Application of electron closures in extended MHD

NASA Astrophysics Data System (ADS)

Held, Eric; Adair, Brett; Taylor, Trevor

2017-10-01

Rigorous closure of the extended MHD equations in plasma fluid codes includes the effects of electron heat conduction along perturbed magnetic fields and contributions of the electron collisional friction and stress to the extended Ohms law. In this work we discuss application of a continuum numerical solution to the Chapman-Enskog-like electron drift kinetic equation using the NIMROD code. The implementation is a tightly-coupled fluid/kinetic system that carefully addresses time-centering in the advance of the fluid variables with their kinetically-computed closures. Comparisons of spatial accuracy, computational efficiency and required velocity space resolution are presented for applications involving growing magnetic islands in cylindrical and toroidal geometry. The reduction in parallel heat conduction due to particle trapping in toroidal geometry is emphasized. Work supported by DOE under Grant Nos. DE-FC02-08ER54973 and DE-FG02-04ER54746.

Exact solutions and low-frequency instability of the adiabatic auroral arc model

NASA Technical Reports Server (NTRS)

Cornwall, John M.

1988-01-01

The adiabatic auroral arc model couples a kinetic theory parallel current driven by mirror forces to horizontal ionospheric currents; the resulting equations are nonlinear. Some exact stationary solutions to these equations, some of them based on the Liouville equation, are developed, with both latitudinal and longitudinal spatial variations. These Liouville equation exact solutions are related to stability boundaries of low-frequency instabilities such as Kelvin-Helmholtz, as shown by a study of a simplified model.

G-bounce

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

Easson, Damien A.; Sawicki, Ignacy; Vikman, Alexander, E-mail: easson@asu.edu, E-mail: ignacy.sawicki@uni-heidelberg.de, E-mail: alexander.vikman@cern.ch

2011-11-01

We present a wide class of models which realise a bounce in a spatially flat Friedmann universe in standard General Relativity. The key ingredient of the theories we consider is a noncanonical, minimally coupled scalar field belonging to the class of theories with Kinetic Gravity Braiding / Galileon-like self-couplings. In these models, the universe smoothly evolves from contraction to expansion, suffering neither from ghosts nor gradient instabilities around the turning point. The end-point of the evolution can be a standard radiation-domination era or an inflationary phase. We formulate necessary restrictions for Lagrangians needed to obtain a healthy bounce and illustratemore » our results with phase portraits for simple systems including the recently proposed Galilean Genesis scenario.« less

Interfacial mixing in high-energy-density matter with a multiphysics kinetic model

NASA Astrophysics Data System (ADS)

Haack, Jeffrey R.; Hauck, Cory D.; Murillo, Michael S.

2017-12-01

We have extended a recently developed multispecies, multitemperature Bhatnagar-Gross-Krook model [Haack et al., J. Stat. Phys. 168, 822 (2017), 10.1007/s10955-017-1824-9], to include multiphysics capabilities that enable modeling of a wider range of physical conditions. In terms of geometry, we have extended from the spatially homogeneous setting to one spatial dimension. In terms of the physics, we have included an atomic ionization model, accurate collision physics across coupling regimes, self-consistent electric fields, and degeneracy in the electronic screening. We apply the model to a warm dense matter scenario in which the ablator-fuel interface of an inertial confinement fusion target is heated, but for larger length and time scales and for much higher temperatures than can be simulated using molecular dynamics. Relative to molecular dynamics, the kinetic model greatly extends the temperature regime and the spatiotemporal scales over which we are able to model. In our numerical results we observe hydrogen from the ablator material jetting into the fuel during the early stages of the implosion and compare the relative size of various diffusion components (Fickean diffusion, electrodiffusion, and barodiffusion) that drive this process. We also examine kinetic effects, such as anisotropic distributions and velocity separation, in order to determine when this problem can be described with a hydrodynamic model.

Hydrolysis kinetics in anaerobic degradation of particulate organic material: an overview.

PubMed

Vavilin, V A; Fernandez, B; Palatsi, J; Flotats, X

2008-01-01

The applicability of different kinetics to the hydrolysis of particulate organic material in anaerobic digestion is discussed. Hydrolysis has traditionally been modelled according to the first-order kinetics. For complex substrate, the first-order kinetics should be modified in order to take into account hardly degradable material. It has been shown that models in which hydrolysis is coupled to the growth of hydrolytic bacteria work well at high or at fluctuant organic loading. In particular, the surface-related two-phase and the Contois models showed good fits to experimental data from a wide range of organic waste. Both models tend to the first-order kinetics at a high biomass-to-waste ratio and, for this reason, they can be considered as more general models. Examples on different inhibition processes that might affect the degradation of solid waste are reported. Acetogenesis or methanogenesis might be the rate-limiting stages in complex waste. In such cases, stimulation of hydrolysis (mechanically, chemically or biologically) may lead to a further inhibition of these stages, which ultimately affects hydrolysis as well. Since the hydrolysis process is characterized by surface and transport phenomena, new developments in spatially distributed models are considered fundamental to provide new insights in this complex process.

Transient Simulation of the Multi-SERTTA Experiment with MAMMOTH

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

Ortensi, Javier; Baker, Benjamin; Wang, Yaqi

This work details the MAMMOTH reactor physics simulations of the Static Environment Rodlet Transient Test Apparatus (SERTTA) conducted at Idaho National Laboratory in FY-2017. TREAT static-environment experiment vehicles are being developed to enable transient testing of Pressurized Water Reactor (PWR) type fuel specimens, including fuel concepts with enhanced accident tolerance (Accident Tolerant Fuels, ATF). The MAMMOTH simulations include point reactor kinetics as well as spatial dynamics for a temperature-limited transient. The strongly coupled multi-physics solutions of the neutron flux and temperature fields are second order accurate both in the spatial and temporal domains. MAMMOTH produces pellet stack powers that are within 1.5% of the Monte Carlo reference solutions. Some discrepancies between the MCNP model used in the design of the flux collars and the Serpent/MAMMOTH models lead to higher power and energy deposition values in Multi-SERTTA unit 1. The TREAT core results compare well with the safety case computed with point reactor kinetics in RELAP5-3D. The reactor period is 44 msec, which corresponds to a reactivity insertion of 2.685% delta k/kmore » $. The peak core power in the spatial dynamics simulation is 431 MW, which the point kinetics model over-predicts by 12%. The pulse width at half the maximum power is 0.177 sec. Subtle transient effects are apparent at the beginning insertion in the experimental samples due to the control rod removal. Additional difference due to transient effects are observed in the sample powers and enthalpy. The time dependence of the power coupling factor (PCF) is calculated for the various fuel stacks of the Multi-SERTTA vehicle. Sample temperatures in excess of 3100 K, the melting point UO$$_2$$, are computed with the adiabatic heat transfer model. The planned shaped-transient might introduce additional effects that cannot be predicted with PRK models. Future modeling will be focused on the shaped-transient by improving the control rod models in MAMMOTH and adding the BISON thermo-elastic models and thermal-fluids heat transfer.« less

Synchronization of three electrochemical oscillators: From local to global coupling

NASA Astrophysics Data System (ADS)

Liu, Yifan; Sebek, Michael; Mori, Fumito; Kiss, István Z.

2018-04-01

We investigate the formation of synchronization patterns in an oscillatory nickel electrodissolution system in a network obtained by superimposing local and global coupling with three electrodes. We explored the behavior through numerical simulations using kinetic ordinary differential equations, Kuramoto type phase models, and experiments, in which the local to global coupling could be tuned by cross resistances between the three nickel wires. At intermediate coupling strength with predominant global coupling, two of the three oscillators, whose natural frequencies are closer, can synchronize. By adding even a relatively small amount of local coupling (about 9%-25%), a spatially organized partially synchronized state can occur where one of the two synchronized elements is in the center. A formula was derived for predicting the critical coupling strength at which full synchronization will occur independent of the permutation of the natural frequencies of the oscillators over the network. The formula correctly predicts the variation of the critical coupling strength as a function of the global coupling fraction, e.g., with local coupling the critical coupling strength is about twice than that required with global coupling. The results show the importance of the topology of the network on the synchronization properties in a simple three-oscillator setup and could provide guidelines for decrypting coupling topology from identification of synchronization patterns.

Spin Hall and Spin Swapping Torques in Diffusive Ferromagnets

NASA Astrophysics Data System (ADS)

Pauyac, Christian Ortiz; Chshiev, Mairbek; Manchon, Aurelien; Nikolaev, Sergey A.

2018-04-01

A complete set of the generalized drift-diffusion equations for a coupled charge and spin dynamics in ferromagnets in the presence of extrinsic spin-orbit coupling is derived from the quantum kinetic approach, covering major transport phenomena, such as the spin and anomalous Hall effects, spin swapping, spin precession, and relaxation processes. We argue that the spin swapping effect in ferromagnets is enhanced due to spin polarization, while the overall spin texture induced by the interplay of spin-orbital and spin precession effects displays a complex spatial dependence that can be exploited to generate torques and nucleate or propagate domain walls in centrosymmetric geometries without the use of external polarizers, as opposed to the conventional understanding of spin-orbit mediated torques.

Interfacial mixing in high energy-density matter with a multiphysics kinetic model

NASA Astrophysics Data System (ADS)

Haack, Jeff; Hauck, Cory; Murillo, Michael

2017-10-01

We have extended a recently-developed multispecies, multitemperature BGK model to include multiphysics capability that allows modeling of a wider range of plasma conditions. In particular, we have extended the model to describe one spatial dimension, and included a multispecies atomic ionization model, accurate collision physics across coupling regimes, self-consistent electric fields, and degeneracy in the electronic screening. We apply the new model to a warm dense matter scenario in which the ablator-fuel interface of an inertial confinement fusion target is heated, similar to a recent molecular dynamics study, but for larger length and time scales and for much higher temperatures. From our numerical results we are able to explore a variety of phenomena, including hydrogen jetting, kinetic effects (non-Maxwellian and anisotropic distributions), plasma physics (size, persistence and role of electric fields) and transport (relative sizes of Fickean diffision, electrodiffusion and barodiffusion). As compared with the recent molecular dynamics work the kinetic model greatly extends the accessible physical domains we are able to model.

Parametrization of Drag and Turbulence for Urban Neighbourhoods with Trees

NASA Astrophysics Data System (ADS)

Krayenhoff, E. S.; Santiago, J.-L.; Martilli, A.; Christen, A.; Oke, T. R.

2015-08-01

Urban canopy parametrizations designed to be coupled with mesoscale models must predict the integrated effect of urban obstacles on the flow at each height in the canopy. To assess these neighbourhood-scale effects, results of microscale simulations may be horizontally-averaged. Obstacle-resolving computational fluid dynamics (CFD) simulations of neutrally-stratified flow through canopies of blocks (buildings) with varying distributions and densities of porous media (tree foliage) are conducted, and the spatially-averaged impacts on the flow of these building-tree combinations are assessed. The accuracy with which a one-dimensional (column) model with a one-equation (-) turbulence scheme represents spatially-averaged CFD results is evaluated. Individual physical mechanisms by which trees and buildings affect flow in the column model are evaluated in terms of relative importance. For the treed urban configurations considered, effects of buildings and trees may be considered independently. Building drag coefficients and length scale effects need not be altered due to the presence of tree foliage; therefore, parametrization of spatially-averaged flow through urban neighbourhoods with trees is greatly simplified. The new parametrization includes only source and sink terms significant for the prediction of spatially-averaged flow profiles: momentum drag due to buildings and trees (and the associated wake production of turbulent kinetic energy), modification of length scales by buildings, and enhanced dissipation of turbulent kinetic energy due to the small scale of tree foliage elements. Coefficients for the Santiago and Martilli (Boundary-Layer Meteorol 137: 417-439, 2010) parametrization of building drag coefficients and length scales are revised. Inclusion of foliage terms from the new parametrization in addition to the Santiago and Martilli building terms reduces root-mean-square difference (RMSD) of the column model streamwise velocity component and turbulent kinetic energy relative to the CFD model by 89 % in the canopy and 71 % above the canopy on average for the highest leaf area density scenarios tested: . RMSD values with the new parametrization are less than 20 % of mean layer magnitude for the streamwise velocity component within and above the canopy, and for above-canopy turbulent kinetic energy; RMSD values for within-canopy turbulent kinetic energy are negligible for most scenarios. The foliage-related portion of the new parametrization is required for scenarios with tree foliage of equal or greater height than the buildings, and for scenarios with foliage below roof height for building plan area densities less than approximately 0.25.

Fabrication of an Absorber-Coupled MKID Detector and Readout for Sub-Millimeter and Far-Infrared Astronomy

NASA Technical Reports Server (NTRS)

Brown, Ari-David; Hsieh, Wen-Ting; Moseley, S. Harvey; Stevenson, Thomas R.; U-yen, Kongpop; Wollack, Edward J.

2010-01-01

We have fabricated absorber-coupled microwave kinetic inductance detector (MKID) arrays for sub-millimeter and far-infrared astronomy. Each detector array is comprised of lambda/2 stepped impedance resonators, a 1.5 micrometer thick silicon membrane, and 380 micrometer thick silicon walls. The resonators consist of parallel plate aluminum transmission lines coupled to low impedance Nb microstrip traces of variable length, which set the resonant frequency of each resonator. This allows for multiplexed microwave readout and, consequently, good spatial discrimination between pixels in the array. The Al transmission lines simultaneously act to absorb optical power and are designed to have a surface impedance and filling fraction so as to match the impedance of free space. Our novel fabrication techniques demonstrate high fabrication yield of MKID arrays on large single crystal membranes and sub-micron front-to-back alignment of the microstrip circuit.

Fabrication of an Absorber-Coupled MKID Detector and Readout for Sub-Millimeter and Far-Infrared Astronomy

NASA Technical Reports Server (NTRS)

Brown, Ari-David; Hsieh, Wen-Ting; Moseley, S. Harvey; Stevenson, Thomas R.; U-yen, Kongpop; Wollack, Edward J.

2010-01-01

We have fabricated absorber-coupled microwave kinetic inductance detector (MKID) arrays for sub-millimeter and farinfrared astronomy. Each detector array is comprised of lambda/2 stepped impedance resonators, a 1.5µm thick silicon membrane, and 380µm thick silicon walls. The resonators consist of parallel plate aluminum transmission lines coupled to low impedance Nb microstrip traces of variable length, which set the resonant frequency of each resonator. This allows for multiplexed microwave readout and, consequently, good spatial discrimination between pixels in the array. The Al transmission lines simultaneously act to absorb optical power and are designed to have a surface impedance and filling fraction so as to match the impedance of free space. Our novel fabrication techniques demonstrate high fabrication yield of MKID arrays on large single crystal membranes and sub-micron front-to-back alignment of the microstrip circuit.

Emergent dynamics of Cucker-Smale particles under the effects of random communication and incompressible fluids

NASA Astrophysics Data System (ADS)

Ha, Seung-Yeal; Xiao, Qinghua; Zhang, Xiongtao

2018-04-01

We study the dynamics of infinitely many Cucker-Smale (C-S) flocking particles under the interplay of random communication and incompressible fluids. For the dynamics of an ensemble of flocking particles, we use the kinetic Cucker-Smale-Fokker-Planck (CS-FP) equation with a degenerate diffusion, whereas for the fluid component, we use the incompressible Navier-Stokes (N-S) equations. These two subsystems are coupled via the drag force. For this coupled model, we present the global existence of weak and strong solutions in Rd (d = 2 , 3). Under the extra regularity assumptions of the initial data, the unique solvability of strong solutions is also established in R2. In a large coupling regime and periodic spatial domain T2 : =R2 /Z2, we show that the velocities of C-S particles and fluids are asymptotically aligned to two constant velocities which may be different.

Hydrogen atom kinetics in capacitively coupled plasmas

NASA Astrophysics Data System (ADS)

Nunomura, Shota; Katayama, Hirotaka; Yoshida, Isao

2017-05-01

Hydrogen (H) atom kinetics has been investigated in capacitively coupled very high frequency (VHF) discharges at powers of 16-780 mW cm-2 and H2 gas pressures of 0.1-2 Torr. The H atom density has been measured using vacuum ultra violet absorption spectroscopy (VUVAS) with a micro-discharge hollow cathode lamp as a VUV light source. The measurements have been performed in two different electrode configurations of discharges: conventional parallel-plate diode and triode with an intermediate mesh electrode. We find that in the triode configuration, the H atom density is strongly reduced across the mesh electrode. The H atom density varies from ˜1012 cm-3 to ˜1010 cm-3 by crossing the mesh with 0.2 mm in thickness and 36% in aperture ratio. The fluid model simulations for VHF discharge plasmas have been performed to study the H atom generation, diffusion and recombination kinetics. The simulations suggest that H atoms are generated in the bulk plasma, by the electron impact dissociation (e + H2 \\to e + 2H) and the ion-molecule reaction (H2 + + H2 \\to {{{H}}}3+ + H). The diffusion of H atoms is strongly limited by a mesh electrode, and thus the mesh geometry influences the spatial distribution of the H atoms. The loss of H atoms is dominated by the surface recombination.

Joint reconstruction of dynamic PET activity and kinetic parametric images using total variation constrained dictionary sparse coding

NASA Astrophysics Data System (ADS)

Yu, Haiqing; Chen, Shuhang; Chen, Yunmei; Liu, Huafeng

2017-05-01

Dynamic positron emission tomography (PET) is capable of providing both spatial and temporal information of radio tracers in vivo. In this paper, we present a novel joint estimation framework to reconstruct temporal sequences of dynamic PET images and the coefficients characterizing the system impulse response function, from which the associated parametric images of the system macro parameters for tracer kinetics can be estimated. The proposed algorithm, which combines statistical data measurement and tracer kinetic models, integrates a dictionary sparse coding (DSC) into a total variational minimization based algorithm for simultaneous reconstruction of the activity distribution and parametric map from measured emission sinograms. DSC, based on the compartmental theory, provides biologically meaningful regularization, and total variation regularization is incorporated to provide edge-preserving guidance. We rely on techniques from minimization algorithms (the alternating direction method of multipliers) to first generate the estimated activity distributions with sub-optimal kinetic parameter estimates, and then recover the parametric maps given these activity estimates. These coupled iterative steps are repeated as necessary until convergence. Experiments with synthetic, Monte Carlo generated data, and real patient data have been conducted, and the results are very promising.

E-H heating mode transition in inductive discharges with different antenna sizes

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

Lee, Hyo-Chang, E-mail: flower4507@hanyang.ac.kr; Chung, Chin-Wook, E-mail: joykang@hanyang.ac.kr

The spatial distribution of plasma density and the transition power for capacitive (E) to inductive (H) mode transition are studied in planar type inductively coupled plasmas with different antenna sizes. The spatial plasma distribution has a relatively flat profile at a low gas pressure, while the plasma profile is affected by the antenna size at higher gas pressure. The transition power for the E to H mode transition is shown to be critically affected by the antenna size. When the discharge is sustained by a small one-turn antenna coil, the transition power has a minimum value at Ar gas ofmore » 20 mTorr. However, the minimum transition power is shown at a relatively high gas pressure (40–60 mTorr) in the case of a large one-turn antenna coil. This change in the transition power can be understood by the thermal transport of the energetic electrons with non-local kinetics to the chamber wall. This non-local kinetic effect indicates that the transition power can also increase even for a small antenna if the antenna is placed near the wall.« less

On the Nonequilibrium Interface Kinetics of Rapid Coupled Eutectic Growth

NASA Astrophysics Data System (ADS)

Dong, H.; Chen, Y. Z.; Shan, G. B.; Zhang, Z. R.; Liu, F.

2017-08-01

Nonequilibrium interface kinetics (NEIK) is expected to play an important role in coupled growth of eutectic alloys, when solidification velocity is high and intermetallic compound or topologically complex phases form in the crystallized product. In order to quantitatively evaluate the effect of NEIK on the rapid coupled eutectic growth, in this work, two nonequilibrium interface kinetic effects, i.e., atom attachment and solute trapping at the solid-liquid interface, were incorporated into the analyses of the coupled eutectic growth under the rapid solidification condition. First, a coupled growth model incorporating the preceding two nonequilibrium kinetic effects was derived. On this basis, an expression of kinetic undercooling (Δ T k), which is used to characterize the NEIK, was defined. The calculations based on the as-derived couple growth model show good agreement with the reported experimental results achieved in rapidly solidified eutectic Al-Sm alloys consisting of a solid solution phase ( α-Al) and an intermetallic compound phase (Al11Sm3). In terms of the definition of Δ T k defined in this work, the role of NEIK in the coupled growth of the Al-Sm eutectic system was analyzed. The results show that with increasing the coupled growth velocity, Δ T k increases continuously, and its ratio to the total undercooling reaches 0.32 at the maximum growth velocity for coupled eutectic growth. Parametric analyses on two key alloy parameters that influence Δ T k, i.e., interface kinetic parameter ( μ i ) and solute distribution coefficient ( k e ), indicate that both μ i and k e influence the NEIK significantly and the decrease of either these two parameters enhances the NEIK effect.

A semi-Lagrangian transport method for kinetic problems with application to dense-to-dilute polydisperse reacting spray flows

NASA Astrophysics Data System (ADS)

Doisneau, François; Arienti, Marco; Oefelein, Joseph C.

2017-01-01

For sprays, as described by a kinetic disperse phase model strongly coupled to the Navier-Stokes equations, the resolution strategy is constrained by accuracy objectives, robustness needs, and the computing architecture. In order to leverage the good properties of the Eulerian formalism, we introduce a deterministic particle-based numerical method to solve transport in physical space, which is simple to adapt to the many types of closures and moment systems. The method is inspired by the semi-Lagrangian schemes, developed for Gas Dynamics. We show how semi-Lagrangian formulations are relevant for a disperse phase far from equilibrium and where the particle-particle coupling barely influences the transport; i.e., when particle pressure is negligible. The particle behavior is indeed close to free streaming. The new method uses the assumption of parcel transport and avoids to compute fluxes and their limiters, which makes it robust. It is a deterministic resolution method so that it does not require efforts on statistical convergence, noise control, or post-processing. All couplings are done among data under the form of Eulerian fields, which allows one to use efficient algorithms and to anticipate the computational load. This makes the method both accurate and efficient in the context of parallel computing. After a complete verification of the new transport method on various academic test cases, we demonstrate the overall strategy's ability to solve a strongly-coupled liquid jet with fine spatial resolution and we apply it to the case of high-fidelity Large Eddy Simulation of a dense spray flow. A fuel spray is simulated after atomization at Diesel engine combustion chamber conditions. The large, parallel, strongly coupled computation proves the efficiency of the method for dense, polydisperse, reacting spray flows.

A semi-Lagrangian transport method for kinetic problems with application to dense-to-dilute polydisperse reacting spray flows

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

Doisneau, François, E-mail: fdoisne@sandia.gov; Arienti, Marco, E-mail: marient@sandia.gov; Oefelein, Joseph C., E-mail: oefelei@sandia.gov

For sprays, as described by a kinetic disperse phase model strongly coupled to the Navier–Stokes equations, the resolution strategy is constrained by accuracy objectives, robustness needs, and the computing architecture. In order to leverage the good properties of the Eulerian formalism, we introduce a deterministic particle-based numerical method to solve transport in physical space, which is simple to adapt to the many types of closures and moment systems. The method is inspired by the semi-Lagrangian schemes, developed for Gas Dynamics. We show how semi-Lagrangian formulations are relevant for a disperse phase far from equilibrium and where the particle–particle coupling barelymore » influences the transport; i.e., when particle pressure is negligible. The particle behavior is indeed close to free streaming. The new method uses the assumption of parcel transport and avoids to compute fluxes and their limiters, which makes it robust. It is a deterministic resolution method so that it does not require efforts on statistical convergence, noise control, or post-processing. All couplings are done among data under the form of Eulerian fields, which allows one to use efficient algorithms and to anticipate the computational load. This makes the method both accurate and efficient in the context of parallel computing. After a complete verification of the new transport method on various academic test cases, we demonstrate the overall strategy's ability to solve a strongly-coupled liquid jet with fine spatial resolution and we apply it to the case of high-fidelity Large Eddy Simulation of a dense spray flow. A fuel spray is simulated after atomization at Diesel engine combustion chamber conditions. The large, parallel, strongly coupled computation proves the efficiency of the method for dense, polydisperse, reacting spray flows.« less

Analytical approach to impurity transport studies: Charge state dynamics in tokamak plasmas

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

Shurygin, V. A.

2006-08-15

Ionization and recombination of plasma impurities govern their charge state kinetics, which is imposed upon the dynamics of ions that implies a superposition of the appropriate probabilities and causes an impurity charge state dynamics. The latter is considered in terms of a vector field of conditional probabilities and presented by a vector charge state distribution function with coupled equations of the Kolmogorov type. Analytical solutions of a diffusion problem are derived with the basic spatial and temporal dimensionless parameters. Analysis shows that the empirical scaling D{sub A}{proportional_to}n{sub e}{sup -1} [K. Krieger, G. Fussmann, and the ASDEX Upgrade Team, Nucl. Fusionmore » 30, 2392 (1990)] can be explained by the ratio of the diffusive and kinetic terms, D{sub A}/(n{sub e}a{sup 2}), being used instead of diffusivity, D{sub A}. The derived time scales of charge state dynamics are given by a sum of the diffusive and kinetic times. Detailed simulations of charge state dynamics are performed for argon impurity and compared with the reference modeling.« less

On the structures and mapping of auroral electrostatic potentials

NASA Technical Reports Server (NTRS)

Chiu, Y. T.; Newman, A. L.; Cornwall, J. M.

1981-01-01

The mapping of magnetospheric and ionospheric electric fields in a kinetic model of magnetospheric-ionospheric electrodynamic coupling proposed for the aurora is examined. One feature is the generalization of the kinetic current-potential relationship to the return current region (identified as a region where the parallel drop from magnetosphere to ionosphere is positive); such a return current always exists unless the ionosphere is electrically charged to grossly unphysical values. A coherent phenomenological picture of both the low energy return current and the high energy precipitation of an inverted-V is given. The mapping between magnetospheric and ionospheric electric fields is phrased in terms of a Green's function which acts as a filter, emphasizing magnetospheric latitudinal spatial scales of order (when mapped to the ionosphere) 50 to 150 km. This same length, when multiplied by electric fields just above the ionosphere, sets the scale for potential drops between the ionosphere and equatorial magnetosphere.

Cyclic Voltammetric Wave-Shapes for Microdisk Electrodes: Coupled Effects of Solution Resistance, Double-Layer Capacitance, and Finite Electrochemical Kinetics

DTIC Science & Technology

1991-05-01

vaveshapea. While the use of high scan rates enhances the effect of electrode kinetics upon the voltametry , the deleterious coupled influence of pa 20...waveshapes. While the use of high scan rates enhances the effect of electrode kinetics upon the voltametry , the deleterious coupled influence of P...2 1 󈧚 Aoki et al have in- 23 vestigated linear sweep voltammetry at microdisks in the reversible case, and Zoski and co-workers have developed

Enhanced reaction kinetics and reactive mixing scale dynamics in mixing fronts under shear flow for arbitrary Damköhler numbers

NASA Astrophysics Data System (ADS)

Bandopadhyay, Aditya; Le Borgne, Tanguy; Méheust, Yves; Dentz, Marco

2017-02-01

Mixing fronts, where fluids of different chemical compositions mix with each other, are known to represent hotspots of chemical reaction in hydrological systems. These fronts are typically subjected to velocity gradients, ranging from the pore scale due to no slip boundary conditions at fluid solid interfaces, to the catchment scale due to permeability variations and complex geometry of the Darcy velocity streamlines. A common trait of these processes is that the mixing interface is strained by shear. Depending on the Péclet number Pe , which represents the ratio of the characteristic diffusion time to the characteristic shear time, and the Damköhler number Da , which represents the ratio of the characteristic diffusion time to the characteristic reaction time, the local reaction rates can be strongly impacted by the dynamics of the mixing interface. So far, this impact has been characterized mostly either in kinetics-limited or in mixing-limited conditions, that is, for either low or high Da. Here the coupling of shear flow and chemical reactivity is investigated for arbitrary Damköhler numbers, for a bimolecular reaction and an initial interface with separated reactants. Approximate analytical expressions for the global production rate and reactive mixing scale are derived based on a reactive lamella approach that allows for a general coupling between stretching enhanced mixing and chemical reactions. While for Pe < Da , reaction kinetics and stretching effects are decoupled, a scenario which we name "weak stretching", for Pe > Da , we uncover a "strong stretching" scenario where new scaling laws emerge from the interplay between reaction kinetics, diffusion, and stretching. The analytical results are validated against numerical simulations. These findings shed light on the effect of flow heterogeneity on the enhancement of chemical reaction and the creation of spatially localized hotspots of reactivity for a broad range of systems ranging from kinetic limited to mixing limited situations.

Fluid-structure interaction of turbulent boundary layer over a compliant surface

NASA Astrophysics Data System (ADS)

Anantharamu, Sreevatsa; Mahesh, Krishnan

2016-11-01

Turbulent flows induce unsteady loads on surfaces in contact with them, which affect material stresses, surface vibrations and far-field acoustics. We are developing a numerical methodology to study the coupled interaction of a turbulent boundary layer with the underlying surface. The surface is modeled as a linear elastic solid, while the fluid follows the spatially filtered incompressible Navier-Stokes equations. An incompressible Large Eddy Simulation finite volume flow approach based on the algorithm of Mahesh et al. is used in the fluid domain. The discrete kinetic energy conserving property of the method ensures robustness at high Reynolds number. The linear elastic model in the solid domain is integrated in space using finite element method and in time using the Newmark time integration method. The fluid and solid domain solvers are coupled using both weak and strong coupling methods. Details of the algorithm, validation, and relevant results will be presented. This work is supported by NSWCCD, ONR.

Numerical Investigations of Subduction of Eighteen Degree Water in the Subtropical Northwest Atlantic Ocean

NASA Astrophysics Data System (ADS)

Zhai, P.; He, R.

2016-02-01

Mode waters are upper-ocean water masses with nearly uniform water properties over a thickness of a few hundred meters. Subduction of mode waters plays an important role in changing atmospheric and oceanic long-term variability because they store "memory" of wintertime air-sea interaction. In this study, we investigated dynamic processes associated with subduction of the Eighteen Degree Water (EDW, the principal mode water) in the subtropical Northwest Atlantic during January to June 2007. Numerical simulations of the temporal and spatial evolutions of EDW were performed using both uncoupled (ocean only) and air-sea coupled configurations and results were contrasted. We find the coupled simulation produced deeper mixed layer depth, stronger eddy kinetic energy, and larger subduction areas than their counterparts in the uncoupled ocean simulation. In both configurations, mesoscale eddies enhance the total subduction and eddy-induced subduction has the same order as the mean component. Resolving strong air-sea coupling and mesoscale eddies is therefore important for understanding EDW dynamics.

Lateral carrier diffusion in InGaAs/GaAs coupled quantum dot-quantum well system

NASA Astrophysics Data System (ADS)

Pieczarka, M.; Syperek, M.; Biegańska, D.; Gilfert, C.; Pavelescu, E. M.; Reithmaier, J. P.; Misiewicz, J.; Sek, G.

2017-05-01

The lateral carrier diffusion process is investigated in coupled InGaAs/GaAs quantum dot-quantum well (QD-QW) structures by means of spatially resolved photoluminescence spectroscopy at low temperature. Under non-resonant photo-excitation above the GaAs bandgap, the lateral carrier transport reflected in the distorted electron-hole pair emission profiles is found to be mainly governed by high energy carriers created within the 3D density of states of GaAs. In contrast, for the case of resonant excitation tuned to the QW-like ground state of the QD-QW system, the emission profiles remain unaffected by the excess kinetic energy of carriers and local phonon heating within the pump spot. The lateral diffusion lengths are determined and present certain dependency on the coupling strength between QW and QDs. While for a strongly coupled structure the diffusion length is found to be around 0.8 μm and monotonically increases up to 1.4 μm with the excitation power density, in weakly coupled structures, it is determined to ca. 1.6 μm and remained virtually independent of the pumping power density.

Inflationary magneto-(non)genesis, increasing kinetic couplings, and the strong coupling problem

NASA Astrophysics Data System (ADS)

Bazrafshan Moghaddam, Hossein; McDonough, Evan; Namba, Ryo; Brandenberger, Robert H.

2018-05-01

We study the generation of magnetic fields during inflation making use of a coupling of the inflaton and moduli fields to electromagnetism via the photon kinetic term, and assuming that the coupling is an increasing function of time. We demonstrate that the strong coupling problem of inflationary magnetogenesis can be avoided by incorporating the destabilization of moduli fields after inflation. The magnetic field always dominates over the electric one, and thus the severe constraints on the latter from backreaction, which are the demanding obstacles in the case of a decreasing coupling function, do not apply to the current scenario. However, we show that this loophole to the strong coupling problem comes at a price: the normalization of the amplitude of magnetic fields is determined by this coupling term and is therefore suppressed by a large factor after the moduli destabilization completes. From this we conclude that there is no self-consistent and generic realization of primordial magnetogenesis producing scale-invariant fields in the case of an increasing kinetic coupling.

Nonminimal kinetic coupled gravity: Inflation on the warped DGP brane

NASA Astrophysics Data System (ADS)

Darabi, F.; Parsiya, A.; Atazadeh, K.

2016-03-01

We consider the nonminimally kinetic coupled version of DGP brane model, where the kinetic term of the scalar field is coupled to the metric and Einstein tensor on the brane by a coupling constant ζ. We obtain the corresponding field equations, using the Friedmann-Robertson-Walker metric and the perfect fluid, and study the inflationary scenario to confront the numerical analysis of six typical scalar field potentials with the current observational results. We find that among the suggested potentials and coupling constants, subject to the e-folding N = 60, the potentials V (ϕ) = σϕ, V (ϕ) = σϕ2 and V (ϕ) = σϕ3 provide the best fits with both Planck+WP+highL data and Planck+WP+highL+BICEP2 data.

Reactor for in situ measurements of spatially resolved kinetic data in heterogeneous catalysis

NASA Astrophysics Data System (ADS)

Horn, R.; Korup, O.; Geske, M.; Zavyalova, U.; Oprea, I.; Schlögl, R.

2010-06-01

The present work describes a reactor that allows in situ measurements of spatially resolved kinetic data in heterogeneous catalysis. The reactor design allows measurements up to temperatures of 1300 °C and 45 bar pressure, i.e., conditions of industrial relevance. The reactor involves reactants flowing through a solid catalyst bed containing a sampling capillary with a side sampling orifice through which a small fraction of the reacting fluid (gas or liquid) is transferred into an analytical device (e.g., mass spectrometer, gas chromatograph, high pressure liquid chromatograph) for quantitative analysis. The sampling capillary can be moved with μm resolution in or against flow direction to measure species profiles through the catalyst bed. Rotation of the sampling capillary allows averaging over several scan lines. The position of the sampling orifice is such that the capillary channel through the catalyst bed remains always occupied by the capillary preventing flow disturbance and fluid bypassing. The second function of the sampling capillary is to provide a well which can accommodate temperature probes such as a thermocouple or a pyrometer fiber. If a thermocouple is inserted in the sampling capillary and aligned with the sampling orifice fluid temperature profiles can be measured. A pyrometer fiber can be used to measure the temperature profile of the solid catalyst bed. Spatial profile measurements are demonstrated for methane oxidation on Pt and methane oxidative coupling on Li/MgO, both catalysts supported on reticulated α -Al2O3 foam supports.

Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling

PubMed Central

Kekenes-Huskey, Peter M.; Eun, Changsun; McCammon, J. A.

2015-01-01

Biochemical reaction networks consisting of coupled enzymes connect substrate signaling events with biological function. Substrates involved in these reactions can be strongly influenced by diffusion “barriers” arising from impenetrable cellular structures and macromolecules, as well as interactions with biomolecules, especially within crowded environments. For diffusion-influenced reactions, the spatial organization of diffusion barriers arising from intracellular structures, non-specific crowders, and specific-binders (buffers) strongly controls the temporal and spatial reaction kinetics. In this study, we use two prototypical biochemical reactions, a Goodwin oscillator, and a reaction with a periodic source/sink term to examine how a diffusion barrier that partitions substrates controls reaction behavior. Namely, we examine how conditions representative of a densely packed cytosol, including reduced accessible volume fraction, non-specific interactions, and buffers, impede diffusion over nanometer length-scales. We find that diffusion barriers can modulate the frequencies and amplitudes of coupled diffusion-influenced reaction networks, as well as give rise to “compartments” of decoupled reactant populations. These effects appear to be intensified in the presence of buffers localized to the diffusion barrier. These findings have strong implications for the role of the cellular environment in tuning the dynamics of signaling pathways. PMID:26342355

Cutoff for extensions of massive gravity and bi-gravity

NASA Astrophysics Data System (ADS)

Matas, Andrew

2016-04-01

Recently there has been interest in extending ghost-free massive gravity, bi-gravity, and multi-gravity by including non-standard kinetic terms and matter couplings. We first review recent proposals for this class of extensions, emphasizing how modifications of the kinetic and potential structure of the graviton and modifications of the coupling to matter are related. We then generalize existing no-go arguments in the metric language to the vielbein language in second-order form. We give an ADM argument to show that the most promising extensions to the kinetic term and matter coupling contain a Boulware-Deser ghost. However, as recently emphasized, we may still be able to view these extensions as effective field theories below some cutoff scale. To address this possibility, we show that there is a decoupling limit where a ghost appears for a wide class of matter couplings and kinetic terms. In particular, we show that there is a decoupling limit where the linear effective vielbein matter coupling contains a ghost. Using the insight we gain from this decoupling limit analysis, we place an upper bound on the cutoff for the linear effective vielbein coupling. This result can be generalized to new kinetic interactions in the vielbein language in second-order form. Combined with recent results, this provides a strong uniqueness argument on the form of ghost-free massive gravity, bi-gravity, and multi-gravity.

TU-C-12A-11: Comparisons Between Cu-ATSM PET and DCE-CT Kinetic Parameters in Canine Sinonasal Tumors

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

La Fontaine, M; Bradshaw, T; Kubicek, L

2014-06-15

Purpose: Regions of poor perfusion within tumors may be associated with higher hypoxic levels. This study aimed to test this hypothesis by comparing measurements of hypoxia from Cu-ATSM PET to vasculature kinetic parameters from DCE-CT kinetic analysis. Methods: Ten canine patients with sinonasal tumors received one Cu-ATSM PET/CT scan and three DCE-CT scans prior to treatment. Cu-ATSM PET/CT and DCE-CT scans were registered and resampled to matching voxel dimensions. Kinetic analysis was performed on DCE-CT scans and for each patient, the resulting kinetic parameter values from the three DCE-CT scans were averaged together. Cu-ATSM SUVs were spatially correlated (r{sub spatial})more » on a voxel-to-voxel basis against the following DCE-CT kinetic parameters: transit time (t{sub 1}), blood flow (F), vasculature fraction (v{sub 1}), and permeability (PS). In addition, whole-tumor comparisons were performed by correlating (r{sub ROI}) the mean Cu-ATSM SUV (SUV{sub mean}) with median kinetic parameter values. Results: The spatial correlations (r{sub spatial}) were poor and ranged from -0.04 to 0.21 for all kinetic parameters. These low spatial correlations may be due to high variability in the DCE-CT kinetic parameter voxel values between scans. In our hypothesis, t{sub 1} was expected to have a positive correlation, while F was expected to have a negative correlation to hypoxia. However, in wholetumor analysis the opposite was found for both t{sub 1} (r{sub ROI} = -0.25) and F (r{sub ROI} = 0.56). PS and v{sub 1} may depict angiogenic responses to hypoxia and found positive correlations to Cu-ATSM SUV for PS (r{sub ROI} = 0.41), and v{sub 1} (r{sub ROI} = 0.57). Conclusion: Low spatial correlations were found between Cu-ATSM uptake and DCE-CT vasculature parameters, implying that poor perfusion is not associated with higher hypoxic regions. Across patients, the most hypoxic tumors tended to have higher blood flow values, which is contrary to our initial hypothesis. Funding: R01 CA136927.« less

Reactive Fluid Flow and Applications to Diagenesis, Mineral Deposits, and Crustal Rocks

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

Rye, Danny M.; Bolton, Edward W.

2002-11-04

The objective is to initiate new: modeling of coupled fluid flow and chemical reactions of geologic environments; experimental and theoretical studies of water-rock reactions; collection and interpretation of stable isotopic and geochemical field data at many spatial scales of systems involving fluid flow and reaction in environments ranging from soils to metamorphic rocks. Theoretical modeling of coupled fluid flow and chemical reactions, involving kinetics, has been employed to understand the differences between equilibrium, steady-state, and non-steady-state behavior of the chemical evolution of open fluid-rock systems. The numerical codes developed in this project treat multi-component, finite-rate reactions combined with advective andmore » dispersive transport in multi-dimensions. The codes incorporate heat, mass, and isotopic transfer in both porous and fractured media. Experimental work has obtained the kinetic rate laws of pertinent silicate-water reactions and the rates of Sr release during chemical weathering. Ab-initio quantum mechanical techniques have been applied to obtain the kinetics and mechanisms of silicate surface reactions and isotopic exchange between water and dissolved species. Geochemical field-based studies were carried out on the Wepawaug metamorphic schist, on the Irish base-metal sediment-hosted ore system, in the Dalradian metamorphic complex in Scotland, and on weathering in the Columbia River flood basalts. The geochemical and isotopic field data, and the experimental and theoretical rate data, were used as constraints on the numerical models and to determine the length and time scales relevant to each of the field areas.« less

Parallel Transport with Sheath and Collisional Effects in Global Electrostatic Turbulent Transport in FRCs

NASA Astrophysics Data System (ADS)

Bao, Jian; Lau, Calvin; Kuley, Animesh; Lin, Zhihong; Fulton, Daniel; Tajima, Toshiki; Tri Alpha Energy, Inc. Team

2017-10-01

Collisional and turbulent transport in a field reversed configuration (FRC) is studied in global particle simulation by using GTC (gyrokinetic toroidal code). The global FRC geometry is incorporated in GTC by using a field-aligned mesh in cylindrical coordinates, which enables global simulation coupling core and scrape-off layer (SOL) across the separatrix. Furthermore, fully kinetic ions are implemented in GTC to treat magnetic-null point in FRC core. Both global simulation coupling core and SOL regions and independent SOL region simulation have been carried out to study turbulence. In this work, the ``logical sheath boundary condition'' is implemented to study parallel transport in the SOL. This method helps to relax time and spatial steps without resolving electron plasma frequency and Debye length, which enables turbulent transports simulation with sheath effects. We will study collisional and turbulent SOL parallel transport with mirror geometry and sheath boundary condition in C2-W divertor.

A numerical study of biofilm growth in a microgravity environment

NASA Astrophysics Data System (ADS)

Aristotelous, A. C.; Papanicolaou, N. C.

2017-10-01

A mathematical model is proposed to investigate the effect of microgravity on biofilm growth. We examine the case of biofilm suspended in a quiescent aqueous nutrient solution contained in a rectangular tank. The bacterial colony is assumed to follow logistic growth whereas nutrient absorption is assumed to follow Monod kinetics. The problem is modeled by a coupled system of nonlinear partial differential equations in two spatial dimensions solved using the Discontinuous Galerkin Finite Element method. Nutrient and biofilm concentrations are computed in microgravity and normal gravity conditions. A preliminary quantitative relationship between the biofilm concentration and the gravity field intensity is derived.

Nanoscale dynamics of Joule heating and bubble nucleation in a solid-state nanopore.

PubMed

Levine, Edlyn V; Burns, Michael M; Golovchenko, Jene A

2016-01-01

We present a mathematical model for Joule heating of an electrolytic solution in a nanopore. The model couples the electrical and thermal dynamics responsible for rapid and extreme superheating of the electrolyte within the nanopore. The model is implemented numerically with a finite element calculation, yielding a time and spatially resolved temperature distribution in the nanopore region. Temperatures near the thermodynamic limit of superheat are predicted to be attained just before the explosive nucleation of a vapor bubble is observed experimentally. Knowledge of this temperature distribution enables the evaluation of related phenomena including bubble nucleation kinetics, relaxation oscillation, and bubble dynamics.

IMPACT OF OXYGEN MEDIATED OXIDATIVE COUPLING ON ADSORPTION KINETICS

EPA Science Inventory

The presence of molecular oxygen in the test environment promotes oxidative coupling (polymer formation) of phenolic compounds on the surface of granular activated carbon (GAC). Both adsorption equilibria and adsorption kinetics are affected by these chemical reactions. Lack of...

Field Effect Transistor in Nanoscale

DTIC Science & Technology

2017-04-26

analogues) and BxCyNz (Napathalene analogues with x+y+z=10) molecules using quantum many body approach coupled with kinetic (master) equations...analogues with x +y+z=10) molecules using quantum many body approach coupled with kinetic (master) equations. Interestingly, various types of non-linear...Small molecules (such as benzene), double quantum dots (like GaAs-based QDs) which are coupled weakly to metallic electrodes have shown their

Percolation, phase separation, and gelation in fluids and mixtures of spheres and rods

NASA Astrophysics Data System (ADS)

Jadrich, Ryan; Schweizer, Kenneth S.

2011-12-01

The relationship between kinetic arrest, connectivity percolation, structure and phase separation in protein, nanoparticle, and colloidal suspensions is a rich and complex problem. Using a combination of integral equation theory, connectivity percolation methods, naïve mode coupling theory, and the activated dynamics nonlinear Langevin equation approach, we study this problem for isotropic one-component fluids of spheres and variable aspect ratio rigid rods, and also percolation in rod-sphere mixtures. The key control parameters are interparticle attraction strength and its (short) spatial range, total packing fraction, and mixture composition. For spherical particles, formation of a homogeneous one-phase kinetically stable and percolated physical gel is predicted to be possible, but depends on non-universal factors. On the other hand, the dynamic crossover to activated dynamics and physical bond formation, which signals discrete cluster formation below the percolation threshold, almost always occurs in the one phase region. Rods more easily gel in the homogeneous isotropic regime, but whether a percolation or kinetic arrest boundary is reached first upon increasing interparticle attraction depends sensitively on packing fraction, rod aspect ratio and attraction range. Overall, the connectivity percolation threshold is much more sensitive to attraction range than either the kinetic arrest or phase separation boundaries. Our results appear to be qualitatively consistent with recent experiments on polymer-colloid depletion systems and brush mediated attractive nanoparticle suspensions.

Theory of activated glassy relaxation, mobility gradients, surface diffusion, and vitrification in free standing thin films

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

Mirigian, Stephen, E-mail: kschweiz@illinois.edu, E-mail: smirigian@gmail.com; Schweizer, Kenneth S., E-mail: kschweiz@illinois.edu, E-mail: smirigian@gmail.com

2015-12-28

We have constructed a quantitative, force level, statistical mechanical theory for how confinement in free standing thin films introduces a spatial mobility gradient of the alpha relaxation time as a function of temperature, film thickness, and location in the film. The crucial idea is that relaxation speeds up due to the reduction of both near-surface barriers associated with the loss of neighbors in the local cage and the spatial cutoff and dynamical softening near the vapor interface of the spatially longer range collective elasticity cost for large amplitude hopping. These two effects are fundamentally coupled. Quantitative predictions are made formore » how an apparent glass temperature depends on the film thickness and experimental probe technique, the emergence of a two-step decay and mobile layers in time domain measurements, signatures of confinement in frequency-domain dielectric loss experiments, the dependence of film-averaged relaxation times and dynamic fragility on temperature and film thickness, surface diffusion, and the relationship between kinetic experiments and pseudo-thermodynamic measurements such as ellipsometry.« less

Theory of activated glassy relaxation, mobility gradients, surface diffusion, and vitrification in free standing thin films.

PubMed

Mirigian, Stephen; Schweizer, Kenneth S

2015-12-28

We have constructed a quantitative, force level, statistical mechanical theory for how confinement in free standing thin films introduces a spatial mobility gradient of the alpha relaxation time as a function of temperature, film thickness, and location in the film. The crucial idea is that relaxation speeds up due to the reduction of both near-surface barriers associated with the loss of neighbors in the local cage and the spatial cutoff and dynamical softening near the vapor interface of the spatially longer range collective elasticity cost for large amplitude hopping. These two effects are fundamentally coupled. Quantitative predictions are made for how an apparent glass temperature depends on the film thickness and experimental probe technique, the emergence of a two-step decay and mobile layers in time domain measurements, signatures of confinement in frequency-domain dielectric loss experiments, the dependence of film-averaged relaxation times and dynamic fragility on temperature and film thickness, surface diffusion, and the relationship between kinetic experiments and pseudo-thermodynamic measurements such as ellipsometry.

A kinetics database and scripts for PHREEQC

NASA Astrophysics Data System (ADS)

Hu, B.; Zhang, Y.; Teng, Y.; Zhu, C.

2017-12-01

Kinetics of geochemical reactions has been increasingly used in numerical models to simulate coupled flow, mass transport, and chemical reactions. However, the kinetic data are scattered in the literature. To assemble a kinetic dataset for a modeling project is an intimidating task for most. In order to facilitate the application of kinetics in geochemical modeling, we assembled kinetics parameters into a database for the geochemical simulation program, PHREEQC (version 3.0). Kinetics data were collected from the literature. Our database includes kinetic data for over 70 minerals. The rate equations are also programmed into scripts with the Basic language. Using the new kinetic database, we simulated reaction path during the albite dissolution process using various rate equations in the literature. The simulation results with three different rate equations gave difference reaction paths at different time scale. Another application involves a coupled reactive transport model simulating the advancement of an acid plume in an acid mine drainage site associated with Bear Creek Uranium tailings pond. Geochemical reactions including calcite, gypsum, and illite were simulated with PHREEQC using the new kinetic database. The simulation results successfully demonstrated the utility of new kinetic database.

Non-equilibrium dynamics of artificial quantum matter

NASA Astrophysics Data System (ADS)

Babadi, Mehrtash

The rapid progress of the field of ultracold atoms during the past two decades has set new milestones in our control over matter. By cooling dilute atomic gases and molecules to nano-Kelvin temperatures, novel quantum mechanical states of matter can be realized and studied on a table-top experimental setup while bulk matter can be tailored to faithfully simulate abstract theoretical models. Two of such models which have witnessed significant experimental and theoretical attention are (1) the two-component Fermi gas with resonant s-wave interactions, and (2) the single-component Fermi gas with dipole-dipole interactions. This thesis is devoted to studying the non-equilibrium collective dynamics of these systems using the general framework of quantum kinetic theory. We present a concise review of the utilized mathematical methods in the first two chapters, including the Schwinger-Keldysh formalism of non-equilibrium quantum fields, two-particle irreducible (2PI) effective actions and the framework of quantum kinetic theory. We study the collective dynamics of the dipolar Fermi gas in a quasi-two-dimensional optical trap in chapter 3 and provide a detailed account of its dynamical crossover from the collisionless to the hydrodynamical regime. Chapter 4 is devoted to studying the dynamics of the attractive Fermi gas in the normal phase. Starting from the self-consistent T-matrix (pairing fluctuation) approximation, we systematically derive a set of quantum kinetic equations and show that they provide a globally valid description of the dynamics of the attractive Fermi gas, ranging from the weak-coupling Fermi liquid phase to the intermediate non-Fermi liquid pairing pseudogap regime and finally the strong-coupling Bose liquid phase. The shortcomings of the self-consistent T-matrix approximation in two spatial dimensions are discussed along with a proposal to overcome its unphysical behaviors. The developed kinetic formalism is finally utilized to reproduce and interpret the findings of a recent experiment done on the collective dynamics of trapped two-dimensional ultracold gases.

Nonequilibrium transition and pattern formation in a linear reaction-diffusion system with self-regulated kinetics

NASA Astrophysics Data System (ADS)

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

2018-02-01

We consider a reaction-diffusion system with linear, stochastic activator-inhibitor kinetics where the time evolution of concentration of a species at any spatial location depends on the relative average concentration of its neighbors. This self-regulating nature of kinetics brings in spatial correlation between the activator and the inhibitor. An interplay of this correlation in kinetics and disparity of diffusivities of the two species leads to symmetry breaking non-equilibrium transition resulting in stationary pattern formation. The role of initial noise strength and the linear reaction terms has been analyzed for pattern selection.

Interpretation of ES, CS, and IOS approximations within a translational-internal coupling scheme. II. Application to atom--diatom kinetic cross sections

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

Coombe, D.A.; Snider, R.F.

1980-02-15

ES, CS, and IOS approximations to atom--diatom kinetic cross sections are derived. In doing so, reduced S-matrices in a translational-internal coupling scheme are stressed. This entails the insertion of recently obtained approximate reduced S-matrices in the translational-internal coupling scheme into previously derived general expressions for the kinetic cross sections. Of special interest is the structure (rotational j quantum number dependence) of the kinetic cross sections associated with the Senftleben Beenakker effects and of pure internal state relaxation phenomena. The viscomagnetic effect is used as an illustrative example. It is found in particular that there is a great similarity of structuremore » between the energy sudden (and IOS) approximation and the previously derived distorted wave Born results.« less

Stability of gravito-coupled complex gyratory astrofluids

NASA Astrophysics Data System (ADS)

Kumar Karmakar, Pralay; Das, Papari

2017-07-01

We analyze the gravitational instability of complex rotating astrofluids in the presence of dynamic role of dark matter in a homogeneous hydrostatic equilibrium framework. The effects of the lowest-order fluid viscoelasticity, Coriolis force, fluid turbulence and inter-layer frictional coupling dynamics are concurrently considered in spatially-flat geometry. The Coriolis rotation is relative to the center of the entire fluid mass distribution, contributed by both the gyratory bright (visible) and dark (invisible) sectors, conjugated via the mutual gravitational interaction. The turbulence effects are included via the modified Larson equation of state. We use a regular Fourier-based linear perturbation analysis over the rotating fluid field equations to obtain a unique form of quartic dispersion relation with variable coefficients. We numerically carry out the dispersion analysis in two extreme limits: hydrodynamic (low-frequency) and kinetic (high-frequency) regimes. It is demonstrated that, in the former regime, the gas as well as dark matter rotations have stabilizing effects on the Jeans instability of the bi-fluidic admixture. In contrast, in the latter, the rotations play destabilizing roles on the instability. An interesting feature noted here is that the magnitude of the group velocity of the fluctuations throughout increases with both the gas and dark matter rotation frequencies, and vice-versa. We, finally, hope that the obtained results could be helpful in understanding the top-down kinetic mechanisms of bounded structure formation via gravitational collapse dynamics.

Electromagnetic studies of redox systems for energy storage

NASA Technical Reports Server (NTRS)

Wu, C. D.; Scherson, D.; Yeager, E.

1981-01-01

Both chromium and iron couples were studied on various electrode surfaces in acidic perchlorate solution by using rotating ring-disk techniques. It was found that chloride which forms inner sphere coordination complexes with the redox species enhances the electrode kinetics dramatically. The effects of lead underpotential deposition and surface alloy formation on the kinetics of the chromium couple on gold were studied using both linear sweep voltammetry and potential step techniques. The lad underpotential deposition was found to slow down the kinetics of the reduction of the Cr species on gold surfaces although increase the hydrogen overvoltage. The effect on the chromium kinetics can be explained in terms of principally a double layer effect. The underpotential deposition lead species with its positive charge results in a decrease in the concentration of the Cr species at the electrode surface. Similar phenomena were also observed with bismuth underpotential deposition on gold for the iron couple.

Hydride Transfer in DHFR by Transition Path Sampling, Kinetic Isotope Effects, and Heavy Enzyme Studies

PubMed Central

Wang, Zhen; Antoniou, Dimitri; Schwartz, Steven D.; Schramm, Vern L.

2016-01-01

Escherichia coli dihydrofolate reductase (ecDHFR) is used to study fundamental principles of enzyme catalysis. It remains controversial whether fast protein motions are coupled to the hydride transfer catalyzed by ecDHFR. Previous studies with heavy ecDHFR proteins labeled with 13C, 15N, and nonexchangeable 2H reported enzyme mass-dependent hydride transfer kinetics for ecDHFR. Here, we report refined experimental and computational studies to establish that hydride transfer is independent of protein mass. Instead, we found the rate constant for substrate dissociation to be faster for heavy DHFR. Previously reported kinetic differences between light and heavy DHFRs likely arise from kinetic steps other than the chemical step. This study confirms that fast (femtosecond to picosecond) protein motions in ecDHFR are not coupled to hydride transfer and provides an integrative computational and experimental approach to resolve fast dynamics coupled to chemical steps in enzyme catalysis. PMID:26652185

Enhanced axion-photon coupling in GUT with hidden photon

NASA Astrophysics Data System (ADS)

Daido, Ryuji; Takahashi, Fuminobu; Yokozaki, Norimi

2018-05-01

We show that the axion coupling to photons can be enhanced in simple models with a single Peccei-Quinn field, if the gauge coupling unification is realized by a large kinetic mixing χ = O (0.1) between hypercharge and unbroken hidden U(1)H. The key observation is that the U(1)H gauge coupling should be rather strong to induce such large kinetic mixing, leading to enhanced contributions of hidden matter fields to the electromagnetic anomaly. We find that the axion-photon coupling is enhanced by about a factor of 10-100 with respect to the GUT-axion models with E / N = 8 / 3.

Shear viscosity for dense plasmas by equilibrium molecular dynamics in asymmetric Yukawa ionic mixtures.

PubMed

Haxhimali, Tomorr; Rudd, Robert E; Cabot, William H; Graziani, Frank R

2015-11-01

We present molecular dynamics (MD) calculations of shear viscosity for asymmetric mixed plasma for thermodynamic conditions relevant to astrophysical and inertial confinement fusion plasmas. Specifically, we consider mixtures of deuterium and argon at temperatures of 100-500 eV and a number density of 10^{25} ions/cc. The motion of 30,000-120,000 ions is simulated in which the ions interact via the Yukawa (screened Coulomb) potential. The electric field of the electrons is included in this effective interaction; the electrons are not simulated explicitly. Shear viscosity is calculated using the Green-Kubo approach with an integral of the shear stress autocorrelation function, a quantity calculated in the equilibrium MD simulations. We systematically study different mixtures through a series of simulations with increasing fraction of the minority high-Z element (Ar) in the D-Ar plasma mixture. In the more weakly coupled plasmas, at 500 eV and low Ar fractions, results from MD compare very well with Chapman-Enskog kinetic results. In the more strongly coupled plasmas, the kinetic theory does not agree well with the MD results. We develop a simple model that interpolates between classical kinetic theories at weak coupling and the Murillo Yukawa viscosity model at higher coupling. This hybrid kinetics-MD viscosity model agrees well with the MD results over the conditions simulated, ranging from moderately weakly coupled to moderately strongly coupled asymmetric plasma mixtures.

Shear viscosity for dense plasmas by equilibrium molecular dynamics in asymmetric Yukawa ionic mixtures

NASA Astrophysics Data System (ADS)

Haxhimali, Tomorr; Rudd, Robert E.; Cabot, William H.; Graziani, Frank R.

2015-11-01

We present molecular dynamics (MD) calculations of shear viscosity for asymmetric mixed plasma for thermodynamic conditions relevant to astrophysical and inertial confinement fusion plasmas. Specifically, we consider mixtures of deuterium and argon at temperatures of 100-500 eV and a number density of 1025 ions/cc. The motion of 30 000-120 000 ions is simulated in which the ions interact via the Yukawa (screened Coulomb) potential. The electric field of the electrons is included in this effective interaction; the electrons are not simulated explicitly. Shear viscosity is calculated using the Green-Kubo approach with an integral of the shear stress autocorrelation function, a quantity calculated in the equilibrium MD simulations. We systematically study different mixtures through a series of simulations with increasing fraction of the minority high-Z element (Ar) in the D-Ar plasma mixture. In the more weakly coupled plasmas, at 500 eV and low Ar fractions, results from MD compare very well with Chapman-Enskog kinetic results. In the more strongly coupled plasmas, the kinetic theory does not agree well with the MD results. We develop a simple model that interpolates between classical kinetic theories at weak coupling and the Murillo Yukawa viscosity model at higher coupling. This hybrid kinetics-MD viscosity model agrees well with the MD results over the conditions simulated, ranging from moderately weakly coupled to moderately strongly coupled asymmetric plasma mixtures.

Evolution and enabling capabilities of spatially resolved techniques for the characterization of heterogeneously catalyzed reactions

DOE PAGES

Morgan, Kevin; Touitou, Jamal; Choi, Jae -Soon; ...

2016-01-15

The development and optimization of catalysts and catalytic processes requires knowledge of reaction kinetics and mechanisms. In traditional catalyst kinetic characterization, the gas composition is known at the inlet, and the exit flow is measured to determine changes in concentration. As such, the progression of the chemistry within the catalyst is not known. Technological advances in electromagnetic and physical probes have made visualizing the evolution of the chemistry within catalyst samples a reality, as part of a methodology commonly known as spatial resolution. Herein, we discuss and evaluate the development of spatially resolved techniques, including the evolutions and achievements ofmore » this growing area of catalytic research. The impact of such techniques is discussed in terms of the invasiveness of physical probes on catalytic systems, as well as how experimentally obtained spatial profiles can be used in conjunction with kinetic modeling. Moreover, some aims and aspirations for further evolution of spatially resolved techniques are considered.« less

1D kinetic simulations of a short glow discharge in helium

NASA Astrophysics Data System (ADS)

Yuan, Chengxun; Bogdanov, E. A.; Eliseev, S. I.; Kudryavtsev, A. A.

2017-07-01

This paper presents a 1D model of a direct current glow discharge based on the solution of the kinetic Boltzmann equation in the two-term approximation. The model takes into account electron-electron coulomb collisions, the corresponding collision integral is written in both detailed and simplified forms. The Boltzmann equation for electrons is coupled with continuity equations for ions and metastable atoms and the Poisson equation for electric potential. Simulations are carried out self-consistently for the whole length of discharge in helium (from cathode to anode) for cases p = 1 Torr, L = 3.6 cm and p = 20 Torr, L = 1.8 mm, so that pL = 3.6 cm.Torr in both cases. It is shown that simulations based on the kinetic approach give lower values of electron temperature in plasma than fluid simulations. Peaks in spatial differential flux corresponding to the electrons originating from superelastic collisions and Penning ionization were observed in simulations. Different approaches of taking coulomb collisions into account give significantly different values of electron density and electron temperature in plasma. Analysis showed that using a simplified approach gives a non-zero contribution to the electron energy balance, which is comparable to energy losses on elastic and inelastic collisions and leads to significant errors and thus is not recommended.

Exploration of two-enzyme coupled catalysis system using scanning electrochemical microscopy.

PubMed

Wu, Zeng-Qiang; Jia, Wen-Zhi; Wang, Kang; Xu, Jing-Juan; Chen, Hong-Yuan; Xia, Xing-Hua

2012-12-18

In biological metabolism, a given metabolic process usually occurs via a group of enzymes working together in sequential pathways. To explore the metabolism mechanism requires the understanding of the multienzyme coupled catalysis systems. In this paper, an approach has been proposed to study the kinetics of a two-enzyme coupled reaction using SECM combining numerical simulations. Acetylcholine esterase and choline oxidase are immobilized on cysteamine self-assembled monolayers on tip and substrate gold electrodes of SECM via electrostatic interactions, respectively. The reaction kinetics of this two-enzyme coupled system upon various separation distance precisely regulated by SECM are measured. An overall apparent Michaelis-Menten constant of this enzyme cascade is thus measured as 2.97 mM at an optimal tip-substrate gap distance of 18 μm. Then, a kinetic model of this enzyme cascade is established for evaluating the kinetic parameters of individual enzyme by using the finite element method. The simulated results demonstrate the choline oxidase catalytic reaction is the rate determining step of this enzyme cascade. The Michaelis-Menten constant of acetylcholine esterase is evaluated as 1.8 mM. This study offers a promising approach to exploring mechanism of other two-enzyme coupled reactions in biological system and would promote the development of biosensors and enzyme-based logic systems.

Performance of Frozen Density Embedding for Modeling Hole Transfer Reactions.

PubMed

Ramos, Pablo; Papadakis, Markos; Pavanello, Michele

2015-06-18

We have carried out a thorough benchmark of the frozen density-embedding (FDE) method for calculating hole transfer couplings. We have considered 10 exchange-correlation functionals, 3 nonadditive kinetic energy functionals, and 3 basis sets. Overall, we conclude that with a 7% mean relative unsigned error, the PBE and PW91 functionals coupled with the PW91k nonadditive kinetic energy functional and a TZP basis set constitute the most stable and accurate levels of theory for hole transfer coupling calculations. The FDE-ET method is found to be an excellent tool for computing diabatic couplings for hole transfer reactions.

Non-Gaussianity in multi-sound-speed disformally coupled inflation

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

De Bruck, Carsten van; Longden, Chris; Koivisto, Tomi, E-mail: C.vandeBruck@sheffield.ac.uk, E-mail: tomi.koivisto@nordita.org, E-mail: cjlongden1@sheffield.ac.uk

Most, if not all, scalar-tensor theories are equivalent to General Relativity with a disformally coupled matter sector. In extra-dimensional theories such a coupling can be understood as a result of induction of the metric on a brane that matter is confined to. This article presents a first look at the non-Gaussianities in disformally coupled inflation, a simple two-field model that features a novel kinetic interaction. Cases with both canonical and Dirac-Born-Infeld (DBI) kinetic terms are taken into account, the latter motivated by the possible extra-dimensional origin of the disformality. The computations are carried out for the equilateral configuration in themore » slow-roll regime, wherein it is found that the non-Gaussianity is typically rather small and negative. This is despite the fact that the new kinetic interaction causes the perturbation modes to propagate with different sounds speeds, which may both significantly deviate from unity during inflation.« less

Multiplexed immunosensing and kinetics monitoring in nanofluidic devices with highly enhanced target capture efficiency

PubMed Central

Lin, Yii-Lih; Huang, Yen-Jun; Teerapanich, Pattamon; Leïchlé, Thierry

2016-01-01

Nanofluidic devices promise high reaction efficiency and fast kinetic responses due to the spatial constriction of transported biomolecules with confined molecular diffusion. However, parallel detection of multiple biomolecules, particularly proteins, in highly confined space remains challenging. This study integrates extended nanofluidics with embedded protein microarray to achieve multiplexed real-time biosensing and kinetics monitoring. Implementation of embedded standard-sized antibody microarray is attained by epoxy-silane surface modification and a room-temperature low-aspect-ratio bonding technique. An effective sample transport is achieved by electrokinetic pumping via electroosmotic flow. Through the nanoslit-based spatial confinement, the antigen-antibody binding reaction is enhanced with ∼100% efficiency and may be directly observed with fluorescence microscopy without the requirement of intermediate washing steps. The image-based data provide numerous spatially distributed reaction kinetic curves and are collectively modeled using a simple one-dimensional convection-reaction model. This study represents an integrated nanofluidic solution for real-time multiplexed immunosensing and kinetics monitoring, starting from device fabrication, protein immobilization, device bonding, sample transport, to data analysis at Péclet number less than 1. PMID:27375819

Explicit integration with GPU acceleration for large kinetic networks

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

Brock, Benjamin; Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830; Belt, Andrew

2015-12-01

We demonstrate the first implementation of recently-developed fast explicit kinetic integration algorithms on modern graphics processing unit (GPU) accelerators. Taking as a generic test case a Type Ia supernova explosion with an extremely stiff thermonuclear network having 150 isotopic species and 1604 reactions coupled to hydrodynamics using operator splitting, we demonstrate the capability to solve of order 100 realistic kinetic networks in parallel in the same time that standard implicit methods can solve a single such network on a CPU. This orders-of-magnitude decrease in computation time for solving systems of realistic kinetic networks implies that important coupled, multiphysics problems inmore » various scientific and technical fields that were intractable, or could be simulated only with highly schematic kinetic networks, are now computationally feasible.« less

Global Magnetosphere Modeling With Kinetic Treatment of Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Toth, G.; Chen, Y.; Gombosi, T. I.; Cassak, P.; Markidis, S.; Peng, B.; Henderson, M. G.

2017-12-01

Global magnetosphere simulations with a kinetic treatment of magnetic reconnection are very challenging because of the large separation of global and kinetic scales. We have developed two algorithms that can overcome these difficulties: 1) the two-way coupling of the global magnetohydrodynamic code with an embedded particle-in-cell model (MHD-EPIC) and 2) the artificial increase of the ion and electron kinetic scales. Both of these techniques improve the efficiency of the simulations by many orders of magnitude. We will describe the techniques and show that they provide correct and meaningful results. Using the coupled model and the increased kinetic scales, we will present global magnetosphere simulations with the PIC domains covering the dayside and/or tail reconnection sites. The simulation results will be compared to and validated with MMS observations.

Imaging with organic indicators and high-speed charge-coupled device cameras in neurons: some applications where these classic techniques have advantages.

PubMed

Ross, William N; Miyazaki, Kenichi; Popovic, Marko A; Zecevic, Dejan

2015-04-01

Dynamic calcium and voltage imaging is a major tool in modern cellular neuroscience. Since the beginning of their use over 40 years ago, there have been major improvements in indicators, microscopes, imaging systems, and computers. While cutting edge research has trended toward the use of genetically encoded calcium or voltage indicators, two-photon microscopes, and in vivo preparations, it is worth noting that some questions still may be best approached using more classical methodologies and preparations. In this review, we highlight a few examples in neurons where the combination of charge-coupled device (CCD) imaging and classical organic indicators has revealed information that has so far been more informative than results using the more modern systems. These experiments take advantage of the high frame rates, sensitivity, and spatial integration of the best CCD cameras. These cameras can respond to the faster kinetics of organic voltage and calcium indicators, which closely reflect the fast dynamics of the underlying cellular events.

A Perspective on Studying G-Protein–Coupled Receptor Signaling with Resonance Energy Transfer Biosensors in Living Organisms

PubMed Central

van Unen, Jakobus; Woolard, Jeanette; Rinken, Ago; Hoffmann, Carsten; Hill, Stephen J.; Goedhart, Joachim; Bruchas, Michael R.; Bouvier, Michel

2015-01-01

The last frontier for a complete understanding of G-protein–coupled receptor (GPCR) biology is to be able to assess GPCR activity, interactions, and signaling in vivo, in real time within biologically intact systems. This includes the ability to detect GPCR activity, trafficking, dimerization, protein-protein interactions, second messenger production, and downstream signaling events with high spatial resolution and fast kinetic readouts. Resonance energy transfer (RET)–based biosensors allow for all of these possibilities in vitro and in cell-based assays, but moving RET into intact animals has proven difficult. Here, we provide perspectives on the optimization of biosensor design, of signal detection in living organisms, and the multidisciplinary development of in vitro and cell-based assays that more appropriately reflect the physiologic situation. In short, further development of RET-based probes, optical microscopy techniques, and mouse genome editing hold great potential over the next decade to bring real-time in vivo GPCR imaging to the forefront of pharmacology. PMID:25972446

Impacts of wind farms on land surface temperature

NASA Astrophysics Data System (ADS)

Zhou, Liming; Tian, Yuhong; Baidya Roy, Somnath; Thorncroft, Chris; Bosart, Lance F.; Hu, Yuanlong

2012-07-01

The wind industry in the United States has experienced a remarkably rapid expansion of capacity in recent years and this fast growth is expected to continue in the future. While converting wind's kinetic energy into electricity, wind turbines modify surface-atmosphere exchanges and the transfer of energy, momentum, mass and moisture within the atmosphere. These changes, if spatially large enough, may have noticeable impacts on local to regional weather and climate. Here we present observational evidence for such impacts based on analyses of satellite data for the period of 2003-2011 over a region in west-central Texas, where four of the world's largest wind farms are located. Our results show a significant warming trend of up to 0.72°C per decade, particularly at night-time, over wind farms relative to nearby non-wind-farm regions. We attribute this warming primarily to wind farms as its spatial pattern and magnitude couples very well with the geographic distribution of wind turbines.

Numerical solution of the quantum Lenard-Balescu equation for a non-degenerate one-component plasma

DOE PAGES

Scullard, Christian R.; Belt, Andrew P.; Fennell, Susan C.; ...

2016-09-01

We present a numerical solution of the quantum Lenard-Balescu equation using a spectral method, namely an expansion in Laguerre polynomials. This method exactly conserves both particles and kinetic energy and facilitates the integration over the dielectric function. To demonstrate the method, we solve the equilibration problem for a spatially homogeneous one-component plasma with various initial conditions. Unlike the more usual Landau/Fokker-Planck system, this method requires no input Coulomb logarithm; the logarithmic terms in the collision integral arise naturally from the equation along with the non-logarithmic order-unity terms. The spectral method can also be used to solve the Landau equation andmore » a quantum version of the Landau equation in which the integration over the wavenumber requires only a lower cutoff. We solve these problems as well and compare them with the full Lenard-Balescu solution in the weak-coupling limit. Finally, we discuss the possible generalization of this method to include spatial inhomogeneity and velocity anisotropy.« less

Spatio-temporal dynamics of turbulence trapped in geodesic acoustic modes

NASA Astrophysics Data System (ADS)

Sasaki, M.; Kobayashi, T.; Itoh, K.; Kasuya, N.; Kosuga, Y.; Fujisawa, A.; Itoh, S.-I.

2018-01-01

The spatio-temporal dynamics of turbulence with the interaction of geodesic acoustic modes (GAMs) are investigated, focusing on the phase-space structure of turbulence, where the phase-space consists of real-space and wavenumber-space. Based on the wave-kinetic framework, the coupling equation between the GAM and the turbulence is numerically solved. The turbulence trapped by the GAM velocity field is obtained. Due to the trapping effect, the turbulence intensity increases where the second derivative of the GAM velocity (curvature of the GAM) is negative. While, in the positive-curvature region, the turbulence is suppressed. Since the trapped turbulence propagates with the GAMs, this relationship is sustained spatially and temporally. The dynamics of the turbulence in the wavenumber spectrum are converted in the evolution of the frequency spectrum, and the simulation result is compared with the experimental observation in JFT-2M tokamak, where the similar patterns are obtained. The turbulence trapping effect is a key to understand the spatial structure of the turbulence in the presence of sheared flows.

Energy and water vapor transport across a simplified cloud-clear air interface

NASA Astrophysics Data System (ADS)

Gallana, L.; Di Savino, S.; De Santi, F.; Iovieno, M.; Tordella, D.

2014-11-01

We consider a simplified physics of the could interface where condensation, evaporation and radiation are neglected and momentum, thermal energy and water vapor transport is represented in terms of the Boussinesq model coupled to a passive scalar transport equation for the vapor. The interface is modeled as a layer separating two isotropic turbulent regions with different kinetic energy and vapor concentration. In particular, we focus on the small scale part of the inertial range of the atmospheric boundary layer as well as on the dissipative range of scales which are important to the micro-physics of warm clouds. We have numerically investigated stably stratified interfaces by locally perturbing at an initial instant the standard temperature lapse rate at the cloud interface and then observing the temporal evolution of the system. When the buoyancy term becomes of the same order of the inertial one, we observe a spatial redistribution of the kinetic energy which produce a concomitant pit of kinetic energy within the mixing layer. In this situation, the mixing layer contains two interfacial regions with opposite kinetic energy gradient, which in turn produces two intermittent sublayers in the velocity fluctuations field. This changes the structure of the field with respect to the corresponding non-stratified shearless mixing: the communication between the two turbulent region is weak, and the growth of the mixing layer stops. These results are discussed with respect to Large Eddy Simulations data for the Planetary Boundary Layers.

How noise and coupling influence leading indicators of population extinction in a spatially extended ecological system.

PubMed

O'Regan, Suzanne M

2018-12-01

Anticipating critical transitions in spatially extended systems is a key topic of interest to ecologists. Gradually declining metapopulations are an important example of a spatially extended biological system that may exhibit a critical transition. Theory for spatially extended systems approaching extinction that accounts for environmental stochasticity and coupling is currently lacking. Here, we develop spatially implicit two-patch models with additive and multiplicative forms of environmental stochasticity that are slowly forced through population collapse, through changing environmental conditions. We derive patch-specific expressions for candidate indicators of extinction and test their performance via a simulation study. Coupling and spatial heterogeneities decrease the magnitude of the proposed indicators in coupled populations relative to isolated populations, and the noise regime and the degree of coupling together determine trends in summary statistics. This theory may be readily applied to other spatially extended ecological systems, such as coupled infectious disease systems on the verge of elimination.

Shear viscosity for dense plasmas by equilibrium molecular dynamics in asymmetric Yukawa ionic mixtures

DOE PAGES

Haxhimali, Tomorr; Rudd, Robert E.; Cabot, William H.; ...

2015-11-24

We present molecular dynamics (MD) calculations of shear viscosity for asymmetric mixed plasma for thermodynamic conditions relevant to astrophysical and inertial confinement fusion plasmas. Specifically, we consider mixtures of deuterium and argon at temperatures of 100–500 eV and a number density of 10 25 ions/cc. The motion of 30 000–120 000 ions is simulated in which the ions interact via the Yukawa (screened Coulomb) potential. The electric field of the electrons is included in this effective interaction; the electrons are not simulated explicitly. Shear viscosity is calculated using the Green-Kubo approach with an integral of the shear stress autocorrelation function,more » a quantity calculated in the equilibrium MD simulations. We systematically study different mixtures through a series of simulations with increasing fraction of the minority high- Z element (Ar) in the D-Ar plasma mixture. In the more weakly coupled plasmas, at 500 eV and low Ar fractions, results from MD compare very well with Chapman-Enskog kinetic results. In the more strongly coupled plasmas, the kinetic theory does not agree well with the MD results. Here, we develop a simple model that interpolates between classical kinetic theories at weak coupling and the Murillo Yukawa viscosity model at higher coupling. Finally, this hybrid kinetics-MD viscosity model agrees well with the MD results over the conditions simulated, ranging from moderately weakly coupled to moderately strongly coupled asymmetric plasma mixtures.« less

On coupling fluid plasma and kinetic neutral physics models

DOE PAGES

Joseph, I.; Rensink, M. E.; Stotler, D. P.; ...

2017-03-01

The coupled fluid plasma and kinetic neutral physics equations are analyzed through theory and simulation of benchmark cases. It is shown that coupling methods that do not treat the coupling rates implicitly are restricted to short time steps for stability. Fast charge exchange, ionization and recombination coupling rates exist, even after constraining the solution by requiring that the neutrals are at equilibrium. For explicit coupling, the present implementation of Monte Carlo correlated sampling techniques does not allow for complete convergence in slab geometry. For the benchmark case, residuals decay with particle number and increase with grid size, indicating that theymore » scale in a manner that is similar to the theoretical prediction for nonlinear bias error. Progress is reported on implementation of a fully implicit Jacobian-free Newton–Krylov coupling scheme. The present block Jacobi preconditioning method is still sensitive to time step and methods that better precondition the coupled system are under investigation.« less

Decay and Spatial Diffusion of Turbulent Kinetic Energy In The Presence of a Linear Kinetic Energy Gradient

NASA Astrophysics Data System (ADS)

Meneveau, Charles

2015-11-01

A topic that elicited the interest of John Lumley is pressure transport in turbulence. In 1978 (JL, in Advances in Applied Mechanics, pages 123-176) he showed that pressure transport likely acts in the opposite direction to the spatial flux of kinetic energy due to triple velocity correlations. Here we examine a flow in which the interplay of turbulent decay and spatial transport is particularly relevant. Specifically, using a specially designed active grid and screens placed in the Corrsin wind tunnel, such a flow is realized. Data are acquired using X-wire thermal anemometry at different spanwise and downstream locations. In order to resolve the dissipation rate accurately, measurements are also acquired using the NSTAP probe developed and manufactured by Princeton researchers and kindly provided to us (M. Hultmark, Y. Fan, L. Smits). The results show power-law decay with downstream distance, with a decay exponent that becomes larger in the high kinetic energy side of the flow. Measurements of the dissipation enable us to obtain the spanwise gradient of the spatial flux. One possible explanation for the observations is upgrading transport of kinetic energy due to pressure-velocity correlations, although its magnitude required to close the budget appears very large. Absence of simultaneous pressure velocity measurement preclude us to fully elucidate the observed trends. In collaboration with Adrien Thormann, Johns Hopkins University. Financial support: National Science Foundation.

Explicit integration with GPU acceleration for large kinetic networks

DOE PAGES

Brock, Benjamin; Belt, Andrew; Billings, Jay Jay; ...

2015-09-15

In this study, we demonstrate the first implementation of recently-developed fast explicit kinetic integration algorithms on modern graphics processing unit (GPU) accelerators. Taking as a generic test case a Type Ia supernova explosion with an extremely stiff thermonuclear network having 150 isotopic species and 1604 reactions coupled to hydrodynamics using operator splitting, we demonstrate the capability to solve of order 100 realistic kinetic networks in parallel in the same time that standard implicit methods can solve a single such network on a CPU. In addition, this orders-of-magnitude decrease in computation time for solving systems of realistic kinetic networks implies thatmore » important coupled, multiphysics problems in various scientific and technical fields that were intractable, or could be simulated only with highly schematic kinetic networks, are now computationally feasible.« less

Diverse Supramolecular Nanofiber Networks Assembled by Functional Low-Complexity Domains.

PubMed

An, Bolin; Wang, Xinyu; Cui, Mengkui; Gui, Xinrui; Mao, Xiuhai; Liu, Yan; Li, Ke; Chu, Cenfeng; Pu, Jiahua; Ren, Susu; Wang, Yanyi; Zhong, Guisheng; Lu, Timothy K; Liu, Cong; Zhong, Chao

2017-07-25

Self-assembling supramolecular nanofibers, common in the natural world, are of fundamental interest and technical importance to both nanotechnology and materials science. Despite important advances, synthetic nanofibers still lack the structural and functional diversity of biological molecules, and the controlled assembly of one type of molecule into a variety of fibrous structures with wide-ranging functional attributes remains challenging. Here, we harness the low-complexity (LC) sequence domain of fused in sarcoma (FUS) protein, an essential cellular nuclear protein with slow kinetics of amyloid fiber assembly, to construct random copolymer-like, multiblock, and self-sorted supramolecular fibrous networks with distinct structural features and fluorescent functionalities. We demonstrate the utilities of these networks in the templated, spatially controlled assembly of ligand-decorated gold nanoparticles, quantum dots, nanorods, DNA origami, and hybrid structures. Owing to the distinguishable nanoarchitectures of these nanofibers, this assembly is structure-dependent. By coupling a modular genetic strategy with kinetically controlled complex supramolecular self-assembly, we demonstrate that a single type of protein molecule can be used to engineer diverse one-dimensional supramolecular nanostructures with distinct functionalities.

An analytical study on excitation of nuclear-coupled thermal-hydraulic instability due to seismically induced resonance in BWR

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

Hirano, Masashi

1997-07-01

This paper describes the results of a scoping study on seismically induced resonance of nuclear-coupled thermal-hydraulic instability in BWRs, which was conducted by using TRAC-BF1 within a framework of a point kinetics model. As a result of the analysis, it is shown that a reactivity insertion could occur accompanied by in-surge of coolant into the core resulted from the excitation of the nuclear-coupled instability by the external acceleration. In order to analyze this phenomenon more in detail, it is necessary to couple a thermal-hydraulic code with a three-dimensional nuclear kinetics code.

Coupled Kinetic-MHD Simulations of Divertor Heat Load with ELM Perturbations

NASA Astrophysics Data System (ADS)

Cummings, Julian; Chang, C. S.; Park, Gunyoung; Sugiyama, Linda; Pankin, Alexei; Klasky, Scott; Podhorszki, Norbert; Docan, Ciprian; Parashar, Manish

2010-11-01

The effect of Type-I ELM activity on divertor plate heat load is a key component of the DOE OFES Joint Research Target milestones for this year. In this talk, we present simulations of kinetic edge physics, ELM activity, and the associated divertor heat loads in which we couple the discrete guiding-center neoclassical transport code XGC0 with the nonlinear extended MHD code M3D using the End-to-end Framework for Fusion Integrated Simulations, or EFFIS. In these coupled simulations, the kinetic code and the MHD code run concurrently on the same massively parallel platform and periodic data exchanges are performed using a memory-to-memory coupling technology provided by EFFIS. The M3D code models the fast ELM event and sends frequent updates of the magnetic field perturbations and electrostatic potential to XGC0, which in turn tracks particle dynamics under the influence of these perturbations and collects divertor particle and energy flux statistics. We describe here how EFFIS technologies facilitate these coupled simulations and discuss results for DIII-D, NSTX and Alcator C-Mod tokamak discharges.

Nanoscale Dynamics of Joule heating and Bubble Nucleation in a Solid-State Nanopore

PubMed Central

Levine, Edlyn V.; Burns, Michael M.; Golovchenko, Jene A.

2016-01-01

We present a mathematical model for Joule heating of an electrolytic solution in a nanopore. The model couples the electrical and thermal dynamics responsible for rapid and extreme superheating of the electrolyte within the nanopore. The model is implemented numerically with a finite element calculation, yielding a time and spatially resolved temperature distribution in the nanopore region. Temperatures near the thermodynamic limit of superheat are predicted to be attained just before the explosive nucleation of a vapor bubble is observed experimentally. Knowledge of this temperature distribution enables the evaluation of related phenomena including bubble nucleation kinetics, relaxation oscillation, and bubble dynamics. PACS numbers 47.55.dp, 47.55.db, 85.35.-p, 05.70Fh PMID:26871171

A particle-particle hybrid method for kinetic and continuum equations

NASA Astrophysics Data System (ADS)

Tiwari, Sudarshan; Klar, Axel; Hardt, Steffen

2009-10-01

We present a coupling procedure for two different types of particle methods for the Boltzmann and the Navier-Stokes equations. A variant of the DSMC method is applied to simulate the Boltzmann equation, whereas a meshfree Lagrangian particle method, similar to the SPH method, is used for simulations of the Navier-Stokes equations. An automatic domain decomposition approach is used with the help of a continuum breakdown criterion. We apply adaptive spatial and time meshes. The classical Sod's 1D shock tube problem is solved for a large range of Knudsen numbers. Results from Boltzmann, Navier-Stokes and hybrid solvers are compared. The CPU time for the hybrid solver is 3-4 times faster than for the Boltzmann solver.

Tight coupling of Na+/K+-ATPase with glycolysis demonstrated in permeabilized rat cardiomyocytes.

PubMed

Sepp, Mervi; Sokolova, Niina; Jugai, Svetlana; Mandel, Merle; Peterson, Pearu; Vendelin, Marko

2014-01-01

The effective integrated organization of processes in cardiac cells is achieved, in part, by the functional compartmentation of energy transfer processes. Earlier, using permeabilized cardiomyocytes, we demonstrated the existence of tight coupling between some of cardiomyocyte ATPases and glycolysis in rat. In this work, we studied contribution of two membrane ATPases and whether they are coupled to glycolysis--sarcoplasmic reticulum Ca2+ ATPase (SERCA) and plasmalemma Na+/K+-ATPase (NKA). While SERCA activity was minor in this preparation in the absence of calcium, major role of NKA was revealed accounting to ∼30% of the total ATPase activity which demonstrates that permeabilized cell preparation can be used to study this pump. To elucidate the contribution of NKA in the pool of ATPases, a series of kinetic measurements was performed in cells where NKA had been inhibited by 2 mM ouabain. In these cells, we recorded: ADP- and ATP-kinetics of respiration, competition for ADP between mitochondria and pyruvate kinase (PK), ADP-kinetics of endogenous PK, and ATP-kinetics of total ATPases. The experimental data was analyzed using a series of mathematical models with varying compartmentation levels. The results show that NKA is tightly coupled to glycolysis with undetectable flux of ATP between mitochondria and NKA. Such tight coupling of NKA to PK is in line with its increased importance in the pathological states of the heart when the substrate preference shifts to glucose.

Multiscale Kinetic Modeling Reveals an Ensemble of Cl–/H+ Exchange Pathways in ClC-ec1 Antiporter

PubMed Central

2018-01-01

Despite several years of research, the ion exchange mechanisms in chloride/proton antiporters and many other coupled transporters are not yet understood at the molecular level. Here, we present a novel approach to kinetic modeling and apply it to ion exchange in ClC-ec1. Our multiscale kinetic model is developed by (1) calculating the state-to-state rate coefficients with reactive and polarizable molecular dynamics simulations, (2) optimizing these rates in a global kinetic network, and (3) predicting new electrophysiological results. The model shows that the robust Cl:H exchange ratio (2.2:1) can indeed arise from kinetic coupling without large protein conformational changes, indicating a possible facile evolutionary connection to chloride channels. The E148 amino acid residue is shown to couple chloride and proton transport through protonation-dependent blockage of the central anion binding site and an anion-dependent pKa value, which influences proton transport. The results demonstrate how an ensemble of different exchange pathways, as opposed to a single series of transitions, culminates in the macroscopic observables of the antiporter, such as transport rates, chloride/proton stoichiometry, and pH dependence. PMID:29332400

Kinetics of microbial reduction of Solid phase U(VI).

PubMed

Liu, Chongxuan; Jeon, Byong-Hun; Zachara, John M; Wang, Zheming; Dohnalkova, Alice; Fredrickson, James K

2006-10-15

Sodium boltwoodite (NaUO2SiO3OH x 1.5 H2O) was used to assess the kinetics of microbial reduction of solid-phase U(VI) by a dissimilatory metal-reducing bacterium (DMRB), Shewanella oneidensis strain MR-1. The bioreduction kinetics was studied with Na-boltwoodite in suspension or within alginate beads in a nongrowth medium with lactate as electron donor at pH 6.8 buffered with PIPES. Concentrations of U(VI)tot and cell number were varied to evaluate the coupling of U(VI) dissolution, diffusion, and microbial activity. Microscopic and spectroscopic analyses with transmission electron microscopy (TEM), energy dispersive spectroscopy (EDS), and laser-induced fluorescence spectroscopy (LIFS) collectively indicated that solid-phase U(VI) was first dissolved and diffused out of grain interiors before it was reduced on bacterial surfaces and/or within the periplasm. The kinetics of solid-phase U(VI) bioreduction was well described by a coupled model of bicarbonate-promoted dissolution of Na-boltwoodite, intragrain uranyl diffusion, and Monod type bioreduction kinetics with respect to dissolved U(VI) concentration. The results demonstrated that microbial reduction of solid-phase U(VI) is controlled by coupled biological, chemical, and physical processes.

A consistent hierarchy of generalized kinetic equation approximations to the master equation applied to surface catalysis.

PubMed

Herschlag, Gregory J; Mitran, Sorin; Lin, Guang

2015-06-21

We develop a hierarchy of approximations to the master equation for systems that exhibit translational invariance and finite-range spatial correlation. Each approximation within the hierarchy is a set of ordinary differential equations that considers spatial correlations of varying lattice distance; the assumption is that the full system will have finite spatial correlations and thus the behavior of the models within the hierarchy will approach that of the full system. We provide evidence of this convergence in the context of one- and two-dimensional numerical examples. Lower levels within the hierarchy that consider shorter spatial correlations are shown to be up to three orders of magnitude faster than traditional kinetic Monte Carlo methods (KMC) for one-dimensional systems, while predicting similar system dynamics and steady states as KMC methods. We then test the hierarchy on a two-dimensional model for the oxidation of CO on RuO2(110), showing that low-order truncations of the hierarchy efficiently capture the essential system dynamics. By considering sequences of models in the hierarchy that account for longer spatial correlations, successive model predictions may be used to establish empirical approximation of error estimates. The hierarchy may be thought of as a class of generalized phenomenological kinetic models since each element of the hierarchy approximates the master equation and the lowest level in the hierarchy is identical to a simple existing phenomenological kinetic models.

Inter-dependent tissue growth and Turing patterning in a model for long bone development

NASA Astrophysics Data System (ADS)

Tanaka, Simon; Iber, Dagmar

2013-10-01

The development of long bones requires a sophisticated spatial organization of cellular signalling, proliferation, and differentiation programs. How such spatial organization emerges on the growing long bone domain is still unresolved. Based on the reported biochemical interactions we developed a regulatory model for the core signalling factors IHH, PTCH1, and PTHrP and included two cell types, proliferating/resting chondrocytes and (pre-)hypertrophic chondrocytes. We show that the reported IHH-PTCH1 interaction gives rise to a Schnakenberg-type Turing kinetics, and that inclusion of PTHrP is important to achieve robust patterning when coupling patterning and tissue dynamics. The model reproduces relevant spatiotemporal gene expression patterns, as well as a number of relevant mutant phenotypes. In summary, we propose that a ligand-receptor based Turing mechanism may control the emergence of patterns during long bone development, with PTHrP as an important mediator to confer patterning robustness when the sensitive Turing system is coupled to the dynamics of a growing and differentiating tissue. We have previously shown that ligand-receptor based Turing mechanisms can also result from BMP-receptor, SHH-receptor, and GDNF-receptor interactions, and that these reproduce the wildtype and mutant patterns during digit formation in limbs and branching morphogenesis in lung and kidneys. Receptor-ligand interactions may thus constitute a general mechanism to generate Turing patterns in nature.

UNRAVELLING THE COMPLEX STRUCTURE OF AGN-DRIVEN OUTFLOWS. II. PHOTOIONIZATION AND ENERGETICS

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

Karouzos, Marios; Woo, Jong-Hak; Bae, Hyun-Jin, E-mail: woo@astro.snu.ac.kr

2016-12-20

Outflows have been shown to be prevalent in galaxies hosting luminous active galactic nuclei (AGNs); they present a physically plausible way to couple the AGN energy output with the interstellar medium of their hosts. Despite their prevalence, accurate characterization of these outflows has been challenging. In the second of a series of papers, we use Gemini Multi-Object Spectrograph integral field unit (IFU) data of six local ( z  < 0.1) and moderate-luminosity Type 2 AGNs to study the ionization properties and energetics of AGN-driven outflows. We find strong evidence connecting the extreme kinematics of the ionized gas to the AGN photoionization.more » The kinematic component related to the AGN-driven outflow is clearly separated from other kinematic components, such as virial motions or rotation, on the velocity and velocity dispersion diagram. Our spatially resolved kinematic analysis reveals that 30 to 90% of the total mass and kinetic energy of the outflow is contained within the central kpc of the galaxy. The spatially integrated mass and kinetic energy of the gas entrained in the outflow correlate well with the AGN bolometric luminosity and results in energy conversion efficiencies between 0.01% and 1%. Intriguingly, we detect ubiquitous signs of ongoing circumnuclear star formation. Their small size, the centrally contained mass and energy, and the universally detected circumnuclear star formation cast doubts on the potency of these AGN-driven outflows as agents of galaxy-scale negative feedback.« less

A combined kinematic and kinetic analysis at the residuum/socket interface of a knee-disarticulation amputee.

PubMed

Tang, Jinghua; McGrath, Michael; Hale, Nick; Jiang, Liudi; Bader, Dan; Laszczak, Piotr; Moser, David; Zahedi, Saeed

2017-11-01

The bespoke interface between a lower limb residuum and a prosthetic socket is critical for an amputee's comfort and overall rehabilitation outcomes. Analysis of interface kinematics and kinetics is important to gain full understanding of the interface biomechanics, which could aid clinical socket fit, rehabilitation and amputee care. This pilot study aims to investigate the dynamic correlation between kinematic movement and kinetic stresses at the interface during walking tests on different terrains. One male, knee disarticulation amputee participated in the study. He was asked to walk on both a level surface and a 5° ramped surface. The movement between the residuum and the socket was evaluated by the angular and axial couplings, based on the outputs from a 3D motion capture system. The corresponding kinetic stresses at anterior-proximal (AP), posterior-proximal (PP) and anterior-distal (AD) locations of the residuum were measured, using individual stress sensors. Approximately 8° of angular coupling and up to 32 mm of axial coupling were measured when walking on different terrains. The direction of the angular coupling shows strong correlation with the pressure difference between the PP and AP sensors. Higher pressure was obtained at the PP location than the AP location during stance phase, associated with the direction of the angular coupling. A strong correlation between axial coupling length, L, and longitudinal shear was also evident at the PP and AD locations i.e. the shortening of L corresponds to the increase of shear in the proximal direction. Although different terrains did not affect these correlations in principle, interface kinematic and kinetic values suggested that gait changes can induce modifications to the interface biomechanics. It is envisaged that the reported techniques could be potentially used to provide combined kinematics and kinetics for the understanding of biomechanics at the residuum/socket interface, which may play an important role in the clinical assessment of prosthetic component settings, including socket fit quality. Copyright © 2017 IPEM. Published by Elsevier Ltd. All rights reserved.

Dynamical analysis for a scalar-tensor model with kinetic and nonminimal couplings

NASA Astrophysics Data System (ADS)

Granda, L. N.; Jimenez, D. F.

We study the autonomous system for a scalar-tensor model of dark energy with nonminimal coupling to curvature and nonminimal kinetic coupling to the Einstein tensor. The critical points describe important stable asymptotic scenarios including quintessence, phantom and de Sitter attractor solutions. Two functional forms for the coupling functions and the scalar potential were considered: power-law and exponential functions of the scalar field. For power-law couplings, the restrictions on stable quintessence and phantom solutions lead to asymptotic freedom regime for the gravitational interaction. For the exponential functions, the stable quintessence, phantom or de Sitter solutions allow asymptotic behaviors where the effective Newtonian coupling can reach either the asymptotic freedom regime or constant value. The phantom solutions could be realized without appealing to ghost degrees of freedom. Transient inflationary and radiation dominated phases can also be described.

Estimation of oceanic subsurface mixing under a severe cyclonic storm using a coupled atmosphere-ocean-wave model

NASA Astrophysics Data System (ADS)

Prakash, Kumar Ravi; Nigam, Tanuja; Pant, Vimlesh

2018-04-01

A coupled atmosphere-ocean-wave model was used to examine mixing in the upper-oceanic layers under the influence of a very severe cyclonic storm Phailin over the Bay of Bengal (BoB) during 10-14 October 2013. The coupled model was found to improve the sea surface temperature over the uncoupled model. Model simulations highlight the prominent role of cyclone-induced near-inertial oscillations in subsurface mixing up to the thermocline depth. The inertial mixing introduced by the cyclone played a central role in the deepening of the thermocline and mixed layer depth by 40 and 15 m, respectively. For the first time over the BoB, a detailed analysis of inertial oscillation kinetic energy generation, propagation, and dissipation was carried out using an atmosphere-ocean-wave coupled model during a cyclone. A quantitative estimate of kinetic energy in the oceanic water column, its propagation, and its dissipation mechanisms were explained using the coupled atmosphere-ocean-wave model. The large shear generated by the inertial oscillations was found to overcome the stratification and initiate mixing at the base of the mixed layer. Greater mixing was found at the depths where the eddy kinetic diffusivity was large. The baroclinic current, holding a larger fraction of kinetic energy than the barotropic current, weakened rapidly after the passage of the cyclone. The shear induced by inertial oscillations was found to decrease rapidly with increasing depth below the thermocline. The dampening of the mixing process below the thermocline was explained through the enhanced dissipation rate of turbulent kinetic energy upon approaching the thermocline layer. The wave-current interaction and nonlinear wave-wave interaction were found to affect the process of downward mixing and cause the dissipation of inertial oscillations.

Development of a fully-consistent reduced order model to study instabilities in boiling water reactors

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

Dykin, V.; Demaziere, C.

2012-07-01

A simple nonlinear Reduced Order Model to study global, regional and local instabilities in Boiling Water Reactors is described. The ROM consists of three submodels: neutron-kinetic, thermal-hydraulic and heat-transfer models. The neutron-kinetic model allows representing the time evolution of the three first neutron kinetic modes: the fundamental, the first and the second azimuthal modes. The thermal-hydraulic model describes four heated channels in order to correctly simulate out-of-phase behavior. The coupling between the different submodels is performed via both void and Doppler feedback mechanisms. After proper spatial homogenization, the governing equations are discretized in the time-domain. Several modifications, compared to othermore » existing ROMs, have been implemented, and are reported in this paper. One novelty of the ROM is the inclusion of both azimuthal modes, which allows to study combined instabilities (in-phase and out-of-phase), as well as to investigate the corresponding interference effects between them. The second modification concerns the precise estimation of so-called reactivity coefficients or C{sub mn}{sup *V,D} - coefficients by using direct cross-section data from SIMULATE-3 combined with the CORE SIM core simulator in order to calculate Eigenmodes. Furthermore, a non-uniform two-step axial power profile is introduced to simulate the separate heat production in the single and two-phase regions, respectively. An iterative procedure was developed to calculate the solution to the coupled neutron-kinetic/thermal-hydraulic static problem prior to solving the time-dependent problem. Besides, the possibility of taking into account the effect of local instabilities is demonstrated in a simplified manner. The present ROM is applied to the investigation of an actual instability that occurred at the Swedish Forsmark-1 BWR in 1996/1997. The results generated by the ROM are compared with real power plant measurements performed during stability tests and show a good qualitative agreement. The present study provides some insight in a deeper understanding of the physical principles which drive both core-wide and local instabilities. (authors)« less

AGN outflows and feedback twenty years on

NASA Astrophysics Data System (ADS)

Harrison, C. M.; Costa, T.; Tadhunter, C. N.; Flütsch, A.; Kakkad, D.; Perna, M.; Vietri, G.

2018-03-01

It is twenty years since the seminal works by Magorrian and co-authors and by Silk and Rees, which, along with other related work, ignited an explosion of publications connecting active galactic nucleus (AGN)-driven outflows to galaxy evolution. With a surge in observations of AGN outflows, studies are attempting to test AGN feedback models directly using the outflow properties. With a focus on outflows traced by optical and CO emission lines, we discuss significant challenges that greatly complicate this task, from both an observational and theoretical perspective. We highlight the observational uncertainties involved and the assumptions required when deriving kinetic coupling efficiencies (that is, outflow kinetic power as a fraction of AGN luminosity) from typical observations. Based on recent models we demonstrate that extreme caution should be taken when comparing observationally derived kinetic coupling efficiencies to coupling efficiencies from fiducial feedback models.

Kinetic coupling of phosphate release, force generation and rate-limiting steps in the cross-bridge cycle.

PubMed

Stehle, Robert; Tesi, Chiara

2017-08-01

A basic goal in muscle research is to understand how the cyclic ATPase activity of cross-bridges is converted into mechanical force. A direct approach to study the chemo-mechanical coupling between P i release and the force-generating step is provided by the kinetics of force response induced by a rapid change in [P i ]. Classical studies on fibres using caged-P i discovered that rapid increases in [P i ] induce fast force decays dependent on final [P i ] whose kinetics were interpreted to probe a fast force-generating step prior to P i release. However, this hypothesis was called into question by studies on skeletal and cardiac myofibrils subjected to P i jumps in both directions (increases and decreases in [P i ]) which revealed that rapid decreases in [P i ] trigger force rises with slow kinetics, similar to those of calcium-induced force development and mechanically-induced force redevelopment at the same [P i ]. A possible explanation for this discrepancy came from imaging of individual sarcomeres in cardiac myofibrils, showing that the fast force decay upon increase in [P i ] results from so-called sarcomere 'give'. The slow force rise upon decrease in [P i ] was found to better reflect overall sarcomeres cross-bridge kinetics and its [P i ] dependence, suggesting that the force generation coupled to P i release cannot be separated from the rate-limiting transition. The reasons for the different conclusions achieved in fibre and myofibril studies are re-examined as the recent findings on cardiac myofibrils have fundamental consequences for the coupling between P i release, rate-limiting steps and force generation. The implications from P i -induced force kinetics of myofibrils are discussed in combination with historical and recent models of the cross-bridge cycle.

Kinetic Monte Carlo simulations of thermally activated magnetization reversal in dual-layer Exchange Coupled Composite recording media

NASA Astrophysics Data System (ADS)

Plumer, M. L.; Almudallal, A. M.; Mercer, J. I.; Whitehead, J. P.; Fal, T. J.

The kinetic Monte Carlo (KMC) method developed for thermally activated magnetic reversal processes in single-layer recording media has been extended to study dual-layer Exchange Coupled Composition (ECC) media used in current and next generations of disc drives. The attempt frequency is derived from the Langer formalism with the saddle point determined using a variant of Bellman Ford algorithm. Complication (such as stagnation) arising from coupled grains having metastable states are addressed. MH-hysteresis loops are calculated over a wide range of anisotropy ratios, sweep rates and inter-layer coupling parameter. Results are compared with standard micromagnetics at fast sweep rates and experimental results at slow sweep rates.

RNA folding: structure prediction, folding kinetics and ion electrostatics.

PubMed

Tan, Zhijie; Zhang, Wenbing; Shi, Yazhou; Wang, Fenghua

2015-01-01

Beyond the "traditional" functions such as gene storage, transport and protein synthesis, recent discoveries reveal that RNAs have important "new" biological functions including the RNA silence and gene regulation of riboswitch. Such functions of noncoding RNAs are strongly coupled to the RNA structures and proper structure change, which naturally leads to the RNA folding problem including structure prediction and folding kinetics. Due to the polyanionic nature of RNAs, RNA folding structure, stability and kinetics are strongly coupled to the ion condition of solution. The main focus of this chapter is to review the recent progress in the three major aspects in RNA folding problem: structure prediction, folding kinetics and ion electrostatics. This chapter will introduce both the recent experimental and theoretical progress, while emphasize the theoretical modelling on the three aspects in RNA folding.

Effective potential kinetic theory for strongly coupled plasmas

NASA Astrophysics Data System (ADS)

Baalrud, Scott D.; Daligault, Jérôme

2016-11-01

The effective potential theory (EPT) is a recently proposed method for extending traditional plasma kinetic and transport theory into the strongly coupled regime. Validation from experiments and molecular dynamics simulations have shown it to be accurate up to the onset of liquid-like correlation parameters (corresponding to Γ ≃ 10-50 for the one-component plasma, depending on the process of interest). Here, this theory is briefly reviewed along with comparisons between the theory and molecular dynamics simulations for self-diffusivity and viscosity of the one-component plasma. A number of new results are also provided, including calculations of friction coefficients, energy exchange rates, stopping power, and mobility. The theory is also cast in the Landau and Fokker-Planck kinetic forms, which may prove useful for enabling efficient kinetic computations.

A Comprehensive Enzyme Kinetic Exercise for Biochemistry

ERIC Educational Resources Information Center

Barton, Janice S.

2011-01-01

This article describes a comprehensive treatment of experimental enzyme kinetics strongly coupled to electronic data acquisition and use of spreadsheets to organize data and perform linear and nonlinear least-squares analyses, all in a manner that promotes development of important reasoning skills. Kinetic parameters are obtained for the stable…

PET/CT Imaging Reveals Unrivaled Placental Avidity for Glucose Compared to Other Tissues

PubMed Central

Sawatzke, Alexander B.; Norris, Andrew W.; Spyropoulos, Fotios; Walsh, Susan A.; Acevedo, Michael R.; Hu, Shanming; Yao, Jianrong; Wang, Chunlin; Sunderland, John J.; Boles Ponto, Laura L.

2014-01-01

Introduction The goal of this study was to define the kinetics of glucose transport from maternal blood to placenta to fetus using real time imaging. Methods Positron emission tomography (PET) imaging of the glucose tracer [18F]fluorodeoxyglucose (FDG) was used to temporally and spatially define, in vivo, the kinetics of glucose transport from maternal blood into placentae and fetuses, in the late gestational gravid rat. Computed tomography (CT), with intravenous contrast, co-registered to the PET images allowed anatomic differentiation of placentae from fetal and maternal tissues. Results FDG was rapidly taken up by placentae and subsequently appeared in fetuses with minimal temporal lag. FDG standardized uptake values in placentae and fetuses approached that of maternal brain. In both anesthetized and awake dams, one quarter of the administered FDG ultimately was accrued in the collective fetuses and placentae. Accordingly, kinetic modeling demonstrated that the placentae had very high avidity for FDG, 2-fold greater than that of the fetus and maternal brain, when accounting for the fact that fetal FDG necessarily must first be taken up by placentae. Consistent with this, placental expression of glucose transporter 1 exceeded that of all other tissues. Discussion Fetal and placental tissues place a substantial glucose metabolic burden on the mother, owing to very high avidity of placentae for glucose coupled with the large relative mass of fetal and placental tissues. Conclusions The placenta has a tremendous capacity to uptake and transport glucose. PET/CT imaging is an ideal means to study metabolite transport kinetics in the fetoplacental unit. PMID:25555498

Remodelling of cellular excitation (reaction) and intercellular coupling (diffusion) by chronic atrial fibrillation represented by a reaction-diffusion system

NASA Astrophysics Data System (ADS)

Zhang, Henggui; Garratt, Clifford J.; Kharche, Sanjay; Holden, Arun V.

2009-06-01

Human atrial tissue is an excitable system, in which myocytes are excitable elements, and cell-to-cell electrotonic interactions are via diffusive interactions of cell membrane potentials. We developed a family of excitable system models for human atrium at cellular, tissue and anatomical levels for both normal and chronic atrial fibrillation (AF) conditions. The effects of AF-induced remodelling of cell membrane ionic channels (reaction kinetics) and intercellular gap junctional coupling (diffusion) on atrial excitability, conduction of excitation waves and dynamics of re-entrant excitation waves are quantified. Both ionic channel and gap junctional coupling remodelling have rate dependent effects on atrial propagation. Membrane channel conductance remodelling allows the propagation of activity at higher rates than those sustained in normal tissue or in tissue with gap junctional remodelling alone. Membrane channel conductance remodelling is essential for the propagation of activity at rates higher than 300/min as seen in AF. Spatially heterogeneous gap junction coupling remodelling increased the risk of conduction block, an essential factor for the genesis of re-entry. In 2D and 3D anatomical models, the dynamical behaviours of re-entrant excitation waves are also altered by membrane channel modelling. This study provides insights to understand the pro-arrhythmic effects of AF-induced reaction and diffusion remodelling in atrial tissue.

A 3D unstructured grid nearshore hydrodynamic model based on the vortex force formalism

NASA Astrophysics Data System (ADS)

Zheng, Peng; Li, Ming; van der A, Dominic A.; van der Zanden, Joep; Wolf, Judith; Chen, Xueen; Wang, Caixia

2017-08-01

A new three-dimensional nearshore hydrodynamic model system is developed based on the unstructured-grid version of the third generation spectral wave model SWAN (Un-SWAN) coupled with the three-dimensional ocean circulation model FVCOM to enable the full representation of the wave-current interaction in the nearshore region. A new wave-current coupling scheme is developed by adopting the vortex-force (VF) scheme to represent the wave-current interaction. The GLS turbulence model is also modified to better reproduce wave-breaking enhanced turbulence, together with a roller transport model to account for the effect of surface wave roller. This new model system is validated first against a theoretical case of obliquely incident waves on a planar beach, and then applied to three test cases: a laboratory scale experiment of normal waves on a beach with a fixed breaker bar, a field experiment of oblique incident waves on a natural, sandy barred beach (Duck'94 experiment), and a laboratory study of normal-incident waves propagating around a shore-parallel breakwater. Overall, the model predictions agree well with the available measurements in these tests, illustrating the robustness and efficiency of the present model for very different spatial scales and hydrodynamic conditions. Sensitivity tests indicate the importance of roller effects and wave energy dissipation on the mean flow (undertow) profile over the depth. These tests further suggest to adopt a spatially varying value for roller effects across the beach. In addition, the parameter values in the GLS turbulence model should be spatially inhomogeneous, which leads to better prediction of the turbulent kinetic energy and an improved prediction of the undertow velocity profile.

Kinetics of Microbial Reduction of Solid Phase U(VI)

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

Liu, Chongxuan; Jeon, Byong Hun; Zachara, John M.

2006-10-01

Sodium boltwoodite (NaUO2SiO3OH ?1.5H2O) was used to assess the kinetics of microbial reduction of solid phase U(VI) by a dissimilatory metal-reducing bacterium (DMRB), Shewanella oneidensis strain MR-1. The bioreduction kinetics was studied with Na-boltwoodite in suspension or within alginate beads. Concentrations of U(VI)tot and cell number were varied to evaluate the coupling of U(VI) dissolution, diffusion, and microbial activity. Batch experiments were performed in a non-growth medium with lactate as electron donor at pH 6.8 buffered with PIPES. Microscopic and spectroscopic analyses with transmission electron microscopy (TEM), energy dispersive spectroscopy (EDS), and laser-induced fluorescence spectroscopy (LIFS) collectively indicated that solidmore » phase U(VI) was first dissolved and diffused out of grain interiors before it was reduced on bacterial surfaces and/or within the periplasm. The kinetics of solid phase U(VI) bioreduction was well described by a coupled model of bicarbonate-promoted dissolution of Na-boltwoodite, intraparticle uranyl diffusion, and Monod type bioreduction kinetics with respect to dissolved U(VI) concentration. The results demonstrated the intimate coupling of biological, chemical, and physical processes in microbial reduction of solid phase U(VI).« less

Beyond mean-field approximations for accurate and computationally efficient models of on-lattice chemical kinetics

NASA Astrophysics Data System (ADS)

Pineda, M.; Stamatakis, M.

2017-07-01

Modeling the kinetics of surface catalyzed reactions is essential for the design of reactors and chemical processes. The majority of microkinetic models employ mean-field approximations, which lead to an approximate description of catalytic kinetics by assuming spatially uncorrelated adsorbates. On the other hand, kinetic Monte Carlo (KMC) methods provide a discrete-space continuous-time stochastic formulation that enables an accurate treatment of spatial correlations in the adlayer, but at a significant computation cost. In this work, we use the so-called cluster mean-field approach to develop higher order approximations that systematically increase the accuracy of kinetic models by treating spatial correlations at a progressively higher level of detail. We further demonstrate our approach on a reduced model for NO oxidation incorporating first nearest-neighbor lateral interactions and construct a sequence of approximations of increasingly higher accuracy, which we compare with KMC and mean-field. The latter is found to perform rather poorly, overestimating the turnover frequency by several orders of magnitude for this system. On the other hand, our approximations, while more computationally intense than the traditional mean-field treatment, still achieve tremendous computational savings compared to KMC simulations, thereby opening the way for employing them in multiscale modeling frameworks.

A hybrid model for coupling kinetic corrections of fusion reactivity to hydrodynamic implosion simulations

NASA Astrophysics Data System (ADS)

Tang, Xian-Zhu; McDevitt, C. J.; Guo, Zehua; Berk, H. L.

2014-03-01

Inertial confinement fusion requires an imploded target in which a central hot spot is surrounded by a cold and dense pusher. The hot spot/pusher interface can take complicated shape in three dimensions due to hydrodynamic mix. It is also a transition region where the Knudsen and inverse Knudsen layer effect can significantly modify the fusion reactivity in comparison with the commonly used value evaluated with background Maxwellians. Here, we describe a hybrid model that couples the kinetic correction of fusion reactivity to global hydrodynamic implosion simulations. The key ingredient is a non-perturbative treatment of the tail ions in the interface region where the Gamow ion Knudsen number approaches or surpasses order unity. The accuracy of the coupling scheme is controlled by the precise criteria for matching the non-perturbative kinetic model to perturbative solutions in both configuration space and velocity space.

Diagnosis of warm dense conditions in foil targets heated by intense femtosecond laser pulses using Kα imaging spectroscopy

DOE PAGES

Bae, L. J.; Zastrau, U.; Chung, H. -K.; ...

2018-03-01

Warm dense conditions in titanium foils irradiated with intense femtosecond laser pulses are diagnosed using an x-ray imaging spectroscopy technique. The line shapes of radially resolved titanium Kα spectra are measured with a toroidally bent GaAs crystal and an x-ray charge-coupled device. Measured spectra are compared with the K-shell emissions modeled using an atomic kinetics – spectroscopy simulation code. Kα line shapes are strongly affected by warm (5-40 eV) bulk electron temperatures and imply multiple temperature distributions in the targets. Finally, the spatial distribution of temperature is dependent on the target thickness, and a thin target shows an advantage tomore » generate uniform warm dense conditions in a large area.« less

Diagnosis of warm dense conditions in foil targets heated by intense femtosecond laser pulses using Kα imaging spectroscopy

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

Bae, L. J.; Zastrau, U.; Chung, H. -K.

Warm dense conditions in titanium foils irradiated with intense femtosecond laser pulses are diagnosed using an x-ray imaging spectroscopy technique. The line shapes of radially resolved titanium Kα spectra are measured with a toroidally bent GaAs crystal and an x-ray charge-coupled device. Measured spectra are compared with the K-shell emissions modeled using an atomic kinetics – spectroscopy simulation code. Kα line shapes are strongly affected by warm (5-40 eV) bulk electron temperatures and imply multiple temperature distributions in the targets. Finally, the spatial distribution of temperature is dependent on the target thickness, and a thin target shows an advantage tomore » generate uniform warm dense conditions in a large area.« less

Development of an integrated chemical weather prediction system for environmental applications at meso to global scales: NMMB/BSC-CHEM

NASA Astrophysics Data System (ADS)

Jorba, O.; Pérez, C.; Karsten, K.; Janjic, Z.; Dabdub, D.; Baldasano, J. M.

2009-09-01

This contribution presents the ongoing developments of a new fully on-line chemical weather prediction system for meso to global scale applications. The modeling system consists of a mineral dust module and a gas-phase chemistry module coupled on-line to a unified global-regional atmospheric driver. This approach allows solving small scale processes and their interactions at local to global scales. Its unified environment maintains the consistency of all the physico-chemical processes involved. The atmospheric driver is the NCEP/NMMB numerical weather prediction model (Janjic and Black, 2007) developed at National Centers for Environmental Prediction (NCEP). It represents an evolution of the operational WRF-NMME model extending from meso to global scales. Its unified non-hydrostatic dynamical core supports regional and global simulations. The Barcelona Supercomputing Center is currently designing and implementing a chemistry transport model coupled online with the new global/regional NMMB. The new modeling system is intended to be a powerful tool for research and to provide efficient global and regional chemical weather forecasts at sub-synoptic and mesoscale resolutions. The online coupling of the chemistry follows the approach similar to that of the mineral dust module already coupled to the atmospheric driver, NMMB/BSC-DUST (Pérez et al., 2008). Chemical species are advected and mixed at the corresponding time steps of the meteorological tracers using the same numerical scheme. Advection is eulerian, positive definite and monotone. The chemical mechanism and chemistry solver is based on the Kinetic PreProcessor KPP (Damian et al., 2002) package with the main purpose of maintaining a wide flexibility when configuring the model. Such approach will allow using a simplified chemical mechanism for global applications or a more complete mechanism for high-resolution local or regional studies. Moreover, it will permit the implementation of a specific configuration for forecasting applications in regional or global domains. An emission process allows the coupling of different emission inventories sources such as RETRO, EDGAR and GEIA for the global domain, EMEP for Europe and HERMES for Spain. The photolysis scheme is based on the Fast-J scheme, coupled with physics of each model layer (e.g., aerosols, clouds, absorbers as ozone) and it considers grid-scale clouds from the atmospheric driver. The dry deposition scheme follows the deposition velocity analogy for gases, enabling the calculation of deposition fluxes from airborne concentrations. No cloud-chemistry processes are included in the system yet (no wet deposition, scavenging and aqueous chemistry). The modeling system developments will be presented and first results of the gas-phase chemistry at global scale will be discussed. REFERENCES Janjic, Z.I., and Black, T.L., 2007. An ESMF unified model for a broad range of spatial and temporal scales, Geophysical Research Abstracts, 9, 05025. Pérez, C., Haustein, K., Janjic, Z.I., Jorba, O., Baldasano, J.M., Black, T.L., and Nickovic, S., 2008. An online dust model within the meso to global NMMB: current progress and plans. AGU Fall Meeting, San Francisco, A41K-03, 2008. Damian, V., Sandu, A., Damian, M., Potra, F., and Carmichael, G.R., 2002. The kinetic preprocessor KPP - A software environment for solving chemical kinetics. Comp. Chem. Eng., 26, 1567-1579. Sandu, A., and Sander, R., 2006. Technical note:Simulating chemical systems in Fortran90 and Matlab with the Kinetic PreProcessor KPP-2.1. Atmos. Chem. and Phys., 6, 187-195.

A Well-Posed, Objective and Dynamic Two-Fluid Model

NASA Astrophysics Data System (ADS)

Chetty, Krishna; Vaidheeswaran, Avinash; Sharma, Subash; Clausse, Alejandro; Lopez de Bertodano, Martin

The transition from dispersed to clustered bubbly flows due to wake entrainment is analyzed with a well-posed and objective one-dimensional (1-D) Two-Fluid Model, derived from variational principles. Modeling the wake entrainment force using the variational technique requires formulation of the inertial coupling coefficient, which defines the kinetic coupling between the phases. The kinetic coupling between a pair of bubbles and the liquid is obtained from potential flow over two-spheres and the results are validated by comparing the virtual mass coefficients with existing literature. The two-body interaction kinetic coupling is then extended to a lumped parameter model for viscous flow over two cylindrical bubbles, to get the Two-Fluid Model for wake entrainment. Linear stability analyses comprising the characteristics and the dispersion relation and non-linear numerical simulations are performed with the 1-D variational Two-Fluid Model to demonstrate the wake entrainment instability leading to clustering of bubbles. Finally, the wavelengths, amplitudes and propagation velocities of the void waves from non-linear simulations are compared with the experimental data.

A Perspective on Studying G-Protein-Coupled Receptor Signaling with Resonance Energy Transfer Biosensors in Living Organisms.

PubMed

van Unen, Jakobus; Woolard, Jeanette; Rinken, Ago; Hoffmann, Carsten; Hill, Stephen J; Goedhart, Joachim; Bruchas, Michael R; Bouvier, Michel; Adjobo-Hermans, Merel J W

2015-09-01

The last frontier for a complete understanding of G-protein-coupled receptor (GPCR) biology is to be able to assess GPCR activity, interactions, and signaling in vivo, in real time within biologically intact systems. This includes the ability to detect GPCR activity, trafficking, dimerization, protein-protein interactions, second messenger production, and downstream signaling events with high spatial resolution and fast kinetic readouts. Resonance energy transfer (RET)-based biosensors allow for all of these possibilities in vitro and in cell-based assays, but moving RET into intact animals has proven difficult. Here, we provide perspectives on the optimization of biosensor design, of signal detection in living organisms, and the multidisciplinary development of in vitro and cell-based assays that more appropriately reflect the physiologic situation. In short, further development of RET-based probes, optical microscopy techniques, and mouse genome editing hold great potential over the next decade to bring real-time in vivo GPCR imaging to the forefront of pharmacology. Copyright © 2015 by The American Society for Pharmacology and Experimental Therapeutics.

Quantification of Dynamic [18F]FDG Pet Studies in Acute Lung Injury.

PubMed

Grecchi, Elisabetta; Veronese, Mattia; Moresco, Rosa Maria; Bellani, Giacomo; Pesenti, Antonio; Messa, Cristina; Bertoldo, Alessandra

2016-02-01

This work aims to investigate lung glucose metabolism using 2-deoxy-2-[(18)F]fluoro-D-glucose ([(18)F]FDG) positron emission tomography (PET) imaging in acute lung injury (ALI) patients. Eleven ALI patients and five healthy controls underwent a dynamic [(18)F]FDG PET/X-ray computed tomography (CT) scan. The standardized uptake values (SUV) and three different methods for the quantification of glucose metabolism (i.e., ratio, Patlak, and spectral analysis iterative filter, SAIF) were applied both at the region and the voxel levels. SUV reported a lower correlation than the ratio with the net tracer uptake. Patlak and SAIF analyses did not show any significant spatial or quantitative (R(2) > 0.80) difference. The additional information provided by SAIF showed that in lung inflammation, elevated tracer uptake is coupled with abnormal tracer exchanges within and between lung tissue compartments. Full kinetic modeling provides a multi-parametric description of glucose metabolism in the lungs. This allows characterizing the spatial distribution of lung inflammation as well as returning the functional state of the tissues.

Coupling effects for separate spatial solitons in a biased series centrosymmetric photorefractive crystal circuit considering grey solitons

NASA Astrophysics Data System (ADS)

Katti, Aavishkar; Yadav, Ram Anjore

2018-02-01

The existence and coupling of grey-grey, grey-bright and grey-dark separate spatial solitons in a biased series centrosymmetric photorefractive crystal circuit is investigated for the first time. The numerical solution of the separate spatial solitons is presented. The coupling between the two separate spatial solitons is analysed for all three cases of separate coupled solitons, namely grey-grey, grey-bright, and grey-dark. Changing the intensity of the soliton in one crystal affects the soliton in both crystals due to flow of the light induced current through the circuit. The effect of the background intensity of each crystal on both the spatial solitons is investigated. Also, the effect of changing the temperature of one crystal affects the soliton in both crystals due to the coupling effect. The soliton width dependence on the temperature is different for each crystal.

Monte carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation.

PubMed

Berry, Hugues

2002-10-01

Conventional equations for enzyme kinetics are based on mass-action laws, that may fail in low-dimensional and disordered media such as biological membranes. We present Monte Carlo simulations of an isolated Michaelis-Menten enzyme reaction on two-dimensional lattices with varying obstacle densities, as models of biological membranes. The model predicts that, as a result of anomalous diffusion on these low-dimensional media, the kinetics are of the fractal type. Consequently, the conventional equations for enzyme kinetics fail to describe the reaction. In particular, we show that the quasi-stationary-state assumption can hardly be retained in these conditions. Moreover, the fractal characteristics of the kinetics are increasingly pronounced as obstacle density and initial substrate concentration increase. The simulations indicate that these two influences are mainly additive. Finally, the simulations show pronounced S-P segregation over the lattice at obstacle densities compatible with in vivo conditions. This phenomenon could be a source of spatial self organization in biological membranes.

Monte carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation.

PubMed Central

Berry, Hugues

2002-01-01

Conventional equations for enzyme kinetics are based on mass-action laws, that may fail in low-dimensional and disordered media such as biological membranes. We present Monte Carlo simulations of an isolated Michaelis-Menten enzyme reaction on two-dimensional lattices with varying obstacle densities, as models of biological membranes. The model predicts that, as a result of anomalous diffusion on these low-dimensional media, the kinetics are of the fractal type. Consequently, the conventional equations for enzyme kinetics fail to describe the reaction. In particular, we show that the quasi-stationary-state assumption can hardly be retained in these conditions. Moreover, the fractal characteristics of the kinetics are increasingly pronounced as obstacle density and initial substrate concentration increase. The simulations indicate that these two influences are mainly additive. Finally, the simulations show pronounced S-P segregation over the lattice at obstacle densities compatible with in vivo conditions. This phenomenon could be a source of spatial self organization in biological membranes. PMID:12324410

Reactive Transport Modeling of Induced Calcite Precipitation Reaction Fronts in Porous Media Using A Parallel, Fully Coupled, Fully Implicit Approach

NASA Astrophysics Data System (ADS)

Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.; Fox, D. T.; Fujita, Y.

2010-12-01

Inducing mineral precipitation in the subsurface is one potential strategy for immobilizing trace metal and radionuclide contaminants. Generating mineral precipitates in situ can be achieved by manipulating chemical conditions, typically through injection or in situ generation of reactants. How these reactants transport, mix and react within the medium controls the spatial distribution and composition of the resulting mineral phases. Multiple processes, including fluid flow, dispersive/diffusive transport of reactants, biogeochemical reactions and changes in porosity-permeability, are tightly coupled over a number of scales. Numerical modeling can be used to investigate the nonlinear coupling effects of these processes which are quite challenging to explore experimentally. Many subsurface reactive transport simulators employ a de-coupled or operator-splitting approach where transport equations and batch chemistry reactions are solved sequentially. However, such an approach has limited applicability for biogeochemical systems with fast kinetics and strong coupling between chemical reactions and medium properties. A massively parallel, fully coupled, fully implicit Reactive Transport simulator (referred to as “RAT”) based on a parallel multi-physics object-oriented simulation framework (MOOSE) has been developed at the Idaho National Laboratory. Within this simulator, systems of transport and reaction equations can be solved simultaneously in a fully coupled, fully implicit manner using the Jacobian Free Newton-Krylov (JFNK) method with additional advanced computing capabilities such as (1) physics-based preconditioning for solution convergence acceleration, (2) massively parallel computing and scalability, and (3) adaptive mesh refinements for 2D and 3D structured and unstructured mesh. The simulator was first tested against analytical solutions, then applied to simulating induced calcium carbonate mineral precipitation in 1D columns and 2D flow cells as analogs to homogeneous and heterogeneous porous media, respectively. In 1D columns, calcium carbonate mineral precipitation was driven by urea hydrolysis catalyzed by urease enzyme, and in 2D flow cells, calcium carbonate mineral forming reactants were injected sequentially, forming migrating reaction fronts that are typically highly nonuniform. The RAT simulation results for the spatial and temporal distributions of precipitates, reaction rates and major species in the system, and also for changes in porosity and permeability, were compared to both laboratory experimental data and computational results obtained using other reactive transport simulators. The comparisons demonstrate the ability of RAT to simulate complex nonlinear systems and the advantages of fully coupled approaches, over de-coupled methods, for accurate simulation of complex, dynamic processes such as engineered mineral precipitation in subsurface environments.

Stability of infinite derivative Abelian Higgs models

NASA Astrophysics Data System (ADS)

Ghoshal, Anish; Mazumdar, Anupam; Okada, Nobuchika; Villalba, Desmond

2018-04-01

Motivated by the stringy effects by modifying the local kinetic term of an Abelian Higgs field by the Gaussian kinetic term, we show that the Higgs field does not possess any instability; the Yukawa coupling between the scalar and the fermion, the gauge coupling, and the self interaction of the Higgs yields exponentially suppressed running at high energies, showing that such class of theory never suffers from vacuum instability. We briefly discuss its implications for the early Universe cosmology.

Phase space analysis for a scalar-tensor model with kinetic and Gauss-Bonnet couplings

NASA Astrophysics Data System (ADS)

Granda, L. N.; Loaiza, E.

2016-09-01

We study the phase space for a scalar-tensor string inspired model of dark energy with nonminimal kinetic and Gauss-Bonnet couplings. The form of the scalar potential and of the coupling terms is of the exponential type, which gives rise to appealing cosmological solutions. The critical points describe a variety of cosmological scenarios that go from a matter or radiation dominated universe to a dark energy dominated universe. Trajectories were found in the phase space departing from unstable or saddle fixed points and arriving at the stable scalar field dominated point corresponding to late-time accelerated expansion.

Model coupling intraparticle diffusion/sorption, nonlinear sorption, and biodegradation processes

USGS Publications Warehouse

Karapanagioti, Hrissi K.; Gossard, Chris M.; Strevett, Keith A.; Kolar, Randall L.; Sabatini, David A.

2001-01-01

Diffusion, sorption and biodegradation are key processes impacting the efficiency of natural attenuation. While each process has been studied individually, limited information exists on the kinetic coupling of these processes. In this paper, a model is presented that couples nonlinear and nonequilibrium sorption (intraparticle diffusion) with biodegradation kinetics. Initially, these processes are studied independently (i.e., intraparticle diffusion, nonlinear sorption and biodegradation), with appropriate parameters determined from these independent studies. Then, the coupled processes are studied, with an initial data set used to determine biodegradation constants that were subsequently used to successfully predict the behavior of a second data set. The validated model is then used to conduct a sensitivity analysis, which reveals conditions where biodegradation becomes desorption rate-limited. If the chemical is not pre-equilibrated with the soil prior to the onset of biodegradation, then fast sorption will reduce aqueous concentrations and thus biodegradation rates. Another sensitivity analysis demonstrates the importance of including nonlinear sorption in a coupled diffusion/sorption and biodegradation model. While predictions based on linear sorption isotherms agree well with solution concentrations, for the conditions evaluated this approach overestimates the percentage of contaminant biodegraded by as much as 50%. This research demonstrates that nonlinear sorption should be coupled with diffusion/sorption and biodegradation models in order to accurately predict bioremediation and natural attenuation processes. To our knowledge this study is unique in studying nonlinear sorption coupled with intraparticle diffusion and biodegradation kinetics with natural media.

Impact of time-of-flight on indirect 3D and direct 4D parametric image reconstruction in the presence of inconsistent dynamic PET data.

PubMed

Kotasidis, F A; Mehranian, A; Zaidi, H

2016-05-07

Kinetic parameter estimation in dynamic PET suffers from reduced accuracy and precision when parametric maps are estimated using kinetic modelling following image reconstruction of the dynamic data. Direct approaches to parameter estimation attempt to directly estimate the kinetic parameters from the measured dynamic data within a unified framework. Such image reconstruction methods have been shown to generate parametric maps of improved precision and accuracy in dynamic PET. However, due to the interleaving between the tomographic and kinetic modelling steps, any tomographic or kinetic modelling errors in certain regions or frames, tend to spatially or temporally propagate. This results in biased kinetic parameters and thus limits the benefits of such direct methods. Kinetic modelling errors originate from the inability to construct a common single kinetic model for the entire field-of-view, and such errors in erroneously modelled regions could spatially propagate. Adaptive models have been used within 4D image reconstruction to mitigate the problem, though they are complex and difficult to optimize. Tomographic errors in dynamic imaging on the other hand, can originate from involuntary patient motion between dynamic frames, as well as from emission/transmission mismatch. Motion correction schemes can be used, however, if residual errors exist or motion correction is not included in the study protocol, errors in the affected dynamic frames could potentially propagate either temporally, to other frames during the kinetic modelling step or spatially, during the tomographic step. In this work, we demonstrate a new strategy to minimize such error propagation in direct 4D image reconstruction, focusing on the tomographic step rather than the kinetic modelling step, by incorporating time-of-flight (TOF) within a direct 4D reconstruction framework. Using ever improving TOF resolutions (580 ps, 440 ps, 300 ps and 160 ps), we demonstrate that direct 4D TOF image reconstruction can substantially prevent kinetic parameter error propagation either from erroneous kinetic modelling, inter-frame motion or emission/transmission mismatch. Furthermore, we demonstrate the benefits of TOF in parameter estimation when conventional post-reconstruction (3D) methods are used and compare the potential improvements to direct 4D methods. Further improvements could possibly be achieved in the future by combining TOF direct 4D image reconstruction with adaptive kinetic models and inter-frame motion correction schemes.

Impact of time-of-flight on indirect 3D and direct 4D parametric image reconstruction in the presence of inconsistent dynamic PET data

NASA Astrophysics Data System (ADS)

Kotasidis, F. A.; Mehranian, A.; Zaidi, H.

2016-05-01

Kinetic parameter estimation in dynamic PET suffers from reduced accuracy and precision when parametric maps are estimated using kinetic modelling following image reconstruction of the dynamic data. Direct approaches to parameter estimation attempt to directly estimate the kinetic parameters from the measured dynamic data within a unified framework. Such image reconstruction methods have been shown to generate parametric maps of improved precision and accuracy in dynamic PET. However, due to the interleaving between the tomographic and kinetic modelling steps, any tomographic or kinetic modelling errors in certain regions or frames, tend to spatially or temporally propagate. This results in biased kinetic parameters and thus limits the benefits of such direct methods. Kinetic modelling errors originate from the inability to construct a common single kinetic model for the entire field-of-view, and such errors in erroneously modelled regions could spatially propagate. Adaptive models have been used within 4D image reconstruction to mitigate the problem, though they are complex and difficult to optimize. Tomographic errors in dynamic imaging on the other hand, can originate from involuntary patient motion between dynamic frames, as well as from emission/transmission mismatch. Motion correction schemes can be used, however, if residual errors exist or motion correction is not included in the study protocol, errors in the affected dynamic frames could potentially propagate either temporally, to other frames during the kinetic modelling step or spatially, during the tomographic step. In this work, we demonstrate a new strategy to minimize such error propagation in direct 4D image reconstruction, focusing on the tomographic step rather than the kinetic modelling step, by incorporating time-of-flight (TOF) within a direct 4D reconstruction framework. Using ever improving TOF resolutions (580 ps, 440 ps, 300 ps and 160 ps), we demonstrate that direct 4D TOF image reconstruction can substantially prevent kinetic parameter error propagation either from erroneous kinetic modelling, inter-frame motion or emission/transmission mismatch. Furthermore, we demonstrate the benefits of TOF in parameter estimation when conventional post-reconstruction (3D) methods are used and compare the potential improvements to direct 4D methods. Further improvements could possibly be achieved in the future by combining TOF direct 4D image reconstruction with adaptive kinetic models and inter-frame motion correction schemes.

Bridging scales through multiscale modeling: a case study on protein kinase A.

PubMed

Boras, Britton W; Hirakis, Sophia P; Votapka, Lane W; Malmstrom, Robert D; Amaro, Rommie E; McCulloch, Andrew D

2015-01-01

The goal of multiscale modeling in biology is to use structurally based physico-chemical models to integrate across temporal and spatial scales of biology and thereby improve mechanistic understanding of, for example, how a single mutation can alter organism-scale phenotypes. This approach may also inform therapeutic strategies or identify candidate drug targets that might otherwise have been overlooked. However, in many cases, it remains unclear how best to synthesize information obtained from various scales and analysis approaches, such as atomistic molecular models, Markov state models (MSM), subcellular network models, and whole cell models. In this paper, we use protein kinase A (PKA) activation as a case study to explore how computational methods that model different physical scales can complement each other and integrate into an improved multiscale representation of the biological mechanisms. Using measured crystal structures, we show how molecular dynamics (MD) simulations coupled with atomic-scale MSMs can provide conformations for Brownian dynamics (BD) simulations to feed transitional states and kinetic parameters into protein-scale MSMs. We discuss how milestoning can give reaction probabilities and forward-rate constants of cAMP association events by seamlessly integrating MD and BD simulation scales. These rate constants coupled with MSMs provide a robust representation of the free energy landscape, enabling access to kinetic, and thermodynamic parameters unavailable from current experimental data. These approaches have helped to illuminate the cooperative nature of PKA activation in response to distinct cAMP binding events. Collectively, this approach exemplifies a general strategy for multiscale model development that is applicable to a wide range of biological problems.

Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents.

PubMed

Reed, Daniel C; Breier, John A; Jiang, Houshuo; Anantharaman, Karthik; Klausmeier, Christopher A; Toner, Brandy M; Hancock, Cathrine; Speer, Kevin; Thurnherr, Andreas M; Dick, Gregory J

2015-08-01

Submarine hydrothermal vents perturb the deep-ocean microbiome by injecting reduced chemical species into the water column that act as an energy source for chemosynthetic organisms. These systems thus provide excellent natural laboratories for studying the response of microbial communities to shifts in marine geochemistry. The present study explores the processes that regulate coupled microbial-geochemical dynamics in hydrothermal plumes by means of a novel mathematical model, which combines thermodynamics, growth and reaction kinetics, and transport processes derived from a fluid dynamics model. Simulations of a plume located in the ABE vent field of the Lau basin were able to reproduce metagenomic observations well and demonstrated that the magnitude of primary production and rate of autotrophic growth are largely regulated by the energetics of metabolisms and the availability of electron donors, as opposed to kinetic parameters. Ambient seawater was the dominant source of microbes to the plume and sulphur oxidisers constituted almost 90% of the modelled community in the neutrally-buoyant plume. Data from drifters deployed in the region allowed the different time scales of metabolisms to be cast in a spatial context, which demonstrated spatial succession in the microbial community. While growth was shown to occur over distances of tens of kilometers, microbes persisted over hundreds of kilometers. Given that high-temperature hydrothermal systems are found less than 100 km apart on average, plumes may act as important vectors between different vent fields and other environments that are hospitable to similar organisms, such as oil spills and oxygen minimum zones.

Carbonyl Sulfide: is it AN Isotope of CO2 on Steroids?

NASA Astrophysics Data System (ADS)

Berry, J. A.; Campbell, J. E.; Baker, I. T.; Whelan, M.; Hilton, T. W.

2015-12-01

The behavior of OCS in the atmosphere is very similar to that of CO2 and reminiscent of an isotopologue. It is stable, has a turnover time of a couple of years (similar to that of 18O in CO2). It can be measured with adequate accuracy - despite the fact that its abundance is one millionth that of CO2, but there is one dramatic difference. The seasonal variation in the concentration of OCS relative to its background concentration can be 6-10 fold larger than the corresponding variation in CO2 concentration. Furthermore there are large spatial gradients in atmospheric OCS, with the concentrations being generally lower over the continents than the ocean, and lower in the atmospheric boundary layer over vegetated surfaces than in the free troposphere. These gradients have been clearly resolved by flask sampling from aircraft and recently by satellite measurements. The dynamics of OCS are larger than any other conserved atmospheric gas and certainly dwarf isotopic gradients. There are strong differences in the kinetics of CO2 and OCS exchange with leaves (similar to an isotopic fractionation), but these are not responsible for the large atmospheric signals. The major driver of these gradients is a large spatial separation between the major sources of OCS (the tropical ocean) and the major sink (the terrestrial biosphere). This talk will review the biogeochemical cycle of OCS; the kinetics of its exchange with leaves and soils; the distribution of sources and sinks, and the local and large scale gradients of OCS concentration in the atmosphere.

Predicting the response of the deep-ocean microbiome to geochemical perturbations by hydrothermal vents

PubMed Central

Reed, Daniel C; Breier, John A; Jiang, Houshuo; Anantharaman, Karthik; Klausmeier, Christopher A; Toner, Brandy M; Hancock, Cathrine; Speer, Kevin; Thurnherr, Andreas M; Dick, Gregory J

2015-01-01

Submarine hydrothermal vents perturb the deep-ocean microbiome by injecting reduced chemical species into the water column that act as an energy source for chemosynthetic organisms. These systems thus provide excellent natural laboratories for studying the response of microbial communities to shifts in marine geochemistry. The present study explores the processes that regulate coupled microbial-geochemical dynamics in hydrothermal plumes by means of a novel mathematical model, which combines thermodynamics, growth and reaction kinetics, and transport processes derived from a fluid dynamics model. Simulations of a plume located in the ABE vent field of the Lau basin were able to reproduce metagenomic observations well and demonstrated that the magnitude of primary production and rate of autotrophic growth are largely regulated by the energetics of metabolisms and the availability of electron donors, as opposed to kinetic parameters. Ambient seawater was the dominant source of microbes to the plume and sulphur oxidisers constituted almost 90% of the modelled community in the neutrally-buoyant plume. Data from drifters deployed in the region allowed the different time scales of metabolisms to be cast in a spatial context, which demonstrated spatial succession in the microbial community. While growth was shown to occur over distances of tens of kilometers, microbes persisted over hundreds of kilometers. Given that high-temperature hydrothermal systems are found less than 100 km apart on average, plumes may act as important vectors between different vent fields and other environments that are hospitable to similar organisms, such as oil spills and oxygen minimum zones. PMID:25658053

Three species one-dimensional kinetic model for weakly ionized plasmas

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

Gonzalez, J., E-mail: jorge.gonzalez@upm.es; Donoso, J. M.; Tierno, S. P.

2016-06-15

A three species one-dimensional kinetic model is presented for a spatially homogeneous weakly ionized plasma subjected to the action of a time varying electric field. Planar geometry is assumed, which means that the plasma evolves in the privileged direction of the field. The energy transmitted to the electric charges is channelized to the neutrals thanks to collisions, a mechanism that influences the plasma dynamics. Charge-charge interactions have been designed as a one-dimensional collision term equivalent to the Landau operator used for fully ionized plasmas. Charge-neutral collisions are modelled by a conservative drift-diffusion operator in the Dougherty's form. The resulting setmore » of coupled integro-differential equations is solved with the stable and robust propagator integral method. This semi–analytical method feasibility accounts for non–linear effects without appealing to linearisation or simplifications, providing conservative physically meaningful solutions even for initial or emerging sharp velocity distribution function profiles. It is found that charge-neutral collisions exert a significant effect since a quite different plasma evolution arises if compared to the collisionless limit. In addition, substantial differences in the system motion are found for constant and temperature dependent collision frequencies cases.« less

Mesoscale phase distribution in single particles of LiFePO4 following lithium deintercalation

PubMed Central

Boesenberg, Ulrike; Meirer, Florian; Liu, Yijin; Shukla, Alpesh K.; Dell’Anna, Rossana; Tyliszczak, Tolek; Chen, Guoying; Andrews, Joy C.; Richardson, Thomas J.; Kostecki, Robert; Cabana, Jordi

2013-01-01

The chemical phase distribution in hydrothermally grown micrometric single crystals LiFePO4 following partial chemical delithiation was investigated. Full field and scanning X-ray microscopy were combined with X-ray absorption spectroscopy at the Fe K- and O K-edges, respectively, to produce maps with high chemical and spatial resolution. The resulting information was compared to morphological insight into the mechanics of the transformation by scanning transmission electron microscopy. This study revealed the interplay at the mesocale between microstructure and phase distribution during the redox process, as morphological defects were found to kinetically determine the progress of the reaction. Lithium deintercalation was also found to induce severe mechanical damage in the crystals, presumably due to the lattice mismatch between LiFePO4 and FePO4. Our results lead to the conclusion that rational design of intercalation-based electrode materials, such as LiFePO4, with optimized utilization and life requires the tailoring of particles that minimize kinetic barriers and mechanical strain. Coupling TXM-XANES with TEM can provide unique insight into the behavior of electrode materials during operation, at scales spanning from nanoparticles to ensembles and complex architectures. PMID:23745016

A texture-component Avrami model for predicting recrystallization textures, kinetics and grain size

NASA Astrophysics Data System (ADS)

Raabe, Dierk

2007-03-01

The study presents an analytical model for predicting crystallographic textures and the final grain size during primary static recrystallization of metals using texture components. The kinetics is formulated as a matrix variant of the Johnson-Mehl-Avrami-Kolmogorov equation. The matrix form is required since the kinetic and crystallographic evolution of the microstructure is described in terms of a limited set of growing (recrystallizing) and swept (deformed) texture components. The number of components required (5-10) defines the order of the matrix since the kinetic coupling occurs between all recrystallizing and all deformed components. Each such couple is characterized by corresponding values for the nucleation energy and grain boundary mobility. The values of these parameters can be obtained by analytical or numerical coarse graining according to a renormalization scheme which replaces many individual grains which grow via recrystallization in a deformed texture component by a single equivalent recrystallization texture component or by fitting to experimental data. Each deformed component is further characterized by an average stored deformation energy. Each element of the kinetic matrix, reflecting one of the possible couplings between a deformed and a recrystallizing texture component, is then derived in each time step by a set of two differential equations. The first equation describes the thermally activated nucleation and growth processes for the expanded (free) volume for a particular couple of a deformed and a recrystallizing texture component and the second equation is used for calculating the constrained (real) volume for that couple which corrects the free volume for those portions of the deformation component which were already swept. The new method is particularly developed for the fast and physically based process simulation of recrystallization textures with respect to processing. The present paper introduces the method and applies it to the primary recrystallization of low carbon steels.

On the mode-coupling treatment of collective density fluctuations for quantum liquids: para-hydrogen and normal liquid helium.

PubMed

Kletenik-Edelman, Orly; Reichman, David R; Rabani, Eran

2011-01-28

A novel quantum mode coupling theory combined with a kinetic approach is developed for the description of collective density fluctuations in quantum liquids characterized by Boltzmann statistics. Three mode-coupling approximations are presented and applied to study the dynamic response of para-hydrogen near the triple point and normal liquid helium above the λ-transition. The theory is compared with experimental results and to the exact imaginary time data generated by path integral Monte Carlo simulations. While for liquid para-hydrogen the combination of kinetic and quantum mode-coupling theory provides semi-quantitative results for both short and long time dynamics, it fails for normal liquid helium. A discussion of this failure based on the ideal gas limit is presented.

Apparatus for direct-to-digital spatially-heterodyned holography

DOEpatents

Thomas, Clarence E.; Hanson, Gregory R.

2006-12-12

An apparatus operable to record a spatially low-frequency heterodyne hologram including spatially heterodyne fringes for Fourier analysis includes: a laser; a beamsplitter optically coupled to the laser; an object optically coupled to the beamsplitter; a focusing lens optically coupled to both the beamsplitter and the object; a digital recorder optically coupled to the focusing lens; and a computer that performs a Fourier transform, applies a digital filter, and performs an inverse Fourier transform. A reference beam and an object beam are focused by the focusing lens at a focal plane of the digital recorder to form a spatially low-frequency heterodyne hologram including spatially heterodyne fringes for Fourier analysis which is recorded by the digital recorder, and the computer transforms the recorded spatially low-frequency heterodyne hologram including spatially heterodyne fringes and shifts axes in Fourier space to sit on top of a heterodyne carrier frequency defined by an angle between the reference beam and the object beam and cuts off signals around an original origin before performing the inverse Fourier transform.

Kinetic compensation effect in logistic distributed activation energy model for lignocellulosic biomass pyrolysis.

PubMed

Xu, Di; Chai, Meiyun; Dong, Zhujun; Rahman, Md Maksudur; Yu, Xi; Cai, Junmeng

2018-06-04

The kinetic compensation effect in the logistic distributed activation energy model (DAEM) for lignocellulosic biomass pyrolysis was investigated. The sum of square error (SSE) surface tool was used to analyze two theoretically simulated logistic DAEM processes for cellulose and xylan pyrolysis. The logistic DAEM coupled with the pattern search method for parameter estimation was used to analyze the experimental data of cellulose pyrolysis. The results showed that many parameter sets of the logistic DAEM could fit the data at different heating rates very well for both simulated and experimental processes, and a perfect linear relationship between the logarithm of the frequency factor and the mean value of the activation energy distribution was found. The parameters of the logistic DAEM can be estimated by coupling the optimization method and isoconversional kinetic methods. The results would be helpful for chemical kinetic analysis using DAEM. Copyright © 2018 Elsevier Ltd. All rights reserved.

Mechanism and Kinetics of Ethanol Coupling to Butanol over Hydroxyapatite

DOE PAGES

Ho, Christopher R.; Shylesh, Sankaranarayanapillai; Bell, Alexis T.

2015-12-23

The mechanism and kinetics for ethanol coupling to n-butanol over hydroxyapatite (HAP) were investigated at 573-613 K. In situ titration experiments show that the active sites for acetaldehyde and butanol formation are different. In combination with FTIR studies, it was found that ethanol dehydrogenation is catalyzed by Ca-O sites, whereas condensation of acetaldehyde is catalyzed by CaO/PO 4 3- pairs. Measurements of the reaction kinetics at various ethanol (3.5-9.4 kPa) and acetaldehyde (0.055-0.12 kPa) partial pressures reveal that direct condensation involving two ethanol molecules does not play a significant role in butanol formation; instead, n-butanol is formed via a Guerbetmore » pathway. At a constant acetaldehyde pressure, enolate formation is rate-limiting, and ethanol inhibits acetaldehyde condensation rates by competitive adsorption. A model of the reaction kinetics consistent with all experimental observations is developed.« less

Kinetic Resolution of α-Hydroxy-Substituted Oxime Ethers by Enantioselective Cu-H-Catalyzed Si-O Coupling.

PubMed

Dong, Xichang; Kita, Yuji; Oestreich, Martin

2018-04-12

A catalyst-controlled enantioselective alcohol silylation by Cu-H-catalyzed dehydrogenative Si-O coupling of hydroxy groups α to an oxime ether and simple hydrosilanes is reported. The selectivity factors reached in this kinetic resolution are generally high (s≈50), and these reactions thereby provide reliable access to highly enantioenriched α-hydroxy-substituted oxime ethers. The synthetic usefulness of these compounds is also demonstrated. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of grain morphology on gas bubble swelling in UMo fuels – A 3D microstructure dependent Booth model

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

Hu, Shenyang; Burkes, Douglas; Lavender, Curt A.

2016-11-01

A three dimensional microstructure dependent swelling model is developed for studying the fission gas swelling kinetics in irradiated nuclear fuels. The model is extended from the Booth model [1] in order to investigate the effect of heterogeneous microstructures on gas bubble swelling kinetics. As an application of the model, the effect of grain morphology, fission gas diffusivity, and spatial dependent fission rate on swelling kinetics are simulated in UMo fuels. It is found that the decrease of grain size, the increase of grain aspect ratio for the grain having the same volume, and the increase of fission gas diffusivity (fissionmore » rate) cause the increase of swelling kinetics. Other heterogeneities such as second phases and spatial dependent thermodynamic properties including diffusivity of fission gas, sink and source strength of defects could be naturally integrated into the model to enhance the model capability.« less

Electron phonon couplings in 2D perovskite probed by ultrafast photoinduced absorption spectroscopy

NASA Astrophysics Data System (ADS)

Huynh, Uyen; Ni, Limeng; Rao, Akshay

We use the time-resolved photoinduced absorption (PIA) spectroscopy with 20fs time resolution to investigate the electron phonon coupling in the self-assembled hybrid organic layered perovskite, the hexyl ammonium lead iodide compound (C6H13NH3)2 (PbI4) . The coupling results in the broadening and asymmetry of its temperature-dependence photoluminescence spectra. The exact time scale of this coupling, however, wasn't reported experimentally. Here we show that using an ultrashort excitation pulse allows us to resolve from PIA kinetics the oscillation of coherent longitudinal optical phonons that relaxes and self-traps electrons to lower energy states within 200 fs. The 200fs relaxation time is equivalent to a coupling strength of 40meV. Two coupled phonon modes are also identified as about 100 cm-1 and 300 cm-1 from the FFT spectrum of the PIA kinetics. The lower energy mode is consistent with previous reports and Raman spectrum but the higher energy one hasn't been observed before.

Computational Study of Thrombus Formation and Clotting Factor Effects under Venous Flow Conditions

PubMed Central

Govindarajan, Vijay; Rakesh, Vineet; Reifman, Jaques; Mitrophanov, Alexander Y.

2016-01-01

A comprehensive understanding of thrombus formation as a physicochemical process that has evolved to protect the integrity of the human vasculature is critical to our ability to predict and control pathological states caused by a malfunctioning blood coagulation system. Despite numerous investigations, the spatial and temporal details of thrombus growth as a multicomponent process are not fully understood. Here, we used computational modeling to investigate the temporal changes in the spatial distributions of the key enzymatic (i.e., thrombin) and structural (i.e., platelets and fibrin) components within a growing thrombus. Moreover, we investigated the interplay between clot structure and its mechanical properties, such as hydraulic resistance to flow. Our model relied on the coupling of computational fluid dynamics and biochemical kinetics, and was validated using flow-chamber data from a previous experimental study. The model allowed us to identify the distinct patterns characterizing the spatial distributions of thrombin, platelets, and fibrin accumulating within a thrombus. Our modeling results suggested that under the simulated conditions, thrombin kinetics was determined predominantly by prothrombinase. Furthermore, our simulations showed that thrombus resistance imparted by fibrin was ∼30-fold higher than that imparted by platelets. Yet, thrombus-mediated bloodflow occlusion was driven primarily by the platelet deposition process, because the height of the platelet accumulation domain was approximately twice that of the fibrin accumulation domain. Fibrinogen supplementation in normal blood resulted in a nonlinear increase in thrombus resistance, and for a supplemented fibrinogen level of 48%, the thrombus resistance increased by ∼2.7-fold. Finally, our model predicted that restoring the normal levels of clotting factors II, IX, and X while simultaneously restoring fibrinogen (to 88% of its normal level) in diluted blood can restore fibrin generation to ∼78% of its normal level and hence improve clot formation under dilution. PMID:27119646

The Challenges to Coupling Dynamic Geospatial Models

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

Goldstein, N

2006-06-23

Many applications of modeling spatial dynamic systems focus on a single system and a single process, ignoring the geographic and systemic context of the processes being modeled. A solution to this problem is the coupled modeling of spatial dynamic systems. Coupled modeling is challenging for both technical reasons, as well as conceptual reasons. This paper explores the benefits and challenges to coupling or linking spatial dynamic models, from loose coupling, where information transfer between models is done by hand, to tight coupling, where two (or more) models are merged as one. To illustrate the challenges, a coupled model of Urbanizationmore » and Wildfire Risk is presented. This model, called Vesta, was applied to the Santa Barbara, California region (using real geospatial data), where Urbanization and Wildfires occur and recur, respectively. The preliminary results of the model coupling illustrate that coupled modeling can lead to insight into the consequences of processes acting on their own.« less

Determination of High-affinity Antibody-antigen Binding Kinetics Using Four Biosensor Platforms.

PubMed

Yang, Danlin; Singh, Ajit; Wu, Helen; Kroe-Barrett, Rachel

2017-04-17

Label-free optical biosensors are powerful tools in drug discovery for the characterization of biomolecular interactions. In this study, we describe the use of four routinely used biosensor platforms in our laboratory to evaluate the binding affinity and kinetics of ten high-affinity monoclonal antibodies (mAbs) against human proprotein convertase subtilisin kexin type 9 (PCSK9). While both Biacore T100 and ProteOn XPR36 are derived from the well-established Surface Plasmon Resonance (SPR) technology, the former has four flow cells connected by serial flow configuration, whereas the latter presents 36 reaction spots in parallel through an improvised 6 x 6 crisscross microfluidic channel configuration. The IBIS MX96 also operates based on the SPR sensor technology, with an additional imaging feature that provides detection in spatial orientation. This detection technique coupled with the Continuous Flow Microspotter (CFM) expands the throughput significantly by enabling multiplex array printing and detection of 96 reaction sports simultaneously. In contrast, the Octet RED384 is based on the BioLayer Interferometry (BLI) optical principle, with fiber-optic probes acting as the biosensor to detect interference pattern changes upon binding interactions at the tip surface. Unlike the SPR-based platforms, the BLI system does not rely on continuous flow fluidics; instead, the sensor tips collect readings while they are immersed in analyte solutions of a 384-well microplate during orbital agitation. Each of these biosensor platforms has its own advantages and disadvantages. To provide a direct comparison of these instruments' ability to provide quality kinetic data, the described protocols illustrate experiments that use the same assay format and the same high-quality reagents to characterize antibody-antigen kinetics that fit the simple 1:1 molecular interaction model.

Cathodal Transcranial Direct Current Stimulation (tDCS) to the Right Cerebellar Hemisphere Affects Motor Adaptation During Gait.

PubMed

Fernandez, Lara; Albein-Urios, Natalia; Kirkovski, Melissa; McGinley, Jennifer L; Murphy, Anna T; Hyde, Christian; Stokes, Mark A; Rinehart, Nicole J; Enticott, Peter G

2017-02-01

The cerebellum appears to play a key role in the development of internal rules that allow fast, predictive adjustments to novel stimuli. This is crucial for adaptive motor processes, such as those involved in walking, where cerebellar dysfunction has been found to increase variability in gait parameters. Motor adaptation is a process that results in a progressive reduction in errors as movements are adjusted to meet demands, and within the cerebellum, this seems to be localised primarily within the right hemisphere. To examine the role of the right cerebellar hemisphere in adaptive gait, cathodal transcranial direct current stimulation (tDCS) was administered to the right cerebellar hemisphere of 14 healthy adults in a randomised, double-blind, crossover study. Adaptation to a series of distinct spatial and temporal templates was assessed across tDCS condition via a pressure-sensitive gait mat (ProtoKinetics Zeno walkway), on which participants walked with an induced 'limp' at a non-preferred pace. Variability was assessed across key spatial-temporal gait parameters. It was hypothesised that cathodal tDCS to the right cerebellar hemisphere would disrupt adaptation to the templates, reflected in a failure to reduce variability following stimulation. In partial support, adaptation was disrupted following tDCS on one of the four spatial-temporal templates used. However, there was no evidence for general effects on either the spatial or temporal domain. This suggests, under specific conditions, a coupling of spatial and temporal processing in the right cerebellar hemisphere and highlights the potential importance of task complexity in cerebellar function.

Internal loop photo-biodegradation reactor used for accelerated quinoline degradation and mineralization.

PubMed

Chang, Ling; Zhang, Yongming; Gan, Lu; Xu, Hua; Yan, Ning; Liu, Rui; Rittmann, Bruce E

2014-07-01

Biofilm biodegradation was coupled with ultra-violet photolysis using the internal loop photobiodegradation reactor for degradation of quinoline. Three protocols-photolysis alone (P), biodegradation alone (B), and intimately coupled photolysis and biodegradation (P&B)-were used for degradation of quinoline in batch and continuous-flow experiments. For a 1,000 mg/L initial quinoline concentration, the volumetric removal rate for quinoline was 38 % higher with P&B than with B in batch experiments, and the P&B kinetics were the sum of kinetics from the P and B experiments. Continuous-flow experiments with an influent quinoline concentration of 1,000 mg/L also gave significantly greater quinoline removal in P&B, and the quinoline-removal kinetics for P&B were approximately equal to the sum of the removal kinetics for P and B. P&B similarly increased the rate and extent of quinoline mineralization, for which the kinetics for P&B were nearly equal to the sum of kinetics for P and B. These findings support that the rate-limiting step for mineralization was transformation of quinoline, which was accelerated by the simultaneous action of photolysis and biodegradation.

Coarse-Grained Theory of Biological Charge Transfer with Spatially and Temporally Correlated Noise.

PubMed

Liu, Chaoren; Beratan, David N; Zhang, Peng

2016-04-21

System-environment interactions are essential in determining charge-transfer (CT) rates and mechanisms. We developed a computationally accessible method, suitable to simulate CT in flexible molecules (i.e., DNA) with hundreds of sites, where the system-environment interactions are explicitly treated with numerical noise modeling of time-dependent site energies and couplings. The properties of the noise are tunable, providing us a flexible tool to investigate the detailed effects of correlated thermal fluctuations on CT mechanisms. The noise is parametrizable by molecular simulation and quantum calculation results of specific molecular systems, giving us better molecular resolution in simulating the system-environment interactions than sampling fluctuations from generic spectral density functions. The spatially correlated thermal fluctuations among different sites are naturally built-in in our method but are not readily incorporated using approximate spectral densities. Our method has quantitative accuracy in systems with small redox potential differences (

Magnetohydrodynamics with Embedded Particle-in-Cell Simulation of Mercury's Magnetosphere

NASA Astrophysics Data System (ADS)

Chen, Y.; Toth, G.; Jia, X.; Gombosi, T. I.; Markidis, S.

2015-12-01

Mercury's magnetosphere is much more dynamic than other planetary magnetospheres because of Mercury's weak intrinsic magnetic field and its proximity to the Sun. Magnetic reconnection and Kelvin-Helmholtz phenomena occur in Mercury's magnetopause and magnetotail at higher frequencies than in other planetary magnetosphere. For instance, chains of flux transfer events (FTEs) on the magnetopause, have been frequentlyobserved by the the MErcury Surface, Space ENvironment, GEochemistry and Ranging (MESSENGER) spacecraft (Slavin et al., 2012). Because ion Larmor radius is comparable to typical spatial scales in Mercury's magnetosphere, finite Larmor radius effects need to be accounted for. In addition, it is important to take in account non-ideal dissipation mechanisms to accurately describe magnetic reconnection. A kinetic approach allows us to model these phenomena accurately. However, kinetic global simulations, even for small-size magnetospheres like Mercury's, are currently unfeasible because of the high computational cost. In this work, we carry out global simulations of Mercury's magnetosphere with the recently developed MHD-EPIC model, which is a two-way coupling of the extended magnetohydrodynamic (XMHD) code BATS-R-US with the implicit Particle-in-Cell (PIC) model iPIC3D. The PIC model can cover the regions where kinetic effects are most important, such as reconnection sites. The BATS-R-US code, on the other hand, can efficiently handle the rest of the computational domain where the MHD or Hall MHD description is sufficient. We will present our preliminary results and comparison with MESSENGER observations.

Kinetic attractor phase diagrams of active nematic suspensions: the dilute regime.

PubMed

Forest, M Gregory; Wang, Qi; Zhou, Ruhai

2015-08-28

Large-scale simulations by the authors of the kinetic-hydrodynamic equations for active polar nematics revealed a variety of spatio-temporal attractors, including steady and unsteady, banded (1d) and cellular (2d) spatial patterns. These particle scale activation-induced attractors arise at dilute nanorod volume fractions where the passive equilibrium phase is isotropic, whereas all previous model simulations have focused on the semi-dilute, nematic equilibrium regime and mostly on low-moment orientation tensor and polarity vector models. Here we extend our previous results to complete attractor phase diagrams for active nematics, with and without an explicit polar potential, to map out novel spatial and dynamic transitions, and to identify some new attractors, over the parameter space of dilute nanorod volume fraction and nanorod activation strength. The particle-scale activation parameter corresponds experimentally to a tunable force dipole strength (so-called pushers with propulsion from the rod tail) generated by active rod macromolecules, e.g., catalysis with the solvent phase, ATP-induced propulsion, or light-activated propulsion. The simulations allow 2d spatial variations in all flow and orientational variables and full spherical orientational degrees of freedom; the attractors correspond to numerical integration of a coupled system of 125 nonlinear PDEs in 2d plus time. The phase diagrams with and without the polar interaction potential are remarkably similar, implying that polar interactions among the rodlike particles are not essential to long-range spatial and temporal correlations in flow, polarity, and nematic order. As a general rule, above a threshold, low volume fractions induce 1d banded patterns, whereas higher yet still dilute volume fractions yield 2d patterns. Again as a general rule, varying activation strength at fixed volume fraction induces novel dynamic transitions. First, stationary patterns saturate the instability of the isotropic state, consisting of discrete 1d banded or 2d cellular patterns depending on nanorod volume fraction. Increasing activation strength further induces a sequence of attractor bifurcations, including oscillations superimposed on the 1d and 2d stationary patterns, a uniform translational motion of 1d and 2d oscillating patterns, and periodic switching between 1d and 2d patterns. These results imply that active macromolecular suspensions are capable of long-range spatial and dynamic organization at isotropic equilibrium concentrations, provided particle-scale activation is sufficiently strong.

Methodology for extracting local constants from petroleum cracking flows

DOEpatents

Chang, Shen-Lin; Lottes, Steven A.; Zhou, Chenn Q.

2000-01-01

A methodology provides for the extraction of local chemical kinetic model constants for use in a reacting flow computational fluid dynamics (CFD) computer code with chemical kinetic computations to optimize the operating conditions or design of the system, including retrofit design improvements to existing systems. The coupled CFD and kinetic computer code are used in combination with data obtained from a matrix of experimental tests to extract the kinetic constants. Local fluid dynamic effects are implicitly included in the extracted local kinetic constants for each particular application system to which the methodology is applied. The extracted local kinetic model constants work well over a fairly broad range of operating conditions for specific and complex reaction sets in specific and complex reactor systems. While disclosed in terms of use in a Fluid Catalytic Cracking (FCC) riser, the inventive methodology has application in virtually any reaction set to extract constants for any particular application and reaction set formulation. The methodology includes the step of: (1) selecting the test data sets for various conditions; (2) establishing the general trend of the parametric effect on the measured product yields; (3) calculating product yields for the selected test conditions using coupled computational fluid dynamics and chemical kinetics; (4) adjusting the local kinetic constants to match calculated product yields with experimental data; and (5) validating the determined set of local kinetic constants by comparing the calculated results with experimental data from additional test runs at different operating conditions.

Relativistic theory of nuclear spin-rotation tensor with kinetically balanced rotational London orbitals

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

Xiao, Yunlong; Zhang, Yong; Liu, Wenjian, E-mail: liuwjbdf@gmail.com

2014-10-28

Both kinetically balanced (KB) and kinetically unbalanced (KU) rotational London orbitals (RLO) are proposed to resolve the slow basis set convergence in relativistic calculations of nuclear spin-rotation (NSR) coupling tensors of molecules containing heavy elements [Y. Xiao and W. Liu, J. Chem. Phys. 138, 134104 (2013)]. While they perform rather similarly, the KB-RLO Ansatz is clearly preferred as it ensures the correct nonrelativistic limit even with a finite basis. Moreover, it gives rise to the same “direct relativistic mapping” between nuclear magnetic resonance shielding and NSR coupling tensors as that without using the London orbitals [Y. Xiao, Y. Zhang, andmore » W. Liu, J. Chem. Theory Comput. 10, 600 (2014)].« less

Ring Current Ion Coupling with Electromagnetic Ion Cyclotron Waves

NASA Technical Reports Server (NTRS)

Khazanov. G. V.; Gamayunov, K. V.; Jordanova, V. K.; Six, N. Frank (Technical Monitor)

2002-01-01

A new ring current global model has been developed that couples the system of two kinetic equations: one equation describes the ring current (RC) ion dynamic, and another equation describes wave evolution of electromagnetic ion cyclotron waves (EMIC). The coupled model is able to simulate, for the first time self-consistently calculated RC ion kinetic and evolution of EMIC waves that propagate along geomagnetic field lines and reflect from the ionosphere. Ionospheric properties affect the reflection index through the integral Pedersen and Hall conductivities. The structure and dynamics of the ring current proton precipitating flux regions, intensities of EMIC global RC energy balance, and some other parameters will be studied in detail for the selected geomagnetic storms.

Lunar Crater Mini-Wakes: Structure, Variability, and Volatiles

NASA Technical Reports Server (NTRS)

Zimmerman, Michael I.; Jackson, T. L.; Farrell, W. M.; Stubbs, T. J.

2012-01-01

Within a permanently shadowed lunar crater the horizontal flow of solar wind is obstructed by upstream topography, forming a regional plasma mini-wake. In the present work kinetic simulations are utilized to investigate how the most prominent structural aspects of a crater mini-wake are modulated during passage of a solar storm. In addition, the simulated particle fluxes are coupled into an equivalent-circuit model of a roving astronaut,. including triboelectric charging due to frictional contact with the lunar regolith, to characterize charging of the astronaut suit during the various stages of the storm. In some cases, triboelectric charging of the astronaut suit becomes effectively perpetual, representing a critical engineering concern for roving within shadowed lunar regions. Finally, the present results suggest that wake structure plays a critical role in modulating the spatial distribution of volatiles at the lunar poles.

Kinetic study of an enzymic cycling system coupled to an enzymic step: determination of alkaline phosphatase activity.

PubMed Central

Valero, E; Varón, R; García-Carmona, F

1995-01-01

A kinetic study is made of a system consisting of a specific enzymic cycling assay coupled to an enzymic reaction. A kinetic analysis of this system is presented, and the accumulation of chromophore involved in the cycle is seen to be parabolic, i.e. the rate of the reaction increases continuously with constant acceleration. The system is illustrated by the measurement of alkaline phosphatase activity using beta-NADP+ as substrate. The enzymes alcohol dehydrogenase and diaphorase are used to cycle beta-NAD+ in the presence of ethanol and p-Iodonitrotetrazolium Violet. During each turn of the cycle, one molecule of the tetrazolium salt is reduced to an intensely coloured formazan. A simple procedure for evaluating the kinetic parameters involved in the system and for optimizing this cycling assay is described. The method is applicable to the measurement of any enzyme, and its amplification capacity as well as the simplicity of determining kinetic parameters enable it to be employed in enzyme immunoassays to increase the magnitude of the measured response. PMID:7619054

Model of Inclusion Evolution During Calcium Treatment in the Ladle Furnace

NASA Astrophysics Data System (ADS)

Tabatabaei, Yousef; Coley, Kenneth S.; Irons, Gordon A.; Sun, Stanley

2018-04-01

Calcium treatment of steel is typically employed to modify alumina inclusions to liquid calcium aluminates. However, injected calcium also reacts with the dissolved sulfur to form calcium sulfide. The current work aims to develop a kinetic model for the evolution of oxide and sulfide inclusions in Al-killed alloyed steel during Ca treatment in the ladle refining process. The model considers dissolution of the calcium from the calcium bubbles into the steel and reduction of calcium oxide in the slag to dissolved calcium. A steel-inclusion kinetic model is used for mass transfer to the inclusion interface and diffusion within the calcium aluminate phases formed on the inclusion. The inclusion-steel kinetic model is then coupled with a previously developed steel-slag kinetic model. The coupled inclusion-steel-slag kinetic model is applied to the chemical composition changes in molten steel, slag, and evolution of inclusions in the ladle. The result of calculations is found to agree well with an industrial heat for species in the steel as well as inclusions during Ca treatment.

Dynamic Model of Basic Oxygen Steelmaking Process Based on Multi-zone Reaction Kinetics: Model Derivation and Validation

NASA Astrophysics Data System (ADS)

Rout, Bapin Kumar; Brooks, Geoff; Rhamdhani, M. Akbar; Li, Zushu; Schrama, Frank N. H.; Sun, Jianjun

2018-04-01

A multi-zone kinetic model coupled with a dynamic slag generation model was developed for the simulation of hot metal and slag composition during the basic oxygen furnace (BOF) operation. The three reaction zones (i) jet impact zone, (ii) slag-bulk metal zone, (iii) slag-metal-gas emulsion zone were considered for the calculation of overall refining kinetics. In the rate equations, the transient rate parameters were mathematically described as a function of process variables. A micro and macroscopic rate calculation methodology (micro-kinetics and macro-kinetics) were developed to estimate the total refining contributed by the recirculating metal droplets through the slag-metal emulsion zone. The micro-kinetics involves developing the rate equation for individual droplets in the emulsion. The mathematical models for the size distribution of initial droplets, kinetics of simultaneous refining of elements, the residence time in the emulsion, and dynamic interfacial area change were established in the micro-kinetic model. In the macro-kinetics calculation, a droplet generation model was employed and the total amount of refining by emulsion was calculated by summing the refining from the entire population of returning droplets. A dynamic FetO generation model based on oxygen mass balance was developed and coupled with the multi-zone kinetic model. The effect of post-combustion on the evolution of slag and metal composition was investigated. The model was applied to a 200-ton top blowing converter and the simulated value of metal and slag was found to be in good agreement with the measured data. The post-combustion ratio was found to be an important factor in controlling FetO content in the slag and the kinetics of Mn and P in a BOF process.

Hydrogen measurement during steam oxidation using coupled thermogravimetric analysis and quadrupole mass spectrometry

DOE PAGES

Parkison, Adam J.; Nelson, Andrew Thomas

2016-01-11

An analytical technique is presented with the goal of measuring reaction kinetics during steam oxidation reactions for three cases in which obtaining kinetics information often requires a prohibitive amount of time and cost. The technique presented relies on coupling thermogravimetric analysis (TGA) with a quantitative hydrogen measurement technique using quadrupole mass spectrometry (QMS). The first case considered is in differentiating between the kinetics of steam oxidation reactions and those for simultaneously reacting gaseous impurities such as nitrogen or oxygen. The second case allows one to independently measure the kinetics of oxide and hydride formation for systems in which both ofmore » these reactions are known to take place during steam oxidation. The third case deals with measuring the kinetics of formation for competing volatile and non-volatile oxides during certain steam oxidation reactions. In order to meet the requirements of the coupled technique, a methodology is presented which attempts to provide quantitative measurement of hydrogen generation using QMS in the presence of an interfering fragmentation species, namely water vapor. This is achieved such that all calibrations and corrections are performed during the TGA baseline and steam oxidation programs, making system operation virtually identical to standard TGA. Benchmarking results showed a relative error in hydrogen measurement of 5.7–8.4% following the application of a correction factor. Lastly, suggestions are made for possible improvements to the presented technique so that it may be better applied to the three cases presented.« less

Weakening gravity on redshift-survey scales with kinetic matter mixing

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

D'Amico, Guido; Huang, Zhiqi; Mancarella, Michele

We explore general scalar-tensor models in the presence of a kinetic mixing between matter and the scalar field, which we call Kinetic Matter Mixing. In the frame where gravity is de-mixed from the scalar this is due to disformal couplings of matter species to the gravitational sector, with disformal coefficients that depend on the gradient of the scalar field. In the frame where matter is minimally coupled, it originates from the so-called beyond Horndeski quadratic Lagrangian. We extend the Effective Theory of Interacting Dark Energy by allowing disformal coupling coefficients to depend on the gradient of the scalar field asmore » well. In this very general approach, we derive the conditions to avoid ghost and gradient instabilities and we define Kinetic Matter Mixing independently of the frame metric used to described the action. We study its phenomenological consequences for a ΛCDM background evolution, first analytically on small scales. Then, we compute the matter power spectrum and the angular spectra of the CMB anisotropies and the CMB lensing potential, on all scales. We employ the public version of COOP, a numerical Einstein-Boltzmann solver that implements very general scalar-tensor modifications of gravity. Rather uniquely, Kinetic Matter Mixing weakens gravity on short scales, predicting a lower σ{sub 8} with respect to the ΛCDM case. We propose this as a possible solution to the tension between the CMB best-fit model and low-redshift observables.« less

Hydrogen measurement during steam oxidation using coupled thermogravimetric analysis and quadrupole mass spectrometry

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

Parkison, Adam J.; Nelson, Andrew Thomas

An analytical technique is presented with the goal of measuring reaction kinetics during steam oxidation reactions for three cases in which obtaining kinetics information often requires a prohibitive amount of time and cost. The technique presented relies on coupling thermogravimetric analysis (TGA) with a quantitative hydrogen measurement technique using quadrupole mass spectrometry (QMS). The first case considered is in differentiating between the kinetics of steam oxidation reactions and those for simultaneously reacting gaseous impurities such as nitrogen or oxygen. The second case allows one to independently measure the kinetics of oxide and hydride formation for systems in which both ofmore » these reactions are known to take place during steam oxidation. The third case deals with measuring the kinetics of formation for competing volatile and non-volatile oxides during certain steam oxidation reactions. In order to meet the requirements of the coupled technique, a methodology is presented which attempts to provide quantitative measurement of hydrogen generation using QMS in the presence of an interfering fragmentation species, namely water vapor. This is achieved such that all calibrations and corrections are performed during the TGA baseline and steam oxidation programs, making system operation virtually identical to standard TGA. Benchmarking results showed a relative error in hydrogen measurement of 5.7–8.4% following the application of a correction factor. Lastly, suggestions are made for possible improvements to the presented technique so that it may be better applied to the three cases presented.« less

Three-dimensional spectral-spatial EPR imaging of free radicals in the heart: a technique for imaging tissue metabolism and oxygenation.

PubMed Central

Kuppusamy, P; Chzhan, M; Vij, K; Shteynbuk, M; Lefer, D J; Giannella, E; Zweier, J L

1994-01-01

It has been hypothesized that free radical metabolism and oxygenation in living organs and tissues such as the heart may vary over the spatially defined tissue structure. In an effort to study these spatially defined differences, we have developed electron paramagnetic resonance imaging instrumentation enabling the performance of three-dimensional spectral-spatial images of free radicals infused into the heart and large vessels. Using this instrumentation, high-quality three-dimensional spectral-spatial images of isolated perfused rat hearts and rabbit aortas are obtained. In the isolated aorta, it is shown that spatially and spectrally accurate images of the vessel lumen and wall could be obtained in this living vascular tissue. In the isolated rat heart, imaging experiments were performed to determine the kinetics of radical clearance at different spatial locations within the heart during myocardial ischemia. The kinetic data show the existence of regional and transmural differences in myocardial free radical clearance. It is further demonstrated that EPR imaging can be used to noninvasively measure spatially localized oxygen concentrations in the heart. Thus, the technique of spectral-spatial EPR imaging is shown to be a powerful tool in providing spatial information regarding the free radical distribution, metabolism, and tissue oxygenation in living biological organs and tissues. Images PMID:8159757

Development of SSUBPIC code for modeling the neutral gas depletion effect in helicon discharges

NASA Astrophysics Data System (ADS)

Kollasch, Jeffrey; Sovenic, Carl; Schmitz, Oliver

2017-10-01

The SSUBPIC (steady-state unstructured-boundary particle-in-cell) code is being developed to model helicon plasma devices. The envisioned modeling framework incorporates (1) a kinetic neutral particle model, (2) a kinetic ion model, (3) a fluid electron model, and (4) an RF power deposition model. The models are loosely coupled and iterated until convergence to steady-state. Of the four required solvers, the kinetic ion and neutral particle simulation can now be done within the SSUBPIC code. Recent SSUBPIC modifications include implementation and testing of a Coulomb collision model (Lemons et al., JCP, 228(5), pp. 1391-1403) allowing efficient coupling of kineticly-treated ions to fluid electrons, and implementation of a neutral particle tracking mode with charge-exchange and electron impact ionization physics. These new simulation capabilities are demonstrated working independently and coupled to ``dummy'' profiles for RF power deposition to converge on steady-state plasma and neutral profiles. The geometry and conditions considered are similar to those of the MARIA experiment at UW-Madison. Initial results qualitatively show the expected neutral gas depletion effect in which neutrals in the plasma core are not replenished at a sufficient rate to sustain a higher plasma density. This work is funded by the NSF CAREER award PHY-1455210 and NSF Grant PHY-1206421.

Implementation of logic functions and computations by chemical kinetics

NASA Astrophysics Data System (ADS)

Hjelmfelt, A.; Ross, J.

We review our work on the computational functions of the kinetics of chemical networks. We examine spatially homogeneous networks which are based on prototypical reactions occurring in living cells and show the construction of logic gates and sequential and parallel networks. This work motivates the study of an important biochemical pathway, glycolysis, and we demonstrate that the switch that controls the flux in the direction of glycolysis or gluconeogenesis may be described as a fuzzy AND operator. We also study a spatially inhomogeneous network which shares features of theoretical and biological neural networks.

Ischemia reperfusion dysfunction changes model-estimated kinetics of myofilament interaction due to inotropic drugs in isolated hearts

PubMed Central

Rhodes, Samhita S; Camara, Amadou KS; Ropella, Kristina M; Audi, Said H; Riess, Matthias L; Pagel, Paul S; Stowe, David F

2006-01-01

Background The phase-space relationship between simultaneously measured myoplasmic [Ca2+] and isovolumetric left ventricular pressure (LVP) in guinea pig intact hearts is altered by ischemic and inotropic interventions. Our objective was to mathematically model this phase-space relationship between [Ca2+] and LVP with a focus on the changes in cross-bridge kinetics and myofilament Ca2+ sensitivity responsible for alterations in Ca2+-contraction coupling due to inotropic drugs in the presence and absence of ischemia reperfusion (IR) injury. Methods We used a four state computational model to predict LVP using experimentally measured, averaged myoplasmic [Ca2+] transients from unpaced, isolated guinea pig hearts as the model input. Values of model parameters were estimated by minimizing the error between experimentally measured LVP and model-predicted LVP. Results We found that IR injury resulted in reduced myofilament Ca2+ sensitivity, and decreased cross-bridge association and dissociation rates. Dopamine (8 μM) reduced myofilament Ca2+ sensitivity before, but enhanced it after ischemia while improving cross-bridge kinetics before and after IR injury. Dobutamine (4 μM) reduced myofilament Ca2+ sensitivity while improving cross-bridge kinetics before and after ischemia. Digoxin (1 μM) increased myofilament Ca2+ sensitivity and cross-bridge kinetics after but not before ischemia. Levosimendan (1 μM) enhanced myofilament Ca2+ affinity and cross-bridge kinetics only after ischemia. Conclusion Estimated model parameters reveal mechanistic changes in Ca2+-contraction coupling due to IR injury, specifically the inefficient utilization of Ca2+ for contractile function with diastolic contracture (increase in resting diastolic LVP). The model parameters also reveal drug-induced improvements in Ca2+-contraction coupling before and after IR injury. PMID:16512898

Analysis of energy relaxation kinetics for control of the electron energy distributions in capacitively coupled RF discharges

NASA Astrophysics Data System (ADS)

Lee, Jung Yeol; Verboncoeur, John P.; Lee, Hae June

2018-04-01

The transition of electron energy probability functions (EEPFs) through the change of heating mode is an important issue in plasma science. A well-known example is that the increase of gas pressure, which was analyzed in terms of the ratio of the energy relaxation mean free path to the electrode gap distance, changes the EEPF from bi-Maxwellian to Maxwellian or Druyvesteyn. In this study, a new aspect of the temporal decay of kinetic energy during the energy relaxation time is theoretically analyzed and compared with a particle-in-cell Monte Carlo collision simulation of capacitively coupled plasmas. A fully kinetic description of electron transport and collisions shows drastic changes of EEPFs with the variation of the driving frequency due to the heating mode transition.

Influence of Proton Acceptors on the Proton-Coupled Electron Transfer Reaction Kinetics of a Ruthenium-Tyrosine Complex.

PubMed

Lennox, J Christian; Dempsey, Jillian L

2017-11-22

A polypyridyl ruthenium complex with fluorinated bipyridine ligands and a covalently bound tyrosine moiety was synthesized, and its photo-induced proton-coupled electron transfer (PCET) reactivity in acetonitrile was investigated with transient absorption spectroscopy. Using flash-quench methodology with methyl viologen as an oxidative quencher, a Ru 3+ species is generated that is capable of initiating the intramolecular PCET oxidation of the tyrosine moiety. Using a series of substituted pyridine bases, the reaction kinetics were found to vary as a function of proton acceptor concentration and identity, with no significant H/D kinetic isotope effect. Through analysis of the kinetics traces and comparison to a control complex without the tyrosine moiety, PCET reactivity was found to proceed through an equilibrium electron transfer followed by proton transfer (ET-PT) pathway in which irreversible deprotonation of the tyrosine radical cation shifts the ET equilibrium, conferring a base dependence on the reaction. Comprehensive kinetics modeling allowed for deconvolution of complex kinetics and determination of rate constants for each elementary step. Across the five pyridine bases explored, spanning a range of 4.2 pK a units, a linear free-energy relationship was found for the proton transfer rate constant with a slope of 0.32. These findings highlight the influence that proton transfer driving force exerts on PCET reaction kinetics.

Understanding titanium-catalysed radical-radical reactions: a DFT study unravels the complex kinetics of ketone-nitrile couplings.

PubMed

Streuff, Jan; Himmel, Daniel; Younas, Sara L

2018-04-03

The computational investigation of a titanium-catalysed reductive radical-radical coupling is reported. The results match the conclusions from an earlier experimental study and enable a further interpretation of the previously observed complex reaction kinetics. Furthermore, the interplay between neutral and cationic reaction pathways in titanium(iii)-catalysed reactions is investigated for the first time. The results show that hydrochloride additives and reaction byproducts play an important role in the respective equilibria. A full reaction profile is assembled and the computed activation barrier is found to be in reasonable agreement with the experiment. The conclusions are of fundamental importance to the field of low-valent titanium catalysis and the understanding of related catalytic radical-radical coupling reactions.

Were inefficient mitochondrial haplogroups selected during migrations of modern humans? A test using modular kinetic analysis of coupling in mitochondria from cybrid cell lines.

PubMed

Amo, Taku; Brand, Martin D

2007-06-01

We introduce a general test of the bioenergetic importance of mtDNA (mitochondrial DNA) variants: modular kinetic analysis of oxidative phosphorylation in mitochondria from cybrid cells with constant nuclear DNA but different mtDNA. We have applied this test to the hypothesis [Ruiz-Pesini, Mishmar, Brandon, Procaccio and Wallace (2004) Science 303, 223-226] that particular mtDNA haplogroups (specific combinations of polymorphisms) that cause lowered coupling efficiency, leading to generation of less ATP and more heat, were positively selected during radiations of modern humans into colder climates. Contrary to the predictions of this hypothesis, mitochondria from Arctic haplogroups had similar or even greater coupling efficiency than mitochondria from tropical haplogroups.

Stability of Einstein static universe in gravity theory with a non-minimal derivative coupling

NASA Astrophysics Data System (ADS)

Huang, Qihong; Wu, Puxun; Yu, Hongwei

2018-01-01

The emergent mechanism provides a possible way to resolve the big-bang singularity problem by assuming that our universe originates from the Einstein static (ES) state. Thus, the existence of a stable ES solution becomes a very crucial prerequisite for the emergent scenario. In this paper, we study the stability of an ES universe in gravity theory with a non-minimal coupling between the kinetic term of a scalar field and the Einstein tensor. We find that the ES solution is stable under both scalar and tensor perturbations when the model parameters satisfy certain conditions, which indicates that the big-bang singularity can be avoided successfully by the emergent mechanism in the non-minimally kinetic coupled gravity.

CALIBRATION OF FULL-SCALE OZONATION SYSTEMS WITH CONSERVATIVE AND REACTIVE TRACERS

EPA Science Inventory

A full-scale ozonation reactor was characterized with respect to the overall oxidation budget by coupling laboratory kinetics with reactor hydraulics. The ozone decomposition kinetics and the ratio of the OH radical to the ozone concentration were determined in laboratory batch ...

Quantum kinetic expansion in the spin-boson model: Matrix formulation and system-bath factorized initial state.

PubMed

Gong, Zhihao; Tang, Zhoufei; Wang, Haobin; Wu, Jianlan

2017-12-28

Within the framework of the hierarchy equation of motion (HEOM), the quantum kinetic expansion (QKE) method of the spin-boson model is reformulated in the matrix representation. The equivalence between the two formulations (HEOM matrices and quantum operators) is numerically verified from the calculation of the time-integrated QKE rates. The matrix formulation of the QKE is extended to the system-bath factorized initial state. Following a one-to-one mapping between HEOM matrices and quantum operators, a quantum kinetic equation is rederived. The rate kernel is modified by an extra term following a systematic expansion over the site-site coupling. This modified QKE is numerically tested for its reliability by calculating the time-integrated rate and non-Markovian population kinetics. For an intermediate-to-strong dissipation strength and a large site-site coupling, the population transfer is found to be significantly different when the initial condition is changed from the local equilibrium to system-bath factorized state.

Model-based analysis of coupled equilibrium-kinetic processes: indirect kinetic studies of thermodynamic parameters using the dynamic data.

PubMed

Emami, Fereshteh; Maeder, Marcel; Abdollahi, Hamid

2015-05-07

Thermodynamic studies of equilibrium chemical reactions linked with kinetic procedures are mostly impossible by traditional approaches. In this work, the new concept of generalized kinetic study of thermodynamic parameters is introduced for dynamic data. The examples of equilibria intertwined with kinetic chemical mechanisms include molecular charge transfer complex formation reactions, pH-dependent degradation of chemical compounds and tautomerization kinetics in micellar solutions. Model-based global analysis with the possibility of calculating and embedding the equilibrium and kinetic parameters into the fitting algorithm has allowed the complete analysis of the complex reaction mechanisms. After the fitting process, the optimal equilibrium and kinetic parameters together with an estimate of their standard deviations have been obtained. This work opens up a promising new avenue for obtaining equilibrium constants through the kinetic data analysis for the kinetic reactions that involve equilibrium processes.

Boundary Conditions for Diffusion-Mediated Processes within Linear Nanopores: Exact Treatment of Coupling to an Equilibrated External Fluid

DOE PAGES

Garcia, Andres; Evans, James W.

2017-04-03

In this paper, we consider a variety of diffusion-mediated processes occurring within linear nanopores, but which involve coupling to an equilibrated external fluid through adsorption and desorption. By determining adsorption and desorption rates through a set of tailored simulations, and by exploiting a spatial Markov property of the models, we develop a formulation for performing efficient pore-only simulations of these processes. Coupling to the external fluid is described exactly through appropriate nontrivial boundary conditions at the pore openings. This formalism is applied to analyze the following: (i) tracer counter permeation (TCP) where different labeled particles adsorb into opposite ends ofmore » the pore and establish a nonequilibrium steady state; (ii) tracer exchange (TE) with exchange of differently labeled particles within and outside the pore; (iii) catalytic conversion reactions where a reactant in the external fluid adsorbs into the pore and converts to a product which may desorb. The TCP analysis also generates a position-dependent generalized tracer diffusion coefficient, the form of which controls behavior in the TE and catalytic conversion processes. We focus on the regime of single-file diffusion within the pore which produces the strongest correlations and largest deviations from mean-field type behavior. Finally, behavior is quantified precisely via kinetic Monte Carlo simulations but is also captured with appropriate analytic treatments.« less

Reaction diffusion in the NiCrAl and CoCrAl systems

NASA Technical Reports Server (NTRS)

Levine, S. R.

1978-01-01

The paper assesses the effect of overlay coating and substrate composition on the kinetics of coating depletion by interdiffusion. This is accomplished by examining the constitution, kinetics and activation energies for a series of diffusion couples primarily of the NiCrAl/Ni-10Cr or CoCrAl/Ni-10Cr type annealed at temperatures in the range 1000-1205 C for times up to 500 hr. A general procedure is developed for analyzing diffusion in multicomponent multiphase systems. It is shown that by introducing the concept of beta-source strength, which can be determined from appropriate phase diagrams, the Wagner solution for consumption of a second phase in a semiinfinite couple is successfully applied to the analysis of MCrAl couples. Thus, correlation of beta-recession rate constants with couple composition, total and diffusional activation energies, and interdiffusion coefficients are determined.

Symmetric Absorber-Coupled Far-Infrared Microwave Kinetic Inductance Detector

NASA Technical Reports Server (NTRS)

U-yen, Kongpop (Inventor); Wollack, Edward J. (Inventor); Brown, Ari D. (Inventor); Stevenson, Thomas R. (Inventor); Patel, Amil A. (Inventor)

2016-01-01

The present invention relates to a symmetric absorber-coupled far-infrared microwave kinetic inductance detector including: a membrane having an absorber disposed thereon in a symmetric cross bar pattern; and a microstrip including a plurality of conductor microstrip lines disposed along all edges of the membrane, and separated from a ground plane by the membrane. The conducting microstrip lines are made from niobium, and the pattern is made from a superconducting material with a transition temperature below niobium, including one of aluminum, titanium nitride, or molybdenum nitride. The pattern is disposed on both a top and a bottom of the membrane, and creates a parallel-plate coupled transmission line on the membrane that acts as a half-wavelength resonator at readout frequencies. The parallel-plate coupled transmission line and the conductor microstrip lines form a stepped impedance resonator. The pattern provides identical power absorption for both horizontal and vertical polarization signals.

Differential segregation in a cell-cell contact interface: the dynamics of the immunological synapse.

PubMed Central

Burroughs, Nigel John; Wülfing, Christoph

2002-01-01

Receptor-ligand couples in the cell-cell contact interface between a T cell and an antigen-presenting cell form distinct geometric patterns and undergo spatial rearrangement within the contact interface. Spatial segregation of the antigen and adhesion receptors occurs within seconds of contact, central aggregation of the antigen receptor then occurring over 1-5 min. This structure, called the immunological synapse, is becoming a paradigm for localized signaling. However, the mechanisms driving its formation, in particular spatial segregation, are currently not understood. With a reaction diffusion model incorporating thermodynamics, elasticity, and reaction kinetics, we examine the hypothesis that differing bond lengths (extracellular domain size) is the driving force behind molecular segregation. We derive two key conditions necessary for segregation: a thermodynamic criterion on the effective bond elasticity and a requirement for the seeding/nucleation of domains. Domains have a minimum length scale and will only spontaneously coalesce/aggregate if the contact area is small or the membrane relaxation distance large. Otherwise, differential attachment of receptors to the cytoskeleton is required for central aggregation. Our analysis indicates that differential bond lengths have a significant effect on synapse dynamics, i.e., there is a significant contribution to the free energy of the interaction, suggesting that segregation by differential bond length is important in cell-cell contact interfaces and the immunological synapse. PMID:12324401

Kinetic theory molecular dynamics and hot dense matter: theoretical foundations.

PubMed

Graziani, F R; Bauer, J D; Murillo, M S

2014-09-01

Electrons are weakly coupled in hot, dense matter that is created in high-energy-density experiments. They are also mildly quantum mechanical and the ions associated with them are classical and may be strongly coupled. In addition, the dynamical evolution of plasmas under these hot, dense matter conditions involve a variety of transport and energy exchange processes. Quantum kinetic theory is an ideal tool for treating the electrons but it is not adequate for treating the ions. Molecular dynamics is perfectly suited to describe the classical, strongly coupled ions but not the electrons. We develop a method that combines a Wigner kinetic treatment of the electrons with classical molecular dynamics for the ions. We refer to this hybrid method as "kinetic theory molecular dynamics," or KTMD. The purpose of this paper is to derive KTMD from first principles and place it on a firm theoretical foundation. The framework that KTMD provides for simulating plasmas in the hot, dense regime is particularly useful since current computational methods are generally limited by their inability to treat the dynamical quantum evolution of the electronic component. Using the N-body von Neumann equation for the electron-proton plasma, three variations of KTMD are obtained. Each variant is determined by the physical state of the plasma (e.g., collisional versus collisionless). The first variant of KTMD yields a closed set of equations consisting of a mean-field quantum kinetic equation for the electron one-particle distribution function coupled to a classical Liouville equation for the protons. The latter equation includes both proton-proton Coulombic interactions and an effective electron-proton interaction that involves the convolution of the electron density with the electron-proton Coulomb potential. The mean-field approach is then extended to incorporate equilibrium electron-proton correlations through the Singwi-Tosi-Land-Sjolander (STLS) ansatz. This is the second variant of KTMD. The STLS contribution produces an effective electron-proton interaction that involves the electron-proton structure factor, thereby extending the usual mean-field theory to correlated but near equilibrium systems. Finally, a third variant of KTMD is derived. It includes dynamical electrons and their correlations coupled to a MD description for the ions. A set of coupled equations for the one-particle electron Wigner function and the electron-electron and electron-proton correlation functions are coupled to a classical Liouville equation for the protons. This latter variation has both time and momentum dependent correlations.

Status of MUSIC, the MUltiwavelength Sub/millimeter Inductance Camera

NASA Astrophysics Data System (ADS)

Golwala, Sunil R.; Bockstiegel, Clint; Brugger, Spencer; Czakon, Nicole G.; Day, Peter K.; Downes, Thomas P.; Duan, Ran; Gao, Jiansong; Gill, Amandeep K.; Glenn, Jason; Hollister, Matthew I.; LeDuc, Henry G.; Maloney, Philip R.; Mazin, Benjamin A.; McHugh, Sean G.; Miller, David; Noroozian, Omid; Nguyen, Hien T.; Sayers, Jack; Schlaerth, James A.; Siegel, Seth; Vayonakis, Anastasios K.; Wilson, Philip R.; Zmuidzinas, Jonas

2012-09-01

We present the status of MUSIC, the MUltiwavelength Sub/millimeter Inductance Camera, a new instrument for the Caltech Submillimeter Observatory. MUSIC is designed to have a 14', diffraction-limited field-of-view instrumented with 2304 detectors in 576 spatial pixels and four spectral bands at 0.87, 1.04, 1.33, and 1.98 mm. MUSIC will be used to study dusty star-forming galaxies, galaxy clusters via the Sunyaev-Zeldovich effect, and star formation in our own and nearby galaxies. MUSIC uses broadband superconducting phased-array slot-dipole antennas to form beams, lumpedelement on-chip bandpass filters to define spectral bands, and microwave kinetic inductance detectors to sense incoming light. The focal plane is fabricated in 8 tiles consisting of 72 spatial pixels each. It is coupled to the telescope via an ambient-temperature ellipsoidal mirror and a cold reimaging lens. A cold Lyot stop sits at the image of the primary mirror formed by the ellipsoidal mirror. Dielectric and metal-mesh filters are used to block thermal infrared and out-ofband radiation. The instrument uses a pulse tube cooler and 3He/ 3He/4He closed-cycle cooler to cool the focal plane to below 250 mK. A multilayer shield attenuates Earth's magnetic field. Each focal plane tile is read out by a single pair of coaxes and a HEMT amplifier. The readout system consists of 16 copies of custom-designed ADC/DAC and IF boards coupled to the CASPER ROACH platform. We focus on recent updates on the instrument design and results from the commissioning of the full camera in 2012.

Transfer matrix approach to electron transport in monolayer MoS2/MoO x heterostructures

NASA Astrophysics Data System (ADS)

Li, Gen

2018-05-01

Oxygen plasma treatment can introduce oxidation into monolayer MoS2 to transfer MoS2 into MoO x , causing the formation of MoS2/MoO x heterostructures. We find the MoS2/MoO x heterostructures have the similar geometry compared with GaAs/Ga1‑x Al x As semiconductor superlattice. Thus, We employ the established transfer matrix method to analyse the electron transport in the MoS2/MoO x heterostructures with double-well and step-well geometries. We also considere the coupling between transverse and longitudinal kinetic energy because the electron effective mass changes spatially in the MoS2/MoO x heterostructures. We find the resonant peaks show red shift with the increasing of transverse momentum, which is similar to the previous work studying the transverse-momentum-dependent transmission in GaAs/Ga1‑x Al x As double-barrier structure. We find electric field can enhance the magnitude of peaks and intensify the coupling between longitudinal and transverse momentums. Moreover, higher bias is applied to optimize resonant tunnelling condition to show negative differential effect can be observed in the MoS2/MoO x system.

A review and guidance for pattern selection in spatiotemporal system

NASA Astrophysics Data System (ADS)

Wang, Chunni; Ma, Jun

2018-03-01

Pattern estimation and selection in media can give important clues to understand the collective response to external stimulus by detecting the observable variables. Both reaction-diffusion systems (RDs) and neuronal networks can be treated as multi-agent systems from molecular level, intrinsic cooperation, competition. An external stimulus or attack can cause collapse of spatial order and distribution, while appropriate noise can enhance the consensus in the spatiotemporal systems. Pattern formation and synchronization stability can bridge isolated oscillators and the network by coupling these nodes with appropriate connection types. As a result, the dynamical behaviors can be detected and discussed by developing different spatial patterns and realizing network synchronization. Indeed, the collective response of network and multi-agent system depends on the local kinetics of nodes and cells. It is better to know the standard bifurcation analysis and stability control schemes before dealing with network problems. In this review, dynamics discussion and synchronization control on low-dimensional systems, pattern formation and synchronization stability on network, wave stability in RDs and neuronal network are summarized. Finally, possible guidance is presented when some physical effects such as polarization field and electromagnetic induction are considered.

Gap junctions between interneurons are required for normal spatial coding in the hippocampus and short-term spatial memory

PubMed Central

Allen, Kevin; Fuchs, Elke C.; Jaschonek, Hannah; Bannerman, David M.; Monyer, Hannah

2011-01-01

Gap junctions containing connexin-36 (Cx36) electrically couple interneurons in many brain regions and synchronize their activity. We used Cx36 knockout mice (Cx36−/−) to study the importance of electrical coupling between interneurons for spatial coding in the hippocampus and for different forms of hippocampus-dependent spatial memory. Recordings in behaving mice revealed that the spatial selectivity of hippocampal pyramidal neurons was reduced and less stable in Cx36−/− mice. Altered network activity was reflected in slower theta oscillations in the mutants. Temporal coding, assessed by determining the presence and characteristics of theta phase precession, had different dynamics in Cx36−/− mice compared to controls. At the behavioral level, Cx36−/− mice displayed impaired short-term spatial memory but normal spatial reference memory. These results highlight the functional role of electrically coupled interneurons for spatial coding and cognition. Moreover, they suggest that the precise spatial selectivity of place cells is not essential for normal performance on spatial tasks assessing associative long-term memory. PMID:21525295

Group-kinetic theory of turbulence

NASA Technical Reports Server (NTRS)

Tchen, C. M.

1986-01-01

The two phases are governed by two coupled systems of Navier-Stokes equations. The couplings are nonlinear. These equations describe the microdynamical state of turbulence, and are transformed into a master equation. By scaling, a kinetic hierarchy is generated in the form of groups, representing the spectral evolution, the diffusivity and the relaxation. The loss of memory in formulating the relaxation yields the closure. The network of sub-distributions that participates in the relaxation is simulated by a self-consistent porous medium, so that the average effect on the diffusivity is to make it approach equilibrium. The kinetic equation of turbulence is derived. The method of moments reverts it to the continuum. The equation of spectral evolution is obtained and the transport properties are calculated. In inertia turbulence, the Kolmogoroff law for weak coupling and the spectrum for the strong coupling are found. As the fluid analog, the nonlinear Schrodinger equation has a driving force in the form of emission of solitons by velocity fluctuations, and is used to describe the microdynamical state of turbulence. In order for the emission together with the modulation to participate in the transport processes, the non-homogeneous Schrodinger equation is transformed into a homogeneous master equation. By group-scaling, the master equation is decomposed into a system of transport equations, replacing the Bogoliubov system of equations of many-particle distributions. It is in the relaxation that the memory is lost when the ensemble of higher-order distributions is simulated by an effective porous medium. The closure is thus found. The kinetic equation is derived and transformed into the equation of spectral flow.

Studies on silicon NMR characterization and kinetic modeling of the structural evolution of siloxane-based materials and their applications in drug delivery and adsorption

NASA Astrophysics Data System (ADS)

Ambati, Jyothirmai

This dissertation presents studies of the synthetic processes and applications of siloxane-based materials. Kinetic investigations of bridged organoalkoxysilanes that are precursors to organic-inorganic hybrid polysilsesquioxanes are a primary focus. Quick gelation despite extensive cyclization is found during the polymerization of bridged silane precursors except for silanes with certain short bridges. This work is an attempt to characterize and understand some of the distinct features of bridged silanes using experimental characterization, kinetic modeling and simulation. In addition to this, the dissertation shows how the properties of siloxane-materials can be engineered for drug delivery and adsorption. The phase behavior of polymerizing mixtures is first investigated to identify the solutions that favor kinetic characterization. Microphase separation is found to cause gradual loss of NMR signal for certain initial compositions. Distortionless Enhancement by Polarization Transfer 29Si NMR is employed to identify the products of polymerization of some short-bridged silanes under no signal loss conditions. This technique requires knowing indirect 29Si-1H scalar coupling constants which sometimes cannot be measured due to second-order effects. However, the B3LYP density functional method with 6-31G basis set is found to predict accurate 29Si- 1H coupling constants of organoalkoxysilanes and siloxanes. The scalar coupling constants thus estimated are employed to resolve non-trivial coupled NMR spectra and quantitative kinetic modeling is performed using the DEPT Si NMR transients. In order to investigate the role of the organic bridging group, the structural evolution of bridged and non-bridged silanes are compared using Monte Carlo simulations. Kinetic and simulation models suggest that cyclization plays a key role right from the onset of polymerization for bridged silanes even more than in non-bridged silanes. The simulations indicate that the carbosiloxane rings formed from short-bridged precursors slow down but do not prevent gelation. The tuning of siloxane-based materials for adsorption technologies are also discussed here. In the first example, antioxidant enzyme loading is investigated as a means to reduce oxidative stress generated by silica nanoparticle drug carriers. Materials are engineered for promising enzyme loading and protection from proteolysis. Second, the potential of copper sulfate impregnation to enhance adsorption of ammonia by silica is explored by molecular simulation. KEYWORDS: Sol-gel Polymerization, Kinetic Investigation, Si NMR, Bridged Silanes, DFT Calculations.

Hippocampal-prefrontal theta-gamma coupling during performance of a spatial working memory task.

PubMed

Tamura, Makoto; Spellman, Timothy J; Rosen, Andrew M; Gogos, Joseph A; Gordon, Joshua A

2017-12-19

Cross-frequency coupling supports the organization of brain rhythms and is present during a range of cognitive functions. However, little is known about whether and how long-range cross-frequency coupling across distant brain regions subserves working memory. Here we report that theta-slow gamma coupling between the hippocampus and medial prefrontal cortex (mPFC) is augmented in a genetic mouse model of cognitive dysfunction. This increased cross-frequency coupling is observed specifically when the mice successfully perform a spatial working memory task. In wild-type mice, increasing task difficulty by introducing a long delay or by optogenetically interfering with encoding, also increases theta-gamma coupling during correct trials. Finally, epochs of high hippocampal theta-prefrontal slow gamma coupling are associated with increased synchronization of neurons within the mPFC. These findings suggest that enhancement of theta-slow gamma coupling reflects a compensatory mechanism to maintain spatial working memory performance in the setting of increased difficulty.

Imaging burst kinetics and spatial coordination during serial killing by single natural killer cells

PubMed Central

Choi, Paul J.; Mitchison, Timothy J.

2013-01-01

Cytotoxic lymphocytes eliminate virus-infected and cancerous cells by immune recognition and killing through the perforin-granzyme pathway. Traditional killing assays measure average target cell lysis at fixed times and high effector:target ratios. Such assays obscure kinetic details that might reveal novel physiology. We engineered target cells to report on granzyme activity, used very low effector:target ratios to observe potential serial killing, and performed low magnification time-lapse imaging to reveal time-dependent statistics of natural killer (NK) killing at the single-cell level. Most kills occurred during serial killing, and a single NK cell killed up to 10 targets over a 6-h assay. The first kill was slower than subsequent kills, especially on poor targets, or when NK signaling pathways were partially inhibited. Spatial analysis showed that sequential kills were usually adjacent. We propose that NK cells integrate signals from the previous and current target, possibly by simultaneous contact. The resulting burst kinetics and spatial coordination may control the activity of NK cells in tissues. PMID:23576740

Vibrational and rotational excitation of CO in comets. Part 1: Non-equilibrium calculations. Part 2: Results of the calculation for standard bright comet, comet Iras-Araki-Alcock and comet Halley

NASA Technical Reports Server (NTRS)

Chin, G.; Weaver, H. A.

1984-01-01

The vibrational and rotational excitation of the CO molecule in cometary comae were investigated using a model which includes IR vibrational pumping by the solar flux, vibrational and rotational radiative decay, and collisional coupling among rotational states. Steady state was not assumed in solving the rate equations. The evolution of a shell of CO gas was monitored as it expanded from the nucleus into the outer coma. Collisional effects were treated using a kinetic temperature profile derived from theoretical work on the coma energy balance. The kinetic temperature was assumed to be extremely cold in the inner coma; this has significant consequences for the CO excitation. If optical depth effects are ignored, only low J transitions will be significantly excited in comets observed at high spatial resolution. Ground-based observations of CO co-vibrational and rotational transitions will be extremely difficult due to lack of sensitivity and/or terrestrial absorption. However, CO should be detectable from a large comet with favorable observing geometry if the CO is a parent molecule present at the 10% level (or greater) relative to H2O. Observations using cooled, spaceborne instruments should be capable of detecting CO emission from even moderately bright comets.

Vibrational and rotational excitation of CO in comets. Part 1: Non-equilibrium calculations. Part 2: Results of the calculation for standard bright comet, comet Iras-Araki-Alcock and comet Halley

NASA Astrophysics Data System (ADS)

Chin, G.; Weaver, H. A.

1984-05-01

The vibrational and rotational excitation of the CO molecule in cometary comae were investigated using a model which includes IR vibrational pumping by the solar flux, vibrational and rotational radiative decay, and collisional coupling among rotational states. Steady state was not assumed in solving the rate equations. The evolution of a shell of CO gas was monitored as it expanded from the nucleus into the outer coma. Collisional effects were treated using a kinetic temperature profile derived from theoretical work on the coma energy balance. The kinetic temperature was assumed to be extremely cold in the inner coma; this has significant consequences for the CO excitation. If optical depth effects are ignored, only low J transitions will be significantly excited in comets observed at high spatial resolution. Ground-based observations of CO co-vibrational and rotational transitions will be extremely difficult due to lack of sensitivity and/or terrestrial absorption. However, CO should be detectable from a large comet with favorable observing geometry if the CO is a parent molecule present at the 10% level (or greater) relative to H2O. Observations using cooled, spaceborne instruments should be capable of detecting CO emission from even moderately bright comets.

Simulating the Reiner Gamma Lunar Swirl: Influence of the Upstream Plasma Conditions

NASA Astrophysics Data System (ADS)

Deca, J.; Gerard, M. J.; Divin, A. V.; Lue, C.; Ahmadi, T.; Lembege, B.; Horanyi, M.

2017-12-01

The Reiner Gamma swirl formation, co-located with one of our Moon's strongest crustal magnetic anomalies, is one of the most prominent lunar surface features. Due to Reiner Gamma's fairly moderate spatial scales, it presents an ideal test case to study the solar wind interaction with its magnetic topology from an ion-electron kinetic perspective. Using a fully kinetic particle-in-cell approach, coupled with a surface vector mapping magnetic field model based on Kaguya and Lunar Prospector observations, we are able to constrain both the reflected as well as the incident flux patterns to the lunar surface. Finding excellent agreement with the in-orbit flux measurements from the SARA:SWIM ion sensor onboard the Chandrayaan-1 spacecraft and the surface albedo images from the Lunar Reconnaissance Orbiter Wide Angle Camera we conclude that (from a pure plasma physics point of view) that solar wind standoff is a viable mechanism for the formation of lunar swirls. Here we show how the reflected and incident flux patterns change under influence of the upstream plasma and magnetic field conditions. The possible consequences of crustal magnetic anomalies for lunar swirl formation are essential for the interpretation of our Moon's geological history and evolution, space weathering, and to evaluate the needs and targets for future lunar exploration opportunities.

Adaptive Nodal Transport Methods for Reactor Transient Analysis

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

Thomas Downar; E. Lewis

2005-08-31

Develop methods for adaptively treating the angular, spatial, and time dependence of the neutron flux in reactor transient analysis. These methods were demonstrated in the DOE transport nodal code VARIANT and the US NRC spatial kinetics code, PARCS.

Multistage adsorption of diffusing macromolecules and viruses

NASA Astrophysics Data System (ADS)

Chou, Tom; D'Orsogna, Maria R.

2007-09-01

We derive the equations that describe adsorption of diffusing particles onto a surface followed by additional surface kinetic steps before being transported across the interface. Multistage surface kinetics occurs during membrane protein insertion, cell signaling, and the infection of cells by virus particles. For example, viral entry into healthy cells is possible only after a series of receptor and coreceptor binding events occurs at the cellular surface. We couple the diffusion of particles in the bulk phase with the multistage surface kinetics and derive an effective, integrodifferential boundary condition that contains a memory kernel embodying the delay induced by the surface reactions. This boundary condition takes the form of a singular perturbation problem in the limit where particle-surface interactions are short ranged. Moreover, depending on the surface kinetics, the delay kernel induces a nonmonotonic, transient replenishment of the bulk particle concentration near the interface. The approach generalizes that of Ward and Tordai [J. Chem. Phys. 14, 453 (1946)] and Diamant and Andelman [Colloids Surf. A 183-185, 259 (2001)] to include surface kinetics, giving rise to qualitatively new behaviors. Our analysis also suggests a simple scheme by which stochastic surface reactions may be coupled to deterministic bulk diffusion.

Decay-ratio calculation in the frequency domain with the LAPUR code using 1D-kinetics

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

Munoz-Cobo, J. L.; Escriva, A.; Garcia, C.

This paper deals with the problem of computing the Decay Ratio in the frequency domain codes as the LAPUR code. First, it is explained how to calculate the feedback reactivity in the frequency domain using slab-geometry i.e. 1D kinetics, also we show how to perform the coupling of the 1D kinetics with the thermal-hydraulic part of the LAPUR code in order to obtain the reactivity feedback coefficients for the different channels. In addition, we show how to obtain the reactivity variation in the complex domain by solving the eigenvalue equation in the frequency domain and we compare this result withmore » the reactivity variation obtained in first order perturbation theory using the 1D neutron fluxes of the base case. Because LAPUR works in the linear regime, it is assumed that in general the perturbations are small. There is also a section devoted to the reactivity weighting factors used to couple the reactivity contribution from the different channels to the reactivity of the entire reactor core in point kinetics and 1D kinetics. Finally we analyze the effects of the different approaches on the DR value. (authors)« less

A CFD model for biomass fast pyrolysis in fluidized-bed reactors

NASA Astrophysics Data System (ADS)

Xue, Qingluan; Heindel, T. J.; Fox, R. O.

2010-11-01

A numerical study is conducted to evaluate the performance and optimal operating conditions of fluidized-bed reactors for fast pyrolysis of biomass to bio-oil. A comprehensive CFD model, coupling a pyrolysis kinetic model with a detailed hydrodynamics model, is developed. A lumped kinetic model is applied to describe the pyrolysis of biomass particles. Variable particle porosity is used to account for the evolution of particle physical properties. The kinetic scheme includes primary decomposition and secondary cracking of tar. Biomass is composed of reference components: cellulose, hemicellulose, and lignin. Products are categorized into groups: gaseous, tar vapor, and solid char. The particle kinetic processes and their interaction with the reactive gas phase are modeled with a multi-fluid model derived from the kinetic theory of granular flow. The gas, sand and biomass constitute three continuum phases coupled by the interphase source terms. The model is applied to investigate the effect of operating conditions on the tar yield in a fluidized-bed reactor. The influence of various parameters on tar yield, including operating temperature and others are investigated. Predicted optimal conditions for tar yield and scale-up of the reactor are discussed.

The Impact of ENSO on Extratropical Low Frequency Noise in Seasonal Forecasts

NASA Technical Reports Server (NTRS)

Schubert, Siegfried D.; Suarez, Max J.; Chang, Yehui; Branstator, Grant

2000-01-01

This study examines the uncertainty in forecasts of the January-February-March (JFM) mean extratropical circulation, and how that uncertainty is modulated by the El Nino/Southern Oscillation (ENSO). The analysis is based on ensembles of hindcasts made with an Atmospheric General Circulation Model (AGCM) forced with sea surface temperatures observed during; the 1983 El Nino and 1989 La Nina events. The AGCM produces pronounced interannual differences in the magnitude of the extratropical seasonal mean noise (intra-ensemble variability). The North Pacific, in particular, shows extensive regions where the 1989 seasonal mean noise kinetic energy (SKE), which is dominated by a "PNA-like" spatial structure, is more than twice that of the 1983 forecasts. The larger SKE in 1989 is associated with a larger than normal barotropic conversion of kinetic energy from the mean Pacific jet to the seasonal mean noise. The generation of SKE due to sub-monthly transients also shows substantial interannual differences, though these are much smaller than the differences in the mean flow conversions. An analysis of the Generation of monthly mean noise kinetic energy (NIKE) and its variability suggests that the seasonal mean noise is predominantly a statistical residue of variability resulting from dynamical processes operating on monthly and shorter times scales. A stochastically-forced barotropic model (linearized about the AGCM's 1983 and 1989 base states) is used to further assess the role of the basic state, submonthly transients, and tropical forcing, in modulating the uncertainties in the seasonal AGCM forecasts. When forced globally with spatially-white noise, the linear model generates much larger variance for the 1989 base state, consistent with the AGCM results. The extratropical variability for the 1989 base state is dominanted by a single eigenmode, and is strongly coupled with forcing over tropical western Pacific and the Indian Ocean, again consistent with the AGCM results. Linear calculations that include forcing from the AGCM variance of the tropical forcing and submonthly transients show a small impact on the variability over the Pacific/North American region compared with that of the base state differences.

Self-Consistent Magnetosphere-Ionosphere Coupling and Associated Plasma Energization Processes

NASA Technical Reports Server (NTRS)

Khazanov, G. V.; Six, N. Frank (Technical Monitor)

2002-01-01

Magnetosphere-Ionosphere (MI) coupling and associated with this process electron and ion energization processes have interested scientists for decades and, in spite of experimental and theoretical research efforts, are still ones of the least well known dynamic processes in space plasma physics. The reason for this is that the numerous physical processes associated with MI coupling occur over multiple spatial lengths and temporal scales. One typical example of MI coupling is large scale ring current (RC) electrodynamic coupling that includes calculation of the magnetospheric electric field that is consistent with the ring current (RC) distribution. A general scheme for numerical simulation of such large-scale magnetosphere-ionosphere coupling processes has been presented earlier in many works. The mathematical formulation of these models are based on "modified frozen-in flux theorem" for an ensemble of adiabatically drifting particles in the magnetosphere. By tracking the flow of particles through the inner magnetosphere, the bounce-averaged phase space density of the hot ions and electrons can be reconstructed and the magnetospheric electric field can be calculated such that it is consistent with the particle distribution in the magnetosphere. The new a self-consistent ring current model has been developed that couples electron and ion magnetospheric dynamics with calculation of electric field. Two new features were taken into account in addition to the RC ions, we solve an electron kinetic equation in our model, self-consistently including these results in the solution. Second, using different analytical relationships, we calculate the height integrated ionospheric conductances as the function of precipitated high energy magnetospheric electrons and ions as produced by our model. This results in fundamental changes to the electric potential pattern in the inner magnetosphere, with a smaller Alfven boundary than previous potential formulations would predict but one consistent with recent satellite observations. This leads to deeper penetration of the plasma sheet ions and electrons into the inner magnetosphere and more effective ring current ions and electron energization.

Information hidden in the velocity distribution of ions and the exact kinetic Bohm criterion

NASA Astrophysics Data System (ADS)

Tsankov, Tsanko V.; Czarnetzki, Uwe

2017-05-01

Non-equilibrium distribution functions of electrons and ions play an important role in plasma physics. A prominent example is the kinetic Bohm criterion. Since its first introduction it has been controversial for theoretical reasons and due to the lack of experimental data, in particular on the ion distribution function. Here we resolve the theoretical as well as the experimental difficulties by an exact solution of the kinetic Boltzmann equation including charge exchange collisions and ionization. This also allows for the first time non-invasive measurement of spatially resolved ion velocity distributions, absolute values of the ion and electron densities, temperatures, and mean energies as well as the electric field and the plasma potential in the entire plasma. The non-invasive access to the spatially resolved distribution functions of electrons and ions is applied to the problem of the kinetic Bohm criterion. Theoretically a so far missing term in the criterion is derived and shown to be of key importance. With the new term the validity of the kinetic criterion at high collisionality and its agreement with the fluid picture are restored. All findings are supported by experimental data, theory and a numerical model with excellent agreement throughout.

Assessing spatial coupling in complex population dynamics using mutual prediction and continuity statistics

USGS Publications Warehouse

Nichols, J.M.; Moniz, L.; Nichols, J.D.; Pecora, L.M.; Cooch, E.

2005-01-01

A number of important questions in ecology involve the possibility of interactions or ?coupling? among potential components of ecological systems. The basic question of whether two components are coupled (exhibit dynamical interdependence) is relevant to investigations of movement of animals over space, population regulation, food webs and trophic interactions, and is also useful in the design of monitoring programs. For example, in spatially extended systems, coupling among populations in different locations implies the existence of redundant information in the system and the possibility of exploiting this redundancy in the development of spatial sampling designs. One approach to the identification of coupling involves study of the purported mechanisms linking system components. Another approach is based on time series of two potential components of the same system and, in previous ecological work, has relied on linear cross-correlation analysis. Here we present two different attractor-based approaches, continuity and mutual prediction, for determining the degree to which two population time series (e.g., at different spatial locations) are coupled. Both approaches are demonstrated on a one-dimensional predator?prey model system exhibiting complex dynamics. Of particular interest is the spatial asymmetry introduced into the model as linearly declining resource for the prey over the domain of the spatial coordinate. Results from these approaches are then compared to the more standard cross-correlation analysis. In contrast to cross-correlation, both continuity and mutual prediction are clearly able to discern the asymmetry in the flow of information through this system.

Simulation and experimental comparison of the thermo-mechanical history and 3D microstructure evolution of 304L stainless steel tubes manufactured using LENS

NASA Astrophysics Data System (ADS)

Johnson, Kyle L.; Rodgers, Theron M.; Underwood, Olivia D.; Madison, Jonathan D.; Ford, Kurtis R.; Whetten, Shaun R.; Dagel, Daryl J.; Bishop, Joseph E.

2018-05-01

Additive manufacturing enables the production of previously unachievable designs in conjunction with time and cost savings. However, spatially and temporally fluctuating thermal histories can lead to residual stress states and microstructural variations that challenge conventional assumptions used to predict part performance. Numerical simulations offer a viable way to explore the root causes of these characteristics, and can provide insight into methods of controlling them. Here, the thermal history of a 304L stainless steel cylinder produced using the Laser Engineered Net Shape process is simulated using finite element analysis (FEA). The resultant thermal history is coupled to both a solid mechanics FEA simulation to predict residual stress and a kinetic Monte Carlo model to predict the three-dimensional grain structure evolution. Experimental EBSD measurements of grain structure and in-process infrared thermal data are compared to the predictions.

Wavelet-based surrogate time series for multiscale simulation of heterogeneous catalysis

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

Savara, Aditya Ashi; Daw, C. Stuart; Xiong, Qingang

We propose a wavelet-based scheme that encodes the essential dynamics of discrete microscale surface reactions in a form that can be coupled with continuum macroscale flow simulations with high computational efficiency. This makes it possible to simulate the dynamic behavior of reactor-scale heterogeneous catalysis without requiring detailed concurrent simulations at both the surface and continuum scales using different models. Our scheme is based on the application of wavelet-based surrogate time series that encodes the essential temporal and/or spatial fine-scale dynamics at the catalyst surface. The encoded dynamics are then used to generate statistically equivalent, randomized surrogate time series, which canmore » be linked to the continuum scale simulation. As a result, we illustrate an application of this approach using two different kinetic Monte Carlo simulations with different characteristic behaviors typical for heterogeneous chemical reactions.« less

A study of the effect of space-dependent neutronics on stochastically-induced bifurcations in BWR dynamics

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

Analytis, G.T.

1995-09-01

A non-linear one-group space-dependent neutronic model for a finite one-dimensional core is coupled with a simple BWR feed-back model. In agreement with results obtained by the authors who originally developed the point-kinetics version of this model, we shall show numerically that stochastic reactivity excitations may result in limit-cycles and eventually in a chaotic behaviour, depending on the magnitude of the feed-back coefficient K. In the framework of this simple space-dependent model, the effect of the non-linearities on the different spatial harmonics is studied and the importance of the space-dependent effects is exemplified and assessed in terms of the importance ofmore » the higher harmonics. It is shown that under certain conditions, when the limit-cycle-type develop, the neutron spectra may exhibit strong space-dependent effects.« less

Simulation and experimental comparison of the thermo-mechanical history and 3D microstructure evolution of 304L stainless steel tubes manufactured using LENS

NASA Astrophysics Data System (ADS)

Johnson, Kyle L.; Rodgers, Theron M.; Underwood, Olivia D.; Madison, Jonathan D.; Ford, Kurtis R.; Whetten, Shaun R.; Dagel, Daryl J.; Bishop, Joseph E.

2017-12-01

Additive manufacturing enables the production of previously unachievable designs in conjunction with time and cost savings. However, spatially and temporally fluctuating thermal histories can lead to residual stress states and microstructural variations that challenge conventional assumptions used to predict part performance. Numerical simulations offer a viable way to explore the root causes of these characteristics, and can provide insight into methods of controlling them. Here, the thermal history of a 304L stainless steel cylinder produced using the Laser Engineered Net Shape process is simulated using finite element analysis (FEA). The resultant thermal history is coupled to both a solid mechanics FEA simulation to predict residual stress and a kinetic Monte Carlo model to predict the three-dimensional grain structure evolution. Experimental EBSD measurements of grain structure and in-process infrared thermal data are compared to the predictions.

The MKID Camera

NASA Astrophysics Data System (ADS)

Maloney, P. R.; Czakon, N. G.; Day, P. K.; Duan, R.; Gao, J.; Glenn, J.; Golwala, S.; Hollister, M.; LeDuc, H. G.; Mazin, B.; Noroozian, O.; Nguyen, H. T.; Sayers, J.; Schlaerth, J.; Vaillancourt, J. E.; Vayonakis, A.; Wilson, P.; Zmuidzinas, J.

2009-12-01

The MKID Camera project is a collaborative effort of Caltech, JPL, the University of Colorado, and UC Santa Barbara to develop a large-format, multi-color millimeter and submillimeter-wavelength camera for astronomy using microwave kinetic inductance detectors (MKIDs). These are superconducting, micro-resonators fabricated from thin aluminum and niobium films. We couple the MKIDs to multi-slot antennas and measure the change in surface impedance produced by photon-induced breaking of Cooper pairs. The readout is almost entirely at room temperature and can be highly multiplexed; in principle hundreds or even thousands of resonators could be read out on a single feedline. The camera will have 576 spatial pixels that image simultaneously in four bands at 750, 850, 1100 and 1300 microns. It is scheduled for deployment at the Caltech Submillimeter Observatory in the summer of 2010. We present an overview of the camera design and readout and describe the current status of testing and fabrication.

The Center for Multiscale Plasma Dynamics, Final Report

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

Gombosi, Tamas I.

The University of Michigan participated in the joint UCLA/Maryland fusion science center focused on plasma physics problems for which the traditional separation of the dynamics into microscale and macroscale processes breaks down. These processes involve large scale flows and magnetic fields tightly coupled to the small scale, kinetic dynamics of turbulence, particle acceleration and energy cascade. The interaction between these vastly disparate scales controls the evolution of the system. The enormous range of temporal and spatial scales associated with these problems renders direct simulation intractable even in computations that use the largest existing parallel computers. Our efforts focused on twomore » main problems: the development of Hall MHD solvers on solution adaptive grids and the development of solution adaptive grids using generalized coordinates so that the proper geometry of inertial confinement can be taken into account and efficient refinement strategies can be obtained.« less

Wavelet-based surrogate time series for multiscale simulation of heterogeneous catalysis

DOE PAGES

Savara, Aditya Ashi; Daw, C. Stuart; Xiong, Qingang; ...

2016-01-28

We propose a wavelet-based scheme that encodes the essential dynamics of discrete microscale surface reactions in a form that can be coupled with continuum macroscale flow simulations with high computational efficiency. This makes it possible to simulate the dynamic behavior of reactor-scale heterogeneous catalysis without requiring detailed concurrent simulations at both the surface and continuum scales using different models. Our scheme is based on the application of wavelet-based surrogate time series that encodes the essential temporal and/or spatial fine-scale dynamics at the catalyst surface. The encoded dynamics are then used to generate statistically equivalent, randomized surrogate time series, which canmore » be linked to the continuum scale simulation. As a result, we illustrate an application of this approach using two different kinetic Monte Carlo simulations with different characteristic behaviors typical for heterogeneous chemical reactions.« less

Diagnosing residual motion via the x-ray self emission from indirectly driven inertial confinement implosions

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

Pak, A., E-mail: pak5@llnl.gov; Field, J. E.; Benedetti, L. R.

2014-11-15

In an indirectly driven implosion, non-radial translational motion of the compressed fusion capsule is a signature of residual kinetic energy not coupled into the compressional heating of the target. A reduction in compression reduces the peak pressure and nuclear performance of the implosion. Measuring and reducing the residual motion of the implosion is therefore necessary to improve performance and isolate other effects that degrade performance. Using the gated x-ray diagnostic, the x-ray Bremsstrahlung emission from the compressed capsule is spatially and temporally resolved at x-ray energies of >8.7 keV, allowing for measurements of the residual velocity. Here details of themore » x-ray velocity measurement and fitting routine will be discussed and measurements will be compared to the velocities inferred from the neutron time of flight detectors.« less

Application of Detailed Chemical Kinetics to Combustion Instability Modeling

DTIC Science & Technology

2016-01-04

Modeling 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Harvazinski, Matt; Talley, Doug; Sankaran, Venke 5d. PROJECT...Chemical Kinetics to Combustion Instability Modeling Matt Harvazinski, Doug Talley, Venke Sankaran Air Force Research Laboratory Edwards AFB, CA...distribution unlimited. 3 Prior Work – Kinetics Used • Simulations : 1) 3D real geometry 2) Unsteady 3) Long run-times 4) Coupled physics • 1- 4

Storm time plasma transport in a unified and inter-coupled global magnetosphere model

NASA Astrophysics Data System (ADS)

Ilie, R.; Liemohn, M. W.; Toth, G.

2014-12-01

We present results from the two-way self-consistent coupling between the kinetic Hot Electron and Ion Drift Integrator (HEIDI) model and the Space Weather Modeling Framework (SWMF). HEIDI solves the time dependent, gyration and bounced averaged kinetic equation for the phase space density of different ring current species and computes full pitch angle distributions for all local times and radial distances. During geomagnetic times the dipole approximation becomes unsuitable even in the inner magnetosphere. Therefore the HEIDI model was generalized to accommodate an arbitrary magnetic field and through the coupling with SWMF it obtains a magnetic field description throughout the HEIDI domain along with a plasma distribution at the model outer boundary from the Block Adaptive Tree Solar Wind Roe Upwind Scheme (BATS-R-US) magnetohydrodynamics (MHD) model within SWMF. Electric field self-consistency is assured by the passing of convection potentials from the Ridley Ionosphere Model (RIM) within SWMF. In this study we test the various levels of coupling between the 3 physics based models, highlighting the role that the magnetic field, plasma sheet conditions and the cross polar cap potential play in the formation and evolution of the ring current. We show that the dynamically changing geospace environment itself plays a key role in determining the geoeffectiveness of the driver. The results of the self-consistent coupling between HEIDI, BATS-R-US and RIM during disturbed conditions emphasize the importance of a kinetic self-consistent approach to the description of geospace.

Were inefficient mitochondrial haplogroups selected during migrations of modern humans? A test using modular kinetic analysis of coupling in mitochondria from cybrid cell lines

PubMed Central

Amo, Taku; Brand, Martin D.

2007-01-01

We introduce a general test of the bioenergetic importance of mtDNA (mitochondrial DNA) variants: modular kinetic analysis of oxidative phosphorylation in mitochondria from cybrid cells with constant nuclear DNA but different mtDNA. We have applied this test to the hypothesis [Ruiz-Pesini, Mishmar, Brandon, Procaccio and Wallace (2004) Science 303, 223–226] that particular mtDNA haplogroups (specific combinations of polymorphisms) that cause lowered coupling efficiency, leading to generation of less ATP and more heat, were positively selected during radiations of modern humans into colder climates. Contrary to the predictions of this hypothesis, mitochondria from Arctic haplogroups had similar or even greater coupling efficiency than mitochondria from tropical haplogroups. PMID:17355224

Analyses of kinetic glass transition in short-range attractive colloids based on time-convolutionless mode-coupling theory.

PubMed

Narumi, Takayuki; Tokuyama, Michio

2017-03-01

For short-range attractive colloids, the phase diagram of the kinetic glass transition is studied by time-convolutionless mode-coupling theory (TMCT). Using numerical calculations, TMCT is shown to recover all the remarkable features predicted by the mode-coupling theory for attractive colloids: the glass-liquid-glass reentrant, the glass-glass transition, and the higher-order singularities. It is also demonstrated through the comparisons with the results of molecular dynamics for the binary attractive colloids that TMCT improves the critical values of the volume fraction. In addition, a schematic model of three control parameters is investigated analytically. It is thus confirmed that TMCT can describe the glass-glass transition and higher-order singularities even in such a schematic model.

Trivial constraints on orbital-free kinetic energy density functionals

NASA Astrophysics Data System (ADS)

Luo, Kai; Trickey, S. B.

2018-03-01

Approximate kinetic energy density functionals (KEDFs) are central to orbital-free density functional theory. Limitations on the spatial derivative dependencies of KEDFs have been claimed from differential virial theorems. We identify a central defect in the argument: the relationships are not true for an arbitrary density but hold only for the minimizing density and corresponding chemical potential. Contrary to the claims therefore, the relationships are not constraints and provide no independent information about the spatial derivative dependencies of approximate KEDFs. A simple argument also shows that validity for arbitrary v-representable densities is not restored by appeal to the density-potential bijection.

Reconciling spatial and temporal soil moisture effects on afternoon rainfall

PubMed Central

Guillod, Benoit P.; Orlowsky, Boris; Miralles, Diego G.; Teuling, Adriaan J.; Seneviratne, Sonia I.

2015-01-01

Soil moisture impacts on precipitation have been strongly debated. Recent observational evidence of afternoon rain falling preferentially over land parcels that are drier than the surrounding areas (negative spatial effect), contrasts with previous reports of a predominant positive temporal effect. However, whether spatial effects relating to soil moisture heterogeneity translate into similar temporal effects remains unknown. Here we show that afternoon precipitation events tend to occur during wet and heterogeneous soil moisture conditions, while being located over comparatively drier patches. Using remote-sensing data and a common analysis framework, spatial and temporal correlations with opposite signs are shown to coexist within the same region and data set. Positive temporal coupling might enhance precipitation persistence, while negative spatial coupling tends to regionally homogenize land surface conditions. Although the apparent positive temporal coupling does not necessarily imply a causal relationship, these results reconcile the notions of moisture recycling with local, spatially negative feedbacks. PMID:25740589

Kinetic operational models of agonism for G-protein-coupled receptors.

PubMed

Hoare, Samuel R J; Pierre, Nicolas; Moya, Arturo Gonzalez; Larson, Brad

2018-06-07

The application of kinetics to research and therapeutic development of G-protein-coupled receptors has become increasingly valuable. Pharmacological models provide the foundation of pharmacology, providing concepts and measurable parameters such as efficacy and potency that have underlain decades of successful drug discovery. Currently there are few pharmacological models that incorporate kinetic activity in such a way as to yield experimentally-accessible drug parameters. In this study, a kinetic model of pharmacological response was developed that provides a kinetic descriptor of efficacy (the transduction rate constant, k τ ) and allows measurement of receptor-ligand binding kinetics from functional data. The model assumes: (1) receptor interacts with a precursor of the response ("Transduction potential") and converts it to the response. (2) The response can decay. Familiar response vs time plots emerge, depending on whether transduction potential is depleted and/or response decays. These are the straight line, the "association" exponential curve, and the rise-and-fall curve. Convenient, familiar methods are described for measuring the model parameters and files are provided for the curve-fitting program Prism (GraphPad Software) that can be used as a guide. The efficacy parameter k τ is straightforward to measure and accounts for receptor reserve; all that is required is measurement of response over time at a maximally-stimulating concentration of agonist. The modular nature of the model framework allows it to be extended. Here this is done to incorporate antagonist-receptor binding kinetics and slow agonist-receptor equilibration. In principle, the modular framework can incorporate other cellular processes, such as receptor desensitization. The kinetic response model described here can be applied to measure kinetic pharmacological parameters than can be used to advance the understanding of GPCR pharmacology and optimize new and improved therapeutics. Copyright © 2018 Elsevier Ltd. All rights reserved.

Local reaction kinetics by imaging☆

PubMed Central

Suchorski, Yuri; Rupprechter, Günther

2016-01-01

In the present contribution we present an overview of our recent studies using the “kinetics by imaging” approach for CO oxidation on heterogeneous model systems. The method is based on the correlation of the PEEM image intensity with catalytic activity: scaled down to the μm-sized surface regions, such correlation allows simultaneous local kinetic measurements on differently oriented individual domains of a polycrystalline metal-foil, including the construction of local kinetic phase diagrams. This allows spatially- and component-resolved kinetic studies and, e.g., a direct comparison of inherent catalytic properties of Pt(hkl)- and Pd(hkl)-domains or supported μm-sized Pd-powder agglomerates, studies of the local catalytic ignition and the role of defects and grain boundaries in the local reaction kinetics. PMID:26865736

Global Particle-in-Cell Simulations of Mercury's Magnetosphere

NASA Astrophysics Data System (ADS)

Schriver, D.; Travnicek, P. M.; Lapenta, G.; Amaya, J.; Gonzalez, D.; Richard, R. L.; Berchem, J.; Hellinger, P.

2017-12-01

Spacecraft observations of Mercury's magnetosphere have shown that kinetic ion and electron particle effects play a major role in the transport, acceleration, and loss of plasma within the magnetospheric system. Kinetic processes include reconnection, the breakdown of particle adiabaticity and wave-particle interactions. Because of the vast range in spatial scales involved in magnetospheric dynamics, from local electron Debye length scales ( meters) to solar wind/planetary magnetic scale lengths (tens to hundreds of planetary radii), fully self-consistent kinetic simulations of a global planetary magnetosphere remain challenging. Most global simulations of Earth's and other planet's magnetosphere are carried out using MHD, enhanced MHD (e.g., Hall MHD), hybrid, or a combination of MHD and particle in cell (PIC) simulations. Here, 3D kinetic self-consistent hybrid (ion particle, electron fluid) and full PIC (ion and electron particle) simulations of the solar wind interaction with Mercury's magnetosphere are carried out. Using the implicit PIC and hybrid simulations, Mercury's relatively small, but highly kinetic magnetosphere will be examined to determine how the self-consistent inclusion of electrons affects magnetic reconnection, particle transport and acceleration of plasma at Mercury. Also the spatial and energy profiles of precipitating magnetospheric ions and electrons onto Mercury's surface, which can strongly affect the regolith in terms of space weathering and particle outflow, will be examined with the PIC and hybrid codes. MESSENGER spacecraft observations are used both to initiate and validate the global kinetic simulations to achieve a deeper understanding of the role kinetic physics play in magnetospheric dynamics.

Two-way coupling of magnetohydrodynamic simulations with embedded particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Makwana, K. D.; Keppens, R.; Lapenta, G.

2017-12-01

We describe a method for coupling an embedded domain in a magnetohydrodynamic (MHD) simulation with a particle-in-cell (PIC) method. In this two-way coupling we follow the work of Daldorff et al. (2014) [19] in which the PIC domain receives its initial and boundary conditions from MHD variables (MHD to PIC coupling) while the MHD simulation is updated based on the PIC variables (PIC to MHD coupling). This method can be useful for simulating large plasma systems, where kinetic effects captured by particle-in-cell simulations are localized but affect global dynamics. We describe the numerical implementation of this coupling, its time-stepping algorithm, and its parallelization strategy, emphasizing the novel aspects of it. We test the stability and energy/momentum conservation of this method by simulating a steady-state plasma. We test the dynamics of this coupling by propagating plasma waves through the embedded PIC domain. Coupling with MHD shows satisfactory results for the fast magnetosonic wave, but significant distortion for the circularly polarized Alfvén wave. Coupling with Hall-MHD shows excellent coupling for the whistler wave. We also apply this methodology to simulate a Geospace Environmental Modeling (GEM) challenge type of reconnection with the diffusion region simulated by PIC coupled to larger scales with MHD and Hall-MHD. In both these cases we see the expected signatures of kinetic reconnection in the PIC domain, implying that this method can be used for reconnection studies.

Measurement of turbulent spatial structure and kinetic energy spectrum by exact temporal-to-spatial mapping

NASA Astrophysics Data System (ADS)

Buchhave, Preben; Velte, Clara M.

2017-08-01

We present a method for converting a time record of turbulent velocity measured at a point in a flow to a spatial velocity record consisting of consecutive convection elements. The spatial record allows computation of dynamic statistical moments such as turbulent kinetic wavenumber spectra and spatial structure functions in a way that completely bypasses the need for Taylor's hypothesis. The spatial statistics agree with the classical counterparts, such as the total kinetic energy spectrum, at least for spatial extents up to the Taylor microscale. The requirements for applying the method are access to the instantaneous velocity magnitude, in addition to the desired flow quantity, and a high temporal resolution in comparison to the relevant time scales of the flow. We map, without distortion and bias, notoriously difficult developing turbulent high intensity flows using three main aspects that distinguish these measurements from previous work in the field: (1) The measurements are conducted using laser Doppler anemometry and are therefore not contaminated by directional ambiguity (in contrast to, e.g., frequently employed hot-wire anemometers); (2) the measurement data are extracted using a correctly and transparently functioning processor and are analysed using methods derived from first principles to provide unbiased estimates of the velocity statistics; (3) the exact mapping proposed herein has been applied to the high turbulence intensity flows investigated to avoid the significant distortions caused by Taylor's hypothesis. The method is first confirmed to produce the correct statistics using computer simulations and later applied to measurements in some of the most difficult regions of a round turbulent jet—the non-equilibrium developing region and the outermost parts of the developed jet. The proposed mapping is successfully validated using corresponding directly measured spatial statistics in the fully developed jet, even in the difficult outer regions of the jet where the average convection velocity is negligible and turbulence intensities increase dramatically. The measurements in the developing region reveal interesting features of an incomplete Richardson-Kolmogorov cascade under development.

Electromagnetic Design of a Magnetically Coupled Spatial Power Combiner

NASA Astrophysics Data System (ADS)

Bulcha, B. T.; Cataldo, G.; Stevenson, T. R.; U-Yen, K.; Moseley, S. H.; Wollack, E. J.

2018-04-01

The design of a two-dimensional spatial beam-combining network employing a parallel-plate superconducting waveguide filled with a monocrystalline silicon dielectric substrate is presented. This component uses arrays of magnetically coupled antenna elements to achieve high coupling efficiency and full sampling of the intensity distribution while avoiding diffractive losses in the multimode waveguide region. These attributes enable the structure's use in realizing compact far-infrared spectrometers for astrophysical and instrumentation applications. If unterminated, reflections within a finite-sized spatial beam combiner can potentially lead to spurious couplings between elements. A planar meta-material electromagnetic absorber is implemented to control this response within the device. This broadband termination absorbs greater than 0.99 of the power over the 1.7:1 operational band at angles ranging from normal to near-parallel incidence. The design approach, simulations and applications of the spatial power combiner and meta-material termination structure are presented.

Optimizing information flow in small genetic networks. IV. Spatial coupling

NASA Astrophysics Data System (ADS)

Sokolowski, Thomas R.; Tkačik, Gašper

2015-06-01

We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the input) by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively different regulatory strategy emerges where individual cells respond to the input in a nearly steplike fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models.

Simultaneous measurement of polymerization stress and curing kinetics for photo-polymerized composites with high filler contents.

PubMed

Wang, Zhengzhi; Landis, Forrest A; Giuseppetti, Anthony A M; Lin-Gibson, Sheng; Chiang, Martin Y M

2014-12-01

Photopolymerized composites are used in a broad range of applications with their performance largely directed by reaction kinetics and contraction accompanying polymerization. The present study was to demonstrate an instrument capable of simultaneously collecting multiple kinetics parameters for a wide range of photopolymerizable systems: degree of conversion (DC), reaction exotherm, and polymerization stress (PS). Our system consisted of a cantilever beam-based instrument (tensometer) that has been optimized to capture a large range of stress generated by lightly-filled to highly-filled composites. The sample configuration allows the tensometer to be coupled to a fast near infrared (NIR) spectrometer collecting spectra in transmission mode. Using our instrument design, simultaneous measurements of PS and DC are performed, for the first time, on a commercial composite with ≈80% (by mass) silica particle fillers. The in situ NIR spectrometer collects more than 10 spectra per second, allowing for thorough characterization of reaction kinetics. With increased instrument sensitivity coupled with the ability to collect real time reaction kinetics information, we show that the external constraint imposed by the cantilever beam during polymerization could affect the rate of cure and final degree of polymerization. The present simultaneous measurement technique is expected to provide new insights into kinetics and property relationships for photopolymerized composites with high filler content such as dental restorative composites. Published by Elsevier Ltd.

Simultaneous Measurement of Polymerization Stress and Curing Kinetics for Photo-polymerized Composites with High Filler Contents

PubMed Central

Wang, Zhengzhi; Landis, Forrest A.; Giuseppetti, Anthony A.M.; Lin-Gibson, Sheng; Chiang, Martin Y.M.

2015-01-01

Objectives Photopolymerized composites are used in a broad range of applications with their performance largely directed by reaction kinetics and contraction accompanying polymerization. The present study was to demonstrate an instrument capable of simultaneously collecting multiple kinetics parameters for a wide range of photopolymerizable systems: degree of conversion (DC), reaction exotherm, and polymerization stress (PS). Methods Our system consisted of a cantilever beam-based instrument (tensometer) that has been optimized to capture a large range of stress generated by lightly-filled to highly-filled composites. The sample configuration allows the tensometer to be coupled to a fast near infrared (NIR) spectrometer collecting spectra in transmission mode. Results Using our instrument design, simultaneous measurements of PS and DC are performed, for the first time, on a commercial composite with ≈ 80 % (by mass) silica particle fillers. The in situ NIR spectrometer collects more than 10 spectra per second, allowing for thorough characterization of reaction kinetics. With increased instrument sensitivity coupled with the ability to collect real time reaction kinetics information, we show that the external constraint imposed by the cantilever beam during polymerization could affect the rate of cure and final degree of polymerization. Significance The present simultaneous measurement technique is expected to provide new insights into kinetics and property relationships for photopolymerized composites with high filler content such as dental restorative composites. PMID:25443160

Coupling glucose fermentation and homoacetogenesis for elevated acetate production: Experimental and mathematical approaches.

PubMed

Ni, Bing-Jie; Liu, He; Nie, Yan-Qiu; Zeng, Raymond J; Du, Guo-Cheng; Chen, Jian; Yu, Han-Qing

2011-02-01

Homoacetogenesis is an important potential hydrogen sink in acetogenesis, in which hydrogen is used to reduce carbon dioxide to acetate. So far the acetate production from homoacetogenesis, especially its kinetics, has not been given sufficient attention. In this work, enhanced production of acetate from anaerobic conversion of glucose through coupling glucose fermentation and homoacetogenesis is investigated with both experimental and mathematical approaches. Experiments are conducted to explore elevated acetate production in a coupled anaerobic system. Acetate production could be achieved by homoacetogenesis with a relative high acetate yield under mixed fermentation conditions. With the experimental observations, a kinetic model is formulated to describe such a homoacetogenic process. The maximum homoacetogenic rate (k(m,homo)) is estimated to be 28.5 ± 1.7 kg COD kg⁻¹ COD day⁻¹ with an uptake affinity constant of 3.7 × 10⁻⁵± 3.1 × 10⁻⁶kg COD m⁻³. The improved calculation of homoacetogenic kinetics by our approach could correct the underestimation of homoacetogenesis in anaerobic fermentation processes, as it often occurs in these systems supported by literature analysis. The model predictions match the experimental results in different cases well and provide insights into the dynamics of anaerobic glucose conversion and acetate production. Furthermore, acetate production via homoacetogenesis increases by about 40% through utilizing the fed-batch coupling system, attributed to a balance between the hydrogen production in the acetogenesis phase and the hydrogen consumption in the homoacetogenesis phase. This work provides an effective way for increased anaerobic acetate production, and gives us a better understanding about the homoacetogenic kinetics in the anaerobic fermentation process. © 2010 Wiley Periodicals, Inc.

Spatial Moment Equations for a Groundwater Plume with Degradation and Rate-Limited Sorption

EPA Science Inventory

In this note, we analytically derive the solution for the spatial moments of groundwater solute concentration distributions simulated by a one-dimensional model that assumes advective-dispersive transport with first-order degradation and rate-limited sorption. Sorption kinetics...

Enhanced electron transfer kinetics through hybrid graphene-carbon nanotube films.

PubMed

Henry, Philémon A; Raut, Akshay S; Ubnoske, Stephen M; Parker, Charles B; Glass, Jeffrey T

2014-11-01

We report the first study of the electrochemical reactivity of a graphenated carbon nanotube (g-CNT) film. The electron transfer kinetics of the ferri-ferrocyanide couple were examined for a g-CNT film and compared to the kinetics to standard carbon nanotubes (CNTs). The g-CNT film exhibited much higher catalytic activity, with a heterogeneous electron-transfer rate constant, k 0 , approximately two orders of magnitude higher than for standard CNTs. Scanning electron microscopy and Raman spectroscopy were used to correlate the higher electron transfer kinetics with the higher edge-density of the g-CNT film.

Microscopic theory of Dzyaloshinsky-Moriya interaction in pyrochlore oxides with spin-orbit coupling

NASA Astrophysics Data System (ADS)

Arakawa, Naoya

2016-10-01

Pyrochlore oxides show several fascinating phenomena, such as the formation of heavy fermions and the thermal Hall effect. Although a key to understanding some phenomena may be the Dzyaloshinsky-Moriya (DM) interaction, its microscopic origin is unclear. To clarify the microscopic origin, we constructed a t2 g-orbital model with the kinetic energy, the trigonal-distortion potential, the multiorbital Hubbard interactions, and the L S coupling, and derived the low-energy effective Hamiltonian for a d1 Mott insulator with the weak L S coupling. We first show that lack of the inversion center of each nearest-neighbor V-V bond causes the odd-mirror interorbital hopping integrals. Those are qualitatively different from the even-mirror hopping integrals, existing even with the inversion center. We next show that the second-order perturbation using the kinetic terms leads to the ferromagnetic and the antiferromagnetic superexchange interactions, whose competition is controllable by tuning the Hubbard interactions. Then, we show the most important result: the third-order perturbation terms using the combination of the even-mirror hopping integral, the odd-mirror hopping integral, and the L S coupling causes the DM interaction due to the mirror-mixing effect, where those hopping integrals are necessary to obtain the antisymmetric kinetic exchange and the L S coupling is necessary to excite the orbital angular momentum at one of two sites. We also show that the magnitude and sign of the DM interaction can be controlled by changing the positions of the O ions and the strength of the Hubbard interactions. We discuss the advantages in comparison with the phenomenological theory and Moriya's microscopic theory, applicability of our mechanism, and the similarities and differences between our case and the strong-L S -coupling case.

Interstitial diffusion and the relationship between compartment modelling and multi-scale spatial-temporal modelling of (18)F-FLT tumour uptake dynamics.

PubMed

Liu, Dan; Chalkidou, Anastasia; Landau, David B; Marsden, Paul K; Fenwick, John D

2014-09-07

Tumour cell proliferation can be imaged via positron emission tomography of the radiotracer 3'-deoxy-3'-18F-fluorothymidine (18F-FLT). Conceptually, the number of proliferating cells might be expected to correlate more closely with the kinetics of 18F-FLT uptake than with uptake at a fixed time. Radiotracer uptake kinetics are standardly visualized using parametric maps of compartment model fits to time-activity-curves (TACs) of individual voxels. However the relationship between the underlying spatiotemporal accumulation of FLT and the kinetics described by compartment models has not yet been explored. In this work tumour tracer uptake is simulated using a mechanistic spatial-temporal model based on a convection-diffusion-reaction equation solved via the finite difference method. The model describes a chain of processes: the flow of FLT between the spatially heterogeneous tumour vasculature and interstitium; diffusion and convection of FLT within the interstitium; transport of FLT into cells; and intracellular phosphorylation. Using values of model parameters estimated from the biological literature, simulated FLT TACs are generated with shapes and magnitudes similar to those seen clinically. Results show that the kinetics of the spatial-temporal model can be recovered accurately by fitting a 3-tissue compartment model to FLT TACs simulated for those tumours or tumour sub-volumes that can be viewed as approximately closed, for which tracer diffusion throughout the interstitium makes only a small fractional change to the quantity of FLT they contain. For a single PET voxel of width 2.5-5 mm we show that this condition is roughly equivalent to requiring that the relative difference in tracer uptake between the voxel and its neighbours is much less than one.

Temporal acceleration of spatially distributed kinetic Monte Carlo simulations

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

Chatterjee, Abhijit; Vlachos, Dionisios G.

The computational intensity of kinetic Monte Carlo (KMC) simulation is a major impediment in simulating large length and time scales. In recent work, an approximate method for KMC simulation of spatially uniform systems, termed the binomial {tau}-leap method, was introduced [A. Chatterjee, D.G. Vlachos, M.A. Katsoulakis, Binomial distribution based {tau}-leap accelerated stochastic simulation, J. Chem. Phys. 122 (2005) 024112], where molecular bundles instead of individual processes are executed over coarse-grained time increments. This temporal coarse-graining can lead to significant computational savings but its generalization to spatially lattice KMC simulation has not been realized yet. Here we extend the binomial {tau}-leapmore » method to lattice KMC simulations by combining it with spatially adaptive coarse-graining. Absolute stability and computational speed-up analyses for spatial systems along with simulations provide insights into the conditions where accuracy and substantial acceleration of the new spatio-temporal coarse-graining method are ensured. Model systems demonstrate that the r-time increment criterion of Chatterjee et al. obeys the absolute stability limit for values of r up to near 1.« less

Spatial Competition: Roughening of an Experimental Interface.

PubMed

Allstadt, Andrew J; Newman, Jonathan A; Walter, Jonathan A; Korniss, G; Caraco, Thomas

2016-07-28

Limited dispersal distance generates spatial aggregation. Intraspecific interactions are then concentrated within clusters, and between-species interactions occur near cluster boundaries. Spread of a locally dispersing invader can become motion of an interface between the invading and resident species, and spatial competition will produce variation in the extent of invasive advance along the interface. Kinetic roughening theory offers a framework for quantifying the development of these fluctuations, which may structure the interface as a self-affine fractal, and so induce a series of temporal and spatial scaling relationships. For most clonal plants, advance should become spatially correlated along the interface, and width of the interface (where invader and resident compete directly) should increase as a power function of time. Once roughening equilibrates, interface width and the relative location of the most advanced invader should each scale with interface length. We tested these predictions by letting white clover (Trifolium repens) invade ryegrass (Lolium perenne). The spatial correlation of clover growth developed as anticipated by kinetic roughening theory, and both interface width and the most advanced invader's lead scaled with front length. However, the scaling exponents differed from those predicted by recent simulation studies, likely due to clover's growth morphology.

Spatial Competition: Roughening of an Experimental Interface

PubMed Central

Allstadt, Andrew J.; Newman, Jonathan A.; Walter, Jonathan A.; Korniss, G.; Caraco, Thomas

2016-01-01

Limited dispersal distance generates spatial aggregation. Intraspecific interactions are then concentrated within clusters, and between-species interactions occur near cluster boundaries. Spread of a locally dispersing invader can become motion of an interface between the invading and resident species, and spatial competition will produce variation in the extent of invasive advance along the interface. Kinetic roughening theory offers a framework for quantifying the development of these fluctuations, which may structure the interface as a self-affine fractal, and so induce a series of temporal and spatial scaling relationships. For most clonal plants, advance should become spatially correlated along the interface, and width of the interface (where invader and resident compete directly) should increase as a power function of time. Once roughening equilibrates, interface width and the relative location of the most advanced invader should each scale with interface length. We tested these predictions by letting white clover (Trifolium repens) invade ryegrass (Lolium perenne). The spatial correlation of clover growth developed as anticipated by kinetic roughening theory, and both interface width and the most advanced invader’s lead scaled with front length. However, the scaling exponents differed from those predicted by recent simulation studies, likely due to clover’s growth morphology. PMID:27465518

Multiscale Models for the Two-Stream Instability

NASA Astrophysics Data System (ADS)

Joseph, Ilon; Dimits, Andris; Banks, Jeffrey; Berger, Richard; Brunner, Stephan; Chapman, Thomas

2017-10-01

Interpenetrating streams of plasma found in many important scenarios in nature and in the laboratory can develop kinetic two-stream instabilities that exchange momentum and energy between the streams. A quasilinear model for the electrostatic two-stream instability is under development as a component of a multiscale model that couples fluid simulations to kinetic theory. Parameters of the model will be validated with comparison to full kinetic simulations using LOKI and efficient strategies for numerical solution of the quasilinear model and for coupling to the fluid model will be discussed. Extending the kinetic models into the collisional regime requires an efficient treatment of the collision operator. Useful reductions of the collision operator relative to the full multi-species Landau-Fokker-Plank operator are being explored. These are further motivated both by careful consideration of the parameter orderings relevant to two-stream scenarios and by the particular 2D+2V phase space used in the LOKI code. Prepared for US DOE by LLNL under Contract DE-AC52-07NA27344 and LDRD project 17- ERD-081.

Effects of self-coupling and asymmetric output on metastable dynamical transient firing patterns in arrays of neurons with bidirectional inhibitory coupling.

PubMed

Horikawa, Yo

2016-04-01

Metastable dynamical transient patterns in arrays of bidirectionally coupled neurons with self-coupling and asymmetric output were studied. First, an array of asymmetric sigmoidal neurons with symmetric inhibitory bidirectional coupling and self-coupling was considered and the bifurcations of its steady solutions were shown. Metastable dynamical transient spatially nonuniform states existed in the presence of a pair of spatially symmetric stable solutions as well as unstable spatially nonuniform solutions in a restricted range of the output gain of a neuron. The duration of the transients increased exponentially with the number of neurons up to the maximum number at which the spatially nonuniform steady solutions were stabilized. The range of the output gain for which they existed reduced as asymmetry in a sigmoidal output function of a neuron increased, while the existence range expanded as the strength of inhibitory self-coupling increased. Next, arrays of spiking neuron models with slow synaptic inhibitory bidirectional coupling and self-coupling were considered with computer simulation. In an array of Class 1 Hindmarsh-Rose type models, in which each neuron showed a graded firing rate, metastable dynamical transient firing patterns were observed in the presence of inhibitory self-coupling. This agreed with the condition for the existence of metastable dynamical transients in an array of sigmoidal neurons. In an array of Class 2 Bonhoeffer-van der Pol models, in which each neuron had a clear threshold between firing and resting, long-lasting transient firing patterns with bursting and irregular motion were observed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Characterizing acid diffusion lengths in chemically amplified resists from measurements of deprotection kinetics

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

Patil, Abhijit A.; Pandey, Yogendra Narayan; Doxastakis, Manolis

2014-10-01

The acid-catalyzed deprotection of glassy poly(4-hydroxystyrene-co-tertbutyl acrylate) films was studied with infrared absorbance spectroscopy and stochastic simulations. Experimental data were interpreted with a simple description of subdiffusive acid transport coupled to second-order acid loss. This model predicts key attributes of observed deprotection rates, such as fast reaction at short times, slow reaction at long times, and a nonlinear dependence on acid loading. Fickian diffusion is approached by increasing the post-exposure bake temperature or adding plasticizing agents to the polymer resin. These findings demonstrate that acid mobility and overall deprotection kinetics are coupled to glassy matrix dynamics. To complement the analysismore » of bulk kinetics, acid diffusion lengths were calculated from the anomalous transport model and compared with nanopattern line widths. The consistent scaling between experiments and simulations suggests that the anomalous diffusion model could be further developed into a predictive lithography tool.« less

Biophysical synaptic dynamics in an analog VLSI network of Hodgkin-Huxley neurons.

PubMed

Yu, Theodore; Cauwenberghs, Gert

2009-01-01

We study synaptic dynamics in a biophysical network of four coupled spiking neurons implemented in an analog VLSI silicon microchip. The four neurons implement a generalized Hodgkin-Huxley model with individually configurable rate-based kinetics of opening and closing of Na+ and K+ ion channels. The twelve synapses implement a rate-based first-order kinetic model of neurotransmitter and receptor dynamics, accounting for NMDA and non-NMDA type chemical synapses. The implemented models on the chip are fully configurable by 384 parameters accounting for conductances, reversal potentials, and pre/post-synaptic voltage-dependence of the channel kinetics. We describe the models and present experimental results from the chip characterizing single neuron dynamics, single synapse dynamics, and multi-neuron network dynamics showing phase-locking behavior as a function of synaptic coupling strength. The 3mm x 3mm microchip consumes 1.29 mW power making it promising for applications including neuromorphic modeling and neural prostheses.

Automatic network coupling analysis for dynamical systems based on detailed kinetic models.

PubMed

Lebiedz, Dirk; Kammerer, Julia; Brandt-Pollmann, Ulrich

2005-10-01

We introduce a numerical complexity reduction method for the automatic identification and analysis of dynamic network decompositions in (bio)chemical kinetics based on error-controlled computation of a minimal model dimension represented by the number of (locally) active dynamical modes. Our algorithm exploits a generalized sensitivity analysis along state trajectories and subsequent singular value decomposition of sensitivity matrices for the identification of these dominant dynamical modes. It allows for a dynamic coupling analysis of (bio)chemical species in kinetic models that can be exploited for the piecewise computation of a minimal model on small time intervals and offers valuable functional insight into highly nonlinear reaction mechanisms and network dynamics. We present results for the identification of network decompositions in a simple oscillatory chemical reaction, time scale separation based model reduction in a Michaelis-Menten enzyme system and network decomposition of a detailed model for the oscillatory peroxidase-oxidase enzyme system.

Inverse electron demand Diels-Alder reactions in chemical biology.

PubMed

Oliveira, B L; Guo, Z; Bernardes, G J L

2017-08-14

The emerging inverse electron demand Diels-Alder (IEDDA) reaction stands out from other bioorthogonal reactions by virtue of its unmatchable kinetics, excellent orthogonality and biocompatibility. With the recent discovery of novel dienophiles and optimal tetrazine coupling partners, attention has now been turned to the use of IEDDA approaches in basic biology, imaging and therapeutics. Here we review this bioorthogonal reaction and its promising applications for live cell and animal studies. We first discuss the key factors that contribute to the fast IEDDA kinetics and describe the most recent advances in the synthesis of tetrazine and dienophile coupling partners. Both coupling partners have been incorporated into proteins for tracking and imaging by use of fluorogenic tetrazines that become strongly fluorescent upon reaction. Selected notable examples of such applications are presented. The exceptional fast kinetics of this catalyst-free reaction, even using low concentrations of coupling partners, make it amenable for in vivo radiolabelling using pretargeting methodologies, which are also discussed. Finally, IEDDA reactions have recently found use in bioorthogonal decaging to activate proteins or drugs in gain-of-function strategies. We conclude by showing applications of the IEDDA reaction in the construction of biomaterials that are used for drug delivery and multimodal imaging, among others. The use and utility of the IEDDA reaction is interdisciplinary and promises to revolutionize chemical biology, radiochemistry and materials science.

Visualizing the kinetic power stroke that drives proton-coupled Zn(II) transport

PubMed Central

Gupta, Sayan; Chai, Jin; Cheng, Jie; D'Mello, Rhijuta; Chance, Mark R.; Fu, Dax

2014-01-01

The proton gradient is a principal energy source for respiration-dependent active transport, but the structural mechanisms of proton-coupled transport processes are poorly understood. YiiP is a proton-coupled zinc transporter found in the cytoplasmic membrane of E. coli, and the transport-site of YiiP receives protons from water molecules that gain access to its hydrophobic environment and transduces the energy of an inward proton gradient to drive Zn(II) efflux1,2. This membrane protein is a well characterized member3-7 of the protein family of cation diffusion facilitators (CDFs) that occurs at all phylogenetic levels8-10. X-ray mediated hydroxyl radical labeling of YiiP and mass spectrometric analysis showed that Zn(II) binding triggered a highly localized, all-or-none change of water accessibility to the transport-site and an adjacent hydrophobic gate. Millisecond time-resolved dynamics revealed a concerted and reciprocal pattern of accessibility changes along a transmembrane helix, suggesting a rigid-body helical reorientation linked to Zn(II) binding that triggers the closing of the hydrophobic gate. The gated water access to the transport-site enables a stationary proton gradient to facilitate the conversion of zinc binding energy to the kinetic power stroke of a vectorial zinc transport. The kinetic details provide energetic insights into a proton-coupled active transport reaction. PMID:25043033

High-resolution Statistics of Solar Wind Turbulence at Kinetic Scales Using the Magnetospheric Multiscale Mission

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

Chasapis, Alexandros; Matthaeus, W. H.; Parashar, T. N.

Using data from the Magnetospheric Multiscale (MMS) and Cluster missions obtained in the solar wind, we examine second-order and fourth-order structure functions at varying spatial lags normalized to ion inertial scales. The analysis includes direct two-spacecraft results and single-spacecraft results employing the familiar Taylor frozen-in flow approximation. Several familiar statistical results, including the spectral distribution of energy, and the sale-dependent kurtosis, are extended down to unprecedented spatial scales of ∼6 km, approaching electron scales. The Taylor approximation is also confirmed at those small scales, although small deviations are present in the kinetic range. The kurtosis is seen to attain verymore » high values at sub-proton scales, supporting the previously reported suggestion that monofractal behavior may be due to high-frequency plasma waves at kinetic scales.« less

Turbulent Radiation Effects in HSCT Combustor Rich Zone

NASA Technical Reports Server (NTRS)

Hall, Robert J.; Vranos, Alexander; Yu, Weiduo

1998-01-01

A joint UTRC-University of Connecticut theoretical program was based on describing coupled soot formation and radiation in turbulent flows using stretched flamelet theory. This effort was involved with using the model jet fuel kinetics mechanism to predict soot growth in flamelets at elevated pressure, to incorporate an efficient model for turbulent thermal radiation into a discrete transfer radiation code, and to couple die soot growth, flowfield, and radiation algorithm. The soot calculations used a recently developed opposed jet code which couples the dynamical equations of size-class dependent particle growth with complex chemistry. Several of the tasks represent technical firsts; among these are the prediction of soot from a detailed jet fuel kinetics mechanism, the inclusion of pressure effects in the soot particle growth equations, and the inclusion of the efficient turbulent radiation algorithm in a combustor code.

Ring Current Ion Coupling with Electromagnetic Ion Cyclotron Waves

NASA Technical Reports Server (NTRS)

Khazanov, George V.

2002-01-01

A new ring current global model has been developed for the first time that couples the system of two kinetic equations: one equation describes the ring current (RC) ion dynamic, and another equation describes wave evolution of electromagnetic ion cyclotron waves (EMIC). The coupled model is able to simulate, for the first time self-consistently calculated RC ion kinetic and evolution of EMIC waves that propagate along geomagnetic field lines and reflect from the ionosphere. Ionospheric properties affect the reflection index through the integral Pedersen and Hall coductivities. The structure and dynamics of the ring current proton precipitating flux regions, intensities of EMIC, global RC energy balance, and some other parameters will be studied in detail for the selected geomagnetic storms. The space whether aspects of RC modelling and comparison with the data will also be discussed.

Spatial localization of excitons and charge carriers in hybrid perovskite thin films

DOE PAGES

Simpson, Mary Jane; Doughty, Benjamin; Yang, Bin; ...

2015-07-21

The fundamental photophysics underlying the remarkably high power conversion efficiency of organic-inorganic hybrid perovskite-based solar cells has been increasingly studied using complementary spectroscopic techniques. The spatially heterogeneous polycrystalline morphology of the photoactive layers owing to the presence of distinct crystalline grains has been generally neglected in optical measurements and therefore the reported results are typically averaged over hundreds or even thousands of such grains. Here, we apply femtosecond transient absorption microscopy to spatially and temporally probe ultrafast electronic excited-state dynamics in pristine methylammonium lead tri-iodide (CH 3NH 3PbI 3) thin films and composite structures. We found that the electronic excited-statemore » relaxation kinetics are extremely sensitive to the sample location probed, which was manifested by position-dependent decay timescales and transient signals. As a result, analysis of transient absorption kinetics acquired at distinct spatial positions enabled us to identify contributions of excitons and free charge carriers.« less

The S4–S5 Linker Acts as a Signal Integrator for hERG K+ Channel Activation and Deactivation Gating

PubMed Central

Ng, Chai Ann; Perry, Matthew D.; Tan, Peter S.; Hill, Adam P.; Kuchel, Philip W.; Vandenberg, Jamie I.

2012-01-01

Human ether-à-go-go-related gene (hERG) K+ channels have unusual gating kinetics. Characterised by slow activation/deactivation but rapid inactivation/recovery from inactivation, the unique gating kinetics underlie the central role hERG channels play in cardiac repolarisation. The slow activation and deactivation kinetics are regulated in part by the S4–S5 linker, which couples movement of the voltage sensor domain to opening of the activation gate at the distal end of the inner helix of the pore domain. It has also been suggested that cytosolic domains may interact with the S4–S5 linker to regulate activation and deactivation kinetics. Here, we show that the solution structure of a peptide corresponding to the S4–S5 linker of hERG contains an amphipathic helix. The effects of mutations at the majority of residues in the S4–S5 linker of hERG were consistent with the previously identified role in coupling voltage sensor movement to the activation gate. However, mutations to Ser543, Tyr545, Gly546 and Ala548 had more complex phenotypes indicating that these residues are involved in additional interactions. We propose a model in which the S4–S5 linker, in addition to coupling VSD movement to the activation gate, also contributes to interactions that stabilise the closed state and a separate set of interactions that stabilise the open state. The S4–S5 linker therefore acts as a signal integrator and plays a crucial role in the slow deactivation kinetics of the channel. PMID:22359612

Spatial variability in land-atmosphere coupling strength at the ARM Southern Great Plains site under different cloud regimes

NASA Astrophysics Data System (ADS)

Tang, Q.; Xie, S.; Zhang, Y.

2016-12-01

The paucity of land/soil observations is a long-standing limitation for land-atmosphere (LA) coupling studies, in particular for estimating the spatial variability in the coupling strengths. Spatially dense atmospheric radiation measurement (ARM) sites deployed at the U.S. Southern Great Plains (SGP) covers a wide range of vegetation, surface, and soil types, and thus allow us to observe the spatial patterns of LA coupling. The upcoming "super site" at SGP will facilitate these studies at even finer scales. While many previous studies have focused only on the observations from the central facility (CF) site or the domain mean from multiple sites, in the present work we examine the robustness of many key surface and land observations (e.g., radiation, turbulence fluxes, soil moisture, etc.) at extended sites besides the CF site for a decade. The coupling strengths are estimated with temporal covariations between important variables. We subsample the data to different categories based on different cloud regimes (e.g., clear sky, shallow cumulus, and deep cumulus. These cloud regimes are strongly impacted by local factors. The spatial variability of coupling strengths at different ARM sites is assessed with respect to dominant drivers (i.e., vegetation, land type, etc.). The results of this study will provide insights for improving the representation of LA coupling in climate models by providing observational constraints to parameterizations, e.g., shallow convective schemes. This work is performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-698523

A second-order theory for transverse ion heating and momentum coupling due to electrostatic ion cyclotron waves

NASA Technical Reports Server (NTRS)

Miller, Ronald H.; Winske, Dan; Gary, S. P.

1992-01-01

A second-order theory for electrostatic instabilities driven by counterstreaming ion beams is developed which describes momentum coupling and heating of the plasma via wave-particle interactions. Exchange rates between the waves and particles are derived, which are suitable for the fluid equations simulating microscopic effects on macroscopic scales. Using a fully kinetic simulation, the electrostatic ion cyclotron instability due to counterstreaming H(+) beams has been simulated. A power spectrum from the kinetic simulation is used to evaluate second-order exchange rates. The calculated heating and momentum loss from second-order theory is compared to the numerical simulation.

Final Report: Mechanisms of sputter ripple formation: coupling among energetic ions, surface kinetics, stress and composition

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

Chason, Eric; Shenoy, Vivek

Self-organized pattern formation enables the creation of nanoscale surface structures over large areas based on fundamental physical processes rather than an applied template. Low energy ion bombardment is one such method that induces the spontaneous formation of a wide variety of interesting morphological features (e.g., sputter ripples and/or quantum dots). This program focused on the processes controlling sputter ripple formation and the kinetics controlling the evolution of surfaces and nanostructures in high flux environments. This was done by using systematic, quantitative experiments to measure ripple formation under a variety of processing conditions coupled with modeling to interpret the results.

Kinetic theory of coupled oscillators.

PubMed

Hildebrand, Eric J; Buice, Michael A; Chow, Carson C

2007-02-02

We present an approach for the description of fluctuations that are due to finite system size induced correlations in the Kuramoto model of coupled oscillators. We construct a hierarchy for the moments of the density of oscillators that is analogous to the Bogoliubov-Born-Green-Kirkwood-Yvon hierarchy in the kinetic theory of plasmas and gases. To calculate the lowest order system size effect, we truncate this hierarchy at second order and solve the resulting closed equations for the two-oscillator correlation function around the incoherent state. We use this correlation function to compute the fluctuations of the order parameter, including the effect of transients, and compare this computation with numerical simulations.

Porosity Development in a Coastal Setting: A Reactive Transport Model to Assess the Influence of Heterogeneity of Hydrological, Geochemical and Lithological Conditions

NASA Astrophysics Data System (ADS)

Maqueda, A.; Renard, P.; Cornaton, F. J.

2014-12-01

Coastal karst networks are formed by mineral dissolution, mainly calcite, in the freshwater-saltwater mixing zone. The problem has been approached first by studying the kinetics of calcite dissolution and then coupling ion-pairing software with flow and mass transport models. Porosity development models require high computational power. A workaround to reduce computational complexity is to assume the calcite dissolution reaction is relatively fast, thus equilibrium chemistry can be used to model it (Sanford & Konikow, 1989). Later developments allowed the full coupling of kinetics and transport in a model. However kinetics effects of calcite dissolution were found negligible under the single set of assumed hydrological and geochemical boundary conditions. A model is implemented with the coupling of FeFlow software as the flow & transport module and PHREEQC4FEFLOW (Wissmeier, 2013) ion-pairing module. The model is used to assess the influence of heterogeneities in hydrological, geochemical and lithological boundary conditions on porosity evolution. The hydrologic conditions present in the karst aquifer of Quintana Roo coast in Mexico are used as a guide for generating inputs for simulations.

Kinetic study on anaerobic oxidation of methane coupled to denitrification.

PubMed

Yu, Hou; Kashima, Hiroyuki; Regan, John M; Hussain, Abid; Elbeshbishy, Elsayed; Lee, Hyung-Sool

2017-09-01

Monod kinetic parameters provide information required for kinetic analysis of anaerobic oxidation of methane coupled to denitrification (AOM-D). This information is critical for engineering AOM-D processes in wastewater treatment facilities. We first experimentally determined Monod kinetic parameters for an AOM-D enriched culture and obtained the following values: maximum specific growth rate (μ max ) 0.121/d, maximum substrate-utilization rate (q max ) 28.8mmol CH 4 /g cells-d, half maximum-rate substrate concentration (K s ) 83μΜ CH 4 , growth yield (Y) 4.76gcells/mol CH 4 , decay coefficient (b) 0.031/d, and threshold substrate concentration (S min ) 28.8μM CH 4 . Clone library analysis of 16S rRNA and mcrA gene fragments suggested that AOM-D reactions might have occurred via the syntrophic interaction between denitrifying bacteria (e.g., Ignavibacterium, Acidovorax, and Pseudomonas spp.) and hydrogenotrophic methanogens (Methanobacterium spp.), supporting reverse methanogenesis-dependent AOM-D in our culture. High μ max and q max , and low K s for the AOM-D enrichment imply that AOM-D could play a significant role in mitigating atmospheric methane efflux. In addition, these high kinetic features suggest that engineered AOM-D systems may provide a sustainable alternative to nitrogen removal in wastewater treatment. Copyright © 2017 Elsevier Inc. All rights reserved.

Coupling DAEM and CFD for simulating biomass fast pyrolysis in fluidized beds

DOE PAGES

Xiong, Qingang; Zhang, Jingchao; Wiggins, Gavin; ...

2015-12-03

We report results from computational simulations of an experimental, lab-scale bubbling bed biomass pyrolysis reactor that include a distributed activation energy model (DAEM) for the kinetics. In this study, we utilized multiphase computational fluid dynamics (CFD) to account for the turbulent hydrodynamics, and this was combined with the DAEM kinetics in a multi-component, multi-step reaction network. Our results indicate that it is possible to numerically integrate the coupled CFD–DAEM system without significantly increasing computational overhead. It is also clear, however, that reactor operating conditions, reaction kinetics, and multiphase flow dynamics all have major impacts on the pyrolysis products exiting themore » reactor. We find that, with the same pre-exponential factors and mean activation energies, inclusion of distributed activation energies in the kinetics can shift the predicted average value of the exit vapor-phase tar flux and its statistical distribution, compared to single-valued activation-energy kinetics. Perhaps the most interesting observed trend is that increasing the diversity of the DAEM activation energies appears to increase the mean tar yield, all else being equal. As a result, these findings imply that accurate resolution of the reaction activation energy distributions will be important for optimizing biomass pyrolysis processes.« less

Mathematical model for internal pH control in immobilized enzyme particles

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

Liou, J.K.; Rousseau, I.

A mathematical model has been developed for the internal pH control in immobilized enzyme particles. This model describes the kinetics of a coupled system of two enzymes, immobilized in particles of either planar, cylindrical, or spherical shape. The enzyme kinetics are assumed to be of a mixed type, including Michaelis-Menten kinetics, uncompetitive substrate inhibition, and competitive and noncompetitive product inhibition. In a case study we have considered the enzyme combination urease and penicillin acylase, whose kinetics are coupled through the pH dependence of the kinetic parameters. The hydrolysis of urea by urease yields ammonia and carbon dioxide, whereas benzylpenicillin (Pen-G)more » is converted to 6-animo penicillanic acid and phenyl acetic acid by penicillin acylase. The production of acids by the latter enzyme will cause a decrease in pH. Because of the presence of the ammonia-carbon dioxide system, however, the pH may be kept under control. In order to obtain information about the optimum performance of this enzymatic pH controller, we have computed the effectiveness factor and the conversion in a CSTR at different enzyme loadings. The results of the computer simulations indicate that a high conversion of Pen-G may be achieved (80-90%) at bulk pH values of about 7.5 - 8. 27 references.« less

Kramers turnover: From energy diffusion to spatial diffusion using metadynamics

PubMed Central

Tiwary, Pratyush; Berne, B. J.

2016-01-01

We consider the rate of transition for a particle between two metastable states coupled to a thermal environment for various magnitudes of the coupling strength using the recently proposed infrequent metadynamics approach [P. Tiwary and M. Parrinello, Phys. Rev. Lett. 111, 230602 (2013)]. We are interested in understanding how this approach for obtaining rate constants performs as the dynamics regime changes from energy diffusion to spatial diffusion. Reassuringly, we find that the approach works remarkably well for various coupling strengths in the strong coupling regime, and to some extent even in the weak coupling regime. PMID:27059558

KINETIC CONTROL OF OXIDATION STATE AT THERMODYNAMICALLY BUFFERED POTENTIALS IN SUBSURFACE WATERS

EPA Science Inventory

Dissolved oxygen (DO) and organic carbon (Corg) are among the highest- and lowest-potential reactants, respectively, of redox couples in natural waters. When DO and Corg are present in subsurface settings, other couples are drawn toward potentials imposed by them, generating a b...

Low-oxygen and chemical kinetic constraints on the geochemical niche of neutrophilic iron(II) oxidizing microorganisms

NASA Astrophysics Data System (ADS)

Druschel, Gregory K.; Emerson, David; Sutka, R.; Suchecki, P.; Luther, George W., III

2008-07-01

Neutrophilic iron oxidizing bacteria (FeOB) must actively compete with rapid abiotic processes governing Fe(II) oxidation and as a result have adapted to primarily inhabit low-O 2 environments where they can more successfully compete with abiotic Fe(II) oxidation. The spatial distribution of these microorganisms can be observed through the chemical gradients they affect, as measured using in situ voltammetric analysis for dissolved Fe(II), Fe(III), O 2, and FeS (aq). Field and laboratory determination of the chemical environments inhabited by the FeOB were coupled with detailed kinetic competition studies for abiotic and biotic oxidation processes using a pure culture of FeOB to quantify the geochemical niche these organisms inhabit. In gradient culture tubes, the maximum oxygen levels, which were associated with growth bands of Sideroxydans lithotrophicus (ES-1, a novel FeOB), were 15-50 μM. Kinetic measurements made on S. lithotrophicus compared biotic/abiotic (killed control) Fe oxidation rates. The biotic rate can be a significant and measurable fraction of the total Fe oxidation rate below O 2 concentrations of approximately 50 μM, but biotic Fe(II) oxidation (via the biotic/abiotic rate comparison) becomes difficult to detect at higher O 2 levels. These results are further supported by observations of conditions supporting FeOB communities in field settings. Variablity in cell densities and cellular activity as well as variations in hydrous ferrous oxide mineral quantities significantly affect the laboratory kinetic rates. The microbial habitat (or geochemical niche) where FeOB are active is thus largely controlled by the competition between abiotic and biotic kinetics, which are dependent on Fe(II) concentration, P O2, temperature and pH in addition to the surface area of hydrous ferric oxide minerals and the cell density/activity of FeOB. Additional field and lab culture observations suggest a potentially important role for the iron-sulfide aqueous molecular cluster, FeS (aq), in the overall cycling of iron associated with the environments these microorganisms inhabit.

Transport Mechanisms and Quality Changes During Frying of Chicken Nuggets--Hybrid Mixture Theory Based Modeling and Experimental Verification.

PubMed

Bansal, Harkirat S; Takhar, Pawan S; Alvarado, Christine Z; Thompson, Leslie D

2015-12-01

Hybrid mixture theory (HMT) based 2-scale fluid transport relations of Takhar coupled with a multiphase heat transfer equation were solved to model water, oil and gas movement during frying of chicken nuggets. A chicken nugget was treated as a heterogeneous material consisting of meat core with wheat-based coating. The coupled heat and fluid transfer equations were solved using the finite element method. Numerical simulations resulted in data on spatial and temporal profiles for moisture, rate of evaporation, temperature, oil, pore pressure, pressure in various phases, and coefficient of elasticity. Results showed that most of the oil stayed in the outer 1.5 mm of the coating region. Temperature values greater than 100 °C were observed in the coating after 30 s of frying. Negative gage-pore pressure (p(w) < p(g)) magnitudes were observed in simulations, which is in agreement with experimental observations of Sandhu and others. It is hypothesized that high water-phase capillary pressure (p(c) > p(g)) in the hydrophilic matrix causes p(w) < p(g), which further results in negative pore pressure. The coefficient of elasticity was the highest at the surface (2.5 × 10(5) Pa) for coating and the interface of coating and core (6 × 10(5) Pa). Kinetics equation for color change obtained from experiments was coupled with the HMT based model to predict the color (L, a, and b) as a function of frying time. © 2015 Institute of Food Technologists®

Strongly coupled fluid-particle flows in vertical channels. I. Reynolds-averaged two-phase turbulence statistics

NASA Astrophysics Data System (ADS)

Capecelatro, Jesse; Desjardins, Olivier; Fox, Rodney O.

2016-03-01

Simulations of strongly coupled (i.e., high-mass-loading) fluid-particle flows in vertical channels are performed with the purpose of understanding the fundamental physics of wall-bounded multiphase turbulence. The exact Reynolds-averaged (RA) equations for high-mass-loading suspensions are presented, and the unclosed terms that are retained in the context of fully developed channel flow are evaluated in an Eulerian-Lagrangian (EL) framework for the first time. A key distinction between the RA formulation presented in the current work and previous derivations of multiphase turbulence models is the partitioning of the particle velocity fluctuations into spatially correlated and uncorrelated components, used to define the components of the particle-phase turbulent kinetic energy (TKE) and granular temperature, respectively. The adaptive spatial filtering technique developed in our previous work for homogeneous flows [J. Capecelatro, O. Desjardins, and R. O. Fox, "Numerical study of collisional particle dynamics in cluster-induced turbulence," J. Fluid Mech. 747, R2 (2014)] is shown to accurately partition the particle velocity fluctuations at all distances from the wall. Strong segregation in the components of granular energy is observed, with the largest values of particle-phase TKE associated with clusters falling near the channel wall, while maximum granular temperature is observed at the center of the channel. The anisotropy of the Reynolds stresses both near the wall and far away is found to be a crucial component for understanding the distribution of the particle-phase volume fraction. In Part II of this paper, results from the EL simulations are used to validate a multiphase Reynolds-stress turbulence model that correctly predicts the wall-normal distribution of the two-phase turbulence statistics.

Strongly coupled fluid-particle flows in vertical channels. I. Reynolds-averaged two-phase turbulence statistics

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

Capecelatro, Jesse, E-mail: jcaps@illinois.edu; Desjardins, Olivier; Fox, Rodney O.

Simulations of strongly coupled (i.e., high-mass-loading) fluid-particle flows in vertical channels are performed with the purpose of understanding the fundamental physics of wall-bounded multiphase turbulence. The exact Reynolds-averaged (RA) equations for high-mass-loading suspensions are presented, and the unclosed terms that are retained in the context of fully developed channel flow are evaluated in an Eulerian–Lagrangian (EL) framework for the first time. A key distinction between the RA formulation presented in the current work and previous derivations of multiphase turbulence models is the partitioning of the particle velocity fluctuations into spatially correlated and uncorrelated components, used to define the components ofmore » the particle-phase turbulent kinetic energy (TKE) and granular temperature, respectively. The adaptive spatial filtering technique developed in our previous work for homogeneous flows [J. Capecelatro, O. Desjardins, and R. O. Fox, “Numerical study of collisional particle dynamics in cluster-induced turbulence,” J. Fluid Mech. 747, R2 (2014)] is shown to accurately partition the particle velocity fluctuations at all distances from the wall. Strong segregation in the components of granular energy is observed, with the largest values of particle-phase TKE associated with clusters falling near the channel wall, while maximum granular temperature is observed at the center of the channel. The anisotropy of the Reynolds stresses both near the wall and far away is found to be a crucial component for understanding the distribution of the particle-phase volume fraction. In Part II of this paper, results from the EL simulations are used to validate a multiphase Reynolds-stress turbulence model that correctly predicts the wall-normal distribution of the two-phase turbulence statistics.« less

Voltage gating by molecular subunits of Na+ and K+ ion channels: higher-dimensional cubic kinetics, rate constants, and temperature

PubMed Central

2015-01-01

The structural similarity between the primary molecules of voltage-gated Na and K channels (alpha subunits) and activation gating in the Hodgkin-Huxley model is brought into full agreement by increasing the model's sodium kinetics to fourth order (m3 → m4). Both structures then virtually imply activation gating by four independent subprocesses acting in parallel. The kinetics coalesce in four-dimensional (4D) cubic diagrams (16 states, 32 reversible transitions) that show the structure to be highly failure resistant against significant partial loss of gating function. Rate constants, as fitted in phase plot data of retinal ganglion cell excitation, reflect the molecular nature of the gating transitions. Additional dimensions (6D cubic diagrams) accommodate kinetically coupled sodium inactivation and gating processes associated with beta subunits. The gating transitions of coupled sodium inactivation appear to be thermodynamically irreversible; response to dielectric surface charges (capacitive displacement) provides a potential energy source for those transitions and yields highly energy-efficient excitation. A comparison of temperature responses of the squid giant axon (apparently Arrhenius) and mammalian channel gating yields kinetic Q10 = 2.2 for alpha unit gating, whose transitions are rate-limiting at mammalian temperatures; beta unit kinetic Q10 = 14 reproduces the observed non-Arrhenius deviation of mammalian gating at low temperatures; the Q10 of sodium inactivation gating matches the rate-limiting component of activation gating at all temperatures. The model kinetics reproduce the physiologically large frequency range for repetitive firing in ganglion cells and the physiologically observed strong temperature dependence of recovery from inactivation. PMID:25867741

Kinetic Modeling of Slow Energy Release in Non-Ideal Carbon Rich Explosives

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

Vitello, P; Fried, L; Glaesemann, K

2006-06-20

We present here the first self-consistent kinetic based model for long time-scale energy release in detonation waves in the non-ideal explosive LX-17. Non-ideal, insensitive carbon rich explosives, such as those based on TATB, are believed to have significant late-time slow release in energy. One proposed source of this energy is diffusion-limited growth of carbon clusters. In this paper we consider the late-time energy release problem in detonation waves using the thermochemical code CHEETAH linked to a multidimensional ALE hydrodynamics model. The linked CHEETAH-ALE model dimensional treats slowly reacting chemical species using kinetic rate laws, with chemical equilibrium assumed for speciesmore » coupled via fast time-scale reactions. In the model presented here we include separate rate equations for the transformation of the un-reacted explosive to product gases and for the growth of a small particulate form of condensed graphite to a large particulate form. The small particulate graphite is assumed to be in chemical equilibrium with the gaseous species allowing for coupling between the instantaneous thermodynamic state and the production of graphite clusters. For the explosive burn rate a pressure dependent rate law was used. Low pressure freezing of the gas species mass fractions was also included to account for regions where the kinetic coupling rates become longer than the hydrodynamic time-scales. The model rate parameters were calibrated using cylinder and rate-stick experimental data. Excellent long time agreement and size effect results were achieved.« less

Spatial layout optimization design of multi-type LEDs lighting source based on photoelectrothermal coupling theory

NASA Astrophysics Data System (ADS)

Xue, Lingyun; Li, Guang; Chen, Qingguang; Rao, Huanle; Xu, Ping

2018-03-01

Multiple LED-based spectral synthesis technology has been widely used in the fields of solar simulator, color mixing, and artificial lighting of plant factory and so on. Generally, amounts of LEDs are spatially arranged with compact layout to obtain the high power density output. Mutual thermal spreading among LEDs will produce the coupled thermal effect which will additionally increase the junction temperature of LED. Affected by the Photoelectric thermal coupling effect of LED, the spectrum of LED will shift and luminous efficiency will decrease. Correspondingly, the spectral synthesis result will mismatch. Therefore, thermal management of LED spatial layout plays an important role for multi-LEDs light source system. In the paper, the thermal dissipation network topology model considering the mutual thermal spreading effect among the LEDs is proposed for multi-LEDs system with various types of power. The junction temperature increment cased by the thermal coupling has the great relation with the spatial arrangement. To minimize the thermal coupling effect, an optimized method of LED spatial layout for the specific light source structure is presented and analyzed. The results showed that layout of LED with high-power are arranged in the corner and low-power in the center. Finally, according to this method, it is convenient to determine the spatial layout of LEDs in a system having any kind of light source structure, and has the advantages of being universally applicable to facilitate adjustment.

A Gas-Kinetic Scheme for Multimaterial Flows and Its Application in Chemical Reaction

NASA Technical Reports Server (NTRS)

Lian, Yongsheng; Xu, Kun

1999-01-01

This paper concerns the extension of the multicomponent gas-kinetic BGK-type scheme to multidimensional chemical reactive flow calculations. In the kinetic model, each component satisfies its individual gas-kinetic BGK equation and the equilibrium states of both components are coupled in space and time due to the momentum and energy exchange in the course of particle collisions. At the same time, according to the chemical reaction rule one component can be changed into another component with the release of energy, where the reactant and product could have different gamma. Many numerical test cases are included in this paper, which show the robustness and accuracy of kinetic approach in the description of multicomponent reactive flows.

Fractal reaction kinetics.

PubMed

Kopelman, R

1988-09-23

Classical reaction kinetics has been found to be unsatisfactory when the reactants are spatially constrained on the microscopic level by either walls, phase boundaries, or force fields. Recently discovered theories of heterogeneous reaction kinetics have dramatic consequences, such as fractal orders for elementary reactions, self-ordering and self-unmixing of reactants, and rate coefficients with temporal "memories." The new theories were needed to explain the results of experiments and supercomputer simulations of reactions that were confined to low dimensions or fractal dimensions or both. Among the practical examples of "fractal-like kinetics" are chemical reactions in pores of membranes, excitation trapping in molecular aggregates, exciton fusion in composite materials, and charge recombination in colloids and clouds.

On electron bunching and stratification of glow discharges

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

Golubovskii, Yuri B.; Kolobov, Vladimir I.; Nekuchaev, Vladimir O.

2013-10-15

Plasma stratification and excitation of ionization waves is one of the fundamental problems in gas discharge physics. Significant progress in this field is associated with the name of Lev Tsendin. He advocated the need for the kinetic approach to this problem contrary to the traditional hydrodynamic approach, introduced the idea of electron bunching in spatially periodic electric fields, and developed a theory of kinetic resonances for analysis of moving striations in rare gases. The present paper shows how Tsendin's ideas have been further developed and applied for understanding the nature of the well-known S-, P-, and R-striations observed in glowmore » discharges of inert gases at low pressures and currents. We review numerical solutions of a Fokker-Planck kinetic equation in spatially periodic electric fields under the effects of elastic and inelastic collisions of electrons with atoms. We illustrate the formation of kinetic resonances at specific field periods for different shapes of injected Electron Distribution Functions (EDF). Computer simulations illustrate how self-organization of the EDFs occurs under nonlocal conditions and how Gaussian-like peaks moving along resonance trajectories are formed in a certain range of discharge conditions. The calculated EDFs agree well with the experimentally measured EDFs for the S, P, and R striations in noble gases. We discuss how kinetic resonances affect dispersion characteristics of moving striations and mention some non-linear effects associated with glow discharge stratification. We propose further studies of stratification phenomena combining physical kinetics and non-linear physics.« less

Large-N kinetic theory for highly occupied systems

NASA Astrophysics Data System (ADS)

Walz, R.; Boguslavski, K.; Berges, J.

2018-06-01

We consider an effective kinetic description for quantum many-body systems, which is not based on a weak-coupling or diluteness expansion. Instead, it employs an expansion in the number of field components N of the underlying scalar quantum field theory. Extending previous studies, we demonstrate that the large-N kinetic theory at next-to-leading order is able to describe important aspects of highly occupied systems, which are beyond standard perturbative kinetic approaches. We analyze the underlying quasiparticle dynamics by computing the effective scattering matrix elements analytically and solve numerically the large-N kinetic equation for a highly occupied system far from equilibrium. This allows us to compute the universal scaling form of the distribution function at an infrared nonthermal fixed point within a kinetic description, and we compare to existing lattice field theory simulation results.

Matching time and spatial scales of rapid solidification: dynamic TEM experiments coupled to CALPHAD-informed phase-field simulations

NASA Astrophysics Data System (ADS)

Perron, Aurelien; Roehling, John D.; Turchi, Patrice E. A.; Fattebert, Jean-Luc; McKeown, Joseph T.

2018-01-01

A combination of dynamic transmission electron microscopy (DTEM) experiments and CALPHAD-informed phase-field simulations was used to study rapid solidification in Cu-Ni thin-film alloys. Experiments—conducted in the DTEM—consisted of in situ laser melting and determination of the solidification kinetics by monitoring the solid-liquid interface and the overall microstructure evolution (time-resolved measurements) during the solidification process. Modelling of the Cu-Ni alloy microstructure evolution was based on a phase-field model that included realistic Gibbs energies and diffusion coefficients from the CALPHAD framework (thermodynamic and mobility databases). DTEM and post mortem experiments highlighted the formation of microsegregation-free columnar grains with interface velocities varying from ˜0.1 to ˜0.6 m s-1. After an ‘incubation’ time, the velocity of the planar solid-liquid interface accelerated until solidification was complete. In addition, a decrease of the temperature gradient induced a decrease in the interface velocity. The modelling strategy permitted the simulation (in 1D and 2D) of the solidification process from the initially diffusion-controlled to the nearly partitionless regimes. Finally, results of DTEM experiments and phase-field simulations (grain morphology, solute distribution, and solid-liquid interface velocity) were consistent at similar time (μs) and spatial scales (μm).

Matching time and spatial scales of rapid solidification: Dynamic TEM experiments coupled to CALPHAD-informed phase-field simulations

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

Perron, Aurelien; Roehling, John D.; Turchi, Patrice E. A.

A combination of dynamic transmission electron microscopy (DTEM) experiments and CALPHAD-informed phase-field simulations was used to study rapid solidification in Cu–Ni thin-film alloys. Experiments—conducted in the DTEM—consisted of in situ laser melting and determination of the solidification kinetics by monitoring the solid–liquid interface and the overall microstructure evolution (time-resolved measurements) during the solidification process. Modelling of the Cu–Ni alloy microstructure evolution was based on a phase-field model that included realistic Gibbs energies and diffusion coefficients from the CALPHAD framework (thermodynamic and mobility databases). DTEM and post mortem experiments highlighted the formation of microsegregation-free columnar grains with interface velocities varying frommore » ~0.1 to ~0.6 m s –1. After an 'incubation' time, the velocity of the planar solid–liquid interface accelerated until solidification was complete. In addition, a decrease of the temperature gradient induced a decrease in the interface velocity. The modelling strategy permitted the simulation (in 1D and 2D) of the solidification process from the initially diffusion-controlled to the nearly partitionless regimes. Lastly, results of DTEM experiments and phase-field simulations (grain morphology, solute distribution, and solid–liquid interface velocity) were consistent at similar time (μs) and spatial scales (μm).« less

Matching time and spatial scales of rapid solidification: Dynamic TEM experiments coupled to CALPHAD-informed phase-field simulations

DOE PAGES

Perron, Aurelien; Roehling, John D.; Turchi, Patrice E. A.; ...

2017-12-05

A combination of dynamic transmission electron microscopy (DTEM) experiments and CALPHAD-informed phase-field simulations was used to study rapid solidification in Cu–Ni thin-film alloys. Experiments—conducted in the DTEM—consisted of in situ laser melting and determination of the solidification kinetics by monitoring the solid–liquid interface and the overall microstructure evolution (time-resolved measurements) during the solidification process. Modelling of the Cu–Ni alloy microstructure evolution was based on a phase-field model that included realistic Gibbs energies and diffusion coefficients from the CALPHAD framework (thermodynamic and mobility databases). DTEM and post mortem experiments highlighted the formation of microsegregation-free columnar grains with interface velocities varying frommore » ~0.1 to ~0.6 m s –1. After an 'incubation' time, the velocity of the planar solid–liquid interface accelerated until solidification was complete. In addition, a decrease of the temperature gradient induced a decrease in the interface velocity. The modelling strategy permitted the simulation (in 1D and 2D) of the solidification process from the initially diffusion-controlled to the nearly partitionless regimes. Lastly, results of DTEM experiments and phase-field simulations (grain morphology, solute distribution, and solid–liquid interface velocity) were consistent at similar time (μs) and spatial scales (μm).« less

Effects of temperature and operation parameters on the galvanic corrosion of Cu coupled to Au in organic solderability preservatives process

NASA Astrophysics Data System (ADS)

Oh, SeKwon; Kim, YoungJun; Jung, KiMin; Kim, JongSoo; Shon, MinYoung; Kwon, HyukSang

2017-03-01

In this work, we quantitatively examined the effects of temperature and operation parameters such as anode (Cu) to cathode (Au) area ratio, stirring speed, and Cu ion concentration on the galvanic corrosion kinetics of Cu coupled to Au (icouple ( Cu-Au)) on print circuit board in organic solderability preservative (OSP) soft etching solution. With the increase of temperature, galvanic corrosion rate (icouple ( Cu-Au) was increased; however, the degree of galvanic corrosion rate (icouple ( Cu-Au) - icorr (Cu)) was decreased owing to the lower activation energy of Cu coupled to Au, than that of Cu alone. With the increase of area ratio (cathode/anode), stirring speed of the system, icouple ( Cu-Au) was increased by the increase of cathodic reaction kinetics. And icouple ( Cu-Au) was decreased by the increase of the Cu-ion concentration in the OSP soft etching solution.

Retarded correlators in kinetic theory: branch cuts, poles and hydrodynamic onset transitions

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

Romatschke, Paul

In this paper, the collective modes of an effective kinetic theory description based on the Boltzmann equation in a relaxation-time approximation applicable to gauge theories at weak but finite coupling and low frequencies are studied. Real time retarded two-point correlators of the energy-momentum tensor and the R-charge current are calculated at finite temperature in flat space-times for large N gauge theories. It is found that the real-time correlators possess logarithmic branch cuts which in the limit of large coupling disappear and give rise to non-hydrodynamic poles that are reminiscent of quasi-normal modes in black holes. In addition to branch cuts,more » correlators can have simple hydrodynamic poles, generalizing the concept of hydrodynamic modes to intermediate wavelength. Surprisingly, the hydrodynamic poles cease to exist for some critical value of the wavelength and coupling reminiscent of the properties of onset transitions.« less

Primordial magnetic fields from a non-singular bouncing cosmology

NASA Astrophysics Data System (ADS)

Membiela, Federico Agustín

2014-08-01

Although inflation is a natural candidate to generate the lengths of coherence of magnetic fields needed to explain current observations, it needs to break conformal invariance of electromagnetism to obtain significant magnetic amplitudes. Of the simplest realizations are the kinetically-coupled theories f2(ϕ)FμνF (or IFF theories). However, these are known to suffer from electric fields backreaction or the strong coupling problem. In this work we shall confirm that such class of theories are problematic to support magnetogenesis during inflationary cosmology. On the contrary, we show that a bouncing cosmology with a contracting phase dominated by an equation of state with p>-ρ/3 can support magnetogenesis, evading the backreaction/strong-coupling problem. Finally, we study safe magnetogenesis in a particular bouncing model with an ekpyrotic-like contracting phase. In this case we found that f2(ϕ)F2-instabilities might arise during the final kinetic-driven expanding phase for steep ekpyrotic potentials.

Retarded correlators in kinetic theory: branch cuts, poles and hydrodynamic onset transitions

DOE PAGES

Romatschke, Paul

2016-06-24

In this paper, the collective modes of an effective kinetic theory description based on the Boltzmann equation in a relaxation-time approximation applicable to gauge theories at weak but finite coupling and low frequencies are studied. Real time retarded two-point correlators of the energy-momentum tensor and the R-charge current are calculated at finite temperature in flat space-times for large N gauge theories. It is found that the real-time correlators possess logarithmic branch cuts which in the limit of large coupling disappear and give rise to non-hydrodynamic poles that are reminiscent of quasi-normal modes in black holes. In addition to branch cuts,more » correlators can have simple hydrodynamic poles, generalizing the concept of hydrodynamic modes to intermediate wavelength. Surprisingly, the hydrodynamic poles cease to exist for some critical value of the wavelength and coupling reminiscent of the properties of onset transitions.« less

Dealloying, Microstructure and the Corrosion/Protection of Cast Magnesium Alloys

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

Sieradzki, Karl; Aiello, Ashlee; McCue, Ian

The purpose of this project was to develop a greater understanding of micro-galvanic corrosion effects in cast magnesium alloys using both experimental and computational methods. Experimental accomplishments have been made in the following areas of interest: characterization, aqueous free-corrosion, atmospheric corrosion, ionic liquid dissolution, rate kinetics of oxide dissolution, and coating investigation. Commercial alloys (AZ91D, AM60, and AZ31B), binary-phase alloys (αMg-2at.%Al, αMg-5at.%Al, and Mg-8at.%Al), and component phases (Mg, Al, β-Mg, β-1%Zn, MnAl3) were obtained and characterized using energy dispersive spectroscopy (EDS), X-ray diffraction (XRD), and scanning electron microscopy (SEM). Full immersion in aqueous chloride was used to characterize the corrosionmore » behavior of alloys. Rotating disc electrodes (RDEs) were used to observe accelerated long-term corrosion behavior. Al surface redistribution for freely corroded samples was analyzed using SEM, EDS, and lithium underpotential deposition (Li UPD). Atmospheric corrosion was observed using contact angle evolution, overnight pH monitoring, and surface pH evolution studies. Ionic liquid corrosion characterization was performed using linear sweep voltammetry and potentiostatic dissolution in 150° choline chloride-urea (cc-urea). Two surface coatings were investigated: (1) Li-carbonate and (2) cc-urea. Li-carbonate coatings were characterized using X-ray photoelectron spectroscopy (XPS), SEM, and aqueous free corrosion potential monitoring. Hydrophobic cc-urea coatings were characterized using contact angle measurements and electrochemical impedance spectroscopy. Oxide dissolution rate kinetics were studied using inductively coupled plasma mass spectroscopy (ICP-MS). Computational accomplishments have been made through the development of Kinetic Monte Carlo (KMC) simulations which model time- and composition-dependent effects on the microstructure due to spatial redistribution of alloying elements during corrosion.« less

Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory.

PubMed

Jakobson, Christopher M; Tullman-Ercek, Danielle; Mangan, Niall M

2018-05-29

Natural biochemical systems are ubiquitously organized both in space and time. Engineering the spatial organization of biochemistry has emerged as a key theme of synthetic biology, with numerous technologies promising improved biosynthetic pathway performance. One strategy, however, may produce disparate results for different biosynthetic pathways. We use a spatially resolved kinetic model to explore this fundamental design choice in systems and synthetic biology. We predict that two example biosynthetic pathways have distinct optimal organization strategies that vary based on pathway-dependent and cell-extrinsic factors. Moreover, we demonstrate that the optimal design varies as a function of kinetic and biophysical properties, as well as culture conditions. Our results suggest that organizing biosynthesis has the potential to substantially improve performance, but that choosing the appropriate strategy is key. The flexible design-space analysis we propose can be adapted to diverse biosynthetic pathways, and lays a foundation to rationally choose organization strategies for biosynthesis.

Numerical simulation of two-phase flow for sediment transport in the inner-surf and swash zones

NASA Astrophysics Data System (ADS)

Bakhtyar, R.; Barry, D. A.; Yeganeh-Bakhtiary, A.; Li, L.; Parlange, J.-Y.; Sander, G. C.

2010-03-01

A two-dimensional two-phase flow framework for fluid-sediment flow simulation in the surf and swash zones was described. Propagation, breaking, uprush and backwash of waves on sloping beaches were studied numerically with an emphasis on fluid hydrodynamics and sediment transport characteristics. The model includes interactive fluid-solid forces and intergranular stresses in the moving sediment layer. In the Euler-Euler approach adopted, two phases were defined using the Navier-Stokes equations with interphase coupling for momentum conservation. The k-ɛ closure model and volume of fluid approach were used to describe the turbulence and tracking of the free surface, respectively. Numerical simulations explored incident wave conditions, specifically spilling and plunging breakers, on both dissipative and intermediate beaches. It was found that the spatial variation of sediment concentration in the swash zone is asymmetric, while the temporal behavior is characterized by maximum sediment concentrations at the start and end of the swash cycle. The numerical results also indicated that the maximum turbulent kinetic energy and sediment flux occurs near the wave-breaking point. These predictions are in general agreement with previous observations, while the model describes the fluid and sediment phase characteristics in much more detail than existing measurements. With direct quantifications of velocity, turbulent kinetic energy, sediment concentration and flux, the model provides a useful approach to improve mechanistic understanding of hydrodynamic and sediment transport in the nearshore zone.

Jeans self gravitational instability of strongly coupled quantum plasma

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

Sharma, Prerana, E-mail: preranaiitd@rediffmail.com; Chhajlani, R. K.

2014-07-15

The Jeans self-gravitational instability is studied for quantum plasma composed of weakly coupled degenerate electron fluid and non-degenerate strongly coupled ion fluid. The formulation for such system is done on the basis of two fluid theory. The dynamics of weakly coupled degenerate electron fluid is governed by inertialess momentum equation. The quantum forces associated with the quantum diffraction effects and the quantum statistical effects act on the degenerate electron fluid. The strong correlation effects of ion are embedded in generalized viscoelastic momentum equation including the viscoelasticity and shear viscosities of ion fluid. The general dispersion relation is obtained using themore » normal mode analysis technique for the two regimes of propagation, i.e., hydrodynamic and kinetic regimes. The Jeans condition of self-gravitational instability is also obtained for both regimes, in the hydrodynamic regime it is observed to be affected by the ion plasma oscillations and quantum parameter while in the kinetic regime in addition to ion plasma oscillations and quantum parameter, it is also affected by the ion velocity which is modified by the viscosity generated compressional effects. The Jeans critical wave number and corresponding critical mass are also obtained for strongly coupled quantum plasma for both regimes.« less

Scaling properties of Arctic sea ice deformation in high-resolution viscous-plastic sea ice models and satellite observations

NASA Astrophysics Data System (ADS)

Hutter, Nils; Losch, Martin; Menemenlis, Dimitris

2017-04-01

Sea ice models with the traditional viscous-plastic (VP) rheology and very high grid resolution can resolve leads and deformation rates that are localised along Linear Kinematic Features (LKF). In a 1-km pan-Arctic sea ice-ocean simulation, the small scale sea-ice deformations in the Central Arctic are evaluated with a scaling analysis in relation to satellite observations of the Envisat Geophysical Processor System (EGPS). A new coupled scaling analysis for data on Eulerian grids determines the spatial and the temporal scaling as well as the coupling between temporal and spatial scales. The spatial scaling of the modelled sea ice deformation implies multi-fractality. The spatial scaling is also coupled to temporal scales and varies realistically by region and season. The agreement of the spatial scaling and its coupling to temporal scales with satellite observations and models with the modern elasto-brittle rheology challenges previous results with VP models at coarse resolution where no such scaling was found. The temporal scaling analysis, however, shows that the VP model does not fully resolve the intermittency of sea ice deformation that is observed in satellite data.

Stochastic calculus of protein filament formation under spatial confinement

NASA Astrophysics Data System (ADS)

Michaels, Thomas C. T.; Dear, Alexander J.; Knowles, Tuomas P. J.

2018-05-01

The growth of filamentous aggregates from precursor proteins is a process of central importance to both normal and aberrant biology, for instance as the driver of devastating human disorders such as Alzheimer's and Parkinson's diseases. The conventional theoretical framework for describing this class of phenomena in bulk is based upon the mean-field limit of the law of mass action, which implicitly assumes deterministic dynamics. However, protein filament formation processes under spatial confinement, such as in microdroplets or in the cellular environment, show intrinsic variability due to the molecular noise associated with small-volume effects. To account for this effect, in this paper we introduce a stochastic differential equation approach for investigating protein filament formation processes under spatial confinement. Using this framework, we study the statistical properties of stochastic aggregation curves, as well as the distribution of reaction lag-times. Moreover, we establish the gradual breakdown of the correlation between lag-time and normalized growth rate under spatial confinement. Our results establish the key role of spatial confinement in determining the onset of stochasticity in protein filament formation and offer a formalism for studying protein aggregation kinetics in small volumes in terms of the kinetic parameters describing the aggregation dynamics in bulk.

Molecular Electronic Coupling Controls Charge Recombination Kinetics in Organic Solar Cells of Low Bandgap Diketopyrrolopyrrole, Carbazole, and Thiophene Polymers

PubMed Central

2013-01-01

Low-bandgap diketopyrrolopyrrole- and carbazole-based polymer bulk-heterojunction solar cells exhibit much faster charge carrier recombination kinetics than that encountered for less-recombining poly(3-hexylthiophene). Solar cells comprising these polymers exhibit energy losses caused by carrier recombination of approximately 100 mV, expressed as reduction in open-circuit voltage, and consequently photovoltaic conversion efficiency lowers in more than 20%. The analysis presented here unravels the origin of that energy loss by connecting the limiting mechanism governing recombination dynamics to the electronic coupling occurring at the donor polymer and acceptor fullerene interfaces. Previous approaches correlate carrier transport properties and recombination kinetics by means of Langevin-like mechanisms. However, neither carrier mobility nor polymer ionization energy helps understanding the variation of the recombination coefficient among the studied polymers. In the framework of the charge transfer Marcus theory, it is proposed that recombination time scale is linked with charge transfer molecular mechanisms at the polymer/fullerene interfaces. As expected for efficient organic solar cells, small electronic coupling existing between donor polymers and acceptor fullerene (Vif < 1 meV) and large reorganization energy (λ ≈ 0.7 eV) are encountered. Differences in the electronic coupling among polymer/fullerene blends suffice to explain the slowest recombination exhibited by poly(3-hexylthiophene)-based solar cells. Our approach reveals how to directly connect photovoltaic parameters as open-circuit voltage to molecular properties of blended materials. PMID:23662167

Kinetic limit of heterogeneous melting in metals.

PubMed

Ivanov, Dmitriy S; Zhigilei, Leonid V

2007-05-11

The velocity and nanoscale shape of the melting front are investigated in a model that combines the molecular dynamics method with a continuum description of the electron heat conduction and electron-phonon coupling. The velocity of the melting front is strongly affected by the local drop of the lattice temperature, defined by the kinetic balance between the transfer of thermal energy to the latent heat of melting, the electron heat conduction from the overheated solid, and the electron-phonon coupling. The maximum velocity of the melting front is found to be below 3% of the room temperature speed of sound in the crystal, suggesting a limited contribution of heterogeneous melting under conditions of fast heating.

Transport in semiconductor nanowire superlattices described by coupled quantum mechanical and kinetic models.

PubMed

Alvaro, M; Bonilla, L L; Carretero, M; Melnik, R V N; Prabhakar, S

2013-08-21

In this paper we develop a kinetic model for the analysis of semiconductor superlattices, accounting for quantum effects. The model consists of a Boltzmann-Poisson type system of equations with simplified Bhatnagar-Gross-Krook collisions, obtained from the general time-dependent Schrödinger-Poisson model using Wigner functions. This system for superlattice transport is supplemented by the quantum mechanical part of the model based on the Ben-Daniel-Duke form of the Schrödinger equation for a cylindrical superlattice of finite radius. The resulting energy spectrum is used to characterize the Fermi-Dirac distribution that appears in the Bhatnagar-Gross-Krook collision, thereby coupling the quantum mechanical and kinetic parts of the model. The kinetic model uses the dispersion relation obtained by the generalized Kronig-Penney method, and allows us to estimate radii of quantum wire superlattices that have the same miniband widths as in experiments. It also allows us to determine more accurately the time-dependent characteristics of superlattices, in particular their current density. Results, for several experimentally grown superlattices, are discussed in the context of self-sustained coherent oscillations of the current density which are important in an increasing range of current and potential applications.

Thermodynamic Analysis of Chemically Reacting Mixtures-Comparison of First and Second Order Models.

PubMed

Pekař, Miloslav

2018-01-01

Recently, a method based on non-equilibrium continuum thermodynamics which derives thermodynamically consistent reaction rate models together with thermodynamic constraints on their parameters was analyzed using a triangular reaction scheme. The scheme was kinetically of the first order. Here, the analysis is further developed for several first and second order schemes to gain a deeper insight into the thermodynamic consistency of rate equations and relationships between chemical thermodynamic and kinetics. It is shown that the thermodynamic constraints on the so-called proper rate coefficient are usually simple sign restrictions consistent with the supposed reaction directions. Constraints on the so-called coupling rate coefficients are more complex and weaker. This means more freedom in kinetic coupling between reaction steps in a scheme, i.e., in the kinetic effects of other reactions on the rate of some reaction in a reacting system. When compared with traditional mass-action rate equations, the method allows a reduction in the number of traditional rate constants to be evaluated from data, i.e., a reduction in the dimensionality of the parameter estimation problem. This is due to identifying relationships between mass-action rate constants (relationships which also include thermodynamic equilibrium constants) which have so far been unknown.

Spatially and time resolved kinetics of indirect magnetoexcitons

NASA Astrophysics Data System (ADS)

Hasling, Matthew; Dorow, Chelsey; Calman, Erica; Butov, Leonid; Wilkes, Joe; Campman, Kenneth; Gossard, Arthur

The small exciton mass and binding energy give the opportunity to realize the high magnetic field regime for excitons in magnetic fields of few Tesla achievable in lab Long lifetimes of indirect exciton give the opportunity to study kinetics of magnetoexciton transport by time-resolved optical imaging of exciton emission. We present spatially and time resolved measurements showing the effect of increased magnetic field on transport of magnetoexcitons. We observe that increased magnetic field leads to slowing down of magnetoexciton transport. Supported by NSF Grant No. 1407277. J.W. was supported by the EPSRC (Grant EP/L022990/1). C.J.D. was supported by the NSF Graduate Research Fellowship Program under Grant No. DGE-1144086.

Spatial Inhomogeneity of Kinetic and Magnetic Dissipations in Thermal Convection

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

Hotta, H.

We investigate the inhomogeneity of kinetic and magnetic dissipations in thermal convection using high-resolution calculations. In statistically steady turbulence, the injected and dissipated energies are balanced. This means that a large amount of energy is continuously converted into internal energy via dissipation. As in thermal convection, downflows are colder than upflows and the inhomogeneity of the dissipation potentially changes the convection structure. Our investigation of the inhomogeneity of the dissipation shows the following. (1) More dissipation is seen around the bottom of the calculation domain, and this tendency is promoted with the magnetic field. (2) The dissipation in the downflowmore » is much larger than that in the upflow. The dissipation in the downflow is more than 80% of the total at maximum. This tendency is also promoted with the magnetic field. (3) Although 2D probability density functions of the kinetic and magnetic dissipations versus the vertical velocity are similar, the kinetic and magnetic dissipations are not well correlated. Our result suggests that the spatial inhomogeneity of the dissipation is significant and should be considered when modeling a small-scale strong magnetic field generated with an efficient small-scale dynamo for low-resolution calculations.« less

A coupled theory for chemically active and deformable solids with mass diffusion and heat conduction

NASA Astrophysics Data System (ADS)

Zhang, Xiaolong; Zhong, Zheng

2017-10-01

To analyse the frequently encountered thermo-chemo-mechanical problems in chemically active material applications, we develop a thermodynamically-consistent continuum theory of coupled deformation, mass diffusion, heat conduction and chemical reaction. Basic balance equations of force, mass and energy are presented at first, and then fully coupled constitutive laws interpreting multi-field interactions and evolving equations governing irreversible fluxes are constructed according to the energy dissipation inequality and the chemical kinetics. To consider the essential distinction between mass diffusion and chemical reactions in affecting free energy and dissipations of a highly coupled system, we regard both the concentrations of diffusive species and the extent of reaction as independent state variables. This new formulation then distinguishes between the energy contribution from the diffusive species entering the solid and that from the subsequent chemical reactions occurring among these species and the host solid, which not only interact with stresses or strains in different manners and on different time scales, but also induce different variations of solid microstructures and material properties. Taking advantage of this new description, we further establish a specialized isothermal model to predict precisely the transient chemo-mechanical response of a swelling solid with a proposed volumetric constraint that accounts for material incompressibility. Coupled kinetics is incorporated to capture the volumetric swelling of the solid caused by imbibition of external species and the simultaneous dilation arised from chemical reactions between the diffusing species and the solid. The model is then exemplified with two numerical examples of transient swelling accompanied by chemical reaction. Various ratios of characteristic times of diffusion and chemical reaction are taken into account to shed light on the dependency on kinetic time scales of evolution patterns for a diffusion-reaction controlled deformable solid.

Microwave Kinetic Inductance Detector with Selective Polarization Coupling

NASA Technical Reports Server (NTRS)

Wollack, Edward; U-yen, Kongpop; Stevenson, Thomas; Brown, Ari; Moseley, Samuel; Hsieh, Wen-Ting

2013-01-01

A conventional low-noise detector requires a technique to both absorb incident power and convert it to an electrical signal at cryogenic temperatures. This innovation combines low-noise detector and readout functionality into one device while maintaining high absorption, controlled polarization sensitivity, and broadband detection capability. The resulting far-infrared detectors can be read out with a simple approach, which is compact and minimizes thermal loading. The proposed microwave kinetic inductance detector (MKID) consists of three basic elements. The first is the absorptive section in which the incident power is coupled to a superconducting resonator at far-infrared frequency above its superconducting critical frequency (where superconductor becomes normal conductor). This absorber's shape effectively absorbs signals in the desired polarization state and is resonant at the radio frequency (RF) used for readout of the device. Control over the metal film used in the absorber allows realization of structures with either a 50% broadband or 100% resonance absorptance over a 30% fractional bandwidth. The second element is a microwave resonator - which is realized from the thin metal films used to make the absorber as transmission lines - whose resonance frequency changes due to a variation in its kinetic inductance. The resonator's kinetic inductance is a function of the power absorbed by the device. A low-loss dielectric (mono-crystalline silicon) is used in a parallel-plate transmission line structure to realize the desired superconducting resonators. There is negligible coupling among the adjacent elements used to define the polarization sensitivity of each detector. The final component of the device is a microwave transmission line, which is coupled to the resonator, and allows detection of changes in resonance frequency for each detector in the focal plane array. The spiral shape of the detector's absorber allows incident power with two polarizations to couple to the detector equally. A stepped impedance resonator was used that allows the incident power absorbed in the detecting membrane area to be uniformly distributed in the detector's transmission line at the RF readout frequency. This maximizes the sensitivity of the detector. The signal is read out via a frequency multiplexing technique that requires a minimum number of interface transmission lines for readout. This reduces the packaging complexity and coupling to the device's thermal environment.

Role of Kinetic Modeling in Biomedical Imaging

PubMed Central

Huang, Sung-Cheng

2009-01-01

Biomedical imaging can reveal clear 3-dimensional body morphology non-invasively with high spatial resolution. Its efficacy, in both clinical and pre-clinical settings, is enhanced with its capability to provide in vivo functional/biological information in tissue. The role of kinetic modeling in providing biological/functional information in biomedical imaging is described. General characteristics and limitations in extracting biological information are addressed and practical approaches to solve the problems are discussed and illustrated with examples. Some future challenges and opportunities for kinetic modeling to expand the capability of biomedical imaging are also presented. PMID:20640185

Voltage gating by molecular subunits of Na+ and K+ ion channels: higher-dimensional cubic kinetics, rate constants, and temperature.

PubMed

Fohlmeister, Jürgen F

2015-06-01

The structural similarity between the primary molecules of voltage-gated Na and K channels (alpha subunits) and activation gating in the Hodgkin-Huxley model is brought into full agreement by increasing the model's sodium kinetics to fourth order (m(3) → m(4)). Both structures then virtually imply activation gating by four independent subprocesses acting in parallel. The kinetics coalesce in four-dimensional (4D) cubic diagrams (16 states, 32 reversible transitions) that show the structure to be highly failure resistant against significant partial loss of gating function. Rate constants, as fitted in phase plot data of retinal ganglion cell excitation, reflect the molecular nature of the gating transitions. Additional dimensions (6D cubic diagrams) accommodate kinetically coupled sodium inactivation and gating processes associated with beta subunits. The gating transitions of coupled sodium inactivation appear to be thermodynamically irreversible; response to dielectric surface charges (capacitive displacement) provides a potential energy source for those transitions and yields highly energy-efficient excitation. A comparison of temperature responses of the squid giant axon (apparently Arrhenius) and mammalian channel gating yields kinetic Q10 = 2.2 for alpha unit gating, whose transitions are rate-limiting at mammalian temperatures; beta unit kinetic Q10 = 14 reproduces the observed non-Arrhenius deviation of mammalian gating at low temperatures; the Q10 of sodium inactivation gating matches the rate-limiting component of activation gating at all temperatures. The model kinetics reproduce the physiologically large frequency range for repetitive firing in ganglion cells and the physiologically observed strong temperature dependence of recovery from inactivation. Copyright © 2015 the American Physiological Society.

The protonation state around TyrD/TyrD• in photosystem II is reflected in its biphasic oxidation kinetics.

PubMed

Sjöholm, Johannes; Ho, Felix; Ahmadova, Nigar; Brinkert, Katharina; Hammarström, Leif; Mamedov, Fikret; Styring, Stenbjörn

2017-02-01

The tyrosine residue D2-Tyr160 (Tyr D ) in photosystem II (PSII) can be oxidized through charge equilibrium with the oxygen evolving complex in PSII. The kinetics of the electron transfer from Tyr D has been followed using time-resolved EPR spectroscopy after triggering the oxidation of pre-reduced Tyr D by a short laser flash. After its oxidation Tyr D is observed as a neutral radical (Tyr D • ) indicating that the oxidation is coupled to a deprotonation event. The redox state of Tyr D was reported to be determined by the two water positions identified in the crystal structure of PSII [Saito et al. (2013) Proc. Natl. Acad. Sci. USA 110, 7690]. To assess the mechanism of the proton coupled electron transfer of Tyr D the oxidation kinetics has been followed in the presence of deuterated buffers, thereby resolving the kinetic isotope effect (KIE) of Tyr D oxidation at different H/D concentrations. Two kinetic phases of Tyr D oxidation - the fast phase (msec-sec time range) and the slow phase (tens of seconds time range) were resolved as was previously reported [Vass and Styring (1991) Biochemistry 30, 830]. In the presence of deuterated buffers the kinetics was significantly slower compared to normal buffers. Furthermore, although the kinetics were faster at both high pH and pD values the observed KIE was found to be similar (~2.4) over the whole pL range investigated. We assign the fast and slow oxidation phases to two populations of PSII centers with different water positions, proximal and distal respectively, and discuss possible deprotonation events in the vicinity of Tyr D . Copyright © 2016 Elsevier B.V. All rights reserved.

Kinetic hindrance of Fe(II) oxidation at alkaline pH and in the presence of nitrate and oxygen in a facultative wastewater stabilization pond.

PubMed

Rockne, Karl J

2007-02-15

To better understand the dynamics of Fe2 + oxidation in facultative wastewater stabilization ponds, water samples from a three-pond system were taken throughout the period of transition from anoxic conditions with high aqueous Fe2 + levels in the early spring to fully aerobic conditions in late spring. Fe2 + levels showed a highly significant correlation with pH but were not correlated with dissolved oxygen (DO). Water column Fe2 + levels were modeled using the kinetic rate law for Fe2 + oxidation of Sung and Morgan.[5] The fitted kinetic coefficients were 5 +/- 3 x 10(6) M(- 2) atm(-1) min(-1); more than six orders of magnitude lower than typically reported. Comparison of four potential Fe redox couples demonstrated that the rhoepsilon was at least 3-4 orders of magnitude higher than would be expected based on internal equilibrium. Surprisingly, measured nitrate and DO (when present) were typically consistent with both nitrate (from denitrification) and DO levels (from aerobic respiration) predicted from equilibrium. Although the hydrous Fe oxide/FeCO3 couple was closest to equilibrium and most consistent with the observed pH dependence (in contrast to predicted lepidocrocite), Fe2 + oxidation is kinetically hindered, resulting in up to 10(7)-fold higher levels than expected based on both kinetic and equilibrium analyses.

EEG source reconstruction reveals frontal-parietal dynamics of spatial conflict processing.

PubMed

Cohen, Michael X; Ridderinkhof, K Richard

2013-01-01

Cognitive control requires the suppression of distracting information in order to focus on task-relevant information. We applied EEG source reconstruction via time-frequency linear constrained minimum variance beamforming to help elucidate the neural mechanisms involved in spatial conflict processing. Human subjects performed a Simon task, in which conflict was induced by incongruence between spatial location and response hand. We found an early (∼200 ms post-stimulus) conflict modulation in stimulus-contralateral parietal gamma (30-50 Hz), followed by a later alpha-band (8-12 Hz) conflict modulation, suggesting an early detection of spatial conflict and inhibition of spatial location processing. Inter-regional connectivity analyses assessed via cross-frequency coupling of theta (4-8 Hz), alpha, and gamma power revealed conflict-induced shifts in cortical network interactions: Congruent trials (relative to incongruent trials) had stronger coupling between frontal theta and stimulus-contrahemifield parietal alpha/gamma power, whereas incongruent trials had increased theta coupling between medial frontal and lateral frontal regions. These findings shed new light into the large-scale network dynamics of spatial conflict processing, and how those networks are shaped by oscillatory interactions.

DURIP: Electrokinetic Injection and Separation System for Analysis of Protein and Peptide Transport, Adsorption and Kinetics Instrumentation Proposal

DTIC Science & Technology

2015-03-18

both the electric double layer that forms at a solid-liquid interface as well as the biomolecules themselves, we can harness the coupled physics of...the biomolecules themselves, we can harness the coupled physics of complex biological fluids in nanofluidic channels towards unique, efficient

Modelling of auroral electrodynamical processes: Magnetosphere to mesosphere

NASA Technical Reports Server (NTRS)

Chiu, Y. T.; Gorney, D. J.; Kishi, A. M.; Newman, A. L.; Schulz, M.; Walterscheid, R. L.; CORNWALL; Prasad, S. S.

1982-01-01

Research conducted on auroral electrodynamic coupling between the magnetosphere and ionosphere-atmosphere in support of the development of a global scale kinetic plasma theory is reviewed. Topics covered include electric potential structure in the evening sector; morning and dayside auroras; auroral plasma formation; electrodynamic coupling with the thermosphere; and auroral electron interaction with the atmosphere.

Collisionless electron heating in inductively coupled discharges

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

Shaing, K.C.; Aydemir, A.Y.

1996-07-01

A kinetic theory of collisionless electron heating is developed for inductively coupled discharges with a finite height L. The novel effect associated with the finite-length system is the resonance between the bounce motion of the electrons and the wave frequency, leading to enhanced heating. The theory is in agreement with results of particle simulations.

Model of quantum kinetics of spin-orbit coupled two-dimensional electron gas in the presence of strong electromagnetic field

NASA Astrophysics Data System (ADS)

Turkin, Yaroslav V.; Kuptsov, Pavel V.

2018-04-01

A quantum model of spin dynamics of spin-orbit coupled two-dimensional electron gas in the presence of strong high- frequency electromagnetic field is suggested. Interaction of electrons with optical phonons is taken into account in the second order of perturbation theory.

Filtering analysis of a direct numerical simulation of the turbulent Rayleigh-Benard problem

NASA Technical Reports Server (NTRS)

Eidson, T. M.; Hussaini, M. Y.; Zang, T. A.

1990-01-01

A filtering analysis of a turbulent flow was developed which provides details of the path of the kinetic energy of the flow from its creation via thermal production to its dissipation. A low-pass spatial filter is used to split the velocity and the temperature field into a filtered component (composed mainly of scales larger than a specific size, nominally the filter width) and a fluctuation component (scales smaller than a specific size). Variables derived from these fields can fall into one of the above two ranges or be composed of a mixture of scales dominated by scales near the specific size. The filter is used to split the kinetic energy equation into three equations corresponding to the three scale ranges described above. The data from a direct simulation of the Rayleigh-Benard problem for conditions where the flow is turbulent are used to calculate the individual terms in the three kinetic energy equations. This is done for a range of filter widths. These results are used to study the spatial location and the scale range of the thermal energy production, the cascading of kinetic energy, the diffusion of kinetic energy, and the energy dissipation. These results are used to evaluate two subgrid models typically used in large-eddy simulations of turbulence. Subgrid models attempt to model the energy below the filter width that is removed by a low-pass filter.

Kinetics of Reactive Fronts in Porous Media: quantification through a laboratory experiment

NASA Astrophysics Data System (ADS)

De Anna, P.; Jimenez-Martinez, J.; Turuban, R.; Tabuteau, H.; Derrien, M.; Le Borgne, T.; Meheust, Y.

2013-12-01

The kinetics of reaction fronts in heterogeneous flows is tightly linked to the mixing dynamics governed by the combined action of stretching, diffusion and dispersion. Focusing on porous media flows, with a new experimental setup we show that the invading solute is organized into stretched lamellae, whose deformation and coalescence control the effective reaction kinetics of the mixing limited bimolecular reaction A + B --> C. While the classic advection-dispersion theory predicts a scaling of the cumulative product mass of C as t^(0.5), we observe two distinct kinetics regimes, one characterized by the stretching and the other by the coalescence of the invading lamellae, in which the mass of C scales faster than t^(0.5). The proposed experimental set up allows for direct quantification of mixing and reactive transport in porous media with a high spatial resolution, at the pore scale. The analogous two dimensional porous medium consists in a Hele-Shaw cell containing a single layer of cylindrical solid grains built by soft lithography. On the one hand, the measurement of the local, intra-pore, conservative concentration field is done using a fluorescent tracer. On the other hand, considering a fast bimolecular advection-dispersion reaction A + B --> C occurring as A displaces B, we quantify the reaction kinetics from the spatially-resolved measurement of the pore scale reaction rate, using a chemiluminescent reaction.

Energy transfer, pressure tensor, and heating of kinetic plasma

NASA Astrophysics Data System (ADS)

Yang, Yan; Matthaeus, William H.; Parashar, Tulasi N.; Haggerty, Colby C.; Roytershteyn, Vadim; Daughton, William; Wan, Minping; Shi, Yipeng; Chen, Shiyi

2017-07-01

Kinetic plasma turbulence cascade spans multiple scales ranging from macroscopic fluid flow to sub-electron scales. Mechanisms that dissipate large scale energy, terminate the inertial range cascade, and convert kinetic energy into heat are hotly debated. Here, we revisit these puzzles using fully kinetic simulation. By performing scale-dependent spatial filtering on the Vlasov equation, we extract information at prescribed scales and introduce several energy transfer functions. This approach allows highly inhomogeneous energy cascade to be quantified as it proceeds down to kinetic scales. The pressure work, - ( P . ∇ ) . u , can trigger a channel of the energy conversion between fluid flow and random motions, which contains a collision-free generalization of the viscous dissipation in collisional fluid. Both the energy transfer and the pressure work are strongly correlated with velocity gradients.

Analysis of the Temporal Response of Coupled Asymmetrical Zero-Power Subcritical Bare Metal Reactor Systems

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

Klain, Kimberly L.

The behavior of symmetrical coupled-core systems has been extensively studied, yet there is a dearth of research on asymmetrical systems due to the increased complexity of the analysis of such systems. In this research, the multipoint kinetics method is applied to asymmetrical zeropower, subcritical, bare metal reactor systems. Existing research on asymmetrical reactor systems assumes symmetry in the neutronic coupling; however, it will be shown that this cannot always be assumed. Deep subcriticality adds another layer of complexity and requires modification of the multipoint kinetics equations to account for the effect of the external neutron source. A modified set ofmore » multipoint kinetics equations is derived with this in mind. Subsequently, the Rossi-alpha equations are derived for a two-region asymmetrical reactor system. The predictive capabilities of the radiation transport code MCNP6 for neutron noise experiments are shown in a comparison to the results of a series of Rossi-alpha measurements performed by J. Mihalczo utilizing a coupled set of symmetrical bare highly-enriched uranium (HEU) cylinders. The ptrac option within MCNP6 can generate time-tagged counts in a cell (list-mode data). The list-mode data can then be processed similarly to measured data to obtain values for system parameters such as the dual prompt neutron decay constants observable in a coupled system. The results from the ptrac simulations agree well with the historical measured values. A series of case studies are conducted to study the effects of geometrical asymmetry in the coupling between two bare metal HEU cylinders. While the coupling behavior of symmetrical systems has been reported on extensively, that of asymmetrical systems remains sparse. In particular, it appears that there has been no previous research in obtaining the coupling time constants for asymmetrically-coupled systems. The difficulty in observing such systems is due in part to the inability to determine the individual coupling coefficients from measurement: unlike the symmetrical cases, only the product of the values can be obtained. A method is proposed utilizing MCNP6 tally ratios to separate the coupling coefficients for such systems. This work provides insight into the behavior of asymmetrically-coupled systems as the separation distance between the two cores is changed and also as the asymmetry is increased. As the asymmetry increases, both the slower and the faster observable prompt neutron decay constants increase in magnitude. The coupling time constants are determined from the measured decay constants. As the separation distance increases, both coupling coefficients decrease as expected. Based on these findings, an effective computational method utilizing MCNP6 and the Rossialpha technique can be applied to the prediction of asymmetrical coupled system measurements.« less

Mechanisms of Coupled Vibrational Relaxation and Dissociation in Carbon Dioxide.

PubMed

Armenise, Iole; Kustova, Elena

2018-05-21

A complete vibrational state-specific kinetic scheme describing dissociating carbon dioxide mixtures is proposed. CO 2 symmetric, bending and asymmetric vibrations and dissociation-recombination are strongly coupled through inter-mode vibrational energy transfers. Comparative study of state-resolved rate coefficients is carried out; the effect of different transitions may vary considerably with temperature. A non-equilibrium 1-D boundary layer flow typical to hypersonic planetary entry is studied in the state-to-state approach. To assess the sensitivity of fluid-dynamic variables and heat transfer to various vibrational transitions and chemical reactions, corresponding processes are successively included to the kinetic scheme. It is shown that vibrational-translational (VT) transitions in the symmetric and asymmetric modes do not alter the flow and can be neglected whereas the VT 2 exchange in the bending mode is the main channel of vibrational relaxation. Inter-mode vibrational exchanges affect the flow implicitly, through energy redistribution enhancing VT relaxation; the dominating role belongs to near-resonant transitions between symmetric and bending modes as well as between CO molecules and CO 2 asymmetric mode. Strong coupling between VT 2 relaxation and chemical reactions is emphasized. While vibrational distributions and average vibrational energy show strong dependence on the kinetic scheme, the heat flux is more sensitive to chemical reactions.

Reconnection in the Martian Magnetotail: Hall-MHD With Embedded Particle-in-Cell Simulations

NASA Astrophysics Data System (ADS)

Ma, Yingjuan; Russell, Christopher T.; Toth, Gabor; Chen, Yuxi; Nagy, Andrew F.; Harada, Yuki; McFadden, James; Halekas, Jasper S.; Lillis, Rob; Connerney, John E. P.; Espley, Jared; DiBraccio, Gina A.; Markidis, Stefano; Peng, Ivy Bo; Fang, Xiaohua; Jakosky, Bruce M.

2018-05-01

Mars Atmosphere and Volatile EvolutioN (MAVEN) mission observations show clear evidence of the occurrence of the magnetic reconnection process in the Martian plasma tail. In this study, we use sophisticated numerical models to help us understand the effects of magnetic reconnection in the plasma tail. The numerical models used in this study are (a) a multispecies global Hall-magnetohydrodynamic (HMHD) model and (b) a global HMHD model two-way coupled to an embedded fully kinetic particle-in-cell code. Comparison with MAVEN observations clearly shows that the general interaction pattern is well reproduced by the global HMHD model. The coupled model takes advantage of both the efficiency of the MHD model and the ability to incorporate kinetic processes of the particle-in-cell model, making it feasible to conduct kinetic simulations for Mars under realistic solar wind conditions for the first time. Results from the coupled model show that the Martian magnetotail is highly dynamic due to magnetic reconnection, and the resulting Mars-ward plasma flow velocities are significantly higher for the lighter ion fluid, which are quantitatively consistent with MAVEN observations. The HMHD with Embedded Particle-in-Cell model predicts that the ion loss rates are more variable but with similar mean values as compared with HMHD model results.

Computational modelling of mesoscale dislocation patterning and plastic deformation of single crystals

NASA Astrophysics Data System (ADS)

Xia, Shengxu; El-Azab, Anter

2015-07-01

We present a continuum dislocation dynamics model that predicts the formation of dislocation cell structure in single crystals at low strains. The model features a set of kinetic equations of the curl type that govern the space and time evolution of the dislocation density in the crystal. These kinetic equations are coupled to stress equilibrium and deformation kinematics using the eigenstrain approach. A custom finite element method has been developed to solve the coupled system of equations of dislocation kinetics and crystal mechanics. The results show that, in general, dislocations self-organize in patterns under their mutual interactions. However, the famous dislocation cell structure has been found to form only when cross slip is implemented in the model. Cross slip is also found to lower the yield point, increase the hardening rate, and sustain an increase in the dislocation density over the hardening regime. Analysis of the cell structure evolution reveals that the average cell size decreases with the applied stress, which is consistent with the similitude principle.

Monte Carlo simulation for kinetic chemotaxis model: An application to the traveling population wave

NASA Astrophysics Data System (ADS)

Yasuda, Shugo

2017-02-01

A Monte Carlo simulation of chemotactic bacteria is developed on the basis of the kinetic model and is applied to a one-dimensional traveling population wave in a microchannel. In this simulation, the Monte Carlo method, which calculates the run-and-tumble motions of bacteria, is coupled with a finite volume method to calculate the macroscopic transport of the chemical cues in the environment. The simulation method can successfully reproduce the traveling population wave of bacteria that was observed experimentally and reveal the microscopic dynamics of bacterium coupled with the macroscopic transports of the chemical cues and bacteria population density. The results obtained by the Monte Carlo method are also compared with the asymptotic solution derived from the kinetic chemotaxis equation in the continuum limit, where the Knudsen number, which is defined by the ratio of the mean free path of bacterium to the characteristic length of the system, vanishes. The validity of the Monte Carlo method in the asymptotic behaviors for small Knudsen numbers is numerically verified.

Kinetic control over pathway complexity in supramolecular polymerization through modulating the energy landscape by rational molecular design.

PubMed

Ogi, Soichiro; Fukui, Tomoya; Jue, Melinda L; Takeuchi, Masayuki; Sugiyasu, Kazunori

2014-12-22

Far-from-equilibrium thermodynamic systems that are established as a consequence of coupled equilibria are the origin of the complex behavior of biological systems. Therefore, research in supramolecular chemistry has recently been shifting emphasis from a thermodynamic standpoint to a kinetic one; however, control over the complex kinetic processes is still in its infancy. Herein, we report our attempt to control the time evolution of supramolecular assembly in a process in which the supramolecular assembly transforms from a J-aggregate to an H-aggregate over time. The transformation proceeds through a delicate interplay of these two aggregation pathways. We have succeeded in modulating the energy landscape of the respective aggregates by a rational molecular design. On the basis of this understanding of the energy landscape, programming of the time evolution was achieved through adjusting the balance between the coupled equilibria. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cross-scale coupling studies with the Heliophysics/Geospace System Observatory: THEMIS/ARTEMIS contributions

NASA Astrophysics Data System (ADS)

Angelopoulos, V.; Hietala, H.; Liu, Z.; Mende, S. B.; Phan, T.; Nishimura, T.; Strangeway, R. J.; Burch, J. L.; Moore, T. E.; Giles, B. L.

2015-12-01

The recent launch of MMS, the impending launch of ERG, the continued availability of space (NASA, NOAA, International) and ground based assets (THEMIS GBOs, TREx, SuperDARN) enable a comprehensive study of global drivers of (and responses to) kinetic processes at the magnetopause, the magnetotail, the inner magnetosphere and the ionosphere. Previously unresolved questions related to the nature of the modes of magnetospheric convection (pseudobreakups, substorms, SMCs and storms) can now be addressed simultaneously at a kinetic level (with multi-spacecraft missions) and at a global level (with the emerging, powerful H/GSO). THEMIS has been tasked to perform orbital changes that will optimize the observatory, and simultaneously place its probes, along with MMS's, at the heart of where critical kinetic processes occur, near sites of magnetic reconnection and magnetic energy conversion, and in optimal view of ground based assets. I will discuss these unique alignments of the H/GSO fleet that can reveal how cross-scale coupling is manifest, allowing us to view old paradigms in a new light.

Metastable dynamical patterns and their stabilization in arrays of bidirectionally coupled sigmoidal neurons

NASA Astrophysics Data System (ADS)

Horikawa, Yo

2013-12-01

Transient patterns in a bistable ring of bidirectionally coupled sigmoidal neurons were studied. When the system had a pair of spatially uniform steady solutions, the instability of unstable spatially nonuniform steady solutions decreased exponentially with the number of neurons because of the symmetry of the system. As a result, transient spatially nonuniform patterns showed dynamical metastability: Their duration increased exponentially with the number of neurons and the duration of randomly generated patterns obeyed a power-law distribution. However, these metastable dynamical patterns were easily stabilized in the presence of small variations in coupling strength. Metastable rotating waves and their pinning in the presence of asymmetry in the direction of coupling and the disappearance of metastable dynamical patterns due to asymmetry in the output function of a neuron were also examined. Further, in a two-dimensional array of neurons with nearest-neighbor coupling, intrinsically one-dimensional patterns were dominant in transients, and self-excitation in these neurons affected the metastable dynamical patterns.

The Einstein-Vlasov System/Kinetic Theory.

PubMed

Andréasson, Håkan

2011-01-01

The main purpose of this article is to provide a guide to theorems on global properties of solutions to the Einstein-Vlasov system. This system couples Einstein's equations to a kinetic matter model. Kinetic theory has been an important field of research during several decades in which the main focus has been on non-relativistic and special relativistic physics, i.e., to model the dynamics of neutral gases, plasmas, and Newtonian self-gravitating systems. In 1990, Rendall and Rein initiated a mathematical study of the Einstein-Vlasov system. Since then many theorems on global properties of solutions to this system have been established. This paper gives introductions to kinetic theory in non-curved spacetimes and then the Einstein-Vlasov system is introduced. We believe that a good understanding of kinetic theory in non-curved spacetimes is fundamental to a good comprehension of kinetic theory in general relativity.

Indirect coupling of phosphate release to de novo tension generation during muscle contraction.

PubMed Central

Davis, J S; Rodgers, M E

1995-01-01

A key question in muscle contraction is how tension generation is coupled to the chemistry of the actomyosin ATPase. Biochemical and mechanochemical experiments link tension generation to a change in structure associated with phosphate release. Length-jump and temperature-jump experiments, on the other hand, implicate phase 2slow, a significantly faster, markedly strain-sensitive kinetic process in tension generation. We use a laser temperature jump to probe the kinetics and mechanism of tension generation in skinned rabbit psoas fibers--an appropriate method since both phosphate release and phase 2slow are readily perturbed by temperature. Kinetics characteristic of the structural change associated with phosphate release are observed only when phosphate is added to fibers. When present, it causes a reduction in fiber tension; otherwise, no force is generated when it is perturbed. We therefore exclude this step from tension generation. The kinetics of de novo tension generation by the temperature-jump equivalent of phase 2slow appear unaffected by phosphate binding. We therefore propose that phosphate release is indirectly coupled to de novo tension generation via a steady-state flux through an irreversible step. We conclude that tension generation occurs in the absence of chemical change as the result of an entropy-driven transition between strongly bound crossbridges in the actomyosin-ADP state. The mechanism resembles the operation of a clock, with phosphate release providing the energy to tension the spring, and the irreversible step functions as the escapement mechanism, which is followed in turn by tension generation as the movement of the hands. Images Fig. 6 PMID:7479824

Direct observation of spatially heterogeneous single-layer graphene oxide reduction kinetics.

PubMed

McDonald, Matthew P; Eltom, Ahmed; Vietmeyer, Felix; Thapa, Janak; Morozov, Yurii V; Sokolov, Denis A; Hodak, Jose H; Vinodgopal, Kizhanipuram; Kamat, Prashant V; Kuno, Masaru

2013-01-01

Graphene oxide (GO) is an important precursor in the production of chemically derived graphene. During reduction, GO's electrical conductivity and band gap change gradually. Doping and chemical functionalization are also possible, illustrating GO's immense potential in creating functional devices through control of its local hybridization. Here we show that laser-induced photolysis controllably reduces individual single-layer GO sheets. The reaction can be followed in real time through sizable decreases in GO's photoluminescence efficiency along with spectral blueshifts. As-produced reduced graphene oxide (rGO) sheets undergo additional photolysis, characterized by dramatic emission enhancements and spectral redshifts. Both GO's reduction and subsequent conversion to photobrightened rGO are captured through movies of their photoluminescence kinetics. Rate maps illustrate sizable spatial and temporal heterogeneities in sp(2) domain growth and reveal how reduction "flows" across GO and rGO sheets. The observed heterogeneous reduction kinetics provides mechanistic insight into GO's conversion to chemically derived graphene and highlights opportunities for overcoming its dynamic, chemical disorder.

Spatially coupled catalytic ignition of CO oxidation on Pt: mesoscopic versus nano-scale

PubMed Central

Spiel, C.; Vogel, D.; Schlögl, R.; Rupprechter, G.; Suchorski, Y.

2015-01-01

Spatial coupling during catalytic ignition of CO oxidation on μm-sized Pt(hkl) domains of a polycrystalline Pt foil has been studied in situ by PEEM (photoemission electron microscopy) in the 10−5 mbar pressure range. The same reaction has been examined under similar conditions by FIM (field ion microscopy) on nm-sized Pt(hkl) facets of a Pt nanotip. Proper orthogonal decomposition (POD) of the digitized FIM images has been employed to analyze spatiotemporal dynamics of catalytic ignition. The results show the essential role of the sample size and of the morphology of the domain (facet) boundary in the spatial coupling in CO oxidation. PMID:26021411

Aviation spatial orientation in relationship to head position, altitude interpretation, and control.

PubMed

Smith, D R; Cacioppo, A J; Hinman, G E

1997-06-01

Recently, a visually driven neck reflex was identified as causing head tilt toward the horizon during VMC flight. If this is the case, then pilots orient about a fixed rather than moving horizon, implying current attitude instruments inaccurately present spatial information. The purpose of this study was to determine if the opto-kinetic cervical neck reflex has an effect dependent on passive (autopilot) or active control of the aircraft. Further, findings could help determine if the opto-kinetic cervical reflex is characteristic of other flight crewmembers. There were 16 military pilots who flew two 13-min VMC low-level routes in a large dome flight simulator. Head position in relation to aircraft bank angle was recorded by a head tracker device. During one low-level route, the pilot had a supervisory role as the autopilot flew the aircraft (passive). The other route was flow manually by the pilot (active). Pilots consistently tilted the head to maintain alignment with the horizon. Similar head tilt angles were found in both the active and passive flight phases. However, head tilt had a faster onset rate in the passive condition. Results indicate the opto-kinetic cervical reflex affects pilots while actively flying or in a supervisory role as the autopilot flies. The consistent head tilt angles in both conditions should be considered in attitude indicator, HUD, and HMD designs. Further, results seem to indicate that non-pilot flight crewmembers are affected by the opto-kinetic cervical reflex which should be considered in spatial disorientation and airsickness discussions.

Chemical Continuous Time Random Walks

NASA Astrophysics Data System (ADS)

Aquino, T.; Dentz, M.

2017-12-01

Traditional methods for modeling solute transport through heterogeneous media employ Eulerian schemes to solve for solute concentration. More recently, Lagrangian methods have removed the need for spatial discretization through the use of Monte Carlo implementations of Langevin equations for solute particle motions. While there have been recent advances in modeling chemically reactive transport with recourse to Lagrangian methods, these remain less developed than their Eulerian counterparts, and many open problems such as efficient convergence and reconstruction of the concentration field remain. We explore a different avenue and consider the question: In heterogeneous chemically reactive systems, is it possible to describe the evolution of macroscopic reactant concentrations without explicitly resolving the spatial transport? Traditional Kinetic Monte Carlo methods, such as the Gillespie algorithm, model chemical reactions as random walks in particle number space, without the introduction of spatial coordinates. The inter-reaction times are exponentially distributed under the assumption that the system is well mixed. In real systems, transport limitations lead to incomplete mixing and decreased reaction efficiency. We introduce an arbitrary inter-reaction time distribution, which may account for the impact of incomplete mixing. This process defines an inhomogeneous continuous time random walk in particle number space, from which we derive a generalized chemical Master equation and formulate a generalized Gillespie algorithm. We then determine the modified chemical rate laws for different inter-reaction time distributions. We trace Michaelis-Menten-type kinetics back to finite-mean delay times, and predict time-nonlocal macroscopic reaction kinetics as a consequence of broadly distributed delays. Non-Markovian kinetics exhibit weak ergodicity breaking and show key features of reactions under local non-equilibrium.

Spatiotemporal chaos of fractional order logistic equation in nonlinear coupled lattices

NASA Astrophysics Data System (ADS)

Zhang, Ying-Qian; Wang, Xing-Yuan; Liu, Li-Yan; He, Yi; Liu, Jia

2017-11-01

We investigate a new spatiotemporal dynamics with fractional order differential logistic map and spatial nonlinear coupling. The spatial nonlinear coupling features such as the higher percentage of lattices in chaotic behaviors for most of parameters and none periodic windows in bifurcation diagrams are held, which are more suitable for encryptions than the former adjacent coupled map lattices. Besides, the proposed model has new features such as the wider parameter range and wider range of state amplitude for ergodicity, which contributes a wider range of key space when applied in encryptions. The simulations and theoretical analyses are developed in this paper.

Multi-Fluid Moment Simulations of Ganymede using the Next-Generation OpenGGCM

NASA Astrophysics Data System (ADS)

Wang, L.; Germaschewski, K.; Hakim, A.; Bhattacharjee, A.; Raeder, J.

2015-12-01

We coupled the multi-fluid moment code Gkeyll[1,2] to the next-generation OpenGGCM[3], and studied the reconnection dynamics at the Ganymede. This work is part of our effort to tackle the grand challenge of integrating kinetic effects into global fluid models. The multi-fluid moment model integrates kinetic effects in that it can capture crucial kinetic physics like pressure tensor effects by evolving moments of the Vlasov equations for each species. This approach has advantages over previous models: desired kinetic effects, together with other important effects like the Hall effect, are self-consistently embedded in the moment equations, and can be efficiently implemented, while not suffering from severe time-step restriction due to plasma oscillation nor artificial whistler modes. This model also handles multiple ion species naturally, which opens up opportunties in investigating the role of oxygen in magnetospheric reconnection and improved coupling to ionosphere models. In this work, the multi-fluid moment solver in Gkeyll was wrapped as a time-stepping module for the high performance, highly flexible next-generation OpenGGCM. Gkeyll is only used to provide the local plasma solver, while computational aspects like parallelization and boundary conditions are handled entirely by OpenGGCM, including interfacing to other models like ionospheric boundary conditions provided by coupling with CTIM [3]. The coupled code is used to study the dynamics near Ganymede, and the results are compared with MHD and Hall MHD results by Dorelli et al. [4]. Hakim, A. (2008). Journal of Fusion Energy, 27, 36-43. Hakim, A., Loverich, J., & Shumlak, U. (2006). Journal of Computational Physics, 219, 418-442. Raeder, J., Larson, D., Li, W., Kepko, E. L., & Fuller-Rowell, T. (2008). Space Science Reviews, 141(1-4), 535-555. Dorelli, J. C., Glocer, A., Collinson, G., & Tóth, G. (2015). Journal of Geophysical Research: Space Physics, 120.

Recent Developments in the Analysis of Couple Oscillator Arrays

NASA Technical Reports Server (NTRS)

Pogorzelski, Ronald J.

2000-01-01

This presentation considers linear arrays of coupled oscillators. Our purpose in coupling oscillators together is to achieve high radiated power through the spatial power combining which results when the oscillators are injection locked to each other. York, et. al. have shown that, left to themselves, the ensemble of injection locked oscillators oscillate at the average of the tuning frequencies of all the oscillators. Coupling these arrays achieves high radiated power through coherent spatial power combining. The coupled oscillators are usually designed to produce constant aperture phase. Oscillators are injection locked to each other or to a master oscillator to produce coherent radiation. Oscillators do not necessarily oscillate at their tuning frequency.

Control of topography gradients on residence time distributions, mixing dynamics and reactive hotspot development

NASA Astrophysics Data System (ADS)

Bandopadhyay, Aditya; Le Borgne, Tanguy; Davy, Philippe

2017-04-01

Topography-driven subsurface flows are thought to play a central role in determining solute turnover and biogeochemical processes at different scales in the critical zone, including river-hyporheic zone exchanges, hillslope solute transport and reactions, and catchment biogeochemical cycles. Hydraulic head gradients, induced by topography gradients at different scales, generate a distribution of streamlines at depth, dictating the spatial distribution of redox sensitive species, the magnitude of surface water - ground water exchanges and ultimately the source/sink function of the subsurface. Flow velocities generally decrease with depth, leading to broad residence time distributions, which have been shown to affect river chemistry and geochemical reactions in catchments. In this presentation, we discuss the impact of topography-driven flows on mixing processes and the formation of localized reactive hotspots. For this, we solve analytically the coupled flow, mixing and reaction equations in two-dimensional vertical cross-sections of subsurface domains with different topography gradients. For a given topography gradient, we derive the spatial distribution of subsurface velocities, the rates of solute mixing accross streamlines and the induced kinetics of redox, precipitation and dissolution reactions using a Lagrangian approach (Le Borgne et al. 2014). We demonstrate that vertical velocity profiles driven by topography variations, act effectively as shear flows, hence stretching continuously the mixing fronts between recently infiltrated and resident water (Bandopadhyay et al. 2017). We thus derive analytical expressions for residence time distributions, mixing rates and kinetics of chemical reactions as a function of the topography gradients. We show that the rates dissolution and precipitation reactions are significantly enhanced by the existence of vertical velocity gradients and that reaction rates reach a maximum in a localized subsurface reactive layer, whose location and intensity depends on topography gradients. As a consequence of these findings, we discuss the links between topography variations, subsurface velocity gradients and biogeochemical processes in the critical zone. References: Bandopadhyay A., T. Le Borgne, Y. Méheust and M. Dentz (2017) Enhanced reaction kinetics and reactive mixing scale dynamics in mixing fronts under shear flow for arbitrary Damkohler numbers, Adv. in Water Resour. Vol. 100, p. 78-95 Le Borgne T., T. Ginn and M. Dentz (2014) Impact of Fluid Deformation on Mixing-Induced Chemical Reactions in Heterogeneous Flows, Geophys. Res. Lett., Vol. 41, 22, p. 7898-790

Multidimensional kinetic simulations using dissipative closures and other reduced Vlasov methods for differing particle magnetizations

NASA Astrophysics Data System (ADS)

Newman, David L.

2006-10-01

Kinetic plasma simulations in which the phase-space distribution functions are advanced directly via the coupled Vlasov and Poisson (or Maxwell) equations---better known simply as Vlasov simulations---provide a valuable low-noise complement to the more commonly employed Particle-in-Cell (PIC) simulations. However, in more than one spatial dimension Vlasov simulations become numerically demanding due to the high dimensionality of x--v phase-space. Methods that can reduce this computational demand are therefore highly desirable. Several such methods will be presented, which treat the phase-space dynamics along a dominant dimension (e.g., parallel to a beam or current) with the full Vlasov propagator, while employing a reduced description, such as moment equations, for the evolution perpendicular to the dominant dimension. A key difference between the moment-based (and other reduced) methods considered here and standard fluid methods is that the moments are now functions of a phase-space coordinate (e.g. moments of vy in z--vz--y phase space, where z is the dominant dimension), rather than functions of spatial coordinates alone. Of course, moment-based methods require closure. For effectively unmagnetized species, new dissipative closure methods inspired by those of Hammett and Perkins [PRL, 64, 3019 (1990)] have been developed, which exactly reproduce the linear electrostatic response for a broad class of distributions with power-law tails, as are commonly measured in space plasmas. The nonlinear response, which requires more care, will also be discussed. For weakly magnetized species (i.e., φs<φs) an alternative algorithm has been developed in which the distributions are assumed to gyrate about the magnetic field with a fixed nominal perpendicular ``thermal'' velocity, thereby reducing the required phase-space dimension by one. These reduced algorithms have been incorporated into 2-D codes used to study the evolution of nonlinear structures such as double layers and electron holes in Earth's auroral zone.

Low-temperature synthesis of homogeneous solid solutions of scheelite-structured Ca 1-xSr xWO 4 and Sr 1-xBa xWO 4 nanocrystals

DOE PAGES

Culver, Sean P.; Greaney, Matthew J.; Tinoco, Antonio; ...

2015-07-24

Here, a series of compositionally complex scheelite-structured nanocrystals of the formula A 1-xA’ xWO 4 (A = Ca, Sr, Ba) have been prepared under benign synthesis conditions using the vapor diffusion sol–gel method. Discrete nanocrystals with sub-20 nm mean diameters were obtained after kinetically controlled hydro- lysis and polycondensation at room temperature, followed by composition-dependent thermal aging at or below 60 °C. Rietveld analysis of X-ray diffraction data and Raman spectroscopy verified the synthesis of continuous and phase-pure nanocrystal solid solutions across the entire composition space for A 1-xA’ xWO 4, where 0 ≤ x ≤ 1. Elemental analysis bymore » X-ray photoelectron and inductively coupled plasma- atomic emission spectroscopies demonstrated excellent agreement between the nominal and experi- mentally determined elemental stoichiometries, while energy dispersive X-ray spectroscopy illustrated good spatial elemental homogeneity within these nanocrystals synthesized under benign conditions.« less

Beginning inflation in an inhomogeneous universe

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

East, William E.; Kleban, Matthew; Linde, Andrei

Using numerical solutions of the full Einstein field equations coupled to a scalar inflaton field in 3+1 dimensions, we study the conditions under which a universe that is initially expanding, highly inhomogeneous and dominated by gradient energy can transition to an inflationary period. If the initial scalar field variations are contained within a sufficiently flat region of the inflaton potential, and the universe is spatially flat or open on average, inflation will occur following the dilution of the gradient and kinetic energy due to expansion. This is the case even when the scale of the inhomogeneities is comparable to themore » initial Hubble length, and overdense regions collapse and form black holes, because underdense regions continue expanding, allowing inflation to eventually begin. In conclusion, this establishes that inflation can arise from highly inhomogeneous initial conditions and solve the horizon and flatness problems, at least as long as the variations in the scalar field do not include values that exceed the inflationary plateau.« less

Beginning inflation in an inhomogeneous universe

DOE PAGES

East, William E.; Kleban, Matthew; Linde, Andrei; ...

2016-09-06

Using numerical solutions of the full Einstein field equations coupled to a scalar inflaton field in 3+1 dimensions, we study the conditions under which a universe that is initially expanding, highly inhomogeneous and dominated by gradient energy can transition to an inflationary period. If the initial scalar field variations are contained within a sufficiently flat region of the inflaton potential, and the universe is spatially flat or open on average, inflation will occur following the dilution of the gradient and kinetic energy due to expansion. This is the case even when the scale of the inhomogeneities is comparable to themore » initial Hubble length, and overdense regions collapse and form black holes, because underdense regions continue expanding, allowing inflation to eventually begin. In conclusion, this establishes that inflation can arise from highly inhomogeneous initial conditions and solve the horizon and flatness problems, at least as long as the variations in the scalar field do not include values that exceed the inflationary plateau.« less

Beginning inflation in an inhomogeneous universe

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

East, William E.; Kleban, Matthew; Linde, Andrei

Using numerical solutions of the full Einstein field equations coupled to a scalar inflaton field in 3+1 dimensions, we study the conditions under which a universe that is initially expanding, highly inhomogeneous and dominated by gradient energy can transition to an inflationary period. If the initial scalar field variations are contained within a sufficiently flat region of the inflaton potential, and the universe is spatially flat or open on average, inflation will occur following the dilution of the gradient and kinetic energy due to expansion. This is the case even when the scale of the inhomogeneities is comparable to themore » initial Hubble length, and overdense regions collapse and form black holes, because underdense regions continue expanding, allowing inflation to eventually begin. This establishes that inflation can arise from highly inhomogeneous initial conditions and solve the horizon and flatness problems, at least as long as the variations in the scalar field do not include values that exceed the inflationary plateau.« less

OH and CH luminescence in opposed flow methane oxy-flames

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

De Leo, Maurizio; Saveliev, Alexei; Kennedy, Lawrence A.

Emission spectroscopy is a 2-D nonintrusive diagnostic technique that offers spatially resolved data for combustion optimization and control. The UV and visible chemiluminescence of the excited radicals CH(A{sup 2}{delta},B{sup 2}{sigma}{sup -}) and OH(A{sup 2}{sigma}{sup +}) is studied experimentally and numerically in opposed-flow diffusion flames of methane and oxygen-enriched air. The oxidized oxygen content is varied from 21 to 100% while the range of the studied strain rates spans from 20 to 40 s{sup -1}. The spectrally resolved imaging is obtained by two different methods: scattering through a grating monochromator and interposition of interference filters along the optical path. Absolute measuredmore » chemiluminescence intensities, coupled with a numerical model based on the opposed flow flame code, are used to evaluate the chemical kinetics of the excited species. The predictions of the selected model are in good agreement with the experimental data over the range of the studied flame conditions. (author)« less

NH2- in a cold ion trap with He buffer gas: Ab initio quantum modeling of the interaction potential and of state-changing multichannel dynamics

NASA Astrophysics Data System (ADS)

Hernández Vera, Mario; Yurtsever, Ersin; Wester, Roland; Gianturco, Franco A.

2018-05-01

We present an extensive range of accurate ab initio calculations, which map in detail the spatial electronic potential energy surface that describes the interaction between the molecular anion NH2 - (1A1) in its ground electronic state and the He atom. The time-independent close-coupling method is employed to generate the corresponding rotationally inelastic cross sections, and then the state-changing rates over a range of temperatures from 10 to 30 K, which is expected to realistically represent the experimental trapping conditions for this ion in a radio frequency ion trap filled with helium buffer gas. The overall evolutionary kinetics of the rotational level population involving the molecular anion in the cold trap is also modelled during a photodetachment experiment and analyzed using the computed rates. The present results clearly indicate the possibility of selectively detecting differences in behavior between the ortho- and para-anions undergoing photodetachment in the trap.

Optimum analysis of a Brownian refrigerator.

PubMed

Luo, X G; Liu, N; He, J Z

2013-02-01

A Brownian refrigerator with the cold and hot reservoirs alternating along a space coordinate is established. The heat flux couples with the movement of the Brownian particles due to an external force in the spatially asymmetric but periodic potential. After using the Arrhenius factor to describe the behaviors of the forward and backward jumps of the particles, the expressions for coefficient of performance (COP) and cooling rate are derived analytically. Then, through maximizing the product of conversion efficiency and heat flux flowing out, a new upper bound only depending on the temperature ratio of the cold and hot reservoirs is found numerically in the reversible situation, and it is a little larger than the so-called Curzon and Ahlborn COP ε(CA)=(1/√[1-τ])-1. After considering the irreversible factor owing to the kinetic energy change of the moving particles, we find the optimized COP is smaller than ε(CA) and the external force even does negative work on the Brownian particles when they jump from a cold to hot reservoir.

Transcriptionally Driven DNA Replication Program of the Human Parasite Leishmania major.

PubMed

Lombraña, Rodrigo; Álvarez, Alba; Fernández-Justel, José Miguel; Almeida, Ricardo; Poza-Carrión, César; Gomes, Fábia; Calzada, Arturo; Requena, José María; Gómez, María

2016-08-09

Faithful inheritance of eukaryotic genomes requires the orchestrated activation of multiple DNA replication origins (ORIs). Although origin firing is mechanistically conserved, how origins are specified and selected for activation varies across different model systems. Here, we provide a complete analysis of the nucleosomal landscape and replication program of the human parasite Leishmania major, building on a better evolutionary understanding of replication organization in Eukarya. We found that active transcription is a driving force for the nucleosomal organization of the L. major genome and that both the spatial and the temporal program of DNA replication can be explained as associated to RNA polymerase kinetics. This simple scenario likely provides flexibility and robustness to deal with the environmental changes that impose alterations in the genetic programs during parasitic life cycle stages. Our findings also suggest that coupling replication initiation to transcription elongation could be an ancient solution used by eukaryotic cells for origin maintenance. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Trapped one-dimensional ideal Fermi gas with a single impurity

NASA Astrophysics Data System (ADS)

Astrakharchik, G. E.; Brouzos, I.

2013-08-01

Ground-state properties of a single impurity in a one-dimensional Fermi gas are investigated in uniform and trapped geometries. The energy of a trapped system is obtained (i) by generalizing the McGuire expression from a uniform to trapped system (ii) within the local density approximation (iii) using the perturbative approach in the case of a weakly interacting impurity and (iv) diffusion Monte Carlo method. We demonstrate that there is a closed formula based on the exact solution of the homogeneous case which provides a precise estimation for the energy of a trapped system even for a small number of fermions and arbitrary coupling constant of the impurity. Using this expression, we analyze energy contributions from kinetic, interaction, and potential components, as well as spatial properties such as the system size and the pair-correlation function. Finally, we calculate the frequency of the breathing mode. Our analysis is directly connected and applicable to the recent experiments in microtraps.

A Computer Program for the Prediction of Solid Propellant Rocket Motor Performance. Volume 3

DTIC Science & Technology

1975-07-01

following losses: two-dimensional/two-phase (coupled), nozzle erosion, kinetics, boundary layer, combustion efficiency, submergence . The program...loss •Two dimensional or divergence less •Finite Rate Kinetics loss •Boundary Layer Loss •Combustion Efficiency - • Submergence Loss •Erosion...counted twice. The iforcmcr.tioned assumptions are describ- ed In Section US, The submergence efficiency, ijgno* ^* rased on an empirical

Using a spatially-distributed hydrologic biogeochemistry model with nitrogen transport to study the spatial variation of carbon stocks and fluxes in a Critical Zone Observatory

NASA Astrophysics Data System (ADS)

Shi, Y.; Eissenstat, D. M.; He, Y.; Davis, K. J.

2017-12-01

Most current biogeochemical models are 1-D and represent one point in space. Therefore, they cannot resolve topographically driven land surface heterogeneity (e.g., lateral water flow, soil moisture, soil temperature, solar radiation) or the spatial pattern of nutrient availability. A spatially distributed forest biogeochemical model with nitrogen transport, Flux-PIHM-BGC, has been developed by coupling a 1-D mechanistic biogeochemical model Biome-BGC (BBGC) with a spatially distributed land surface hydrologic model, Flux-PIHM, and adding an advection dominated nitrogen transport module. Flux-PIHM is a coupled physically based model, which incorporates a land-surface scheme into the Penn State Integrated Hydrologic Model (PIHM). The land surface scheme is adapted from the Noah land surface model, and is augmented by adding a topographic solar radiation module. Flux-PIHM is able to represent the link between groundwater and the surface energy balance, as well as land surface heterogeneities caused by topography. In the coupled Flux-PIHM-BGC model, each Flux-PIHM model grid couples a 1-D BBGC model, while nitrogen is transported among model grids via surface and subsurface water flow. In each grid, Flux-PIHM provides BBGC with soil moisture, soil temperature, and solar radiation, while BBGC provides Flux-PIHM with spatially-distributed leaf area index. The coupled Flux-PIHM-BGC model has been implemented at the Susquehanna/Shale Hills Critical Zone Observatory. The model-predicted aboveground vegetation carbon and soil carbon distributions generally agree with the macro patterns observed within the watershed. The importance of abiotic variables (including soil moisture, soil temperature, solar radiation, and soil mineral nitrogen) in predicting aboveground carbon distribution is calculated using a random forest. The result suggests that the spatial pattern of aboveground carbon is controlled by the distribution of soil mineral nitrogen. A Flux-PIHM-BGC simulation without the nitrogen transport module is also executed. The model without nitrogen transport fails in predicting the spatial patterns of vegetation carbon, which indicates the importance of having a nitrogen transport module in spatially distributed ecohydrologic modeling.

Fiber-coupling efficiency of Gaussian-Schell model beams through an ocean to fiber optical communication link

NASA Astrophysics Data System (ADS)

Hu, Beibei; Shi, Haifeng; Zhang, Yixin

2018-06-01

We theoretically study the fiber-coupling efficiency of Gaussian-Schell model beams propagating through oceanic turbulence. The expression of the fiber-coupling efficiency is derived based on the spatial power spectrum of oceanic turbulence and the cross-spectral density function. Our work shows that the salinity fluctuation has a greater impact on the fiber-coupling efficiency than temperature fluctuation does. We can select longer λ in the "ocean window" and higher spatial coherence of light source to improve the fiber-coupling efficiency of the communication link. We also can achieve the maximum fiber-coupling efficiency by choosing design parameter according specific oceanic turbulence condition. Our results are able to help the design of optical communication link for oceanic turbulence to fiber sensor.

Interarticulator coordination in children with and without cerebral palsy

PubMed Central

Nip, Ignatius S. B.

2017-01-01

The current study investigates how interarticulator coordination changes across speaking tasks varying in articulatory and linguistic demands for children with CP and their typically-developing peers. Articulatory movements from 12 children with spastic CP (7M, 5F, 4–15 years of age) and 12 typically-developing age- and sex-matched peers were cross-correlated to determine the degree of spatial and temporal coupling between the upper lip and jaw, lower lip and jaw, and upper and lower lips. Spatial and temporal coupling were also correlated with intelligibility. Results indicated that children with CP have reduced spatial coupling between the upper and lower lips and reduced temporal coupling between all articulators as compared to their typically-developing peers. For all participants, sentences were produced with the greatest degree of interarticulator coordination when compared to the diadochokinetic and syllable repetition tasks. Measures of interarticulator coordination were correlated with intelligibility for the speakers with CP. PMID:25905558

Residential outdoor water use in Tucson, Arizona: Geospatial, demographic and temporal perspectives

NASA Astrophysics Data System (ADS)

Himmel, Alexander I.

Outdoor water use by single-family residences in the desert city of Tucson, Arizona is investigated as a multi-scaled coupled human-environment system, using remotely sensed images, GIS data, household water use records and survey responses. Like many desert cities, Tucson's municipal water system faces stresses at multiple spatial and temporal scales: rising demand, limited supplies, competition for distant resources and the likelihood of shortages due to regional climate change. Though the need for demand management is recognized, conflict between the long-term regional scale of the ecosystem that sustains Tucson's water supply and the short-term, local scale of the municipal utility results in a "lack of fit", shown here as the inability to reduce consumption to sustainable levels. While direct regulation of outdoor water use has not been successful, geographic research suggests that modification of the built environment, the focus of the three studies comprising this dissertation, holds promise as a demand management strategy. The first study is a spatial analysis of survey responses on outdoor water use practices during a drought. Next, the potential for substituting common amenities (irrigated landscapes and swimming pools) for private ones is investigated. Residential use was found to be sensitive to park proximity, greenness (proxied by the Normalized Difference Vegetation Index), size and presence of a park pool. Most small parks were net water savers; large parks offered the opportunity to substitute reclaimed water for potable supplies. The last study correlates long-term Landsat-based vegetation and water use trends and integrates these with a spatial analysis of kinetic temperatures. Findings indicate that despite reduced water use, Tucson became greener over the 1995 -- 2008 period. This effect is attributed to a pulse of vegetation establishment in response to a shift in the El Nino -- Southern Oscillation (ENSO) and Pacific Decadal Oscillation (PDO) around 1976 and to irrigation prior to the study period. I conclude that although the coupled human-environment system of Tucson's municipal water supply and use practices is complex, there are scale-dependent competitive advantages to be gained through thoughtful modification of the built environment.

ONR Far East Scientific Information Bulletin

DTIC Science & Technology

1990-09-01

In bone, grafting onto a polymer chain, inter- continuous processes, such as reactive extru- chain reactions, formation of interpenetrat- sion and...reaction kinetics, rheology, and side- and end-chain grafting , homopolymer transport phenomena occurring during REX. chain coupling, polymer...the Grafting reactions yield block or graft coupling species becomes a part of the chain, copolymers. Polyethylene, polypropylene, or by

Electron magnetic reconnection without ion coupling in Earth's turbulent magnetosheath

NASA Astrophysics Data System (ADS)

Phan, T. D.; Eastwood, J. P.; Shay, M. A.; Drake, J. F.; Sonnerup, B. U. Ö.; Fujimoto, M.; Cassak, P. A.; Øieroset, M.; Burch, J. L.; Torbert, R. B.; Rager, A. C.; Dorelli, J. C.; Gershman, D. J.; Pollock, C.; Pyakurel, P. S.; Haggerty, C. C.; Khotyaintsev, Y.; Lavraud, B.; Saito, Y.; Oka, M.; Ergun, R. E.; Retino, A.; Le Contel, O.; Argall, M. R.; Giles, B. L.; Moore, T. E.; Wilder, F. D.; Strangeway, R. J.; Russell, C. T.; Lindqvist, P. A.; Magnes, W.

2018-05-01

Magnetic reconnection in current sheets is a magnetic-to-particle energy conversion process that is fundamental to many space and laboratory plasma systems. In the standard model of reconnection, this process occurs in a minuscule electron-scale diffusion region1,2. On larger scales, ions couple to the newly reconnected magnetic-field lines and are ejected away from the diffusion region in the form of bi-directional ion jets at the ion Alfvén speed3-5. Much of the energy conversion occurs in spatially extended ion exhausts downstream of the diffusion region6. In turbulent plasmas, which contain a large number of small-scale current sheets, reconnection has long been suggested to have a major role in the dissipation of turbulent energy at kinetic scales7-11. However, evidence for reconnection plasma jetting in small-scale turbulent plasmas has so far been lacking. Here we report observations made in Earth's turbulent magnetosheath region (downstream of the bow shock) of an electron-scale current sheet in which diverging bi-directional super-ion-Alfvénic electron jets, parallel electric fields and enhanced magnetic-to-particle energy conversion were detected. Contrary to the standard model of reconnection, the thin reconnecting current sheet was not embedded in a wider ion-scale current layer and no ion jets were detected. Observations of this and other similar, but unidirectional, electron jet events without signatures of ion reconnection reveal a form of reconnection that can drive turbulent energy transfer and dissipation in electron-scale current sheets without ion coupling.

Electron magnetic reconnection without ion coupling in Earth's turbulent magnetosheath.

PubMed

Phan, T D; Eastwood, J P; Shay, M A; Drake, J F; Sonnerup, B U Ö; Fujimoto, M; Cassak, P A; Øieroset, M; Burch, J L; Torbert, R B; Rager, A C; Dorelli, J C; Gershman, D J; Pollock, C; Pyakurel, P S; Haggerty, C C; Khotyaintsev, Y; Lavraud, B; Saito, Y; Oka, M; Ergun, R E; Retino, A; Le Contel, O; Argall, M R; Giles, B L; Moore, T E; Wilder, F D; Strangeway, R J; Russell, C T; Lindqvist, P A; Magnes, W

2018-05-01

Magnetic reconnection in current sheets is a magnetic-to-particle energy conversion process that is fundamental to many space and laboratory plasma systems. In the standard model of reconnection, this process occurs in a minuscule electron-scale diffusion region 1,2 . On larger scales, ions couple to the newly reconnected magnetic-field lines and are ejected away from the diffusion region in the form of bi-directional ion jets at the ion Alfvén speed 3-5 . Much of the energy conversion occurs in spatially extended ion exhausts downstream of the diffusion region 6 . In turbulent plasmas, which contain a large number of small-scale current sheets, reconnection has long been suggested to have a major role in the dissipation of turbulent energy at kinetic scales 7-11 . However, evidence for reconnection plasma jetting in small-scale turbulent plasmas has so far been lacking. Here we report observations made in Earth's turbulent magnetosheath region (downstream of the bow shock) of an electron-scale current sheet in which diverging bi-directional super-ion-Alfvénic electron jets, parallel electric fields and enhanced magnetic-to-particle energy conversion were detected. Contrary to the standard model of reconnection, the thin reconnecting current sheet was not embedded in a wider ion-scale current layer and no ion jets were detected. Observations of this and other similar, but unidirectional, electron jet events without signatures of ion reconnection reveal a form of reconnection that can drive turbulent energy transfer and dissipation in electron-scale current sheets without ion coupling.

A new ionospheric electron precipitation module coupled with RAM-SCB within the geospace general circulation model

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

Yu, Yiqun; Jordanova, Vania K.; Ridley, Aaron J.

Electron precipitation down to the atmosphere due to wave-particle scattering in the magnetosphere contributes significantly to the auroral ionospheric conductivity. In order to obtain the auroral conductivity in global MHD models that are incapable of capturing kinetic physics in the magnetosphere, MHD parameters are often used to estimate electron precipitation flux for the conductivity calculation. Such an MHD approach, however, lacks self-consistency in representing the magnetosphere-ionosphere coupling processes. In this study we improve the coupling processes in global models with a more physical method. We calculate the physics-based electron precipitation from the ring current and map it to the ionosphericmore » altitude for solving the ionospheric electrodynamics. In particular, we use the BATS-R-US (Block Adaptive Tree Scheme-Roe type-Upstream) MHD model coupled with the kinetic ring current model RAM-SCB (Ring current-Atmosphere interaction Model with Self-Consistent Magnetic field (B)) that solves pitch angle-dependent electron distribution functions, to study the global circulation dynamics during the 25–26 January 2013 storm event. Since the electron precipitation loss is mostly governed by wave-particle resonant scattering in the magnetosphere, we further investigate two loss methods of specifying electron precipitation loss associated with wave-particle interactions: (1) using pitch angle diffusion coefficients D αα(E,α) determined from the quasi-linear theory, with wave spectral and plasma density obtained from statistical observations (named as “diffusion coefficient method”) and (2) using electron lifetimes τ(E) independent on pitch angles inferred from the above diffusion coefficients (named as “lifetime method”). We found that both loss methods demonstrate similar temporal evolution of the trapped ring current electrons, indicating that the impact of using different kinds of loss rates is small on the trapped electron population. Furthermore, for the precipitated electrons, the lifetime method hardly captures any precipitation in the large L shell (i.e., 4 < L < 6.5) region, while the diffusion coefficient method produces much better agreement with NOAA/POES measurements, including the spatial distribution and temporal evolution of electron precipitation in the region from the premidnight through the dawn to the dayside. Further comparisons of the precipitation energy flux to DMSP observations indicates that the new physics-based precipitation approach using diffusion coefficients for the ring current electron loss can explain the diffuse electron precipitation in the dawn sector, such as the enhanced precipitation flux at auroral latitudes and flux drop near the subauroral latitudes, but the traditional MHD approach largely overestimates the precipitation flux at lower latitudes.« less

A new ionospheric electron precipitation module coupled with RAM-SCB within the geospace general circulation model

DOE PAGES

Yu, Yiqun; Jordanova, Vania K.; Ridley, Aaron J.; ...

2016-09-01

Electron precipitation down to the atmosphere due to wave-particle scattering in the magnetosphere contributes significantly to the auroral ionospheric conductivity. In order to obtain the auroral conductivity in global MHD models that are incapable of capturing kinetic physics in the magnetosphere, MHD parameters are often used to estimate electron precipitation flux for the conductivity calculation. Such an MHD approach, however, lacks self-consistency in representing the magnetosphere-ionosphere coupling processes. In this study we improve the coupling processes in global models with a more physical method. We calculate the physics-based electron precipitation from the ring current and map it to the ionosphericmore » altitude for solving the ionospheric electrodynamics. In particular, we use the BATS-R-US (Block Adaptive Tree Scheme-Roe type-Upstream) MHD model coupled with the kinetic ring current model RAM-SCB (Ring current-Atmosphere interaction Model with Self-Consistent Magnetic field (B)) that solves pitch angle-dependent electron distribution functions, to study the global circulation dynamics during the 25–26 January 2013 storm event. Since the electron precipitation loss is mostly governed by wave-particle resonant scattering in the magnetosphere, we further investigate two loss methods of specifying electron precipitation loss associated with wave-particle interactions: (1) using pitch angle diffusion coefficients D αα(E,α) determined from the quasi-linear theory, with wave spectral and plasma density obtained from statistical observations (named as “diffusion coefficient method”) and (2) using electron lifetimes τ(E) independent on pitch angles inferred from the above diffusion coefficients (named as “lifetime method”). We found that both loss methods demonstrate similar temporal evolution of the trapped ring current electrons, indicating that the impact of using different kinds of loss rates is small on the trapped electron population. Furthermore, for the precipitated electrons, the lifetime method hardly captures any precipitation in the large L shell (i.e., 4 < L < 6.5) region, while the diffusion coefficient method produces much better agreement with NOAA/POES measurements, including the spatial distribution and temporal evolution of electron precipitation in the region from the premidnight through the dawn to the dayside. Further comparisons of the precipitation energy flux to DMSP observations indicates that the new physics-based precipitation approach using diffusion coefficients for the ring current electron loss can explain the diffuse electron precipitation in the dawn sector, such as the enhanced precipitation flux at auroral latitudes and flux drop near the subauroral latitudes, but the traditional MHD approach largely overestimates the precipitation flux at lower latitudes.« less

a Novel Approach to Link the Structure and the Metabolic Rate of Biofilms

NASA Astrophysics Data System (ADS)

Freixa, A.; Rubol, S.; Romaní, A.; Sanchez-Vila, X.

2013-12-01

Biofilms are complex natural system and exhibits heterogeneity both in space and time. In this study, we aim to 1) investigate the effect of this spatially behavior of oxygen metabolic activity (measured as the rate of O2 consumption) for different temperatures (10°C and 20°C) and light conditions (dark and light) in biofilms and 2) link the oxygen consumption rate to the biofilm structure. To meet this objective, we used a novel optical sensor plus imaging technology called VisiSens (PreSens Precision Sensing) that gave us a unique opportunity to obtain percentage air saturation of biofilm in time and space using the images of the surface of the developing biofilm at a set interval (every 20 seconds for 40 minutes). Biofilm oxygen consumption was measured after glucose and humic acid addition in order to study metabolic differences depending on organic matter source. Each of these series of images (each consisting of 120 images) were analyzed for spatial statistical analysis (e.g. histogram) and kinetic rates of consumption were determined for one-week and two-week-old biofilms. In addition, the one week old biofilm structures were determined for both dark and light condition and for both temperatures by using a confocal microscope .The 2D and 3D images obtained were then used to determine the variogram of each treatment. Information obtained by the two approaches was then coupled. To the best of our knowledge this is the first work which attempt to link the biofilm spatial structure to its metabolism at this fine scale.

Frustration of resonant preheating by exotic kinetic terms

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

Rahmati, Shohreh; Seahra, Sanjeev S., E-mail: srahmati@unb.ca, E-mail: sseahra@unb.ca

2014-10-01

We study the effects of exotic kinetic terms on parametric resonance during the preheating epoch of the early universe. Specifically, we consider modifications to the action of ordinary matter fields motivated by generalized uncertainty principles, polymer quantization, as well as Dirac-Born-Infeld and k-essence models. To leading order in an ''exotic physics'' scale, the equations of motion derived from each of these models have the same algebraic form involving a nonlinear self-interaction in the matter sector. Neglecting spatial dependence, we show that the nonlinearity effectively shuts down the parametric resonance after a finite time period. We find numeric evidence that themore » frustration of parametric resonance persists to spatially inhomogenous matter in (1+1)-dimensions.« less

A Kinetic Study of Microwave Start-up of Tokamak Plasmas

NASA Astrophysics Data System (ADS)

du Toit, E. J.; O'Brien, M. R.; Vann, R. G. L.

2017-07-01

A kinetic model for studying the time evolution of the distribution function for microwave startup is presented. The model for the distribution function is two dimensional in momentum space, but, for simplicity and rapid calculations, has no spatial dependence. Experiments on the Mega Amp Spherical Tokamak have shown that the plasma current is carried mainly by electrons with energies greater than 70 keV, and effects thought to be important in these experiments are included, i.e. particle sources, orbital losses, the loop voltage and microwave heating, with suitable volume averaging where necessary to give terms independent of spatial dimensions. The model predicts current carried by electrons with the same energies as inferred from the experiments, though the current drive efficiency is smaller.

Power-law spatial dispersion from fractional Liouville equation

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

Tarasov, Vasily E.

2013-10-15

A microscopic model in the framework of fractional kinetics to describe spatial dispersion of power-law type is suggested. The Liouville equation with the Caputo fractional derivatives is used to obtain the power-law dependence of the absolute permittivity on the wave vector. The fractional differential equations for electrostatic potential in the media with power-law spatial dispersion are derived. The particular solutions of these equations for the electric potential of point charge in this media are considered.

Coupled enzyme reactions performed in heterogeneous reaction media: experiments and modeling for glucose oxidase and horseradish peroxidase in a PEG/citrate aqueous two-phase system.

PubMed

Aumiller, William M; Davis, Bradley W; Hashemian, Negar; Maranas, Costas; Armaou, Antonios; Keating, Christine D

2014-03-06

The intracellular environment in which biological reactions occur is crowded with macromolecules and subdivided into microenvironments that differ in both physical properties and chemical composition. The work described here combines experimental and computational model systems to help understand the consequences of this heterogeneous reaction media on the outcome of coupled enzyme reactions. Our experimental model system for solution heterogeneity is a biphasic polyethylene glycol (PEG)/sodium citrate aqueous mixture that provides coexisting PEG-rich and citrate-rich phases. Reaction kinetics for the coupled enzyme reaction between glucose oxidase (GOX) and horseradish peroxidase (HRP) were measured in the PEG/citrate aqueous two-phase system (ATPS). Enzyme kinetics differed between the two phases, particularly for the HRP. Both enzymes, as well as the substrates glucose and H2O2, partitioned to the citrate-rich phase; however, the Amplex Red substrate necessary to complete the sequential reaction partitioned strongly to the PEG-rich phase. Reactions in ATPS were quantitatively described by a mathematical model that incorporated measured partitioning and kinetic parameters. The model was then extended to new reaction conditions, i.e., higher enzyme concentration. Both experimental and computational results suggest mass transfer across the interface is vital to maintain the observed rate of product formation, which may be a means of metabolic regulation in vivo. Although outcomes for a specific system will depend on the particulars of the enzyme reactions and the microenvironments, this work demonstrates how coupled enzymatic reactions in complex, heterogeneous media can be understood in terms of a mathematical model.

Kinetics and thermochemistry of polyatomic free radicals: New results and new understandings

NASA Technical Reports Server (NTRS)

Gutman, David; Slagle, Irene R.

1990-01-01

An experimental facility for the study of the chemical kinetics of polyatomic free radicals is described which consists of a heatable tubular reactor coupled to a photoionization mass spectrometer. Its use in different kinds of chemical kinetic studies is also discussed. Examples presented include studies of the C2H3 + O2, C2H3 + HC1, CH3 + O, and CH3 + CH3 reactions. The heat of formation of C2H3 was obtained from the results of the study of the C2H3 + HC1 reaction.

Effects of Convective Transport of Solute and Impurities on Defect-Causing Kinetics Instabilities in Protein Crystallization

NASA Technical Reports Server (NTRS)

Vekilov, Peter G.

2002-01-01

The objective of the proposed research is to obtain further insight into the onset and development of the defect-causing instabilities that anise due to the coupling of the bulk transport and nonlinear-interfacial kinetics during growth in the mixed regime, utilizing the reduction of the convective contribution to the bulk transport under microgravity. These studies will build upon the data on the effects of quantitative variations of the forced convection velocity on the averaged and time-dependent kinetic behavior of protein crystal growth systems that have recently been obtained in our laboratory.

Interactions of toroidally coupled tearing modes in the KSTAR tokamak

NASA Astrophysics Data System (ADS)

Kim, Gnan; Yun, Gunsu S.; Woo, Minho; Park, Hyeon K.; KSTAR Team2, the

2018-03-01

The evolutions of toroidally coupled radially-distant and radially-adjacent tearing modes are visualized in 2D in detail on the Korea superconducting tokamak for advanced research. The coupled tearing modes are in-phase on the out-board mid-plane and become destabilized or compete with each other depending on their spatial separation. When two coupled tearing modes are far apart, both are increasingly destabilized. On the other hand, when they become close to each other, one becomes stabilized while the other becomes destabilized. In such cases, an additional tearing mode is often formed on outer rational flux surface and the three tearing modes compete. The competitions suggest that spatial overlap (merging) of coupled magnetic islands is difficult.

Coordinated prefrontal-hippocampal activity and navigation strategy-related prefrontal firing during spatial memory formation.

PubMed

Negrón-Oyarzo, Ignacio; Espinosa, Nelson; Aguilar, Marcelo; Fuenzalida, Marco; Aboitiz, Francisco; Fuentealba, Pablo

2018-06-18

Learning the location of relevant places in the environment is crucial for survival. Such capacity is supported by a distributed network comprising the prefrontal cortex and hippocampus, yet it is not fully understood how these structures cooperate during spatial reference memory formation. Hence, we examined neural activity in the prefrontal-hippocampal circuit in mice during acquisition of spatial reference memory. We found that interregional oscillatory coupling increased with learning, specifically in the slow-gamma frequency (20 to 40 Hz) band during spatial navigation. In addition, mice used both spatial and nonspatial strategies to navigate and solve the task, yet prefrontal neuronal spiking and oscillatory phase coupling were selectively enhanced in the spatial navigation strategy. Lastly, a representation of the behavioral goal emerged in prefrontal spiking patterns exclusively in the spatial navigation strategy. These results suggest that reference memory formation is supported by enhanced cortical connectivity and evolving prefrontal spiking representations of behavioral goals.

Fractional Order Spatiotemporal Chaos with Delay in Spatial Nonlinear Coupling

NASA Astrophysics Data System (ADS)

Zhang, Yingqian; Wang, Xingyuan; Liu, Liyan; Liu, Jia

We investigate the spatiotemporal dynamics with fractional order differential logistic map with delay under nonlinear chaotic maps for spatial coupling connections. Here, the coupling methods between lattices are the nonlinear chaotic map coupling of lattices. The fractional order differential logistic map with delay breaks the limits of the range of parameter μ ∈ [3.75, 4] in the classical logistic map for chaotic states. The Kolmogorov-Sinai entropy density and universality, and bifurcation diagrams are employed to investigate the chaotic behaviors of the proposed model in this paper. The proposed model can also be applied for cryptography, which is verified in a color image encryption scheme in this paper.

Chemistry with spatial control using particles and streams†

PubMed Central

Kalinin, Yevgeniy V.; Murali, Adithya

2012-01-01

Spatial control of chemical reactions, with micro- and nanometer scale resolution, has important consequences for one pot synthesis, engineering complex reactions, developmental biology, cellular biochemistry and emergent behavior. We review synthetic methods to engineer this spatial control using chemical diffusion from spherical particles, shells and polyhedra. We discuss systems that enable both isotropic and anisotropic chemical release from isolated and arrayed particles to create inhomogeneous and spatially patterned chemical fields. In addition to such finite chemical sources, we also discuss spatial control enabled with laminar flow in 2D and 3D microfluidic networks. Throughout the paper, we highlight applications of spatially controlled chemistry in chemical kinetics, reaction-diffusion systems, chemotaxis and morphogenesis. PMID:23145348

EEG Source Reconstruction Reveals Frontal-Parietal Dynamics of Spatial Conflict Processing

PubMed Central

Cohen, Michael X; Ridderinkhof, K. Richard

2013-01-01

Cognitive control requires the suppression of distracting information in order to focus on task-relevant information. We applied EEG source reconstruction via time-frequency linear constrained minimum variance beamforming to help elucidate the neural mechanisms involved in spatial conflict processing. Human subjects performed a Simon task, in which conflict was induced by incongruence between spatial location and response hand. We found an early (∼200 ms post-stimulus) conflict modulation in stimulus-contralateral parietal gamma (30–50 Hz), followed by a later alpha-band (8–12 Hz) conflict modulation, suggesting an early detection of spatial conflict and inhibition of spatial location processing. Inter-regional connectivity analyses assessed via cross-frequency coupling of theta (4–8 Hz), alpha, and gamma power revealed conflict-induced shifts in cortical network interactions: Congruent trials (relative to incongruent trials) had stronger coupling between frontal theta and stimulus-contrahemifield parietal alpha/gamma power, whereas incongruent trials had increased theta coupling between medial frontal and lateral frontal regions. These findings shed new light into the large-scale network dynamics of spatial conflict processing, and how those networks are shaped by oscillatory interactions. PMID:23451201

Thermodynamic and Kinetic Properties of Shocks in Two-Dimensional Yukawa Systems [Thermodynamic and Kinetic Properties of Shocks in 2D Yukawa Systems

DOE PAGES

Marciante, Mathieu; Murillo, Michael Sean

2017-01-10

Particle-level simulations of shocked plasmas are carried out to examine kinetic properties not captured by hydrodynamic models. In particular, molecular dynamics simulations of 2D Yukawa plasmas with variable couplings and screening lengths are used to examine shock features unique to plasmas, including the presence of dispersive shock structures for weak shocks. A phase-space analysis reveals several kinetic properties, including anisotropic velocity distributions, non-Maxwellian tails, and the presence of fast particles ahead of the shock, even for moderately low Mach numbers. As a result, we also examine the thermodynamics (Rankine-Hugoniot relations) of recent experiments and find no anomalies in their equationsmore » of state.« less

Thermodynamic and Kinetic Properties of Shocks in Two-Dimensional Yukawa Systems [Thermodynamic and Kinetic Properties of Shocks in 2D Yukawa Systems

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

Marciante, Mathieu; Murillo, Michael Sean

Particle-level simulations of shocked plasmas are carried out to examine kinetic properties not captured by hydrodynamic models. In particular, molecular dynamics simulations of 2D Yukawa plasmas with variable couplings and screening lengths are used to examine shock features unique to plasmas, including the presence of dispersive shock structures for weak shocks. A phase-space analysis reveals several kinetic properties, including anisotropic velocity distributions, non-Maxwellian tails, and the presence of fast particles ahead of the shock, even for moderately low Mach numbers. As a result, we also examine the thermodynamics (Rankine-Hugoniot relations) of recent experiments and find no anomalies in their equationsmore » of state.« less

Optimization of coupled multiphysics methodology for safety analysis of pebble bed modular reactor

NASA Astrophysics Data System (ADS)

Mkhabela, Peter Tshepo

The research conducted within the framework of this PhD thesis is devoted to the high-fidelity multi-physics (based on neutronics/thermal-hydraulics coupling) analysis of Pebble Bed Modular Reactor (PBMR), which is a High Temperature Reactor (HTR). The Next Generation Nuclear Plant (NGNP) will be a HTR design. The core design and safety analysis methods are considerably less developed and mature for HTR analysis than those currently used for Light Water Reactors (LWRs). Compared to LWRs, the HTR transient analysis is more demanding since it requires proper treatment of both slower and much longer transients (of time scale in hours and days) and fast and short transients (of time scale in minutes and seconds). There is limited operation and experimental data available for HTRs for validation of coupled multi-physics methodologies. This PhD work developed and verified reliable high fidelity coupled multi-physics models subsequently implemented in robust, efficient, and accurate computational tools to analyse the neutronics and thermal-hydraulic behaviour for design optimization and safety evaluation of PBMR concept The study provided a contribution to a greater accuracy of neutronics calculations by including the feedback from thermal hydraulics driven temperature calculation and various multi-physics effects that can influence it. Consideration of the feedback due to the influence of leakage was taken into account by development and implementation of improved buckling feedback models. Modifications were made in the calculation procedure to ensure that the xenon depletion models were accurate for proper interpolation from cross section tables. To achieve this, the NEM/THERMIX coupled code system was developed to create the system that is efficient and stable over the duration of transient calculations that last over several tens of hours. Another achievement of the PhD thesis was development and demonstration of full-physics, three-dimensional safety analysis methodology for the PBMR to provide reference solutions. Investigation of different aspects of the coupled methodology and development of efficient kinetics treatment for the PBMR were carried out, which accounts for all feedback phenomena in an efficient manner. The OECD/NEA PBMR-400 coupled code benchmark was used as a test matrix for the proposed investigations. The integrated thermal-hydraulics and neutronics (multi-physics) methods were extended to enable modeling of a wider range of transients pertinent to the PBMR. First, the effect of the spatial mapping schemes (spatial coupling) was studied and quantified for different types of transients, which resulted in implementation of improved mapping methodology based on user defined criteria. The second aspect that was studied and optimized is the temporal coupling and meshing schemes between the neutronics and thermal-hydraulics time step selection algorithms. The coupled code convergence was achieved supplemented by application of methods to accelerate it. Finally, the modeling of all feedback phenomena in PBMRs was investigated and a novel treatment of cross-section dependencies was introduced for improving the representation of cross-section variations. The added benefit was that in the process of studying and improving the coupled multi-physics methodology more insight was gained into the physics and dynamics of PBMR, which will help also to optimize the PBMR design and improve its safety. One unique contribution of the PhD research is the investigation of the importance of the correct representation of the three-dimensional (3-D) effects in the PBMR analysis. The performed studies demonstrated that explicit 3-D modeling of control rod movement is superior and removes the errors associated with the grey curtain (2-D homogenized) approximation.

Mechanism of the coupling of diazonium to single-walled carbon nanotubes and its consequences.

PubMed

Schmidt, Grégory; Gallon, Salomé; Esnouf, Stéphane; Bourgoin, Jean-Philippe; Chenevier, Pascale

2009-01-01

On the tube: The coupling of diazonium ions onto single-walled carbon nanotubes is shown to proceed through a radical chain reaction by kinetic analysis of the absorption peak drop (see picture). Radical species are also revealed by ESR. Metallic (m) nanotubes play a special catalytic role in the functionalization of semiconducting (sc) nanotubes.Due to its simplicity and versatility, diazonium coupling is the most widely used method for carbon nanotube (CNT) functionalization to increase CNT processability and add new functionalities. Yet, its mechanism is so far mostly unknown. Herein, we use kinetic analysis to shed light on this complex mechanism. A free-radical chain reaction is revealed by absorption spectroscopy and ESR. Metallic CNTs are shown to play an unexpected catalytic role. The step determining the selectivity towards metallic CNTs is identified by a Hammett correlation. A mechanistic model is proposed that predicts reactivity and selectivity as a function of diazonium electrophilicity and metallic-to-semiconducting CNT ratio, thus opening perspectives of controlled high-yield functionalization and purification.

The kinetics and mechanism of the ferrate(VI) oxidation of hydroxylamines.

PubMed

Johnson, Michael D; Hornstein, Brooks J

2003-10-20

Aqueous solutions of potassium ferrate(VI) cleanly and rapidly oxidize hydroxylamine to nitrous oxide, N-methylhydroxylamine to nitrosomethane, N-phenylhydroxylamine to nitrosobenzene, and O-methylhydroxylamine to methanol and nitrogen. The kinetics show first-order behavior with respect to each reactant and a two term component representing acid dependent and independent pathways. A general mechanism involving intermediate formation coupled with a two-electron oxidation is proposed.

Non-equilibrium plasma kinetics of reacting CO: an improved state to state approach

NASA Astrophysics Data System (ADS)

Pietanza, L. D.; Colonna, G.; Capitelli, M.

2017-12-01

Non-equilibrium plasma kinetics of reacting CO for conditions typically met in microwave discharges have been developed based on the coupling of excited state kinetics and the Boltzmann equation for the electron energy distribution function (EEDF). Particular attention is given to the insertion in the vibrational kinetics of a complete set of electron molecule resonant processes linking the whole vibrational ladder of the CO molecule, as well as to the role of Boudouard reaction, i.e. the process of forming CO2 by two vibrationally excited CO molecules, in shaping the vibrational distribution of CO and promoting reaction channels assisted by vibrational excitation (pure vibrational mechanisms, PVM). PVM mechanisms can become competitive with electron impact dissociation processes (DEM) in the activation of CO. A case study reproducing the conditions of a microwave discharge has been considered following the coupled kinetics also in the post discharge conditions. Results include the evolution of EEDF in discharge and post discharge conditions highlighting the role of superelastic vibrational and electronic collisions in shaping the EEDF. Moreover, PVM rate coefficients and DEM ones are studied as a function of gas temperature, showing a non-Arrhenius behavior, i.e. the rate coefficients increase with decreasing gas temperature as a result of a vibrational-vibrational (V-V) pumping up mechanism able to form plateaux in the vibrational distribution function. The accuracy of the results is discussed in particular in connection to the present knowledge of the activation energy of the Boudouard process.

Determining Li+-Coupled Redox Targeting Reaction Kinetics of Battery Materials with Scanning Electrochemical Microscopy.

PubMed

Yan, Ruiting; Ghilane, Jalal; Phuah, Kia Chai; Pham Truong, Thuan Nguyen; Adams, Stefan; Randriamahazaka, Hyacinthe; Wang, Qing

2018-02-01

The redox targeting reaction of Li + -storage materials with redox mediators is the key process in redox flow lithium batteries, a promising technology for next-generation large-scale energy storage. The kinetics of the Li + -coupled heterogeneous charge transfer between the energy storage material and redox mediator dictates the performance of the device, while as a new type of charge transfer process it has been rarely studied. Here, scanning electrochemical microscopy (SECM) was employed for the first time to determine the interfacial charge transfer kinetics of LiFePO 4 /FePO 4 upon delithiation and lithiation by a pair of redox shuttle molecules FcBr 2 + and Fc. The effective rate constant k eff was determined to be around 3.70-6.57 × 10 -3 cm/s for the two-way pseudo-first-order reactions, which feature a linear dependence on the composition of LiFePO 4 , validating the kinetic process of interfacial charge transfer rather than bulk solid diffusion. In addition, in conjunction with chronoamperometry measurement, the SECM study disproves the conventional "shrinking-core" model for the delithiation of LiFePO 4 and presents an intriguing way of probing the phase boundary propagations induced by interfacial redox reactions. This study demonstrates a reliable method for the kinetics of redox targeting reactions, and the results provide useful guidance for the optimization of redox targeting systems for large-scale energy storage.

Pair correlation function and nonlinear kinetic equation for a spatially uniform polarizable nonideal plasma

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

Belyi, V.V.; Kukharenko, Y.A.; Wallenborn, J.

Taking into account the first non-Markovian correction to the Balescu-Lenard equation, we have derived an expression for the pair correlation function and a nonlinear kinetic equation valid for a nonideal polarized classical plasma. This last equation allows for the description of the correlational energy evolution and shows the global conservation of energy with dynamical polarization. {copyright} {ital 1996 The American Physical Society.}

Exploring the performance of thin-film superconducting multilayers as kinetic inductance detectors for low-frequency detection

NASA Astrophysics Data System (ADS)

Zhao, Songyuan; Goldie, D. J.; Withington, S.; Thomas, C. N.

2018-01-01

We have solved numerically the diffusive Usadel equations that describe the spatially varying superconducting proximity effect in Ti-Al thin-film bi- and trilayers with thickness values that are suitable for kinetic inductance detectors (KIDs) to operate as photon detectors with detection thresholds in the frequency range of 50-90 GHz. Using Nam’s extension of the Mattis-Bardeen calculation of the superconductor complex conductivity, we show how to calculate the surface impedance for the spatially varying case, and hence the surface impedance quality factor. In addition, we calculate energy-and spatially-averaged quasiparticle lifetimes at temperatures well-below the transition temperature and compare to calculation in Al. Our results for the pair-breaking threshold demonstrate differences between bilayers and trilayers with the same total film thicknesses. We also predict high quality factors and long multilayer-averaged quasiparticle recombination times compared to thin-film Al. Our calculations give a route for designing KIDs to operate in this scientifically-important frequency regime.

Pulsed IR Heating Studies of Single-Molecule DNA Duplex Dissociation Kinetics and Thermodynamics

PubMed Central

Holmstrom, Erik D.; Dupuis, Nicholas F.; Nesbitt, David J.

2014-01-01

Single-molecule fluorescence spectroscopy is a powerful technique that makes it possible to observe the conformational dynamics associated with biomolecular processes. The addition of precise temperature control to these experiments can yield valuable thermodynamic information about equilibrium and kinetic rate constants. To accomplish this, we have developed a microscopy technique based on infrared laser overtone/combination band absorption to heat small (≈10−11 liter) volumes of water. Detailed experimental characterization of this technique reveals three major advantages over conventional stage heating methods: 1), a larger range of steady-state temperatures (20–100°C); 2), substantially superior spatial (≤20 μm) control; and 3), substantially superior temporal (≈1 ms) control. The flexibility and breadth of this spatial and temporally resolved laser-heating approach is demonstrated in single-molecule fluorescence assays designed to probe the dissociation of a 21 bp DNA duplex. These studies are used to support a kinetic model based on nucleic acid end fraying that describes dissociation for both short (<10 bp) and long (>10 bp) DNA duplexes. These measurements have been extended to explore temperature-dependent kinetics for the 21 bp construct, which permit determination of single-molecule activation enthalpies and entropies for DNA duplex dissociation. PMID:24411254

Monitoring of the spatio-temporal change in the interplate coupling at northeastern Japan subduction zone based on the spatial gradients of surface velocity field

NASA Astrophysics Data System (ADS)

Iinuma, Takeshi

2018-04-01

A monitoring method to grasp the spatio-temporal change in the interplate coupling in a subduction zone based on the spatial gradients of surface displacement rate fields is proposed. I estimated the spatio-temporal change in the interplate coupling along the plate boundary in northeastern (NE) Japan by applying the proposed method to the surface displacement rates based on global positioning system observations. The gradient of the surface velocities is calculated in each swath configured along the direction normal to the Japan Trench for time windows such as 0.5, 1, 2, 3 and 5 yr being shifted by one week during the period of 1997-2016. The gradient of the horizontal velocities is negative and has a large magnitude when the interplate coupling at the shallow part (less than approximately 50 km in depth) beneath the profile is strong, and the sign of the gradient of the vertical velocity is sensitive to the existence of the coupling at the deep part (greater than approximately 50 km in depth). The trench-parallel variation of the spatial gradients of a displacement rate field clearly corresponds to the trench-parallel variation of the amplitude of the interplate coupling on the plate interface, as well as the rupture areas of previous interplate earthquakes. Temporal changes in the trench-parallel variation of the spatial gradient of the displacement rate correspond to the strengthening or weakening of the interplate coupling. We can monitor the temporal change in the interplate coupling state by calculating the spatial gradients of the surface displacement rate field to some extent without performing inversion analyses with applying certain constraint conditions that sometimes cause over- and/or underestimation at areas of limited spatial resolution far from the observation network. The results of the calculation confirm known interplate events in the NE Japan subduction zone, such as the post-seismic slip of the 2003 M8.0 Tokachi-oki and 2005 M7.2 Miyagi-oki earthquakes and the recovery of the interplate coupling around the rupture area of the 1994 M7.6 Sanriku-Haruka-oki earthquake. The results also indicate the semi-periodic occurrence of slow slip events and the expansion of the area of slow slip events before the 2011 Tohoku-oki earthquake (M9.0) approaching the hypocentre of the Tohoku-oki earthquake.

Coupled stochastic spatial and non-spatial simulations of ErbB1 signaling pathways demonstrate the importance of spatial organization in signal transduction.

PubMed

Costa, Michelle N; Radhakrishnan, Krishnan; Wilson, Bridget S; Vlachos, Dionisios G; Edwards, Jeremy S

2009-07-23

The ErbB family of receptors activates intracellular signaling pathways that control cellular proliferation, growth, differentiation and apoptosis. Given these central roles, it is not surprising that overexpression of the ErbB receptors is often associated with carcinogenesis. Therefore, extensive laboratory studies have been devoted to understanding the signaling events associated with ErbB activation. Systems biology has contributed significantly to our current understanding of ErbB signaling networks. However, although computational models have grown in complexity over the years, little work has been done to consider the spatial-temporal dynamics of receptor interactions and to evaluate how spatial organization of membrane receptors influences signaling transduction. Herein, we explore the impact of spatial organization of the epidermal growth factor receptor (ErbB1/EGFR) on the initiation of downstream signaling. We describe the development of an algorithm that couples a spatial stochastic model of membrane receptors with a nonspatial stochastic model of the reactions and interactions in the cytosol. This novel algorithm provides a computationally efficient method to evaluate the effects of spatial heterogeneity on the coupling of receptors to cytosolic signaling partners. Mathematical models of signal transduction rarely consider the contributions of spatial organization due to high computational costs. A hybrid stochastic approach simplifies analyses of the spatio-temporal aspects of cell signaling and, as an example, demonstrates that receptor clustering contributes significantly to the efficiency of signal propagation from ligand-engaged growth factor receptors.

NMR analysis of lignins in CAD-deficient plants. Part 1, Incorporation of hydroxycinnamaldehydes and hydroxybenzaldehydes into lignins

Treesearch

Hoon Kim; John Ralph; Fachuang Lu; Sally A. Ralph; Alain-M. Boudett; John J. MacKay; Ronald R. Sederoff; Takashi Ito; Shingo Kawai; Hideo Ohashi; Takayoshi Higuchi

2003-01-01

Peroxidase/H2O2-mediated radical coupling of 4-hydroxycinnamaldehydes produces 8–O–4-, 8–5-, and 8–8-coupled dehydrodimers as has been documented earlier, as well as the 5-5-coupled dehydrodimer. The 8–5- dehydrodimer is however produced kinetically in its cyclic phenylcoumaran form at neutral pH. Synthetic polymers produced from mixtures of hydroxycinnamaldehydes and...

Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms

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

Arampatzis, Giorgos, E-mail: garab@math.uoc.gr; Katsoulakis, Markos A., E-mail: markos@math.umass.edu; Plechac, Petr, E-mail: plechac@math.udel.edu

2012-10-01

We present a mathematical framework for constructing and analyzing parallel algorithms for lattice kinetic Monte Carlo (KMC) simulations. The resulting algorithms have the capacity to simulate a wide range of spatio-temporal scales in spatially distributed, non-equilibrium physiochemical processes with complex chemistry and transport micro-mechanisms. Rather than focusing on constructing exactly the stochastic trajectories, our approach relies on approximating the evolution of observables, such as density, coverage, correlations and so on. More specifically, we develop a spatial domain decomposition of the Markov operator (generator) that describes the evolution of all observables according to the kinetic Monte Carlo algorithm. This domain decompositionmore » corresponds to a decomposition of the Markov generator into a hierarchy of operators and can be tailored to specific hierarchical parallel architectures such as multi-core processors or clusters of Graphical Processing Units (GPUs). Based on this operator decomposition, we formulate parallel Fractional step kinetic Monte Carlo algorithms by employing the Trotter Theorem and its randomized variants; these schemes, (a) are partially asynchronous on each fractional step time-window, and (b) are characterized by their communication schedule between processors. The proposed mathematical framework allows us to rigorously justify the numerical and statistical consistency of the proposed algorithms, showing the convergence of our approximating schemes to the original serial KMC. The approach also provides a systematic evaluation of different processor communicating schedules. We carry out a detailed benchmarking of the parallel KMC schemes using available exact solutions, for example, in Ising-type systems and we demonstrate the capabilities of the method to simulate complex spatially distributed reactions at very large scales on GPUs. Finally, we discuss work load balancing between processors and propose a re-balancing scheme based on probabilistic mass transport methods.« less

Cosmology with nonminimal kinetic coupling and a Higgs-like potential

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

Matsumoto, Jiro; Sushkov, Sergey V., E-mail: jmatsumoto@kpfu.ru, E-mail: sergey_sushkov@mail.ru

2015-11-01

We consider cosmological dynamics in the theory of gravity with the scalar field possessing the nonminimal kinetic coupling to curvature given as κG{sup μν}φ{sub ,μ}φ{sub ,ν}, and the Higgs-like potential . Using the dynamical system method, we analyze stationary points, their stability, and all possible asymptotical regimes of the model under consideration. We show that the Higgs field with the kinetic coupling provides an existence of accelerated regimes of the Universe evolution. There are three possible cosmological scenarios with acceleration: (i) The late-time de Sitter epoch when the Hubble parameter tends to the constant value, as t → ∞, while the scalarmore » field tends to zero, 0φ(t)→ , so that the Higgs potential reaches its local maximum . (ii) The Big Rip when H(t)∼(t{sub *}−t){sup −1} → ∞ and φ(t)∼(t{sub *}−t){sup −2} → ∞ as t →  t{sub *}. (iii) The Little Rip when H(t)∼ t{sup 1/2} → ∞ and φ(t)∼ t{sup 1/4} → ∞ as t → ∞. Also, we derive modified slow-roll conditions for the Higgs field and demonstrate that they lead to the Little Rip scenario.« less

Study of shear viscosity for dense plasmas by equilibrium molecular dynamics in asymmetric Yukawa ionic mixtures

NASA Astrophysics Data System (ADS)

Haxhimali, Tomorr; Rudd, Robert; Cabot, William; Graziani, Frank

2015-11-01

We present molecular dynamics (MD) calculations of shear viscosity for asymmetric mixed plasma for thermodynamic conditions relevant to astrophysical and Inertial Confinement Fusion plasmas. Specifically, we consider mixtures of deuterium and argon at temperatures of 100-500 eV and a number density of 1025 ions/cc. The motion of 30000-120000 ions is simulated in which the ions interact via the Yukawa (screened Coulomb) potential. The electric field of the electrons is included in this effective interaction. Shear viscosity is calculated using the Green-Kubo approach with an integral of the shear stress autocorrelation function, a quantity calculated in the equilibrium MD simulations. We study different mixtures with increasing fraction of the minority high-Z element (Ar) in the D-Ar plasma mixture. In the more weakly coupled plasmas, at 500 eV and low Ar fractions, results from MD compare very well with Chapman-Enskog kinetic results. We introduce a model that interpolates between a screened-plasma kinetic theory at weak coupling and the Murillo Yukawa viscosity model at higher coupling. This hybrid kinetics-MD viscosity model agrees well with the MD results over the conditions simulated. This work was performed under the auspices of the US Dept. of Energy by Lawrence Livermore National Security, LLC under Contract DE-AC52-07NA27344.

Continuous variables logic via coupled automata using a DNAzyme cascade with feedback.

PubMed

Lilienthal, S; Klein, M; Orbach, R; Willner, I; Remacle, F; Levine, R D

2017-03-01

The concentration of molecules can be changed by chemical reactions and thereby offer a continuous readout. Yet computer architecture is cast in textbooks in terms of binary valued, Boolean variables. To enable reactive chemical systems to compute we show how, using the Cox interpretation of probability theory, one can transcribe the equations of chemical kinetics as a sequence of coupled logic gates operating on continuous variables. It is discussed how the distinct chemical identity of a molecule allows us to create a common language for chemical kinetics and Boolean logic. Specifically, the logic AND operation is shown to be equivalent to a bimolecular process. The logic XOR operation represents chemical processes that take place concurrently. The values of the rate constants enter the logic scheme as inputs. By designing a reaction scheme with a feedback we endow the logic gates with a built in memory because their output then depends on the input and also on the present state of the system. Technically such a logic machine is an automaton. We report an experimental realization of three such coupled automata using a DNAzyme multilayer signaling cascade. A simple model verifies analytically that our experimental scheme provides an integrator generating a power series that is third order in time. The model identifies two parameters that govern the kinetics and shows how the initial concentrations of the substrates are the coefficients in the power series.

Carbon-fluorine bond activation coupled with carbon-hydrogen bond formation alpha to iridium: kinetics, mechanism, and diastereoselectivity.

PubMed

Garratt, Shaun A; Hughes, Russell P; Kovacik, Ivan; Ward, Antony J; Willemsen, Stefan; Zhang, Donghui

2005-11-09

Reactions of iridium(fluoroalkyl)hydride complexes CpIr(PMe(3))(CF(2)R(F))Y (R(F) = F, CF(3); Y = H, D) with LutHX (Lut = 2,6-dimethylpyridine; X = Cl, I) results in C-F activation coupled with hydride migration to give CpIr(PMe(3))(CYFR(F))X as variable mixtures of diastereomers. Solution conformations and relative diastereomer configurations of the products have been determined by (19)F{(1)H}HOESY NMR to be (S(C), S(Ir))(R(C), R(Ir)) for the kinetic diastereomer and (R(C), S(Ir))(S(C), R(Ir)) for its thermodynamic counterpart. Isotope labeling experiments using LutDCl/CpIr(PMe(3))(CF(2)R(F))H and CpIr(PMe(3))(CF(2)R(F))D/LutHCl) showed that, unlike a previously studied system, H/D exchange is faster than protonation of the alpha-CF bond, giving an identical mixture of product isotopologues from both reaction mixtures. The kinetic rate law shows a first-order dependence on the concentration of iridium substrate, but a half-order dependence on that of LutHCl; this is interpreted to mean that LutHCl dissociates to give HCl as the active protic source for C-F bond activation. Detailed kinetic studies are reported, which demonstrate that lack of complete diastereoselectivity is not a function of the C-F bond activation/H migration steps but that a cationic intermediate plays a double role in loss of diastereoselectivity; the intermediate can undergo epimerization at iridium before being trapped by halide and can also catalyze the epimerization of kinetic diastereomer product to thermodynamic product. A detailed mechanism is proposed and simulations performed to fit the kinetic data.

MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations

NASA Astrophysics Data System (ADS)

Dibak, Manuel; del Razo, Mauricio J.; De Sancho, David; Schütte, Christof; Noé, Frank

2018-06-01

Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long time-scale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large length scales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time and length scales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step toward MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B ⇌ C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported.

On the efficiency and reversibility of active ligand transport induced by alternating rectangular electric pulses.

PubMed Central

Chen, Y; Tsong, T Y

1994-01-01

The stationary-state kinetic properties of a simplified two-state electro-conformational coupling model (ECC) in the presence of alternating rectangular electric potential pulses are derived analytically. Analytic expressions for the transport flux, the rate of electric energy dissipation, and the efficiency of the transducing system are obtained as a function of the amplitude and frequency of the oscillation. These formulas clarify some fundamental concept of the ECC model and are directly applicable to the interpretation and design of experiments. Based on these formulas, the reversibility and the degree of coupling of the system can be studied quantitatively. It is found that the oscillation-induced free energy transduction is reversible and tight-coupled only when the amplitude of the oscillating electric field is infinitely large. In general, the coupling is not tight when the amplitude of the electric field is finite. Furthermore, depending on the kinetic parameters of the model, there may exist a "critical" electric field amplitude, below which free energy transduction is not reversible. That is, energy may be transduced from the electric to the chemical, but not from the chemical to the electric. PMID:8075348

μ-Rainbow: CdSe Nanocrystal Photoluminescence Gradients via Laser Spike Annealing for Kinetic Investigations and Tunable Device Design.

PubMed

Treml, Benjamin E; Jacobs, Alan G; Bell, Robert T; Thompson, Michael O; Hanrath, Tobias

2016-02-10

Much of the promise of nanomaterials derives from their size-dependent, and hence tunable, properties. Impressive advances have been made in the synthesis of nanoscale building blocks with precisely tailored size, shape and composition. Significant attention is now turning toward creating thin film structures in which size-dependent properties can be spatially programmed with high fidelity. Nonequilibrium processing techniques present exciting opportunities to create nanostructured thin films with unprecedented spatial control over their optical and electronic properties. Here, we demonstrate single scan laser spike annealing (ssLSA) on CdSe nanocrystal (NC) thin films as an experimental test bed to illustrate how the size-dependent photoluminescence (PL) emission can be tuned throughout the visible range and in spatially defined profiles during a single annealing step. Through control of the annealing temperature and time, we discovered that NC fusion is a kinetically limited process with a constant activation energy in over 2 orders of magnitude of NC growth rate. To underscore the broader technological implications of this work, we demonstrate the scalability of LSA to process large area NC films with periodically modulated PL emission, resulting in tunable emission properties of a large area film. New insights into the processing-structure-property relationships presented here offer significant advances in our fundamental understanding of kinetics of nanomaterials as well as technological implications for the production of nanomaterial films.

Near-Field Infrared Pump-Probe Imaging of Surface Phonon Coupling in Boron Nitride Nanotubes.

PubMed

Gilburd, Leonid; Xu, Xiaoji G; Bando, Yoshio; Golberg, Dmitri; Walker, Gilbert C

2016-01-21

Surface phonon modes are lattice vibrational modes of a solid surface. Two common surface modes, called longitudinal and transverse optical modes, exhibit lattice vibration along or perpendicular to the direction of the wave. We report a two-color, infrared pump-infrared probe technique based on scattering type near-field optical microscopy (s-SNOM) to spatially resolve coupling between surface phonon modes. Spatially varying couplings between the longitudinal optical and surface phonon polariton modes of boron nitride nanotubes are observed, and a simple model is proposed.

Fully coupled approach to modeling shallow water flow, sediment transport, and bed evolution in rivers

NASA Astrophysics Data System (ADS)

Li, Shuangcai; Duffy, Christopher J.

2011-03-01

Our ability to predict complex environmental fluid flow and transport hinges on accurate and efficient simulations of multiple physical phenomenon operating simultaneously over a wide range of spatial and temporal scales, including overbank floods, coastal storm surge events, drying and wetting bed conditions, and simultaneous bed form evolution. This research implements a fully coupled strategy for solving shallow water hydrodynamics, sediment transport, and morphological bed evolution in rivers and floodplains (PIHM_Hydro) and applies the model to field and laboratory experiments that cover a wide range of spatial and temporal scales. The model uses a standard upwind finite volume method and Roe's approximate Riemann solver for unstructured grids. A multidimensional linear reconstruction and slope limiter are implemented, achieving second-order spatial accuracy. Model efficiency and stability are treated using an explicit-implicit method for temporal discretization with operator splitting. Laboratory-and field-scale experiments were compiled where coupled processes across a range of scales were observed and where higher-order spatial and temporal accuracy might be needed for accurate and efficient solutions. These experiments demonstrate the ability of the fully coupled strategy in capturing dynamics of field-scale flood waves and small-scale drying-wetting processes.

Local dynamics measured by hydrogen/deuterium exchange and mass spectrometry of creatine kinase digested by two proteases.

PubMed

Mazon, Hortense; Marcillat, Olivier; Forest, Eric; Vial, Christian

2005-12-01

Hydrogen/deuterium exchange coupled to mass spectrometry has been used to investigate the structure and dynamics of native dimeric cytosolic muscle creatine kinase. The protein was incubated in D2O for various time. After H/D exchange and rapid quenching of the reaction, the partially deuterated protein was cleaved in parallel by two different proteases (pepsin or type XIII protease from Aspergillus saitoi) to increase the sequence coverage and spatial resolution of deuterium incorporation. The resulting peptides were analyzed by liquid chromatography coupled to mass spectrometry. In comparison with the 3D structure of MM-CK, the analysis of the two independent proteolysis deuteration patterns allowed us to get new insights into CK local dynamics as compared to a previous study using pepsin [Mazon et al. Protein Science 13 (2004) 476-486]. In particular, we obtained more information on the kinetics and extent of deuterium exchange in the N- and C-terminal extremities represented by the 1-22 and 362-380 pepsin peptides. Indeed, we observed a very different behaviour of the 1-12 and 13-22 type XIII protease peptides, and similarly for the 362-373 and 374-380 peptides. Moreover, comparison of the deuteration patterns of type XIII protease segments of the large 90-126 pepsin peptide led us to identify a small relatively dynamic region (108-114).

Impact of the IMF conditions on the high latitude geomagnetic field fluctuations at Swarm altitude

NASA Astrophysics Data System (ADS)

De Michelis, Paola; Consolini, Giuseppe; Tozzi, Roberta

2016-04-01

Several space-plasma media are characterized by turbulent fluctuations covering a wide range of temporal and spatial scales from the MHD domain down to the kinetic region, which substantially affect the overall dynamics of these media. In the framework of ionosphere-magnetosphere coupling, magnetic field and plasma disturbances are driven by different current systems responsible for the coupling. These disturbances manifest in the plasma parameters inhomogeneity and in the magnetic field fluctuations, which are capable of affecting the ionospheric conditions. The present work focuses on the analysis of the statistical features of high latitude magnetic field fluctuations at Swarm altitude. The multi-satellite mission, Swarm, is equipped with several instruments which observe electric and magnetic fields as well as ionospheric parameters of the near-Earth space environment. Using these data we investigate the scaling properties of the magnetic field fluctuations at ionospheric altitude and high latitudes in the Northern and Southern hemispheres according to different interplanetary magnetic field conditions and Earth's seasons. The aim of this work is to characterize the different features of ionospheric turbulence in order to better understand the nature and possible drivers of magnetic field variability and to discuss the results in the framework of Sun-Earth relationship and ionospheric polar convection. This work is supported by the Italian National Program for Antarctic Research (PNRA) Research Project 2013/AC3.08

Convective drying of osmo-dehydrated apple slices: kinetics and spatial behavior of effective mass diffusivity and moisture content

NASA Astrophysics Data System (ADS)

de Farias Aires, Juarez Everton; da Silva, Wilton Pereira; de Almeida Farias Aires, Kalina Lígia Cavalcante; da Silva Júnior, Aluízio Freire; da Silva e Silva, Cleide Maria Diniz Pereira

2018-04-01

The main objective of this study is the presentation of a numerical model of liquid diffusion for the description of the convective drying of apple slices submitted to pretreatment of osmotic dehydration able of predicting the spatial distribution of effective mass diffusivity values in apple slabs. Two models that use numerical solutions of the two-dimensional diffusion equation in Cartesian coordinates with the boundary condition of third kind were proposed to describe drying. The first one does not consider the shrinkage of the product and assumes that the process parameters remain constant along the convective drying. The second one considers the shrinkage of the product and assumes that the effective mass diffusivity of water varies according to the local value of the water content in the apple samples. Process parameters were estimated from experimental data through an optimizer coupled to the numerical solutions. The osmotic pretreatment did not reduce the drying time in relation to the fresh fruits when the drying temperature was equal to 40 °C. The use of the temperature of 60 °C led to a reduction in the drying time. The model that considers the variations in the dimensions of the product and the variation in the effective mass diffusivity proved to be more adequate to describe the process.

Nonlinear plasma wave models in 3D fluid simulations of laser-plasma interaction

NASA Astrophysics Data System (ADS)

Chapman, Thomas; Berger, Richard; Arrighi, Bill; Langer, Steve; Banks, Jeffrey; Brunner, Stephan

2017-10-01

Simulations of laser-plasma interaction (LPI) in inertial confinement fusion (ICF) conditions require multi-mm spatial scales due to the typical laser beam size and durations of order 100 ps in order for numerical laser reflectivities to converge. To be computationally achievable, these scales necessitate a fluid-like treatment of light and plasma waves with a spatial grid size on the order of the light wave length. Plasma waves experience many nonlinear phenomena not naturally described by a fluid treatment, such as frequency shifts induced by trapping, a nonlinear (typically suppressed) Landau damping, and mode couplings leading to instabilities that can cause the plasma wave to decay rapidly. These processes affect the onset and saturation of stimulated Raman and Brillouin scattering, and are of direct interest to the modeling and prediction of deleterious LPI in ICF. It is not currently computationally feasible to simulate these Debye length-scale phenomena in 3D across experimental scales. Analytically-derived and/or numerically benchmarked models of processes occurring at scales finer than the fluid simulation grid offer a path forward. We demonstrate the impact of a range of kinetic processes on plasma reflectivity via models included in the LPI simulation code pF3D. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Phase behavior of a simple dipolar fluid under shear flow in an electric field.

PubMed

McWhirter, J Liam

2008-01-21

Nonequilibrium molecular dynamics simulations are performed on a dense simple dipolar fluid under a planar Couette shear flow. Shear generates heat, which is removed by thermostatting terms added to the equations of motion of the fluid particles. The spatial structure of simple fluids at high shear rates is known to depend strongly on the thermostatting mechanism chosen. Kinetic thermostats are either biased or unbiased: biased thermostats neglect the existence of secondary flows that appear at high shear rates superimposed upon the linear velocity profile of the fluid. Simulations that employ a biased thermostat produce a string phase where particles align in strings with hexagonal symmetry along the direction of the flow. This phase is known to be a simulation artifact of biased thermostatting, and has not been observed by experiments on colloidal suspensions under shear flow. In this paper, we investigate the possibility of using a suitably directed electric field, which is coupled to the dipole moments of the fluid particles, to stabilize the string phase. We explore several thermostatting mechanisms where either the kinetic or configurational fluid degrees of freedom are thermostated. Some of these mechanisms do not yield a string phase, but rather a shear-thickening phase; in this case, we find the influence of the dipolar interactions and external field on the packing structure, and in turn their influence on the shear viscosity at the onset of this shear-thickening regime.

Reliability of spatiotemporal and kinetic gait parameters determined by a new instrumented treadmill system.

PubMed

Reed, Lloyd F; Urry, Stephen R; Wearing, Scott C

2013-08-21

Despite the emerging use of treadmills integrated with pressure platforms as outcome tools in both clinical and research settings, published evidence regarding the measurement properties of these new systems is limited. This study evaluated the within- and between-day repeatability of spatial, temporal and vertical ground reaction force parameters measured by a treadmill system instrumented with a capacitance-based pressure platform. Thirty three healthy adults (mean age, 21.5 ± 2.8 years; height, 168.4 ± 9.9 cm; and mass, 67.8 ± 18.6 kg), walked barefoot on a treadmill system (FDM-THM-S, Zebris Medical GmbH) on three separate occasions. For each testing session, participants set their preferred pace but were blinded to treadmill speed. Spatial (foot rotation, step width, stride and step length), temporal (stride and step times, duration of stance, swing and single and double support) and peak vertical ground reaction force variables were collected over a 30-second capture period, equating to an average of 52 ± 5 steps of steady-state walking. Testing was repeated one week following the initial trial and again, for a third time, 20 minutes later. Repeated measures ANOVAs within a generalized linear modelling framework were used to assess between-session differences in gait parameters. Agreement between gait parameters measured within the same day (session 2 and 3) and between days (session 1 and 2; 1 and 3) were evaluated using the 95% repeatability coefficient. There were statistically significant differences in the majority (14/16) of temporal, spatial and kinetic gait parameters over the three test sessions (P < .01). The minimum change that could be detected with 95% confidence ranged between 3% and 17% for temporal parameters, 14% and 33% for spatial parameters, and 4% and 20% for kinetic parameters between days. Within-day repeatability was similar to that observed between days. Temporal and kinetic gait parameters were typically more consistent than spatial parameters. The 95% repeatability coefficient for vertical force peaks ranged between ± 53 and ± 63 N. The limits of agreement in spatial parameters and ground reaction forces for the treadmill system encompass previously reported changes with neuromuscular pathology and footwear interventions. These findings provide clinicians and researchers with an indication of the repeatability and sensitivity of the Zebris treadmill system to detect changes in common spatiotemporal gait parameters and vertical ground reaction forces.

Resolving vorticity-driven lateral fire spread using the WRF-Fire coupled atmosphere-fire numerical model

NASA Astrophysics Data System (ADS)

Simpson, C. C.; Sharples, J. J.; Evans, J. P.

2014-05-01

Fire channelling is a form of dynamic fire behaviour, during which a wildland fire spreads rapidly across a steep lee-facing slope in a direction transverse to the background winds, and is often accompanied by a downwind extension of the active flaming region and extreme pyro-convection. Recent work using the WRF-Fire coupled atmosphere-fire model has demonstrated that fire channelling can be characterised as vorticity-driven lateral fire spread (VDLS). In this study, 16 simulations are conducted using WRF-Fire to examine the sensitivity of resolving VDLS to spatial resolution and atmosphere-fire coupling within the WRF-Fire model framework. The horizontal grid spacing is varied between 25 and 90 m, and the two-way atmosphere-fire coupling is either enabled or disabled. At high spatial resolution, the atmosphere-fire coupling increases the peak uphill and lateral spread rate by a factor of up to 2.7 and 9.5. The enhancement of the uphill and lateral spread rate diminishes at coarser spatial resolution, and VDLS is not modelled for a horizontal grid spacing of 90 m. The laterally spreading fire fronts become the dominant contributors of the extreme pyro-convection. The resolved fire-induced vortices responsible for driving the lateral spread in the coupled simulations have non-zero vorticity along each unit vector direction, and develop due to an interaction between the background winds and vertical return circulations generated at the flank of the fire front as part of the pyro-convective updraft. The results presented in this study demonstrate that both high spatial resolution and two-way atmosphere-fire coupling are required to reproduce VDLS within the current WRF-Fire model framework.

Kinetic effects on the velocity-shear-driven instability

NASA Technical Reports Server (NTRS)

Wang, Z.; Pritchett, P. L.; Ashour-Abdalla, M.

1992-01-01

A comparison is made between the properties of the low-frequency long-wavelength velocity-shear-driven instability in kinetic theory and magnetohydrodynamics (MHD). The results show that the removal of adiabaticity along the magnetic field line in kinetic theory leads to modifications in the nature of the instability. Although the threshold for the instability in the two formalisms is the same, the kinetic growth rate and the unstable range in wave-number space can be larger or smaller than the MHD values depending on the ratio between the thermal speed, Alfven speed, and flow speed. When the thermal speed is much larger than the flow speed and the flow speed is larger than the Alfven speed, the kinetic formalism gives a larger maximum growth rate and broader unstable range in wave-number space. In this regime, the normalized wave number for instability can be larger than unity, while in MHD it is always less than unity. The normal mode profile in the kinetic case has a wider spatial extent across the shear layer.

Theory and modeling of atmospheric turbulence, part 1

NASA Technical Reports Server (NTRS)

1984-01-01

The cascade transfer which is the only function to describe the mode coupling as the result of the nonlinear hydrodynamic state of turbulence is discussed. A kinetic theory combined with a scaling procedure was developed. The transfer function governs the non-linear mode coupling in strong turbulence. The master equation is consistent with the hydrodynamical system that describes the microdynamic state of turbulence and has the advantages to be homogeneous and have fewer nonlinear terms. The modes are scaled into groups to decipher the governing transport processes and statistical characteristics. An equation of vorticity transport describes the microdynamic state of two dimensional, isotropic and homogeneous, geostrophic turbulence. The equation of evolution of the macrovorticity is derived from group scaling in the form of the Fokker-Planck equation with memory. The microdynamic state of turbulence is transformed into the Liouville equation to derive the kinetic equation of the singlet distribution in turbulence. The collision integral contains a memory, which is analyzed with pair collision and the multiple collision. Two other kinetic equations are developed in parallel for the propagator and the transition probability for the interaction among the groups.

GPU based 3D feature profile simulation of high-aspect ratio contact hole etch process under fluorocarbon plasmas

NASA Astrophysics Data System (ADS)

Chun, Poo-Reum; Lee, Se-Ah; Yook, Yeong-Geun; Choi, Kwang-Sung; Cho, Deog-Geun; Yu, Dong-Hun; Chang, Won-Seok; Kwon, Deuk-Chul; Im, Yeon-Ho

2013-09-01

Although plasma etch profile simulation has been attracted much interest for developing reliable plasma etching, there still exist big gaps between current research status and predictable modeling due to the inherent complexity of plasma process. As an effort to address this issue, we present 3D feature profile simulation coupled with well-defined plasma-surface kinetic model for silicon dioxide etching process under fluorocarbon plasmas. To capture the realistic plasma surface reaction behaviors, a polymer layer based surface kinetic model was proposed to consider the simultaneous polymer deposition and oxide etching. Finally, the realistic plasma surface model was used for calculation of speed function for 3D topology simulation, which consists of multiple level set based moving algorithm, and ballistic transport module. In addition, the time consumable computations in the ballistic transport calculation were improved drastically by GPU based numerical computation, leading to the real time computation. Finally, we demonstrated that the surface kinetic model could be coupled successfully for 3D etch profile simulations in high-aspect ratio contact hole plasma etching.

Sensitivity analysis of a coupled hydrodynamic-vegetation model using the effectively subsampled quadratures method

USGS Publications Warehouse

Kalra, Tarandeep S.; Aretxabaleta, Alfredo; Seshadri, Pranay; Ganju, Neil K.; Beudin, Alexis

2017-01-01

Coastal hydrodynamics can be greatly affected by the presence of submerged aquatic vegetation. The effect of vegetation has been incorporated into the Coupled-Ocean-Atmosphere-Wave-Sediment Transport (COAWST) Modeling System. The vegetation implementation includes the plant-induced three-dimensional drag, in-canopy wave-induced streaming, and the production of turbulent kinetic energy by the presence of vegetation. In this study, we evaluate the sensitivity of the flow and wave dynamics to vegetation parameters using Sobol' indices and a least squares polynomial approach referred to as Effective Quadratures method. This method reduces the number of simulations needed for evaluating Sobol' indices and provides a robust, practical, and efficient approach for the parameter sensitivity analysis. The evaluation of Sobol' indices shows that kinetic energy, turbulent kinetic energy, and water level changes are affected by plant density, height, and to a certain degree, diameter. Wave dissipation is mostly dependent on the variation in plant density. Performing sensitivity analyses for the vegetation module in COAWST provides guidance for future observational and modeling work to optimize efforts and reduce exploration of parameter space.

Modelling the influence of ionic and fluid transport on rebars corrosion in unsaturated cement systems

NASA Astrophysics Data System (ADS)

Dridi, W.; Dangla, P.; Foct, F.; Petre-Lazar, I.

2006-11-01

This paper deals with numerical modelling of rebar corrosion kinetics in unsaturated concrete structures. The corrosion kinetics is investigated in terms of mechanistic coupling between reaction rates at the steel surface and the ionic transport processes in the concrete pore system. The ionic and mass transport model consists of time-dependent equations for the concentration of dissolved species, the liquid pressure and the electrical potential. The complete set of nonlinear equations is solved using the finite-volume method. The nonlinear boundary conditions dealing with corrosion are introduced at the steel-concrete interface where they are implicitly coupled with the mass transport model in the concrete structure. Both the case of free corrosion and potentiostatic polarisation are discussed in a one dimensional model.

First passage times for multiple particles with reversible target-binding kinetics

NASA Astrophysics Data System (ADS)

Grebenkov, Denis S.

2017-10-01

We investigate the first passage problem for multiple particles that diffuse towards a target, partially adsorb there, and then desorb after a finite exponentially distributed residence time. We search for the first time when m particles undergoing such reversible target-binding kinetics are found simultaneously on the target that may trigger an irreversible chemical reaction or a biophysical event. Even if the particles are independent, the finite residence time on the target yields an intricate temporal coupling between particles. We compute analytically the mean first passage time (MFPT) for two independent particles by mapping the original problem to higher-dimensional surface-mediated diffusion and solving the coupled partial differential equations. The respective effects of the adsorption and desorption rates on the MFPT are revealed and discussed.

Fuzzy Performance between Surface Fitting and Energy Distribution in Turbulence Runner

PubMed Central

Liang, Zhongwei; Liu, Xiaochu; Ye, Bangyan; Brauwer, Richard Kars

2012-01-01

Because the application of surface fitting algorithms exerts a considerable fuzzy influence on the mathematical features of kinetic energy distribution, their relation mechanism in different external conditional parameters must be quantitatively analyzed. Through determining the kinetic energy value of each selected representative position coordinate point by calculating kinetic energy parameters, several typical algorithms of complicated surface fitting are applied for constructing microkinetic energy distribution surface models in the objective turbulence runner with those obtained kinetic energy values. On the base of calculating the newly proposed mathematical features, we construct fuzzy evaluation data sequence and present a new three-dimensional fuzzy quantitative evaluation method; then the value change tendencies of kinetic energy distribution surface features can be clearly quantified, and the fuzzy performance mechanism discipline between the performance results of surface fitting algorithms, the spatial features of turbulence kinetic energy distribution surface, and their respective environmental parameter conditions can be quantitatively analyzed in detail, which results in the acquirement of final conclusions concerning the inherent turbulence kinetic energy distribution performance mechanism and its mathematical relation. A further turbulence energy quantitative study can be ensured. PMID:23213287

Air-coupled laser vibrometry: analysis and applications.

PubMed

Solodov, Igor; Döring, Daniel; Busse, Gerd

2009-03-01

Acousto-optic interaction between a narrow laser beam and acoustic waves in air is analyzed theoretically. The photoelastic relation in air is used to derive the phase modulation of laser light in air-coupled reflection vibrometry induced by angular spatial spectral components comprising the acoustic beam. Maximum interaction was found for the zero spatial acoustic component propagating normal to the laser beam. The angular dependence of the imaging efficiency is determined for the axial and nonaxial acoustic components with the regard for the laser beam steering in the scanning mode. The sensitivity of air-coupled vibrometry is compared with conventional "Doppler" reflection vibrometry. Applications of the methodology for visualization of linear and nonlinear air-coupled fields are demonstrated.

Parameters assessment of the inductively-coupled circuit for wireless power transfer

NASA Astrophysics Data System (ADS)

Isaev, Yu N.; Vasileva, O. V.; Budko, A. A.; Lefebvre, S.

2017-02-01

In this paper, a wireless power transfer model through the example of inductively-coupled coils of irregular shape in software package COMSOL Multiphysics is studied. Circuit parameters, such as inductance, coil resistance and self-capacitance were defined through electromagnetic energy by the finite-element method. The study was carried out according to Helmholtz equation. Spatial distribution of current per unit depending on frequency and the coupling coefficient for analysis of resonant frequency and spatial distribution of the vector magnetic potential at different distances between coils were presented. The resulting algorithm allows simulating the wireless power transfer between the inductively coupled coils of irregular shape with the assessment of the optimal parameters.

ATLASGAL-selected massive clumps in the inner Galaxy. VI. Kinetic temperature and spatial density measured with formaldehyde

NASA Astrophysics Data System (ADS)

Tang, X. D.; Henkel, C.; Wyrowski, F.; Giannetti, A.; Menten, K. M.; Csengeri, T.; Leurini, S.; Urquhart, J. S.; König, C.; Güsten, R.; Lin, Y. X.; Zheng, X. W.; Esimbek, J.; Zhou, J. J.

2018-03-01

Context. Formaldehyde (H2CO) is a reliable tracer to accurately measure the physical parameters of dense gas in star-forming regions. Aim. We aim to determine directly the kinetic temperature and spatial density with formaldehyde for the 100 brightest ATLASGAL-selected clumps (the TOP100 sample) at 870 μm representing various evolutionary stages of high-mass star formation. Methods: Ten transitions (J = 3-2 and 4-3) of ortho- and para-H2CO near 211, 218, 225, and 291 GHz were observed with the Atacama Pathfinder EXperiment (APEX) 12 m telescope. Results: Using non-LTE models with RADEX, we derived the gas kinetic temperature and spatial density with the measured para-H2CO 321-220/303-202, 422-321/404-303, and 404-303/303-202 ratios. The gas kinetic temperatures derived from the para-H2CO 321-220/303-202 and 422-321/404-303 line ratios are high, ranging from 43 to >300 K with an unweighted average of 91 ± 4 K. Deduced Tkin values from the J = 3-2 and 4-3 transitions are similar. Spatial densities of the gas derived from the para-H2CO 404-303/303-202 line ratios yield 0.6-8.3 × 106 cm-3 with an unweighted average of 1.5 (±0.1) × 106 cm-3. A comparison of kinetic temperatures derived from para-H2CO, NH3, and dust emission indicates that para-H2CO traces a distinctly higher temperature than the NH3 (2, 2)/(1, 1) transitions and the dust, tracing heated gas more directly associated with the star formation process. The H2CO line widths are found to be correlated with bolometric luminosity and increase with the evolutionary stage of the clumps, which suggests that higher luminosities tend to be associated with a more turbulent molecular medium. It seems that the spatial densities measured with H2CO do not vary significantly with the evolutionary stage of the clumps. However, averaged gas kinetic temperatures derived from H2CO increase with time through the evolution of the clumps. The high temperature of the gas traced by H2CO may be mainly caused by radiation from embedded young massive stars and the interaction of outflows with the ambient medium. For Lbol/Mclump ≳ 10 L⊙/M⊙, we find a rough correlation between gas kinetic temperature and this ratio, which is indicative of the evolutionary stage of the individual clumps. The strong relationship between H2CO line luminosities and clump masses is apparently linear during the late evolutionary stages of the clumps, indicating that LH_2CO does reliably trace the mass of warm dense molecular gas. In our massive clumps H2CO line luminosities are approximately linearly correlated with bolometric luminosities over about four orders of magnitude in Lbol, which suggests that the mass of dense molecular gas traced by the H2CO line luminosity is well correlated with star formation. Source and H2CO parameters (Tables A.1-A.7) are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/611/A6

Numerical study of radiometric forces via the direct solution of the Boltzmann kinetic equation

NASA Astrophysics Data System (ADS)

Anikin, Yu. A.

2011-07-01

The two-dimensional rarefied gas motion in a Crookes radiometer and the resulting radiometric forces are studied by numerically solving the Boltzmann kinetic equation. The collision integral is directly evaluated using a projection method, and second-order accurate TVD schemes are used to solve the advection equation. The radiometric forces are found as functions of the Knudsen number and the temperatures, and their spatial distribution is analyzed.

Programmed coherent coupling in a synthetic DNA-based excitonic circuit

NASA Astrophysics Data System (ADS)

Boulais, Étienne; Sawaya, Nicolas P. D.; Veneziano, Rémi; Andreoni, Alessio; Banal, James L.; Kondo, Toru; Mandal, Sarthak; Lin, Su; Schlau-Cohen, Gabriela S.; Woodbury, Neal W.; Yan, Hao; Aspuru-Guzik, Alán; Bathe, Mark

2018-02-01

Natural light-harvesting systems spatially organize densely packed chromophore aggregates using rigid protein scaffolds to achieve highly efficient, directed energy transfer. Here, we report a synthetic strategy using rigid DNA scaffolds to similarly program the spatial organization of densely packed, discrete clusters of cyanine dye aggregates with tunable absorption spectra and strongly coupled exciton dynamics present in natural light-harvesting systems. We first characterize the range of dye-aggregate sizes that can be templated spatially by A-tracts of B-form DNA while retaining coherent energy transfer. We then use structure-based modelling and quantum dynamics to guide the rational design of higher-order synthetic circuits consisting of multiple discrete dye aggregates within a DX-tile. These programmed circuits exhibit excitonic transport properties with prominent circular dichroism, superradiance, and fast delocalized exciton transfer, consistent with our quantum dynamics predictions. This bottom-up strategy offers a versatile approach to the rational design of strongly coupled excitonic circuits using spatially organized dye aggregates for use in coherent nanoscale energy transport, artificial light-harvesting, and nanophotonics.

Role of N-terminal domain and accessory subunits in controlling deactivation-inactivation coupling of Kv4.2 channels.

PubMed

Barghaan, Jan; Tozakidou, Magdalini; Ehmke, Heimo; Bähring, Robert

2008-02-15

We examined the relationship between deactivation and inactivation in Kv4.2 channels. In particular, we were interested in the role of a Kv4.2 N-terminal domain and accessory subunits in controlling macroscopic gating kinetics and asked if the effects of N-terminal deletion and accessory subunit coexpression conform to a kinetic coupling of deactivation and inactivation. We expressed Kv4.2 wild-type channels and N-terminal deletion mutants in the absence and presence of Kv channel interacting proteins (KChIPs) and dipeptidyl aminopeptidase-like proteins (DPPs) in human embryonic kidney 293 cells. Kv4.2-mediated A-type currents at positive and deactivation tail currents at negative membrane potentials were recorded under whole-cell voltage-clamp and analyzed by multi-exponential fitting. The observed changes in Kv4.2 macroscopic inactivation kinetics caused by N-terminal deletion, accessory subunit coexpression, or a combination of the two maneuvers were compared with respective changes in deactivation kinetics. Extensive correlation analyses indicated that modulatory effects on deactivation closely parallel respective effects on inactivation, including both onset and recovery kinetics. Searching for the structural determinants, which control deactivation and inactivation, we found that in a Kv4.2 Delta 2-10 N-terminal deletion mutant both the initial rapid phase of macroscopic inactivation and tail current deactivation were slowed. On the other hand, the intermediate and slow phase of A-type current decay, recovery from inactivation, and tail current decay kinetics were accelerated in Kv4.2 Delta 2-10 by KChIP2 and DPPX. Thus, a Kv4.2 N-terminal domain, which may control both inactivation and deactivation, is not necessary for active modulation of current kinetics by accessory subunits. Our results further suggest distinct mechanisms for Kv4.2 gating modulation by KChIPs and DPPs.

Nuclear-coupled thermal-hydraulic stability analysis of boiling water reactors

NASA Astrophysics Data System (ADS)

Karve, Atul A.

We have studied the nuclear-coupled thermal-hydraulic stability of boiling water reactors (BWRs) using a model we developed from: the space-time modal neutron kinetics equations based on spatial omega-modes, the equations for two-phase flow in parallel boiling channels, the fuel rod heat conduction equations, and a simple model for the recirculation loop. The model is represented as a dynamical system comprised of time-dependent nonlinear ordinary differential equations, and it is studied using stability analysis, modern bifurcation theory, and numerical simulations. We first determine the stability boundary (SB) in the most relevant parameter plane, the inlet-subcooling-number/external-pressure-drop plane, for a fixed control rod induced external reactivity equal to the 100% rod line value and then transform the SB to the practical power-flow map. Using this SB, we show that the normal operating point at 100% power is very stable, stability of points on the 100% rod line decreases as the flow rate is reduced, and that points are least stable in the low-flow/high-power region. We also determine the SB when the modal kinetics is replaced by simple point reactor kinetics and show that the first harmonic mode has no significant effect on the SB. Later we carry out the relevant numerical simulations where we first show that the Hopf bifurcation, that occurs as a parameter is varied across the SB is subcritical, and that, in the important low-flow/high-power region, growing oscillations can result following small finite perturbations of stable steady-states on the 100% rod line. Hence, a point on the 100% rod line in the low-flow/high-power region, although stable, may nevertheless be a point at which a BWR should not be operated. Numerical simulations are then done to calculate the decay ratios (DRs) and frequencies of oscillations for various points on the 100% rod line. It is determined that the NRC requirement of DR < 0.75-0.8 is not rigorously satisfied in the low-flow/high-power region and hence these points should be avoided during normal startup and shutdown operations. The frequency of oscillation is shown to decrease as the flow rate is reduced and the frequency of 0.5Hz observed in the low-flow/high-power region is consistent with those observed during actual instability incidents. Additional numerical simulations show that in the low-flow/high-power region, for the same initial conditions, the use of point kinetics leads to damped oscillations, whereas the model that includes the modal kinetics equations results in growing nonlinear oscillations. Thus, we show that side-by-side out-of-phase growing power oscillations result due to the very important first harmonic mode effect and that the use of point kinetics, which fails to predict these growing oscillations, leads to dramatically nonconservative results. Finally, the effect of a simple recirculation loop model that we develop is studied by carrying out additional stability analyses and additional numerical simulations. It is shown that the loop has a stabilizing effect on certain points on the 100% rod line for time delays equal to integer multiples of the natural period of oscillation, whereas it has a destabilizing effect for half-integer multiples. However, for more practical time delays, it is determined that the overall effect generally is destabilizing.

On the sub-model errors of a generalized one-way coupling scheme for linking models at different scales

NASA Astrophysics Data System (ADS)

Zeng, Jicai; Zha, Yuanyuan; Zhang, Yonggen; Shi, Liangsheng; Zhu, Yan; Yang, Jinzhong

2017-11-01

Multi-scale modeling of the localized groundwater flow problems in a large-scale aquifer has been extensively investigated under the context of cost-benefit controversy. An alternative is to couple the parent and child models with different spatial and temporal scales, which may result in non-trivial sub-model errors in the local areas of interest. Basically, such errors in the child models originate from the deficiency in the coupling methods, as well as from the inadequacy in the spatial and temporal discretizations of the parent and child models. In this study, we investigate the sub-model errors within a generalized one-way coupling scheme given its numerical stability and efficiency, which enables more flexibility in choosing sub-models. To couple the models at different scales, the head solution at parent scale is delivered downward onto the child boundary nodes by means of the spatial and temporal head interpolation approaches. The efficiency of the coupling model is improved either by refining the grid or time step size in the parent and child models, or by carefully locating the sub-model boundary nodes. The temporal truncation errors in the sub-models can be significantly reduced by the adaptive local time-stepping scheme. The generalized one-way coupling scheme is promising to handle the multi-scale groundwater flow problems with complex stresses and heterogeneity.

New Multi-group Transport Neutronics (PHISICS) Capabilities for RELAP5-3D and its Application to Phase I of the OECD/NEA MHTGR-350 MW Benchmark

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

Gerhard Strydom; Cristian Rabiti; Andrea Alfonsi

2012-10-01

PHISICS is a neutronics code system currently under development at the Idaho National Laboratory (INL). Its goal is to provide state of the art simulation capability to reactor designers. The different modules for PHISICS currently under development are a nodal and semi-structured transport core solver (INSTANT), a depletion module (MRTAU) and a cross section interpolation (MIXER) module. The INSTANT module is the most developed of the mentioned above. Basic functionalities are ready to use, but the code is still in continuous development to extend its capabilities. This paper reports on the effort of coupling the nodal kinetics code package PHISICSmore » (INSTANT/MRTAU/MIXER) to the thermal hydraulics system code RELAP5-3D, to enable full core and system modeling. This will enable the possibility to model coupled (thermal-hydraulics and neutronics) problems with more options for 3D neutron kinetics, compared to the existing diffusion theory neutron kinetics module in RELAP5-3D (NESTLE). In the second part of the paper, an overview of the OECD/NEA MHTGR-350 MW benchmark is given. This benchmark has been approved by the OECD, and is based on the General Atomics 350 MW Modular High Temperature Gas Reactor (MHTGR) design. The benchmark includes coupled neutronics thermal hydraulics exercises that require more capabilities than RELAP5-3D with NESTLE offers. Therefore, the MHTGR benchmark makes extensive use of the new PHISICS/RELAP5-3D coupling capabilities. The paper presents the preliminary results of the three steady state exercises specified in Phase I of the benchmark using PHISICS/RELAP5-3D.« less

MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions

NASA Astrophysics Data System (ADS)

Novosad, Philip; Reader, Andrew J.

2016-06-01

Recent advances in dynamic positron emission tomography (PET) reconstruction have demonstrated that it is possible to achieve markedly improved end-point kinetic parameter maps by incorporating a temporal model of the radiotracer directly into the reconstruction algorithm. In this work we have developed a highly constrained, fully dynamic PET reconstruction algorithm incorporating both spectral analysis temporal basis functions and spatial basis functions derived from the kernel method applied to a co-registered T1-weighted magnetic resonance (MR) image. The dynamic PET image is modelled as a linear combination of spatial and temporal basis functions, and a maximum likelihood estimate for the coefficients can be found using the expectation-maximization (EM) algorithm. Following reconstruction, kinetic fitting using any temporal model of interest can be applied. Based on a BrainWeb T1-weighted MR phantom, we performed a realistic dynamic [18F]FDG simulation study with two noise levels, and investigated the quantitative performance of the proposed reconstruction algorithm, comparing it with reconstructions incorporating either spectral analysis temporal basis functions alone or kernel spatial basis functions alone, as well as with conventional frame-independent reconstruction. Compared to the other reconstruction algorithms, the proposed algorithm achieved superior performance, offering a decrease in spatially averaged pixel-level root-mean-square-error on post-reconstruction kinetic parametric maps in the grey/white matter, as well as in the tumours when they were present on the co-registered MR image. When the tumours were not visible in the MR image, reconstruction with the proposed algorithm performed similarly to reconstruction with spectral temporal basis functions and was superior to both conventional frame-independent reconstruction and frame-independent reconstruction with kernel spatial basis functions. Furthermore, we demonstrate that a joint spectral/kernel model can also be used for effective post-reconstruction denoising, through the use of an EM-like image-space algorithm. Finally, we applied the proposed algorithm to reconstruction of real high-resolution dynamic [11C]SCH23390 data, showing promising results.

MR-guided dynamic PET reconstruction with the kernel method and spectral temporal basis functions.

PubMed

Novosad, Philip; Reader, Andrew J

2016-06-21

Recent advances in dynamic positron emission tomography (PET) reconstruction have demonstrated that it is possible to achieve markedly improved end-point kinetic parameter maps by incorporating a temporal model of the radiotracer directly into the reconstruction algorithm. In this work we have developed a highly constrained, fully dynamic PET reconstruction algorithm incorporating both spectral analysis temporal basis functions and spatial basis functions derived from the kernel method applied to a co-registered T1-weighted magnetic resonance (MR) image. The dynamic PET image is modelled as a linear combination of spatial and temporal basis functions, and a maximum likelihood estimate for the coefficients can be found using the expectation-maximization (EM) algorithm. Following reconstruction, kinetic fitting using any temporal model of interest can be applied. Based on a BrainWeb T1-weighted MR phantom, we performed a realistic dynamic [(18)F]FDG simulation study with two noise levels, and investigated the quantitative performance of the proposed reconstruction algorithm, comparing it with reconstructions incorporating either spectral analysis temporal basis functions alone or kernel spatial basis functions alone, as well as with conventional frame-independent reconstruction. Compared to the other reconstruction algorithms, the proposed algorithm achieved superior performance, offering a decrease in spatially averaged pixel-level root-mean-square-error on post-reconstruction kinetic parametric maps in the grey/white matter, as well as in the tumours when they were present on the co-registered MR image. When the tumours were not visible in the MR image, reconstruction with the proposed algorithm performed similarly to reconstruction with spectral temporal basis functions and was superior to both conventional frame-independent reconstruction and frame-independent reconstruction with kernel spatial basis functions. Furthermore, we demonstrate that a joint spectral/kernel model can also be used for effective post-reconstruction denoising, through the use of an EM-like image-space algorithm. Finally, we applied the proposed algorithm to reconstruction of real high-resolution dynamic [(11)C]SCH23390 data, showing promising results.

Spatial Stochastic Intracellular Kinetics: A Review of Modelling Approaches.

PubMed

Smith, Stephen; Grima, Ramon

2018-05-21

Models of chemical kinetics that incorporate both stochasticity and diffusion are an increasingly common tool for studying biology. The variety of competing models is vast, but two stand out by virtue of their popularity: the reaction-diffusion master equation and Brownian dynamics. In this review, we critically address a number of open questions surrounding these models: How can they be justified physically? How do they relate to each other? How do they fit into the wider landscape of chemical models, ranging from the rate equations to molecular dynamics? This review assumes no prior knowledge of modelling chemical kinetics and should be accessible to a wide range of readers.

Integration agent-based models and GIS as a virtual urban dynamic laboratory

NASA Astrophysics Data System (ADS)

Chen, Peng; Liu, Miaolong

2007-06-01

Based on the Agent-based Model and spatial data model, a tight-coupling integrating method of GIS and Agent-based Model (ABM) is to be discussed in this paper. The use of object-orientation for both spatial data and spatial process models facilitates their integration, which can allow exploration and explanation of spatial-temporal phenomena such as urban dynamic. In order to better understand how tight coupling might proceed and to evaluate the possible functional and efficiency gains from such a tight coupling, the agent-based model and spatial data model are discussed, and then the relationships affecting spatial data model and agent-based process models interaction. After that, a realistic crowd flow simulation experiment is presented. Using some tools provided by general GIS systems and a few specific programming languages, a new software system integrating GIS and MAS as a virtual laboratory applicable for simulating pedestrian flows in a crowd activity centre has been developed successfully. Under the environment supported by the software system, as an applicable case, a dynamic evolution process of the pedestrian's flows (dispersed process for the spectators) in a crowds' activity center - The Shanghai Stadium has been simulated successfully. At the end of the paper, some new research problems have been pointed out for the future.

Experiments and Reaction Models of Fundamental Combustion Properties

DTIC Science & Technology

2010-05-31

in liquid hydrocarbon flames Lennard - Jones 12-6 potential parameters were estimated for n-alkanes and 1-alkenes with carbon numbers ranging from 5...hydrocarbons, were studied both experimentally and numerically. The fuel mixtures were chosen in order to gain insight into potential kinetic couplings...initio electronic structure theory, transition state theory, and master equation modelling. The potential energy surface was examined with the coupled

Interfacial reactions between metal and gallium arsenide

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

Lin, J.C.; Schulz, K.J.; Hsieh, K.C.

1989-10-01

The phase formation sequence for GaAs/metal ternary diffusion couples is discussed. The diffusion path concept is introduced and is used with the phase diagram to understand interfacial reactions between GaAs and metal. The correlation between growth kinetics and interface morphology is discussed. Studies of bulk and thin film couples in two systems, GaAs/Pd and GaAs/Pt, are given to illustrate these concepts.

Protein control of true, gated, and coupled electron transfer reactions.

PubMed

Davidson, Victor L

2008-06-01

Electron transfer (ET) through and between proteins is a fundamental biological process. The rates of ET depend upon the thermodynamic driving force, the reorganization energy, and the degree of electronic coupling between the reactant and product states. The analysis of protein ET reactions is complicated by the fact that non-ET processes might influence the observed ET rate in kinetically complex biological systems. This Account describes studies of the methylamine dehydrogenase-amicyanin-cytochrome c-551i protein ET complex that have revealed the influence of several features of the protein structure on the magnitudes of the physical parameters for true ET reactions and how they dictate the kinetic mechanisms of non-ET processes that sometimes influence protein ET reactions. Kinetic and thermodynamic studies, coupled with structural information and biochemical data, are necessary to fully describe the ET reactions of proteins. Site-directed mutagenesis can be used to elucidate specific structure-function relationships. When mutations selectively alter the electronic coupling, reorganization energy, or driving force for the ET reaction, it becomes possible to use the parameters of the ET process to determine how specific amino acid residues and other features of the protein structure influence the ET rates. When mutations alter the kinetic mechanism for ET, one can determine the mechanisms by which non-ET processes, such as protein conformational changes or proton transfers, control the rates of ET reactions and how specific amino acid residues and certain features of the protein structure influence these non-ET reactions. A complete description of the mechanism of regulation of biological ET reactions enhances our understanding of metabolism, respiration, and photosynthesis at the molecular level. Such information has important medical relevance. Defective protein ET leads to production of the reactive oxygen species and free radicals that are associated with aging and many disease states. Defective ET within the respiratory chain also causes certain mitochondrial myopathies. An understanding of the mechanisms of regulation of protein ET is also of practical value because it provides a logical basis for the design of applications utilizing redox enzymes, such as enzyme-based electrode sensors and fuel cells.

A methodology for analysing lateral coupled behavior of high speed railway vehicles and structures

NASA Astrophysics Data System (ADS)

Antolín, P.; Goicolea, J. M.; Astiz, M. A.; Alonso, A.

2010-06-01

Continuous increment of the speed of high speed trains entails the increment of kinetic energy of the trains. The main goal of this article is to study the coupled lateral behavior of vehicle-structure systems for high speed trains. Non linear finite element methods are used for structures whereas multibody dynamics methods are employed for vehicles. Special attention must be paid when dealing with contact rolling constraints for coupling bridge decks and train wheels. The dynamic models must include mixed variables (displacements and creepages). Additionally special attention must be paid to the contact algorithms adequate to wheel-rail contact. The coupled vehicle-structure system is studied in a implicit dynamic framework. Due to the presence of very different systems (trains and bridges), different frequencies are involved in the problem leading to stiff systems. Regarding to contact methods, a main branch is studied in normal contact between train wheels and bridge decks: penalty method. According to tangential contact FastSim algorithm solves the tangential contact at each time step solving a differential equation involving relative displacements and creepage variables. Integration for computing the total forces in the contact ellipse domain is performed for each train wheel and each solver iteration. Coupling between trains and bridges requires a special treatment according to the kinetic constraints imposed in the wheel-rail pair and the load transmission. A numerical example is performed.

Investigation of Iso-octane Ignition and Validation of a Multizone Modeling Method in an Ignition Quality Tester

DOE PAGES

Osecky, Eric M.; Bogin, Gregory E.; Villano, Stephanie M.; ...

2016-08-18

An ignition quality tester was used to characterize the autoignition delay times of iso-octane. The experimental data were characterized between temperatures of 653 and 996 K, pressures of 1.0 and 1.5 MPa, and global equivalence ratios of 0.7 and 1.05. A clear negative temperature coefficient behavior was seen at both pressures in the experimental data. These data were used to characterize the effectiveness of three modeling methods: a single-zone homogeneous batch reactor, a multizone engine model, and a three-dimensional computational fluid dynamics (CFD) model. A detailed 874 species iso-octane ignition mechanism (Mehl, M.; Curran, H. J.; Pitz, W. J.; Westbrook,more » C. K.Chemical kinetic modeling of component mixtures relevant to gasoline. Proceedings of the European Combustion Meeting; Vienna, Austria, April 14-17, 2009) was reduced to 89 species for use in these models, and the predictions of the reduced mechanism were consistent with ignition delay times predicted by the detailed chemical mechanism across a broad range of temperatures, pressures, and equivalence ratios. The CFD model was also run without chemistry to characterize the extent of mixing of fuel and air in the chamber. The calculations predicted that the main part of the combustion chamber was fairly well-mixed at longer times (> ~30 ms), suggesting that the simpler models might be applicable in this quasi-homogeneous region. The multizone predictions, where the combustion chamber was divided into 20 zones of temperature and equivalence ratio, were quite close to the coupled CFD-kinetics results, but the calculation time was ~11 times faster than the coupled CFD-kinetics model. Although the coupled CFD-kinetics model captured the observed negative temperature coefficient behavior and pressure dependence, discrepancies remain between the predictions and the observed ignition time delays, suggesting improvements are still needed in the kinetic mechanism and/or the CFD model. This approach suggests a combined modeling approach, wherein the CFD calculations (without chemistry) can be used to examine the sensitivity of various model inputs to in-cylinder temperature and equivalence ratios. In conclusion, these values can be used as inputs to the multizone model to examine the impact on ignition delay. Additionally, the speed of the multizone model also makes it feasible to quickly test more detailed kinetic mechanisms for comparison to experimental data and sensitivity analysis.« less

Investigation of Iso-octane Ignition and Validation of a Multizone Modeling Method in an Ignition Quality Tester

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

Osecky, Eric M.; Bogin, Gregory E.; Villano, Stephanie M.

An ignition quality tester was used to characterize the autoignition delay times of iso-octane. The experimental data were characterized between temperatures of 653 and 996 K, pressures of 1.0 and 1.5 MPa, and global equivalence ratios of 0.7 and 1.05. A clear negative temperature coefficient behavior was seen at both pressures in the experimental data. These data were used to characterize the effectiveness of three modeling methods: a single-zone homogeneous batch reactor, a multizone engine model, and a three-dimensional computational fluid dynamics (CFD) model. A detailed 874 species iso-octane ignition mechanism (Mehl, M.; Curran, H. J.; Pitz, W. J.; Westbrook,more » C. K.Chemical kinetic modeling of component mixtures relevant to gasoline. Proceedings of the European Combustion Meeting; Vienna, Austria, April 14-17, 2009) was reduced to 89 species for use in these models, and the predictions of the reduced mechanism were consistent with ignition delay times predicted by the detailed chemical mechanism across a broad range of temperatures, pressures, and equivalence ratios. The CFD model was also run without chemistry to characterize the extent of mixing of fuel and air in the chamber. The calculations predicted that the main part of the combustion chamber was fairly well-mixed at longer times (> ~30 ms), suggesting that the simpler models might be applicable in this quasi-homogeneous region. The multizone predictions, where the combustion chamber was divided into 20 zones of temperature and equivalence ratio, were quite close to the coupled CFD-kinetics results, but the calculation time was ~11 times faster than the coupled CFD-kinetics model. Although the coupled CFD-kinetics model captured the observed negative temperature coefficient behavior and pressure dependence, discrepancies remain between the predictions and the observed ignition time delays, suggesting improvements are still needed in the kinetic mechanism and/or the CFD model. This approach suggests a combined modeling approach, wherein the CFD calculations (without chemistry) can be used to examine the sensitivity of various model inputs to in-cylinder temperature and equivalence ratios. In conclusion, these values can be used as inputs to the multizone model to examine the impact on ignition delay. Additionally, the speed of the multizone model also makes it feasible to quickly test more detailed kinetic mechanisms for comparison to experimental data and sensitivity analysis.« less

Using a spatially-distributed hydrologic biogeochemistry model to study the spatial variation of carbon processes in a Critical Zone Observatory

NASA Astrophysics Data System (ADS)

Shi, Y.; Eissenstat, D. M.; Davis, K. J.; He, Y.

2016-12-01

Forest carbon processes are affected by, among other factors, soil moisture, soil temperature, soil nutrients and solar radiation. Most of the current biogeochemical models are 1-D and represent one point in space. Therefore, they cannot resolve the topographically driven hill-slope land surface heterogeneity or the spatial pattern of nutrient availability. A spatially distributed forest ecosystem model, Flux-PIHM-BGC, has been developed by coupling a 1-D mechanistic biogeochemical model Biome-BGC (BBGC) with a spatially distributed land surface hydrologic model, Flux-PIHM. Flux-PIHM is a coupled physically based model, which incorporates a land-surface scheme into the Penn State Integrated Hydrologic Model (PIHM). The land surface scheme is adapted from the Noah land surface model. Flux-PIHM is able to represent the link between groundwater and the surface energy balance, as well as the land surface heterogeneities caused by topography. In the coupled Flux-PIHM-BGC model, each Flux-PIHM model grid couples a 1-D BBGC model, while soil nitrogen is transported among model grids via subsurface water flow. In each grid, Flux-PIHM provides BBGC with soil moisture, soil temperature, and solar radiation information, while BBGC provides Flux-PIHM with leaf area index. The coupled Flux-PIHM-BGC model has been implemented at the Susquehanna/Shale Hills critical zone observatory (SSHCZO). Model results suggest that the vegetation and soil carbon distribution is primarily constrained by nitorgen availability (affected by nitorgen transport via topographically driven subsurface flow), and also constrained by solar radiation and root zone soil moisture. The predicted vegetation and soil carbon distribution generally agrees with the macro pattern observed within the watershed. The coupled ecosystem-hydrologic model provides an important tool to study the impact of topography on watershed carbon processes, as well as the impact of climate change on water resources.

Observed Thermal Impacts of Wind Farms Over Northern Illinois.

PubMed

Slawsky, Lauren M; Zhou, Liming; Baidya Roy, Somnath; Xia, Geng; Vuille, Mathias; Harris, Ronald A

2015-06-25

This paper assesses impacts of three wind farms in northern Illinois using land surface temperature (LST) data from the Moderate Resolution Imaging Spectroradiometer (MODIS) instruments onboard the Terra and Aqua satellites for the period 2003-2013. Changes in LST between two periods (before and after construction of the wind turbines) and between wind farm pixels and nearby non-wind-farm pixels are quantified. An areal mean increase in LST by 0.18-0.39 °C is observed at nighttime over the wind farms, with the geographic distribution of this warming effect generally spatially coupled with the layout of the wind turbines (referred to as the spatial coupling), while there is no apparent impact on daytime LST. The nighttime LST warming effect varies with seasons, with the strongest warming in winter months of December-February, and the tightest spatial coupling in summer months of June-August. Analysis of seasonal variations in wind speed and direction from weather balloon sounding data and Automated Surface Observing System hourly observations from nearby stations suggest stronger winds correspond to seasons with greater warming and larger downwind impacts. The early morning soundings in Illinois are representative of the nighttime boundary layer and exhibit strong temperature inversions across all seasons. The strong and relatively shallow inversion in summer leaves warm air readily available to be mixed down and spatially well coupled with the turbine. Although the warming effect is strongest in winter, the spatial coupling is more erratic and spread out than in summer. These results suggest that the observed warming signal at nighttime is likely due to the net downward transport of heat from warmer air aloft to the surface, caused by the turbulent mixing in the wakes of the spinning turbine rotor blades.

Observed Thermal Impacts of Wind Farms Over Northern Illinois

PubMed Central

Slawsky, Lauren M.; Zhou, Liming; Baidya Roy, Somnath; Xia, Geng; Vuille, Mathias; Harris, Ronald A.

2015-01-01

This paper assesses impacts of three wind farms in northern Illinois using land surface temperature (LST) data from the Moderate Resolution Imaging Spectroradiometer (MODIS) instruments onboard the Terra and Aqua satellites for the period 2003–2013. Changes in LST between two periods (before and after construction of the wind turbines) and between wind farm pixels and nearby non-wind-farm pixels are quantified. An areal mean increase in LST by 0.18–0.39 °C is observed at nighttime over the wind farms, with the geographic distribution of this warming effect generally spatially coupled with the layout of the wind turbines (referred to as the spatial coupling), while there is no apparent impact on daytime LST. The nighttime LST warming effect varies with seasons, with the strongest warming in winter months of December-February, and the tightest spatial coupling in summer months of June-August. Analysis of seasonal variations in wind speed and direction from weather balloon sounding data and Automated Surface Observing System hourly observations from nearby stations suggest stronger winds correspond to seasons with greater warming and larger downwind impacts. The early morning soundings in Illinois are representative of the nighttime boundary layer and exhibit strong temperature inversions across all seasons. The strong and relatively shallow inversion in summer leaves warm air readily available to be mixed down and spatially well coupled with the turbine. Although the warming effect is strongest in winter, the spatial coupling is more erratic and spread out than in summer. These results suggest that the observed warming signal at nighttime is likely due to the net downward transport of heat from warmer air aloft to the surface, caused by the turbulent mixing in the wakes of the spinning turbine rotor blades. PMID:26121613

Anomalous dispersion in correlated porous media: a coupled continuous time random walk approach

NASA Astrophysics Data System (ADS)

Comolli, Alessandro; Dentz, Marco

2017-09-01

We study the causes of anomalous dispersion in Darcy-scale porous media characterized by spatially heterogeneous hydraulic properties. Spatial variability in hydraulic conductivity leads to spatial variability in the flow properties through Darcy's law and thus impacts on solute and particle transport. We consider purely advective transport in heterogeneity scenarios characterized by broad distributions of heterogeneity length scales and point values. Particle transport is characterized in terms of the stochastic properties of equidistantly sampled Lagrangian velocities, which are determined by the flow and conductivity statistics. The persistence length scales of flow and transport velocities are imprinted in the spatial disorder and reflect the distribution of heterogeneity length scales. Particle transitions over the velocity length scales are kinematically coupled with the transition time through velocity. We show that the average particle motion follows a coupled continuous time random walk (CTRW), which is fully parameterized by the distribution of flow velocities and the medium geometry in terms of the heterogeneity length scales. The coupled CTRW provides a systematic framework for the investigation of the origins of anomalous dispersion in terms of heterogeneity correlation and the distribution of conductivity point values. We derive analytical expressions for the asymptotic scaling of the moments of the spatial particle distribution and first arrival time distribution (FATD), and perform numerical particle tracking simulations of the coupled CTRW to capture the full average transport behavior. Broad distributions of heterogeneity point values and lengths scales may lead to very similar dispersion behaviors in terms of the spatial variance. Their mechanisms, however are very different, which manifests in the distributions of particle positions and arrival times, which plays a central role for the prediction of the fate of dissolved substances in heterogeneous natural and engineered porous materials. Contribution to the Topical Issue "Continuous Time Random Walk Still Trendy: Fifty-year History, Current State and Outlook", edited by Ryszard Kutner and Jaume Masoliver.

The monocarboxylate carrier from rat liver mitochondria. Purification and kinetic characterization in a reconstituted system.

PubMed

Capuano, F; Di Paola, M; Azzi, A; Papa, S

1990-02-12

The monocarboxylate (pyruvate) carrier was extracted from rat liver mitochondria with Triton X-100 in the presence of asolectin and partially purified by chromatography on HTP. The HTP eluate reconstituted in liposomes was shown to catalyze active pyruvatein/acetoacetateout and acetoacetatein/pyruvateout counter-exchange. Kinetic characterization of the reconstituted pyruvate carrier was achieved by an original spectrophotometric method consisting of determination of substrate release from proteoliposomes with a coupled enzymatic assay.

Ensemble-Based Parameter Estimation in a Coupled GCM Using the Adaptive Spatial Average Method

DOE PAGES

Liu, Y.; Liu, Z.; Zhang, S.; ...

2014-05-29

Ensemble-based parameter estimation for a climate model is emerging as an important topic in climate research. And for a complex system such as a coupled ocean–atmosphere general circulation model, the sensitivity and response of a model variable to a model parameter could vary spatially and temporally. An adaptive spatial average (ASA) algorithm is proposed to increase the efficiency of parameter estimation. Refined from a previous spatial average method, the ASA uses the ensemble spread as the criterion for selecting “good” values from the spatially varying posterior estimated parameter values; these good values are then averaged to give the final globalmore » uniform posterior parameter. In comparison with existing methods, the ASA parameter estimation has a superior performance: faster convergence and enhanced signal-to-noise ratio.« less

Coupling of kinetic Monte Carlo simulations of surface reactions to transport in a fluid for heterogeneous catalytic reactor modeling.

PubMed

Schaefer, C; Jansen, A P J

2013-02-07

We have developed a method to couple kinetic Monte Carlo simulations of surface reactions at a molecular scale to transport equations at a macroscopic scale. This method is applicable to steady state reactors. We use a finite difference upwinding scheme and a gap-tooth scheme to efficiently use a limited amount of kinetic Monte Carlo simulations. In general the stochastic kinetic Monte Carlo results do not obey mass conservation so that unphysical accumulation of mass could occur in the reactor. We have developed a method to perform mass balance corrections that is based on a stoichiometry matrix and a least-squares problem that is reduced to a non-singular set of linear equations that is applicable to any surface catalyzed reaction. The implementation of these methods is validated by comparing numerical results of a reactor simulation with a unimolecular reaction to an analytical solution. Furthermore, the method is applied to two reaction mechanisms. The first is the ZGB model for CO oxidation in which inevitable poisoning of the catalyst limits the performance of the reactor. The second is a model for the oxidation of NO on a Pt(111) surface, which becomes active due to lateral interaction at high coverages of oxygen. This reaction model is based on ab initio density functional theory calculations from literature.

A Global Modeling Framework for Plasma Kinetics: Development and Applications

NASA Astrophysics Data System (ADS)

Parsey, Guy Morland

The modern study of plasmas, and applications thereof, has developed synchronously with com- puter capabilities since the mid-1950s. Complexities inherent to these charged-particle, many- body, systems have resulted in the development of multiple simulation methods (particle-in-cell, fluid, global modeling, etc.) in order to both explain observed phenomena and predict outcomes of plasma applications. Recognizing that different algorithms are chosen to best address specific topics of interest, this thesis centers around the development of an open-source global model frame- work for the focused study of non-equilibrium plasma kinetics. After verification and validation of the framework, it was used to study two physical phenomena: plasma-assisted combustion and the recently proposed optically-pumped rare gas metastable laser. Global models permeate chemistry and plasma science, relying on spatial averaging to focus attention on the dynamics of reaction networks. Defined by a set of species continuity and energy conservation equations, the required data and constructed systems are conceptually similar across most applications, providing a light platform for exploratory and result-search parameter scan- ning. Unfortunately, it is common practice for custom code to be developed for each application-- an enormous duplication of effort which negatively affects the quality of the software produced. Presented herein, the Python-based Kinetic Global Modeling framework (KGMf) was designed to support all modeling phases: collection and analysis of reaction data, construction of an exportable system of model ODEs, and a platform for interactive evaluation and post-processing analysis. A symbolic ODE system is constructed for interactive manipulation and generation of a Jacobian, both of which are compiled as operation-optimized C-code. Plasma-assisted combustion and ignition (PAC/PAI) embody the modernization of burning fuel by opening up new avenues of control and optimization. With applications ranging from engineefficiency and pollution control to stabilized operation of scramjet technology in hypersonic flows, developing an understanding of the underlying plasma chemistry is of the utmost importance. While the use of equilibrium (thermal) plasmas in the combustion process extends back to the ad- vent of the spark-ignition engine, works from the last few decades have demonstrated fundamental differences between PAC and classical combustion theory. The KGMf is applied to nanosecond- discharge systems in order to analyze the effects of electron energy distribution assumptions on reaction kinetics and highlight the usefulness of 0D modeling in systems defined by coupled and complex physics. With fundamentally different principles involved, the concept of optically-pumped rare gas metastable lasing (RGL) presents a novel opportunity for scalable high-powered lasers by taking advantage of similarities in the electronic structure of elements while traversing the periodic ta- ble. Building from the proven concept of diode-pumped alkali vapor lasers (DPAL), RGL systems demonstrate remarkably similar spectral characteristics without problems associated with heated caustic vapors. First introduced in 2012, numerical studies on the latent kinetics remain immature. This work couples an analytic model developed for DPAL with KGMf plasma chemistry to bet- ter understand the interaction of a non-equilibrium plasma with the induced laser processes and determine if optical pumping could be avoided through careful discharge selection.

Spatio-temporal kinetics of growth hormone receptor signaling in single cells using FRET microscopy.

PubMed

Biener-Ramanujan, Eva; Ramanujan, V Krishnan; Herman, Brian; Gertler, Arieh

2006-08-01

The growth hormone (GH) receptor (R)-mediated JAK2 (Janus kinase-2)-STAT5 (signaling transducer and activator of transcription-5) pathway involves a cascade of protein-protein interactions and tyrosine phosphorylations that occur in a spatially and temporally sensitive manner in cells. To study GHR dimerization or GH-induced conformational change of predimerized GHRs and STAT5 activation kinetics in intact cells, fluorescence resonance energy transfer (FRET) and live-cell imaging methods were employed. FRET measurements at the membrane of HEK-293T cells co-expressing GHRs tagged at the C-terminus with cyan (C) and yellow (Y) fluorescent proteins (FPs) revealed transient GHR dimerization lasting 2-3 min, with a maximum at 3 min after GH stimulation, which was sufficient to induce STAT5 activation. The transient nature of the dimerization or GH-induced conformational change of predimerized GHRs kinetics was not a result of GHR internalization, as neither potassium- nor cholesterol-depletion treatments prolonged the FRET signal. YFP-tagged STAT5 recruitment to the membrane, binding to GHR-CFP, and phosphorylation, occurred within minutes of GH stimulation. Activated STAT5a-YFP did not show nuclear accumulation, despite nuclear pSTAT5 increase, suggesting high turnover of STAT5 nuclear shuttling. Although GHR dimerization and STAT5 activation have been reported previously, this is the first spatially resolved demonstration of GHR-signaling kinetics in intact cells.

CC, CS, and IOS generalized phenomenological cross sections for atom--diatom mixtures

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

Fitz, D.E.; Kouri, D.J.; Evans, D.

1981-05-01

Close coupled expressions for phenomenological cross sections which describe transport properties of atom--diatom mixtures are obtained in the total-J coupling scheme and are related to the bracket integrals of kinetic theory. Coupled states and infinite order sudden expressions for the generalized phenomenological cross sections using initial, final, and average l-labeling are also given. Particular care is taken to use a phase convention for the CS and IOS approximations which is consistent with the Arthurs--Dalgarno formalism and which gives the correct behavior of degeneracy averaged differential cross sections.

Weak and strong coupling equilibration in nonabelian gauge theories

NASA Astrophysics Data System (ADS)

Keegan, Liam; Kurkela, Aleksi; Romatschke, Paul; van der Schee, Wilke; Zhu, Yan

2016-04-01

We present a direct comparison studying equilibration through kinetic theory at weak coupling and through holography at strong coupling in the same set-up. The set-up starts with a homogeneous thermal state, which then smoothly transitions through an out-of-equilibrium phase to an expanding system undergoing boost-invariant flow. This first apples-to-apples comparison of equilibration provides a benchmark for similar equilibration processes in heavy-ion collisions, where the equilibration mechanism is still under debate. We find that results at weak and strong coupling can be smoothly connected by simple, empirical power-laws for the viscosity, equilibration time and entropy production of the system.

Phase transitions in coupled map lattices and in associated probabilistic cellular automata.

PubMed

Just, Wolfram

2006-10-01

Analytical tools are applied to investigate piecewise linear coupled map lattices in terms of probabilistic cellular automata. The so-called disorder condition of probabilistic cellular automata is closely related with attracting sets in coupled map lattices. The importance of this condition for the suppression of phase transitions is illustrated by spatially one-dimensional systems. Invariant densities and temporal correlations are calculated explicitly. Ising type phase transitions are found for one-dimensional coupled map lattices acting on repelling sets and for a spatially two-dimensional Miller-Huse-like system with stable long time dynamics. Critical exponents are calculated within a finite size scaling approach. The relevance of detailed balance of the resulting probabilistic cellular automaton for the critical behavior is pointed out.

Effects of electric field methods on modeling the midlatitude ionospheric electrodynamics and inner magnetosphere dynamics

DOE PAGES

Yu, Yiqun; Jordanova, Vania Koleva; Ridley, Aaron J.; ...

2017-05-10

Here, we report a self-consistent electric field coupling between the midlatitude ionospheric electrodynamics and inner magnetosphere dynamics represented in a kinetic ring current model. This implementation in the model features another self-consistency in addition to its already existing self-consistent magnetic field coupling with plasma. The model is therefore named as Ring current-Atmosphere interaction Model with Self-Consistent magnetic (B) and electric (E) fields, or RAM-SCB-E. With this new model, we explore, by comparing with previously employed empirical Weimer potential, the impact of using self-consistent electric fields on the modeling of storm time global electric potential distribution, plasma sheet particle injection, andmore » the subauroral polarization streams (SAPS) which heavily rely on the coupled interplay between the inner magnetosphere and midlatitude ionosphere. We find the following phenomena in the self-consistent model: (1) The spatially localized enhancement of electric field is produced within 2.5 < L < 4 during geomagnetic active time in the dusk-premidnight sector, with a similar dynamic penetration as found in statistical observations. (2) The electric potential contours show more substantial skewing toward the postmidnight than the Weimer potential, suggesting the resistance on the particles from directly injecting toward the low-L region. (3) The proton flux indeed indicates that the plasma sheet inner boundary at the dusk-premidnight sector is located further away from the Earth than in the Weimer potential, and a “tongue” of low-energy protons extends eastward toward the dawn, leading to the Harang reversal. (4) SAPS are reproduced in the subauroral region, and their magnitude and latitudinal width are in reasonable agreement with data.« less

Effects of electric field methods on modeling the midlatitude ionospheric electrodynamics and inner magnetosphere dynamics

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

Yu, Yiqun; Jordanova, Vania Koleva; Ridley, Aaron J.

Here, we report a self-consistent electric field coupling between the midlatitude ionospheric electrodynamics and inner magnetosphere dynamics represented in a kinetic ring current model. This implementation in the model features another self-consistency in addition to its already existing self-consistent magnetic field coupling with plasma. The model is therefore named as Ring current-Atmosphere interaction Model with Self-Consistent magnetic (B) and electric (E) fields, or RAM-SCB-E. With this new model, we explore, by comparing with previously employed empirical Weimer potential, the impact of using self-consistent electric fields on the modeling of storm time global electric potential distribution, plasma sheet particle injection, andmore » the subauroral polarization streams (SAPS) which heavily rely on the coupled interplay between the inner magnetosphere and midlatitude ionosphere. We find the following phenomena in the self-consistent model: (1) The spatially localized enhancement of electric field is produced within 2.5 < L < 4 during geomagnetic active time in the dusk-premidnight sector, with a similar dynamic penetration as found in statistical observations. (2) The electric potential contours show more substantial skewing toward the postmidnight than the Weimer potential, suggesting the resistance on the particles from directly injecting toward the low-L region. (3) The proton flux indeed indicates that the plasma sheet inner boundary at the dusk-premidnight sector is located further away from the Earth than in the Weimer potential, and a “tongue” of low-energy protons extends eastward toward the dawn, leading to the Harang reversal. (4) SAPS are reproduced in the subauroral region, and their magnitude and latitudinal width are in reasonable agreement with data.« less

Effects of electric field methods on modeling the midlatitude ionospheric electrodynamics and inner magnetosphere dynamics

NASA Astrophysics Data System (ADS)

Yu, Yiqun; Jordanova, Vania K.; Ridley, Aaron J.; Toth, Gabor; Heelis, Roderick

2017-05-01

We report a self-consistent electric field coupling between the midlatitude ionospheric electrodynamics and inner magnetosphere dynamics represented in a kinetic ring current model. This implementation in the model features another self-consistency in addition to its already existing self-consistent magnetic field coupling with plasma. The model is therefore named as Ring current-Atmosphere interaction Model with Self-Consistent magnetic (B) and electric (E) fields, or RAM-SCB-E. With this new model, we explore, by comparing with previously employed empirical Weimer potential, the impact of using self-consistent electric fields on the modeling of storm time global electric potential distribution, plasma sheet particle injection, and the subauroral polarization streams (SAPS) which heavily rely on the coupled interplay between the inner magnetosphere and midlatitude ionosphere. We find the following phenomena in the self-consistent model: (1) The spatially localized enhancement of electric field is produced within 2.5 < L < 4 during geomagnetic active time in the dusk-premidnight sector, with a similar dynamic penetration as found in statistical observations. (2) The electric potential contours show more substantial skewing toward the postmidnight than the Weimer potential, suggesting the resistance on the particles from directly injecting toward the low-L region. (3) The proton flux indeed indicates that the plasma sheet inner boundary at the dusk-premidnight sector is located further away from the Earth than in the Weimer potential, and a "tongue" of low-energy protons extends eastward toward the dawn, leading to the Harang reversal. (4) SAPS are reproduced in the subauroral region, and their magnitude and latitudinal width are in reasonable agreement with data.

Synchrony, waves and ripple in spatially coupled Kuramoto oscillators with Mexican hat connectivity.

PubMed

Heitmann, Stewart; Ermentrout, G Bard

2015-06-01

Spatiotemporal waves of synchronized activity are known to arise in oscillatory neural networks with lateral inhibitory coupling. How such patterns respond to dynamic changes in coupling strength is largely unexplored. The present study uses analysis and simulation to investigate the evolution of wave patterns when the strength of lateral inhibition is varied dynamically. Neural synchronization was modeled by a spatial ring of Kuramoto oscillators with Mexican hat lateral coupling. Broad bands of coexisting stable wave solutions were observed at all levels of inhibition. The stability of these waves was formally analyzed in both the infinite ring and the finite ring. The broad range of multi-stability predicted hysteresis in transitions between neighboring wave solutions when inhibition is slowly varied. Numerical simulation confirmed the predicted transitions when inhibition was ramped down from a high initial value. However, non-wave solutions emerged from the uniform solution when inhibition was ramped upward from zero. These solutions correspond to spatially periodic deviations of phase that we call ripple states. Numerical continuation showed that stable ripple states emerge from synchrony via a supercritical pitchfork bifurcation. The normal form of this bifurcation was derived analytically, and its predictions compared against the numerical results. Ripple states were also found to bifurcate from wave solutions, but these were locally unstable. Simulation also confirmed the existence of hysteresis and ripple states in two spatial dimensions. Our findings show that spatial synchronization patterns can remain structurally stable despite substantial changes in network connectivity.

Constant DI pacing suppresses cardiac alternans formation in numerical cable models

NASA Astrophysics Data System (ADS)

Zlochiver, S.; Johnson, C.; Tolkacheva, E. G.

2017-09-01

Cardiac repolarization alternans describe the sequential alternation of the action potential duration (APD) and can develop during rapid pacing. In the ventricles, such alternans may rapidly turn into life risking arrhythmias under conditions of spatial heterogeneity. Thus, suppression of alternans by artificial pacing protocols, or alternans control, has been the subject of numerous theoretical, numerical, and experimental studies. Yet, previous attempts that were inspired by chaos control theories were successful only for a short spatial extent (<2 cm) from the pacing electrode. Previously, we demonstrated in a single cell model that pacing with a constant diastolic interval (DI) can suppress the formation of alternans at high rates of activation. We attributed this effect to the elimination of feedback between the pacing cycle length and the last APD, effectively preventing restitution-dependent alternans from developing. Here, we extend this idea into cable models to study the extent by which constant DI pacing can control alternans during wave propagation conditions. Constant DI pacing was applied to ventricular cable models of up to 5 cm, using human kinetics. Our results show that constant DI pacing significantly shifts the onset of both cardiac alternans and conduction blocks to higher pacing rates in comparison to pacing with constant cycle length. We also demonstrate that constant DI pacing reduces the propensity of spatially discordant alternans, a precursor of wavebreaks. We finally found that the protective effect of constant DI pacing is stronger for increased electrotonic coupling along the fiber in the sense that the onset of alternans is further shifted to higher activation rates. Overall, these results support the potential clinical applicability of such type of pacing in improving protocols of implanted pacemakers, in order to reduce the risk of life-threatening arrhythmias. Future research should be conducted in order to experimentally validate these promising results.

Slow Proton Transfer Coupled to Unfolding Explains the Puzzling Results of Single-Molecule Experiments on BBL, a Paradigmatic Downhill Folding Protein

PubMed Central

Cerminara, Michele; Campos, Luis A.; Ramanathan, Ravishankar; Muñoz, Victor

2013-01-01

A battery of thermodynamic, kinetic, and structural approaches has indicated that the small α-helical protein BBL folds-unfolds via the one-state downhill scenario. Yet, single-molecule fluorescence spectroscopy offers a more conflicting view. Single-molecule experiments at pH 6 show a unique half-unfolded conformational ensemble at mid denaturation, whereas other experiments performed at higher pH show a bimodal distribution, as expected for two-state folding. Here we use thermodynamic and laser T-jump kinetic experiments combined with theoretical modeling to investigate the pH dependence of BBL stability, folding kinetics and mechanism within the pH 6–11 range. We find that BBL unfolding is tightly coupled to the protonation of one of its residues with an apparent pKa of ∼7. Therefore, in chemical denaturation experiments around neutral pH BBL unfolds gradually, and also converts in binary fashion to the protonated species. Moreover, under the single-molecule experimental conditions (denaturant midpoint and 279 K), we observe that proton transfer is much slower than the ∼15 microseconds folding-unfolding kinetics of BBL. The relaxation kinetics is distinctly biphasic, and the overall relaxation time (i.e. 0.2–0.5 ms) becomes controlled by the proton transfer step. We then show that a simple theoretical model of protein folding coupled to proton transfer explains quantitatively all these results as well as the two sets of single-molecule experiments, including their more puzzling features. Interestingly, this analysis suggests that BBL unfolds following a one-state downhill folding mechanism at all conditions. Accordingly, the source of the bimodal distributions observed during denaturation at pH 7–8 is the splitting of the unique conformational ensemble of BBL onto two slowly inter-converting protonation species. Both, the unprotonated and protonated species unfold gradually (one-state downhill), but they exhibit different degree of unfolding at any given condition because the native structure is less stable for the protonated form. PMID:24205082

Partial Overhaul and Initial Parallel Optimization of KINETICS, a Coupled Dynamics and Chemistry Atmosphere Model

NASA Technical Reports Server (NTRS)

Nguyen, Howard; Willacy, Karen; Allen, Mark

2012-01-01

KINETICS is a coupled dynamics and chemistry atmosphere model that is data intensive and computationally demanding. The potential performance gain from using a supercomputer motivates the adaptation from a serial version to a parallelized one. Although the initial parallelization had been done, bottlenecks caused by an abundance of communication calls between processors led to an unfavorable drop in performance. Before starting on the parallel optimization process, a partial overhaul was required because a large emphasis was placed on streamlining the code for user convenience and revising the program to accommodate the new supercomputers at Caltech and JPL. After the first round of optimizations, the partial runtime was reduced by a factor of 23; however, performance gains are dependent on the size of the data, the number of processors requested, and the computer used.

Phantom energy mediates a long-range repulsive force.

PubMed

Amendola, Luca

2004-10-29

Scalar field models with nonstandard kinetic terms have been proposed in the context of k inflation, of Born-Infeld Lagrangians, of phantom energy and, more in general, of low-energy string theory. In general, scalar fields are expected to couple to matter inducing a new interaction. In this Letter I derive the cosmological perturbation equations and the Yukawa correction to gravity for such general models. I find three interesting results: first, when the field behaves as phantom energy (equation of state less than -1), then the coupling strength is negative, inducing a long-range repulsive force; second, the dark-energy field might cluster on astrophysical scales; third, applying the formalism to a Brans-Dicke theory with a general kinetic term it is shown that its Newtonian effects depend on a single parameter that generalizes the Brans-Dicke constant.

Utilization of rotor kinetic energy storage for hybrid vehicles

DOEpatents

Hsu, John S [Oak Ridge, TN

2011-05-03

A power system for a motor vehicle having an internal combustion engine, the power system comprises an electric machine (12) further comprising a first excitation source (47), a permanent magnet rotor (28) and a magnetic coupling rotor (26) spaced from the permanent magnet rotor and at least one second excitation source (43), the magnetic coupling rotor (26) also including a flywheel having an inertial mass to store kinetic energy during an initial acceleration to an operating speed; and wherein the first excitation source is electrically connected to the second excitation source for power cycling such that the flywheel rotor (26) exerts torque on the permanent magnet rotor (28) to assist braking and acceleration of the permanent magnet rotor (28) and consequently, the vehicle. An axial gap machine and a radial gap machine are disclosed and methods of the invention are also disclosed.

Elementary solutions of coupled model equations in the kinetic theory of gases

NASA Technical Reports Server (NTRS)

Kriese, J. T.; Siewert, C. E.; Chang, T. S.

1974-01-01

The method of elementary solutions is employed to solve two coupled integrodifferential equations sufficient for determining temperature-density effects in a linearized BGK model in the kinetic theory of gases. Full-range completeness and orthogonality theorems are proved for the developed normal modes and the infinite-medium Green's function is constructed as an illustration of the full-range formalism. The appropriate homogeneous matrix Riemann problem is discussed, and half-range completeness and orthogonality theorems are proved for a certain subset of the normal modes. The required existence and uniqueness theorems relevant to the H matrix, basic to the half-range analysis, are proved, and an accurate and efficient computational method is discussed. The half-space temperature-slip problem is solved analytically, and a highly accurate value of the temperature-slip coefficient is reported.

Evanescent field microscopy techniques for studying dynamics at the surface of living cells

NASA Astrophysics Data System (ADS)

Sund, Susan E.

This thesis presents two distinct optical microscopy techniques for applications in cell biophysics: (a)the extension to living cells of an established technique, total internal reflection/fluorescence recovery after photobleaching (TIR/FRAP) for the first time in imaging mode; and (b)the novel development of polarized total internal reflection fluorescence (p- TIRF) to study membrane orientation in living cells. Although reversible chemistry is crucial to dynamical processes in living cells, relatively little is known about the relevant chemical kinetic rates in vivo. TIR/FRAP, an established technique which can measure reversible biomolecular kinetic rates at surfaces, is extended here to measure kinetic parameters of microinjected rhodamine actin at the cytofacial surface of the plasma membrane of living cultured smooth muscle cells. For the first time, spatial imaging (with a CCD camera) is used in conjunction with TIR/FRAP. TIR/FRAP imaging allows production of spatially resolved images of kinetic data, and calculation of correlation distances, cell-wide gradients, and kinetic parameter dependence on initial fluorescence intensity. In living cells, membrane curvature occurs both in easily imaged large scale morphological features, and also in less visualizable submicroscopic regions of activity such as endocytosis, exocytosis, and cell surface ruffling. A fluorescence microscopic method, p-TIRF, is introduced here to visualize such regions. The method is based on fluorescence of the oriented membrane probe diI- C18-(3) (diI) excited by evanescent field light polarized either perpendicular or parallel to the plane of the substrate coverslip. The excitation efficiency from each polarization depends on the membrane orientation, and thus the ratio of the observed fluorescence excited by these two polarizations vividly shows regions of microscopic and submicroscopic curvature of the membrane. A theoretical background of the technique and experimental verifications are presented in samples of protein solutions, model lipid bilayers, and living cells. Sequential digital images of the polarized TIR fluorescence ratios show spatially-resolved time- course maps of membrane orientations on diI labeled macrophages from which low visibility membrane structures can be identified and quantified. The TIR images are sharpened and contrast-enhanced by deconvoluting them with an experimentally-measured point spread function.

Dark matter cosmic string in the gravitational field of a black hole

NASA Astrophysics Data System (ADS)

Nakonieczny, Łukasz; Nakonieczna, Anna; Rogatko, Marek

2018-03-01

We examined analytically and proposed a numerical model of an Abelian Higgs dark matter vortex in the spacetime of a stationary axisymmetric Kerr black hole. In analytical calculations the dark matter sector was modeled by an addition of a U(1)-gauge field coupled to the visible sector. The backreaction analysis revealed that the impact of the dark vortex presence is far more complicated than causing only a deficit angle. The vortex causes an ergosphere shift and the event horizon velocity is also influenced by its presence. These phenomena are more significant than in the case of a visible vortex sector. The area of the event horizon of a black hole is diminished and this decline is larger in comparison to the Kerr black hole with an Abelian Higgs vortex case. After analyzing the gravitational properties for the general setup, we focused on the subset of models that are motivated by particle physics. We retained the Abelian Higgs model as a description of the dark matter sector (this sector contained a heavy dark photon and an additional complex scalar) and added a real scalar representing the real component of the Higgs doublet in the unitary gauge, as well as an additional U(1)-gauge field representing an ordinary electromagnetic field. Moreover, we considered two coupling channels between the visible and dark sectors, which were the kinetic mixing between the gauge fields and a quartic coupling between the scalar fields. After solving the equations of motion for the matter fields numerically we analyzed properties of the cosmic string in the dark matter sector and its influence on the visible sector fields that are directly coupled to it. We found out that the presence of the cosmic string induced spatial variation in the vacuum expectation value of the Higgs field and a nonzero electromagnetic field around the black hole.

Mulliken Hush elucidation of the encounter (precursor) complex in intermolecular electron transfer via self-exchange of tetracyanoethylene anion-radical

NASA Astrophysics Data System (ADS)

Rosokha, S. V.; Newton, M. D.; Head-Gordon, M.; Kochi, J. K.

2006-05-01

The paramagnetic [1:1] encounter complex (TCNE)2-rad is established as the important precursor in the kinetics and mechanism of electron-transfer for the self-exchange between tetracyanoethylene acceptor ( TCNE) and its radical-anion as the donor. Spectroscopic observation of the dimeric complex (TCNE)2-rad by its intervalence absorption band at the solvent-dependent wavelength of λIV ˜ 1500 nm facilitates the application of Mulliken-Hush theory which reveals the significant electronic interaction extant between the pair of cofacial TCNE moieties with the sizable coupling of HDA = 1000 cm -1. The transient existence of such an encounter complex provides the critical link in the electron-transfer kinetics by lowering the classical Marcus reorganization barrier by the amount of HDA in this strongly adiabatic system. Ab initio quantum-mechanical methods as applied to independent theoretical computations of both the reorganization energy ( λ) and the electronic coupling element ( HDA) confirm the essential correctness of the Mulliken-Hush formalism for fast electron transfer via strongly coupled donor/acceptor encounter complexes.

Design and Performance of the Antenna-Coupled Lumped-Element Kinetic Inductance Detector

NASA Astrophysics Data System (ADS)

Barry, P. S.; Doyle, S.; Hornsby, A. L.; Kofman, A.; Mayer, E.; Nadolski, A.; Tang, Q. Y.; Vieira, J.; Shirokoff, E.

2018-05-01

Focal plane arrays consisting of low-noise, polarisation-sensitive detectors have made possible the pioneering advances in the study of the cosmic microwave background (CMB). To make further progress, the next generation of CMB experiments (e.g. CMB-S4) will require a substantial increase in the number of detectors compared to current instruments. Arrays of kinetic inductance detectors (KIDs) provide a possible path to realising such large-format arrays owing to their intrinsic multiplexing advantage and relative cryogenic simplicity. In this paper, we report on the design of a variant of the traditional KID design: the antenna-coupled lumped-element KID. A polarisation-sensitive twin-slot antenna placed behind an optimised hemispherical lens couples power onto a thin-film superconducting microstrip line. The power is then guided into the inductive section of an aluminium KID, where it is absorbed and modifies both the resonant frequency and quality factor of the KID. We present the various aspects of the design and preliminary results from the first set of seven-element prototype arrays and compare to the expected modelled performance.

Evaluation of the Role of G Protein-Coupled Receptor Kinase 3 in Desensitization of Mouse Odorant Receptors in a Mammalian Cell Line and in Olfactory Sensory Neurons

PubMed Central

Kato, Aya; Reisert, Johannes; Ihara, Sayoko; Yoshikawa, Keiichi

2014-01-01

Thousands of odors are sensed and discriminated by G protein-coupled odorant receptors (ORs) expressed in olfactory sensory neurons (OSNs). G protein-coupled receptor kinases (GRKs) may have a role in desensitization of ORs. However, whether ORs are susceptible to agonist-dependent desensitization and whether GRKs affect odorant responsiveness of OSNs are currently unknown. Here we show that GRK3 attenuated the agonist responsiveness of a specific mouse odorant receptor for eugenol (mOR-EG) upon agonist pretreatment in HEK293 cells, but GRK3 did not affect the response amplitude or the recovery kinetics upon repeated agonist stimulation. We performed electrophysiological recordings of single OSNs which expressed mOR-EG and green fluorescent protein (GFP) in the presence or absence of GRK3. The kinetics and amplitude of agonist responsiveness of individual GFP-labeled mOR-EG neurons were not significantly affected by the absence of GRK3. These results indicate that the role of GRK3 in attenuating ORs responsiveness in OSNs may have been overestimated. PMID:25313015

Serpentinization as a reactive transport process: The brucite silicification reaction

NASA Astrophysics Data System (ADS)

Tutolo, B. M.; Luhmann, A. J.; Tosca, N. J.; Seyfried, W. E., Jr.

2017-12-01

Serpentinization plays a fundamental role in the biogeochemical and tectonic evolution of the Earth and perhaps many other rocky planetary bodies. Yet, geochemical models still fail to produce accurate predictions of the various modes of serpentinization, which limits our ability to predict a variety of related geological phenomena over many spatial and temporal scales. Here, we utilize kinetic and reactive transport experiments to parameterize the brucite silicification reaction and provide fundamental constraints on SiO2 transport during serpentinization. We show that, at temperatures characteristic of the sub-seafloor at the serpentinite-hosted Lost City Hydrothermal Field, the assembly of Si tetrahedra onto MgOH2 (i.e., brucite) surfaces is a rate-limiting elementary reaction in the production of serpentine and/or talc from olivine. Moreover, a kinetic rate law extracted from our laboratory experiments shows that this reaction is exponentially dependent on the activity of aqueous silica (aSiO2(aq)), such that its rate is orders of magnitude slower near-equilibrium than it is far-from-equilibrium. Calculations performed with this rate law demonstrate that both brucite and Si are surprisingly persistent in serpentinizing environments, leading to elevated Si concentrations in fluids that can be transported over comparatively large distances without equilibrating with brucite. Moreover, applying this rate law to an open-system reactive transport experiment indicates that advection, preferential flow pathways, and reactive surface area armoring can diminish the net rate of Si uptake resulting from this reaction even further. Because brucite silicification is a fundamentally rate-limiting elementary reaction for the production of both serpentine and talc from forsterite, our new constraints are applicable across the many environments where serpentinization occurs. The unexpected but highly consequential behavior of this simple reaction emphasizes the need for considering serpentinization and many other hydrothermal processes in a reactive transport framework whereby fluid, solute, and heat transport are intimately coupled to kinetically-controlled reactions.

Three-dimensional simulation of beam propagation and heat transfer in static gas Cs DPALs using wave optics and fluid dynamics models

NASA Astrophysics Data System (ADS)

Waichman, Karol; Barmashenko, Boris D.; Rosenwaks, Salman

2017-10-01

Analysis of beam propagation, kinetic and fluid dynamic processes in Cs diode pumped alkali lasers (DPALs), using wave optics model and gasdynamic code, is reported. The analysis is based on a three-dimensional, time-dependent computational fluid dynamics (3D CFD) model. The Navier-Stokes equations for momentum, heat and mass transfer are solved by a commercial Ansys FLUENT solver based on the finite volume discretization technique. The CFD code which solves the gas conservation equations includes effects of natural convection and temperature diffusion of the species in the DPAL mixture. The DPAL kinetic processes in the Cs/He/C2H6 gas mixture dealt with in this paper involve the three lowest energy levels of Cs, (1) 62S1/2, (2) 62P1/2 and (3) 62P3/2. The kinetic processes include absorption due to the 1->3 D2 transition followed by relaxation the 3 to 2 fine structure levels and stimulated emission due to the 2->1 D1 transition. Collisional quenching of levels 2 and 3 and spontaneous emission from these levels are also considered. The gas flow conservation equations are coupled to fast-Fourier-transform algorithm for transverse mode propagation to obtain a solution of the scalar paraxial propagation equation for the laser beam. The wave propagation equation is solved by the split-step beam propagation method where the gain and refractive index in the DPAL medium affect the wave amplitude and phase. Using the CFD and beam propagation models, the gas flow pattern and spatial distributions of the pump and laser intensities in the resonator were calculated for end-pumped Cs DPAL. The laser power, DPAL medium temperature and the laser beam quality were calculated as a function of pump power. The results of the theoretical model for laser power were compared to experimental results of Cs DPAL.

Identifying functional zones of denitrification in heterogeneous aquifer systems by numerical simulations - a case study

NASA Astrophysics Data System (ADS)

Jang, E.; Kalbacher, T.; He, W.; Shao, H.; Schueth, C.; Kolditz, O.

2014-12-01

Nitrate contamination in shallow groundwater is still one of the common problems in many countries. Because of its high solubility and anionic nature, nitrate can easily leach through soil and persist in groundwater for decades. High nitrate concentration has been suggested as a major cause of accelerated eutrophication, methemoglobinemia and gastric cancer. There are several factors influencing the fate of nitrate in groundwater system, which is e.g. distribution of N- sources to soil and groundwater, distribution and amount of reactive substances maintaining denitrification, rate of nitrate degradation and its kinetics, and geological characteristics of the aquifer. Nitrate transport and redox transformation processes are closely linked to complex and spatially distributed physical and chemical interaction, therefore it is difficult to predict and quantify in the field and laboratory experiment. Models can play a key role in elucidation of nitrate reduction pathway in groundwater system and in the design and evaluation of field tests to investigate in situ remediation technologies as well. The goal of the current study is to predict groundwater vulnerability to nitrate, to identify functional zones of denitrification in heterogeneous aquifer systems and to describe the uncertainty of the predictions due to scale effects. For this aim, we developed a kinetic model using multi-component mass transport code OpenGeoSys coupling with IPhreeqc module of the geochemical solver PHREEQC. The developed model included sequential aerobic and nitrate-based respiration, multi-Monod kinetics, multi-species biogeochemical reactions, and geological characteristics of the groundwater aquifer. Moreover water-rock interaction such as secondary mineral precipitation was also included in this model. In this presentation, we focused on the general modelling approach and present the simulation results of nitrate transport simulation in a hypothetical aquifer systems based on data from Hessian Ried, an important groundwater resource for the densely populated Rhine-Main region in Germany.

Geometry Genetics and Evolution

NASA Astrophysics Data System (ADS)

Siggia, Eric

2011-03-01

Darwin argued that highly perfected organs such as the vertebrate eye could evolve by a series of small changes, each of which conferred a selective advantage. In the context of gene networks, this idea can be recast into a predictive algorithm, namely find networks that can be built by incremental adaptation (gradient search) to perform some task. It embodies a ``kinetic'' view of evolution where a solution that is quick to evolve is preferred over a global optimum. Examples of biochemical kinetic networks were evolved for temporal adaptation, temperature compensated entrainable clocks, explore-exploit trade off in signal discrimination, will be presented as well as networks that model the spatially periodic somites (vertebrae) and HOX gene expression in the vertebrate embryo. These models appear complex by the criterion of 19th century applied mathematics since there is no separation of time or spatial scales, yet they are all derivable by gradient optimization of simple functions (several in the Pareto evolution) often based on the Shannon entropy of the time or spatial response. Joint work with P. Francois, Physics Dept. McGill University. With P. Francois, Physics Dept. McGill University

Crystallographic Lattice Boltzmann Method

PubMed Central

Namburi, Manjusha; Krithivasan, Siddharth; Ansumali, Santosh

2016-01-01

Current approaches to Direct Numerical Simulation (DNS) are computationally quite expensive for most realistic scientific and engineering applications of Fluid Dynamics such as automobiles or atmospheric flows. The Lattice Boltzmann Method (LBM), with its simplified kinetic descriptions, has emerged as an important tool for simulating hydrodynamics. In a heterogeneous computing environment, it is often preferred due to its flexibility and better parallel scaling. However, direct simulation of realistic applications, without the use of turbulence models, remains a distant dream even with highly efficient methods such as LBM. In LBM, a fictitious lattice with suitable isotropy in the velocity space is considered to recover Navier-Stokes hydrodynamics in macroscopic limit. The same lattice is mapped onto a cartesian grid for spatial discretization of the kinetic equation. In this paper, we present an inverted argument of the LBM, by making spatial discretization as the central theme. We argue that the optimal spatial discretization for LBM is a Body Centered Cubic (BCC) arrangement of grid points. We illustrate an order-of-magnitude gain in efficiency for LBM and thus a significant progress towards feasibility of DNS for realistic flows. PMID:27251098

Protein Crystallization: Specific Phenomena and General Insights on Crystallization Kinetics

NASA Technical Reports Server (NTRS)

Rosenberger, F.

1998-01-01

Experimental and simulation studies of the nucleation and growth kinetics of proteins have revealed phenomena that are specific for macromolecular crystallization, and others that provide a more detailed understanding of solution crystallization in general. The more specific phenomena, which include metastable liquid-liquid phase separations and gelation prior to solid nucleation, are due to the small ratio of the intermolecular interaction-range to the size of molecules involved. The apparently more generally applicable mechanisms include the cascade-like formation of macrosteps, as an intrinsic morphological instability that roots in the coupled bulk transport and nonlinear interface kinetics in systems with mixed growth rate control. Analyses of this nonlinear response provide (a) criteria for the choice of bulk transport conditions to minimize structural defect formation, and (b) indications that the "slow" protein crystallization kinetics stems from the mutual retardation of growth steps.

Synchronization as Aggregation: Cluster Kinetics of Pulse-Coupled Oscillators.

PubMed

O'Keeffe, Kevin P; Krapivsky, P L; Strogatz, Steven H

2015-08-07

We consider models of identical pulse-coupled oscillators with global interactions. Previous work showed that under certain conditions such systems always end up in sync, but did not quantify how small clusters of synchronized oscillators progressively coalesce into larger ones. Using tools from the study of aggregation phenomena, we obtain exact results for the time-dependent distribution of cluster sizes as the system evolves from disorder to synchrony.

Coupling of exothermic and endothermic hydrogen storage materials

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

Brooks, Kriston P.; Bowden, Mark E.; Karkamkar, Abhijeet J.

2016-08-01

Chemical hydrogen storage (CHS) materials are a high-storage-density alternative to the gaseous compressed hydrogen currently used to provide hydrogen for fuel cell vehicles. One of the challenges of CHS materials is addressing the thermodynamic and kinetic barriers required to break the chemical bonds and release the hydrogen. Coupling CHS reactions that are endothermic and exothermic during the dehydrogenation can improve the system on-board energy efficiency and thermal control, making such materials viable. Acceptable coupling between reactions requires both thermodynamic and kinetics considerations. Models were developed to predict the reaction enthalpy and rate required to achieve high conversions for both reactionsmore » based on experimental measurements. These modeling results show that the efficiency of coupling of an exothermic and endothermic reaction is more sensitive the magnitude of the ratio of the exothermic and endothermic enthalpies than the ratio of the rates of the two steps. The modeling shows further that a slower rate of the endothermic step is desirable to permit sufficient heating of the reactor by the exothermic step. We look at two examples of a sequential and parallel reaction scheme and provide some of the first insight into the required temperature range to maximize the H2 release from 1,2-BN cyclohexane and indoline.« less

Inference of the sparse kinetic Ising model using the decimation method

NASA Astrophysics Data System (ADS)

Decelle, Aurélien; Zhang, Pan

2015-05-01

In this paper we study the inference of the kinetic Ising model on sparse graphs by the decimation method. The decimation method, which was first proposed in Decelle and Ricci-Tersenghi [Phys. Rev. Lett. 112, 070603 (2014), 10.1103/PhysRevLett.112.070603] for the static inverse Ising problem, tries to recover the topology of the inferred system by setting the weakest couplings to zero iteratively. During the decimation process the likelihood function is maximized over the remaining couplings. Unlike the ℓ1-optimization-based methods, the decimation method does not use the Laplace distribution as a heuristic choice of prior to select a sparse solution. In our case, the whole process can be done auto-matically without fixing any parameters by hand. We show that in the dynamical inference problem, where the task is to reconstruct the couplings of an Ising model given the data, the decimation process can be applied naturally into a maximum-likelihood optimization algorithm, as opposed to the static case where pseudolikelihood method needs to be adopted. We also use extensive numerical studies to validate the accuracy of our methods in dynamical inference problems. Our results illustrate that, on various topologies and with different distribution of couplings, the decimation method outperforms the widely used ℓ1-optimization-based methods.

Efficient Coupling of Fluid-Plasma and Monte-Carlo-Neutrals Models for Edge Plasma Transport

NASA Astrophysics Data System (ADS)

Dimits, A. M.; Cohen, B. I.; Friedman, A.; Joseph, I.; Lodestro, L. L.; Rensink, M. E.; Rognlien, T. D.; Sjogreen, B.; Stotler, D. P.; Umansky, M. V.

2017-10-01

UEDGE has been valuable for modeling transport in the tokamak edge and scrape-off layer due in part to its efficient fully implicit solution of coupled fluid neutrals and plasma models. We are developing an implicit coupling of the kinetic Monte-Carlo (MC) code DEGAS-2, as the neutrals model component, to the UEDGE plasma component, based on an extension of the Jacobian-free Newton-Krylov (JFNK) method to MC residuals. The coupling components build on the methods and coding already present in UEDGE. For the linear Krylov iterations, a procedure has been developed to ``extract'' a good preconditioner from that of UEDGE. This preconditioner may also be used to greatly accelerate the convergence rate of a relaxed fixed-point iteration, which may provide a useful ``intermediate'' algorithm. The JFNK method also requires calculation of Jacobian-vector products, for which any finite-difference procedure is inaccurate when a MC component is present. A semi-analytical procedure that retains the standard MC accuracy and fully kinetic neutrals physics is therefore being developed. Prepared for US DOE by LLNL under Contract DE-AC52-07NA27344 and LDRD project 15-ERD-059, by PPPL under Contract DE-AC02-09CH11466, and supported in part by the U.S. DOE, OFES.

Thermalization of oscillator chains with onsite anharmonicity and comparison with kinetic theory

DOE PAGES

Mendl, Christian B.; Lu, Jianfeng; Lukkarinen, Jani

2016-12-02

We perform microscopic molecular dynamics simulations of particle chains with an onsite anharmonicity to study relaxation of spatially homogeneous states to equilibrium, and directly compare the simulations with the corresponding Boltzmann-Peierls kinetic theory. The Wigner function serves as a common interface between the microscopic and kinetic level. We demonstrate quantitative agreement after an initial transient time interval. In particular, besides energy conservation, we observe the additional quasiconservation of the phonon density, defined via an ensemble average of the related microscopic field variables and exactly conserved by the kinetic equations. On superkinetic time scales, density quasiconservation is lost while energy remainsmore » conserved, and we find evidence for eventual relaxation of the density to its canonical ensemble value. Furthermore, the precise mechanism remains unknown and is not captured by the Boltzmann-Peierls equations.« less

Thermalization of oscillator chains with onsite anharmonicity and comparison with kinetic theory

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

Mendl, Christian B.; Lu, Jianfeng; Lukkarinen, Jani

We perform microscopic molecular dynamics simulations of particle chains with an onsite anharmonicity to study relaxation of spatially homogeneous states to equilibrium, and directly compare the simulations with the corresponding Boltzmann-Peierls kinetic theory. The Wigner function serves as a common interface between the microscopic and kinetic level. We demonstrate quantitative agreement after an initial transient time interval. In particular, besides energy conservation, we observe the additional quasiconservation of the phonon density, defined via an ensemble average of the related microscopic field variables and exactly conserved by the kinetic equations. On superkinetic time scales, density quasiconservation is lost while energy remainsmore » conserved, and we find evidence for eventual relaxation of the density to its canonical ensemble value. Furthermore, the precise mechanism remains unknown and is not captured by the Boltzmann-Peierls equations.« less

The Einstein-Vlasov System/Kinetic Theory.

PubMed

Andréasson, Håkan

2005-01-01

The main purpose of this article is to provide a guide to theorems on global properties of solutions to the Einstein-Vlasov system. This system couples Einstein's equations to a kinetic matter model. Kinetic theory has been an important field of research during several decades in which the main focus has been on nonrelativistic and special relativistic physics, i.e. to model the dynamics of neutral gases, plasmas, and Newtonian self-gravitating systems. In 1990, Rendall and Rein initiated a mathematical study of the Einstein-Vlasov system. Since then many theorems on global properties of solutions to this system have been established. The Vlasov equation describes matter phenomenologically, and it should be stressed that most of the theorems presented in this article are not presently known for other such matter models (i.e. fluid models). This paper gives introductions to kinetic theory in non-curved spacetimes and then the Einstein-Vlasov system is introduced. We believe that a good understanding of kinetic theory in non-curved spacetimes is fundamental to good comprehension of kinetic theory in general relativity.

The Einstein-Vlasov System/Kinetic Theory.

PubMed

Andréasson, Håkan

2002-01-01

The main purpose of this article is to provide a guide to theorems on global properties of solutions to the Einstein-Vlasov system. This system couples Einstein's equations to a kinetic matter model. Kinetic theory has been an important field of research during several decades in which the main focus has been on nonrelativistic and special relativistic physics, i.e. to model the dynamics of neutral gases, plasmas, and Newtonian self-gravitating systems. In 1990, Rendall and Rein initiated a mathematical study of the Einstein-Vlasov system. Since then many theorems on global properties of solutions to this system have been established. The Vlasov equation describes matter phenomenologically, and it should be stressed that most of the theorems presented in this article are not presently known for other such matter models (i.e. fluid models). This paper gives introductions to kinetic theory in non-curved spacetimes and then the Einstein-Vlasov system is introduced. We believe that a good understanding of kinetic theory in non-curved spacetimes is fundamental to good comprehension of kinetic theory in general relativity.

Nucleation and Growth Kinetics from LaMer Burst Data.

PubMed

Chu, Daniel B K; Owen, Jonathan S; Peters, Baron

2017-10-12

In LaMer burst nucleation, the individual nucleation events happen en masse, quasi-simultaneously, and at nearly identical homogeneous conditions. These properties make LaMer burst nucleation important for applications that require monodispersed particles and also for theoretical analyses. Sugimoto and co-workers predicted that the number of nuclei generated during a LaMer burst depends only on the solute supply rate and the growth rate, independent of the nucleation kinetics. Some experiments confirm that solute supply kinetics control the number of nuclei, but flaws in the original theoretical analysis raise questions about the predicted roles of growth and nucleation kinetics. We provide a rigorous analysis of the coupled equations that govern concentrations of nuclei and solutes. Our analysis confirms that the number of nuclei is largely determined by the solute supply and growth rates, but our predicted relationship differs from that of Sugimoto et al. Moreover, we find that additional nucleus size dependent corrections should emerge in systems with slow growth kinetics. Finally, we show how the nucleation kinetics determine the particle size distribution. We suggest that measured particle size distributions might therefore provide ways to test theoretical models of homogeneous nucleation kinetics.

Implementation of an online chemical mechanism within a global-regional atmospheric model: design and initial steps

NASA Astrophysics Data System (ADS)

Jorba, O.; Pérez, C.; Baldasano, J. M.

2009-04-01

Chemical processes in air quality modelling systems are usually treated independently from the meteorological models. This approach is computationally attractive since off-line chemical transport simulations only require a single meteorological dataset to produce many chemical simulations. However, this separation of chemistry and meteorology produces a loss of important information about atmospheric processes and does not allow for feedbacks between chemistry and meteorology. To take into account such processes current models are evolving to an online coupling of chemistry and meteorology to produce consistent chemical weather predictions. The Earth Sciences Department of the Barcelona Supercomputing Center (BSC) develops the NMMB/BSC-DUST (Pérez et al., 2008), an online dust model within the global-regional NCEP/NMMB numerical weather prediction model (Janjic and Black, 2007) under development at National Centers for Environmental Prediction (NCEP). Current implementation is based on the well established regional dust model and forecast system DREAM (Nickovic et al., 2001). The most relevant characteristics of NMMB/BSC-DUST are its on-line coupling of the dust scheme with the meteorological driver, the wide range of applications from meso to global scales, and the inclusion of dust radiative effects allowing feedbacks between aerosols and meteorology. In order to complement such development, BSC works also in the implementation of a fully coupled online chemical mechanism within NMMB/BSC-DUST. The final objective is to develop a fully chemical weather prediction system able to resolve gas-aerosol-meteorology interactions from global to local scales. In this contribution we will present the design of the chemistry coupling and the current progress of its implementation. Following the NCEP/NMMB approach, the chemistry part will be coupled through the Earth System Modeling Framework (ESMF) as a pluggable component. The chemical mechanism and chemistry solver is based on the Kinetic PreProcessor KPP (Sandu and Sander, 2006) package with the main purpose to maintain a wide flexibility when configuring the model. Such approach will allow using a simple general chemical mechanism for global applications or a more complex mechanism for regional to local applications at higher resolution. REFERENCES Janjic, Z.I., and Black, T.L., 2007. An ESMF unified model for a broad range of spatial and temporal scales, Geophysical Research Abstracts, 9, 05025. Nickovic, S., Papadopoulos, A., Kakaliagou, O., and Kallos, G., 2001. Model for prediciton of desert dust cycle in the atmosphere. J. Geophys. Res., 106, 18113-18129. Pérez, C., Haustein, K., Janjic, Z.I., Jorba, O., Baldasano, J.M., Black, T.L., and Nickovic, S., 2008. An online dust model within the meso to global NMMB: current progress and plans. AGU Fall Meeting, San Francisco, A41K-03, 2008. Sandu, A., and Sander, R., 2006. Technical note:Simulating chemical systems in Fortran90 and Matlab with the Kinetic PreProcessor KPP-2.1. Atmos. Chem. and Phys., 6, 187-195.

Spectral kinetic energy transfer in turbulent premixed reacting flows.

PubMed

Towery, C A Z; Poludnenko, A Y; Urzay, J; O'Brien, J; Ihme, M; Hamlington, P E

2016-05-01

Spectral kinetic energy transfer by advective processes in turbulent premixed reacting flows is examined using data from a direct numerical simulation of a statistically planar turbulent premixed flame. Two-dimensional turbulence kinetic-energy spectra conditioned on the planar-averaged reactant mass fraction are computed through the flame brush and variations in the spectra are connected to terms in the spectral kinetic energy transport equation. Conditional kinetic energy spectra show that turbulent small-scale motions are suppressed in the burnt combustion products, while the energy content of the mean flow increases. An analysis of spectral kinetic energy transfer further indicates that, contrary to the net down-scale transfer of energy found in the unburnt reactants, advective processes transfer energy from small to large scales in the flame brush close to the products. Triadic interactions calculated through the flame brush show that this net up-scale transfer of energy occurs primarily at spatial scales near the laminar flame thermal width. The present results thus indicate that advective processes in premixed reacting flows contribute to energy backscatter near the scale of the flame.

Kinetic energy budgets in areas of convection

NASA Technical Reports Server (NTRS)

Fuelberg, H. E.

1979-01-01

Synoptic scale budgets of kinetic energy are computed using 3 and 6 h data from three of NASA's Atmospheric Variability Experiments (AVE's). Numerous areas of intense convection occurred during the three experiments. Large kinetic energy variability, with periods as short as 6 h, is observed in budgets computed over each entire experiment area and over limited volumes that barely enclose the convection and move with it. Kinetic energy generation and transport processes in the smaller volumes are often a maximum when the enclosed storms are near peak intensity, but the nature of the various energy processes differs between storm cases and seems closely related to the synoptic conditions. A commonly observed energy budget for peak storm intensity indicates that generation of kinetic energy by cross-contour flow is the major energy source while dissipation to subgrid scales is the major sink. Synoptic scale vertical motion transports kinetic energy from lower to upper levels of the atmosphere while low-level horizontal flux convergence and upper-level horizontal divergence also occur. Spatial fields of the energy budget terms show that the storm environment is a major center of energy activity for the entire area.

Combustion and Magnetohydrodynamic Processes in Advanced Pulse Detonation Rocket Engines

NASA Astrophysics Data System (ADS)

Cole, Lord Kahil

A number of promising alternative rocket propulsion concepts have been developed over the past two decades that take advantage of unsteady combustion waves in order to produce thrust. These concepts include the Pulse Detonation Rocket Engine (PDRE), in which repetitive ignition, propagation, and reflection of detonations and shocks can create a high pressure chamber from which gases may be exhausted in a controlled manner. The Pulse Detonation Rocket Induced Magnetohydrodynamic Ejector (PDRIME) is a modification of the basic PDRE concept, developed by Cambier (1998), which has the potential for performance improvements based on magnetohydrodynamic (MHD) thrust augmentation. The PDRIME has the advantage of both low combustion chamber seeding pressure, per the PDRE concept, and efficient energy distribution in the system, per the rocket-induced MHD ejector (RIME) concept of Cole, et al. (1995). In the initial part of this thesis, we explore flow and performance characteristics of different configurations of the PDRIME, assuming quasi-one-dimensional transient flow and global representations of the effects of MHD phenomena on the gas dynamics. By utilizing high-order accurate solvers, we thus are able to investigate the fundamental physical processes associated with the PDRIME and PDRE concepts and identify potentially promising operating regimes. In the second part of this investigation, the detailed coupling of detonations and electric and magnetic fields are explored. First, a one-dimensional spark-ignited detonation with complex reaction kinetics is fully evaluated and the mechanisms for the different instabilities are analyzed. It is found that complex kinetics in addition to sufficient spatial resolution are required to be able to quantify high frequency as well as low frequency detonation instability modes. Armed with this quantitative understanding, we then examine the interaction of a propagating detonation and the applied MHD, both in one-dimensional and two-dimensional transient simulations. The dynamics of the detonation are found to be affected by the application of magnetic and electric fields. We find that the regularity of one-dimensional cesium-seeded detonations can be significantly altered by reasonable applied magnetic fields (Bz ≤ 8T), but that it takes a stronger applied field (Bz > 16T) to significantly alter the cellular structure and detonation velocity of a two-dimensional detonation in the time in which these phenomena were observed. This observation is likely attributed to the additional coupling of the two-dimensional detonation with the transverse waves, which are not captured in the one-dimensional simulations. Future studies involving full ionization kinetics including collisional-radiative processes, will be used to examine these processes in further detail.

Magnetospheric discontinuities and interfaces as roots of discrete auroral arcs: modeling and comparison with in-situ data

NASA Astrophysics Data System (ADS)

Echim, M.; Maggiolo, R.; de Keyser, J. M.; Roth, M. A.

2009-12-01

We discuss the quasi-stationary coupling between magnetospheric sharp plasma interfaces and discrete auroral arcs. The magnetospheric generator is described by a Vlasov equilibrium similar to the kinetic models of tangential discontinuities. It provides the self-consistent profile of the magnetospheric convergent electric field, Φm. A kinetic current-voltage relationship gives the field-aligned current density flowing into and out of the ionosphere as a function of the potential difference between the magnetospheric generator and the ionospheric load. The electric potential in the ionosphere, Φi, is computed from the current continuity equation taking into account the variation of the Pedersen conductance, ΣP, with the energy flux of the precipitating magnetospheric electrons (ɛem). We discuss results obtained for the interface between the Plasma Sheet Boundary Layer (PSBL) and the lobes and respectively for the inner edge of the Low Latitude Boundary Layer (LLBL). This type of interfaces provides a field-aligned potential drop, ΔΦ=Φi-Φm, of the order of several kilovolts and field-aligned current densities, j||, of the order of tens of μA/m2 . The precipitating particles are confined in thin regions whose thickness is of the order of several kilometers at 200 km altitude. We show that visible auroral arcs form when the velocity shear across the generator magnetospheric plasma interface is above a threshold depending also on the kinetic properties of the generator. Brighter arcs forms for larger velocity shear in the magnetospheric generator. The field-aligned potential drop tends to decrease when the density gradient across the interface increases. Conjugated observations on April 28, 2001 by Cluster and DMSP-F14 give us the opportunity to validate the model with data gathered simultaneously below and above the acceleration region. The magnetospheric module of the coupling model provides a good estimation of the plasma parameters measured by Cluster across the magnetospheric interface: the electric potential, the plasma density and the parallel flux of downgoing electrons and upgoing Oxygen ions. The results of the ionospheric module of the model are in good agreement with the DMSP-F14 measurements of the field-aligned current density, the flux of precipitating energy and the accelerating field-aligned potential drop. A synthetic electron energy spectrum derived from the computed field-aligned potential drop retrieves the spatial scale and spectral width of the inverted-V event observed by DMSP-F14.

An observationally-driven kinetic approach to coronal heating

NASA Astrophysics Data System (ADS)

Moraitis, K.; Toutountzi, A.; Isliker, H.; Georgoulis, M.; Vlahos, L.; Chintzoglou, G.

2016-11-01

Aims: Coronal heating through the explosive release of magnetic energy remains an open problem in solar physics. Recent hydrodynamical models attempt an investigation by placing swarms of "nanoflares" at random sites and times in modeled one-dimensional coronal loops. We investigate the problem in three dimensions, using extrapolated coronal magnetic fields of observed solar active regions. Methods: We applied a nonlinear force-free field extrapolation above an observed photospheric magnetogram of NOAA active region (AR) 11 158. We then determined the locations, energy contents, and volumes of "unstable" areas, namely areas prone to releasing magnetic energy due to locally accumulated electric current density. Statistical distributions of these volumes and their fractal dimension are inferred, investigating also their dependence on spatial resolution. Further adopting a simple resistivity model, we inferred the properties of the fractally distributed electric fields in these volumes. Next, we monitored the evolution of 105 particles (electrons and ions) obeying an initial Maxwellian distribution with a temperature of 10 eV, by following their trajectories and energization when subjected to the resulting electric fields. For computational convenience, the length element of the magnetic-field extrapolation is 1 arcsec, or 725 km, much coarser than the particles' collisional mean free path in the low corona (0.1-1 km). Results: The presence of collisions traps the bulk of the plasma around the unstable volumes, or current sheets (UCS), with only a tail of the distribution gaining substantial energy. Assuming that the distance between UCS is similar to the collisional mean free path we find that the low active-region corona is heated to 100-200 eV, corresponding to temperatures exceeding 2 MK, within tens of seconds for electrons and thousands of seconds for ions. Conclusions: Fractally distributed, nanoflare-triggening fragmented UCS in the active-region corona can heat electrons and ions with minor enhancements of the local resistivity. This statistical result is independent from the nature of the extrapolation and the spatial resolution of the modeled active-region corona. This finding should be coupled with a complete plasma treatment to determine whether a quasi-steady temperature similar to that of the ambient corona can be maintained, either via a kinetic or via a hybrid, kinetic and fluid, plasma treatment. The finding can also be extended to the quiet solar corona, provided that the currently undetected nanoflares are frequent enough to account for the lower (compared to active regions) energy losses in this case.

Kinetic energy and scalar spectra in high Rayleigh number axially homogeneous buoyancy driven turbulence

NASA Astrophysics Data System (ADS)

Pawar, Shashikant S.; Arakeri, Jaywant H.

2016-06-01

Kinetic energy and scalar spectra from the measurements in high Rayleigh number axially homogeneous buoyancy driven turbulent flow are presented. Kinetic energy and concentration (scalar) spectra are obtained from the experiments wherein density difference is created using brine and fresh water and temperature spectra are obtained from the experiments in which heat is used. Scaling of the frequency spectra of lateral and longitudinal velocity near the tube axis is closer to the Kolmogorov-Obukhov scaling, while the scalar spectra show some evidence of dual scaling, Bolgiano-Obukhov scaling followed by Obukhov-Corrsin scaling. These scalings are also observed in the corresponding second order spatial structure functions of velocity and concentration fluctuations.

Interpretation of ES, CS, and IOS approximations within a translational--internal coupling scheme. IV. ES and IOS molecule--molecule cross sections

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

Snider, R.F.; Parvatiyar, M.G.

1981-05-15

Properties of energy sudden and infinite order sudden translational--internal reduced S matrices are given for general molecule--molecule collisions. Formal similarities with the distorted wave Born approximation are discussed. Structural simplifications of energy dependent and kinetic cross sections associated with making the ES approximation are described. Conceptual difficulties associated with applying the ES and IOS approximations to kinetic processes dominated by energetically inelastic collisions are pointed out.

Convective cell generation by kinetic Alfven wave turbulence in the auroral ionosphere

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

Zhao, J. S.; Wu, D. J.; Yu, M. Y.

2012-06-15

Modulation of convective cells by kinetic Alfven wave (KAW) turbulence is investigated. The interaction is governed by a nonlinear dispersion relation for the convective cells. It is shown that KAW turbulence is disrupted by excitation of the large-scale convective motion through a resonant instability. Application of the results to the auroral ionosphere shows that cross-scale coupling of the KAW turbulence and convective cells plays an important role in the evolution of ionospheric plasma turbulence.

Final Technical Report: Mathematical Foundations for Uncertainty Quantification in Materials Design

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

Plechac, Petr; Vlachos, Dionisios G.

We developed path-wise information theory-based and goal-oriented sensitivity analysis and parameter identification methods for complex high-dimensional dynamics and in particular of non-equilibrium extended molecular systems. The combination of these novel methodologies provided the first methods in the literature which are capable to handle UQ questions for stochastic complex systems with some or all of the following features: (a) multi-scale stochastic models such as (bio)chemical reaction networks, with a very large number of parameters, (b) spatially distributed systems such as Kinetic Monte Carlo or Langevin Dynamics, (c) non-equilibrium processes typically associated with coupled physico-chemical mechanisms, driven boundary conditions, hybrid micro-macro systems,more » etc. A particular computational challenge arises in simulations of multi-scale reaction networks and molecular systems. Mathematical techniques were applied to in silico prediction of novel materials with emphasis on the effect of microstructure on model uncertainty quantification (UQ). We outline acceleration methods to make calculations of real chemistry feasible followed by two complementary tasks on structure optimization and microstructure-induced UQ.« less

Dynamical inversion of the energy landscape promotes non-equilibrium self-assembly of binary mixtures

DOE PAGES

Pestana, Luis Ruiz; Minnetian, Natalie; Lammers, Laura Nielsen; ...

2018-01-02

When driven out of equilibrium, many diverse systems can form complex spatial and dynamical patterns, even in the absence of attractive interactions. Using kinetic Monte Carlo simulations, we investigate the phase behavior of a binary system of particles of dissimilar size confined between semiflexible planar surfaces, in which the nanoconfinement introduces a non-local coupling between particles, which we model as an activation energy barrier to diffusion that decreases with the local fraction of the larger particle. The system autonomously reaches a cyclical non-equilibrium state characterized by the formation and dissolution of metastable micelle-like clusters with the small particles in themore » core and the large ones in the surrounding corona. The power spectrum of the fluctuations in the aggregation number exhibits 1/f noise reminiscent of self-organized critical systems. Finally, we suggest that the dynamical metastability of the micellar structures arises from an inversion of the energy landscape, in which the relaxation dynamics of one of the species induces a metastable phase for the other species.« less

Dynamical inversion of the energy landscape promotes non-equilibrium self-assembly of binary mixtures

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

Pestana, Luis Ruiz; Minnetian, Natalie; Lammers, Laura Nielsen

When driven out of equilibrium, many diverse systems can form complex spatial and dynamical patterns, even in the absence of attractive interactions. Using kinetic Monte Carlo simulations, we investigate the phase behavior of a binary system of particles of dissimilar size confined between semiflexible planar surfaces, in which the nanoconfinement introduces a non-local coupling between particles, which we model as an activation energy barrier to diffusion that decreases with the local fraction of the larger particle. The system autonomously reaches a cyclical non-equilibrium state characterized by the formation and dissolution of metastable micelle-like clusters with the small particles in themore » core and the large ones in the surrounding corona. The power spectrum of the fluctuations in the aggregation number exhibits 1/f noise reminiscent of self-organized critical systems. Finally, we suggest that the dynamical metastability of the micellar structures arises from an inversion of the energy landscape, in which the relaxation dynamics of one of the species induces a metastable phase for the other species.« less

Formation and dynamics of plasma bullets in a non-thermal plasma jet: influence of the high-voltage parameters on the plume characteristics

NASA Astrophysics Data System (ADS)

Jarrige, Julien; Laroussi, Mounir; Karakas, Erdinc

2010-12-01

Non-thermal plasma jets in open air are composed of ionization waves commonly known as 'plasma bullets' propagating at high velocities. We present in this paper an experimental study of plasma bullets produced in a dielectric barrier discharge linear-field reactor fed with helium and driven by microsecond high-voltage pulses. Two discharges were produced between electrodes for every pulse (at the rising and falling edge), but only one bullet was generated. Fast intensified charge coupled device camera imaging showed that bullet velocity and diameter increase with applied voltage. Spatially resolved optical emission spectroscopy measurements provided evidence of the hollow structure of the jet and its contraction. It was shown that the pulse amplitude significantly enhances electron energy and production of active species. The plasma bullet appeared to behave like a surface discharge in the tube, and like a positive streamer in air. A kinetics mechanism based on electron impact, Penning effect and charge transfer reactions is proposed to explain the propagation of the ionization front and temporal behavior of the radiative species.

Scaling Properties of Arctic Sea Ice Deformation in a High‐Resolution Viscous‐Plastic Sea Ice Model and in Satellite Observations

PubMed Central

Losch, Martin; Menemenlis, Dimitris

2018-01-01

Abstract Sea ice models with the traditional viscous‐plastic (VP) rheology and very small horizontal grid spacing can resolve leads and deformation rates localized along Linear Kinematic Features (LKF). In a 1 km pan‐Arctic sea ice‐ocean simulation, the small‐scale sea ice deformations are evaluated with a scaling analysis in relation to satellite observations of the Envisat Geophysical Processor System (EGPS) in the Central Arctic. A new coupled scaling analysis for data on Eulerian grids is used to determine the spatial and temporal scaling and the coupling between temporal and spatial scales. The spatial scaling of the modeled sea ice deformation implies multifractality. It is also coupled to temporal scales and varies realistically by region and season. The agreement of the spatial scaling with satellite observations challenges previous results with VP models at coarser resolution, which did not reproduce the observed scaling. The temporal scaling analysis shows that the VP model, as configured in this 1 km simulation, does not fully resolve the intermittency of sea ice deformation that is observed in satellite data. PMID:29576996

Scaling Properties of Arctic Sea Ice Deformation in a High-Resolution Viscous-Plastic Sea Ice Model and in Satellite Observations

NASA Astrophysics Data System (ADS)

Hutter, Nils; Losch, Martin; Menemenlis, Dimitris

2018-01-01

Sea ice models with the traditional viscous-plastic (VP) rheology and very small horizontal grid spacing can resolve leads and deformation rates localized along Linear Kinematic Features (LKF). In a 1 km pan-Arctic sea ice-ocean simulation, the small-scale sea ice deformations are evaluated with a scaling analysis in relation to satellite observations of the Envisat Geophysical Processor System (EGPS) in the Central Arctic. A new coupled scaling analysis for data on Eulerian grids is used to determine the spatial and temporal scaling and the coupling between temporal and spatial scales. The spatial scaling of the modeled sea ice deformation implies multifractality. It is also coupled to temporal scales and varies realistically by region and season. The agreement of the spatial scaling with satellite observations challenges previous results with VP models at coarser resolution, which did not reproduce the observed scaling. The temporal scaling analysis shows that the VP model, as configured in this 1 km simulation, does not fully resolve the intermittency of sea ice deformation that is observed in satellite data.

Scaling Properties of Arctic Sea Ice Deformation in a High-Resolution Viscous-Plastic Sea Ice Model and in Satellite Observations.

PubMed

Hutter, Nils; Losch, Martin; Menemenlis, Dimitris

2018-01-01

Sea ice models with the traditional viscous-plastic (VP) rheology and very small horizontal grid spacing can resolve leads and deformation rates localized along Linear Kinematic Features (LKF). In a 1 km pan-Arctic sea ice-ocean simulation, the small-scale sea ice deformations are evaluated with a scaling analysis in relation to satellite observations of the Envisat Geophysical Processor System (EGPS) in the Central Arctic. A new coupled scaling analysis for data on Eulerian grids is used to determine the spatial and temporal scaling and the coupling between temporal and spatial scales. The spatial scaling of the modeled sea ice deformation implies multifractality. It is also coupled to temporal scales and varies realistically by region and season. The agreement of the spatial scaling with satellite observations challenges previous results with VP models at coarser resolution, which did not reproduce the observed scaling. The temporal scaling analysis shows that the VP model, as configured in this 1 km simulation, does not fully resolve the intermittency of sea ice deformation that is observed in satellite data.

Phase coupling and synchrony in the spatiotemporal dynamics of muskrat and mink populations across Canada

PubMed Central

Haydon, D. T.; Stenseth, N. C.; Boyce, M. S.; Greenwood, P. E.

2001-01-01

Population ecologists have traditionally focused on the patterns and causes of population variation in the temporal domain for which a substantial body of practical analytic techniques have been developed. More recently, numerous studies have documented how populations may fluctuate synchronously over large spatial areas; analyses of such spatially extended time-series have started to provide additional clues regarding the causes of these population fluctuations and explanations for their synchronous occurrence. Here, we report on the development of a phase-based method for identifying coupling between temporally coincident but spatially distributed cyclic time-series, which we apply to the numbers of muskrat and mink recorded at 81 locations across Canada. The analysis reveals remarkable parallel clines in the strength of coupling between proximate populations of both species—declining from west to east—together with a corresponding increase in observed synchrony between these populations the further east they are located. PMID:11606729

Nuclear spatial delocalization silences electron density oscillations in 2-phenyl-ethyl-amine (PEA) and 2-phenylethyl-N,N-dimethylamine (PENNA) cations

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

Jenkins, Andrew J.; Vacher, Morgane; Bearpark, Michael J.

2016-03-14

We simulate electron dynamics following ionization in 2-phenyl-ethyl-amine and 2-phenylethyl-N,N-dimethylamine as examples of systems where 3 coupled cationic states are involved. We study two nuclear effects on electron dynamics: (i) coupled electron-nuclear motion and (ii) nuclear spatial delocalization as a result of the zero-point energy in the neutral molecule. Within the Ehrenfest approximation, our calculations show that the coherent electron dynamics in these molecules is not lost as a result of coupled electron-nuclear motion. In contrast, as a result of nuclear spatial delocalization, dephasing of the oscillations occurs on a time scale of only a few fs, long before anymore » significant nuclear motion can occur. The results have been rationalized using a semi-quantitative model based upon the gradients of the potential energy surfaces.« less

Kinetic Simulations of Type II Radio Burst Emission Processes

NASA Astrophysics Data System (ADS)

Ganse, U.; Spanier, F. A.; Vainio, R. O.

2011-12-01

The fundamental emission process of Type II Radio Bursts has been under discussion for many decades. While analytic deliberations point to three wave interaction as the source for fundamental and harmonic radio emissions, sparse in-situ observational data and high computational demands for kinetic simulations have not allowed for a definite conclusion to be reached. A popular model puts the radio emission into the foreshock region of a coronal mass ejection's shock front, where shock drift acceleration can create eletrcon beam populations in the otherwise quiescent foreshock plasma. Beam-driven instabilities are then assumed to create waves, forming the starting point of three wave interaction processes. Using our kinetic particle-in-cell code, we have studied a number of emission scenarios based on electron beam populations in a CME foreshock, with focus on wave-interaction microphysics on kinetic scales. The self-consistent, fully kinetic simulations with completely physical mass-ratio show fundamental and harmonic emission of transverse electromagnetic waves and allow for detailled statistical analysis of all contributing wavemodes and their couplings.

A general theory of kinetics and thermodynamics of steady-state copolymerization.

PubMed

Shu, Yao-Gen; Song, Yong-Shun; Ou-Yang, Zhong-Can; Li, Ming

2015-06-17

Kinetics of steady-state copolymerization has been investigated since the 1940s. Irreversible terminal and penultimate models were successfully applied to a number of comonomer systems, but failed for systems where depropagation is significant. Although a general mathematical treatment of the terminal model with depropagation was established in the 1980s, a penultimate model and higher-order terminal models with depropagation have not been systematically studied, since depropagation leads to hierarchically-coupled and unclosed kinetic equations which are hard to solve analytically. In this work, we propose a truncation method to solve the steady-state kinetic equations of any-order terminal models with depropagation in a unified way, by reducing them into closed steady-state equations which give the exact solution of the original kinetic equations. Based on the steady-state equations, we also derive a general thermodynamic equality in which the Shannon entropy of the copolymer sequence is explicitly introduced as part of the free energy dissipation of the whole copolymerization system.

Simulation of the effects of sub-breakdown electric fields on the chemical kinetics in nonpremixed counterflow methane/air flames

NASA Astrophysics Data System (ADS)

Belhi, Memdouh; Im, Hong; Computational Reacting Flows Laboratory, Clean Combustion Research Center Team

2017-11-01

The effects of an electric field on the combustion kinetics in nonpremixed counterflow methane/air flames were investigated via one-dimensional numerical simulations. A classical fluid model coupling Poison's equation with transport equations for combustion species and electric field-induced particles was used. A methane-air reaction mechanism accounting for the natural ionization in flames was combined with a set of reactions that describe the formation of active particles induced by the electric field. Kinetic parameters for electron-impact reactions and transport coefficients of electrons were modeled as functions of reduced electric field via solutions to the Boltzmann kinetic equation using the BOLSIG code. Mobility of ions was computed based on the (n,6,4) and coulomb interaction potentials, while the diffusion coefficient was approximated from the mobility using Einstein relation. Contributions of electron dissociation, excitation and ionization processes were characterized quantitatively. An analysis to identify the plasma regime where the electric field can alter the combustion kinetic was proposed.

An induction reactor for studying crude-oil oxidation relevant to in situ combustion.

PubMed

Bazargan, Mohammad; Lapene, Alexandre; Chen, Bo; Castanier, Louis M; Kovscek, Anthony R

2013-07-01

In a conventional ramped temperature oxidation kinetics cell experiment, an electrical furnace is used to ramp temperature at a prescribed rate. Thus, the heating rate of a kinetics cell experiment is limited by furnace performance to heating rates of about 0.5-3 °C/min. A new reactor has been designed to overcome this limit. It uses an induction heating method to ramp temperature. Induction heating is fast and easily controlled. The new reactor covers heating rates from 1 to 30 °C/min. This is the first time that the oxidation profiles of a crude oil are available over such a wide range of heating rate. The results from an induction reactor and a conventional kinetics cell at roughly 2 °C/min are compared to illustrate consistency between the two reactors. The results at low heating rate are the same as the conventional kinetics cell. As presented in the paper, the new reactor couples well with the isoconversional method for interpretation of reaction kinetics.

Diffusion of point defects in crystalline silicon using the kinetic activation-relaxation technique method

DOE PAGES

Trochet, Mickaël; Béland, Laurent Karim; Joly, Jean -François; ...

2015-06-16

We study point-defect diffusion in crystalline silicon using the kinetic activation-relaxation technique (k-ART), an off-lattice kinetic Monte Carlo method with on-the-fly catalog building capabilities based on the activation-relaxation technique (ART nouveau), coupled to the standard Stillinger-Weber potential. We focus more particularly on the evolution of crystalline cells with one to four vacancies and one to four interstitials in order to provide a detailed picture of both the atomistic diffusion mechanisms and overall kinetics. We show formation energies, activation barriers for the ground state of all eight systems, and migration barriers for those systems that diffuse. Additionally, we characterize diffusion pathsmore » and special configurations such as dumbbell complex, di-interstitial (IV-pair+2I) superdiffuser, tetrahedral vacancy complex, and more. In conclusion, this study points to an unsuspected dynamical richness even for this apparently simple system that can only be uncovered by exhaustive and systematic approaches such as the kinetic activation-relaxation technique.« less

Kinetics of Cation and Oxyanion Adsorption and Desorption on Ferrihydrite: Roles of Ferrihydrite Binding Sites and a Unified Model.

PubMed

Tian, Lei; Shi, Zhenqing; Lu, Yang; Dohnalkova, Alice C; Lin, Zhang; Dang, Zhi

2017-09-19

Quantitative understanding the kinetics of toxic ion reactions with various heterogeneous ferrihydrite binding sites is crucial for accurately predicting the dynamic behavior of contaminants in environment. In this study, kinetics of As(V), Cr(VI), Cu(II), and Pb(II) adsorption and desorption on ferrihydrite was studied using a stirred-flow method, which showed that metal adsorption/desorption kinetics was highly dependent on the reaction conditions and varied significantly among four metals. High resolution scanning transmission electron microscopy coupled with energy-dispersive X-ray spectroscopy showed that all four metals were distributed within the ferrihydrite aggregates homogeneously after adsorption reactions. Based on the equilibrium model CD-MUSIC, we developed a novel unified kinetics model applicable for both cation and oxyanion adsorption and desorption on ferrihydrite, which is able to account for the heterogeneity of ferrihydrite binding sites, different binding properties of cations and oxyanions, and variations of solution chemistry. The model described the kinetic results well. We quantitatively elucidated how the equilibrium properties of the cation and oxyanion binding to various ferrihydrite sites and the formation of various surface complexes controlled the adsorption and desorption kinetics at different reaction conditions and time scales. Our study provided a unified modeling method for the kinetics of ion adsorption/desorption on ferrihydrite.

On the cross-field diffusion of ions in one- and two-dimensional hybrid simulations of collisionless shocks

NASA Technical Reports Server (NTRS)

Giacalone, Joe

1994-01-01

It can be demonstrated analytically that under certain geometries used in numerical simulations of collisionless shocks in which there is at least one ignorable spatial coordinate, the transport of particles across the magnetic field is essentially zero. This notion is tested using one- and two-dimensional hybrid simulations (kinetic ions/fluid electrons). We find, as the theorem predicts, the particles treated kinetically are tied to the same field line on which they start.

Kinetic Modeling of Accelerated Stability Testing Enabled by Second Harmonic Generation Microscopy.

PubMed

Song, Zhengtian; Sarkar, Sreya; Vogt, Andrew D; Danzer, Gerald D; Smith, Casey J; Gualtieri, Ellen J; Simpson, Garth J

2018-04-03

The low limits of detection afforded by second harmonic generation (SHG) microscopy coupled with image analysis algorithms enabled quantitative modeling of the temperature-dependent crystallization of active pharmaceutical ingredients (APIs) within amorphous solid dispersions (ASDs). ASDs, in which an API is maintained in an amorphous state within a polymer matrix, are finding increasing use to address solubility limitations of small-molecule APIs. Extensive stability testing is typically performed for ASD characterization, the time frame for which is often dictated by the earliest detectable onset of crystal formation. Here a study of accelerated stability testing on ritonavir, a human immunodeficiency virus (HIV) protease inhibitor, has been conducted. Under the condition for accelerated stability testing at 50 °C/75%RH and 40 °C/75%RH, ritonavir crystallization kinetics from amorphous solid dispersions were monitored by SHG microscopy. SHG microscopy coupled by image analysis yielded limits of detection for ritonavir crystals as low as 10 ppm, which is about 2 orders of magnitude lower than other methods currently available for crystallinity detection in ASDs. The four decade dynamic range of SHG microscopy enabled quantitative modeling with an established (JMAK) kinetic model. From the SHG images, nucleation and crystal growth rates were independently determined.

Quantum path integral simulation of isotope effects in the melting temperature of ice Ih.

PubMed

Ramírez, R; Herrero, C P

2010-10-14

The isotope effect in the melting temperature of ice Ih has been studied by free energy calculations within the path integral formulation of statistical mechanics. Free energy differences between isotopes are related to the dependence of their kinetic energy on the isotope mass. The water simulations were performed by using the q-TIP4P/F model, a point charge empirical potential that includes molecular flexibility and anharmonicity in the OH stretch of the water molecule. The reported melting temperature at ambient pressure of this model (T=251 K) increases by 6.5±0.5 and 8.2±0.5 K upon isotopic substitution of hydrogen by deuterium and tritium, respectively. These temperature shifts are larger than the experimental ones (3.8 and 4.5 K, respectively). In the classical limit, the melting temperature is nearly the same as that for tritiated ice. This unexpected behavior is rationalized by the coupling between intermolecular interactions and molecular flexibility. This coupling makes the kinetic energy of the OH stretching modes larger in the liquid than in the solid phase. However, the opposite behavior is found for intramolecular modes, which display larger kinetic energy in ice than in liquid water.

Magneto-optical relaxation measurements for the characterization of biomolecular interactions

NASA Astrophysics Data System (ADS)

Aurich, K.; Glöckl, G.; Romanus, E.; Weber, P.; Nagel, S.; Weitschies, W.

2006-09-01

Measurements of the magneto-optical relaxation of ferrofluids (MORFF) were applied as a novel homogeneous immunoassay for the investigation of biomolecular interactions. The technique is based on magnetic nanoparticles (MNP) functionalized with antibodies. The relaxation time of the optical birefringence that occurs when a pulsed magnetic field is applied to the nanoparticle suspension depends on the particle size. This enables the detection of particle aggregates formed after the addition of the antigen coupling partner. MORFF size measurements on the original ferrofluid and its fractions obtained by magnetic fractionation are comparable with results from other methods such as atomic force microscopy and photon correlation spectroscopy. In kinetic studies, the binding properties of five antigens and their polyclonal antibodies were investigated: human immunoglobulin G (hIgG), human immunoglobulin M (hIgM), human Eotaxin (hEotaxin), human carcinoembryonic antigen (hCEA), and human insulin (hInsulin). The enlargement of the relaxation time observed during the coupling experiments is expressed in terms of a size distribution function, which includes MNP monomers as well as aggregates. The kinetic process can be described by a model of stepwise polymerization. The kinetic parameters obtained are compared to results of surface plasmon resonance measurements.

Sensitivity analysis of a coupled hydrodynamic-vegetation model using the effectively subsampled quadratures method (ESQM v5.2)

NASA Astrophysics Data System (ADS)

Kalra, Tarandeep S.; Aretxabaleta, Alfredo; Seshadri, Pranay; Ganju, Neil K.; Beudin, Alexis

2017-12-01

Coastal hydrodynamics can be greatly affected by the presence of submerged aquatic vegetation. The effect of vegetation has been incorporated into the Coupled Ocean-Atmosphere-Wave-Sediment Transport (COAWST) modeling system. The vegetation implementation includes the plant-induced three-dimensional drag, in-canopy wave-induced streaming, and the production of turbulent kinetic energy by the presence of vegetation. In this study, we evaluate the sensitivity of the flow and wave dynamics to vegetation parameters using Sobol' indices and a least squares polynomial approach referred to as the Effective Quadratures method. This method reduces the number of simulations needed for evaluating Sobol' indices and provides a robust, practical, and efficient approach for the parameter sensitivity analysis. The evaluation of Sobol' indices shows that kinetic energy, turbulent kinetic energy, and water level changes are affected by plant stem density, height, and, to a lesser degree, diameter. Wave dissipation is mostly dependent on the variation in plant stem density. Performing sensitivity analyses for the vegetation module in COAWST provides guidance to optimize efforts and reduce exploration of parameter space for future observational and modeling work.

Spatial Noise in Coupling Strength and Natural Frequency within a Pacemaker Network; Consequences for Development of Intestinal Motor Patterns According to a Weakly Coupled Phase Oscillator Model

PubMed Central

Parsons, Sean P.; Huizinga, Jan D.

2016-01-01

Pacemaker activities generated by networks of interstitial cells of Cajal (ICC), in conjunction with the enteric nervous system, orchestrate most motor patterns in the gastrointestinal tract. It was our objective to understand the role of network features of ICC associated with the myenteric plexus (ICC-MP) in the shaping of motor patterns of the small intestine. To that end, a model of weakly coupled oscillators (oscillators influence each other's phase but not amplitude) was created with most parameters derived from experimental data. The ICC network is a uniform two dimensional network coupled by gap junctions. All ICC generate pacemaker (slow wave) activity with a frequency gradient in mice from 50/min at the proximal end of the intestine to 40/min at the distal end. Key features of motor patterns, directly related to the underlying pacemaker activity, are frequency steps and dislocations. These were accurately mimicked by reduction of coupling strength at a point in the chain of oscillators. When coupling strength was expressed as a product of gap junction density and conductance, and gap junction density was varied randomly along the chain (i.e., spatial noise) with a long-tailed distribution, plateau steps occurred at pointsof low density. As gap junction conductance was decreased, the number of plateaus increased, mimicking the effect of the gap junction inhibitor carbenoxolone. When spatial noise was added to the natural interval gradient, as gap junction conductance decreased, the number of plateaus increased as before but in addition the phase waves frequently changed direction of apparent propagation, again mimicking the effect of carbenoxolone. In summary, key features of the motor patterns that are governed by pacemaker activity may be a direct consequence of biological noise, specifically spatial noise in gap junction coupling and pacemaker frequency. PMID:26869875

Using a spatially-distributed hydrologic biogeochemistry model with a nitrogen transport module to study the spatial variation of carbon processes in a Critical Zone Observatory

DOE PAGES

Shi, Yuning; Eissenstat, David M.; He, Yuting; ...

2018-05-12

Terrestrial carbon processes are affected by soil moisture, soil temperature, nitrogen availability and solar radiation, among other factors. Most of the current ecosystem biogeochemistry models represent one point in space, and have limited characterization of hydrologic processes. Therefore these models can neither resolve the topographically driven spatial variability of water, energy, and nutrient, nor their effects on carbon processes. A spatially-distributed land surface hydrologic biogeochemistry model, Flux-PIHM-BGC, is developed by coupling the Biome-BGC model with a physically-based land surface hydrologic model, Flux-PIHM. In the coupled system, each Flux-PIHM model grid couples a 1-D Biome-BGC model. In addition, a topographic solarmore » radiation module and an advection-driven nitrogen transport module are added to represent the impact of topography on nutrient transport and solar energy distribution. Because Flux-PIHM is able to simulate lateral groundwater flow and represent the land surface heterogeneities caused by topography, Flux-PIHM-BGC is capable of simulating the complex interaction among water, energy, nutrient, and carbon in time and space. The Flux-PIHM-BGC model is tested at the Susquehanna/Shale Hills Critical Zone Observatory. Model results show that distributions of carbon and nitrogen stocks and fluxes are strongly affected by topography and landscape position, and tree growth is nitrogen limited. The predicted aboveground and soil carbon distributions generally agree with the macro patterns observed. Although the model underestimates the spatial variation, the predicted watershed average values are close to the observations. Lastly, the coupled Flux-PIHM-BGC model provides an important tool to study spatial variations in terrestrial carbon and nitrogen processes and their interactions with environmental factors, and to predict the spatial structure of the responses of ecosystems to climate change.« less

Using a spatially-distributed hydrologic biogeochemistry model with a nitrogen transport module to study the spatial variation of carbon processes in a Critical Zone Observatory

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

Shi, Yuning; Eissenstat, David M.; He, Yuting

Terrestrial carbon processes are affected by soil moisture, soil temperature, nitrogen availability and solar radiation, among other factors. Most of the current ecosystem biogeochemistry models represent one point in space, and have limited characterization of hydrologic processes. Therefore these models can neither resolve the topographically driven spatial variability of water, energy, and nutrient, nor their effects on carbon processes. A spatially-distributed land surface hydrologic biogeochemistry model, Flux-PIHM-BGC, is developed by coupling the Biome-BGC model with a physically-based land surface hydrologic model, Flux-PIHM. In the coupled system, each Flux-PIHM model grid couples a 1-D Biome-BGC model. In addition, a topographic solarmore » radiation module and an advection-driven nitrogen transport module are added to represent the impact of topography on nutrient transport and solar energy distribution. Because Flux-PIHM is able to simulate lateral groundwater flow and represent the land surface heterogeneities caused by topography, Flux-PIHM-BGC is capable of simulating the complex interaction among water, energy, nutrient, and carbon in time and space. The Flux-PIHM-BGC model is tested at the Susquehanna/Shale Hills Critical Zone Observatory. Model results show that distributions of carbon and nitrogen stocks and fluxes are strongly affected by topography and landscape position, and tree growth is nitrogen limited. The predicted aboveground and soil carbon distributions generally agree with the macro patterns observed. Although the model underestimates the spatial variation, the predicted watershed average values are close to the observations. Lastly, the coupled Flux-PIHM-BGC model provides an important tool to study spatial variations in terrestrial carbon and nitrogen processes and their interactions with environmental factors, and to predict the spatial structure of the responses of ecosystems to climate change.« less

Fabrication of an Absorber-Coupled MKID Detector

NASA Technical Reports Server (NTRS)

Brown, Ari; Hsieh, Wen-Ting; Moseley, Samuel; Stevenson, Thomas; U-Yen, Kongpop; Wollack, Edward

2012-01-01

Absorber-coupled microwave kinetic inductance detector (MKID) arrays were developed for submillimeter and far-infrared astronomy. These sensors comprise arrays of lambda/2 stepped microwave impedance resonators patterned on a 1.5-mm-thick silicon membrane, which is optimized for optical coupling. The detector elements are supported on a 380-mm-thick micro-machined silicon wafer. The resonators consist of parallel plate aluminum transmission lines coupled to low-impedance Nb microstrip traces of variable length, which set the resonant frequency of each resonator. This allows for multiplexed microwave readout and, consequently, good spatial discrimination between pixels in the array. The transmission lines simultaneously act to absorb optical power and employ an appropriate surface impedance and effective filling fraction. The fabrication techniques demonstrate high-fabrication yield of MKID arrays on large, single-crystal membranes and sub-micron front-to-back alignment of the micro strip circuit. An MKID is a detector that operates upon the principle that a superconducting material s kinetic inductance and surface resistance will change in response to being exposed to radiation with a power density sufficient to break its Cooper pairs. When integrated as part of a resonant circuit, the change in surface impedance will result in a shift in its resonance frequency and a decrease of its quality factor. In this approach, incident power creates quasiparticles inside a superconducting resonator, which is configured to match the impedance of free space in order to absorb the radiation being detected. For this reason MKIDs are attractive for use in large-format focal plane arrays, because they are easily multiplexed in the frequency domain and their fabrication is straightforward. The fabrication process can be summarized in seven steps: (1) Alignment marks are lithographically patterned and etched all the way through a silicon on insulator (SOI) wafer, which consists of a thin silicon membrane bonded to a thick silicon handle wafer. (2) The metal microwave circuitry on the front of the membrane is patterned and etched. (3) The wafer is then temporarily bonded with wafer wax to a Pyrex wafer, with the SOI side abutting the Pyrex. (4) The silicon handle component of the SOI wafer is subsequently etched away so as to expose the membrane backside. (5) The wafer is flipped over, and metal microwave circuitry is patterned and etched on the membrane backside. Furthermore, cuts in the membrane are made so as to define the individual detector array chips. (6) Silicon frames are micromachined and glued to the silicon membrane. (7) The membranes, which are now attached to the frames, are released from the Pyrex wafer via dissolution of the wafer wax in acetone.

Proton-pumping mechanism of cytochrome c oxidase: A kinetic master-equation approach

PubMed Central

Kim, Young C.; Hummer, Gerhard

2011-01-01

Cytochrome c oxidase (CcO) is an efficient energy transducer that reduces oxygen to water and converts the released chemical energy into an electrochemical membrane potential. As a true proton pump, CcO translocates protons across the membrane against this potential. Based on a wealth of experiments and calculations, an increasingly detailed picture of the reaction intermediates in the redox cycle has emerged. However, the fundamental mechanism of proton pumping coupled to redox chemistry remains largely unresolved. Here we examine and extend a kinetic master-equation approach to gain insight into redox-coupled proton pumping in CcO. Basic principles of the CcO proton pump emerge from an analysis of the simplest kinetic models that retain essential elements of the experimentally determined structure, energetics, and kinetics, and that satisfy fundamental physical principles. The master-equation models allow us to address the question of how pumping can be achieved in a system in which all reaction steps are reversible. Whereas proton pumping does not require the direct modulation of microscopic reaction barriers, such kinetic gating greatly increases the pumping efficiency. Further efficiency gains can be achieved by partially decoupling the proton uptake pathway from the ative-site region. Such a mechanism is consistent with the proposed Glu valve, in which the side chain of a key glutamic acid shuttles between the D channel and the active-site region. We also show that the models predict only small proton leaks even in the absence of turnover. The design principles identified here for CcO provide a blueprint for novel biology-inspired fuel cells, and the master-equation formulation should prove useful also for other molecular machines. PMID:21946020

120W, NA_0.15 fiber coupled LD module with 125-μm clad/NA 0.22 fiber by spatial coupling method

NASA Astrophysics Data System (ADS)

Ishige, Yuta; Kaji, Eisaku; Katayama, Etsuji; Ohki, Yutaka; Gajdátsy, Gábor; Cserteg, András.

2018-02-01

We have fabricated a fiber coupled semiconductor laser diode module by means of spatial beam combining of single emitter broad area semiconductor laser diode chips in the 9xx nm band. In the spatial beam multiplexing method, the numerical aperture of the output light from the optical fiber increases by increasing the number of laser diodes coupled into the fiber. To reduce it, we have tried the approach to improving assembly process technology. As a result, we could fabricate laser diode modules having a light output power of 120W or more and 95% power within NA of 0.15 or less from a single optical fiber with 125-μm cladding diameter. Furthermore, we have obtained that the laser diode module maintaining high coupling efficiency can be realized even around the fill factor of 0.95. This has been achieved by improving the optical alignment method regarding the fast axis stack pitch of the laser diodes in the laser diode module. Therefore, without using techniques such as polarization combining and wavelength combining, high output power was realized while keeping small numerical aperture. This contributes to a reduction in unit price per light output power of the pumping laser diode module.

Weak and strong coupling equilibration in nonabelian gauge theories

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

Keegan, Liam; Kurkela, Aleksi; Romatschke, Paul

2016-04-06

In this study, we present a direct comparison studying equilibration through kinetic theory at weak coupling and through holography at strong coupling in the same set-up. The set-up starts with a homogeneous thermal state, which then smoothly transitions through an out-of-equilibrium phase to an expanding system undergoing boost-invariant flow. This first apples-to-apples comparison of equilibration provides a benchmark for similar equilibration processes in heavy-ion collisions, where the equilibration mechanism is still under debate. We find that results at weak and strong coupling can be smoothly connected by simple, empirical power-laws for the viscosity, equilibration time and entropy production of themore » system.« less

Rh(I)-Catalyzed Intermolecular Hydroacylation: Enantioselective Cross-Coupling of Aldehydes and Ketoamides

PubMed Central

2015-01-01

Under Rh(I) catalysis, α-ketoamides undergo intermolecular hydroacylation with aliphatic aldehydes. A newly designed Josiphos ligand enables access to α-acyloxyamides with high atom-economy and enantioselectivity. On the basis of mechanistic and kinetic studies, we propose a pathway in which rhodium plays a dual role in activating the aldehyde for cross-coupling. A stereochemical model is provided to rationalize the sense of enantioinduction observed. PMID:24937681

The cryomechanical design of MUSIC: a novel imaging instrument for millimeter-wave astrophysics at the Caltech Submillimeter Observatory

NASA Astrophysics Data System (ADS)

Hollister, Matthew I.; Czakon, Nicole G.; Day, Peter K.; Downes, Thomas P.; Duan, Ran; Gao, Jiansong; Glenn, Jason; Golwala, Sunil R.; LeDuc, Henry G.; Maloney, Philip R.; Mazin, Benjamin A.; Nguyen, Hien Trong; Noroozian, Omid; Sayers, Jack; Schlaerth, James; Siegel, Seth; Vaillancourt, John E.; Vayonakis, Anastasios; Wilson, Philip; Zmuidzinas, Jonas

2010-07-01

MUSIC (Multicolor Submillimeter kinetic Inductance Camera) is a new facility instrument for the Caltech Submillimeter Observatory (Mauna Kea, Hawaii) developed as a collaborative effect of Caltech, JPL, the University of Colorado at Boulder and UC Santa Barbara, and is due for initial commissioning in early 2011. MUSIC utilizes a new class of superconducting photon detectors known as microwave kinetic inductance detectors (MKIDs), an emergent technology that offers considerable advantages over current types of detectors for submillimeter and millimeter direct detection. MUSIC will operate a focal plane of 576 spatial pixels, where each pixel is a slot line antenna coupled to multiple detectors through on-chip, lumped-element filters, allowing simultaneously imaging in four bands at 0.86, 1.02, 1.33 and 2.00 mm. The MUSIC instrument is designed for closed-cycle operation, combining a pulse tube cooler with a two-stage Helium-3 adsorption refrigerator, providing a focal plane temperature of 0.25 K with intermediate temperature stages at approximately 50, 4 and 0.4 K for buffering heat loads and heat sinking of optical filters. Detector readout is achieved using semi-rigid coaxial cables from room temperature to the focal plane, with cryogenic HEMT amplifiers operating at 4 K. Several hundred detectors may be multiplexed in frequency space through one signal line and amplifier. This paper discusses the design of the instrument cryogenic hardware, including a number of features unique to the implementation of superconducting detectors. Predicted performance data for the instrument system will also be presented and discussed.

Formation of Polar Stratospheric Clouds in the Atmosphere

NASA Astrophysics Data System (ADS)

Aloyan, Artash; Yermakov, Alex; Arutyunyan, Vardan; Larin, Igor

2014-05-01

A new mathematical model of the global transport of gaseous species and aerosols in the atmosphere and the formation of polar stratospheric clouds (PSCs) in both hemispheres was constructed. PSCs play a significant role in ozone chemistry since heterogeneous reactions proceed on their particle surfaces and in the bulk, affecting the gas composition of the atmosphere, specifically, the content of chlorine and nitrogen compounds, which are actively involved in the destruction of ozone. Stratospheric clouds are generated by co-condensation of water vapor and nitric acid on sulfate particles and in some cases during the freezing of supercooled water as well as when nitric acid vapors are dissolved in sulfate aerosol particles [1]. These clouds differ in their chemical composition and microphysics [2]. In this study, we propose new kinetic equations describing the variability of species in the gas and condensed phases to simulate the formation of PSCs. Most models for the formation of PSCs use constant background values of sulfate aerosols in the lower stratosphere. This approach is too simplistic since sulfate aerosols in the stratosphere are characterized by considerably nonuniform spatial and temporal variations. Two PSC types are considered: Type 1 refers to the formation of nitric acid trihydrate (NAT) and Type 2 refers to the formation of particles composed of different proportions of H2SO4/HNO3/H2O. Their formation is coupled with the spatial problem of sulfate aerosol generation in the upper troposphere and lower stratosphere incorporating the chemical and kinetic transformation processes (photochemistry, nucleation, condensation/evaporation, and coagulation) and using a non-equilibrium particle-size distribution [3]. In this formulation, the system of equations is closed and allows an adequate description of the PSC dynamics in the stratosphere. Using the model developed, numerical experiments were performed to reproduce the spatial and temporal variability of polar clouds in both hemispheres for the winter time period. The numerical experiments were performed in the following sequence. In the first stage, we address the transport of multicomponent gaseous species, the formation of sulfate aerosols in the troposphere and lower stratosphere (spherical atmosphere), the chemical and kinetic transformations, and the biogenic and anthropogenic emissions of related chemical components [3]. This model makes it possible to reproduce the distribution of sulfate particles in the size range from 3 nm to 1 mcm. Next, the base model was improved by using a new module describing the dynamics of phase transition of substances in gaseous and condensed phases that are typical for different types of PSCs. Here, we used the methods of thermodynamics. Conclusions •The model developed allow us to reproduce the size distribution of sulfate particles generated from precursor gases in the troposphere and stratosphere; •The numerical experiments show that the model adequately reproduces the spatial characteristics of the PSC formation in the atmosphere. References 1.Carslaw K.S., Peter T., Clegg S.L. Modeling the composition of liquid stratospheric clouds. Rev. Geophys. 35, 125, 1997 2.Drdla, K., Shoeberl, M.R., and Browell, E.V., Microphysical modeling of the 1999-2000 Arctic winter. J. Geophys. Res., 2003, vol. 108, No. D5, p. 8312. 3.Aloyan, A.E., Yermakov, A.N., Arutyunyan, V.O., Sulfate aerosol formation in the troposphere and lower stratosphere, in Possibilities of Climate Stabilization by Using Novel Technologies, Moscow: Rosgidromet, 2012, pp. 75-98.

A multi-point perspective on the formation of polar cap arcs: kinetic modeling and observations by Cluster and TIMED

NASA Astrophysics Data System (ADS)

de Keyser, J. M.; Maggiolo, R.; Echim, M.; Simon, C.; Zhang, Y.; Trotignon, J.

2010-12-01

On April 1st, 2004 the GUVI imager onboard the TIMED spacecraft spots an isolated and elongated polar cap arc. Simultaneously, the Cluster spacecraft detects an isolated upflowing ion beam above the polar cap. Cluster observations show that the ions are accelerated upward by a quasi-stationary electric field. The field-aligned potential drop is estimated to about 600 V and the upflowing ions are accompanied by a tenuous population of isotropic protons with a temperature of about 300eV. The footprint of the magnetic field line on which the Cluster spacecraft are situated, is located just outside the GUVI field of view in the prolongation of the polar cap arc. This suggests that the upflowing ion beam and the polar cap arc may be different signatures of the same phenomenon, as suggested by a recent statistical study of polar cap ion beams using Cluster data. We use Cluster observations at high altitude as input to a quasi-stationary magnetosphere-ionosphere (MI) coupling model. Using a Knight-type current-voltage relationship and the current continuity at the topside ionosphere, the model computes the energy spectrum of precipitating electrons at ionospheric altitudes corresponding to the generator electric field observed by Cluster. The MI coupling model provides a field-aligned potential drop in agreement with Cluster observations of upflowing ions and a spatial scale of the polar cap arc consistent with the optical observations by TIMED. The energy spectrum of the precipitating electrons provided by the model is introduced as input to the Trans4 ionospheric transport code. This 1-D model, based on Boltzmann's kinetic formalism, takes into account ionospheric processes like photoionisation and electron/proton precipitation, and computes the optical and UV emissions due to precipitating electrons. The emission rates provided by the Trans4 code are then compared to the optical observations by TIMED. Data and modeling results are consistent with quasi-static acceleration of precipitating magnetospheric electrons. We also discuss possible implications of our modeling results for optical observations of polar cap arcs.

Global Three-dimensional Simulation of the Solar Wind-Magnetosphere Interaction Using a Two-way Coupled Magnetohydrodynamics with Embedded Particle-in-Cell Model

NASA Astrophysics Data System (ADS)

Chen, Y.; Toth, G.; Cassak, P.; Jia, X.; Gombosi, T. I.; Slavin, J. A.; Welling, D. T.; Markidis, S.; Peng, I. B.; Jordanova, V. K.; Henderson, M. G.

2017-12-01

We perform a three-dimensional (3D) global simulation of Earth's magnetosphere with kinetic reconnection physics to study the interaction between the solar wind and Earth's magnetosphere. In this global simulation with magnetohydrodynamics with embedded particle-in-cell model (MHD-EPIC), both the dayside magnetopause reconnection region and the magnetotail reconnection region are covered with a kinetic particle-in-cell code iPIC3D, which is two-way coupled with the global MHD model BATS-R-US. We will describe the dayside reconnection related phenomena, such as the lower hybrid drift instability (LHDI) and the evolution of the flux transfer events (FTEs) along the magnetopause, and compare the simulation results with observations. We will also discuss the response of the magnetotail to the southward IMF. The onset of the tail reconnection and the properties of the magnetotail flux ropes will be discussed.

Final Report: Molecular mechanisms and kinetics of microbial anaerobic nitrate-dependent U(IV) and Fe(II) oxidation

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

O'Day, Peggy A.; Asta, Maria P.; Kanematsu, Masakazu

2015-02-27

In this project, we combined molecular genetic, spectroscopic, and microscopic techniques with kinetic and reactive transport studies to describe and quantify biotic and abiotic mechanisms underlying anaerobic, nitrate-dependent U(IV) and Fe(II) oxidation, which influences the long-term efficacy of in situ reductive immobilization of uranium at DOE sites. In these studies, Thiobacillus denitrificans, an autotrophic bacterium that catalyzes anaerobic U(IV) and Fe(II) oxidation, was used to examine coupled oxidation-reduction processes under either biotic (enzymatic) or abiotic conditions in batch and column experiments with biogenically produced UIVO2(s). Synthesis and quantitative analysis of coupled chemical and transport processes were done with the reactivemore » transport modeling code Crunchflow. Research focused on identifying the primary redox proteins that catalyze metal oxidation, environmental factors that influence protein expression, and molecular-scale geochemical factors that control the rates of biotic and abiotic oxidation.« less

A novel iron-lead redox flow battery for large-scale energy storage

NASA Astrophysics Data System (ADS)

Zeng, Y. K.; Zhao, T. S.; Zhou, X. L.; Wei, L.; Ren, Y. X.

2017-04-01

The redox flow battery (RFB) is one of the most promising large-scale energy storage technologies for the massive utilization of intermittent renewables especially wind and solar energy. This work presents a novel redox flow battery that utilizes inexpensive and abundant Fe(II)/Fe(III) and Pb/Pb(II) redox couples as redox materials. Experimental results show that both the Fe(II)/Fe(III) and Pb/Pb(II) redox couples have fast electrochemical kinetics in methanesulfonic acid, and that the coulombic efficiency and energy efficiency of the battery are, respectively, as high as 96.2% and 86.2% at 40 mA cm-2. Furthermore, the battery exhibits stable performance in terms of efficiencies and discharge capacities during the cycle test. The inexpensive redox materials, fast electrochemical kinetics and stable cycle performance make the present battery a promising candidate for large-scale energy storage applications.

Quantum Transmission Conditions for Diffusive Transport in Graphene with Steep Potentials

NASA Astrophysics Data System (ADS)

Barletti, Luigi; Negulescu, Claudia

2018-05-01

We present a formal derivation of a drift-diffusion model for stationary electron transport in graphene, in presence of sharp potential profiles, such as barriers and steps. Assuming the electric potential to have steep variations within a strip of vanishing width on a macroscopic scale, such strip is viewed as a quantum interface that couples the classical regions at its left and right sides. In the two classical regions, where the potential is assumed to be smooth, electron and hole transport is described in terms of semiclassical kinetic equations. The diffusive limit of the kinetic model is derived by means of a Hilbert expansion and a boundary layer analysis, and consists of drift-diffusion equations in the classical regions, coupled by quantum diffusive transmission conditions through the interface. The boundary layer analysis leads to the discussion of a four-fold Milne (half-space, half-range) transport problem.

Investigating Uranium Concentrations in Groundwaters in the State of Idaho Using Kinetic Phosphorescence Analysis and Inductively Coupled Plasma Mass Spectrometry.

PubMed

Tkavadze, Levan; Dunker, Roy E; Brey, Richard R; Dudgeon, John

2016-11-01

The determination of uranium concentrations in natural water samples is of great interest due to the environmental consequences of this radionuclide. In this study, 380 groundwater samples from various locations within the state of Idaho were analyzed using two different techniques. The first method was Kinetic Phosphorescence Analysis (KPA), which gives the total uranium concentrations in water samples. The second analysis method was inductively coupled plasma mass spectrometry (ICP- MS). This method determines the total uranium concentration as well as the separate isotope concentrations of uranium. The U/U isotopic ratio was also measured for each sample to confirm that there was no depleted or enriched uranium present. The results were compared and mapped separately from each other. The study also found that in some areas of the state, natural uranium concentrations are relatively high.

Simulations of moving effect of coastal vegetation on tsunami damping

NASA Astrophysics Data System (ADS)

Tsai, Ching-Piao; Chen, Ying-Chi; Octaviani Sihombing, Tri; Lin, Chang

2017-05-01

A coupled wave-vegetation simulation is presented for the moving effect of the coastal vegetation on tsunami wave height damping. The problem is idealized by solitary wave propagation on a group of emergent cylinders. The numerical model is based on general Reynolds-averaged Navier-Stokes equations with renormalization group turbulent closure model by using volume of fluid technique. The general moving object (GMO) model developed in computational fluid dynamics (CFD) code Flow-3D is applied to simulate the coupled motion of vegetation with wave dynamically. The damping of wave height and the turbulent kinetic energy along moving and stationary cylinders are discussed. The simulated results show that the damping of wave height and the turbulent kinetic energy by the moving cylinders are clearly less than by the stationary cylinders. The result implies that the wave decay by the coastal vegetation may be overestimated if the vegetation was represented as stationary state.

Modeling quantum cascade lasers: Coupled electron and phonon transport far from equilibrium and across disparate spatial scales

DOE PAGES

Shi, Y. B.; Mei, S.; Jonasson, O.; ...

2016-12-28

Quantum cascade lasers (QCLs) are high-power coherent light sources in the midinfrared and terahertz parts of the electromagnetic spectrum. They are devices in which the electronic and lattice systems are far from equilibrium, strongly coupled to one another, and the problem bridges disparate spatial scales. Here, we present our ongoing work on the multiphysics and multiscale simulation of far-from-equilibrium transport of charge and heat in midinfrared QCLs.

Space- and time-resolved raman and breakdown spectroscopy: advanced lidar techniques

NASA Astrophysics Data System (ADS)

Silviu, Gurlui; Marius Mihai, Cazacu; Adrian, Timofte; Oana, Rusu; Georgiana, Bulai; Dimitriu, Dan

2018-04-01

DARLIOES - the advanced LIDAR is based on space- and time-resolved RAMAN and breakdown spectroscopy, to investigate chemical and toxic compounds, their kinetics and physical properties at high temporal (2 ns) and spatial (1 cm) resolution. The high spatial and temporal resolution are needed to resolve a large variety of chemical troposphere compounds, emissions from aircraft, the self-organization space charges induced light phenomena, temperature and humidity profiles, ice nucleation, etc.

Kinetic modeling and exploratory numerical simulation of chloroplastic starch degradation

PubMed Central

2011-01-01

Background Higher plants and algae are able to fix atmospheric carbon dioxide through photosynthesis and store this fixed carbon in large quantities as starch, which can be hydrolyzed into sugars serving as feedstock for fermentation to biofuels and precursors. Rational engineering of carbon flow in plant cells requires a greater understanding of how starch breakdown fluxes respond to variations in enzyme concentrations, kinetic parameters, and metabolite concentrations. We have therefore developed and simulated a detailed kinetic ordinary differential equation model of the degradation pathways for starch synthesized in plants and green algae, which to our knowledge is the most complete such model reported to date. Results Simulation with 9 internal metabolites and 8 external metabolites, the concentrations of the latter fixed at reasonable biochemical values, leads to a single reference solution showing β-amylase activity to be the rate-limiting step in carbon flow from starch degradation. Additionally, the response coefficients for stromal glucose to the glucose transporter kcat and KM are substantial, whereas those for cytosolic glucose are not, consistent with a kinetic bottleneck due to transport. Response coefficient norms show stromal maltopentaose and cytosolic glucosylated arabinogalactan to be the most and least globally sensitive metabolites, respectively, and β-amylase kcat and KM for starch to be the kinetic parameters with the largest aggregate effect on metabolite concentrations as a whole. The latter kinetic parameters, together with those for glucose transport, have the greatest effect on stromal glucose, which is a precursor for biofuel synthetic pathways. Exploration of the steady-state solution space with respect to concentrations of 6 external metabolites and 8 dynamic metabolite concentrations show that stromal metabolism is strongly coupled to starch levels, and that transport between compartments serves to lower coupling between metabolic subsystems in different compartments. Conclusions We find that in the reference steady state, starch cleavage is the most significant determinant of carbon flux, with turnover of oligosaccharides playing a secondary role. Independence of stationary point with respect to initial dynamic variable values confirms a unique stationary point in the phase space of dynamically varying concentrations of the model network. Stromal maltooligosaccharide metabolism was highly coupled to the available starch concentration. From the most highly converged trajectories, distances between unique fixed points of phase spaces show that cytosolic maltose levels depend on the total concentrations of arabinogalactan and glucose present in the cytosol. In addition, cellular compartmentalization serves to dampen much, but not all, of the effects of one subnetwork on another, such that kinetic modeling of single compartments would likely capture most dynamics that are fast on the timescale of the transport reactions. PMID:21682905

Molecular details of dimerization kinetics reveal negligible populations of transient µ-opioid receptor homodimers at physiological concentrations.

PubMed

Meral, Derya; Provasi, Davide; Prada-Gracia, Diego; Möller, Jan; Marino, Kristen; Lohse, Martin J; Filizola, Marta

2018-05-16

Various experimental and computational techniques have been employed over the past decade to provide structural and thermodynamic insights into G Protein-Coupled Receptor (GPCR) dimerization. Here, we use multiple microsecond-long, coarse-grained, biased and unbiased molecular dynamics simulations (a total of ~4 milliseconds) combined with multi-ensemble Markov state models to elucidate the kinetics of homodimerization of a prototypic GPCR, the µ-opioid receptor (MOR), embedded in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/cholesterol lipid bilayer. Analysis of these computations identifies kinetically distinct macrostates comprising several different short-lived dimeric configurations of either inactive or activated MOR. Calculated kinetic rates and fractions of dimers at different MOR concentrations suggest a negligible population of MOR homodimers at physiological concentrations, which is supported by acceptor photobleaching fluorescence resonance energy transfer (FRET) experiments. This study provides a rigorous, quantitative explanation for some conflicting experimental data on GPCR oligomerization.

A kinetic model for the transport of electrons in a graphene layer

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

Fermanian Kammerer, Clotilde, E-mail: Clotilde.Fermanian@u-pec.fr; Méhats, Florian, E-mail: florian.mehats@univ-rennes1.fr

In this article, we propose a new numerical scheme for the computation of the transport of electrons in a graphene device. The underlying quantum model for graphene is a massless Dirac equation, whose eigenvalues display a conical singularity responsible for non-adiabatic transitions between the two modes. We first derive a kinetic model which takes the form of two Boltzmann equations coupled by a collision operator modeling the non-adiabatic transitions. This collision term includes a Landau–Zener transfer term and a jump operator whose presence is essential in order to ensure a good energy conservation during the transitions. We propose an algorithmicmore » realization of the semi-group solving the kinetic model, by a particle method. We give analytic justification of the model and propose a series of numerical experiments studying the influences of the various sources of errors between the quantum and the kinetic models.« less

Coulomb-driven energy boost of heavy ions for laser-plasma acceleration.

PubMed

Braenzel, J; Andreev, A A; Platonov, K; Klingsporn, M; Ehrentraut, L; Sandner, W; Schnürer, M

2015-03-27

An unprecedented increase of kinetic energy of laser accelerated heavy ions is demonstrated. Ultrathin gold foils have been irradiated by an ultrashort laser pulse at a peak intensity of 8×10^{19}  W/  cm^{2}. Highly charged gold ions with kinetic energies up to >200  MeV and a bandwidth limited energy distribution have been reached by using 1.3 J laser energy on target. 1D and 2D particle in cell simulations show how a spatial dependence on the ion's ionization leads to an enhancement of the accelerating electrical field. Our theoretical model considers a spatial distribution of the ionization inside the thin target, leading to a field enhancement for the heavy ions by Coulomb explosion. It is capable of explaining the energy boost of highly charged ions, enabling a higher efficiency for the laser-driven heavy ion acceleration.

Cooperativity in Monomeric Enzymes with Single Ligand-Binding Sites

PubMed Central

Porter, Carol M.

2011-01-01

Cooperativity is widespread in biology. It empowers a variety of regulatory mechanisms and impacts both the kinetic and thermodynamic properties of macromolecular systems. Traditionally, cooperativity is viewed as requiring the participation of multiple, spatially distinct binding sites that communicate via ligand-induced structural rearrangements; however, cooperativity requires neither multiple ligand binding events nor multimeric assemblies. An underappreciated manifestation of cooperativity has been observed in the non-Michaelis-Menten kinetic response of certain monomeric enzymes that possess only a single ligand-binding site. In this review, we present an overview of kinetic cooperativity in monomeric enzymes. We discuss the primary mechanisms postulated to give rise to monomeric cooperativity and highlight modern experimental methods that could offer new insights into the nature of this phenomenon. We conclude with an updated list of single subunit enzymes that are suspected of displaying cooperativity, and a discussion of the biological significance of this unique kinetic response. PMID:22137502

Reductive dechlorination of trichloroethene DNAPL source zones: source zone architecture versus electron donor availability

NASA Astrophysics Data System (ADS)

Krol, M.; Kokkinaki, A.; Sleep, B.

2014-12-01

The persistence of dense-non-aqueous-phase liquids (DNAPLs) in the subsurface has led practitioners and regulatory agencies to turn towards low-maintenance, low-cost remediation methods. Biological degradation has been suggested as a possible solution, based on the well-proven ability of certain microbial species to break down dissolved chlorinated ethenes under favorable conditions. However, the biodegradation of pure phase chlorinated ethenes is subject to additional constraints: the continuous release of electron acceptor at a rate governed by mass transfer kinetics, and the temporal and spatial heterogeneity of DNAPL source zones which leads to spatially and temporally variable availability of the reactants for reductive dechlorination. In this work, we investigate the relationship between various DNAPL source zone characteristics and reaction kinetics using COMPSIM, a multiphase groundwater model that considers non-equilibrium mass transfer and Monod-type kinetics for reductive dechlorination. Numerical simulations are performed for simple, homogeneous trichloroethene DNAPL source zones to demonstrate the effect of single source zone characteristics, as well as for larger, more realistic heterogeneous source zones. It is shown that source zone size, and mass transfer kinetics may have a decisive effect on the predicted bio-enhancement. Finally, we evaluate the performance of DNAPL bioremediation for realistic, thermodynamically constrained, concentrations of electron donor. Our results indicate that the latter may be the most important limitation for the success of DNAPL bioremediation, leading to reduced bio-enhancement and, in many cases, comparable performance with water flooding.

The Eschenmoser coupling reaction under continuous-flow conditions

PubMed Central

Singh, Sukhdeep; Köhler, J Michael; Schober, Andreas

2011-01-01

Summary The Eschenmoser coupling is a useful carbon–carbon bond forming reaction which has been used in various different synthesis strategies. The reaction proceeds smoothly if S-alkylated ternary thioamides or thiolactames are used. In the case of S-alkylated secondary thioamides or thiolactames, the Eschenmoser coupling needs prolonged reaction times and elevated temperatures to deliver valuable yields. We have used a flow chemistry system to promote the Eschenmoser coupling under enhanced reaction conditions in order to convert the demanding precursors such as S-alkylated secondary thioamides and thiolactames in an efficient way. Under pressurized reaction conditions at about 220 °C, the desired Eschenmoser coupling products were obtained within 70 s residence time. The reaction kinetics was investigated and 15 examples of different building block combinations are given. PMID:21915222