar to human behavior on matching or probability classification tasks. When informed that a Markov chain assigned reward probabilities, subjects (n = 3) learned to select the greatest reward probability more often, bringing them close to behavior that maximizes reward. On sessions where reward magnitude varied across stimuli, subjects (n = 6) demonstrated preferences for both greater reward probability and greater reward magnitude, resulting in a preference for greater expected value (the product of reward probability and magnitude). These results demonstrate that Markov chains can be used to dynamically assign probabilities that are rapidly exploited by human subjects during saccade target selection. PMID:18330552

Saccade selection when reward probability is dynamically manipulated using Markov chains.

PubMed

Nummela, Samuel U; Lovejoy, Lee P; Krauzlis, Richard J

2008-05-01

Markov chains (stochastic processes where probabilities are assigned based on the previous outcome) are commonly used to examine the transitions between behavioral states, such as those that occur during foraging or social interactions. However, relatively little is known about how well primates can incorporate knowledge about Markov chains into their behavior. Saccadic eye movements are an example of a simple behavior influenced by information about probability, and thus are good candidates for testing whether subjects can learn Markov chains. In addition, when investigating the influence of probability on saccade target selection, the use of Markov chains could provide an alternative method that avoids confounds present in other task designs. To investigate these possibilities, we evaluated human behavior on a task in which stimulus reward probabilities were assigned using a Markov chain. On each trial, the subject selected one of four identical stimuli by saccade; after selection, feedback indicated the rewarded stimulus. Each session consisted of 200-600 trials, and on some sessions, the reward magnitude varied. On sessions with a uniform reward, subjects (n = 6) learned to select stimuli at a frequency close to reward probability, which is similar to human behavior on matching or probability classification tasks. When informed that a Markov chain assigned reward probabilities, subjects (n = 3) learned to select the greatest reward probability more often, bringing them close to behavior that maximizes reward. On sessions where reward magnitude varied across stimuli, subjects (n = 6) demonstrated preferences for both greater reward probability and greater reward magnitude, resulting in a preference for greater expected value (the product of reward probability and magnitude). These results demonstrate that Markov chains can be used to dynamically assign probabilities that are rapidly exploited by human subjects during saccade target selection.

Conformational dynamics of helix 8 in the GPCR rhodopsin controls arrestin activation in the desensitization process.

PubMed

Kirchberg, Kristina; Kim, Tai-Yang; Möller, Martina; Skegro, Darko; Dasara Raju, Gayathri; Granzin, Joachim; Büldt, Georg; Schlesinger, Ramona; Alexiev, Ulrike

2011-11-15

Arrestins are regulatory molecules for G-protein coupled receptor function. In visual rhodopsin, selective binding of arrestin to the cytoplasmic side of light-activated, phosphorylated rhodopsin (P-Rh*) terminates signaling via the G-protein transducin. While the "phosphate-sensor" of arrestin for the recognition of receptor-attached phosphates is identified, the molecular mechanism of arrestin binding and the involvement of receptor conformations in this process are still largely hypothetic. Here we used fluorescence pump-probe and time-resolved fluorescence depolarization measurements to investigate the kinetics of arrestin conformational changes and the corresponding nanosecond dynamical changes at the receptor surface. We show that at least two sequential conformational changes of arrestin occur upon interaction with P-Rh*, thus providing a kinetic proof for the suggested multistep nature of arrestin binding. At the cytoplasmic surface of P-Rh*, the structural dynamics of the amphipathic helix 8 (H8), connecting transmembrane helix 7 and the phosphorylated C-terminal tail, depends on the arrestin interaction state. We find that a high mobility of H8 is required in the low-affinity (prebinding) but not in the high-affinity binding state. High-affinity arrestin binding is inhibited when a bulky, inflexible group is bound to H8, indicating close interaction. We further show that this close steric interaction of H8 with arrestin is mandatory for the transition from prebinding to high-affinity binding; i.e., for arrestin activation. This finding implies a regulatory role for H8 in activation of visual arrestin, which shows high selectivity to P-Rh* in contrast to the broad receptor specificity displayed by the two nonvisual arrestins.

Conformational dynamics of helix 8 in the GPCR rhodopsin controls arrestin activation in the desensitization process

PubMed Central

Kirchberg, Kristina; Kim, Tai-Yang; Möller, Martina; Skegro, Darko; Dasara Raju, Gayathri; Granzin, Joachim; Büldt, Georg; Schlesinger, Ramona; Alexiev, Ulrike

2011-01-01

Arrestins are regulatory molecules for G-protein coupled receptor function. In visual rhodopsin, selective binding of arrestin to the cytoplasmic side of light-activated, phosphorylated rhodopsin (P-Rh*) terminates signaling via the G-protein transducin. While the “phosphate-sensor” of arrestin for the recognition of receptor-attached phosphates is identified, the molecular mechanism of arrestin binding and the involvement of receptor conformations in this process are still largely hypothetic. Here we used fluorescence pump-probe and time-resolved fluorescence depolarization measurements to investigate the kinetics of arrestin conformational changes and the corresponding nanosecond dynamical changes at the receptor surface. We show that at least two sequential conformational changes of arrestin occur upon interaction with P-Rh*, thus providing a kinetic proof for the suggested multistep nature of arrestin binding. At the cytoplasmic surface of P-Rh*, the structural dynamics of the amphipathic helix 8 (H8), connecting transmembrane helix 7 and the phosphorylated C-terminal tail, depends on the arrestin interaction state. We find that a high mobility of H8 is required in the low-affinity (prebinding) but not in the high-affinity binding state. High-affinity arrestin binding is inhibited when a bulky, inflexible group is bound to H8, indicating close interaction. We further show that this close steric interaction of H8 with arrestin is mandatory for the transition from prebinding to high-affinity binding; i.e., for arrestin activation. This finding implies a regulatory role for H8 in activation of visual arrestin, which shows high selectivity to P-Rh* in contrast to the broad receptor specificity displayed by the two nonvisual arrestins. PMID:22039220

Molecular dynamics and crystallization phenomenon of supercooled and glassy DNA and RNA nucleosides: β-adenosine, β-thymidine, and β-uridine

NASA Astrophysics Data System (ADS)

Adrjanowicz, K.; Wojnarowska, Z.; Grzybowska, K.; Hawelek, L.; Kaminski, K.; Paluch, M.; Kasprzycka, A.; Walczak, K.

2011-11-01

Nucleosides are chemical compounds that have an extremely important biological role; they can be found in all types of living organisms. They are crucial components from which DNA and RNA acids are built. In addition, nucleosides are key regulators of many physiological processes. In this paper, the molecular dynamics in the liquid and glassy state of three selected nucleosides, β-adenosine, β-thymidine, and β-uridine, was investigated by means of dielectric spectroscopy. Our results revealed multiple relaxation processes associated with different types of molecular motions. Besides the primary α relaxation, two secondary modes in the glassy states of examined compounds were identified. Crystallization progress monitored by dielectric spectroscopy and x-ray diffraction technique at isostructural relaxation conditions revealed that the examined nucleosides possess completely different tendencies to recrystallize from the liquid as well as the glassy state. We have also made an attempt to predict the time scale of molecular motion below the glass transition temperatures of the respective nucleosides to discuss their potential stability at room temperature over prolonged storage time. Finally, combination of molecular mobility studies with evaluation of thermodynamic parameters from calorimetric measurements allowed us to discuss the fundamental roles of both kinetic and thermodynamic factors in governing the physical stability of the glassy state.

Adiabatic fast passage application in solid state NMR study of cross relaxation and molecular dynamics in heteronuclear systems.

PubMed

Baranowski, M; Woźniak-Braszak, A; Jurga, K

2016-01-01

The paper presents the benefits of using fast adiabatic passage for the study of molecular dynamics in the solid state heteronuclear systems in the laboratory frame. A homemade pulse spectrometer operating at the frequency of 30.2MHz and 28.411MHz for protons and fluorines, respectively, has been enhanced with microcontroller direct digital synthesizer DDS controller [1-4]. This work briefly describes how to construct a low-cost and easy-to-assemble adiabatic extension set for homemade and commercial spectrometers based on recently very popular Arduino shields. The described set was designed for fast adiabatic generation. Timing and synchronization problems are discussed. The cross-relaxation experiments with different initial states of the two spin systems have been performed. Contrary to our previous work [5] where the steady-state NOE experiments were conducted now proton spins (1)H are polarized in the magnetic field B0 while fluorine spins (19)F are perturbed by selective saturation for a short time and then the system is allowed to evolve for a period in the absence of a saturating field. The adiabatic passage application leads to a reversal of magnetization of fluorine spins and increases the amplitude of the signal. Copyright © 2015 Elsevier Inc. All rights reserved.

Cybersecurity Dynamics

DTIC Science & Technology

2014-08-20

of Cybersecurity Dynamics emerged. Intuitively, Cybersecurity Dynamics describes the evolution of cybersecurity state as caused by cyber attack...Dynamics emerged. Intuitively, Cybersecurity Dynamics describes the evolution of cybersecurity state as caused by cyber attack-defense interactions...evolution of cyberse- curity state as caused by cyber attack-defense interactions. By studying Cybersecurity Dynamics, we can characterize the

Binding Pathway of Opiates to μ-Opioid Receptors Revealed by Machine Learning

NASA Astrophysics Data System (ADS)

Barati Farimani, Amir; Feinberg, Evan; Pande, Vijay

2018-02-01

Many important analgesics relieve pain by binding to the $\\mu$-Opioid Receptor ($\\mu$OR), which makes the $\\mu$OR among the most clinically relevant proteins of the G Protein Coupled Receptor (GPCR) family. Despite previous studies on the activation pathways of the GPCRs, the mechanism of opiate binding and the selectivity of $\\mu$OR are largely unknown. We performed extensive molecular dynamics (MD) simulation and analysis to find the selective allosteric binding sites of the $\\mu$OR and the path opiates take to bind to the orthosteric site. In this study, we predicted that the allosteric site is responsible for the attraction and selection of opiates. Using Markov state models and machine learning, we traced the pathway of opiates in binding to the orthosteric site, the main binding pocket. Our results have important implications in designing novel analgesics.

Human aquaporin 4 gating dynamics under and after nanosecond-scale static and alternating electric-field impulses: a molecular dynamics study of field effects and relaxation.

PubMed

Reale, Riccardo; English, Niall J; Garate, José-Antonio; Marracino, Paolo; Liberti, Micaela; Apollonio, Francesca

2013-11-28

Water self-diffusion and the dipolar response of the selectivity filter within human aquaporin 4 have been studied using molecular dynamics (MD) simulations in the absence and presence of pulses of external static and alternating electric fields. The pulses were approximately 50 and 100 ns in duration and 0.0065 V/Å in (r.m.s.) intensity and were either static or else 2.45 or 100 GHz in frequency and applied both along and perpendicular to the channels. In addition, the relaxation of the aquaporin, water self-diffusion and gating dynamics following cessation of the impulses was studied. In previous work it was determined that switches in the dihedral angle of the selectivity filter led to boosting of water permeation events within the channels, in the presence of identical external static and alternating electric fields, although applied continuously. Here the application of field impulses (and subsequently, upon removal) has shown that it is the dipolar orientation of the histidine-201 residue in the selectivity filter which governs the dihedral angle, and hence influences water self-diffusion; this constitutes an appropriate order parameter. The dipolar response of this residue to the applied field leads to the adoption of four distinct states, which we modelled as time-homogeneous Markov jump processes, and may be distinguished in the potential of mean force (PMF) as a function of the dipolar orientation of histidine-201. The observations of enhanced "dipolar flipping" of H201 serve to explain increased levels of water self-diffusion within aquaporin channels during, and immediately following, field impulses, although the level of statistical certainty here is lower. Given the appreciable size of the energy barriers evident in PMFs computed directly from deterministic MD (whether in the absence or presence of external fields), metadynamics calculations were undertaken to explore the free-energy landscape of histidine-201 orientation with greater accuracy and precision. These indicate that electric fields do alter the free-energy profile of the H201 side-chain orientation, wherein a perturbation of the symmetric bimodal state evident in the zero-field case is observed. These effects are dependent on the field intensities.

Dynamic Hop Service Differentiation Model for End-to-End QoS Provisioning in Multi-Hop Wireless Networks

NASA Astrophysics Data System (ADS)

Youn, Joo-Sang; Seok, Seung-Joon; Kang, Chul-Hee

This paper presents a new QoS model for end-to-end service provisioning in multi-hop wireless networks. In legacy IEEE 802.11e based multi-hop wireless networks, the fixed assignment of service classes according to flow's priority at every node causes priority inversion problem when performing end-to-end service differentiation. Thus, this paper proposes a new QoS provisioning model called Dynamic Hop Service Differentiation (DHSD) to alleviate the problem and support effective service differentiation between end-to-end nodes. Many previous works for QoS model through the 802.11e based service differentiation focus on packet scheduling on several service queues with different service rate and service priority. Our model, however, concentrates on a dynamic class selection scheme, called Per Hop Class Assignment (PHCA), in the node's MAC layer, which selects a proper service class for each packet, in accordance with queue states and service requirement, in every node along the end-to-end route of the packet. The proposed QoS solution is evaluated using the OPNET simulator. The simulation results show that the proposed model outperforms both best-effort and 802.11e based strict priority service models in mobile ad hoc environments.

Trees Wanted—Dead or Alive! Host Selection and Population Dynamics in Tree-Killing Bark Beetles

PubMed Central

Kausrud, Kyrre L.; Grégoire, Jean-Claude; Skarpaas, Olav; Erbilgin, Nadir; Gilbert, Marius; Økland, Bjørn; Stenseth, Nils Chr.

2011-01-01

Bark beetles (Coleoptera: Curculionidae, Scolytinae) feed and breed in dead or severely weakened host trees. When their population densities are high, some species aggregate on healthy host trees so that their defences may be exhausted and the inner bark successfully colonized, killing the tree in the process. Here we investigate under what conditions participating with unrelated conspecifics in risky mass attacks on living trees is an adaptive strategy, and what this can tell us about bark beetle outbreak dynamics. We find that the outcome of individual host selection may deviate from the ideal free distribution in a way that facilitates the emergence of tree-killing (aggressive) behavior, and that any heritability on traits governing aggressiveness seems likely to exist in a state of flux or cycles consistent with variability observed in natural populations. This may have implications for how economically and ecologically important species respond to environmental changes in climate and landscape (forest) structure. The population dynamics emerging from individual behavior are complex, capable of switching between “endemic” and “epidemic” regimes spontaneously or following changes in host availability or resistance. Model predictions are compared to empirical observations, and we identify some factors determining the occurrence and self-limitation of epidemics. PMID:21647433

Experiments with bosonic atoms for quantum gas assembly

NASA Astrophysics Data System (ADS)

Brown, Mark; Lin, Yiheng; Lester, Brian; Kaufman, Adam; Ball, Randall; Brossard, Ludovic; Isaev, Leonid; Thiele, Tobias; Lewis-Swan, Robert; Schymik, Kai-Niklas; Rey, Ana Maria; Regal, Cindy

2017-04-01

Quantum gas assembly is a promising platform for preparing and observing neutral atom systems on the single-atom level. We have developed a toolbox that includes ground-state laser cooling, high-fidelity loading techniques, addressable spin control, and dynamic spatial control and coupling of atoms. Already, this platform has enabled us to pursue a number of experiments studying entanglement and interference of pairs of bosonic atoms. We discuss our recent work in probabilistically entangling neutral atoms via interference, measurement, and post-selection as well as our future pursuits of interesting spin-motion dynamics of larger arrays of atoms. This work was supported by the David and Lucile Packard Foundation, National Science Foundation Physics Frontier Centers, and the National Defense Science and Engineering Graduate Fellowships program.

Solution landscapes in nematic microfluidics

NASA Astrophysics Data System (ADS)

Crespo, M.; Majumdar, A.; Ramos, A. M.; Griffiths, I. M.

2017-08-01

We study the static equilibria of a simplified Leslie-Ericksen model for a unidirectional uniaxial nematic flow in a prototype microfluidic channel, as a function of the pressure gradient G and inverse anchoring strength, B. We numerically find multiple static equilibria for admissible pairs (G , B) and classify them according to their winding numbers and stability. The case G = 0 is analytically tractable and we numerically study how the solution landscape is transformed as G increases. We study the one-dimensional dynamical model, the sensitivity of the dynamic solutions to initial conditions and the rate of change of G and B. We provide a physically interesting example of how the time delay between the applications of G and B can determine the selection of the final steady state.

Nanowires: Enhanced Optoelectronic Performance of a Passivated Nanowire-Based Device: Key Information from Real-Space Imaging Using 4D Electron Microscopy (Small 17/2016).

PubMed

Khan, Jafar I; Adhikari, Aniruddha; Sun, Jingya; Priante, Davide; Bose, Riya; Shaheen, Basamat S; Ng, Tien Khee; Zhao, Chao; Bakr, Osman M; Ooi, Boon S; Mohammed, Omar F

2016-05-01

Selective mapping of surface charge carrier dynamics of InGaN nanowires before and after surface passivation with octadecylthiol (ODT) is reported by O. F. Mohammed and co-workers on page 2313, using scanning ultrafast electron microscopy. In a typical experiment, the 343 nm output of the laser beam is used to excite the microscope tip to generate pulsed electrons for probing, and the 515 nm output is used as a clocking excitation pulse to initiate dynamics. Time-resolved images demonstrate clearly that carrier recombination is significantly slowed after ODT treatment, which supports the efficient removal of surface trap states. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A novel framework to simulating non-stationary, non-linear, non-Normal hydrological time series using Markov Switching Autoregressive Models

NASA Astrophysics Data System (ADS)

Birkel, C.; Paroli, R.; Spezia, L.; Tetzlaff, D.; Soulsby, C.

2012-12-01

In this paper we present a novel model framework using the class of Markov Switching Autoregressive Models (MSARMs) to examine catchments as complex stochastic systems that exhibit non-stationary, non-linear and non-Normal rainfall-runoff and solute dynamics. Hereby, MSARMs are pairs of stochastic processes, one observed and one unobserved, or hidden. We model the unobserved process as a finite state Markov chain and assume that the observed process, given the hidden Markov chain, is conditionally autoregressive, which means that the current observation depends on its recent past (system memory). The model is fully embedded in a Bayesian analysis based on Markov Chain Monte Carlo (MCMC) algorithms for model selection and uncertainty assessment. Hereby, the autoregressive order and the dimension of the hidden Markov chain state-space are essentially self-selected. The hidden states of the Markov chain represent unobserved levels of variability in the observed process that may result from complex interactions of hydroclimatic variability on the one hand and catchment characteristics affecting water and solute storage on the other. To deal with non-stationarity, additional meteorological and hydrological time series along with a periodic component can be included in the MSARMs as covariates. This extension allows identification of potential underlying drivers of temporal rainfall-runoff and solute dynamics. We applied the MSAR model framework to streamflow and conservative tracer (deuterium and oxygen-18) time series from an intensively monitored 2.3 km2 experimental catchment in eastern Scotland. Statistical time series analysis, in the form of MSARMs, suggested that the streamflow and isotope tracer time series are not controlled by simple linear rules. MSARMs showed that the dependence of current observations on past inputs observed by transport models often in form of the long-tailing of travel time and residence time distributions can be efficiently explained by non-stationarity either of the system input (climatic variability) and/or the complexity of catchment storage characteristics. The statistical model is also capable of reproducing short (event) and longer-term (inter-event) and wet and dry dynamical "hydrological states". These reflect the non-linear transport mechanisms of flow pathways induced by transient climatic and hydrological variables and modified by catchment characteristics. We conclude that MSARMs are a powerful tool to analyze the temporal dynamics of hydrological data, allowing for explicit integration of non-stationary, non-linear and non-Normal characteristics.

Using a physically-based water flow model to explore the dynamics of transit times and mixing in a small agricultural catchment

NASA Astrophysics Data System (ADS)

Yang, Jie; Heidbüchel, Ingo; Musolff, Andreas; Fleckenstein, Jan H.

2017-04-01

Catchment-scale transit time distributions (TTDs) for discharge and residence time distributions of the water in storage (RTDs) are promising tools to characterize the discharge and mixing behavior of a catchment and can help to interpret the associated solute loads to the stream in a spatially implicit way. TTDs and RTDs are dynamic in time, influenced by dynamic rainfall and evapotranspiration forcing, and changing groundwater storage in the catchment. In order to understand the links between the dynamics of TTDs and groundwater mixing in the small agricultural catchment Schäfertal, in central Germany, a 3D hydrological model was set up for the catchment using the fully coupled surface-subsurface numerical model HydroGeoSphere (HGS). The model is calibrated using discharge and groundwater level measurements, and runs transiently for a period of 10 years from 1997 to 2007. A particle tracking tool was implemented in HGS to track the movement of water parcels in the subsurface, outputting TTDs of channel discharge and RTDs of groundwater storage at daily intervals. Results show that the mean age of the discharge water is significantly younger than that of the water in storage, indicating a poorly mixed subsurface. Discharge preferentially samples faster flowing younger water originating from the more conductive top parts of the aquifer. Spatial variations of the age of water in storage are observed, highly influenced by aquifer heterogeneity. Computed StorAge Selection (SAS) functions [Rinaldo et al. 2015] show clear shifts in the discharge sampling preferences between wet and dry states: during wet states in winter and spring, discharge has a preference for younger water because the shallow flow paths are active due to high groundwater levels and low evapotranspiration. Conversely, during dry states in summer and autumn, discharge has a preference for older water because the shallow flow paths are inactive due to low groundwater levels and stronger evapotranspiration. Measured nitrate (NO3) loads in discharge, mainly originating from fertilizer in shallow soils, decrease significantly with decreasing wetness of the catchment. This trend confirms the shifts of discharge sampling preferences between wet and dry states. Reference: Rinaldo, A., P. Benettin, C. J. Harman, M. Hrachowitz, K. J. McGuire, Y. van der Velde, E. Bertuzzo, and G. Botter (2015), Storage selection functions: A coherent framework for quantifying how catchments store and release water and solutes, Water Resour. Res., 51, 4840-4847, doi:10.1002/2015WR017273.

Novel and lost forests in the Upper Midwestern United States, from new estimates of settlement-era composition, stem density, and biomass

USGS Publications Warehouse

Goring, Simon; Mladenoff, David J.; Cogbill, Charles; Record, Sydne; Paciorek, Christopher J.; Dietze, Michael C.; Dawson, Andria; Matthes, Jaclyn; McLachlan, Jason S.; Williams, John W.

2016-01-01

EuroAmerican land-use and its legacies have transformed forest structure and composition across the United States (US). More accurate reconstructions of historical states are critical to understanding the processes governing past, current, and future forest dynamics. Here we present new gridded (8x8km) reconstructions of pre-settlement (1800s) forest composition and structure from the upper Midwestern US (Minnesota, Wisconsin, and most of Michigan), using 19th Century Public Land Survey System (PLSS), with estimates of relative composition, above-ground biomass, stem density, and basal area for 28 tree types. This mapping is more robust than past efforts, using spatially varying correction factors to accommodate sampling design, azimuthal censoring, and biases in tree selection.

Multiple loop conformations of peptides predicted by molecular dynamics simulations are compatible with nuclear magnetic resonance.

PubMed

Carstens, Heiko; Renner, Christian; Milbradt, Alexander G; Moroder, Luis; Tavan, Paul

2005-03-29

The affinity and selectivity of protein-protein interactions can be fine-tuned by varying the size, flexibility, and amino acid composition of involved surface loops. As a model for such surface loops, we study the conformational landscape of an octapeptide, whose flexibility is chemically steered by a covalent ring closure integrating an azobenzene dye into and by a disulfide bridge additionally constraining the peptide backbone. Because the covalently integrated azobenzene dyes can be switched by light between a bent cis state and an elongated trans state, six cyclic peptide models of strongly different flexibilities are obtained. The conformational states of these peptide models are sampled by NMR and by unconstrained molecular dynamics (MD) simulations. Prototypical conformations and the free-energy landscapes in the high-dimensional space spanned by the phi/psi angles at the peptide backbone are obtained by clustering techniques from the MD trajectories. Multiple open-loop conformations are shown to be predicted by MD particularly in the very flexible cases and are shown to comply with the NMR data despite the fact that such open-loop conformations are missing in the refined NMR structures.

Quantumness-generating capability of quantum dynamics

NASA Astrophysics Data System (ADS)

Li, Nan; Luo, Shunlong; Mao, Yuanyuan

2018-04-01

We study quantumness-generating capability of quantum dynamics, where quantumness refers to the noncommutativity between the initial state and the evolving state. In terms of the commutator of the square roots of the initial state and the evolving state, we define a measure to quantify the quantumness-generating capability of quantum dynamics with respect to initial states. Quantumness-generating capability is absent in classical dynamics and hence is a fundamental characteristic of quantum dynamics. For qubit systems, we present an analytical form for this measure, by virtue of which we analyze several prototypical dynamics such as unitary dynamics, phase damping dynamics, amplitude damping dynamics, and random unitary dynamics (Pauli channels). Necessary and sufficient conditions for the monotonicity of quantumness-generating capability are also identified. Finally, we compare these conditions for the monotonicity of quantumness-generating capability with those for various Markovianities and illustrate that quantumness-generating capability and quantum Markovianity are closely related, although they capture different aspects of quantum dynamics.

A Data Filter for Identifying Steady-State Operating Points in Engine Flight Data for Condition Monitoring Applications

NASA Technical Reports Server (NTRS)

Simon, Donald L.; Litt, Jonathan S.

2010-01-01

This paper presents an algorithm that automatically identifies and extracts steady-state engine operating points from engine flight data. It calculates the mean and standard deviation of select parameters contained in the incoming flight data stream. If the standard deviation of the data falls below defined constraints, the engine is assumed to be at a steady-state operating point, and the mean measurement data at that point are archived for subsequent condition monitoring purposes. The fundamental design of the steady-state data filter is completely generic and applicable for any dynamic system. Additional domain-specific logic constraints are applied to reduce data outliers and variance within the collected steady-state data. The filter is designed for on-line real-time processing of streaming data as opposed to post-processing of the data in batch mode. Results of applying the steady-state data filter to recorded helicopter engine flight data are shown, demonstrating its utility for engine condition monitoring applications.

Temporal Tuning of Word- and Face-selective Cortex.

PubMed

Yeatman, Jason D; Norcia, Anthony M

2016-11-01

Sensitivity to temporal change places fundamental limits on object processing in the visual system. An emerging consensus from the behavioral and neuroimaging literature suggests that temporal resolution differs substantially for stimuli of different complexity and for brain areas at different levels of the cortical hierarchy. Here, we used steady-state visually evoked potentials to directly measure three fundamental parameters that characterize the underlying neural response to text and face images: temporal resolution, peak temporal frequency, and response latency. We presented full-screen images of text or a human face, alternated with a scrambled image, at temporal frequencies between 1 and 12 Hz. These images elicited a robust response at the first harmonic that showed differential tuning, scalp topography, and delay for the text and face images. Face-selective responses were maximal at 4 Hz, but text-selective responses, by contrast, were maximal at 1 Hz. The topography of the text image response was strongly left-lateralized at higher stimulation rates, whereas the response to the face image was slightly right-lateralized but nearly bilateral at all frequencies. Both text and face images elicited steady-state activity at more than one apparent latency; we observed early (141-160 msec) and late (>250 msec) text- and face-selective responses. These differences in temporal tuning profiles are likely to reflect differences in the nature of the computations performed by word- and face-selective cortex. Despite the close proximity of word- and face-selective regions on the cortical surface, our measurements demonstrate substantial differences in the temporal dynamics of word- versus face-selective responses.

A statistical state dynamics approach to wall turbulence.

PubMed

Farrell, B F; Gayme, D F; Ioannou, P J

2017-03-13

This paper reviews results obtained using statistical state dynamics (SSD) that demonstrate the benefits of adopting this perspective for understanding turbulence in wall-bounded shear flows. The SSD approach used in this work employs a second-order closure that retains only the interaction between the streamwise mean flow and the streamwise mean perturbation covariance. This closure restricts nonlinearity in the SSD to that explicitly retained in the streamwise constant mean flow together with nonlinear interactions between the mean flow and the perturbation covariance. This dynamical restriction, in which explicit perturbation-perturbation nonlinearity is removed from the perturbation equation, results in a simplified dynamics referred to as the restricted nonlinear (RNL) dynamics. RNL systems, in which a finite ensemble of realizations of the perturbation equation share the same mean flow, provide tractable approximations to the SSD, which is equivalent to an infinite ensemble RNL system. This infinite ensemble system, referred to as the stochastic structural stability theory system, introduces new analysis tools for studying turbulence. RNL systems provide computationally efficient means to approximate the SSD and produce self-sustaining turbulence exhibiting qualitative features similar to those observed in direct numerical simulations despite greatly simplified dynamics. The results presented show that RNL turbulence can be supported by as few as a single streamwise varying component interacting with the streamwise constant mean flow and that judicious selection of this truncated support or 'band-limiting' can be used to improve quantitative accuracy of RNL turbulence. These results suggest that the SSD approach provides new analytical and computational tools that allow new insights into wall turbulence.This article is part of the themed issue 'Toward the development of high-fidelity models of wall turbulence at large Reynolds number'. © 2017 The Author(s).

A statistical state dynamics approach to wall turbulence

PubMed Central

Gayme, D. F.; Ioannou, P. J.

2017-01-01

This paper reviews results obtained using statistical state dynamics (SSD) that demonstrate the benefits of adopting this perspective for understanding turbulence in wall-bounded shear flows. The SSD approach used in this work employs a second-order closure that retains only the interaction between the streamwise mean flow and the streamwise mean perturbation covariance. This closure restricts nonlinearity in the SSD to that explicitly retained in the streamwise constant mean flow together with nonlinear interactions between the mean flow and the perturbation covariance. This dynamical restriction, in which explicit perturbation–perturbation nonlinearity is removed from the perturbation equation, results in a simplified dynamics referred to as the restricted nonlinear (RNL) dynamics. RNL systems, in which a finite ensemble of realizations of the perturbation equation share the same mean flow, provide tractable approximations to the SSD, which is equivalent to an infinite ensemble RNL system. This infinite ensemble system, referred to as the stochastic structural stability theory system, introduces new analysis tools for studying turbulence. RNL systems provide computationally efficient means to approximate the SSD and produce self-sustaining turbulence exhibiting qualitative features similar to those observed in direct numerical simulations despite greatly simplified dynamics. The results presented show that RNL turbulence can be supported by as few as a single streamwise varying component interacting with the streamwise constant mean flow and that judicious selection of this truncated support or ‘band-limiting’ can be used to improve quantitative accuracy of RNL turbulence. These results suggest that the SSD approach provides new analytical and computational tools that allow new insights into wall turbulence. This article is part of the themed issue ‘Toward the development of high-fidelity models of wall turbulence at large Reynolds number’. PMID:28167577

Benefits Analysis of Multi-Center Dynamic Weather Routes

NASA Technical Reports Server (NTRS)

Sheth, Kapil; McNally, David; Morando, Alexander; Clymer, Alexis; Lock, Jennifer; Petersen, Julien

2014-01-01

Dynamic weather routes are flight plan corrections that can provide airborne flights more than user-specified minutes of flying-time savings, compared to their current flight plan. These routes are computed from the aircraft's current location to a flight plan fix downstream (within a predefined limit region), while avoiding forecasted convective weather regions. The Dynamic Weather Routes automation has been continuously running with live air traffic data for a field evaluation at the American Airlines Integrated Operations Center in Fort Worth, TX since July 31, 2012, where flights within the Fort Worth Air Route Traffic Control Center are evaluated for time savings. This paper extends the methodology to all Centers in United States and presents benefits analysis of Dynamic Weather Routes automation, if it was implemented in multiple airspace Centers individually and concurrently. The current computation of dynamic weather routes requires a limit rectangle so that a downstream capture fix can be selected, preventing very large route changes spanning several Centers. In this paper, first, a method of computing a limit polygon (as opposed to a rectangle used for Fort Worth Center) is described for each of the 20 Centers in the National Airspace System. The Future ATM Concepts Evaluation Tool, a nationwide simulation and analysis tool, is used for this purpose. After a comparison of results with the Center-based Dynamic Weather Routes automation in Fort Worth Center, results are presented for 11 Centers in the contiguous United States. These Centers are generally most impacted by convective weather. A breakdown of individual Center and airline savings is presented and the results indicate an overall average savings of about 10 minutes of flying time are obtained per flight.

Model of ultrafast demagnetization driven by spin-orbit coupling in a photoexcited antiferromagnetic insulator Cr2O3

NASA Astrophysics Data System (ADS)

Guo, Feng; Zhang, Na; Jin, Wei; Chang, Jun

2017-06-01

We theoretically study the dynamic time evolution following laser pulse pumping in an antiferromagnetic insulator Cr2O3. From the photoexcited high-spin quartet states to the long-lived low-spin doublet states, the ultrafast demagnetization processes are investigated by solving the dissipative Schrödinger equation. We find that the demagnetization times are of the order of hundreds of femtoseconds, in good agreement with recent experiments. The switching times could be strongly reduced by properly tuning the energy gaps between the multiplet energy levels of Cr3+. Furthermore, the relaxation times also depend on the hybridization of atomic orbitals in the first photoexcited state. Our results suggest that the selective manipulation of the electronic structure by engineering stress-strain or chemical substitution allows effective control of the magnetic state switching in photoexcited insulating transition-metal oxides.

Design of crystal-like aperiodic solids with selective disorder–phonon coupling

PubMed Central

Overy, Alistair R.; Cairns, Andrew B.; Cliffe, Matthew J.; Simonov, Arkadiy; Tucker, Matthew G.; Goodwin, Andrew L.

2016-01-01

Functional materials design normally focuses on structurally ordered systems because disorder is considered detrimental to many functional properties. Here we challenge this paradigm by showing that particular types of strongly correlated disorder can give rise to useful characteristics that are inaccessible to ordered states. A judicious combination of low-symmetry building unit and high-symmetry topological template leads to aperiodic ‘procrystalline' solids that harbour this type of disorder. We identify key classes of procrystalline states together with their characteristic diffraction behaviour, and establish mappings onto known and target materials. The strongly correlated disorder found in these systems is associated with specific sets of modulation periodicities distributed throughout the Brillouin zone. Lattice dynamical calculations reveal selective disorder-driven phonon broadening that resembles the poorly understood ‘waterfall' effect observed in relaxor ferroelectrics. This property of procrystalline solids suggests a mechanism by which strongly correlated topological disorder might allow independently optimized thermal and electronic transport behaviour, such as required for high-performance thermoelectrics. PMID:26842772

Pluripotency factors in embryonic stem cells regulate differentiation into germ layers.

PubMed

Thomson, Matt; Liu, Siyuan John; Zou, Ling-Nan; Smith, Zack; Meissner, Alexander; Ramanathan, Sharad

2011-06-10

Cell fate decisions are fundamental for development, but we do not know how transcriptional networks reorganize during the transition from a pluripotent to a differentiated cell state. Here, we asked how mouse embryonic stem cells (ESCs) leave the pluripotent state and choose between germ layer fates. By analyzing the dynamics of the transcriptional circuit that maintains pluripotency, we found that Oct4 and Sox2, proteins that maintain ESC identity, also orchestrate germ layer fate selection. Oct4 suppresses neural ectodermal differentiation and promotes mesendodermal differentiation; Sox2 inhibits mesendodermal differentiation and promotes neural ectodermal differentiation. Differentiation signals continuously and asymmetrically modulate Oct4 and Sox2 protein levels, altering their binding pattern in the genome, and leading to cell fate choice. The same factors that maintain pluripotency thus also integrate external signals and control lineage selection. Our study provides a framework for understanding how complex transcription factor networks control cell fate decisions in progenitor cells. Copyright © 2011 Elsevier Inc. All rights reserved.

Significant Transient Mobility of Platinum Clusters via a Hot Precursor State on the Alumina Surface.

PubMed

Beniya, Atsushi; Hirata, Hirohito; Watanabe, Yoshihide

2016-11-17

Relaxation dynamics of hot metal clusters on oxide surfaces play a crucial role in a variety of physical and chemical processes. However, their transient mobility has not been investigated as much as other systems such as atoms and molecules on metal surfaces due to experimental difficulties. To study the role of the transient mobility of clusters on the oxide surface, we investigated the initial adsorption process of size-selected Pt clusters on a thin Al 2 O 3 film. Soft-landing the size-selected clusters while suppressing the thermal migration resulted in the transient migration controlling the initial adsorption states as an isolated and aggregated cluster, as revealed using scanning tunneling microscopy. We demonstrate that transient migration significantly contributes to the initial cluster adsorption process; the cross section for aggregation is seven times larger than the expected value from geometrical considerations, indicating that metal clusters are highly mobile during a energy dissipation process on the oxide surface.

Aircraft Dynamic Response to Damaged and Repaired Runways.

DTIC Science & Technology

1982-08-01

is particularly beneficial in giving the engineer a fast understanding of problems encountered. This can extend, if required, to computer animation of...pitch response following a repair for a selection of ’critical’ initial states o animation of time history responses o routines, for the multiple repair...forms L𔄀&alit6 so produit on css do glissement avao ~ed i/~ Ct am :ooefficient do laminago do l’huilo, eat dittdrant ontro is d6tonte at i’ontonoeent at

Ion Correlation Effects in Salt-Doped Block Copolymers

NASA Astrophysics Data System (ADS)

Brown, Jonathan R.; Seo, Youngmi; Hall, Lisa M.

2018-03-01

We apply classical density functional theory to study how salt changes the microphase morphology of diblock copolymers. Polymers are freely jointed and one monomer type favorably interacts with ions, to account for the selective solvation that arises from different dielectric constants of the microphases. By including correlations from liquid state theory of an unbound reference fluid, the theory can treat chain behavior, microphase separation, ion correlations, and preferential solvation, at the same coarse-grained level. We show good agreement with molecular dynamics simulations.

Evaluation of Bridges Subjected to Military Loading and Dynamic Hydraulic Effects: Review of Design Regulations, Selection Criteria, and Inspection Procedures for Bridge Railing Systems

DTIC Science & Technology

2011-08-01

Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington VA 22202-4302. Respondents should be aware that notwithstanding any...may be required by the United States Customs and Immigration Services, in connection with the operation of an international bridge or tunnel. ERDC...significant effect on the operation , service quality, and safety of road networks by restricting the traffic volume and vehicle weight that can be

Towards Real-Time Maneuver Detection: Automatic State and Dynamics Estimation with the Adaptive Optimal Control Based Estimator

NASA Astrophysics Data System (ADS)

Lubey, D.; Scheeres, D.

Tracking objects in Earth orbit is fraught with complications. This is due to the large population of orbiting spacecraft and debris that continues to grow, passive (i.e. no direct communication) and data-sparse observations, and the presence of maneuvers and dynamics mismodeling. Accurate orbit determination in this environment requires an algorithm to capture both a system's state and its state dynamics in order to account for mismodelings. Previous studies by the authors yielded an algorithm called the Optimal Control Based Estimator (OCBE) - an algorithm that simultaneously estimates a system's state and optimal control policies that represent dynamic mismodeling in the system for an arbitrary orbit-observer setup. The stochastic properties of these estimated controls are then used to determine the presence of mismodelings (maneuver detection), as well as characterize and reconstruct the mismodelings. The purpose of this paper is to develop the OCBE into an accurate real-time orbit tracking and maneuver detection algorithm by automating the algorithm and removing its linear assumptions. This results in a nonlinear adaptive estimator. In its original form the OCBE had a parameter called the assumed dynamic uncertainty, which is selected by the user with each new measurement to reflect the level of dynamic mismodeling in the system. This human-in-the-loop approach precludes real-time application to orbit tracking problems due to their complexity. This paper focuses on the Adaptive OCBE, a version of the estimator where the assumed dynamic uncertainty is chosen automatically with each new measurement using maneuver detection results to ensure that state uncertainties are properly adjusted to account for all dynamic mismodelings. The paper also focuses on a nonlinear implementation of the estimator. Originally, the OCBE was derived from a nonlinear cost function then linearized about a nominal trajectory, which is assumed to be ballistic (i.e. the nominal optimal control policy is zero for all times). In this paper, we relax this assumption on the nominal trajectory in order to allow for controlled nominal trajectories. This allows the estimator to be iterated to obtain a more accurate nonlinear solution for both the state and control estimates. Beyond these developments to the estimator, this paper also introduces a modified distance metric for maneuver detection. The original metric used in the OCBE only accounted for the estimated control and its uncertainty. This new metric accounts for measurement deviation and a priori state deviations, such that it accounts for all three major forms of uncertainty in orbit determination. This allows the user to understand the contributions of each source of uncertainty toward the total system mismodeling so that the user can properly account for them. Together these developments create an accurate orbit determination algorithm that is automated, robust to mismodeling, and capable of detecting and reconstructing the presence of mismodeling. These qualities make this algorithm a good foundation from which to approach the problem of real-time maneuver detection and reconstruction for Space Situational Awareness applications. This is further strengthened by the algorithm's general formulation that allows it to be applied to problems with an arbitrary target and observer.

Local control theory using trajectory surface hopping and linear-response time-dependent density functional theory.

PubMed

Curchod, Basile F E; Penfold, Thomas J; Rothlisberger, Ursula; Tavernelli, Ivano

2013-01-01

The implementation of local control theory using nonadiabatic molecular dynamics within the framework of linear-response time-dependent density functional theory is discussed. The method is applied to study the photoexcitation of lithium fluoride, for which we demonstrate that this approach can efficiently generate a pulse, on-the-fly, able to control the population transfer between two selected electronic states. Analysis of the computed control pulse yields insights into the photophysics of the process identifying the relevant frequencies associated to the curvature of the initial and final state potential energy curves and their energy differences. The limitations inherent to the use of the trajectory surface hopping approach are also discussed.

Appearance of Unstable Monopoly State Caused by Selective and Concentrative Mergers in Business Networks.

PubMed

Goto, Hayato; Viegas, Eduardo; Jensen, Henrik Jeldtoft; Takayasu, Hideki; Takayasu, Misako

2017-07-11

Recently, growth mechanism of firms in complex business networks became new targets of scientific study owing to increasing availability of high quality business firms' data. Here, we paid attention to comprehensive data of M&A events for 40 years and derived empirical laws by applying methods and concepts of aggregation dynamics of aerosol physics. It is found that the probability of merger between bigger firms is bigger than that between smaller ones, and such tendency is enhancing year by year. We introduced a numerical model simulating the whole ecosystem of firms and showed that the system is already in an unstable monopoly state in which growth of middle sized firms are suppressed.

Role of Dynamic Nucleation at Moving Boundaries in Phase and Microstructure Selection

NASA Technical Reports Server (NTRS)

Karma, Alain; Trivedi, Rohit

1999-01-01

Solidification microstructures that form under steady-state growth conditions (cells, dendrites, regular eutectics, etc.) are reasonably well understood in comparison to other, more complex microstructures, which form under intrinsically non-steady-state growth conditions due to the competition between the nucleation and growth of several phases. Some important practical examples in this latter class include microstructures forming in peritectic systems in highly undercooled droplets, and in strip cast stainless steels. Prediction of phase and microstructure selection in these systems has been traditionally based on (1) heterogeneous nucleation on a static interface, and (2) comparing the relative growth rate of different phase/microstructures under steady-state growth conditions. The formation of new phases, however, occurs via nucleation on, or ahead of, a moving boundary. In addition, the actual selection process is controlled by a complex interaction between the nucleation process and the growth competition between the nuclei and the pre-existing phase under non-steady-state conditions. As a result, it is often difficult to predict which microstructure will form and which phases will be selected under prescribed processing conditions. This research addresses this critical role of nucleation at moving boundaries in the selection of phases and solidification microstructures through quantitative experiments and numerical modeling in peritectic systems. In order to create a well characterized system in which to study this problem, we focus on the directional solidification of hypo- and hyper-peritectic alloys in the two-phase region, imposing a large enough ratio of temperature gradient/growth rate (G/V(sub p)) to suppress the morphological instability of both the parent (alpha) and peritectic (Beta) phases, i.e. each phase alone would grow as a planar front. Our combined experimental and theoretical results show that, already in this simplified case, the growth competition of these two phases leads to a rich variety of microstructures that depend sensitively upon the relative importance of nucleation, diffusion, and convection.

Numerical study on the selective excitation of Helmholtz-Gauss beams in end-pumped solid-state digital lasers with the control of the laser gain transverse position provided by off-axis end pumping

NASA Astrophysics Data System (ADS)

Tsai, Ko-Fan; Chu, Shu-Chun

2018-03-01

This study proposes a complete and unified method for selective excitation of any specified nearly nondiffracting Helmholtz-Gauss (HzG) beam in end-pumped solid-state digital lasers. Four types of the HzG beams: cosine-Gauss beams, Bessel-Gauss beams, Mathieu-Gauss beams, and, in particular, parabolic-Gauss beams are successfully demonstrated to be generated with the proposed methods. To the best of the authors’ knowledge, parabolic-Gauss beams have not yet been directly generated from any kind of laser system. The numerical results of this study show that one can successfully achieve any lasing HzG beams directly from the solid-state digital lasers with only added control of the laser gain transverse position provided by off-axis end pumping. This study also presents a practical digital laser set-up for easily manipulating off-axis pumping in order to achieve the control of the laser gain transverse gain position in digital lasers. The reported results in this study provide advancement of digital lasers in dynamically generating nondiffracting beams. The control of the digital laser cavity gain position creates the possibility of achieving real-time selection of more laser modes in digital lasers, and it is worth further investigation in the future.

Detecting Selection on Protein Stability through Statistical Mechanical Models of Folding and Evolution

PubMed Central

Bastolla, Ugo

2014-01-01

The properties of biomolecules depend both on physics and on the evolutionary process that formed them. These two points of view produce a powerful synergism. Physics sets the stage and the constraints that molecular evolution has to obey, and evolutionary theory helps in rationalizing the physical properties of biomolecules, including protein folding thermodynamics. To complete the parallelism, protein thermodynamics is founded on the statistical mechanics in the space of protein structures, and molecular evolution can be viewed as statistical mechanics in the space of protein sequences. In this review, we will integrate both points of view, applying them to detecting selection on the stability of the folded state of proteins. We will start discussing positive design, which strengthens the stability of the folded against the unfolded state of proteins. Positive design justifies why statistical potentials for protein folding can be obtained from the frequencies of structural motifs. Stability against unfolding is easier to achieve for longer proteins. On the contrary, negative design, which consists in destabilizing frequently formed misfolded conformations, is more difficult to achieve for longer proteins. The folding rate can be enhanced by strengthening short-range native interactions, but this requirement contrasts with negative design, and evolution has to trade-off between them. Finally, selection can accelerate functional movements by favoring low frequency normal modes of the dynamics of the native state that strongly correlate with the functional conformation change. PMID:24970217

Relating dynamic brain states to dynamic machine states: Human and machine solutions to the speech recognition problem

PubMed Central

Liu, Xunying; Zhang, Chao; Woodland, Phil; Fonteneau, Elisabeth

2017-01-01

There is widespread interest in the relationship between the neurobiological systems supporting human cognition and emerging computational systems capable of emulating these capacities. Human speech comprehension, poorly understood as a neurobiological process, is an important case in point. Automatic Speech Recognition (ASR) systems with near-human levels of performance are now available, which provide a computationally explicit solution for the recognition of words in continuous speech. This research aims to bridge the gap between speech recognition processes in humans and machines, using novel multivariate techniques to compare incremental ‘machine states’, generated as the ASR analysis progresses over time, to the incremental ‘brain states’, measured using combined electro- and magneto-encephalography (EMEG), generated as the same inputs are heard by human listeners. This direct comparison of dynamic human and machine internal states, as they respond to the same incrementally delivered sensory input, revealed a significant correspondence between neural response patterns in human superior temporal cortex and the structural properties of ASR-derived phonetic models. Spatially coherent patches in human temporal cortex responded selectively to individual phonetic features defined on the basis of machine-extracted regularities in the speech to lexicon mapping process. These results demonstrate the feasibility of relating human and ASR solutions to the problem of speech recognition, and suggest the potential for further studies relating complex neural computations in human speech comprehension to the rapidly evolving ASR systems that address the same problem domain. PMID:28945744

Localization of Non-Linearly Modeled Autonomous Mobile Robots Using Out-of-Sequence Measurements

PubMed Central

Besada-Portas, Eva; Lopez-Orozco, Jose A.; Lanillos, Pablo; de la Cruz, Jesus M.

2012-01-01

This paper presents a state of the art of the estimation algorithms dealing with Out-of-Sequence (OOS) measurements for non-linearly modeled systems. The state of the art includes a critical analysis of the algorithm properties that takes into account the applicability of these techniques to autonomous mobile robot navigation based on the fusion of the measurements provided, delayed and OOS, by multiple sensors. Besides, it shows a representative example of the use of one of the most computationally efficient approaches in the localization module of the control software of a real robot (which has non-linear dynamics, and linear and non-linear sensors) and compares its performance against other approaches. The simulated results obtained with the selected OOS algorithm shows the computational requirements that each sensor of the robot imposes to it. The real experiments show how the inclusion of the selected OOS algorithm in the control software lets the robot successfully navigate in spite of receiving many OOS measurements. Finally, the comparison highlights that not only is the selected OOS algorithm among the best performing ones of the comparison, but it also has the lowest computational and memory cost. PMID:22736962

Localization of non-linearly modeled autonomous mobile robots using out-of-sequence measurements.

PubMed

Besada-Portas, Eva; Lopez-Orozco, Jose A; Lanillos, Pablo; de la Cruz, Jesus M

2012-01-01

This paper presents a state of the art of the estimation algorithms dealing with Out-of-Sequence (OOS) measurements for non-linearly modeled systems. The state of the art includes a critical analysis of the algorithm properties that takes into account the applicability of these techniques to autonomous mobile robot navigation based on the fusion of the measurements provided, delayed and OOS, by multiple sensors. Besides, it shows a representative example of the use of one of the most computationally efficient approaches in the localization module of the control software of a real robot (which has non-linear dynamics, and linear and non-linear sensors) and compares its performance against other approaches. The simulated results obtained with the selected OOS algorithm shows the computational requirements that each sensor of the robot imposes to it. The real experiments show how the inclusion of the selected OOS algorithm in the control software lets the robot successfully navigate in spite of receiving many OOS measurements. Finally, the comparison highlights that not only is the selected OOS algorithm among the best performing ones of the comparison, but it also has the lowest computational and memory cost.

Mechanistic Insights from Discrete Molecular Dynamics Simulations of Pesticide-Nanoparticle Interactions.

PubMed

Geitner, Nicholas K; Zhao, Weilu; Ding, Feng; Chen, Wei; Wiesner, Mark R

2017-08-01

Nanoscale particles have the potential to modulate the transport, lifetimes, and ultimate uptake of pesticides that may otherwise be bound to agricultural soils. Engineered nanoparticles provide a unique platform for studying these interactions. In this study, we utilized discrete molecular dynamics (DMD) as a screening tool for examining nanoparticle-pesticide adsorptive interactions. As a proof-of-concept, we selected a library of 15 pesticides common in the United States and 4 nanomaterials with likely natural or incidental sources, and simulated all possible nanoparticle-pesticide pairs. The resulting adsorption coefficients derived from DMD simulations ranged over several orders of magnitude, and in many cases were significantly stronger than pesticide adsorption on clay surfaces, highlighting the significance of specific nanoscale phases as a preferential media with which pesticides may associate. Binding was found to be significantly enhanced by the capacity to form hydrogen bonds with slightly hydroxylated fullerols, highlighting the importance of considering the precise nature of weathered nanomaterials as opposed to pristine precursors. Results were compared to experimental adsorption studies using selected pesticides, with a Pearson correlation coefficient of 0.97.

A boundary PDE feedback control approach for the stabilization of mortgage price dynamics

NASA Astrophysics Data System (ADS)

Rigatos, G.; Siano, P.; Sarno, D.

2017-11-01

Several transactions taking place in financial markets are dependent on the pricing of mortgages (loans for the purchase of residences, land or farms). In this article, a method for stabilization of mortgage price dynamics is developed. It is considered that mortgage prices follow a PDE model which is equivalent to a multi-asset Black-Scholes PDE. Actually it is a diffusion process evolving in a 2D assets space, where the first asset is the house price and the second asset is the interest rate. By applying semi-discretization and a finite differences scheme this multi-asset PDE is transformed into a state-space model consisting of ordinary nonlinear differential equations. For the local subsystems, into which the mortgage PDE is decomposed, it becomes possible to apply boundary-based feedback control. The controller design proceeds by showing that the state-space model of the mortgage price PDE stands for a differentially flat system. Next, for each subsystem which is related to a nonlinear ODE, a virtual control input is computed, that can invert the subsystem's dynamics and can eliminate the subsystem's tracking error. From the last row of the state-space description, the control input (boundary condition) that is actually applied to the multi-factor mortgage price PDE system is found. This control input contains recursively all virtual control inputs which were computed for the individual ODE subsystems associated with the previous rows of the state-space equation. Thus, by tracing the rows of the state-space model backwards, at each iteration of the control algorithm, one can finally obtain the control input that should be applied to the mortgage price PDE system so as to assure that all its state variables will converge to the desirable setpoints. By showing the feasibility of such a control method it is also proven that through selected modification of the PDE boundary conditions the price of the mortgage can be made to converge and stabilize at specific reference values.

Mode localization in the cooperative dynamics of protein recognition

NASA Astrophysics Data System (ADS)

Copperman, J.; Guenza, M. G.

2016-07-01

The biological function of proteins is encoded in their structure and expressed through the mediation of their dynamics. This paper presents a study on the correlation between local fluctuations, binding, and biological function for two sample proteins, starting from the Langevin Equation for Protein Dynamics (LE4PD). The LE4PD is a microscopic and residue-specific coarse-grained approach to protein dynamics, which starts from the static structural ensemble of a protein and predicts the dynamics analytically. It has been shown to be accurate in its prediction of NMR relaxation experiments and Debye-Waller factors. The LE4PD is solved in a set of diffusive modes which span a vast range of time scales of the protein dynamics, and provides a detailed picture of the mode-dependent localization of the fluctuation as a function of the primary structure of the protein. To investigate the dynamics of protein complexes, the theory is implemented here to treat the coarse-grained dynamics of interacting macromolecules. As an example, calculations of the dynamics of monomeric and dimerized HIV protease and the free Insulin Growth Factor II Receptor (IGF2R) domain 11 and its IGF2R:IGF2 complex are presented. Either simulation-derived or experimentally measured NMR conformers are used as input structural ensembles to the theory. The picture that emerges suggests a dynamical heterogeneous protein where biologically active regions provide energetically comparable conformational states that are trapped by a reacting partner in agreement with the conformation-selection mechanism of binding.

Neural field model to reconcile structure with function in primary visual cortex.

PubMed

Rankin, James; Chavane, Frédéric

2017-10-01

Voltage-sensitive dye imaging experiments in primary visual cortex (V1) have shown that local, oriented visual stimuli elicit stable orientation-selective activation within the stimulus retinotopic footprint. The cortical activation dynamically extends far beyond the retinotopic footprint, but the peripheral spread stays non-selective-a surprising finding given a number of anatomo-functional studies showing the orientation specificity of long-range connections. Here we use a computational model to investigate this apparent discrepancy by studying the expected population response using known published anatomical constraints. The dynamics of input-driven localized states were simulated in a planar neural field model with multiple sub-populations encoding orientation. The realistic connectivity profile has parameters controlling the clustering of long-range connections and their orientation bias. We found substantial overlap between the anatomically relevant parameter range and a steep decay in orientation selective activation that is consistent with the imaging experiments. In this way our study reconciles the reported orientation bias of long-range connections with the functional expression of orientation selective neural activity. Our results demonstrate this sharp decay is contingent on three factors, that long-range connections are sufficiently diffuse, that the orientation bias of these connections is in an intermediate range (consistent with anatomy) and that excitation is sufficiently balanced by inhibition. Conversely, our modelling results predict that, for reduced inhibition strength, spurious orientation selective activation could be generated through long-range lateral connections. Furthermore, if the orientation bias of lateral connections is very strong, or if inhibition is particularly weak, the network operates close to an instability leading to unbounded cortical activation.

Multistate and phase change selection in constitutional multivalent systems.

PubMed

Barboiu, Mihail

2012-01-01

Molecular architectures and materials can be constitutionally self-sorted in the presence of different biomolecular targets or external physical stimuli or chemical effectors, thus responding to an external selection pressure. The high selectivity and specificity of different bioreceptors or self-correlated internal interactions may be used to describe the complex constitutional behaviors through multistate component selection from a dynamic library. The self-selection may result in the dynamic amplification of self-optimized architectures during the phase change process. The sol-gel resolution of dynamic molecular/supramolecular libraries leads to higher self-organized constitutional hybrid materials, in which organic (supramolecular)/inorganic domains are reversibily connected.

Study of skeletal muscle cross-bridge population dynamics by second harmonic generation

NASA Astrophysics Data System (ADS)

Nucciotti, V.; Stringari, C.; Sacconi, L.; Vanzi, F.; Tesi, C.; Pirrodi, N.; Poggesi, C.; Castiglioni, C.; Milani, A.; Linari, M.; Piazzesi, G.; Lombardi, V.; Pavone, F. S.

2007-02-01

The high degree of structural order in skeletal muscle allows imaging of this tissue by Second Harmonic Generation (SHG). Biochemical and colocalization studies have gathered an increasing wealth of clues for the attribution of the molecular origin of the muscle SHG signal to the motor protein myosin. Thus, SHG represents a potentially very powerful tool in the investigation of structural dynamics occurring in muscle during active production of force and/or shortening. A full characterization of the polarization-dependence of the SHG signal represents a very selective information on the orientation of the emitting proteins and their dynamics during contraction, provided that different physiological states of muscle (relaxed, rigor and active) exhibit distinct patterns of SHG polarization dependence. Here polarization data are obtained from single frog muscle fibers at rest and during isometric contraction and interpreted, by means of a model, in terms of an average orientation of the SHG emitters which are structured with a cylindrical symmetry about the fiber axis. The setup is optimized for accurate polarization measurements with SHG, combined with a line scan imaging method allowing acquisition of SHG polarization curves in different physiological states. We demonstrate that muscle fiber displays a measurable variation of the orientation of SHG emitters with the transition from rest to isometric contraction.

Real-time sensor validation and fusion for distributed autonomous sensors

NASA Astrophysics Data System (ADS)

Yuan, Xiaojing; Li, Xiangshang; Buckles, Bill P.

2004-04-01

Multi-sensor data fusion has found widespread applications in industrial and research sectors. The purpose of real time multi-sensor data fusion is to dynamically estimate an improved system model from a set of different data sources, i.e., sensors. This paper presented a systematic and unified real time sensor validation and fusion framework (RTSVFF) based on distributed autonomous sensors. The RTSVFF is an open architecture which consists of four layers - the transaction layer, the process fusion layer, the control layer, and the planning layer. This paradigm facilitates distribution of intelligence to the sensor level and sharing of information among sensors, controllers, and other devices in the system. The openness of the architecture also provides a platform to test different sensor validation and fusion algorithms and thus facilitates the selection of near optimal algorithms for specific sensor fusion application. In the version of the model presented in this paper, confidence weighted averaging is employed to address the dynamic system state issue noted above. The state is computed using an adaptive estimator and dynamic validation curve for numeric data fusion and a robust diagnostic map for decision level qualitative fusion. The framework is then applied to automatic monitoring of a gas-turbine engine, including a performance comparison of the proposed real-time sensor fusion algorithms and a traditional numerical weighted average.

Supramolecular control of the spin-dependent dynamics of long-lived charge-separated states at the micellar interface as studied by magnetic field effect.

PubMed

Miura, Tomoaki

2013-05-30

Spin selectivity in long-lived charge separation at the micellar interface is studied using the magnetic field effect (MFE). An amphiphilic viologen is complexed with a nonionic surfactant to form a supramolecular acceptor cage, of which the size is controlled by the acceptor concentration, as confirmed by dynamic light scattering measurement. Photoinduced electron transfer (ET) from a guest polyaromatic molecule to the viologen moiety is observed spin-dependently with time-resolved fluorescence (trFL) and transient absorption (TA). A negative MFE on the radical yield is successfully observed, which indicates generation of singlet-born long-lived radical pair that is realized by supramolecular control of the donor-acceptor (D-A) distances. The dominance of the singlet-precursor MFE is sensitive to the acceptor concentration, which presumably affects the D-A distance as well as the cage size. However, theoretical analysis of the MFE gives large recombination rates of ca. 10(8) s(-1), which indicate the contribution of spin-allowed recombination of the pseudocontact radical pair generated by still active in-cage diffusion. Dependence of the viologen concentration and alkyl chain length on the recombination and escape dynamics is discussed in terms of precursor spin states and the microenvironments in the cage.

The dynamic Atg13-free conformation of the Atg1 EAT domain is required for phagophore expansion.

PubMed

Lin, Mary G; Schöneberg, Johannes; Davies, Christopher W; Ren, Xuefeng; Hurley, James H

2018-05-15

Yeast macroautophagy begins with the de novo formation of a double-membrane phagophore at the preautophagosomal structure/phagophore assembly site (PAS), followed by its expansion into the autophagosome responsible for cargo engulfment. The kinase Atg1 is recruited to the PAS by Atg13 through interactions between the EAT domain of the former and the tMIM motif of the latter. Mass-spectrometry data have shown that, in the absence of Atg13, the EAT domain structure is strikingly dynamic, but the function of this Atg13-free dynamic state has been unclear. We used structure-based mutational analysis and quantitative and superresolution microscopy to show that Atg1 is present on autophagic puncta at, on average, twice the stoichiometry of Atg13. Moreover, Atg1 colocalizes with the expanding autophagosome in a manner dependent on Atg8 but not Atg13. We used isothermal titration calorimetry and crystal structure information to design an EAT domain mutant allele ATG1 DD that selectively perturbs the function of the Atg13-free state. Atg1 DD shows reduced PAS formation and does not support phagophore expansion, showing that the EAT domain has an essential function that is separate from its Atg13-dependent role in autophagy initiation.

Molecular dynamics studies of protein folding and aggregation

NASA Astrophysics Data System (ADS)

Ding, Feng

This thesis applies molecular dynamics simulations and statistical mechanics to study: (i) protein folding; and (ii) protein aggregation. Most small proteins fold into their native states via a first-order-like phase transition with a major free energy barrier between the folded and unfolded states. A set of protein conformations corresponding to the free energy barrier, Delta G >> kBT, are the folding transition state ensemble (TSE). Due to their evasive nature, TSE conformations are hard to capture (probability ∝ exp(-DeltaG/k BT)) and characterize. A coarse-grained discrete molecular dynamics model with realistic steric constraints is constructed to reproduce the experimentally observed two-state folding thermodynamics. A kinetic approach is proposed to identify the folding TSE. A specific set of contacts, common to the TSE conformations, is identified as the folding nuclei which are necessary to be formed in order for the protein to fold. Interestingly, the amino acids at the site of the identified folding nuclei are highly conserved for homologous proteins sharing the same structures. Such conservation suggests that amino acids that are important for folding kinetics are under selective pressure to be preserved during the course of molecular evolution. In addition, studies of the conformations close to the transition states uncover the importance of topology in the construction of order parameter for protein folding transition. Misfolded proteins often form insoluble aggregates, amyloid fibrils, that deposit in the extracellular space and lead to a type of disease known as amyloidosis. Due to its insoluble and non-crystalline nature, the aggregation structure and, thus the aggregation mechanism, has yet to be uncovered. Discrete molecular dynamics studies reveal an aggregate structure with the same structural signatures as in experimental observations and show a nucleation aggregation scenario. The simulations also suggest a generic aggregation mechanism that globular proteins under a denaturing environment partially unfold and aggregate by forming stabilizing hydrogen bonds between the backbones of the partial folded substructures. Proteins or peptides rich in alpha-helices also aggregate into beta-rich amyloid fibrils. Upon aggregation, the protein or peptide undergoes a conformational transition from alpha-helices to beta-sheets. The transition of alpha-helix to beta-hairpin (two-stranded beta-sheet) is studied in an all-heavy-atom discrete molecular dynamics model of a polyalanine chain. An entropical driving scenario for the alpha-helix to beta-hairpin transition is discovered.

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: The case of domain motions

NASA Astrophysics Data System (ADS)

Naritomi, Yusuke; Fuchigami, Sotaro

2011-02-01

Protein dynamics on a long time scale was investigated using all-atom molecular dynamics (MD) simulation and time-structure based independent component analysis (tICA). We selected the lysine-, arginine-, ornithine-binding protein (LAO) as a target protein and focused on its domain motions in the open state. A MD simulation of the LAO in explicit water was performed for 600 ns, in which slow and large-amplitude domain motions of the LAO were observed. After extracting domain motions by rigid-body domain analysis, the tICA was applied to the obtained rigid-body trajectory, yielding slow modes of the LAO's domain motions in order of decreasing time scale. The slowest mode detected by the tICA represented not a closure motion described by a largest-amplitude mode determined by the principal component analysis but a twist motion with a time scale of tens of nanoseconds. The slow dynamics of the LAO were well described by only the slowest mode and were characterized by transitions between two basins. The results show that tICA is promising for describing and analyzing slow dynamics of proteins.

Slow dynamics in protein fluctuations revealed by time-structure based independent component analysis: the case of domain motions.

PubMed

Naritomi, Yusuke; Fuchigami, Sotaro

2011-02-14

Protein dynamics on a long time scale was investigated using all-atom molecular dynamics (MD) simulation and time-structure based independent component analysis (tICA). We selected the lysine-, arginine-, ornithine-binding protein (LAO) as a target protein and focused on its domain motions in the open state. A MD simulation of the LAO in explicit water was performed for 600 ns, in which slow and large-amplitude domain motions of the LAO were observed. After extracting domain motions by rigid-body domain analysis, the tICA was applied to the obtained rigid-body trajectory, yielding slow modes of the LAO's domain motions in order of decreasing time scale. The slowest mode detected by the tICA represented not a closure motion described by a largest-amplitude mode determined by the principal component analysis but a twist motion with a time scale of tens of nanoseconds. The slow dynamics of the LAO were well described by only the slowest mode and were characterized by transitions between two basins. The results show that tICA is promising for describing and analyzing slow dynamics of proteins.

Lane-changing model with dynamic consideration of driver's propensity

NASA Astrophysics Data System (ADS)

Wang, Xiaoyuan; Wang, Jianqiang; Zhang, Jinglei; Ban, Xuegang Jeff

2015-07-01

Lane-changing is the driver's selection result of the satisfaction degree in different lane driving conditions. There are many different factors influencing lane-changing behavior, such as diversity, randomicity and difficulty of measurement. So it is hard to accurately reflect the uncertainty of drivers' lane-changing behavior. As a result, the research of lane-changing models is behind that of car-following models. Driver's propensity is her/his emotion state or the corresponding preference of a decision or action toward the real objective traffic situations under the influence of various dynamic factors. It represents the psychological characteristics of the driver in the process of vehicle operation and movement. It is an important factor to influence lane-changing. In this paper, dynamic recognition of driver's propensity is considered during simulation based on its time-varying discipline and the analysis of the driver's psycho-physic characteristics. The Analytic Hierarchy Process (AHP) method is used to quantify the hierarchy of driver's dynamic lane-changing decision-making process, especially the influence of the propensity. The model is validated using real data. Test results show that the developed lane-changing model with the dynamic consideration of a driver's time-varying propensity and the AHP method are feasible and with improved accuracy.