Modeling the detailed kinetics of mitochondrial cytochrome c oxidase: Catalytic mechanism and nitric oxide inhibition

PubMed Central

Pannala, Venkat R.; Camara, Amadou K. S.

2016-01-01

Cytochrome c oxidase (CcO) catalyzes the exothermic reduction of O2 to H2O by using electrons from cytochrome c, and hence plays a crucial role in ATP production. Although details on the enzyme structure and redox centers involved in O2 reduction have been known, there still remains a considerable ambiguity on its mechanism of action, e.g., the number of sequential electrons donated to O2 in each catalytic step, the sites of protonation and proton pumping, and nitric oxide (NO) inhibition mechanism. In this work, we developed a thermodynamically constrained mechanistic mathematical model for the catalytic action of CcO based on available kinetic data. The model considers a minimal number of redox centers on CcO and couples electron transfer and proton pumping driven by proton motive force (PMF), and accounts for the inhibitory effects of NO on the reaction kinetics. The model is able to fit well all the available kinetic data under diverse experimental conditions with a physiologically realistic unique parameter set. The model predictions show that: 1) the apparent Km of O2 varies considerably and increases from fully reduced to fully oxidized cytochrome c depending on pH and the energy state of mitochondria, and 2) the intermediate enzyme states depend on pH and cytochrome c redox fraction and play a central role in coupling mitochondrial respiration to PMF. The developed CcO model can easily be integrated into existing mitochondrial bioenergetics models to understand the role of the enzyme in controlling oxidative phosphorylation in normal and disease conditions. PMID:27633738

Development of high performance particle in cell code for the exascale age

NASA Astrophysics Data System (ADS)

Lapenta, Giovanni; Amaya, Jorge; Gonzalez, Diego; Deep-Est H2020 Consortium Collaboration

2017-10-01

Magnetized plasmas are most effectively described by magneto-hydrodynamics, MHD, a fluid theory based on describing some fields defined in space: electromagnetic fields, density, velocity and temperature of the plasma. However, microphysics processes need kinetic theory, where statistical distributions of particles are governed by the Boltzmann equation. While fluid models are based on the ordinary space and time, kinetic models require a six dimensional space, called phase space, besides time. The two methods are not separated but rather interact to determine the system evolution. Arriving at a single self-consistent model is the goal of our research. We present a new approach developed with the goal of extending the reach of kinetic models to the fluid scales. Kinetic models are a higher order description and all fluid effects are included in them. However, the cost in terms of computing power is much higher and it has been so far prohibitively expensive to treat space weather events fully kinetically. We have now designed a new method capable of reducing that cost by several orders of magnitude making it possible for kinetic models to study macroscopic systems. H2020 Deep-EST consortium (European Commission).

Effect of nonlinearity in hybrid kinetic Monte Carlo-continuum models.

PubMed

Balter, Ariel; Lin, Guang; Tartakovsky, Alexandre M

2012-01-01

Recently there has been interest in developing efficient ways to model heterogeneous surface reactions with hybrid computational models that couple a kinetic Monte Carlo (KMC) model for a surface to a finite-difference model for bulk diffusion in a continuous domain. We consider two representative problems that validate a hybrid method and show that this method captures the combined effects of nonlinearity and stochasticity. We first validate a simple deposition-dissolution model with a linear rate showing that the KMC-continuum hybrid agrees with both a fully deterministic model and its analytical solution. We then study a deposition-dissolution model including competitive adsorption, which leads to a nonlinear rate, and show that in this case the KMC-continuum hybrid and fully deterministic simulations do not agree. However, we are able to identify the difference as a natural result of the stochasticity coming from the KMC surface process. Because KMC captures inherent fluctuations, we consider it to be more realistic than a purely deterministic model. Therefore, we consider the KMC-continuum hybrid to be more representative of a real system.

Extended MHD modeling of nonlinear instabilities in fusion and space plasmas

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

Germaschewski, Kai

A number of different sub-projects where pursued within this DOE early career project. The primary focus was on using fully nonlinear, curvilinear, extended MHD simulations of instabilities with applications to fusion and space plasmas. In particular, we performed comprehensive studies of the dynamics of the double tearing mode in different regimes and confi gurations, using Cartesian and cyclindrical geometry and investigating both linear and non-linear dynamics. In addition to traditional extended MHD involving Hall term and electron pressure gradient, we also employed a new multi-fluid moment model, which shows great promise to incorporate kinetic effects, in particular off-diagonal elements ofmore » the pressure tensor, in a fluid model, which is naturally computationally much cheaper than fully kinetic particle or Vlasov simulations. We used our Vlasov code for detailed studies of how weak collisions effect plasma echos. In addition, we have played an important supporting role working with the PPPL theory group around Will Fox and Amitava Bhattacharjee on providing simulation support for HED plasma experiments performed at high-powered laser facilities like OMEGA-EP in Rochester, NY. This project has support a great number of computational advances in our fluid and kinetic plasma models, and has been crucial to winning multiple INCITE computer time awards that supported our computational modeling.« less

A two-fluid study of oblique tearing modes in a force-free current sheet

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

Akçay, Cihan, E-mail: akcay@lanl.gov; Daughton, William; Lukin, Vyacheslav S.

2016-01-15

Kinetic simulations have demonstrated that three-dimensional reconnection in collisionless regimes proceeds through the formation and interaction of magnetic flux ropes, which are generated due to the growth of tearing instabilities at multiple resonance surfaces. Since kinetic simulations are intrinsically expensive, it is desirable to explore the feasibility of reduced two-fluid models to capture this complex evolution, particularly, in the strong guide field regime, where two-fluid models are better justified. With this goal in mind, this paper compares the evolution of the collisionless tearing instability in a force-free current sheet with a two-fluid model and fully kinetic simulations. Our results indicatemore » that the most unstable modes are oblique for guide fields larger than the reconnecting field, in agreement with the kinetic results. The standard two-fluid tearing theory is extended to address the tearing instability at oblique angles. The resulting theory yields a flat oblique spectrum and underestimates the growth of oblique modes in a similar manner to kinetic theory relative to kinetic simulations.« less

A two-fluid study of oblique tearing modes in a force-free current sheet

DOE PAGES

Akçay, Cihan; Daughton, William; Lukin, Vyacheslav S.; ...

2016-01-01

Kinetic simulations have demonstrated that three-dimensional reconnection in collisionless regimes proceeds through the formation and interaction of magnetic flux ropes, which are generated due to the growth of tearing instabilities at multiple resonance surfaces. Because kinetic simulations are intrinsically expensive, it is desirable to explore the feasibility of reduced two-fluid models to capture this complex evolution, particularly, in the strong guide field regime, where two-fluid models are better justified. With this goal in mind, this paper compares the evolution of the collisionless tearing instability in a force-free current sheet with a two-fluid model and fully kinetic simulations. Our results indicatemore » that the most unstable modes are oblique for guide fields larger than the reconnecting field, in agreement with the kinetic results. The standard two-fluid tearing theory is extended to address the tearing instability at oblique angles. As a results this theory yields a flat oblique spectrum and underestimates the growth of oblique modes in a similar manner to kinetic theory relative to kinetic simulations.« less

Statistical model of a flexible inextensible polymer chain: The effect of kinetic energy.

PubMed

Pergamenshchik, V M; Vozniak, A B

2017-01-01

Because of the holonomic constraints, the kinetic energy contribution in the partition function of an inextensible polymer chain is difficult to find, and it has been systematically ignored. We present the first thermodynamic calculation incorporating the kinetic energy of an inextensible polymer chain with the bending energy. To explore the effect of the translation-rotation degrees of freedom, we propose and solve a statistical model of a fully flexible chain of N+1 linked beads which, in the limit of smooth bending, is equivalent to the well-known wormlike chain model. The partition function with the kinetic and bending energies and correlations between orientations of any pair of links and velocities of any pair of beads are found. This solution is precise in the limits of small and large rigidity-to-temperature ratio b/T. The last exact solution is essential as even very "harmless" approximation results in loss of the important effects when the chain is very rigid. For very high b/T, the orientations of different links become fully correlated. Nevertheless, the chain does not go over into a hard rod even in the limit b/T→∞: While the velocity correlation length diverges, the correlations themselves remain weak and tend to the value ∝T/(N+1). The N dependence of the partition function is essentially determined by the kinetic energy contribution. We demonstrate that to obtain the correct energy and entropy in a constrained system, the T derivative of the partition function has to be applied before integration over the constraint-setting variable.

Statistical model of a flexible inextensible polymer chain: The effect of kinetic energy

NASA Astrophysics Data System (ADS)

Pergamenshchik, V. M.; Vozniak, A. B.

2017-01-01

Because of the holonomic constraints, the kinetic energy contribution in the partition function of an inextensible polymer chain is difficult to find, and it has been systematically ignored. We present the first thermodynamic calculation incorporating the kinetic energy of an inextensible polymer chain with the bending energy. To explore the effect of the translation-rotation degrees of freedom, we propose and solve a statistical model of a fully flexible chain of N +1 linked beads which, in the limit of smooth bending, is equivalent to the well-known wormlike chain model. The partition function with the kinetic and bending energies and correlations between orientations of any pair of links and velocities of any pair of beads are found. This solution is precise in the limits of small and large rigidity-to-temperature ratio b /T . The last exact solution is essential as even very "harmless" approximation results in loss of the important effects when the chain is very rigid. For very high b /T , the orientations of different links become fully correlated. Nevertheless, the chain does not go over into a hard rod even in the limit b /T →∞ : While the velocity correlation length diverges, the correlations themselves remain weak and tend to the value ∝T /(N +1 ). The N dependence of the partition function is essentially determined by the kinetic energy contribution. We demonstrate that to obtain the correct energy and entropy in a constrained system, the T derivative of the partition function has to be applied before integration over the constraint-setting variable.

Recent advances in parametric neuroreceptor mapping with dynamic PET: basic concepts and graphical analyses.

PubMed

Seo, Seongho; Kim, Su Jin; Lee, Dong Soo; Lee, Jae Sung

2014-10-01

Tracer kinetic modeling in dynamic positron emission tomography (PET) has been widely used to investigate the characteristic distribution patterns or dysfunctions of neuroreceptors in brain diseases. Its practical goal has progressed from regional data quantification to parametric mapping that produces images of kinetic-model parameters by fully exploiting the spatiotemporal information in dynamic PET data. Graphical analysis (GA) is a major parametric mapping technique that is independent on any compartmental model configuration, robust to noise, and computationally efficient. In this paper, we provide an overview of recent advances in the parametric mapping of neuroreceptor binding based on GA methods. The associated basic concepts in tracer kinetic modeling are presented, including commonly-used compartment models and major parameters of interest. Technical details of GA approaches for reversible and irreversible radioligands are described, considering both plasma input and reference tissue input models. Their statistical properties are discussed in view of parametric imaging.

A continued fraction resummation form of bath relaxation effect in the spin-boson model

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

Gong, Zhihao; Tang, Zhoufei; Wu, Jianlan, E-mail: jianlanwu@zju.edu.cn

2015-02-28

In the spin-boson model, a continued fraction form is proposed to systematically resum high-order quantum kinetic expansion (QKE) rate kernels, accounting for the bath relaxation effect beyond the second-order perturbation. In particular, the analytical expression of the sixth-order QKE rate kernel is derived for resummation. With higher-order correction terms systematically extracted from higher-order rate kernels, the resummed quantum kinetic expansion approach in the continued fraction form extends the Pade approximation and can fully recover the exact quantum dynamics as the expansion order increases.

Attenuation characteristics of electromagnetic waves in a weak collisional and fully ionized dusty plasma

NASA Astrophysics Data System (ADS)

Dan, Li; Guo, Li-Xin; Li, Jiang-Ting; Chen, Wei; Yan, Xu; Huang, Qing-Qing

2017-09-01

The expression of complex dielectric permittivity for non-magnetized fully ionized dusty plasma is obtained based on the kinetic equation in the Fokker-Planck-Landau collision model and the charging equation of the statistical theory. The influences of density, average size of dust grains, and balanced charging of the charge number of dust particles on the attenuation properties of electromagnetic waves in fully ionized dusty plasma are investigated by calculating the attenuation constant. In addition, the attenuation characteristics of weakly ionized and fully ionized dusty plasmas are compared. Results enriched the physical mechanisms of microwave attenuation for fully ionized dusty plasma and provide a theoretical basis for future studies.

Electromagnetic particle-in-cell simulations of the solar wind interaction with lunar magnetic anomalies.

PubMed

Deca, J; Divin, A; Lapenta, G; Lembège, B; Markidis, S; Horányi, M

2014-04-18

We present the first three-dimensional fully kinetic and electromagnetic simulations of the solar wind interaction with lunar crustal magnetic anomalies (LMAs). Using the implicit particle-in-cell code iPic3D, we confirm that LMAs may indeed be strong enough to stand off the solar wind from directly impacting the lunar surface forming a mini-magnetosphere, as suggested by spacecraft observations and theory. In contrast to earlier magnetohydrodynamics and hybrid simulations, the fully kinetic nature of iPic3D allows us to investigate the space charge effects and in particular the electron dynamics dominating the near-surface lunar plasma environment. We describe for the first time the interaction of a dipole model centered just below the lunar surface under plasma conditions such that only the electron population is magnetized. The fully kinetic treatment identifies electromagnetic modes that alter the magnetic field at scales determined by the electron physics. Driven by strong pressure anisotropies, the mini-magnetosphere is unstable over time, leading to only temporal shielding of the surface underneath. Future human exploration as well as lunar science in general therefore hinges on a better understanding of LMAs.

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.

Symmetry breaking patterns for inflation

NASA Astrophysics Data System (ADS)

Klein, Remko; Roest, Diederik; Stefanyszyn, David

2018-06-01

We study inflationary models where the kinetic sector of the theory has a non-linearly realised symmetry which is broken by the inflationary potential. We distinguish between kinetic symmetries which non-linearly realise an internal or space-time group, and which yield a flat or curved scalar manifold. This classification leads to well-known inflationary models such as monomial inflation and α-attractors, as well as a new model based on fixed couplings between a dilaton and many axions which non-linearly realises higher-dimensional conformal symmetries. In this model, inflation can be realised along the dilatonic direction, leading to a tensor-to-scalar ratio r ˜ 0 .01 and a spectral index n s ˜ 0 .975. We refer to the new model as ambient inflation since inflation proceeds along an isometry of an anti-de Sitter ambient space-time, which fully determines the kinetic sector.

Carbonic Anhydrase, Calcification Dynamics and Stable Isotope Vital Effects: Deep Sea Corals and Beyond

NASA Astrophysics Data System (ADS)

Chen, S.; Gagnon, A. C.; Adkins, J. F.

2017-12-01

The stable isotope compositions of biogenic carbonates have been used for paleoceanographic and paleoclimatic reconstructions for decades, and produced some of the most iconic records in the field. However, we still lack a fully mechanistic understanding of the stable isotope proxies, especially the biological overprint on the environmental signals termed "vital effects". A ubiquitous feature of stable isotope vital effects in marine calcifying organisms is a strong correlation between δ18O and δ13C in a range of values that are depleted from equilibrium. Two mechanisms have been proposed to explain this correlation, one based on kinetic isotope effects during CO2(aq)-HCO3- inter-conversion, the other based on equilibrium isotope exchange during pH dependent speciation of the dissolved inorganic carbon pool. Neither mechanism explains all the stable isotope features observed in biogenic carbonates. Here we present a fully kinetic model of biomineralization and its isotope effects using deep sea corals as a test organism. A key component of our model is the consideration of the enzyme carbonic anhydrase in catalyzing the CO2(aq)-HCO3- inter-conversion reactions in the extracellular calcifying fluid (ECF). We find that the amount of carbonic anhydrase not only modulates the carbonate chemistry of the calcifying fluid, but also helps explain the slope of the δ18O-δ13C correlation. With this model, we are not only able to fit deep sea coral data, but also explain the stable isotope vital effects of other calcifying organisms. This fully kinetic model of stable isotope vital effects and the underlying calcification dynamics may also help us better understand mechanisms of other paleoceanographic tracers in biogenic carbonates, including boron isotopes and trace metal proxies.

Arctic Ocean Cyclostratigraphy: An Alternative to Marine Oxygen Isotope curves as measures of Cryospheric and Sea-Level History

NASA Astrophysics Data System (ADS)

Cronin, T. M.; Marzen, R.; O'Regan, M.; Dwyer, G. S.

2016-12-01

The stable isotope compositions of biogenic carbonates have been used for paleoceanographic and paleoclimatic reconstructions for decades, and produced some of the most iconic records in the field. However, we still lack a fully mechanistic understanding of the stable isotope proxies, especially the biological overprint on the environmental signals termed "vital effects". A ubiquitous feature of stable isotope vital effects in marine calcifying organisms is a strong correlation between δ18O and δ13C in a range of values that are depleted from equilibrium. Two mechanisms have been proposed to explain this correlation, one based on kinetic isotope effects during CO2(aq)-HCO3- inter-conversion, the other based on equilibrium isotope exchange during pH dependent speciation of the dissolved inorganic carbon pool. Neither mechanism explains all the stable isotope features observed in biogenic carbonates. Here we present a fully kinetic model of biomineralization and its isotope effects using deep sea corals as a test organism. A key component of our model is the consideration of the enzyme carbonic anhydrase in catalyzing the CO2(aq)-HCO3- inter-conversion reactions in the extracellular calcifying fluid (ECF). We find that the amount of carbonic anhydrase not only modulates the carbonate chemistry of the calcifying fluid, but also helps explain the slope of the δ18O-δ13C correlation. With this model, we are not only able to fit deep sea coral data, but also explain the stable isotope vital effects of other calcifying organisms. This fully kinetic model of stable isotope vital effects and the underlying calcification dynamics may also help us better understand mechanisms of other paleoceanographic tracers in biogenic carbonates, including boron isotopes and trace metal proxies.

On the relationship between kinetic and fluid formalisms for convection in the inner magnetosphere

NASA Astrophysics Data System (ADS)

Song, Yang; Sazykin, Stanislav; Wolf, Richard A.

2008-08-01

In the inner magnetosphere, the plasma flows are mostly slow compared to thermal or Alfvén speeds, but the convection is far away from the ideal magnetohydrodynamic regime since the gradient/curvature drifts become significant. Both kinetic (Wolf, 1983) and two-fluid (Peymirat and Fontaine, 1994; Heinemann, 1999) formalisms have been used to describe plasma dynamics, but it is not fully understood how they relate to each other. We explore the relations among kinetic, fluid, and recently developed "average" (Liu, 2006) models in an attempt to find the simplest yet realistic way to describe the convection. First, we prove analytically that the model of (Liu, 2006), when closed with the assumption of a Maxwellian distribution, is equivalent to the fluid model of (Heinemann, 1999). Second, we analyze the transport of both one-dimensional and two-dimensional Gaussian-shaped blob of hot plasma. For the kinetic case, it is known that the time evolution of such a blob is gradual spreading in time. For the fluid case, Heinemann and Wolf (2001a, 2001b) showed that in a one-dimensional idealized case, the blob separates into two drifting at different speeds. We present a fully nonlinear solution of this case, confirming this behavior but demonstrating what appears to be a shocklike steepening of the faster drifting secondary blob. A new, more realistic two-dimensional example using the dipole geometry with a uniform electric field confirms the one-dimensional solutions. Implications for the numerical simulations of magnetospheric dynamics are discussed.

3D nozzle flow simulations including state-to-state kinetics calculation

NASA Astrophysics Data System (ADS)

Cutrone, L.; Tuttafesta, M.; Capitelli, M.; Schettino, A.; Pascazio, G.; Colonna, G.

2014-12-01

In supersonic and hypersonic flows, thermal and chemical non-equilibrium is one of the fundamental aspects that must be taken into account for the accurate characterization of the plasma. In this paper, we present an optimized methodology to approach plasma numerical simulation by state-to-state kinetics calculations in a fully 3D Navier-Stokes CFD solver. Numerical simulations of an expanding flow are presented aimed at comparing the behavior of state-to-state chemical kinetics models with respect to the macroscopic thermochemical non-equilibrium models that are usually used in the numerical computation of high temperature hypersonic flows. The comparison is focused both on the differences in the numerical results and on the computational effort associated with each approach.

Computation of turbulent boundary layer flows with an algebraic stress turbulence model

NASA Technical Reports Server (NTRS)

Kim, Sang-Wook; Chen, Yen-Sen

1986-01-01

An algebraic stress turbulence model is presented, characterized by the following: (1) the eddy viscosity expression is derived from the Reynolds stress turbulence model; (2) the turbulent kinetic energy dissipation rate equation is improved by including a production range time scale; and (3) the diffusion coefficients for turbulence equations are adjusted so that the kinetic energy profile extends further into the free stream region found in most experimental data. The turbulent flow equations were solved using a finite element method. Examples include: fully developed channel flow, fully developed pipe flow, flat plate boundary layer flow, plane jet exhausting into a moving stream, circular jet exhausting into a moving stream, and wall jet flow. Computational results compare favorably with experimental data for most of the examples considered. Significantly improved results were obtained for the plane jet flow, the circular jet flow, and the wall jet flow; whereas the remainder are comparable to those obtained by finite difference methods using the standard kappa-epsilon turbulence model. The latter seems to be promising with further improvement of the expression for the eddy viscosity coefficient.

Three dimensional fluid-kinetic model of a magnetically guided plasma jet

NASA Astrophysics Data System (ADS)

Ramos, Jesús J.; Merino, Mario; Ahedo, Eduardo

2018-06-01

A fluid-kinetic model of the collisionless plasma flow in a convergent-divergent magnetic nozzle is presented. The model combines the leading-order Vlasov equation and the fluid continuity and perpendicular momentum equation for magnetized electrons, and the fluid equations for cold ions, which must be solved iteratively to determine the self-consistent plasma response in a three-dimensional magnetic field. The kinetic electron solution identifies three electron populations and provides the plasma density and pressure tensor. The far downstream asymptotic behavior shows the anisotropic cooling of the electron populations. The fluid equations determine the electric potential and the fluid velocities. In the small ion-sound gyroradius case, the solution is constructed one magnetic line at a time. In the large ion-sound gyroradius case, ion detachment from magnetic lines makes the problem fully three-dimensional.

Origami Arrays as Substrates for the Determination of Reaction Kinetics Using High-Speed Atomic Force Microscopy.

PubMed

Rahman, Masudur; Day, B Scott; Neff, David; Norton, Michael L

2017-08-01

DNA nanostructures (DN) are powerful platforms for the programmable assembly of nanomaterials. As applications for DN both as a structural material and as a support for functional biomolecular sensing systems develop, methods enabling the determination of reaction kinetics in real time become increasingly important. In this report, we present a study of the kinetics of streptavidin binding onto biotinylated DN constructs enabled by these planar structures. High-speed AFM was employed at a 2.5 frame/s rate to evaluate the kinetics and indicates that the binding fully saturates in less than 60 s. When the the data was fitted with an adsorption-limited kinetic model, a forward rate constant of 5.03 × 10 5 s -1 was found.

Towards a fully kinetic 3D electromagnetic particle-in-cell model of streamer formation and dynamics in high-pressure electronegative gases

NASA Astrophysics Data System (ADS)

Rose, D. V.; Welch, D. R.; Clark, R. E.; Thoma, C.; Zimmerman, W. R.; Bruner, N.; Rambo, P. K.; Atherton, B. W.

2011-09-01

Streamer and leader formation in high pressure devices is dynamic process involving a broad range of physical phenomena. These include elastic and inelastic particle collisions in the gas, radiation generation, transport and absorption, and electrode interactions. Accurate modeling of these physical processes is essential for a number of applications, including high-current, laser-triggered gas switches. Towards this end, we present a new 3D implicit particle-in-cell simulation model of gas breakdown leading to streamer formation in electronegative gases. The model uses a Monte Carlo treatment for all particle interactions and includes discrete photon generation, transport, and absorption for ultra-violet and soft x-ray radiation. Central to the realization of this fully kinetic particle treatment is an algorithm that manages the total particle count by species while preserving the local momentum distribution functions and conserving charge [D. R. Welch, T. C. Genoni, R. E. Clark, and D. V. Rose, J. Comput. Phys. 227, 143 (2007)]. The simulation model is fully electromagnetic, making it capable of following, for example, the evolution of a gas switch from the point of laser-induced localized breakdown of the gas between electrodes through the successive stages of streamer propagation, initial electrode current connection, and high-current conduction channel evolution, where self-magnetic field effects are likely to be important. We describe the model details and underlying assumptions used and present sample results from 3D simulations of streamer formation and propagation in SF6.

Modeling of kinetic, ionospheric and auroral contributions to the 557.7-nm nightglow

NASA Astrophysics Data System (ADS)

Campbell, L.; Brunger, M. J.

2010-11-01

Emission of 557.7-nm radiation from the Earth's upper atmosphere is produced by kinetic, ionospheric and auroral excitation of oxygen atoms. The mechanisms and hence the relative contributions of these three sources are not fully understood. A ground-based mid-latitude recording of the 557.7-nm emissions over the previous solar cycle facilitates a comparison of measurements with theoretical predictions. In this paper the predicted kinetic and ionospheric contributions are simulated and compared with the observations. Semi-quantitative agreement is found between the kinetic contribution and the observations, particularly in the presence of annual, semi-annual and solar cycle variations. An observed enhancement in the emissions in the years following solar maximum is not predicted by the kinetic model. However, correlation analysis reveals a component in the observed values that is related to the auroral hemispheric power. When this extra component is included, a better fit to the pre-midnight observations over the full solar cycle is found.

Electron inertia and quasi-neutrality in the Weibel instability

NASA Astrophysics Data System (ADS)

Camporeale, Enrico; Tronci, Cesare

2017-06-01

While electron kinetic effects are well known to be of fundamental importance in several situations, the electron mean-flow inertia is often neglected when length scales below the electron skin depth become irrelevant. This has led to the formulation of different reduced models, where electron inertia terms are discarded while retaining some or all kinetic effects. Upon considering general full-orbit particle trajectories, this paper compares the dispersion relations emerging from such models in the case of the Weibel instability. As a result, the question of how length scales below the electron skin depth can be neglected in a kinetic treatment emerges as an unsolved problem, since all current theories suffer from drawbacks of different nature. Alternatively, we discuss fully kinetic theories that remove all these drawbacks by restricting to frequencies well below the plasma frequency of both ions and electrons. By giving up on the length scale restrictions appearing in previous works, these models are obtained by assuming quasi-neutrality in the full Vlasov-Maxwell system.

A finite element computation of turbulent boundary layer flows with an algebraic stress turbulence model

NASA Technical Reports Server (NTRS)

Kim, Sang-Wook; Chen, Yen-Sen

1988-01-01

An algebraic stress turbulence model and a computational procedure for turbulent boundary layer flows which is based on the semidiscrete Galerkin FEM are discussed. In the algebraic stress turbulence model, the eddy viscosity expression is obtained from the Reynolds stress turbulence model, and the turbulent kinetic energy dissipation rate equation is improved by including a production range time scale. Good agreement with experimental data is found for the examples of a fully developed channel flow, a fully developed pipe flow, a flat plate boundary layer flow, a plane jet exhausting into a moving stream, a circular jet exhausting into a moving stream, and a wall jet flow.

Instabilities and Turbulence Generation by Pick-Up Ion Distributions in the Outer Heliosheath

NASA Astrophysics Data System (ADS)

Weichman, K.; Roytershteyn, V.; Delzanno, G. L.; Pogorelov, N.

2017-12-01

Pick-up ions (PUIs) play a significant role in the dynamics of the heliosphere. One problem that has attracted significant attention is the stability of ring-like distributions of PUIs and the electromagnetic fluctuations that could be generated by PUI distributions. For example, PUI stability is relevant to theories attempting to identify the origins of the IBEX ribbon. PUIs have previously been investigated by linear stability analysis of model (e.g. Gaussian) rings and corresponding computer simulations. The majority of these simulations utilized particle-in-cell methods which suffer from accuracy limitations imposed by the statistical noise associated with representing the plasma by a relatively small number of computational particles. In this work, we utilize highly accurate spectral Vlasov simulations conducted using the fully kinetic implicit code SPS (Spectral Plasma Solver) to investigate the PUI distributions inferred from a global heliospheric model (Heerikhuisen et al., 2016). Results are compared with those obtained by hybrid and fully kinetic particle-in-cell methods.

3D CFD Modeling of the LMF System: Desulfurization Kinetics

NASA Astrophysics Data System (ADS)

Cao, Qing; Pitts, April; Zhang, Daojie; Nastac, Laurentiu; Williams, Robert

A fully transient 3D CFD modeling approach capable of predicting the three phase (gas, slag and steel) fluid flow characteristics and behavior of the slag/steel interface in the argon gas bottom stirred ladle with two off-centered porous plugs (Ladle Metallurgical Furnace or LMF) has been recently developed. The model predicts reasonably well the fluid flow characteristics in the LMF system and the observed size of the slag eyes for both the high-stirring and low-stirring conditions. A desulfurization reaction kinetics model considering metal/slag interface characteristics is developed in conjunction with the CFD modeling approach. The model is applied in this study to determine the effects of processing time, and gas flow rate on the efficiency of desulfurization in the studied LMF system.

Kinetic theory of age-structured stochastic birth-death processes

NASA Astrophysics Data System (ADS)

Greenman, Chris D.; Chou, Tom

2016-01-01

Classical age-structured mass-action models such as the McKendrick-von Foerster equation have been extensively studied but are unable to describe stochastic fluctuations or population-size-dependent birth and death rates. Stochastic theories that treat semi-Markov age-dependent processes using, e.g., the Bellman-Harris equation do not resolve a population's age structure and are unable to quantify population-size dependencies. Conversely, current theories that include size-dependent population dynamics (e.g., mathematical models that include carrying capacity such as the logistic equation) cannot be easily extended to take into account age-dependent birth and death rates. In this paper, we present a systematic derivation of a new, fully stochastic kinetic theory for interacting age-structured populations. By defining multiparticle probability density functions, we derive a hierarchy of kinetic equations for the stochastic evolution of an aging population undergoing birth and death. We show that the fully stochastic age-dependent birth-death process precludes factorization of the corresponding probability densities, which then must be solved by using a Bogoliubov--Born--Green--Kirkwood--Yvon-like hierarchy. Explicit solutions are derived in three limits: no birth, no death, and steady state. These are then compared with their corresponding mean-field results. Our results generalize both deterministic models and existing master equation approaches by providing an intuitive and efficient way to simultaneously model age- and population-dependent stochastic dynamics applicable to the study of demography, stem cell dynamics, and disease evolution.

3D Hall MHD-EPIC Simulations of Ganymede's Magnetosphere

NASA Astrophysics Data System (ADS)

Zhou, H.; Toth, G.; Jia, X.

2017-12-01

Fully kinetic modeling of a complete 3D magnetosphere is still computationally expensive and not feasible on current computers. While magnetohydrodynamic (MHD) models have been successfully applied to a wide range of plasma simulation, they cannot capture some important kinetic effects. We have recently developed a new modeling tool to embed the implicit particle-in-cell (PIC) model iPIC3D into the Block-Adaptive-Tree-Solarwind-Roe-Upwind-Scheme (BATS-R-US) magnetohydrodynamic model. This results in a kinetic model of the regions where kinetic effects are important. In addition to the MHD-EPIC modeling of the magnetosphere, the improved model presented here is now able to represent the moon as a resistive body. We use a stretched spherical grid with adaptive mesh refinement (AMR) to capture the resistive body and its boundary. A semi-implicit scheme is employed for solving the magnetic induction equation to allow time steps that are not limited by the resistivity. We have applied the model to Ganymede, the only moon in the solar system known to possess a strong intrinsic magnetic field, and included finite resistivity beneath the moon`s surface to model the electrical properties of the interior in a self-consistent manner. The kinetic effects of electrons and ions on the dayside magnetopause and tail current sheet are captured with iPIC3D. Magnetic reconnections under different upstream background conditions of several Galileo flybys are simulated to study the global reconnection rate and the magnetospheric dynamics

Modeling Disturbance Dynamics in Transitional and Turbulent Boundary Layers

NASA Technical Reports Server (NTRS)

Grosch, C. E.; Gatski, T. B. (Technical Monitor)

2002-01-01

The dynamics of an ensemble of linear disturbances in boundary-layer flows at various Reynolds numbers is studied through an analysis of the transport equations for the mean disturbance kinetic energy and energy dissipation rate. Effects of adverse and favorable pressure-gradients on the disturbance dynamics are also included in the analysis. Unlike the fully turbulent regime where nonlinear phase scrambling of the fluctuations affects the flow field even in proximity to the wall, the early stage transition regime fluctuations studied here are influenced across the boundary layer by the solid boundary. In addition, the dominating dynamics in the disturbance kinetic energy equation is governed by the energy production, pressure-transport and viscous diffusion - also in contrast to the fully turbulent regime. For the disturbance dissipation rate, a dynamic balance exists between the destruction and diffusion of dissipation.

Modeling of near-wall turbulence

NASA Technical Reports Server (NTRS)

Shih, T. H.; Mansour, N. N.

1990-01-01

An improved k-epsilon model and a second order closure model is presented for low Reynolds number turbulence near a wall. For the k-epsilon model, a modified form of the eddy viscosity having correct asymptotic near wall behavior is suggested, and a model for the pressure diffusion term in the turbulent kinetic energy equation is proposed. For the second order closure model, the existing models are modified for the Reynolds stress equations to have proper near wall behavior. A dissipation rate equation for the turbulent kinetic energy is also reformulated. The proposed models satisfy realizability and will not produce unphysical behavior. Fully developed channel flows are used for model testing. The calculations are compared with direct numerical simulations. It is shown that the present models, both the k-epsilon model and the second order closure model, perform well in predicting the behavior of the near wall turbulence. Significant improvements over previous models are obtained.

Zonal PANS: evaluation of different treatments of the RANS-LES interface

NASA Astrophysics Data System (ADS)

Davidson, L.

2016-03-01

The partially Reynolds-averaged Navier-Stokes (PANS) model can be used to simulate turbulent flows either as RANS, large eddy simulation (LES) or DNS. Its main parameter is fk whose physical meaning is the ratio of the modelled to the total turbulent kinetic energy. In RANS fk = 1, in DNS fk = 0 and in LES fk takes values between 0 and 1. Three different ways of prescribing fk are evaluated for decaying grid turbulence and fully developed channel flow: fk = 0.4, fk = k3/2tot/ɛ and, from its definition, fk = k/ktot where ktot is the sum of the modelled, k, and resolved, kres, turbulent kinetic energy. It is found that the fk = 0.4 gives the best results. In Girimaji and Wallin, a method was proposed to include the effect of the gradient of fk. This approach is used at RANS- LES interface in the present study. Four different interface models are evaluated in fully developed channel flow and embedded LES of channel flow: in both cases, PANS is used as a zonal model with fk = 1 in the unsteady RANS (URANS) region and fk = 0.4 in the LES region. In fully developed channel flow, the RANS- LES interface is parallel to the wall (horizontal) and in embedded LES, it is parallel to the inlet (vertical). The importance of the location of the horizontal interface in fully developed channel flow is also investigated. It is found that the location - and the choice of the treatment at the interface - may be critical at low Reynolds number or if the interface is placed too close to the wall. The reason is that the modelled turbulent shear stress at the interface is large and hence the relative strength of the resolved turbulence is small. In RANS, the turbulent viscosity - and consequently also the modelled Reynolds shear stress - is only weakly dependent on Reynolds number. It is found in the present work that it also applies in the URANS region.

Modelling Precipitation Kinetics During Aging of Al-Mg-Si Alloys

NASA Astrophysics Data System (ADS)

Du, Qiang; Friis, Jepser

A classical Kaufmann-Wagner numerical model is employed to predict the evolution of precipitate size distribution during the aging treatment of Al-Mg-Si alloys. One feature of the model is its fully coupling with CALPHAD database, and with the input of interfacial energy from ab-initial calculation, it is able to capture the morphological change of the precipitates. The simulation results will be compared with the experimental measurements.

Reynolds-Stress and Triple-Product Models Applied to a Flow with Rotation and Curvature

NASA Technical Reports Server (NTRS)

Olsen, Michael E.

2016-01-01

Turbulence models, with increasing complexity, up to triple product terms, are applied to the flow in a rotating pipe. The rotating pipe is a challenging case for turbulence models as it contains significant rotational and curvature effects. The flow field starts with the classic fully developed pipe flow, with a stationary pipe wall. This well defined condition is then subjected to a section of pipe with a rotating wall. The rotating wall introduces a second velocity scale, and creates Reynolds shear stresses in the radial-circumferential and circumferential-axial planes. Furthermore, the wall rotation introduces a flow stabilization, and actually reduces the turbulent kinetic energy as the flow moves along the rotating wall section. It is shown in the present work that the Reynolds stress models are capable of predicting significant reduction in the turbulent kinetic energy, but triple product improves the predictions of the centerline turbulent kinetic energy, which is governed by convection, dissipation and transport terms, as the production terms vanish on the pipe axis.

Combustion Of Metals In Reduced Gravity And Extraterrestrial Environments

NASA Technical Reports Server (NTRS)

Abbud-Madrid, A.; Modak, A.; Branch, M. C.

2003-01-01

The recent focus of this research project has been to model the combustion of isolated metal droplets and, in particular, to couple the existing theories and formulations of phenomena such as condensation, reaction kinetics, radiation, and surface reactions to formulate a more complete combustion model. A fully transient, one-dimensional (spherical symmetry) numerical model that uses detailed chemical kinetics, multi-component molecular transport mechanisms, condensation kinetics, and gas phase radiation heat transfer was developed. A coagulation model was used to simulate the particulate formation of MgO. The model was used to simulate the combustion of an Mg droplet in pure O2 and CO2. Methanol droplet combustion is considered as a test case for the solution method for both quasi-steady and fully transient simulations. Although some important processes unique to methanol combustion, such as water absorption at the surface, are not included in the model, the results are in sufficient agreement with the published data. Since the major part of the heat released in combustion of Mg, and in combustion of metals in general, is due to the condensation of the metal oxide, it is very important to capture the condensation processes correctly. Using the modified nucleation theory, an Arrhenius type rate expression is derived to calculate the condensation rate of MgO. This expression can be easily included in the CHEMKIN reaction mechanism format. Although very little property data is available for MgO, the condensation rate expression derived using the existing data is able to capture the condensation of MgO. An appropriate choice of the reference temperature to calculate the rate coefficients allows the model to correctly predict the subsequent heat release and hence the flame temperature.

Matrix Characterization and Development for the Vacuum Assisted Resin Transfer Molding Process

NASA Technical Reports Server (NTRS)

Grimsley, B. W.; Hubert, P.; Hou, T. H.; Cano, R. J.; Loos, A. C.; Pipes, R. B.

2001-01-01

The curing kinetics and viscosity of an epoxy resin system, SI-ZG-5A, have been characterized for application in the vacuum assisted resin transfer molding (VARTM) process. Impregnation of a typical carbon fiber perform provided the test bed for the characterization. Process simulations were carried out using the process model, COMPRO, to examine heat transfer and curing kinetics for a fully impregnated panel, neglecting resin flow. The predicted viscosity profile and final degree of cure were found to be in good agreement with experimental observations.

Non-equilibrium radiation from viscous chemically reacting two-phase exhaust plumes

NASA Technical Reports Server (NTRS)

Penny, M. M.; Smith, S. D.; Mikatarian, R. R.; Ring, L. R.; Anderson, P. G.

1976-01-01

A knowledge of the structure of the rocket exhaust plumes is necessary to solve problems involving plume signatures, base heating, plume/surface interactions, etc. An algorithm is presented which treats the viscous flow of multiphase chemically reacting fluids in a two-dimensional or axisymmetric supersonic flow field. The gas-particle flow solution is fully coupled with the chemical kinetics calculated using an implicit scheme to calculate chemical production rates. Viscous effects include chemical species diffusion with the viscosity coefficient calculated using a two-equation turbulent kinetic energy model.

Study of electron transport in a Hall thruster by axial–radial fully kinetic particle simulation

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

Cho, Shinatora, E-mail: choh.shinatora@jaxa.jp; Kubota, Kenichi; Funaki, Ikkoh

2015-10-15

Electron transport across a magnetic field in a magnetic-layer-type Hall thruster was numerically investigated for the future predictive modeling of Hall thrusters. The discharge of a 1-kW-class magnetic-layer-type Hall thruster designed for high-specific-impulse operation was modeled using an r-z two-dimensional fully kinetic particle code with and without artificial electron-diffusion models. The thruster performance results showed that both electron transport models captured the experimental result within discrepancies less than 20% in thrust and discharge current for all the simulated operation conditions. The electron cross-field transport mechanism of the so-called anomalous diffusion was self-consistently observed in the simulation without artificial diffusion models;more » the effective electron mobility was two orders of magnitude higher than the value obtained using the classical diffusion theory. To account for the self-consistently observed anomalous transport, the oscillation of plasma properties was speculated. It was suggested that the enhanced random-walk diffusion due to the velocity oscillation of low-frequency electron flow could explain the observed anomalous diffusion within an order of magnitude. The dominant oscillation mode of the electron flow velocity was found to be 20 kHz, which was coupled to electrostatic oscillation excited by global ionization instability.« less

A multiple-time-scale turbulence model based on variable partitioning of turbulent kinetic energy spectrum

NASA Technical Reports Server (NTRS)

Kim, S.-W.; Chen, C.-P.

1987-01-01

A multiple-time-scale turbulence model of a single point closure and a simplified split-spectrum method is presented. In the model, the effect of the ratio of the production rate to the dissipation rate on eddy viscosity is modeled by use of the multiple-time-scales and a variable partitioning of the turbulent kinetic energy spectrum. The concept of a variable partitioning of the turbulent kinetic energy spectrum and the rest of the model details are based on the previously reported algebraic stress turbulence model. Example problems considered include: a fully developed channel flow, a plane jet exhausting into a moving stream, a wall jet flow, and a weakly coupled wake-boundary layer interaction flow. The computational results compared favorably with those obtained by using the algebraic stress turbulence model as well as experimental data. The present turbulence model, as well as the algebraic stress turbulence model, yielded significantly improved computational results for the complex turbulent boundary layer flows, such as the wall jet flow and the wake boundary layer interaction flow, compared with available computational results obtained by using the standard kappa-epsilon turbulence model.

A multiple-time-scale turbulence model based on variable partitioning of the turbulent kinetic energy spectrum

NASA Technical Reports Server (NTRS)

Kim, S.-W.; Chen, C.-P.

1989-01-01

A multiple-time-scale turbulence model of a single point closure and a simplified split-spectrum method is presented. In the model, the effect of the ratio of the production rate to the dissipation rate on eddy viscosity is modeled by use of the multiple-time-scales and a variable partitioning of the turbulent kinetic energy spectrum. The concept of a variable partitioning of the turbulent kinetic energy spectrum and the rest of the model details are based on the previously reported algebraic stress turbulence model. Example problems considered include: a fully developed channel flow, a plane jet exhausting into a moving stream, a wall jet flow, and a weakly coupled wake-boundary layer interaction flow. The computational results compared favorably with those obtained by using the algebraic stress turbulence model as well as experimental data. The present turbulence model, as well as the algebraic stress turbulence model, yielded significantly improved computational results for the complex turbulent boundary layer flows, such as the wall jet flow and the wake boundary layer interaction flow, compared with available computational results obtained by using the standard kappa-epsilon turbulence model.

A scalable, fully implicit algorithm for the reduced two-field low-β extended MHD model

DOE PAGES

Chacon, Luis; Stanier, Adam John

2016-12-01

Here, we demonstrate a scalable fully implicit algorithm for the two-field low-β extended MHD model. This reduced model describes plasma behavior in the presence of strong guide fields, and is of significant practical impact both in nature and in laboratory plasmas. The model displays strong hyperbolic behavior, as manifested by the presence of fast dispersive waves, which make a fully implicit treatment very challenging. In this study, we employ a Jacobian-free Newton–Krylov nonlinear solver, for which we propose a physics-based preconditioner that renders the linearized set of equations suitable for inversion with multigrid methods. As a result, the algorithm ismore » shown to scale both algorithmically (i.e., the iteration count is insensitive to grid refinement and timestep size) and in parallel in a weak-scaling sense, with the wall-clock time scaling weakly with the number of cores for up to 4096 cores. For a 4096 × 4096 mesh, we demonstrate a wall-clock-time speedup of ~6700 with respect to explicit algorithms. The model is validated linearly (against linear theory predictions) and nonlinearly (against fully kinetic simulations), demonstrating excellent agreement.« less

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data

NASA Astrophysics Data System (ADS)

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-01

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

Machine learning-based kinetic modeling: a robust and reproducible solution for quantitative analysis of dynamic PET data.

PubMed

Pan, Leyun; Cheng, Caixia; Haberkorn, Uwe; Dimitrakopoulou-Strauss, Antonia

2017-05-07

A variety of compartment models are used for the quantitative analysis of dynamic positron emission tomography (PET) data. Traditionally, these models use an iterative fitting (IF) method to find the least squares between the measured and calculated values over time, which may encounter some problems such as the overfitting of model parameters and a lack of reproducibility, especially when handling noisy data or error data. In this paper, a machine learning (ML) based kinetic modeling method is introduced, which can fully utilize a historical reference database to build a moderate kinetic model directly dealing with noisy data but not trying to smooth the noise in the image. Also, due to the database, the presented method is capable of automatically adjusting the models using a multi-thread grid parameter searching technique. Furthermore, a candidate competition concept is proposed to combine the advantages of the ML and IF modeling methods, which could find a balance between fitting to historical data and to the unseen target curve. The machine learning based method provides a robust and reproducible solution that is user-independent for VOI-based and pixel-wise quantitative analysis of dynamic PET data.

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.

Full particle-in-cell simulations of kinetic equilibria and the role of the initial current sheet on steady asymmetric magnetic reconnection

NASA Astrophysics Data System (ADS)

Dargent, J.; Aunai, N.; Belmont, G.; Dorville, N.; Lavraud, B.; Hesse, M.

2016-06-01

> Tangential current sheets are ubiquitous in space plasmas and yet hard to describe with a kinetic equilibrium. In this paper, we use a semi-analytical model, the BAS model, which provides a steady ion distribution function for a tangential asymmetric current sheet and we prove that an ion kinetic equilibrium produced by this model remains steady in a fully kinetic particle-in-cell simulation even if the electron distribution function does not satisfy the time independent Vlasov equation. We then apply this equilibrium to look at the dependence of magnetic reconnection simulations on their initial conditions. We show that, as the current sheet evolves from a symmetric to an asymmetric upstream plasma, the reconnection rate is impacted and the X line and the electron flow stagnation point separate from one another and start to drift. For the simulated systems, we investigate the overall evolution of the reconnection process via the classical signatures discussed in the literature and searched in the Magnetospheric MultiScale data. We show that they seem robust and do not depend on the specific details of the internal structure of the initial current sheet.

Particle-In-Cell Modeling For MJ Dense Plasma Focus with Varied Anode Shape

NASA Astrophysics Data System (ADS)

Link, A.; Halvorson, C.; Schmidt, A.; Hagen, E. C.; Rose, D.; Welch, D.

2014-10-01

Megajoule scale dense plasma focus (DPF) Z-pinches with deuterium gas fill are compact devices capable of producing 1012 neutrons per shot but past predictive models of large-scale DPF have not included kinetic effects such as ion beam formation or anomalous resistivity. We report on progress of developing a predictive DPF model by extending our 2D axisymmetric collisional kinetic particle-in-cell (PIC) simulations to the 1 MJ, 2 MA Gemini DPF using the PIC code LSP. These new simulations incorporate electrodes, an external pulsed-power driver circuit, and model the plasma from insulator lift-off through the pinch phase. The simulations were performed using a new hybrid fluid-to-kinetic model transitioning from a fluid description to a fully kinetic PIC description during the run-in phase. Simulations are advanced through the final pinch phase using an adaptive variable time-step to capture the fs and sub-mm scales of the kinetic instabilities involved in the ion beam formation and neutron production. Results will be present on the predicted effects of different anode configurations. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory (LLNL) under Contract DE-AC52-07NA27344 and supported by the Laboratory Directed Research and Development Program (11-ERD-063) and the Computing Grand Challenge program at LLNL. This work supported by Office of Defense Nuclear Nonproliferation Research and Development within U.S. Department of Energy's National Nuclear Security Administration.

Kinetics and thermodynamics of living copolymerization processes

PubMed Central

2016-01-01

Theoretical advances are reported on the kinetics and thermodynamics of free and template-directed living copolymerizations. Until recently, the kinetic theory of these processes had only been established in the fully irreversible regime, in which the attachment rates are only considered. However, the entropy production is infinite in this regime and the approach to thermodynamic equilibrium cannot be investigated. For this purpose, the detachment rates should also be included. Inspite of this complication, the kinetics can be exactly solved in the regimes of steady growth and depolymerization. In this way, analytical expressions are obtained for the mean growth velocity, the statistical properties of the copolymer sequences, as well as the thermodynamic entropy production. The results apply to DNA replication, transcription and translation, allowing us to understand important aspects of molecular evolution. This article is part of the themed issue ‘Multiscale modelling at the physics–chemistry–biology interface’. PMID:27698043

Kinetics and thermodynamics of living copolymerization processes.

PubMed

Gaspard, Pierre

2016-11-13

Theoretical advances are reported on the kinetics and thermodynamics of free and template-directed living copolymerizations. Until recently, the kinetic theory of these processes had only been established in the fully irreversible regime, in which the attachment rates are only considered. However, the entropy production is infinite in this regime and the approach to thermodynamic equilibrium cannot be investigated. For this purpose, the detachment rates should also be included. Inspite of this complication, the kinetics can be exactly solved in the regimes of steady growth and depolymerization. In this way, analytical expressions are obtained for the mean growth velocity, the statistical properties of the copolymer sequences, as well as the thermodynamic entropy production. The results apply to DNA replication, transcription and translation, allowing us to understand important aspects of molecular evolution.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'. © 2016 The Author(s).

Kinetics and thermodynamics of living copolymerization processes

NASA Astrophysics Data System (ADS)

Gaspard, Pierre

2016-11-01

Theoretical advances are reported on the kinetics and thermodynamics of free and template-directed living copolymerizations. Until recently, the kinetic theory of these processes had only been established in the fully irreversible regime, in which the attachment rates are only considered. However, the entropy production is infinite in this regime and the approach to thermodynamic equilibrium cannot be investigated. For this purpose, the detachment rates should also be included. Inspite of this complication, the kinetics can be exactly solved in the regimes of steady growth and depolymerization. In this way, analytical expressions are obtained for the mean growth velocity, the statistical properties of the copolymer sequences, as well as the thermodynamic entropy production. The results apply to DNA replication, transcription and translation, allowing us to understand important aspects of molecular evolution. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

An analysis of artificial viscosity effects on reacting flows using a spectral multi-domain technique

NASA Technical Reports Server (NTRS)

Macaraeg, M. G.; Streett, C. L.; Hussaini, M. Y.

1987-01-01

Standard techniques used to model chemically-reacting flows require an artificial viscosity for stability in the presence of strong shocks. The resulting shock is smeared over at least three computational cells, so that the thickness of the shock is dictated by the structure of the overall mesh and not the shock physics. A gas passing through a strong shock is thrown into a nonequilibrium state and subsequently relaxes down over some finite distance to an equilibrium end state. The artificial smearing of the shock envelops this relaxation zone which causes the chemical kinetics of the flow to be altered. A method is presented which can investigate these issues by following the chemical kinetics and flow kinetics of a gas passing through a fully resolved shock wave at hypersonic Mach numbers. A nonequilibrium chemistry model for air is incorporated into a spectral multidomain Navier-Stokes solution method. Since no artificial viscosity is needed for stability of the multidomain technique, the precise effect of this artifice on the chemical kinetics and relevant flow features can be determined.

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.

Spacecraft Solar Particle Event (SPE) Shielding: Shielding Effectiveness as a Function of SPE model as Determined with the FLUKA Radiation Transport Code

NASA Technical Reports Server (NTRS)

Koontz, Steve; Atwell, William; Reddell, Brandon; Rojdev, Kristina

2010-01-01

Analysis of both satellite and surface neutron monitor data demonstrate that the widely utilized Exponential model of solar particle event (SPE) proton kinetic energy spectra can seriously underestimate SPE proton flux, especially at the highest kinetic energies. The more recently developed Band model produces better agreement with neutron monitor data ground level events (GLEs) and is believed to be considerably more accurate at high kinetic energies. Here, we report the results of modeling and simulation studies in which the radiation transport code FLUKA (FLUktuierende KAskade) is used to determine the changes in total ionizing dose (TID) and single-event environments (SEE) behind aluminum, polyethylene, carbon, and titanium shielding masses when the assumed form (i. e., Band or Exponential) of the solar particle event (SPE) kinetic energy spectra is changed. FLUKA simulations have fully three dimensions with an isotropic particle flux incident on a concentric spherical shell shielding mass and detector structure. The effects are reported for both energetic primary protons penetrating the shield mass and secondary particle showers caused by energetic primary protons colliding with shielding mass nuclei. Our results, in agreement with previous studies, show that use of the Exponential form of the event

Detailed kinetics and regulation of mammalian 2-oxoglutarate dehydrogenase

PubMed Central

2011-01-01

Background Mitochondrial 2-oxoglutarate (α-ketoglutarate) dehydrogenase complex (OGDHC), a key regulatory point of tricarboxylic acid (TCA) cycle, plays vital roles in multiple pathways of energy metabolism and biosynthesis. The catalytic mechanism and allosteric regulation of this large enzyme complex are not fully understood. Here computer simulation is used to test possible catalytic mechanisms and mechanisms of allosteric regulation of the enzyme by nucleotides (ATP, ADP), pH, and metal ion cofactors (Ca2+ and Mg2+). Results A model was developed based on an ordered ter-ter enzyme kinetic mechanism combined with con-formational changes that involve rotation of one lipoic acid between three catalytic sites inside the enzyme complex. The model was parameterized using a large number of kinetic data sets on the activity of OGDHC, and validated by comparison of model predictions to independent data. Conclusions The developed model suggests a hybrid rapid-equilibrium ping-pong random mechanism for the kinetics of OGDHC, consistent with previously reported mechanisms, and accurately describes the experimentally observed regulatory effects of cofactors on the OGDHC activity. This analysis provides a single consistent theoretical explanation for a number of apparently contradictory results on the roles of phosphorylation potential, NAD (H) oxidation-reduction state ratio, as well as the regulatory effects of metal ions on ODGHC function. PMID:21943256

Modeling of the Effect of Path Planning on Thermokinetic Evolutions in Laser Powder Deposition Process

NASA Astrophysics Data System (ADS)

Foroozmehr, Ehsan; Kovacevic, Radovan

2011-07-01

A thermokinetic model coupling finite-element heat transfer with transformation kinetics is developed to determine the effect of deposition patterns on the phase-transformation kinetics of laser powder deposition (LPD) process of a hot-work tool steel. The finite-element model is used to define the temperature history of the process used in an empirical-based kinetic model to analyze the tempering effect of the heating and cooling cycles of the deposition process. An area is defined to be covered by AISI H13 on a substrate of AISI 1018 with three different deposition patterns: one section, two section, and three section. The two-section pattern divides the area of the one-section pattern into two sections, and the three-section pattern divides that area into three sections. The results show that dividing the area under deposition into smaller areas can influence the phase transformation kinetics of the process and, consequently, change the final hardness of the deposited material. The two-section pattern shows a higher average hardness than the one-section pattern, and the three-section pattern shows a fully hardened surface without significant tempered zones of low hardness. To verify the results, a microhardness test and scanning electron microscope were used.

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.

Reverse Stability Kinetics of Meat Pigment Oxidation in Aqueous Extract from Fresh Beef.

PubMed

Frelka, John C; Phinney, David M; Wick, Macdonald P; Heldman, Dennis R

2017-12-01

The use of kinetic models is an evolving approach to describing quality changes in foods during processes, including storage. Previous studies indicate that the oxidation rate of myoglobin is accelerated under frozen storage conditions, a phenomenon termed reverse stability. The goal of this study was to develop a model for meat pigment oxidation to incorporate the phenomenon of reverse stability. In this investigation, the model system was an aqueous extract from beef which was stored under a range of temperatures, both unfrozen and frozen. The kinetic analysis showed that in unfrozen solutions, the temperature dependence of oxidation rate followed Arrhenius kinetics. However, under in frozen solutions the rate of oxidation increased with decreasing temperature until reaching a local maximum around -20 °C. The addition of NaCl to the model system increased oxidation rates at all temperatures, even above the initial freezing temperature. This observation suggests that this reaction is dependent on the ionic strength of the solution as well as temperature. The mechanism of this deviant kinetic behavior is not fully understood, but this study shows that the interplay of temperature and composition on the rate of oxidation of meat pigments is complicated and may involve multiple mechanisms. A better understanding of the kinetics of quality loss in a meat system allows for a re-examination of the current recommendations for frozen storage. The deviant kinetic behavior observed in this study indicates that the relationship between quality loss and temperature in a frozen food is not as simple as once thought. Product-specific recommendations could be implemented in the future that would allow for a decrease in energy consumption without a significant loss of quality. © 2017 Institute of Food Technologists®.

Kinetic models of gene expression including non-coding RNAs

NASA Astrophysics Data System (ADS)

Zhdanov, Vladimir P.

2011-03-01

In cells, genes are transcribed into mRNAs, and the latter are translated into proteins. Due to the feedbacks between these processes, the kinetics of gene expression may be complex even in the simplest genetic networks. The corresponding models have already been reviewed in the literature. A new avenue in this field is related to the recognition that the conventional scenario of gene expression is fully applicable only to prokaryotes whose genomes consist of tightly packed protein-coding sequences. In eukaryotic cells, in contrast, such sequences are relatively rare, and the rest of the genome includes numerous transcript units representing non-coding RNAs (ncRNAs). During the past decade, it has become clear that such RNAs play a crucial role in gene expression and accordingly influence a multitude of cellular processes both in the normal state and during diseases. The numerous biological functions of ncRNAs are based primarily on their abilities to silence genes via pairing with a target mRNA and subsequently preventing its translation or facilitating degradation of the mRNA-ncRNA complex. Many other abilities of ncRNAs have been discovered as well. Our review is focused on the available kinetic models describing the mRNA, ncRNA and protein interplay. In particular, we systematically present the simplest models without kinetic feedbacks, models containing feedbacks and predicting bistability and oscillations in simple genetic networks, and models describing the effect of ncRNAs on complex genetic networks. Mathematically, the presentation is based primarily on temporal mean-field kinetic equations. The stochastic and spatio-temporal effects are also briefly discussed.

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

Chacon, Luis; Stanier, Adam John

Here, we demonstrate a scalable fully implicit algorithm for the two-field low-β extended MHD model. This reduced model describes plasma behavior in the presence of strong guide fields, and is of significant practical impact both in nature and in laboratory plasmas. The model displays strong hyperbolic behavior, as manifested by the presence of fast dispersive waves, which make a fully implicit treatment very challenging. In this study, we employ a Jacobian-free Newton–Krylov nonlinear solver, for which we propose a physics-based preconditioner that renders the linearized set of equations suitable for inversion with multigrid methods. As a result, the algorithm ismore » shown to scale both algorithmically (i.e., the iteration count is insensitive to grid refinement and timestep size) and in parallel in a weak-scaling sense, with the wall-clock time scaling weakly with the number of cores for up to 4096 cores. For a 4096 × 4096 mesh, we demonstrate a wall-clock-time speedup of ~6700 with respect to explicit algorithms. The model is validated linearly (against linear theory predictions) and nonlinearly (against fully kinetic simulations), demonstrating excellent agreement.« less

Extended MHD Turbulence and Its Applications to the Solar Wind

NASA Astrophysics Data System (ADS)

Abdelhamid, Hamdi M.; Lingam, Manasvi; Mahajan, Swadesh M.

2016-10-01

Extended MHD is a one-fluid model that incorporates two-fluid effects such as electron inertia and the Hall drift. This model is used to construct fully nonlinear Alfvénic wave solutions, and thereby derive the kinetic and magnetic spectra by resorting to a Kolmogorov-like hypothesis based on the constant cascading rates of the energy and generalized helicities of this model. The magnetic and kinetic spectra are derived in the ideal (k\\lt 1/{λ }I), Hall (1/{λ }I\\lt k\\lt 1/{λ }e), and electron inertia (k\\gt 1/{λ }e) regimes; k is the wavenumber and {λ }s=c/{ω }{ps} is the skin depth of species “s.” In the Hall regime, it is shown that the emergent results are fully consistent with previous numerical and analytical studies, especially in the context of the solar wind. The focus is primarily on the electron inertia regime, where magnetic energy spectra with power-law indexes of -11/3 and -13/3 are always recovered. The latter, in particular, is quite close to recent observational evidence from the solar wind with a potential slope of approximately -4 in this regime. It is thus plausible that these spectra may constitute a part of the (extended) inertial range, as opposed to the standard “dissipation” range paradigm.

Drift-free kinetic equations for turbulent dispersion

NASA Astrophysics Data System (ADS)

Bragg, A.; Swailes, D. C.; Skartlien, R.

2012-11-01

The dispersion of passive scalars and inertial particles in a turbulent flow can be described in terms of probability density functions (PDFs) defining the statistical distribution of relevant scalar or particle variables. The construction of transport equations governing the evolution of such PDFs has been the subject of numerous studies, and various authors have presented formulations for this type of equation, usually referred to as a kinetic equation. In the literature it is often stated, and widely assumed, that these PDF kinetic equation formulations are equivalent. In this paper it is shown that this is not the case, and the significance of differences among the various forms is considered. In particular, consideration is given to which form of equation is most appropriate for modeling dispersion in inhomogeneous turbulence and most consistent with the underlying particle equation of motion. In this regard the PDF equations for inertial particles are considered in the limit of zero particle Stokes number and assessed against the fully mixed (zero-drift) condition for fluid points. A long-standing question regarding the validity of kinetic equations in the fluid-point limit is answered; it is demonstrated formally that one version of the kinetic equation (derived using the Furutsu-Novikov method) provides a model that satisfies this zero-drift condition exactly in both homogeneous and inhomogeneous systems. In contrast, other forms of the kinetic equation do not satisfy this limit or apply only in a limited regime.

Drift-free kinetic equations for turbulent dispersion.

PubMed

Bragg, A; Swailes, D C; Skartlien, R

2012-11-01

The dispersion of passive scalars and inertial particles in a turbulent flow can be described in terms of probability density functions (PDFs) defining the statistical distribution of relevant scalar or particle variables. The construction of transport equations governing the evolution of such PDFs has been the subject of numerous studies, and various authors have presented formulations for this type of equation, usually referred to as a kinetic equation. In the literature it is often stated, and widely assumed, that these PDF kinetic equation formulations are equivalent. In this paper it is shown that this is not the case, and the significance of differences among the various forms is considered. In particular, consideration is given to which form of equation is most appropriate for modeling dispersion in inhomogeneous turbulence and most consistent with the underlying particle equation of motion. In this regard the PDF equations for inertial particles are considered in the limit of zero particle Stokes number and assessed against the fully mixed (zero-drift) condition for fluid points. A long-standing question regarding the validity of kinetic equations in the fluid-point limit is answered; it is demonstrated formally that one version of the kinetic equation (derived using the Furutsu-Novikov method) provides a model that satisfies this zero-drift condition exactly in both homogeneous and inhomogeneous systems. In contrast, other forms of the kinetic equation do not satisfy this limit or apply only in a limited regime.

Prospects of in vivo singlet oxygen luminescence monitoring: Kinetics at different locations on living mice.

PubMed

Pfitzner, Michael; Schlothauer, Jan C; Bastien, Estelle; Hackbarth, Steffen; Bezdetnaya, Lina; Lassalle, Henri-Pierre; Röder, Beate

2016-06-01

Singlet oxygen observation is considered a valuable tool to assess and optimize PDT treatment. In complex systems, such as tumors in vivo, only the direct, time-resolved singlet oxygen luminescence detection can give reliable information about generation and interaction of singlet oxygen. Up to now, evaluation of kinetics was not possible due to insufficient signal-to-noise ratio. Here we present high signal-to-noise ratio singlet oxygen luminescence kinetics obtained in mouse tumor model under PDT relevant conditions. A highly optimized system based on a custom made laser diode excitation source and a high aperture multi-furcated fiber, utilizing a photomultiplier tube with a multi photon counting device was used. Luminescence kinetics with unsurpassed signal-to-noise ratio were gained from tumor bearing nude mice in vivo upon topic application, subcutaneous injection as well as intravenous injection of different photosensitizers (chlorin e6 and dendrimer formulations of chlorin e6). Singlet oxygen kinetics in appropriate model systems are discussed to facilitate the interpretation of complex kinetics obtained from in vivo tumor tissue. This is the first study addressing the complexity of singlet oxygen luminescence kinetics in tumor tissue. At present, further investigations are needed to fully explain the processes involved. Nevertheless, the high signal-to-noise ratio proves the applicability of direct time-resolved singlet oxygen luminescence detection as a prospective tool for monitoring photodynamic therapy. Copyright © 2016 Elsevier B.V. All rights reserved.

A KDE-Based Random Walk Method for Modeling Reactive Transport With Complex Kinetics in Porous Media

NASA Astrophysics Data System (ADS)

Sole-Mari, Guillem; Fernà ndez-Garcia, Daniel; Rodríguez-Escales, Paula; Sanchez-Vila, Xavier

2017-11-01

In recent years, a large body of the literature has been devoted to study reactive transport of solutes in porous media based on pure Lagrangian formulations. Such approaches have also been extended to accommodate second-order bimolecular reactions, in which the reaction rate is proportional to the concentrations of the reactants. Rather, in some cases, chemical reactions involving two reactants follow more complicated rate laws. Some examples are (1) reaction rate laws written in terms of powers of concentrations, (2) redox reactions incorporating a limiting term (e.g., Michaelis-Menten), or (3) any reaction where the activity coefficients vary with the concentration of the reactants, just to name a few. We provide a methodology to account for complex kinetic bimolecular reactions in a fully Lagrangian framework where each particle represents a fraction of the total mass of a specific solute. The method, built as an extension to the second-order case, is based on the concept of optimal Kernel Density Estimator, which allows the concentrations to be written in terms of particle locations, hence transferring the concept of reaction rate to that of particle location distribution. By doing so, we can update the probability of particles reacting without the need to fully reconstruct the concentration maps. The performance and convergence of the method is tested for several illustrative examples that simulate the Advection-Dispersion-Reaction Equation in a 1-D homogeneous column. Finally, a 2-D application example is presented evaluating the need of fully describing non-bilinear chemical kinetics in a randomly heterogeneous porous medium.

Combination of Markov state models and kinetic networks for the analysis of molecular dynamics simulations of peptide folding.

PubMed

Radford, Isolde H; Fersht, Alan R; Settanni, Giovanni

2011-06-09

Atomistic molecular dynamics simulations of the TZ1 beta-hairpin peptide have been carried out using an implicit model for the solvent. The trajectories have been analyzed using a Markov state model defined on the projections along two significant observables and a kinetic network approach. The Markov state model allowed for an unbiased identification of the metastable states of the system, and provided the basis for commitment probability calculations performed on the kinetic network. The kinetic network analysis served to extract the main transition state for folding of the peptide and to validate the results from the Markov state analysis. The combination of the two techniques allowed for a consistent and concise characterization of the dynamics of the peptide. The slowest relaxation process identified is the exchange between variably folded and denatured species, and the second slowest process is the exchange between two different subsets of the denatured state which could not be otherwise identified by simple inspection of the projected trajectory. The third slowest process is the exchange between a fully native and a partially folded intermediate state characterized by a native turn with a proximal backbone H-bond, and frayed side-chain packing and termini. The transition state for the main folding reaction is similar to the intermediate state, although a more native like side-chain packing is observed.

Phenomenological and molecular-level Petri net modeling and simulation of long-term potentiation.

PubMed

Hardy, S; Robillard, P N

2005-10-01

Petri net-based modeling methods have been used in many research projects to represent biological systems. Among these, the hybrid functional Petri net (HFPN) was developed especially for biological modeling in order to provide biologists with a more intuitive Petri net-based method. In the literature, HFPNs are used to represent kinetic models at the molecular level. We present two models of long-term potentiation previously represented by differential equations which we have transformed into HFPN models: a phenomenological synapse model and a molecular-level model of the CaMKII regulation pathway. Through simulation, we obtained results similar to those of previous studies using these models. Our results open the way to a new type of modeling for systems biology where HFPNs are used to combine different levels of abstraction within one model. This approach can be useful in fully modeling a system at the molecular level when kinetic data is missing or when a full study of a system at the molecular level it is not within the scope of the research.

A third-order gas-kinetic CPR method for the Euler and Navier-Stokes equations on triangular meshes

NASA Astrophysics Data System (ADS)

Zhang, Chao; Li, Qibing; Fu, Song; Wang, Z. J.

2018-06-01

A third-order accurate gas-kinetic scheme based on the correction procedure via reconstruction (CPR) framework is developed for the Euler and Navier-Stokes equations on triangular meshes. The scheme combines the accuracy and efficiency of the CPR formulation with the multidimensional characteristics and robustness of the gas-kinetic flux solver. Comparing with high-order finite volume gas-kinetic methods, the current scheme is more compact and efficient by avoiding wide stencils on unstructured meshes. Unlike the traditional CPR method where the inviscid and viscous terms are treated differently, the inviscid and viscous fluxes in the current scheme are coupled and computed uniformly through the kinetic evolution model. In addition, the present scheme adopts a fully coupled spatial and temporal gas distribution function for the flux evaluation, achieving high-order accuracy in both space and time within a single step. Numerical tests with a wide range of flow problems, from nearly incompressible to supersonic flows with strong shocks, for both inviscid and viscous problems, demonstrate the high accuracy and efficiency of the present scheme.

Martensite Embryology

NASA Astrophysics Data System (ADS)

Reid, Andrew C. E.; Olson, Gregory B.

2000-03-01

Heterogeneous nucleation of martensite is modeled by examining the strain field of a dislocation array in a nonlinear, nonlocal continuum elastic matrix. The dislocations are modeled by including effects from atomic length scales, which control the dislocation Burger's vector, into a mesoscopic continuum model. The dislocation array models the heterogeneous nucleation source of the Olson/Cohen defect dissociation model, and depending on the potency can give rise to embryos of different character. High potency dislocations give rise to fully developed, classical pre-existing embryos, whereas low-potency dislocations result in the formation of highly nonclassical strain embryos. Heterogeneous nucleation theory is related to nucleation kinetics through the critical driving force for nucleation at a defect of a given potency. Recent stereological and calorimetric kinetic studies in thermoelastic TiNi alloys confirm that these materials exhibit the same form of defect potency distribution and resulting sample-size dependent Martensite start temperature, M_s, as nonthermoelastic FeNi systems. These results together point towards a broad theory of heterogeneous nucleation for both thermoelastic and nonthermoelastic martensites.

Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study

NASA Astrophysics Data System (ADS)

Kouza, Maksim; Co, Nguyen Truong; Li, Mai Suan; Kmiecik, Sebastian; Kolinski, Andrzej; Kloczkowski, Andrzej; Buhimschi, Irina Alexandra

2018-06-01

Fibril formation resulting from protein misfolding and aggregation is a hallmark of several neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. Despite much progress in the understanding of the protein aggregation process, the factors governing fibril formation rates and fibril stability have not been fully understood. Using lattice models, we have shown that the fibril formation time is controlled by the kinetic stability of the fibril state but not by its energy. Having performed all-atom explicit solvent molecular dynamics simulations with the GROMOS43a1 force field for full-length amyloid beta peptides Aβ40 and Aβ42 and truncated peptides, we demonstrated that kinetic stability can be accessed via mechanical stability in such a way that the higher the mechanical stability or the kinetic stability, the faster the fibril formation. This result opens up a new way for predicting fibril formation rates based on mechanical stability that may be easily estimated by steered molecular dynamics.

Peptide concentration alters intermediate species in amyloid β fibrillation kinetics

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

Garvey, M., E-mail: megan.garvey@molbiotech.rwth-aachen.de; Morgado, I., E-mail: immorgado@ualg.pt

2013-04-12

Highlights: ► Aβ(1–40) aggregation in vitro has been monitored at different concentrations. ► Aβ(1–40) fibrillation does not always follow conventional kinetic mechanisms. ► We demonstrate non-linear features in the kinetics of Aβ(1–40) fibril formation. ► At high Aβ(1–40) concentrations secondary processes dictate fibrillation speed. ► Intermediate species may play significant roles on final amyloid fibril development. -- Abstract: The kinetic mechanism of amyloid aggregation remains to be fully understood. Investigations into the species present in the different kinetic phases can assist our comprehension of amyloid diseases and further our understanding of the mechanism behind amyloid β (Aβ) (1–40) peptide aggregation.more » Thioflavin T (ThT) fluorescence and transmission electron microscopy (TEM) have been used in combination to monitor Aβ(1–40) aggregation in vitro at both normal and higher than standard concentrations. The observed fibrillation behaviour deviates, in several respects, from standard concepts of the nucleation–polymerisation models and shows such features as concentration-dependent non-linear effects in the assembly mechanism. Aβ(1–40) fibrillation kinetics do not always follow conventional kinetic mechanisms and, specifically at high concentrations, intermediate structures become populated and secondary processes may further modify the fibrillation mechanism.« less

Particle-in-cell modeling for MJ scale dense plasma focus with varied anode shape

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

Link, A., E-mail: link6@llnl.gov; Halvorson, C., E-mail: link6@llnl.gov; Schmidt, A.

2014-12-15

Megajoule scale dense plasma focus (DPF) Z-pinches with deuterium gas fill are compact devices capable of producing 10{sup 12} neutrons per shot but past predictive models of large-scale DPF have not included kinetic effects such as ion beam formation or anomalous resistivity. We report on progress of developing a predictive DPF model by extending our 2D axisymmetric collisional kinetic particle-in-cell (PIC) simulations from the 4 kJ, 200 kA LLNL DPF to 1 MJ, 2 MA Gemini DPF using the PIC code LSP. These new simulations incorporate electrodes, an external pulsed-power driver circuit, and model the plasma from insulator lift-off throughmore » the pinch phase. To accommodate the vast range of relevant spatial and temporal scales involved in the Gemini DPF within the available computational resources, the simulations were performed using a new hybrid fluid-to-kinetic model. This new approach allows single simulations to begin in an electron/ion fluid mode from insulator lift-off through the 5-6 μs run-down of the 50+ cm anode, then transition to a fully kinetic PIC description during the run-in phase, when the current sheath is 2-3 mm from the central axis of the anode. Simulations are advanced through the final pinch phase using an adaptive variable time-step to capture the fs and sub-mm scales of the kinetic instabilities involved in the ion beam formation and neutron production. Validation assessments are being performed using a variety of different anode shapes, comparing against experimental measurements of neutron yield, neutron anisotropy and ion beam production.« less

Simulating the Solar Wind Interaction with Comet 67P/Churyumov-Gerasimenko: Latest Results

NASA Astrophysics Data System (ADS)

Deca, J.; Divin, A. V.; Henri, P.; Eriksson, A. I.; Markidis, S.; Olshevsky, V.; Goldstein, R.; Myllys, M. E.; Horanyi, M.

2017-12-01

First observed in 1969, comet 67P/Churyumov-Gerasimenko was escorted for almost two years along its 6.45-yr elliptical orbit by ESA's Rosetta orbiter spacecraft. When a comet is sufficiently close to the Sun, the sublimation of ice leads to an outgassing atmosphere and the formation of a coma, and a dust and plasma tail. Comets are critical to decipher the physics of gas release processes in space. The latter result in mass-loaded plasmas, which more than three decades after the Active Magnetospheric Particle Tracer Explorers (AMPTE) space release experiments are still not fully understood. Using a 3D fully kinetic approach, we study the solar wind interaction with comet 67P/Churyumov-Gerasimenko, focusing in particular on the ion-electron dynamics for various outgassing rates. A detailed kinetic treatment of the electron dynamics is critical to fully capture the complex physics of mass-loading plasmas and to describe the strongly inhomogeneous plasma dynamics observed by Rosetta, down to electron kinetic scales.

Kinetic performance comparison of fully and superficially porous particles with a particle size of 5 µm: intrinsic evaluation and application to the impurity analysis of griseofulvin.

PubMed

Kahsay, Getu; Broeckhoven, Ken; Adams, Erwin; Desmet, Gert; Cabooter, Deirdre

2014-05-01

After the great commercial success of sub-3 µm superficially porous particles, vendors are now also starting to commercialize 5 µm superficially porous particles, as an alternative to their fully porous counterparts which are routinely used in pharmaceutical analysis. In this study, the performance of 5 µm superficially porous particles was compared to that of fully porous 5 µm particles in terms of efficiency, separation performance and loadability on a conventional HPLC instrument. Van Deemter and kinetic plots were first used to evaluate the efficiency and performance of both particle types using alkylphenones as a test mixture. The van Deemter and kinetic plots showed that the superficially porous particles provide a superior kinetic performance compared to the fully porous particles over the entire relevant range of separation conditions, when both support types were evaluated at the same operating pressure. The same observations were made both for isocratic and gradient analysis. The superior performance was further demonstrated for the separation of a pharmaceutical compound (griseofulvin) and its impurities, where a gain in analysis time of around 2 could be obtained using the superficially porous particles. Finally, both particle types were evaluated in terms of loadability by plotting the resolution of the active pharmaceutical ingredient and its closest impurity as a function of the signal-to-noise ratio obtained for the smallest impurity. It was demonstrated that the superficially porous particles show better separation performance for griseofulvin and its impurities without significantly compromising sensitivity due to loadability issues in comparison with their fully porous counterparts. Moreover these columns can be used on conventional equipment without modifications to obtain a significant improvement in analysis time. Copyright © 2014 Elsevier B.V. All rights reserved.

The Kinetic Energy of a Rotating Figure Skater.

ERIC Educational Resources Information Center

Chen, Wei R.; Troelstra, Arne A.

1998-01-01

When a rotating figure skater's fully extended arms are pulled back toward the torso, the angular velocity is noticeably increased and the kinetic energy of the skater can also be shown to increase. Discusses the change of the kinetic energy during such a process, and the work necessary for such an increase is derived using a dynamic equilibrium…

Coupling Fluid and Kineitc Effects in Space Weather: an interdisciplinary task

NASA Astrophysics Data System (ADS)

Lapenta, Giovanni; González-Herrero, Diego; Boella, Elisabetta; Siddi, Lorenzo; Cazzola, Emanuele

2017-04-01

Two agents are key to space weather: electromagentic fields and energetic particles. Magnetic fields carried by plasmas in the solar wind interact with the Earth magnetosphere and solar energetic particles produced by solar events or in cosmic rays affect the space environment. Describing both is challenging. Magnetized plasmas are most effectively described by magneto-hydrodynamics, MHD, a fluid theory based on describing some fields defined in space: electromagnetic fields, density, velocity and temperature of the plasma. High energy particles, instead need a more detailed approach , kinetic theory, where statistical distributions of particles are governed by the Boltzmann equation. While fluid models are based on the ordinary space and time, kinetic models require a six dimensional space, called phase space, besides time. The two methods are not separated, the processes leading to the production of energetic particles are the same that involve space plasamas and fields. Arriving at a single self-consistent model has been the goal of the Swiff project funded by the EC in FP7 and it is now a key goal of the ongoing DEEP-ER project. We present a new approach developed with the goal of extending the reach of kinetic models to the fluid scales. Kinetic models are a higher order description and all fluid effects are included in them. However, the cost in terms of computing power is much higher and it has been so far prohibitively expensive to treat space weather events fully kinetically. We have now designed a new method capable of reducing that cost by several orders of magnitude making it possible for kinetic models to study space weather events [1,2]. We will report the new methodology and show its application to space weather mdeling. [1] Giovanni Lapenta,Exactly Energy Conserving Semi-Implicit Particle in Cell Formulation, to appear, JCP, arXiv:1602.06326 [2] Giovanni Lapenta, Diego Gonzalez-Herrero, Elisabetta Boella, Multiple scale kinetic simulations with the energy conserving semi implicit particle in cell (PIC) method, submitted JPP, arXiv:1612.08289

Remarks on the chemical Fokker-Planck and Langevin equations: Nonphysical currents at equilibrium.

PubMed

Ceccato, Alessandro; Frezzato, Diego

2018-02-14

The chemical Langevin equation and the associated chemical Fokker-Planck equation are well-known continuous approximations of the discrete stochastic evolution of reaction networks. In this work, we show that these approximations suffer from a physical inconsistency, namely, the presence of nonphysical probability currents at the thermal equilibrium even for closed and fully detailed-balanced kinetic schemes. An illustration is given for a model case.

Effect of Nonlinearity in Hybrid Kinetic Monte Carlo-Continuum Models

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

Balter, Ariel I.; Lin, Guang; Tartakovsky, Alexandre M.

2012-04-23

Recently there has been interest in developing efficient ways to model heterogeneous surface reactions with hybrid computational models that couple a KMC model for a surface to a finite difference model for bulk diffusion in a continuous domain. We consider two representative problems that validate a hybrid method and also show that this method captures the combined effects of nonlinearity and stochasticity. We first validate a simple deposition/dissolution model with a linear rate showing that the KMC-continuum hybrid agrees with both a fully deterministic model and its analytical solution. We then study a deposition/dissolution model including competitive adsorption, which leadsmore » to a nonlinear rate, and show that, in this case, the KMC-continuum hybrid and fully deterministic simulations do not agree. However, we are able to identify the difference as a natural result of the stochasticity coming from the KMC surface process. Because KMC captures inherent fluctuations, we consider it to be more realistic than a purely deterministic model. Therefore, we consider the KMC-continuum hybrid to be more representative of a real system.« less

There is more than one way to model an elephant. Experiment-driven modeling of the actin cytoskeleton.

PubMed

Ditlev, Jonathon A; Mayer, Bruce J; Loew, Leslie M

2013-02-05

Mathematical modeling has established its value for investigating the interplay of biochemical and mechanical mechanisms underlying actin-based motility. Because of the complex nature of actin dynamics and its regulation, many of these models are phenomenological or conceptual, providing a general understanding of the physics at play. But the wealth of carefully measured kinetic data on the interactions of many of the players in actin biochemistry cries out for the creation of more detailed and accurate models that could permit investigators to dissect interdependent roles of individual molecular components. Moreover, no human mind can assimilate all of the mechanisms underlying complex protein networks; so an additional benefit of a detailed kinetic model is that the numerous binding proteins, signaling mechanisms, and biochemical reactions can be computationally organized in a fully explicit, accessible, visualizable, and reusable structure. In this review, we will focus on how comprehensive and adaptable modeling allows investigators to explain experimental observations and develop testable hypotheses on the intracellular dynamics of the actin cytoskeleton. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

There is More Than One Way to Model an Elephant. Experiment-Driven Modeling of the Actin Cytoskeleton

PubMed Central

Ditlev, Jonathon A.; Mayer, Bruce J.; Loew, Leslie M.

2013-01-01

Mathematical modeling has established its value for investigating the interplay of biochemical and mechanical mechanisms underlying actin-based motility. Because of the complex nature of actin dynamics and its regulation, many of these models are phenomenological or conceptual, providing a general understanding of the physics at play. But the wealth of carefully measured kinetic data on the interactions of many of the players in actin biochemistry cries out for the creation of more detailed and accurate models that could permit investigators to dissect interdependent roles of individual molecular components. Moreover, no human mind can assimilate all of the mechanisms underlying complex protein networks; so an additional benefit of a detailed kinetic model is that the numerous binding proteins, signaling mechanisms, and biochemical reactions can be computationally organized in a fully explicit, accessible, visualizable, and reusable structure. In this review, we will focus on how comprehensive and adaptable modeling allows investigators to explain experimental observations and develop testable hypotheses on the intracellular dynamics of the actin cytoskeleton. PMID:23442903

Purification and characterization of two fully deuterated enzymes

NASA Technical Reports Server (NTRS)

Crespi, H. L.; Katz, J. J.; Parmerter, S.; Rokop, S.

1969-01-01

Comparative data reveal little difference between kinetic and thermal stabilities of pure preparations of two ordinary enzymes and their fully deuterated counterparts. The effects of temperature on the enzymes proved to be consistent with earlier results.

Fully Parallel MHD Stability Analysis Tool

NASA Astrophysics Data System (ADS)

Svidzinski, Vladimir; Galkin, Sergei; Kim, Jin-Soo; Liu, Yueqiang

2014-10-01

Progress on full parallelization of the plasma stability code MARS will be reported. MARS calculates eigenmodes in 2D axisymmetric toroidal equilibria in MHD-kinetic plasma models. It is a powerful tool for studying MHD and MHD-kinetic instabilities and it is widely used by fusion community. Parallel version of MARS is intended for simulations on local parallel clusters. It will be an efficient tool for simulation of MHD instabilities with low, intermediate and high toroidal mode numbers within both fluid and kinetic plasma models, already implemented in MARS. Parallelization of the code includes parallelization of the construction of the matrix for the eigenvalue problem and parallelization of the inverse iterations algorithm, implemented in MARS for the solution of the formulated eigenvalue problem. Construction of the matrix is parallelized by distributing the load among processors assigned to different magnetic surfaces. Parallelization of the solution of the eigenvalue problem is made by repeating steps of the present MARS algorithm using parallel libraries and procedures. Initial results of the code parallelization will be reported. Work is supported by the U.S. DOE SBIR program.

Combined Recirculatory-compartmental Population Pharmacokinetic Modeling of Arterial and Venous Plasma S(+) and R(-) Ketamine Concentrations.

PubMed

Henthorn, Thomas K; Avram, Michael J; Dahan, Albert; Gustafsson, Lars L; Persson, Jan; Krejcie, Tom C; Olofsen, Erik

2018-05-16

The pharmacokinetics of infused drugs have been modeled without regard for recirculatory or mixing kinetics. We used a unique ketamine dataset with simultaneous arterial and venous blood sampling, during and after separate S(+) and R(-) ketamine infusions, to develop a simplified recirculatory model of arterial and venous plasma drug concentrations. S(+) or R(-) ketamine was infused over 30 min on two occasions to 10 healthy male volunteers. Frequent, simultaneous arterial and forearm venous blood samples were obtained for up to 11 h. A multicompartmental pharmacokinetic model with front-end arterial mixing and venous blood components was developed using nonlinear mixed effects analyses. A three-compartment base pharmacokinetic model with additional arterial mixing and arm venous compartments and with shared S(+)/R(-) distribution kinetics proved superior to standard compartmental modeling approaches. Total pharmacokinetic flow was estimated to be 7.59 ± 0.36 l/min (mean ± standard error of the estimate), and S(+) and R(-) elimination clearances were 1.23 ± 0.04 and 1.06 ± 0.03 l/min, respectively. The arm-tissue link rate constant was 0.18 ± 0.01 min and the fraction of arm blood flow estimated to exchange with arm tissue was 0.04 ± 0.01. Arterial drug concentrations measured during drug infusion have two kinetically distinct components: partially or lung-mixed drug and fully mixed-recirculated drug. Front-end kinetics suggest the partially mixed concentration is proportional to the ratio of infusion rate and total pharmacokinetic flow. This simplified modeling approach could lead to more generalizable models for target-controlled infusions and improved methods for analyzing pharmacokinetic-pharmacodynamic data.

Reacting Flow in the Entrance to a Channel with Surface and Gas-Phase Kinetics

NASA Astrophysics Data System (ADS)

Mikolaitis, David; Griffen, Patrick

2006-11-01

In many catalytic reactors the conversion process is most intense at the very beginning of the channel where the flow is not yet fully developed; hence there will be important interactions between the developing flow field and reaction. To study this problem we have written an object-oriented code for the analysis of reacting flow in the entrance of a channel where both surface reaction and gas-phase reaction are modeled with detailed kinetics. Fluid mechanical momentum and energy equations are modeled by parabolic ``boundary layer''-type equations where streamwise gradient terms are small and the pressure is constant in the transverse direction. Transport properties are modeled with mixture-averaging and the chemical kinetic sources terms are evaluated using Cantera. Numerical integration is done with Matlab using the function pdepe. Calculations were completed using mixtures of methane and air flowing through a channel with platinum walls held at a fixed temperature. GRI-Mech 3.0 was used to describe the gas-phase chemistry and Deutchmann's methane-air-platinum model was used for the surface chemistry. Ignition in the gas phase is predicted for high enough wall temperatures. A hot spot forms away from the walls just before ignition that is fed by radicals produced at the surface.

Demonstration of Anisotropic Fluid Closure Capturing the Kinetic Structure of Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Ohia, Obioma

2012-10-01

Magnetic reconnection in collisionless plasmas plays an important role in space and laboratory plasmas. Allowing magnetic stress to be reduced by a rearrangement of magnetic line topology, this process is often accompanied by a large release of magnetic field energy, which can heat the plasma, drive large scale flows, or accelerate particles. Reconnection has been widely studied through fluid models and kinetic simulations. While two-fluid models often reproduce the fast reconnection that is observed in nature and seen in kinetic simulations, it is found that the structure surrounding the electron diffusion region and the electron current layer differ vastly between fluid models and kinetic simulations [1]. Recently, using an adiabatic solution of the Vlasov equation, a new fluid closure has been obtained for electrons that relate parallel and perpendicular pressures to the density and magnetic field [2]. Here we present the results of fluid simulation, developed using the HiFi framework [3], that implements new equations of state for guide-field reconnection. The new fluid closure accurately accounts for the anisotropic electron pressure that builds in the reconnection region due to electric and magnetic trapping of electrons. In contrast to previous fluid models, our fluid simulation reproduces the detailed reconnection region as observed in fully kinetic simulations [4]. We hereby demonstrate that the new fluid closure self-consistently captures all the physics relevant to the structure of the reconnection region, providing a gateway to a renewed and deeper theoretical understanding for reconnection in weakly collisional regimes.[4pt] [1] Daughton W et al., Phys. Plasmas 13, 072101 (2006).[0pt] [2] Le A et al., Phys. Rev. Lett. 102, 085001 (2009). [0pt] [3] Lukin VS, Linton MG, Nonlinear Proc. Geoph. 18, 871 (2011). [0pt] [4] Ohia O, et al., Phys. Rev. Lett. In Press (2012).

Effect of Temperature and Sheet Temper on Isothermal Solidification Kinetics in Clad Aluminum Brazing Sheet

NASA Astrophysics Data System (ADS)

Benoit, Michael J.; Whitney, Mark A.; Wells, Mary A.; Winkler, Sooky

2016-09-01

Isothermal solidification (IS) is a phenomenon observed in clad aluminum brazing sheets, wherein the amount of liquid clad metal is reduced by penetration of the liquid clad into the core. The objective of the current investigation is to quantify the rate of IS through the use of a previously derived parameter, the Interface Rate Constant (IRC). The effect of peak temperature and initial sheet temper on IS kinetics were investigated. The results demonstrated that IS is due to the diffusion of silicon (Si) from the liquid clad layer into the solid core. Reduced amounts of liquid clad at long liquid duration times, a roughened sheet surface, and differences in resolidified clad layer morphology between sheet tempers were observed. Increased IS kinetics were predicted at higher temperatures by an IRC model as well as by experimentally determined IRC values; however, the magnitudes of these values are not in good agreement due to deficiencies in the model when applied to alloys. IS kinetics were found to be higher for sheets in the fully annealed condition when compared with work-hardened sheets, due to the influence of core grain boundaries providing high diffusivity pathways for Si diffusion, resulting in more rapid liquid clad penetration.

Kinetic evidence for folding and unfolding intermediates in staphylococcal nuclease.

PubMed

Walkenhorst, W F; Green, S M; Roder, H

1997-05-13

The complex kinetic behavior commonly observed in protein folding studies suggests that a heterogeneous population of molecules exists in solution and that a number of discrete steps are involved in the conversion of unfolded molecules to the fully native form. A central issue in protein folding is whether any of these kinetic events represent conformational steps important for efficient folding rather than side reactions caused by slow steps such as proline isomerization or misfolding of the polypeptide chain. In order to address this question, we used stopped-flow fluorescence techniques to characterize the kinetic mechanism of folding and unfolding for a Pro- variant of SNase in which all six proline residues were replaced by glycines or alanines. Compared to the wild-type protein, which exhibits a series of proline-dependent slow folding phases, the folding kinetics of Pro- SNase were much simpler, which made quantitative kinetic analysis possible. Despite the absence of prolines or other complicating factors, the folding kinetics still contain several phases and exhibit a complex denaturant dependence. The GuHCl dependence of the major observable folding phase and a distinct lag in the appearance of the native state provide clear evidence for an early folding intermediate. The fluorescence of Trp140 in the alpha-helical domain is insensitive to the formation of this early intermediate, which is consistent with a partially folded state with a stable beta-domain and a largely disordered alpha-helical region. A second intermediate is required to model the kinetics of unfolding for the Pro- variant, which shows evidence for a denaturant-induced change in the rate-limiting unfolding step. With the inclusion of these two intermediates, we are able to completely model the major phase(s) in both folding and unfolding across a wide range of denaturant concentrations using a sequential four-state folding mechanism. In order to model the minor slow phase observed for the Pro- mutant, a six-state scheme containing a parallel pathway originating from a distinct unfolded state was required. The properties of this alternate unfolded conformation are consistent with those expected due to the presence of a non-prolyl cis peptide bond. To test the kinetic model, we used simulations based on the six-state scheme and were able to completely reproduce the folding kinetics for Pro- SNase across a range of denaturant concentrations.

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

Rao, Rekha R.; Celina, Mathias C.; Giron, Nicholas Henry

We are developing computational models to help understand manufacturing processes, final properties and aging of structural foam, polyurethane PMDI. Th e resulting model predictions of density and cure gradients from the manufacturing process will be used as input to foam heat transfer and mechanical models. BKC 44306 PMDI-10 and BKC 44307 PMDI-18 are the most prevalent foams used in structural parts. Experiments needed to parameterize models of the reaction kinetics and the equations of motion during the foam blowing stages were described for BKC 44306 PMDI-10 in the first of this report series (Mondy et al. 2014). BKC 44307 PMDI-18more » is a new foam that will be used to make relatively dense structural supports via over packing. It uses a different catalyst than those in the BKC 44306 family of foams; hence, we expect that the reaction kineti cs models must be modified. Here we detail the experiments needed to characteriz e the reaction kinetics of BKC 44307 PMDI-18 and suggest parameters for the model based on these experiments. In additi on, the second part of this report describes data taken to provide input to the preliminary nonlinear visco elastic structural response model developed for BKC 44306 PMDI-10 foam. We show that the standard cu re schedule used by KCP does not fully cure the material, and, upon temperature elevation above 150°C, oxidation or decomposition reactions occur that alter the composition of the foam. These findings suggest that achieving a fully cured foam part with this formulation may be not be possible through therma l curing. As such, visco elastic characterization procedures developed for curing thermosets can provide only approximate material properties, since the state of the material continuously evolves during tests.« less

Computational modeling of fully-ionized, magnetized plasmas using the fluid approximation

NASA Astrophysics Data System (ADS)

Schnack, Dalton

2005-10-01

Strongly magnetized plasmas are rich in spatial and temporal scales, making a computational approach useful for studying these systems. The most accurate model of a magnetized plasma is based on a kinetic equation that describes the evolution of the distribution function for each species in six-dimensional phase space. However, the high dimensionality renders this approach impractical for computations for long time scales in relevant geometry. Fluid models, derived by taking velocity moments of the kinetic equation [1] and truncating (closing) the hierarchy at some level, are an approximation to the kinetic model. The reduced dimensionality allows a wider range of spatial and/or temporal scales to be explored. Several approximations have been used [2-5]. Successful computational modeling requires understanding the ordering and closure approximations, the fundamental waves supported by the equations, and the numerical properties of the discretization scheme. We review and discuss several ordering schemes, their normal modes, and several algorithms that can be applied to obtain a numerical solution. The implementation of kinetic parallel closures is also discussed [6].[1] S. Chapman and T.G. Cowling, ``The Mathematical Theory of Non-Uniform Gases'', Cambridge University Press, Cambridge, UK (1939).[2] R.D. Hazeltine and J.D. Meiss, ``Plasma Confinement'', Addison-Wesley Publishing Company, Redwood City, CA (1992).[3] L.E. Sugiyama and W. Park, Physics of Plasmas 7, 4644 (2000).[4] J.J. Ramos, Physics of Plasmas, 10, 3601 (2003).[5] P.J. Catto and A.N. Simakov, Physics of Plasmas, 11, 90 (2004).[6] E.D. Held et al., Phys. Plasmas 11, 2419 (2004)

Integration of Extended MHD and Kinetic Effects in Global Magnetosphere Models

NASA Astrophysics Data System (ADS)

Germaschewski, K.; Wang, L.; Maynard, K. R. M.; Raeder, J.; Bhattacharjee, A.

2015-12-01

Computational models of Earth's geospace environment are an important tool to investigate the science of the coupled solar-wind -- magnetosphere -- ionosphere system, complementing satellite and ground observations with a global perspective. They are also crucial in understanding and predicting space weather, in particular under extreme conditions. Traditionally, global models have employed the one-fluid MHD approximation, which captures large-scale dynamics quite well. However, in Earth's nearly collisionless plasma environment it breaks down on small scales, where ion and electron dynamics and kinetic effects become important, and greatly change the reconnection dynamics. A number of approaches have recently been taken to advance global modeling, e.g., including multiple ion species, adding Hall physics in a Generalized Ohm's Law, embedding local PIC simulations into a larger fluid domain and also some work on simulating the entire system with hybrid or fully kinetic models, the latter however being to computationally expensive to be run at realistic parameters. We will present an alternate approach, ie., a multi-fluid moment model that is derived rigorously from the Vlasov-Maxwell system. The advantage is that the computational cost remains managable, as we are still solving fluid equations. While the evolution equation for each moment is exact, it depends on the next higher-order moment, so that truncating the hiearchy and closing the system to capture the essential kinetic physics is crucial. We implement 5-moment (density, momentum, scalar pressure) and 10-moment (includes pressure tensor) versions of the model, and use local approximations for the heat flux to close the system. We test these closures by local simulations where we can compare directly to PIC / hybrid codes, and employ them in global simulations using the next-generation OpenGGCM to contrast them to MHD / Hall-MHD results and compare with observations.

Solute-defect interactions in Al-Mg alloys from diffusive variational Gaussian calculations

NASA Astrophysics Data System (ADS)

Dontsova, E.; Rottler, J.; Sinclair, C. W.

2014-11-01

Resolving atomic-scale defect topologies and energetics with accurate atomistic interaction models provides access to the nonlinear phenomena inherent at atomic length and time scales. Coarse graining the dynamics of such simulations to look at the migration of, e.g., solute atoms, while retaining the rich atomic-scale detail required to properly describe defects, is a particular challenge. In this paper, we present an adaptation of the recently developed "diffusive molecular dynamics" model to describe the energetics and kinetics of binary alloys on diffusive time scales. The potential of the technique is illustrated by applying it to the classic problems of solute segregation to a planar boundary (stacking fault) and edge dislocation in the Al-Mg system. Our approach provides fully dynamical solutions in situations with an evolving energy landscape in a computationally efficient way, where atomistic kinetic Monte Carlo simulations are difficult or impractical to perform.

Characterization of the efficiency of microbore liquid chromatography columns by van Deemter and kinetic plot analysis.

PubMed

Hetzel, Terence; Loeker, Denise; Teutenberg, Thorsten; Schmidt, Torsten C

2016-10-01

The efficiency of miniaturized liquid chromatography columns with inner diameters between 200 and 300 μm has been investigated using a dedicated micro-liquid chromatography system. Fully porous, core-shell and monolithic commercially available stationary phases were compared applying van Deemter and kinetic plot analysis. The sub-2 μm fully porous as well as the 2.7 μm core-shell particle packed columns showed superior efficiency and similar values for the minimum reduced plate heights (2.56-2.69) before correction for extra-column contribution compared to normal-bore columns. Moreover, the influence of extra-column contribution was investigated to demonstrate the difference between apparent and intrinsic efficiency by replacing the column by a zero dead volume union to determine the band spreading caused by the system. It was demonstrated that 72% of the intrinsic efficiency could be reached. The results of the kinetic plot analysis indicate the superior performance of the sub-2 μm fully porous particle packed column for ultra-fast liquid chromatography. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A unified model of Grignard reagent formation.

PubMed

Shao, Yunqi; Liu, Zhen; Huang, Pan; Liu, Boping

2018-04-25

Grignard reagents are among the most fundamental reagents in organic synthesis, yet studies have hitherto failed to fully explain the selectivity and kinetics of Grignard reagent formation (GRF). The present study provides new insights into the intermediates and pathways of GRF using density functional theory (DFT) calculations. Potential energy surfaces of RX dissociation along different directions reveal the origin of configuration retention of alkenyl and aromatic halides. Radical intermediates participate solely in the dissociation stage, and depend on the geometry of the reactant halide. Dissociation of organic halides yields stabilized surface anions, and the rest of the reaction is ionic in nature. MgX+/RMg+ were proposed as the key intermediates of Mg leaving from the surface in the self-activation of GRF, which explains the accelerated kinetics upon addition of RMgX or MgX2. The intermediacy of the cations was supported by a simple electrochemical experiment. To the best of our knowledge, this is the first unified ionic model (I-model) developed for resolving the controversial issues of GRF.

Theory favors a stepwise mechanism of porphyrin degradation by a ferric hydroperoxide model of the active species of heme oxygenase.

PubMed

Kumar, Devesh; de Visser, Samuël P; Shaik, Sason

2005-06-08

The report uses density functional theory to address the mechanism of heme degradation by the enzyme heme oxygenase (HO) using a model ferric hydroperoxide complex. HO is known to trap heme molecules and degrade them to maintain iron homeostasis in the biosystem. The degradation is initiated by complexation of the heme, then formation of the iron-hydroperoxo species, which subsequently oxidizes the meso position of the porphyrin by hydroxylation, thereby enabling eventually the cleavage of the porphyrin ring. Kinetic isotope effect studies indicate that the mechanism is assisted by general acid catalysis, via a chain of water molecules, and that all the events occur in concert. However, previous theoretical treatments indicated that the concerted mechanism has a high barrier, much higher than an alternative mechanism that is initiated by O-O bond homolysis of iron-hydroperoxide. The present contribution studies the stepwise and concerted acid-catalyzed mechanisms using H(3)O(+)(H(2)O)(n)(), n = 0-2. The effect of the acid strength is tested using the H(4)N(+)(H(2)O)(2) cluster and a fully protonated ferric hydroperoxide. All the calculations show that a stepwise mechanism that involves proton relay and O-O homolysis, in the rate-determining step, has a much lower barrier (>10 kcal/mol) than the corresponding fully concerted mechanism. The best fit of the calculated solvent kinetic isotope effect, to the experimental data, is obtained for the H(3)O(+)(H(2)O)(2) cluster. The calculated alpha-deuterium secondary kinetic isotope effect is inverse (0.95-0.98), but much less so than the experimental value (0.7). Possible reasons for this quantitative difference are discussed. Some probes are suggested that may enable experiment to distinguish the stepwise from the concerted mechanism.

A Kinetic Model of Trp-Cage Folding from Multiple Biased Molecular Dynamics Simulations

PubMed Central

Marinelli, Fabrizio; Pietrucci, Fabio; Laio, Alessandro; Piana, Stefano

2009-01-01

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins. Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For the Trp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap. Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at of 4.4 Å from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the and chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data. PMID:19662155

A kinetic model of trp-cage folding from multiple biased molecular dynamics simulations.

PubMed

Marinelli, Fabrizio; Pietrucci, Fabio; Laio, Alessandro; Piana, Stefano

2009-08-01

Trp-cage is a designed 20-residue polypeptide that, in spite of its size, shares several features with larger globular proteins.Although the system has been intensively investigated experimentally and theoretically, its folding mechanism is not yet fully understood. Indeed, some experiments suggest a two-state behavior, while others point to the presence of intermediates. In this work we show that the results of a bias-exchange metadynamics simulation can be used for constructing a detailed thermodynamic and kinetic model of the system. The model, although constructed from a biased simulation, has a quality similar to those extracted from the analysis of long unbiased molecular dynamics trajectories. This is demonstrated by a careful benchmark of the approach on a smaller system, the solvated Ace-Ala3-Nme peptide. For theTrp-cage folding, the model predicts that the relaxation time of 3100 ns observed experimentally is due to the presence of a compact molten globule-like conformation. This state has an occupancy of only 3% at 300 K, but acts as a kinetic trap.Instead, non-compact structures relax to the folded state on the sub-microsecond timescale. The model also predicts the presence of a state at Calpha-RMSD of 4.4 A from the NMR structure in which the Trp strongly interacts with Pro12. This state can explain the abnormal temperature dependence of the Pro12-delta3 and Gly11-alpha3 chemical shifts. The structures of the two most stable misfolded intermediates are in agreement with NMR experiments on the unfolded protein. Our work shows that, using biased molecular dynamics trajectories, it is possible to construct a model describing in detail the Trp-cage folding kinetics and thermodynamics in agreement with experimental data.

Fully kinetic Biermann battery and associated generation of pressure anisotropy

NASA Astrophysics Data System (ADS)

Schoeffler, K. M.; Loureiro, N. F.; Silva, L. O.

2018-03-01

The dynamical evolution of a fully kinetic, collisionless system with imposed background density and temperature gradients is investigated analytically. The temperature gradient leads to the generation of temperature anisotropy, with the temperature along the gradient becoming larger than that in the direction perpendicular to it. This causes the system to become unstable to pressure anisotropy driven instabilities, dominantly to the electron Weibel instability. When both density and temperature gradients are present and nonparallel to each other, we obtain a Biermann-like linear-in-time magnetic field growth. Accompanying particle-in-cell numerical simulations are shown to confirm our analytical results.

Center for Extended Magnetohydrodynamics Modeling - Final Technical Report

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

Parker, Scott

This project funding supported approximately 74 percent of a Ph.D. graduate student, not including costs of travel and supplies. We had a highly successful research project including the development of a second-order implicit electromagnetic kinetic ion hybrid model [Cheng 2013, Sturdevant 2016], direct comparisons with the extended MHD NIMROD code and kinetic simulation [Schnack 2013], modeling of slab tearing modes using the fully kinetic ion hybrid model and finally, modeling global tearing modes in cylindrical geometry using gyrokinetic simulation [Chen 2015, Chen 2016]. We developed an electromagnetic second-order implicit kinetic ion fluid electron hybrid model [Cheng 2013]. As a firstmore » step, we assumed isothermal electrons, but have included drift-kinetic electrons in similar models [Chen 2011]. We used this simulation to study the nonlinear evolution of the tearing mode in slab geometry, including nonlinear evolution and saturation [Cheng 2013]. Later, we compared this model directly to extended MHD calculations using the NIMROD code [Schnack 2013]. In this study, we investigated the ion-temperature-gradient instability with an extended MHD code for the first time and got reasonable agreement with the kinetic calculation in terms of linear frequency, growth rate and mode structure. We then extended this model to include orbit averaging and sub-cycling of the ions and compared directly to gyrokinetic theory [Sturdevant 2016]. This work was highlighted in an Invited Talk at the International Conference on the Numerical Simulation of Plasmas in 2015. The orbit averaging sub-cycling multi-scale algorithm is amenable to hybrid architectures with GPUS or math co-processors. Additionally, our participation in the Center for Extend Magnetohydrodynamics motivated our research on developing the capability for gyrokinetic simulation to model a global tearing mode. We did this in cylindrical geometry where the results could be benchmarked with existing eigenmode calculations. First, we developed a gyrokinetic code capable of simulating long wavelengths using a fluid electron model [Chen 2015]. We benchmarked this code with an eigenmode calculation. Besides having to rewrite the field solver due to the breakdown in the gyrokinetic ordering for long wavelengths, very high radial resolution was required. We developed a technique where we used the solution from the eigenmode solver to specify radial boundary conditions allowing for a very high radial resolution of the inner solution. Using this technique enabled us to use our direct algorithm with gyrokinetic ions and drift kinetic electrons [Chen 2016]. This work was highlighted in an Invited Talk at the American Physical Society - Division of Plasma Physics in 2015.« less

Understanding Yield Anomalies in ICF Implosions via Fully Kinetic Simulations

NASA Astrophysics Data System (ADS)

Taitano, William

2017-10-01

In the quest towards ICF ignition, plasma kinetic effects are among prime candidates for explaining some significant discrepancies between experimental observations and rad-hydro simulations. To assess their importance, high-fidelity fully kinetic simulations of ICF capsule implosions are needed. Owing to the extremely multi-scale nature of the problem, kinetic codes have to overcome nontrivial numerical and algorithmic challenges, and very few options are currently available. Here, we present resolutions of some long-standing yield discrepancy conundrums using a novel, LANL-developed, 1D-2V Vlasov-Fokker-Planck code iFP. iFP possesses an unprecedented fidelity and features fully implicit time-stepping, exact mass, momentum, and energy conservation, and optimal grid adaptation in phase space, all of which are critically important for ensuring long-time numerical accuracy of the implosion simulations. Specifically, we concentrate on several anomalous yield degradation instances observed in Omega campaigns, with the so-called ``Rygg effect'', or an anomalous yield scaling with the fuel composition, being a prime example. Understanding the physical mechanisms responsible for such degradations in non-ignition-grade Omega experiments is of great interest, as such experiments are often used for platform and diagnostic development, which are then used in ignition-grade experiments on NIF. In the case of Rygg's experiments, effects of a kinetic stratification of fuel ions on the yield have been previously proposed as the anomaly explanation, studied with a kinetic code FPION, and found unimportant. We have revisited this issue with iFP and obtained excellent yield-over-clean agreement with the original Rygg results, and several subsequent experiments. This validates iFP and confirms that the kinetic fuel stratification is indeed at the root of the observed yield degradation. This work was sponsored by the Metropolis Postdoctoral Fellowship, LDRD office, Thermonuclear Burn Initiative of ASC, and the LANL Institutional Computing. This work was performed under the NNSA of the USDOE at LANL under contract DE-AC52-06NA25396.

The H2A-H2B dimeric kinetic intermediate is stabilized by widespread hydrophobic burial with few fully native interactions.

PubMed

Guyett, Paul J; Gloss, Lisa M

2012-01-20

The H2A-H2B histone heterodimer folds via monomeric and dimeric kinetic intermediates. Within ∼5 ms, the H2A and H2B polypeptides associate in a nearly diffusion limited reaction to form a dimeric ensemble, denoted I₂ and I₂*, the latter being a subpopulation characterized by a higher content of nonnative structure (NNS). The I₂ ensemble folds to the native heterodimer, N₂, through an observable, first-order kinetic phase. To determine the regions of structure in the I₂ ensemble, we characterized 26 Ala mutants of buried hydrophobic residues, spanning the three helices of the canonical histone folds of H2A and H2B and the H2B C-terminal helix. All but one targeted residue contributed significantly to the stability of I₂, the transition state and N₂; however, only residues in the hydrophobic core of the dimer interface perturbed the I₂* population. Destabilization of I₂* correlated with slower folding rates, implying that NNS is not a kinetic trap but rather accelerates folding. The pattern of Φ values indicated that residues forming intramolecular interactions in the peripheral helices contributed similar stability to I₂ and N₂, but residues involved in intermolecular interactions in the hydrophobic core are only partially folded in I₂. These findings suggest a dimerize-then-rearrange model. Residues throughout the histone fold contribute to the stability of I₂, but after the rapid dimerization reaction, the hydrophobic core of the dimer interface has few fully native interactions. In the transition state leading to N₂, more native-like interactions are developed and nonnative interactions are rearranged. Copyright © 2011 Elsevier Ltd. All rights reserved.

Simulation and optimization of ammonia removal at low temperature for a double channel oxidation ditch based on fully coupled activated sludge model (FCASM): a full-scale study.

PubMed

Yang, Min; Sun, Peide; Wang, Ruyi; Han, Jingyi; Wang, Jianqiao; Song, Yingqi; Cai, Jing; Tang, Xiudi

2013-09-01

An optimal operating condition for ammonia removal at low temperature, based on fully coupled activated sludge model (FCASM), was determined in a full-scale oxidation ditch process wastewater treatment plant (WWTP). The FCASM-based mechanisms model was calibrated and validated with the data measured on site. Several important kinetic parameters of the modified model were tested through respirometry experiment. Validated model was used to evaluate the relationship between ammonia removal and operating parameters, such as temperature (T), dissolved oxygen (DO), solid retention time (SRT) and hydraulic retention time of oxidation ditch (HRT). The simulated results showed that low temperature have a negative effect on the ammonia removal. Through orthogonal simulation tests of the last three factors and combination with the analysis of variance, the optimal operating mode acquired of DO, SRT, HRT for the WWTP at low temperature were 3.5 mg L(-1), 15 d and 14 h, respectively. Copyright © 2013 Elsevier Ltd. All rights reserved.

Prediction of heat release effects on a mixing layer

NASA Technical Reports Server (NTRS)

Farshchi, M.

1986-01-01

A fully second-order closure model for turbulent reacting flows is suggested based on Favre statistics. For diffusion flames the local thermodynamic state is related to single conserved scalar. The properties of pressure fluctuations are analyzed for turbulent flows with fluctuating density. Closure models for pressure correlations are discussed and modeled transport equations for Reynolds stresses, turbulent kinetic energy dissipation, density-velocity correlations, scalar moments and dissipation are presented and solved, together with the mean equations for momentum and mixture fraction. Solutions of these equations are compared with the experimental data for high heat release free mixing layers of fluorine and hydrogen in a nitrogen diluent.

Explosion of comet Shoemaker-Levy 9 on entry into the Jovian atmosphere

NASA Technical Reports Server (NTRS)

Mac Low, Mordecai-Mark; Zahnle, Kevin

1994-01-01

We use the astrophysical hydrocode ZEUS to compute high-resolution models of the disruption and deceleration of cometary fragments striking Jupiter. We find that simple analytic and semianalytic models work well for kilometer-size impactors. We show that previous numerical models that placed the explosion much deeper in the atmosphere failed to fully resolve important gasdynamical instabilities. These instabilities tear the comet apart, greatly increase its effective cross section, and bring it to an abrupt halt. A 1 km diameter fragment loses over 90% of its kinetic energy within a single scale height at an atmospheric pressure of order 10 bars. For all practical purposes, it explodes.

Effect of driver impedance on dense plasma focus Z-pinch neutron yield

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

Sears, Jason, E-mail: sears8@llnl.gov, E-mail: schmidt36@llnl.gov; Link, Anthony, E-mail: sears8@llnl.gov, E-mail: schmidt36@llnl.gov; Schmidt, Andrea, E-mail: sears8@llnl.gov, E-mail: schmidt36@llnl.gov

2014-12-15

The Z-pinch phase of a dense plasma focus (DPF) heats the plasma by rapid compression and accelerates ions across its intense electric fields, producing neutrons through both thermonuclear and beam-target fusion. Driver characteristics have empirically been shown to affect performance, as measured by neutron yield per unit of stored energy. We are exploring the effect of driver characteristics on DPF performance using particle-in-cell (PIC) simulations of a kJ scale DPF. In this work, our PIC simulations are fluid for the run-down phase and transition to fully kinetic for the pinch phase, capturing kinetic instabilities, anomalous resistivity, and beam formation duringmore » the pinch. The anode-cathode boundary is driven by a circuit model of the capacitive driver, including system inductance, the load of the railgap switches, the guard resistors, and the coaxial transmission line parameters. It is known that the driver impedance plays an important role in the neutron yield: first, it sets the peak current achieved at pinch time; and second, it affects how much current continues to flow through the pinch when the pinch inductance and resistance suddenly increase. Here we show from fully kinetic simulations how total neutron yield depends on the impedance of the driver and the distributed parameters of the transmission circuit. Direct comparisons between the experiment and simulations enhance our understanding of these plasmas and provide predictive design capability for neutron source applications.« less

Expression and Characterization of Hyperthermostable Exo-polygalacturonase TtGH28 from Thermotoga thermophilus.

PubMed

Wagschal, Kurt; Rose Stoller, J; Chan, Victor J; Lee, Charles C; Grigorescu, Arabela A; Jordan, Douglas B

2016-07-01

D-galacturonic acid is a potential platform chemical comprising the principal component of pectin in the citrus processing waste stream. Several enzyme activities are required for the enzymatic production of galacturonic acid from pectin, including exo- and endo-polygalacturonases. The gene TtGH28 encoding a putative GH28 polygalacturonase from Pseudothermotoga thermarum DSM 5069 (Theth_0397, NCBI# AEH50492.1) was synthesized, expressed in Escherichia coli, and characterized. Alignment of the amino acid sequence of gene product TtGH28 with other GH28 proteins whose structures and details of their catalytic mechanism have been elucidated shows that three catalytic Asp residues and several other key active site residues are strictly conserved. Purified TtGH28 was dimeric and hyperthermostable, with K t (0.5)  = 86.3 °C. Kinetic parameters for activity on digalacturonic acid, trigalacturonic acid, and polygalacturonic acid were obtained. No substrate inhibition was observed for polygalacturonate, while the K si values for the oligogalacturonides were in the low mM range, and K i for product galacturonic acid was in the low μM range. Kinetic modeling of the progress of reaction showed that the enzyme is both fully exo- and fully non-processional.

Coincident measurements of prompt fission γ rays and fission fragments at DANCE

NASA Astrophysics Data System (ADS)

Walker, C. L.; Baramsai, B.; Jandel, M.; Rusev, G.; Couture, A.; Mosby, S.; Ullmann, J.; Kawano, T.; Stetcu, I.; Talou, P.

2015-10-01

Modern statistical approaches to modeling fission involve the calculation of not only average quantities but also fully correlated distributions of all fission products. Applications such as those involving the detection of special nuclear materials also rely on fully correlated data of fission products. Experimental measurements of correlated data are thus critical to the validation of theory and the development of important applications. The goal of this experiment was to measure properties of prompt fission gamma-ray emission as a function of fission fragments' total kinetic energy in the spontaneous fission of 252Cf. The measurement was carried out at the Detector for Advanced Neutron Capture Experiments (DANCE), a 4 π γ-ray calorimeter. A prototype design consisting of two silicon detectors was installed in the center of DANCE, allowing simultaneous measurement of fission fragments and γ rays. Effort has been taken to simulate fragment kinetic energy losses as well as γ-ray attenuation in DANCE using such tools as GEANT4 and SRIM. Theoretical predictions generated by the code CGMF were also incorporated as input for these simulations. Results from the experiment and simulations will be presented, along with plans for future measurements.

Fully Parallel MHD Stability Analysis Tool

NASA Astrophysics Data System (ADS)

Svidzinski, Vladimir; Galkin, Sergei; Kim, Jin-Soo; Liu, Yueqiang

2015-11-01

Progress on full parallelization of the plasma stability code MARS will be reported. MARS calculates eigenmodes in 2D axisymmetric toroidal equilibria in MHD-kinetic plasma models. It is a powerful tool for studying MHD and MHD-kinetic instabilities and it is widely used by fusion community. Parallel version of MARS is intended for simulations on local parallel clusters. It will be an efficient tool for simulation of MHD instabilities with low, intermediate and high toroidal mode numbers within both fluid and kinetic plasma models, already implemented in MARS. Parallelization of the code includes parallelization of the construction of the matrix for the eigenvalue problem and parallelization of the inverse iterations algorithm, implemented in MARS for the solution of the formulated eigenvalue problem. Construction of the matrix is parallelized by distributing the load among processors assigned to different magnetic surfaces. Parallelization of the solution of the eigenvalue problem is made by repeating steps of the present MARS algorithm using parallel libraries and procedures. Results of MARS parallelization and of the development of a new fix boundary equilibrium code adapted for MARS input will be reported. Work is supported by the U.S. DOE SBIR program.

Quantitative modeling of the reaction/diffusion kinetics of two-chemistry photopolymers

NASA Astrophysics Data System (ADS)

Kowalski, Benjamin Andrew

Optically driven diffusion in photopolymers is an appealing material platform for a broad range of applications, in which the recorded refractive index patterns serve either as images (e.g. data storage, display holography) or as optical elements (e.g. custom GRIN components, integrated optical devices). A quantitative understanding of the reaction/diffusion kinetics is difficult to obtain directly, but is nevertheless necessary in order to fully exploit the wide array of design freedoms in these materials. A general strategy for characterizing these kinetics is proposed, in which key processes are decoupled and independently measured. This strategy enables prediction of a material's potential refractive index change, solely on the basis of its chemical components. The degree to which a material does not reach this potential reveals the fraction of monomer that has participated in unwanted reactions, reducing spatial resolution and dynamic range. This approach is demonstrated for a model material similar to commercial media, achieving quantitative predictions of index response over three orders of exposure dose (~1 to ~103 mJ cm-2) and three orders of feature size (0.35 to 500 microns). The resulting insights enable guided, rational design of new material formulations with demonstrated performance improvement.

Kinetics-based phase change approach for VOF method applied to boiling flow

NASA Astrophysics Data System (ADS)

Cifani, Paolo; Geurts, Bernard; Kuerten, Hans

2014-11-01

Direct numerical simulations of boiling flows are performed to better understand the interaction of boiling phenomena with turbulence. The multiphase flow is simulated by solving a single set of equations for the whole flow field according to the one-fluid formulation, using a VOF interface capturing method. Interface terms, related to surface tension, interphase mass transfer and latent heat, are added at the phase boundary. The mass transfer rate across the interface is derived from kinetic theory and subsequently coupled with the continuum representation of the flow field. The numerical model was implemented in OpenFOAM and validated against 3 cases: evaporation of a spherical uniformly heated droplet, growth of a spherical bubble in a superheated liquid and two dimensional film boiling. The computational model will be used to investigate the change in turbulence intensity in a fully developed channel flow due to interaction with boiling heat and mass transfer. In particular, we will focus on the influence of the vapor bubble volume fraction on enhancing heat and mass transfer. Furthermore, we will investigate kinetic energy spectra in order to identify the dynamics associated with the wakes of vapor bubbles. Department of Applied Mathematics, 7500 AE Enschede, NL.

Kinetic analysis of MgB2 layer formation in advanced internal magnesium infiltration (AIMI) processed MgB2 wires

PubMed Central

Li, G. Z.; Sumption, M. D.; Collings, E. W.

2015-01-01

Significantly enhanced critical current density (Jc) for MgB2 superconducting wires can be obtained following the advanced internal Mg infiltration (AIMI) route. But unless suitable precautions are taken, the AIMI-processed MgB2 wires will exhibit incomplete MgB2 layer formation, i.e. reduced superconductor core size and hence suppressed current-carrying capability. Microstructural characterization of AIMI MgB2 wires before and after the heat treatment reveals that the reaction mechanism changes from a “Mg infiltration-reaction” at the beginning of the heat treatment to a “Mg diffusion-reaction” once a dense MgB2 layer is formed. A drastic drop in the Mg transport rate from infiltration to diffusion causes the termination of the MgB2 core growth. To quantify this process, a two-stage kinetic model is built to describe the MgB2 layer formation and growth. The derived kinetic model and the associated experimental observations indicate that fully reacted AIMI-processed MgB2 wires can be achieved following the optimization of B particle size, B powder packing density, MgB2 reaction activation energy and its response to the additions of dopants. PMID:26973431

Sinusoidal voltage protocols for rapid characterisation of ion channel kinetics.

PubMed

Beattie, Kylie A; Hill, Adam P; Bardenet, Rémi; Cui, Yi; Vandenberg, Jamie I; Gavaghan, David J; de Boer, Teun P; Mirams, Gary R

2018-03-24

Ion current kinetics are commonly represented by current-voltage relationships, time constant-voltage relationships and subsequently mathematical models fitted to these. These experiments take substantial time, which means they are rarely performed in the same cell. Rather than traditional square-wave voltage clamps, we fitted a model to the current evoked by a novel sum-of-sinusoids voltage clamp that was only 8 s long. Short protocols that can be performed multiple times within a single cell will offer many new opportunities to measure how ion current kinetics are affected by changing conditions. The new model predicts the current under traditional square-wave protocols well, with better predictions of underlying currents than literature models. The current under a novel physiologically relevant series of action potential clamps is predicted extremely well. The short sinusoidal protocols allow a model to be fully fitted to individual cells, allowing us to examine cell-cell variability in current kinetics for the first time. Understanding the roles of ion currents is crucial to predict the action of pharmaceuticals and mutations in different scenarios, and thereby to guide clinical interventions in the heart, brain and other electrophysiological systems. Our ability to predict how ion currents contribute to cellular electrophysiology is in turn critically dependent on our characterisation of ion channel kinetics - the voltage-dependent rates of transition between open, closed and inactivated channel states. We present a new method for rapidly exploring and characterising ion channel kinetics, applying it to the hERG potassium channel as an example, with the aim of generating a quantitatively predictive representation of the ion current. We fitted a mathematical model to currents evoked by a novel 8 second sinusoidal voltage clamp in CHO cells overexpressing hERG1a. The model was then used to predict over 5 minutes of recordings in the same cell in response to further protocols: a series of traditional square step voltage clamps, and also a novel voltage clamp comprising a collection of physiologically relevant action potentials. We demonstrate that we can make predictive cell-specific models that outperform the use of averaged data from a number of different cells, and thereby examine which changes in gating are responsible for cell-cell variability in current kinetics. Our technique allows rapid collection of consistent and high quality data, from single cells, and produces more predictive mathematical ion channel models than traditional approaches. © 2018 The Authors. The Journal of Physiology published by John Wiley & Sons Ltd on behalf of The Physiological Society.

Accelerated hydrolysis of substituted cellulose for potential biofuel production: kinetic study and modeling.

PubMed

Mu, Bingnan; Xu, Helan; Yang, Yiqi

2015-11-01

In this work, kinetics of substitution accelerated cellulose hydrolysis with multiple reaction stages was investigated to lay foundation for mechanism study and molecular design of substituting compounds. High-efficiency hydrolysis of cellulose is critical for cellulose-based bioethanol production. It is known that, substitution could substantially decrease activation energy and increase reaction rate of acidic hydrolysis of glycosidic bonds in cellulose. However, reaction kinetics and mechanism of the accelerated hydrolysis were not fully revealed. In this research, it was proved that substitution therefore accelerated hydrolysis only occurred in amorphous regions of cellulose fibers, and was a process with multiple reaction stages. With molar ratio of substitution less than 1%, the overall hydrolysis rate could be increased for around 10 times. We also quantified the relationship between the hydrolysis rate of individual reaction stage and its major influences, including molar ratio of substitution, activation energy of acidic hydrolysis, pH and temperature. Copyright © 2015 Elsevier Ltd. All rights reserved.

Experimental effect of shots caused by projectiles fired from air guns with kinetic energy below 17 J.

PubMed

Smędra-Kaźmirska, Anna; Barzdo, Maciej; Kędzierski, Maciej; Antoszczyk, Łukasz; Szram, Stefan; Berent, Jarosław

2013-09-01

Pursuant to the Polish Weapons and Ammunitions Law (Legal Gazette No 53/1999 item 549 with subsequent amendments), air guns with kinetic energy of the fired projectiles below 17 J are not regarded as weapons. The aim of the study was to assess the potential effect of shots caused by projectiles of various mass and structure fired from air guns with kinetic energy below 17 J on human soft tissues. As a model of soft tissue, we used 20% gelatin blocks. After shooting, we measured the depth of gelatin block penetration by pellets fired from various distances and compared these results with autopsy findings. The results demonstrated that examined pneumatic guns may cause serious injuries, including damage to the pleura, pericardium, liver, spleen, kidneys, femoral artery, and thoracic and abdominal aorta. Experiment shown that gelatin blocks do not reflect fully the properties of the human body. © 2013 American Academy of Forensic Sciences.

A biomechanical analysis of upper extremity kinetics in children with cerebral palsy using anterior and posterior walkers.

PubMed

Konop, Katherine A; Strifling, Kelly M B; Wang, Mei; Cao, Kevin; Schwab, Jeffrey P; Eastwood, Daniel; Jackson, Scott; Ackman, Jeffrey D; Harris, Gerald F

2009-10-01

Upper extremity (UE) joint kinetics during aided ambulation is an area of research that is not well characterized in the current literature. Biped UE joints are not anatomically designed to be weight bearing, therefore it is important to quantify UE kinetics during assisted gait. This will help to better understand the biomechanical implications of UE weight bearing, and enable physicians to prescribe more effective methods for treatment and therapy, perhaps minimizing excessive loads and torques. To address this challenge, an UE model that incorporates both kinematics and kinetics has been developed for use with walkers instrumented with load cells. In this study, the UE joint kinetics are calculated for 10 children with cerebral palsy using both anterior and posterior walkers. Three-dimensional joint reaction forces and moments are fully characterized for the wrist, elbow, and shoulder (glenohumeral) joints for both walker types. Statistical analysis methods are used to quantify the differences in forces or moments between the two walker types. Comparisons showed no significant differences in kinetic joint parameters between walker types. Results from a power analysis of the current data are provided which may be useful for planning longer term clinical studies. If risk factors for UE joint pathology can be identified early, perhaps a change in gait training routine, walker prescription, or walker design could prevent further harm.

Supersymmetric quantum mechanics method for the Fokker-Planck equation with applications to protein folding dynamics

NASA Astrophysics Data System (ADS)

Polotto, Franciele; Drigo Filho, Elso; Chahine, Jorge; Oliveira, Ronaldo Junio de

2018-03-01

This work developed analytical methods to explore the kinetics of the time-dependent probability distributions over thermodynamic free energy profiles of protein folding and compared the results with simulation. The Fokker-Planck equation is mapped onto a Schrödinger-type equation due to the well-known solutions of the latter. Through a semi-analytical description, the supersymmetric quantum mechanics formalism is invoked and the time-dependent probability distributions are obtained with numerical calculations by using the variational method. A coarse-grained structure-based model of the two-state protein Tm CSP was simulated at a Cα level of resolution and the thermodynamics and kinetics were fully characterized. Analytical solutions from non-equilibrium conditions were obtained with the simulated double-well free energy potential and kinetic folding times were calculated. It was found that analytical folding time as a function of temperature agrees, quantitatively, with simulations and experiments from the literature of Tm CSP having the well-known 'U' shape of the Chevron Plots. The simple analytical model developed in this study has a potential to be used by theoreticians and experimentalists willing to explore, quantitatively, rates and the kinetic behavior of their system by informing the thermally activated barrier. The theory developed describes a stochastic process and, therefore, can be applied to a variety of biological as well as condensed-phase two-state systems.

Electrochemical kinetic and mass transfer model for direct ethanol alkaline fuel cell (DEAFC)

NASA Astrophysics Data System (ADS)

Abdullah, S.; Kamarudin, S. K.; Hasran, U. A.; Masdar, M. S.; Daud, W. R. W.

2016-07-01

A mathematical model is developed for a liquid-feed DEAFC incorporating an alkaline anion-exchange membrane. The one-dimensional mass transport of chemical species is modelled using isothermal, single-phase and steady-state assumptions. The anode and cathode electrochemical reactions use the Tafel kinetics approach, with two limiting cases, for the reaction order. The model fully accounts for the mixed potential effects of ethanol oxidation at the cathode due to ethanol crossover via an alkaline anion-exchange membrane. In contrast to a polymer electrolyte membrane model, the current model considers the flux of ethanol at the membrane as the difference between diffusive and electroosmotic effects. The model is used to investigate the effects of the ethanol and alkali inlet feed concentrations at the anode. The model predicts that the cell performance is almost identical for different ethanol concentrations at a low current density. Moreover, the model results show that feeding the DEAFC with 5 M NaOH and 3 M ethanol at specific operating conditions yields a better performance at a higher current density. Furthermore, the model indicates that crossover effects on the DEAFC performance are significant. The cell performance decrease from its theoretical value when a parasitic current is enabled in the model.

Impact of polymer structure and composition on fully resorbable endovascular scaffold performance

PubMed Central

Ferdous, Jahid; Kolachalama, Vijaya B.; Shazly, Tarek

2014-01-01

Fully erodible endovascular scaffolds are being increasingly considered for the treatment of obstructive arterial disease owing to their potential to mitigate long-term risks associated with permanent alternatives. While complete scaffold erosion facilitates vessel healing, generation and release of material degradation by-products from candidate materials such as poly-l-lactide (PLLA) may elicit local inflammatory responses that limit implant efficacy. We developed a computational framework to quantify how the compositional and structural parameters of PLLA-based fully erodible endovascular scaffolds affect degradation kinetics, erosion kinetics and the transient accumulation of material by-products within the arterial wall. Parametric studies reveal that, while some material properties have similar effects on these critical processes, others induce qualitatively opposing responses. For example, scaffold degradation is only mildly responsive to changes in either PLLA polydispersity or the initial degree of crystallinity, while the erosion kinetics is comparatively sensitive to crystallinity. Moreover, lactide doping can effectively tune both scaffold degradation and erosion, but a concomitant increase in local byproduct accumulation raises concerns about implant safety. Optimized erodible endovascular scaffolds must precisely balance therapeutic function and biological response over the implant lifetime, where compositional and structural parameters will have differential effects on implant performance. PMID:23261926

The Effect of Polymer Char on Nitridation Kinetics of Silicon

NASA Technical Reports Server (NTRS)

Chan, Rickmond C.; Bhatt, Ramakrishna T.

1994-01-01

Effects of polymer char on nitridation kinetics of attrition milled silicon powder have been investigated from 1200 to 1350 C. Results indicate that at and above 1250 C, the silicon compacts containing 3.5 wt percent polymer char were fully converted to Si3N4 after 24 hr exposure in nitrogen. In contrast, the silicon compacts without polymer char could not be fully converted to Si3N4 at 1350 C under similar exposure conditions. At 1250 and 1350 C, the silicon compacts with polymer char showed faster nitridation kinetics than those without the polymer char. As the polymer char content is increased, the amount of SiC in the nitrided material is also increased. By adding small amounts (approx. 2.5 wt percent) of NiO, the silicon compacts containing polymer char can be completely nitrided at 1200 C. The probable mechanism for the accelerated nitridation of silicon containing polymer char is discussed.

An Improved K-Epsilon Model for Near-Wall Turbulence and Comparison with Direct Numerical Simulation

NASA Technical Reports Server (NTRS)

Shih, T. H.

1990-01-01

An improved k-epsilon model for low Reynolds number turbulence near a wall is presented. The near-wall asymptotic behavior of the eddy viscosity and the pressure transport term in the turbulent kinetic energy equation is analyzed. Based on this analysis, a modified eddy viscosity model, having correct near-wall behavior, is suggested, and a model for the pressure transport term in the k-equation is proposed. In addition, a modeled dissipation rate equation is reformulated. Fully developed channel flows were used for model testing. The calculations using various k-epsilon models are compared with direct numerical simulations. The results show that the present k-epsilon model performs well in predicting the behavior of near-wall turbulence. Significant improvement over previous k-epsilon models is obtained.

Self-consistent particle-in-cell simulations of fundamental and harmonic radio plasma emission mechanisms

NASA Astrophysics Data System (ADS)

Tsiklauri, D.; Thurgood, J. O.

2015-12-01

first co-author Jonathan O. Thurgood (QMUL) The simulation of three-wave interaction based plasma emission, an underlying mechanism for type III solar radio bursts, is a challenging task requiring fully-kinetic, multi-dimensional models. This paper aims to resolve a contradiction in past attempts, whereby some authors report that no such processes occur and others draw conflicting conclusions, by using 2D, fully kinetic, particle-in-cell simulations of relaxing electron beams. Here we present the results of particle-in-cell simulations which for different physical parameters permit or prohibit the plasma emission. We show that the possibility of plasma emission is contingent upon the frequency of the initial electrostatic waves generated by the bump-in-tail instability, and that these waves may be prohibited from participating in the necessary three-wave interactions due to the frequency beat requirements. We caution against simulating astrophysical radio bursts using unrealistically dense beams (a common approach which reduces run time), as the resulting non-Langmuir characteristics of the initial wave modes significantly suppresses the emission. Comparison of our results indicates that, contrary to the suggestions of previous authors, a plasma emission mechanism based on two counter-propagating beams is unnecessary in astrophysical context. Finally, we also consider the action of the Weibel instability, which generates an electromagnetic beam mode. As this provides a stronger contribution to electromagnetic energy than the emission, we stress that evidence of plasma emission in simulations must disentangle the two contributions and not simply interpret changes in total electromagnetic energy as the evidence of plasma emission. In summary, we present the first self-consistent demonstration of fundamental and harmonic plasma emission from a single-beam system via fully kinetic numerical simulation. Pre-print can be found at http://astro.qmul.ac.uk/~tsiklauri/jtdt1.pdf

First Observation of Switch-Off Slow Shocks in Fully Kinetic Particle in Cell Simulation of Magnetic Reconnection

NASA Astrophysics Data System (ADS)

Lapenta, G.; Sanna, L.; Goldman, M. V.; Newman, D. L.; Markidis, S.

2014-12-01

A perduring challenge in the study of reconnection it has long been the failing attempts to reconcile the large scale MHD view based on the Petschek model with the small scale view based on kinetic theory. The first is based on the existence of standing switch off slow shocks (SSS) that eliminate the horizontal (the x component in the usual GSM coordinates) reconnecting magnetic field component forming vertical magnetic field lines. The second is based on nested diffusion regions where the magnetic field lines become decoupled first from ions and then from electrons. The kinetic picture when observed superficially does seem to have seem resemblance to the Petschek topology, despite the nested boxes being more of a Sweet-Parker concept. Nevertheless, the question has always been: if expanded to sufficiently large scales, does the kinetic description eventually lead tot the formation os SSS? The question remains answered. Recently a first negative answer has been proposed in Ref. [1]. The proposed answer is in essence that SSS are made impossible by the presence of a firehose instability in the reconnection exhaust and by the formation of a plateau in the firehose parameter at a value of 0.25 corresponding to the condition where nonlinear slow and intermediate wave become degenerate. We report a new series of simulations where we demonstrate that this is not the case in general. While for the specific case used in Ref [1], we indeed re-obtain the same conclusions reached by the authors. But our study demonstrates that case to be very peculiar and not representative of the more general kinetic answer. We will report direct evidence of the presence of extended SSS (over regions of hundreds of ion inertial lengths) in fully kinetic simulations for parameters typical of the magntotail and of the solar wind. Our results indicate that SSS are the natural extension of kinetic reconnection to large scales. The simulations required for the study are heroic and were conducted with state of the art massively parallel computers provided by the PRACE system in Europe (specifically the Curie and SuperMUC computers) and by NASA Pleiades. The present work was funded by the NASA MMS mission and by the EC-funded project eHeroes (www.eheroes.eu)[1] Liu, Yi-Hsin, et al., PoP 18.6 (2011): 062110.

Numerical Investigation of Desulfurization Kinetics in Gas-Stirred Ladles by a Quick Modeling Analysis Approach

NASA Astrophysics Data System (ADS)

Cao, Qing; Nastac, Laurentiu; Pitts-Baggett, April; Yu, Qiulin

2018-03-01

A quick modeling analysis approach for predicting the slag-steel reaction and desulfurization kinetics in argon gas-stirred ladles has been developed in this study. The model consists of two uncoupled components: (i) a computational fluid dynamics (CFD) model for predicting the fluid flow and the characteristics of slag-steel interface, and (ii) a multicomponent reaction kinetics model for calculating the desulfurization evolution. The steel-slag interfacial area and mass transfer coefficients predicted by the CFD simulation are used as the processing data for the reaction model. Since the desulfurization predictions are uncoupled from the CFD simulation, the computational time of this uncoupled predictive approach is decreased by at least 100 times for each case study when compared with the CFD-reaction kinetics fully coupled model. The uncoupled modeling approach was validated by comparing the evolution of steel and slag compositions with the experimentally measured data during ladle metallurgical furnace (LMF) processing at Nucor Steel Tuscaloosa, Inc. Then, the validated approach was applied to investigate the effects of the initial steel and slag compositions, as well as different types of additions during the refining process on the desulfurization efficiency. The results revealed that the sulfur distribution ratio and the desulfurization reaction can be promoted by making Al and CaO additions during the refining process. It was also shown that by increasing the initial Al content in liquid steel, both Al oxidation and desulfurization rates rapidly increase. In addition, it was found that the variation of the initial Si content in steel has no significant influence on the desulfurization rate. Lastly, if the initial CaO content in slag is increased or the initial Al2O3 content is decreased in the fluid-slag compositional range, the desulfurization rate can be improved significantly during the LMF process.

Numerical Investigation of Desulfurization Kinetics in Gas-Stirred Ladles by a Quick Modeling Analysis Approach

NASA Astrophysics Data System (ADS)

Cao, Qing; Nastac, Laurentiu; Pitts-Baggett, April; Yu, Qiulin

2018-06-01

A quick modeling analysis approach for predicting the slag-steel reaction and desulfurization kinetics in argon gas-stirred ladles has been developed in this study. The model consists of two uncoupled components: (i) a computational fluid dynamics (CFD) model for predicting the fluid flow and the characteristics of slag-steel interface, and (ii) a multicomponent reaction kinetics model for calculating the desulfurization evolution. The steel-slag interfacial area and mass transfer coefficients predicted by the CFD simulation are used as the processing data for the reaction model. Since the desulfurization predictions are uncoupled from the CFD simulation, the computational time of this uncoupled predictive approach is decreased by at least 100 times for each case study when compared with the CFD-reaction kinetics fully coupled model. The uncoupled modeling approach was validated by comparing the evolution of steel and slag compositions with the experimentally measured data during ladle metallurgical furnace (LMF) processing at Nucor Steel Tuscaloosa, Inc. Then, the validated approach was applied to investigate the effects of the initial steel and slag compositions, as well as different types of additions during the refining process on the desulfurization efficiency. The results revealed that the sulfur distribution ratio and the desulfurization reaction can be promoted by making Al and CaO additions during the refining process. It was also shown that by increasing the initial Al content in liquid steel, both Al oxidation and desulfurization rates rapidly increase. In addition, it was found that the variation of the initial Si content in steel has no significant influence on the desulfurization rate. Lastly, if the initial CaO content in slag is increased or the initial Al2O3 content is decreased in the fluid-slag compositional range, the desulfurization rate can be improved significantly during the LMF process.

Exact solutions for kinetic models of macromolecular dynamics.

PubMed

Chemla, Yann R; Moffitt, Jeffrey R; Bustamante, Carlos

2008-05-15

Dynamic biological processes such as enzyme catalysis, molecular motor translocation, and protein and nucleic acid conformational dynamics are inherently stochastic processes. However, when such processes are studied on a nonsynchronized ensemble, the inherent fluctuations are lost, and only the average rate of the process can be measured. With the recent development of methods of single-molecule manipulation and detection, it is now possible to follow the progress of an individual molecule, measuring not just the average rate but the fluctuations in this rate as well. These fluctuations can provide a great deal of detail about the underlying kinetic cycle that governs the dynamical behavior of the system. However, extracting this information from experiments requires the ability to calculate the general properties of arbitrarily complex theoretical kinetic schemes. We present here a general technique that determines the exact analytical solution for the mean velocity and for measures of the fluctuations. We adopt a formalism based on the master equation and show how the probability density for the position of a molecular motor at a given time can be solved exactly in Fourier-Laplace space. With this analytic solution, we can then calculate the mean velocity and fluctuation-related parameters, such as the randomness parameter (a dimensionless ratio of the diffusion constant and the velocity) and the dwell time distributions, which fully characterize the fluctuations of the system, both commonly used kinetic parameters in single-molecule measurements. Furthermore, we show that this formalism allows calculation of these parameters for a much wider class of general kinetic models than demonstrated with previous methods.

Comparison of ACCENT 2000 Shuttle Plume Data with SIMPLE Model Predictions

NASA Astrophysics Data System (ADS)

Swaminathan, P. K.; Taylor, J. C.; Ross, M. N.; Zittel, P. F.; Lloyd, S. A.

2001-12-01

The JHU/APL Stratospheric IMpact of PLume Effluents (SIMPLE)model was employed to analyze the trace species in situ composition data collected during the ACCENT 2000 intercepts of the space shuttle Space Transportation Launch System (STS) rocket plume as a function of time and radial location within the cold plume. The SIMPLE model is initialized using predictions for species depositions calculated using an afterburning model based on standard TDK/SPP nozzle and SPF plume flowfield codes with an expanded chemical kinetic scheme. The time dependent ambient stratospheric chemistry is fully coupled to the plume species evolution whose transport is based on empirically derived diffusion. Model/data comparisons are encouraging through capturing observed local ozone recovery times as well as overall morphology of chlorine chemistry.

Analytical Model for Mean Flow and Fluxes of Momentum and Energy in Very Large Wind Farms

NASA Astrophysics Data System (ADS)

Markfort, Corey D.; Zhang, Wei; Porté-Agel, Fernando

2018-01-01

As wind-turbine arrays continue to be installed and the array size continues to grow, there is an increasing need to represent very large wind-turbine arrays in numerical weather prediction models, for wind-farm optimization, and for environmental assessment. We propose a simple analytical model for boundary-layer flow in fully-developed wind-turbine arrays, based on the concept of sparsely-obstructed shear flows. In describing the vertical distribution of the mean wind speed and shear stress within wind farms, our model estimates the mean kinetic energy harvested from the atmospheric boundary layer, and determines the partitioning between the wind power captured by the wind turbines and that absorbed by the underlying land or water. A length scale based on the turbine geometry, spacing, and performance characteristics, is able to estimate the asymptotic limit for the fully-developed flow through wind-turbine arrays, and thereby determine if the wind-farm flow is fully developed for very large turbine arrays. Our model is validated using data collected in controlled wind-tunnel experiments, and its usefulness for the prediction of wind-farm performance and optimization of turbine-array spacing are described. Our model may also be useful for assessing the extent to which the extraction of wind power affects the land-atmosphere coupling or air-water exchange of momentum, with implications for the transport of heat, moisture, trace gases such as carbon dioxide, methane, and nitrous oxide, and ecologically important oxygen.

Modeling of microstructure evolution of magnesium alloy during the high pressure die casting process

NASA Astrophysics Data System (ADS)

Wu, Mengwu; Xiong, Shoumei

2012-07-01

Two important microstructure characteristics of high pressure die cast magnesium alloy are the externally solidified crystals (ESCs) and the fully divorced eutectic which form at the filling stage of the shot sleeve and at the last stage of solidification in the die cavity, respectively. Both of them have a significant influence on the mechanical properties and performance of magnesium alloy die castings. In the present paper, a numerical model based on the cellular automaton (CA) method was developed to simulate the microstructure evolution of magnesium alloy during cold-chamber high pressure die casting (HPDC) process. Modeling of dendritic growth of magnesium alloy with six-fold symmetry was achieved by defining a special neighbourhood configuration and calculating of the growth kinetics from complete solution of the transport equations. Special attention was paid to establish a nucleation model considering both of the nucleation of externally solidified crystals in the shot sleeve and the massive nucleation in the die cavity. Meanwhile, simulation of the formation of fully divorced eutectic was also taken into account in the present CA model. Validation was performed and the capability of the present model was addressed by comparing the simulated results with those obtained by experiments.

Investigation of unsteadiness in Shock-particle cloud interaction: Fully resolved two-dimensional simulation and one-dimensional modeling

NASA Astrophysics Data System (ADS)

Hosseinzadeh-Nik, Zahra; Regele, Jonathan D.

2015-11-01

Dense compressible particle-laden flow, which has a complex nature, exists in various engineering applications. Shock waves impacting a particle cloud is a canonical problem to investigate this type of flow. It has been demonstrated that large flow unsteadiness is generated inside the particle cloud from the flow induced by the shock passage. It is desirable to develop models for the Reynolds stress to capture the energy contained in vortical structures so that volume-averaged models with point particles can be simulated accurately. However, the previous work used Euler equations, which makes the prediction of vorticity generation and propagation innacurate. In this work, a fully resolved two dimensional (2D) simulation using the compressible Navier-Stokes equations with a volume penalization method to model the particles has been performed with the parallel adaptive wavelet-collocation method. The results still show large unsteadiness inside and downstream of the particle cloud. A 1D model is created for the unclosed terms based upon these 2D results. The 1D model uses a two-phase simple low dissipation AUSM scheme (TSLAU) developed by coupled with the compressible two phase kinetic energy equation.

An alternative explicit model expression equivalent to the integrated michaelis-menten equation and its application to nonlinear saturation pharmacokinetics.

PubMed

Goličnik, Marko

2011-06-01

Many pharmacodynamic processes can be described by the nonlinear saturation kinetics that are most frequently based on the hyperbolic Michaelis-Menten equation. Thus, various time-dependent solutions for drugs obeying such kinetics can be expressed in terms of the Lambert W(x)-omega function. However, unfortunately, computer programs that can perform the calculations for W(x) are not widely available. To avoid this problem, the replacement of the integrated Michaelis-Menten equation with an empiric integrated 1--exp alternative model equation was proposed recently by Keller et al. (Ther Drug Monit. 2009;31:783-785), although, as shown here, it was not necessary. Simulated concentrations of model drugs obeying Michaelis-Menten elimination kinetics were generated by two approaches: 1) calculation of time-course data based on an approximation equation W2*(x) performed using Microsoft Excel; and 2) calculation of reference time-course data based on an exact W(x) function built in to the Wolfram Mathematica. I show here that the W2*(x) function approximates the actual W(x) accurately. W2*(x) is expressed in terms of elementary mathematical functions and, consequently, it can be easily implemented using any of the widely available software. Hence, with the example of a hypothetical drug, I demonstrate here that an equation based on this approximation is far better, because it is nearly equivalent to the original solution, whereas the same characteristics cannot be fully confirmed for the 1--exp model equation. The W2*(x) equation proposed here might have an important role as a useful shortcut in optional software to estimate kinetic parameters from experimental data for drugs, and it might represent an easy and universal analytical tool for simulating and designing dosing regimens.

Physical Model Study of the Fully Developed Wind Turbine Array Boundary Layer in the UNH Flow Physics Facility

NASA Astrophysics Data System (ADS)

Turner, John; Wosnik, Martin

2015-11-01

Results from an experimental study of an array of up to 100 model wind turbines with 0.25 m diameter are reported. The study was conducted in the UNH Flow Physics Facility (FPF), which has test section dimensions of 6.0 m wide, 2.7 m high and 72.0 m long. For a given configuration (spacing, initial conditions, etc.), the model wind farm reaches a ``fully developed'' condition, in which turbulence statistics remain the same from one row to the next within and above the wind turbine array. Of interest is the transport of kinetic energy within the wind turbine array boundary layer (WTABL). Model wind farms of up to 20 rows are possible in the FPF at the wind turbine scale used. The present studies in the FPF are able to achieve the fully developed WTABL condition, which can provide valuable insight to the optimization of wind farm energy production. The FPF can achieve a boundary layer height on the order of 1 m at the beginning of the wind turbine array. The wind turbine array was constructed of porous disks, which where drag (thrust) matched to wind turbines at typical operating conditions and therefore act as momentum sinks similar to wind turbines. The flow in the WTABL was measured with constant temperature anemometry using an X-wire.

Verification of nonlinear particle simulation of radio frequency waves in fusion plasmas

NASA Astrophysics Data System (ADS)

Kuley, Animesh; Bao, Jian; Lin, Zhihong

2015-11-01

Nonlinear global particle simulation model has been developed in GTC to study the nonlinear interactions of radio frequency (RF) waves with plasmas in tokamak. In this model, ions are considered as fully kinetic particles using the Vlasov equation and electrons are treated as guiding centers using the drift kinetic. Boris push scheme for the ion motion has been implemented in the toroidal geometry using magnetic coordinates and successfully verified for the ion cyclotron, ion Bernstein and lower hybrid waves. The nonlinear GTC simulation of the lower hybrid wave shows that the amplitude of the electrostatic potential is oscillatory due to the trapping of resonant electrons by the electric field of the lower hybrid wave. The nonresonant parametric decay is observed an IBW sideband and an ion cyclotron quasimode (ICQM). The ICQM induces an ion perpendicular heating with a heating rate proportional to the pump wave intensity. This work is supported by PPPL subcontract number S013849-F and US Department of Energy (DOE) SciDAC GSEP Program.

Current Driven Instabilities and Anomalous Mobility in Hall-effect Thrusters

NASA Astrophysics Data System (ADS)

Tran, Jonathan; Eckhardt, Daniel; Martin, Robert

2017-10-01

Due to the extreme cost of fully resolving the Debye length and plasma frequency, hybrid plasma simulations utilizing kinetic ions and quasi-steady state fluid electrons have long been the principle workhorse methodology for Hall-effect thruster (HET) modeling. Plasma turbulence and the resulting anomalous electron transport in HETs is a promising candidate for developing predictive models for the observed anomalous transport. In this work, we investigate the implementation of an anomalous electron cross field transport model for hybrid HET simulations such a HPHall. A theory for anomalous transport in HETs and current driven instabilities has been recently studied by Lafleur et al. This work has shown collective electron-wave scattering due to large amplitude azimuthal fluctuations of the electric field. We will further adapt the previous results for related current driven instabilities to electric propulsion relevant mass ratios and conduct a preliminary study of resolving this instability with a modified hybrid (fluid electron and kinetic ion) simulation with the hope of integration with established hybrid HET simulations. This work is supported by the Air Force Office of Scientific Research award FA9950-17RQCOR465.

Fully kinetic simulations of collisionless, mesothermal plasma emission: Macroscopic plume structure and microscopic electron characteristics

NASA Astrophysics Data System (ADS)

Hu, Yuan; Wang, Joseph

2017-03-01

This paper presents a fully kinetic particle particle-in-cell simulation study on the emission of a collisionless plasma plume consisting of cold beam ions and thermal electrons. Results are presented for both the two-dimensional macroscopic plume structure and the microscopic electron kinetic characteristics. We find that the macroscopic plume structure exhibits several distinctive regions, including an undisturbed core region, an electron cooling expansion region, and an electron isothermal expansion region. The properties of each region are determined by microscopic electron kinetic characteristics. The division between the undisturbed region and the cooling expansion region approximately matches the Mach line generated at the edge of the emission surface, and that between the cooling expansion region and the isothermal expansion region approximately matches the potential well established in the beam. The interactions between electrons and the potential well lead to a new, near-equilibrium state different from the initial distribution for the electrons in the isothermal expansion region. The electron kinetic characteristics in the plume are also very anisotropic. As the electron expansion process is mostly non-equilibrium and anisotropic, the commonly used assumption that the electrons in a collisionless, mesothermal plasma plume may be treated as a single equilibrium fluid in general is not valid.

Similarity between turbulent kinetic energy and temperature spectra in the near-wall region

NASA Technical Reports Server (NTRS)

Antonia, R. A.; Kim, J.

1991-01-01

The similarity between turbulent kinetic energy and temperature spectra, previously confirmed using experimental data in various turbulent shear flows, is validated in the near-wall region using direct numerical simulation data in a fully developed turbulent channel flow. The dependence of this similarity on the molecular Prandtl number is also examined.

Evolution of a mini-scale biphasic dissolution model: Impact of model parameters on partitioning of dissolved API and modelling of in vivo-relevant kinetics.

PubMed

Locher, Kathrin; Borghardt, Jens M; Frank, Kerstin J; Kloft, Charlotte; Wagner, Karl G

2016-08-01

Biphasic dissolution models are proposed to have good predictive power for the in vivo absorption. The aim of this study was to improve our previously introduced mini-scale dissolution model to mimic in vivo situations more realistically and to increase the robustness of the experimental model. Six dissolved APIs (BCS II) were tested applying the improved mini-scale biphasic dissolution model (miBIdi-pH-II). The influence of experimental model parameters including various excipients, API concentrations, dual paddle and its rotation speed was investigated. The kinetics in the biphasic model was described applying a one- and four-compartment pharmacokinetic (PK) model. The improved biphasic dissolution model was robust related to differing APIs and excipient concentrations. The dual paddle guaranteed homogenous mixing in both phases; the optimal rotation speed was 25 and 75rpm for the aqueous and the octanol phase, respectively. A one-compartment PK model adequately characterised the data of fully dissolved APIs. A four-compartment PK model best quantified dissolution, precipitation, and partitioning also of undissolved amounts due to realistic pH profiles. The improved dissolution model is a powerful tool for investigating the interplay between dissolution, precipitation and partitioning of various poorly soluble APIs (BCS II). In vivo-relevant PK parameters could be estimated applying respective PK models. Copyright © 2016 Elsevier B.V. All rights reserved.

Anelastic Models of Fully-Convective Stars: Differential Rotation, Meridional Circulation and Residual Entropy

NASA Astrophysics Data System (ADS)

Sainsbury-Martinez, Felix; Browning, Matthew; Miesch, Mark; Featherstone, Nicholas A.

2018-01-01

Low-Mass stars are typically fully convective, and as such their dynamics may differ significantly from sun-like stars. Here we present a series of 3D anelastic HD and MHD simulations of fully convective stars, designed to investigate how the meridional circulation, the differential rotation, and residual entropy are affected by both varying stellar parameters, such as the luminosity or the rotation rate, and by the presence of a magnetic field. We also investigate, more specifically, a theoretical model in which isorotation contours and residual entropy (σ‧ = σ ‑ σ(r)) are intrinsically linked via the thermal wind equation (as proposed in the Solar context by Balbus in 2009). We have selected our simulation parameters in such as way as to span the transition between Solar-like differential rotation (fast equator + slow poles) and ‘anti-Solar’ differential rotation (slow equator + fast poles), as characterised by the convective Rossby number and △Ω. We illustrate the transition from single-celled to multi-celled MC profiles, and from positive to negative latitudinal entropy gradients. We show that an extrapolation involving both TWB and the σ‧/Ω link provides a reasonable estimate for the interior profile of our fully convective stars. Finally, we also present a selection of MHD simulations which exhibit an almost unsuppressed differential rotation profile, with energy balances remaining dominated by kinetic components.

Hydrologic Transport of Dissolved Inorganic Carbon and Its Control on Chemical Weathering

NASA Astrophysics Data System (ADS)

Calabrese, Salvatore; Parolari, Anthony J.; Porporato, Amilcare

2017-10-01

Chemical weathering is one of the major processes interacting with climate and tectonics to form clays, supply nutrients to soil microorganisms and plants, and sequester atmospheric CO2. Hydrology and dissolution kinetics have been emphasized as factors controlling chemical weathering rates. However, the interaction between hydrology and transport of dissolved inorganic carbon (DIC) in controlling weathering has received less attention. In this paper, we present an analytical model that couples subsurface water and chemical molar balance equations to analyze the roles of hydrology and DIC transport on chemical weathering. The balance equations form a dynamical system that fully determines the dynamics of the weathering zone chemistry as forced by the transport of DIC. The model is formulated specifically for the silicate mineral albite, but it can be extended to other minerals, and is studied as a function of percolation rate and water transit time. Three weathering regimes are elucidated. For very small or large values of transit time, the weathering is limited by reaction kinetics or transport, respectively. For intermediate values, the system is transport controlled and is sensitive to transit time. We apply the model to a series of watersheds for which we estimate transit times and identify the type of weathering regime. The results suggest that hydrologic transport of DIC may be as important as reaction kinetics and dilution in determining chemical weathering rates.

Kinetics versus thermodynamics in materials modeling: The case of the di-vacancy in iron

NASA Astrophysics Data System (ADS)

Djurabekova, F.; Malerba, L.; Pasianot, R. C.; Olsson, P.; Nordlund, K.

2010-07-01

Monte Carlo models are widely used for the study of microstructural and microchemical evolution of materials under irradiation. However, they often link explicitly the relevant activation energies to the energy difference between local equilibrium states. We provide a simple example (di-vacancy migration in iron) in which a rigorous activation energy calculation, by means of both empirical interatomic potentials and density functional theory methods, clearly shows that such a link is not granted, revealing a migration mechanism that a thermodynamics-linked activation energy model cannot predict. Such a mechanism is, however, fully consistent with thermodynamics. This example emphasizes the importance of basing Monte Carlo methods on models where the activation energies are rigorously calculated, rather than deduced from widespread heuristic equations.

Fully kinetic simulations of magnetic reconnction in semi-collisional plasmas

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

Daughton, William S; Roytershteyn, Vadim S; Albright, Brian J

2009-01-01

The influence of Coulomb collisions on the dynamics of magnetic reconnection is examined using fully kinetic simulations with a Monte-Carlo treatment of the Fokker-Planck collision operator. This powerful first-principles approach offers a bridge between kinetic and fluid regimes, which may prove useful for understanding the applicability of various fluid models. In order to lay the necessary groundwork, the collision algorithm is first carefully bench marked for a homogeneous plasma against theoretical predictions for beam-plasma interactions and electrical resistivity. Next, the collisional decay of a current layer is examined as a function of guide field, allowing direct comparisons with transport theorymore » for the parallel and perpendicular resistivity as well as the thermoelectric force. Finally, the transition between collisional and collision less reconnection is examined in neutral sheet geometry. For modest Lundquist numbers S {approx}< 1000, a distinct transition is observed when the thickness of the Sweet-Parker layers falls below the ion inertia length {delta}{sub sp} {approx}< d,. At higher Lundquist number, deviations from the Sweet-Parker scaling are observed due to the growth of plasmoids (secondary-islands) within the elongated resistive layer. In certain cases, this instability leads to the onset of fast reconnection sooner than expected from {delta}{sub sp} {approx} d, condition. After the transition to fast reconnection, elongated electron current layers are formed which are unstable to the formation of new plasmoids. The structure and time-dependence of the electron diffusion region in these semi-collisional regimes is profoundly different than reported in two-fluid simulations.« less

Epidermal Homeostasis and Radiation Responses in a Multiscale Tissue Modeling Framework

NASA Technical Reports Server (NTRS)

Hu, Shaowen; Cucinotta, Francis A.

2013-01-01

The surface of skin is lined with several thin layers of epithelial cells that are maintained throughout life time by a small population of stem cells. High dose radiation exposures could injure and deplete the underlying proliferative cells and induce cutaneous radiation syndrome. In this work we propose a multiscale computational model for skin epidermal dynamics that links phenomena occurring at the subcellular, cellular, and tissue levels of organization, to simulate the experimental data of the radiation response of swine epidermis, which is closely similar to human epidermis. Incorporating experimentally measured histological and cell kinetic parameters, we obtain results of population kinetics and proliferation indexes comparable to observations in unirradiated and acutely irradiated swine experiments. At the sub-cellular level, several recently published Wnt signaling controlled cell-cycle models are applied and the roles of key components and parameters are analyzed. Based on our simulation results, we demonstrate that a moderate increase of proliferation rate for the survival proliferative cells is sufficient to fully repopulate the area denuded by high dose radiation, as long as the integrity of underlying basement membrane is maintained. Our work highlights the importance of considering proliferation kinetics as well as the spatial organization of tissues when conducting in vivo investigations of radiation responses. This integrated model allow us to test the validity of several basic biological rules at the cellular level and sub-cellular mechanisms by qualitatively comparing simulation results with published research, and enhance our understanding of the pathophysiological effects of ionizing radiation on skin.

Molecular Dynamics Studies of Self-Assembling Biomolecules and DNA-functionalized Gold Nanoparticles

NASA Astrophysics Data System (ADS)

Cho, Vince Y.

This thesis is organized as following. In Chapter 2, we use fully atomistic MD simulations to study the conformation of DNA molecules that link gold nanoparticles to form nanoparticle superlattice crystals. In Chapter 3, we study the self-assembly of peptide amphiphiles (PAs) into a cylindrical micelle fiber by using CGMD simulations. Compared to fully atomistic MD simulations, CGMD simulations prove to be computationally cost-efficient and reasonably accurate for exploring self-assembly, and are used in all subsequent chapters. In Chapter 4, we apply CGMD methods to study the self-assembly of small molecule-DNA hybrid (SMDH) building blocks into well-defined cage-like dimers, and reveal the role of kinetics and thermodynamics in this process. In Chapter 5, we extend the CGMD model for this system and find that the assembly of SMDHs can be fine-tuned by changing parameters. In Chapter 6, we explore superlattice crystal structures of DNA-functionalized gold nanoparticles (DNA-AuNP) with the CGMD model and compare the hybridization.

Towards full-Braginskii implicit extended MHD

NASA Astrophysics Data System (ADS)

Chacon, Luis

2009-05-01

Recently, viable algorithms have been proposed for the scalable, fully-implicit temporal integration of 3D resistive MHD and cold-ion extended MHD models. While significant, these achievements must be tempered by the fact that such models lack predictive capabilities in regimes of interest for magnetic fusion. Short of including kinetic closures, a natural evolution path towards predictability starts by considering additional terms as described in Braginskii's fluid closures in the collisional regime. Here, we focus on the inclusion of two fundamental elements of relevance for fusion plasmas: anisotropic parallel electron transport, and warm-ion physics (i.e., ion finite Larmor radius effects, included via gyroviscosity). Both these elements introduce significant numerical difficulties, due to the strong anisotropy in the former, and the presence of dispersive waves in the latter. In this presentation, we will discuss progress in our fully implicit algorithmic formulation towards the inclusion of both these elements. L. Chac'on, Phys. Plasmas, 15, 056103 (2008) L. Chac'on, J. Physics: Conf. Series, 125, 012041 (2008)

Continuum kinetic modeling of the tokamak plasma edge

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

Dorf, M. A.; Dorr, M. R.; Hittinger, J. A.

2016-05-15

The first 4D (axisymmetric) high-order continuum gyrokinetic transport simulations that span the magnetic separatrix of a tokamak are presented. The modeling is performed with the COGENT code, which is distinguished by fourth-order finite-volume discretization combined with mapped multiblock grid technology to handle the strong anisotropy of plasma transport and the complex X-point divertor geometry with high accuracy. The calculations take into account the effects of fully nonlinear Fokker-Plank collisions, electrostatic potential variations, and anomalous radial transport. Topics discussed include: (a) ion orbit loss and the associated toroidal rotation and (b) edge plasma relaxation in the presence of anomalous radial transport.

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.

Fully Nonlinear Edge Gyrokinetic Simulations of Kinetic Geodesic-Acoustic Modes and Boundary Flows

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

Xu, X Q; Belli, E; Bodi, K

We present edge gyrokinetic neoclassical simulations of tokamak plasmas using the fully nonlinear (full-f) continuum code TEMPEST. A nonlinear Boltzmann model is used for the electrons. The electric field is obtained by solving the 2D gyrokinetic Poisson Equation. We demonstrate the following: (1) High harmonic resonances (n > 2) significantly enhance geodesic-acoustic mode (GAM) damping at high-q (tokamak safety factor), and are necessary to explain both the damping observed in our TEMPEST q-scans and experimental measurements of the scaling of the GAM amplitude with edge q{sub 95} in the absence of obvious evidence that there is a strong q dependencemore » of the turbulent drive and damping of the GAM. (2) The kinetic GAM exists in the edge for steep density and temperature gradients in the form of outgoing waves, its radial scale is set by the ion temperature profile, and ion temperature inhomogeneity is necessary for GAM radial propagation. (3) The development of the neoclassical electric field evolves through different phases of relaxation, including GAMs, their radial propagation, and their long-time collisional decay. (4) Natural consequences of orbits in the pedestal and scrape-off layer region in divertor geometry are substantial non-Maxwellian ion distributions and flow characteristics qualitatively like those observed in experiments.« less

The singing comet 67P: utilizing fully kinetic simulations to study its interaction with the solar wind plasma

NASA Astrophysics Data System (ADS)

Deca, J.; Divin, A. V.; Horanyi, M.; Henri, P.

2016-12-01

We present preliminary results of the first 3-D fully kinetic and electromagnetic simulations of the solar wind interaction with 67P/Churyumov-Gerasimenko at 3 AU, before the comet transitions into its high-activity phase. We focus on the global cometary environment and the electron-kinetic activity of the interaction. In addition to the background solar wind plasma flow, our model includes also plasma-driven ionization of cometary neutrals and collisional effects. We approximate mass loading of cold cometary oxygen and hydrogen using a hyperbolic relation with distance to the comet. We consider two primary cases: a weak outgassing comet (with the peak ion density 10x the solar wind density) and a moderately outgassing comet (with the peak ion density 50x the solar wind density). The weak comet is characterized by the formation of a narrow region containing a compressed solar wind (the density of the solar wind ion population is 3x the value far upstream of the comet) and a magnetic barrier ( 2x to 4x the interplanetary magnetic field). Blobs of plasma are detached continuously from this sheath region. Standing electromagnetic waves are excited in the cometary wake due to a strong anisotropy in the plasma pressure, as the density and the magnetic field magnitude are anti-correlated.The moderate mass-loading case shows more dynamics at the dayside region. The stagnation of the solar wind flow is accompanied by the formation of elongated density stripes, indicating the presence of a Rayleigh-Taylor instability. These density cavities are elongated in the direction of the magnetic field and encompass the dayside ionopause. To conclude, we believe that our results provide vital information to disentangle the observations made by the Rosetta spacecraft and compose a global solar wind - comet interaction model.

Enhancing charge transfer kinetics by nanoscale catalytic cermet interlayer.

PubMed

An, Jihwan; Kim, Young-Beom; Gür, Turgut M; Prinz, Fritz B

2012-12-01

Enhancing the density of catalytic sites is crucial for improving the performance of energy conversion devices. This work demonstrates the kinetic role of 2 nm thin YSZ/Pt cermet layers on enhancing the oxygen reduction kinetics for low temperature solid oxide fuel cells. Cermet layers were deposited between the porous Pt cathode and the dense YSZ electrolyte wafer using atomic layer deposition (ALD). Not only the catalytic role of the cermet layer itself but the mixing effect in the cermet was explored. For cells with unmixed and fully mixed cermet interlayers, the maximum power density was enhanced by a factor of 1.5 and 1.8 at 400 °C, and by 2.3 and 2.7 at 450 °C, respectively, when compared to control cells with no cermet interlayer. The observed enhancement in cell performance is believed to be due to the increased triple phase boundary (TPB) density in the cermet interlayer. We also believe that the sustained kinetics for the fully mixed cermet layer sample stems from better thermal stability of Pt islands separated by the ALD YSZ matrix, which helped to maintain the high-density TPBs even at elevated temperature.

Turbulence dissipation challenge: particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Roytershteyn, V.; Karimabadi, H.; Omelchenko, Y.; Germaschewski, K.

2015-12-01

We discuss application of three particle in cell (PIC) codes to the problems relevant to turbulence dissipation challenge. VPIC is a fully kinetic code extensively used to study a variety of diverse problems ranging from laboratory plasmas to astrophysics. PSC is a flexible fully kinetic code offering a variety of algorithms that can be advantageous to turbulence simulations, including high order particle shapes, dynamic load balancing, and ability to efficiently run on Graphics Processing Units (GPUs). Finally, HYPERS is a novel hybrid (kinetic ions+fluid electrons) code, which utilizes asynchronous time advance and a number of other advanced algorithms. We present examples drawn both from large-scale turbulence simulations and from the test problems outlined by the turbulence dissipation challenge. Special attention is paid to such issues as the small-scale intermittency of inertial range turbulence, mode content of the sub-proton range of scales, the formation of electron-scale current sheets and the role of magnetic reconnection, as well as numerical challenges of applying PIC codes to simulations of astrophysical turbulence.

A surprisingly complex aqueous chemistry of the simplest amino acid. A pulse radiolysis and theoretical study on H/D kinetic isotope effects in the reaction of glycine anions with hydroxyl radicals.

PubMed

Stefanić, I; Ljubić, I; Bonifacić, M; Sabljić, A; Asmus, K-D; Armstrong, D A

2009-04-07

A pulse radiolysis study was carried out of the reaction rate constants and kinetic isotope effects of hydroxyl-radical-induced H/D abstraction from the most-simple alpha-amino acid glycine in its anionic form in water. The rate constants and yields of three predominantly formed radical products, glycyl (NH2-*CH-CO2-), aminomethyl (NH2-*CH2), and aminyl (*NH-CH2-CO2-) radicals, as well as of their partially or fully deuterated analogs, were found to be of comparable magnitude. The primary, secondary, and primary/secondary H/D kinetic isotope effects on the rate constants were determined with respect to each of the three radicals. The unusual variety of products for such an elementary reaction between two small and simple species indicates a complex mechanism with several reactions taking place simultaneously. Thus, a theoretical modeling of the reaction mechanism and kinetics in the gas- and aqueous phase was performed by using the unrestricted density functional theory with the BB1K functional (employing the polarizable continuum model for the aqueous phase), unrestricted coupled cluster UCCSD(T) method, and improved canonical variational theory. Several hydrogen-bonded prereaction complexes and transition states were detected. In particular, the calculations pointed to a significant mechanistic role of the three-electron two-orbital (sigma/sigma* N therefore O) hemibonded prereaction complexes in the aqueous phase. A good agreement with the experimental rate constants and kinetic isotope effects was achieved by downshifting the calculated reaction barriers by 3 kcal mol(-1) and damping the NH(D) stretching frequency by a factor of 0.86.

Dynamic single photon emission computed tomography—basic principles and cardiac applications

PubMed Central

Gullberg, Grant T; Reutter, Bryan W; Sitek, Arkadiusz; Maltz, Jonathan S; Budinger, Thomas F

2011-01-01

The very nature of nuclear medicine, the visual representation of injected radiopharmaceuticals, implies imaging of dynamic processes such as the uptake and wash-out of radiotracers from body organs. For years, nuclear medicine has been touted as the modality of choice for evaluating function in health and disease. This evaluation is greatly enhanced using single photon emission computed tomography (SPECT), which permits three-dimensional (3D) visualization of tracer distributions in the body. However, to fully realize the potential of the technique requires the imaging of in vivo dynamic processes of flow and metabolism. Tissue motion and deformation must also be addressed. Absolute quantification of these dynamic processes in the body has the potential to improve diagnosis. This paper presents a review of advancements toward the realization of the potential of dynamic SPECT imaging and a brief history of the development of the instrumentation. A major portion of the paper is devoted to the review of special data processing methods that have been developed for extracting kinetics from dynamic cardiac SPECT data acquired using rotating detector heads that move as radiopharmaceuticals exchange between biological compartments. Recent developments in multi-resolution spatiotemporal methods enable one to estimate kinetic parameters of compartment models of dynamic processes using data acquired from a single camera head with slow gantry rotation. The estimation of kinetic parameters directly from projection measurements improves bias and variance over the conventional method of first reconstructing 3D dynamic images, generating time–activity curves from selected regions of interest and then estimating the kinetic parameters from the generated time–activity curves. Although the potential applications of SPECT for imaging dynamic processes have not been fully realized in the clinic, it is hoped that this review illuminates the potential of SPECT for dynamic imaging, especially in light of new developments that enable measurement of dynamic processes directly from projection measurements. PMID:20858925

TOPICAL REVIEW: Dynamic single photon emission computed tomography—basic principles and cardiac applications

NASA Astrophysics Data System (ADS)

Gullberg, Grant T.; Reutter, Bryan W.; Sitek, Arkadiusz; Maltz, Jonathan S.; Budinger, Thomas F.

2010-10-01

The very nature of nuclear medicine, the visual representation of injected radiopharmaceuticals, implies imaging of dynamic processes such as the uptake and wash-out of radiotracers from body organs. For years, nuclear medicine has been touted as the modality of choice for evaluating function in health and disease. This evaluation is greatly enhanced using single photon emission computed tomography (SPECT), which permits three-dimensional (3D) visualization of tracer distributions in the body. However, to fully realize the potential of the technique requires the imaging of in vivo dynamic processes of flow and metabolism. Tissue motion and deformation must also be addressed. Absolute quantification of these dynamic processes in the body has the potential to improve diagnosis. This paper presents a review of advancements toward the realization of the potential of dynamic SPECT imaging and a brief history of the development of the instrumentation. A major portion of the paper is devoted to the review of special data processing methods that have been developed for extracting kinetics from dynamic cardiac SPECT data acquired using rotating detector heads that move as radiopharmaceuticals exchange between biological compartments. Recent developments in multi-resolution spatiotemporal methods enable one to estimate kinetic parameters of compartment models of dynamic processes using data acquired from a single camera head with slow gantry rotation. The estimation of kinetic parameters directly from projection measurements improves bias and variance over the conventional method of first reconstructing 3D dynamic images, generating time-activity curves from selected regions of interest and then estimating the kinetic parameters from the generated time-activity curves. Although the potential applications of SPECT for imaging dynamic processes have not been fully realized in the clinic, it is hoped that this review illuminates the potential of SPECT for dynamic imaging, especially in light of new developments that enable measurement of dynamic processes directly from projection measurements.

Inverse energy cascades in three-dimensional turbulence

NASA Technical Reports Server (NTRS)

Hossain, Murshed

1991-01-01

Fully three-dimensional magnetohydrodynamic (MHD) turbulence at large kinetic and low magnetic Reynolds numbers is considered in the presence of a strong uniform magnetic field. It is shown by numerical simulation of a model of MHD that the energy inverse cascades to longer length scales when the interaction parameter is large. While the steady-state dynamics of the driven problem is three-dimensional in character, the behavior has resemblance to two-dimensional hydrodynamics. These results have implications in turbulence theory, MHD power generator, planetary dynamos, and fusion reactor blanket design.

Isocratic and gradient impedance plot analysis and comparison of some recently introduced large size core-shell and fully porous particles.

PubMed

Vanderheyden, Yoachim; Cabooter, Deirdre; Desmet, Gert; Broeckhoven, Ken

2013-10-18

The intrinsic kinetic performance of three recently commercialized large size (≥4μm) core-shell particles packed in columns with different lengths has been measured and compared with that of standard fully porous particles of similar and smaller size (5 and 3.5μm, respectively). The kinetic performance is compared in both absolute (plot of t0 versus the plate count N or the peak capacity np for isocratic and gradient elution, respectively) and dimensionless units. The latter is realized by switching to so-called impedance plots, a format which has been previously introduced (as a plot of t0/N(2) or E0 versus Nopt/N) and has in the present study been extended from isocratic to gradient elution (where the impedance plot corresponds to a plot of t0/np(4) versus np,opt(2)/np(2)). Both the isocratic and gradient impedance plot yielded a very similar picture: the clustered impedance plot curves divide into two distinct groups, one for the core-shell particles (lowest values, i.e. best performance) and one for the fully porous particles (highest values), confirming the clear intrinsic kinetic advantage of core-shell particles. If used around their optimal flow rate, the core-shell particles displayed a minimal separation impedance that is about 40% lower than the fully porous particles. Even larger gains in separation speed can be achieved in the C-term regime. Copyright © 2013 Elsevier B.V. All rights reserved.

Comparison of three-way and four-way calibration for the real-time quantitative analysis of drug hydrolysis in complex dynamic samples by excitation-emission matrix fluorescence.

PubMed

Yin, Xiao-Li; Gu, Hui-Wen; Liu, Xiao-Lu; Zhang, Shan-Hui; Wu, Hai-Long

2018-03-05

Multiway calibration in combination with spectroscopic technique is an attractive tool for online or real-time monitoring of target analyte(s) in complex samples. However, how to choose a suitable multiway calibration method for the resolution of spectroscopic-kinetic data is a troubling problem in practical application. In this work, for the first time, three-way and four-way fluorescence-kinetic data arrays were generated during the real-time monitoring of the hydrolysis of irinotecan (CPT-11) in human plasma by excitation-emission matrix fluorescence. Alternating normalization-weighted error (ANWE) and alternating penalty trilinear decomposition (APTLD) were used as three-way calibration for the decomposition of the three-way kinetic data array, whereas alternating weighted residual constraint quadrilinear decomposition (AWRCQLD) and alternating penalty quadrilinear decomposition (APQLD) were applied as four-way calibration to the four-way kinetic data array. The quantitative results of the two kinds of calibration models were fully compared from the perspective of predicted real-time concentrations, spiked recoveries of initial concentration, and analytical figures of merit. The comparison study demonstrated that both three-way and four-way calibration models could achieve real-time quantitative analysis of the hydrolysis of CPT-11 in human plasma under certain conditions. However, it was also found that both of them possess some critical advantages and shortcomings during the process of dynamic analysis. The conclusions obtained in this paper can provide some helpful guidance for the reasonable selection of multiway calibration models to achieve the real-time quantitative analysis of target analyte(s) in complex dynamic systems. Copyright © 2017 Elsevier B.V. All rights reserved.

Fracture-tough, corrosion-resistant bearing steels

NASA Technical Reports Server (NTRS)

Olson, Gregory B.

1990-01-01

The fundamental principles allowing design of stainless bearing steels with enhanced toughness and stress corrosion resistance has involved both investigation of basic phenomena in model alloys and evaluation of a prototype bearing steel based on a conceptual design exercise. Progress in model studies has included a scanning Auger microprobe (SAM) study of the kinetics of interfacial segregation of embrittling impurities which compete with the kinetics of alloy carbide precipitation in secondary hardening steels. These results can define minimum allowable carbide precipitation rates and/or maximum allowable free impurity contents in these ultrahigh strength steels. Characterization of the prototype bearing steel designed to combine precipitated austenite transformation toughening with secondary hardening shows good agreement between predicted and observed solution treatment response including the nature of the high temperature carbides. An approximate equilibrium constraint applied in the preliminary design calculations to maintain a high martensitic temperature proved inadequate, and the solution treated alloy remained fully austenitic down to liquid nitrogen temperature rather than transforming above 200 C. The alloy can be martensitically transformed by cryogenic deformation, and material so processed will be studied further to test predicted carbide and austenite precipitation behavior. A mechanistically-based martensitic kinetic model was developed and parameters are being evaluated from available kinetic data to allow precise control of martensitic temperatures of high alloy steels in future designs. Preliminary calculations incorporating the prototype stability results suggest that the transformation-toughened secondary-hardening martensitic-stainless design concept is still viable, but may require lowering Cr content to 9 wt. pct. and adding 0.5 to 1.0 wt. pct. Al. An alternative design approach based on strain-induced martensitic transformation during cryogenic forming, thus removing the high martensitic constraint, may permit alloy compositions offering higher fracture roughness.

Energy Dissipation and Phase-Space Dynamics in Eulerian Vlasov-Maxwell Turbulence

NASA Astrophysics Data System (ADS)

Tenbarge, Jason; Juno, James; Hakim, Ammar

2017-10-01

Turbulence in a magnetized plasma is a primary mechanism responsible for transforming energy at large injection scales into small-scale motions, which are ultimately dissipated as heat in systems such as the solar corona, wind, and other astrophysical objects. At large scales, the turbulence is well described by fluid models of the plasma; however, understanding the processes responsible for heating a weakly collisional plasma such as the solar wind requires a kinetic description. We present a fully kinetic Eulerian Vlasov-Maxwell study of turbulence using the Gkeyll simulation framework, including studies of the cascade of energy in phase space and formation and dissipation of coherent structures. We also leverage the recently developed field-particle correlations to diagnose the dominant sources of dissipation and compare the results of the field-particle correlation to other dissipation measures. NSF SHINE AGS-1622306 and DOE DE-AC02-09CH11466.

Consistent transport coefficients in astrophysics

NASA Technical Reports Server (NTRS)

Fontenla, Juan M.; Rovira, M.; Ferrofontan, C.

1986-01-01

A consistent theory for dealing with transport phenomena in stellar atmospheres starting with the kinetic equations and introducing three cases (LTE, partial LTE, and non-LTE) was developed. The consistent hydrodynamical equations were presented for partial-LTE, the transport coefficients defined, and a method shown to calculate them. The method is based on the numerical solution of kinetic equations considering Landau, Boltzmann, and Focker-Planck collision terms. Finally a set of results for the transport coefficients derived for a partially ionized hydrogen gas with radiation was shown, considering ionization and recombination as well as elastic collisions. The results obtained imply major changes is some types of theoretical model calculations and can resolve some important current problems concerning energy and mass balance in the solar atmosphere. It is shown that energy balance in the lower solar transition region can be fully explained by means of radiation losses and conductive flux.

Kinetic simulations of gas breakdown in the dense plasma focus

NASA Astrophysics Data System (ADS)

Bennett, N.; Blasco, M.; Breeding, K.; DiPuccio, V.; Gall, B.; Garcia, M.; Gardner, S.; Gatling, J.; Hagen, E. C.; Luttman, A.; Meehan, B. T.; Molnar, S.; O'Brien, R.; Ormond, E.; Robbins, L.; Savage, M.; Sipe, N.; Welch, D. R.

2017-06-01

The first fully kinetic, collisional, and electromagnetic simulations of the breakdown phase of a MA-scale dense plasma focus are described and shown to agree with measured electrical characteristics, including breakdown time. In the model, avalanche ionization is driven by cathode electron emission, and this results in incomplete gas breakdown along the insulator. This reinforces the importance of the conditioning process that creates a metallic layer on the insulator surface. The simulations, nonetheless, help explain the relationship between the gas pressure, the insulator length, and the coaxial gap width. Previously, researchers noted three breakdown patterns related to pressure. Simulation and analytical results show that at low pressures, long ionization path lengths lead to volumetric breakdown, while high pressures lead to breakdown across the relatively small coaxial electrode gap. In an intermediate pressure regime, ionization path lengths are comparable to the insulator length which promotes ideal breakdown along the insulator surface.

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

An integral turbulent kinetic energy analysis of free shear flows

NASA Technical Reports Server (NTRS)

Peters, C. E.; Phares, W. J.

1973-01-01

Mixing of coaxial streams is analyzed by application of integral techniques. An integrated turbulent kinetic energy (TKE) equation is solved simultaneously with the integral equations for the mean flow. Normalized TKE profile shapes are obtained from incompressible jet and shear layer experiments and are assumed to be applicable to all free turbulent flows. The shear stress at the midpoint of the mixing zone is assumed to be directly proportional to the local TKE, and dissipation is treated with a generalization of the model developed for isotropic turbulence. Although the analysis was developed for ducted flows, constant-pressure flows were approximated with the duct much larger than the jet. The axisymmetric flows under consideration were predicted with reasonable accuracy. Fairly good results were also obtained for the fully developed two-dimensional shear layers, which were computed as thin layers at the boundary of a large circular jet.

Multidimensional, fully implicit, exactly conserving electromagnetic particle-in-cell simulations

NASA Astrophysics Data System (ADS)

Chacon, Luis

2015-09-01

We discuss a new, conservative, fully implicit 2D-3V particle-in-cell algorithm for non-radiative, electromagnetic kinetic plasma simulations, based on the Vlasov-Darwin model. Unlike earlier linearly implicit PIC schemes and standard explicit PIC schemes, fully implicit PIC algorithms are unconditionally stable and allow exact discrete energy and charge conservation. This has been demonstrated in 1D electrostatic and electromagnetic contexts. In this study, we build on these recent algorithms to develop an implicit, orbit-averaged, time-space-centered finite difference scheme for the Darwin field and particle orbit equations for multiple species in multiple dimensions. The Vlasov-Darwin model is very attractive for PIC simulations because it avoids radiative noise issues in non-radiative electromagnetic regimes. The algorithm conserves global energy, local charge, and particle canonical-momentum exactly, even with grid packing. The nonlinear iteration is effectively accelerated with a fluid preconditioner, which allows efficient use of large timesteps, O(√{mi/me}c/veT) larger than the explicit CFL. In this presentation, we will introduce the main algorithmic components of the approach, and demonstrate the accuracy and efficiency properties of the algorithm with various numerical experiments in 1D and 2D. Support from the LANL LDRD program and the DOE-SC ASCR office.

Active galactic nuclei feedback, quiescence and circumgalactic medium metal enrichment in early-type galaxies

NASA Astrophysics Data System (ADS)

Eisenreich, Maximilian; Naab, Thorsten; Choi, Ena; Ostriker, Jeremiah P.; Emsellem, Eric

2017-06-01

We present three-dimensional hydrodynamical simulations showing the effect of kinetic and radiative active galactic nuclei (AGN) feedback on a model galaxy representing a massive quiescent low-redshift early-type galaxy of M* = 8.41 × 1010 M⊙, harbouring an MBH = 4 × 108 M⊙ black hole surrounded by a cooling gaseous halo. We show that, for a total baryon fraction of ˜20 per cent of the cosmological value, feedback from the AGN can keep the galaxy quiescent for about 4.35 Gyr and with properties consistent with black hole mass and X-ray luminosity scaling relations. However, this can only be achieved if the AGN feedback model includes both kinetic and radiative feedback modes. The simulation with only kinetic feedback fails to keep the model galaxy fully quiescent, while one with only radiative feedback leads to excessive black hole growth. For higher baryon fractions (e.g. 50 per cent of the cosmological value), the X-ray luminosities exceed observed values by at least one order of magnitude, and rapid cooling results in a star-forming galaxy. The AGN plays a major role in keeping the circumgalactic gas at observed metallicities of Z/Z⊙ ≳ 0.3 within the central ˜30 kpc by venting nuclear gas enriched with metals from residual star formation activity. As indicated by previous cosmological simulations, our results are consistent with a model for which the black hole mass and the total baryon fraction are set at higher redshifts z > 1 and the AGN alone can keep the model galaxy on observed scaling relations. Models without AGN feedback violate both the quiescence criterion as well as circumgalactic medium metallicity constraints.

Monte Carlo kinetics simulations of ice-mantle formation on interstellar grains

NASA Astrophysics Data System (ADS)

Garrod, Robin

2015-08-01

The majority of interstellar dust-grain chemical kinetics models use rate equations, or alternative population-based simulation methods, to trace the time-dependent formation of grain-surface molecules and ice mantles. Such methods are efficient, but are incapable of considering explicitly the morphologies of the dust grains, the structure of the ices formed thereon, or the influence of local surface composition on the chemistry.A new Monte Carlo chemical kinetics model, MIMICK, is presented here, whose prototype results were published recently (Garrod 2013, ApJ, 778, 158). The model calculates the strengths and positions of the potential mimima on the surface, on the fly, according to the individual pair-wise (van der Waals) bonds between surface species, allowing the structure of the ice to build up naturally as surface diffusion and chemistry occur. The prototype model considered contributions to a surface particle's potential only from contiguous (or "bonded") neighbors; the full model considers contributions from surface constituents from short to long range. Simulations are conducted on a fully 3-D user-generated dust-grain with amorphous surface characteristics. The chemical network has also been extended from the simple water system previously published, and now includes 33 chemical species and 55 reactions. This allows the major interstellar ice components to be simulated, such as water, methane, ammonia and methanol, as well as a small selection of more complex molecules, including methyl formate (HCOOCH3).The new model results indicate that the porosity of interstellar ices are dependent on multiple variables, including gas density, the dust temperature, and the relative accretion rates of key gas-phase species. The results presented also have implications for the formation of complex organic molecules on dust-grain surfaces at very low temperatures.

Correlation lengths in hydrodynamic models of active nematics.

PubMed

Hemingway, Ewan J; Mishra, Prashant; Marchetti, M Cristina; Fielding, Suzanne M

2016-09-28

We examine the scaling with activity of the emergent length scales that control the nonequilibrium dynamics of an active nematic liquid crystal, using two popular hydrodynamic models that have been employed in previous studies. In both models we find that the chaotic spatio-temporal dynamics in the regime of fully developed active turbulence is controlled by a single active scale determined by the balance of active and elastic stresses, regardless of whether the active stress is extensile or contractile in nature. The observed scaling of the kinetic energy and enstrophy with activity is consistent with our single-length scale argument and simple dimensional analysis. Our results provide a unified understanding of apparent discrepancies in the previous literature and demonstrate that the essential physics is robust to the choice of model.

Exact and approximate solutions for the decades-old Michaelis-Menten equation: Progress-curve analysis through integrated rate equations.

PubMed

Goličnik, Marko

2011-01-01

The Michaelis-Menten rate equation can be found in most general biochemistry textbooks, where the time derivative of the substrate is a hyperbolic function of two kinetic parameters (the limiting rate V, and the Michaelis constant K(M) ) and the amount of substrate. However, fundamental concepts of enzyme kinetics can be difficult to understand fully, or can even be misunderstood, by students when based only on the differential form of the Michaelis-Menten equation, and the variety of methods available to calculate the kinetic constants from rate versus substrate concentration "textbook data." Consequently, enzyme kinetics can be confusing if an analytical solution of the Michaelis-Menten equation is not available. Therefore, the still rarely known exact solution to the Michaelis-Menten equation is presented here through the explicit closed-form equation in terms of the Lambert W(x) function. Unfortunately, as the W(x) is not available in standard curve-fitting computer programs, the practical use of this direct solution is limited for most life-science students. Thus, the purpose of this article is to provide analytical approximations to the equation for modeling Michaelis-Menten kinetics. The elementary and explicit nature of these approximations can provide students with direct and simple estimations of kinetic parameters from raw experimental time-course data. The Michaelis-Menten kinetics studied in the latter context can provide an ideal alternative to the 100-year-old problems of data transformation, graphical visualization, and data analysis of enzyme-catalyzed reactions. Hence, the content of the course presented here could gradually become an important component of the modern biochemistry curriculum in the 21st century. Copyright © 2011 Wiley Periodicals, Inc.

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.

The photoexcitation of crystalline ice and amorphous solid water: A molecular dynamics study of outcomes at 11 K and 125 K.

PubMed

Crouse, J; Loock, H-P; Cann, N M

2015-07-21

Photoexcitation of crystalline ice Ih and amorphous solid water at 7-9 eV is examined using molecular dynamics simulations and a fully flexible water model. The probabilities of photofragment desorption, trapping, and recombination are examined for crystalline ice at 11 K and at 125 K and for amorphous solid water at 11 K. For 11 K crystalline ice, a fully rigid water model is also employed for comparison. The kinetic energy of desorbed H atoms and the distance travelled by trapped fragments are correlated to the location and the local environment of the photoexcited water molecule. In all cases, H atom desorption is found to be the most likely outcome in the top bilayer while trapping of all photofragments is most probable deeper in the solid where the likelihood for recombination of the fragments into H2O molecules also rises. Trajectory analysis indicates that the local hydrogen bonding network in amorphous solid water is more easily distorted by a photodissociation event compared to crystalline ice. Also, simulations indicate that desorption of OH radicals and H2O molecules are more probable in amorphous solid water. The kinetic energy distributions for desorbed H atoms show a peak at high energy in crystalline ice, arising from photoexcited water molecules in the top monolayer. This peak is less pronounced in amorphous solid water. H atoms that are trapped may be displaced by up to ∼10 water cages, but migrate on average 3 water cages. Trapped OH fragments tend to stay near the original solvent cage.

Kinetics and mechanisms of the conversion of silicate (45S5), borate, and borosilicate glasses to hydroxyapatite in dilute phosphate solutions.

PubMed

Huang, Wenhai; Day, Delbert E; Kittiratanapiboon, Kanisa; Rahaman, Mohamed N

2006-07-01

Bioactive glasses with controllable conversion rates to hydroxyapatite (HA) may provide a novel class of scaffold materials for bone tissue engineering. The objective of the present work was to comprehensively characterize the conversion of a silicate bioactive glass (45S5), a borate glass, and two intermediate borosilicate glass compositions to HA in a dilute phosphate solution at 37 degrees Celsius. The borate glass and the borosilicate glasses were derived from the 45S5 glass by fully or partially replacing the SiO(2) with B(2)O(3). Higher B(2)O(3) content produced a more rapid conversion of the glass to HA and a lower pH value of the phosphate solution. Whereas the borate glass was fully converted to HA in less than 4 days, the silicate (45S5) and borosilicate compositions were only partially converted even after 70 days, and contained residual SiO(2) in a Na-depleted core. The concentration of Na(+) in the phosphate solution increased with reaction time whereas the PO(4) (3-) concentration decreased, both reaching final limiting values at a rate that increased with the B(2)O(3) content of the glass. However, the Ca(2+) concentration in the solution remained low, below the detection limit of atomic absorption, throughout the reaction. Immersion of the glasses in a mixed solution of K(2)HPO(4) and K(2)CO(3) produced a carbonate-substituted HA but the presence of the K(2)CO(3) had little effect on the kinetics of conversion to HA. The kinetics and mechanisms of the conversion process of the four glasses to HA are compared and used to develop a model for the process.

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

Continuum kinetic modeling of the tokamak plasma edge

DOE PAGES

Dorf, M. A.; Dorr, M.; Rognlien, T.; ...

2016-03-10

In this study, the first 4D (axisymmetric) high-order continuum gyrokinetic transport simulations that span the magnetic separatrix of a tokamak are presented. The modeling is performed with the COGENT code, which is distinguished by fourth-order finite-volume discretization combined with mapped multiblock grid technology to handle the strong anisotropy of plasmatransport and the complex X-point divertor geometry with high accuracy. The calculations take into account the effects of fully nonlinear Fokker-Plank collisions, electrostatic potential variations, and anomalous radial transport. Topics discussed include: (a) ion orbit loss and the associated toroidal rotation and (b) edge plasma relaxation in the presence of anomalousmore » radial transport.« less

PDF turbulence modeling and DNS

NASA Technical Reports Server (NTRS)

Hsu, A. T.

1992-01-01

The problem of time discontinuity (or jump condition) in the coalescence/dispersion (C/D) mixing model is addressed in probability density function (pdf). A C/D mixing model continuous in time is introduced. With the continuous mixing model, the process of chemical reaction can be fully coupled with mixing. In the case of homogeneous turbulence decay, the new model predicts a pdf very close to a Gaussian distribution, with finite higher moments also close to that of a Gaussian distribution. Results from the continuous mixing model are compared with both experimental data and numerical results from conventional C/D models. The effect of Coriolis forces on compressible homogeneous turbulence is studied using direct numerical simulation (DNS). The numerical method used in this study is an eight order compact difference scheme. Contrary to the conclusions reached by previous DNS studies on incompressible isotropic turbulence, the present results show that the Coriolis force increases the dissipation rate of turbulent kinetic energy, and that anisotropy develops as the Coriolis force increases. The Taylor-Proudman theory does apply since the derivatives in the direction of the rotation axis vanishes rapidly. A closer analysis reveals that the dissipation rate of the incompressible component of the turbulent kinetic energy indeed decreases with a higher rotation rate, consistent with incompressible flow simulations (Bardina), while the dissipation rate of the compressible part increases; the net gain is positive. Inertial waves are observed in the simulation results.

On the thermodynamic and kinetic investigations of a [c2]daisy chain polymer

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

Hmadeh, Mohamad; Fang, Lei; Trabolsi, Ali

2010-01-01

We report a variety of [c2]daisy chain molecules which undergo quantitative, efficient, and fully reversible molecular movements upon the addition of base/acid in organic solvents. Such externally triggered molecular movements can induce the contraction and extension of the [c2]daisy chain molecule as a whole. A linear polymer of such a bistable [c2]daisy chain exerts similar types of movements and can be looked upon as a candidate for the development of artificial muscles. The spectrophotometric investigations of both the monomeric and polymeric bistable [c2]daisy chains, as well as the corresponding model compounds, were performed in MeCN at room temperature, in ordermore » to obtain the thermodynamic parameters for these mechanically interlocked molecules. Based on their spectrophotometric and thermodynamic characteristics, kinetic analysis of the acid/base-induced contraction and extension of the [c2]daisy chain monomer and polymer were conducted by employing a stopped-flow technique. These kinetic data suggest that the rates of contraction and extension for these [c2]daisy chain molecules are determined by the thermodynamic stabilities of the corresponding kinetic intermediates. Faster switching rates for both the contraction and extension processes of the polymeric [c2]daisy chain were observed when compared to those of its monomeric counterpart. These kinetic and thermodynamic investigations on [c2]daisy chain-based muscle-like compounds provide important information for those seeking an understanding of the mechanisms of actuation in mechanically interlocked macromolecules.« less

The Disintegration Process in Microcrystalline Cellulose Based Tablets, Part 1: Influence of Temperature, Porosity and Superdisintegrants

PubMed Central

Yassin, Samy; Goodwin, Daniel J; Anderson, Andrew; Sibik, Juraj; Wilson, D Ian; Gladden, Lynn F; Zeitler, J Axel

2015-01-01

Disintegration performance was measured by analysing both water ingress and tablet swelling of pure microcrystalline cellulose (MCC) and in mixture with croscarmellose sodium using terahertz pulsed imaging (TPI). Tablets made from pure MCC with porosities of 10% and 15% showed similar swelling and transport kinetics: within the first 15 s, tablets had swollen by up to 33% of their original thickness and water had fully penetrated the tablet following Darcy flow kinetics. In contrast, MCC tablets with a porosity of 5% exhibited much slower transport kinetics, with swelling to only 17% of their original thickness and full water penetration reached after 100 s, dominated by case II transport kinetics. The effect of adding superdisintegrant to the formulation and varying the temperature of the dissolution medium between 20°C and 37°C on the swelling and transport process was quantified. We have demonstrated that TPI can be used to non-invasively analyse the complex disintegration kinetics of formulations that take place on timescales of seconds and is a promising tool to better understand the effect of dosage form microstructure on its performance. By relating immediate-release formulations to mathematical models used to describe controlled release formulations, it becomes possible to use this data for formulation design. © 2015 The Authors. Journal of Pharmaceutical Sciences published by Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 104:3440–3450, 2015 PMID:26073446

Mutation-induced protein interaction kinetics changes affect apoptotic network dynamic properties and facilitate oncogenesis

PubMed Central

Zhao, Linjie; Sun, Tanlin; Pei, Jianfeng; Ouyang, Qi

2015-01-01

It has been a consensus in cancer research that cancer is a disease caused primarily by genomic alterations, especially somatic mutations. However, the mechanism of mutation-induced oncogenesis is not fully understood. Here, we used the mitochondrial apoptotic pathway as a case study and performed a systematic analysis of integrating pathway dynamics with protein interaction kinetics to quantitatively investigate the causal molecular mechanism of mutation-induced oncogenesis. A mathematical model of the regulatory network was constructed to establish the functional role of dynamic bifurcation in the apoptotic process. The oncogenic mutation enrichment of each of the protein functional domains involved was found strongly correlated with the parameter sensitivity of the bifurcation point. We further dissected the causal mechanism underlying this correlation by evaluating the mutational influence on protein interaction kinetics using molecular dynamics simulation. We analyzed 29 matched mutant–wild-type and 16 matched SNP—wild-type protein systems. We found that the binding kinetics changes reflected by the changes of free energy changes induced by protein interaction mutations, which induce variations in the sensitive parameters of the bifurcation point, were a major cause of apoptosis pathway dysfunction, and mutations involved in sensitive interaction domains show high oncogenic potential. Our analysis provided a molecular basis for connecting protein mutations, protein interaction kinetics, network dynamics properties, and physiological function of a regulatory network. These insights provide a framework for coupling mutation genotype to tumorigenesis phenotype and help elucidate the logic of cancer initiation. PMID:26170328

Stratified Simulations of Collisionless Accretion Disks

NASA Astrophysics Data System (ADS)

Hirabayashi, Kota; Hoshino, Masahiro

2017-06-01

This paper presents a series of stratified-shearing-box simulations of collisionless accretion disks in the recently developed framework of kinetic magnetohydrodynamics (MHD), which can handle finite non-gyrotropy of a pressure tensor. Although a fully kinetic simulation predicted a more efficient angular-momentum transport in collisionless disks than in the standard MHD regime, the enhanced transport has not been observed in past kinetic-MHD approaches to gyrotropic pressure anisotropy. For the purpose of investigating this missing link between the fully kinetic and MHD treatments, this paper explores the role of non-gyrotropic pressure and makes the first attempt to incorporate certain collisionless effects into disk-scale, stratified disk simulations. When the timescale of gyrotropization was longer than, or comparable to, the disk-rotation frequency of the orbit, we found that the finite non-gyrotropy selectively remaining in the vicinity of current sheets contributes to suppressing magnetic reconnection in the shearing-box system. This leads to increases both in the saturated amplitude of the MHD turbulence driven by magnetorotational instabilities and in the resultant efficiency of angular-momentum transport. Our results seem to favor the fast advection of magnetic fields toward the rotation axis of a central object, which is required to launch an ultra-relativistic jet from a black hole accretion system in, for example, a magnetically arrested disk state.

A study of hydriding kinetics of metal hydrides using a physically based model

NASA Astrophysics Data System (ADS)

Voskuilen, Tyler G.

The reaction of hydrogen with metals to form metal hydrides has numerous potential energy storage and management applications. The metal hydrogen system has a high volumetric energy density and is often reversible with a high cycle life. The stored hydrogen can be used to produce energy through combustion, reaction in a fuel cell, or electrochemically in metal hydride batteries. The high enthalpy of the metal-hydrogen reaction can also be used for rapid heat removal or delivery. However, improving the often poor gravimetric performance of such systems through the use of lightweight metals usually comes at the cost of reduced reaction rates or the requirement of pressure and temperature conditions far from the desired operating conditions. In this work, a 700 bar Sievert system was developed at the Purdue Hydrogen Systems Laboratory to study the kinetic and thermodynamic behavior of high pressure hydrogen absorption under near-ambient temperatures. This system was used to determine the kinetic and thermodynamic properties of TiCrMn, an intermetallic metal hydride of interest due to its ambient temperature performance for vehicular applications. A commonly studied intermetallic hydride, LaNi5, was also characterized as a base case for the phase field model. The analysis of the data obtained from such a system necessitate the use of specialized techniques to decouple the measured reaction rates from experimental conditions. These techniques were also developed as a part of this work. Finally, a phase field model of metal hydride formation in mass-transport limited interstitial solute reactions based on the regular solution model was developed and compared with measured kinetics of LaNi5 and TiCrMn. This model aided in the identification of key reaction features and was used to verify the proposed technique for the analysis of gas-solid reaction rates determined volumetrically. Additionally, the phase field model provided detailed quantitative predictions of the effects of multidimensional phase growth and transitions between rate-limiting processes on the experimentally determined reaction rates. Unlike conventional solid state reaction analysis methods, this model relies fully on rate parameters based on the physical mechanisms occurring in the hydride reaction and can be extended to reactions in any dimension.

Interrogating the Effects of Radiation Damage Annealing on Helium Diffusion Kinetics in Apatite

NASA Astrophysics Data System (ADS)

Willett, C. D.; Fox, M.; Shuster, D. L.

2015-12-01

Apatite (U-Th)/He thermochronology is commonly used to study landscape evolution and potential links between climate, erosion and tectonics. The technique relies on a quantitative understanding of (i) helium diffusion kinetics in apatite, (ii) an evolving 4He concentration, (iii) accumulating damage to the crystal lattice caused by radioactive decay[1], and (iv) the thermal annealing of such damage[2],[3], which are each functions of both time and temperature. Uncertainty in existing models of helium diffusion kinetics has resulted in conflicting conclusions, especially in settings involving burial heating through geologic time. The effects of alpha recoil damage annealing are currently assumed to follow the kinetics of fission track annealing (e.g., reference [3]), although this assumption is difficult to fully validate. Here, we present results of modeling exercises and a suite of experiments designed to interrogate the effects of damage annealing on He diffusivity in apatite that are independent of empirical calibrations of fission track annealing. We use the existing experimental results for Durango apatite[2] to develop and calibrate a new function that predicts the effects of annealing temperature and duration on measured diffusivity. We also present a suite of experiments conducted on apatite from Sierra Nevada, CA granite to establish whether apatites with different chemical compositions have the same behavior as Durango apatite. Crystals were heated under vacuum to temperatures between 250 and 500°C for 1, 10, or 100 hours. The samples were then irradiated with ~220 MeV protons to produce spallogenic 3He, the diffusant then used in step-heating diffusion experiments. We compare the results of these experiments and model calibrations to existing models. Citations: [1]Shuster, D., Flowers R., and Farley K., (2006), EPSL 249(3-4), 148-161; [2]Shuster, D. and Farley, K., (2009), GCA 73 (1), 6183-6196; [3]Flowers, R., Ketcham, R., Shuster, D. and Farley, K., (2009), GCA 73, 2347-2365.

Atomic-Scale Design of Iron Fischer-Tropsch Catalysts; A Combined Computational Chemistry, Experimental, and Microkinetic Modeling Approach

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

Manos Mavrikakis; James Dumesic; Rahul Nabar

2008-09-29

This work focuses on (1) searching/summarizing published Fischer-Tropsch synthesis (FTS) mechanistic and kinetic studies of FTS reactions on iron catalysts; (2) preparation and characterization of unsupported iron catalysts with/without potassium/platinum promoters; (3) measurement of H{sub 2} and CO adsorption/dissociation kinetics on iron catalysts using transient methods; (3) analysis of the transient rate data to calculate kinetic parameters of early elementary steps in FTS; (4) construction of a microkinetic model of FTS on iron, and (5) validation of the model from collection of steady-state rate data for FTS on iron catalysts. Three unsupported iron catalysts and three alumina-supported iron catalysts weremore » prepared by non-aqueous-evaporative deposition (NED) or aqueous impregnation (AI) and characterized by chemisorption, BET, temperature-programmed reduction (TPR), extent-of-reduction, XRD, and TEM methods. These catalysts, covering a wide range of dispersions and metal loadings, are well-reduced and relatively thermally stable up to 500-600 C in H{sub 2} and thus ideal for kinetic and mechanistic studies. Kinetic parameters for CO adsorption, CO dissociation, and surface carbon hydrogenation on these catalysts were determined from temperature-programmed desorption (TPD) of CO and temperature programmed surface hydrogenation (TPSR), temperature-programmed hydrogenation (TPH), and isothermal, transient hydrogenation (ITH). A microkinetic model was constructed for the early steps in FTS on polycrystalline iron from the kinetic parameters of elementary steps determined experimentally in this work and from literature values. Steady-state rate data were collected in a Berty reactor and used for validation of the microkinetic model. These rate data were fitted to 'smart' Langmuir-Hinshelwood rate expressions derived from a sequence of elementary steps and using a combination of fitted steady-state parameters and parameters specified from the transient measurements. The results provide a platform for further development of microkinetic models of FTS on Fe and a basis for more precise modeling of FTS activity of Fe catalysts. Calculations using periodic, self-consistent Density Functional Theory (DFT) methods were performed on various realistic models of industrial, Fe-based FTS catalysts. Close-packed, most stable Fe(110) facet was analyzed and subsequently carbide formation was found to be facile leading to the choice of the FeC(110) model representing a Fe facet with a sub-surface C atom. The Pt adatom (Fe{sup Pt}(110)) was found to be the most stable model for our studies into Pt promotion and finally the role of steps was elucidated by recourse to the defected Fe(211) facet. Binding Energies(BEs), preferred adsorption sites and geometries for all FTS relevant stable species and intermediates were evaluated on each model catalyst facet. A mechanistic model (comprising of 32 elementary steps involving 19 species) was constructed and each elementary step therein was fully characterized with respect to its thermochemistry and kinetics. Kinetic calculations involved evaluation of the Minimum Energy Pathways (MEPs) and activation energies (barriers) for each step. Vibrational frequencies were evaluated for the preferred adsorption configuration of each species with the aim of evaluating entropy-changes, pre exponential factors and serving as a useful connection with experimental surface science techniques. Comparative analysis among these four facets revealed important trends in their relative behavior and roles in FTS catalysis. Overall the First Principles Calculations afforded us a new insight into FTS catalysis on Fe and modified-Fe catalysts.« less

Kinetic modeling of x-ray laser-driven solid Al plasmas via particle-in-cell simulation

NASA Astrophysics Data System (ADS)

Royle, R.; Sentoku, Y.; Mancini, R. C.; Paraschiv, I.; Johzaki, T.

2017-06-01

Solid-density plasmas driven by intense x-ray free-electron laser (XFEL) radiation are seeded by sources of nonthermal photoelectrons and Auger electrons that ionize and heat the target via collisions. Simulation codes that are commonly used to model such plasmas, such as collisional-radiative (CR) codes, typically assume a Maxwellian distribution and thus instantaneous thermalization of the source electrons. In this study, we present a detailed description and initial applications of a collisional particle-in-cell code, picls, that has been extended with a self-consistent radiation transport model and Monte Carlo models for photoionization and K L L Auger ionization, enabling the fully kinetic simulation of XFEL-driven plasmas. The code is used to simulate two experiments previously performed at the Linac Coherent Light Source investigating XFEL-driven solid-density Al plasmas. It is shown that picls-simulated pulse transmissions using the Ecker-Kröll continuum-lowering model agree much better with measurements than do simulations using the Stewart-Pyatt model. Good quantitative agreement is also found between the time-dependent picls results and those of analogous simulations by the CR code scfly, which was used in the analysis of the experiments to accurately reproduce the observed K α emissions and pulse transmissions. Finally, it is shown that the effects of the nonthermal electrons are negligible for the conditions of the particular experiments under investigation.

Effects of perturbations and radial profiles on ignition of inertial confinement fusion hotspots

NASA Astrophysics Data System (ADS)

Taylor, S.; Chittenden, J. P.

2014-06-01

Perturbations of inertial confinement fusion hotspots from spherical symmetry cause an increase in the implosion velocity required for ignition, as investigated analytically by [R. Kishony and D. Shvarts, Phys. Plasmas 8, 4925 (2001)] and in numerical studies by many authors. In this paper, we analyse the mechanisms behind this effect by comparing fully 3D fluid simulations of National Ignition Facility targets to a novel analytic model of the thermal energy balance of the hotspot. The analytic model takes into account the radial variation of the state variables within the hotspot and provides an accurate relationship between the hotspot's 0D parameters (ρc, Tc, R , uR, and q) and its heating and cooling rates. The dominant effect of perturbations appears to be an increase in the inflow velocity at the hotspot's surface due to transverse flow of material between perturbation structures, causing premature thermalisation of kinetic energy before the hotspot is fully compressed. In hotspots with a broad perturbation spectrum, thermalisation of energy is inhibited by nonradial motion introduced by mode-mode interaction, reducing the yield further.

Energy transfer dynamics in strongly inhomogeneous hot-dense-matter systems

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

Stillman, C. R.; Nilson, P. M.; Sefkow, A. B.

Direct measurements of energy transfer across steep density and temperature gradients in a hot-dense-matter system are presented. Hot dense plasma conditions were generated by high-intensity laser irradiation of a thin-foil target containing a buried metal layer. Energy transfer to the layer was measured using picosecond time-resolved x-ray emission spectroscopy. Here, the data show two x-ray flashes in time. Fully explicit, coupled particle-in-cell and collisional-radiative atomic kinetics model predictions reproduce these observations, connecting the two x-ray flashes with staged radial energy transfer within the target.

Energy transfer dynamics in strongly inhomogeneous hot-dense-matter systems

DOE PAGES

Stillman, C. R.; Nilson, P. M.; Sefkow, A. B.; ...

2018-06-25

Direct measurements of energy transfer across steep density and temperature gradients in a hot-dense-matter system are presented. Hot dense plasma conditions were generated by high-intensity laser irradiation of a thin-foil target containing a buried metal layer. Energy transfer to the layer was measured using picosecond time-resolved x-ray emission spectroscopy. Here, the data show two x-ray flashes in time. Fully explicit, coupled particle-in-cell and collisional-radiative atomic kinetics model predictions reproduce these observations, connecting the two x-ray flashes with staged radial energy transfer within the target.

Exploring the limits of the ``SNB'' multi-group diffusion nonlocal model

NASA Astrophysics Data System (ADS)

Brodrick, Jonathan; Ridgers, Christopher; Kingham, Robert

2014-10-01

A correct treatment of nonlocal transport in the presence of steep temperature gradients found in laser and inertial fusion plasmas has long been highly desirable over the use of an ad-hoc flux limiter. Therefore, an implementation of the ``SNB'' nonlocal model (G P Schurtz, P D Nicolaï & M Busquet, Phys. Plas. 7, 4238 (2000)) has been benchmarked against a fully-implicit kinetic code: IMPACT. A variety of scenarios, including relaxation of temperature sinusoids and Gaussians in addition to continuous laser heating have been investigated. Results highlight the effect of neglecting electron inertia (∂f1/∂ t) as well as question the feasibility of a nonlocal model that does not continuously track the evolution of the distribution function. Deviations from the Spitzer electric fields used in the model across steep gradients are also investigated. Regimes of validity for such a model are identified and discussed, and possible improvements to the model are suggested.

Characterization of peak capacity of microbore liquid chromatography columns using gradient kinetic plots.

PubMed

Hetzel, Terence; Blaesing, Christina; Jaeger, Martin; Teutenberg, Thorsten; Schmidt, Torsten C

2017-02-17

The performance of micro-liquid chromatography columns with an inner diameter of 0.3mm was investigated on a dedicated micro-LC system for gradient elution. Core-shell as well as fully porous particle packed columns were compared on the basis of peak capacity and gradient kinetic plot limits. The results for peak capacity showed the superior performance of columns packed with sub-2μm fully porous particles compared to 3.0μm fully porous and 2.7μm core-shell particles within a range of different gradient time to column void time ratios. For ultra-fast chromatography a maximum peak capacity of 16 can be obtained using a 30s gradient for the sub-2μm fully porous particle packed column. A maximum peak capacity of 121 can be achieved using a 5min gradient. In addition, the influence of an alternative detector cell on the basis of optical waveguide technology and contributing less to system variance was investigated showing an increased peak capacity for all applied gradient time/column void time ratios. Finally, the influence of pressure was evaluated indicating increased peak capacity for maximum performance whereas a limited benefit for ultra-fast chromatography with gradient times below 30s was observed. Copyright © 2017 Elsevier B.V. All rights reserved.

Kinetic limitation of chemical ordering in Bi2Te3-x Se x layers grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Schreyeck, S.; Brunner, K.; Kirchner, A.; Bass, U.; Grauer, S.; Schumacher, C.; Gould, C.; Karczewski, G.; Geurts, J.; Molenkamp, L. W.

2016-04-01

We study the chemical ordering in Bi2Te3-x Se x grown by molecular beam epitaxy on Si substrates. We produce films in the full composition range from x  =  0 to 3, and determine their material properties using energy dispersive x-ray spectroscopy, x-ray diffraction and Raman spectroscopy. By fitting the parameters of a kinetic growth model to these results, we obtain a consistent description of growth at a microscopic level. Our main finding is that despite the incorporation of Se in the central layer being much more probable than that of Te, the formation of a fully ordered Te-Bi-Se-Bi-Te layer is prevented by kinetic of the growth process. Indeed, the Se concentration in the central layer of Bi2Te2Se1 reaches a maximum of only  ≈75% even under ideal growth conditions. A second finding of our work is that the intensity ratio of the 0 0 12 and 0 0 6 x-ray reflections serves as an experimentally accessible quantitative measure of the degree of ordering in these films.

Kinetic performance comparison of fully and superficially porous particles with sizes ranging between 2.7 μm and 5 μm: Intrinsic evaluation and application to a pharmaceutical test compound

PubMed Central

Broeckhoven, K.; Cabooter, D.; Desmet, G.

2012-01-01

The reintroduction of superficially porous particles has resulted in a leap forward for the separation performance in liquid chromatography. The underlying reasons for the higher efficiency of columns packed with these particles are discussed. The performance of the newly introduced 5 μm superficially porous particles is evaluated and compared to 2.7 μm superficially porous and 3.5 and 5 μm fully porous columns using typical test compounds (alkylphenones) and a relevant pharmaceutical compound (impurity of amoxicillin). The 5 μm superficially porous particles provide a superior kinetic performance compared to both the 3.5 and 5 μm fully porous particles over the entire relevant range of separation conditions. The performance of the superficially porous particles, however, appears to depend strongly on retention and analyte properties, emphasizing the importance of comparing different columns under realistic conditions (high enough k) and using the compound of interest. PMID:29403833

A survey of kinetic data of compounds containing flourine

NASA Technical Reports Server (NTRS)

Brewer, D. A.

1976-01-01

Chlorofluoromethanes may have a significant effect on the level of ozone in the atmosphere. However, the role of fluroine-containing compounds has not been examined fully. A tabulation of a search of the chemical kinetic literature published between 1953 and July 1975, is presented. The data are then evaluated with respect to acceptability and importance to the overall reaction balance in the atmosphere. Possible future research to elucidate important reaction processes is discussed.

TEMPEST simulations of the plasma transport in a single-null tokamak geometry

NASA Astrophysics Data System (ADS)

Xu, X. Q.; Bodi, K.; Cohen, R. H.; Krasheninnikov, S.; Rognlien, T. D.

2010-06-01

We present edge kinetic ion transport simulations of tokamak plasmas in magnetic divertor geometry using the fully nonlinear (full-f) continuum code TEMPEST. Besides neoclassical transport, a term for divergence of anomalous kinetic radial flux is added to mock up the effect of turbulent transport. To study the relative roles of neoclassical and anomalous transport, TEMPEST simulations were carried out for plasma transport and flow dynamics in a single-null tokamak geometry, including the pedestal region that extends across the separatrix into the scrape-off layer and private flux region. A series of TEMPEST simulations were conducted to investigate the transition of midplane pedestal heat flux and flow from the neoclassical to the turbulent limit and the transition of divertor heat flux and flow from the kinetic to the fluid regime via an anomalous transport scan and a density scan. The TEMPEST simulation results demonstrate that turbulent transport (as modelled by large diffusion) plays a similar role to collisional decorrelation of particle orbits and that the large turbulent transport (large diffusion) leads to an apparent Maxwellianization of the particle distribution. We also show the transition of parallel heat flux and flow at the entrance to the divertor plates from the fluid to the kinetic regime. For an absorbing divertor plate boundary condition, a non-half-Maxwellian is found due to the balance between upstream radial anomalous transport and energetic ion endloss.

Shock interactions with heterogeneous energetic materials

NASA Astrophysics Data System (ADS)

Yarrington, Cole D.; Wixom, Ryan R.; Damm, David L.

2018-03-01

The complex physical phenomenon of shock wave interaction with material heterogeneities has significant importance and nevertheless remains little understood. In many materials, the observed macroscale response to shock loading is governed by characteristics of the microstructure. Yet, the majority of computational studies aimed at predicting phenomena affected by these processes, such as the initiation and propagation of detonation waves in explosives or shock propagation in geological materials, employ continuum material and reactive burn model treatment. In an effort to highlight the grain-scale processes that underlie the observable effects in an energetic system, a grain-scale model for hexanitrostilbene (HNS) has been developed. The measured microstructures were used to produce synthetic computational representations of the pore structure, and a density functional theory molecular dynamics derived equation of state (EOS) was used for the fully dense HNS matrix. The explicit inclusion of the microstructure along with a fully dense EOS resulted in close agreement with historical shock compression experiments. More recent experiments on the dynamic reaction threshold were also reproduced by inclusion of a global kinetics model. The complete model was shown to reproduce accurately the expected response of this heterogeneous material to shock loading. Mesoscale simulations were shown to provide a clear insight into the nature of threshold behavior and are a way to understand complex physical phenomena.

Shock interactions with heterogeneous energetic materials

DOE PAGES

Yarrington, Cole D.; Wixom, Ryan R.; Damm, David L.

2018-03-14

The complex physical phenomenon of shock wave interaction with material heterogeneities has significant importance and nevertheless remains little understood. In many materials, the observed macroscale response to shock loading is governed by characteristics of the microstructure. Yet the majority of computational studies aimed at predicting phenomena affected by these processes, such as initiation and propagation of detonation waves in explosives, or shock propagation in geological materials, employ continuum material and reactive burn model treatment. In an effort to highlight the grain-scale processes that underlie the observable effects in an energetic system, a grain-scale model for hexanitrostilbene (HNS) has been developed.more » Measured microstructures were used to produce synthetic computational representations of the pore structure, and a density functional theory molecular dynamics (DFT-MD) derived equation of state (EOS) was used for the fully dense HNS matrix. The explicit inclusion of microstructure along with a fully-dense EOS resulted in close agreement with historical shock compression experiments. More recent experiments on dynamic reaction threshold were also reproduced by inclusion of a global kinetics model. The complete model was shown to reproduce accurately the expected response of this heterogeneous material to shock loading. Mesoscale simulations were shown to provide clear insight into the nature of threshold behavior, and are a way to understand complex physical phenomena.« less

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

Yarrington, Cole D.; Wixom, Ryan R.; Damm, David L.

The complex physical phenomenon of shock wave interaction with material heterogeneities has significant importance and nevertheless remains little understood. In many materials, the observed macroscale response to shock loading is governed by characteristics of the microstructure. Yet the majority of computational studies aimed at predicting phenomena affected by these processes, such as initiation and propagation of detonation waves in explosives, or shock propagation in geological materials, employ continuum material and reactive burn model treatment. In an effort to highlight the grain-scale processes that underlie the observable effects in an energetic system, a grain-scale model for hexanitrostilbene (HNS) has been developed.more » Measured microstructures were used to produce synthetic computational representations of the pore structure, and a density functional theory molecular dynamics (DFT-MD) derived equation of state (EOS) was used for the fully dense HNS matrix. The explicit inclusion of microstructure along with a fully-dense EOS resulted in close agreement with historical shock compression experiments. More recent experiments on dynamic reaction threshold were also reproduced by inclusion of a global kinetics model. The complete model was shown to reproduce accurately the expected response of this heterogeneous material to shock loading. Mesoscale simulations were shown to provide clear insight into the nature of threshold behavior, and are a way to understand complex physical phenomena.« less

Fully-kinetic Ion Simulation of Global Electrostatic Turbulent Transport in C-2U

NASA Astrophysics Data System (ADS)

Fulton, Daniel; Lau, Calvin; Bao, Jian; Lin, Zhihong; Tajima, Toshiki; TAE Team

2017-10-01

Understanding the nature of particle and energy transport in field-reversed configuration (FRC) plasmas is a crucial step towards an FRC-based fusion reactor. The C-2U device at Tri Alpha Energy (TAE) achieved macroscopically stable plasmas and electron energy confinement time which scaled favorably with electron temperature. This success led to experimental and theoretical investigation of turbulence in C-2U, including gyrokinetic ion simulations with the Gyrokinetic Toroidal Code (GTC). A primary objective of TAE's new C-2W device is to explore transport scaling in an extended parameter regime. In concert with the C-2W experimental campaign, numerical efforts have also been extended in A New Code (ANC) to use fully-kinetic (FK) ions and a Vlasov-Poisson field solver. Global FK ion simulations are presented. Future code development is also discussed.

Modeling Momentum Transfer from Kinetic Impacts: Implications for Redirecting Asteroids

DOE PAGES

Stickle, A. M.; Atchison, J. A.; Barnouin, O. S.; ...

2015-05-19

Kinetic impactors are one way to deflect a potentially hazardous object headed for Earth. The Asteroid Impact and Deflection Assessment (AIDA) mission is designed to test the effectiveness of this approach and is a joint effort between NASA and ESA. The NASA-led portion is the Double Asteroid Redirect Test (DART) and is composed of a ~300-kg spacecraft designed to impact the moon of the binary system 65803 Didymos. The deflection of the moon will be measured by the ESA-led Asteroid Impact Mission (AIM) (which will characterize the moon) and from ground-based observations. Because the material properties and internal structure ofmore » the target are poorly constrained, however, analytical models and numerical simulations must be used to understand the range of potential outcomes. Here, we describe a modeling effort combining analytical models and CTH simulations to determine possible outcomes of the DART impact. We examine a wide parameter space and provide predictions for crater size, ejecta mass, and momentum transfer following the impact into the moon of the Didymos system. For impacts into “realistic” asteroid types, these models produce craters with diameters on the order of 10 m, an imparted Δv of 0.5–2 mm/s and a momentum enhancement of 1.07 to 5 for a highly porous aggregate to a fully dense rock.« less

Modelling the Krebs cycle and oxidative phosphorylation.

PubMed

Korla, Kalyani; Mitra, Chanchal K

2014-01-01

The Krebs cycle and oxidative phosphorylation are the two most important sets of reactions in a eukaryotic cell that meet the major part of the total energy demands of a cell. In this paper, we present a computer simulation of the coupled reactions using open source tools for simulation. We also show that it is possible to model the Krebs cycle with a simple black box with a few inputs and outputs. However, the kinetics of the internal processes has been modelled using numerical tools. We also show that the Krebs cycle and oxidative phosphorylation together can be combined in a similar fashion - a black box with a few inputs and outputs. The Octave script is flexible and customisable for any chosen set-up for this model. In several cases, we had no explicit idea of the underlying reaction mechanism and the rate determining steps involved, and we have used the stoichiometric equations that can be easily changed as and when more detailed information is obtained. The script includes the feedback regulation of the various enzymes of the Krebs cycle. For the electron transport chain, the pH gradient across the membrane is an essential regulator of the kinetics and this has been modelled empirically but fully consistent with experimental results. The initial conditions can be very easily changed and the simulation is potentially very useful in a number of cases of clinical importance.

Nipah virion entry kinetics, composition, and conformational changes determined by enzymatic virus-like particles and new flow virometry tools.

PubMed

Landowski, Matthew; Dabundo, Jeffrey; Liu, Qian; Nicola, Anthony V; Aguilar, Hector C

2014-12-01

Virus-cell membrane fusion is essential for enveloped virus infections. However, mechanistic viral membrane fusion studies have predominantly focused on cell-cell fusion models, largely due to the low availability of technologies capable of characterizing actual virus-cell membrane fusion. Although cell-cell fusion assays are valuable, they do not fully recapitulate all the variables of virus-cell membrane fusion. Drastic differences between viral and cellular membrane lipid and protein compositions and curvatures exist. For biosafety level 4 (BSL4) pathogens such as the deadly Nipah virus (NiV), virus-cell fusion mechanistic studies are notably cumbersome. To circumvent these limitations, we used enzymatic Nipah virus-like-particles (NiVLPs) and developed new flow virometric tools. NiV's attachment (G) and fusion (F) envelope glycoproteins mediate viral binding to the ephrinB2/ephrinB3 cell receptors and virus-cell membrane fusion, respectively. The NiV matrix protein (M) can autonomously induce NiV assembly and budding. Using a β-lactamase (βLa) reporter/NiV-M chimeric protein, we produced NiVLPs expressing NiV-G and wild-type or mutant NiV-F on their surfaces. By preloading target cells with the βLa fluorescent substrate CCF2-AM, we obtained viral entry kinetic curves that correlated with the NiV-F fusogenic phenotypes, validating NiVLPs as suitable viral entry kinetic tools and suggesting overall relatively slower viral entry than cell-cell fusion kinetics. Additionally, the proportions of F and G on individual NiVLPs and the extent of receptor-induced conformational changes in NiV-G were measured via flow virometry, allowing the proper interpretation of the viral entry kinetic phenotypes. The significance of these findings in the viral entry field extends beyond NiV to other paramyxoviruses and enveloped viruses. Virus-cell membrane fusion is essential for enveloped virus infections. However, mechanistic viral membrane fusion studies have predominantly focused on cell-cell fusion models, largely due to the low availability of technologies capable of characterizing actual virus-cell membrane fusion. Although cell-cell fusion assays are valuable, they do not fully recapitulate all the variables of virus-cell membrane fusion. For example, drastic differences between viral and cellular membrane lipid and protein compositions and curvatures exist. For biosafety level 4 (BSL4) pathogens such as the deadly Nipah virus (NiV), virus-cell fusion mechanistic studies are especially cumbersome. To circumvent these limitations, we used enzymatic Nipah virus-like-particles (NiVLPs) and developed new flow virometric tools. Our new tools allowed us the high-throughput measurement of viral entry kinetics, glycoprotein proportions on individual viral particles, and receptor-induced conformational changes in viral glycoproteins on viral surfaces. The significance of these findings extends beyond NiV to other paramyxoviruses and enveloped viruses. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

A gas kinetic scheme for hybrid simulation of partially rarefied flows

NASA Astrophysics Data System (ADS)

Colonia, S.; Steijl, R.; Barakos, G.

2017-06-01

Approaches to predict flow fields that display rarefaction effects incur a cost in computational time and memory considerably higher than methods commonly employed for continuum flows. For this reason, to simulate flow fields where continuum and rarefied regimes coexist, hybrid techniques have been introduced. In the present work, analytically defined gas-kinetic schemes based on the Shakhov and Rykov models for monoatomic and diatomic gas flows, respectively, are proposed and evaluated with the aim to be used in the context of hybrid simulations. This should reduce the region where more expensive methods are needed by extending the validity of the continuum formulation. Moreover, since for high-speed rare¦ed gas flows it is necessary to take into account the nonequilibrium among the internal degrees of freedom, the extension of the approach to employ diatomic gas models including rotational relaxation process is a mandatory first step towards realistic simulations. Compared to previous works of Xu and coworkers, the presented scheme is de¦ned directly on the basis of kinetic models which involve a Prandtl number correction. Moreover, the methods are defined fully analytically instead of making use of Taylor expansion for the evaluation of the required derivatives. The scheme has been tested for various test cases and Mach numbers proving to produce reliable predictions in agreement with other approaches for near-continuum flows. Finally, the performance of the scheme, in terms of memory and computational time, compared to discrete velocity methods makes it a compelling alternative in place of more complex methods for hybrid simulations of weakly rarefied flows.

Systematic Constraint Selection Strategy for Rate-Controlled Constrained-Equilibrium Modeling of Complex Nonequilibrium Chemical Kinetics

NASA Astrophysics Data System (ADS)

Beretta, Gian Paolo; Rivadossi, Luca; Janbozorgi, Mohammad

2018-04-01

Rate-Controlled Constrained-Equilibrium (RCCE) modeling of complex chemical kinetics provides acceptable accuracies with much fewer differential equations than for the fully Detailed Kinetic Model (DKM). Since its introduction by James C. Keck, a drawback of the RCCE scheme has been the absence of an automatable, systematic procedure to identify the constraints that most effectively warrant a desired level of approximation for a given range of initial, boundary, and thermodynamic conditions. An optimal constraint identification has been recently proposed. Given a DKM with S species, E elements, and R reactions, the procedure starts by running a probe DKM simulation to compute an S-vector that we call overall degree of disequilibrium (ODoD) because its scalar product with the S-vector formed by the stoichiometric coefficients of any reaction yields its degree of disequilibrium (DoD). The ODoD vector evolves in the same (S-E)-dimensional stoichiometric subspace spanned by the R stoichiometric S-vectors. Next we construct the rank-(S-E) matrix of ODoD traces obtained from the probe DKM numerical simulation and compute its singular value decomposition (SVD). By retaining only the first C largest singular values of the SVD and setting to zero all the others we obtain the best rank-C approximation of the matrix of ODoD traces whereby its columns span a C-dimensional subspace of the stoichiometric subspace. This in turn yields the best approximation of the evolution of the ODoD vector in terms of only C parameters that we call the constraint potentials. The resulting order-C RCCE approximate model reduces the number of independent differential equations related to species, mass, and energy balances from S+2 to C+E+2, with substantial computational savings when C ≪ S-E.

New Insight into the Catalytic Mechanism of Bacterial MraY from Enzyme Kinetics and Docking Studies*

PubMed Central

Liu, Yao; Rodrigues, João P. G. L. M.; Bonvin, Alexandre M. J. J.; Zaal, Esther A.; Berkers, Celia R.; Heger, Michal; Gawarecka, Katarzyna; Swiezewska, Ewa; Breukink, Eefjan; Egmond, Maarten R.

2016-01-01

Phospho-MurNAc-pentapeptide translocase (MraY) catalyzes the synthesis of Lipid I, a bacterial peptidoglycan precursor. As such, MraY is essential for bacterial survival and therefore is an ideal target for developing novel antibiotics. However, the understanding of its catalytic mechanism, despite the recently determined crystal structure, remains limited. In the present study, the kinetic properties of Bacillus subtilis MraY (BsMraY) were investigated by fluorescence enhancement using dansylated UDP-MurNAc-pentapeptide and heptaprenyl phosphate (C35-P, short-chain homolog of undecaprenyl phosphate, the endogenous substrate of MraY) as second substrate. Varying the concentrations of both of these substrates and fitting the kinetics data to two-substrate models showed that the concomitant binding of both UDP-MurNAc-pentapeptide-DNS and C35-P to the enzyme is required before the release of the two products, Lipid I and UMP. We built a model of BsMraY and performed docking studies with the substrate C35-P to further deepen our understanding of how MraY accommodates this lipid substrate. Based on these modeling studies, a novel catalytic role was put forward for a fully conserved histidine residue in MraY (His-289 in BsMraY), which has been experimentally confirmed to be essential for MraY activity. Using the current model of BsMraY, we propose that a small conformational change is necessary to relocate the His-289 residue, such that the translocase reaction can proceed via a nucleophilic attack of the phosphate moiety of C35-P on bound UDP-MurNAc-pentapeptide. PMID:27226570

Simulation studies of plasma waves in the electron foreshock - The transition from reactive to kinetic instability

NASA Technical Reports Server (NTRS)

Dum, C. T.

1990-01-01

Particle simulation experiments were used to analyze the electron beam-plasma instability. It is shown that there is a transition from the reactive state of the electron beam-plasma instability to the kinetic instability of Langmuir waves. Quantitative tests, which include an evaluation of the dispersion relation for the evolving non-Maxwellian beam distribution, show that a quasi-linear theory describes the onset of this transition and applies again fully to the kinetic stage. This stage is practically identical to the late stage seen in simulations of plasma waves in the electron foreshock described by Dum (1990).

The photoexcitation of crystalline ice and amorphous solid water: A molecular dynamics study of outcomes at 11 K and 125 K

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

Crouse, J.; Loock, H.-P., E-mail: hploock@chem.queensu.ca; Cann, N. M., E-mail: ncann@chem.queensu.ca

2015-07-21

Photoexcitation of crystalline ice Ih and amorphous solid water at 7-9 eV is examined using molecular dynamics simulations and a fully flexible water model. The probabilities of photofragment desorption, trapping, and recombination are examined for crystalline ice at 11 K and at 125 K and for amorphous solid water at 11 K. For 11 K crystalline ice, a fully rigid water model is also employed for comparison. The kinetic energy of desorbed H atoms and the distance travelled by trapped fragments are correlated to the location and the local environment of the photoexcited water molecule. In all cases, H atommore » desorption is found to be the most likely outcome in the top bilayer while trapping of all photofragments is most probable deeper in the solid where the likelihood for recombination of the fragments into H{sub 2}O molecules also rises. Trajectory analysis indicates that the local hydrogen bonding network in amorphous solid water is more easily distorted by a photodissociation event compared to crystalline ice. Also, simulations indicate that desorption of OH radicals and H{sub 2}O molecules are more probable in amorphous solid water. The kinetic energy distributions for desorbed H atoms show a peak at high energy in crystalline ice, arising from photoexcited water molecules in the top monolayer. This peak is less pronounced in amorphous solid water. H atoms that are trapped may be displaced by up to ∼10 water cages, but migrate on average 3 water cages. Trapped OH fragments tend to stay near the original solvent cage.« less

Rubisco, Rubisco activase, and global climate change.

PubMed

Sage, Rowan F; Way, Danielle A; Kubien, David S

2008-01-01

Global warming and the rise in atmospheric CO(2) will increase the operating temperature of leaves in coming decades, often well above the thermal optimum for photosynthesis. Presently, there is controversy over the limiting processes controlling photosynthesis at elevated temperature. Leading models propose that the reduction in photosynthesis at elevated temperature is a function of either declining capacity of electron transport to regenerate RuBP, or reductions in the capacity of Rubisco activase to maintain Rubisco in an active configuration. Identifying which of these processes is the principal limitation at elevated temperature is complicated because each may be regulated in response to a limitation in the other. Biochemical and gas exchange assessments can disentangle these photosynthetic limitations; however, comprehensive assessments are often difficult and, for many species, virtually impossible. It is proposed that measurement of the initial slope of the CO(2) response of photosynthesis (the A/C(i) response) can be a useful means to screen for Rubisco activase limitations. This is because a reduction in the Rubisco activation state should be most apparent at low CO(2) when Rubisco capacity is generally limiting. In sweet potato, spinach, and tobacco, the initial slope of the A/C(i) response shows no evidence of activase limitations at high temperature, as the slope can be accurately modelled using the kinetic parameters of fully activated Rubisco. In black spruce (Picea mariana), a reduction in the initial slope above 30 degrees C cannot be explained by the known kinetics of fully activated Rubisco, indicating that activase may be limiting at high temperatures. Because black spruce is the dominant species in the boreal forest of North America, Rubisco activase may be an unusually important factor determining the response of the boreal biome to climate change.

Multiphase chemical kinetics of OH radical uptake by molecular organic markers of biomass burning aerosols: humidity and temperature dependence, surface reaction, and bulk diffusion.

PubMed

Arangio, Andrea M; Slade, Jonathan H; Berkemeier, Thomas; Pöschl, Ulrich; Knopf, Daniel A; Shiraiwa, Manabu

2015-05-14

Multiphase reactions of OH radicals are among the most important pathways of chemical aging of organic aerosols in the atmosphere. Reactive uptake of OH by organic compounds has been observed in a number of studies, but the kinetics of mass transport and chemical reaction are still not fully understood. Here we apply the kinetic multilayer model of gas-particle interactions (KM-GAP) to experimental data from OH exposure studies of levoglucosan and abietic acid, which serve as surrogates and molecular markers of biomass burning aerosol (BBA). The model accounts for gas-phase diffusion within a cylindrical coated-wall flow tube, reversible adsorption of OH, surface-bulk exchange, bulk diffusion, and chemical reactions at the surface and in the bulk of the condensed phase. The nonlinear dependence of OH uptake coefficients on reactant concentrations and time can be reproduced by KM-GAP. We find that the bulk diffusion coefficient of the organic molecules is approximately 10(-16) cm(2) s(-1), reflecting an amorphous semisolid state of the organic substrates. The OH uptake is governed by reaction at or near the surface and can be kinetically limited by surface-bulk exchange or bulk diffusion of the organic reactants. Estimates of the chemical half-life of levoglucosan in 200 nm particles in a biomass burning plume increase from 1 day at high relative humidity to 1 week under dry conditions. In BBA particles transported to the free troposphere, the chemical half-life of levoglucosan can exceed 1 month due to slow bulk diffusion in a glassy matrix at low temperature.

Refolding dynamics of stretched biopolymers upon force quench

PubMed Central

Hyeon, Changbong; Morrison, Greg; Pincus, David L.; Thirumalai, D.

2009-01-01

Single-molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse of RNA and proteins upon force quench by using simulations of an RNA hairpin and theory based on the de Gennes model for homopolymer collapse. The folding time, τF, depends asymmetrically on δfS = f S − f m and δf Q = f m − f Q where f S (f Q) is the stretch (quench) force and f m is the transition midforce of the RNA hairpin. In accord with experiments, the relaxation kinetics of the molecular extension, R(t), occurs in three stages: A rapid initial decrease in the extension is followed by a plateau and finally, an abrupt reduction in R(t) occurs as the native state is approached. The duration of the plateau increases as λ = τ Q/τ F decreases (where τ Q is the time in which the force is reduced from f S to f Q). Variations in the mechanisms of force-quench relaxation as λ is altered are reflected in the experimentally measurable time-dependent entropy, which is computed directly from the folding trajectories. An analytical solution of the de Gennes model under tension reproduces the multistage stage kinetics in R(t). The prediction that the initial stages of collapse should also be a generic feature of polymers is validated by simulation of the kinetics of toroid (globule) formation in semiflexible (flexible) homopolymers in poor solvents upon quenching the force from a fully stretched state. Our findings give a unified explanation for multiple disparate experimental observations of protein folding. PMID:19915145

Stratified Simulations of Collisionless Accretion Disks

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

Hirabayashi, Kota; Hoshino, Masahiro, E-mail: hirabayashi-k@eps.s.u-tokyo.ac.jp

This paper presents a series of stratified-shearing-box simulations of collisionless accretion disks in the recently developed framework of kinetic magnetohydrodynamics (MHD), which can handle finite non-gyrotropy of a pressure tensor. Although a fully kinetic simulation predicted a more efficient angular-momentum transport in collisionless disks than in the standard MHD regime, the enhanced transport has not been observed in past kinetic-MHD approaches to gyrotropic pressure anisotropy. For the purpose of investigating this missing link between the fully kinetic and MHD treatments, this paper explores the role of non-gyrotropic pressure and makes the first attempt to incorporate certain collisionless effects into disk-scale,more » stratified disk simulations. When the timescale of gyrotropization was longer than, or comparable to, the disk-rotation frequency of the orbit, we found that the finite non-gyrotropy selectively remaining in the vicinity of current sheets contributes to suppressing magnetic reconnection in the shearing-box system. This leads to increases both in the saturated amplitude of the MHD turbulence driven by magnetorotational instabilities and in the resultant efficiency of angular-momentum transport. Our results seem to favor the fast advection of magnetic fields toward the rotation axis of a central object, which is required to launch an ultra-relativistic jet from a black hole accretion system in, for example, a magnetically arrested disk state.« less

Two-dimensional implosion simulations with a kinetic particle code [2D implosion simulations with a kinetic particle code

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

Sagert, Irina; Even, Wesley Paul; Strother, Terrance Timothy

Here, we perform two-dimensional implosion simulations using a Monte Carlo kinetic particle code. The application of a kinetic transport code is motivated, in part, by the occurrence of nonequilibrium effects in inertial confinement fusion capsule implosions, which cannot be fully captured by hydrodynamic simulations. Kinetic methods, on the other hand, are able to describe both continuum and rarefied flows. We perform simple two-dimensional disk implosion simulations using one-particle species and compare the results to simulations with the hydrodynamics code rage. The impact of the particle mean free path on the implosion is also explored. In a second study, we focusmore » on the formation of fluid instabilities from induced perturbations. We find good agreement with hydrodynamic studies regarding the location of the shock and the implosion dynamics. Differences are found in the evolution of fluid instabilities, originating from the higher resolution of rage and statistical noise in the kinetic studies.« less

Two-dimensional implosion simulations with a kinetic particle code [2D implosion simulations with a kinetic particle code

DOE PAGES

Sagert, Irina; Even, Wesley Paul; Strother, Terrance Timothy

2017-05-17

Here, we perform two-dimensional implosion simulations using a Monte Carlo kinetic particle code. The application of a kinetic transport code is motivated, in part, by the occurrence of nonequilibrium effects in inertial confinement fusion capsule implosions, which cannot be fully captured by hydrodynamic simulations. Kinetic methods, on the other hand, are able to describe both continuum and rarefied flows. We perform simple two-dimensional disk implosion simulations using one-particle species and compare the results to simulations with the hydrodynamics code rage. The impact of the particle mean free path on the implosion is also explored. In a second study, we focusmore » on the formation of fluid instabilities from induced perturbations. We find good agreement with hydrodynamic studies regarding the location of the shock and the implosion dynamics. Differences are found in the evolution of fluid instabilities, originating from the higher resolution of rage and statistical noise in the kinetic studies.« less

Drosophila QVR/SSS modulates the activation and C-type inactivation kinetics of Shaker K+ channels

PubMed Central

Dean, Terry; Xu, Rong; Joiner, William; Sehgal, Amita; Hoshi, Toshinori

2011-01-01

The quiver/sleepless (qvr/sss) gene encodes a small, glycosylphosphatidylinositol-anchored protein that plays a critical role in the regulation of sleep in Drosophila. Loss-of-function mutations in qvr/sss severely suppress sleep and effect multiple changes in in situ Shaker K+ currents, including decreased magnitude, slower time-to-peak, and cumulative inactivation. Recently, we demonstrated that SLEEPLESS (SSS) protein modulates Shaker channel activity, possibly through a direct interaction at the plasma membrane. We show here that SSS accelerates the activation of heterologously expressed Shaker channels with no effect on deactivation or fast N-type inactivation. Furthermore, this SSS-induced acceleration is sensitive to the pharmacological disruption of lipid rafts and sufficiently accounts for the slower time-to-peak of in situ Shaker currents seen in qvr/sss mutants. We also find that SSS decreases the rate of C-type inactivation of heterologously expressed Shaker channels, providing a potential mechanism for the cumulative inactivation phenotype induced by qvr/sss loss of function mutations. Kinetic modeling based on the in vitro results suggests that the SSS-dependent regulation of channel kinetics accounts for nearly 40% of the decrease in Shaker current magnitude in flies lacking SSS. Sleep duration in qvr/sss null mutants is restored to normal by a qvr/sss transgene that fully rescues the Shaker kinetic phenotypes but only partially rescues the decrease in current magnitude. Together, these results suggest that the role of SSS in the regulation of sleep in Drosophila correlates more strongly with the effects of SSS on Shaker kinetics than current magnitude. PMID:21813698

Drosophila QVR/SSS modulates the activation and C-type inactivation kinetics of Shaker K(+) channels.

PubMed

Dean, Terry; Xu, Rong; Joiner, William; Sehgal, Amita; Hoshi, Toshinori

2011-08-03

The quiver/sleepless (qvr/sss) gene encodes a small, glycosylphosphatidylinositol-anchored protein that plays a critical role in the regulation of sleep in Drosophila. Loss-of-function mutations in qvr/sss severely suppress sleep and effect multiple changes in in situ Shaker K(+) currents, including decreased magnitude, slower time-to-peak, and cumulative inactivation. Recently, we demonstrated that SLEEPLESS (SSS) protein modulates Shaker channel activity, possibly through a direct interaction at the plasma membrane. We show here that SSS accelerates the activation of heterologously expressed Shaker channels with no effect on deactivation or fast N-type inactivation. Furthermore, this SSS-induced acceleration is sensitive to the pharmacological disruption of lipid rafts and sufficiently accounts for the slower time-to-peak of in situ Shaker currents seen in qvr/sss mutants. We also find that SSS decreases the rate of C-type inactivation of heterologously expressed Shaker channels, providing a potential mechanism for the cumulative inactivation phenotype induced by qvr/sss loss-of-function mutations. Kinetic modeling based on the in vitro results suggests that the SSS-dependent regulation of channel kinetics accounts for nearly 40% of the decrease in Shaker current magnitude in flies lacking SSS. Sleep duration in qvr/sss-null mutants is restored to normal by a qvr/sss transgene that fully rescues the Shaker kinetic phenotypes but only partially rescues the decrease in current magnitude. Together, these results suggest that the role of SSS in the regulation of sleep in Drosophila correlates more strongly with the effects of SSS on Shaker kinetics than current magnitude.

The Disintegration Process in Microcrystalline Cellulose Based Tablets, Part 1: Influence of Temperature, Porosity and Superdisintegrants.

PubMed

Yassin, Samy; Goodwin, Daniel J; Anderson, Andrew; Sibik, Juraj; Wilson, D Ian; Gladden, Lynn F; Zeitler, J Axel

2015-10-01

Disintegration performance was measured by analysing both water ingress and tablet swelling of pure microcrystalline cellulose (MCC) and in mixture with croscarmellose sodium using terahertz pulsed imaging (TPI). Tablets made from pure MCC with porosities of 10% and 15% showed similar swelling and transport kinetics: within the first 15 s, tablets had swollen by up to 33% of their original thickness and water had fully penetrated the tablet following Darcy flow kinetics. In contrast, MCC tablets with a porosity of 5% exhibited much slower transport kinetics, with swelling to only 17% of their original thickness and full water penetration reached after 100 s, dominated by case II transport kinetics. The effect of adding superdisintegrant to the formulation and varying the temperature of the dissolution medium between 20°C and 37°C on the swelling and transport process was quantified. We have demonstrated that TPI can be used to non-invasively analyse the complex disintegration kinetics of formulations that take place on timescales of seconds and is a promising tool to better understand the effect of dosage form microstructure on its performance. By relating immediate-release formulations to mathematical models used to describe controlled release formulations, it becomes possible to use this data for formulation design. © 2015 The Authors. Journal of Pharmaceutical Sciences published by Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 104:3440-3450, 2015. © 2015 The Authors. Journal of Pharmaceutical Sciences published by Wiley Periodicals, Inc. and the American Pharmacists Association.

Modeling aerosol surface chemistry and gas-particle interaction kinetics with K2-SURF: PAH oxidation

NASA Astrophysics Data System (ADS)

Shiraiwa, M.; Garland, R.; Pöschl, U.

2009-04-01

Atmospheric aerosols are ubiquitous in the atmosphere. They have the ability to impact cloud properties, radiative balance and provide surfaces for heterogeneous reactions. The uptake of gaseous species on aerosol surfaces impacts both the aerosol particles and the atmospheric budget of trace gases. These subsequent changes to the aerosol can in turn impact the aerosol chemical and physical properties. However, this uptake, as well as the impact on the aerosol, is not fully understood. This uncertainty is due not only to limited measurement data, but also a dearth of comprehensive and applicable modeling formalizations used for the analysis, interpretation and description of these heterogeneous processes. Without a common model framework, comparing and extrapolating experimental data is difficult. In this study, a novel kinetic surface model (K2-SURF) [Ammann & Pöschl, 2007; Pöschl et al., 2007] was used to describe the oxidation of a variety of polycyclic aromatic hydrocarbons (PAHs). Integrated into this consistent and universally applicable kinetic and thermodynamic process model are the concepts, terminologies and mathematical formalizations essential to the description of atmospherically relevant physicochemical processes involving organic and mixed organic-inorganic aerosols. Within this process model framework, a detailed master mechanism, simplified mechanism and parameterizations of atmospheric aerosol chemistry are being developed and integrated in analogy to existing mechanisms and parameterizations of atmospheric gas-phase chemistry. One of the key aspects to this model is the defining of a clear distinction between various layers of the particle and surrounding gas phase. The processes occurring at each layer can be fully described using known fluxes and kinetic parameters. Using this system there is a clear separation of gas phase, gas-surface and surface bulk transport and reactions. The partitioning of compounds can be calculated using the flux values between the layers. By describing these layers unambiguously, the interactions of all species in the system can be appropriately modeled. In describing the oxidation of PAHs, the focus was on the interactions between the sorption layer and quasi-static surface layer. The results from a variety of published experimental studies [Pöschl et al., 2001; Kahan et al., 2006; Kwamena et al., 2004, 2006, 2007; Mmereki and Donaldson, 2003; Mmereki et al., 2004; Dubowski et al., 2004; Donaldson et al., 2005; Segal-Rosenheimer and Dubowski, 2007] were analyzed and compared utilizing K2-SURF. The heterogeneous reaction of PAH and O3 are found to follow a Langmuir-Hinshelwood mechanism, in which ozone first absorbs to the surface and then reacts with PAH. The Langmuir equilibrium constants and second-order-rate coefficients of surface reaction were estimated. In PAH/O3/solid substrate system, they showed similar reaction rate (×10), but large difference (×1000) in adsorption. The mean residence time and adsorption enthalpy were estimated for O3 at the surface of substrates, suggesting the chemisorption of O3 molecules or O atoms, respectively. Initial uptake coefficients of O3 under different conditions were also investigated. The observed dependence on gas-phase O3 concentration was well explained with K2-SURF model in five-order range. In addition, competitive adsorption of other gas phase species (NO2, H2O) was well described by the model. Possible mechanism of PAH degradation system and atmospheric implications are discussed.

Mass accommodation of water: bridging the gap between molecular dynamics simulations and kinetic condensation models.

PubMed

Julin, Jan; Shiraiwa, Manabu; Miles, Rachael E H; Reid, Jonathan P; Pöschl, Ulrich; Riipinen, Ilona

2013-01-17

The condensational growth of submicrometer aerosol particles to climate relevant sizes is sensitive to their ability to accommodate vapor molecules, which is described by the mass accommodation coefficient. However, the underlying processes are not yet fully understood. We have simulated the mass accommodation and evaporation processes of water using molecular dynamics, and the results are compared to the condensation equations derived from the kinetic gas theory to shed light on the compatibility of the two. Molecular dynamics simulations were performed for a planar TIP4P-Ew water surface at four temperatures in the range 268-300 K as well as two droplets, with radii of 1.92 and 4.14 nm at T = 273.15 K. The evaporation flux from molecular dynamics was found to be in good qualitative agreement with that predicted by the simple kinetic condensation equations. Water droplet growth was also modeled with the kinetic multilayer model KM-GAP of Shiraiwa et al. [Atmos. Chem. Phys. 2012, 12, 2777]. It was found that, due to the fast transport across the interface, the growth of a pure water droplet is controlled by gas phase diffusion. These facts indicate that the simple kinetic treatment is sufficient in describing pure water condensation and evaporation. The droplet size was found to have minimal effect on the value of the mass accommodation coefficient. The mass accommodation coefficient was found to be unity (within 0.004) for all studied surfaces, which is in agreement with previous simulation work. Additionally, the simulated evaporation fluxes imply that the evaporation coefficient is also unity. Comparing the evaporation rates of the mass accommodation and evaporation simulations indicated that the high collision flux, corresponding to high supersaturation, present in typical molecular dynamics mass accommodation simulations can under certain conditions lead to an increase in the evaporation rate. Consequently, in such situations the mass accommodation coefficient can be overestimated, but in the present cases the corrected values were still close to unity with the lowest value at ≈0.99.

Mass Accommodation of Water: Bridging the Gap Between Molecular Dynamics Simulations and Kinetic Condensation Models

PubMed Central

2012-01-01

The condensational growth of submicrometer aerosol particles to climate relevant sizes is sensitive to their ability to accommodate vapor molecules, which is described by the mass accommodation coefficient. However, the underlying processes are not yet fully understood. We have simulated the mass accommodation and evaporation processes of water using molecular dynamics, and the results are compared to the condensation equations derived from the kinetic gas theory to shed light on the compatibility of the two. Molecular dynamics simulations were performed for a planar TIP4P-Ew water surface at four temperatures in the range 268–300 K as well as two droplets, with radii of 1.92 and 4.14 nm at T = 273.15 K. The evaporation flux from molecular dynamics was found to be in good qualitative agreement with that predicted by the simple kinetic condensation equations. Water droplet growth was also modeled with the kinetic multilayer model KM-GAP of Shiraiwa et al. [Atmos. Chem. Phys.2012, 117, 2777]. It was found that, due to the fast transport across the interface, the growth of a pure water droplet is controlled by gas phase diffusion. These facts indicate that the simple kinetic treatment is sufficient in describing pure water condensation and evaporation. The droplet size was found to have minimal effect on the value of the mass accommodation coefficient. The mass accommodation coefficient was found to be unity (within 0.004) for all studied surfaces, which is in agreement with previous simulation work. Additionally, the simulated evaporation fluxes imply that the evaporation coefficient is also unity. Comparing the evaporation rates of the mass accommodation and evaporation simulations indicated that the high collision flux, corresponding to high supersaturation, present in typical molecular dynamics mass accommodation simulations can under certain conditions lead to an increase in the evaporation rate. Consequently, in such situations the mass accommodation coefficient can be overestimated, but in the present cases the corrected values were still close to unity with the lowest value at ≈0.99. PMID:23253100

Electromagnetic Torque in Tokamaks with Toroidal Asymmetries

NASA Astrophysics Data System (ADS)

Logan, Nikolas Christopher

Toroidal rotation and rotation shear strongly influences stability and confinement in tokamaks. Breaking of the toroidal symmetry by fields orders of magnitude smaller than the axisymmetric field can, however, produce electromagnetic torques that significantly affect the plasma rotation, stability and confinement. These electromagnetic torques are the study of this thesis. There are two typical types of electromagnetic torques in tokamaks: 1) "resonant torques" for which a plasma current defined by a single toroidal and single poloidal harmonic interact with external currents and 2) "nonresonant torques" for which the global plasma response to nonaxisymmetric fields is phase shifted by kinetic effects that drive the rotation towards a neoclassical offset. This work describes the diagnostics and analysis necessary to evaluate the torque by measuring the rate of momentum transfer per unit area in the vacuum region between the plasma and external currents using localized magnetic sensors to measure the Maxwell stress. These measurements provide model independent quantification of both the resonant and nonresonant electromagnetic torques, enabling direct verification of theoretical models. Measured values of the nonresonant torque are shown to agree well with the perturbed equilibrium nonambipolar transport (PENT) code calculation of torque from cross field transport in nonaxisymmetric equilibria. A combined neoclassical toroidal viscosity (NTV) theory, valid across a wide range of kinetic regimes, is fully implemented for the first time in general aspect ratio and shaped plasmas. The code captures pitch angle resonances, reproducing previously inaccessible collisionality limits in the model. The complete treatment of the model enables benchmarking to the hybrid kinetic MHD stability codes MARS-K and MISK, confirming the energy-torque equivalency principle in perturbed equilibria. Experimental validations of PENT results confirm the torque applied by nonaxisymmetric coils is often proportional to the energy put into the dominant ideal MHD kink mode. This reduces the control of nonresonant torque to a single mode model, enabling efficient feed forward optimization of applied fields. Initial results including the anisotropic kinetic pressure tensor directly in the plasma eigenmode calculations are presented here, and may eventually provide accurate metrics for multimodal coupling similar to the established single mode metrics.

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

CFD analysis of municipal solid waste combustion using detailed chemical kinetic modelling.

PubMed

Frank, Alex; Castaldi, Marco J

2014-08-01

Nitrogen oxides (NO x ) emissions from the combustion of municipal solid waste (MSW) in waste-to-energy (WtE) facilities are receiving renewed attention to reduce their output further. While NO x emissions are currently 60% below allowed limits, further reductions will decrease the air pollution control (APC) system burden and reduce consumption of NH3. This work combines the incorporation of the GRI 3.0 mechanism as a detailed chemical kinetic model (DCKM) into a custom three-dimensional (3D) computational fluid dynamics (CFD) model fully to understand the NO x chemistry in the above-bed burnout zones. Specifically, thermal, prompt and fuel NO formation mechanisms were evaluated for the system and a parametric study was utilized to determine the effect of varying fuel nitrogen conversion intermediates between HCN, NH3 and NO directly. Simulation results indicate that the fuel nitrogen mechanism accounts for 92% of the total NO produced in the system with thermal and prompt mechanisms accounting for the remaining 8%. Results also show a 5% variation in final NO concentration between HCN and NH3 inlet conditions, demonstrating that the fuel nitrogen intermediate assumed is not significant. Furthermore, the conversion ratio of fuel nitrogen to NO was 0.33, revealing that the majority of fuel nitrogen forms N2. © The Author(s) 2014.

Free-energy landscape of protein oligomerization from atomistic simulations

PubMed Central

Barducci, Alessandro; Bonomi, Massimiliano; Prakash, Meher K.; Parrinello, Michele

2013-01-01

In the realm of protein–protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage. PMID:24248370

The reaction mechanism with free energy barriers at constant potentials for the oxygen evolution reaction at the IrO 2 (110) surface

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

Ping, Yuan; Nielsen, Robert J.; Goddard, William A.

How to efficiently oxidize H 2O to O 2 (oxygen evolution reaction, OER) in photoelectrochemical cells (PEC) is a great challenge due to its complex charge transfer process, high overpotential, and corrosion. So far no OER mechanism has been fully explained atomistically with both thermodynamic and kinetics. IrO 2 is the only known OER catalyst with both high catalytic activity and stability in acidic conditions. This is important because PEC experiments often operate at extreme pH conditions. In this work, we performed first-principles calculations integrated with implicit solvation at constant potentials to examine the detailed atomistic reaction mechanism of OERmore » at the IrO 2 (110) surface. We determined the surface phase diagram, explored the possible reaction pathways including kinetic barriers, and computed reaction rates based on the microkinetic models. Furthermore, this allowed us to resolve several long-standing puzzles about the atomistic OER mechanism.« less

The reaction mechanism with free energy barriers at constant potentials for the oxygen evolution reaction at the IrO 2 (110) surface

DOE PAGES

Ping, Yuan; Nielsen, Robert J.; Goddard, William A.

2016-12-09

How to efficiently oxidize H 2O to O 2 (oxygen evolution reaction, OER) in photoelectrochemical cells (PEC) is a great challenge due to its complex charge transfer process, high overpotential, and corrosion. So far no OER mechanism has been fully explained atomistically with both thermodynamic and kinetics. IrO 2 is the only known OER catalyst with both high catalytic activity and stability in acidic conditions. This is important because PEC experiments often operate at extreme pH conditions. In this work, we performed first-principles calculations integrated with implicit solvation at constant potentials to examine the detailed atomistic reaction mechanism of OERmore » at the IrO 2 (110) surface. We determined the surface phase diagram, explored the possible reaction pathways including kinetic barriers, and computed reaction rates based on the microkinetic models. Furthermore, this allowed us to resolve several long-standing puzzles about the atomistic OER mechanism.« less

Kinetic simulations of gas breakdown in the dense plasma focus

DOE PAGES

Bennett, N.; Blasco, M.; Breeding, K.; ...

2017-06-09

We describe the first fully-kinetic, collisional, and electromagnetic simulations of the breakdown phase of a MA-scale dense plasma focus and are shown to agree with measured electrical characteristics, including breakdown time. In the model, avalanche ionization is driven by cathode electron emission and this results in incomplete gas breakdown along the insulator. This reinforces the importance of the conditioning process that creates a metallic layer on the insulator surface. The simulations, nonetheless, help explain the relationship between the gas pressure, the insulator length, and the coaxial gap width. In the past, researchers noted three breakdown patterns related to pressure. Simulationmore » and analytic results show that at low pressures, long ionization path lengths lead to volumetric breakdown, while high pressures lead to breakdown across the relatively small coaxial electrode gap. In an intermediate pressure regime, ionization path lengths are comparable to the insulator length which promotes ideal breakdown along the insulator surface.« less

Free-energy landscape of protein oligomerization from atomistic simulations.

PubMed

Barducci, Alessandro; Bonomi, Massimiliano; Prakash, Meher K; Parrinello, Michele

2013-12-03

In the realm of protein-protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most experimental investigations. Molecular simulations provide a unique tool to shed light onto these complex processes complementing experimental data. Here we combine advanced sampling techniques, such as metadynamics and parallel tempering, to characterize the oligomerization landscape of fibritin foldon domain. This system is an evolutionarily optimized trimerization motif that represents an ideal model for experimental and computational mechanistic studies. Our results are fully consistent with previous experimental nuclear magnetic resonance and kinetic data, but they provide a unique insight into fibritin foldon assembly. In particular, our simulations unveil the role of nonspecific interactions and suggest that an interplay between thermodynamic bias toward native structure and residual conformational disorder may provide a kinetic advantage.

Progress with the COGENT Edge Kinetic Code: Implementing the Fokker-Plank Collision Operator

DOE PAGES

Dorf, M. A.; Cohen, R. H.; Dorr, M.; ...

2014-06-20

Here, COGENT is a continuum gyrokinetic code for edge plasma simulations being developed by the Edge Simulation Laboratory collaboration. The code is distinguished by application of a fourth-order finite-volume (conservative) discretization, and mapped multiblock grid technology to handle the geometric complexity of the tokamak edge. The distribution function F is discretized in v∥ – μ (parallel velocity – magnetic moment) velocity coordinates, and the code presently solves an axisymmetric full-f gyro-kinetic equation coupled to the long-wavelength limit of the gyro-Poisson equation. COGENT capabilities are extended by implementing the fully nonlinear Fokker-Plank operator to model Coulomb collisions in magnetized edge plasmas.more » The corresponding Rosenbluth potentials are computed by making use of a finite-difference scheme and multipole-expansion boundary conditions. Details of the numerical algorithms and results of the initial verification studies are discussed. (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)« less

Capabilities of Fully Parallelized MHD Stability Code MARS

NASA Astrophysics Data System (ADS)

Svidzinski, Vladimir; Galkin, Sergei; Kim, Jin-Soo; Liu, Yueqiang

2016-10-01

Results of full parallelization of the plasma stability code MARS will be reported. MARS calculates eigenmodes in 2D axisymmetric toroidal equilibria in MHD-kinetic plasma models. Parallel version of MARS, named PMARS, has been recently developed at FAR-TECH. Parallelized MARS is an efficient tool for simulation of MHD instabilities with low, intermediate and high toroidal mode numbers within both fluid and kinetic plasma models, implemented in MARS. Parallelization of the code included parallelization of the construction of the matrix for the eigenvalue problem and parallelization of the inverse vector iterations algorithm, implemented in MARS for the solution of the formulated eigenvalue problem. Construction of the matrix is parallelized by distributing the load among processors assigned to different magnetic surfaces. Parallelization of the solution of the eigenvalue problem is made by repeating steps of the MARS algorithm using parallel libraries and procedures. Parallelized MARS is capable of calculating eigenmodes with significantly increased spatial resolution: up to 5,000 adapted radial grid points with up to 500 poloidal harmonics. Such resolution is sufficient for simulation of kink, tearing and peeling-ballooning instabilities with physically relevant parameters. Work is supported by the U.S. DOE SBIR program.

A three-state kinetic agent-based model to analyze tax evasion dynamics

NASA Astrophysics Data System (ADS)

Crokidakis, Nuno

2014-11-01

In this work we study the problem of tax evasion on a fully-connected population. For this purpose, we consider that the agents may be in three different states, namely honest tax payers, tax evaders and undecided, that are individuals in an intermediate class among honests and evaders. Every individual can change his/her state following a kinetic exchange opinion dynamics, where the agents interact by pairs with competitive negative (with probability q) and positive (with probability 1-q) couplings, representing agreement/disagreement between pairs of agents. In addition, we consider the punishment rules of the Zaklan econophysics model, for which there is a probability pa of an audit each agent is subject to in every period and a length of time k detected tax evaders remain honest. Our results suggest that below the critical point qc=1/4 of the opinion dynamics the compliance is high, and the punishment rules have a small effect in the population. On the other hand, for q>qc the tax evasion can be considerably reduced by the enforcement mechanism. We also discuss the impact of the presence of the undecided agents in the evolution of the system.

Fragment-based lead generation: identification of seed fragments by a highly efficient fragment screening technology

NASA Astrophysics Data System (ADS)

Neumann, Lars; Ritscher, Allegra; Müller, Gerhard; Hafenbradl, Doris

2009-08-01

For the detection of the precise and unambiguous binding of fragments to a specific binding site on the target protein, we have developed a novel reporter displacement binding assay technology. The application of this technology for the fragment screening as well as the fragment evolution process with a specific modelling based design strategy is demonstrated for inhibitors of the protein kinase p38alpha. In a fragment screening approach seed fragments were identified which were then used to build compounds from the deep-pocket towards the hinge binding area of the protein kinase p38alpha based on a modelling approach. BIRB796 was used as a blueprint for the alignment of the fragments. The fragment evolution of these deep-pocket binding fragments towards the fully optimized inhibitor BIRB796 included the modulation of the residence time as well as the affinity. The goal of our study was to evaluate the robustness and efficiency of our novel fragment screening technology at high fragment concentrations, compare the screening data with biochemical activity data and to demonstrate the evolution of the hit fragments with fast kinetics, into slow kinetic inhibitors in an in silico approach.

Stopping dynamics of ions passing through correlated honeycomb clusters

NASA Astrophysics Data System (ADS)

Balzer, Karsten; Schlünzen, Niclas; Bonitz, Michael

2016-12-01

A combined nonequilibrium Green functions-Ehrenfest dynamics approach is developed that allows for a time-dependent study of the energy loss of a charged particle penetrating a strongly correlated system at zero and finite temperatures. Numerical results are presented for finite inhomogeneous two-dimensional Fermi-Hubbard models, where the many-electron dynamics in the target are treated fully quantum mechanically and the motion of the projectile is treated classically. The simulations are based on the solution of the two-time Dyson (Keldysh-Kadanoff-Baym) equations using the second-order Born, third-order, and T -matrix approximations of the self-energy. As application, we consider protons and helium nuclei with a kinetic energy between 1 and 500 keV/u passing through planar fragments of the two-dimensional honeycomb lattice and, in particular, examine the influence of electron-electron correlations on the energy exchange between projectile and electron system. We investigate the time dependence of the projectile's kinetic energy (stopping power), the electron density, the double occupancy, and the photoemission spectrum. Finally, we show that, for a suitable choice of the Hubbard model parameters, the results for the stopping power are in fair agreement with ab initio simulations for particle irradiation of single-layer graphene.

Near-inertial kinetic energy budget of the mixed layer and shear evolution in the transition layer in the Arabian Sea during the monsoons

NASA Astrophysics Data System (ADS)

Majumder, Sudip; Tandon, Amit; Rudnick, Daniel L.; Thomas Farrar, J.

2015-09-01

We present the horizontal kinetic energy (KE) balance of near-inertial currents in the mixed layer and explain shear evolution in the transition layer using observations from a mooring at 15.26° N in the Arabian Sea during the southwest monsoon. The highly sheared and stratified transition layer at the mixed-layer base varies between 5 m and 35 m and correlates negatively with the wind stress. Results from the mixed layer near-inertial KE (NIKE) balance suggest that wind energy at times can energize the transition layer and at other times is fully utilized within the mixed layer. A simple two layer model is utilized to study the shear evolution in the transition layer and shown to match well with observations. The shear production in this model arises from alignment of wind stress and shear. Although the winds are unidirectional during the monsoon, the shear in the transition layer is predominantly near-inertial. The near-inertial shear bursts in the observations show the same phasing and magnitude at near-inertial frequencies as the wind-shear alignment term.

Comparisons of time explicit hybrid kinetic-fluid code Architect for Plasma Wakefield Acceleration with a full PIC code

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

Massimo, F., E-mail: francesco.massimo@ensta-paristech.fr; Dipartimento SBAI, Università di Roma “La Sapienza“, Via A. Scarpa 14, 00161 Roma; Atzeni, S.

Architect, a time explicit hybrid code designed to perform quick simulations for electron driven plasma wakefield acceleration, is described. In order to obtain beam quality acceptable for applications, control of the beam-plasma-dynamics is necessary. Particle in Cell (PIC) codes represent the state-of-the-art technique to investigate the underlying physics and possible experimental scenarios; however PIC codes demand the necessity of heavy computational resources. Architect code substantially reduces the need for computational resources by using a hybrid approach: relativistic electron bunches are treated kinetically as in a PIC code and the background plasma as a fluid. Cylindrical symmetry is assumed for themore » solution of the electromagnetic fields and fluid equations. In this paper both the underlying algorithms as well as a comparison with a fully three dimensional particle in cell code are reported. The comparison highlights the good agreement between the two models up to the weakly non-linear regimes. In highly non-linear regimes the two models only disagree in a localized region, where the plasma electrons expelled by the bunch close up at the end of the first plasma oscillation.« less

cDF Theory Software for mesoscopic modeling of equilibrium and transport phenomena

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

2015-12-01

The approach is based on classical Density Functional Theory ((cDFT) coupled with the Poisson-Nernst-Planck (PNP) transport kinetics model and quantum mechanical description of short-range interaction and elementary transport processes. The model we proposed and implemented is fully atomistic, taking into account pairwise short-range and manybody long-range interactions. But in contrast to standard molecular dynamics (MD) simulations, where long-range manybody interactions are evaluated as a sum of pair-wise atom-atom contributions, we include them analytically based on wellestablished theories of electrostatic and excluded volume interactions in multicomponent systems. This feature of the PNP/cDFT approach allows us to reach well beyond the length-scalesmore » accessible to MD simulations, while retaining the essential physics of interatomic interactions from first principles and in a parameter-free fashion.« less

A coupled model of transport-reaction-mechanics with trapping. Part I - Small strain analysis

NASA Astrophysics Data System (ADS)

Salvadori, A.; McMeeking, R.; Grazioli, D.; Magri, M.

2018-05-01

A fully coupled model for mass and heat transport, mechanics, and chemical reactions with trapping is proposed. It is rooted in non-equilibrium rational thermodynamics and assumes that displacements and strains are small. Balance laws for mass, linear and angular momentum, energy, and entropy are stated. Thermodynamic restrictions are identified, based on an additive strain decomposition and on the definition of the Helmholtz free energy. Constitutive theory and chemical kinetics are studied in order to finally write the governing equations for the multi-physics problem. The field equations are solved numerically with the finite element method, stemming from a three-fields variational formulation. Three case-studies on vacancies redistribution in metals, hydrogen embrittlement, and the charge-discharge of active particles in Li-ion batteries demonstrate the features and the potential of the proposed model.

Implicit Plasma Kinetic Simulation Using The Jacobian-Free Newton-Krylov Method

NASA Astrophysics Data System (ADS)

Taitano, William; Knoll, Dana; Chacon, Luis

2009-11-01

The use of fully implicit time integration methods in kinetic simulation is still area of algorithmic research. A brute-force approach to simultaneously including the field equations and the particle distribution function would result in an intractable linear algebra problem. A number of algorithms have been put forward which rely on an extrapolation in time. They can be thought of as linearly implicit methods or one-step Newton methods. However, issues related to time accuracy of these methods still remain. We are pursuing a route to implicit plasma kinetic simulation which eliminates extrapolation, eliminates phase-space from the linear algebra problem, and converges the entire nonlinear system within a time step. We accomplish all this using the Jacobian-Free Newton-Krylov algorithm. The original research along these lines considered particle methods to advance the distribution function [1]. In the current research we are advancing the Vlasov equations on a grid. Results will be presented which highlight algorithmic details for single species electrostatic problems and coupled ion-electron electrostatic problems. [4pt] [1] H. J. Kim, L. Chac'on, G. Lapenta, ``Fully implicit particle in cell algorithm,'' 47th Annual Meeting of the Division of Plasma Physics, Oct. 24-28, 2005, Denver, CO

A physical model of the photo- and radiation-induced degradation of ytterbium-doped silica optical fibres

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

Mady, Franck, E-mail: franck.mady@unice.fr; Duchez, Jean-Bernard, E-mail: franck.mady@unice.fr; Mebrouk, Yasmine, E-mail: franck.mady@unice.fr

2014-10-21

We propose a model to describe the photo- or/and the radiation-induced darkening of ytterbium-doped silica optical fibers. This model accounts for the well-established experimental features of photo-darkening. Degradation behaviors predicted for fibers pumped in harsh environments are also fully confirmed by experimental data reported in the work by Duchez et al. (this proceeding), which gives a detailed characterization of the interplay between the effects of the pump and those of a superimposed ionizing irradiation (actual operation conditions in space-based applications for instance). In particular, dependences of the darkening build-up on the pump power, the total ionizing dose and the dosemore » rate are all correctly reproduced. The presented model is a ‘sufficient’ one, including the minimal physical ingredients required to reproduce experimental features. Refinements could be proposed to improve, e.g., quantitative kinetics.« less

Study of High Lift Configurations

NASA Technical Reports Server (NTRS)

Edward, Jack R.; Hassan, Hassan A.

2000-01-01

This project focus on the implementation of the Warren-Hassan transition / turbulence model (Journal of Aircraft, Vol. 35, No. 5) into the NASA code CFL3D and its testing for multi-element airfoils in landing configuration at different angles of attack. The Warren-Hassan transition model solves an evolution equation for a kinetic energy characteristic of non-turbulent fluctuations. This is combined with an empirical estimate of the frequency of the most amplified first-mode disturbance to yield an expression for an eddy viscosity characteristic of non-turbulent fluctuations. This is combined with the k - zeta model for fully turbulent flow to yield a unified approach capable of predicting both transition onset and extent. Blending of the non-turbulent and turbulent components of the model is accomplished by an intermittency function based on the work of Dhawan and Narasimha (Journal of Fluid Mechanics, Vol. 3, No. 4).

Vectorization of copper complexes via biocompatible and biodegradable PLGA nanoparticles.

PubMed

Courant, T; Roullin, V G; Cadiou, C; Delavoie, F; Molinari, M; Andry, M C; Gafa, V; Chuburu, F

2010-04-23

A double emulsion-solvent diffusion approach with fully biocompatible materials was used to encapsulate copper complexes within biodegradable nanoparticles, for which the release kinetics profiles have highlighted their potential use for a prolonged circulating administration.

Fluid preconditioning for Newton–Krylov-based, fully implicit, electrostatic particle-in-cell simulations

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

Chen, G., E-mail: gchen@lanl.gov; Chacón, L.; Leibs, C.A.

2014-02-01

A recent proof-of-principle study proposes an energy- and charge-conserving, nonlinearly implicit electrostatic particle-in-cell (PIC) algorithm in one dimension [9]. The algorithm in the reference employs an unpreconditioned Jacobian-free Newton–Krylov method, which ensures nonlinear convergence at every timestep (resolving the dynamical timescale of interest). Kinetic enslavement, which is one key component of the algorithm, not only enables fully implicit PIC as a practical approach, but also allows preconditioning the kinetic solver with a fluid approximation. This study proposes such a preconditioner, in which the linearized moment equations are closed with moments computed from particles. Effective acceleration of the linear GMRES solvemore » is demonstrated, on both uniform and non-uniform meshes. The algorithm performance is largely insensitive to the electron–ion mass ratio. Numerical experiments are performed on a 1D multi-scale ion acoustic wave test problem.« less

The Thermochronologist's Progress

NASA Astrophysics Data System (ADS)

Zeitler, P. K.

2011-12-01

We owe our current understanding of thermochronology less to a series of revolutionary insights than to a somewhat uneven intellectual pilgrimage that over fifty years has progressed in fits and starts. Though hampered at times by overenthusiasm, oversimplification, and misunderstandings, on balance the field advanced thanks to a blend of curiosity-driven research, tool-building motivated by new ideas about Earth science, and improvements in technology. But now that we've exploited most radiogenic systems and the major minerals that host them, and now that our models can devour CPU time along with the best of them, are we done? Have we reached peak thermochron? The answer of course is no, and papers in this session will demonstrate what new technologies and techniques might have to offer in the coming years. However, I will argue that the discipline as a whole has matured to a point where if thermochronology is to remain a mainstream tool as opposed to a weekend sport, we need to get serious about several challenges. The most fundamental challenge is that current geodynamic models (and even more complex models we can envision coding) have outpaced our meagre stockpile of kinetic calibrations, our understanding of detailed isotope systematics, and our ability to generate data with sufficient throughput. These issues will not be addressed adequately through the business-as-usual approach that brought us to our current knowledge, and some community effort will probably be needed to coordinate the hard work that will be required. But any serious attempt to answer important questions with accurate thermal histories that have low and well-defined uncertainties will require that we actually know the kinetics for the specific samples we are analyzing, that we fully understand scatter in the data, that we work with the large sample numbers that are required for some problems like landscape evolution, and that inversion tools fully explore the important aspects of both the geochemical and geodynamical parameter spaces.

Transient Droplet Behavior and Droplet Breakup during Bulk and Confined Shear Flow in Blends with One Viscoelastic Component: Experiments, Modelling and Simulations

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

Cardinaels, Ruth; Verhulst, Kristof; Moldenaers, Paula

2008-07-07

The transient droplet deformation and droplet orientation after inception of shear, the shape relaxation after cessation of shear and droplet breakup during shear, are microscopically studied, both under bulk and confined conditions. The studied blends contain one viscoelastic Boger fluid phase. A counter rotating setup, based on a Paar Physica MCR300, is used for the droplet visualisation. For bulk shear flow, it is shown that the droplet deformation during startup of shear flow and the shape relaxation after cessation of shear flow are hardly influenced by droplet viscoelasticity, even at moderate to high capillary and Deborah numbers. The effects ofmore » droplet viscoelasticity only become visible close to the critical conditions and a novel break-up mechanism is observed. Matrix viscoelasticity has a more pronounced effect, causing overshoots in the deformation and significantly inhibiting relaxation. However, different applied capillary numbers prior to cessation of shear flow, with the Deborah number fixed, still result in a single master curve for shape retraction, as in fully Newtonian systems. The long tail in the droplet relaxation can be qualitatively described with a phenomenological model for droplet deformation, when using a 5-mode Giesekus model for the fluid rheology. It is found that the shear flow history significantly affects the droplet shape evolution and the breakup process in blends with one viscoelastic component. Confining a droplet between two plates accelerates the droplet deformation kinetics, similar to fully Newtonian systems. However, the increased droplet deformation, due to wall effects, causes the steady state to be reached at a later instant in time. Droplet relaxation is less sensitive to confinement, leading to slower relaxation kinetics only for highly confined droplets. For the blend with a viscoelastic droplet, a non-monotonous trend is found for the critical capillary number as a function of the confinement ratio. Finally, experimental data are compared with 3D simulations, performed with a volume-of-fluid algorithm.« less

Dynamic Kinetic Asymmetric Transformations of β-Stereogenic-α-Keto Esters via Direct Aldolization

PubMed Central

Corbett, Michael T.; Johnson, Jeffrey S.

2014-01-01

Dynamic kinetic asymmetric transformations (DyKAT) of racemic β-bromo-α-keto esters via direct aldolization of nitromethane and acetone provide access to fully substituted α-glycolic acid derivatives bearing a β-stereocenter. The aldol adducts are obtained in excellent yield with high relative and absolute stereocontrol under mild reaction conditions. Mechanistic studies determined that the reactions proceed through a facile catalyst-mediated racemization of the β-bromo-α-keto esters under a DyKAT Type I manifold. PMID:24222195

Online optimal experimental re-design in robotic parallel fed-batch cultivation facilities.

PubMed

Cruz Bournazou, M N; Barz, T; Nickel, D B; Lopez Cárdenas, D C; Glauche, F; Knepper, A; Neubauer, P

2017-03-01

We present an integrated framework for the online optimal experimental re-design applied to parallel nonlinear dynamic processes that aims to precisely estimate the parameter set of macro kinetic growth models with minimal experimental effort. This provides a systematic solution for rapid validation of a specific model to new strains, mutants, or products. In biosciences, this is especially important as model identification is a long and laborious process which is continuing to limit the use of mathematical modeling in this field. The strength of this approach is demonstrated by fitting a macro-kinetic differential equation model for Escherichia coli fed-batch processes after 6 h of cultivation. The system includes two fully-automated liquid handling robots; one containing eight mini-bioreactors and another used for automated at-line analyses, which allows for the immediate use of the available data in the modeling environment. As a result, the experiment can be continually re-designed while the cultivations are running using the information generated by periodical parameter estimations. The advantages of an online re-computation of the optimal experiment are proven by a 50-fold lower average coefficient of variation on the parameter estimates compared to the sequential method (4.83% instead of 235.86%). The success obtained in such a complex system is a further step towards a more efficient computer aided bioprocess development. Biotechnol. Bioeng. 2017;114: 610-619. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

CFD-Modeling of the Multistage Gasifier Capacity of 30 KW

NASA Astrophysics Data System (ADS)

Levin, A. A.; Kozlov, A. N.; Svishchev, D. A.; Donskoy, I. G.

2017-11-01

Single-stage fuel gasification processes have been developed and widely studied in Russia and abroad throughout the 20th century. They are fundamental to the creation and design of modern gas generator equipment. Many studies have shown that single-stage gasification process, have already reached the limit of perfection, which was a significant improvement in their performance becomes impossible and unprofitable. The most fully meet modern technical requirements of multistage gasification technology. In the first step of the process, is organized allothermic biomass pyrolysis using heat of exhaust gas and generating power plant. At this stage, the yield of volatile products (gas and tar) of fuel. In the second step, the layer of fuel is, the tar is decomposed by the action of hot air and steam, steam-gas mixture is formed further reacts with the charcoal in the third process stage. The paper presents a model developed by the authors of the multi-stage gasifier for wood chips. The model is made with the use of CFD-modeling software package (COMSOL Multiphisics). To describe the kinetics of wood pyrolysis and gasification of charcoal studies were carried out using a set of simultaneous thermal analysis. For this complex developed original methods of interpretation of measurements, including methods of technical analysis of fuels and determine the parameters of the detailed kinetics and mechanism of pyrolysis.

Numerical study of shock-induced combustion in methane-air mixtures

NASA Technical Reports Server (NTRS)

Yungster, Shaye; Rabinowitz, Martin J.

1993-01-01

The shock-induced combustion of methane-air mixtures in hypersonic flows is investigated using a new reaction mechanism consisting of 19 reacting species and 52 elementary reactions. This reduced model is derived from a full kinetic mechanism via the Detailed Reduction technique. Zero-dimensional computations of several shock-tube experiments are presented first. The reaction mechanism is then combined with a fully implicit Navier-Stokes computational fluid dynamics (CFD) code to conduct numerical simulations of two-dimensional and axisymmetric shock-induced combustion experiments of stoichiometric methane-air mixtures at a Mach number of M = 6.61. Applications to the ram accelerator concept are also presented.

The effective compliance of spatially evolving planar wing-cracks

NASA Astrophysics Data System (ADS)

Ayyagari, R. S.; Daphalapurkar, N. P.; Ramesh, K. T.

2018-02-01

We present an analytic closed form solution for anisotropic change in compliance due to the spatial evolution of planar wing-cracks in a material subjected to largely compressive loading. A fully three-dimensional anisotropic compliance tensor is defined and evaluated considering the wing-crack mechanism, using a mixed-approach based on kinematic and energetic arguments to derive the coefficients in incremental compliance. Material, kinematic and kinetic parametric influences on the increments in compliance are studied in order to understand their physical implications on material failure. Model verification is carried out through comparisons to experimental uniaxial compression results to showcase the predictive capabilities of the current study.

Comparing the mechanism of water condensation and evaporation in glassy aerosol.

PubMed

Bones, David L; Reid, Jonathan P; Lienhard, Daniel M; Krieger, Ulrich K

2012-07-17

Atmospheric models generally assume that aerosol particles are in equilibrium with the surrounding gas phase. However, recent observations that secondary organic aerosols can exist in a glassy state have highlighted the need to more fully understand the kinetic limitations that may control water partitioning in ambient particles. Here, we explore the influence of slow water diffusion in the condensed aerosol phase on the rates of both condensation and evaporation, demonstrating that significant inhibition in mass transfer occurs for ultraviscous aerosol, not just for glassy aerosol. Using coarse mode (3-4 um radius) ternary sucrose/sodium chloride/aqueous droplets as a proxy for multicomponent ambient aerosol, we demonstrate that the timescale for particle equilibration correlates with bulk viscosity and can be ≫10(3) s. Extrapolation of these timescales to particle sizes in the accumulation mode (e.g., approximately 100 nm) by applying the Stokes-Einstein equation suggests that the kinetic limitations imposed on mass transfer of water by slow bulk phase diffusion must be more fully investigated for atmospheric aerosol. Measurements have been made on particles covering a range in dynamic viscosity from < 0.1 to > 10(13) Pa s. We also retrieve the radial inhomogeneities apparent in particle composition during condensation and evaporation and contrast the dynamics of slow dissolution of a viscous core into a labile shell during condensation with the slow percolation of water during evaporation through a more homogeneous viscous particle bulk.

Field, laboratory and numerical approaches to studying flow through mangrove pneumatophores

NASA Astrophysics Data System (ADS)

Chua, V. P.

2014-12-01

The circulation of water in riverine mangrove swamps is expected to be influenced by mangrove roots, which in turn affect the nutrients, pollutants and sediments transport in these systems. Field studies were carried out in mangrove areas along the coastline of Singapore where Avicennia marina and Sonneratia alba pneumatophore species are found. Geometrical properties, such as height, diameter and spatial density of the mangrove roots were assessed through the use of photogrammetric methods. Samples of these roots were harvested from mangrove swamps and their material properties, such as bending strength and Young's modulus were determined in the laboratory. It was found that the pneumatophores under hydrodynamic loadings in a mangrove environment could be regarded as fairly rigid. Artificial root models of pneumatophores were fabricated from downscaling based on field observations of mangroves. Flume experiments were performed and measurements of mean flow velocities, Reynolds stress and turbulent kinetic energy were made. The boundary layer formed over the vegetation patch is fully developed after x = 6 m with a linear mean velocity profile. High shear stresses and turbulent kinetic energy were observed at the interface between the top portion of the roots and the upper flow. The experimental data was employed to calibrate and validate three-dimensional simulations of flow in pneumatophores. The simulations were performed with the Delft3D-FLOW model, where the vegetation effect is introduced by adding a depth-distributed resistance force and modifying the k-ɛ turbulence model. The model-predicted profiles for mean velocity, turbulent kinetic energy and concentration were compared with experimental data. The model calibration is performed by adjusting the horizontal and vertical eddy viscosities and diffusivities. A skill assessment of the model is performed using statistical measures that include the Pearson correlation coefficient (r), the mean absolute error (MAE), and the root-mean-squared error (RMSE).

Simulations of Hall reconnection in partially ionized plasmas

NASA Astrophysics Data System (ADS)

Innocenti, Maria Elena; Jiang, Wei; Lapenta, Giovanni

2017-04-01

Magnetic reconnection occurs in the Hall, partially ionized regime in environments as diverse as molecular clouds, protostellar disks and regions of the solar chromosphere. While much is known about Hall reconnection in fully ionized plasmas, Hall reconnection in partially ionized plasmas is, in comparison, still relatively unexplored. This notwithstanding the fact that partial ionization is expected to affect fundamental processes in reconnection such as the transition from the slow, fluid to the fast, kinetic regime, the value of the reconnection rate and the dimensions of the diffusion regions [Malyshkin and Zweibel 2011 , Zweibel et al. 2011]. We present here the first, to our knowledge, fully kinetic simulations of Hall reconnection in partially ionized plasmas. The interaction of electrons and ions with the neutral background is realistically modelled via a Monte Carlo plug-in coded into the semi-implicit, fully kinetic code iPic3D [Markidis 2010]. We simulate a plasma with parameters compatible with the MRX experiments illustrated in Zweibel et al. 2011 and Lawrence et al. 2013, to be able to compare our simulation results with actual experiments. The gas and ion temperature is T=3 eV, the ion to electron temperature ratio is Tr=0.44, ion and electron thermal velocities are calculated accordingly resorting to a reduced mass ratio and a reduced value of the speed of light to reduce the computational costs of the simulations. The initial density of the plasma is set at n= 1.1 1014 cm-3 and is then left free to change during the simulation as a result of gas-plasma interaction. A set of simulations with initial ionisation percentage IP= 0.01, 0.1, 0.2, 0.6 is presented and compared with a reference simulation where no background gas is present (full ionization). In this first set of simulations, we assume to be able to externally control the initial relative densities of gas and plasma. Within this parameter range, the ion but not the electron population is heavily affected by collisions with the neutrals. In line with experimental results, we observe reduction of the reconnection rate and no variation of the half-thickness of the ion diffusion region with decreasing IP (increasing gas density). Contrarily to the experiments, we can confidently state that these effects are not influenced by boundary constraints. We then provide an explanation for the behaviour observed.

Kinetic scale structure of low-frequency waves and fluctuations

NASA Astrophysics Data System (ADS)

Lopez Herrera, R. A.; Figueroa-Vinas, A.; Araneda, J. A.; Yoon, P. H.

2017-12-01

The dissipation of solar wind turbulence at kinetic scales is believed to be important for heating the corona and accelerating the wind. Linear Vlasov kinetic theory is a useful tool in identifying various wave modes, including kinetic Alfvén, fast magnetosonic/whistler, ion-acoustic (or kinetic slow mode), and their possible roles in the dissipation. However, kinetic mode structure near the vicinity of ion cyclotron modes is not clearly understood. The present poster aims to further elucidate the structure of these low-frequency waves by introducing discrete particle effects through hybrid simulations and Klimontovich formalism of spontaneous emission theory. The theory and simulation of spontaneously emitted low-frequency fluctuations are employed to identify and distinguish the detailed mode structures associated with ion Bernstein versus quasi modes. The spontaneous emission theory and simulation also confirm the findings of Vlasov theory in that the kinetic Alfvén wave can be defined over a wide range of frequencies, including the proton cyclotron frequency and its harmonics, especially for high beta plasmas. This implies that these low-frequency modes may play predominant roles even in the fully kinetic description of kinetic scale turbulence and dissipation despite the fact that cyclotron harmonic and Bernstein modes may also play important roles in wave-particle interactions.

Particle Acceleration and Heating Processes at the Dayside Magnetopause

NASA Astrophysics Data System (ADS)

Berchem, J.; Lapenta, G.; Richard, R. L.; El-Alaoui, M.; Walker, R. J.; Schriver, D.

2017-12-01

It is well established that electrons and ions are accelerated and heated during magnetic reconnection at the dayside magnetopause. However, a detailed description of the actual physical mechanisms driving these processes and where they are operating is still incomplete. Many basic mechanisms are known to accelerate particles, including resonant wave-particle interactions as well as stochastic, Fermi, and betatron acceleration. In addition, acceleration and heating processes can occur over different scales. We have carried out kinetic simulations to investigate the mechanisms by which electrons and ions are accelerated and heated at the dayside magnetopause. The simulation model uses the results of global magnetohydrodynamic (MHD) simulations to set the initial state and the evolving boundary conditions of fully kinetic implicit particle-in-cell (iPic3D) simulations for different solar wind and interplanetary magnetic field conditions. This approach allows us to include large domains both in space and energy. In particular, some of these regional simulations include both the magnetopause and bow shock in the kinetic domain, encompassing range of particle energies from a few eV in the solar wind to keV in the magnetospheric boundary layer. We analyze the results of the iPic3D simulations by discussing wave spectra and particle velocity distribution functions observed in the different regions of the simulation domain, as well as using large-scale kinetic (LSK) computations to follow particles' time histories. We discuss the relevance of our results by comparing them with local observations by the MMS spacecraft.

Possibilities and limitations of the kinetic plot method in supercritical fluid chromatography.

PubMed

De Pauw, Ruben; Desmet, Gert; Broeckhoven, Ken

2013-08-30

Although supercritical fluid chromatography (SFC) is becoming a technique of increasing importance in the field of analytical chromatography, methods to compare the performance of SFC-columns and separations in an unbiased way are not fully developed. The present study uses mathematical models to investigate the possibilities and limitations of the kinetic plot method in SFC as this easily allows to investigate a wide range of operating pressures, retention and mobile phase conditions. The variable column length (L) kinetic plot method was further investigated in this work. Since the pressure history is identical for each measurement, this method gives the true kinetic performance limit in SFC. The deviations of the traditional way of measuring the performance as a function of flow rate (fixed back pressure and column length) and the isopycnic method with respect to this variable column length method were investigated under a wide range of operational conditions. It is found that using the variable L method, extrapolations towards other pressure drops are not valid in SFC (deviation of ∼15% for extrapolation from 50 to 200bar pressure drop). The isopycnic method provides the best prediction but its use is limited when operating closer towards critical point conditions. When an organic modifier is used, the predictions are improved for both methods with respect to the variable L method (e.g. deviations decreases from 20% to 2% when 20mol% of methanol is added). Copyright © 2013 Elsevier B.V. All rights reserved.

TEMPEST Simulations of the Plasma Transport in a Single-Null Tokamak Geometry

DOE PAGES

X. Q. Xu; Bodi, K.; Cohen, R. H.; ...

2010-05-28

We present edge kinetic ion transport simulations of tokamak plasmas in magnetic divertor geometry using the fully nonlinear (full-f) continuum code TEMPEST. Besides neoclassical transport, a term for divergence of anomalous kinetic radial flux is added to mock up the effect of turbulent transport. In order to study the relative roles of neoclassical and anomalous transport, TEMPEST simulations were carried out for plasma transport and flow dynamics in a single-null tokamak geometry, including the pedestal region that extends across the separatrix into the scrape-off layer and private flux region. In a series of TEMPEST simulations were conducted to investigate themore » transition of midplane pedestal heat flux and flow from the neoclassical to the turbulent limit and the transition of divertor heat flux and flow from the kinetic to the fluid regime via an anomalous transport scan and a density scan. The TEMPEST simulation results demonstrate that turbulent transport (as modelled by large diffusion) plays a similar role to collisional decorrelation of particle orbits and that the large turbulent transport (large diffusion) leads to an apparent Maxwellianization of the particle distribution. Moreover, we show the transition of parallel heat flux and flow at the entrance to the divertor plates from the fluid to the kinetic regime. For an absorbing divertor plate boundary condition, a non-half-Maxwellian is found due to the balance between upstream radial anomalous transport and energetic ion endloss.« less

TEMPEST Simulations of the Plasma Transport in a Single-Null Tokamak Geometry

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

X. Q. Xu; Bodi, K.; Cohen, R. H.

We present edge kinetic ion transport simulations of tokamak plasmas in magnetic divertor geometry using the fully nonlinear (full-f) continuum code TEMPEST. Besides neoclassical transport, a term for divergence of anomalous kinetic radial flux is added to mock up the effect of turbulent transport. In order to study the relative roles of neoclassical and anomalous transport, TEMPEST simulations were carried out for plasma transport and flow dynamics in a single-null tokamak geometry, including the pedestal region that extends across the separatrix into the scrape-off layer and private flux region. In a series of TEMPEST simulations were conducted to investigate themore » transition of midplane pedestal heat flux and flow from the neoclassical to the turbulent limit and the transition of divertor heat flux and flow from the kinetic to the fluid regime via an anomalous transport scan and a density scan. The TEMPEST simulation results demonstrate that turbulent transport (as modelled by large diffusion) plays a similar role to collisional decorrelation of particle orbits and that the large turbulent transport (large diffusion) leads to an apparent Maxwellianization of the particle distribution. Moreover, we show the transition of parallel heat flux and flow at the entrance to the divertor plates from the fluid to the kinetic regime. For an absorbing divertor plate boundary condition, a non-half-Maxwellian is found due to the balance between upstream radial anomalous transport and energetic ion endloss.« less

Efficient Ligation of the Schistosoma Hammerhead Ribozyme †

PubMed Central

Canny, Marella D.; Jucker, Fiona M.; Pardi, Arthur

2011-01-01

The hammerhead ribozyme from Schistosoma mansoni is the best characterized of the natural hammerhead ribozymes. Biophysical, biochemical, and structural studies have shown that the formation of the loop-loop tertiary interaction between stems I and II alters the global folding, cleavage kinetics, and conformation of the catalytic core of this hammerhead, leading to a ribozyme that is readily cleaved under physiological conditions. This study investigates the ligation kinetics and the internal equilibrium between cleavage and ligation for the Schistosoma hammerhead. Single turnover kinetic studies on a construct where the ribozyme cleaves and ligates substrate(s) in trans showed up to 23% ligation when starting from fully cleaved products. This was achieved by a ~2,000-fold increase in the rate of ligation compared to a minimal hammerhead without the loop-loop tertiary interaction, yielding an internal equilibrium that ranges from 2–3 at physiological Mg2+ ion concentrations (0.1 –1 mM). Thus, the natural Schistosoma hammerhead ribozyme is almost as efficient at ligation as it is at cleavage. The results here are consistent with a model where formation of the loop-loop tertiary interaction leads to a higher population of catalytically active molecules, and where formation of this tertiary interaction has a much larger effect on the ligation than the cleavage activity of the Schistosoma hammerhead ribozyme. PMID:17319693

Selective deuteration illuminates the importance of tunneling in the unimolecular decay of Criegee intermediates to hydroxyl radical products

DOE PAGES

Green, Amy M.; Barber, Victoria P.; Fang, Yi; ...

2017-11-06

Ozonolysis of alkenes, an important nonphotolytic source of hydroxyl (OH) radicals in the atmosphere, proceeds through unimolecular decay of Criegee intermediates. Here, we report a large kinetic isotope effect associated with the rate-limiting hydrogen-transfer step that releases OH radicals for a prototypical Criegee intermediate, CH 3CHOO. IR excitation of selectively deuterated syn-CD 3CHOO is shown to result in deuterium atom transfer and release OD radical products. Vibrational activation of syn-CD 3CHOO is coupled with direct time-resolved detection of OD products to measure a 10-fold slower rate of unimolecular decay upon deuteration in the vicinity of the transition state barrier, whichmore » is confirmed by microcanonical statistical theory that incorporates quantum mechanical tunneling. The corresponding kinetic isotope effect of ~10 is attributed primarily to the decreased probability of D-atom vs. H-atom transfer arising from tunneling. Master equation modeling is utilized to compute the thermal unimolecular decay rates for selectively and fully deuterated syn methyl-substituted Criegee intermediates under atmospheric conditions. Lastly, at 298 K (1 atm), tunneling is predicted to enhance the thermal decay rate of syn-CH 3CHOO compared with the deuterated species, giving rise to a significant kinetic isotope effect of ~50.« less

Statistics of Magnetic Reconnection X-Lines in Kinetic Turbulence

NASA Astrophysics Data System (ADS)

Haggerty, C. C.; Parashar, T.; Matthaeus, W. H.; Shay, M. A.; Wan, M.; Servidio, S.; Wu, P.

2016-12-01

In this work we examine the statistics of magnetic reconnection (x-lines) and their associated reconnection rates in intermittent current sheets generated in turbulent plasmas. Although such statistics have been studied previously for fluid simulations (e.g. [1]), they have not yet been generalized to fully kinetic particle-in-cell (PIC) simulations. A significant problem with PIC simulations, however, is electrostatic fluctuations generated due to numerical particle counting statistics. We find that analyzing gradients of the magnetic vector potential from the raw PIC field data identifies numerous artificial (or non-physical) x-points. Using small Orszag-Tang vortex PIC simulations, we analyze x-line identification and show that these artificial x-lines can be removed using sub-Debye length filtering of the data. We examine how turbulent properties such as the magnetic spectrum and scale dependent kurtosis are affected by particle noise and sub-Debye length filtering. We subsequently apply these analysis methods to a large scale kinetic PIC turbulent simulation. Consistent with previous fluid models, we find a range of normalized reconnection rates as large as ½ but with the bulk of the rates being approximately less than to 0.1. [1] Servidio, S., W. H. Matthaeus, M. A. Shay, P. A. Cassak, and P. Dmitruk (2009), Magnetic reconnection and two-dimensional magnetohydrodynamic turbulence, Phys. Rev. Lett., 102, 115003.

Development of a Grid-Based Gyro-Kinetic Simulation Code

NASA Astrophysics Data System (ADS)

Lapillonne, Xavier; Brunetti, Maura; Tran, Trach-Minh; Brunner, Stephan

2006-10-01

A grid-based semi-Lagrangian code using cubic spline interpolation is being developed at CRPP, for solving the electrostatic drift-kinetic equations [M. Brunetti et. al, Comp. Phys. Comm. 163, 1 (2004)] in a cylindrical system. This 4-dim code, CYGNE, is part of a project with long term aim of studying microturbulence in toroidal fusion devices, in the more general frame of gyro-kinetic equations. Towards their non-linear phase, the simulations from this code are subject to significant overshoot problems, reflected by the development of negative value regions of the distribution function, which leads to bad energy conservation. This has motivated the study of alternative schemes. On the one hand, new time integration algorithms are considered in the semi-Lagrangian frame. On the other hand, fully Eulerian schemes, which separate time and space discretisation (method of lines), are investigated. In particular, the Essentially Non Oscillatory (ENO) approach, constructed so as to minimize the overshoot problem, has been considered. All these methods have first been tested in the simpler case of the 2-dim guiding-center model for the Kelvin-Helmholtz instability, which enables to address the specific issue of the E xB drift also met in the more complex gyrokinetic-type equations. Based on these preliminary studies, the most promising methods are being implemented and tested in CYGNE.

Selective deuteration illuminates the importance of tunneling in the unimolecular decay of Criegee intermediates to hydroxyl radical products

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

Green, Amy M.; Barber, Victoria P.; Fang, Yi

Ozonolysis of alkenes, an important nonphotolytic source of hydroxyl (OH) radicals in the atmosphere, proceeds through unimolecular decay of Criegee intermediates. Here, we report a large kinetic isotope effect associated with the rate-limiting hydrogen-transfer step that releases OH radicals for a prototypical Criegee intermediate, CH 3CHOO. IR excitation of selectively deuterated syn-CD 3CHOO is shown to result in deuterium atom transfer and release OD radical products. Vibrational activation of syn-CD 3CHOO is coupled with direct time-resolved detection of OD products to measure a 10-fold slower rate of unimolecular decay upon deuteration in the vicinity of the transition state barrier, whichmore » is confirmed by microcanonical statistical theory that incorporates quantum mechanical tunneling. The corresponding kinetic isotope effect of ~10 is attributed primarily to the decreased probability of D-atom vs. H-atom transfer arising from tunneling. Master equation modeling is utilized to compute the thermal unimolecular decay rates for selectively and fully deuterated syn methyl-substituted Criegee intermediates under atmospheric conditions. Lastly, at 298 K (1 atm), tunneling is predicted to enhance the thermal decay rate of syn-CH 3CHOO compared with the deuterated species, giving rise to a significant kinetic isotope effect of ~50.« less

Selective deuteration illuminates the importance of tunneling in the unimolecular decay of Criegee intermediates to hydroxyl radical products.

PubMed

Green, Amy M; Barber, Victoria P; Fang, Yi; Klippenstein, Stephen J; Lester, Marsha I

2017-11-21

Ozonolysis of alkenes, an important nonphotolytic source of hydroxyl (OH) radicals in the atmosphere, proceeds through unimolecular decay of Criegee intermediates. Here, we report a large kinetic isotope effect associated with the rate-limiting hydrogen-transfer step that releases OH radicals for a prototypical Criegee intermediate, CH 3 CHOO. IR excitation of selectively deuterated syn -CD 3 CHOO is shown to result in deuterium atom transfer and release OD radical products. Vibrational activation of syn -CD 3 CHOO is coupled with direct time-resolved detection of OD products to measure a 10-fold slower rate of unimolecular decay upon deuteration in the vicinity of the transition state barrier, which is confirmed by microcanonical statistical theory that incorporates quantum mechanical tunneling. The corresponding kinetic isotope effect of ∼10 is attributed primarily to the decreased probability of D-atom vs. H-atom transfer arising from tunneling. Master equation modeling is utilized to compute the thermal unimolecular decay rates for selectively and fully deuterated syn methyl-substituted Criegee intermediates under atmospheric conditions. At 298 K (1 atm), tunneling is predicted to enhance the thermal decay rate of syn -CH 3 CHOO compared with the deuterated species, giving rise to a significant kinetic isotope effect of ∼50.

Selective deuteration illuminates the importance of tunneling in the unimolecular decay of Criegee intermediates to hydroxyl radical products

PubMed Central

Green, Amy M.; Barber, Victoria P.; Fang, Yi; Klippenstein, Stephen J.; Lester, Marsha I.

2017-01-01

Ozonolysis of alkenes, an important nonphotolytic source of hydroxyl (OH) radicals in the atmosphere, proceeds through unimolecular decay of Criegee intermediates. Here, we report a large kinetic isotope effect associated with the rate-limiting hydrogen-transfer step that releases OH radicals for a prototypical Criegee intermediate, CH3CHOO. IR excitation of selectively deuterated syn-CD3CHOO is shown to result in deuterium atom transfer and release OD radical products. Vibrational activation of syn-CD3CHOO is coupled with direct time-resolved detection of OD products to measure a 10-fold slower rate of unimolecular decay upon deuteration in the vicinity of the transition state barrier, which is confirmed by microcanonical statistical theory that incorporates quantum mechanical tunneling. The corresponding kinetic isotope effect of ∼10 is attributed primarily to the decreased probability of D-atom vs. H-atom transfer arising from tunneling. Master equation modeling is utilized to compute the thermal unimolecular decay rates for selectively and fully deuterated syn methyl-substituted Criegee intermediates under atmospheric conditions. At 298 K (1 atm), tunneling is predicted to enhance the thermal decay rate of syn-CH3CHOO compared with the deuterated species, giving rise to a significant kinetic isotope effect of ∼50. PMID:29109292

Multiscale simulations of the early stages of the growth of graphene on copper

NASA Astrophysics Data System (ADS)

Gaillard, P.; Chanier, T.; Henrard, L.; Moskovkin, P.; Lucas, S.

2015-07-01

We have performed multiscale simulations of the growth of graphene on defect-free copper (111) in order to model the nucleation and growth of graphene flakes during chemical vapour deposition and potentially guide future experimental work. Basic activation energies for atomic surface diffusion were determined by ab initio calculations. Larger scale growth was obtained within a kinetic Monte Carlo approach (KMC) with parameters based on the ab initio results. The KMC approach counts the first and second neighbours to determine the probability of surface diffusion. We report qualitative results on the size and shape of the graphene islands as a function of deposition flux. The dominance of graphene zigzag edges for low deposition flux, also observed experimentally, is explained by its larger dynamical stability that the present model fully reproduced.

Effect of heating rate and kinetic model selection on activation energy of nonisothermal crystallization of amorphous felodipine.

PubMed

Chattoraj, Sayantan; Bhugra, Chandan; Li, Zheng Jane; Sun, Changquan Calvin

2014-12-01

The nonisothermal crystallization kinetics of amorphous materials is routinely analyzed by statistically fitting the crystallization data to kinetic models. In this work, we systematically evaluate how the model-dependent crystallization kinetics is impacted by variations in the heating rate and the selection of the kinetic model, two key factors that can lead to significant differences in the crystallization activation energy (Ea ) of an amorphous material. Using amorphous felodipine, we show that the Ea decreases with increase in the heating rate, irrespective of the kinetic model evaluated in this work. The model that best describes the crystallization phenomenon cannot be identified readily through the statistical fitting approach because several kinetic models yield comparable R(2) . Here, we propose an alternate paired model-fitting model-free (PMFMF) approach for identifying the most suitable kinetic model, where Ea obtained from model-dependent kinetics is compared with those obtained from model-free kinetics. The most suitable kinetic model is identified as the one that yields Ea values comparable with the model-free kinetics. Through this PMFMF approach, nucleation and growth is identified as the main mechanism that controls the crystallization kinetics of felodipine. Using this PMFMF approach, we further demonstrate that crystallization mechanism from amorphous phase varies with heating rate. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

Comparison of multi-fluid moment models with particle-in-cell simulations of collisionless magnetic reconnection

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

Wang, Liang, E-mail: liang.wang@unh.edu; Germaschewski, K.; Hakim, Ammar H.

2015-01-15

We introduce an extensible multi-fluid moment model in the context of collisionless magnetic reconnection. This model evolves full Maxwell equations and simultaneously moments of the Vlasov-Maxwell equation for each species in the plasma. Effects like electron inertia and pressure gradient are self-consistently embedded in the resulting multi-fluid moment equations, without the need to explicitly solving a generalized Ohm's law. Two limits of the multi-fluid moment model are discussed, namely, the five-moment limit that evolves a scalar pressures for each species and the ten-moment limit that evolves the full anisotropic, non-gyrotropic pressure tensor for each species. We first demonstrate analytically andmore » numerically that the five-moment model reduces to the widely used Hall magnetohydrodynamics (Hall MHD) model under the assumptions of vanishing electron inertia, infinite speed of light, and quasi-neutrality. Then, we compare ten-moment and fully kinetic particle-in-cell (PIC) simulations of a large scale Harris sheet reconnection problem, where the ten-moment equations are closed with a local linear collisionless approximation for the heat flux. The ten-moment simulation gives reasonable agreement with the PIC results regarding the structures and magnitudes of the electron flows, the polarities and magnitudes of elements of the electron pressure tensor, and the decomposition of the generalized Ohm's law. Possible ways to improve the simple local closure towards a nonlocal fully three-dimensional closure are also discussed.« less

Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics.

PubMed

Marquez-Lago, Tatiana T; Burrage, Kevin

2007-09-14

In cell biology, cell signaling pathway problems are often tackled with deterministic temporal models, well mixed stochastic simulators, and/or hybrid methods. But, in fact, three dimensional stochastic spatial modeling of reactions happening inside the cell is needed in order to fully understand these cell signaling pathways. This is because noise effects, low molecular concentrations, and spatial heterogeneity can all affect the cellular dynamics. However, there are ways in which important effects can be accounted without going to the extent of using highly resolved spatial simulators (such as single-particle software), hence reducing the overall computation time significantly. We present a new coarse grained modified version of the next subvolume method that allows the user to consider both diffusion and reaction events in relatively long simulation time spans as compared with the original method and other commonly used fully stochastic computational methods. Benchmarking of the simulation algorithm was performed through comparison with the next subvolume method and well mixed models (MATLAB), as well as stochastic particle reaction and transport simulations (CHEMCELL, Sandia National Laboratories). Additionally, we construct a model based on a set of chemical reactions in the epidermal growth factor receptor pathway. For this particular application and a bistable chemical system example, we analyze and outline the advantages of our presented binomial tau-leap spatial stochastic simulation algorithm, in terms of efficiency and accuracy, in scenarios of both molecular homogeneity and heterogeneity.

2D Implosion Simulations with a Kinetic Particle Code

NASA Astrophysics Data System (ADS)

Sagert, Irina; Even, Wesley; Strother, Terrance

2017-10-01

Many problems in laboratory and plasma physics are subject to flows that move between the continuum and the kinetic regime. We discuss two-dimensional (2D) implosion simulations that were performed using a Monte Carlo kinetic particle code. The application of kinetic transport theory is motivated, in part, by the occurrence of non-equilibrium effects in inertial confinement fusion (ICF) capsule implosions, which cannot be fully captured by hydrodynamics simulations. Kinetic methods, on the other hand, are able to describe both, continuum and rarefied flows. We perform simple 2D disk implosion simulations using one particle species and compare the results to simulations with the hydrodynamics code RAGE. The impact of the particle mean-free-path on the implosion is also explored. In a second study, we focus on the formation of fluid instabilities from induced perturbations. I.S. acknowledges support through the Director's fellowship from Los Alamos National Laboratory. This research used resources provided by the LANL Institutional Computing Program.

Modeling of thermal degradation kinetics of the C-glucosyl xanthone mangiferin in an aqueous model solution as a function of pH and temperature and protective effect of honeybush extract matrix.

PubMed

Beelders, Theresa; de Beer, Dalene; Kidd, Martin; Joubert, Elizabeth

2018-01-01

Mangiferin, a C-glucosyl xanthone, abundant in mango and honeybush, is increasingly targeted for its bioactive properties and thus to enhance functional properties of food. The thermal degradation kinetics of mangiferin at pH3, 4, 5, 6 and 7 were each modeled at five temperatures ranging between 60 and 140°C. First-order reaction models were fitted to the data using non-linear regression to determine the reaction rate constant at each pH-temperature combination. The reaction rate constant increased with increasing temperature and pH. Comparison of the reaction rate constants at 100°C revealed an exponential relationship between the reaction rate constant and pH. The data for each pH were also modeled with the Arrhenius equation using non-linear and linear regression to determine the activation energy and pre-exponential factor. Activation energies decreased slightly with increasing pH. Finally, a multi-linear model taking into account both temperature and pH was developed for mangiferin degradation. Sterilization (121°C for 4min) of honeybush extracts dissolved at pH4, 5 and 7 did not cause noticeable degradation of mangiferin, although the multi-linear model predicted 34% degradation at pH7. The extract matrix is postulated to exert a protective effect as changes in potential precursor content could not fully explain the stability of mangiferin. Copyright © 2017 Elsevier Ltd. All rights reserved.

Space debris characterization in support of a satellite breakup model

NASA Technical Reports Server (NTRS)

Fortson, Bryan H.; Winter, James E.; Allahdadi, Firooz A.

1992-01-01

The Space Kinetic Impact and Debris Branch began an ambitious program to construct a fully analytical model of the breakup of a satellite under hypervelocity impact. In order to provide empirical data with which to substantiate the model, debris from hypervelocity experiments conducted in a controlled laboratory environment were characterized to provide information of its mass, velocity, and ballistic coefficient distributions. Data on the debris were collected in one master data file, and a simple FORTRAN program allows users to describe the debris from any subset of these experiments that may be of interest to them. A statistical analysis was performed, allowing users to determine the precision of the velocity measurements for the data. Attempts are being made to include and correlate other laboratory data, as well as those data obtained from the explosion or collision of spacecraft in low earth orbit.

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

Gorelenkov, N. N.; Heidbrink, W. W.; Kramer, G. J.

The redistribution and potential loss of energetic particles due to MHD modes can limit the performance of fusion plasmas by reducing the plasma heating rate. In this work, we present validation studies of the 1.5D critical gradient model (CGM) for Alfvén eigenmode (AE) induced EP transport in NSTX and DIII-D neutral beam heated plasmas. In previous comparisons with a single DIII-D L-mode case, the CGM model was found to be responsible for 75% of measured AE induced neutron deficit [1]. A fully kinetic HINST is used to compute mode stability for the non-perturbative version of CGM (or nCGM). We have found that AEs show strong local instability drive up tomore » $$\\gamma /\\omega \\sim 20\\%$$ violating assumptions of perturbative approaches used in NOVA-K code. Lastly, we demonstrate that both models agree with each other and both underestimate the neutron deficit measured in DIII-D shot by approximately a factor of 2.« less

The Stimulated Glycolytic Pathway Is Able to Maintain ATP Levels and Kinetic Patterns of Bovine Epididymal Sperm Subjected to Mitochondrial Uncoupling.

PubMed

Losano, João D A; Padín, Juan Fernando; Méndez-López, Iago; Angrimani, Daniel S R; García, Antonio G; Barnabe, Valquiria H; Nichi, Marcilio

2017-01-01

Studies have reported the importance of mitochondria in sperm functionality. However, for some species, the glycolytic pathway appears to be as important as oxidative phosphorylation in ATP synthesis and sperm kinetics. These mechanisms have not been fully elucidated for bovine spermatozoa. Therefore, the aim of this study was to evaluate the role of mitochondria and the glycolytic pathway in ATP synthesis, sperm movement patterns, and oxidative homeostasis of epididymal spermatozoa in bovine specimens. We observed that mitochondrial uncoupling with protonophores significantly reduced ATP levels. However, these levels were reestablished after stimulation of the glycolytic pathway. We verified the same pattern of results for sperm kinetic variables and the production of reactive oxygen species (ROS). Thus, we suggest that, after its appropriate stimulation, the glycolytic pathway is capable of maintaining ATP levels, sperm kinetic patterns, and oxidative balance of bovine epididymal spermatozoa submitted to mitochondrial uncoupling.

Bifunctional anion-exchange resins with improved selectivity and exchange kinetics

DOEpatents

Alexandratos, Spiro D.; Brown, Gilbert M.; Bonnesen, Peter V.; Moyer, Bruce A.

2000-01-01

Disclosed herein are a class of anion exchange resins containing two different exchange sites with improved selectivity and sorptive capability for chemical species in solution, such as heptavalent technetium (as pertechnetate anion, TcO.sub.4.sup.-). The resins are prepared by first reacting haloalkylated crosslinked copolymer beads with a large tertiary amine in a solvent in which the resin beads can swell, followed by reaction with a second, smaller, tertiary amine to more fully complete the functionalization of the resin. The resins have enhanced selectivity, capacity, and exchange kinetics.

How many molecules are required to measure a cyclic voltammogram?

NASA Astrophysics Data System (ADS)

Cutress, Ian J.; Compton, Richard G.

2011-05-01

The stochastic limit at which fully-reversible cyclic voltammetry can accurately be measured is investigated. Specifically, Monte Carlo GPU simulation is used to study low concentration cyclic voltammetry at a microdisk electrode over a range of scan rates and concentrations, and the results compared to the statistical limit as predicted by finite difference simulation based on Fick's Laws of Diffusion. Both Butler-Volmer and Marcus-Hush electrode kinetics are considered, simulated via random-walk methods, and shown to give identical results in the fast kinetic limit.

Temperature for a dynamic spin ensemble

NASA Astrophysics Data System (ADS)

Ma, Pui-Wai; Dudarev, S. L.; Semenov, A. A.; Woo, C. H.

2010-09-01

In molecular dynamics simulations, temperature is evaluated, via the equipartition principle, by computing the mean kinetic energy of atoms. There is no similar recipe yet for evaluating temperature of a dynamic system of interacting spins. By solving semiclassical Langevin spin-dynamics equations, and applying the fluctuation-dissipation theorem, we derive an equation for the temperature of a spin ensemble, expressed in terms of dynamic spin variables. The fact that definitions for the kinetic and spin temperatures are fully consistent is illustrated using large-scale spin dynamics and spin-lattice dynamics simulations.

Dynamic kinetic asymmetric cross-benzoin additions of β-stereogenic α-keto esters.

PubMed

Goodman, C Guy; Johnson, Jeffrey S

2014-10-22

The dynamic kinetic resolution of β-halo α-keto esters via an asymmetric cross-benzoin reaction is described. A chiral N-heterocyclic carbene catalyzes the umpolung addition of aldehydes to racemic α-keto esters. The resulting fully substituted β-halo glycolic ester products are obtained with high levels of enantio- and diastereocontrol. The high chemoselectivity observed is a result of greater electrophilicity of the α-keto ester toward the Breslow intermediate. The reaction products are shown to undergo highly diastereoselective substrate-controlled reduction to give highly functionalized stereotriads.

Dynamic Kinetic Asymmetric Cross-Benzoin Additions of β-Stereogenic α-Keto Esters

PubMed Central

2015-01-01

The dynamic kinetic resolution of β-halo α-keto esters via an asymmetric cross-benzoin reaction is described. A chiral N-heterocyclic carbene catalyzes the umpolung addition of aldehydes to racemic α-keto esters. The resulting fully substituted β-halo glycolic ester products are obtained with high levels of enantio- and diastereocontrol. The high chemoselectivity observed is a result of greater electrophilicity of the α-keto ester toward the Breslow intermediate. The reaction products are shown to undergo highly diastereoselective substrate-controlled reduction to give highly functionalized stereotriads. PMID:25299730

Factor analysis for delineation of organ structures, creation of in- and output functions, and standardization of multicenter kinetic modeling

NASA Astrophysics Data System (ADS)

Schiepers, Christiaan; Hoh, Carl K.; Dahlbom, Magnus; Wu, Hsiao-Ming; Phelps, Michael E.

1999-05-01

PET imaging can quantify metabolic processes in-vivo; this requires the measurement of an input function which is invasive and labor intensive. A non-invasive, semi-automated, image based method of input function generation would be efficient, patient friendly, and allow quantitative PET to be applied routinely. A fully automated procedure would be ideal for studies across institutions. Factor analysis (FA) was applied as processing tool for definition of temporally changing structures in the field of view. FA has been proposed earlier, but the perceived mathematical difficulty has prevented widespread use. FA was utilized to delineate structures and extract blood and tissue time-activity-curves (TACs). These TACs were used as input and output functions for tracer kinetic modeling, the results of which were compared with those from an input function obtained with serial blood sampling. Dynamic image data of myocardial perfusion studies with N-13 ammonia, O-15 water, or Rb-82, cancer studies with F-18 FDG, and skeletal studies with F-18 fluoride were evaluated. Correlation coefficients of kinetic parameters obtained with factor and plasma input functions were high. Linear regression usually furnished a slope near unity. Processing time was 7 min/patient on an UltraSPARC. Conclusion: FA can non-invasively generate input functions from image data eliminating the need for blood sampling. Output (tissue) functions can be simultaneously generated. The method is simple, requires no sophisticated operator interaction and has little inter-operator variability. FA is well suited for studies across institutions and standardized evaluations.

A probabilistic approach to identify putative drug targets in biochemical networks.

PubMed

Murabito, Ettore; Smallbone, Kieran; Swinton, Jonathan; Westerhoff, Hans V; Steuer, Ralf

2011-06-06

Network-based drug design holds great promise in clinical research as a way to overcome the limitations of traditional approaches in the development of drugs with high efficacy and low toxicity. This novel strategy aims to study how a biochemical network as a whole, rather than its individual components, responds to specific perturbations in different physiological conditions. Proteins exerting little control over normal cells and larger control over altered cells may be considered as good candidates for drug targets. The application of network-based drug design would greatly benefit from using an explicit computational model describing the dynamics of the system under investigation. However, creating a fully characterized kinetic model is not an easy task, even for relatively small networks, as it is still significantly hampered by the lack of data about kinetic mechanisms and parameters values. Here, we propose a Monte Carlo approach to identify the differences between flux control profiles of a metabolic network in different physiological states, when information about the kinetics of the system is partially or totally missing. Based on experimentally accessible information on metabolic phenotypes, we develop a novel method to determine probabilistic differences in the flux control coefficients between the two observable phenotypes. Knowledge of how differences in flux control are distributed among the different enzymatic steps is exploited to identify points of fragility in one of the phenotypes. Using a prototypical cancerous phenotype as an example, we demonstrate how our approach can assist researchers in developing compounds with high efficacy and low toxicity. © 2010 The Royal Society

Fully kinetic simulations of magnetic reconnection in partially ionised gases

NASA Astrophysics Data System (ADS)

Innocenti, M. E.; Jiang, W.; Lapenta, G.; Markidis, S.

2016-12-01

Magnetic reconnection has been explored for decades as a way to convert magnetic energy into kinetic energy and heat and to accelerate particles in environments as different as the solar surface, planetary magnetospheres, the solar wind, accretion disks, laboratory plasmas. When studying reconnection via simulations, it is usually assumed that the plasma is fully ionised, as it is indeed the case in many of the above-mentioned cases. There are, however, exceptions, the most notable being the lower solar atmosphere. Small ionisation fractions are registered also in the warm neutral interstellar medium, in dense interstellar clouds, in protostellar and protoplanetary accreditation disks, in tokamak edge plasmas and in ad-hoc laboratory experiments [1]. We study here how magnetic reconnection is modified by the presence of a neutral background, i.e. when the majority of the gas is not ionised. The ionised plasma is simulated with the fully kinetic Particle-In-Cell (PIC) code iPic3D [2]. Collisions with the neutral background are introduced via a Monte Carlo plug-in. The standard Monte Carlo procedure [3] is employed to account for elastic, excitation and ionization electron-neutral collisions, as well as for elastic scattering and charge exchange ion-neutral collisions. Collisions with the background introduce resistivity in an otherwise collisionless plasma and modifications of the particle distribution functions: particles (and ions at a faster rate) tend to thermalise to the background. To pinpoint the consequences of this, we compare reconnection simulations with and without background. References [1] E E Lawrence et al. Physical review letters, 110(1):015001, 2013. [2] S Markidis et al. Mathematics and Computers in Simulation, 80(7):1509-1519, 2010. [3] K Nanbu. IEEE Transactions on plasma science, 28(3):971-990, 2000.

Modelling Of Flotation Processes By Classical Mathematical Methods - A Review

NASA Astrophysics Data System (ADS)

Jovanović, Ivana; Miljanović, Igor

2015-12-01

Flotation process modelling is not a simple task, mostly because of the process complexity, i.e. the presence of a large number of variables that (to a lesser or a greater extent) affect the final outcome of the mineral particles separation based on the differences in their surface properties. The attempts toward the development of the quantitative predictive model that would fully describe the operation of an industrial flotation plant started in the middle of past century and it lasts to this day. This paper gives a review of published research activities directed toward the development of flotation models based on the classical mathematical rules. The description and systematization of classical flotation models were performed according to the available references, with emphasize exclusively given to the flotation process modelling, regardless of the model application in a certain control system. In accordance with the contemporary considerations, models were classified as the empirical, probabilistic, kinetic and population balance types. Each model type is presented through the aspects of flotation modelling at the macro and micro process levels.

Kinetic Scale Structure of Low-frequency Waves and Fluctuations

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

López, Rodrigo A.; Yoon, Peter H.; Viñas, Adolfo F.

The dissipation of solar wind turbulence at kinetic scales is believed to be important for the heating of the corona and for accelerating the wind. The linear Vlasov kinetic theory is a useful tool for identifying various wave modes, including kinetic Alfvén, fast magnetosonic/whistler, and ion-acoustic (or kinetic slow), and their possible roles in the dissipation. However, the kinetic mode structure in the vicinity of ion-cyclotron modes is not clearly understood. The present paper aims to further elucidate the structure of these low-frequency waves by introducing discrete particle effects through hybrid simulations and Klimontovich formalism of spontaneous emission theory. Themore » theory and simulation of spontaneously emitted low-frequency fluctuations are employed to identify and distinguish the detailed mode structures associated with ion-Bernstein modes versus quasi-modes. The spontaneous emission theory and simulation also confirm the findings of the Vlasov theory in that the kinetic Alfvén waves can be defined over a wide range of frequencies, including the proton cyclotron frequency and its harmonics, especially for high-beta plasmas. This implies that these low-frequency modes may play predominant roles even in the fully kinetic description of kinetic scale turbulence and dissipation despite the fact that cyclotron harmonic and Bernstein modes may also play important roles in wave–particle interactions.« less

On the relativistic large-angle electron collision operator for runaway avalanches in plasmas

NASA Astrophysics Data System (ADS)

Embréus, O.; Stahl, A.; Fülöp, T.

2018-02-01

Large-angle Coulomb collisions lead to an avalanching generation of runaway electrons in a plasma. We present the first fully conservative large-angle collision operator, derived from the relativistic Boltzmann operator. The relation to previous models for large-angle collisions is investigated, and their validity assessed. We present a form of the generalized collision operator which is suitable for implementation in a numerical kinetic equation solver, and demonstrate the effect on the runaway-electron growth rate. Finally we consider the reverse avalanche effect, where runaways are slowed down by large-angle collisions, and show that the choice of operator is important if the electric field is close to the avalanche threshold.

Numerical solutions of nonlinear STIFF initial value problems by perturbed functional iterations

NASA Technical Reports Server (NTRS)

Dey, S. K.

1982-01-01

Numerical solution of nonlinear stiff initial value problems by a perturbed functional iterative scheme is discussed. The algorithm does not fully linearize the system and requires only the diagonal terms of the Jacobian. Some examples related to chemical kinetics are presented.

A fully-implicit Particle-In-Cell Monte Carlo Collision code for the simulation of inductively coupled plasmas

NASA Astrophysics Data System (ADS)

Mattei, S.; Nishida, K.; Onai, M.; Lettry, J.; Tran, M. Q.; Hatayama, A.

2017-12-01

We present a fully-implicit electromagnetic Particle-In-Cell Monte Carlo collision code, called NINJA, written for the simulation of inductively coupled plasmas. NINJA employs a kinetic enslaved Jacobian-Free Newton Krylov method to solve self-consistently the interaction between the electromagnetic field generated by the radio-frequency coil and the plasma response. The simulated plasma includes a kinetic description of charged and neutral species as well as the collision processes between them. The algorithm allows simulations with cell sizes much larger than the Debye length and time steps in excess of the Courant-Friedrichs-Lewy condition whilst preserving the conservation of the total energy. The code is applied to the simulation of the plasma discharge of the Linac4 H- ion source at CERN. Simulation results of plasma density, temperature and EEDF are discussed and compared with optical emission spectroscopy measurements. A systematic study of the energy conservation as a function of the numerical parameters is presented.

Adsorption Behavior, Thermodynamics, and Kinetics of the Methanol Decomposition Reaction on defective graphene-supported Pt13

NASA Astrophysics Data System (ADS)

Gasper, Raymond; Ramasubramaniam, Ashwin

Defective graphene has been shown experimentally to be an excellent support for transition-metal electrocatalysts in direct methanol fuel cells. Prior computational modeling has shown that the improved catalytic activity of graphene-supported metal clusters is in part due to increased resistance to catalyst sintering and CO poisoning, but the increased reaction rate for the methanol decomposition reaction (MDR) is not yet fully explained. Using DFT, we investigate the adsorption of MDR intermediates and reaction thermodynamics on defective graphene-supported Pt13 nanoclusters with realistic, low-symmetry morphologies. We find that the support-induced shifts in Pt13 electronic structure correlate well with a rigid shift in adsorption of MDR intermediates, and that adsorption energy scaling relationships perform well on the low-symmetry surface. We investigate the reaction kinetics and thermodynamics, including testing the effectiveness of scaling relationships for predicting reaction barriers on the nanoclusters. Using these fundamental data, we perform microkinetic modeling to quantify the effect of the support on the MDR, and to understand how the support influences surface coverages, CO poisoning, and the relationships between reaction pathways. Funded by U.S. Department of Energy under Award Number DE-SC0010610. Computational resources were provided by National Energy Research Scientific Computing Center.

Nanoscale wear as a stress-assisted chemical reaction

NASA Astrophysics Data System (ADS)

Jacobs, Tevis D. B.; Carpick, Robert W.

2013-02-01

Wear of sliding contacts leads to energy dissipation and device failure, resulting in massive economic and environmental costs. Typically, wear phenomena are described empirically, because physical and chemical interactions at sliding interfaces are not fully understood at any length scale. Fundamental insights from individual nanoscale contacts are crucial for understanding wear at larger length scales, and to enable reliable nanoscale devices, manufacturing and microscopy. Observable nanoscale wear mechanisms include fracture and plastic deformation, but recent experiments and models propose another mechanism: wear via atom-by-atom removal (`atomic attrition'), which can be modelled using stress-assisted chemical reaction kinetics. Experimental evidence for this has so far been inferential. Here, we quantitatively measure the wear of silicon--a material relevant to small-scale devices--using in situ transmission electron microscopy. We resolve worn volumes as small as 25 +/- 5 nm3, a factor of 103 lower than is achievable using alternative techniques. Wear of silicon against diamond is consistent with atomic attrition, and inconsistent with fracture or plastic deformation, as shown using direct imaging. The rate of atom removal depends exponentially on stress in the contact, as predicted by chemical rate kinetics. Measured activation parameters are consistent with an atom-by-atom process. These results, by direct observation, establish atomic attrition as the primary wear mechanism of silicon in vacuum at low loads.

Low Mach-number collisionless electrostatic shocks and associated ion acceleration

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

Pusztai, Istvan; TenBarge, Jason; Csapó, Aletta N.

The existence and properties of low Mach-number (M >~ 1) electrostatic collisionless shocks are investigated with a semi-analytical solution for the shock structure. We show that the properties of the shock obtained in the semi-analytical model can be well reproduced in fully kinetic Eulerian Vlasov-Poisson simulations, where the shock is generated by the decay of an initial density discontinuity. By using this semi-analytical model, we also study the effect of electron-to-ion temperature ratio and presence of impurities on both the maximum shock potential and Mach number. We find that even a small amount of impurities can influence the shock propertiesmore » significantly, including the reflected light ion fraction, which can change several orders of magnitude. Electrostatic shocks in heavy ion plasmas reflect most of the hydrogen impurity ions.« less

Low Mach-number collisionless electrostatic shocks and associated ion acceleration

DOE PAGES

Pusztai, Istvan; TenBarge, Jason; Csapó, Aletta N.; ...

2017-12-19

The existence and properties of low Mach-number (M >~ 1) electrostatic collisionless shocks are investigated with a semi-analytical solution for the shock structure. We show that the properties of the shock obtained in the semi-analytical model can be well reproduced in fully kinetic Eulerian Vlasov-Poisson simulations, where the shock is generated by the decay of an initial density discontinuity. By using this semi-analytical model, we also study the effect of electron-to-ion temperature ratio and presence of impurities on both the maximum shock potential and Mach number. We find that even a small amount of impurities can influence the shock propertiesmore » significantly, including the reflected light ion fraction, which can change several orders of magnitude. Electrostatic shocks in heavy ion plasmas reflect most of the hydrogen impurity ions.« less

From Glass Formation to Icosahedral Ordering by Curving Three-Dimensional Space.

PubMed

Turci, Francesco; Tarjus, Gilles; Royall, C Patrick

2017-05-26

Geometric frustration describes the inability of a local molecular arrangement, such as icosahedra found in metallic glasses and in model atomic glass formers, to tile space. Local icosahedral order, however, is strongly frustrated in Euclidean space, which obscures any causal relationship with the observed dynamical slowdown. Here we relieve frustration in a model glass-forming liquid by curving three-dimensional space onto the surface of a 4-dimensional hypersphere. For sufficient curvature, frustration vanishes and the liquid "freezes" in a fully icosahedral structure via a sharp "transition." Frustration increases upon reducing the curvature, and the transition to the icosahedral state smoothens while glassy dynamics emerge. Decreasing the curvature leads to decoupling between dynamical and structural length scales and the decrease of kinetic fragility. This sheds light on the observed glass-forming behavior in Euclidean space.

Effect of increased surface hydrophobicity via drug conjugation on the clearance of inhaled PEGylated polylysine dendrimers.

PubMed

Haque, Shadabul; McLeod, Victoria M; Jones, Seth; Fung, Sandy; Whittaker, Michael; McIntosh, Michelle; Pouton, Colin; Owen, David J; Porter, Christopher J H; Kaminskas, Lisa M

2017-10-01

PEGylated polylysine dendrimers are attractive and well tolerated inhalable drug delivery platforms that have the potential to control the release, absorption kinetics and lung retention time of conjugated drugs. The clinical application of these systems though, would likely require partial substitution of surface PEG groups with drug molecules that are anticipated to alter their lung clearance kinetics and clearance pathways. In the current study, we therefore evaluated the impact of increased surface hydrophobicity via substitution of 50% surface PEG groups with a model hydrophobic drug (α-carboxyl OtButylated methotrexate) on the lung clearance of a Generation 5 PEGylated polylysine dendrimer in rats. PEG substitution with OtBu-methotrexate accelerated lung clearance of the dendrimer by increasing polylysine scaffold catabolism, improving systemic absorption of the intact dendrimer and low molecular weight products of scaffold catabolism, and enhancing mucociliary clearance. These results suggest that the conjugation of hydrophobic drug on the surface of a PEGylated dendrimer is likely to accelerate lung clearance when compared to a fully PEGylated dendrimer. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Oil shale powders and their interactions with ciprofloxacin, ofloxacin, and oxytetracycline antibiotics.

PubMed

Gouza, Asmae; Saoiabi, Sanaa; El Karbane, Miloud; Masse, Sylvie; Laurent, Guillaume; Rami, Ahmed; Saoiabi, Ahmed; Laghzizil, Abdelaziz; Coradin, Thibaud

2017-11-01

The interaction of oil shale, as a widespread sedimentary rock, with common antibiotics ofloxacine, oxytetracycline, and ciprofloxacine was studied. The selected Moroccan deposit and its thermally treated forms were fully characterized from a chemical and structural point of view, indicating the prevalence of quartz as a mineral component together with aluminum- and iron-rich phase that are converted into Al-doped iron oxide phases upon heating. The presence of 4 wt% organics was also detected, which was removed at 550 °C without significant loss of specific surface area. The pseudo-second-order kinetic model and Langmuir equation were found the most adequate to reproduce the kinetics and isothermal sorption experiments. These analyses enlighten the contribution of the organic matter on antibiotic retention as well as the key role of hydrophobic interactions on the molecule-mineral surface interactions. Our results emphasize the possible contribution of raw oil shale in the accumulation of antibiotics in soils and suggest that thermally treated oil shell powders can constitute cheap mineral sorbents for environmental cleaning.

Arbitrary-order Hilbert Spectral Analysis and Intermittency in Solar Wind Density Fluctuations

NASA Astrophysics Data System (ADS)

Carbone, Francesco; Sorriso-Valvo, Luca; Alberti, Tommaso; Lepreti, Fabio; Chen, Christopher H. K.; Němeček, Zdenek; Šafránková, Jana

2018-05-01

The properties of inertial- and kinetic-range solar wind turbulence have been investigated with the arbitrary-order Hilbert spectral analysis method, applied to high-resolution density measurements. Due to the small sample size and to the presence of strong nonstationary behavior and large-scale structures, the classical analysis in terms of structure functions may prove to be unsuccessful in detecting the power-law behavior in the inertial range, and may underestimate the scaling exponents. However, the Hilbert spectral method provides an optimal estimation of the scaling exponents, which have been found to be close to those for velocity fluctuations in fully developed hydrodynamic turbulence. At smaller scales, below the proton gyroscale, the system loses its intermittent multiscaling properties and converges to a monofractal process. The resulting scaling exponents, obtained at small scales, are in good agreement with those of classical fractional Brownian motion, indicating a long-term memory in the process, and the absence of correlations around the spectral-break scale. These results provide important constraints on models of kinetic-range turbulence in the solar wind.

Surface Interaction Kinetics of GaAs (100) Surfaces Under Electron Cyclotron Resonance Nitrogen Plasma Exposure

NASA Astrophysics Data System (ADS)

O'Steen, M. L.; Hauenstein, R. J.; Bandić, Z. Z.; Feenstra, R. M.; Hwang, S. J.; McGill, T. C.

1996-03-01

GaN is a robust semiconducting material offering a large, direct bandgap appropriate for use in blue-green to UV light emitting diodes and laser diodes. Attainment of device quality GaN has been difficult due to the lack of substrate materials that are suitably matched to the unusually small lattice parameter of GaN. To better control heteroepitaxial growth quality, a fundamental study of the initial stages of GaN growth by Electron Cyclotron Resonance Nitrogen Plasma-Assisted Molecular Beam Epitaxy (ECR-MBE) has been performed. The effect of an ECR Nitrogen plasma on a GaAs (100) surface is examined through time resolved reflection high energy electron diffraction, high resolution x-ray diffraction, and cross-sectional scanning tunneling microscopy. Fully commensurate GaN_yAs_1-y/GaAs heterostructures involving ultrathin GaN_yAs_1-y layers are obtained, and thermally activated microscopic growth processes are identified and quantitatively characterized through the aid of a specially developed kinetic model. The implications for ECR-MBE growth of GaN/GaAs mutilayers is discussed.

Direct parametric reconstruction in dynamic PET myocardial perfusion imaging: in vivo studies.

PubMed

Petibon, Yoann; Rakvongthai, Yothin; El Fakhri, Georges; Ouyang, Jinsong

2017-05-07

Dynamic PET myocardial perfusion imaging (MPI) used in conjunction with tracer kinetic modeling enables the quantification of absolute myocardial blood flow (MBF). However, MBF maps computed using the traditional indirect method (i.e. post-reconstruction voxel-wise fitting of kinetic model to PET time-activity-curves-TACs) suffer from poor signal-to-noise ratio (SNR). Direct reconstruction of kinetic parameters from raw PET projection data has been shown to offer parametric images with higher SNR compared to the indirect method. The aim of this study was to extend and evaluate the performance of a direct parametric reconstruction method using in vivo dynamic PET MPI data for the purpose of quantifying MBF. Dynamic PET MPI studies were performed on two healthy pigs using a Siemens Biograph mMR scanner. List-mode PET data for each animal were acquired following a bolus injection of ~7-8 mCi of 18 F-flurpiridaz, a myocardial perfusion agent. Fully-3D dynamic PET sinograms were obtained by sorting the coincidence events into 16 temporal frames covering ~5 min after radiotracer administration. Additionally, eight independent noise realizations of both scans-each containing 1/8th of the total number of events-were generated from the original list-mode data. Dynamic sinograms were then used to compute parametric maps using the conventional indirect method and the proposed direct method. For both methods, a one-tissue compartment model accounting for spillover from the left and right ventricle blood-pools was used to describe the kinetics of 18 F-flurpiridaz. An image-derived arterial input function obtained from a TAC taken in the left ventricle cavity was used for tracer kinetic analysis. For the indirect method, frame-by-frame images were estimated using two fully-3D reconstruction techniques: the standard ordered subset expectation maximization (OSEM) reconstruction algorithm on one side, and the one-step late maximum a posteriori (OSL-MAP) algorithm on the other side, which incorporates a quadratic penalty function. The parametric images were then calculated using voxel-wise weighted least-square fitting of the reconstructed myocardial PET TACs. For the direct method, parametric images were estimated directly from the dynamic PET sinograms using a maximum a posteriori (MAP) parametric reconstruction algorithm which optimizes an objective function comprised of the Poisson log-likelihood term, the kinetic model and a quadratic penalty function. Maximization of the objective function with respect to each set of parameters was achieved using a preconditioned conjugate gradient algorithm with a specifically developed pre-conditioner. The performance of the direct method was evaluated by comparing voxel- and segment-wise estimates of [Formula: see text], the tracer transport rate (ml · min -1 · ml -1 ), to those obtained using the indirect method applied to both OSEM and OSL-MAP dynamic reconstructions. The proposed direct reconstruction method produced [Formula: see text] maps with visibly lower noise than the indirect method based on OSEM and OSL-MAP reconstructions. At normal count levels, the direct method was shown to outperform the indirect method based on OSL-MAP in the sense that at matched level of bias, reduced regional noise levels were obtained. At lower count levels, the direct method produced [Formula: see text] estimates with significantly lower standard deviation across noise realizations than the indirect method based on OSL-MAP at matched bias level. In all cases, the direct method yielded lower noise and standard deviation than the indirect method based on OSEM. Overall, the proposed direct reconstruction offered a better bias-variance tradeoff than the indirect method applied to either OSEM and OSL-MAP. Direct parametric reconstruction as applied to in vivo dynamic PET MPI data is therefore a promising method for producing MBF maps with lower variance.

Direct parametric reconstruction in dynamic PET myocardial perfusion imaging: in-vivo studies

PubMed Central

Petibon, Yoann; Rakvongthai, Yothin; Fakhri, Georges El; Ouyang, Jinsong

2017-01-01

Dynamic PET myocardial perfusion imaging (MPI) used in conjunction with tracer kinetic modeling enables the quantification of absolute myocardial blood flow (MBF). However, MBF maps computed using the traditional indirect method (i.e. post-reconstruction voxel-wise fitting of kinetic model to PET time-activity-curves -TACs) suffer from poor signal-to-noise ratio (SNR). Direct reconstruction of kinetic parameters from raw PET projection data has been shown to offer parametric images with higher SNR compared to the indirect method. The aim of this study was to extend and evaluate the performance of a direct parametric reconstruction method using in-vivo dynamic PET MPI data for the purpose of quantifying MBF. Dynamic PET MPI studies were performed on two healthy pigs using a Siemens Biograph mMR scanner. List-mode PET data for each animal were acquired following a bolus injection of ~7-8 mCi of 18F-flurpiridaz, a myocardial perfusion agent. Fully-3D dynamic PET sinograms were obtained by sorting the coincidence events into 16 temporal frames covering ~5 min after radiotracer administration. Additionally, eight independent noise realizations of both scans - each containing 1/8th of the total number of events - were generated from the original list-mode data. Dynamic sinograms were then used to compute parametric maps using the conventional indirect method and the proposed direct method. For both methods, a one-tissue compartment model accounting for spillover from the left and right ventricle blood-pools was used to describe the kinetics of 18F-flurpiridaz. An image-derived arterial input function obtained from a TAC taken in the left ventricle cavity was used for tracer kinetic analysis. For the indirect method, frame-by-frame images were estimated using two fully-3D reconstruction techniques: the standard Ordered Subset Expectation Maximization (OSEM) reconstruction algorithm on one side, and the One-Step Late Maximum a Posteriori (OSL-MAP) algorithm on the other side, which incorporates a quadratic penalty function. The parametric images were then calculated using voxel-wise weighted least-square fitting of the reconstructed myocardial PET TACs. For the direct method, parametric images were estimated directly from the dynamic PET sinograms using a maximum a posteriori (MAP) parametric reconstruction algorithm which optimizes an objective function comprised of the Poisson log-likelihood term, the kinetic model and a quadratic penalty function. Maximization of the objective function with respect to each set of parameters was achieved using a preconditioned conjugate gradient algorithm with a specifically developed pre-conditioner. The performance of the direct method was evaluated by comparing voxel- and segment-wise estimates of K1, the tracer transport rate (mL.min−1.mL−1), to those obtained using the indirect method applied to both OSEM and OSL-MAP dynamic reconstructions. The proposed direct reconstruction method produced K1 maps with visibly lower noise than the indirect method based on OSEM and OSL-MAP reconstructions. At normal count levels, the direct method was shown to outperform the indirect method based on OSL-MAP in the sense that at matched level of bias, reduced regional noise levels were obtained. At lower count levels, the direct method produced K1 estimates with significantly lower standard deviation across noise realizations than the indirect method based on OSL-MAP at matched bias level. In all cases, the direct method yielded lower noise and standard deviation than the indirect method based on OSEM. Overall, the proposed direct reconstruction offered a better bias-variance tradeoff than the indirect method applied to either OSEM and OSL-MAP. Direct parametric reconstruction as applied to in-vivo dynamic PET MPI data is therefore a promising method for producing MBF maps with lower variance. PMID:28379843

Direct parametric reconstruction in dynamic PET myocardial perfusion imaging: in vivo studies

NASA Astrophysics Data System (ADS)

Petibon, Yoann; Rakvongthai, Yothin; El Fakhri, Georges; Ouyang, Jinsong

2017-05-01

Dynamic PET myocardial perfusion imaging (MPI) used in conjunction with tracer kinetic modeling enables the quantification of absolute myocardial blood flow (MBF). However, MBF maps computed using the traditional indirect method (i.e. post-reconstruction voxel-wise fitting of kinetic model to PET time-activity-curves-TACs) suffer from poor signal-to-noise ratio (SNR). Direct reconstruction of kinetic parameters from raw PET projection data has been shown to offer parametric images with higher SNR compared to the indirect method. The aim of this study was to extend and evaluate the performance of a direct parametric reconstruction method using in vivo dynamic PET MPI data for the purpose of quantifying MBF. Dynamic PET MPI studies were performed on two healthy pigs using a Siemens Biograph mMR scanner. List-mode PET data for each animal were acquired following a bolus injection of ~7-8 mCi of 18F-flurpiridaz, a myocardial perfusion agent. Fully-3D dynamic PET sinograms were obtained by sorting the coincidence events into 16 temporal frames covering ~5 min after radiotracer administration. Additionally, eight independent noise realizations of both scans—each containing 1/8th of the total number of events—were generated from the original list-mode data. Dynamic sinograms were then used to compute parametric maps using the conventional indirect method and the proposed direct method. For both methods, a one-tissue compartment model accounting for spillover from the left and right ventricle blood-pools was used to describe the kinetics of 18F-flurpiridaz. An image-derived arterial input function obtained from a TAC taken in the left ventricle cavity was used for tracer kinetic analysis. For the indirect method, frame-by-frame images were estimated using two fully-3D reconstruction techniques: the standard ordered subset expectation maximization (OSEM) reconstruction algorithm on one side, and the one-step late maximum a posteriori (OSL-MAP) algorithm on the other side, which incorporates a quadratic penalty function. The parametric images were then calculated using voxel-wise weighted least-square fitting of the reconstructed myocardial PET TACs. For the direct method, parametric images were estimated directly from the dynamic PET sinograms using a maximum a posteriori (MAP) parametric reconstruction algorithm which optimizes an objective function comprised of the Poisson log-likelihood term, the kinetic model and a quadratic penalty function. Maximization of the objective function with respect to each set of parameters was achieved using a preconditioned conjugate gradient algorithm with a specifically developed pre-conditioner. The performance of the direct method was evaluated by comparing voxel- and segment-wise estimates of {{K}1} , the tracer transport rate (ml · min-1 · ml-1), to those obtained using the indirect method applied to both OSEM and OSL-MAP dynamic reconstructions. The proposed direct reconstruction method produced {{K}1} maps with visibly lower noise than the indirect method based on OSEM and OSL-MAP reconstructions. At normal count levels, the direct method was shown to outperform the indirect method based on OSL-MAP in the sense that at matched level of bias, reduced regional noise levels were obtained. At lower count levels, the direct method produced {{K}1} estimates with significantly lower standard deviation across noise realizations than the indirect method based on OSL-MAP at matched bias level. In all cases, the direct method yielded lower noise and standard deviation than the indirect method based on OSEM. Overall, the proposed direct reconstruction offered a better bias-variance tradeoff than the indirect method applied to either OSEM and OSL-MAP. Direct parametric reconstruction as applied to in vivo dynamic PET MPI data is therefore a promising method for producing MBF maps with lower variance.

Fully dynamical simulation of central nuclear collisions.

PubMed

van der Schee, Wilke; Romatschke, Paul; Pratt, Scott

2013-11-27

We present a fully dynamical simulation of central nuclear collisions around midrapidity at LHC energies. Unlike previous treatments, we simulate all phases of the collision, including the equilibration of the system. For the simulation, we use numerical relativity solutions to anti-de Sitter space/conformal field theory for the preequilibrium stage, viscous hydrodynamics for the plasma equilibrium stage, and kinetic theory for the low-density hadronic stage. Our preequilibrium stage provides initial conditions for hydrodynamics, resulting in sizable radial flow. The resulting light particle spectra reproduce the measurements from the ALICE experiment at all transverse momenta.

Rate Kinetics and Molecular Dynamics of the Structural Transitions in Amyloidogenic Proteins

NASA Astrophysics Data System (ADS)

Steckmann, Timothy M.

Amyloid fibril aggregation is associated with several horrific diseases such as Alzheimer's, Creutzfeld-Jacob, diabetes, Parkinson's and others. The process of amyloid aggregation involves forming myriad different metastable intermediate aggregates. Amyloid fibrils are composed of proteins that originate in an innocuous alpha-helix or random-coil structure. The alpha-helices convert their structure to beta-strands that aggregate into beta-sheets, and then into protofibrils, and ultimately into fully formed amyloid fibrils. On the basis of experimental data, I have developed a mathematical model for the kinetics of the reaction pathways and determined rate parameters for peptide secondary structural conversion and aggregation during the entire fibrillogenesis process from random coil to fibrils, including the molecular species that accelerate the conversions. The specific steps of the model and the rate constants that are determined by fitting to experimental data provide insight on the molecular species involved in the fibril formation process. To better understand the molecular basis of the protein structural transitions and aggregation, I report on molecular dynamics (MD) computational studies on the formation of amyloid protofibrillar structures in the small model protein ccbeta, which undergoes many of the structural transitions of the larger, naturally occurring amyloid forming proteins. Two different structural transition processes involving hydrogen bonds are observed for aggregation into fibrils: the breaking of intrachain hydrogen bonds to allow beta-hairpin proteins to straighten, and the subsequent formation of interchain hydrogen bonds during aggregation into amyloid fibrils. For my MD simulations, I found that the temperature dependence of these two different structural transition processes results in the existence of a temperature window that the ccbeta protein experiences during the process of forming protofibrillar structures. Both the mathematical modeling of the kinetics and the MD simulations show that molecular structural heterogeneity is a major factor in the process. The MD simulations also show that intrachain and interchain hydrogen bonds breaking and forming is strongly correlated to the process of amyloid formation.

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.

Theoretical Basis for Estimated Test Times and Conditions for Drop Tower and Space-Based Droplet Burning Experiments With Methanol and N-Heptane

NASA Technical Reports Server (NTRS)

Marchese, Anthony J.; Dryer, Fredrick L.; Choi, Mun Y.

1994-01-01

In order to develop an extensive envelope of test conditions for NASA's space-based Droplet Combustion Experiment (DCE) as well those droplet experiments which can be performed using a drop tower, the transient vaporization and combustion of methanol and n-heptane droplets were simulated using a recently developed fully time-dependent, spherically symmetric droplet combustion model. The transient vaporization of methanol and n-heptane was modeled to characterize the instantaneous gas phase composition surrounding the droplet prior to the introduction of an ignition source. The results for methanol/air showed that the entire gas phase surrounding a 2 mm methanol droplet deployed in zero-g .quickly falls outside the lean flammability limit. The gas phase surrounding an identically-sized n-heptane droplet, on the other hand, remains flammable. The combustion of methanol was then modeled considering a detailed gas phase chemical kinetic mechanism (168 steps, 26 species) and the effect of the dissolution of flame-generated water into the liquid droplet. These results were used to determine the critical ignition diameter required to achieve quasi-steady droplet combustion in a given oxidizing environment. For droplet diameters greater than the critical ignition diameter, the model predicted a finite diameter at which the flame would extinguish. These extinction diameters were found to vary significantly with initial droplet diameter. This phenomenon appears to be unique to the transient heat transfer, mass transfer and chemical kinetics of the system and thus has not been reported elsewhere to date. The extinction diameter was also shown to vary significantly with the liquid phase Lewis number since the amount of water present in the droplet at extinction is largely governed by the rate at which water is transported into the droplet via mass diffusion. Finally, the numerical results for n-heptane combustion were obtained using both 2 step and 96 step semi-emperical chemical kinetic mechanisms. Neither mechanism exhibited the variation of extinction diameter with initial diameter.

Wave Attenuation and Gas Exchange Velocity in Marginal Sea Ice Zone

NASA Astrophysics Data System (ADS)

Bigdeli, A.; Hara, T.; Loose, B.; Nguyen, A. T.

2018-03-01

The gas transfer velocity in marginal sea ice zones exerts a strong control on the input of anthropogenic gases into the ocean interior. In this study, a sea state-dependent gas exchange parametric model is developed based on the turbulent kinetic energy dissipation rate. The model is tuned to match the conventional gas exchange parametrization in fetch-unlimited, fully developed seas. Next, fetch limitation is introduced in the model and results are compared to fetch limited experiments in lakes, showing that the model captures the effects of finite fetch on gas exchange with good fidelity. Having validated the results in fetch limited waters such as lakes, the model is next applied in sea ice zones using an empirical relation between the sea ice cover and the effective fetch, while accounting for the sea ice motion effect that is unique to sea ice zones. The model results compare favorably with the available field measurements. Applying this parametric model to a regional Arctic numerical model, it is shown that, under the present conditions, gas flux into the Arctic Ocean may be overestimated by 10% if a conventional parameterization is used.

Presenting a new kinetic model for methanol to light olefins reactions over a hierarchical SAPO-34 catalyst using the Langmuir-Hinshelwood-Hougen-Watson mechanism

NASA Astrophysics Data System (ADS)

Javad Azarhoosh, Mohammad; Halladj, Rouein; Askari, Sima

2017-10-01

In this study, a new kinetic model for methanol to light olefins (MTO) reactions over a hierarchical SAPO-34 catalyst using the Langmuir-Hinshelwood-Hougen-Watson (LHHW) mechanism was presented and the kinetic parameters was obtained using a genetic algorithm (GA) and genetic programming (GP). Several kinetic models for the MTO reactions have been presented. However, due to the complexity of the reactions, most reactions are considered lumped and elementary, which cannot be deemed a completely accurate kinetic model of the process. Therefore, in this study, the LHHW mechanism is presented as kinetic models of MTO reactions. Because of the non-linearity of the kinetic models and existence of many local optimal points, evolutionary algorithms (GA and GP) are used in this study to estimate the kinetic parameters in the rate equations. Via the simultaneous connection of the code related to modelling the reactor and the GA and GP codes in the MATLAB R2013a software, optimization of the kinetic models parameters was performed such that the least difference between the results from the kinetic models and experiential results was obtained and the best kinetic parameters of MTO process reactions were achieved. A comparison of the results from the model with experiential results showed that the present model possesses good accuracy.

Kinetic memory based on the enzyme-limited competition.

PubMed

Hatakeyama, Tetsuhiro S; Kaneko, Kunihiko

2014-08-01

Cellular memory, which allows cells to retain information from their environment, is important for a variety of cellular functions, such as adaptation to external stimuli, cell differentiation, and synaptic plasticity. Although posttranslational modifications have received much attention as a source of cellular memory, the mechanisms directing such alterations have not been fully uncovered. It may be possible to embed memory in multiple stable states in dynamical systems governing modifications. However, several experiments on modifications of proteins suggest long-term relaxation depending on experienced external conditions, without explicit switches over multi-stable states. As an alternative to a multistability memory scheme, we propose "kinetic memory" for epigenetic cellular memory, in which memory is stored as a slow-relaxation process far from a stable fixed state. Information from previous environmental exposure is retained as the long-term maintenance of a cellular state, rather than switches over fixed states. To demonstrate this kinetic memory, we study several models in which multimeric proteins undergo catalytic modifications (e.g., phosphorylation and methylation), and find that a slow relaxation process of the modification state, logarithmic in time, appears when the concentration of a catalyst (enzyme) involved in the modification reactions is lower than that of the substrates. Sharp transitions from a normal fast-relaxation phase into this slow-relaxation phase are revealed, and explained by enzyme-limited competition among modification reactions. The slow-relaxation process is confirmed by simulations of several models of catalytic reactions of protein modifications, and it enables the memorization of external stimuli, as its time course depends crucially on the history of the stimuli. This kinetic memory provides novel insight into a broad class of cellular memory and functions. In particular, applications for long-term potentiation are discussed, including dynamic modifications of calcium-calmodulin kinase II and cAMP-response element-binding protein essential for synaptic plasticity.

Stellar Mixing: I. Formalism

NASA Technical Reports Server (NTRS)

Canuto, V .M.

2011-01-01

In this paper we use the Reynolds stress models (RSM) to derive algebraic expressions for the following variables: a) heat fluxes; b) J.l fluxes; and c) momentum fluxes. These relations, which are fully 3D, include: 1) stable and unstable stratification, represented by the Brunt-Vaislila frequency, N(exp 2) =-g/H(sub p_(del - del(sub ad))(1 - RI(sub mu)); 2) double diffusion, salt-fingers, and semi-convection, represented by the density ratio R(sub mu) = del(sub mu)/(del - del(sub ad)); 3) shear (differential rotation), represented by the mean squared shear Sigma(exp 2) or by the Richardson number, Ri =N(exp 2)Sigma(exp -2); 4) radiative losses represented by a Peclet number, Pe; 5) a complete analytical solution of the ID version of the model. In general, the model requires the solution of two differential equations for the eddy kinetic energy K and its rate of dissipation, epsilon. In the local and stationary cases, when production equals dissipation, the model equations are all algebraic.

Validating predictive models for fast ion profile relaxation in burning plasmas

DOE PAGES

Gorelenkov, N. N.; Heidbrink, W. W.; Kramer, G. J.; ...

2016-07-22

The redistribution and potential loss of energetic particles due to MHD modes can limit the performance of fusion plasmas by reducing the plasma heating rate. In this work, we present validation studies of the 1.5D critical gradient model (CGM) for Alfvén eigenmode (AE) induced EP transport in NSTX and DIII-D neutral beam heated plasmas. In previous comparisons with a single DIII-D L-mode case, the CGM model was found to be responsible for 75% of measured AE induced neutron deficit [1]. A fully kinetic HINST is used to compute mode stability for the non-perturbative version of CGM (or nCGM). We have found that AEs show strong local instability drive up tomore » $$\\gamma /\\omega \\sim 20\\%$$ violating assumptions of perturbative approaches used in NOVA-K code. Lastly, we demonstrate that both models agree with each other and both underestimate the neutron deficit measured in DIII-D shot by approximately a factor of 2.« less

On the modeling of wave-enhanced turbulence nearshore

NASA Astrophysics Data System (ADS)

Moghimi, Saeed; Thomson, Jim; Özkan-Haller, Tuba; Umlauf, Lars; Zippel, Seth

2016-07-01

A high resolution k-ω two-equation turbulence closure model, including surface wave forcing was employed to fully resolve turbulence dissipation rate profiles close to the ocean surface. Model results were compared with observations from Surface Wave Instrument Floats with Tracking (SWIFTs) in the nearshore region at New River Inlet, North Carolina USA, in June 2012. A sensitivity analysis for different physical parameters and wave and turbulence formulations was performed. The flux of turbulent kinetic energy (TKE) prescribed by wave dissipation from a numerical wave model was compared with the conventional prescription using the wind friction velocity. A surface roughness length of 0.6 times the significant wave height was proposed, and the flux of TKE was applied at a distance below the mean sea surface that is half of this roughness length. The wave enhanced layer had a total depth that is almost three times the significant wave height. In this layer the non-dimensionalized Terray scaling with power of - 1.8 (instead of - 2) was applicable.

Phosphoryl transfer is not rate-limiting for the ROCK I-catalyzed kinase reaction.

PubMed

Futer, Olga; Saadat, Ahmad R; Doran, John D; Raybuck, Scott A; Pazhanisamy, S

2006-06-27

Rho-associated coiled-coil kinase, ROCK, is implicated in Rho-mediated cell adhesion and smooth muscle contraction. Animal models suggest that the inhibition of ROCK can ameliorate conditions, such as vasospasm, hypertension, and inflammation. As part of our effort to design novel inhibitors of ROCK, we investigated the kinetic mechanism of ROCK I. Steady-state bisubstrate kinetics, inhibition kinetics, isotope partition analysis, viscosity effects, and presteady-state kinetics were used to explore the kinetic mechanism. Plots of reciprocals of initial rates obtained in the presence of nonhydrolyzable ATP analogues and the small molecule inhibitor of ROCK, Y-27632, against the reciprocals of the peptide concentrations yielded parallel lines (uncompetitive pattern). This pattern is indicative of an ordered binding mechanism, with the peptide adding first. The staurosporine analogue K252a, however, gave a noncompetitive pattern. When a pulse of (33)P-gamma-ATP mixed with ROCK was chased with excess unlabeled ATP and peptide, 0.66 enzyme equivalent of (33)P-phosphate was incorporated into the product in the first turnover. The presence of ATPase activity coupled with the isotope partition data is a clear evidence for the existence of a viable [E-ATP] complex in the kinase reaction and implicates a random binding mechanism. The k(cat)/K(m) parameters were fully sensitive to viscosity (viscosity effects of 1.4 +/- 0.2 and 0.9 +/- 0.3 for ATP and peptide 5, respectively), and therefore, the barriers to dissociation of either substrate are higher than the barrier for the phosphoryl transfer step. As a consequence, not all the binding steps are at fast equilibrium. The observation of a burst in presteady-state kinetics (k(b) = 10.2 +/- 2.1 s(-)(1)) and the viscosity effect on k(cat) of 1.3 +/- 0.2 characterize the phosphoryl transfer step to be fast and the release of product and/or the enzyme isomerization step accompanying it as rate-limiting at V(max) conditions. From the multiple kinetic studies, most of the rate constants for the individual steps were either evaluated or estimated.

Large eddy simulation study of the kinetic energy entrainment by energetic turbulent flow structures in large wind farms

NASA Astrophysics Data System (ADS)

VerHulst, Claire; Meneveau, Charles

2014-02-01

In this study, we address the question of how kinetic energy is entrained into large wind turbine arrays and, in particular, how large-scale flow structures contribute to such entrainment. Previous research has shown this entrainment to be an important limiting factor in the performance of very large arrays where the flow becomes fully developed and there is a balance between the forcing of the atmospheric boundary layer and the resistance of the wind turbines. Given the high Reynolds numbers and domain sizes on the order of kilometers, we rely on wall-modeled large eddy simulation (LES) to simulate turbulent flow within the wind farm. Three-dimensional proper orthogonal decomposition (POD) analysis is then used to identify the most energetic flow structures present in the LES data. We quantify the contribution of each POD mode to the kinetic energy entrainment and its dependence on the layout of the wind turbine array. The primary large-scale structures are found to be streamwise, counter-rotating vortices located above the height of the wind turbines. While the flow is periodic, the geometry is not invariant to all horizontal translations due to the presence of the wind turbines and thus POD modes need not be Fourier modes. Differences of the obtained modes with Fourier modes are documented. Some of the modes are responsible for a large fraction of the kinetic energy flux to the wind turbine region. Surprisingly, more flow structures (POD modes) are needed to capture at least 40% of the turbulent kinetic energy, for which the POD analysis is optimal, than are needed to capture at least 40% of the kinetic energy flux to the turbines. For comparison, we consider the cases of aligned and staggered wind turbine arrays in a neutral atmospheric boundary layer as well as a reference case without wind turbines. While the general characteristics of the flow structures are robust, the net kinetic energy entrainment to the turbines depends on the presence and relative arrangement of the wind turbines in the domain.

Kinetics of silicide formation over a wide range of heating rates spanning six orders of magnitude

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

Molina-Ruiz, Manel; Lopeandía, Aitor F.; Gonzalez-Silveira, Marta

Kinetic processes involving intermediate phase formation are often assumed to follow an Arrhenius temperature dependence. This behavior is usually inferred from limited data over narrow temperature intervals, where the exponential dependence is generally fully satisfied. However, direct evidence over wide temperature intervals is experimentally challenging and data are scarce. Here, we report a study of silicide formation between a 12 nm film of palladium and 15 nm of amorphous silicon in a wide range of heating rates, spanning six orders of magnitude, from 0.1 to 10{sup 5 }K/s, or equivalently more than 300 K of variation in reaction temperature. The calorimetric traces exhibit severalmore » distinct exothermic events related to interdiffusion, nucleation of Pd{sub 2}Si, crystallization of amorphous silicon, and vertical growth of Pd{sub 2}Si. Interestingly, the thickness of the initial nucleation layer depends on the heating rate revealing enhanced mass diffusion at the fastest heating rates during the initial stages of the reaction. In spite of this, the formation of the silicide strictly follows an Arrhenius temperature dependence over the whole temperature interval explored. A kinetic model is used to fit the calorimetric data over the complete heating rate range. Calorimetry is complemented by structural analysis through transmission electron microscopy and both standard and in-situ synchrotron X-ray diffraction.« less

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.

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models.

PubMed

Cotten, Cameron; Reed, Jennifer L

2013-01-30

Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets.

Mechanistic analysis of multi-omics datasets to generate kinetic parameters for constraint-based metabolic models

PubMed Central

2013-01-01

Background Constraint-based modeling uses mass balances, flux capacity, and reaction directionality constraints to predict fluxes through metabolism. Although transcriptional regulation and thermodynamic constraints have been integrated into constraint-based modeling, kinetic rate laws have not been extensively used. Results In this study, an in vivo kinetic parameter estimation problem was formulated and solved using multi-omic data sets for Escherichia coli. To narrow the confidence intervals for kinetic parameters, a series of kinetic model simplifications were made, resulting in fewer kinetic parameters than the full kinetic model. These new parameter values are able to account for flux and concentration data from 20 different experimental conditions used in our training dataset. Concentration estimates from the simplified kinetic model were within one standard deviation for 92.7% of the 790 experimental measurements in the training set. Gibbs free energy changes of reaction were calculated to identify reactions that were often operating close to or far from equilibrium. In addition, enzymes whose activities were positively or negatively influenced by metabolite concentrations were also identified. The kinetic model was then used to calculate the maximum and minimum possible flux values for individual reactions from independent metabolite and enzyme concentration data that were not used to estimate parameter values. Incorporating these kinetically-derived flux limits into the constraint-based metabolic model improved predictions for uptake and secretion rates and intracellular fluxes in constraint-based models of central metabolism. Conclusions This study has produced a method for in vivo kinetic parameter estimation and identified strategies and outcomes of kinetic model simplification. We also have illustrated how kinetic constraints can be used to improve constraint-based model predictions for intracellular fluxes and biomass yield and identify potential metabolic limitations through the integrated analysis of multi-omics datasets. PMID:23360254

How to model supernovae in simulations of star and galaxy formation

NASA Astrophysics Data System (ADS)

Hopkins, Philip F.; Wetzel, Andrew; Kereš, Dušan; Faucher-Giguère, Claude-André; Quataert, Eliot; Boylan-Kolchin, Michael; Murray, Norman; Hayward, Christopher C.; El-Badry, Kareem

2018-06-01

We study the implementation of mechanical feedback from supernovae (SNe) and stellar mass loss in galaxy simulations, within the Feedback In Realistic Environments (FIRE) project. We present the FIRE-2 algorithm for coupling mechanical feedback, which can be applied to any hydrodynamics method (e.g. fixed-grid, moving-mesh, and mesh-less methods), and black hole as well as stellar feedback. This algorithm ensures manifest conservation of mass, energy, and momentum, and avoids imprinting `preferred directions' on the ejecta. We show that it is critical to incorporate both momentum and thermal energy of mechanical ejecta in a self-consistent manner, accounting for SNe cooling radii when they are not resolved. Using idealized simulations of single SN explosions, we show that the FIRE-2 algorithm, independent of resolution, reproduces converged solutions in both energy and momentum. In contrast, common `fully thermal' (energy-dump) or `fully kinetic' (particle-kicking) schemes in the literature depend strongly on resolution: when applied at mass resolution ≳100 M⊙, they diverge by orders of magnitude from the converged solution. In galaxy-formation simulations, this divergence leads to orders-of-magnitude differences in galaxy properties, unless those models are adjusted in a resolution-dependent way. We show that all models that individually time-resolve SNe converge to the FIRE-2 solution at sufficiently high resolution (<100 M⊙). However, in both idealized single-SN simulations and cosmological galaxy-formation simulations, the FIRE-2 algorithm converges much faster than other sub-grid models without re-tuning parameters.

Modelling the competition between photo-darkening and photo-bleaching effects in high-power ytterbium-doped fibre amplifiers

NASA Astrophysics Data System (ADS)

Jolly, A.; Vinçont, C.; Pierre, Ch.; Boullet, J.

2017-08-01

We propose an innovative, fully space-time model to take into account the seed-dependent nature of ageing penalties in high-power ytterbium-doped fibre amplifiers. Ageing is shown to be based on the on-going competition between photo-darkening and photo-bleaching phenomena. Our approach is based on the natural interplay between the excited states of co-existing ytterbium pairs and colour centres in highly doped fibres, in the presence of thermal coupling between the closely spaced excited states. As initiated from IR photons, the excitation of colour centres up to the UV band is supposed to be governed by multi-photon absorption. The interactions of interest in the kinetics of photo-bleaching then take the form of highly efficient charge transfers, which imply the reduction of some fraction of the basically trivalent ions to their divalent state. Due to the activation of ytterbium pairs by means of energy transfer up-conversion, these interactions get more and more effective at elevated operating powers. Computational results using these principles actually help to fit our experimental data regarding seeding effects, as well as fully generic trends already evidenced in the literature. This gives a fine demonstration for the need to discriminate co-active pump and signal contributions. Our self-consistent, still simplified model then consists of a valuable tool to help for a deeper understanding of the ageing issues. Furthermore, considering higher-order ytterbium aggregates, this should open new routes towards more comprehensive models.

A quantification method for numerical dissipation in quasi-DNS and under-resolved DNS, and effects of numerical dissipation in quasi-DNS and under-resolved DNS of turbulent channel flows

NASA Astrophysics Data System (ADS)

Komen, E. M. J.; Camilo, L. H.; Shams, A.; Geurts, B. J.; Koren, B.

2017-09-01

LES for industrial applications with complex geometries is mostly characterised by: a) a finite volume CFD method using a non-staggered arrangement of the flow variables and second order accurate spatial and temporal discretisation schemes, b) an implicit top-hat filter, where the filter length is equal to the local computational cell size, and c) eddy-viscosity type LES models. LES based on these three main characteristics is indicated as industrial LES in this paper. It becomes increasingly clear that the numerical dissipation in CFD codes typically used in industrial applications with complex geometries may inhibit the predictive capabilities of explicit LES. Therefore, there is a need to quantify the numerical dissipation rate in such CFD codes. In this paper, we quantify the numerical dissipation rate in physical space based on an analysis of the transport equation for the mean turbulent kinetic energy. Using this method, we quantify the numerical dissipation rate in a quasi-Direct Numerical Simulation (DNS) and in under-resolved DNS of, as a basic demonstration case, fully-developed turbulent channel flow. With quasi-DNS, we indicate a DNS performed using a second order accurate finite volume method typically used in industrial applications. Furthermore, we determine and explain the trends in the performance of industrial LES for fully-developed turbulent channel flow for four different Reynolds numbers for three different LES mesh resolutions. The presented explanation of the mechanisms behind the observed trends is based on an analysis of the turbulent kinetic energy budgets. The presented quantitative analyses demonstrate that the numerical errors in the industrial LES computations of the considered turbulent channel flows result in a net numerical dissipation rate which is larger than the subgrid-scale dissipation rate. No new computational methods are presented in this paper. Instead, the main new elements in this paper are our detailed quantification method for the numerical dissipation rate, the application of this method to a quasi-DNS and under-resolved DNS of fully-developed turbulent channel flow, and the explanation of the effects of the numerical dissipation on the observed trends in the performance of industrial LES for fully-developed turbulent channel flows.

Towards a microscopic description of the free-energy landscape of water.

PubMed

Prada-Gracia, Diego; Shevchuk, Roman; Hamm, Peter; Rao, Francesco

2012-10-14

Free-energy landscape theory is often used to describe complex molecular systems. Here, a microscopic description of water structure and dynamics based on configuration-space-networks and molecular dynamics simulations of the TIP4P/2005 model is applied to investigate the free-energy landscape of water. The latter is built on top of a large set of water microstates describing the kinetic stability of local hydrogen-bond arrangements up to the second solvation shell. In temperature space, the landscape displays three different regimes. At around ambient conditions, the free-energy surface is characterized by many short-lived basins of attraction which are structurally well-defined (inhomogeneous regime). At lower temperatures instead, the liquid rapidly becomes homogeneous. In this regime, the free energy is funneled-like, with fully coordinated water arrangements at the bottom of the funnel. Finally, a third regime develops below the temperature of maximal compressibility (Widom line) where the funnel becomes steeper with few interconversions between microstates other than the fully coordinated ones. Our results present a way to manage the complexity of water structure and dynamics, connecting microscopic properties to its ensemble behavior.

Reducing the surface roughness beyond the pulsed-laser-deposition limit.

PubMed

Vasco, E; Polop, C; Sacedón, J L

2009-10-01

Here, we outline the theoretical fundamentals of a promising growth kinetics of films from the vapor phase, in which pulsed fluxes are combined with temperature transients to enable short-range surface relaxations (e.g., species rearrangements) and to inhibit long-range relaxations (atomic exchange between species). A group of physical techniques (fully pulsed thermal and/or laser depositions) based on this kinetics is developed that can be used to prepare films with roughnesses even lower than those obtained with pulsed-laser deposition, which is the physical vapor-phase deposition technique that has produced the flattest films reported so far.

Convergent synthesis of proteins by kinetically controlled ligation

DOEpatents

Kent, Stephen; Pentelute, Brad; Bang, Duhee; Johnson, Erik; Durek, Thomas

2010-03-09

The present invention concerns methods and compositions for synthesizing a polypeptide using kinetically controlled reactions involving fragments of the polypeptide for a fully convergent process. In more specific embodiments, a ligation involves reacting a first peptide having a protected cysteyl group at its N-terminal and a phenylthioester at its C-terminal with a second peptide having a cysteine residue at its N-termini and a thioester at its C-termini to form a ligation product. Subsequent reactions may involve deprotecting the cysteyl group of the resulting ligation product and/or converting the thioester into a thiophenylester.

Kinetic parameter estimation model for anaerobic co-digestion of waste activated sludge and microalgae.

PubMed

Lee, Eunyoung; Cumberbatch, Jewel; Wang, Meng; Zhang, Qiong

2017-03-01

Anaerobic co-digestion has a potential to improve biogas production, but limited kinetic information is available for co-digestion. This study introduced regression-based models to estimate the kinetic parameters for the co-digestion of microalgae and Waste Activated Sludge (WAS). The models were developed using the ratios of co-substrates and the kinetic parameters for the single substrate as indicators. The models were applied to the modified first-order kinetics and Monod model to determine the rate of hydrolysis and methanogenesis for the co-digestion. The results showed that the model using a hyperbola function was better for the estimation of the first-order kinetic coefficients, while the model using inverse tangent function closely estimated the Monod kinetic parameters. The models can be used for estimating kinetic parameters for not only microalgae-WAS co-digestion but also other substrates' co-digestion such as microalgae-swine manure and WAS-aquatic plants. Copyright © 2016 Elsevier Ltd. All rights reserved.

Radial k-t SPIRiT: autocalibrated parallel imaging for generalized phase-contrast MRI.

PubMed

Santelli, Claudio; Schaeffter, Tobias; Kozerke, Sebastian

2014-11-01

To extend SPIRiT to additionally exploit temporal correlations for highly accelerated generalized phase-contrast MRI and to compare the performance of the proposed radial k-t SPIRiT method relative to frame-by-frame SPIRiT and radial k-t GRAPPA reconstruction for velocity and turbulence mapping in the aortic arch. Free-breathing navigator-gated two-dimensional radial cine imaging with three-directional multi-point velocity encoding was implemented and fully sampled data were obtained in the aortic arch of healthy volunteers. Velocities were encoded with three different first gradient moments per axis to permit quantification of mean velocity and turbulent kinetic energy. Velocity and turbulent kinetic energy maps from up to 14-fold undersampled data were compared for k-t SPIRiT, frame-by-frame SPIRiT, and k-t GRAPPA relative to the fully sampled reference. Using k-t SPIRiT, improvements in magnitude and velocity reconstruction accuracy were found. Temporally resolved magnitude profiles revealed a reduction in spatial blurring with k-t SPIRiT compared with frame-by-frame SPIRiT and k-t GRAPPA for all velocity encodings, leading to improved estimates of turbulent kinetic energy. k-t SPIRiT offers improved reconstruction accuracy at high radial undersampling factors and hence facilitates the use of generalized phase-contrast MRI for routine use. Copyright © 2013 Wiley Periodicals, Inc.

Intermittency, coherent structures and dissipation in plasma turbulence

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

Wan, M.; Matthaeus, W. H.; Parashar, T. N.

Collisionless dissipation in turbulent plasmas such as the solar wind and the solar corona has been an intensively studied subject recently, with new insights often emerging from numerical simulation. Here we report results from high resolution, fully kinetic simulations of plasma turbulence in both two (2D) and three (3D) dimensions, studying the relationship between intermittency and dissipation. The simulations show development of turbulent coherent structures, characterized by sheet-like current density structures spanning a range of scales. An approximate dissipation measure is employed, based on work done by the electromagnetic field in the local electron fluid frame. This surrogate dissipation measuremore » is highly concentrated in small subvolumes in both 2D and 3D simulations. Fully kinetic simulations are also compared with magnetohydrodynamics (MHD) simulations in terms of coherent structures and dissipation. The interesting result emerges that the conditional averages of dissipation measure scale very similarly with normalized current density J in 2D and 3D particle-in-cell and in MHD. To the extent that the surrogate dissipation measure is accurate, this result implies that on average dissipation scales as ∼J{sup 2} in turbulent kinetic plasma. Multifractal intermittency is seen in the inertial range in both 2D and 3D, but at scales ∼ion inertial length, the scaling is closer to monofractal.« less

Transition in Electron Physics of Magnetic Reconnection in Weakly Collisional Plasma

NASA Astrophysics Data System (ADS)

Le, A.; Roytershteyn, V.; Karimabadi, H.; Daughton, W. S.; Egedal, J.; Forest, C.

2013-12-01

Using self-consistent fully kinetic simulations with a Monte-Carlo treatment of the Coulomb collision operator, we explore the transition between collisional and kinetic regimes of magnetic reconnection in high-Lundquist-number current sheets. Recent research in collisionless reconnection has shown that electron kinetic physics plays a key role in the evolution. Large-scale electron current sheets may form, leading to secondary island formation and turbulent flux rope interactions in 3D. The new collisional simulations demonstrate how increasing collisionality modifies or eliminates these electron structures in the kinetic regimes. Additional basic questions that are addressed include how the reconnection rate and the release of magnetic energy into electrons and ions vary with collisionality. The numerical study provides insight into reconnection in dense regions of the solar corona, the solar wind, and upcoming laboratory experiments at MRX (Princeton) and MPDX (UW-Madison). The implications of these results for studies of turbulence dissipation in weakly collisional plasmas are discussed.

Cyclic voltammetry of fast conducting electrocatalytic films.

PubMed

Costentin, Cyrille; Savéant, Jean-Michel

2015-07-15

In the framework of contemporary energy challenges, cyclic voltammetry is a particularly useful tool for deciphering the kinetics of catalytic films. The case of fast conducting films is analyzed, whether conduction is of the ohmic type or proceeds through rapid electron hopping. The rate-limiting factors are then the diffusion of the substrate in solution and through the film as well as the catalytic reaction itself. The dimensionless combination of the characteristics of these factors allows reducing the number of actual parameters to a maximum of two. The kinetics of the system may then be fully analyzed with the help of a kinetic zone diagram. Observing the variations of the current-potential responses with operational parameters such as film thickness, the potential scan rate and substrate concentration allows a precise assessment of the interplay between these factors and of the values of the rate controlling factors. A series of thought experiments is described in order to render the kinetic analysis more palpable.

Characterization of High-Frequency Excitation of a Wake by Simulation

NASA Technical Reports Server (NTRS)

Cain, Alan B.; Rogers, Michael M.; Kibens, Valdis; Mansour, Nagi (Technical Monitor)

2003-01-01

Insights into the effects of high-frequency forcing on free shear layer evolution are gained through analysis of several direct numerical simulations. High-frequency forcing of a fully turbulent plane wake results in only a weak transient effect. On the other hand, significant changes in the developed turbulent state may result when high-frequency forcing is applied to a transitional wake. The impacts of varying the characteristics of the high-frequency forcing are examined, particularly, the streamwise wavenumber band in which forcing is applied and the initial amplitude of the forcing. The high-frequency excitation is found to increase the dissipation rate of turbulent kinetic energy, to reduce the turbulent kinetic energy production rate, and to reduce the turbulent kinetic energy suppression increases with forcing amplitude once a threshold level has been reached. For a given initial forcing energy, the largest reduction in turbulent kinetic energy density was achieved by forcing wavenumbers that are about two to three times the neutral wavenumber determined from linear stability theory.

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.

Surface correlations of hydrodynamic drag for transitionally rough engineering surfaces

NASA Astrophysics Data System (ADS)

Thakkar, Manan; Busse, Angela; Sandham, Neil

2017-02-01

Rough surfaces are usually characterised by a single equivalent sand-grain roughness height scale that typically needs to be determined from laboratory experiments. Recently, this method has been complemented by a direct numerical simulation approach, whereby representative surfaces can be scanned and the roughness effects computed over a range of Reynolds number. This development raises the prospect over the coming years of having enough data for different types of rough surfaces to be able to relate surface characteristics to roughness effects, such as the roughness function that quantifies the downward displacement of the logarithmic law of the wall. In the present contribution, we use simulation data for 17 irregular surfaces at the same friction Reynolds number, for which they are in the transitionally rough regime. All surfaces are scaled to the same physical roughness height. Mean streamwise velocity profiles show a wide range of roughness function values, while the velocity defect profiles show a good collapse. Profile peaks of the turbulent kinetic energy also vary depending on the surface. We then consider which surface properties are important and how new properties can be incorporated into an empirical model, the accuracy of which can then be tested. Optimised models with several roughness parameters are systematically developed for the roughness function and profile peak turbulent kinetic energy. In determining the roughness function, besides the known parameters of solidity (or frontal area ratio) and skewness, it is shown that the streamwise correlation length and the root-mean-square roughness height are also significant. The peak turbulent kinetic energy is determined by the skewness and root-mean-square roughness height, along with the mean forward-facing surface angle and spanwise effective slope. The results suggest feasibility of relating rough-wall flow properties (throughout the range from hydrodynamically smooth to fully rough) to surface parameters.

Numerical simulations of stick-slip in fluid saturated granular fault gouge

NASA Astrophysics Data System (ADS)

Dorostkar, O.; Johnson, P. A.; Guyer, R. A.; Marone, C.; Carmeliet, J.

2016-12-01

Fluids play a key role in determining the frictional strength and stability of faults. For example, fluid flow and fluid-solid interaction in fault gouge can trigger seismicity, alter earthquake nucleation properties and cause fault zone weakening. We present results of 3D numerical simulations of stick-slip behavior in dry and saturated granular fault gouge. In the saturated case, the gouge is fully saturated and drainage is possible through the boundaries. We model the solid phase (particles) with the discrete element method (DEM) while the fluid is described by the Navier-Stokes equations and solved by computational fluid dynamics (CFD). In our model, granular gouge is sheared between two rough plates under boundary conditions of constant normal stress and constant shearing velocity at the layer boundaries. A phase-space study including shearing velocity and normal stress is taken to identify the conditions for stick-slip regime. We analyzed slip events for dry and saturated cases to determine shear stress drop, released kinetic energy and compaction. The presence of fluid tends to cause larger slip events. We observe a close correlation between the kinetic energy of the particles and of the fluid. In short, during slip, fluid flow induced by the failure and compaction of the granular system, mobilizes the particles, which increases their kinetic energy, leading to greater slip. We further observe that the solid-fluid interaction forces are equal or larger than the solid-solid interaction forces during the slip event, indicating the important influence of the fluid on the granular system. Our simulations can explain the behaviors observed in experimental studies and we are working to apply our results to tectonic faults.

Kinetic limitations on tracer partitioning in ganglia dominated source zones.

PubMed

Ervin, Rhiannon E; Boroumand, Ali; Abriola, Linda M; Ramsburg, C Andrew

2011-11-01

Quantification of the relationship between dense nonaqueous phase liquid (DNAPL) source strength, source longevity and spatial distribution is increasingly recognized as important for effective remedial design. Partitioning tracers are one tool that may permit interrogation of DNAPL architecture. Tracer data are commonly analyzed under the assumption of linear, equilibrium partitioning, although the appropriateness of these assumptions has not been fully explored. Here we focus on elucidating the nonlinear and nonequilibrium partitioning behavior of three selected alcohol tracers - 1-pentanol, 1-hexanol and 2-octanol in a series of batch and column experiments. Liquid-liquid equilibria for systems comprising water, TCE and the selected alcohol illustrate the nonlinear distribution of alcohol between the aqueous and organic phases. Complete quantification of these equilibria facilitates delineation of the limits of applicability of the linear partitioning assumption, and assessment of potential inaccuracies associated with measurement of partition coefficients at a single concentration. Column experiments were conducted under conditions of non-equilibrium to evaluate the kinetics of the reversible absorption of the selected tracers in a sandy medium containing a uniform entrapped saturation of TCE-DNAPL. Experimental tracer breakthrough data were used, in conjunction with mathematical models and batch measurements, to evaluate alternative hypotheses for observed deviations from linear equilibrium partitioning behavior. Analyses suggest that, although all tracers accumulate at the TCE-DNAPL/aqueous interface, surface accumulation does not influence transport at concentrations typically employed for tracer tests. Moreover, results reveal that the kinetics of the reversible absorption process are well described using existing mass transfer correlations originally developed to model aqueous boundary layer resistance for pure-component NAPL dissolution. Copyright © 2011 Elsevier B.V. All rights reserved.

Neutron Compton scattering from selectively deuterated acetanilide

NASA Astrophysics Data System (ADS)

Wanderlingh, U. N.; Fielding, A. L.; Middendorf, H. D.

With the aim of developing the application of neutron Compton scattering (NCS) to molecular systems of biophysical interest, we are using the Compton spectrometer EVS at ISIS to characterize the momentum distribution of protons in peptide groups. In this contribution we present NCS measurements of the recoil peak (Compton profile) due to the amide proton in otherwise fully deuterated acetanilide (ACN), a widely studied model system for H-bonding and energy transfer in biomolecules. We obtain values for the average width of the potential well of the amide proton and its mean kinetic energy. Deviations from the Gaussian form of the Compton profile, analyzed on the basis of an expansion due to Sears, provide data relating to the Laplacian of the proton potential.

Combinatoric analysis of heterogeneous stochastic self-assembly.

PubMed

D'Orsogna, Maria R; Zhao, Bingyu; Berenji, Bijan; Chou, Tom

2013-09-28

We analyze a fully stochastic model of heterogeneous nucleation and self-assembly in a closed system with a fixed total particle number M, and a fixed number of seeds Ns. Each seed can bind a maximum of N particles. A discrete master equation for the probability distribution of the cluster sizes is derived and the corresponding cluster concentrations are found using kinetic Monte-Carlo simulations in terms of the density of seeds, the total mass, and the maximum cluster size. In the limit of slow detachment, we also find new analytic expressions and recursion relations for the cluster densities at intermediate times and at equilibrium. Our analytic and numerical findings are compared with those obtained from classical mass-action equations and the discrepancies between the two approaches analyzed.

Kinetic energy flux budget across air-sea interface

NASA Astrophysics Data System (ADS)

Fan, Yalin; Hwang, Paul

2017-12-01

The kinetic energy (KE) fluxes into subsurface currents (EFc) is an important boundary condition for ocean circulation models. Traditionally, numerical models assume the KE flux from wind (EFair) is identical to EFc, that is, no net KE is gained (or lost) by surface waves. This assumption, however, is invalid when the surface wave field is not fully developed, and acquires KE when it grows in space or time. In this study, numerical experiments are performed to investigate the KE flux budget across the air-sea interface under both uniform and idealized tropical cyclone (TC) winds. The wave fields are simulated using the WAVEWATCH III model under different wind forcing. The difference between EFair and EFc is estimated using an air-sea KE budget model. To address the uncertainty of these estimates resides in the variation of source functions, two source function packages are used for this study: the ST4 source package (Ardhuin et al, 2010), and the ST6 source package (Babanin, 2011). The modeled EFc is significantly reduced relative to EFair under growing seas for both the uniform and TC experiments. The reduction can be as large as 20%, and the variation of this ratio is highly dependent on the choice of source function for the wave model. Normalized EFc are found to be consistent with analytical expressions by Hwang and Sletten (2008) and Hwang and Walsh (2016) and field observations by Terray et al. (1996) and Drennan et al. (1996), while the scatters are more widely in the TC cases due to the complexity of the associated wave field. The waves may even give up KE to subsurface currents in the left rear quadrant of fast moving storms. Our results also suggest that the normalized KE fluxes may depend on both wave age and friction velocity (u*).

Higher Order Chemistry Models in the CFD Simulation of Laser-Ablated Carbon Plumes

NASA Technical Reports Server (NTRS)

Greendyke, R. B.; Creel, J. R.; Payne, B. T.; Scott, C. D.

2005-01-01

Production of single-walled carbon nanotubes (SWNT) has taken place for a number of years and by a variety of methods such as laser ablation, chemical vapor deposition, and arc-jet ablation. Yet, little is actually understood about the exact chemical kinetics and processes that occur in SWNT formation. In recent time, NASA Johnson Space Center has devoted a considerable effort to the experimental evaluation of the laser ablation production process for SWNT originally developed at Rice University. To fully understand the nature of the laser ablation process it is necessary to understand the development of the carbon plume dynamics within the laser ablation oven. The present work is a continuation of previous studies into the efforts to model plume dynamics using computational fluid dynamics (CFD). The ultimate goal of the work is to improve understanding of the laser ablation process, and through that improved understanding, refine the laser ablation production of SWNT.

Implementation of a kappa-epsilon turbulence model to RPLUS3D code

NASA Technical Reports Server (NTRS)

Chitsomboon, Tawit

1992-01-01

The RPLUS3D code has been developed at the NASA Lewis Research Center to support the National Aerospace Plane (NASP) project. The code has the ability to solve three dimensional flowfields with finite rate combustion of hydrogen and air. The combustion process of the hydrogen-air system are simulated by an 18 reaction path, 8 species chemical kinetic mechanism. The code uses a Lower-Upper (LU) decomposition numerical algorithm as its basis, making it a very efficient and robust code. Except for the Jacobian matrix for the implicit chemistry source terms, there is no inversion of a matrix even though a fully implicit numerical algorithm is used. A k-epsilon turbulence model has recently been incorporated into the code. Initial validations have been conducted for a flow over a flat plate. Results of the validation studies are shown. Some difficulties in implementing the k-epsilon equations to the code are also discussed.

Implementation of a kappa-epsilon turbulence model to RPLUS3D code

NASA Astrophysics Data System (ADS)

Chitsomboon, Tawit

1992-02-01

The RPLUS3D code has been developed at the NASA Lewis Research Center to support the National Aerospace Plane (NASP) project. The code has the ability to solve three dimensional flowfields with finite rate combustion of hydrogen and air. The combustion process of the hydrogen-air system are simulated by an 18 reaction path, 8 species chemical kinetic mechanism. The code uses a Lower-Upper (LU) decomposition numerical algorithm as its basis, making it a very efficient and robust code. Except for the Jacobian matrix for the implicit chemistry source terms, there is no inversion of a matrix even though a fully implicit numerical algorithm is used. A k-epsilon turbulence model has recently been incorporated into the code. Initial validations have been conducted for a flow over a flat plate. Results of the validation studies are shown. Some difficulties in implementing the k-epsilon equations to the code are also discussed.

Optimizing Dense Plasma Focus Neutron Yields with Fast Gas Jets

NASA Astrophysics Data System (ADS)

McMahon, Matthew; Kueny, Christopher; Stein, Elizabeth; Link, Anthony; Schmidt, Andrea

2016-10-01

We report a study using the particle-in-cell code LSP to perform fully kinetic simulations modeling dense plasma focus (DPF) devices with high density gas jets on axis. The high density jet models fast gas puffs which allow for more mass on axis while maintaining the optimal pressure for the DPF. As the density of the jet compared to the background fill increases we find the neutron yield increases, as does the variability in the neutron yield. Introducing perturbations in the jet density allow for consistent seeding of the m =0 instability leading to more consistent ion acceleration and higher neutron yields with less variability. Jets with higher on axis density are found to have the greatest yield. The optimal jet configuration is explored. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Stress drop with constant, scale independent seismic efficiency and overshoot

USGS Publications Warehouse

Beeler, N.M.

2001-01-01

To model dissipated and radiated energy during earthquake stress drop, I calculate dynamic fault slip using a single degree of freedom spring-slider block and a laboratory-based static/kinetic fault strength relation with a dynamic stress drop proportional to effective normal stress. The model is scaled to earthquake size assuming a circular rupture; stiffness varies inversely with rupture radius, and rupture duration is proportional to radius. Calculated seismic efficiency, the ratio of radiated to total energy expended during stress drop, is in good agreement with laboratory and field observations. Predicted overshoot, a measure of how much the static stress drop exceeds the dynamic stress drop, is higher than previously published laboratory and seismic observations and fully elasto-dynamic calculations. Seismic efficiency and overshoot are constant, independent of normal stress and scale. Calculated variation of apparent stress with seismic moment resembles the observational constraints of McGarr [1999].

Symmetry breaking by heating in a continuous opinion model

NASA Astrophysics Data System (ADS)

Anteneodo, Celia; Crokidakis, Nuno

2017-04-01

We study the critical behavior of a continuous opinion model, driven by kinetic exchanges in a fully connected population. Opinions range in the real interval [-1 ,1 ] , representing the different shades of opinions against and for an issue under debate. Individuals' opinions evolve through pairwise interactions, with couplings that are typically positive, but a fraction p of negative ones is allowed. Moreover, a social temperature parameter T controls the tendency of the individual responses toward neutrality. Depending on p and T , different collective states emerge: symmetry broken (one side wins), symmetric (tie of opposite sides), and absorbing neutral (indecision wins). We find the critical points and exponents that characterize the phase transitions between them. The symmetry breaking transition belongs to the usual Ising mean-field universality class, but the absorbing-phase transitions, with β =0.5 , are out of the paradigmatic directed percolation class. Moreover, ordered phases can emerge by increasing social temperature.

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

PubMed

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

2017-08-09

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

Predicting heavy metals' adsorption edges and adsorption isotherms on MnO2 with the parameters determined from Langmuir kinetics.

PubMed

Hu, Qinghai; Xiao, Zhongjin; Xiong, Xinmei; Zhou, Gongming; Guan, Xiaohong

2015-01-01

Although surface complexation models have been widely used to describe the adsorption of heavy metals, few studies have verified the feasibility of modeling the adsorption kinetics, edge, and isotherm data with one pH-independent parameter. A close inspection of the derivation process of Langmuir isotherm revealed that the equilibrium constant derived from the Langmuir kinetic model, KS-kinetic, is theoretically equivalent to the adsorption constant in Langmuir isotherm, KS-Langmuir. The modified Langmuir kinetic model (MLK model) and modified Langmuir isotherm model (MLI model) incorporating pH factor were developed. The MLK model was employed to simulate the adsorption kinetics of Cu(II), Co(II), Cd(II), Zn(II) and Ni(II) on MnO2 at pH3.2 or 3.3 to get the values of KS-kinetic. The adsorption edges of heavy metals could be modeled with the modified metal partitioning model (MMP model), and the values of KS-Langmuir were obtained. The values of KS-kinetic and KS-Langmuir are very close to each other, validating that the constants obtained by these two methods are basically the same. The MMP model with KS-kinetic constants could predict the adsorption edges of heavy metals on MnO2 very well at different adsorbent/adsorbate concentrations. Moreover, the adsorption isotherms of heavy metals on MnO2 at various pH levels could be predicted reasonably well by the MLI model with the KS-kinetic constants. Copyright © 2014. Published by Elsevier B.V.

Equilibrium and kinetics of DNA overstretching modeled with a quartic energy landscape.

PubMed

Argudo, David; Purohit, Prashant K

2014-11-04

It is well known that the dsDNA molecule undergoes a phase transition from B-DNA into an overstretched state at high forces. For some time, the structure of the overstretched state remained unknown and highly debated, but recent advances in experimental techniques have presented evidence of more than one possible phase (or even a mixed phase) depending on ionic conditions, temperature, and basepair sequence. Here, we present a theoretical model to study the overstretching transition with the possibility that the overstretched state is a mixture of two phases: a structure with portions of inner strand separation (melted or M-DNA), and an extended phase that retains the basepair structure (S-DNA). We model the double-stranded DNA as a chain composed of n segments of length l, where the transition is studied by means of a Landau quartic potential with statistical fluctuations. The length l is a measure of cooperativity of the transition and is key to characterizing the overstretched phase. By analyzing the different values of l corresponding to a wide spectrum of experiments, we find that for a range of temperatures and ionic conditions, the overstretched form is likely to be a mix of M-DNA and S-DNA. For a transition close to a pure S-DNA state, where the change in extension is close to 1.7 times the original B-DNA length, we find l ? 25 basepairs regardless of temperature and ionic concentration. Our model is fully analytical, yet it accurately reproduces the force-extension curves, as well as the transient kinetic behavior, seen in DNA overstretching experiments.

Fully solar-driven thermo- and electrochemistry for advanced oxidation processes (STEP-AOPs) of 2-nitrophenol wastewater.

PubMed

Nie, Chunhong; Shao, Nan; Wang, Baohui; Yuan, Dandan; Sui, Xin; Wu, Hongjun

2016-07-01

The STEP (Solar Thermal Electrochemical Process) for Advanced Oxidation Processes (AOPs, combined to STEP-AOPs), fully driven by solar energy without the input of any other forms of energy and chemicals, is introduced and demonstrated from the theory to experiments. Exemplified by the persistent organic pollutant 2-nitrophenol in water, the fundamental model and practical system are exhibited for the STEP-AOPs to efficiently transform 2-nitrophenol into carbon dioxide, water, and the other substances. The results show that the STEP-AOPs system performs more effectively than classical AOPs in terms of the thermodynamics and kinetics of pollutant oxidation. Due to the combination of solar thermochemical reactions with electrochemistry, the STEP-AOPs system allows the requisite electrolysis voltage of 2-nitrophenol to be experimentally decreased from 1.00 V to 0.84 V, and the response current increases from 18 mA to 40 mA. STEP-AOPs also greatly improve the kinetics of the oxidation at 30 °C and 80 °C. As a result, the removal rate of 2-nitrophenol after 1 h increased from 19.50% at 30 °C to 32.70% at 80 °C at constant 1.90 V. Mechanistic analysis reveals that the oxidation pathway is favorably changed because of thermal effects. The tracking of the reaction displayed that benzenediol and hydroquinone are initial products, with maleic acid and formic acid as sequential carboxylic acid products, and carbon dioxide as the final product. The theory and experiments on STEP-AOPs system exemplified by the oxidation of 2-nitrophenol provide a broad basis for extension of the STEP and AOPs for rapid and efficient treatment of organic wastewater. Copyright © 2016 Elsevier Ltd. All rights reserved.

On Kinetic Slow Modes, Fluid Slow Modes, and Pressure-balanced Structures in the Solar Wind

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

Verscharen, Daniel; Chen, Christopher H. K.; Wicks, Robert T., E-mail: daniel.verscharen@unh.edu, E-mail: christopher.chen@imperial.ac.uk, E-mail: r.wicks@ucl.ac.uk

Observations in the solar wind suggest that the compressive component of inertial-range solar-wind turbulence is dominated by slow modes. The low collisionality of the solar wind allows for nonthermal features to survive, which suggests the requirement of a kinetic plasma description. The least-damped kinetic slow mode is associated with the ion-acoustic (IA) wave and a nonpropagating (NP) mode. We derive analytical expressions for the IA-wave dispersion relation in an anisotropic plasma in the framework of gyrokinetics and then compare them to fully kinetic numerical calculations, results from two-fluid theory, and magnetohydrodynamics (MHD). This comparison shows major discrepancies in the predictedmore » wave phase speeds from MHD and kinetic theory at moderate to high β . MHD and kinetic theory also dictate that all plasma normal modes exhibit a unique signature in terms of their polarization. We quantify the relative amplitude of fluctuations in the three lowest particle velocity moments associated with IA and NP modes in the gyrokinetic limit and compare these predictions with MHD results and in situ observations of the solar-wind turbulence. The agreement between the observations of the wave polarization and our MHD predictions is better than the kinetic predictions, which suggests that the plasma behaves more like a fluid in the solar wind than expected.« less

Application of powder densification models to the consolidation processing of composites

NASA Technical Reports Server (NTRS)

Wadley, H. N. G.; Elzey, D. M.

1991-01-01

Unidirectional fiber reinforced metal matrix composite tapes (containing a single layer of parallel fibers) can now be produced by plasma deposition. These tapes can be stacked and subjected to a thermomechanical treatment that results in a fully dense near net shape component. The mechanisms by which this consolidation step occurs are explored, and models to predict the effect of different thermomechanical conditions (during consolidation) upon the kinetics of densification are developed. The approach is based upon a methodology developed by Ashby and others for the simpler problem of HIP of spherical powders. The complex problem is devided into six, much simpler, subproblems, and then their predicted contributions are added to densification. The initial problem decomposition is to treat the two extreme geometries encountered (contact deformation occurring between foils and shrinkage of isolated, internal pores). Deformation of these two geometries is modelled for plastic, power law creep and diffusional flow. The results are reported in the form of a densification map.

Generation and comparison of CRISPR-Cas9 and Cre-mediated genetically engineered mouse models of sarcoma

PubMed Central

Huang, Jianguo; Chen, Mark; Whitley, Melodi Javid; Kuo, Hsuan-Cheng; Xu, Eric S.; Walens, Andrea; Mowery, Yvonne M.; Van Mater, David; Eward, William C.; Cardona, Diana M.; Luo, Lixia; Ma, Yan; Lopez, Omar M.; Nelson, Christopher E.; Robinson-Hamm, Jacqueline N.; Reddy, Anupama; Dave, Sandeep S.; Gersbach, Charles A.; Dodd, Rebecca D.; Kirsch, David G.

2017-01-01

Genetically engineered mouse models that employ site-specific recombinase technology are important tools for cancer research but can be costly and time-consuming. The CRISPR-Cas9 system has been adapted to generate autochthonous tumours in mice, but how these tumours compare to tumours generated by conventional recombinase technology remains to be fully explored. Here we use CRISPR-Cas9 to generate multiple subtypes of primary sarcomas efficiently in wild type and genetically engineered mice. These data demonstrate that CRISPR-Cas9 can be used to generate multiple subtypes of soft tissue sarcomas in mice. Primary sarcomas generated with CRISPR-Cas9 and Cre recombinase technology had similar histology, growth kinetics, copy number variation and mutational load as assessed by whole exome sequencing. These results show that sarcomas generated with CRISPR-Cas9 technology are similar to sarcomas generated with conventional modelling techniques and suggest that CRISPR-Cas9 can be used to more rapidly generate genotypically and phenotypically similar cancers. PMID:28691711

Fundamental Scaling of Microplasmas and Tunable UV Light Generation.

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

Manginell, Ronald P.; Sillerud, Colin Halliday; Hopkins, Matthew M.

2016-11-01

The temporal evolution of spectral lines from microplasma devices (MD) was studied, including impurity transitions. Long-wavelength emission diminishes more rapidly than deep UV with decreasing pulse width and RF operation. Thus, switching from DC to short pulsed or RF operation, UV emissions can be suppressed, allowing for real-time tuning of the ionization energy of a microplasma photo-ionization source, which is useful for chemical and atomic physics. Scaling allows MD to operate near atmospheric pressure where excimer states are efficiently created and emit down to 65 nm; laser emissions fall off below 200 nm, making MD light sources attractive for deepmore » UV use. A first fully-kinetic three-dimensional model was developed that explicitly calculates electron-energy distribution function. This, and non-continuum effects, were studied with the model and how they are impacted by geometry and transient or DC operation. Finally, a global non-dimensional model was developed to help explain general trends MD physics.« less

Using engineered single-chain antibodies to correlate molecular binding properties and nanoparticle adhesion dynamics.

PubMed

Haun, Jered B; Pepper, Lauren R; Boder, Eric T; Hammer, Daniel A

2011-11-15

Elucidation of the relationship between targeting molecule binding properties and the adhesive behavior of therapeutic or diagnostic nanocarriers would aid in the design of optimized vectors and lead to improved efficacy. We measured the adhesion of 200-nm-diameter particles under fluid flow that was mediated by a diverse array of molecular interactions, including recombinant single-chain antibodies (scFvs), full antibodies, and the avidin/biotin interaction. Within the panel of scFvs, we used a family of mutants that display a spectrum of binding kinetics, allowing us to compare nanoparticle adhesion to bond chemistry. In addition, we explored the effect of molecular size by inserting a protein linker into the scFv fusion construct and by employing scFvs that are specific for targets with vastly different sizes. Using computational models, we extracted multivalent kinetic rate constants for particle attachment and detachment from the adhesion data and correlated the results to molecular binding properties. Our results indicate that the factors that increase encounter probability, such as adhesion molecule valency and size, directly enhance the rate of nanoparticle attachment. Bond kinetics had no influence on scFv-mediated nanoparticle attachment within the kinetic range tested, however, but did appear to affect antibody/antigen and avidin/biotin mediated adhesion. We attribute this finding to a combination of multivalent binding and differences in bond mechanical strength between recombinant scFvs and the other adhesion molecules. Nanoparticle detachment probability correlated directly with adhesion molecule valency and size, as well as the logarithm of the affinity for all molecules tested. On the basis of this work, scFvs can serve as viable targeting receptors for nanoparticles, but improvements to their bond mechanical strength would likely be required to fully exploit their tunable kinetic properties and maximize the adhesion efficiency of nanoparticles that bear them.

Stability of sub-Alfvenic plasma expansions

NASA Technical Reports Server (NTRS)

Huba, J. D.; Hassam, A. B.; Winske, D.

1990-01-01

A theoretical treatment of the linear stability of sub-Alfvenic plasma expansion is developed. The theory is fully kinetic and includes finite-beta effects, collisional effects, and neutral gas flow. A variety of results are obtained, and are applied to the the AMPTE magnetotail release, the NRL laser experiment, and the upcoming CRRES GTO releases.

Investigating EMIC Wave Dynamics with RAM-SCB-E

NASA Astrophysics Data System (ADS)

Jordanova, V. K.; Fu, X.; Henderson, M. G.; Morley, S.; Welling, D. T.; Yu, Y.

2017-12-01

The distribution of ring current ions and electrons in the inner magnetosphere depends strongly on their transport in realistic electric (E) and magnetic (B) fields and concurrent energization or loss. To investigate the high variability of energetic particle (H+, He+, O+, and electron) fluxes during storms selected by the GEM Surface Charging Challenge, we use our kinetic ring current model (RAM) two-way coupled with a 3-D magnetic field code (SCB). This model was just extended to include electric field calculations, making it a unique, fully self-consistent, anisotropic ring current-atmosphere interactions model, RAM-SCB-E. Recently we investigated electromagnetic ion cyclotron (EMIC) instability in a local plasma using both linear theory and nonlinear hybrid simulations and derived a scaling formula that relates the saturation EMIC wave amplitude to initial plasma conditions. Global dynamic EMIC wave maps obtained with our RAM-SCB-E model using this scaling will be presented and compared with statistical models. These plasma waves can affect significantly both ion and electron precipitation into the atmosphere and the subsequent patterns of ionospheric conductance, as well as the global ring current dynamics.

Probing the Structure of Our Solar System's Edge

NASA Astrophysics Data System (ADS)

Hensley, Kerry

2018-02-01

The boundary between the solar wind and the interstellar medium (ISM) at the distant edge of our solar system has been probed remotely and directly by spacecraft, but questions about its properties persist. What can models tell us about the structure of this region?The Heliopause: A Dynamic BoundarySchematic illustrating different boundaries of our solar system and the locations of the Voyager spacecraft. [Walt Feimer/NASA GSFCs Conceptual Image Lab]As our solar system travels through interstellar space, the magnetized solar wind flows outward and pushes back on the oncoming ISM, forming a bubble called the heliosphere. The clash of plasmas generates a boundary region called the heliopause, the shape of which depends strongly on the properties of the solar wind and the local ISM.Much of our understanding of the outer heliosphere and the local ISM comes from observations made by the International Boundary Explorer (IBEX) and the Voyager 1 and Voyager 2 spacecraft. IBEX makes global maps of the flux of neutral atoms, while Voyagers 1 and 2 record the plasma density and magnetic field parameters along their trajectories as they exit the solar system. In order to interpret the IBEX and Voyager observations, astronomers rely on complex models that must capture both global and local effects.Simulations of the plasma density in the meridional plane of the heliosphere due to the interaction of the solar wind with the ISM for the case of a relatively dense ISM with a weak magnetic field. [Adapted from Pogorelov et al. 2017]Modeling the Edge of the Solar SystemIn this study, Nikolai Pogorelov (University of Alabama in Huntsville) and collaborators use a hybrid magneto-hydrodynamical (MHD) and kinetic simulation to capture fully the physical processes happening in the outer heliosphere.MHD models have been used to understand many aspects of plasma flow in the heliosphere. However, they struggle to capture processes that are better described kinetically, like charge exchange or plasma instabilities. Fully kinetic models, on the other hand, are too computationally expensive to be used for global time-dependent simulations.In order to combine the strengths of MHD and kinetic models, the authors also use adaptive mesh refinement a technique in which the grid size is whittled down at key locations where small-scale physics can have a large effect to resolve the important kinetic processes taking place at the heliopause while lowering the overall computational cost.Physics of the BorderTop: Simulation results for the plasma density observed by Voyager 1 along its trajectory. Bottom: Voyager 1 observations of plasma waves. An increase in the plasma wave frequency corresponds to an increase in the ambient plasma density. Click for a closer look. [Adapted from Pogorelov et al. 2017]The authors varied the ISMs density and magnetic field, exploring how this changed the interaction between the ISM and the solar wind. Among their many results, the authors found:There exists a plasma density drop and magnetic field strength increase in the ISM, just beyond the heliopause. This narrow boundary region is similar to a plasma depletion layer formed upstream from the Earths magnetopause as the solar wind streams around it.The authors model for the plasma density along the trajectory of Voyager 1 is consistent with the actual plasma density inferred from Voyager 1s measurements.The heliospheric magnetic field likely dissipates in the region between the termination shock the point at which the solar wind speed drops below the speed of sound and the heliopause.While this work by Pogorelov and collaborators has brought to light new aspects of the boundary between the solar wind and the ISM, the challenge of linking data and models continues. Future simulations will help us further interpret observations by IBEX and the Voyager spacecraft and advance our understanding of how our solar system interacts with the surrounding ISM.CitationN. V. Pogorelov et al 2017ApJ8459. doi:10.3847/1538-4357/aa7d4f

Phase field approaches of bone remodeling based on TIP

NASA Astrophysics Data System (ADS)

Ganghoffer, Jean-François; Rahouadj, Rachid; Boisse, Julien; Forest, Samuel

2016-01-01

The process of bone remodeling includes a cycle of repair, renewal, and optimization. This adaptation process, in response to variations in external loads and chemical driving factors, involves three main types of bone cells: osteoclasts, which remove the old pre-existing bone; osteoblasts, which form the new bone in a second phase; osteocytes, which are sensing cells embedded into the bone matrix, trigger the aforementioned sequence of events. The remodeling process involves mineralization of the bone in the diffuse interface separating the marrow, which contains all specialized cells, from the newly formed bone. The main objective advocated in this contribution is the setting up of a modeling and simulation framework relying on the phase field method to capture the evolution of the diffuse interface between the new bone and the marrow at the scale of individual trabeculae. The phase field describes the degree of mineralization of this diffuse interface; it varies continuously between the lower value (no mineral) and unity (fully mineralized phase, e.g. new bone), allowing the consideration of a diffuse moving interface. The modeling framework is the theory of continuous media, for which field equations for the mechanical, chemical, and interfacial phenomena are written, based on the thermodynamics of irreversible processes. Additional models for the cellular activity are formulated to describe the coupling of the cell activity responsible for bone production/resorption to the kinetics of the internal variables. Kinetic equations for the internal variables are obtained from a pseudo-potential of dissipation. The combination of the balance equations for the microforce associated to the phase field and the kinetic equations lead to the Ginzburg-Landau equation satisfied by the phase field with a source term accounting for the dissipative microforce. Simulations illustrating the proposed framework are performed in a one-dimensional situation showing the evolution of the diffuse interface separating new bone from marrow.

Kinetic modeling of cell metabolism for microbial production.

PubMed

Costa, Rafael S; Hartmann, Andras; Vinga, Susana

2016-02-10

Kinetic models of cellular metabolism are important tools for the rational design of metabolic engineering strategies and to explain properties of complex biological systems. The recent developments in high-throughput experimental data are leading to new computational approaches for building kinetic models of metabolism. Herein, we briefly survey the available databases, standards and software tools that can be applied for kinetic models of metabolism. In addition, we give an overview about recently developed ordinary differential equations (ODE)-based kinetic models of metabolism and some of the main applications of such models are illustrated in guiding metabolic engineering design. Finally, we review the kinetic modeling approaches of large-scale networks that are emerging, discussing their main advantages, challenges and limitations. Copyright © 2015 Elsevier B.V. All rights reserved.

Spectral method for a kinetic swarming model

DOE PAGES

Gamba, Irene M.; Haack, Jeffrey R.; Motsch, Sebastien

2015-04-28

Here we present the first numerical method for a kinetic description of the Vicsek swarming model. The kinetic model poses a unique challenge, as there is a distribution dependent collision invariant to satisfy when computing the interaction term. We use a spectral representation linked with a discrete constrained optimization to compute these interactions. To test the numerical scheme we investigate the kinetic model at different scales and compare the solution with the microscopic and macroscopic descriptions of the Vicsek model. Lastly, we observe that the kinetic model captures key features such as vortex formation and traveling waves.

Biodegradation kinetics for pesticide exposure assessment.

PubMed

Wolt, J D; Nelson, H P; Cleveland, C B; van Wesenbeeck, I J

2001-01-01

Understanding pesticide risks requires characterizing pesticide exposure within the environment in a manner that can be broadly generalized across widely varied conditions of use. The coupled processes of sorption and soil degradation are especially important for understanding the potential environmental exposure of pesticides. The data obtained from degradation studies are inherently variable and, when limited in extent, lend uncertainty to exposure characterization and risk assessment. Pesticide decline in soils reflects dynamically coupled processes of sorption and degradation that add complexity to the treatment of soil biodegradation data from a kinetic perspective. Additional complexity arises from study design limitations that may not fully account for the decline in microbial activity of test systems, or that may be inadequate for considerations of all potential dissipation routes for a given pesticide. Accordingly, kinetic treatment of data must accommodate a variety of differing approaches starting with very simple assumptions as to reaction dynamics and extending to more involved treatments if warranted by the available experimental data. Selection of the appropriate kinetic model to describe pesticide degradation should rely on statistical evaluation of the data fit to ensure that the models used are not overparameterized. Recognizing the effects of experimental conditions and methods for kinetic treatment of degradation data is critical for making appropriate comparisons among pesticide biodegradation data sets. Assessment of variability in soil half-life among soils is uncertain because for many pesticides the data on soil degradation rate are limited to one or two soils. Reasonable upper-bound estimates of soil half-life are necessary in risk assessment so that estimated environmental concentrations can be developed from exposure models. Thus, an understanding of the variable and uncertain distribution of soil half-lives in the environment is necessary to estimate bounding values. Statistical evaluation of measures of central tendency for multisoil kinetic studies shows that geometric means better represent the distribution in soil half-lives than do the arithmetic or harmonic means. Estimates of upper-bound soil half-life values based on the upper 90% confidence bound on the geometric mean tend to accurately represent the upper bound when pesticide degradation rate is biologically driven but appear to overestimate the upper bound when there is extensive coupling of biodegradation with sorptive processes. The limited data available comparing distribution in pesticide soil half-lives between multisoil laboratory studies and multilocation field studies suggest that the probability density functions are similar. Thus, upper-bound estimates of pesticide half-life determined from laboratory studies conservatively represent pesticide biodegradation in the field environment for the purposes of exposure and risk assessment. International guidelines and approaches used for interpretations of soil biodegradation reflect many common elements, but differ in how the source and nature of variability in soil kinetic data are considered. Harmonization of approaches for the use of soil biodegradation data will improve the interpretative power of these data for the purposes of exposure and risk assessment.

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.

General kinetic solution for the Biermann battery with an associated pressure anisotropy generation

NASA Astrophysics Data System (ADS)

Schoeffler, K. M.; Silva, L. O.

2018-01-01

Fully kinetic analytic calculations of an initially Maxwellian distribution with arbitrary density and temperature gradients exhibit the development of temperature anisotropies and magnetic field growth associated with the Biermann battery. The calculation, performed by taking a small order expansion of the ratio of the Debye length to the gradient scale, predicts anisotropies and magnetic fields as a function of space given an arbitrary temperature and density profile. These predictions are shown to qualitatively match the values measured from particle-in-cell simulations, where the development of the Weibel instability occurs at the same location and with a wavenumber aligned with the predicted temperature anisotropy.

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.

Application of Petri net based analysis techniques to signal transduction pathways.

PubMed

Sackmann, Andrea; Heiner, Monika; Koch, Ina

2006-11-02

Signal transduction pathways are usually modelled using classical quantitative methods, which are based on ordinary differential equations (ODEs). However, some difficulties are inherent in this approach. On the one hand, the kinetic parameters involved are often unknown and have to be estimated. With increasing size and complexity of signal transduction pathways, the estimation of missing kinetic data is not possible. On the other hand, ODEs based models do not support any explicit insights into possible (signal-) flows within the network. Moreover, a huge amount of qualitative data is available due to high-throughput techniques. In order to get information on the systems behaviour, qualitative analysis techniques have been developed. Applications of the known qualitative analysis methods concern mainly metabolic networks. Petri net theory provides a variety of established analysis techniques, which are also applicable to signal transduction models. In this context special properties have to be considered and new dedicated techniques have to be designed. We apply Petri net theory to model and analyse signal transduction pathways first qualitatively before continuing with quantitative analyses. This paper demonstrates how to build systematically a discrete model, which reflects provably the qualitative biological behaviour without any knowledge of kinetic parameters. The mating pheromone response pathway in Saccharomyces cerevisiae serves as case study. We propose an approach for model validation of signal transduction pathways based on the network structure only. For this purpose, we introduce the new notion of feasible t-invariants, which represent minimal self-contained subnets being active under a given input situation. Each of these subnets stands for a signal flow in the system. We define maximal common transition sets (MCT-sets), which can be used for t-invariant examination and net decomposition into smallest biologically meaningful functional units. The paper demonstrates how Petri net analysis techniques can promote a deeper understanding of signal transduction pathways. The new concepts of feasible t-invariants and MCT-sets have been proven to be useful for model validation and the interpretation of the biological system behaviour. Whereas MCT-sets provide a decomposition of the net into disjunctive subnets, feasible t-invariants describe subnets, which generally overlap. This work contributes to qualitative modelling and to the analysis of large biological networks by their fully automatic decomposition into biologically meaningful modules.

Application of Petri net based analysis techniques to signal transduction pathways

PubMed Central

Sackmann, Andrea; Heiner, Monika; Koch, Ina

2006-01-01

Background Signal transduction pathways are usually modelled using classical quantitative methods, which are based on ordinary differential equations (ODEs). However, some difficulties are inherent in this approach. On the one hand, the kinetic parameters involved are often unknown and have to be estimated. With increasing size and complexity of signal transduction pathways, the estimation of missing kinetic data is not possible. On the other hand, ODEs based models do not support any explicit insights into possible (signal-) flows within the network. Moreover, a huge amount of qualitative data is available due to high-throughput techniques. In order to get information on the systems behaviour, qualitative analysis techniques have been developed. Applications of the known qualitative analysis methods concern mainly metabolic networks. Petri net theory provides a variety of established analysis techniques, which are also applicable to signal transduction models. In this context special properties have to be considered and new dedicated techniques have to be designed. Methods We apply Petri net theory to model and analyse signal transduction pathways first qualitatively before continuing with quantitative analyses. This paper demonstrates how to build systematically a discrete model, which reflects provably the qualitative biological behaviour without any knowledge of kinetic parameters. The mating pheromone response pathway in Saccharomyces cerevisiae serves as case study. Results We propose an approach for model validation of signal transduction pathways based on the network structure only. For this purpose, we introduce the new notion of feasible t-invariants, which represent minimal self-contained subnets being active under a given input situation. Each of these subnets stands for a signal flow in the system. We define maximal common transition sets (MCT-sets), which can be used for t-invariant examination and net decomposition into smallest biologically meaningful functional units. Conclusion The paper demonstrates how Petri net analysis techniques can promote a deeper understanding of signal transduction pathways. The new concepts of feasible t-invariants and MCT-sets have been proven to be useful for model validation and the interpretation of the biological system behaviour. Whereas MCT-sets provide a decomposition of the net into disjunctive subnets, feasible t-invariants describe subnets, which generally overlap. This work contributes to qualitative modelling and to the analysis of large biological networks by their fully automatic decomposition into biologically meaningful modules. PMID:17081284

Catalysis by Metallic Nanoparticles in Solution: Thermosensitive Microgels as Nanoreactors

NASA Astrophysics Data System (ADS)

Roa, Rafael; Angioletti-Uberti, Stefano; Lu, Yan; Dzubiella, Joachim; Piazza, Francesco; Ballauff, Matthias

2018-05-01

Metallic nanoparticles have been used as catalysts for various reactions, and the huge literature on the subject is hard to overlook. In many applications, the nanoparticles must be affixed to a colloidal carrier for easy handling during catalysis. These "passive carriers" (e.g. dendrimers) serve for a controlled synthesis of the nanoparticles and prevent coagulation during catalysis. Recently, hybrids from nanoparticles and polymers have been developed that allow us to change the catalytic activity of the nanoparticles by external triggers. In particular, single nanoparticles embedded in a thermosensitive network made from poly(N-isopropylacrylamide) (PNIPAM) have become the most-studied examples of such hybrids: immersed in cold water, the PNIPAM network is hydrophilic and fully swollen. In this state, hydrophilic substrates can diffuse easily through the network, and react at the surface of the nanoparticles. Above the volume transition located at 32°C, the network becomes hydrophobic and shrinks. Now hydrophobic substrates will preferably diffuse through the network and react with other substrates in the reaction catalyzed by the enclosed nanoparticle. Such "active carriers", may thus be viewed as true nanoreactors that open new ways for the use of nanoparticles in catalysis. In this review, we give a survey on recent work done on these hybrids and their application in catalysis. The aim of this review is threefold: we first review hybrid systems composed of nanoparticles and thermosensitive networks and compare these "active carriers" to other colloidal and polymeric carriers (e.g. dendrimers). In a second step we discuss the model reactions used to obtain precise kinetic data on the catalytic activity of nanoparticles in various carriers and environments. These kinetic data allow us to present a fully quantitative comparison of different nanoreactors. In a final section we shall present the salient points of recent efforts in the theoretical modeling of these nanoreactors. By accounting for the presence of a free-energy landscape for the reactants' diffusive approach towards the catalytic nanoparticle, arising from solvent-reactant and polymeric shell-reactant interactions, these models are capable of explaining the emergence of all the important features observed so far in studies of nanoreactors. The present survey also suggests that such models may be used for the design of future carrier systems adapted to a given reaction and solvent.

A paradigm for modeling and computation of gas dynamics

NASA Astrophysics Data System (ADS)

Xu, Kun; Liu, Chang

2017-02-01

In the continuum flow regime, the Navier-Stokes (NS) equations are usually used for the description of gas dynamics. On the other hand, the Boltzmann equation is applied for the rarefied flow. These two equations are based on distinguishable modeling scales for flow physics. Fortunately, due to the scale separation, i.e., the hydrodynamic and kinetic ones, both the Navier-Stokes equations and the Boltzmann equation are applicable in their respective domains. However, in real science and engineering applications, they may not have such a distinctive scale separation. For example, around a hypersonic flying vehicle, the flow physics at different regions may correspond to different regimes, where the local Knudsen number can be changed significantly in several orders of magnitude. With a variation of flow physics, theoretically a continuous governing equation from the kinetic Boltzmann modeling to the hydrodynamic Navier-Stokes dynamics should be used for its efficient description. However, due to the difficulties of a direct modeling of flow physics in the scale between the kinetic and hydrodynamic ones, there is basically no reliable theory or valid governing equations to cover the whole transition regime, except resolving flow physics always down to the mean free path scale, such as the direct Boltzmann solver and the Direct Simulation Monte Carlo (DSMC) method. In fact, it is an unresolved problem about the exact scale for the validity of the NS equations, especially in the small Reynolds number cases. The computational fluid dynamics (CFD) is usually based on the numerical solution of partial differential equations (PDEs), and it targets on the recovering of the exact solution of the PDEs as mesh size and time step converging to zero. This methodology can be hardly applied to solve the multiple scale problem efficiently because there is no such a complete PDE for flow physics through a continuous variation of scales. For the non-equilibrium flow study, the direct modeling methods, such as DSMC, particle in cell, and smooth particle hydrodynamics, play a dominant role to incorporate the flow physics into the algorithm construction directly. It is fully legitimate to combine the modeling and computation together without going through the process of constructing PDEs. In other words, the CFD research is not only to obtain the numerical solution of governing equations but to model flow dynamics as well. This methodology leads to the unified gas-kinetic scheme (UGKS) for flow simulation in all flow regimes. Based on UGKS, the boundary for the validation of the Navier-Stokes equations can be quantitatively evaluated. The combination of modeling and computation provides a paradigm for the description of multiscale transport process.

Probing static disorder in Arrhenius kinetics by single-molecule force spectroscopy.

PubMed

Kuo, Tzu-Ling; Garcia-Manyes, Sergi; Li, Jingyuan; Barel, Itay; Lu, Hui; Berne, Bruce J; Urbakh, Michael; Klafter, Joseph; Fernández, Julio M

2010-06-22

The widely used Arrhenius equation describes the kinetics of simple two-state reactions, with the implicit assumption of a single transition state with a well-defined activation energy barrier DeltaE, as the rate-limiting step. However, it has become increasingly clear that the saddle point of the free-energy surface in most reactions is populated by ensembles of conformations, leading to nonexponential kinetics. Here we present a theory that generalizes the Arrhenius equation to include static disorder of conformational degrees of freedom as a function of an external perturbation to fully account for a diverse set of transition states. The effect of a perturbation on static disorder is best examined at the single-molecule level. Here we use force-clamp spectroscopy to study the nonexponential kinetics of single ubiquitin proteins unfolding under force. We find that the measured variance in DeltaE shows both force-dependent and independent components, where the force-dependent component scales with F(2), in excellent agreement with our theory. Our study illustrates a novel adaptation of the classical Arrhenius equation that accounts for the microscopic origins of nonexponential kinetics, which are essential in understanding the rapidly growing body of single-molecule data.

Kinetic studies of the stability of Pt for No oxidation: effect of sulfur and long-term aging.

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

Pazmino, J. H.; Miller, J. T.; Mulla, S. S.

2011-01-01

The stability of Pt catalysts for NO oxidation was analyzed by observing the effect of pre-adsorbed sulfur on the reaction kinetics using a series of Pt/SBA-15 catalysts with varying Pt particle sizes (ca 2-9 nm). Our results indicate that sulfur addition did not influence catalyst deactivation of any of the Pt catalysts, resulting in unchanged turnover rates (TOR) and reaction kinetics. The presence of sulfur on Pt was confirmed by X-ray absorption fine structure spectroscopy (EXAFS) under reducing environments. However, exposure of the catalyst to NO oxidation conditions displaced sulfur from the first coordination shell of Pt, yielding Pt-O bondsmore » instead. Re-reduction fully recovered the Pt-S backscattering, implying that sulfur remained near the Pt under oxidizing conditions. X-ray photoelectron spectroscopy (XPS) and chemisorption measurements confirmed the presence of sulfur near platinum. The invariance of the NO oxidation reaction to sulfur poisoning is explained by sulfur displacement to interfacial sites and/or sulfur binding on kinetically irrelevant sites. Formation of Pt oxides remains as the main source of catalyst deactivation as observed by kinetic and X-ray absorption spectroscopy (XAS) measurements.« less

Kinetics of bacterial phospholipase C activity at micellar interfaces: effect of substrate aggregate microstructure and a model for the kinetic parameters.

PubMed

Singh, Jasmeet; Ranganathan, Radha; Hajdu, Joseph

2008-12-25

Activity at micellar interfaces of bacterial phospholipase C from Bacillus cereus on phospholipids solubilized in micelles was investigated with the goal of elucidating the role of the interface microstructure and developing further an existing kinetic model. Enzyme kinetics and physicochemical characterization of model substrate aggregates were combined, thus enabling the interpretation of kinetics in the context of the interface. Substrates were diacylphosphatidylcholine of different acyl chain lengths in the form of mixed micelles with dodecyldimethylammoniopropanesulfonate. An early kinetic model, reformulated to reflect the interfacial nature of the kinetics, was applied to the kinetic data. A better method of data treatment is proposed, use of which makes the presence of microstructure effects quite transparent. Models for enzyme-micelle binding and enzyme-lipid binding are developed, and expressions incorporating the microstructural properties are derived for the enzyme-micelle dissociation constant K(s) and the interface Michaelis-Menten constant, K(M). Use of these expressions in the interface kinetic model brings excellent agreement between the kinetic data and the model. Numerical values for the thermodynamic and kinetic parameters are determined. Enzyme-lipid binding is found to be an activated process with an acyl chain length dependent free energy of activation that decreases with micelle lipid molar fraction with a coefficient of about -15RT and correlates with the tightness of molecular packing in the substrate aggregate. Thus, the physical insight obtained includes a model for the kinetic parameters that shows that these parameters depend on the substrate concentration and acyl chain length of the lipid. Enzyme-micelle binding is indicated to be hydrophobic and solvent mediated with a dissociation constant of 1.2 mM.

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.

Aerobic sludge digestion under low dissolved oxygen concentrations.

PubMed

Arunachalam, RaviSankar; Shah, Hemant K; Ju, Lu-Kwang

2004-01-01

Low dissolved oxygen (DO) concentrations occur commonly in aerobic digesters treating thickened sludge, with benefits of smaller digester size, much reduced aeration cost, and higher digestion temperature (especially important for plants in colder areas). The effects of low DO concentrations on digestion kinetics were studied using the sludge from municipal wastewater treatment plants in Akron, Ohio, and Los Lunas, New Mexico. The experiments were conducted in both batch digestion and a mixed mode of continuous, fed-batch, and batch operations. The low DO condition was clearly advantageous in eliminating the need for pH control because of the simultaneous occurrence of nitrification and denitrification. However, when compared with fully aerobic (high DO) systems under constant pH control (rare in full-scale plants), low DO concentrations and a higher solids loading had a negative effect on the specific volatile solids (VS) digestion kinetics. Nonetheless, the overall (volumetric) digestion performance depends not only on the specific digestion kinetics, but also the solids concentration, pH, and digester temperature. All of the latter factors favor the low DO digestion of thickened sludge. The significant effect of temperature on low DO digestion was confirmed in the mixed-mode study with the Akron sludge. When compared with the well-known empirical correlation between VS reduction and the product (temperature x solids retention time), the experimental data followed the same trend, but were lower than the correlation predictions. The latter was attributed to the lower digestible VS in the Akron sludge, the slower digestion at low DO concentrations, or both. Through model simulation, the first-order decay constant (kd) was estimated as 0.004 h(-1) in the mixed-mode operations, much lower than those (0.011 to 0.029 h(-1)) obtained in batch digestion. The findings suggested that the interactions among sludges with different treatment ages may have a substantially negative effect on digestion kinetics. The use of multistage digesters, especially with small front-end reactors, may be advantageous in both "process" kinetics and "biological reaction" kinetics for sludge digestion.

Laboratory and numerical investigations of kinetic interface sensitive tracers transport for immiscible two-phase flow porous media systems

NASA Astrophysics Data System (ADS)

Tatomir, Alexandru Bogdan A. C.; Sauter, Martin

2017-04-01

A number of theoretical approaches estimating the interfacial area between two fluid phases are available (Schaffer et al.,2013). Kinetic interface sensitive (KIS) tracers are used to describe the evolution of fluid-fluid interfaces advancing in two phase porous media systems (Tatomir et al., 2015). Initially developed to offer answers about the supercritical (sc)CO2 plume movement and the efficiency of trapping in geological carbon storage reservoirs, KIS tracers are tested in dynamic controlled laboratory conditions. N-octane and water, analogue to a scCO2 - brine system, are used. The KIS tracer is dissolved in n-octane, which is injected as the non-wetting phase in a fully water saturated porous media column. The porous system is made up of spherical glass beads with sizes of 100-250 μm. Subsequently, the KIS tracer follows a hydrolysis reaction over the n-octane - water interface resulting in an acid and phenol which are both water soluble. The fluid-fluid interfacial area is described numerically with the help of constitutive-relationships derived from the Brooks-Corey model. The specific interfacial area is determined numerically from pore scale calculations, or from different literature sources making use of pore network model calculations (Joekar-Niasar et al., 2008). This research describes the design of the laboratory setup and compares the break-through curves obtained with the forward model and in the laboratory experiment. Furthermore, first results are shown in the attempt to validate the immiscible two phase flow reactive transport numerical model with dynamic laboratory column experiments. Keywords: Fluid-fluid interfacial area, KIS tracers, model validation, CCS, geological storage of CO2

Modelling dimercaptosuccinic acid (DMSA) plasma kinetics in humans.

PubMed

van Eijkeren, Jan C H; Olie, J Daniël N; Bradberry, Sally M; Vale, J Allister; de Vries, Irma; Meulenbelt, Jan; Hunault, Claudine C

2016-11-01

No kinetic models presently exist which simulate the effect of chelation therapy on lead blood concentrations in lead poisoning. Our aim was to develop a kinetic model that describes the kinetics of dimercaptosuccinic acid (DMSA; succimer), a commonly used chelating agent, that could be used in developing a lead chelating model. This was a kinetic modelling study. We used a two-compartment model, with a non-systemic gastrointestinal compartment (gut lumen) and the whole body as one systemic compartment. The only data available from the literature were used to calibrate the unknown model parameters. The calibrated model was then validated by comparing its predictions with measured data from three different experimental human studies. The model predicted total DMSA plasma and urine concentrations measured in three healthy volunteers after ingestion of DMSA 10 mg/kg. The model was then validated by using data from three other published studies; it predicted concentrations within a factor of two, representing inter-human variability. A simple kinetic model simulating the kinetics of DMSA in humans has been developed and validated. The interest of this model lies in the future potential to use it to predict blood lead concentrations in lead-poisoned patients treated with DMSA.

Kinetic Modeling of a Heterogeneous Fenton Oxidative Treatment of Petroleum Refining Wastewater

PubMed Central

Basheer Hasan, Diya'uddeen; Abdul Raman, Abdul Aziz; Wan Daud, Wan Mohd Ashri

2014-01-01

The mineralisation kinetics of petroleum refinery effluent (PRE) by Fenton oxidation were evaluated. Within the ambit of the experimental data generated, first-order kinetic model (FKM), generalised lumped kinetic model (GLKM), and generalized kinetic model (GKM) were tested. The obtained apparent kinetic rate constants for the initial oxidation step (k 2′), their final oxidation step (k 1′), and the direct conversion to endproducts step (k 3′) were 10.12, 3.78, and 0.24 min−1 for GKM; 0.98, 0.98, and nil min−1 for GLKM; and nil, nil, and >0.005 min−1 for FKM. The findings showed that GKM is superior in estimating the mineralization kinetics. PMID:24592152

The spatial-temporal characteristics of type I collagen-based extracellular matrix.

PubMed

Jones, Christopher Allen Rucksack; Liang, Long; Lin, Daniel; Jiao, Yang; Sun, Bo

2014-11-28

Type I collagen abounds in mammalian extracellular matrix (ECM) and is crucial to many biophysical processes. While previous studies have mostly focused on bulk averaged properties, here we provide a comprehensive and quantitative spatial-temporal characterization of the microstructure of type I collagen-based ECM as the gelation temperature varies. The structural characteristics including the density and nematic correlation functions are obtained by analyzing confocal images of collagen gels prepared at a wide range of gelation temperatures (from 16 °C to 36 °C). As temperature increases, the gel microstructure varies from a "bundled" network with strong orientational correlation between the fibers to an isotropic homogeneous network with no significant orientational correlation, as manifested by the decaying of length scales in the correlation functions. We develop a kinetic Monte-Carlo collagen growth model to better understand how ECM microstructure depends on various environmental or kinetic factors. We show that the nucleation rate, growth rate, and an effective hydrodynamic alignment of collagen fibers fully determines the spatiotemporal fluctuations of the density and orientational order of collagen gel microstructure. Also the temperature dependence of the growth rate and nucleation rate follow the prediction of classical nucleation theory.

Kinetic Modeling of RF Breakdown in High-Pressure Gas-filled Cavities

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

Tollestrup, A. V.; Yonehara, K.; Byrd, J. M.

2012-05-01

Recent studies have shown that high gradients can be achieved quickly in high-pressure gas-filled cavities without the need for long conditioning times, because the dense gas can dramatically reduce dark currents and multipacting. In this proj ect we use this high pressure technique to suppress effects of residual vacuum and geometry found in evacuated cavities to isolate and study the role of the metallic surfaces in RF cavity breakdown as a function of radiofrequency and surface preparation. A series of experiments at 805 MHz using hydrogen fill pressures up to 0.01 g/cm3 of H2 have demonstrated high electric field gradientsmore » and scaling with the DC Paschen law limit, up to ~30 MV/m, depending on the choice of electrode material. For higher fi eld stresses, the breakdown characteristics deviate from the Paschen law scaling. Fully-kinetic 0D collisional particle-in-cell (PIC) simulations give breakdown characteristics in H2 and H2/SF6 mixtures in good agreement with the 805 MHz experimental resu lts below this field stress threshold. The impact of these results on gas-filled RF accelerating cavity design will be discussed.« less

Characterization of the mammalian miRNA turnover landscape

PubMed Central

Guo, Yanwen; Liu, Jun; Elfenbein, Sarah J.; Ma, Yinghong; Zhong, Mei; Qiu, Caihong; Ding, Ye; Lu, Jun

2015-01-01

Steady state cellular microRNA (miRNA) levels represent the balance between miRNA biogenesis and turnover. The kinetics and sequence determinants of mammalian miRNA turnover during and after miRNA maturation are not fully understood. Through a large-scale study on mammalian miRNA turnover, we report the co-existence of multiple cellular miRNA pools with distinct turnover kinetics and biogenesis properties and reveal previously unrecognized sequence features for fast turnover miRNAs. We measured miRNA turnover rates in eight mammalian cell types with a combination of expression profiling and deep sequencing. While most miRNAs are stable, a subset of miRNAs, mostly miRNA*s, turnovers quickly, many of which display a two-step turnover kinetics. Moreover, different sequence isoforms of the same miRNA can possess vastly different turnover rates. Fast turnover miRNA isoforms are enriched for 5′ nucleotide bias against Argonaute-(AGO)-loading, but also additional 3′ and central sequence features. Modeling based on two fast turnover miRNA*s miR-222-5p and miR-125b-1-3p, we unexpectedly found that while both miRNA*s are associated with AGO, they strongly differ in HSP90 association and sensitivity to HSP90 inhibition. Our data characterize the landscape of genome-wide miRNA turnover in cultured mammalian cells and reveal differential HSP90 requirements for different miRNA*s. Our findings also implicate rules for designing stable small RNAs, such as siRNAs. PMID:25653157

An overlapping region between the two terminal folding units of the outer surface protein A (OspA) controls its folding behavior.

PubMed

Makabe, Koki; Nakamura, Takashi; Dhar, Debanjan; Ikura, Teikichi; Koide, Shohei; Kuwajima, Kunihiro

2018-04-27

Although many naturally occurring proteins consist of multiple domains, most studies on protein folding to date deal with single-domain proteins or isolated domains of multi-domain proteins. Studies of multi-domain protein folding are required for further advancing our understanding of protein folding mechanisms. Borrelia outer surface protein A (OspA) is a β-rich two-domain protein, in which two globular domains are connected by a rigid and stable single-layer β-sheet. Thus, OspA is particularly suited as a model system for studying the interplays of domains in protein folding. Here, we studied the equilibria and kinetics of the urea-induced folding-unfolding reactions of OspA probed with tryptophan fluorescence and ultraviolet circular dichroism. Global analysis of the experimental data revealed compelling lines of evidence for accumulation of an on-pathway intermediate during kinetic refolding and for the identity between the kinetic intermediate and a previously described equilibrium unfolding intermediate. The results suggest that the intermediate has the fully native structure in the N-terminal domain and the single layer β-sheet, with the C-terminal domain still unfolded. The observation of the productive on-pathway folding intermediate clearly indicates substantial interactions between the two domains mediated by the single-layer β-sheet. We propose that a rigid and stable intervening region between two domains creates an overlap between two folding units and can energetically couple their folding reactions. Copyright © 2018. Published by Elsevier Ltd.

Mark R. Nimlos | NREL

Science.gov Websites

, reaction kinetics, computational modeling, photochemistry, and molecular spectroscopy. Nimlos has served as Chemical reaction energetics and kinetics Biomass pyrolysis and gasification Heterogeneous catalysis in zeolites Quantum modeling and kinetic modeling of reaction Molecular dynamics modeling

Magnetosphere Modeling: From Cartoons to Simulations

NASA Astrophysics Data System (ADS)

Gombosi, T. I.

2017-12-01

Over the last half a century physics-based global computer simulations became a bridge between experiment and basic theory and now it represents the "third pillar" of geospace research. Today, many of our scientific publications utilize large-scale simulations to interpret observations, test new ideas, plan campaigns, or design new instruments. Realistic simulations of the complex Sun-Earth system have been made possible by the dramatically increased power of both computing hardware and numerical algorithms. Early magnetosphere models were based on simple E&M concepts (like the Chapman-Ferraro cavity) and hydrodynamic analogies (bow shock). At the beginning of the space age current system models were developed culminating in the sophisticated Tsyganenko-type description of the magnetic configuration. The first 3D MHD simulations of the magnetosphere were published in the early 1980s. A decade later there were several competing global models that were able to reproduce many fundamental properties of the magnetosphere. The leading models included the impact of the ionosphere by using a height-integrated electric potential description. Dynamic coupling of global and regional models started in the early 2000s by integrating a ring current and a global magnetosphere model. It has been recognized for quite some time that plasma kinetic effects play an important role. Presently, global hybrid simulations of the dynamic magnetosphere are expected to be possible on exascale supercomputers, while fully kinetic simulations with realistic mass ratios are still decades away. In the 2010s several groups started to experiment with PIC simulations embedded in large-scale 3D MHD models. Presently this integrated MHD-PIC approach is at the forefront of magnetosphere simulations and this technique is expected to lead to some important advances in our understanding of magnetosheric physics. This talk will review the evolution of magnetosphere modeling from cartoons to current systems, to global MHD to MHD-PIC and discuss the role of state-of-the-art models in forecasting space weather.

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.

Fully kinetic 3D simulations of the Hermean magnetosphere under realistic conditions: a new approach

NASA Astrophysics Data System (ADS)

Amaya, Jorge; Gonzalez-Herrero, Diego; Lembège, Bertrand; Lapenta, Giovanni

2017-04-01

Simulations of the magnetosphere of planets are usually performed using the MHD and the hybrid approaches. However, these two methods still rely on approximations for the computation of the pressure tensor, and require the neutrality of the plasma at every point of the domain by construction. These approximations undermine the role of electrons on the emergence of plasma features in the magnetosphere of planets. The high mobility of electrons, their characteristic time and space scales, and the lack of perfect neutrality, are the source of many observed phenomena in the magnetospheres, including the turbulence energy cascade, the magnetic reconnection, the particle acceleration in the shock front and the formation of current systems around the magnetosphere. Fully kinetic codes are extremely demanding of computing time, and have been unable to perform simulations of the full magnetosphere at the real scales of a planet with realistic plasma conditions. This is caused by two main reasons: 1) explicit codes must resolve the electron scales limiting the time and space discretisation, and 2) current versions of semi-implicit codes are unstable for cell sizes larger than a few Debye lengths. In this work we present new simulations performed with ECsim, an Energy Conserving semi-implicit method [1], that can overcome these two barriers. We compare the solutions obtained with ECsim with the solutions obtained by the classic semi-implicit code iPic3D [2]. The new simulations with ECsim demand a larger computational effort, but the time and space discretisations are larger than those in iPic3D allowing for a faster simulation time of the full planetary environment. The new code, ECsim, can reach a resolution allowing the capture of significant large scale physics without loosing kinetic electron information, such as wave-electron interaction and non-Maxwellian electron velocity distributions [3]. The code is able to better capture the thickness of the different boundary layers of the magnetosphere of Mercury. Electron kinetics are consistent with the spatial and temporal scale resolutions. Simulations are compared with measurements from the MESSENGER spacecraft showing a better fit when compared against the classic fully kinetic code iPic3D. These results show that the new generation of Energy Conserving semi-implicit codes can be used for an accurate analysis and interpretation of particle data from magnetospheric missions like BepiColombo and MMS, including electron velocity distributions and electron temperature anisotropies. [1] Lapenta, G. (2016). Exactly Energy Conserving Implicit Moment Particle in Cell Formulation. arXiv preprint arXiv:1602.06326. [2] Markidis, S., & Lapenta, G. (2010). Multi-scale simulations of plasma with iPIC3D. Mathematics and Computers in Simulation, 80(7), 1509-1519. [3] Lapenta, G., Gonzalez-Herrero, D., & Boella, E. (2016). Multiple scale kinetic simulations with the energy conserving semi implicit particle in cell (PIC) method. arXiv preprint arXiv:1612.08289.

Kinetics of Methylmercury Production Revisited

DOE PAGES

Olsen, Todd A.; Muller, Katherine A.; Painter, Scott L.; ...

2018-01-27

Laboratory measurements of the biologically mediated methylation of mercury (Hg) to the neurotoxin monomethylmercury (MMHg) often exhibit kinetics that are inconsistent with first-order kinetic models. Using time-resolved measurements of filter passing Hg and MMHg during methylation/demethylation assays, a multisite kinetic sorption model, and reanalyses of previous assays, we show in this paper that competing kinetic sorption reactions can lead to time-varying availability and apparent non-first-order kinetics in Hg methylation and MMHg demethylation. The new model employing a multisite kinetic sorption model for Hg and MMHg can describe the range of behaviors for time-resolved methylation/demethylation data reported in the literature includingmore » those that exhibit non-first-order kinetics. Additionally, we show that neglecting competing sorption processes can confound analyses of methylation/demethylation assays, resulting in rate constant estimates that are systematically biased low. Finally, simulations of MMHg production and transport in a hypothetical periphyton biofilm bed illustrate the implications of our new model and demonstrate that methylmercury production may be significantly different than projected by single-rate first-order models.« less

Fully Kinetic Large-scale Simulations of the Collisionless Magnetorotational Instability

NASA Astrophysics Data System (ADS)

Inchingolo, Giannandrea; Grismayer, Thomas; Loureiro, Nuno F.; Fonseca, Ricardo A.; Silva, Luis O.

2018-06-01

We present two-dimensional particle-in-cell simulations of the fully kinetic collisionless magnetorotational instability (MRI) in weakly magnetized (high β) pair plasma. The central result of this numerical analysis is the emergence of a self-induced turbulent regime in the saturation state of the collisionless MRI, which can only be captured for large enough simulation domains. One of the underlying mechanisms for the development of this turbulent state is the drift-kink instability (DKI) of the current sheets resulting from the nonlinear evolution of the channel modes. The onset of the DKI can only be observed for simulation domain sizes exceeding several linear MRI wavelengths. The DKI and ensuing magnetic reconnection activate the turbulent motion of the plasma in the late stage of the nonlinear evolution of the MRI. At steady-state, the magnetic energy has an MHD-like spectrum with a slope of k ‑5/3 for kρ < 1 and k ‑3 for sub-Larmor scale (kρ > 1). We also examine the role of the collisionless MRI and associated magnetic reconnection in the development of pressure anisotropy. We study the stability of the system due to this pressure anisotropy, observing the development of mirror instability during the early-stage of the MRI. We further discuss the importance of magnetic reconnection for particle acceleration during the turbulence regime. In particular, consistent with reconnection studies, we show that at late times the kinetic energy presents a characteristic slope of ɛ ‑2 in the high-energy region.

Ablation, Thermal Response, and Chemistry Program for Analysis of Thermal Protection Systems

NASA Technical Reports Server (NTRS)

Milos, Frank S.; Chen, Yih-Kanq

2010-01-01

In previous work, the authors documented the Multicomponent Ablation Thermochemistry (MAT) and Fully Implicit Ablation and Thermal response (FIAT) programs. In this work, key features from MAT and FIAT were combined to create the new Fully Implicit Ablation, Thermal response, and Chemistry (FIATC) program. FIATC is fully compatible with FIAT (version 2.5) but has expanded capabilities to compute the multispecies surface chemistry and ablation rate as part of the surface energy balance. This new methodology eliminates B' tables, provides blown species fractions as a function of time, and enables calculations that would otherwise be impractical (e.g. 4+ dimensional tables) such as pyrolysis and ablation with kinetic rates or unequal diffusion coefficients. Equations and solution procedures are presented, then representative calculations of equilibrium and finite-rate ablation in flight and ground-test environments are discussed.

Multi-dimensional, fully implicit, exactly conserving electromagnetic particle-in-cell simulations in curvilinear geometry

NASA Astrophysics Data System (ADS)

Chen, Guangye; Chacon, Luis

2015-11-01

We discuss a new, conservative, fully implicit 2D3V Vlasov-Darwin particle-in-cell algorithm in curvilinear geometry for non-radiative, electromagnetic kinetic plasma simulations. Unlike standard explicit PIC schemes, fully implicit PIC algorithms are unconditionally stable and allow exact discrete energy and charge conservation. Here, we extend these algorithms to curvilinear geometry. The algorithm retains its exact conservation properties in curvilinear grids. The nonlinear iteration is effectively accelerated with a fluid preconditioner for weakly to modestly magnetized plasmas, which allows efficient use of large timesteps, O (√{mi/me}c/veT) larger than the explicit CFL. In this presentation, we will introduce the main algorithmic components of the approach, and demonstrate the accuracy and efficiency properties of the algorithm with various numerical experiments in 1D (slow shock) and 2D (island coalescense).

Integrating Multiple Approaches to Solving Solar Wind Turbulence Problems (Invited)

NASA Astrophysics Data System (ADS)

Karimabadi, H.; Roytershteyn, V.

2013-12-01

The ultimate understanding of the solar wind turbulence must explain the physical process and their connection at all scales ranging from the largest down to electron kinetic scales. This is a daunting task and as a result a more piecemeal approach to the problem has been followed. For example, the role of each wave has been explored in isolation and in simulations with scales limited to those of the underlying waves. In this talk, we present several issues with this approach and offer an alternative with an eye towards more realistic simulations of solar wind turbulence. The main simulation techniques used have been MHD, Hall MHD, hybrid, fully kinetic, and gyrokinetic. We examine the limitations of each approach and their viability for studies of solar wind turbulence. Finally, the effect of initial conditions on the resulting turbulence and their comparison with solar wind are demonstrated through several kinetic simulations.

ER-PM Contacts Define Actomyosin Kinetics for Proper Contractile Ring Assembly.

PubMed

Zhang, Dan; Bidone, Tamara C; Vavylonis, Dimitrios

2016-03-07

The cortical endoplasmic reticulum (ER), an elaborate network of tubules and cisternae [1], establishes contact sites with the plasma membrane (PM) through tethering machinery involving a set of conserved integral ER proteins [2]. The physiological consequences of forming ER-PM contacts are not fully understood. Here, we reveal a kinetic restriction role of ER-PM contacts over ring compaction process for proper actomyosin ring assembly in Schizosaccharomyces pombe. We show that fission yeast cells deficient in ER-PM contacts exhibit aberrant equatorial clustering of actin cables during ring assembly and are particularly susceptible to compromised actin filament crosslinking activity. Using quantitative image analyses and computer simulation, we demonstrate that ER-PM contacts function to modulate the distribution of ring components and to constrain their compaction kinetics. We propose that ER-PM contacts have evolved as important physical modulators to ensure robust ring assembly. Copyright © 2016 Elsevier Ltd. All rights reserved.

Crystal nucleation in amorphous (Au/100-y/Cu/y/)77Si9Ge14 alloys

NASA Technical Reports Server (NTRS)

Thompson, C. V.; Greer, A. L.; Spaepen, F.

1983-01-01

Because, unlike most metallic glasses, melt-spun alloys of the series (Au/100-y/Cu/y/)77Si9Ge14 exhibit well separated glass transition and kinetic crystallization temperatures, crystallization can be studied in the fully relaxed amorphous phase. An isothermal calorimetric analysis of the devitrification kinetics of the amorphous alloy indicates sporadic nucleation and a constant growth rate. It is found for the cases of alloys with y values lower than 25 that the classical theory of homogeneous nucleation is consistent with observations, including transient effects. An analysis of the crystallization kinetics shows that slow crystal growth rates play an important role in glass formation in these alloys. Although the reduced glass transition temperature increases with Cu content, glass formation is more difficult at high Cu contents, perhaps because of a difference in nucleus composition.

Extracting surface diffusion coefficients from batch adsorption measurement data: application of the classic Langmuir kinetics model.

PubMed

Chu, Khim Hoong

2017-11-09

Surface diffusion coefficients may be estimated by fitting solutions of a diffusion model to batch kinetic data. For non-linear systems, a numerical solution of the diffusion model's governing equations is generally required. We report here the application of the classic Langmuir kinetics model to extract surface diffusion coefficients from batch kinetic data. The use of the Langmuir kinetics model in lieu of the conventional surface diffusion model allows derivation of an analytical expression. The parameter estimation procedure requires determining the Langmuir rate coefficient from which the pertinent surface diffusion coefficient is calculated. Surface diffusion coefficients within the 10 -9 to 10 -6  cm 2 /s range obtained by fitting the Langmuir kinetics model to experimental kinetic data taken from the literature are found to be consistent with the corresponding values obtained from the traditional surface diffusion model. The virtue of this simplified parameter estimation method is that it reduces the computational complexity as the analytical expression involves only an algebraic equation in closed form which is easily evaluated by spreadsheet computation.

Astrophysical Gyrokinetics: Kinetic and Fluid Turbulent Cascades in Magnetized Weakly Collisional Plasmas

NASA Astrophysics Data System (ADS)

Schekochihin, A. A.; Cowley, S. C.; Dorland, W.; Hammett, G. W.; Howes, G. G.; Quataert, E.; Tatsuno, T.

2009-05-01

This paper presents a theoretical framework for understanding plasma turbulence in astrophysical plasmas. It is motivated by observations of electromagnetic and density fluctuations in the solar wind, interstellar medium and galaxy clusters, as well as by models of particle heating in accretion disks. All of these plasmas and many others have turbulent motions at weakly collisional and collisionless scales. The paper focuses on turbulence in a strong mean magnetic field. The key assumptions are that the turbulent fluctuations are small compared to the mean field, spatially anisotropic with respect to it and that their frequency is low compared to the ion cyclotron frequency. The turbulence is assumed to be forced at some system-specific outer scale. The energy injected at this scale has to be dissipated into heat, which ultimately cannot be accomplished without collisions. A kinetic cascade develops that brings the energy to collisional scales both in space and velocity. The nature of the kinetic cascade in various scale ranges depends on the physics of plasma fluctuations that exist there. There are four special scales that separate physically distinct regimes: the electron and ion gyroscales, the mean free path and the electron diffusion scale. In each of the scale ranges separated by these scales, the fully kinetic problem is systematically reduced to a more physically transparent and computationally tractable system of equations, which are derived in a rigorous way. In the "inertial range" above the ion gyroscale, the kinetic cascade separates into two parts: a cascade of Alfvénic fluctuations and a passive cascade of density and magnetic-field-strength fluctuations. The former are governed by the reduced magnetohydrodynamic (RMHD) equations at both the collisional and collisionless scales; the latter obey a linear kinetic equation along the (moving) field lines associated with the Alfvénic component (in the collisional limit, these compressive fluctuations become the slow and entropy modes of the conventional MHD). In the "dissipation range" below ion gyroscale, there are again two cascades: the kinetic-Alfvén-wave (KAW) cascade governed by two fluid-like electron reduced magnetohydrodynamic (ERMHD) equations and a passive cascade of ion entropy fluctuations both in space and velocity. The latter cascade brings the energy of the inertial-range fluctuations that was Landau-damped at the ion gyroscale to collisional scales in the phase space and leads to ion heating. The KAW energy is similarly damped at the electron gyroscale and converted into electron heat. Kolmogorov-style scaling relations are derived for all of these cascades. The relationship between the theoretical models proposed in this paper and astrophysical applications and observations is discussed in detail.

The structure of turbulence in fully developed pipe flow

NASA Technical Reports Server (NTRS)

Laufer, John

1954-01-01

Measurements, principally with a hot-wire anemometer, were made in fully developed turbulent flow in a 10-inch pipe at speeds of approximately 10 and 100 feet per second. Emphasis was placed on turbulence and conditions near the wall. The results include relevant mean and statistical quantities, such as Reynolds stresses, triple correlations, turbulent dissipation, and energy spectra. It is shown that rates of turbulent-energy production, dissipation, and diffusion have sharp maximums near the edge of the laminar sublayer and that there exist a strong movement of kinetic energy away from this point and an equally strong movement of pressure energy toward it.

Viral kinetic modeling: state of the art

DOE PAGES

Canini, Laetitia; Perelson, Alan S.

2014-06-25

Viral kinetic modeling has led to increased understanding of the within host dynamics of viral infections and the effects of therapy. Here we review recent developments in the modeling of viral infection kinetics with emphasis on two infectious diseases: hepatitis C and influenza. We review how viral kinetic modeling has evolved from simple models of viral infections treated with a drug or drug cocktail with an assumed constant effectiveness to models that incorporate drug pharmacokinetics and pharmacodynamics, as well as phenomenological models that simply assume drugs have time varying-effectiveness. We also discuss multiscale models that include intracellular events in viralmore » replication, models of drug-resistance, models that include innate and adaptive immune responses and models that incorporate cell-to-cell spread of infection. Overall, viral kinetic modeling has provided new insights into the understanding of the disease progression and the modes of action of several drugs. In conclusion, we expect that viral kinetic modeling will be increasingly used in the coming years to optimize drug regimens in order to improve therapeutic outcomes and treatment tolerability for infectious diseases.« less

Double Asteroid Redirection Test (DART) element of AIDA mission

NASA Astrophysics Data System (ADS)

Cheng, A.; Michel, P.; Rivkin, A.; Barnouin, O.; Stickle, A.; Miller, P.; Chesley, S.; Richardson, D.

2017-09-01

The AIDA mission, an international cooperation between NASA and ESA, will be the first demonstration of a kinetic impactor spacecraft to deflect an asteroid. AIDA will perform the first hypervelocity impact on an asteroid where the impact conditions are fully known and the target properties are also characterized. AIDA will reduce risks for any future asteroid hazard mitigation.

SPH simulations of WBC adhesion to the endothelium: the role of haemodynamics and endothelial binding kinetics.

PubMed

Gholami, Babak; Comerford, Andrew; Ellero, Marco

2015-11-01

A multiscale Lagrangian particle solver introduced in our previous work is extended to model physiologically realistic near-wall cell dynamics. Three-dimensional simulation of particle trajectories is combined with realistic receptor-ligand adhesion behaviour to cover full cell interactions in the vicinity of the endothelium. The selected stochastic adhesion model, which is based on a Monte Carlo acceptance-rejection method, fits in our Lagrangian framework and does not compromise performance. Additionally, appropriate inflow/outflow boundary conditions are implemented for our SPH solver to enable realistic pulsatile flow simulation. The model is tested against in-vitro data from a 3D geometry with a stenosis and sudden expansion. In both steady and pulsatile flow conditions, results show close agreement with the experimental ones. Furthermore we demonstrate, in agreement with experimental observations, that haemodynamics alone does not account for adhesion of white blood cells, in this case U937 monocytic human cells. Our findings suggest that the current framework is fully capable of modelling cell dynamics in large arteries in a realistic and efficient manner.

A study of the kinetic energy generation with general circulation models

NASA Technical Reports Server (NTRS)

Chen, T.-C.; Lee, Y.-H.

1983-01-01

The history data of winter simulation by the GLAS climate model and the NCAR community climate model are used to examine the generation of atmospheric kinetic energy. The contrast between the geographic distributions of the generation of kinetic energy and divergence of kinetic energy flux shows that kinetic energy is generated in the upstream side of jets, transported to the downstream side and destroyed there. The contributions from the time-mean and transient modes to the counterbalance between generation of kinetic energy and divergence of kinetic energy flux are also investigated. It is observed that the kinetic energy generated by the time-mean mode is essentially redistributed by the time-mean flow, while that generated by the transient flow is mainly responsible for the maintenance of the kinetic energy of the entire atmospheric flow.

Kinetic control of the coverage of oil droplets by DNA-functionalized colloids

PubMed Central

Joshi, Darshana; Bargteil, Dylan; Caciagli, Alessio; Burelbach, Jerome; Xing, Zhongyang; Nunes, André S.; Pinto, Diogo E. P.; Araújo, Nuno A. M.; Brujic, Jasna; Eiser, Erika

2016-01-01

We report a study of reversible adsorption of DNA-coated colloids on complementary functionalized oil droplets. We show that it is possible to control the surface coverage of oil droplets using colloidal particles by exploiting the fact that, during slow adsorption, compositional arrest takes place well before structural arrest occurs. As a consequence, we can prepare colloid-coated oil droplets with a “frozen” degree of loading but with fully ergodic colloidal dynamics on the droplets. We illustrate the equilibrium nature of the adsorbed colloidal phase by exploring the quasi–two-dimensional phase behavior of the adsorbed colloids under the influence of depletion interactions and present simulations of a simple model that illustrates the nature of the compositional arrest and the structural ergodicity. PMID:27532053

Nucleation and Growth of Crystalline Grains in RF-Sputtered TiO 2 Films

DOE PAGES

Johnson, J. C.; Ahrenkiel, S. P.; Dutta, P.; ...

2009-01-01

Amore » morphous TiO 2 thin films were radio frequency sputtered onto siliconmonoxide and carbon support films on molybdenum transmission electron microscope (TEM) grids and observed during in situ annealing in a TEM heating stage at 250 ∘ C. The evolution of crystallization is consistent with a classical model of homogeneous nucleation and isotropic grain growth. The two-dimensional grain morphology of the TEM foil allowed straightforward recognition of amorphous and crystallized regions of the films, for measurement of crystalline volume fraction and grain number density. By assuming that the kinetic parameters remain constant beyond the onset of crystallization, the final average grain size was computed, using an analytical extrapolation to the fully crystallized state. Electron diffraction reveals a predominance of the anatase crystallographic phase.« less

Probing the Intermediacy of Covalent RNA Enzyme Complexes in RNA Modification Enzymes

PubMed Central

Chervin, Stephanie M.; Kittendorf, Jeffrey D.; Garcia, George A.

2009-01-01

Within the large and diverse group of RNA-modifying enzymes, a number of enzymes seem to form stable covalent linkages to their respective RNA substrates. A complete understanding of the chemical and kinetic mechanisms of these enzymes, some of which have identified pathological roles, is lacking. As part of our ongoing work studying the posttranscriptional modification of tRNA with queuine, we wish to understand fully the chemical and kinetic mechanisms involved in this key transglycosylation reaction. In our previous investigations, we have used a gel mobility-shift assay to characterize an apparent covalent enzyme-RNA intermediate believed to be operative in the catalytic pathway. However, the simple observation of a covalent complex is not sufficient to prove intermediacy. To be a true intermediate, the complex must be both chemically and kinetically competent. As a case study for the proof of intermediacy, we report the use of this gel-shift assay under mildly denaturing conditions to probe the kinetic competency of the covalent association between RNA and the tRNA modifying enzyme tRNA-guanine transglycosylase (TGT). PMID:17673081

Automated smoother for the numerical decoupling of dynamics models.

PubMed

Vilela, Marco; Borges, Carlos C H; Vinga, Susana; Vasconcelos, Ana Tereza R; Santos, Helena; Voit, Eberhard O; Almeida, Jonas S

2007-08-21

Structure identification of dynamic models for complex biological systems is the cornerstone of their reverse engineering. Biochemical Systems Theory (BST) offers a particularly convenient solution because its parameters are kinetic-order coefficients which directly identify the topology of the underlying network of processes. We have previously proposed a numerical decoupling procedure that allows the identification of multivariate dynamic models of complex biological processes. While described here within the context of BST, this procedure has a general applicability to signal extraction. Our original implementation relied on artificial neural networks (ANN), which caused slight, undesirable bias during the smoothing of the time courses. As an alternative, we propose here an adaptation of the Whittaker's smoother and demonstrate its role within a robust, fully automated structure identification procedure. In this report we propose a robust, fully automated solution for signal extraction from time series, which is the prerequisite for the efficient reverse engineering of biological systems models. The Whittaker's smoother is reformulated within the context of information theory and extended by the development of adaptive signal segmentation to account for heterogeneous noise structures. The resulting procedure can be used on arbitrary time series with a nonstationary noise process; it is illustrated here with metabolic profiles obtained from in-vivo NMR experiments. The smoothed solution that is free of parametric bias permits differentiation, which is crucial for the numerical decoupling of systems of differential equations. The method is applicable in signal extraction from time series with nonstationary noise structure and can be applied in the numerical decoupling of system of differential equations into algebraic equations, and thus constitutes a rather general tool for the reverse engineering of mechanistic model descriptions from multivariate experimental time series.

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.

Effects of Step Length, Age, and Fall History on Hip and Knee Kinetics and Knee Co-contraction during the Maximum Step Length Test

PubMed Central

Schulz, Brian W.; Jongprasithporn, Manutchanok; Hart-Hughes, Stephanie J.; Bulat, Tatjana

2017-01-01

Background Maximum step length is a brief clinical test involving stepping out and back as far as possible with the arms folded across the chest. This test has been shown to predict fall risk, but the biomechanics of this test are not fully understood. Knee and hip kinetics (moments and powers) are greater for longer steps and for younger subjects, but younger subjects also step farther. Methods To separate effects of step length, age, and fall history on joint kinetics; 14 healthy younger, 14 older non-fallers, and 11 older fallers (27(5), 72(5), 75(6) years respectively) all stepped to the same relative target distances of 20-80% of their height. Knee and hip kinetics and knee co-contraction were calculated. Findings Hip and knee kinetics and knee co-contraction all increased with step length, but older non-fallers and fallers utilized greater stepping hip and less stepping knee extensor kinetics. Fallers had greater stepping knee co-contraction than non-fallers. Stance knee co-contraction of non-fallers was similar to young for shorter steps and similar to fallers for longer steps. Interpretation Age had minimal effects and fall history had no effects on joint kinetics of steps to similar distances. Effects of age and fall history on knee co-contraction may contribute to age-related kinetic differences and shorter maximal step lengths of older non-fallers and fallers, but step length correlated with every variable tested. Thus, declines in maximum step length could indicate declines in hip and knee extensor kinetics and impaired performance on similar tasks like recovering from a trip. PMID:23978310

Reversible photocapture of a [2]rotaxane harnessing a barbiturate template.

PubMed

Tron, Arnaud; Thornton, Peter J; Lincheneau, Christophe; Desvergne, Jean-Pierre; Spencer, Neil; Tucker, James H R; McClenaghan, Nathan D

2015-01-16

Photoirradiation of a hydrogen-bonded molecular complex comprising acyclic components, namely, a stoppered thread (1) with a central barbiturate motif and an optimized doubly anthracene-terminated acyclic Hamilton-like receptor (2b), leads to an interlocked architecture, which was isolated and fully characterized. The sole isolated interlocked photoproduct (Φ = 0.06) is a [2]rotaxane, with the dimerized anthracenes assuming a head-to-tail geometry, as evidenced by NMR spectroscopy and consistent with molecular modeling (PM6). A different behavior was observed on irradiating homologous molecular complexes 1⊂2a, 1⊂2b, and 1⊂2c, where the spacers of 2a, 2b, and 2c incorporated 3, 6, and 9 methylene units, respectively. While no evidence of interlocked structure formation was observed following irradiation of 1⊂2a, a kinetically labile rotaxane was obtained on irradiating the complex 1⊂2c, and ring slippage was revealed. A more stable [2]rotaxane was formed on irradiating 1⊂2b, whose capture is found to be fully reversible upon heating, thereby resetting the system, with some fatigue (38%) after four irradiation–thermal reversion cycles.

The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models

PubMed Central

2013-01-01

Background The complexity and multiscale nature of the mammalian immune response provides an excellent test bed for the potential of mathematical modeling and simulation to facilitate mechanistic understanding. Historically, mathematical models of the immune response focused on subsets of the immune system and/or specific aspects of the response. Mathematical models have been developed for the humoral side of the immune response, or for the cellular side, or for cytokine kinetics, but rarely have they been proposed to encompass the overall system complexity. We propose here a framework for integration of subset models, based on a system biology approach. Results A dynamic simulator, the Fully-integrated Immune Response Model (FIRM), was built in a stepwise fashion by integrating published subset models and adding novel features. The approach used to build the model includes the formulation of the network of interacting species and the subsequent introduction of rate laws to describe each biological process. The resulting model represents a multi-organ structure, comprised of the target organ where the immune response takes place, circulating blood, lymphoid T, and lymphoid B tissue. The cell types accounted for include macrophages, a few T-cell lineages (cytotoxic, regulatory, helper 1, and helper 2), and B-cell activation to plasma cells. Four different cytokines were accounted for: IFN-γ, IL-4, IL-10 and IL-12. In addition, generic inflammatory signals are used to represent the kinetics of IL-1, IL-2, and TGF-β. Cell recruitment, differentiation, replication, apoptosis and migration are described as appropriate for the different cell types. The model is a hybrid structure containing information from several mammalian species. The structure of the network was built to be physiologically and biochemically consistent. Rate laws for all the cellular fate processes, growth factor production rates and half-lives, together with antibody production rates and half-lives, are provided. The results demonstrate how this framework can be used to integrate mathematical models of the immune response from several published sources and describe qualitative predictions of global immune system response arising from the integrated, hybrid model. In addition, we show how the model can be expanded to include novel biological findings. Case studies were carried out to simulate TB infection, tumor rejection, response to a blood borne pathogen and the consequences of accounting for regulatory T-cells. Conclusions The final result of this work is a postulated and increasingly comprehensive representation of the mammalian immune system, based on physiological knowledge and susceptible to further experimental testing and validation. We believe that the integrated nature of FIRM has the potential to simulate a range of responses under a variety of conditions, from modeling of immune responses after tuberculosis (TB) infection to tumor formation in tissues. FIRM also has the flexibility to be expanded to include both complex and novel immunological response features as our knowledge of the immune system advances. PMID:24074340

Phase-field Model for Interstitial Loop Growth Kinetics and Thermodynamic and Kinetic Models of Irradiated Fe-Cr Alloys

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

Li, Yulan; Hu, Shenyang Y.; Sun, Xin

2011-06-15

Microstructure evolution kinetics in irradiated materials has strongly spatial correlation. For example, void and second phases prefer to nucleate and grow at pre-existing defects such as dislocations, grain boundaries, and cracks. Inhomogeneous microstructure evolution results in inhomogeneity of microstructure and thermo-mechanical properties. Therefore, the simulation capability for predicting three dimensional (3-D) microstructure evolution kinetics and its subsequent impact on material properties and performance is crucial for scientific design of advanced nuclear materials and optimal operation conditions in order to reduce uncertainty in operational and safety margins. Very recently the meso-scale phase-field (PF) method has been used to predict gas bubblemore » evolution, void swelling, void lattice formation and void migration in irradiated materials,. Although most results of phase-field simulations are qualitative due to the lake of accurate thermodynamic and kinetic properties of defects, possible missing of important kinetic properties and processes, and the capability of current codes and computers for large time and length scale modeling, the simulations demonstrate that PF method is a promising simulation tool for predicting 3-D heterogeneous microstructure and property evolution, and providing microstructure evolution kinetics for higher scale level simulations of microstructure and property evolution such as mean field methods. This report consists of two parts. In part I, we will present a new phase-field model for predicting interstitial loop growth kinetics in irradiated materials. The effect of defect (vacancy/interstitial) generation, diffusion and recombination, sink strength, long-range elastic interaction, inhomogeneous and anisotropic mobility on microstructure evolution kinetics is taken into account in the model. The model is used to study the effect of elastic interaction on interstitial loop growth kinetics, the interstitial flux, and sink strength of interstitial loop for interstitials. In part II, we present a generic phase field model and discuss the thermodynamic and kinetic properties in phase-field models including the reaction kinetics of radiation defects and local free energy of irradiated materials. In particular, a two-sublattice thermodynamic model is suggested to describe the local free energy of alloys with irradiated defects. Fe-Cr alloy is taken as an example to explain the required thermodynamic and kinetic properties for quantitative phase-field modeling. Finally the great challenges in phase-field modeling will be discussed.« less

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.

Enhancement of 3D guide field magnetic reconnection by self-generated kinetic turbulence

NASA Astrophysics Data System (ADS)

Alejandro Munoz Sepulveda, Patricio; Buechner, Joerg

2017-04-01

Kinetic plasma turbulence is ubiquitous in magnetic reconnection in laboratory, space and astrophysical plasmas. Most of previous investigations focused on the role of low-frequency/Alfvénic turbulence in homogeneous plasmas. High-frequency/electron-scale turbulence in the reconnecting current sheets, however, have been rarely addressed. Our aim is to investigate the role of this self-generated turbulence via kinetic instabilities in 3D magnetic reconnection. For this sake, we carried out 3D fully-kinetic Particle-in-Cell (PiC) code numerical simulations of force free current sheets with a guide magnetic field, a common situation in the plasmas of interest. We show that the dynamically evolving kinetic turbulence spectra is broadband, with a power-law spectrum between the lower hybrid and up to the electron frequencies with a spectral index near 2.7 at the reconnection site. This result is directly in the frequency-domain, without change of frame of reference assuming Taylor's hypothesis. The evolution of the turbulence correlates with the growth and rate of magnetic reconnection and can be explained by unstable waves caused by (kinetic) streaming instabilities driven by electron current. This provides a plausible explanation for the enhancement of magnetic reconnection due to turbulence observed in laboratory experiments like MRX, VTF and VINETA-II, as well as of in-situ measurements in the Earth's magnetosphere by the MMS spacecraft.

Large scale structures in the kinetic gravity braiding model that can be unbraided

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

Kimura, Rampei; Yamamoto, Kazuhiro, E-mail: rampei@theo.phys.sci.hiroshima-u.ac.jp, E-mail: kazuhiro@hiroshima-u.ac.jp

2011-04-01

We study cosmological consequences of a kinetic gravity braiding model, which is proposed as an alternative to the dark energy model. The kinetic braiding model we study is characterized by a parameter n, which corresponds to the original galileon cosmological model for n = 1. We find that the background expansion of the universe of the kinetic braiding model is the same as the Dvali-Turner's model, which reduces to that of the standard cold dark matter model with a cosmological constant (ΛCDM model) for n equal to infinity. We also find that the evolution of the linear cosmological perturbation inmore » the kinetic braiding model reduces to that of the ΛCDM model for n = ∞. Then, we focus our study on the growth history of the linear density perturbation as well as the spherical collapse in the nonlinear regime of the density perturbations, which might be important in order to distinguish between the kinetic braiding model and the ΛCDM model when n is finite. The theoretical prediction for the large scale structure is confronted with the multipole power spectrum of the luminous red galaxy sample of the Sloan Digital Sky survey. We also discuss future prospects of constraining the kinetic braiding model using a future redshift survey like the WFMOS/SuMIRe PFS survey as well as the cluster redshift distribution in the South Pole Telescope survey.« less

Modeling of autocatalytic hydrolysis of adefovir dipivoxil in solid formulations.

PubMed

Dong, Ying; Zhang, Yan; Xiang, Bingren; Deng, Haishan; Wu, Jingfang

2011-04-01

The stability and hydrolysis kinetics of a phosphate prodrug, adefovir dipivoxil, in solid formulations were studied. The stability relationship between five solid formulations was explored. An autocatalytic mechanism for hydrolysis could be proposed according to the kinetic behavior which fits the Prout-Tompkins model well. For the classical kinetic models could hardly describe and predict the hydrolysis kinetics of adefovir dipivoxil in solid formulations accurately when the temperature is high, a feedforward multilayer perceptron (MLP) neural network was constructed to model the hydrolysis kinetics. The build-in approaches in Weka, such as lazy classifiers and rule-based learners (IBk, KStar, DecisionTable and M5Rules), were used to verify the performance of MLP. The predictability of the models was evaluated by 10-fold cross-validation and an external test set. It reveals that MLP should be of general applicability proposing an alternative efficient way to model and predict autocatalytic hydrolysis kinetics for phosphate prodrugs.

A Study of the Optimal Model of the Flotation Kinetics of Copper Slag from Copper Mine BOR

NASA Astrophysics Data System (ADS)

Stanojlović, Rodoljub D.; Sokolović, Jovica M.

2014-10-01

In this study the effect of mixtures of copper slag and flotation tailings from copper mine Bor, Serbia on the flotation results of copper recovery and flotation kinetics parameters in a batch flotation cell has been investigated. By simultaneous adding old flotation tailings in the ball mill at the rate of 9%, it is possible to increase copper recovery for about 20%. These results are compared with obtained copper recovery of pure copper slag. The results of batch flotation test were fitted by MatLab software for modeling the first-order flotation kinetics in order to determine kinetics parameters and define an optimal model of the flotation kinetics. Six kinetic models are tested on the batch flotation copper recovery against flotation time. All models showed good correlation, however the modified Kelsall model provided the best fit.

Jovian Plasmas Torus Interaction with Europa. Plasma Wake Structure and Effect of Inductive Magnetic Field: 3D Hybrid Kinetic Simulation

NASA Technical Reports Server (NTRS)

Lipatov, A. S.; Cooper, J F.; Paterson, W. R.; Sittler, E. C., Jr.; Hartle, R. E.; Simpson, David G.

2013-01-01

The hybrid kinetic model supports comprehensive simulation of the interaction between different spatial and energetic elements of the Europa moon-magnetosphere system with respect to a variable upstream magnetic field and flux or density distributions of plasma and energetic ions, electrons, and neutral atoms. This capability is critical for improving the interpretation of the existing Europa flyby measurements from the Galileo Orbiter mission, and for planning flyby and orbital measurements (including the surface and atmospheric compositions) for future missions. The simulations are based on recent models of the atmosphere of Europa (Cassidy et al., 2007; Shematovich et al., 2005). In contrast to previous approaches with MHD simulations, the hybrid model allows us to fully take into account the finite gyroradius effect and electron pressure, and to correctly estimate the ion velocity distribution and the fluxes along the magnetic field (assuming an initial Maxwellian velocity distribution for upstream background ions). Photoionization, electron-impact ionization, charge exchange and collisions between the ions and neutrals are also included in our model. We consider the models with Oþ þ and Sþ þ background plasma, and various betas for background ions and electrons, and pickup electrons. The majority of O2 atmosphere is thermal with an extended non-thermal population (Cassidy et al., 2007). In this paper, we discuss two tasks: (1) the plasma wake structure dependence on the parameters of the upstream plasma and Europa's atmosphere (model I, cases (a) and (b) with a homogeneous Jovian magnetosphere field, an inductive magnetic dipole and high oceanic shell conductivity); and (2) estimation of the possible effect of an induced magnetic field arising from oceanic shell conductivity. This effect was estimated based on the difference between the observed and modeled magnetic fields (model II, case (c) with an inhomogeneous Jovian magnetosphere field, an inductive magnetic dipole and low oceanic shell conductivity).

Novel recirculating loop reactor for studies on model catalysts: CO oxidation on Pt/TiO2(110)

NASA Astrophysics Data System (ADS)

Tenney, Samuel A.; Xie, Kangmin; Monnier, John R.; Rodriguez, Abraham; Galhenage, Randima P.; Duke, Audrey S.; Chen, Donna A.

2013-10-01

A novel recirculating loop microreactor coupled to an ultrahigh vacuum (UHV) chamber has been constructed for the kinetic evaluation of model catalysts, which can be fully characterized by UHV surface science techniques. The challenge for this reactor design is to attain sufficient sensitivity to detect reactions on model single-crystal surfaces, which have a low number of active sites compared to conventional catalysts of equivalent mass. To this end, the total dead volume of the reactor system is minimized (32 cm3), and the system is operated in recirculation mode so that product concentrations build up to detectable levels over time. The injection of gas samples into the gas chromatography column and the refilling of the recirculation loop with fresh feed gas are achieved with computer-controlled, automated switching valves. In this manner, product concentrations can be followed over short time intervals (15 min) for extended periods of time (24 h). A proof of principle study in this reactor for CO oxidation at 145-165 °C on Pt clusters supported on a rutile TiO2(110) single crystal yields kinetic parameters that are comparable to those reported in the literature for CO oxidation on Pt clusters on powdered oxide supports, as well as on Pt(100). The calculated activation energy is 16.4 ± 0.7 kcal/mol, the turnover frequency is 0.03-0.06 molecules/(site.s) over the entire temperature range, and the reaction orders in O2 and CO at 160 °C are 0.9 ± 0.2 and -0.82 ± 0.03, respectively.

Quasiclassical Theory of Spin Dynamics in Superfluid ^3He: Kinetic Equations in the Bulk and Spin Response of Surface Majorana States

NASA Astrophysics Data System (ADS)

Silaev, M. A.

2018-06-01

We develop a theory based on the formalism of quasiclassical Green's functions to study the spin dynamics in superfluid ^3He. First, we derive kinetic equations for the spin-dependent distribution function in the bulk superfluid reproducing the results obtained earlier without quasiclassical approximation. Then, we consider spin dynamics near the surface of fully gapped ^3He-B-phase taking into account spin relaxation due to the transitions in the spectrum of localized fermionic states. The lifetimes of longitudinal and transverse spin waves are calculated taking into account the Fermi-liquid corrections which lead to a crucial modification of fermionic spectrum and spin responses.

Kinetic and dynamic Delaunay tetrahedralizations in three dimensions

NASA Astrophysics Data System (ADS)

Schaller, Gernot; Meyer-Hermann, Michael

2004-09-01

We describe algorithms to implement fully dynamic and kinetic three-dimensional unconstrained Delaunay triangulations, where the time evolution of the triangulation is not only governed by moving vertices but also by a changing number of vertices. We use three-dimensional simplex flip algorithms, a stochastic visibility walk algorithm for point location and in addition, we propose a new simple method of deleting vertices from an existing three-dimensional Delaunay triangulation while maintaining the Delaunay property. As an example, we analyse the performance in various cases of practical relevance. The dual Dirichlet tessellation can be used to solve differential equations on an irregular grid, to define partitions in cell tissue simulations, for collision detection etc.

Electric currents in E-like planetary ionospheres

NASA Technical Reports Server (NTRS)

Cole, K. D.

1990-01-01

In this paper an MHD approach is used to consider the conduction of electric current in a lightly ionized gas, taking into account the gradients of pressure in the ion and electron gases, in addition to the electric field. The coefficients of electrical conductivity are found for each driver of current. New expressions for the components of heat dissipation associated with each driver of current are developed, which are fully consistent with kinetic theory. The relationship of the results to those obtained by kinetic theory is discussed. New components of currents associated with planetary equatorial electrojets are found. A new diffusion equation for magnetic induction is found, applicable in E-like regions of planetary ionospheres, and stellar photospheres.

Direct estimation of tracer-kinetic parameter maps from highly undersampled brain dynamic contrast enhanced MRI.

PubMed

Guo, Yi; Lingala, Sajan Goud; Zhu, Yinghua; Lebel, R Marc; Nayak, Krishna S

2017-10-01

The purpose of this work was to develop and evaluate a T 1 -weighted dynamic contrast enhanced (DCE) MRI methodology where tracer-kinetic (TK) parameter maps are directly estimated from undersampled (k,t)-space data. The proposed reconstruction involves solving a nonlinear least squares optimization problem that includes explicit use of a full forward model to convert parameter maps to (k,t)-space, utilizing the Patlak TK model. The proposed scheme is compared against an indirect method that creates intermediate images by parallel imaging and compressed sensing before to TK modeling. Thirteen fully sampled brain tumor DCE-MRI scans with 5-second temporal resolution are retrospectively undersampled at rates R = 20, 40, 60, 80, and 100 for each dynamic frame. TK maps are quantitatively compared based on root mean-squared-error (rMSE) and Bland-Altman analysis. The approach is also applied to four prospectively R = 30 undersampled whole-brain DCE-MRI data sets. In the retrospective study, the proposed method performed statistically better than indirect method at R ≥ 80 for all 13 cases. This approach provided restoration of TK parameter values with less errors in tumor regions of interest, an improvement compared to a state-of-the-art indirect method. Applied prospectively, the proposed method provided whole-brain, high-resolution TK maps with good image quality. Model-based direct estimation of TK maps from k,t-space DCE-MRI data is feasible and is compatible up to 100-fold undersampling. Magn Reson Med 78:1566-1578, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Hybrid-PIC modeling of laser-plasma interactions and hot electron generation in gold hohlraum walls

NASA Astrophysics Data System (ADS)

Thoma, C.; Welch, D. R.; Clark, R. E.; Rose, D. V.; Golovkin, I. E.

2017-06-01

The walls of the hohlraum used in experiments at the national ignition facility are heated by laser beams with intensities ˜ 10 15 W/cm2, a wavelength of ˜ 1 / 3 μm, and pulse lengths on the order of a ns, with collisional absorption believed to be the primary heating mechanism. X-rays generated by the hot ablated plasma at the gold walls are then used to implode a target in the hohlraum interior. In addition to the collisional absorption of laser energy at the walls, non-linear laser-plasma interactions (LPI), such as stimulated Raman scattering and two plasmon decay, are believed to generate a population of supra-thermal electrons which, if present in the hohlraum, can have a deleterious effect on target implosion. We describe results of hohlraum modeling using a hybrid particle-in-cell code. To enable this work, new particle-based algorithms for a multiple-ion magneto-hydrodynamic (MHD) treatment, and a particle-based ray-tracing model were developed. The use of such hybrid methods relaxes the requirement to resolve the laser wavelength, and allows for relatively large-scale hohlraum simulations with a reasonable number of cells. But the non-linear effects which are believed to be the cause of hot electron generation can only be captured by fully kinetic simulations with good resolution of the laser wavelength. For this reason, we employ a two-tiered approach to hohlraum modeling. Large-scale simulations of the collisional absorption process can be conducted using the fast quasi-neutral MHD algorithm with fluid particle species. From these simulations, we can observe the time evolution of the hohlraum walls and characterize the density and temperature profiles. From these results, we can transition to smaller-scale highly resolved simulations using traditional kinetic particle-in-cell methods, from which we can fully model all of the non-linear laser-plasma interactions, as well as assess the details of the electron distribution function. We find that vacuum hohlraums should be stable to both two plasmon decay and stimulated Raman scattering instabilities for intensities ≤ 10 15 W/cm2. In gas-filled hohlraums, shocks may be induced in the blowoff gold plasma, which leads to more complex density and temperatures profiles. The resulting effect on LPI stability depends strongly on the details of the profile, and it is possible for the gas-filled hohlraum to become unstable to two plasmon decay at 1015 W/cm2 if the quarter-critical surface reaches temperatures exceeding 1 keV.

An improved k-epsilon model for near wall turbulence

NASA Technical Reports Server (NTRS)

Shih, T. H.; Hsu, Andrew T.

1991-01-01

An improved k-epsilon model for low Reynolds number turbulence near a wall is presented. In the first part of this work, the near-wall asymptotic behavior of the eddy viscosity and the pressure transport term in the turbulent kinetic energy equation are analyzed. Based on these analyses, a modified eddy viscosity model with the correct near-wall behavior is suggested, and a model for the pressure transport term in the k-equation is proposed. In addition, a modeled dissipation rate equation is reformulated, and a boundary condition for the dissipation rate is suggested. In the second part of the work, one of the deficiencies of the existing k-epsilon models, namely, the wall distance dependency of the equations and the damping functions, is examined. An improved model that does not depend on any wall distance is introduced. Fully developed turbulent channel flows and turbulent boundary layers over a flat plate are studied as validations for the proposed new models. Numerical results obtained from the present and other previous k-epsilon models are compared with data from direct numerical simulation. The results show that the present k-epsilon model, with added robustness, performs as well as or better than other existing models in predicting the behavior of near-wall turbulence.

Kinetic Model of Growth of Arthropoda Populations

NASA Astrophysics Data System (ADS)

Ershov, Yu. A.; Kuznetsov, M. A.

2018-05-01

Kinetic equations were derived for calculating the growth of crustacean populations ( Crustacea) based on the biological growth model suggested earlier using shrimp ( Caridea) populations as an example. The development cycle of successive stages for populations can be represented in the form of quasi-chemical equations. The kinetic equations that describe the development cycle of crustaceans allow quantitative prediction of the development of populations depending on conditions. In contrast to extrapolation-simulation models, in the developed kinetic model of biological growth the kinetic parameters are the experimental characteristics of population growth. Verification and parametric identification of the developed model on the basis of the experimental data showed agreement with experiment within the error of the measurement technique.

Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

PubMed

Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

2018-06-13

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

Wheelchair pushrim kinetics measurement: A method to cancel inaccuracies due to pushrim weight and wheel camber.

PubMed

Chénier, Félix; Aissaoui, Rachid; Gauthier, Cindy; Gagnon, Dany H

2017-02-01

The commercially available SmartWheel TM is largely used in research and increasingly used in clinical practice to measure the forces and moments applied on the wheelchair pushrims by the user. However, in some situations (i.e. cambered wheels or increased pushrim weight), the recorded kinetics may include dynamic offsets that affect the accuracy of the measurements. In this work, an automatic method to identify and cancel these offsets is proposed and tested. First, the method was tested on an experimental bench with different cambers and pushrim weights. Then, the method was generalized to wheelchair propulsion. Nine experienced wheelchair users propelled their own wheelchairs instrumented with two SmartWheels with anti-slip pushrim covers. The dynamic offsets were correctly identified using the propulsion acquisition, without needing a separate baseline acquisition. A kinetic analysis was performed with and without dynamic offset cancellation using the proposed method. The most altered kinetic variables during propulsion were the vertical and total forces, with errors of up to 9N (p<0.001, large effect size of 5). This method is simple to implement, fully automatic and requires no further acquisitions. Therefore, we advise to use it systematically to enhance the accuracy of existing and future kinetic measurements. Copyright © 2016 IPEM. Published by Elsevier Ltd. All rights reserved.

Fundamental Statistical Descriptions of Plasma Turbulence in Magnetic Fields

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

John A. Krommes

2001-02-16

A pedagogical review of the historical development and current status (as of early 2000) of systematic statistical theories of plasma turbulence is undertaken. Emphasis is on conceptual foundations and methodology, not practical applications. Particular attention is paid to equations and formalism appropriate to strongly magnetized, fully ionized plasmas. Extensive reference to the literature on neutral-fluid turbulence is made, but the unique properties and problems of plasmas are emphasized throughout. Discussions are given of quasilinear theory, weak-turbulence theory, resonance-broadening theory, and the clump algorithm. Those are developed independently, then shown to be special cases of the direct-interaction approximation (DIA), which providesmore » a central focus for the article. Various methods of renormalized perturbation theory are described, then unified with the aid of the generating-functional formalism of Martin, Siggia, and Rose. A general expression for the renormalized dielectric function is deduced and discussed in detail. Modern approaches such as decimation and PDF methods are described. Derivations of DIA-based Markovian closures are discussed. The eddy-damped quasinormal Markovian closure is shown to be nonrealizable in the presence of waves, and a new realizable Markovian closure is presented. The test-field model and a realizable modification thereof are also summarized. Numerical solutions of various closures for some plasma-physics paradigms are reviewed. The variational approach to bounds on transport is developed. Miscellaneous topics include Onsager symmetries for turbulence, the interpretation of entropy balances for both kinetic and fluid descriptions, self-organized criticality, statistical interactions between disparate scales, and the roles of both mean and random shear. Appendices are provided on Fourier transform conventions, dimensional and scaling analysis, the derivations of nonlinear gyrokinetic and gyrofluid equations, stochasticity criteria for quasilinear theory, formal aspects of resonance-broadening theory, Novikov's theorem, the treatment of weak inhomogeneity, the derivation of the Vlasov weak-turbulence wave kinetic equation from a fully renormalized description, some features of a code for solving the direct-interaction approximation and related Markovian closures, the details of the solution of the EDQNM closure for a solvable three-wave model, and the notation used in the article.« less

Carotene Degradation and Isomerization during Thermal Processing: A Review on the Kinetic Aspects.

PubMed

Colle, Ines J P; Lemmens, Lien; Knockaert, Griet; Van Loey, Ann; Hendrickx, Marc

2016-08-17

Kinetic models are important tools for process design and optimization to balance desired and undesired reactions taking place in complex food systems during food processing and preservation. This review covers the state of the art on kinetic models available to describe heat-induced conversion of carotenoids, in particular lycopene and β-carotene. First, relevant properties of these carotenoids are discussed. Second, some general aspects of kinetic modeling are introduced, including both empirical single-response modeling and mechanism-based multi-response modeling. The merits of multi-response modeling to simultaneously describe carotene degradation and isomerization are demonstrated. The future challenge in this research field lies in the extension of the current multi-response models to better approach the real reaction pathway and in the integration of kinetic models with mass transfer models in case of reaction in multi-phase food systems.

Asymmetric kinetic equilibria: Generalization of the BAS model for rotating magnetic profile and non-zero electric field

NASA Astrophysics Data System (ADS)

Dorville, Nicolas; Belmont, Gérard; Aunai, Nicolas; Dargent, Jérémy; Rezeau, Laurence

2015-09-01

Finding kinetic equilibria for non-collisional/collisionless tangential current layers is a key issue as well for their theoretical modeling as for our understanding of the processes that disturb them, such as tearing or Kelvin Helmholtz instabilities. The famous Harris equilibrium [E. Harris, Il Nuovo Cimento Ser. 10 23, 115-121 (1962)] assumes drifting Maxwellian distributions for ions and electrons, with constant temperatures and flow velocities; these assumptions lead to symmetric layers surrounded by vacuum. This strongly particular kind of layer is not suited for the general case: asymmetric boundaries between two media with different plasmas and different magnetic fields. The standard method for constructing more general kinetic equilibria consists in using Jeans theorem, which says that any function depending only on the Hamiltonian constants of motion is a solution to the steady Vlasov equation [P. J. Channell, Phys. Fluids (1958-1988) 19, 1541 (1976); M. Roth et al., Space Sci. Rev. 76, 251-317 (1996); and F. Mottez, Phys. Plasmas 10, 1541-1545 (2003)]. The inverse implication is however not true: when using the motion invariants as variables instead of the velocity components, the general stationary particle distributions keep on depending explicitly of the position, in addition to the implicit dependence introduced by these invariants. The standard approach therefore strongly restricts the class of solutions to the problem and probably does not select the most physically reasonable. The BAS (Belmont-Aunai-Smets) model [G. Belmont et al., Phys. Plasmas 19, 022108 (2012)] used for the first time the concept of particle accessibility to find new solutions: considering the case of a coplanar-antiparallel magnetic field configuration without electric field, asymmetric solutions could be found while the standard method can only lead to symmetric ones. These solutions were validated in a hybrid simulation [N. Aunai et al., Phys. Plasmas (1994-present) 20, 110702 (2013)], and more recently in a fully kinetic simulation as well [J. Dargent and N. Aunai, Phys. Plasmas (submitted)]. Nevertheless, in most asymmetric layers like the terrestrial magnetopause, one would indeed expect a magnetic field rotation from one direction to another without going through zero [J. Berchem and C. T. Russell, J. Geophys. Res. 87, 8139-8148 (1982)], and a non-zero normal electric field. In this paper, we propose the corresponding generalization: in the model presented, the profiles can be freely imposed for the magnetic field rotation (although restricted to a 180 rotation hitherto) and for the normal electric field. As it was done previously, the equilibrium is tested with a hybrid simulation.

Detonation initiation in a model of explosive: Comparative atomistic and hydrodynamics simulations

NASA Astrophysics Data System (ADS)

Murzov, S. A.; Sergeev, O. V.; Dyachkov, S. A.; Egorova, M. S.; Parshikov, A. N.; Zhakhovsky, V. V.

2016-11-01

Here we extend consistent simulations to reactive materials by the example of AB model explosive. The kinetic model of chemical reactions observed in a molecular dynamics (MD) simulation of self-sustained detonation wave can be used in hydrodynamic simulation of detonation initiation. Kinetic coefficients are obtained by minimization of difference between profiles of species calculated from the kinetic model and observed in MD simulations of isochoric thermal decomposition with a help of downhill simplex method combined with random walk in multidimensional space of fitting kinetic model parameters.

Kinetic Description of the Impedance Probe

NASA Astrophysics Data System (ADS)

Oberrath, Jens; Lapke, Martin; Mussenbrock, Thomas; Brinkmann, Ralf

2011-10-01

Active plasma resonance spectroscopy is a well known diagnostic method. Many concepts of this method are theoretically investigated and realized as a diagnostic tool, one of which is the impedance probe (IP). The application of such a probe in plasmas with pressures of a few Pa raises the question whether kinetic effects have to be taken into account or not. To address this question a kinetic model is necessary. A general kinetic model for an electrostatic concept of active plasma spectroscopy was presented by R.P. Brinkmann and can be used to describe the multipole resonance probe (MRP). In principle the IP is interpretable as a special case of the MRP in lower order. Thus, we are able to describe the IP by the kinetic model of the MRP. Based on this model we derive a solution to investigate the influence of kinetic effects to the resonance behavior of the IP. Active plasma resonance spectroscopy is a well known diagnostic method. Many concepts of this method are theoretically investigated and realized as a diagnostic tool, one of which is the impedance probe (IP). The application of such a probe in plasmas with pressures of a few Pa raises the question whether kinetic effects have to be taken into account or not. To address this question a kinetic model is necessary. A general kinetic model for an electrostatic concept of active plasma spectroscopy was presented by R.P. Brinkmann and can be used to describe the multipole resonance probe (MRP). In principle the IP is interpretable as a special case of the MRP in lower order. Thus, we are able to describe the IP by the kinetic model of the MRP. Based on this model we derive a solution to investigate the influence of kinetic effects to the resonance behavior of the IP. The authors acknowledge the support by the Deutsche Forschungsgemeinschaft (DFG) via the Ruhr University Research School and the Federal Ministry of Education and Research in frame of the PluTO project.

A Self Consistent RF Discharge, Plasma Chemistry and Surface Model for Plasma Enhanced Chemical Vapor Deposition

DTIC Science & Technology

1988-06-30

consists of three submodels for the electron kinetics, plasma chemistry , and surface deposition kinetics for a-Si:H deposited from radio frequency...properties. Plasma enhanced, Chemical vapor deposition, amorphous silicon, Modeling, Electron kinetics, Plasma chemistry , Deposition kinetics, Rf discharge, Silane, Film properties, Silicon.

A note on the maintenance of the atmospheric kinetic energy

NASA Technical Reports Server (NTRS)

Chen, T.-C.; Lee, Y.-H.

1982-01-01

The winter simulations of the GLAS climate model and the NCAR community climate model are used to examine the maintenance of the atmospheric kinetic energy. It is found that the kinetic energy is generated in the lower latitudes south of the maximum westerlies, transported northward and then, destroyed in the midlatitudes north of the maximum westerlies. Therefore, the atmospheric kinetic energy is maintained by the counterbalance between the divergence (convergence) of kinetic energy flux and generation (destruction) of kinetic energy in lower (middle) latitudes.

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.

Kinetic analysis of overlapping multistep thermal decomposition comprising exothermic and endothermic processes: thermolysis of ammonium dinitramide.

PubMed

Muravyev, Nikita V; Koga, Nobuyoshi; Meerov, Dmitry B; Pivkina, Alla N

2017-01-25

This study focused on kinetic modeling of a specific type of multistep heterogeneous reaction comprising exothermic and endothermic reaction steps, as exemplified by the practical kinetic analysis of the experimental kinetic curves for the thermal decomposition of molten ammonium dinitramide (ADN). It is known that the thermal decomposition of ADN occurs as a consecutive two step mass-loss process comprising the decomposition of ADN and subsequent evaporation/decomposition of in situ generated ammonium nitrate. These reaction steps provide exothermic and endothermic contributions, respectively, to the overall thermal effect. The overall reaction process was deconvoluted into two reaction steps using simultaneously recorded thermogravimetry and differential scanning calorimetry (TG-DSC) curves by considering the different physical meanings of the kinetic data derived from TG and DSC by P value analysis. The kinetic data thus separated into exothermic and endothermic reaction steps were kinetically characterized using kinetic computation methods including isoconversional method, combined kinetic analysis, and master plot method. The overall kinetic behavior was reproduced as the sum of the kinetic equations for each reaction step considering the contributions to the rate data derived from TG and DSC. During reproduction of the kinetic behavior, the kinetic parameters and contributions of each reaction step were optimized using kinetic deconvolution analysis. As a result, the thermal decomposition of ADN was successfully modeled as partially overlapping exothermic and endothermic reaction steps. The logic of the kinetic modeling was critically examined, and the practical usefulness of phenomenological modeling for the thermal decomposition of ADN was illustrated to demonstrate the validity of the methodology and its applicability to similar complex reaction processes.

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

NASA Astrophysics Data System (ADS)

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

2017-08-01

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

Three dimensional Particle-in-Cell (PIC) simulations of the 67P environment

NASA Astrophysics Data System (ADS)

Divin, Andrey; Deca, Jan; Henri, Pierre; Horanyi, Mihaly; Markidis, Stefano; Lapenta, Giovanni; Olshevsky, Vyacheslav; Eriksson, Anders

2017-04-01

ESA's Rosetta orbiter spacecraft escorted comet 67P/Churyumov-Gerasimenko for two years, carrying 21 scientific instruments. Five of those were dedicated to plasma measurements. The mission revealed for the first time, and in unprecedented detail, the fascinating evolution of a comet and its interaction with our Sun as it races along its 6.45yr elliptical orbit around the Sun. Using a self-consistent 3-D fully kinetic electromagnetic particle-in-cell approach, we focus on the global cometary environment and, in particular, on the collisionless electron-kinetic interaction. We include cometary ions and electrons produced by the ionization of the outgassing cometary atmosphere in addition to the solar wind ion and electron plasma flow. We approximate mass-loading of the cold cometary ion and electron populations using a 1/r relation with distance to the comet with a total neutral production rate of Q = 1026 s-1. Our simulation results disentangle for the first time the kinetic ion and electron dynamics of the solar wind interaction with a weakly outgassing comet. The simulated global structure of the solar wind-comet interaction confirms the results reported in hybrid simulations of the induced cometary magnetosphere. Moreover, we show that cometary and solar wind electrons neutralize the solar wind protons and cometary ions, respectively, in the region of influence around the comet, representing to first order a four-fluid behavior. The electron energy distribution close to the comet is shown to be a mix of cometary and solar wind electrons that appear as, respectively, a thermal and a suprathermal components. Analyzing ion and electron energy distribution functions, and comparing with plasma measurements from ESA's Rosetta mission to comet 67P/Churyumov-Gerasimenko, we conclude that a detailed kinetic treatment of the electron dynamics is critical to fully capture the complex physics of mass-loading plasmas.

Development and assessement of the GECKO-A multiphase modelling tool for the atmospheric oxidation of biogenic organic compounds

NASA Astrophysics Data System (ADS)

Valorso, Richard; Raventos-Duran, Teresa; Aumont, Bernard; Camredon, Marie; Ng, Nga L.; Seinfeld, John H.

2010-05-01

The evaluation of the impacts of secondary organics on pollution episodes, climate and the tropospheric oxidizing capacity requires modelling tools that track the identity and reactivity of organic carbon in the various stages down to the ultimate oxidation products. The fully explicit representation of hydrocarbon oxidation, from the initial compounds to the final product CO2, requires a very large number of chemical reactions and intermediate species, far in excess of the number that can be reasonably written manually. We developed a "self generating approach" to explicitly describe (i) the gas phase oxidation schemes of organic compounds under general tropospheric conditions and (ii) the partitioning of secondary organics between gas and condensed phases. This approach was codified in a computer program, GECKO-A (Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere). This method allows prediction of multiphase mass budget using first principles. However, due to computational limitations, fully explicit chemical schemes can only be generated for species up to C8. We recently implemented a reduction protocol in GECKO-A to allow the generation of oxidation schemes for long chain organics. This protocol was applied to develop highly detailed oxidation schemes for biogenic compounds. The relevance of the generated schemes was assessed using experiments performed in the Caltech smog chamber for various NOx conditions. The first results show a systematic overestimation of the simulated SOA concentrations by GECKO-A. Several hypotheses were tested to find the origin of the discrepancies beetwen model and measurements.

Modeling of Turbulent Swirling Flows

NASA Technical Reports Server (NTRS)

Shih, Tsan-Hsing; Zhu, Jiang; Liou, William; Chen, Kuo-Huey; Liu, Nan-Suey; Lumley, John L.

1997-01-01

Aircraft engine combustors generally involve turbulent swirling flows in order to enhance fuel-air mixing and flame stabilization. It has long been recognized that eddy viscosity turbulence models are unable to appropriately model swirling flows. Therefore, it has been suggested that, for the modeling of these flows, a second order closure scheme should be considered because of its ability in the modeling of rotational and curvature effects. However, this scheme will require solution of many complicated second moment transport equations (six Reynolds stresses plus other scalar fluxes and variances), which is a difficult task for any CFD implementations. Also, this scheme will require a large amount of computer resources for a general combustor swirling flow. This report is devoted to the development of a cubic Reynolds stress-strain model for turbulent swirling flows, and was inspired by the work of Launder's group at UMIST. Using this type of model, one only needs to solve two turbulence equations, one for the turbulent kinetic energy k and the other for the dissipation rate epsilon. The cubic model developed in this report is based on a general Reynolds stress-strain relationship. Two flows have been chosen for model evaluation. One is a fully developed rotating pipe flow, and the other is a more complex flow with swirl and recirculation.

Microbial Kinetic Model for the Degradation of Poorly Soluble Organic Materials

EPA Science Inventory

A novel mechanistic model is presented that describes the aerobic biodegradation kinetics of soybean biodiesel and petroleum diesel in batch experiments. The model was built on the assumptions that biodegradation takes place in the aqueous phase according to Monod kinetics, and ...

Kinetic modeling of a bi-enzymatic system for efficient conversion of lactose to lactobionic acid.

PubMed

Van Hecke, Wouter; Bhagwat, Aditya; Ludwig, Roland; Dewulf, Jo; Haltrich, Dietmar; Van Langenhove, Herman

2009-04-01

A model has been developed to describe the interaction between two enzymes and an intermediary redox mediator. In this bi-enzymatic process, the enzyme cellobiose dehydrogenase oxidizes lactose at the C-1 position of the reducing sugar moiety to lactobionolactone, which spontaneously hydrolyzes to lactobionic acid. 2,2'-Azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt is used as electron acceptor and is continuously regenerated by laccase. Oxygen is the terminal electron acceptor and is fully reduced to water by laccase, a copper-containing oxidase. Oxygen is added to the system by means of bubble-free oxygenation. Using the model, the productivity of the process is investigated by simultaneous solution of the rate equations for varying enzyme quantities and redox mediator concentrations, solved with the aid of a numerical solution. The isocharts developed in this work provide an easy-to-use graphical tool to determine optimal process conditions. The model allows the optimization of the employed activities of the two enzymes and the redox mediator concentration for a given overall oxygen mass transfer coefficient by using the isocharts. Model predictions are well in agreement with the experimental data.

Gyrokinetic neoclassical study of the bootstrap current in the tokamak edge pedestal with fully non-linear Coulomb collisions

DOE PAGES

Hager, Robert; Chang, C. S.

2016-04-08

As a follow-up on the drift-kinetic study of the non-local bootstrap current in the steep edge pedestal of tokamak plasma by Koh et al. [Phys. Plasmas 19, 072505 (2012)], a gyrokinetic neoclassical study is performed with gyrokinetic ions and drift-kinetic electrons. Besides the gyrokinetic improvement of ion physics from the drift-kinetic treatment, a fully non-linear Fokker-Planck collision operator—that conserves mass, momentum, and energy—is used instead of Koh et al.'s linearized collision operator in consideration of the possibility that the ion distribution function is non-Maxwellian in the steep pedestal. An inaccuracy in Koh et al.'s result is found in the steepmore » edge pedestal that originated from a small error in the collisional momentum conservation. The present study concludes that (1) the bootstrap current in the steep edge pedestal is generally smaller than what has been predicted from the small banana-width (local) approximation [e.g., Sauter et al., Phys. Plasmas 6, 2834 (1999) and Belli et al., Plasma Phys. Controlled Fusion 50, 095010 (2008)], (2) the plasma flow evaluated from the local approximation can significantly deviate from the non-local results, and (3) the bootstrap current in the edge pedestal, where the passing particle region is small, can be dominantly carried by the trapped particles in a broad trapped boundary layer. In conclusion, a new analytic formula based on numerous gyrokinetic simulations using various magnetic equilibria and plasma profiles with self-consistent Grad-Shafranov solutions is constructed.« less

Gyrokinetic neoclassical study of the bootstrap current in the tokamak edge pedestal with fully non-linear Coulomb collisions

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

Hager, Robert; Chang, C. S.

As a follow-up on the drift-kinetic study of the non-local bootstrap current in the steep edge pedestal of tokamak plasma by Koh et al. [Phys. Plasmas 19, 072505 (2012)], a gyrokinetic neoclassical study is performed with gyrokinetic ions and drift-kinetic electrons. Besides the gyrokinetic improvement of ion physics from the drift-kinetic treatment, a fully non-linear Fokker-Planck collision operator—that conserves mass, momentum, and energy—is used instead of Koh et al.'s linearized collision operator in consideration of the possibility that the ion distribution function is non-Maxwellian in the steep pedestal. An inaccuracy in Koh et al.'s result is found in the steepmore » edge pedestal that originated from a small error in the collisional momentum conservation. The present study concludes that (1) the bootstrap current in the steep edge pedestal is generally smaller than what has been predicted from the small banana-width (local) approximation [e.g., Sauter et al., Phys. Plasmas 6, 2834 (1999) and Belli et al., Plasma Phys. Controlled Fusion 50, 095010 (2008)], (2) the plasma flow evaluated from the local approximation can significantly deviate from the non-local results, and (3) the bootstrap current in the edge pedestal, where the passing particle region is small, can be dominantly carried by the trapped particles in a broad trapped boundary layer. In conclusion, a new analytic formula based on numerous gyrokinetic simulations using various magnetic equilibria and plasma profiles with self-consistent Grad-Shafranov solutions is constructed.« less

Gyrokinetic neoclassical study of the bootstrap current in the tokamak edge pedestal with fully non-linear Coulomb collisions

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

Hager, Robert, E-mail: rhager@pppl.gov; Chang, C. S., E-mail: cschang@pppl.gov

As a follow-up on the drift-kinetic study of the non-local bootstrap current in the steep edge pedestal of tokamak plasma by Koh et al. [Phys. Plasmas 19, 072505 (2012)], a gyrokinetic neoclassical study is performed with gyrokinetic ions and drift-kinetic electrons. Besides the gyrokinetic improvement of ion physics from the drift-kinetic treatment, a fully non-linear Fokker-Planck collision operator—that conserves mass, momentum, and energy—is used instead of Koh et al.'s linearized collision operator in consideration of the possibility that the ion distribution function is non-Maxwellian in the steep pedestal. An inaccuracy in Koh et al.'s result is found in the steepmore » edge pedestal that originated from a small error in the collisional momentum conservation. The present study concludes that (1) the bootstrap current in the steep edge pedestal is generally smaller than what has been predicted from the small banana-width (local) approximation [e.g., Sauter et al., Phys. Plasmas 6, 2834 (1999) and Belli et al., Plasma Phys. Controlled Fusion 50, 095010 (2008)], (2) the plasma flow evaluated from the local approximation can significantly deviate from the non-local results, and (3) the bootstrap current in the edge pedestal, where the passing particle region is small, can be dominantly carried by the trapped particles in a broad trapped boundary layer. A new analytic formula based on numerous gyrokinetic simulations using various magnetic equilibria and plasma profiles with self-consistent Grad-Shafranov solutions is constructed.« less

Incoherent manipulation of the photoactive yellow protein photocycle with dispersed pump-dump-probe spectroscopy.

PubMed

Larsen, Delmar S; van Stokkum, Ivo H M; Vengris, Mikas; van Der Horst, Michael A; de Weerd, Frank L; Hellingwerf, Klaas J; van Grondelle, Rienk

2004-09-01

Photoactive yellow protein is the protein responsible for initiating the "blue-light vision" of Halorhodospira halophila. The dynamical processes responsible for triggering the photoactive yellow protein photocycle have been disentangled with the use of a novel application of dispersed ultrafast pump-dump-probe spectroscopy, where the photocycle can be started and interrupted with appropriately tuned and timed laser pulses. This "incoherent" manipulation of the photocycle allows for the detailed spectroscopic investigation of the underlying photocycle dynamics and the construction of a fully self-consistent dynamical model. This model requires three kinetically distinct excited-state intermediates, two (ground-state) photocycle intermediates, I(0) and pR, and a ground-state intermediate through which the protein, after unsuccessful attempts at initiating the photocycle, returns to the equilibrium ground state. Also observed is a previously unknown two-photon ionization channel that generates a radical and an ejected electron into the protein environment. This second excitation pathway evolves simultaneously with the pathway containing the one-photon photocycle intermediates.

Incoherent Manipulation of the Photoactive Yellow Protein Photocycle with Dispersed Pump-Dump-Probe Spectroscopy

PubMed Central

Larsen, Delmar S.; van Stokkum, Ivo H. M.; Vengris, Mikas; van der Horst, Michael A.; de Weerd, Frank L.; Hellingwerf, Klaas J.; van Grondelle, Rienk

2004-01-01

Photoactive yellow protein is the protein responsible for initiating the “blue-light vision” of Halorhodospira halophila. The dynamical processes responsible for triggering the photoactive yellow protein photocycle have been disentangled with the use of a novel application of dispersed ultrafast pump-dump-probe spectroscopy, where the photocycle can be started and interrupted with appropriately tuned and timed laser pulses. This “incoherent” manipulation of the photocycle allows for the detailed spectroscopic investigation of the underlying photocycle dynamics and the construction of a fully self-consistent dynamical model. This model requires three kinetically distinct excited-state intermediates, two (ground-state) photocycle intermediates, I0 and pR, and a ground-state intermediate through which the protein, after unsuccessful attempts at initiating the photocycle, returns to the equilibrium ground state. Also observed is a previously unknown two-photon ionization channel that generates a radical and an ejected electron into the protein environment. This second excitation pathway evolves simultaneously with the pathway containing the one-photon photocycle intermediates. PMID:15345564

Failure Resistance of Fiber-Reinforced Ultra-High Performance Concrete (FRUHPC) Subjected to Blast Loading

NASA Astrophysics Data System (ADS)

Ellis, Brett; Zhou, Min; McDowell, David

2011-06-01

As part of a hierarchy-based computational materials design program, a fully dynamic 3D mesoscale model is developed to quantify the effects of energy storage and dissipation mechanisms in Fiber-Reinforced Ultra-High Performance Concretes (FRUHPCs) subjected to blast loading. This model accounts for three constituent components: reinforcement fibers, cementitious matrix, and fiber-matrix interfaces. Microstructure instantiations encompass a range of fiber volume fraction (0-2%), fiber length (10-15 mm), and interfacial bonding strength (1-100 MPa). Blast loading with scaled distances between 5 and 10 m/kg1/3 are considered. Calculations have allowed the delineation and characterization of the evolutions of kinetic energy, strain energy, work expended on interfacial damage and failure, frictional dissipation along interfaces, and bulk dissipation through granular flow as functions of microstructure, loading and constituent attributes. The relations obtained point out avenues for designing FRUHPCs with properties tailored for specific load environments and reveal trade-offs between various design scenarios.

A Theoretical Study of Phosphoryl Transfers of Tyrosyl-DNA Phosphodiesterase I (Tdp1) and the Possibility of a "Dead-End" Phosphohistidine Intermediate.

PubMed

DeYonker, Nathan J; Webster, Charles Edwin

2015-07-14

Tyrosyl-DNA phosphodiesterase I (Tdp1) is a DNA repair enzyme conserved across eukaryotes that catalyzes the hydrolysis of the phosphodiester bond between the tyrosine residue of topoisomerase I and the 3'-phosphate of DNA. Atomic level details of the mechanism of Tdp1 are proposed and analyzed using a fully quantum mechanical, geometrically constrained model. The structural basis for the computational model is the vanadate-inhibited crystal structure of human Tdp1 (hTdp1, Protein Data Bank entry 1RFF ). Density functional theory computations are used to acquire thermodynamic and kinetic data along the catalytic pathway, including the phosphoryl transfer and subsequent hydrolysis. Located transition states and intermediates along the reaction coordinate suggest an associative phosphoryl transfer mechanism with five-coordinate phosphorane intermediates. Similar to both theoretical and experimental results for phospholipase D, the proposed mechanism for hTdp1 also includes the thermodynamically favorable possibility of a four-coordinate phosphohistidine "dead-end" product.

Kinetics of Cd(ii) adsorption and desorption on ferrihydrite: experiments and modeling.

PubMed

Liang, Yuzhen; Tian, Lei; Lu, Yang; Peng, Lanfang; Wang, Pei; Lin, Jingyi; Cheng, Tao; Dang, Zhi; Shi, Zhenqing

2018-05-15

The kinetics of Cd(ii) adsorption/desorption on ferrihydrite is an important process affecting the fate, transport, and bioavailability of Cd(ii) in the environment, which was rarely systematically studied and understood at quantitative levels. In this work, a combination of stirred-flow kinetic experiments, batch adsorption equilibrium experiments, high-resolution transmission electron microscopy (HR-TEM), and mechanistic kinetic modeling were used to study the kinetic behaviors of Cd(ii) adsorption/desorption on ferrihydrite. HR-TEM images showed the open, loose, and sponge-like structure of ferrihydrite. The batch adsorption equilibrium experiments revealed that higher pH and initial metal concentration increased Cd(ii) adsorption on ferrihydrite. The stirred-flow kinetic results demonstrated the increased adsorption rate and capacity as a result of the increased pH, influent concentration, and ferrihydrite concentration. The mechanistic kinetic model successfully described the kinetic behaviors of Cd(ii) during the adsorption and desorption stages under various chemistry conditions. The model calculations showed that the adsorption rate coefficients varied as a function of solution chemistry, and the relative contributions of the weak and strong ferrihydrite sites for Cd(ii) binding varied with time at different pH and initial metal concentrations. Our model is able to quantitatively assess the contributions of each individual ferrihydrite binding site to the overall Cd(ii) adsorption/desorption kinetics. This study provided insights into the dynamic behavior of Cd(ii) and a predictive modeling tool for Cd(ii) adsorption/desorption kinetics when ferrihydrite is present, which may be helpful for the risk assessment and management of Cd contaminated sites.

Topological and kinetic determinants of the modal matrices of dynamic models of metabolism

PubMed Central

2017-01-01

Large-scale kinetic models of metabolism are becoming increasingly comprehensive and accurate. A key challenge is to understand the biochemical basis of the dynamic properties of these models. Linear analysis methods are well-established as useful tools for characterizing the dynamic response of metabolic networks. Central to linear analysis methods are two key matrices: the Jacobian matrix (J) and the modal matrix (M-1) arising from its eigendecomposition. The modal matrix M-1 contains dynamically independent motions of the kinetic model near a reference state, and it is sparse in practice for metabolic networks. However, connecting the structure of M-1 to the kinetic properties of the underlying reactions is non-trivial. In this study, we analyze the relationship between J, M-1, and the kinetic properties of the underlying network for kinetic models of metabolism. Specifically, we describe the origin of mode sparsity structure based on features of the network stoichiometric matrix S and the reaction kinetic gradient matrix G. First, we show that due to the scaling of kinetic parameters in real networks, diagonal dominance occurs in a substantial fraction of the rows of J, resulting in simple modal structures with clear biological interpretations. Then, we show that more complicated modes originate from topologically-connected reactions that have similar reaction elasticities in G. These elasticities represent dynamic equilibrium balances within reactions and are key determinants of modal structure. The work presented should prove useful towards obtaining an understanding of the dynamics of kinetic models of metabolism, which are rooted in the network structure and the kinetic properties of reactions. PMID:29267329

HYDRATE v1.5 OPTION OF TOUGH+ v1.5

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

Moridis, George

HYDRATE v1.5 is a numerical code that for the simulation of the behavior of hydrate-bearing geologic systems, and represents the third update of the code since its first release [Moridis et al., 2008]. It is an option of TOUGH+ v1.5 [Moridis and Pruess, 2014], a successor to the TOUGH2 [Pruess et al., 1999, 2012] family of codes for multi-component, multiphase fluid and heat flow developed at the Lawrence Berkeley National Laboratory. HYDRATE v1.5 needs the TOUGH+ v1.5 core code in order to compile and execute. It is written in standard FORTRAN 95/2003, and can be run on any computational platformmore » (workstation, PC, Macintosh) for which such compilers are available. By solving the coupled equations of mass and heat balance, the fully operational TOUGH+HYDRATE code can model the non-isothermal gas release, phase behavior and flow of fluids and heat under conditions typical of common natural CH 4-hydrate deposits (i.e., in the permafrost and in deep ocean sediments) in complex geological media at any scale (from laboratory to reservoir) at which Darcy's law is valid. TOUGH+HYDRATE v1.5 includes both an equilibrium and a kinetic model of hydrate formation and dissociation. The model accounts for heat and up to four mass components, i.e., water, CH 4, hydrate, and water-soluble inhibitors such as salts or alcohols. These are partitioned among four possible phases (gas phase, liquid phase, ice phase and hydrate phase). Hydrate dissociation or formation, phase changes and the corresponding thermal effects are fully described, as are the effects of inhibitors. The model can describe all possible hydrate dissociation mechanisms, i.e., depressurization, thermal stimulation, salting-out effects and inhibitor-induced effects.« less

Second-order kinetic model for the sorption of cadmium onto tree fern: a comparison of linear and non-linear methods.

PubMed

Ho, Yuh-Shan

2006-01-01

A comparison was made of the linear least-squares method and a trial-and-error non-linear method of the widely used pseudo-second-order kinetic model for the sorption of cadmium onto ground-up tree fern. Four pseudo-second-order kinetic linear equations are discussed. Kinetic parameters obtained from the four kinetic linear equations using the linear method differed but they were the same when using the non-linear method. A type 1 pseudo-second-order linear kinetic model has the highest coefficient of determination. Results show that the non-linear method may be a better way to obtain the desired parameters.

Adsorption dynamics of methyl violet onto granulated mesoporous carbon: Facile synthesis and adsorption kinetics.

PubMed

Kim, Yohan; Bae, Jiyeol; Park, Hosik; Suh, Jeong-Kwon; You, Young-Woo; Choi, Heechul

2016-09-15

A new and facile one-step synthesis method for preparing granulated mesoporous carbon (GMC) with three-dimensional spherical mesoporous symmetry is prepared to remove large molecular weight organic compounds in aqueous phase. GMC is synthesized in a single step using as-synthesized mesoporous carbon particles and organic binders through a simple and economical synthesis approach involving a simultaneous calcination and carbonization process. Characterization results obtained from SEM, XRD, as well as surface and porosity analysis indicate that the synthesized GMC has similar physical properties to those of the powdered mesoporous carbon and maintains the Brunauer-Emmett-Teller (BET) surface area and pore volume because the new synthesis method prevents the collapse of the pores during the granulation process. Batch adsorption experiments revealed GMC showed a substantial adsorption capacity (202.8 mg/g) for the removal of methyl violet as a target large molecular contaminant in aqueous phase. The mechanisms and dynamics modeling of GMC adsorption were also fully examined, which revealed that surface diffusion was rate limiting step on adsorption process of GMC. Adsorption kinetics of GMC enables 3 times faster than that of granular activated carbon in terms of surface diffusion coefficient. This is the first study, to the best of our knowledge, to synthesize GMC as an adsorbent for water purification by using facile granulation method and to investigate the adsorption kinetics and characteristics of GMC. This study introduces a new and simple method for the synthesis of GMC and reveals its adsorption characteristics for large molecular compounds in a water treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Kinetics, bioavailability, and metabolism of RRR-alpha-tocopherol in humans supports lower requirement for vitamin E

USDA-ARS?s Scientific Manuscript database

Kinetic models enable nutrient needs and kinetic behaviors to be quantified and provide mechanistic insights into metabolism. Therefore, we modeled and quantified the kinetics, bioavailability and metabolism of RRR-alpha-tocopherol in 12 healthy adults. Six men and six women, aged 27 ± 6 y, each i...

Fluid dynamic modeling and numerical simulation of low-density hypersonic flow

NASA Astrophysics Data System (ADS)

Cheng, H. K.; Wong, Eric Y.

1988-06-01

The concept of a viscous shock-layer and several related versions of continuum theories/methods are examined for their adequacy as a viable framework to study flow physics and aerothermodynamics of relevance to sustained hypersonic flights. Considering the flat plate at angle of attack, or the wedge, as a generic example for the major aerodynamic component of a hypersonic vehicle, the relative importance of the molecular-transport effects behind the shock (in the form of the 'shock slip') and the wall-slip effects are studied. In the flow regime where the shock-transition-zone thickness remains small compared to the shock radius of curvature, a quasi-one-dimensional shock structure under the Burnett/thirteen-moment approximation, as well as particulate/collisional models, can be consistently developed. The fully viscous version of the shock-layer model is shown to provide the crucial boundary condition downstream the shock in this case. The gas-kinetic basis of the continuum description for the flow behind the bow shock, and certain features affecting the non-equilibrium flow chemistry, are also discussed.

Fluid dynamic modeling and numerical simulation of low-density hypersonic flow

NASA Technical Reports Server (NTRS)

Cheng, H. K.; Wong, Eric Y.

1988-01-01

The concept of a viscous shock-layer and several related versions of continuum theories/methods are examined for their adequacy as a viable framework to study flow physics and aerothermodynamics of relevance to sustained hypersonic flights. Considering the flat plate at angle of attack, or the wedge, as a generic example for the major aerodynamic component of a hypersonic vehicle, the relative importance of the molecular-transport effects behind the shock (in the form of the 'shock slip') and the wall-slip effects are studied. In the flow regime where the shock-transition-zone thickness remains small compared to the shock radius of curvature, a quasi-one-dimensional shock structure under the Burnett/thirteen-moment approximation, as well as particulate/collisional models, can be consistently developed. The fully viscous version of the shock-layer model is shown to provide the crucial boundary condition downstream the shock in this case. The gas-kinetic basis of the continuum description for the flow behind the bow shock, and certain features affecting the non-equilibrium flow chemistry, are also discussed.

Particle model of a cylindrical inductively coupled ion source

NASA Astrophysics Data System (ADS)

Ippolito, N. D.; Taccogna, F.; Minelli, P.; Cavenago, M.; Veltri, P.

2017-08-01

In spite of the wide use of RF sources, a complete understanding of the mechanisms regulating the RF-coupling of the plasma is still lacking so self-consistent simulations of the involved physics are highly desirable. For this reason we are developing a 2.5D fully kinetic Particle-In-Cell Monte-Carlo-Collision (PIC-MCC) model of a cylindrical ICP-RF source, keeping the time step of the simulation small enough to resolve the plasma frequency scale. The grid cell dimension is now about seven times larger than the average Debye length, because of the large computational demand of the code. It will be scaled down in the next phase of the development of the code. The filling gas is Xenon, in order to minimize the time lost by the MCC collision module in the first stage of development of the code. The results presented here are preliminary, with the code already showing a good robustness. The final goal will be the modeling of the NIO1 (Negative Ion Optimization phase 1) source, operating in Padua at Consorzio RFX.

Dynamic Metabolic Model Building Based on the Ensemble Modeling Approach

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

Liao, James C.

2016-10-01

Ensemble modeling of kinetic systems addresses the challenges of kinetic model construction, with respect to parameter value selection, and still allows for the rich insights possible from kinetic models. This project aimed to show that constructing, implementing, and analyzing such models is a useful tool for the metabolic engineering toolkit, and that they can result in actionable insights from models. Key concepts are developed and deliverable publications and results are presented.

An improved kinetics approach to describe the physical stability of amorphous solid dispersions.

PubMed

Yang, Jiao; Grey, Kristin; Doney, John

2010-01-15

The recrystallization of amorphous solid dispersions may lead to a loss in the dissolution rate, and consequently reduce bioavailability. The purpose of this work is to understand factors governing the recrystallization of amorphous drug-polymer solid dispersions, and develop a kinetics model capable of accurately predicting their physical stability. Recrystallization kinetics was measured using differential scanning calorimetry for initially amorphous efavirenz-polyvinylpyrrolidone solid dispersions stored at controlled temperature and relative humidity. The experimental measurements were fitted by a new kinetic model to estimate the recrystallization rate constant and microscopic geometry of crystal growth. The new kinetics model was used to illustrate the governing factors of amorphous solid dispersions stability. Temperature was found to affect efavirenz recrystallization in an Arrhenius manner, while recrystallization rate constant was shown to increase linearly with relative humidity. Polymer content tremendously inhibited the recrystallization process by increasing the crystallization activation energy and decreasing the equilibrium crystallinity. The new kinetic model was validated by the good agreement between model fits and experiment measurements. A small increase in polyvinylpyrrolidone resulted in substantial stability enhancements of efavirenz amorphous solid dispersion. The new established kinetics model provided more accurate predictions than the Avrami equation.

Assessment of kinetic models on Fe adsorption in groundwater using high-quality limestone

NASA Astrophysics Data System (ADS)

Akbar, N. A.; Kamil, N. A. F. Mohd; Zin, N. S. Md; Adlan, M. N.; Aziz, H. A.

2018-04-01

During the groundwater pumping process, dissolved Fe2+ is oxidized into Fe3+ and produce rust-coloured iron mineral. Adsorption kinetic models are used to evaluate the performance of limestone adsorbent and describe the mechanism of adsorption and the diffusion processes of Fe adsorption in groundwater. This work presents the best kinetic model of Fe adsorption, which was chosen based on a higher value of coefficient correlation, R2. A batch adsorption experiment was conducted for various contact times ranging from 0 to 135 minutes. From the results of the batch study, three kinetic models were analyzed for Fe removal onto limestone sorbent, including the pseudo-first order (PFO), pseudo-second order (PSO) and intra-particle diffusion (IPD) models. Results show that the adsorption kinetic models follow the sequence: PSO > PFO > IPD, where the values of R2 are 0.997 > 0.919 > 0.918. A high value of R2 (0.997) reveals better fitted experimental data. Furthermore, the value of qe cal in the PSO kinetic model is very near to qe exp rather than that in other models. This finding therefore suggests that the PSO kinetic model has the good fitted with the experimental data which involved chemisorption process of divalent Fe removal in groundwater solution. Thus, limestone adsorbent media found to be an alternative and effective treatment of Fe removal from groundwater.

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.

Kinetics of heavy metal adsorption and desorption in soil: Developing a unified model based on chemical speciation

NASA Astrophysics Data System (ADS)

Peng, Lanfang; Liu, Paiyu; Feng, Xionghan; Wang, Zimeng; Cheng, Tao; Liang, Yuzhen; Lin, Zhang; Shi, Zhenqing

2018-03-01

Predicting the kinetics of heavy metal adsorption and desorption in soil requires consideration of multiple heterogeneous soil binding sites and variations of reaction chemistry conditions. Although chemical speciation models have been developed for predicting the equilibrium of metal adsorption on soil organic matter (SOM) and important mineral phases (e.g. Fe and Al (hydr)oxides), there is still a lack of modeling tools for predicting the kinetics of metal adsorption and desorption reactions in soil. In this study, we developed a unified model for the kinetics of heavy metal adsorption and desorption in soil based on the equilibrium models WHAM 7 and CD-MUSIC, which specifically consider metal kinetic reactions with multiple binding sites of SOM and soil minerals simultaneously. For each specific binding site, metal adsorption and desorption rate coefficients were constrained by the local equilibrium partition coefficients predicted by WHAM 7 or CD-MUSIC, and, for each metal, the desorption rate coefficients of various binding sites were constrained by their metal binding constants with those sites. The model had only one fitting parameter for each soil binding phase, and all other parameters were derived from WHAM 7 and CD-MUSIC. A stirred-flow method was used to study the kinetics of Cd, Cu, Ni, Pb, and Zn adsorption and desorption in multiple soils under various pH and metal concentrations, and the model successfully reproduced most of the kinetic data. We quantitatively elucidated the significance of different soil components and important soil binding sites during the adsorption and desorption kinetic processes. Our model has provided a theoretical framework to predict metal adsorption and desorption kinetics, which can be further used to predict the dynamic behavior of heavy metals in soil under various natural conditions by coupling other important soil processes.

Evaluation of a Stochastic Inactivation Model for Heat-Activated Spores of Bacillus spp. ▿

PubMed Central

Corradini, Maria G.; Normand, Mark D.; Eisenberg, Murray; Peleg, Micha

2010-01-01

Heat activates the dormant spores of certain Bacillus spp., which is reflected in the “activation shoulder” in their survival curves. At the same time, heat also inactivates the already active and just activated spores, as well as those still dormant. A stochastic model based on progressively changing probabilities of activation and inactivation can describe this phenomenon. The model is presented in a fully probabilistic discrete form for individual and small groups of spores and as a semicontinuous deterministic model for large spore populations. The same underlying algorithm applies to both isothermal and dynamic heat treatments. Its construction does not require the assumption of the activation and inactivation kinetics or knowledge of their biophysical and biochemical mechanisms. A simplified version of the semicontinuous model was used to simulate survival curves with the activation shoulder that are reminiscent of experimental curves reported in the literature. The model is not intended to replace current models to predict dynamic inactivation but only to offer a conceptual alternative to their interpretation. Nevertheless, by linking the survival curve's shape to probabilities of events at the individual spore level, the model explains, and can be used to simulate, the irregular activation and survival patterns of individual and small groups of spores, which might be involved in food poisoning and spoilage. PMID:20453137

Science case for the Asteroid Impact Mission (AIM): A component of the Asteroid Impact & Deflection Assessment (AIDA) mission

NASA Astrophysics Data System (ADS)

Michel, Patrick; Cheng, A.; Küppers, M.; Pravec, P.; Blum, J.; Delbo, M.; Green, S. F.; Rosenblatt, P.; Tsiganis, K.; Vincent, J. B.; Biele, J.; Ciarletti, V.; Hérique, A.; Ulamec, S.; Carnelli, I.; Galvez, A.; Benner, L.; Naidu, S. P.; Barnouin, O. S.; Richardson, D. C.; Rivkin, A.; Scheirich, P.; Moskovitz, N.; Thirouin, A.; Schwartz, S. R.; Campo Bagatin, A.; Yu, Y.

2016-06-01

The Asteroid Impact & Deflection Assessment (AIDA) mission is a joint cooperation between European and US space agencies that consists of two separate and independent spacecraft that will be launched to a binary asteroid system, the near-Earth asteroid Didymos, to test the kinetic impactor technique to deflect an asteroid. The European Asteroid Impact Mission (AIM) is set to rendezvous with the asteroid system to fully characterize the smaller of the two binary components a few months prior to the impact by the US Double Asteroid Redirection Test (DART) spacecraft. AIM is a unique mission as it will be the first time that a spacecraft will investigate the surface, subsurface, and internal properties of a small binary near-Earth asteroid. In addition it will perform various important technology demonstrations that can serve other space missions. The knowledge obtained by this mission will have great implications for our understanding of the history of the Solar System. Having direct information on the surface and internal properties of small asteroids will allow us to understand how the various processes they undergo work and transform these small bodies as well as, for this particular case, how a binary system forms. Making these measurements from up close and comparing them with ground-based data from telescopes will also allow us to calibrate remote observations and improve our data interpretation of other systems. With DART, thanks to the characterization of the target by AIM, the mission will be the first fully documented impact experiment at asteroid scale, which will include the characterization of the target's properties and the outcome of the impact. AIDA will thus offer a great opportunity to test and refine our understanding and models at the actual scale of an asteroid, and to check whether the current extrapolations of material strength from laboratory-scale targets to the scale of AIDA's target are valid. Moreover, it will offer a first check of the validity of the kinetic impactor concept to deflect a small body and lead to improved efficiency for future kinetic impactor designs. This paper focuses on the science return of AIM, the current knowledge of its target from ground-based observations, and the instrumentation planned to get the necessary data.

Study of Electron-scale Dissipation near the X-line During Magnetic Reconnection in a Laboratory Plasma

NASA Astrophysics Data System (ADS)

Ji, H.; Yoo, J.; Dorfman, S. E.; Jara-Almonte, J.; Yamada, M.; Swanson, C.; Daughton, W. S.; Roytershteyn, V.; Kuwahata, A.; Ii, T.; Inomoto, M.; Ono, Y.; von Stechow, A.; Grulke, O.; Phan, T.; Mozer, F.; Bale, S. D.

2013-12-01

Despite its disruptive influences on the large-scale structures of space and solar plasmas, the crucial topological changes and associated dissipation during magnetic reconnection take place only near an X-line within thin singular layers. In the modern collisionless models where electrons and ions are allowed to move separately, it has been predicted that ions exhaust efficiently through a thicker, ion-scale dissipative layer while mobile electrons can evacuate through a thinner, electron-scale dissipation layer, allowing for efficient release of magnetic energy. While ion dissipation layers have been frequently detected, the existence of election layers near the X-line and the associated dissipation structures and mechanisms are still an open question, and will be a main subject of the coming MMS mission. In this presentation, we will summarize our efforts in the past a few years to study electron-scale dissipation in a well-controlled and well-diagnosed reconnecting current sheet in a laboratory plasma, with close comparisons with the state-of-the-art, 2D and 3D fully kinetic simulations. Key results include: (1) positive identification of electromagnetic waves detected at the current sheet center as long wave-length, lower-hybrid drift instabilities (EM-LHDI), (2) however, there is strong evidence that this EM-LHDI cannot provide the required force to support the reconnection electric field, (3) detection of 3D flux-rope-like magnetic structures during impulsive reconnection events, and (4) electrons are heated through non-classical mechanisms near the X-line with a small but clear temperature anisotropy. These results, unfortunately, do not resolve the outstanding discrepancies on electron layer thickness between best available experiments and fully kinetic simulations. To make further progress, we are continuously pushing in the both experimental and numerical frontiers. Experimentally, we started investigations on EM-LHDI and electron heating as a function of guide field strength and symmetry of reconnection geometry, with new attempts to measure non-thermal electrons and higher frequency fluctuations. Numerically, we started investigations of kinetic simulations at realistic ratios of electron plasma frequency to cyclotron frequency, and also at realistic ratios of ion mass to electron mass. The most updated results of these new projects will be presented with discussions on the relevance to space observations.

Scaling of Magnetic Reconnection in Relativistic Collisionless Pair Plasmas

NASA Technical Reports Server (NTRS)

Liu, Yi-Hsin; Guo, Fan; Daughton, William; Li, Hui; Hesse, Michael

2015-01-01

Using fully kinetic simulations, we study the scaling of the inflow speed of collisionless magnetic reconnection in electron-positron plasmas from the non-relativistic to ultra-relativistic limit. In the anti-parallel configuration, the inflow speed increases with the upstream magnetization parameter sigma and approaches the speed of light when sigma is greater than O(100), leading to an enhanced reconnection rate. In all regimes, the divergence of the pressure tensor is the dominant term responsible for breaking the frozen-in condition at the x-line. The observed scaling agrees well with a simple model that accounts for the Lorentz contraction of the plasma passing through the diffusion region. The results demonstrate that the aspect ratio of the diffusion region, modified by the compression factor of proper density, remains approximately 0.1 in both the non-relativistic and relativistic limits.

Kinetic Framework for the Magnetosphere-Ionosphere-Plasmasphere-Polar Wind System: Modeling Ion Outflow

NASA Astrophysics Data System (ADS)

Schunk, R. W.; Barakat, A. R.; Eccles, V.; Karimabadi, H.; Omelchenko, Y.; Khazanov, G. V.; Glocer, A.; Kistler, L. M.

2014-12-01

A Kinetic Framework for the Magnetosphere-Ionosphere-Plasmasphere-Polar Wind System is being developed in order to provide a rigorous approach to modeling the interaction of hot and cold particle interactions. The framework will include ion and electron kinetic species in the ionosphere, plasmasphere and polar wind, and kinetic ion, super-thermal electron and fluid electron species in the magnetosphere. The framework is ideally suited to modeling ion outflow from the ionosphere and plasmasphere, where a wide range for fluid and kinetic processes are important. These include escaping ion interactions with (1) photoelectrons, (2) cusp/auroral waves, double layers, and field-aligned currents, (3) double layers in the polar cap due to the interaction of cold ionospheric and hot magnetospheric electrons, (4) counter-streaming ions, and (5) electromagnetic wave turbulence. The kinetic ion interactions are particularly strong during geomagnetic storms and substorms. The presentation will provide a brief description of the models involved and discuss the effect that kinetic processes have on the ion outflow.

Virus Neutralisation: New Insights from Kinetic Neutralisation Curves

PubMed Central

Magnus, Carsten

2013-01-01

Antibodies binding to the surface of virions can lead to virus neutralisation. Different theories have been proposed to determine the number of antibodies that must bind to a virion for neutralisation. Early models are based on chemical binding kinetics. Applying these models lead to very low estimates of the number of antibodies needed for neutralisation. In contrast, according to the more conceptual approach of stoichiometries in virology a much higher number of antibodies is required for virus neutralisation by antibodies. Here, we combine chemical binding kinetics with (virological) stoichiometries to better explain virus neutralisation by antibody binding. This framework is in agreement with published data on the neutralisation of the human immunodeficiency virus. Knowing antibody reaction constants, our model allows us to estimate stoichiometrical parameters from kinetic neutralisation curves. In addition, we can identify important parameters that will make further analysis of kinetic neutralisation curves more valuable in the context of estimating stoichiometries. Our model gives a more subtle explanation of kinetic neutralisation curves in terms of single-hit and multi-hit kinetics. PMID:23468602

The Ω-loop lid domain of phosphoenolpyruvate carboxykinase is essential for catalytic function

PubMed Central

Johnson, Troy A.; Holyoak, Todd

2012-01-01

Phosphoenolpyruvate carboxykinase (PEPCK) is an essential metabolic enzyme operating in the gluconeogenesis and glyceroneogenesis pathways. Recent studies have demonstrated that the enzyme contains a mobile active site lid domain that transitions between an open/disorded conformation to a closed/ordered conformation as the enzyme progresses through the catalytic cycle. The understanding of how this mobile domain functions in catalysis is incomplete. Previous studies show that the closure of the lid domain stabilizes the reaction intermediate and protects the reactive intermediate from spurious protonation and thus contributes to the fidelity of the enzyme. In order to more fully investigate the roles of the lid domain in PEPCK function we created three mutations that replaced the 11-residue lid domain with one, two or three glycine residues. Kinetic analysis of the mutant enzymes demonstrates that none of the enzyme constructs exhibit any measurable kinetic activity resulting in a decrease in the catalytic parameters by at least 106. Structural characterization of the mutants in complexes representing the catalytic cycle suggest that the inactivity is due to a role for the lid domain in the formation of the fully closed state of the enzyme that is required for catalytic function. In the absence of the lid domain, the enzyme is unable to achieve the fully closed state and is rendered inactive despite possessing all of the residues and substrates required for catalytic function. This work demonstrates how enzyme catalytic function can be abolished through the alteration of conformational equilibria despite all elements required for chemical conversion of substrates to products remaining intact. PMID:23127136

Parameter Balancing in Kinetic Models of Cell Metabolism†

PubMed Central

2010-01-01

Kinetic modeling of metabolic pathways has become a major field of systems biology. It combines structural information about metabolic pathways with quantitative enzymatic rate laws. Some of the kinetic constants needed for a model could be collected from ever-growing literature and public web resources, but they are often incomplete, incompatible, or simply not available. We address this lack of information by parameter balancing, a method to complete given sets of kinetic constants. Based on Bayesian parameter estimation, it exploits the thermodynamic dependencies among different biochemical quantities to guess realistic model parameters from available kinetic data. Our algorithm accounts for varying measurement conditions in the input data (pH value and temperature). It can process kinetic constants and state-dependent quantities such as metabolite concentrations or chemical potentials, and uses prior distributions and data augmentation to keep the estimated quantities within plausible ranges. An online service and free software for parameter balancing with models provided in SBML format (Systems Biology Markup Language) is accessible at www.semanticsbml.org. We demonstrate its practical use with a small model of the phosphofructokinase reaction and discuss its possible applications and limitations. In the future, parameter balancing could become an important routine step in the kinetic modeling of large metabolic networks. PMID:21038890

Si1-yCy/Si(001) gas-source molecular beam epitaxy from Si2H6 and CH3SiH3: Surface reaction paths and growth kinetics

NASA Astrophysics Data System (ADS)

Foo, Y. L.; Bratland, K. A.; Cho, B.; Desjardins, P.; Greene, J. E.

2003-04-01

In situ surface probes and postdeposition analyses were used to follow surface reaction paths and growth kinetics of Si1-yCy alloys grown on Si(001) by gas-source molecular-beam epitaxy from Si2H6/CH3SiH3 mixtures as a function of C concentration y (0-2.6 at %) and temperature Ts (500-600 °C). High-resolution x-ray diffraction reciprocal lattice maps show that all layers are in tension and fully coherent with their substrates. Film growth rates R decrease with both y and Ts, and the rate of decrease in R as a function of y increases rapidly with Ts. In situ isotopically tagged D2 temperature-programmed desorption (TPD) measurements reveal that C segregation during steady-state Si1-yCy(001) growth results in charge transfer from Si surface dangling bonds to second-layer C atoms, which have a higher electronegativity than Si. From the TPD results, we obtain the coverage θSi*(y,Ts) of Si* surface sites with C backbonds as well as H2 desorption energies Ed from both Si and Si* surface sites. θSi* increases with increasing y and Ts in the kinetically limited segregation regime while Ed decreases from 2.52 eV for H2 desorption from Si surface sites with Si back bonds to 2.22 eV from Si* surface sites. This leads to an increase in the H2 desorption rate, and hence should yield higher film deposition rates, with increasing y and/or Ts during Si1-yCy(001) growth. The effect, however, is more than offset by the decrease in Si2H6 reactive sticking probabilities at Si* surface sites. Film growth rates R(Ts,JSi2H6,JCH3SiH3) calculated using a simple transition-state kinetic model, together with measured kinetic parameters, were found to be in excellent agreement with the experimental data.

The Effect of Ethanol Addition to Gasoline on Low- and Intermediate-Temperature Heat Release under Boosted Conditions in Kinetically Controlled Engines

NASA Astrophysics Data System (ADS)

Vuilleumier, David Malcolm

The detailed study of chemical kinetics in engines has become required to further advance engine efficiency while simultaneously lowering engine emissions. This push for higher efficiency engines is not caused by a lack of oil, but by efforts to reduce anthropogenic carbon dioxide emissions, that cause global warming. To operate in more efficient manners while reducing traditional pollutant emissions, modern internal combustion piston engines are forced to operate in regimes in which combustion is no longer fully transport limited, and instead is at least partially governed by chemical kinetics of combusting mixtures. Kinetically-controlled combustion allows the operation of piston engines at high compression ratios, with partially-premixed dilute charges; these operating conditions simultaneously provide high thermodynamic efficiency and low pollutant formation. The investigations presented in this dissertation study the effect of ethanol addition on the low-temperature chemistry of gasoline type fuels in engines. These investigations are carried out both in a simplified, fundamental engine experiment, named Homogeneous Charge Compression Ignition, as well as in more applied engine systems, named Gasoline Compression Ignition engines and Partial Fuel Stratification engines. These experimental investigations, and the accompanying modeling work, show that ethanol is an effective scavenger of radicals at low temperatures, and this inhibits the low temperature pathways of gasoline oxidation. Further, the investigations measure the sensitivity of gasoline auto-ignition to system pressure at conditions that are relevant to modern engines. It is shown that at pressures above 40 bar and temperatures below 850 Kelvin, gasoline begins to exhibit Low-Temperature Heat Release. However, the addition of 20% ethanol raises the pressure requirement to 60 bar, while the temperature requirement remains unchanged. These findings have major implications for a range of modern engines. Low-Temperature Heat Release significantly enhances the auto-ignition process, which limits the conditions under which advanced combustion strategies may operate. As these advanced combustion strategies are required to meet emissions and fuel-economy regulations, the findings of this dissertation may benefit and be incorporated into future engine design toolkits, such as detailed chemical kinetic mechanisms.

In silico synchronization reveals regulators of nuclear ruptures in lamin A/C deficient model cells

NASA Astrophysics Data System (ADS)

Robijns, J.; Molenberghs, F.; Sieprath, T.; Corne, T. D. J.; Verschuuren, M.; de Vos, W. H.

2016-07-01

The nuclear lamina is a critical regulator of nuclear structure and function. Nuclei from laminopathy patient cells experience repetitive disruptions of the nuclear envelope, causing transient intermingling of nuclear and cytoplasmic components. The exact causes and consequences of these events are not fully understood, but their stochastic occurrence complicates in-depth analyses. To resolve this, we have established a method that enables quantitative investigation of spontaneous nuclear ruptures, based on co-expression of a firmly bound nuclear reference marker and a fluorescent protein that shuttles between the nucleus and cytoplasm during ruptures. Minimally invasive imaging of both reporters, combined with automated tracking and in silico synchronization of individual rupture events, allowed extracting information on rupture frequency and recovery kinetics. Using this approach, we found that rupture frequency correlates inversely with lamin A/C levels, and can be reduced in genome-edited LMNA knockout cells by blocking actomyosin contractility or inhibiting the acetyl-transferase protein NAT10. Nuclear signal recovery followed a kinetic that is co-determined by the severity of the rupture event, and could be prolonged by knockdown of the ESCRT-III complex component CHMP4B. In conclusion, our approach reveals regulators of nuclear rupture induction and repair, which may have critical roles in disease development.

Kinetics, Assembling and Conformation Control of L-Cysteine Adsorption on Pt by In Situ FTIR Spectroscopy and QCM-D.

PubMed

Cordoba de Torresi, Susana Ines; Dourado, Andre H B; Silva, Rubens A; Torresi, Roberto M; Sumodjo, Paulo T A; Arenz, Matthias

2018-06-05

A quartz crystal microbalance method with dissipation (QCM-D) and attenuated total reflection infrared (ATR-FTIRS) spectroscopy were used to study the adsorption of L-cysteine (L-Cys) on Pt. Using QCM-D, it was possible to verify that the viscoelastic properties of the adsorbed species play an important role in the adsorption, rendering Sauerbrey's equation inapplicable. The modelling of QCM-D data exposed two different processes for the adsorption reaction. The first one had an activation time and is fast, whereas the second is slow. These processes were also resolved by ATR-FTIRS identified to be water and anion adsorption preceded by L-Cys adsorption. Both techniques reveal that the degree of surface coverage is pH dependent. Spectroscopic data indicate that the conformation of L-Cys(ads) changes with pH and that the structures do not fully agree with those proposed in literature for other metallic surfaces. The assembling of the adsorbed monolayer appeared to be very fast, and it was not possible to determine or quantify this kinetics. The conformation is also controlled by applied potential, and the anion adsorption and interfacial water depends on the conformation of the adsorbed molecules. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Effect of Size of Red Cells on the Kinetics of Their Oxygen Uptake

PubMed Central

Holland, R. A. B.; Forster, R. E.

1966-01-01

Using a double-beam stopped-flow apparatus estimations were made of the velocity constant for the initial uptake of oxygen by fully reduced erythrocytes (k'c). Mammalian cells were studied with volumes varying from 20 µ3 (goat) to 90 µ3 (man), as were bullfrog cells (680 µ3). Measurements were made under physiological conditions of pH, P CO2, and temperature. In man k'c was 80 mM -1 sec-1 and in other species smaller cells generally had a greater value for k'c than did the larger cells. In the goat it was 1.8 times as great as the human value; in the bullfrog it was only one-fifth as great. These differences could not be accounted for by interspecific differences in hemoglobin kinetics. The differences probably represent a true effect of size conferring some biological advantage on the species with the smaller cells. The cell membrane offered resistance to oxygen passage. Using the usual red cell model of an infinite sheet of reduced hemoglobin, membrane permeability appeared to differ among mammals. If, as is likely, the effective cell halfthickness differs among mammals, actual membrane permeability differences may be less. A method for measurement of oxygen saturation of dilute cell suspensions is also described. PMID:5943611

Dynamics of kinetic geodesic-acoustic modes and the radial electric field in tokamak neoclassical plasmas

NASA Astrophysics Data System (ADS)

Xu, X. Q.; Belli, E.; Bodi, K.; Candy, J.; Chang, C. S.; Cohen, R. H.; Colella, P.; Dimits, A. M.; Dorr, M. R.; Gao, Z.; Hittinger, J. A.; Ko, S.; Krasheninnikov, S.; McKee, G. R.; Nevins, W. M.; Rognlien, T. D.; Snyder, P. B.; Suh, J.; Umansky, M. V.

2009-06-01

We present edge gyrokinetic simulations of tokamak plasmas using the fully non-linear (full-f) continuum code TEMPEST. A non-linear Boltzmann model is used for the electrons. The electric field is obtained by solving the 2D gyrokinetic Poisson equation. We demonstrate the following. (1) High harmonic resonances (n > 2) significantly enhance geodesic-acoustic mode (GAM) damping at high q (tokamak safety factor), and are necessary to explain the damping observed in our TEMPEST q-scans and consistent with the experimental measurements of the scaling of the GAM amplitude with edge q95 in the absence of obvious evidence that there is a strong q-dependence of the turbulent drive and damping of the GAM. (2) The kinetic GAM exists in the edge for steep density and temperature gradients in the form of outgoing waves, its radial scale is set by the ion temperature profile, and ion temperature inhomogeneity is necessary for GAM radial propagation. (3) The development of the neoclassical electric field evolves through different phases of relaxation, including GAMs, their radial propagation and their long-time collisional decay. (4) Natural consequences of orbits in the pedestal and scrape-off layer region in divertor geometry are substantial non-Maxwellian ion distributions and parallel flow characteristics qualitatively like those observed in experiments.

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.

Diagnosing entropy production and dissipation in fully kinetic plasmas

NASA Astrophysics Data System (ADS)

Juno, James; Tenbarge, Jason; Hakim, Ammar; Dorland, William; Cagas, Petr

2017-10-01

Many plasma systems, from the core of a tokamak to the outer heliosphere, are weakly collisional and thus most accurately described by kinetic theory. The typical approach to solving the kinetic equation has been the particle-in-cell algorithm, which, while a powerful tool, introduces counting noise into the particle distribution function. The counting noise is particularly problematic when attempting to study grand challenge problems such as entropy production from phenomena like shocks and turbulence. In this poster, we present studies of entropy production and dissipation processes present in simple turbulence and shock calculations using the continuum Vlasov-Maxwell solver in the Gkeyll framework. Particular emphasis is placed on a novel diagnostic, the field-particle correlation, which is especially efficient at separating the secular energy transfer into its constituent components, for example, cyclotron damping, Landau damping, or transit-time damping, when applied to a noise-free distribution function. National Science Foundation SHINE award No. AGS-1622306 and the UMD DOE Grant DE-FG02-93ER54197.

Automated placement of interfaces in conformational kinetics calculations using machine learning

NASA Astrophysics Data System (ADS)

Grazioli, Gianmarc; Butts, Carter T.; Andricioaei, Ioan

2017-10-01

Several recent implementations of algorithms for sampling reaction pathways employ a strategy for placing interfaces or milestones across the reaction coordinate manifold. Interfaces can be introduced such that the full feature space describing the dynamics of a macromolecule is divided into Voronoi (or other) cells, and the global kinetics of the molecular motions can be calculated from the set of fluxes through the interfaces between the cells. Although some methods of this type are exact for an arbitrary set of cells, in practice, the calculations will converge fastest when the interfaces are placed in regions where they can best capture transitions between configurations corresponding to local minima. The aim of this paper is to introduce a fully automated machine-learning algorithm for defining a set of cells for use in kinetic sampling methodologies based on subdividing the dynamical feature space; the algorithm requires no intuition about the system or input from the user and scales to high-dimensional systems.

Diagnosing entropy production and dissipation in fully kinetic plasmas

NASA Astrophysics Data System (ADS)

Juno, J.; TenBarge, J. M.; Hakim, A.; Dorland, W.

2017-12-01

Many plasma systems, from the core of a tokamak to the outer heliosphere, are weakly collisional and thus most accurately described by kinetic theory. The typical approach to solving the kinetic equation has been the particle-in-cell algorithm, which, while a powerful tool, introduces counting noise into the particle distribution function. The counting noise is particularly problematic when attempting to study grand challenge problems such as entropy production from phenomena like shocks and turbulence. In this poster, we present studies of entropy production and dissipation processes present in simple turbulence and shock calculations using the continuum Vlasov-Maxwell solver in the Gkeyll framework. Particular emphasis is placed on a novel diagnostic, the field-particle correlation, which is especially efficient at separating the secular energy transfer into its constituent components, for example, cyclotron damping, Landau damping, or transit-time damping, when applied to a noise-free distribution function. Using reduced systems such as completely transverse electromagnetic shocks, we also explore the signatures of perpendicular, non-resonant, energization mechanisms.

Cutting Edge: Protection by Antiviral Memory CD8 T Cells Requires Rapidly Produced Antigen in Large Amounts.

PubMed

Remakus, Sanda; Ma, Xueying; Tang, Lingjuan; Xu, Ren-Huan; Knudson, Cory; Melo-Silva, Carolina R; Rubio, Daniel; Kuo, Yin-Ming; Andrews, Andrew; Sigal, Luis J

2018-05-15

Numerous attempts to produce antiviral vaccines by harnessing memory CD8 T cells have failed. A barrier to progress is that we do not know what makes an Ag a viable target of protective CD8 T cell memory. We found that in mice susceptible to lethal mousepox (the mouse homolog of human smallpox), a dendritic cell vaccine that induced memory CD8 T cells fully protected mice when the infecting virus produced Ag in large quantities and with rapid kinetics. Protection did not occur when the Ag was produced in low amounts, even with rapid kinetics, and protection was only partial when the Ag was produced in large quantities but with slow kinetics. Hence, the amount and timing of Ag expression appear to be key determinants of memory CD8 T cell antiviral protective immunity. These findings may have important implications for vaccine design. Copyright © 2018 by The American Association of Immunologists, Inc.

The Use of a Multidimensional Measure of Dialysis Adequacy—Moving beyond Small Solute Kinetics

PubMed Central

Perl, Jeffrey; Dember, Laura M.; Bargman, Joanne M.; Browne, Teri; Charytan, David M.; Flythe, Jennifer E.; Hickson, LaTonya J.; Hung, Adriana M.; Jadoul, Michel; Lee, Timmy Chang; Meyer, Klemens B.; Moradi, Hamid; Shafi, Tariq; Teitelbaum, Isaac; Wong, Leslie P.

2017-01-01

Urea removal has become a key measure of the intensity of dialysis treatment for kidney failure. Small solute removal, exemplified by Kt/Vurea, has been broadly applied as a means to quantify the dose of thrice weekly hemodialysis. Yet, the reliance on small solute clearances alone as a measure of dialysis adequacy fails fully to quantify the intended clinical effects of dialysis therapy. This review aims to (1) understand the strengths and limitations of small solute kinetics as a surrogate marker of dialysis dose, and (2) present the prospect of a more comprehensive construct for dialysis dose, one that considers more broadly the goals of ESRD care to maximize both quality of life and survival. On behalf of the American Society of Nephrology Dialysis Advisory Group, we propose the need to ascertain the validity and utility of a multidimensional measure that moves beyond small solute kinetics alone to quantify optimal dialysis derived from both patient-reported and comprehensive clinical and dialysis-related measures. PMID:28314806

Kinetic Behavior and Microstructure of Pearlite Isothermal Transformation Under High Undercooling

NASA Astrophysics Data System (ADS)

Liang, Yu; Xu, Pingwei; Xiang, Song; Liang, Yilong; Xiong, Hu; Li, Jing

2018-06-01

The kinetic behavior of highly undercooled austenite and its effects on the microstructural evolution and mechanical properties of high-carbon steel are studied. The undercooling degree is increased through a temporary undercooling treatment at the bainite transformation temperature of 380 °C to 450 °C before the pearlite isothermal transformation at 500 °C to 620 °C. The transformation kinetics reveals an increased nose temperature and a rightward shift of the transformation curve under high undercooling conditions. In addition, the undercooling treatment leads to an increased driving force during pearlite transformation, which is responsible for the refined hierarchical structures of pearlite. As a result, a 20 to 40 pct size reduction is achieved for pearlite colonies and lamellae. Such refinement is in turn attributed to an 26 pct increase in reduction in area. This work provides both a new understanding of high-performance fully pearlitic steels for practical applications and new perspectives for potential technological applications in drawing processes for hypoeutectoid steels.

Automated placement of interfaces in conformational kinetics calculations using machine learning.

PubMed

Grazioli, Gianmarc; Butts, Carter T; Andricioaei, Ioan

2017-10-21

Several recent implementations of algorithms for sampling reaction pathways employ a strategy for placing interfaces or milestones across the reaction coordinate manifold. Interfaces can be introduced such that the full feature space describing the dynamics of a macromolecule is divided into Voronoi (or other) cells, and the global kinetics of the molecular motions can be calculated from the set of fluxes through the interfaces between the cells. Although some methods of this type are exact for an arbitrary set of cells, in practice, the calculations will converge fastest when the interfaces are placed in regions where they can best capture transitions between configurations corresponding to local minima. The aim of this paper is to introduce a fully automated machine-learning algorithm for defining a set of cells for use in kinetic sampling methodologies based on subdividing the dynamical feature space; the algorithm requires no intuition about the system or input from the user and scales to high-dimensional systems.

Effect of electron thermal anisotropy on the kinetic cross-field streaming instability

NASA Technical Reports Server (NTRS)

Tsai, S. T.; Tanaka, M.; Gaffey, J. D., Jr.; Wu, C. S.; Da Jornada, E. H.; Ziebell, L. F.

1984-01-01

The investigation of the kinetic cross-field streaming instability, motivated by the research of collisionless shock waves and previously studied by Wu et al. (1983), is discussed more fully. Since in the ramp region of a quasi-perpendicular shock electrons can be preferentially heated in the direction transverse to the ambient magnetic field, it is both desirable and necessary to include the effect of the thermal anisotropy on the instability associated with a shock. It is found that Te-perpendicular greater than Te-parallel can significantly enhance the peak growth rate of the cross-field streaming instability when the electron beta is sufficiently high. Furthermore, the present analysis also improves the analytical and numerical solutions previously obtained.

Kinetic Simulations of Plasma Energization and Particle Acceleration in Interacting Magnetic Flux Ropes

NASA Astrophysics Data System (ADS)

Du, S.; Guo, F.; Zank, G. P.; Li, X.; Stanier, A.

2017-12-01

The interaction between magnetic flux ropes has been suggested as a process that leads to efficient plasma energization and particle acceleration (e.g., Drake et al. 2013; Zank et al. 2014). However, the underlying plasma dynamics and acceleration mechanisms are subject to examination of numerical simulations. As a first step of this effort, we carry out 2D fully kinetic simulations using the VPIC code to study the plasma energization and particle acceleration during coalescence of two magnetic flux ropes. Our analysis shows that the reconnection electric field and compression effect are important in plasma energization. The results may help understand the energization process associated with magnetic flux ropes frequently observed in the solar wind near the heliospheric current sheet.

Kinetics of heterotrophic biomass and storage mechanism in wetland cores measured by respirometry.

PubMed

Ortigara, A R C; Foladori, P; Andreottola, G

2011-01-01

Although oxygen uptake rate has been widely used in activated sludge for measuring kinetic and stoichiometric parameters or for wastewater characterization, its application in constructed wetlands (CWs) cores has been recently proposed. The aim of this research is to estimate the kinetic and stoichiometric parameters of the heterotrophic biomass in CW cores. Respirometric tests were carried out with pure carbonaceous substrate and real wastewater. Endogenous respiration was about 2 gO2 m(-3) h(-1) (per unit of bed volume), while the kinetic parameters obtained for COD oxidation were very high (maximum rate per unit of bed volume of 10.7-26.8 gCOD m(-3) h(-1)) which indicates high biodegradation potential in fully aerobic environment. Regarding to stoichiometric parameter, the maximum growth yield, Y(H), was 0.56-0.59 mgCOD/mgCOD, while the storage yield, Y(STO), was 0.75-0.77 mgCOD/mgCOD. The storage mechanism was observed in CW cores during COD oxidation, which leads to the transformation of the external soluble substrate in internal storage products, probably as response to intermittent loads applied in CW systems, transient concentrations of readily biodegradable substrate and alternance of feast/famine periods.

Movement variability in the golf swing.

PubMed

Langdown, Ben L; Bridge, Matt; Li, Francois-Xavier

2012-06-01

Traditionally, golf biomechanics has focused upon achieving consistency in swing kinematics and kinetics, whilst variability was considered to be noise and dysfunctional. There has been a growing argument that variability is an intrinsic aspect of skilled motor performance and plays a functional role. Two types of variability are described: 'strategic shot selection' and 'movement variability'. In 'strategic shot selection', the outcome remains consistent, but the swing kinematics/kinetics (resulting in the desired ball flight) are free to vary; 'movement variability' is the changes in swing kinematics and kinetics from trial to trial when the golfer attempts to hit the same shot. These changes will emerge due to constraints of the golfer's body, the environment, and the task. Biomechanical research has focused upon aspects of technique such as elite versus non-elite kinematics, kinetics, kinematic sequencing, peak angular velocities of body segments, wrist function, ground reaction forces, and electromyography, mainly in the search for greater distance and clubhead velocity. To date very little is known about the impact of variability on this complex motor skill, and it has yet to be fully researched to determine where the trade-off between functional and detrimental variability lies when in pursuit of enhanced performance outcomes.

Multispecies diffusion models: A study of uranyl species diffusion

NASA Astrophysics Data System (ADS)

Liu, Chongxuan; Shang, Jianying; Zachara, John M.

2011-12-01

Rigorous numerical description of multispecies diffusion requires coupling of species, charge, and aqueous and surface complexation reactions that collectively affect diffusive fluxes. The applicability of a fully coupled diffusion model is, however, often constrained by the availability of species self-diffusion coefficients, as well as by computational complication in imposing charge conservation. In this study, several diffusion models with variable complexity in charge and species coupling were formulated and compared to describe reactive multispecies diffusion in groundwater. Diffusion of uranyl [U(VI)] species was used as an example in demonstrating the effectiveness of the models in describing multispecies diffusion. Numerical simulations found that a diffusion model with a single, common diffusion coefficient for all species was sufficient to describe multispecies U(VI) diffusion under a steady state condition of major chemical composition, but not under transient chemical conditions. Simulations revealed that for multispecies U(VI) diffusion under transient chemical conditions, a fully coupled diffusion model could be well approximated by a component-based diffusion model when the diffusion coefficient for each chemical component was properly selected. The component-based diffusion model considers the difference in diffusion coefficients between chemical components, but not between the species within each chemical component. This treatment significantly enhanced computational efficiency at the expense of minor charge conservation. The charge balance in the component-based diffusion model can be enforced, if necessary, by adding a secondary migration term resulting from model simplification. The effect of ion activity coefficient gradients on multispecies diffusion is also discussed. The diffusion models were applied to describe U(VI) diffusive mass transfer in intragranular domains in two sediments collected from U.S. Department of Energy's Hanford 300A, where intragranular diffusion is a rate-limiting process controlling U(VI) adsorption and desorption. The grain-scale reactive diffusion model was able to describe U(VI) adsorption/desorption kinetics that had been previously described using a semiempirical, multirate model. Compared with the multirate model, the diffusion models have the advantage to provide spatiotemporal speciation evolution within the diffusion domains.

Cell survival fraction estimation based on the probability densities of domain and cell nucleus specific energies using improved microdosimetric kinetic models.

PubMed

Sato, Tatsuhiko; Furusawa, Yoshiya

2012-10-01

Estimation of the survival fractions of cells irradiated with various particles over a wide linear energy transfer (LET) range is of great importance in the treatment planning of charged-particle therapy. Two computational models were developed for estimating survival fractions based on the concept of the microdosimetric kinetic model. They were designated as the double-stochastic microdosimetric kinetic and stochastic microdosimetric kinetic models. The former model takes into account the stochastic natures of both domain and cell nucleus specific energies, whereas the latter model represents the stochastic nature of domain specific energy by its approximated mean value and variance to reduce the computational time. The probability densities of the domain and cell nucleus specific energies are the fundamental quantities for expressing survival fractions in these models. These densities are calculated using the microdosimetric and LET-estimator functions implemented in the Particle and Heavy Ion Transport code System (PHITS) in combination with the convolution or database method. Both the double-stochastic microdosimetric kinetic and stochastic microdosimetric kinetic models can reproduce the measured survival fractions for high-LET and high-dose irradiations, whereas a previously proposed microdosimetric kinetic model predicts lower values for these fractions, mainly due to intrinsic ignorance of the stochastic nature of cell nucleus specific energies in the calculation. The models we developed should contribute to a better understanding of the mechanism of cell inactivation, as well as improve the accuracy of treatment planning of charged-particle therapy.

Comparison of frictional resistance of esthetic and semi-esthetic self-ligating brackets

PubMed Central

Kannan, M. S.; Murali, R. V.; Kishorekumar, S.; Gnanashanmugam, K.; Jayanth, V.

2015-01-01

Aim: The frictional resistance encountered during sliding mechanics has been well established in the orthodontic literature, and it consists of complex interactions between the bracket, archwire, and method of ligation the claim of reduced friction with self-ligating brackets is often cited as a primary advantage over conventional brackets. This study was done to compare and evaluate the frictional forces generated between fully esthetic brackets and semi-aesthetic self-ligating brackets, which are of passive form and SEM (scanning electron microscope) study of the Brackets after Frictional evaluation. Materials and Methods: Two types of self-ligating esthetic brackets, Damon clear (Ormco) made of fully ceramic and Opal (Ultradent Products, USA) and, Two types of self-ligating semi-esthetic brackets, Clarity SL (3M Unitek) and Damon 3 (Ormco) both of which are made of ceramic with metal slot. Arch wires with different dimensions and quality 17 × 25, 19 × 25 Titanium Molybdenum Alloy (TMA) and 17 × 25, 19 × 25 stainless steel that came from plain strands of wire were used for frictional comparison test. The brackets used in this study had 0.022 × 0.028 inch slot. Results: The statistical tests showed significantly smaller amount of kinetic frictional forces is generated by Damon 3 (semi-esthetic self-ligating brackets). For each wire used, Damon 3 displayed significantly lower frictional forces (P ≤ 0.05) than any of the self-ligating system, followed by Opal (fully esthetic self-ligating brackets) which generated smaller amount of frictional forces but relatively on the higher side when compared with Damon 3. Damon clear (fully esthetic self-ligating brackets) generated the maximum amount of kinetic forces with all types of wire dimensions and properties when compared to the other three types of self-ligating system. Clarity SL (semi-esthetic self-ligating brackets) generated smaller amount of frictional forces when compared with Damon clear and relatively higher amount of frictional forces when compared to Opal and Damon 3 PMID:26015687

Comparison of frictional resistance of esthetic and semi-esthetic self-ligating brackets.

PubMed

Kannan, M S; Murali, R V; Kishorekumar, S; Gnanashanmugam, K; Jayanth, V

2015-04-01

The frictional resistance encountered during sliding mechanics has been well established in the orthodontic literature, and it consists of complex interactions between the bracket, archwire, and method of ligation the claim of reduced friction with self-ligating brackets is often cited as a primary advantage over conventional brackets. This study was done to compare and evaluate the frictional forces generated between fully esthetic brackets and semi-aesthetic self-ligating brackets, which are of passive form and SEM (scanning electron microscope) study of the Brackets after Frictional evaluation. Two types of self-ligating esthetic brackets, Damon clear (Ormco) made of fully ceramic and Opal (Ultradent Products, USA) and, Two types of self-ligating semi-esthetic brackets, Clarity SL (3M Unitek) and Damon 3 (Ormco) both of which are made of ceramic with metal slot. Arch wires with different dimensions and quality 17 × 25, 19 × 25 Titanium Molybdenum Alloy (TMA) and 17 × 25, 19 × 25 stainless steel that came from plain strands of wire were used for frictional comparison test. The brackets used in this study had 0.022 × 0.028 inch slot. The statistical tests showed significantly smaller amount of kinetic frictional forces is generated by Damon 3 (semi-esthetic self-ligating brackets). For each wire used, Damon 3 displayed significantly lower frictional forces (P ≤ 0.05) than any of the self-ligating system, followed by Opal (fully esthetic self-ligating brackets) which generated smaller amount of frictional forces but relatively on the higher side when compared with Damon 3. Damon clear (fully esthetic self-ligating brackets) generated the maximum amount of kinetic forces with all types of wire dimensions and properties when compared to the other three types of self-ligating system. Clarity SL (semi-esthetic self-ligating brackets) generated smaller amount of frictional forces when compared with Damon clear and relatively higher amount of frictional forces when compared to Opal and Damon 3.

Feasible Muscle Activation Ranges Based on Inverse Dynamics Analyses of Human Walking

PubMed Central

Simpson, Cole S.; Sohn, M. Hongchul; Allen, Jessica L.; Ting, Lena H.

2015-01-01

Although it is possible to produce the same movement using an infinite number of different muscle activation patterns owing to musculoskeletal redundancy, the degree to which observed variations in muscle activity can deviate from optimal solutions computed from biomechanical models is not known. Here, we examined the range of biomechanically permitted activation levels in individual muscles during human walking using a detailed musculoskeletal model and experimentally-measured kinetics and kinematics. Feasible muscle activation ranges define the minimum and maximum possible level of each muscle’s activation that satisfy inverse dynamics joint torques assuming that all other muscles can vary their activation as needed. During walking, 73% of the muscles had feasible muscle activation ranges that were greater than 95% of the total muscle activation range over more than 95% of the gait cycle, indicating that, individually, most muscles could be fully active or fully inactive while still satisfying inverse dynamics joint torques. Moreover, the shapes of the feasible muscle activation ranges did not resemble previously-reported muscle activation patterns nor optimal solutions, i.e. static optimization and computed muscle control, that are based on the same biomechanical constraints. Our results demonstrate that joint torque requirements from standard inverse dynamics calculations are insufficient to define the activation of individual muscles during walking in healthy individuals. Identifying feasible muscle activation ranges may be an effective way to evaluate the impact of additional biomechanical and/or neural constraints on possible versus actual muscle activity in both normal and impaired movements. PMID:26300401

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.

Noncollisional kinetic model for non-neutral plasmas in a Penning trap: General properties and stationary solutions

NASA Astrophysics Data System (ADS)

Coppa, G. G.; Ricci, Paolo

2002-10-01

This work deals with a noncollisional kinetic model for non-neutral plasmas in a Penning trap. Using the spatial coordinates r, θ, z and the axial velocity vz as phase-space variables, a kinetic model is developed starting from the kinetic equation for the distribution function f(r,θ,z,vz,t). In order to reduce the complexity of the model, the kinetic equations are integrated along the axial direction by assuming an ergodic distribution in the phase space (z,vz) for particles of the same axial energy ɛ and the same planar position. In this way, a kinetic equation for the z-integrated electron distribution F(r,θ,ɛ,t) is obtained taking into account implicitly the three-dimensionality of the problem. The general properties of the model are discussed, in particular the conservation laws. The model is also related to the fluid model that was introduced by Finn et al. [Phys. Plasmas 6, 3744 (1999); Phys. Rev. Lett. 84, 2401 (2000)] and developed by Coppa et al. [Phys. Plasmas 8, 1133 (2001)]. Finally, numerical investigations are presented regarding the stationary solutions of the model.

Multivariate curve resolution-alternating least squares and kinetic modeling applied to near-infrared data from curing reactions of epoxy resins: mechanistic approach and estimation of kinetic rate constants.

PubMed

Garrido, M; Larrechi, M S; Rius, F X

2006-02-01

This study describes the combination of multivariate curve resolution-alternating least squares with a kinetic modeling strategy for obtaining the kinetic rate constants of a curing reaction of epoxy resins. The reaction between phenyl glycidyl ether and aniline is monitored by near-infrared spectroscopy under isothermal conditions for several initial molar ratios of the reagents. The data for all experiments, arranged in a column-wise augmented data matrix, are analyzed using multivariate curve resolution-alternating least squares. The concentration profiles recovered are fitted to a chemical model proposed for the reaction. The selection of the kinetic model is assisted by the information contained in the recovered concentration profiles. The nonlinear fitting provides the kinetic rate constants. The optimized rate constants are in agreement with values reported in the literature.

Emergence of HGF/SF-Induced Coordinated Cellular Motility

PubMed Central

Zaritsky, Assaf; Natan, Sari; Ben-Jacob, Eshel; Tsarfaty, Ilan

2012-01-01

Collective cell migration plays a major role in embryonic morphogenesis, tissue remodeling, wound repair and cancer invasion. Despite many decades of extensive investigations, only few analytical tools have been developed to enhance the biological understanding of this important phenomenon. Here we present a novel quantitative approach to analyze long term kinetics of bright field time-lapse wound healing. Fully-automated spatiotemporal measures and visualization of cells' motility and implicit morphology were proven to be sound, repetitive and highly informative compared to single-cell tracking analysis. We study cellular collective migration induced by tyrosine kinase-growth factor signaling (Met-Hepatocyte Growth Factor/Scatter Factor (HGF/SF)). Our quantitative approach is applied to demonstrate that collective migration of the adenocarcinoma cell lines is characterized by simple morpho-kinetics. HGF/SF induces complex morpho-kinetic coordinated collective migration: cells at the front move faster and are more spread than those further away from the wound edge. As the wound heals, distant cells gradually accelerate and enhance spread and elongation –resembling the epithelial to mesenchymal transition (EMT), and then the cells become more spread and maintain higher velocity than cells located closer to the wound. Finally, upon wound closure, front cells halt, shrink and round up (resembling mesenchymal to epithelial transition (MET) phenotype) while distant cells undergo the same process gradually. Met inhibition experiments further validate that Met signaling dramatically alters the morpho-kinetic dynamics of the healing wound. Machine-learning classification was applied to demonstrate the generalization of our findings, revealing even subtle changes in motility patterns induced by Met-inhibition. It is concluded that activation of Met-signaling induces an elaborated model in which cells lead a coordinated increased motility along with gradual differentiation-based collective cell motility dynamics. Our quantitative phenotypes may guide future investigation on the molecular and cellular mechanisms of tyrosine kinase-induced coordinate cell motility and morphogenesis in metastasis. PMID:22970283