Kinetic Model for 1D aggregation of yeast ``prions''
NASA Astrophysics Data System (ADS)
Kunes, Kay; Cox, Daniel; Singh, Rajiv
2004-03-01
Mammalian prion proteins (PrP) are of public health interest because of mad cow and chronic wasting diseases. Yeast have proteins which can undergo similar reconformation and aggregation processes to PrP; yeast forms are simpler to experimentally study and model. Recent in vitro studies of the SUP35 protein(1), showed long aggregates and pure exponential growth of the misfolded form. To explain this data, we have extended a previous model of aggregation kinetics(2). The model assumes reconformation only upon aggregation, and includes aggregate fissioning and an initial nucleation barrier. We find for sufficiently small nucleation rates or seeding by small dimer concentrations that we can achieve the requisite exponential growth and long aggregates. We will compare to a more realistic stochastic kinetics model and present prelimary attempts to describe recent experiments on SUP35 strains. *-Supported by U.S. Army Congressionally Mandated Research Fund. 1) P. Chien and J.S. Weissman, Nature 410, 223 (2001); http://online.kitp.ucsb.edu/online/bionet03/collins/. 2) J. Masel, V.A.> Jansen, M.A. Nowak, Biophys. Chem. 77, 139 (1999).
Kinetic and Stochastic Models of 1D yeast ``prions"
NASA Astrophysics Data System (ADS)
Kunes, Kay
2005-03-01
Mammalian prion proteins (PrP) are of public health interest because of mad cow and chronic wasting diseases. Yeasts have proteins, which can undergo similar reconformation and aggregation processes to PrP; yeast ``prions" are simpler to experimentally study and model. Recent in vitro studies of the SUP35 protein (1), showed long aggregates and pure exponential growth of the misfolded form. To explain this data, we have extended a previous model of aggregation kinetics along with our own stochastic approach (2). Both models assume reconformation only upon aggregation, and include aggregate fissioning and an initial nucleation barrier. We find for sufficiently small nucleation rates or seeding by small dimer concentrations that we can achieve the requisite exponential growth and long aggregates.
HELIOS-CR A 1-D radiation-magnetohydrodynamics code with inline atomic kinetics modeling
NASA Astrophysics Data System (ADS)
Macfarlane, J. J.; Golovkin, I. E.; Woodruff, P. R.
2006-05-01
HELIOS-CR is a user-oriented 1D radiation-magnetohydrodynamics code to simulate the dynamic evolution of laser-produced plasmas and z-pinch plasmas. It includes an in-line collisional-radiative (CR) model for computing non-LTE atomic level populations at each time step of the hydrodynamics simulation. HELIOS-CR has been designed for ease of use, and is well-suited for experimentalists, as well as graduate and undergraduate student researchers. The energy equations employed include models for laser energy deposition, radiation from external sources, and high-current discharges. Radiative transport can be calculated using either a multi-frequency flux-limited diffusion model, or a multi-frequency, multi-angle short characteristics model. HELIOS-CR supports the use of SESAME equation of state (EOS) tables, PROPACEOS EOS/multi-group opacity data tables, and non-LTE plasma properties computed using the inline CR modeling. Time-, space-, and frequency-dependent results from HELIOS-CR calculations are readily displayed with the HydroPLOT graphics tool. In addition, the results of HELIOS simulations can be post-processed using the SPECT3D Imaging and Spectral Analysis Suite to generate images and spectra that can be directly compared with experimental measurements. The HELIOS-CR package runs on Windows, Linux, and Mac OSX platforms, and includes online documentation. We will discuss the major features of HELIOS-CR, and present example results from simulations.
NASA Technical Reports Server (NTRS)
Dobson, Chris C.; Hrbud, Ivana
2004-01-01
Electron density measurements have been made in steady-state plasmas in a spherical inertial electrostatic confinement (IEC) discharge using microwave interferometry. Plasma cores interior to two cathodes, having diameters of 15 and 23 cm, respectively, were probed over a transverse range of 10 cm with a spatial resolution of about 1.4 cm for buffer gas pressures from 0.2 to 6 Pa in argon and deuterium. The transverse profiles are generally flat, in some cases with eccentric symmetric minima, and give mean densities of from approx. = 0.4 to 7x 10(exp 10)/cu cm, the density generally increasing with the neutral gas pressure. Numerical solutions of the 1-D Poisson equation for EC plasmas are reviewed and energy distribution functions are identified which give flat transverse profiles. These functions are used with the plasma approximation to obtain solutions which also give densities consistent with the measurements, and a double potential well solution is obtained which has minima qualitatively similar to those observed. Explicit consideration is given to the compatibility of the solutions interior and exterior to the cathode, and to grid transparency. Deuterium fusion neutron emission rates were also measured and found to be isotropic, to within the measurement error, over two simultaneous directions. Anisotropy was observed in residual emissions during operation with non-fusing hydrogen-1. The deuterium rates are consistent with predictions from the model.
NOKIN1D: one-dimensional neutron kinetics based on a nodal collocation method
NASA Astrophysics Data System (ADS)
Verdú, G.; Ginestar, D.; Miró, R.; Jambrina, A.; Barrachina, T.; Soler, Amparo; Concejal, Alberto
2014-06-01
The TRAC-BF1 one-dimensional kinetic model is a formulation of the neutron diffusion equation in the two energy groups' approximation, based on the analytical nodal method (ANM). The advantage compared with a zero-dimensional kinetic model is that the axial power profile may vary with time due to thermal-hydraulic parameter changes and/or actions of the control systems but at has the disadvantages that in unusual situations it fails to converge. The nodal collocation method developed for the neutron diffusion equation and applied to the kinetics resolution of TRAC-BF1 thermal-hydraulics, is an adaptation of the traditional collocation methods for the discretization of partial differential equations, based on the development of the solution as a linear combination of analytical functions. It has chosen to use a nodal collocation method based on a development of Legendre polynomials of neutron fluxes in each cell. The qualification is carried out by the analysis of the turbine trip transient from the NEA benchmark in Peach Bottom NPP using both the original 1D kinetics implemented in TRAC-BF1 and the 1D nodal collocation method.
O(1D) kinetic study of key ozone depleting substances and greenhouse gases.
Baasandorj, Munkhbayar; Fleming, Eric L; Jackman, Charles H; Burkholder, James B
2013-03-28
A key stratospheric loss process for ozone depleting substances (ODSs) and greenhouse gases (GHGs) is reaction with the O((1)D) atom. In this study, rate coefficients, k, for the O((1)D) atom reaction were measured for the following key halocarbons: chlorofluorocarbons (CFCs) CFCl3 (CFC-11), CF2Cl2 (CFC-12), CFCl2CF2Cl (CFC-113), CF2ClCF2Cl (CFC-114), CF3CF2Cl (CFC-115); hydrochlorofluorocarbons (HCFCs) CHF2Cl (HCFC-22), CH3CClF2 (HCFC-142b); and hydrofluorocarbons (HFCs) CHF3 (HFC-23), CHF2CF3 (HFC-125), CH3CF3 (HFC-143a), and CF3CHFCF3 (HFC-227ea). Total rate coefficients, kT, corresponding to the loss of the O((1)D) atom, were measured over the temperature range 217-373 K using a competitive reactive technique. kT values for the CFC and HCFC reactions were >1 × 10(-10) cm(3) molecule(-1) s(-1), except for CFC-115, and the rate coefficients for the HFCs were in the range (0.095-0.72) × 10(-10) cm(3) molecule(-1) s(-1). Rate coefficients for the CFC-12, CFC-114, CFC-115, HFC-23, HFC-125, HFC-143a, and HFC-227ea reactions were observed to have a weak negative temperature dependence, E/R ≈ -25 K. Reactive rate coefficients, kR, corresponding to the loss of the halocarbon, were measured for CFC-11, CFC-115, HCFC-22, HCFC-142b, HFC-23, HFC-125, HFC-143a, and HFC-227ea using a relative rate technique. The reactive branching ratio obtained was dependent on the composition of the halocarbon and the trend in O((1)D) reactivity with the extent of hydrogen and chlorine substitution is discussed. The present results are critically compared with previously reported kinetic data and the discrepancies are discussed. 2D atmospheric model calculations were used to evaluate the local and global annually averaged atmospheric lifetimes of the halocarbons and the contribution of O((1)D) chemistry to their atmospheric loss. The O((1)D) reaction was found to be a major global loss process for CFC-114 and CFC-115 and a secondary global loss process for the other molecules included
Brady 1D seismic velocity model ambient noise prelim
Mellors, Robert J.
2013-10-25
Preliminary 1D seismic velocity model derived from ambient noise correlation. 28 Green's functions filtered between 4-10 Hz for Vp, Vs, and Qs were calculated. 1D model estimated for each path. The final model is a median of the individual models. Resolution is best for the top 1 km. Poorly constrained with increasing depth.
GIS-BASED 1-D DIFFUSIVE WAVE OVERLAND FLOW MODEL
KALYANAPU, ALFRED; MCPHERSON, TIMOTHY N.; BURIAN, STEVEN J.
2007-01-17
This paper presents a GIS-based 1-d distributed overland flow model and summarizes an application to simulate a flood event. The model estimates infiltration using the Green-Ampt approach and routes excess rainfall using the 1-d diffusive wave approximation. The model was designed to use readily available topographic, soils, and land use/land cover data and rainfall predictions from a meteorological model. An assessment of model performance was performed for a small catchment and a large watershed, both in urban environments. Simulated runoff hydrographs were compared to observations for a selected set of validation events. Results confirmed the model provides reasonable predictions in a short period of time.
Non-cooperative Brownian donkeys: A solvable 1D model
NASA Astrophysics Data System (ADS)
Jiménez de Cisneros, B.; Reimann, P.; Parrondo, J. M. R.
2003-12-01
A paradigmatic 1D model for Brownian motion in a spatially symmetric, periodic system is tackled analytically. Upon application of an external static force F the system's response is an average current which is positive for F < 0 and negative for F > 0 (absolute negative mobility). Under suitable conditions, the system approaches 100% efficiency when working against the external force F.
Deconvolution of Complex 1D NMR Spectra Using Objective Model Selection.
Hughes, Travis S; Wilson, Henry D; de Vera, Ian Mitchelle S; Kojetin, Douglas J
2015-01-01
Fluorine (19F) NMR has emerged as a useful tool for characterization of slow dynamics in 19F-labeled proteins. One-dimensional (1D) 19F NMR spectra of proteins can be broad, irregular and complex, due to exchange of probe nuclei between distinct electrostatic environments; and therefore cannot be deconvoluted and analyzed in an objective way using currently available software. We have developed a Python-based deconvolution program, decon1d, which uses Bayesian information criteria (BIC) to objectively determine which model (number of peaks) would most likely produce the experimentally obtained data. The method also allows for fitting of intermediate exchange spectra, which is not supported by current software in the absence of a specific kinetic model. In current methods, determination of the deconvolution model best supported by the data is done manually through comparison of residual error values, which can be time consuming and requires model selection by the user. In contrast, the BIC method used by decond1d provides a quantitative method for model comparison that penalizes for model complexity helping to prevent over-fitting of the data and allows identification of the most parsimonious model. The decon1d program is freely available as a downloadable Python script at the project website (https://github.com/hughests/decon1d/). PMID:26241959
Structural stability of a 1D compressible viscoelastic fluid model
NASA Astrophysics Data System (ADS)
Huo, Xiaokai; Yong, Wen-An
2016-07-01
This paper is concerned with a compressible viscoelastic fluid model proposed by Öttinger. Although the model has a convex entropy, the Hessian matrix of the entropy does not symmetrize the system of first-order partial differential equations due to the non-conservative terms in the constitutive equation. We show that the corresponding 1D model is symmetrizable hyperbolic and dissipative and satisfies the Kawashima condition. Based on these, we prove the global existence of smooth solutions near equilibrium and justify the compatibility of the model with the Navier-Stokes equations.
Kinetic Modeling of Divertor Plasma
NASA Astrophysics Data System (ADS)
Ishiguro, Seiji; Hasegawa, Hiroki; Pianpanit, Theerasarn
2015-11-01
Particle-in-Cell (PIC) simulation with the Monte Carlo collisions and the cumulative scattering angle coulomb collision can present kinetic dynamics of divertor plasmas. We are developing two types of PIC codes. The first one is the three dimensional bounded PIC code where three dimensional kinetic dynamics of blob is studied and current flow structures related to sheath formation are unveiled. The second one is the one spatial three velocity space dimensional (1D3V) PIC code with the Monte Carlo collisions where formation of detach plasma is studied. First target of our research is to construct self-consistent full kinetic simulation modeling of the linear divertor simulation experiments. This work is performed with the support and under the auspices of NIFS Collaboration Research program (NIFS15KNSS059, NIFS14KNXN279, and NIFS13KNSS038) and the Research Cooperation Program on Hierarchy and Holism in Natural Science at NINS.
A 1-D morphodynamic model of postglacial valley incision
NASA Astrophysics Data System (ADS)
Tunnicliffe, Jon F.; Church, Michael
2015-11-01
Chilliwack River is typical of many Cordilleran valley river systems that have undergone dramatic Holocene degradation of valley fills that built up over the course of Pleistocene glaciation. Downstream controls on base level, mainly blockage of valleys by glaciers, led to aggradation of significant glaciofluvial and glaciolacustrine valley fills and fan deposits, subsequently incised by fluvial action. Models of such large-scale, long-term degradation present a number of important challenges since the evolution of model parameters, such as the rate of bedload transport and grain size characteristics, are governed by the nature of the deposit. Sediment sampling in the Chilliwack Valley reveals a complex sequence of very coarse to fine textural modes. We present a 1-D numerical morphodynamic model for the river-floodplain system tailored to conditions in the valley. The model is adapted to dynamically adjust channel width to optimize sediment transporting capacity and to integrate relict valley fill material as the channel incises through valley deposits. Sensitivity to model parameters is studied using four principal criteria: profile concavity, rate of downstream grain size fining, bed surface sand content, and the timescale to equilibrium. Model results indicate that rates of abrasion and coarsening of the grain size distributions exert the strongest controls on all of the interrelated model performance criteria. While there are a number of difficulties in satisfying all model criteria simultaneously, results indicate that 1-D models of valley bottom sedimentary systems can provide a suitable framework for integrating results from sediment budget studies and chronologies of sediment evacuation established from dating.
Decay-ratio calculation in the frequency domain with the LAPUR code using 1D-kinetics
Munoz-Cobo, J. L.; Escriva, A.; Garcia, C.; Berna, C.
2012-07-01
This paper deals with the problem of computing the Decay Ratio in the frequency domain codes as the LAPUR code. First, it is explained how to calculate the feedback reactivity in the frequency domain using slab-geometry i.e. 1D kinetics, also we show how to perform the coupling of the 1D kinetics with the thermal-hydraulic part of the LAPUR code in order to obtain the reactivity feedback coefficients for the different channels. In addition, we show how to obtain the reactivity variation in the complex domain by solving the eigenvalue equation in the frequency domain and we compare this result with the reactivity variation obtained in first order perturbation theory using the 1D neutron fluxes of the base case. Because LAPUR works in the linear regime, it is assumed that in general the perturbations are small. There is also a section devoted to the reactivity weighting factors used to couple the reactivity contribution from the different channels to the reactivity of the entire reactor core in point kinetics and 1D kinetics. Finally we analyze the effects of the different approaches on the DR value. (authors)
Emergent kinetics and fractionalized charge in 1D spin-orbit coupled flatband optical lattices.
Lin, Fei; Zhang, Chuanwei; Scarola, V W
2014-03-21
Recent ultracold atomic gas experiments implementing synthetic spin-orbit coupling allow access to flatbands that emphasize interactions. We model spin-orbit coupled fermions in a one-dimensional flatband optical lattice. We introduce an effective Luttinger-liquid theory to show that interactions generate collective excitations with emergent kinetics and fractionalized charge, analogous to properties found in the two-dimensional fractional quantum Hall regime. Observation of these excitations would provide an important platform for exploring exotic quantum states derived solely from interactions. PMID:24702335
Examination of 1D Solar Cell Model Limitations Using 3D SPICE Modeling: Preprint
McMahon, W. E.; Olson, J. M.; Geisz, J. F.; Friedman, D. J.
2012-06-01
To examine the limitations of one-dimensional (1D) solar cell modeling, 3D SPICE-based modeling is used to examine in detail the validity of the 1D assumptions as a function of sheet resistance for a model cell. The internal voltages and current densities produced by this modeling give additional insight into the differences between the 1D and 3D models.
1-D Modeling of Massive Particle Injection (MPI) in Tokamaks
NASA Astrophysics Data System (ADS)
Wu, W.; Parks, P. B.; Izzo, V. A.
2008-11-01
A 1-D Fast Current Quench (FCQ) model is developed to study current evolution and runaway electron suppression under massive density increase. The model consists of coupled toroidal electric field and energy equations, and it is solved numerically for DIII-D and ITER operating conditions. Simulation results suggest that fast shutdown by D2 liquid jet/pellet injection is in principle achievable for the desired plasma cooling time (˜15 ms for DIII-D and ˜50 ms for ITER) under ˜150x or higher densification. The current density and pressure profile are practically unaltered during the initial phase of jet propagation when dilution cooling dominates. With subsequent radiation cooling, the densified discharge enters the strongly collisional regime where Pfirsch-Schluter thermal diffusion can inhibit current contraction on the magnetic axis. Often the 1/1 kink instability, addressed by Kadomtsev's magnetic reconnection model, can be prevented. Our results are compared with NIMROD simulations in which the plasma is suddenly densified by ˜100x and experiences instantaneous dilution cooling, allowing for use of actual (lower) Lundquist numbers.
Multidimensional reactor kinetics modeling
Diamond, D.J.
1996-11-01
There is general agreement that for many light water reactor transient calculations, it is-necessary to use a multidimensional neutron kinetics model coupled to a thermal-hydraulics model for satisfactory results. These calculations are needed for a variety of applications for licensing safety analysis, probabilistic risk assessment (PRA), operational support, and training. The latter three applications have always required best-estimate models, but in the past applications for licensing could be satisfied with relatively simple models. By using more sophisticated best-estimate models, the consequences of these calculations are better understood, and the potential for gaining relief from restrictive operating limits increases. Hence, for all of the aforementioned applications, it is important to have the ability to do best-estimate calculations with multidimensional neutron kinetics models. coupled to sophisticated thermal-hydraulic models. Specifically, this paper reviews the status of multidimensional neutron kinetics modeling which would be used in conjunction with thermal-hydraulic models to do core dynamics calculations, either coupled to a complete NSSS representation or in isolation. In addition, the paper makes recommendations as to what should be the state-of-the-art for the next ten years. The review is an update to a previous review of the status as of ten years ago. The general requirements for a core dynamics code and the modeling available for such a code, discussed in that review, are still applicable. The emphasis in the current review is on the neutron kinetics assuming that the necessary thermal-hydraulic capability exists. In addition to discussing the basic neutron kinetics, discussion is given of related modeling (other than thermal- hydraulics). The capabilities and limitations of current computer codes are presented to understand the state-of-the-art and to help clarify the future direction of model development in this area.
Development of a hybrid deterministic/stochastic method for 1D nuclear reactor kinetics
NASA Astrophysics Data System (ADS)
Terlizzi, Stefano; Rahnema, Farzad; Zhang, Dingkang; Dulla, Sandra; Ravetto, Piero
2015-12-01
A new method has been implemented for solving the time-dependent neutron transport equation efficiently and accurately. This is accomplished by coupling the hybrid stochastic-deterministic steady-state coarse-mesh radiation transport (COMET) method [1,2] with the new predictor-corrector quasi-static method (PCQM) developed at Politecnico di Torino [3]. In this paper, the coupled method is implemented and tested in 1D slab geometry.
Development of a hybrid deterministic/stochastic method for 1D nuclear reactor kinetics
Terlizzi, Stefano; Dulla, Sandra; Ravetto, Piero; Rahnema, Farzad; Zhang, Dingkang
2015-12-31
A new method has been implemented for solving the time-dependent neutron transport equation efficiently and accurately. This is accomplished by coupling the hybrid stochastic-deterministic steady-state coarse-mesh radiation transport (COMET) method [1,2] with the new predictor-corrector quasi-static method (PCQM) developed at Politecnico di Torino [3]. In this paper, the coupled method is implemented and tested in 1D slab geometry.
LLNL Chemical Kinetics Modeling Group
Pitz, W J; Westbrook, C K; Mehl, M; Herbinet, O; Curran, H J; Silke, E J
2008-09-24
The LLNL chemical kinetics modeling group has been responsible for much progress in the development of chemical kinetic models for practical fuels. The group began its work in the early 1970s, developing chemical kinetic models for methane, ethane, ethanol and halogenated inhibitors. Most recently, it has been developing chemical kinetic models for large n-alkanes, cycloalkanes, hexenes, and large methyl esters. These component models are needed to represent gasoline, diesel, jet, and oil-sand-derived fuels.
XCHEM-1D: A Heat Transfer/Chemical Kinetics Computer Program for multilayered reactive materials
Gross, R.J.; Baer, M.R.; Hobbs, M.L.
1993-10-01
An eXplosive CHEMical kinetics code, XCHEM, has been developed to solve the reactive diffusion equations associated with thermal ignition of energetic materials. This method-of-lines code uses stiff numerical methods and adaptive meshing to resolve relevant combustion physics. Solution accuracy is maintained between multilayered materials consisting of blends of reactive components and/or inert materials. Phase change and variable properties are included in one-dimensional slab, cylindrical and spherical geometries. Temperature-dependent thermal properties have been incorporated and the modification of thermal conductivities to include decomposition effects are estimated using solid/gas volume fractions determined by species fractions. Gas transport properties, including high pressure corrections, have also been included. Time varying temperature, heat flux, convective and thermal radiation boundary conditions, and layer to layer contact resistances have also been implemented.
Westbrook, C.K.; Pitz, W.J.
1993-12-01
This project emphasizes numerical modeling of chemical kinetics of combustion, including applications in both practical combustion systems and in controlled laboratory experiments. Elementary reaction rate parameters are combined into mechanisms which then describe the overall reaction of the fuels being studied. Detailed sensitivity analyses are used to identify those reaction rates and product species distributions to which the results are most sensitive and therefore warrant the greatest attention from other experimental and theoretical research programs. Experimental data from a variety of environments are combined together to validate the reaction mechanisms, including results from laminar flames, shock tubes, flow systems, detonations, and even internal combustion engines.
Quasi 1D Modeling of Mixed Compression Supersonic Inlets
NASA Technical Reports Server (NTRS)
Kopasakis, George; Connolly, Joseph W.; Paxson, Daniel E.; Woolwine, Kyle J.
2012-01-01
The AeroServoElasticity task under the NASA Supersonics Project is developing dynamic models of the propulsion system and the vehicle in order to conduct research for integrated vehicle dynamic performance. As part of this effort, a nonlinear quasi 1-dimensional model of the 2-dimensional bifurcated mixed compression supersonic inlet is being developed. The model utilizes computational fluid dynamics for both the supersonic and subsonic diffusers. The oblique shocks are modeled utilizing compressible flow equations. This model also implements variable geometry required to control the normal shock position. The model is flexible and can also be utilized to simulate other mixed compression supersonic inlet designs. The model was validated both in time and in the frequency domain against the legacy LArge Perturbation INlet code, which has been previously verified using test data. This legacy code written in FORTRAN is quite extensive and complex in terms of the amount of software and number of subroutines. Further, the legacy code is not suitable for closed loop feedback controls design, and the simulation environment is not amenable to systems integration. Therefore, a solution is to develop an innovative, more simplified, mixed compression inlet model with the same steady state and dynamic performance as the legacy code that also can be used for controls design. The new nonlinear dynamic model is implemented in MATLAB Simulink. This environment allows easier development of linear models for controls design for shock positioning. The new model is also well suited for integration with a propulsion system model to study inlet/propulsion system performance, and integration with an aero-servo-elastic system model to study integrated vehicle ride quality, vehicle stability, and efficiency.
Validation of 1-D transport and sawtooth models for ITER
Connor, J.W.; Turner, M.F.; Attenberger, S.E.; Houlberg, W.A.
1996-12-31
In this paper the authors describe progress on validating a number of local transport models by comparing their predictions with relevant experimental data from a range of tokamaks in the ITER profile database. This database, the testing procedure and results are discussed. In addition a model for sawtooth oscillations is used to investigate their effect in an ITER plasma with alpha-particles.
A 1D model of the arterial circulation in mice.
Aslanidou, Lydia; Trachet, Bram; Reymond, Philippe; Fraga-Silva, Rodrigo A; Segers, Patrick; Stergiopulos, Nikolaos
2016-01-01
At a time of growing concern over the ethics of animal experimentation, mouse models are still an indispensable source of insight into the cardiovascular system and its most frequent pathologies. Nevertheless, reference data on the murine cardiovascular anatomy and physiology are lacking. In this work, we developed and validated an in silico, one dimensional model of the murine systemic arterial tree consisting of 85 arterial segments. Detailed aortic dimensions were obtained in vivo from contrast-enhanced micro-computed tomography in 3 male, C57BL/6J anesthetized mice and 3 male ApoE(-/-) mice, all 12-weeks old. Physiological input data were gathered from a wide range of literature data. The integrated form of the Navier-Stokes equations was solved numerically to yield pressures and flows throughout the arterial network. The resulting model predictions have been validated against invasive pressure waveforms and non-invasive velocity and diameter waveforms that were measured in vivo on an independent set of 47 mice. In conclusion, we present a validated one-dimensional model of the anesthetized murine cardiovascular system that can serve as a versatile tool in the field of preclinical cardiovascular research. PMID:26555250
Zakynthinaki, Maria S.
2015-01-01
The objective of the present study was to formulate a simple and at the same time effective mathematical model of heart rate kinetics in response to movement (exercise). Based on an existing model, a system of two coupled differential equations which give the rate of change of heart rate and the rate of change of exercise intensity is used. The modifications introduced to the existing model are justified and discussed in detail, while models of blood lactate accumulation in respect to time and exercise intensity are also presented. The main modification is that the proposed model has now only one parameter which reflects the overall cardiovascular condition of the individual. The time elapsed after the beginning of the exercise, the intensity of the exercise, as well as blood lactate are also taken into account. Application of the model provides information regarding the individual’s cardiovascular condition and is able to detect possible changes in it, across the data recording periods. To demonstrate examples of successful numerical fit of the model, constant intensity experimental heart rate data sets of two individuals have been selected and numerical optimization was implemented. In addition, numerical simulations provided predictions for various exercise intensities and various cardiovascular condition levels. The proposed model can serve as a powerful tool for a complete means of heart rate analysis, not only in exercise physiology (for efficiently designing training sessions for healthy subjects) but also in the areas of cardiovascular health and rehabilitation (including application in population groups for which direct heart rate recordings at intense exercises are not possible or not allowed, such as elderly or pregnant women). PMID:25876164
Modelling heart rate kinetics.
Zakynthinaki, Maria S
2015-01-01
The objective of the present study was to formulate a simple and at the same time effective mathematical model of heart rate kinetics in response to movement (exercise). Based on an existing model, a system of two coupled differential equations which give the rate of change of heart rate and the rate of change of exercise intensity is used. The modifications introduced to the existing model are justified and discussed in detail, while models of blood lactate accumulation in respect to time and exercise intensity are also presented. The main modification is that the proposed model has now only one parameter which reflects the overall cardiovascular condition of the individual. The time elapsed after the beginning of the exercise, the intensity of the exercise, as well as blood lactate are also taken into account. Application of the model provides information regarding the individual's cardiovascular condition and is able to detect possible changes in it, across the data recording periods. To demonstrate examples of successful numerical fit of the model, constant intensity experimental heart rate data sets of two individuals have been selected and numerical optimization was implemented. In addition, numerical simulations provided predictions for various exercise intensities and various cardiovascular condition levels. The proposed model can serve as a powerful tool for a complete means of heart rate analysis, not only in exercise physiology (for efficiently designing training sessions for healthy subjects) but also in the areas of cardiovascular health and rehabilitation (including application in population groups for which direct heart rate recordings at intense exercises are not possible or not allowed, such as elderly or pregnant women). PMID:25876164
GaAs solar cell photoresponse modeling using PC-1D V2.1
NASA Technical Reports Server (NTRS)
Huber, D. A.; Olsen, L. C.; Dunham, G.; Addis, F. W.
1991-01-01
Photoresponse data of high efficiency GaAs solar cells were analyzed using PC-1D V2.1. The approach required to use PC-1D for photoresponse data analysis, and the physical insights gained from performing the analysis are discussed. In particular, the effect of Al(x)Ga(1-x)As heteroface quality was modeled. Photoresponse or spectral quantum efficiency is an important tool in characterizing material quality and predicting cell performance. The strength of the photoresponse measurement lies in the ability to precisely fit the experimental data with a physical model. PC-1D provides a flexible platform for calculations based on these physical models.
Potent neutralizing anti-CD1d antibody reduces lung cytokine release in primate asthma model
Nambiar, Jonathan; Clarke, Adam W; Shim, Doris; Mabon, David; Tian, Chen; Windloch, Karolina; Buhmann, Chris; Corazon, Beau; Lindgren, Matilda; Pollard, Matthew; Domagala, Teresa; Poulton, Lynn; Doyle, Anthony G
2015-01-01
CD1d is a receptor on antigen-presenting cells involved in triggering cell populations, particularly natural killer T (NKT) cells, to release high levels of cytokines. NKT cells are implicated in asthma pathology and blockade of the CD1d/NKT cell pathway may have therapeutic potential. We developed a potent anti-human CD1d antibody (NIB.2) that possesses high affinity for human and cynomolgus macaque CD1d (KD ∼100 pM) and strong neutralizing activity in human primary cell-based assays (IC50 typically <100 pM). By epitope mapping experiments, we showed that NIB.2 binds to CD1d in close proximity to the interface of CD1d and the Type 1 NKT cell receptor β-chain. Together with data showing that NIB.2 inhibited stimulation via CD1d loaded with different glycolipids, this supports a mechanism whereby NIB.2 inhibits NKT cell activation by inhibiting Type 1 NKT cell receptor β-chain interactions with CD1d, independent of the lipid antigen in the CD1d antigen-binding cleft. The strong in vitro potency of NIB.2 was reflected in vivo in an Ascaris suum cynomolgus macaque asthma model. Compared with vehicle control, NIB.2 treatment significantly reduced bronchoalveolar lavage (BAL) levels of Ascaris-induced cytokines IL-5, IL-8 and IL-1 receptor antagonist, and significantly reduced baseline levels of GM-CSF, IL-6, IL-15, IL-12/23p40, MIP-1α, MIP-1β, and VEGF. At a cellular population level NIB.2 also reduced numbers of BAL lymphocytes and macrophages, and blood eosinophils and basophils. We demonstrate that anti-CD1d antibody blockade of the CD1d/NKT pathway modulates inflammatory parameters in vivo in a primate inflammation model, with therapeutic potential for diseases where the local cytokine milieu is critical. PMID:25751125
Grinberg, L; Cheever, E; Anor, T; Madsen, J R; Karniadakis, G E
2011-01-01
We compare results from numerical simulations of pulsatile blood flow in two patient-specific intracranial arterial networks using one-dimensional (1D) and three-dimensional (3D) models. Specifically, we focus on the pressure and flowrate distribution at different segments of the network computed by the two models. Results obtained with 1D and 3D models with rigid walls show good agreement in massflow distribution at tens of arterial junctions and also in pressure drop along the arteries. The 3D simulations with the rigid walls predict higher amplitude of the flowrate and pressure temporal oscillations than the 1D simulations with compliant walls at various segments even for small time-variations in the arterial cross-sectional areas. Sensitivity of the flow and pressure with respect to variation in the elasticity parameters is investigated with the 1D model. PMID:20661645
Stochastic kinetic mean field model
NASA Astrophysics Data System (ADS)
Erdélyi, Zoltán; Pasichnyy, Mykola; Bezpalchuk, Volodymyr; Tomán, János J.; Gajdics, Bence; Gusak, Andriy M.
2016-07-01
This paper introduces a new model for calculating the change in time of three-dimensional atomic configurations. The model is based on the kinetic mean field (KMF) approach, however we have transformed that model into a stochastic approach by introducing dynamic Langevin noise. The result is a stochastic kinetic mean field model (SKMF) which produces results similar to the lattice kinetic Monte Carlo (KMC). SKMF is, however, far more cost-effective and easier to implement the algorithm (open source program code is provided on
Bengoechea, Rocio; Pittman, Sara K; Tuck, Elizabeth P; True, Heather L; Weihl, Conrad C
2015-12-01
Limb-girdle muscular dystrophy type 1D (LGMD1D) is caused by dominantly inherited missense mutations in DNAJB6, an Hsp40 co-chaperone. LGMD1D muscle has rimmed vacuoles and inclusion bodies containing DNAJB6, Z-disc proteins and TDP-43. DNAJB6 is expressed as two isoforms; DNAJB6a and DNAJB6b. Both isoforms contain LGMD1D mutant residues and are expressed in human muscle. To identify which mutant isoform confers disease pathogenesis and generate a mouse model of LGMD1D, we evaluated DNAJB6 expression and localization in skeletal muscle as well as generating DNAJB6 isoform specific expressing transgenic mice. DNAJB6a localized to myonuclei while DNAJB6b was sarcoplasmic. LGMD1D mutations in DNAJB6a or DNAJB6b did not alter this localization in mouse muscle. Transgenic mice expressing the LGMD1D mutant, F93L, in DNAJB6b under a muscle-specific promoter became weak, had early lethality and developed muscle pathology consistent with myopathy after 2 months; whereas mice expressing the same F93L mutation in DNAJB6a or overexpressing DNAJB6a or DNAJB6b wild-type transgenes remained unaffected after 1 year. DNAJB6b localized to the Z-disc and DNAJB6b-F93L expressing mouse muscle had myofibrillar disorganization and desmin inclusions. Consistent with DNAJB6 dysfunction, keratin 8/18, a DNAJB6 client also accumulated in DNAJB6b-F93L expressing mouse muscle. The RNA-binding proteins hnRNPA1 and hnRNPA2/B1 accumulated and co-localized with DNAJB6 at sarcoplasmic stress granules suggesting that these proteins maybe novel DNAJB6b clients. Similarly, hnRNPA1 and hnRNPA2/B1 formed sarcoplasmic aggregates in patients with LGMD1D. Our data support that LGMD1D mutations in DNAJB6 disrupt its sarcoplasmic function suggesting a role for DNAJB6b in Z-disc organization and stress granule kinetics. PMID:26362252
Kinetic models of hydrocarbon generation
Burnham, A.K.; Sweeney, J.J.
1990-10-25
We are carrying out an integrated program of laboratory experiments, kinetics modeling, and basin thermal history modeling in order to better understand the natural breakdown of organic matter into oil and gas. Our kinetic models of organic maturation are being used to better understand the coupling of generation, cracking, expulsion, and overpressuring in both the laboratory and geologic setting. Currently we are carrying out chemical experiments and developing more efficient chemical kinetic modeling schemes to obtain a better understanding of expulsion and cracking from lean source rocks and from hydrogen-poor (terrestrial) organic source material. We verify the chemical kinetic models by integrating them with thermal history models of hydrocarbon-producing sediments and comparing predicted and observed characteristics of the hydrocarbon occurrence in a variety of settings. We intend to apply this approach to evaluate the potential for deep gas resources in the Pacific Northwest and in the Louisiana Gulf Coast. 11 refs., 4 figs.
Two-loop effective action of O(N) spin models in 1/D expansion
NASA Astrophysics Data System (ADS)
Matsui, T.; Kleinert, H.; Ami, S.
1984-08-01
We calculate the two-loop effective action of O(N) spin models on the lattice in a 1/D expansion to order 1/D2. The resulting free energy depends on β = 1/T and the order parameter Φ. It matches the high and low temperature regimes and is quite reliable close to the phase transition where it has a simple Landau expansion.
Benchmarks and models for 1-D radiation transport in stochastic participating media
Miller, D S
2000-08-21
Benchmark calculations for radiation transport coupled to a material temperature equation in a 1-D slab and 1-D spherical geometry binary random media are presented. The mixing statistics are taken to be homogeneous Markov statistics in the 1-D slab but only approximately Markov statistics in the 1-D sphere. The material chunk sizes are described by Poisson distribution functions. The material opacities are first taken to be constant and then allowed to vary as a strong function of material temperature. Benchmark values and variances for time evolution of the ensemble average of material temperature energy density and radiation transmission are computed via a Monte Carlo type method. These benchmarks are used as a basis for comparison with three other approximate methods of solution. One of these approximate methods is simple atomic mix. The second approximate model is an adaptation of what is commonly called the Levermore-Pomraning model and which is referred to here as the standard model. It is shown that recasting the temperature coupling as a type of effective scattering can be useful in formulating the third approximate model, an adaptation of a model due to Su and Pomraning which attempts to account for the effects of scattering in a stochastic context. This last adaptation shows consistent improvement over both the atomic mix and standard models when used in the 1-D slab geometry but shows limited improvement in the 1-D spherical geometry. Benchmark values are also computed for radiation transmission from the 1-D sphere without material heating present. This is to evaluate the performance of the standard model on this geometry--something which has never been done before. All of the various tests demonstrate the importance of stochastic structure on the solution. Also demonstrated are the range of usefulness and limitations of a simple atomic mix formulation.
A Mathematical Model of T1D Acceleration and Delay by Viral Infection.
Moore, James R; Adler, Fred
2016-03-01
Type 1 diabetes (T1D) is often triggered by a viral infection, but the T1D prevalence is rising among populations that have a lower exposure to viral infection. In an animal model of T1D, the NOD mouse, viral infection at different ages may either accelerate or delay disease depending on the age of infection and the type of virus. Viral infection may affect the progression of T1D via multiple mechanisms: triggering inflammation, bystander activation of self-reactive T-cells, inducing a competitive immune response, or inducing a regulatory immune response. In this paper, we create mathematical models of the interaction of viral infection with T1D progression, incorporating each of these four mechanisms. Our goal is to understand how each viral mechanism interacts with the age of infection. The model predicts that each viral mechanism has a unique pattern of interaction with disease progression. Viral inflammation always accelerates disease, but the effect decreases with age of infection. Bystander activation has little effect at younger ages and actually decreases incidence at later ages while accelerating disease in mice that do get the disease. A competitive immune response to infection can decrease incidence at young ages and increase it at older ages, with the effect decreasing over time. Finally, an induced Treg response decreases incidence at any age of infection, but the effect decreases with age. Some of these patterns resemble those seen experimentally. PMID:27030351
Comparison of 1D and 2D modelling with soil erosion model SMODERP
NASA Astrophysics Data System (ADS)
Kavka, Petr; Weyskrabova, Lenka; Zajicek, Jan
2013-04-01
The contribution presents a comparison of a runoff simulated by profile method (1D) and spatially distributed method (2D). Simulation model SMODERP is used for calculation and prediction of soil erosion and surface runoff from agricultural land. SMODERP is physically based model that includes the processes of infiltration (Phillips equation), surface runoff (kinematic wave based equation), surface retention, surface roughness and vegetation impact on runoff. 1D model was developed in past, new 2D model was developed in last two years. The model is being developed at the Department of Irrigation, Drainage and Landscape Engineering, Civil Engineering Faculty, CTU in Prague. 2D model was developed as a tool for widespread GIS software ArcGIS. The physical relations were implemented through Python script. This script uses ArcGIS system tools for raster and vectors treatment of the inputs. Flow direction is calculated by Steepest Descent algorithm in the preliminary version of 2D model. More advanced multiple flow algorithm is planned in the next version. Spatially distributed models enable to estimate not only surface runoff but also flow in the rills. Surface runoff is described in the model by kinematic wave equation. Equation uses Manning roughness coefficient for surface runoff. Parameters for five different soil textures were calibrated on the set of forty measurements performed on the laboratory rainfall simulator. For modelling of the rills a specific sub model was created. This sub model uses Manning formula for flow estimation. Numerical stability of the model is solved by Courant criterion. Spatial scale is fixed. Time step is dynamically changed depending on how flow is generated and developed. SMODERP is meant to be used not only for the research purposes, but mainly for the engineering practice. We also present how the input data can be obtained based on available resources (soil maps and data, land use, terrain models, field research, etc.) and how can
HYDRUS-1D Modeling of an Irrigated Agricultural Plot with Application to Aquifer Recharge Estimation
Technology Transfer Automated Retrieval System (TEKTRAN)
A variety of methods are available for estimating aquifer recharge in semi-arid regions, each with advantages and disadvantages. We are investigating a procedure for estimating recharge in an irrigated basin. The method involves computing irrigation return flows based on HYDRUS-1D modeling of root z...
Minimum 1D P- and S- Velocity Models for Montenegro and Vicinity
NASA Astrophysics Data System (ADS)
Vucic, Ljiljana; Kissling, Edi; Spakman, Wim; Glavatovic, Branislav
2015-04-01
The territory of Montenegro and its vicinity are characterized by high-seismicity rate and very complex tectonics. Namely, southern Adria microplate subducts beneath Eurasia, forming the Dinarides fold-and-thrust belt which spreads through whole Montenegro and the western Balkans. Present-day lithosphere structure of the Adria-Dinarides collision zone in general is not constrained very well and, consequently, there is a lack of three-dimensional (3D) velocity models in this region. For these reasons, high resolution 3D tomography modeling of this area is considered to be of great importance. As part of preparatory phase for conducting a 3D local earthquake tomography study, a substantial amount of waveform data was collected, from all surroundings national seismic networks including 130 seismic stations from 11 countries. The data set comprises waveforms from 1452 earthquakes in the region recorded during time period 1990 - 2014. The collected data were obtained in different formats and the data base was harmonized by converting and integrating all data to miniseed format. The potential resolution of collected data for seismic tomography purpose was analyzed by ray density testing, using specially developed software for this specific purpose. The result is expressed as the number of rays between selected group of earthquake hypocenters and seismic stations, penetrating through the 3D model of the Earth crust and it documents the great potential of the data set for 3D seismic tomography. As a prerequisite to 3D tomography and for consistent high-precision earthquake locations, a minimum 1D velocity model has been calculated. The data set of around 400 earthquakes was selected from the main database and consistent wave onsets picking was performed, including seismic phase interpretation and its quality assessment. This highly consistent travel time data set is used for calculation of 1D velocity models for the region under study. The minimum 1D models were derived
West, W.P.; Evans, T.E.; Brooks, N.H.
1996-10-01
NEWT1D, a one dimensional multifluid model of the scrape-off layer and divertor plasma, has been used to model the plasma including the distribution of carbon ionization states in the SOL and divertor of ELMing H-mode at two injected power levels in DIII-D. Comparison of the code predictions to the measured divertor and scrape-off layer (SOL) plasma density and temperature shows good agreement. Comparison of the predicted line emissions to the spectroscopic data suggests that physically sputtered carbon from the strike point is not transported up the flux tube; a distributed source of carbon a few centimeters up the flux tube is required to achieve reasonable agreement.
First Author = C.Z. Cheng; Jay R. Johnson
1998-07-10
A nonlinear kinetic-fluid model for high-beta plasmas with multiple ion species which can be applied to multiscale phenomena is presented. The model embeds important kinetic effects due to finite ion Larmor radius (FLR), wave-particle resonances, magnetic particle trapping, etc. in the framework of simple fluid descriptions. When further restricting to low frequency phenomena with frequencies less than the ion cyclotron frequency the kinetic-fluid model takes a simpler form in which the fluid equations of multiple ion species collapse into single-fluid density and momentum equations and a low frequency generalized Ohm's law. The kinetic effects are introduced via plasma pressure tensors for ions and electrons which are computed from particle distribution functions that are governed by the Vlasov equation or simplified plasma dynamics equations such as the gyrokinetic equation. The ion FLR effects provide a finite parallel electric field, a perpendicular velocity that modifies the ExB drift, and a gyroviscosity tensor, all of which are neglected in the usual one-fluid MHD description. Eigenmode equations are derived which include magnetosphere-ionosphere coupling effects for low frequency waves (e.g., kinetic/inertial Alfven waves and ballooning-mirror instabilities).
Chemical kinetics and combustion modeling
Miller, J.A.
1993-12-01
The goal of this program is to gain qualitative insight into how pollutants are formed in combustion systems and to develop quantitative mathematical models to predict their formation rates. The approach is an integrated one, combining low-pressure flame experiments, chemical kinetics modeling, theory, and kinetics experiments to gain as clear a picture as possible of the process in question. These efforts are focused on problems involved with the nitrogen chemistry of combustion systems and on the formation of soot and PAH in flames.
Review of Zero-D and 1-D Models of Blood Flow in the Cardiovascular System
2011-01-01
Background Zero-dimensional (lumped parameter) and one dimensional models, based on simplified representations of the components of the cardiovascular system, can contribute strongly to our understanding of circulatory physiology. Zero-D models provide a concise way to evaluate the haemodynamic interactions among the cardiovascular organs, whilst one-D (distributed parameter) models add the facility to represent efficiently the effects of pulse wave transmission in the arterial network at greatly reduced computational expense compared to higher dimensional computational fluid dynamics studies. There is extensive literature on both types of models. Method and Results The purpose of this review article is to summarise published 0D and 1D models of the cardiovascular system, to explore their limitations and range of application, and to provide an indication of the physiological phenomena that can be included in these representations. The review on 0D models collects together in one place a description of the range of models that have been used to describe the various characteristics of cardiovascular response, together with the factors that influence it. Such models generally feature the major components of the system, such as the heart, the heart valves and the vasculature. The models are categorised in terms of the features of the system that they are able to represent, their complexity and range of application: representations of effects including pressure-dependent vessel properties, interaction between the heart chambers, neuro-regulation and auto-regulation are explored. The examination on 1D models covers various methods for the assembly, discretisation and solution of the governing equations, in conjunction with a report of the definition and treatment of boundary conditions. Increasingly, 0D and 1D models are used in multi-scale models, in which their primary role is to provide boundary conditions for sophisticate, and often patient-specific, 2D and 3D models
Coupled 1D-3D hydrodynamic modelling, with application to the Pearl River Delta
NASA Astrophysics Data System (ADS)
Twigt, Daniel J.; de Goede, Erik D.; Zijl, Firmijn; Schwanenberg, Dirk; Chiu, Alex Y. W.
2009-12-01
Within the hydrodynamic modelling community, it is common practice to apply different modelling systems for coastal waters and river systems. Whereas for coastal waters 3D finite difference or finite element grids are commonly used, river systems are generally modelled using 1D networks. Each of these systems is tailored towards specific applications. Three-dimensional coastal water models are designed to model the horizontal and vertical variability in coastal waters and are less well suited for representing the complex geometry and cross-sectional areas of river networks. On the other hand, 1D river network models are designed to accurately represent complex river network geometries and complex structures like weirs, barrages and dams. A disadvantage, however, is that they are unable to resolve complex spatial flow variability. In real life, however, coastal oceans and rivers interact. In deltaic estuaries, both tidal intrusion of seawater into the upstream river network and river discharge into open waters play a role. This is frequently approached by modelling the systems independently, with off-line coupling of the lateral boundary forcing. This implies that the river and the coastal model run sequentially, providing lateral discharge (1D) and water level (3D) forcing to each other without the possibility of direct feedback or interaction between these processes. An additional disadvantage is that due to the time aggregation usually applied to exchanged quantities, mass conservation is difficult to ensure. In this paper, we propose an approach that couples a 3D hydrodynamic modelling system for coastal waters (Delft3D) with a 1D modelling system for river hydraulics (SOBEK) online. This implies that contrary to off-line coupling, the hydrodynamic quantities are exchanged between the 1D and 3D domains during runtime to resolve the real-time exchange and interaction between the coastal waters and river network. This allows for accurate and mass conserving
Zero finite-temperature charge stiffness within the half-filled 1D Hubbard model
Carmelo, J.M.P.; Gu, Shi-Jian; Sacramento, P.D.
2013-12-15
Even though the one-dimensional (1D) Hubbard model is solvable by the Bethe ansatz, at half-filling its finite-temperature T>0 transport properties remain poorly understood. In this paper we combine that solution with symmetry to show that within that prominent T=0 1D insulator the charge stiffness D(T) vanishes for T>0 and finite values of the on-site repulsion U in the thermodynamic limit. This result is exact and clarifies a long-standing open problem. It rules out that at half-filling the model is an ideal conductor in the thermodynamic limit. Whether at finite T and U>0 it is an ideal insulator or a normal resistor remains an open question. That at half-filling the charge stiffness is finite at U=0 and vanishes for U>0 is found to result from a general transition from a conductor to an insulator or resistor occurring at U=U{sub c}=0 for all finite temperatures T>0. (At T=0 such a transition is the quantum metal to Mott–Hubbard-insulator transition.) The interplay of the η-spin SU(2) symmetry with the hidden U(1) symmetry beyond SO(4) is found to play a central role in the unusual finite-temperature charge transport properties of the 1D half-filled Hubbard model. -- Highlights: •The charge stiffness of the half-filled 1D Hubbard model is evaluated. •Its value is controlled by the model symmetry operator algebras. •We find that there is no charge ballistic transport at finite temperatures T>0. •The hidden U(1) symmetry controls the U=0 phase transition for T>0.
Thermodynamic nature of vitrification in a 1D model of a structural glass former
NASA Astrophysics Data System (ADS)
Semenov, A. N.
2015-07-01
We propose a new spin-glass model with no positional quenched disorder which is regarded as a coarse-grained model of a structural glass-former. The model is analyzed in the 1D case when the number N of states of a primary cell is large. For N → ∞, the model exhibits a sharp freezing transition of the thermodynamic origin. It is shown both analytically and numerically that the glass transition is accompanied by a significant growth of a static length scale ξ pointing to the structural (equilibrium) nature of dynamical slowdown effects in supercooled liquids.
Thermodynamic nature of vitrification in a 1D model of a structural glass former.
Semenov, A N
2015-07-28
We propose a new spin-glass model with no positional quenched disorder which is regarded as a coarse-grained model of a structural glass-former. The model is analyzed in the 1D case when the number N of states of a primary cell is large. For N → ∞, the model exhibits a sharp freezing transition of the thermodynamic origin. It is shown both analytically and numerically that the glass transition is accompanied by a significant growth of a static length scale ξ pointing to the structural (equilibrium) nature of dynamical slowdown effects in supercooled liquids. PMID:26233148
SILVA: EDF two-phase 1D annular model of a CFB boiler furnace
Montat, D.; Fauquet, P.; Lafanechere, L.; Bursi, J.M.
1997-12-31
Aiming to improve its knowledge of CFB boilers, EDF has initiated a R and D program including: laboratory work on mock-ups, numerical modelling and on-site tests in CFB power plants. One of the objectives of this program is the development of a comprehensive steady-state 1D model of the solid circulation loop, named SILVA, for plant operation and design evaluation purposes. This paper describes its mathematical and physical modelling. Promising validation of the model on cold mock-up and industrial CFB is presented.
Thermodynamic nature of vitrification in a 1D model of a structural glass former
Semenov, A. N.
2015-07-28
We propose a new spin-glass model with no positional quenched disorder which is regarded as a coarse-grained model of a structural glass-former. The model is analyzed in the 1D case when the number N of states of a primary cell is large. For N → ∞, the model exhibits a sharp freezing transition of the thermodynamic origin. It is shown both analytically and numerically that the glass transition is accompanied by a significant growth of a static length scale ξ pointing to the structural (equilibrium) nature of dynamical slowdown effects in supercooled liquids.
Assessment of improved root growth representation in a 1-D, field scale crop model
NASA Astrophysics Data System (ADS)
Miltin Mboh, Cho; Gaiser, Thomas; Ewert, Frank
2015-04-01
Many 1-D, field scale crop models over-simplify root growth. The over-simplification of this "hidden half" of the crop may have significant consequences on simulated root water and nutrient uptake with a corresponding reflection on the simulated crop yields. Poor representation of root growth in crop models may therefore constitute a major source of uncertainty propagation. In this study we assess the effect of an improved representation of root growth in a model solution of the model framework SIMPLACE (Scientific Impact assessment and Modeling PLatform for Advanced Crop and Ecosystem management) compared to conventional 1-D approaches. The LINTUL5 crop growth model is coupled to the Hillflow soil water balance model within the SIMPLACE modeling framework (Gaiser et al, 2013). Root water uptake scenarios in the soil hydrological simulator Hillflow (Bronstert, 1995) together with an improved representation of root growth is compared to scenarios for which root growth is simplified. The improvement of root growth is achieved by integrating root growth solutions from R-SWMS (Javaux et al., 2008) into the SIMPLACE model solution. R-SWMS is a three dimensional model for simultaneous modeling of root growth, soil water fluxes and solute transport and uptake. These scenarios are tested by comparing how well the simulated water contents match with the observed soil water dynamics. The impacts of the scenarios on above ground biomass and wheat grain are assessed
Kinetic Modeling of Biological Systems
Petzold, Linda; Pettigrew, Michel F.
2010-01-01
The dynamics of how the constituent components of a natural system interact defines the spatio-temporal response of the system to stimuli. Modeling the kinetics of the processes that represent a biophysical system has long been pursued with the aim of improving our understanding of the studied system. Due to the unique properties of biological systems, in addition to the usual difficulties faced in modeling the dynamics of physical or chemical systems, biological simulations encounter difficulties that result from intrinsic multiscale and stochastic nature of the biological processes. This chapter discusses the implications for simulation of models involving interacting species with very low copy numbers, which often occur in biological systems and give rise to significant relative fluctuations. The conditions necessitating the use of stochastic kinetic simulation methods and the mathematical foundations of the stochastic simulation algorithms are presented. How the well-organized structural hierarchies often seen in biological systems can lead to multiscale problems, and possible ways to address the encountered computational difficulties are discussed. We present the details of the existing kinetic simulation methods, and discuss their strengths and shortcomings. A list of the publicly available kinetic simulation tools and our reflections for future prospects are also provided. PMID:19381542
Box model and 1D longitudinal model of flow and transport in Bosten Lake, China
NASA Astrophysics Data System (ADS)
Li, Ning; Kinzelbach, Wolfgang; Li, WenPeng; Dong, XinGuang
2015-05-01
Bosten Lake in the southeast of Yanqi Catchment, China, supports the downstream agricultural and natural environments. Over the last few decades the intensive agricultural activities in Yanqi Catchment resulted in decreased lake levels and deteriorated lake water quality. A two-box model is constructed to understand the evolution of lake level and salinity between 1958 and 2008. The two-box model of the lake indicates that the evaporation does have the same trend as the observed lake area and the annual average evaporation agrees with the value obtained from the Penman-Monteith approach. To achieve a correct salt balance, the ratio of outflow concentration and average lake concentration has to be around 0.7. This is due to the incomplete mixing of the lake caused by short-circuiting between tributary inflow and the main outflow via the pump stations abstracting water from the lake. This short-circuiting is investigated in more detail by a 1D numerical flow and transport model of the lake calibrated with observations of lake level and lake concentrations. The distributed model reproduces the correct time-varying outflow concentration. It is used for the assessment of two basic management options: increasing river discharge (by water saving irrigation, reduction of phreatic evaporation or reduction of agricultural area) and diverting saline drainage water to the desert. Increasing river discharge to the lake by 20% reduces the east basin salt concentration by 0.55 kg/m3, while capturing all the drainage water and discharging it to depressions instead of the lake reduces the east basin salt concentration by 0.63 kg/m3. A combination of increasing river inflow and decreasing drainage salt flux is sufficient to bring future lake TDS below the required 1 kg/m3, to keep a lake level that sustains the lake ecosystem, and to supply more water for downstream development and ecosystem rehabilitation.
NASA Astrophysics Data System (ADS)
Lipatov, A. S.; Sibeck, D. G.
2015-12-01
We use a new hybrid kinetic model to simulate the response of ring current, outer radiation belt, and plasmasphere particle populations to impulsive interplanetary shocks. Since particle distributions attending the interplanetary shock waves and in the ring current and radiation belts are non-Maxwellian, wave-particle interactions play a crucial role in energy transport within the inner magnetosphere. Finite gyroradius effects become important in mass loading the shock waves with the background plasma in the presence of higher energy ring current and radiation belt ions and electrons. Initial results show that the shock causes strong deformations in the global structure of the ring current, radiation belt, and plasmasphere. The ion velocity distribution functions at the shock front, in the ring current, and in the radiation belt help us to determine energy transport through the Earth's inner magnetosphere. We compare our predictions with THEMIS and Van Allen Probes spacecraft observations.
Kinetic Modeling of Microbiological Processes
Liu, Chongxuan; Fang, Yilin
2012-08-26
Kinetic description of microbiological processes is vital for the design and control of microbe-based biotechnologies such as waste water treatment, petroleum oil recovery, and contaminant attenuation and remediation. Various models have been proposed to describe microbiological processes. This editorial article discusses the advantages and limiation of these modeling approaches in cluding tranditional, Monod-type models and derivatives, and recently developed constraint-based approaches. The article also offers the future direction of modeling researches that best suit for petroleum and environmental biotechnologies.
Verification and comparison of four numerical schemes for a 1D viscoelastic blood flow model.
Wang, Xiaofei; Fullana, Jose-Maria; Lagrée, Pierre-Yves
2015-01-01
A reliable and fast numerical scheme is crucial for the 1D simulation of blood flow in compliant vessels. In this paper, a 1D blood flow model is incorporated with a Kelvin-Voigt viscoelastic arterial wall. This leads to a nonlinear hyperbolic-parabolic system, which is then solved with four numerical schemes, namely: MacCormack, Taylor-Galerkin, monotonic upwind scheme for conservation law and local discontinuous Galerkin. The numerical schemes are tested on a single vessel, a simple bifurcation and a network with 55 arteries. The numerical solutions are checked favorably against analytical, semi-analytical solutions or clinical observations. Among the numerical schemes, comparisons are made in four important aspects: accuracy, ability to capture shock-like phenomena, computational speed and implementation complexity. The suitable conditions for the application of each scheme are discussed. PMID:25145651
NASA Astrophysics Data System (ADS)
Raybaud, V.; Nival, P.; Prieur, L.
2011-01-01
Modelling was used as a tool to better understand the physical and biological processes observed during the multidisciplinary cruise DYNAPROC 2 (DYNAmic of rapid PROCesses in the water column), which took place in the Ligurian Sea in September-October 2004. The aim of the cruise was to study the short time-scale physical and biological processes that occur when the ecosystem switches from summer oligotrophy to autumnal mesotrophy. In this study, we have tested two 1D physical-biological coupled models. The first was a classical model in which surface layer dynamics were obtained using the turbulent kinetic energy model of Gaspar [Gaspar et al., 1990]. The simulated food-web took into account ten state variables: three nutrients, three classes of phytoplankton, two classes of zooplankton and two types of detritus. The second model (called IDA, Isopycnals Depth Adjustment) was based on the initial one but it took into account the measured variations of isopycnals depths. The results showed that the IDA model most efficiently reproduced the observed ecosystem dynamics. We have therefore used the IDA model to show that physical processes observed during the cruise had a major effect on biological compartment, mainly on nano- and picophytoplankton.
Nested 1D-2D approach for urban surface flood modeling
NASA Astrophysics Data System (ADS)
Murla, Damian; Willems, Patrick
2015-04-01
Floods in urban areas as a consequence of sewer capacity exceedance receive increased attention because of trends in urbanization (increased population density and impermeability of the surface) and climate change. Despite the strong recent developments in numerical modeling of water systems, urban surface flood modeling is still a major challenge. Whereas very advanced and accurate flood modeling systems are in place and operation by many river authorities in support of flood management along rivers, this is not yet the case in urban water management. Reasons include the small scale of the urban inundation processes, the need to have very high resolution topographical information available, and the huge computational demands. Urban drainage related inundation modeling requires a 1D full hydrodynamic model of the sewer network to be coupled with a 2D surface flood model. To reduce the computational times, 0D (flood cones), 1D/quasi-2D surface flood modeling approaches have been developed and applied in some case studies. In this research, a nested 1D/2D hydraulic model has been developed for an urban catchment at the city of Gent (Belgium), linking the underground sewer (minor system) with the overland surface (major system). For the overland surface flood modelling, comparison was made of 0D, 1D/quasi-2D and full 2D approaches. The approaches are advanced by considering nested 1D-2D approaches, including infiltration in the green city areas, and allowing the effects of surface storm water storage to be simulated. An optimal nested combination of three different mesh resolutions was identified; based on a compromise between precision and simulation time for further real-time flood forecasting, warning and control applications. Main streets as mesh zones together with buildings as void regions constitute one of these mesh resolution (3.75m2 - 15m2); they have been included since they channel most of the flood water from the manholes and they improve the accuracy of
Evaluation of 2 1-D cloud models for the analysis of VAS soundings
NASA Technical Reports Server (NTRS)
Emmitt, G. D.
1984-01-01
Evaluation of the satellite Visual Infrared Spin Scan Radiometer Atmospheric Sounder (VISSR) has begun to document several of its critical shortcomings as far as numerical cloud models are concerned: excessive smoothing of thermal inversions; imprecise measurement of boundary layer moisture; and tendency to exaggerate atmospheric stability. The sensitivity of 1-D cloud models to their required inputs is stressed with special attention to those parameters obtained from atmospheric soundings taken by the VAS or rawinsonde. In addition to performing model experiments using temperature and moisture profiles having the general characteristics of VAS soundings, standard input sensitivity tests were made and 1-D model performance was compared with observations and the results of a 2-D model experiment using AVE/VAS data (Atmospheric Variability Experiment). Although very encouraging, the results are not sufficient to make any specific conclusions. In general, the VAS soundings are likely to be inadequate to provide the cloud base (and subcloud layer) information needed for inputs to current cumulus models. Above cloud base, the tendency to exaggerate the stability of the atmosphere requires solution before meaningful model experiments are run.
Optimisation of A 1d-ecosystem Model To Observations In The North Atlantic Ocean
NASA Astrophysics Data System (ADS)
Schartau, M.; Oschlies, A.
An optimisation experiment is performed with a vertically resolved, nitrogen based ecosystem model, comprising four state variables (1D-NPZD model): dissolved inor- ganic nitrogen (N), phytoplankton (P), herbivorous zooplankton (Z) and detritus (D). Parameter values of the NPZD-model are optimised while regarding observational data from three locations in the North Atlantic simultaneously: Bermuda Atlantic Time-series Study (BATS), data of the North Atlantic Bloom Experiment (NABE) and observations from Ocean Weather Ship-India (OWS-INDIA). The simultaneous opti- misation yields a best parameter set which can be utilized for basin wide simulations in coupled physical-biological (general circulation) models of the North Atlantic. After optimisation of the 1D-NPZD model, systematic discrepancies between 14C-fixation rates and modelled primary production are emphasized. Using the optimal parame- ter estimates for coupled 3D-simulations, the biogeochemical fluxes show substantial differences in contrast to previous model results. For instance, rapid recycling of or- ganic matter enhances primary production rates. This becomes most evident within the oligotrophic regions of the subtropical gyre.
Prediction of car cabin environment by means of 1D and 3D cabin model
NASA Astrophysics Data System (ADS)
Fišer, J.; Pokorný, J.; Jícha, M.
2012-04-01
Thermal comfort and also reduction of energy requirements of air-conditioning system in vehicle cabins are currently very intensively investigated and up-to-date issues. The article deals with two approaches of modelling of car cabin environment; the first model was created in simulation language Modelica (typical 1D approach without cabin geometry) and the second one was created in specialized software Theseus-FE (3D approach with cabin geometry). Performance and capabilities of this tools are demonstrated on the example of the car cabin and the results from simulations are compared with the results from the real car cabin climate chamber measurements.
Kinetic model of HIV infection
Zhdanov, V. P.
2007-10-15
Recent experiments clarifying the details of exhaustion of CD8 T cells specific to various strains of human immunodeficiency virus (HIV) are indicative of slow irreversible (on a one-year time scale) deterioration of the immune system. The conventional models of HIV kinetics do not take this effect into account. Removing this shortcoming, we show the likely influence of such changes on the escape of HIV from control of the immune system.
A 1-D model study of Arctic sea-ice salinity
NASA Astrophysics Data System (ADS)
Griewank, P. J.; Notz, D.
2014-03-01
We use a 1-D model to study how salinity evolves in Arctic sea ice. To do so, we first explore how sea-ice surface melt and flooding can be incorporated into the 1-D thermodynamic SAMSIM sea-ice model presented by Griewank and Notz (2013). We introduce flooding and a flushing parametrization which treats sea ice as a hydraulic network of horizontal and vertical fluxes. Forcing SAMSIM with 36 years of ERA-interim atmospheric reanalysis data, we obtain a modeled Arctic sea-ice salinity that agrees well with ice-core measurements. The simulations hence allow us to identify the main drivers of the observed mean salinity profile in Arctic sea ice. Our results show a 1.5-4 g kg-1 decrease of bulk salinity via gravity drainage after ice growth has ceased and before flushing sets in, which hinders approximating bulk salinity from ice thickness beyond the first growth season. In our simulations, salinity variability of first-year ice is mostly restricted to the top 20 cm. We find that ice thickness, thermal resistivity, freshwater column, and stored energy change by less than 5% on average when the full salinity parametrization is replaced with a prescribed salinity profile. We conclude that for earth system models the impact of fully parametrizing the Arctic temporal salinity evolution is too small to justify the increase in computational cost and model complexity.
Assessing the impact of different sources of topographic data on 1-D hydraulic modelling of floods
NASA Astrophysics Data System (ADS)
Ali, A. Md; Solomatine, D. P.; Di Baldassarre, G.
2015-01-01
Topographic data, such as digital elevation models (DEMs), are essential input in flood inundation modelling. DEMs can be derived from several sources either through remote sensing techniques (spaceborne or airborne imagery) or from traditional methods (ground survey). The Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), the Shuttle Radar Topography Mission (SRTM), the light detection and ranging (lidar), and topographic contour maps are some of the most commonly used sources of data for DEMs. These DEMs are characterized by different precision and accuracy. On the one hand, the spatial resolution of low-cost DEMs from satellite imagery, such as ASTER and SRTM, is rather coarse (around 30 to 90 m). On the other hand, the lidar technique is able to produce high-resolution DEMs (at around 1 m), but at a much higher cost. Lastly, contour mapping based on ground survey is time consuming, particularly for higher scales, and may not be possible for some remote areas. The use of these different sources of DEM obviously affects the results of flood inundation models. This paper shows and compares a number of 1-D hydraulic models developed using HEC-RAS as model code and the aforementioned sources of DEM as geometric input. To test model selection, the outcomes of the 1-D models were also compared, in terms of flood water levels, to the results of 2-D models (LISFLOOD-FP). The study was carried out on a reach of the Johor River, in Malaysia. The effect of the different sources of DEMs (and different resolutions) was investigated by considering the performance of the hydraulic models in simulating flood water levels as well as inundation maps. The outcomes of our study show that the use of different DEMs has serious implications to the results of hydraulic models. The outcomes also indicate that the loss of model accuracy due to re-sampling the highest resolution DEM (i.e. lidar 1 m) to lower resolution is much less than the loss of model accuracy due
Periodic solutions for a 1D-model with nonlocal velocity via mass transport
NASA Astrophysics Data System (ADS)
Ferreira, Lucas C. F.; Valencia-Guevara, Julio C.
2016-05-01
This paper concerns periodic solutions for a 1D-model with nonlocal velocity given by the periodic Hilbert transform. There is a rich literature showing, via numerics and rigorous analysis, that this model presents singular behavior of solutions. For instance, they can blow up by forming mass-concentration. We develop a global well-posedness theory for periodic measure initial data that allows, in particular, to analyze how the model evolves from those singularities. Our results are based on periodic mass transport theory and the abstract gradient flow theory in metric spaces developed by Ambrosio et al. (2005). A viscous version of the model is also analyzed and inviscid limit properties are obtained.
Optimal modeling of 1D azimuth correlations in the context of Bayesian inference
NASA Astrophysics Data System (ADS)
De Kock, Michiel B.; Eggers, Hans C.; Trainor, Thomas A.
2015-09-01
Analysis and interpretation of spectrum and correlation data from high-energy nuclear collisions is currently controversial because two opposing physics narratives derive contradictory implications from the same data, one narrative claiming collision dynamics is dominated by dijet production and projectile-nucleon fragmentation, the other claiming collision dynamics is dominated by a dense, flowing QCD medium. Opposing interpretations seem to be supported by alternative data models, and current model-comparison schemes are unable to distinguish between them. There is clearly need for a convincing new methodology to break the deadlock. In this study we introduce Bayesian inference (BI) methods applied to angular correlation data as a basis to evaluate competing data models. For simplicity the data considered are projections of two-dimensional (2D) angular correlations onto a 1D azimuth from three centrality classes of 200-GeV Au-Au collisions. We consider several data models typical of current model choices, including Fourier series (FS) and a Gaussian plus various combinations of individual cosine components. We evaluate model performance with BI methods and with power-spectrum analysis. We find that FS-only models are rejected in all cases by Bayesian analysis, which always prefers a Gaussian. A cylindrical quadrupole cos(2 ϕ ) is required in some cases but rejected for 0%-5%-central Au-Au collisions. Given a Gaussian centered at the azimuth origin, "higher harmonics" cos(m ϕ ) for m >2 are rejected. A model consisting of Gaussian +dipole cos(ϕ )+quadrupole cos(2 ϕ ) provides good 1D data descriptions in all cases.
Reactive Transport Modeling of Microbially-Mediated Chromate Reduction in 1-D Soil Columns
NASA Astrophysics Data System (ADS)
Qiu, H.; Viamajala, S.; Alam, M. M.; Peyton, B. M.; Petersen, J. N.; Yonge, D. R.
2002-12-01
Cr(VI) reduction tests were performed with the well known metal reducing bacterium Shewanella oneidensis MR-1 in liquid phase batch reactors and continuous flow soil columns under anaerobic conditions. In the batch tests, the cultures were grown with fumarate as the terminal electron acceptor and lactate as the electron donor in a simulated groundwater medium to determine yield coefficients and specific growth rates. The bench-scale soil column experiments were carried out with MR-1 to test the hypothesis that the kinetic parameters obtained in batch studies, combined with microbial attachment /detachment processes, will accurately predict reactive transport of Cr(VI) during bacterial Cr(VI) reduction in a soil matrix. Cr(VI)-free simulated groundwater media containing fumarate as the limiting substrate and lactate was supplied to a 2.1cm (ID) x 15 cm soil column inoculated with MR-1 for a duration of 9 residence times to allow for biomass to build-up in the column. Thereafter the column was supplied with both Cr(VI) and substrate. The concentrations of effluent substrate, biomass and Cr(VI) were monitored on a periodic basis and attached biomass in the column was measured in the termination of each column test. A reactive transport model was developed in which 6 governing equations deal with Cr(VI) bioreaction, fumarate (as electron donor) consumption, aqueous biomass growth and transport, solid biomass detachment and attachment kinetics, aqueous and solid phase enzyme reaction and transport, respectively. The model incorporating the enzyme reaction kinetics for Cr(VI) reduction, Monod kinetic expressions for substrate depletion, nonlinear attachment and detachment kinetics for aqueous and solid phase microorganism concentration, was solved by a fully implicit, finite-difference procedure using RT3D (A Modular Computer Code for Reactive Multi-species Transport in 3-Dimensional Groundwater Systems) platform in one dimension. Cr(VI)-free column data was used to
Kinetic models of conjugated metabolic cycles
NASA Astrophysics Data System (ADS)
Ershov, Yu. A.
2016-01-01
A general method is developed for the quantitative kinetic analysis of conjugated metabolic cycles in the human organism. This method is used as a basis for constructing a kinetic graph and model of the conjugated citric acid and ureapoiesis cycles. The results from a kinetic analysis of the model for these cycles are given.
Survey of Multi-Material Closure Models in 1D Lagrangian Hydrodynamics
Maeng, Jungyeoul Brad; Hyde, David Andrew Bulloch
2015-07-28
Accurately treating the coupled sub-cell thermodynamics of computational cells containing multiple materials is an inevitable problem in hydrodynamics simulations, whether due to initial configurations or evolutions of the materials and computational mesh. When solving the hydrodynamics equations within a multi-material cell, we make the assumption of a single velocity field for the entire computational domain, which necessitates the addition of a closure model to attempt to resolve the behavior of the multi-material cells’ constituents. In conjunction with a 1D Lagrangian hydrodynamics code, we present a variety of both the popular as well as more recently proposed multi-material closure models and survey their performances across a spectrum of examples. We consider standard verification tests as well as practical examples using combinations of fluid, solid, and composite constituents within multi-material mixtures. Our survey provides insights into the advantages and disadvantages of various multi-material closure models in different problem configurations.
Modelling reaction kinetics inside cells
Grima, Ramon; Schnell, Santiago
2009-01-01
In the past decade, advances in molecular biology such as the development of non-invasive single molecule imaging techniques have given us a window into the intricate biochemical activities that occur inside cells. In this article we review four distinct theoretical and simulation frameworks: (1) non-spatial and deterministic, (2) spatial and deterministic, (3) non-spatial and stochastic and (4) spatial and stochastic. Each framework can be suited to modelling and interpreting intracellular reaction kinetics. By estimating the fundamental length scales, one can roughly determine which models are best suited for the particular reaction pathway under study. We discuss differences in prediction between the four modelling methodologies. In particular we show that taking into account noise and space does not simply add quantitative predictive accuracy but may also lead to qualitatively different physiological predictions, unaccounted for by classical deterministic models. PMID:18793122
This technical report describes the new one-dimensional (1D) hydrodynamic and sediment transport model EFDC1D. This model that can be applied to stream networks. The model code and two sample data sets are included on the distribution CD. EFDC1D can simulate bi-directional unstea...
Evaluation of a Revised Interplanetary Shock Prediction Model: 1D CESE-HD-2 Solar-Wind Model
NASA Astrophysics Data System (ADS)
Zhang, Y.; Du, A. M.; Du, D.; Sun, W.
2014-08-01
We modified the one-dimensional conservation element and solution element (CESE) hydrodynamic (HD) model into a new version [ 1D CESE-HD-2], by considering the direction of the shock propagation. The real-time performance of the 1D CESE-HD-2 model during Solar Cycle 23 (February 1997 - December 2006) is investigated and compared with those of the Shock Time of Arrival Model ( STOA), the Interplanetary-Shock-Propagation Model ( ISPM), and the Hakamada-Akasofu-Fry version 2 ( HAFv.2). Of the total of 584 flare events, 173 occurred during the rising phase, 166 events during the maximum phase, and 245 events during the declining phase. The statistical results show that the success rates of the predictions by the 1D CESE-HD-2 model for the rising, maximum, declining, and composite periods are 64 %, 62 %, 57 %, and 61 %, respectively, with a hit window of ± 24 hours. The results demonstrate that the 1D CESE-HD-2 model shows the highest success rates when the background solar-wind speed is relatively fast. Thus, when the background solar-wind speed at the time of shock initiation is enhanced, the forecasts will provide potential values to the customers. A high value (27.08) of χ 2 and low p-value (< 0.0001) for the 1D CESE-HD-2 model give considerable confidence for real-time forecasts by using this new model. Furthermore, the effects of various shock characteristics (initial speed, shock duration, background solar wind, longitude, etc.) and background solar wind on the forecast are also investigated statistically.
Fluid friction and wall viscosity of the 1D blood flow model.
Wang, Xiao-Fei; Nishi, Shohei; Matsukawa, Mami; Ghigo, Arthur; Lagrée, Pierre-Yves; Fullana, Jose-Maria
2016-02-29
We study the behavior of the pulse waves of water into a flexible tube for application to blood flow simulations. In pulse waves both fluid friction and wall viscosity are damping factors, and difficult to evaluate separately. In this paper, the coefficients of fluid friction and wall viscosity are estimated by fitting a nonlinear 1D flow model to experimental data. In the experimental setup, a distensible tube is connected to a piston pump at one end and closed at another end. The pressure and wall displacements are measured simultaneously. A good agreement between model predictions and experiments was achieved. For amplitude decrease, the effect of wall viscosity on the pulse wave has been shown as important as that of fluid viscosity. PMID:26862041
NASA Astrophysics Data System (ADS)
Klimeck, Gerhard
2001-03-01
The quantum mechanical functionality of commercially pursued heterostructure devices such as resonant tunneling diodes (RTDs), quantum well infrared photodetectors, and quantum well lasers are enabled by material variations on an atomic scale. The creation of these heterostructure devices is realized in a vast design space of material compositions, layer thicknesses and doping profiles. The full experimental exploration of this design space is unfeasible and a reliable design tool is needed. The Nanoelectronic Modeling tool (NEMO) is one of the first commercial grade attempts for such a modeling tool. NEMO was developed as a general-purpose quantum mechanics-based 1-D device design and analysis tool from 1993-97 by the Central Research Laboratory of Texas Instruments (later Raytheon Systems). NEMO enables(R. Lake, G. Klimeck, R. C. Bowen, and D. Jovanovic, J. Appl. Phys. 81), 7845 (1997). the fundamentally sound inclusion of the required(G. Klimeck et al.), in the 1997 55th Annual Device Research Conference Digest, (IEEE, NJ, 1997), p. 92^,(R. C. Bowen et al.), J. Appl. Phys 81, 3207 (1997). physics: bandstructure, scattering, and charge self-consistency based on the non-equilibrium Green function approach. A new class of devices which require full 3-D quantum mechanics based models is starting to emerge: quantum dots, or in general semiconductor based deca-nano devices. We are currently building a 3-D modeling tool based on NEMO to include the important physics to understand electronic stated in such superscaled structures. This presentation will overview various facets of the NEMO 1-D tool such electron transport physics in RTDs, numerical technology, software engineering and graphical user interface. The lessons learned from that work are now entering the NEMO 3-D development and first results using the NEMO 3-D prototype will be shown. More information about
NASA Astrophysics Data System (ADS)
Gloesener, Elodie; Karatekin, Özgür; Dehant, Véronique
2016-04-01
MSL Rover Environmental Monitoring Station (REMS) performed high-resolution measurements of temperature and relative humidity during more than one Martian year. In this work, a 1D subsurface model is used to study water vapor exchange between the atmosphere and the subsurface at Gale crater using REMS data. The thermal model used includes several layers of varying thickness with depth and properties that can be changed to correspond to those of Martian rocks at locations studied. It also includes the transport of water vapor through porous Martian regolith and the different phases considered are vapor, ice and adsorbed H2O. The total mass flux is given by the sum of diffusive and advective transport. The role of an adsorbing regolith on water transfer as well as the range of parameters with significant effect on water transport in Martian conditions are investigated. In addition, kinetics of the adsorption process is considered to examine its influence on the water vapor exchange between the subsurface and the atmosphere.
NASA Astrophysics Data System (ADS)
Pradel, J.-L.; David, C.; Quinebèche, S.; Blondel, P.
2014-05-01
Industrial scale-up (or scale down) in Compounding and Reactive Extrusion processes is one of the most critical R&D challenges. Indeed, most of High Performances Polymers are obtained within a reactive compounding involving chemistry: free radical grafting, in situ compatibilization, rheology control... but also side reactions: oxidation, branching, chain scission... As described by basic Arrhenius and kinetics laws, the competition between all chemical reactions depends on residence time distribution and temperature. Then, to ensure the best possible scale up methodology, we need tools to match thermal history of the formulation along the screws from a lab scale twin screw extruder to an industrial one. This paper proposes a comparison between standard scale-up laws and the use of Computer modeling Software such as Ludovic® applied and compared to experimental data. Scaling data from a compounding line to another one, applying general rules (for example at constant specific mechanical energy), shows differences between experimental and computed data, and error depends on the screw speed range. For more accurate prediction, 1D-Computer Modeling could be used to optimize the process conditions to ensure the best scale-up product, especially in temperature sensitive reactive extrusion processes. When the product temperature along the screws is the key, Ludovic® software could help to compute the temperature profile along the screws and extrapolate conditions, even screw profile, on industrial extruders.
Full Waveform 3D Synthetic Seismic Algorithm for 1D Layered Anelastic Models
NASA Astrophysics Data System (ADS)
Schwaiger, H. F.; Aldridge, D. F.; Haney, M. M.
2007-12-01
Numerical calculation of synthetic seismograms for 1D layered earth models remains a significant aspect of amplitude-offset investigations, surface wave studies, microseismic event location approaches, and reflection interpretation or inversion processes. Compared to 3D finite-difference algorithms, memory demand and execution time are greatly reduced, enabling rapid generation of seismic data within workstation or laptop computational environments. We have developed a frequency-wavenumber forward modeling algorithm adapted to realistic 1D geologic media, for the purpose of calculating seismograms accurately and efficiently. The earth model consists of N layers bounded by two halfspaces. Each layer/halfspace is a homogeneous and isotropic anelastic (attenuative and dispersive) solid, characterized by a rectangular relaxation spectrum of absorption mechanisms. Compressional and shear phase speeds and quality factors are specified at a particular reference frequency. Solution methodology involves 3D Fourier transforming the three coupled, second- order, integro-differential equations for particle displacements to the frequency-horizontal wavenumber domain. An analytic solution of the resulting ordinary differential system is obtained. Imposition of welded interface conditions (continuity of displacement and stress) at all interfaces, as well as radiation conditions in the two halfspaces, yields a system of 6(N+1) linear algebraic equations for the coefficients in the ODE solution. An optimized inverse 2D Fourier transform to the space domain gives the seismic wavefield on a horizontal plane. Finally, three-component seismograms are obtained by accumulating frequency spectra at designated receiver positions on this plane, followed by a 1D inverse FFT from angular frequency ω to time. Stress-free conditions may be applied at the top or bottom interfaces, and seismic waves are initiated by force or moment density sources. Examples reveal that including attenuation
1D numerical model of muddy subaqueous and subaerial debris flows
Imran, J.; Parker, G.; Locat, J.; Lee, H.
2001-01-01
A 1D numerical model of the downslope flow and deposition of muddy subaerial and subaqueous debris flows is presented. The model incorporates the Herschel-Bulkley and bilinear rheologies of viscoplastic fluid. The more familiar Bingham model is integrated into the Herschel-Bulkley rheological model. The conservation equations of mass and momentum of single-phase laminar debris flow are layer-integrated using the slender flow approximation. They are then expressed in a Lagrangian framework and solved numerically using an explicit finite difference scheme. Starting from a given initial shape, a debris flow is allowed to collapse and propagate over a specified topography. Comparison between the model predictions and laboratory experiments shows reasonable agreement. The model is used to study the effect of the ambient fluid density, initial shape of the failed mass, and rheological model on the simulated propagation of the front and runout characteristics of muddy debris flows. It is found that initial failure shape influence the front velocity but has little bearing on the final deposit shape. In the Bingham model, the excess of shear stress above the yield strength is proportional to the strain rate to the first power. This exponent is free to vary in the Herschel-Bulkley model. When it is set at a value lower than unity, the resulting final deposits are thicker and shorter than in the case of the Bingham rheology. The final deposit resulting from the bilinear model is longer and thinner than that from the Bingham model due to the fact that the debris flow is allowed to act as a Newtonian fluid at low shear rate in the bilinear model.
Uniform Contractivity in Wasserstein Metric for the Original 1D Kac's Model
NASA Astrophysics Data System (ADS)
Hauray, Maxime
2016-03-01
We study here a very popular 1D jump model introduced by Kac: it consists of N velocities encountering random binary collisions at which they randomly exchange energy. We show the uniform (in N) exponential contractivity of the dynamics in a non-standard Monge-Kantorovich-Wasserstein: precisely the MKW metric of order 2 on the energy. The result is optimal in the sense that for each N, the contractivity constant is equal to the L^2 spectral gap of the generator associated to Kac's dynamic. As a corollary, we get an uniform but non optimal contractivity in the MKW metric of order 4. We use a simple coupling that works better that the parallel one. The estimates are simple and new (to the best of our knowledge).
Initial Stage of the Microwave Ionization Wave Within a 1D Model
NASA Astrophysics Data System (ADS)
Semenov, V. E.; Rakova, E. I.; Glyavin, M. Yu.; Nusinovich, G. S.
2016-06-01
The dynamics of the microwave breakdown in a gas is simulated numerically within a simple 1D model which takes into account such processes as the impact ionization of gas molecules, the attachment of electrons to neutral molecules, and plasma diffusion. Calculations are carried out for different spatial distributions of seed electrons with account for reflection of the incident electromagnetic wave from the plasma. The results reveal considerable dependence of the ionization wave evolution on the relation between the field frequency and gas pressure, as well as on the existence of extended rarefied halo of seed electrons. At relatively low gas pressures (or high field frequencies), the breakdown process is accompanied by the stationary ionization wave moving towards the incident electromagnetic wave. In the case of a high gas pressure (or a relatively low field frequency), the peculiarities of the breakdown are associated with the formation of repetitive jumps of the ionization front.
Application of HYDRUS 1D model for assessment of phenol-soil adsorption dynamics.
Pal, Supriya; Mukherjee, Somnath; Ghosh, Sudipta
2014-04-01
Laboratory-scale batch, vertical, and horizontal column experiments were conducted to investigate the attenuative capacity of a fine-grained clayey soil of local origin in the surrounding of a steel plant wastewater discharge site in West Bengal, India, for removal of phenol. Linear, Langmuir, and Freundlich isotherm plots from batch experimental data revealed that Freundlich isotherm model was reasonably fitted (R (2) = 0.94). The breakthrough column experiments were also carried out with different soil bed heights (5, 10, and 15 cm) under uniform flow to study the hydraulic movements of phenol by evaluating time concentration flow behavior using bromide as a tracer. The horizontal migration test was also conducted in the laboratory using adsorptive phenol and nonreactive bromide tracer to explore the movement of solute in a horizontal distance. The hydrodynamic dispersion coefficients (D) in the vertical and horizontal directions in the soil were estimated using nonlinear least-square parameter optimization method in CXTFIT model. In addition, the equilibrium convection dispersion model in HYDRUS 1D was also examined to simulate the fate and transport of phenol in vertical and horizontal directions using Freundlich isotherm constants and estimated hydrodynamic parameters as input in the model. The model efficacy and validation were examined through statistical parameters such as the coefficient of determination (R (2)), root mean square error and design of index (d). PMID:24407784
Spectral method for a kinetic swarming model
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.
Spectral method for a kinetic swarming model
NASA Astrophysics Data System (ADS)
Gamba, Irene M.; Haack, Jeffrey R.; Motsch, Sebastien
2015-09-01
In this paper 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. We observe that the kinetic model captures key features such as vortex formation and traveling waves.
NASA Astrophysics Data System (ADS)
Shen, Linhan; Bui, Thinh Q.; Chen, Pin; Okumura, Mitchio
2014-11-01
Martian atmospheric methane (CH4) concentrations observed from satellite orbiter and Earth based telescopes have shown significant time and spatial variations. Recent MSL measurements observed very low methane concentrations (0.18 ± 0.67 ppbv). In order to reconcile these findings, a search of missing methane sinks is needed. In this study, we investigated the kinetic isotope effect (KIE) of methane oxidation reaction by O(1D) as a function of temperature, which will provide an important constraint to the loss of methane. The KIE of major methane isotopologues (13CH4 and 12CH3D) are measured as a function of temperature. The experiments were carried out by photolyzing a mixture of N2O, isotope enriched methane, and He at 193 nm in a temperature controlled cell between 155 K and 300 K. The N2O molecules were used as an O(1D) source, while He was used to collisionally quench translationally hot O(1D) radicals. The concentrations of all major methane isotopologues before and after photolysis were analyzed using a frequency stabilized cavity ringdown (FS-CRDS) spectrometer. The spectrometer employs coupling of two orthogonally polarized cw lasers into a ringdown cavity for simultaneous spectral measurements over the full wavelength range of 1.45 - 1.65 µm and is capable of measuring isotopes of methane of enriched samples to a very high precision (D < 0.03% and 13C < 0.01%). We measured for the first time the D-KIE and 13C-KIE at temperatures relative to the Martian conditions. Our measurements observed D-KIE(155 K) = 1.133(20), and 13C-KIE(115 K) = 1.149(22).
Assessing the habitability of planets with Earth-like atmospheres with 1D and 3D climate modeling
NASA Astrophysics Data System (ADS)
Godolt, M.; Grenfell, J. L.; Kitzmann, D.; Kunze, M.; Langematz, U.; Patzer, A. B. C.; Rauer, H.; Stracke, B.
2016-07-01
Context. The habitable zone (HZ) describes the range of orbital distances around a star where the existence of liquid water on the surface of an Earth-like planet is in principle possible. The applicability of one-dimensional (1D) climate models for the estimation of the HZ boundaries has been questioned by recent three-dimensional (3D) climate studies. While 3D studies can calculate the water vapor, ice albedo, and cloud feedback self-consistently and therefore allow for a deeper understanding and the identification of relevant climate processes, 1D model studies rely on fewer model assumptions and can be more easily applied to the large parameter space possible for extrasolar planets. Aims: We evaluate the applicability of 1D climate models to estimate the potential habitability of Earth-like extrasolar planets by comparing our 1D model results to those of 3D climate studies in the literature. We vary the two important planetary properties, surface albedo and relative humidity, in the 1D model. These depend on climate feedbacks that are not treated self-consistently in most 1D models. Methods: We applied a cloud-free 1D radiative-convective climate model to calculate the climate of Earth-like planets around different types of main-sequence stars with varying surface albedo and relative humidity profile. We compared the results to those of 3D model calculations available in the literature and investigated to what extent the 1D model can approximate the surface temperatures calculated by the 3D models. Results: The 1D parameter study results in a large range of climates possible for an Earth-sized planet with an Earth-like atmosphere and water reservoir at a certain stellar insolation. At some stellar insolations the full spectrum of climate states could be realized, i.e., uninhabitable conditions due to surface temperatures that are too high or too low as well as habitable surface conditions, depending only on the relative humidity and surface albedo assumed. When
Testing the accuracy of a 1-D volcanic plume model in estimating mass eruption rate
Mastin, Larry G.
2014-01-01
During volcanic eruptions, empirical relationships are used to estimate mass eruption rate from plume height. Although simple, such relationships can be inaccurate and can underestimate rates in windy conditions. One-dimensional plume models can incorporate atmospheric conditions and give potentially more accurate estimates. Here I present a 1-D model for plumes in crosswind and simulate 25 historical eruptions where plume height Hobs was well observed and mass eruption rate Mobs could be calculated from mapped deposit mass and observed duration. The simulations considered wind, temperature, and phase changes of water. Atmospheric conditions were obtained from the National Center for Atmospheric Research Reanalysis 2.5° model. Simulations calculate the minimum, maximum, and average values (Mmin, Mmax, and Mavg) that fit the plume height. Eruption rates were also estimated from the empirical formula Mempir = 140Hobs4.14 (Mempir is in kilogram per second, Hobs is in kilometer). For these eruptions, the standard error of the residual in log space is about 0.53 for Mavg and 0.50 for Mempir. Thus, for this data set, the model is slightly less accurate at predicting Mobs than the empirical curve. The inability of this model to improve eruption rate estimates may lie in the limited accuracy of even well-observed plume heights, inaccurate model formulation, or the fact that most eruptions examined were not highly influenced by wind. For the low, wind-blown plume of 14–18 April 2010 at Eyjafjallajökull, where an accurate plume height time series is available, modeled rates do agree better with Mobs than Mempir.
1D Chemical Modeling of coupled snow-atmosphere chemistry at Dome C Antarctica
NASA Astrophysics Data System (ADS)
Gil, Jaime E.; Thomas, Jennie; von Glasgow, Roland; Bekki, Slimane; Kukui, Alexandre; Frey, Markus; Jourdain, Bruno; Kerbrat, Michel; Genthon, Christophe; Preuknert, Susanne; Legrand, Michel
2013-04-01
High levels of nitrogen oxides NOx (NOx=NO+NO2) generated by the photolysis of nitrate present in surface snow profoundly impact atmospheric composition and oxidizing capacity in the Antarctic boundary layer. In particular, NOx emissions from sunlit snow increase OH values by effectively recycling HO2 to OH. In order to better characterize this chemistry the OPALE campaign was conducted in December 2011/January 2012 at Dome C, Antarctica (altitude of 3,233 meters, 75 ° S, 123 ° E). The campaign included boundary layer profiling, measurements of the physical properties of snow, as well as a comprehensive suite of atmospheric chemistry measurements (including NOx, HONO, OH and RO2, H2O2, CH2O, O3). We present results using the 1-D coupled snow-boundary layer model MISTRA-SNOW in combination with observations made during the measurement campaign to understand this chemistry. The model includes both chemistry at the surface of snow grains (aqueous chemistry), in firn air (gas phase chemistry), and gas/aerosol chemistry in the boundary layer. Model predictions of NOx mixing ratios using a model sensitivity analysis approach are presented. The model was initialized using measured snow properties, including temperature, density, and snow grain size. In addition, the model dynamics are driven using the measured surface temperature at Dome C. To calculate the rate of snowpack ventilation, measured wind speeds during the campaign were used. The model was run varying the amount of nitrate and bromide available for reaction at the surface of snow grains and results are compared to measurements made in the atmospheric boundary from 2-4 January 2012. We test the hypothesis that very low concentrations of bromine may alter the ratio of NO/NO2. We also investigate the influence of NOx emissions from snow, and bromine (if present), on OH concentrations in the boundary layer on the Antarctic plateau.
The optimization of high resolution topographic data for 1D hydrodynamic models
NASA Astrophysics Data System (ADS)
Ales, Ronovsky; Michal, Podhoranyi
2016-06-01
The main focus of our research presented in this paper is to optimize and use high resolution topographical data (HRTD) for hydrological modelling. Optimization of HRTD is done by generating adaptive mesh by measuring distance of coarse mesh and the surface of the dataset and adapting the mesh from the perspective of keeping the geometry as close to initial resolution as possible. Technique described in this paper enables computation of very accurate 1-D hydrodynamic models. In the paper, we use HEC-RAS software as a solver. For comparison, we have chosen the amount of generated cells/grid elements (in whole discretization domain and selected cross sections) with respect to preservation of the accuracy of the computational domain. Generation of the mesh for hydrodynamic modelling is strongly reliant on domain size and domain resolution. Topographical dataset used in this paper was created using LiDAR method and it captures 5.9km long section of a catchment of the river Olše. We studied crucial changes in topography for generated mesh. Assessment was done by commonly used statistical and visualization methods.
A 1-D evolutionary model for icy satellites, applied to Enceladus
NASA Astrophysics Data System (ADS)
Malamud, Uri; Prialnik, Dina
2016-04-01
We develop a long-term 1-D evolution model for icy satellites that couples multiple processes: water migration and differentiation, geochemical reactions and silicate phase transitions, compaction by self-gravity, and ablation. The model further considers the following energy sources and sinks: tidal heating, radiogenic heating, geochemical energy released by serpentinization or absorbed by mineral dehydration, gravitational energy and insolation, and heat transport by conduction, convection, and advection. We apply the model to Enceladus, by guessing the initial conditions that would render a structure compatible with present-day observations, assuming the initial structure to have been homogeneous. Assuming the satellite has been losing water continually along its evolution, we postulate that it was formed as a more massive, more icy and more porous satellite, and gradually transformed into its present day state due to sustained long-term tidal heating. We consider several initial compositions and evolution scenarios and follow the evolution for the age of the Solar System, testing the present day model results against the available observational constraints. Our model shows the present configuration to be differentiated into a pure icy mantle, several tens of km thick, overlying a rocky core, composed of dehydrated rock at the center and hydrated rock in the outer part. For Enceladus, it predicts a higher rock/ice mass ratio than previously assumed and a thinner ice mantle, compatible with recent estimates based on gravity field measurements. Although, obviously, the model cannot be used to explain local phenomena, it sheds light on the internal structure invoked in explanations of localized features and activities.
Kinetic modelling of mitochondrial translation.
Korla, Kalyani; Mitra, Chanchal K
2014-01-01
Mitochondrial genome contains 13 protein coding genes, all being part of the oxidative phosphorylation complexes. The process of translation of these protein coding mRNAs in mitochondrial matrix is a good miniature model of translation in cytoplasm. In this work, we have simulated three phases of mitochondrial translation viz. initiation, elongation and termination (including ribosome recycling). The kinetic equations for these phases have been deduced based on the information available in literature. Various factors involved in the process have been included explicitly. Kinetic simulation was done using Octave, open source software. Scripts were written individually for each phase. Initiation begins with mitoribosome, mRNA, fMet-tRNA and initiation factors. The final product of the initiation script, the initiation complex, was introduced as the start point in the successive step, i.e. elongation. Elongation is a particular extensive process where the various aminoacyl-tRNAs already present in the matrix check for matching with the triplet codon in A-site of mitoribosome. This script consists of two parts: one with the time behaviour of the factors involved in the molecular process (using ordinary differential equation solver) and the other including the reading of triplet codon on the mRNA and incorporating the corresponding aminoacyl-tRNA, and then at each step elongating the peptide chain (using loops and conditions). The peptide chain thus formed in the elongation step (in the loops and conditions segment) was released in the termination step. This was followed by mitoribosome recycling where the mitoribosome reached the native state and was ready for the next cycle of translation. PMID:24028553
Topological order in 1D super-lattice Bose-Hubbard models
NASA Astrophysics Data System (ADS)
Fleischhauer, Michael; Grusdt, Fabian; Hoening, Michael
2013-05-01
After the discovery of topological insulators as a new state of matter and their consequent classification for free fermions, the question arises what kind of topological order can be supported by incompressible systems of interacting bosons. We consider a 1D super-lattice Hamiltonian with a non-trivial band structure (the Su-Schrieffer-Heeger model) and show that its Mott-insulating (MI) states can be classified by a quantized many-body winding number. This quantization is protected by sub-lattice and time-reversal symmetries, and it allows the implementation of a quantized cyclic pumping process (Thouless pump) in a simple super-lattice Bose-Hubbard model (BHM). For extended BHMs we discuss a connection of such a pump with the fractional quantum Hall effect. Furthermore we show that the quantization of the winding number leads to localized, protected edge states at sharp interfaces between topologically distinct MI phases which can be experimentally realized using Bose-Fermi mixtures in optical superlattices. DMRG simulations show that these edge states manifest themself either in localized density maxima or localized density minima, which can easily be detected. Supported by research center OPTIMAS and graduate school MAINZ.
1D Tight-Binding Models Render Quantum First Passage Time "Speakable"
NASA Astrophysics Data System (ADS)
Ranjith, V.; Kumar, N.
2015-12-01
The calculation of First Passage Time (moreover, even its probability density in time) has so far been generally viewed as an ill-posed problem in the domain of quantum mechanics. The reasons can be summarily seen in the fact that the quantum probabilities in general do not satisfy the Kolmogorov sum rule: the probabilities for entering and non-entering of Feynman paths into a given region of space-time do not in general add up to unity, much owing to the interference of alternative paths. In the present work, it is pointed out that a special case exists (within quantum framework), in which, by design, there exists one and only one available path (i.e., door-way) to mediate the (first) passage -no alternative path to interfere with. Further, it is identified that a popular family of quantum systems - namely the 1d tight binding Hamiltonian systems - falls under this special category. For these model quantum systems, the first passage time distributions are obtained analytically by suitably applying a method originally devised for classical (stochastic) mechanics (by Schroedinger in 1915). This result is interesting especially given the fact that the tight binding models are extensively used in describing everyday phenomena in condense matter physics.
1D-3D hybrid modeling—from multi-compartment models to full resolution models in space and time
Grein, Stephan; Stepniewski, Martin; Reiter, Sebastian; Knodel, Markus M.; Queisser, Gillian
2014-01-01
Investigation of cellular and network dynamics in the brain by means of modeling and simulation has evolved into a highly interdisciplinary field, that uses sophisticated modeling and simulation approaches to understand distinct areas of brain function. Depending on the underlying complexity, these models vary in their level of detail, in order to cope with the attached computational cost. Hence for large network simulations, single neurons are typically reduced to time-dependent signal processors, dismissing the spatial aspect of each cell. For single cell or networks with relatively small numbers of neurons, general purpose simulators allow for space and time-dependent simulations of electrical signal processing, based on the cable equation theory. An emerging field in Computational Neuroscience encompasses a new level of detail by incorporating the full three-dimensional morphology of cells and organelles into three-dimensional, space and time-dependent, simulations. While every approach has its advantages and limitations, such as computational cost, integrated and methods-spanning simulation approaches, depending on the network size could establish new ways to investigate the brain. In this paper we present a hybrid simulation approach, that makes use of reduced 1D-models using e.g., the NEURON simulator—which couples to fully resolved models for simulating cellular and sub-cellular dynamics, including the detailed three-dimensional morphology of neurons and organelles. In order to couple 1D- and 3D-simulations, we present a geometry-, membrane potential- and intracellular concentration mapping framework, with which graph- based morphologies, e.g., in the swc- or hoc-format, are mapped to full surface and volume representations of the neuron and computational data from 1D-simulations can be used as boundary conditions for full 3D simulations and vice versa. Thus, established models and data, based on general purpose 1D-simulators, can be directly coupled to
NASA Astrophysics Data System (ADS)
Hassan, Kazi; Allen, Deonie; Haynes, Heather
2016-04-01
This paper considers 1D hydraulic model data on the effect of high flow clusters and sequencing on sediment transport. Using observed flow gauge data from the River Caldew, England, a novel stochastic modelling approach was developed in order to create alternative 50 year flow sequences. Whilst the observed probability density of gauge data was preserved in all sequences, the order in which those flows occurred was varied using the output from a Hidden Markov Model (HMM) with generalised Pareto distribution (GP). In total, one hundred 50 year synthetic flow series were generated and used as the inflow boundary conditions for individual flow series model runs using the 1D sediment transport model HEC-RAS. The model routed graded sediment through the case study river reach to define the long-term morphological changes. Comparison of individual simulations provided a detailed understanding of the sensitivity of channel capacity to flow sequence. Specifically, each 50 year synthetic flow sequence was analysed using a 3-month, 6-month or 12-month rolling window approach and classified for clusters in peak discharge. As a cluster is described as a temporal grouping of flow events above a specified threshold, the threshold condition used herein is considered as a morphologically active channel forming discharge event. Thus, clusters were identified for peak discharges in excess of 10%, 20%, 50%, 100% and 150% of the 1 year Return Period (RP) event. The window of above-peak flows also required cluster definition and was tested for timeframes 1, 2, 10 and 30 days. Subsequently, clusters could be described in terms of the number of events, maximum peak flow discharge, cumulative flow discharge and skewness (i.e. a description of the flow sequence). The model output for each cluster was analysed for the cumulative flow volume and cumulative sediment transport (mass). This was then compared to the total sediment transport of a single flow event of equivalent flow volume
1D-coupled photochemical model of neutrals, cations and anions in the atmosphere of Titan
NASA Astrophysics Data System (ADS)
Dobrijevic, M.; Loison, J. C.; Hickson, K. M.; Gronoff, G.
2016-04-01
Many models with different characteristics have been published so far to study the chemical processes at work in Titan's atmosphere. Some models focus on neutral species in the stratosphere or ionic species in the ionosphere, but few of them couple all the species throughout the whole atmosphere. Very few of these emphasize the importance of uncertainties in the chemical scheme and study their propagation in the model. We have developed a new 1D-photochemical model of Titan's atmosphere coupling neutral species with positive and negative ions from the lower atmosphere up to the ionosphere and have compared our results with observations to have a comprehensive view of the chemical processes driving the composition of the stratosphere and ionosphere of Titan. We have updated the neutral, positive ion and negative ion chemistry and have improved the description of N2 photodissociation by introducing high resolution N2 absorption cross sections. We performed for the first time an uncertainty propagation study in a fully coupled ion-neutral model. We determine how uncertainties on rate constants on both neutral and ionic reactions influence the model results and pinpoint the key reactions responsible for this behavior. We find very good agreement between our model results and observations in both the stratosphere and in the ionosphere for most neutral compounds. Our results are also in good agreement with an average INMS mass spectrum and specific flybys in the dayside suggesting that our chemical model (for both neutral and ions) provides a good approximation of Titan's atmospheric chemistry as a whole. Our uncertainty propagation study highlights the difficulty to interpret the INMS mass spectra for masses 14, 31, 41 and we identified the key reactions responsible for these ambiguities. Despite an overall improvement in the chemical model, disagreement for some specific compounds (HC3N, C2H5CN, C2H4) highlights the role that certain physical processes could play
Cenozoic ice volume and temperature simulations with a 1-D ice-sheet model
NASA Astrophysics Data System (ADS)
de Boer, B.; van de Wal, R. S. W.; Bintanja, R.; Lourens, L. J.; Tuenter, E.
2009-04-01
Ice volume and temperature for the past 35 Million years is investigated with a 1-D ice-sheet model, simulating ice-sheets on both hemispheres. The simulations include two continental Northern Hemisphere (NH) ice-sheets representative for glaciation on the two major continents, i.e. Eurasia (EAZ) and North America (NAM). Antarctic glaciation is simulated with two separate ice-sheets, respectively for West and East Antarctica. The surface air temperature is reconstructed with an inventive inverse procedure, forced with benthic δ18O data. The procedure linearly relates the temperature to the difference between the modelled and observed marine δ18O 100 years later. The derived temperature, representative for the NH, is used to run the ice-sheet model over 100 years, to obtain a mutually consistent record of marine δ18O, sea level and temperature for the last 35 Ma of the Cenozoic. For Northern Hemispheric glaciations results are good compared to similar simulations performed with a much more comprehensive 3-D ice-sheet model. On average, differences are only 1.9 ˚ C for temperature and 6.1 m for sea level. Results with ice-sheets on both hemispheres are very similar. Most notably, the reconstructed ice volume as function of temperature shows a transition from climate dominated by Antarctic ice volume variation towards NH ice-sheets controlled climate. The transition period falls within the range of interglacials (about -2 to +8 ˚ C with respect to present day) and is thus characterized by lower ice volume changes per ˚ C. The relationship between temperature, sea level and δ18O input is tested with an equilibrium experiment, which results in a linear and symmetric relationship for both temperature and total sea level, providing limited evidence for hysteresis, though transient behaviour is still important. Furthermore results show a rather good comparison with other simulations of Antarctic ice volume and observed sea level and deep-sea temperature.
Self-assembling morphologies in a 1D model of two-inclusion-containing lipid membranes
NASA Astrophysics Data System (ADS)
Zhou, Ling; Cheng, Mingfei; Fang, Jinghuai; Peng, Ju
2016-08-01
The self-assembling morphologies in a 1D model of two-inclusion-containing lipid membranes are investigated by using self-consistent field theory. It is found that the shape and overall volume fraction of lipids, the hydrophobic strength and the distance of inclusions play important roles in the morphology of lipid membrane. The membrane consisting of cylindrical lipids with a symmetrical head and tail only forms the well-known normal morphology. However, for the membrane consisting of cone-like lipids with a relatively big head, the increase of the hydrophobic strength of inclusions can realize the membrane transition from the normal morphology to the pore morphologies. With increasing distance between two inclusions, two pores, three pores and four pores appear in turn. Conversely, the increase of the overall volume fraction of lipids can make the membrane undergo a reentrant transition from pore morphologies to normal morphologies. The results may be helpful in our understanding of the pore-forming mechanism.
Modelling hydrology of a single bioretention system with HYDRUS-1D.
Meng, Yingying; Wang, Huixiao; Chen, Jiangang; Zhang, Shuhan
2014-01-01
A study was carried out on the effectiveness of bioretention systems to abate stormwater using computer simulation. The hydrologic performance was simulated for two bioretention cells using HYDRUS-1D, and the simulation results were verified by field data of nearly four years. Using the validated model, the optimization of design parameters of rainfall return period, filter media depth and type, and surface area was discussed. And the annual hydrologic performance of bioretention systems was further analyzed under the optimized parameters. The study reveals that bioretention systems with underdrains and impervious boundaries do have some detention capability, while their total water retention capability is extremely limited. Better detention capability is noted for smaller rainfall events, deeper filter media, and design storms with a return period smaller than 2 years, and a cost-effective filter media depth is recommended in bioretention design. Better hydrologic effectiveness is achieved with a higher hydraulic conductivity and ratio of the bioretention surface area to the catchment area, and filter media whose conductivity is between the conductivity of loamy sand and sandy loam, and a surface area of 10% of the catchment area is recommended. In the long-term simulation, both infiltration volume and evapotranspiration are critical for the total rainfall treatment in bioretention systems. PMID:25133240
Modelling Hydrology of a Single Bioretention System with HYDRUS-1D
Meng, Yingying; Wang, Huixiao; Chen, Jiangang; Zhang, Shuhan
2014-01-01
A study was carried out on the effectiveness of bioretention systems to abate stormwater using computer simulation. The hydrologic performance was simulated for two bioretention cells using HYDRUS-1D, and the simulation results were verified by field data of nearly four years. Using the validated model, the optimization of design parameters of rainfall return period, filter media depth and type, and surface area was discussed. And the annual hydrologic performance of bioretention systems was further analyzed under the optimized parameters. The study reveals that bioretention systems with underdrains and impervious boundaries do have some detention capability, while their total water retention capability is extremely limited. Better detention capability is noted for smaller rainfall events, deeper filter media, and design storms with a return period smaller than 2 years, and a cost-effective filter media depth is recommended in bioretention design. Better hydrologic effectiveness is achieved with a higher hydraulic conductivity and ratio of the bioretention surface area to the catchment area, and filter media whose conductivity is between the conductivity of loamy sand and sandy loam, and a surface area of 10% of the catchment area is recommended. In the long-term simulation, both infiltration volume and evapotranspiration are critical for the total rainfall treatment in bioretention systems. PMID:25133240
Investigating the Response of Greenland Outlet Glaciers to Perturbations Using a 1D Flowline Model
NASA Astrophysics Data System (ADS)
Petrakopoulos, K.; Stearns, L. A.; van der Veen, C. J.
2015-12-01
Over the past two decades, the behavior of many Greenland tidewater outlet glaciers has been characterized by dramatic acceleration, thinning, and retreat. In some cases this behavior is followed by re-advance, thickening and deceleration. The mechanisms that control glacier stability are not fully understood, and hinder ice sheet mass balance projections. Many studies suggest that accelerations are caused exclusively by processes at the terminus, namely by mechanisms that result in increases in iceberg calving rates. In this study we investigate whether comparable accelerations can initiate at different places along the glacier trunk due to changes in subglacial processes or shear margin evolution. We begin our experiments using a prognostic depth integrated (1-D) flowline model applied to Helheim Glacier, and investigate its flow response to perturbations at the terminus and up-flow. Our work shows that large-scale accelerations could have initiated up-flow far from the terminus. The results of this study will contribute to the long-lasting debate about the role of terminus dynamics, and thus ocean conditions, in modulating ice sheet mass balance.
Spectral functions in the 1D and 2D Bose Hubbard model
NASA Astrophysics Data System (ADS)
Ivancic, Robert; Duchon, Eric; Trivedi, Nandini
2014-03-01
We use state of the art numerical techniques including quantum Monte Carlo and maximum entropy methods to obtain the low energy excitation spectra in the superfluid and Mott-insulator phases of the Bose Hubbard model. These results are checked in 1D against Bethe Ansatz and tDMRG results and extended to 2D where such approaches are impossible. In the superfluid, we find linearly dispersing Bogoliubov sound modes as well as additional gapped modes broadened by interaction effects. In the Mott insulator, we find evidence for a finite gap and well defined quasiparticle excitations. We examine properties such as the excitation lifetime, density of states, and speed of sound as the system is tuned across the quantum phase transition that separates the superfluid and Mott states. These results provide an important theoretical framework for upcoming ultracold atom experiments in one and two dimensions. We acknowledge support from the NSF DMR-0907275 (R.I., E.D. and N.T.).
Column Testing and 1D Reactive Transport Modeling to Evaluate Uranium Plume Persistence Processes
NASA Astrophysics Data System (ADS)
Johnson, R. H.; Morrison, S.; Morris, S.; Tigar, A.; Dam, W. L.; Dayvault, J.
2015-12-01
At many U.S. Department of Energy Office of Legacy Management sites, 100 year natural flushing was selected as a remedial option for groundwater uranium plumes. However, current data indicate that natural flushing is not occurring as quickly as expected and solid-phase and aqueous uranium concentrations are persistent. At the Grand Junction, Colorado office site, column testing was completed on core collected below an area where uranium mill tailings have been removed. The total uranium concentration in this core was 13.2 mg/kg and the column was flushed with laboratory-created water with no uranium and chemistry similar to the nearby Gunnison River. The core was flushed for a total of 91 pore volumes producing a maximum effluent uranium concentration of 6,110 μg/L at 2.1 pore volumes and a minimum uranium concentration of 36.2 μg/L at the final pore volume. These results indicate complex geochemical reactions at small pore volumes and a long tailing affect at greater pore volumes. Stop flow data indicate the occurrence of non-equilibrium processes that create uranium concentration rebound. These data confirm the potential for plume persistence, which is occurring at the field scale. 1D reactive transport modeling was completed using PHREEQC (geochemical model) and calibrated to the column test data manually and using PEST (inverse modeling calibration routine). Processes of sorption, dual porosity with diffusion, mineral dissolution, dispersion, and cation exchange were evaluated separately and in combination. The calibration results indicate that sorption and dual porosity are major processes in explaining the column test data. These processes are also supported by fission track photographs that show solid-phase uranium residing in less mobile pore spaces. These procedures provide valuable information on plume persistence and secondary source processes that may be used to better inform and evaluate remedial strategies, including natural flushing.
1-D/3-D geologic model of the Western Canada Sedimentary Basin
Higley, D.K.; Henry, M.; Roberts, L.N.R.; Steinshouer, D.W.
2005-01-01
The 3-D geologic model of the Western Canada Sedimentary Basin comprises 18 stacked intervals from the base of the Devonian Woodbend Group and age equivalent formations to ground surface; it includes an estimated thickness of eroded sediments based on 1-D burial history reconstructions for 33 wells across the study area. Each interval for the construction of the 3-D model was chosen on the basis of whether it is primarily composed of petroleum system elements of reservoir, hydrocarbon source, seal, overburden, or underburden strata, as well as the quality and areal distribution of well and other data. Preliminary results of the modeling support the following interpretations. Long-distance migration of hydrocarbons east of the Rocky Mountains is indicated by oil and gas accumulations in areas within which source rocks are thermally immature for oil and (or) gas. Petroleum systems in the basin are segmented by the northeast-trending Sweetgrass Arch; hydrocarbons west of the arch were from source rocks lying near or beneath the Rocky Mountains, whereas oil and gas east of the arch were sourced from the Williston Basin. Hydrocarbon generation and migration are primarily due to increased burial associated with the Laramide Orogeny. Hydrocarbon sources and migration were also influenced by the Lower Cretaceous sub-Mannville unconformity. In the Peace River Arch area of northern Alberta, Jurassic and older formations exhibit high-angle truncations against the unconformity. Potential Paleozoic though Mesozoic hydrocarbon source rocks are in contact with overlying Mannville Group reservoir facies. In contrast, in Saskatchewan and southern Alberta the contacts are parallel to sub-parallel, with the result that hydrocarbon source rocks are separated from the Mannville Group by seal-forming strata within the Jurassic. Vertical and lateral movement of hydrocarbons along the faults in the Rocky Mountains deformed belt probably also resulted in mixing of oil and gas from numerous
1D and 2D urban dam-break flood modelling in Istanbul, Turkey
NASA Astrophysics Data System (ADS)
Ozdemir, Hasan; Neal, Jeffrey; Bates, Paul; Döker, Fatih
2014-05-01
Urban flood events are increasing in frequency and severity as a consequence of several factors such as reduced infiltration capacities due to continued watershed development, increased construction in flood prone areas due to population growth, the possible amplification of rainfall intensity due to climate change, sea level rise which threatens coastal development, and poorly engineered flood control infrastructure (Gallegos et al., 2009). These factors will contribute to increased urban flood risk in the future, and as a result improved modelling of urban flooding according to different causative factor has been identified as a research priority (Gallegos et al., 2009; Ozdemir et al. 2013). The flooding disaster caused by dam failures is always a threat against lives and properties especially in urban environments. Therefore, the prediction of dynamics of dam-break flows plays a vital role in the forecast and evaluation of flooding disasters, and is of long-standing interest for researchers. Flooding occurred on the Ayamama River (Istanbul-Turkey) due to high intensity rainfall and dam-breaching of Ata Pond in 9th September 2009. The settlements, industrial areas and transportation system on the floodplain of the Ayamama River were inundated. Therefore, 32 people were dead and millions of Euros economic loses were occurred. The aim of this study is 1 and 2-Dimensional flood modelling of the Ata Pond breaching using HEC-RAS and LISFLOOD-Roe models and comparison of the model results using the real flood extent. The HEC-RAS model solves the full 1-D Saint Venant equations for unsteady open channel flow whereas LISFLOOD-Roe is the 2-D shallow water model which calculates the flow according to the complete Saint Venant formulation (Villanueva and Wright, 2006; Neal et al., 2011). The model consists a shock capturing Godunov-type scheme based on the Roe Riemann solver (Roe, 1981). 3 m high resolution Digital Surface Model (DSM), natural characteristics of the pond
Kinetic model for erythrocyte aggregation.
Bertoluzzo, S M; Bollini, A; Rasia, M; Raynal, A
1999-01-01
It is well known that light transmission through blood is the most widely utilized method for the study of erythrocyte aggregation. The curves obtained had been considered empirically as exponential functions. In consequence, the process becomes characterized by an only parameter that varies with all the process factors without discrimination. In the present paper a mathematical model for RBC aggregation process is deduced in accordance with von Smoluchowski's theory about the kinetics of colloidal particles agglomeration. The equation fitted the experimental pattern of the RBC suspension optical transmittance closely and contained two parameters that estimate the most important characteristics of the aggregation process separately, i.e., (1) average size of rouleaux at equilibrium and (2) aggregation rate. The evaluation of the method was assessed by some factors affecting erythrocyte aggregation, such as temperature, plasma dilutions, Dextran 500, Dextran 70 and PVP 360, at different media concentrations, cellular membrane alteration by the alkylating agent TCEA, and decrease of medium osmolarity. Results were interpreted considering the process characteristics estimated by the parameters, and there were also compared with similar studies carried out by other authors with other methods. This analysis allowed us to conclude that the equation proposed is reliable and useful to study erythrocyte aggregation. PMID:10660481
A 1-D radiative conductive model to study the SOIR/VEx thermal profiles
NASA Astrophysics Data System (ADS)
Mahieux, Arnaud; Erwin, Justin T.; Chamberlain, Sarah; Robert, Séverine; Carine Vandaele, Ann; Wilquet, Valérie; Thomas, Ian; Yelle, Roger V.; Bertaux, Jean-Loup
2015-04-01
SOIR is an infrared spectrometer on board Venus Express that probes the Venus terminator region since 2006. The measurements are taken on the morning and evening sides of the terminator, covering all latitudes from the North Pole to the South Pole. Its wavelength range - 2.2 to 4.3 μm - allows a detailed chemical inventory of the Venus atmosphere [1-5], such as CO2, CO, H2O, HCl, HF, SO2 and aerosols. CO2 is detected from 70 km up to 165 km, CO from 70 km to 140 km, and the minor species typically below 110 km down to 70 km. Number density profiles of these species are computed from the measured spectra. Temperature profiles are obtained while computing the spectral inversion of the CO2 spectra combined with the hydrostatic law [6]. These temperature measurements show a striking permanent temperature minimum (at 125 km) and a weaker temperature maximum (over 100-115 km). The time variability of the CO2 density profiles spans over two orders of magnitude, and a clear trend is seen with latitude. The temperature variations are also important, of the order of 35 K for a given pressure level, but the latitude variation are small. Miss-RT, a 1D radiative transfer model has been developed to reproduce the SOIR terminator profiles, derived from the Mars thermosphere code presented in [7]. This model has been expanded to better account for the CO2, CO, and O non-LTE radiative heating and cooling processes which have to be considered in the dense atmosphere of Venus. Radiative cooling by minor species detected by SOIR (e.g. HCl, SO2, and H2O) are found to be small in comparison to the 15 μm CO2 cooling. Aerosol cooling in the 60-90km altitude range may be important to the thermal balance. There is a good agreement between the 1D model temperature profile and the mean SOIR temperature profile. Further we can suggest parameters that can be adjusted to improve the agreement between the model and measurements. The remaining differences can be attributed to the atmosphere
Comprehensive 1D Modelling of Reactive Chemical Transport in Unsaturated Soil
NASA Astrophysics Data System (ADS)
Wissmeier, L.; Barry, D. A.
2007-12-01
Computer models for simulating environmental processes of water flow, solute transport and geochemical reactions have greatly advanced during recent years. However, there is still demand for the development of programs that a capable of simulating the numerous interactions between physical transport processes and biogeochemical reactions in natural soils. We present a new tool for simulating transient vadose zone flow and solute transport according to the moisture- based form of Richards' equation within the widely used geochemical software PHREEQC. The direct implementation into the geochemical framework provides access to comprehensive geochemical models, giving capabilities beyond existing software for coupled unsaturated flow and reaction. Possible reactions include complex aqueous speciation, cation exchange, equilibrium phase dissolution and precipitation, formation of solid solutions, redox reactions, gas phase exchange, surface adsorption considering electrostatics and kinetic reactions with user-defined rate equations, among others. As a result of the close coupling procedure, the influence of geochemical reactions on water content, e.g., through dissolution or precipitation of water-containing phases, can be investigated. For the solution of the partial differential equations of flow and transport, an explicit finite-difference formulation with a second-order space discretization and first-order time discretization was employed. The use of integrated diffusivities transforms Richards' equation into a simple advection-diffusion equation. Changes in water content and solute concentration were conceptualized as local kinetic reactions of individual elements where changes in moisture content result from fluxes of oxygen and hydrogen across cell boundaries. Reactions and chemical element transport are coupled via sequential two-step operator splitting. The scheme was implemented into PHREEQC without any source code modification such that it can be applied by
Liang, Xiaoyan; Schnaper, H. William; Matsusaka, Taiji; Pastan, Ira; Ledbetter, Steve; Hayashida, Tomoko
2016-01-01
Fibrosis is a final common pathway leading to loss of kidney function, in which the fibrogenic cytokine, transforming growth factor β (TGF-β), plays a central role. While previous studies showed that TGF-β antagonism by various means prevents fibrosis in mouse models, clinical approaches based on these findings remain elusive. 1D11 is a neutralizing antibody to all three isoforms of TGF-β. In both adriamycin (ADR)-induced nephropathy and NEP25 podocyte ablation nephropathy, thrice-weekly intraperitoneal administration of 1D11 from the day of disease induction until the mice were sacrificed (day 14 for ADR and day 28 for NEP25), significantly reduced glomerular COL1A2 mRNA accumulation and histological changes. Consistent with our previous findings, proteinuria remained overt in the mice treated with 1D11, suggesting distinct mechanisms for proteinuria and fibrogenesis. Podocyte numbers determined by WT1 staining were significantly reduced in NEP25-model glomeruli as expected, while WT1-positive cells were preserved in mice receiving 1D11. Even when 1D11 was administered after the onset of proteinuria on day 3, 1D11 preserved WT1-positive cell numbers in glomeruli and significantly reduced glomerular scar score (2.5 ± 0.2 [control IgG] vs. 1.8 ± 0.2 [1D11], P < 0.05) and glomerular COL1A2 mRNA expression (19.3 ± 4.4 [control IgG] vs. 8.4 ± 2.4 [1D11] fold increase over the healthy control, P < 0.05). Transmission electron microscopy revealed loss of podocytes and denuded glomerular basement membrane in NEP25 mice with disease, whereas podocytes remained attached to the basement membrane, though effaced and swollen, in those receiving 1D11 from day 3. Together, these data suggest that TGF-β neutralization by 1D11 prevents glomerular fibrosis even when started after the onset of proteinuria. While overt proteinuria and podocyte effacement persist, 1D11 prevents total podocytes detachment, which might be a key event activating fibrogenic events in glomeruli
NASA Astrophysics Data System (ADS)
Carmelo, J. M. P.; Čadež, T.
2016-03-01
A modified version of the metallic-phase pseudofermion dynamical theory (PDT) of the 1D Hubbard model is introduced for the spin dynamical correlation functions of the half-filled 1D Hubbard model Mott-Hubbard phase. The Mott-Hubbard insulator phase PDT is applied to the study of the model longitudinal and transverse spin dynamical structure factors at finite magnetic field h, focusing in particular on the singularities at excitation energies in the vicinity of the lower thresholds. The relation of our theoretical results to both condensed-matter and ultra-cold atom systems is discussed.
Rayleigh Wave Dispersion and A 1d S-velocity Model of The Fennoscandian Mantle
NASA Astrophysics Data System (ADS)
Funke, S.; Friederich, W.; Sstwg, The
We derive a Rayleigh wave dispersion curve from surface wave data recorded at the SVEKALAPKO tomographic array deployed in Southern Finland from September 1998 to March 1999. After a suite of processing steps, complex spectral amplitudes of the Rayleigh wave train are determined for each available seismogram. The process- ing includes low-pass filtering, instrument correction, deconvolution using a standard earth model to compress the Rayleigh wave train, computation of Gabor matrices (sonograms) to pick group travel times, and finally estimation of complex spectral amplitudes in a Gaussian time window of frequency-dependent width centered on the group travel time. Spectral amplitude values are only accepted if the signal-to-noise ratio in the considered frequency interval is above a pre-chosen threshold and if the picked group travel time does not deviate too strongly from that predicted by a stan- dard earth model. The final dataset contains spectral amplitude values at 34 selected periods from 52 earthquakes observed at on average 25 stations. For each selected frequency, we determine a phase velocity by fitting plane waves propagating across the array with this velocity to the complex spectral amplitudes of all earthquakes and stations. Errors are estimated with a bootstrap method. We obtain reliable phase velocities in the frequency band from 8 mHz to 50 mHz. Phase veloci- ties for lower frequencies exhibit large errors due to the lack of big earthquakes during the time of deployment. The phase velocities are substantially higher than predicted by standard earth model ak135 below 20 mHz and slightly lower above 25 mHz. We have inverted the dispersion curve for a 1D shear wave velocity model down to about 400 km depth and obtain a 50 km thick crust and a fast upper mantle with a sub- Moho velocity of 4.7 km/s. Our data do not require a low-velocity zone in the upper mantle. Indeed, the dispersion curve can be explained by a nearly straight velocity profile from
Development of a 1D canopy module to couple mesoscale meteorogical model with building energy model
NASA Astrophysics Data System (ADS)
Mauree, Dasaraden; Kohler, Manon; Blond, Nadège; Clappier, Alain
2013-04-01
The actual global warming, highlighted by the scientific community, is due to the greenhouse gases emissions resulting from our energy consumption. This energy is mainly produced in cities (about 70% of the total energy use). Around 36% of this energy are used in buildings (residential/tertiary) and this accounts for about 20% of the greenhouse gases emissions. Moreover, the world population is more and more concentrated in urban areas, 50% of the actual world population already lives in cities and this ratio is expected to reach 70% by 2050. With the obviously increasing responsibility of cities in climate change in the future, it is of great importance to go toward more sustainable cities that would reduce the energy consumption in urban areas. The energy use inside buildings is driven by two factors: (1) the level of comfort wished by the inhabitants and (2) the urban climate. On the other hand, the urban climate is influenced by the presence of buildings. Indeed, artificial surfaces of urban areas modify the energy budget of the Earth's surface and furthermore, heat is released into the atmosphere due to the energy used by buildings. Modifications at the building scale (micro-scale) can thus have an influence on the climate of the urban areas and surroundings (meso-scale), and vice and versa. During the last decades, meso-scale models have been developed to simulate the atmospheric conditions for domain of 100-1000km wide with a resolution of few kilometers. Due to their low resolution, the effects of small obstacles (such as buildings, trees, ...) near the ground are not reproduced properly and parameterizations have been developed to represent such effects in meso-scale models. On the other side, micro-scale models have a higher resolution (around 1 meter) and consequently can better simulate the impact of obstacles on the atmospheric heat flux exchanges with the earth surface. However, only a smaller domain (less than 1km) can be simulated for the same
Diesel Engine performance improvement in a 1-D engine model using Particle Swarm Optimization
NASA Astrophysics Data System (ADS)
Karra, Prashanth
2015-12-01
A particle swarm optimization (PSO) technique was implemented to improve the engine development and optimization process to simultaneously reduce emissions and improve the fuel efficiency. The optimization was performed on a 4-stroke 4-cylinder GT-Power based 1-D diesel engine model. To achieve the multi-objective optimization, a merit function was defined which included the parameters to be optimized: Nitrogen Oxides (NOx), Nonmethyl hydro carbons (NMHC), Carbon Monoxide (CO), Brake Specific Fuel Consumption (BSFC). EPA Tier 3 emissions standards for non-road diesel engines between 37 and 75 kW of output were chosen as targets for the optimization. The combustion parameters analyzed in this study include: Start of main Injection, Start of Pilot Injection, Pilot fuel quantity, Swirl, and Tumble. The PSO was found to be very effective in quickly arriving at a solution that met the target criteria as defined in the merit function. The optimization took around 40-50 runs to find the most favourable engine operating condition under the constraints specified in the optimization. In a favourable case with a high merit function values, the NOx+NMHC and CO values were reduced to as low as 2.9 and 0.014 g/kWh, respectively. The operating conditions at this point were: 10 ATDC Main SOI, -25 ATDC Pilot SOI, 0.25 mg of pilot fuel, 0.45 Swirl and 0.85 tumble. These results indicate that late main injections preceded by a close, small pilot injection are most favourable conditions at the operating condition tested.
Testing the early Mars H2-CO2 greenhouse hypothesis with a 1-D photochemical model
NASA Astrophysics Data System (ADS)
Batalha, Natasha; Domagal-Goldman, Shawn D.; Ramirez, Ramses; Kasting, James F.
2015-09-01
A recent study by Ramirez et al. (Ramirez, R.M. et al. [2014]. Nat. Geosci. 7(1), 59-63.) demonstrated that an atmosphere with 1.3-4 bar of CO2 and H2O, in addition to 5-20% H2, could have raised the mean annual and global surface temperature of early Mars above the freezing point of water. Such warm temperatures appear necessary to generate the rainfall (or snowfall) amounts required to carve the ancient martian valleys. Here, we use our best estimates for early martian outgassing rates, along with a 1-D photochemical model, to assess the conversion efficiency of CO, CH4, and H2S to CO2, SO2, and H2. Our outgassing estimates assume that Mars was actively recycling volatiles between its crust and interior, as Earth does today. H2 production from serpentinization and deposition of banded iron-formations is also considered. Under these assumptions, maintaining an H2 concentration of ˜1-2% by volume is achievable, but reaching 5% H2 requires additional H2 sources or a slowing of the hydrogen escape rate below the diffusion limit. If the early martian atmosphere was indeed H2-rich, we might be able to see evidence of this in the rock record. The hypothesis proposed here is consistent with new data from the Curiosity Rover, which show evidence for a long-lived lake in Gale Crater near Mt. Sharp. It is also consistent with measured oxygen fugacities of martian meteorites, which show evidence for progressive mantle oxidation over time.
Modeling of general 1-D periodic leaky-wave antennas in layered media using EIGER.
Wilton, Donald R.; Basilio, Lorena I.; Celepcikay, Ferhat T.; Johnson, William Arthur; Baccarelli, Paolo; Valerio, Guido; Paulotto, Simone; Langston, William L.; Jackson, David R.
2010-09-01
This paper presents a mixed-potential integral-equation formulation for analyzing 1-D periodic leaky-wave antennas in layered media. The structures are periodic in one dimension and finite in the other two dimensions. The unit cell consists of an arbitrary-shaped metallic/dielectric structure. The formulation has been implemented in the EIGER{trademark} code in order to obtain the real and complex propagation wavenumbers of the bound and leaky modes of such structures. Validation results presented here include a 1-D periodic planar leaky-wave antenna and a fully 3-D waveguide test case.
Modeling of general 1-D periodic leaky-wave antennas in layered media with EIGER.
Wilton, Donald R.; Basilio, Lorena I.; Celepcikay, F. T.; Johnson, William Arthur; Baccarelli, Paolo; Valerio, G.; Paulotto, Simone; Langston, William L.; Jackson, David R.
2010-06-01
This paper presents a mixed-potential integral-equation formulation for analyzing 1-D periodic leaky-wave antennas in layered media. The structures are periodic in one dimension and finite in the other two dimensions. The unit cell consists of an arbitrary-shaped metallic/dielectric structure. The formulation has been implemented in the EIGER{trademark} code in order to obtain the real and complex propagation wavenumbers of the bound and leaky modes of such structures. Validation results presented here include a 1-D periodic planar leaky-wave antenna and a fully 3-D waveguide test case.
NASA Astrophysics Data System (ADS)
Subin, Z. M.; Riley, W. J.
2009-12-01
Compared to solid ground, lakes tend to have decreased albedo, increased ground heat conductance, and increased effective ground heat capacity. These features alter local surface fluxes compared to nearby vegetation, which in turn alter the climate of the nearby atmosphere and surrounding land areas. Interest in feedbacks between lake behavior and climate change provides motivation for including lakes in global climate models, as does the desire to do effective regional downscaling of climate model predictions over regions with large lake area fraction, like the Great Lakes region. Finally, the initiation, warming, and expansion of Arctic thermokarst lakes could provide an important geophysical and biogeochemical feedback to climate warming. The Community Land Model (CLM) 3.5 currently uses a 1D Hostetler lake scheme. We have updated this model to improve the characterization of surface fluxes, eddy diffusivity, and convective mixing. We also link the lake model with the full snow physics found over other land surface types (including 5 snow layers, aerosol deposition, partial transparency of snow layers, and snow aging), add phase change & ice physics to the lake model, and include soil layers beneath lakes. These soil layers will be an important component of future thermokarst lake modeling, as thermokarst lakes tend to form regions of unfrozen soil (talik) beneath them that become active sites for anaerobic decomposition of pre-modern peat. We have also integrated the updated lake model into a modified version of the Weather Research and Forecasting (WRF) Model 3.0. We will present comparisons between predicted and observed thermal conditions, snow and ice depths, and surface energy fluxes at several lake sites, using local meteorological forcing or integrated regional atmospheric coupling. The thermal predictions are generally reasonable and show a marked improvement from runs performed with the baseline CLM 3.5 version of the lake model. Over Sparkling Lake
Viral kinetic modeling: state of the art
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 viral 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.
Viral kinetic modeling: state of the art
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
1D Runoff-runon stochastic model in the light of queueing theory : heterogeneity and connectivity
NASA Astrophysics Data System (ADS)
Harel, M.-A.; Mouche, E.; Ledoux, E.
2012-04-01
Runoff production on a hillslope during a rainfall event may be simplified as follows. Given a soil of constant infiltrability I, which is the maximum amount of water that the soil can infiltrate, and a constant rainfall intensity R, runoff is observed where R is greater than I. The infiltration rate equals the infiltrability when runoff is produced, R otherwise. When ponding time, topography, and overall spatial and temporal variations of physical parameters, such as R and I, are neglected, the runoff equation remains simple. In this study, we consider soils of spatially variable infiltrability. As runoff can re-infiltrate on down-slope areas of higher infiltrabilities (runon), the resulting process is highly non-linear. The stationary runoff equation is: Qn+1 = max(Qn + (R - In)*Δx , 0) where Qn is the runoff arriving on pixel n of size Δx [L2/T], R and In the rainfall intensity and infiltrability on that same pixel [L/T]. The non-linearity is due to the dependence of infiltration on R and Qn, that is runon. This re-infiltration process generates patterns of runoff along the slope, patterns that organise and connect to each other differently depending on the rainfall intensity and the nature of the soil heterogeneity. The runoff connectivity, assessed using the connectivity function of Allard (1993), affects greatly the dynamics of the runoff hillslope. Our aim is to assess, in a stochastic framework, the runoff organization on 1D slopes with random infiltrabilities (log-normal, exponential, bimodal and uniform distributions) by means of theoretical developments and numerical simulations. This means linking the nature of soil heterogeneity with the resulting runoff organisation. In term of connectivity, we investigate the relations between structural (infiltrability) and functional (runoff) connectivity. A theoretical framework based on the queueing theory is developed. We implement the idea of Jones et al. (2009), who remarked that the above formulation is
Comparison of the 1D flux theory with a 2D hydrodynamic secondary settling tank model.
Ekama, G A; Marais, P
2004-01-01
The applicability of the 1D idealized flux theory (1DFT) for design of secondary settling tanks (SSTs) is evaluated by comparing its predicted maximum surface overflow (SOR) and solids loading (SLR) rates with that calculated from the 2D hydrodynamic model SettlerCAD using as a basis 35 full scale SST stress tests conducted on different SSTs with diameters from 30 to 45m and 2.25 to 4.1 m side water depth, with and without Stamford baffles. From the simulations, a relatively consistent pattern appeared, i.e. that the 1DFT can be used for design but its predicted maximum SLR needs to be reduced by an appropriate flux rating, the magnitude of which depends mainly on SST depth and hydraulic loading rate (HLR). Simulations of the sloping bottom shallow (1.5-2.5 m SWD) Dutch SSTs tested by STOWa and the Watts et al. SST, all with doubled SWDs, and the Darvill new (4.1 m) and old (2.5 m) SSTs with interchanged depths, were run to confirm the sensitivity of the flux rating to depth and HLR. Simulations with and without a Stamford baffle were also done. While the design of the internal features of the SST, such as baffling, have a marked influence on the effluent SS concentration for underloaded SSTs, these features appeared to have only a small influence on the flux rating, i.e. capacity, of the SST, In the meantime until more information is obtained, it would appear that from the simulations so far that the flux rating of 0.80 of the 1DFT maximum SLR recommended by Ekama and Marais remains a reasonable value to apply in the design of full scale SSTs--for deep SSTs (4 m SWD) the flux rating could be increased to 0.85 and for shallow SSTs (2.5 m SWD) decreased to 0.75. It is recommended that (i) while the apparent interrelationship between SST flux rating and depth suggests some optimization of the volume of the SST, that this be avoided and that (ii) the depth of the SST be designed independently of the surface area as is usually the practice and once selected, the
A One-Dimensional (1-D) Three-Region Model for a Bubbling Fluidized-Bed Adsorber
Lee, Andrew; Miller, David C.
2012-01-01
A general one-dimensional (1-D), three-region model for a bubbling fluidized-bed adsorber with internal heat exchangers has been developed. The model can predict the hydrodynamics of the bed and provides axial profiles for all temperatures, concentrations, and velocities. The model is computationally fast and flexible and allows for any system of adsorption and desorption reactions to be modeled, making the model applicable to any adsorption process. The model has been implemented in both gPROMS and Aspen Custom Modeler, and the behavior of the model has been verified.
Sabtaji, Agung E-mail: agung.sabtaji@bmkg.go.id; Nugraha, Andri Dian
2015-04-24
West Papua region has fairly high of seismicity activities due to tectonic setting and many inland faults. In addition, the region has a unique and complex tectonic conditions and this situation lead to high potency of seismic hazard in the region. The precise earthquake hypocenter location is very important, which could provide high quality of earthquake parameter information and the subsurface structure in this region to the society. We conducted 1-D P-wave velocity using earthquake data catalog from BMKG for April, 2009 up to March, 2014 around West Papua region. The obtained 1-D seismic velocity then was used as input for improving hypocenter location using double-difference method. The relocated hypocenter location shows fairly clearly the pattern of intraslab earthquake beneath New Guinea Trench (NGT). The relocated hypocenters related to the inland fault are also observed more focus in location around the fault.
Chemical Kinetic Modeling of Advanced Transportation Fuels
PItz, W J; Westbrook, C K; Herbinet, O
2009-01-20
Development of detailed chemical kinetic models for advanced petroleum-based and nonpetroleum based fuels is a difficult challenge because of the hundreds to thousands of different components in these fuels and because some of these fuels contain components that have not been considered in the past. It is important to develop detailed chemical kinetic models for these fuels since the models can be put into engine simulation codes used for optimizing engine design for maximum efficiency and minimal pollutant emissions. For example, these chemistry-enabled engine codes can be used to optimize combustion chamber shape and fuel injection timing. They also allow insight into how the composition of advanced petroleum-based and non-petroleum based fuels affect engine performance characteristics. Additionally, chemical kinetic models can be used separately to interpret important in-cylinder experimental data and gain insight into advanced engine combustion processes such as HCCI and lean burn engines. The objectives are: (1) Develop detailed chemical kinetic reaction models for components of advanced petroleum-based and non-petroleum based fuels. These fuels models include components from vegetable-oil-derived biodiesel, oil-sand derived fuel, alcohol fuels and other advanced bio-based and alternative fuels. (2) Develop detailed chemical kinetic reaction models for mixtures of non-petroleum and petroleum-based components to represent real fuels and lead to efficient reduced combustion models needed for engine modeling codes. (3) Characterize the role of fuel composition on efficiency and pollutant emissions from practical automotive engines.
Marin-Valencia, Isaac; Good, Levi B.; Ma, Qian; Duarte, Joao; Bottiglieri, Teodoro; Sinton, Christopher M.; Heilig, Charles W.; Pascual, Juan M.
2012-01-01
Brain glucose supplies most of the carbon required for acetyl-coenzyme A (acetyl-CoA) generation (an important step for myelin synthesis) and for neurotransmitter production via further metabolism of acetyl-CoA in the tricarboxylic acid (TCA) cycle. However, it is not known whether reduced brain glucose transporter type I (GLUT-1) activity, the hallmark of the GLUT-1 deficiency (G1D) syndrome, leads to acetyl-CoA, TCA or neurotransmitter depletion. This question is relevant because, in its most common form in man, G1D is associated with cerebral hypomyelination (manifested as microcephaly) and epilepsy, suggestive of acetyl-CoA depletion and neurotransmitter dysfunction, respectively. Yet, brain metabolism in G1D remains underexplored both theoretically and experimentally, partly because computational models of limited brain glucose transport are subordinate to metabolic assumptions and partly because current hemizygous G1D mouse models manifest a mild phenotype not easily amenable to investigation. In contrast, adult antisense G1D mice replicate the human phenotype of spontaneous epilepsy associated with robust thalamocortical electrical oscillations. Additionally, and in consonance with human metabolic imaging observations, thalamus and cerebral cortex display the lowest GLUT-1 expression and glucose uptake in the mutant mouse. This depletion of brain glucose is associated with diminished plasma fatty acids and elevated ketone body levels, and with decreased brain acetyl-CoA and fatty acid contents, consistent with brain ketone body consumption and with stimulation of brain beta-oxidation and/or diminished cerebral lipid synthesis. In contrast with other epilepsies, astrocyte glutamine synthetase expression, cerebral TCA cycle intermediates, amino acid and amine neurotransmitter contents are also intact in G1D. The data suggest that the TCA cycle is preserved in G1D because reduced glycolysis and acetyl-CoA formation can be balanced by enhanced ketone body
Diomede, P.; Longo, S.; Capitelli, M.
2005-05-16
We present a 1D(r)2D(v) particle code for capacitively coupled radio frequency discharge plasmas in hydrogen, which includes a rigorous kinetic modeling of ion transport and several solutions to speed up the convergence. In a test case the effect of surface atom recombination and molecule vibrational deactivation on H- concentration is investigated.
Algebraic operator approach to gas kinetic models
NASA Astrophysics Data System (ADS)
Il'ichov, L. V.
1997-02-01
Some general properties of the linear Boltzmann kinetic equation are used to present it in the form ∂ tϕ = - Â†Âϕ with the operators ÂandÂ† possessing some nontrivial algebraic properties. When applied to the Keilson-Storer kinetic model, this method gives an example of quantum ( q-deformed) Lie algebra. This approach provides also a natural generalization of the “kangaroo model”.
NASA Astrophysics Data System (ADS)
Harley, P.; Spence, S.; Early, J.; Filsinger, D.; Dietrich, M.
2013-12-01
Single-zone modelling is used to assess different collections of impeller 1D loss models. Three collections of loss models have been identified in literature, and the background to each of these collections is discussed. Each collection is evaluated using three modern automotive turbocharger style centrifugal compressors; comparisons of performance for each of the collections are made. An empirical data set taken from standard hot gas stand tests for each turbocharger is used as a baseline for comparison. Compressor range is predicted in this study; impeller diffusion ratio is shown to be a useful method of predicting compressor surge in 1D, and choke is predicted using basic compressible flow theory. The compressor designer can use this as a guide to identify the most compatible collection of losses for turbocharger compressor design applications. The analysis indicates the most appropriate collection for the design of automotive turbocharger centrifugal compressors.
NASA Astrophysics Data System (ADS)
Matrullo, Emanuela; De Matteis, Raffaella; Satriano, Claudio; Amoroso, Ortensia; Zollo, Aldo
2013-10-01
We present a 1-D velocity model of the Earth's crust in Campania-Lucania region obtained by solving the coupled hypocentre-velocity inverse problem for 1312 local earthquakes recorded at a dense regional network. The model is constructed using the VELEST program, which calculates 1-D `minimum' velocity model from body wave traveltimes, together with station corrections, which account for deviations from the simple 1-D structure. The spatial distribution of station corrections correlates with the P-wave velocity variations of a preliminary 3-D crustal velocity model that has been obtained from the tomographic inversion of the same data set of P traveltimes. We found that station corrections reflect not only inhomogeneous near-surface structures, but also larger-scale geological features associated to the transition between carbonate platform outcrops at Southwest and Miocene sedimentary basins at Northeast. We observe a significant trade-off between epicentral locations and station corrections, related to the existence of a thick low-velocity layer to the NE. This effect is taken into account and minimized by re-computing station corrections, fixing the position of a subset of well-determined hypocentres, located in the 3-D tomographic model.
NASA Astrophysics Data System (ADS)
Sutanto, S. J.; Wenninger, J.; Coenders-Gerrits, A. M. J.; Uhlenbrook, S.
2012-08-01
Knowledge of the water fluxes within the soil-vegetation-atmosphere system is crucial to improve water use efficiency in irrigated land. Many studies have tried to quantify these fluxes, but they encountered difficulties in quantifying the relative contribution of evaporation and transpiration. In this study, we compared three different methods to estimate evaporation fluxes during simulated summer conditions in a grass-covered lysimeter in the laboratory. Only two of these methods can be used to partition total evaporation into transpiration, soil evaporation and interception. A water balance calculation (whereby rainfall, soil moisture and percolation were measured) was used for comparison as a benchmark. A HYDRUS-1D model and isotope measurements were used for the partitioning of total evaporation. The isotope mass balance method partitions total evaporation of 3.4 mm d-1 into 0.4 mm d-1 for soil evaporation, 0.3 mm d-1 for interception and 2.6 mm d-1 for transpiration, while the HYDRUS-1D partitions total evaporation of 3.7 mm d-1 into 1 mm d-1 for soil evaporation, 0.3 mm d-1 for interception and 2.3 mm d-1 for transpiration. From the comparison, we concluded that the isotope mass balance is better for low temporal resolution analysis than the HYDRUS-1D. On the other hand, HYDRUS-1D is better for high temporal resolution analysis than the isotope mass balance.
A 1D Model For Describing Ion Cyclotron Resonance Heating At Arbitrary Cyclotron Harmonics
NASA Astrophysics Data System (ADS)
Van Eester, Dirk; Lerche, Ernesto
2011-12-01
Both at low and higher cyclotron harmonics, properly accounting for finite Larmor radius effects is crucial in many ICRF heating scenario's creating high energy tails. The present paper discusses an extension of the 1D TOMCAT wave equation solver [1] to arbitrary harmonics and arbitrary wavelengths. Rather than adopting the particle position, the guiding center position is used as the independent variable when writing down an expression for the dielectric response that is suitable for numerical application. This choice of variable yields symmetric and intuitive expressions, and guarantees that a positive definite power absorption is obtained for any of the wave modes in the plasma. Rather than relying on a truncated Taylor series expansion of the dielectric response, an integro-differential approach is proposed. To keep the required computation time for this generalized description reasonable tabulation of integrals is intensively used. An example is provided to illustrate the potential of the new wave code.
Model-Independent Bounds on Kinetic Mixing
Hook, Anson; Izaguirre, Eder; Wacker, Jay G.
2011-01-01
New Abelimore » an vector bosons can kinetically mix with the hypercharge gauge boson of the Standard Model. This letter computes the model-independent limits on vector bosons with masses from 1 GeV to 1 TeV. The limits arise from the numerous e + e − experiments that have been performed in this energy range and bound the kinetic mixing by ϵ ≲ 0.03 for most of the mass range studied, regardless of any additional interactions that the new vector boson may have.« less
Model Independent Bounds on Kinetic Mixing
Hook, Anson; Izaguirre, Eder; Wacker, Jay G.; /SLAC
2011-08-22
New Abelian vector bosons can kinetically mix with the hypercharge gauge boson of the Standard Model. This letter computes the model independent limits on vector bosons with masses from 1 GeV to 1 TeV. The limits arise from the numerous e{sup +}e{sup -} experiments that have been performed in this energy range and bound the kinetic mixing by {epsilon} {approx}< 0.03 for most of the mass range studied, regardless of any additional interactions that the new vector boson may have.
Kinetic Analysis of Protein Folding Lattice Models
NASA Astrophysics Data System (ADS)
Chen, Hu; Zhou, Xin; Liaw, Chih Young; Koh, Chan Ghee
Based on two-dimensional square lattice models of proteins, the relation between folding time and temperature is studied by Monte Carlo simulation. The results can be represented by a kinetic model with three states — random coil, molten globule, and native state. The folding process is composed of nonspecific collapse and final searching for the native state. At high temperature, it is easy to escape from local traps in the folding process. With decreasing temperature, because of the trapping in local traps, the final searching speed decreases. Then the folding shows chevron rollover. Through the analysis of the fitted parameters of the kinetic model, it is found that the main difference between the energy landscapes of the HP model and the Go model is that the number of local minima of the Go model is less than that of the HP model.
Joseph, S; Caridade, P J S B; Varandas, A J C
2011-07-14
The recently proposed ab initio single-sheeted double many-body expansion potential energy for the methylene molecule has been used to perform quasiclassical trajectory (QCT) calculations for the title reaction. Thermal and initial state-specific (v = 0, j = 0) rate constants for the C((1)D) + H(2)/HD/D(2) reactions have been obtained over a wide range of temperatures. Cross sections for the reaction C((1)D) + H(2) and its deuterated isotopes have also been calculated, as well as the CD/CH branching ratios for the C((1)D) + HD reaction. It is found that the CD + H product channel in the C((1)D) + HD reaction is preferred relative to the CH + D channel. The estimated rate constants are predicted to be in the order k(H2) > k(HD) > k(D2) and the calculated cross sections and rate constants compared with available theoretical and experimental data. PMID:21644798
NASA Astrophysics Data System (ADS)
Haji Mohammadi, M.; Kang, S.; Sotiropoulos, F.
2011-12-01
It is well-known that meander bends impose local losses of energy to the flow in rivers. These local losses should be added together with friction loss to get the total loss of energy. In this work, we strive to develop a framework that considers the effect of bends in meandering rivers for one-dimensional (1-D) homogenous equations of flow. Our objective is to develop a simple, yet physically sound, and efficient model for carrying out engineering computations of flow through meander bends. We consider several approaches for calculating 1-D hydraulic properties of meandering rivers such as friction factor and Manning coefficient. The method of Kasper et al. (2005), which is based on channel top width, aspect ratio and radius of curvature, is adopted for further calculations. In this method, a correction is implemented in terms of local energy loss, due to helical motion and secondary currents of fluid particles driven by centrifugal force, in meanders. To validate the model, several test cases are simulated and the computed results are compared with the reported data in the literature in terms of water surface elevation, shear velocity, etc. For all cases the computed results are in reasonable agreement with the experimental data. 3-D RANS turbulent flow simulations are also carried out, using the method of Kang et al. (Adv. In Water Res., vol. 34, 2011), for different geometrical parameters of Kinoshita Rivers to determine the spatial distribution of shear stress on river bed and banks, which is the key factor in scour/deposition patterns. The 3-D solutions are then cross-sectionally averaged and compared with the respective solutions from the 1-D model. The comparisons show that the improved 1D model, which incorporates the effect of local bend loss, captures key flow parameters with reasonable accuracy. Our results also underscore the range of validity and limitations of 1D models for meander bend simulations. This work was supported by NSF Grants (as part of
Immersed boundary method for Boltzmann model kinetic equations
NASA Astrophysics Data System (ADS)
Pekardan, Cem; Chigullapalli, Sruti; Sun, Lin; Alexeenko, Alina
2012-11-01
Three different immersed boundary method formulations are presented for Boltzmann model kinetic equations such as Bhatnagar-Gross-Krook (BGK) and Ellipsoidal statistical Bhatnagar-Gross-Krook (ESBGK) model equations. 1D unsteady IBM solution for a moving piston is compared with the DSMC results and 2D quasi-steady microscale gas damping solutions are verified by a conformal finite volume method solver. Transient analysis for a sinusoidally moving beam is also carried out for the different pressure conditions (1 atm, 0.1 atm and 0.01 atm) corresponding to Kn=0.05,0.5 and 5. Interrelaxation method (Method 2) is shown to provide a faster convergence as compared to the traditional interpolation scheme used in continuum IBM formulations. Unsteady damping in rarefied regime is characterized by a significant phase-lag which is not captured by quasi-steady approximations.
Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark
NASA Astrophysics Data System (ADS)
Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.
2014-12-01
Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.
KINETICS MODEL AND OZONE ISOPLETH PLOTTING PACKAGE
The Kinetics Model and Ozone Isopleth Plotting Package (OZIPP) computer program can be used to simulate ozone formation in urban atmospheres. OZIPP calculates maximum one-hour average ozone concentrations given a set of input assumptions about initial precursor concentrations, li...
Deterministic Modelling of BAK Activation Kinetics
NASA Astrophysics Data System (ADS)
Grills, C.; Chacko, A.; Crawford, N.; Johnston, P. G.; Fennell, D. A.; O'Rourke, S. F. C.
2009-08-01
The molecular mechanism underlying mitochondrial BAK activation during apoptosis remains highly controversial. Two seemingly conflicting models have been proposed. In the activation model, BAK requires so-called activating BH3 only proteins (aBH3) to initiate its conformation change. In the other, displacement from inhibitory pro-survival BCL-2 proteins (PBPs) and monomerization of BAK by PBP restricted dissociator BH3-only proteins (dBH3) is sufficient. To better understand the kinetic implications of these models and reconcile these conflicting but highly evidence-based models, we have employed dynamical systems analysis to explore the kinetics underlying BAK activation as a non-linear reaction system. Our findings accommodate both pure agonism and dissociation as mutually exclusive mechanisms capable of initiating BAK activation. In addition we find our work supports a modelling based approach for predicting resistance to therapeutically relevant small molecules BH3 mimetics.
1D Nonisothermal Fiber Spinning Models for Thermotropic Polymeric Liquid Crystals
NASA Astrophysics Data System (ADS)
Zhou, Hong; Forest, M. Gregory; Wang, Qi
1997-11-01
Previous slender one-dimensional models for axisymmetric filaments of liquid crystalline polymers (LCPs) are extended to include temperature-dependent material behavior and an energy equation. A two-phase model is posited, where below the glass transition temperature the material is modeled as a rigid cooling LCP fiber. We present families of numerical steady boundary-value solutions for thermal spinning flows; effects of temperature-dependent viscosity, LCP relaxation, excluded-volume potential, and viscous heating are modeled and exhibited. The predictions focus on thermal influence on spun fiber performance properties, such as birefringence and axial force, and process stability. A cooling ambient clearly contributes to faster stable spinning speeds.
Chemical Kinetic Modeling of Hydrogen Combustion Limits
Pitz, W J; Westbrook, C K
2008-04-02
A detailed chemical kinetic model is used to explore the flammability and detonability of hydrogen mixtures. In the case of flammability, a detailed chemical kinetic mechanism for hydrogen is coupled to the CHEMKIN Premix code to compute premixed, laminar flame speeds. The detailed chemical kinetic model reproduces flame speeds in the literature over a range of equivalence ratios, pressures and reactant temperatures. A series of calculation were performed to assess the key parameters determining the flammability of hydrogen mixtures. Increased reactant temperature was found to greatly increase the flame speed and the flammability of the mixture. The effect of added diluents was assessed. Addition of water and carbon dioxide were found to reduce the flame speed and thus the flammability of a hydrogen mixture approximately equally well and much more than the addition of nitrogen. The detailed chemical kinetic model was used to explore the detonability of hydrogen mixtures. A Zeldovich-von Neumann-Doring (ZND) detonation model coupled with detailed chemical kinetics was used to model the detonation. The effectiveness on different diluents was assessed in reducing the detonability of a hydrogen mixture. Carbon dioxide was found to be most effective in reducing the detonability followed by water and nitrogen. The chemical action of chemical inhibitors on reducing the flammability of hydrogen mixtures is discussed. Bromine and organophosphorus inhibitors act through catalytic cycles that recombine H and OH radicals in the flame. The reduction in H and OH radicals reduces chain branching in the flame through the H + O{sub 2} = OH + O chain branching reaction. The reduction in chain branching and radical production reduces the flame speed and thus the flammability of the hydrogen mixture.
Kinetics model development of cocoa bean fermentation
NASA Astrophysics Data System (ADS)
Kresnowati, M. T. A. P.; Gunawan, Agus Yodi; Muliyadini, Winny
2015-12-01
Although Indonesia is one of the biggest cocoa beans producers in the world, Indonesian cocoa beans are oftenly of low quality and thereby frequently priced low in the world market. In order to improve the quality, adequate post-harvest cocoa processing techniques are required. Fermentation is the vital stage in series of cocoa beans post harvest processing which could improve the quality of cocoa beans, in particular taste, aroma, and colours. During the fermentation process, combination of microbes grow producing metabolites that serve as the precursors for cocoa beans flavour. Microbial composition and thereby their activities will affect the fermentation performance and influence the properties of cocoa beans. The correlation could be reviewed using a kinetic model that includes unstructured microbial growth, substrate utilization and metabolic product formation. The developed kinetic model could be further used to design cocoa bean fermentation process to meet the expected quality. Further the development of kinetic model of cocoa bean fermentation also serve as a good case study of mixed culture solid state fermentation, that has rarely been studied. This paper presents the development of a kinetic model for solid-state cocoa beans fermentation using an empirical approach. Series of lab scale cocoa bean fermentations, either natural fermentations without starter addition or fermentations with mixed yeast and lactic acid bacteria starter addition, were used for model parameters estimation. The results showed that cocoa beans fermentation can be modelled mathematically and the best model included substrate utilization, microbial growth, metabolites production and its transport. Although the developed model still can not explain the dynamics in microbial population, this model can sufficiently explained the observed changes in sugar concentration as well as metabolic products in the cocoa bean pulp.
Modeling Inhomogeneous DNA Replication Kinetics
Gauthier, Michel G.; Norio, Paolo; Bechhoefer, John
2012-01-01
In eukaryotic organisms, DNA replication is initiated at a series of chromosomal locations called origins, where replication forks are assembled proceeding bidirectionally to replicate the genome. The distribution and firing rate of these origins, in conjunction with the velocity at which forks progress, dictate the program of the replication process. Previous attempts at modeling DNA replication in eukaryotes have focused on cases where the firing rate and the velocity of replication forks are homogeneous, or uniform, across the genome. However, it is now known that there are large variations in origin activity along the genome and variations in fork velocities can also take place. Here, we generalize previous approaches to modeling replication, to allow for arbitrary spatial variation of initiation rates and fork velocities. We derive rate equations for left- and right-moving forks and for replication probability over time that can be solved numerically to obtain the mean-field replication program. This method accurately reproduces the results of DNA replication simulation. We also successfully adapted our approach to the inverse problem of fitting measurements of DNA replication performed on single DNA molecules. Since such measurements are performed on specified portion of the genome, the examined DNA molecules may be replicated by forks that originate either within the studied molecule or outside of it. This problem was solved by using an effective flux of incoming replication forks at the model boundaries to represent the origin activity outside the studied region. Using this approach, we show that reliable inferences can be made about the replication of specific portions of the genome even if the amount of data that can be obtained from single-molecule experiments is generally limited. PMID:22412853
Computational model for Halorhodopsin photocurrent kinetics
NASA Astrophysics Data System (ADS)
Bravo, Jaime; Stefanescu, Roxana; Talathi, Sachin
2013-03-01
Optogenetics is a rapidly developing novel optical stimulation technique that employs light activated ion channels to excite (using channelrhodopsin (ChR)) or suppress (using halorhodopsin (HR)) impulse activity in neurons with high temporal and spatial resolution. This technique holds enormous potential to externally control activity states in neuronal networks. The channel kinetics of ChR and HR are well understood and amenable for mathematical modeling. Significant progress has been made in recent years to develop models for ChR channel kinetics. To date however, there is no model to mimic photocurrents produced by HR. Here, we report the first model developed for HR photocurrents based on a four-state model of the HR photocurrent kinetics. The model provides an excellent fit (root-mean-square error of 3.1862x10-4, to an empirical profile of experimentally measured HR photocurrents. In combination, mathematical models for ChR and HR photocurrents can provide effective means to design test light based control systems to regulate neural activity, which in turn may have implications for the development of novel light based stimulation paradigms for brain disease control. I would like to thank the University of Florida and the Physics Research Experience for Undergraduates (REU) program, funded through NSF DMR-1156737. This research was also supported through start-up funds provided to Dr. Sachin Talathi
NASA Astrophysics Data System (ADS)
Pekşen, Ertan; Yas, Türker; Kıyak, Alper
2014-09-01
We examine the one-dimensional direct current method in anisotropic earth formation. We derive an analytic expression of a simple, two-layered anisotropic earth model. Further, we also consider a horizontally layered anisotropic earth response with respect to the digital filter method, which yields a quasi-analytic solution over anisotropic media. These analytic and quasi-analytic solutions are useful tests for numerical codes. A two-dimensional finite difference earth model in anisotropic media is presented in order to generate a synthetic data set for a simple one-dimensional earth. Further, we propose a particle swarm optimization method for estimating the model parameters of a layered anisotropic earth model such as horizontal and vertical resistivities, and thickness. The particle swarm optimization is a naturally inspired meta-heuristic algorithm. The proposed method finds model parameters quite successfully based on synthetic and field data. However, adding 5 % Gaussian noise to the synthetic data increases the ambiguity of the value of the model parameters. For this reason, the results should be controlled by a number of statistical tests. In this study, we use probability density function within 95 % confidence interval, parameter variation of each iteration and frequency distribution of the model parameters to reduce the ambiguity. The result is promising and the proposed method can be used for evaluating one-dimensional direct current data in anisotropic media.
NASA Astrophysics Data System (ADS)
Hooshyar, M.; Hagen, S. C.; Wang, D.
2014-12-01
Hydrodynamic models are widely applied to coastal areas in order to predict water levels and flood inundation and typically involve solving a form of the Shallow Water Equations (SWE). The SWE are routinely discretized by applying numerical methods, such as the finite element method. Like other numerical models, hydrodynamic models include uncertainty. Uncertainties are generated due to errors in the discrete approximation of coastal geometry, bathymetry, bottom friction and forcing functions such as tides and wind fields. Methods to counteract these uncertainties should always begin with improvements to physical characterization of: the geometric description through increased resolution, parameters that describe land cover variations in the natural and urban environment, parameters that enhance transfer of surface forcings to the water surface, open boundary forcings, and the wetting/drying brought upon by flood and ebb cycles. When the best possible physical representation is achieved, we are left with calibration and data assimilation to reduce model uncertainty. Data assimilation has been applied to coastal hydrodynamic models to better estimate system states and/or system parameters by incorporating observed data into the model. Kalman Filter is one of the most studied data assimilation methods that minimizes the mean square errors between model state estimations and the observed data in linear systems (Kalman , 1960). For nonlinear systems, as with hydrodynamic models, a variation of Kalman filter called Ensemble Kalman Filter (EnKF), is applied to update the system state according to error statistics in the context of Monte Carlo simulations (Evensen , 2003) & (Hitoshi et. al, 2014). In this research, Kalman Filter is incorporated to simultaneously estimate an influential parameter used in the shallow water equations, bottom roughness, and to adjust the physical feature of bathymetry. Starting from an initial estimate of bottom roughness and bathymetry, and
NASA Astrophysics Data System (ADS)
Ingeman-Nielsen, Thomas; Baumgartner, François
2006-11-01
We have constructed a forward modelling code in Matlab, capable of handling several commonly used electrical and electromagnetic methods in a 1D environment. We review the implemented electromagnetic field equations for grounded wires, frequency and transient soundings and present new solutions in the case of a non-magnetic first layer. The CR1Dmod code evaluates the Hankel transforms occurring in the field equations using either the Fast Hankel Transform based on digital filter theory, or a numerical integration scheme applied between the zeros of the Bessel function. A graphical user interface allows easy construction of 1D models and control of the parameters. Modelling results are in agreement with other authors, but the time of computation is less efficient than other available codes. Nevertheless, the CR1Dmod routine handles complex resistivities and offers solutions based on the full EM-equations as well as the quasi-static approximation. Thus, modelling of effects based on changes in the magnetic permeability and the permittivity is also possible.
Assessing the impact of different sources of topographic data on 1-D hydraulic modelling of floods
NASA Astrophysics Data System (ADS)
Ali, A. Md; Solomatine, D. P.; Di Baldassarre, G.
2014-07-01
Topographic data, such as digital elevation models (DEMs), are essential input in flood inundation modelling. DEMs can be derived from several sources either through remote sensing techniques (space-borne or air-borne imagery) or from traditional methods (ground survey). The Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), the Shuttle Radar Topography Mission (SRTM), the Light Detection and Ranging (LiDAR), and topographic contour maps are some of the most commonly used sources of data for DEMs. These DEMs are characterized by different precision and accuracy. On the one hand, the spatial resolution of low-cost DEMs from satellite imagery, such as ASTER and SRTM, is rather coarse (around 30-90 m). On the other hand, LiDAR technique is able to produce a high resolution DEMs (around 1m), but at a much higher cost. Lastly, contour mapping based on ground survey is time consuming, particularly for higher scales, and may not be possible for some remote areas. The use of these different sources of DEM obviously affects the results of flood inundation models. This paper shows and compares a number of hydraulic models developed using HEC-RAS as model code and the aforementioned sources of DEM as geometric input. The study was carried out on a reach of the Johor River, in Malaysia. The effect of the different sources of DEMs (and different resolutions) was investigated by considering the performance of the hydraulic models in simulating flood water levels as well as inundation maps. The outcomes of our study show that the use of different DEMs has serious implications to the results of hydraulic models. The outcomes also indicates the loss of model accuracy due to re-sampling the highest resolution DEM (i.e. LiDAR 1 m) to lower resolution are much less compared to the loss of model accuracy due to the use of low-cost DEM that have not only a lower resolution, but also a lower quality. Lastly, to better explore the sensitivity of the hydraulic models
Space-based Observational Constraints for 1-D Plume Rise Models
NASA Technical Reports Server (NTRS)
Martin, Maria Val; Kahn, Ralph A.; Logan, Jennifer A.; Paguam, Ronan; Wooster, Martin; Ichoku, Charles
2012-01-01
We use a space-based plume height climatology derived from observations made by the Multi-angle Imaging SpectroRadiometer (MISR) instrument aboard the NASA Terra satellite to evaluate the ability of a plume-rise model currently embedded in several atmospheric chemical transport models (CTMs) to produce accurate smoke injection heights. We initialize the plume-rise model with assimilated meteorological fields from the NASA Goddard Earth Observing System and estimated fuel moisture content at the location and time of the MISR measurements. Fire properties that drive the plume-rise model are difficult to estimate and we test the model with four estimates for active fire area and four for total heat flux, obtained using empirical data and Moderate Resolution Imaging Spectroradiometer (MODIS) re radiative power (FRP) thermal anomalies available for each MISR plume. We show that the model is not able to reproduce the plume heights observed by MISR over the range of conditions studied (maximum r2 obtained in all configurations is 0.3). The model also fails to determine which plumes are in the free troposphere (according to MISR), key information needed for atmospheric models to simulate properly smoke dispersion. We conclude that embedding a plume-rise model using currently available re constraints in large-scale atmospheric studies remains a difficult proposition. However, we demonstrate the degree to which the fire dynamical heat flux (related to active fire area and sensible heat flux), and atmospheric stability structure influence plume rise, although other factors less well constrained (e.g., entrainment) may also be significant. Using atmospheric stability conditions, MODIS FRP, and MISR plume heights, we offer some constraints on the main physical factors that drive smoke plume rise. We find that smoke plumes reaching high altitudes are characterized by higher FRP and weaker atmospheric stability conditions than those at low altitude, which tend to remain confined
NASA Astrophysics Data System (ADS)
Kim, Seongryong; Rhie, Junkee; Kim, Geunyoung
2011-04-01
We propose a full-grid search procedure for broad-band waveform modelling to determine a 1-D crustal velocity model. The velocity model can be more constrained because of the use of broad-band waveforms instead of traveltimes for the crustal phases, although only a small number of event-station pairs were employed. Despite the time-consuming nature of the full-grid search method to search the whole model parameter space, the use of an empirical relationship between the P- and S-wave velocities can significantly reduce computation time. The proposed method was applied to a case in the southern Korean Peninsula. Broad-band waveforms obtained from two inland earthquakes that occurred on 2007 January 20 (Mw 4.6) and 2004 April 26 (Mw 3.6) were used to test the method. The three-layers over half-space crustal velocity model of the P- and S-wave velocities was estimated. Comparisons of waveform fitness between the final model and previously published models demonstrate advancements in the average value of waveform fitness for the inland earthquakes. In addition, 1-D velocity models were determined for three distinct tectonic regions, namely, the Gyonggi Massif, the Okcheon Belt and the Gyeongsang Basin, which are all located inside the study area. A comparison between the three models demonstrates that the crustal thickness of the southern Korean Peninsula increases from NW to SE and that the lower crustal composition of the Okcheon belt differs from that of the other tectonic regions.
Data Assimilation Using a Variational Method for a 1D Radiation Belt Diffusion Model
NASA Astrophysics Data System (ADS)
Marchand, R.; Degeling, A. W.; O'Donnell, S.; Rankin, R.; Kabin, K.
2009-12-01
A variational data assimilation algorithm has been developed to incorporate electron flux time-series data from satellites into a simple one dimensional diffusion model for the radial transport of radiation belt electrons. The model developed assumes a power law scaling for the radial diffusion coefficient with L shell. The effectiveness of this method is investigated by means of a series of identical twin numerical experiments. This involves using the diffusion model to produce synthetic observations along various satellite trajectories. These observations are in turn used to estimate time-dependent parameters input to the diffusion model, which are compared against the values initially used. The data assimilation algorithm considers the time dependent source located at the outer boundary as a function to be determined. Using synthetic satellite electron flux observations, the algorithm computes a source function that, when used as an input to the diffusion model, most closely reproduces the synthetic observations in a least-squares sense. Observational errors are taken into account, and an estimate of the uncertainty in the output source function is also produced. This uncertainty is found to consistently reflect the quality of the source function estimation during identical twin numerical experiments. Initial tests indicate that the quality of the outer boundary source estimation is strongly dependent on the satellite location, indicating that the outer boundary source estimation becomes poor as information relating to the outer boundary contained in the observations is reduced. The potential of using this data assimilation method to estimate one or more parameters that determine the radial diffusion coefficient, and the possibility of determining whether physical processes affecting the observations are missing in the dynamical model will be discussed.
PROM4: 1D isothermal and isobaric modeler for solar prominences
NASA Astrophysics Data System (ADS)
Gouttebroze, P.; Labrosse, N.
2013-06-01
PROM4 computes simple models of solar prominences which consist of plane-parallel slabs standing vertically above the solar surface. Each model is defined by 5 parameters: temperature, density, geometrical thickness, microturbulent velocity and height above the solar surface. PROM4 solves the equations of radiative transfer, statistical equilibrium, ionization and pressure equilibria, and computes electron and hydrogen level populations and hydrogen line profiles. Written in Fortran 90 and with two versions available (one with text in English, one with text in French), the code needs 64-bit arithmetic for real numbers.
Urea kinetic modeling: comparing the options.
Hoenich, N A; Keir, M J; Hildreth, K; Woffindin, C; Goodall, R; Vanholder, R; Ward, M K
1993-09-01
In this study 6 commercially produced kinetic modeling packages utilizing a variable volume, single pool urea model, as well as formulae to determine the delivery of therapy, have been compared by applying to each the same set of rigorously collected data for a group of 12 patients. Comparison of the kinetically derived parameters (urea generation rate [G], urea distribution volume [V], delivery of therapy [Kt/V], and normalized protein catabolic rate [nPCR]) showed that the values obtained for both G and V differed between packages owing to the numerical methods and the clearance used in the solution of the differential equations. Although a broad agreement between the values established for Kt/V and nPCR was noted, the 95% limits of agreement indicated that it would be prudent to exercise caution when comparing results established by different modeling packages. PMID:8240076
Strong decays of excited 1D charmed(-strange) mesons in the covariant oscillator quark model
NASA Astrophysics Data System (ADS)
Maeda, Tomohito; Yoshida, Kento; Yamada, Kenji; Ishida, Shin; Oda, Masuho
2016-05-01
Recently observed charmed mesons, D1* (2760), D3* (2760) and charmed-strange mesons, Ds1 * (2860), Ds3 * (2860), by BaBar and LHCb collaborations are considered to be plausible candidates for c q ¯ 13 DJ (q = u, d, s) states. We calculate the strong decays with one pion (kaon) emission of these states including well-established 1S and 1P charmed(-strange) mesons within the framework of the covariant oscillator quark model. The results obtained are compared with the experimental data and the typical nonrelativistic quark-model calculations. Concerning the results for 1S and 1P states, we find that, thanks to the relativistic effects of decay form factors, our model parameters take reasonable values, though our relativistic approach and the nonrelativistic quark model give similar decay widths in agreement with experiment. While the results obtained for 13 DJ=1,3 states are roughly consistent with the present data, they should be checked by the future precise measurement.
Stochastic Heat Equation Limit of a (2 + 1)d Growth Model
NASA Astrophysics Data System (ADS)
Borodin, Alexei; Corwin, Ivan; Toninelli, Fabio Lucio
2016-07-01
We determine a {q to 1} limit of the two-dimensional q-Whittaker driven particle system on the torus studied previously in Corwin and Toninelli (Electron. Commun. Probab. 21(44):1-12, 2016). This has an interpretation as a (2 + 1)-dimensional stochastic interface growth model, which is believed to belong to the so-called anisotropic Kardar-Parisi-Zhang (KPZ) class. This limit falls into a general class of two-dimensional systems of driven linear SDEs which have stationary measures on gradients. Taking the number of particles to infinity we demonstrate Gaussian free field type fluctuations for the stationary measure. Considering the temporal evolution of the stationary measure, we determine that along characteristics, correlations are asymptotically given by those of the (2 + 1)-dimensional additive stochastic heat equation. This confirms (for this model) the prediction that the non-linearity for the anisotropic KPZ equation in (2 + 1)-dimension is irrelevant.
Prediction of the expansion velocity of ultracold 1D quantum gases for integrable models
NASA Astrophysics Data System (ADS)
Mei, Zhongtao; Vidmar, Lev; Heidrich-Meisner, Fabian; Bolech, Carlos
In the theory of Bethe-ansatz integrable quantum systems, rapidities play an important role as they are used to specify many-body states. The physical interpretation of rapidities going back to Sutherland is that they are the asymptotic momenta after letting a quantum gas expand into a larger volume rendering it dilute and noninteracting. We exploit this picture to calculate the expansion velocity of a one-dimensional Fermi-Hubbard model by using the distribution of rapidities defined by the initial state. Our results are consistent with the ones from time-dependent density-matrix renormalization. We show in addition that an approximate Bethe-ansatz solution works well also for the Bose-Hubbard model. Our results are of interests for future sudden-expansion experiments with ultracold quantum gases.
A 1-D Model of the 4 Bed Molecular Sieve of the Carbon Dioxide Removal Assembly
NASA Technical Reports Server (NTRS)
Coker, Robert; Knox, Jim
2015-01-01
Developments to improve system efficiency and reliability for water and carbon dioxide separation systems on crewed vehicles combine sub-scale systems testing and multi-physics simulations. This paper describes the development of COMSOL simulations in support of the Life Support Systems (LSS) project within NASA's Advanced Exploration Systems (AES) program. Specifically, we model the 4 Bed Molecular Sieve (4BMS) of the Carbon Dioxide Removal Assembly (CDRA) operating on the International Space Station (ISS).
A Simplified 1-D Model for Calculating CO2 Leakage through Conduits
Zhang, Y.; Oldenburg, C.M.
2011-02-15
In geological CO{sub 2} storage projects, a cap rock is generally needed to prevent CO{sub 2} from leaking out of the storage formation. However, the injected CO{sub 2} may still encounter some discrete flow paths such as a conductive well or fault (here referred to as conduits) through the cap rock allowing escape of CO{sub 2} from the storage formation. As CO{sub 2} migrates upward, it may migrate into the surrounding formations. The amount of mass that is lost to the formation is called attenuation. This report describes a simplified model to calculate the CO{sub 2} mass flux at different locations of the conduit and the amount of attenuation to the surrounding formations. From the comparison among the three model results, we can conclude that the steady-state conduit model (SSCM) provides a more accurate solution than the PMC at a given discretization. When there is not a large difference between the permeability of the surrounding formation and the permeability of the conduits, and there is leak-off at the bottom formation (the formation immediately above the CO{sub 2} plume), a fine discretization is needed for an accurate solution. Based on this comparison, we propose to use the SSCM in the rapid prototype for now given it does not produce spurious oscillations, and is already in FORTRAN and therefore can be easily made into a dll for use in GoldSim.
NASA Astrophysics Data System (ADS)
Lauer, Wesley; Viparelli, Enrica; Piegay, Herve
2014-05-01
Sedimentary deposits adjacent to rivers can represent important sources and sinks for bed material sediment, particularly on decadal and longer timescales. The Morphodynamics and Sediment Tracers in 1-D model (MAST-1D) is a size-specific sediment transport model that allows for active exchange between channel and floodplain sediment on river reaches of tens to hundreds of kilometers in length. The model is intended to provide a mechanism for performing a first-order assessment of the likely importance of off-channel sediment exchange in controlling decadal-scale geomorphic trends, thereby helping plan and/or prioritize field data collection and higher resolution modeling work. The model develops a sediment budget for short segments of an alluvial valley. Each segment encompasses several active river bends. In each segment, a sediment transport capacity computation is performed to determine the downstream flux of bed material sediment, following the approach of most other 1-D sediment transport models. However, the model differs from most other bed evolution models in that sediment can be exchanged with the floodplain in each segment, and mass conservation is applied to both the active layer and floodplain sediment storage reservoirs. The potential for net imbalances in overall exchange as well as the size specific nature of the computations allows the model to simulate reach-scale aggradation/degradation and/or changes in bed texture. The inclusion of fine sediment in the model allows it to track geochemical tracer material and also provides a mechanism to simulate, to first order, the effects of changes in the supply of silt and clay on overall channel hydraulic capacity. The model is applied to a ~40 km reach of the Ain River, a tributary of the Rhône River in eastern France that has experienced a significant sediment deficit as a result of the construction of several dams between 1920 and 1970. MAST-1D simulations result in both incision and the formation of a
Constraining the temporal evolution of a deep hypersaline anoxic basin by 1D geochemical modelling
NASA Astrophysics Data System (ADS)
Goldhammer, Tobias; Aiello, Ivano; Zabel, Matthias
2014-05-01
Deep hypersaline anoxic basins (DHABs) are seafloor features of the accretionary prism of the Mediterranean Ridge. They have formed by the dissolution of exhumed shallow Messinian evaporites and subsequent concentration of the ultra-saline solutions in depressions on the seafloor. As an example, the horseshoe-shaped Urania basin is a DHAB south of the Peloponnese peninsula contains one of the most saline (about six times higher than Mediterranean seawater) and sulfidic (up to 15mM) water bodies of the Earth. Furthermore, its deepest part is underlain by a mud volcano that is responsible for the injection of fluid mud beneath the brine lake, with exceptionally sharp chemoclines between water column, brine, and mud layer. We here present a model approach to reconstruct the temporal aspects of the formation, dynamics and persistence of the brine-mud-system in the deep pit of the Urania Basin. Based on data from a sampling campaign with RV Meteor (Cruise M84/1 in February 2011), we set up a one-dimensional geochemical model that integrates diffusion, reaction and advective transport and mixing. Using a set of model preconditions, we aimed to answer (1) which processes are required to maintain the current situation of steep chemical gradients of the brine-mud-system, (2) how fast the current situation could have developed under different scenarios, and (3) how long such extraordinary conditions could have persisted through Earth's history. We further discuss the consequences of the temporal framework for the evolution of prokaryotic life in this extreme habitat.
Dynamical correlation functions of the 1D Bose gas (Lieb Liniger model)
NASA Astrophysics Data System (ADS)
Caux, Jean-Sebastien; Calabrese, Pasquale
2007-03-01
The momentum- and frequency-dependent correlation functions (one-body and density-density) of the one-dimensional interacting Bose gas (Lieb-Liniger model) are obtained for any value (repulsive or attractive) of the interaction parameter. In the repulsive regime, we use the Algebraic Bethe Ansatz and the ABACUS method to reconstruct the correlators to high accuracy for systems with finite but large numbers of particles. For attractive interactions, the correlations are computed analytically. Our results are discussed, with particular emphasis on their applications to quasi-one-dimensional atomic gases.
State to State and Charged Particle Kinetic Modeling of Time Filtering and Cs Addition
Capitelli, M.; Gorse, C.; Longo, S.; Diomede, P.; Pagano, D.
2007-08-10
We present here an account on the progress of kinetic simulation of non equilibrium plasmas in conditions of interest for negative ion production by using the 1D Bari code for hydrogen plasma simulation. The model includes the state to state kinetics of the vibrational level population of hydrogen molecules, plus a PIC/MCC module for the multispecies dynamics of charged particles. In particular we present new results for the modeling of two issues of great interest: the time filtering and the Cs addition via surface coverage.
Zeng, Y; Albertus, P; Klein, R; Chaturvedi, N; Kojic, A; Bazant, MZ; Christensen, J
2013-06-07
Mathematical models of batteries which make use of the intercalation of a species into a solid phase need to solve the corresponding mass transfer problem. Because solving this equation can significantly add to the computational cost of a model, various methods have been devised to reduce the computational time. In this paper we focus on a comparison of the formulation, accuracy, and order of the accuracy for two numerical methods of solving the spherical diffusion problem with a constant or non-constant diffusion coefficient: the finite volume method and the control volume method. Both methods provide perfect mass conservation and second order accuracy in mesh spacing, but the control volume method provides the surface concentration directly, has a higher accuracy for a given numbers of mesh points and can also be easily extended to variable mesh spacing. Variable mesh spacing can significantly reduce the number of points that are required to achieve a given degree of accuracy in the surface concentration (which is typically coupled to the other battery equations) by locating more points where the concentration gradients are highest. (C) 2013 The Electrochemical Society. All rights reserved.
NASA Astrophysics Data System (ADS)
Jahromi, Amir E.; Miller, Franklin K.
2016-03-01
A sub Kelvin Active Magnetic Regenerative Refrigerator (AMRR) is being developed at the University of Wisconsin - Madison. This AMRR consists of two circulators, two regenerators, one superleak, one cold heat exchanger, and two warm heat exchangers. The circulators are novel non-moving part pumps that reciprocate a superfluid mixture of 4He-3He in the system. Heat from the mixture is removed within the two regenerators of this tandem system. An accurate model of the regenerators in this AMRR is necessary in order to predict the performance of these components, which in turn helps predicting the overall performance of the AMRR system. This work presents modeling methodology along with results from a 1-D transient numerical model of the regenerators of an AMRR capable of removing 2.5 mW at 850 mK at cyclic steady state.
Pool Formation in Boulder-Bed Streams: Implications From 1-D and 2-D Numerical Modeling
NASA Astrophysics Data System (ADS)
Harrison, L. R.; Keller, E. A.
2003-12-01
In mountain rivers of Southern California, boulder-large roughness elements strongly influence flow hydraulics and pool formation and maintenance. In these systems, boulders appear to control the stream morphology by converging flow and producing deep pools during channel forming discharges. Our research goal is to develop quantitative relationships between boulder roughness elements, temporal patterns of scour and fill, and geomorphic processes that are important in producing pool habitat. The longitudinal distribution of shear stress, unit stream power and velocity were estimated along a 48 m reach on Rattlesnake Creek, using the HEC-RAS v 3.0 and River 2-D numerical models. The reach has an average slope of 0.02 and consists of a pool-riffle sequence with a large boulder constriction directly above the pool. Model runs were performed for a range of stream discharges to test if scour and fill thresholds for pool and riffle environments could be identified. Results from the HEC-RAS simulations identified that thresholds in shear stress, unit stream power and mean velocity occur above a discharge of 5.0 cms. Results from the one-dimensional analysis suggest that the reversal in competency is likely due to changes in cross-sectional width at varying flows. River 2-D predictions indicated that strong transverse velocity gradients were present through the pool at higher modeled discharges. At a flow of 0.5 cms (roughly 1/10th bankfull discharge), velocities are estimated at 0.6 m/s and 1.3 m/s for the pool and riffle, respectively. During discharges of 5.15 cms (approximate bankfull discharge), the maximum velocity in the pool center increased to nearly 3.0 m/s, while the maximum velocity over the riffle is estimated at approximately 2.5 cms. These results are consistent with those predicted by HEC-RAS, though the reversal appears to be limited to a narrow jet that occurs through the pool head and pool center. Model predictions suggest that the velocity reversal is
Hyperbolic reformulation of a 1D viscoelastic blood flow model and ADER finite volume schemes
Montecinos, Gino I.; Müller, Lucas O.; Toro, Eleuterio F.
2014-06-01
The applicability of ADER finite volume methods to solve hyperbolic balance laws with stiff source terms in the context of well-balanced and non-conservative schemes is extended to solve a one-dimensional blood flow model for viscoelastic vessels, reformulated as a hyperbolic system, via a relaxation time. A criterion for selecting relaxation times is found and an empirical convergence rate assessment is carried out to support this result. The proposed methodology is validated by applying it to a network of viscoelastic vessels for which experimental and numerical results are available. The agreement between the results obtained in the present paper and those available in the literature is satisfactory. Key features of the present formulation and numerical methodologies, such as accuracy, efficiency and robustness, are fully discussed in the paper.
Existence of a metallic phase in a 1D Holstein Hubbard model at half filling
NASA Astrophysics Data System (ADS)
Krishna, Phani Murali; Chatterjee, Ashok
2007-06-01
The one-dimensional half-filled Holstein-Hubbard model is studied using a series of canonical transformations including phonon coherence effect that partly depends on the electron density and is partly independent and also incorporating the on-site and the nearest-neighbour phonon correlations and the exact Bethe-ansatz solution of Lieb and Wu. It is shown that choosing a better variational phonon state makes the polarons more mobile and widens the intermediate metallic region at the charge-density-wave-spin-density-wave crossover recently predicted by Takada and Chatterjee. The presence of this metallic phase is indeed a favourable situation from the point of view of high temperature superconductivity.
Development of a 3D to 1D Particle Transport Model to Predict Deposition in the Lungs
NASA Astrophysics Data System (ADS)
Oakes, Jessica M.; Grandmont, Celine; Shadden, Shawn C.; Vignon-Clementel, Irene E.
2014-11-01
Aerosolized particles are commonly used for therapeutic drug delivery as they can be delivered to the body systemically or be used to treat lung diseases. Recent advances in computational resources have allowed for sophisticated pulmonary simulations, however it is currently impossible to solve for airflow and particle transport for all length and time scales of the lung. Instead, multi-scale methods must be used. In our recent work, where computational methods were employed to solve for airflow and particle transport in the rat airways (Oakes et al. (2014), Annals of Biomedical Engineering 42, 899), the number of particles to exit downstream of the 3D domain was determined. In this current work, the time-dependent Lagrangian description of particles was used to numerically solve a 1D convection-diffusion model (trumpet model, Taulbee and Yu (1975), Journal of Applied Physiology, 38, 77) parameterized specifically for the lung. The expansion of the airway dimensions was determined based on data collected from our aerosol exposure experiments (Oakes et al. (2014), Journal of Applied Physiology, 116, 1561). This 3D-1D framework enables us to predict the fate of particles in the whole lung. This work was supported by the Whitaker Foundation at the IIE, a INRIA Associated Team Postdoc Grant, and a UC Presidential Fellowship.
Exact solution of the 1D Hubbard model with NN and NNN interactions in the narrow-band limit
NASA Astrophysics Data System (ADS)
Mancini, Ferdinando; Plekhanov, Evgeny; Sica, Gerardo
2013-10-01
We present the exact solution, obtained by means of the Transfer Matrix (TM) method, of the 1D Hubbard model with nearest-neighbor (NN) and next-nearest-neighbor (NNN) Coulomb interactions in the atomic limit ( t = 0). The competition among the interactions ( U, V 1, and V 2) generates a plethora of T = 0 phases in the whole range of fillings. U, V 1, and V 2 are the intensities of the local, NN and NNN interactions, respectively. We report the T = 0 phase diagram, in which the phases are classified according to the behavior of the principal correlation functions, and reconstruct a representative electronic configuration for each phase. In order to do that, we make an analytic limit T → 0 in the transfer matrix, which allows us to obtain analytic expressions for the ground state energies even for extended transfer matrices. Such an extension of the standard TM technique can be easily applied to a wide class of 1D models with the interaction range beyond NN distance, allowing for a complete determination of the T = 0 phase diagrams.
NASA Astrophysics Data System (ADS)
Hayden-Lesmeister, A.; Remo, J. W.; Piazza, B.
2015-12-01
The Atchafalaya River (AR) in Louisiana is the principal distributary of the Mississippi River (MR), and its basin contains the largest contiguous area of baldcypress-water tupelo swamp forests in North America. After designation of the Atchafalaya River Basin (ARB) as a federal floodway following the destructive 1927 MR flood, it was extensively modified to accommodate a substantial portion of the MR flow (~25%) to mitigate flooding in southern Louisiana. These modifications and increased flows resulted in substantial incision along large portions of the AR, altering connectivity between the river and its associated waterbodies. As a result of incision, the hydroperiod has been substantially altered, which has contributed to a decline in ecological health of the ARB's baldcypress-water tupelo forests. While it is recognized that the altered hydroperiod has negatively affected natural baldcypress regeneration, it is unclear whether proposed projects designed to enhance flow connectivity will increase long-term survival of these forests. In this study, we have constructed a 1D2D hydrodynamic model using SOBEK 2.12 to realistically model key physical parameters such as residence times, inundation extent, water-surface elevations (WSELs), and flow velocities to increase our understanding of the ARB's altered hydroperiod and the consequences for baldcypress-water tupelo forests. While the model encompasses a majority of the ARB, our modeling effort is focused on the Flat Lake Water Management Unit located in the southern portion of the ARB, where it will also be used to evaluate flow connectivity enhancement projects within the management unit. We believe our 1D2D hybrid hydraulic modeling approach will provide the flexibility and accuracy needed to guide connectivity enhancement efforts in the ARB and may provide a model framework for guiding similar efforts along other highly-altered river systems.
Chemical kinetics models for semiconductor processing
Coltrin, M.E.; Creighton, J.R.; Meeks, E.; Grcar, J.F.; Houf, W.G.; Kee, R.J.
1997-12-31
Chemical reactions in the gas-phase and on surfaces are important in the deposition and etching of materials for microelectronic applications. A general software framework for describing homogeneous and heterogeneous reaction kinetics utilizing the Chemkin suite of codes is presented. Experimental, theoretical and modeling approaches to developing chemical reaction mechanisms are discussed. A number of TCAD application modules for simulating the chemically reacting flow in deposition and etching reactors have been developed and are also described.
Vlasov dynamics of 1D models with long-range interactions
NASA Astrophysics Data System (ADS)
Druken, Kelsey A.
Subduction zones, mid-ocean spreading centers and mantle plumes are three of the largest sources for volcanism on Earth. With subduction as the driving tectonic force, these systems are responsible for the evolution of both the crust and mantle and as a result are important processes in our understanding of the solid Earth. Mantle plume processes, however, are still strongly debated within the community, particularly when occurring near subduction zones. Using both laboratory (i.e. analog) and numerical modeling techniques, we examine the dynamic interaction between subduction-driven and plume-driven flow. Results highlight the weak nature of buoyant plumes in comparison to the dominant slab-induced circulation. As a consequence of the subduction-induced flow, surface expressions differ significantly from traditional plume expectations. Variations in slab sinking style and plume position lead to a range in plume head and conduit melting signatures, as well as migrating hotspots. Motivated by the debated origin of recent (< 20 Ma) volcanism in the Northwest U.S., we also report results of the evolution of finite strain within rollback-induced as well as plume-driven flow fields. If the patterns differ between background subduction and plume structures, seismic anisotropy observations could help distinguish the plume and non plume models that are suggested for the region. We find rollback-induced horizontal shear causes predominantly trench-normal strain alignment in the backarc mantle wedge in contrast to longitudinal subduction which, despite the simple flow field, results in complex and variable orientations from the lack of strong horizontal shear. Splitting observations from the High Lava Plains region with the Northwest U.S. are in good agreement with the trench-normal laboratory predictions of strain alignment. Alignment within plume heads are found to exhibit striking tangential patterns that are perpendicular to the plume-driven flow. While we show that
A 1D pulse wave propagation model of the hemodynamics of calf muscle pump function.
Keijsers, J M T; Leguy, C A D; Huberts, W; Narracott, A J; Rittweger, J; van de Vosse, F N
2015-07-01
The calf muscle pump is a mechanism which increases venous return and thereby compensates for the fluid shift towards the lower body during standing. During a muscle contraction, the embedded deep veins collapse and venous return increases. In the subsequent relaxation phase, muscle perfusion increases due to increased perfusion pressure, as the proximal venous valves temporarily reduce the distal venous pressure (shielding). The superficial and deep veins are connected via perforators, which contain valves allowing flow in the superficial-to-deep direction. The aim of this study is to investigate and quantify the physiological mechanisms of the calf muscle pump, including the effect of venous valves, hydrostatic pressure, and the superficial venous system. Using a one-dimensional pulse wave propagation model, a muscle contraction is simulated by increasing the extravascular pressure in the deep venous segments. The hemodynamics are studied in three different configurations: a single artery-vein configuration with and without valves and a more detailed configuration including a superficial vein. Proximal venous valves increase effective venous return by 53% by preventing reflux. Furthermore, the proximal valves shielding function increases perfusion following contraction. Finally, the superficial system aids in maintaining the perfusion during the contraction phase and reduces the refilling time by 37%. PMID:25766693
Phase transitions at strong coupling in the 2+1-d abelian Higgs model
NASA Astrophysics Data System (ADS)
MacKenzie, R. B.; Nebia-Rahal, Faïza; Paranjape, M. B.
2013-12-01
We study, using numerical Monte-Carlo simulations, an effective description of the 2+1 dimensional Abelian Higgs model which is valid at strong coupling, in the broken symmetry sector. In this limit, the massive gauge boson and the massive neutral Higgs decouple leaving only the massive vortices. The vortices have no long range interactions. We find a phase transition as the mass of the vortices is made lighter and lighter. At the transition, the contributions to the functional integral come from a so-called infinite vortex anti-vortex loop. Adding the Chern-Simons term simply counts the linking number between the vortices. We find that the Wilson loop exhibits perimeter law behaviour in both phases, although the polarization cloud increases by an order of magnitude at the transition. We also study the 't Hooft loop. We find the 't Hooft loop exhibits perimeter law behaviour in the presence of the Chern-Simons term but is trivial in its absence. Thus we have a theory with perimeter law for both the Wilson loop and the 't Hooft loop, but contains no massless particles.
A 1D pulse wave propagation model of the hemodynamics of calf muscle pump function
Keijsers, J M T; Leguy, C A D; Huberts, W; Narracott, A J; Rittweger, J; van de Vosse, F N
2015-01-01
The calf muscle pump is a mechanism which increases venous return and thereby compensates for the fluid shift towards the lower body during standing. During a muscle contraction, the embedded deep veins collapse and venous return increases. In the subsequent relaxation phase, muscle perfusion increases due to increased perfusion pressure, as the proximal venous valves temporarily reduce the distal venous pressure (shielding). The superficial and deep veins are connected via perforators, which contain valves allowing flow in the superficial-to-deep direction. The aim of this study is to investigate and quantify the physiological mechanisms of the calf muscle pump, including the effect of venous valves, hydrostatic pressure, and the superficial venous system. Using a one-dimensional pulse wave propagation model, a muscle contraction is simulated by increasing the extravascular pressure in the deep venous segments. The hemodynamics are studied in three different configurations: a single artery–vein configuration with and without valves and a more detailed configuration including a superficial vein. Proximal venous valves increase effective venous return by 53% by preventing reflux. Furthermore, the proximal valves shielding function increases perfusion following contraction. Finally, the superficial system aids in maintaining the perfusion during the contraction phase and reduces the refilling time by 37%. © 2015 The Authors. International Journal for Numerical Methods in Biomedical Engineering published by John Wiley & Sons Ltd. PMID:25766693
A kinetic model for chemical neurotransmission
NASA Astrophysics Data System (ADS)
Ramirez-Santiago, Guillermo; Martinez-Valencia, Alejandro; Fernandez de Miguel, Francisco
Recent experimental observations in presynaptic terminals at the neuromuscular junction indicate that there are stereotyped patterns of cooperativeness in the fusion of adjacent vesicles. That is, a vesicle in hemifusion process appears on the side of a fused vesicle and which is followed by another vesicle in a priming state while the next one is in a docking state. In this talk we present a kinetic model for this morphological pattern in which each vesicle state previous to the exocytosis is represented by a kinetic state. This chain states kinetic model can be analyzed by means of a Master equation whose solution is simulated with the stochastic Gillespie algorithm. With this approach we have reproduced the responses to the basal release in the absence of stimulation evoked by the electrical activity and the phenomena of facilitation and depression of neuromuscular synapses. This model offers new perspectives to understand the underlying phenomena in chemical neurotransmission based on molecular interactions that result in the cooperativity between vesicles during neurotransmitter release. DGAPA Grants IN118410 and IN200914 and Conacyt Grant 130031.
Compartmental model of leucine kinetics in humans.
Cobelli, C; Saccomani, M P; Tessari, P; Biolo, G; Luzi, L; Matthews, D E
1991-10-01
The complexity of amino acid and protein metabolism has limited the development of comprehensive, accurate whole body kinetic models. For leucine, simplified approaches are in use to measure in vivo leucine fluxes, but their domain of validity is uncertain. We propose here a comprehensive compartmental model of the kinetics of leucine and alpha-ketoisocaproate (KIC) in humans. Data from a multiple-tracer administration were generated with a two-stage (I and II) experiment. Six normal subjects were studied. In experiment I, labeled leucine and KIC were simultaneously injected into plasma. Four plasma leucine and KIC tracer concentration curves and label in the expired CO2 were measured. In experiment II, labeled bicarbonate was injected into plasma, and labeled CO2 in the expired air was measured. Radioactive (L-[1-14C]leucine, [4,5-3H]KIC, [14C]bicarbonate) and stable isotope (L-[1-13C]leucine, [5,5,5-2H3]KIC, [13C]bicarbonate) tracers were employed. The input format was a bolus (impulse) dose in the radioactive case and a constant infusion in the stable isotope case. A number of physiologically based, linear time-invariant compartmental models were proposed and tested against the data. The model finally chosen for leucine-KIC kinetics has 10 compartments: 4 for leucine, 3 for KIC, and 3 for bicarbonate. The model is a priori uniquely identifiable, and its parameters were estimated with precision from the five curves of experiment I. The separate assessment of bicarbonate kinetics (experiment II) was shown to be unnecessary. The model defines masses and fluxes of leucine in the organism, in particular its intracellular appearance from protein breakdown, its oxidation, and its incorporation into proteins. An important feature of the model is its ability to estimate leucine oxidation by resolving the bicarbonate model in each individual subject. Finally, the model allows the assessment of the domain of validity of the simpler commonly used models. PMID:1928344
Adhikari, K; Pal, S; Chakraborty, B; Mukherjee, S N; Gangopadhyay, A
2014-10-01
The movement of contaminants through soil imparts a variety of geo-environmental problem inclusive of lithospheric pollution. Near-surface aquifers are often vulnerable to contamination from surface source if overlying soil possesses poor resilience or contaminant attenuation capacity. The prediction of contaminant transport through soil is urged to protect groundwater from sources of pollutants. Using field simulation through column experiments and mathematical modeling like HYDRUS-1D, assessment of soil resilience and movement of contaminants through the subsurface to reach aquifers can be predicted. An outfall site of effluents of a coke oven plant comprising of alarming concentration of phenol (4-12.2 mg/L) have been considered for studying groundwater condition and quality, in situ soil characterization, and effluent characterization. Hydrogeological feature suggests the presence of near-surface aquifers at the effluent discharge site. Analysis of groundwater of nearby locality reveals the phenol concentration (0.11-0.75 mg/L) exceeded the prescribed limit of WHO specification (0.002 mg/L). The in situ soil, used in column experiment, possess higher saturated hydraulic conductivity (KS = 5.25 × 10(-4) cm/s). The soil containing 47 % silt, 11 % clay, and 1.54% organic carbon content was found to be a poor absorber of phenol (24 mg/kg). The linear phenol adsorption isotherm model showed the best fit (R(2) = 0.977, RMSE = 1.057) to the test results. Column experiments revealed that the phenol removal percent and the length of the mass transfer zone increased with increasing bed heights. The overall phenol adsorption efficiency was found to be 42-49%. Breakthrough curves (BTCs) predicted by HYDRUS-1D model appears to be close fitting with the BTCs derived from the column experiments. The phenol BTC predicted by the HYDRUS-1D model for 1.2 m depth subsurface soil, i.e., up to the depth of groundwater in the study area, showed that the exhaustion
NASA Astrophysics Data System (ADS)
Minárik, Stanislav
2015-08-01
In this paper, we propose theoretical basis for investigation of dynamics of acoustic phonons in a thin layers containing nano-scale structural inhomogeneities. One-dimensional (1D) model of a crystal lattice was considered to reveal specific features of the processes arising in such system of phonons in equilibrium state. Standard quantization of energy of 1D ionic chain vibrating by acoustic frequencies was carried out while the presence of foreign ions in this chain was taken into account. Since only two dimensions are dominant in thin layers, only longitudinal vibrations of the chain in the plane of the layer were considered. Results showed that foreign ions affect the energy quantization. Phonon-phonon interaction between two phonon`s modes can be expected if the mass of foreign ions implanted by ion-beam differs from the mass of ions in the initial layer. We believe that the obtained results will help to understand the character of phonon systems in nanostructured thin layers prepared by ion-bem technology, and will allow better explain some thermal and electrical phenomena associated with lattice dynamics in such layers.
NASA Astrophysics Data System (ADS)
Zhou, Tianci; Chen, Xiao; Fradkin, Eduardo
We investigate the entanglement entropy(EE) of circular entangling surfaces in the 2+1d quantum Lifshitz model, where the spatially conformal invariant ground state is a Rokhsar-Kivelson state with Gibbs weight of 2d free Boson. We use cut-off independent mutual information regulator to define and calculate the subleading correction in the EE. The subtlety due to the Boson compactification in the replica trick is carefully taken care of. Our results show that for circular entangling surface, the subleading term is a constant on both the sphere of arbitrary radius and infinite plane. For the latter case, it parallels the constancy of disk EE in 2+1d conformal field theory, despite the lack of full space time conformal invariance. In the end, we present the mutual information of two disjoint disks and compare its scaling function in the small parameter regime (radii much smaller than their separation) with Cardy's general CFT results. This work was supported in part by the National Science Foundation Grants NSF-DMR-13-06011(TZ) and DMR-1408713 (XC, EF).
Cluster kinetics model for mixtures of glassformers.
Brenskelle, Lisa A; McCoy, Benjamin J
2007-10-14
For glassformers we propose a binary mixture relation for parameters in a cluster kinetics model previously shown to represent pure compound data for viscosity and dielectric relaxation as functions of either temperature or pressure. The model parameters are based on activation energies and activation volumes for cluster association-dissociation processes. With the mixture parameters, we calculated dielectric relaxation times and compared the results to experimental values for binary mixtures. Mixtures of sorbitol and glycerol (seven compositions), sorbitol and xylitol (three compositions), and polychloroepihydrin and polyvinylmethylether (three compositions) were studied. PMID:17935407
Aggregation kinetics in a model colloidal suspension
Bastea, S
2005-08-08
The authors present molecular dynamics simulations of aggregation kinetics in a colloidal suspension modeled as a highly asymmetric binary mixture. Starting from a configuration with largely uncorrelated colloidal particles the system relaxes by coagulation-fragmentation dynamics to a structured state of low-dimensionality clusters with an exponential size distribution. The results show that short range repulsive interactions alone can give rise to so-called cluster phases. For the present model and probably other, more common colloids, the observed clusters appear to be equilibrium phase fluctuations induced by the entropic inter-colloidal attractions.
Cluster kinetics model for mixtures of glassformers
NASA Astrophysics Data System (ADS)
Brenskelle, Lisa A.; McCoy, Benjamin J.
2007-10-01
For glassformers we propose a binary mixture relation for parameters in a cluster kinetics model previously shown to represent pure compound data for viscosity and dielectric relaxation as functions of either temperature or pressure. The model parameters are based on activation energies and activation volumes for cluster association-dissociation processes. With the mixture parameters, we calculated dielectric relaxation times and compared the results to experimental values for binary mixtures. Mixtures of sorbitol and glycerol (seven compositions), sorbitol and xylitol (three compositions), and polychloroepihydrin and polyvinylmethylether (three compositions) were studied.
An analytical 1-D model for vertical momentum and energy flux through a fully developed wind farm
NASA Astrophysics Data System (ADS)
Markfort, Corey D.; Zhang, Wei; Porté-Agel, Fernando
2014-05-01
Wind farms capture momentum from the atmospheric boundary layer (ABL) both at the leading edge and from the atmosphere above. Momentum is advected into the wind farm and wake turbulence draws excess momentum in from between turbines until momentum is only available from above the wind farm. This distance can be described by the so-called drag development length scale, which arises from the canopy drag force term in the momentum equation. At this point the flow can be considered fully developed. The horizontally-averaged velocity profile for a fully developed wind farm flow exhibits a characteristic inflection point near the top of the wind farm, similar to that of sparse canopy-type flows (Markfort et al., JoT, 2012). The inflected vertical velocity profile is associated with the presence of a dominant characteristic turbulence scale, which may be responsible for a significant portion of the vertical momentum flux. We evaluate an analytical canopy-type flow model for wind farm-atmosphere interaction by testing it against wind-tunnel experimental data of flow through a model wind farm. The model is adapted to predict the mean flow, vertical momentum flux, and the mean kinetic energy flux as well as kinetic energy dissipation within the wind farm. This model is particularly useful for wind farm configuration optimization, considering wind turbine spacing and surface roughness and can also be useful to represent wind farms in regional scale atmospheric simulations.
NASA Astrophysics Data System (ADS)
Zhu, D.; Nakamura, N.
2009-12-01
Spontaneous formation of a vorticity staircase and multiple jets is simulated using a one dimensional barotropic model on a beta-plane with parameterized eddy mixing. The model represents nearly inviscid geostrophic turbulence characterized by a uniform forcing of pseudomomentum, nonuniform dissipation due to mixing, and no frictional damping of the mean flow. The dissipation of pseudomomentum (diffusive flux of vorticity) is modeled with the effective diffusivity parameterization proposed recently by Ferrari and Nikurashin(2009). Rossby wave dynamics and upscale energy cascade are not modeled explicitly but implicit in the parameterization. The parameterized effective diffusivity is a decreasing function of squared vorticity gradient, revealing the active role of (potential) vorticity gradient as a barrier to mixing, consistent with the Rossby elasticity idea. Not only does the parameterized diffusivity agree well with the effective diffusivity of a direct numerical simulation, but it allows the 1D model to reproduce other salient features of the direct simulation, most notably the formation of a welldefined vorticity staircase from a uniform vorticity gradient, through inhomogeneous mixing of vorticity. The staircase formation starts as a small-scale, antidiffusive instability in vorticity gradient that develops when the eddy scale is comparable to the Rhines scale. This spawns numerous gaps (barriers) in diffusivity and corresponding small steps in vorticity, but many of them become unstable and disappear later, until a few stable ones remain. The final number of barriers (vorticity steps) is predictable to a good approximation with a few model parameters.
Equilibrium, kinetic, and reactive transport models for plutonium
NASA Astrophysics Data System (ADS)
Schwantes, Jon Michael
Equilibrium, kinetic, and reactive transport models for plutonium (Pu) have been developed to help meet environmental concerns posed by past war-related and present and future peacetime nuclear technologies. A thorough review of the literature identified several hurdles that needed to be overcome in order to develop capable predictive tools for Pu. These hurdles include: (1) missing or ill-defined chemical equilibrium and kinetic constants for environmentally important Pu species; (2) no adequate conceptual model describing the formation of Pu oxy/hydroxide colloids and solids; and (3) an inability of two-phase reactive transport models to adequately simulate Pu behavior in the presence of colloids. A computer program called INVRS K was developed that integrates the geochemical modeling software of PHREEQC with a nonlinear regression routine. This program provides a tool for estimating equilibrium and kinetic constants from experimental data. INVRS K was used to regress on binding constants for Pu sorbing onto various mineral and humic surfaces. These constants enhance the thermodynamic database for Pu and improve the capability of current predictive tools. Time and temperature studies of the Pu intrinsic colloid were also conducted and results of these studies were presented here. Formation constants for the fresh and aged Pu intrinsic colloid were regressed upon using INVRS K. From these results, it was possible to develop a cohesive diagenetic model that describes the formation of Pu oxy/hydroxide colloids and solids. This model provides for the first time a means of deciphering historically unexplained observations with respect to the Pu intrinsic colloid, as well as a basis for simulating the behavior within systems containing these solids. Discussion of the development and application of reactive transport models is also presented and includes: (1) the general application of a 1-D in flow, three-phase (i.e., dissolved, solid, and colloidal), reactive
2D Axisymmetric vs 1D: A PIC/DSMC Model of Breakdown in Triggered Vacuum Spark Gaps
NASA Astrophysics Data System (ADS)
Moore, Stan; Moore, Chris; Boerner, Jeremiah
2015-09-01
Last year at GEC14, we presented results of one-dimensional PIC/DSMC simulations of breakdown in triggered vacuum spark gaps. In this talk, we extend the model to two-dimensional axisymmetric and compare the results to the previous 1D case. Specially, we vary the fraction of the cathode that emits electrons and neutrals (holding the total injection rates over the cathode surface constant) and show the effects of the higher dimensionality on the time to breakdown. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U. S. Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Chemical kinetics and modeling of planetary atmospheres
NASA Technical Reports Server (NTRS)
Yung, Yuk L.
1990-01-01
A unified overview is presented for chemical kinetics and chemical modeling in planetary atmospheres. The recent major advances in the understanding of the chemistry of the terrestrial atmosphere make the study of planets more interesting and relevant. A deeper understanding suggests that the important chemical cycles have a universal character that connects the different planets and ultimately link together the origin and evolution of the solar system. The completeness (or incompleteness) of the data base for chemical kinetics in planetary atmospheres will always be judged by comparison with that for the terrestrial atmosphere. In the latter case, the chemistry of H, O, N, and Cl species is well understood. S chemistry is poorly understood. In the atmospheres of Jovian planets and Titan, the C-H chemistry of simple species (containing 2 or less C atoms) is fairly well understood. The chemistry of higher hydrocarbons and the C-N, P-N chemistry is much less understood. In the atmosphere of Venus, the dominant chemistry is that of chlorine and sulfur, and very little is known about C1-S coupled chemistry. A new frontier for chemical kinetics both in the Earth and planetary atmospheres is the study of heterogeneous reactions. The formation of the ozone hole on Earth, the ubiquitous photochemical haze on Venus and in the Jovian planets and Titan all testify to the importance of heterogeneous reactions. It remains a challenge to connect the gas phase chemistry to the production of aerosols.
Brittle failure kinetics model for concrete
Silling, S.A.
1997-03-01
A new constitutive model is proposed for the modeling of penetration and large stress waves in concrete. Rate effects are incorporated explicitly into the damage evolution law, hence the term brittle failure kinetics. The damage variable parameterizes a family of Mohr-Coulomb strength curves. The model, which has been implemented in the CTH code, has been shown to reproduce some distinctive phenomena that occur in penetration of concrete targets. Among these are the sharp spike in deceleration of a rigid penetrator immediately after impact. Another is the size scale effect, which leads to a nonlinear scaling of penetration depth with penetrator size. This paper discusses the theory of the model and some results of an extensive validation effort.
NASA Astrophysics Data System (ADS)
Graves, R. W.
2012-12-01
I have performed low frequency (f < 1 Hz) ground motion simulations for the 2008 Mw 5.23 Mt. Carmel, Illinois and 2011 Mw 5.74 Mineral, Virginia earthquakes to calibrate a rock-site 1D crustal velocity and Q structure model for central and eastern US (CEUS). For each earthquake, the observed ground motions were simulated at sites extending out to about 900 km from the epicenter. Sites within the Mississippi embayment are not included in the modeling. The initial 1D velocity model was developed by averaging profiles extracted from the CUS V1.3 3D velocity model (Ramirez-Guzman et al, 2012) at each of the recording sites, with the surface shear wave velocity set at 2200 m/s. The Mt. Carmel earthquake is represented as a point double couple (strike=25, dip=90, rake=-175) at a depth of 14 km and a slip-rate function having a Brune corner frequency of 0.89 Hz (Hartzell and Mendoza, 2011). The Mineral earthquake is represented as a point double couple (strike=26, dip=55, rake=108) at a depth of 6 km and a slip-rate function having a corner frequency of 0.50 Hz. Full waveform Green's functions were computed using the FK method of Zhu and Rivera (2002). The initial model does well at reproducing the median level of observed response spectral acceleration (Sa) for most sites out to 300 km at periods of 2 to 5 sec, including the observed flattening in distance attenuation between 70 and 150 km. However, this model under predicts the motions beyond about 400 km distance. Increasing Q in the mid- and lower crust from the original value of 700 to 5000 removes this under prediction of the larger distance motions. Modified Mercalli Intensity (MMI) estimates have been computed from the simulations using the ground motion-intensity conversion equations of Atkinson and Kaka (2007; AK2007) and Dangkua and Cramer (2011; DC2011-ENA) for comparison against the observed "Did You Feel It" intensity estimates. Given the bandwidth limitations of the simulations, I use the conversion
Wealth redistribution in conservative linear kinetic models
NASA Astrophysics Data System (ADS)
Toscani, G.
2009-10-01
We introduce and discuss kinetic models for wealth distribution which include both taxation and uniform redistribution. The evolution of the continuous density of wealth obeys a linear Boltzmann equation where the background density represents the action of an external subject on the taxation mechanism. The case in which the mean wealth is conserved is analyzed in full details, by recovering the analytical form of the steady states. These states are probability distributions of convergent random series of a special structure, called perpetuities. Among others, Gibbs distribution appears as steady state in case of total taxation and uniform redistribution.
The kinetic regime of the Vicsek model
NASA Astrophysics Data System (ADS)
Chepizhko, A. A.; Kulinskii, V. L.
2009-12-01
We consider the dynamics of the system of self-propelling particles modeled via the Vicsek algorithm in continuum time limit. It is shown that the alignment process for the velocities can be subdivided into two regimes: "fast" kinetic and "slow" hydrodynamic ones. In fast kinetic regime the alignment of the particle velocity to the local neighborhood takes place with characteristic relaxation time. So, that the bigger regions arise with the velocity alignment. These regions align their velocities thus giving rise to hydrodynamic regime of the dynamics. We propose the mean-field-like approach in which we take into account the correlations between density and velocity. The comparison of the theoretical predictions with the numerical simulations is given. The relation between Vicsek model in the zero velocity limit and the Kuramoto model is stated. The mean-field approach accounting for the dynamic change of the neighborhood is proposed. The nature of the discontinuity of the dependence of the order parameter in case of vectorial noise revealed in Gregorie and Chaite, Phys. Rev. Lett., 92, 025702 (2004) is discussed and the explanation of it is proposed.
A Kinetic Model of Active Extensile Bundles
NASA Astrophysics Data System (ADS)
Goldstein, Daniel; Chakraborty, Bulbul; Baskaran, Aparna
Recent experiments in active filament networks reveal interesting rheological properties (Dan Chen: APS March Meeting 2015 D49.00001). This system consumes ATP to produce an extensile motion in bundles of microtubules. This extension then leads to self generated stresses and spontaneous flows. We propose a minimal model where the activity is modeled by self-extending bundles that are part of a cross linked network. This network can reorganize itself through buckling of extending filaments and merging events that alter the topology of the network. We numerically simulate this minimal kinetic model and examine the emergent rheological properties and determine how stresses are generated by the extensile activity. We will present results that focus on the effects of confinement and network connectivity of the bundles on stress fluctuations and response of an active gel.
On Kinetics Modeling of Vibrational Energy Transfer
NASA Technical Reports Server (NTRS)
Gilmore, John O.; Sharma, Surendra P.; Cavolowsky, John A. (Technical Monitor)
1996-01-01
Two models of vibrational energy exchange are compared at equilibrium to the elementary vibrational exchange reaction for a binary mixture. The first model, non-linear in the species vibrational energies, was derived by Schwartz, Slawsky, and Herzfeld (SSH) by considering the detailed kinetics of vibrational energy levels. This model recovers the result demanded at equilibrium by the elementary reaction. The second model is more recent, and is gaining use in certain areas of computational fluid dynamics. This model, linear in the species vibrational energies, is shown not to recover the required equilibrium result. Further, this more recent model is inconsistent with its suggested rate constants in that those rate constants were inferred from measurements by using the SSH model to reduce the data. The non-linear versus linear nature of these two models can lead to significant differences in vibrational energy coupling. Use of the contemporary model may lead to significant misconceptions, especially when integrated in computer codes considering multiple energy coupling mechanisms.
Kinetic model solves visbreaker constraint control problem
Iscovici, R.S. )
1994-05-01
A kinetic model of the visbreaking process was developed and used in an advanced control algorithm implemented in a distributed control system (DCS). During development, model predictions were checked against unit history data and compared to the actual unit performance with respect to fuel oil stability vs. cracking conversion. In the first stage, the algorithm was used in open-loop supervisory control. In the second stage the advanced control loop was closed and the visbreaking units was run automatically. The visbreaker control, based on process kinetics, is simple enough to be developed and implemented in a DCS, eliminating need for higher-power computers at the information system (IS) level, and reducing to a minimum data transfer from them to the process regulatory control level based on the DCS. The advanced control application led to profits estimated at $4.5 million annually, more than expected. The visbreaker advanced control showed how process engineering knowledge used in powerful and versatile DCSs could increase profit, shorten pay-out time and ease the workload on unit operators.
NASA Astrophysics Data System (ADS)
Li, Zhanhui; Huang, Qinghua; Xie, Xingbing; Tang, Xingong; Chang, Liao
2016-08-01
We present a generic 1D forward modeling and inversion algorithm for transient electromagnetic (TEM) data with an arbitrary horizontal transmitting loop and receivers at any depth in a layered earth. Both the Hankel and sine transforms required in the forward algorithm are calculated using the filter method. The adjoint-equation method is used to derive the formulation of data sensitivity at any depth in non-permeable media. The inversion algorithm based on this forward modeling algorithm and sensitivity formulation is developed using the Gauss-Newton iteration method combined with the Tikhonov regularization. We propose a new data-weighting method to minimize the initial model dependence that enhances the convergence stability. On a laptop with a CPU of i7-5700HQ@3.5 GHz, the inversion iteration of a 200 layered input model with a single receiver takes only 0.34 s, while it increases to only 0.53 s for the data from four receivers at a same depth. For the case of four receivers at different depths, the inversion iteration runtime increases to 1.3 s. Modeling the data with an irregular loop and an equal-area square loop indicates that the effect of the loop geometry is significant at early times and vanishes gradually along the diffusion of TEM field. For a stratified earth, inversion of data from more than one receiver is useful in noise reducing to get a more credible layered earth. However, for a resistive layer shielded below a conductive layer, increasing the number of receivers on the ground does not have significant improvement in recovering the resistive layer. Even with a down-hole TEM sounding, the shielded resistive layer cannot be recovered if all receivers are above the shielded resistive layer. However, our modeling demonstrates remarkable improvement in detecting the resistive layer with receivers in or under this layer.
NASA Astrophysics Data System (ADS)
Li, Zhanhui; Huang, Qinghua; Xie, Xingbing; Tang, Xingong; Chang, Liao
2016-07-01
We present a generic 1D forward modeling and inversion algorithm for transient electromagnetic (TEM) data with an arbitrary horizontal transmitting loop and receivers at any depth in a layered earth. Both the Hankel and sine transforms required in the forward algorithm are calculated using the filter method. The adjoint-equation method is used to derive the formulation of data sensitivity at any depth in non-permeable media. The inversion algorithm based on this forward modeling algorithm and sensitivity formulation is developed using the Gauss-Newton iteration method combined with the Tikhonov regularization. We propose a new data-weighting method to minimize the initial model dependence that enhances the convergence stability. On a laptop with a CPU of i7-5700HQ@3.5 GHz, the inversion iteration of a 200 layered input model with a single receiver takes only 0.34 s, while it increases to only 0.53 s for the data from four receivers at a same depth. For the case of four receivers at different depths, the inversion iteration runtime increases to 1.3 s. Modeling the data with an irregular loop and an equal-area square loop indicates that the effect of the loop geometry is significant at early times and vanishes gradually along the diffusion of TEM field. For a stratified earth, inversion of data from more than one receiver is useful in noise reducing to get a more credible layered earth. However, for a resistive layer shielded below a conductive layer, increasing the number of receivers on the ground does not have significant improvement in recovering the resistive layer. Even with a down-hole TEM sounding, the shielded resistive layer cannot be recovered if all receivers are above the shielded resistive layer. However, our modeling demonstrates remarkable improvement in detecting the resistive layer with receivers in or under this layer.
NASA Astrophysics Data System (ADS)
Ashworth, K.; Chung, S. H.; Griffin, R. J.; Chen, J.; Forkel, R.; Bryan, A. M.; Steiner, A. L.
2015-11-01
Biosphere-atmosphere interactions play a critical role in governing atmospheric composition, mediating the concentrations of key species such as ozone and aerosol, thereby influencing air quality and climate. The exchange of reactive trace gases and their oxidation products (both gas and particle phase) is of particular importance in this process. The FORCAsT (FORest Canopy Atmosphere Transfer) 1-D model is developed to study the emission, deposition, chemistry and transport of volatile organic compounds (VOCs) and their oxidation products in the atmosphere within and above the forest canopy. We include an equilibrium partitioning scheme, making FORCAsT one of the few canopy models currently capable of simulating the formation of secondary organic aerosols (SOAs) from VOC oxidation in a forest environment. We evaluate the capability of FORCAsT to reproduce observed concentrations of key gas-phase species and report modeled SOA concentrations within and above a mixed forest at the University of Michigan Biological Station (UMBS) during the Community Atmosphere-Biosphere Interactions Experiment (CABINEX) field campaign in the summer of 2009. We examine the impact of two different gas-phase chemical mechanisms on modelled concentrations of short-lived primary emissions, such as isoprene and monoterpenes, and their oxidation products. While the two chemistry schemes perform similarly under high-NOx conditions, they diverge at the low levels of NOx at UMBS. We identify peroxy radical and alkyl nitrate chemistry as the key causes of the differences, highlighting the importance of this chemistry in understanding the fate of biogenic VOCs (bVOCs) for both the modelling and measurement communities.
Detailed Kinetic Modeling of Gasoline Surrogate Mixtures
Mehl, M; Curran, H J; Pitz, W J; Westbrook, C K
2009-03-09
Real fuels are complex mixtures of thousands of hydrocarbon compounds including linear and branched paraffins, naphthenes, olefins and aromatics. It is generally agreed that their behavior can be effectively reproduced by simpler fuel surrogates containing a limited number of components. In this work, a recently revised version of the kinetic model by the authors is used to analyze the combustion behavior of several components relevant to gasoline surrogate formulation. Particular attention is devoted to linear and branched saturated hydrocarbons (PRF mixtures), olefins (1-hexene) and aromatics (toluene). Model predictions for pure components, binary mixtures and multi-component gasoline surrogates are compared with recent experimental information collected in rapid compression machine, shock tube and jet stirred reactors covering a wide range of conditions pertinent to internal combustion engines. Simulation results are discussed focusing attention on the mixing effects of the fuel components.
A single-phase model for liquid-feed DMFCs with non-Tafel kinetics
NASA Astrophysics Data System (ADS)
Vera, Marcos
An isothermal single-phase 3D/1D model for liquid-feed direct methanol fuel cells (DMFC) is presented. Three-dimensional (3D) mass, momentum and species transport in the anode channels and gas diffusion layer is modeled using a commercial, finite-volume based, computational fluid dynamics (CFD) software complemented with user supplied subroutines. The 3D model is locally coupled to a one-dimensional (1D) model accounting for the electrochemical reactions in both the anode and the cathode, which provides a physically sound boundary condition for the velocity and methanol concentration fields at the anode gas diffusion layer/catalyst interface. The 1D model - comprising the membrane-electrode assembly, cathode gas diffusion layer, and cathode channel - assumes non-Tafel kinetics to describe the complex kinetics of the multi-step methanol oxidation reaction at the anode, and accounts for the mixed potential associated with methanol crossover, induced both by diffusion and electro-osmotic drag. Polarization curves computed for various methanol feed concentrations, temperatures, and methanol feed velocities show good agreement with recent experimental results. The spatial distribution of methanol in the anode channels, together with the distributions of current density, methanol crossover and fuel utilization at the anode catalyst layer, are also presented for different opperating conditions.
Monochloramination of resorcinol: mechanism and kinetic modeling.
Cimetiere, Nicolas; Dossier-Berne, Florence; De Laat, Joseph
2009-12-15
The kinetics of monochloramination of resorcinol, 4-chlororesorcinol, and 4,6-dichlororesorcinol have been investigated over the pH range of 5-12, at 23 +/- 2 degrees C. Monochloramine solutions were prepared with ammonia-to-chlorine ratios (N/Cl) ranging from 1.08 to 31 mol/mol. Under conditions that minimize free chlorine reactions (N/Cl > 2 mol/mol), the apparent second-order rate constants of monochloramination of resorcinol compounds show a maximum at pH values between 8.6 and 10.2. The intrinsic second-order rate constants for the reaction of monochloramine with the acid-base forms of the dihydroxybenzenes (Ar(OH)(2), Ar(OH)O(-), and Ar(O(-))(2)) were calculated from the apparent second-order rate constants. The stoichiometric coefficients for the formation of 4-chlororesorcinol by monochloramination of resorcinol and 4,6-dichlororesorcinol by monochloramination of 4-chlororesorcinol were found to be equal to 0.66 +/- 0.05 and 0.25 +/- 0.02 mol/mol, respectively at pH 8.6. A kinetic model that incorporates reactions of free chlorine and monochloramine with the different acid-base forms of resorcinol compounds simulated well the initial rates of degradation of resorcinol compounds and was useful to evaluate the contribution of free chlorine reactions to the overall rates of degradation of resorcinol at low N/Cl ratios. PMID:20000532
Napier, C; Stewart, M; Melrose, H; Hopkins, B; McHarg, A; Wallis, R
1999-03-01
The affinity of eletriptan ((R)-3-(1-methyl-2-pyrrolidinylmethyl)-5-[2-(phenylsulphonyl )ethyl]-1H-indole) for a range of 5-HT receptors was compared to values obtained for other 5-HT1B/1D receptor agonists known to be effective in the treatment of migraine. Eletriptan, like sumatriptan, zolmitriptan, naratriptan and rizatriptan had highest affinity for the human 5-HT1B, 5-HT1D and putative 5-ht1f receptor. Kinetic studies comparing the binding of [3H]eletriptan and [3H]sumatriptan to the human recombinant 5-HT1B and 5-HT1D receptors expressed in HeLa cells revealed that both radioligands bound with high specificity (>90%) and reached equilibrium within 10-15 min. However, [3H]eletriptan had over 6-fold higher affinity than [3H]sumatriptan at the 5-HT1D receptor (K(D)): 0.92 and 6.58 nM, respectively) and over 3-fold higher affinity than [3H]sumatriptan at the 5-HT1B receptor (K(D): 3.14 and 11.07 nM, respectively). Association and dissociation rates for both radioligands could only be accurately determined at the 5-HT1D receptor and then only at 4 degrees C. At this temperature, [3H]eletriptan had a significantly (P<0.05) faster association rate (K(on) 0.249 min(-1) nM(-1)) than [3H]sumatriptan (K(on) 0.024 min(-1) nM(-1)) and a significantly (P<0.05) slower off-rate (K(off) 0.027 min(-1) compared to 0.037 min(-1) for [3H]sumatriptan). These data indicate that eletriptan is a potent ligand at the human 5-HT1B, 5-HT1D, and 5-ht1f receptors and are consistent with its potent vasoconstrictor activity and use as a drug for the acute treatment of migraine headache. PMID:10193663
Novel phase-space Monte-Carlo method for quench dynamics in 1D and 2D spin models
NASA Astrophysics Data System (ADS)
Pikovski, Alexander; Schachenmayer, Johannes; Rey, Ana Maria
2015-05-01
An important outstanding problem is the effcient numerical computation of quench dynamics in large spin systems. We propose a semiclassical method to study many-body spin dynamics in generic spin lattice models. The method, named DTWA, is based on a novel type of discrete Monte-Carlo sampling in phase-space. We demonstare the power of the technique by comparisons with analytical and numerically exact calculations. It is shown that DTWA captures the dynamics of one- and two-point correlations 1D systems. We also use DTWA to study the dynamics of correlations in 2D systems with many spins and different types of long-range couplings, in regimes where other numerical methods are generally unreliable. Computing spatial and time-dependent correlations, we find a sharp change in the speed of propagation of correlations at a critical range of interactions determined by the system dimension. The investigations are relevant for a broad range of systems including solids, atom-photon systems and ultracold gases of polar molecules, trapped ions, Rydberg, and magnetic atoms. This work has been financially supported by JILA-NSF-PFC-1125844, NSF-PIF-1211914, ARO, AFOSR, AFOSR-MURI.
Thermal characterization of large size lithium-ion pouch cell based on 1d electro-thermal model
NASA Astrophysics Data System (ADS)
Vertiz, G.; Oyarbide, M.; Macicior, H.; Miguel, O.; Cantero, I.; Fernandez de Arroiabe, P.; Ulacia, I.
2014-12-01
Thermal management is one of the key factors to keep lithium-ion cells in optimum electrical performance, under safe working conditions and into a reasonably low ageing process. This issue is becoming particularly relevant due to the heterogeneous heat generation along the cell. Cell working temperature is determined by ambient temperature, heat generation and evacuation capacity. Therefore, thermal management is established by: i) the intrinsic thermal properties (heat capacity & thermal conductivity) and ii) the heat generation electro-thermal parameters (internal resistance, open circuit voltage & entropic factor). In this research, different methods - calculated and experimental - are used to characterize the main heat properties of a 14Ah -LiFePO4/graphite-commercial large sizes pouch cell. In order to evaluate the accuracy of methods, two comparisons were performed. First, Newman heat generation estimations were compared with experimental heat measurements. Secondly, empirical thermal cell behaviour was match with 1D electro-thermal model response. Finally, considering the results, the most adequate methodology to evaluate the key thermal parameters of a large size Lithium-ion pouch cell are proposed to be: i) pulse method for internal resistance, ii)heat loss method for entropic factor; and iii)experimental measurement (ARC calorimeter and C-177-97 standard method) for heat capacity and thermal conductivity.
NASA Astrophysics Data System (ADS)
Dzierzbicka-Glowacka, L.; Maciejewska, A.; Osiński, R.; Jakacki, J.; Jędrasik, J.
2009-04-01
This paper presents a one-dimensional Ecosystem Model. Mathematically, the pelagic variables in the model are described by a second-order partial differential equation of the diffusion type with biogeochemical sources and sinks. The temporal changes in the phytoplankton biomass are caused by primary production, respiration, mortality, grazing by zooplankton and sinking. The zooplankton biomass is affected by ingestion, excretion, respiration, fecal production, mortality, and carnivorous grazing. The changes in the pelagic detritus concentration are determined by input of: dead phytoplankton and zooplankton, natural mortality of predators, fecal pellets, and sinks: sedimentation, zooplankton grazing and decomposition. The nutrient concentration is caused by nutrient release, zooplankton excretion, predator excretion, detritus decomposition and benthic regeneration as sources and by nutrient uptake by phytoplankton as sinks. However, the benthic detritus is described by phytoplankton sedimentation, detritus sedimentation and remineralisation. The particulate organic carbon concentration is determined as the sum of phytoplankton, zooplankton and dead organic matter (detritus) concentrations. The 1D ecosystem model was used to simulate the seasonal dynamics of pelagic variables (phytoplankton, zooplankton, pelagic detritus and POC) in the southern Baltic Sea (Gdańsk Deep, Bornholm Deep and Gotland Deep). The calculations were made assuming: 1) increase in the water temperature in the upper layer - 0.008oC per year, 2) increase in the available light - 0.2% per year. Based on this trend, daily, monthly and seasonal and annual variability of phytoplankton, zooplankton, pelagic detritus and particulate organic carbon in different areas of the southern Baltic Sea (Gdańsk Deep, Borrnholm Deep and Gotland Deep) in the euphotic layer was calculated for the years: 2000, 2010, 2020, 2030, 2040 and 2050.
Kinetic Modeling of Esterification of Ethylene Glycol with Acetic Acid
NASA Astrophysics Data System (ADS)
Yadav, Vishnu P.; Mukherjee, Rudra Palash; Bantraj, Kandi; Maity, Sunil K.
2010-10-01
The reaction kinetics of the esterification of ethylene glycol with acetic acid in the presence of cation exchange resin has been studied and kinetic models based on empirical and Langmuir approach has been developed. The Langmuir based model involving eight kinetic parameters fits experimental data much better compared to empirical model involving four kinetic parameters. The effect of temperature and catalyst loading on the reaction system has been analyzed. Further, the activation energy and frequency factor of the rate constants for Langmuir based model has been estimated.
Aerosol kinetic code "AERFORM": Model, validation and simulation results
NASA Astrophysics Data System (ADS)
Gainullin, K. G.; Golubev, A. I.; Petrov, A. M.; Piskunov, V. N.
2016-06-01
The aerosol kinetic code "AERFORM" is modified to simulate droplet and ice particle formation in mixed clouds. The splitting method is used to calculate condensation and coagulation simultaneously. The method is calibrated with analytic solutions of kinetic equations. Condensation kinetic model is based on cloud particle growth equation, mass and heat balance equations. The coagulation kinetic model includes Brownian, turbulent and precipitation effects. The real values are used for condensation and coagulation growth of water droplets and ice particles. The model and the simulation results for two full-scale cloud experiments are presented. The simulation model and code may be used autonomously or as an element of another code.
Kinetic Modeling of Esterification of Ethylene Glycol with Acetic Acid
Yadav, Vishnu P.; Maity, Sunil K.; Mukherjee, Rudra Palash; Bantraj, Kandi
2010-10-26
The reaction kinetics of the esterification of ethylene glycol with acetic acid in the presence of cation exchange resin has been studied and kinetic models based on empirical and Langmuir approach has been developed. The Langmuir based model involving eight kinetic parameters fits experimental data much better compared to empirical model involving four kinetic parameters. The effect of temperature and catalyst loading on the reaction system has been analyzed. Further, the activation energy and frequency factor of the rate constants for Langmuir based model has been estimated.
Kinetic modelling of vinyl ester resin polymerization
Dhulipala, R.; Kreig. G.; Hawley, M.C.
1993-12-31
The study of kinetics offers a substantional incentive in the endeavor to manufacture polymer matrix composites at high speeds. The study enables one to optimize the curing cycle based on the specific curing characteristics of the resin and also makes it possible to simulate the curing process. This paper reports the results of the modelling of the thermal curing of the vinyl ester resin. The parameters for the proposed model have been calculated based on conversion-vs-data generated at various temperatures and Benzoyl peroxide (initiator) concentrations. The extent of cure of the resin mixture was determined using Fourier Transform Infrared Spectroscopy. In this model the termination rate constant is considered to drop with extent of cure until a limiting value is reached. The limiting value is a consequence of the active chain ends possessing a degree of mobility due to the propagation reaction even though the translational motion of the growing for radicals in increasingly restricted with conversion. Good agreements is observed between the model predictions and the experimental data.
NASA Astrophysics Data System (ADS)
Reynolds, Dylan; Wood, Stephen E.; Bapst, Jonathan; Mehlhaff, Joshua; Griffiths, Stephen G.
2014-11-01
We have applied a self-consistent 1-D model for heat diffusion, vapor diffusion, and ice condensation/sublimation, and surface energy balance to investigate our hypothesis for the source of the recently observed water vapor around Ceres [1]. As described in a companion presentation [2], we find that the estimated global flux of 6 kg/s can be produced by steady-state sublimation of subsurface ice driven by the “geothermal” temperature gradient for a heat flux of 1 mW/m2 - the value estimated for a chondritic abundance of heat-producing elements [3,4]. We will present a detailed description of our Ceres cryothermal diffusion model and comparisons with previous models. One key difference is the use of a new physics-based analytic model (‘MaxRTCM’) for calculating the thermal conductivity (Kth) of planetary regolith [5] that has been validated by comparisons to a wide range of laboratory data [6]. MaxRTCM predicts much lower Kth values in the upper regolith than those in previous work [3]. It also accounts for a process first modeled in a study of unstable equatorial ground ice on Mars [7,8], where vapor diffusing up from a receding ice table toward the surface can recondense at shallower depths - eventually forming a steady-state profile of pore ice volume fraction that increases with depth and maintains a constant flux of vapor at all depths [7]. Using MaxRTCM we calculate the corresponding Kth(z) profiles and will present predictions and implications of the resulting temperature profile in the upper few kilometers of Ceres’ megaregolith.References: [1] Küppers et al. (2014), Nature, 505(7484), 525-527. [2] Wood et al., 2014, this meeting. [3] Fanale & Salvail (1989) Icarus 82, 97-110. [4] McCord and Sotin (2005) JGR 110, E05009. [5] Wood (2013) LPSC Abs. 44, 3077. [6] Wood (2014), Icarus, in revision. [7] Mellon et al. (1997), JGR, 102, 19357-69. [8] Clifford (1993), JGR, 98, 10973-11016.
NASA Astrophysics Data System (ADS)
Manful, D. Y.; Kaule, G.; Wieprecht, S.; Rees, J.; Hu, W.
2009-12-01
Hydroelectric Power (HEP) is proving to be a good alternative to carbon based energy. In the past hydropower especially large scale hydro attracted significant criticism as a result of its impact on the environment. A new breed of hydroelectric dam is in the offing. The aim is to have as little a footprint as possible on the environment in both pre and post construction phases and thus minimize impact on biodiversity whilst producing clean renewable energy. The Bui dam is 400 MW scheme currently under development on the Black Volta River in the Bui national park in Ghana. The reservoir created by the Bui barrage is expected to impact (through inundation) the habitat of two species of hippos know to exist in the park, the Hippopotamus amphibius and the Choeropsis liberiensis. Computer-based models present a unique opportunity to assess quantitatively the impact of the new reservoir on the habitat of the target species in this case the H. amphibious. Until this undertaking, there were very few studies documenting the habitat of the H. amphibious let alone model it. The work and subsequent presentation will show the development of a habitat model for the Hippopotamus amphibius. The Habitat Information retrieval Program based on Streamflow Analysis, in short HIPStrA, is a one dimensional (1D) in-stream, spatially explicit hybrid construct that combines physico-chemical evidence and expert knowledge to forecast river habitat suitability (Hs) for the Hippopotamus amphibius. The version of the model presented is specifically developed to assess the impact of a reservoir created by a hydroelectric dam on potential dwelling areas in the Bui gorge for hippos. Accordingly, this version of HIPStrA simulates a special reservoir suitability index (Rsi), a metric that captures the”hippo friendliness” of any lake or reservoir. The impact of measured and simulated flood events as well as low flows, representing extreme events is also assessed. Recommendations are made for the
Mg line formation in late-type stellar atmospheres. II. Calculations in a grid of 1D models
NASA Astrophysics Data System (ADS)
Osorio, Y.; Barklem, P. S.
2016-02-01
Context. Mg is the α element of choice for Galactic population and chemical evolution studies because it is easily detectable in all late-type stars. Such studies require precise elemental abundances, and thus departures from local thermodynamic equilibrium (LTE) need to be accounted for. Aims: Our goal is to provide reliable departure coefficients and equivalent widths in non-LTE, and for reference in LTE, for diagnostic lines of Mg studied in late-type stars. These can be used, for example, to correct LTE spectra and abundances. Methods: Using the model atom built and tested in the preceding paper in this series, we performed non-LTE radiative transfer calculations in a grid of 3945 stellar 1D atmospheric models. We used a sub-grid of 86 models to explore the propagation of errors in the recent atomic collision calculations to the radiative transfer results. Results: We obtained departure coefficients for all the levels and equivalent widths (in LTE and non-LTE) for all the radiative transitions included in the "final" model atom presented in Paper I. Here we present and describe our results and show some examples of applications of the data. The errors that result from uncertainties in the collisional data are investigated and tabulated. The results for equivalent widths and departure coefficients are made freely available. Conclusions: Giants tend to have negative abundance corrections while dwarfs have positive, though small, corrections. Error analysis results show that uncertainties related to the atomic collision data are typically on the order of 0.01 dex or less, although for few stellar models in specific lines uncertainties can be as large as 0.03 dex. As these errors are less than or on the same order as typical corrections, we expect that we can use these results to extract Mg abundances from high-quality spectra more reliably than from classical LTE analysis. Full Table 1 is only available at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130
Nonlinear kinetic modeling of stimulated Raman scattering
NASA Astrophysics Data System (ADS)
Benisti, Didier
2011-10-01
Despite its importance for many applications, such as or Raman amplification or inertial confinement fusion, deriving a nonlinear estimate of Raman reflectivity in a plasma has remained quite a challenge for decades. This is mainly due to the nonlinear modification of the electron distribution function induced by the plasma wave (EPW), which, in turn, modifies the propagation of this wave. In this paper is derived an envelope equation for the EPW valid in 3D and which accounts for the nonlinear change of its collisionless (Landau-like) damping rate, group velocity, coupling to the electromagnetic drive, frequency and wave number. Our theoretical predictions for each of these terms are carefully compared against results from Vlasov simulations of stimulated Raman scattering (SRS), as well as with other theories. Moreover, our envelope model shows to be as accurate as a Vlasov code in predicting Raman threshold in 1D. Making comparisons with experimental results nevertheless requires including transverse dimensions and letting Raman start from noise. To this end, we performed a completely new derivation of the electrostatic fluctuations in a plasma, which accounts nonlinear effects. Moreover, based on our Multi-D simulations of Raman scattering with our envelope code BRAMA, we discuss the effect on SRS of wave front bowing, transverse detrapping and of a completely new defocussing effect due to the local change in the direction of the EPW group velocity induced by the nonlinear decrease of Landau damping.
Chemical Kinetic Modeling of Biofuel Combustion
NASA Astrophysics Data System (ADS)
Sarathy, Subram Maniam
Bioalcohols, such as bioethanol and biobutanol, are suitable replacements for gasoline, while biodiesel can replace petroleum diesel. Improving biofuel engine performance requires understanding its fundamental combustion properties and the pathways of combustion. This study's contribution is experimentally validated chemical kinetic combustion mechanisms for biobutanol and biodiesel. Fundamental combustion data and chemical kinetic mechanisms are presented and discussed to improve our understanding of biofuel combustion. The net environmental impact of biobutanol (i.e., n-butanol) has not been studied extensively, so this study first assesses the sustainability of n-butanol derived from corn. The results indicate that technical advances in fuel production are required before commercializing biobutanol. The primary contribution of this research is new experimental data and a novel chemical kinetic mechanism for n-butanol combustion. The results indicate that under the given experimental conditions, n-butanol is consumed primarily via abstraction of hydrogen atoms to produce fuel radical molecules, which subsequently decompose to smaller hydrocarbon and oxygenated species. The hydroxyl moiety in n-butanol results in the direct production of the oxygenated species such as butanal, acetaldehyde, and formaldehyde. The formation of these compounds sequesters carbon from forming soot precursors, but they may introduce other adverse environmental and health effects. Biodiesel is a mixture of long chain fatty acid methyl esters derived from fats and oils. This research study presents high quality experimental data for one large fatty acid methyl ester, methyl decanoate, and models its combustion using an improved skeletal mechanism. The results indicate that methyl decanoate is consumed via abstraction of hydrogen atoms to produce fuel radicals, which ultimately lead to the production of alkenes. The ester moiety in methyl decanoate leads to the formation of low molecular
Kinetic modelling of krypton fluoride laser systems
Jancaitis, K.S.
1983-11-01
A kinetic model has been developed for the KrF* rare gas halide laser system, specifically for electron-beam pumped mixtures of krypton, fluorine, and either helium or argon. The excitation produced in the laser gas by the e-beam was calculated numerically using an algorithm checked by comparing the predicted ionization yields in the pure rare gases with their experimental values. The excitation of the laser media by multi-kilovolt x-rays was also modeled and shown to be similar to that produced by high energy electrons. A system of equations describing the transfer of the initial gas excitation into the laser upper level was assembled using reaction rate constants from both experiment and theory. A one-dimensional treatment of the interaction of the laser radiation with the gas was formulated which considered spontaneous and stimulated emission and absorption. The predictions of this model were in good agreement with the fluorescence signals and gain and absorption measured experimentally.
Percolation in a kinetic opinion exchange model
NASA Astrophysics Data System (ADS)
Chandra, Anjan Kumar
2012-02-01
We study the percolation transition of the geometrical clusters in the square-lattice LCCC model [a kinetic opinion exchange model introduced by Lallouache, Chakrabarti, Chakraborti, and Chakrabarti, Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.82.056112 82, 056112 (2010)] with the change in conviction and influencing parameter. The cluster is comprised of the adjacent sites having an opinion value greater than or equal to a prefixed threshold value of opinion (Ω). The transition point is different from that obtained for the transition of the order parameter (average opinion value) found by Lallouache Although the transition point varies with the change in the threshold value of the opinion, the critical exponents for the percolation transition obtained from the data collapses of the maximum cluster size, the cluster size distribution, and the Binder cumulant remain the same. The exponents are also independent of the values of conviction and influencing parameters, indicating the robustness of this transition. The exponents do not match any other known percolation exponents (e.g., the static Ising, dynamic Ising, and standard percolation). This means that the LCCC model belongs to a separate universality class.
1D-Var multilayer assimilation of X-band SAR data into a detailed snowpack model
NASA Astrophysics Data System (ADS)
Phan, X. V.; Ferro-Famil, L.; Gay, M.; Durand, Y.; Dumont, M.; Morin, S.; Allain, S.; D'Urso, G.; Girard, A.
2014-10-01
The structure and physical properties of a snowpack and their temporal evolution may be simulated using meteorological data and a snow metamorphism model. Such an approach may meet limitations related to potential divergences and accumulated errors, to a limited spatial resolution, to wind or topography-induced local modulations of the physical properties of a snow cover, etc. Exogenous data are then required in order to constrain the simulator and improve its performance over time. Synthetic-aperture radars (SARs) and, in particular, recent sensors provide reflectivity maps of snow-covered environments with high temporal and spatial resolutions. The radiometric properties of a snowpack measured at sufficiently high carrier frequencies are known to be tightly related to some of its main physical parameters, like its depth, snow grain size and density. SAR acquisitions may then be used, together with an electromagnetic backscattering model (EBM) able to simulate the reflectivity of a snowpack from a set of physical descriptors, in order to constrain a physical snowpack model. In this study, we introduce a variational data assimilation scheme coupling TerraSAR-X radiometric data into the snowpack evolution model Crocus. The physical properties of a snowpack, such as snow density and optical diameter of each layer, are simulated by Crocus, fed by the local reanalysis of meteorological data (SAFRAN) at a French Alpine location. These snowpack properties are used as inputs of an EBM based on dense media radiative transfer (DMRT) theory, which simulates the total backscattering coefficient of a dry snow medium at X and higher frequency bands. After evaluating the sensitivity of the EBM to snowpack parameters, a 1D-Var data assimilation scheme is implemented in order to minimize the discrepancies between EBM simulations and observations obtained from TerraSAR-X acquisitions by modifying the physical parameters of the Crocus-simulated snowpack. The algorithm then re
Reflected kinetics model for nuclear space reactor kinetics and control scoping calculations
Washington, K.E.
1986-05-01
The objective of this research is to develop a model that offers an alternative to the point kinetics (PK) modelling approach in the analysis of space reactor kinetics and control studies. Modelling effort will focus on the explicit treatment of control drums as reactivity input devices so that the transition to automatic control can be smoothly done. The proposed model is developed for the specific integration of automatic control and the solution of the servo mechanism problem. The integration of the kinetics model with an automatic controller will provide a useful tool for performing space reactor scoping studies for different designs and configurations. Such a tool should prove to be invaluable in the design phase of a space nuclear system from the point of view of kinetics and control limitations.
A marching in space and time (MAST) solver of the shallow water equations. Part I: The 1D model
NASA Astrophysics Data System (ADS)
Aricò, C.; Tucciarelli, T.
2007-05-01
A new approach is presented for the numerical solution of the complete 1D Saint-Venant equations. At each time step, the governing system of partial differential equations (PDEs) is split, using a fractional time step methodology, into a convective prediction system and a diffusive correction system. Convective prediction system is further split into a convective prediction and a convective correction system, according to a specified approximated potential. If a scalar exact potential of the flow field exists, correction vanishes and the solution of the convective correction system is the same solution of the prediction system. Both convective prediction and correction systems are shown to have at each x - t point a single characteristic line, and a corresponding eigenvalue equal to the local velocity. A marching in space and time (MAST) technique is used for the solution of the two systems. MAST solves a system of two ordinary differential equations (ODEs) in each computational cell, using for the time discretization a self-adjusting fraction of the original time step. The computational cells are ordered and solved according to the decreasing value of the potential in the convective prediction step and to the increasing value of the same potential in the convective correction step. The diffusive correction system is solved using an implicit scheme, that leads to the solution of a large linear system, with the same order of the cell number, but sparse, symmetric and well conditioned. The numerical model shows unconditional stability with regard of the Courant-Friedrichs-Levi (CFL) number, requires no special treatment of the source terms and a computational effort almost proportional to the cell number. Several tests have been carried out and results of the proposed scheme are in good agreement with analytical solutions, as well as with experimental data.
Fully implicit kinetic modelling of collisional plasmas
Mousseau, V.A.
1996-05-01
This dissertation describes a numerical technique, Matrix-Free Newton Krylov, for solving a simplified Vlasov-Fokker-Planck equation. This method is both deterministic and fully implicit, and may not have been a viable option before current developments in numerical methods. Results are presented that indicate the efficiency of the Matrix-Free Newton Krylov method for these fully-coupled, nonlinear integro-differential equations. The use and requirement for advanced differencing is also shown. To this end, implementations of Chang-Cooper differencing and flux limited Quadratic Upstream Interpolation for Convective Kinematics (QUICK) are presented. Results are given for a fully kinetic ion-electron problem with a self consistent electric field calculated from the ion and electron distribution functions. This numerical method, including advanced differencing, provides accurate solutions, which quickly converge on workstation class machines. It is demonstrated that efficient steady-state solutions can be achieved to the non-linear integro-differential equation, obtaining quadratic convergence, without incurring the large memory requirements of an integral operator. Model problems are presented which simulate plasma impinging on a plate with both high and low neutral particle recycling typical of a divertor in a Tokamak device. These model problems demonstrate the performance of the new solution method.
Kinetic modeling of cell metabolism for microbial production.
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. PMID:26724578
NASA Astrophysics Data System (ADS)
Augustins, L.; Billardon, R.; Hild, F.
2016-07-01
One of the critical points of the thermomechanical fatigue design process is the correct description of the cyclic behavior of the material. This work focuses on the material of automotive brake discs, namely flake graphite cast iron. The specificity of this material is its asymmetric behavior under tensile and compressive loadings, which is due to the shape of graphite that acts as small cracks. Multiscale models inspired from the literature are first presented. They lead to a good description of the material behavior under cyclic loadings. An elastoviscoplastic constitutive model is then proposed in a one-dimensional setting in order to accurately describe cyclic tests from room temperature up to {600^{circ}{C}}.
Santos-Villalobos, Hector J; Gregor, Jens; Bingham, Philip R
2014-01-01
At the present, neutron sources cannot be fabricated small and powerful enough in order to achieve high resolution radiography while maintaining an adequate flux. One solution is to employ computational imaging techniques such as a Magnified Coded Source Imaging (CSI) system. A coded-mask is placed between the neutron source and the object. The system resolution is increased by reducing the size of the mask holes and the flux is increased by increasing the size of the coded-mask and/or the number of holes. One limitation of such system is that the resolution of current state-of-the-art scintillator-based detectors caps around 50um. To overcome this challenge, the coded-mask and object are magnified by making the distance from the coded-mask to the object much smaller than the distance from object to detector. In previous work, we have shown via synthetic experiments that our least squares method outperforms other methods in image quality and reconstruction precision because of the modeling of the CSI system components. However, the validation experiments were limited to simplistic neutron sources. In this work, we aim to model the flux distribution of a real neutron source and incorporate such a model in our least squares computational system. We provide a full description of the methodology used to characterize the neutron source and validate the method with synthetic experiments.
Chemical kinetic modeling of exhaust hydrocarbon oxidation
Wu, K.C.; Hochgreb, S.; Norris, M.B. . Dept. of Mechanical Engineering)
1995-01-01
Numerical simulations of the oxidation of unburned hydrocarbons from spark ignition engines were made based on full-chemistry, zero-dimensional models and compared with experiments for engine-out hydrocarbons and exhaust port oxidation. Simple correlations can be drawn between calculated results for hydrocarbon oxidation half-lives in plug or stirred reactors and measured hydrocarbon emissions. the extent of reaction through the exhaust port was simulated using calculated temperature histories for each burned gas mass element leaving the cylinder, coupled to detailed chemical kinetic rate equations. The results show that, for the fuels considered, the extent of oxidation of the remaining unburned fuel measured through the exhaust can be bracketed by the calculated results for the well-mixed (average) and core (adiabatically expanded) temperatures in the exhaust. Most of the oxidation is shown to occur at the very early exhaust times. For the paraffins considered, comparisons of simulations and experiments suggest that fuel oxidation is partially controlled by the mixing of cold gases at the initial stages of exhaust, where temperatures are high and the cold unburned mixture emerges from the wall layers into the exhaust jet. These conclusions are supported by the relatively small measured dependence on fuel type of the extent of oxidation in the exhaust, and by the resulting ratio of fuel to nonfuel hydrocarbons in the exhaust port exit.
Noack Watt, Kristin E; Achilleos, Annita; Neben, Cynthia L; Merrill, Amy E; Trainor, Paul A
2016-07-01
Ribosome biogenesis is a global process required for growth and proliferation of all cells, yet perturbation of ribosome biogenesis during human development often leads to tissue-specific defects termed ribosomopathies. Transcription of the ribosomal RNAs (rRNAs) by RNA polymerases (Pol) I and III, is considered a rate limiting step of ribosome biogenesis and mutations in the genes coding for RNA Pol I and III subunits, POLR1C and POLR1D cause Treacher Collins syndrome, a rare congenital craniofacial disorder. Our understanding of the functions of individual RNA polymerase subunits, however, remains poor. We discovered that polr1c and polr1d are dynamically expressed during zebrafish embryonic development, particularly in craniofacial tissues. Consistent with this pattern of activity, polr1c and polr1d homozygous mutant zebrafish exhibit cartilage hypoplasia and cranioskeletal anomalies characteristic of humans with Treacher Collins syndrome. Mechanistically, we discovered that polr1c and polr1d loss-of-function results in deficient ribosome biogenesis, Tp53-dependent neuroepithelial cell death and a deficiency of migrating neural crest cells, which are the primary progenitors of the craniofacial skeleton. More importantly, we show that genetic inhibition of tp53 can suppress neuroepithelial cell death and ameliorate the skeletal anomalies in polr1c and polr1d mutants, providing a potential avenue to prevent the pathogenesis of Treacher Collins syndrome. Our work therefore has uncovered tissue-specific roles for polr1c and polr1d in rRNA transcription, ribosome biogenesis, and neural crest and craniofacial development during embryogenesis. Furthermore, we have established polr1c and polr1d mutant zebrafish as models of Treacher Collins syndrome together with a unifying mechanism underlying its pathogenesis and possible prevention. PMID:27448281
Achilleos, Annita; Neben, Cynthia L.; Merrill, Amy E.; Trainor, Paul A.
2016-01-01
Ribosome biogenesis is a global process required for growth and proliferation of all cells, yet perturbation of ribosome biogenesis during human development often leads to tissue-specific defects termed ribosomopathies. Transcription of the ribosomal RNAs (rRNAs) by RNA polymerases (Pol) I and III, is considered a rate limiting step of ribosome biogenesis and mutations in the genes coding for RNA Pol I and III subunits, POLR1C and POLR1D cause Treacher Collins syndrome, a rare congenital craniofacial disorder. Our understanding of the functions of individual RNA polymerase subunits, however, remains poor. We discovered that polr1c and polr1d are dynamically expressed during zebrafish embryonic development, particularly in craniofacial tissues. Consistent with this pattern of activity, polr1c and polr1d homozygous mutant zebrafish exhibit cartilage hypoplasia and cranioskeletal anomalies characteristic of humans with Treacher Collins syndrome. Mechanistically, we discovered that polr1c and polr1d loss-of-function results in deficient ribosome biogenesis, Tp53-dependent neuroepithelial cell death and a deficiency of migrating neural crest cells, which are the primary progenitors of the craniofacial skeleton. More importantly, we show that genetic inhibition of tp53 can suppress neuroepithelial cell death and ameliorate the skeletal anomalies in polr1c and polr1d mutants, providing a potential avenue to prevent the pathogenesis of Treacher Collins syndrome. Our work therefore has uncovered tissue-specific roles for polr1c and polr1d in rRNA transcription, ribosome biogenesis, and neural crest and craniofacial development during embryogenesis. Furthermore, we have established polr1c and polr1d mutant zebrafish as models of Treacher Collins syndrome together with a unifying mechanism underlying its pathogenesis and possible prevention. PMID:27448281
Enskog-like kinetic models for vehicular traffic
Klar, A.; Wegener, R.
1997-04-01
In the present paper a general criticism of kinetic equations for vehicular traffic is given. The necessity of introducing an Enskog-type correction into these equations is shown. An Enskog-like kinetic traffic flow equation is presented and fluid dynamic equations are derived. This derivation yields new coefficients for the standard fluid dynamic equations of vehicular traffic. Numerical simulations for inhomogeneous traffic flow situations are shown together with a comparison between kinetic and fluid dynamics models.
NASA Astrophysics Data System (ADS)
Marcq, E.
2012-01-01
In order to understand the early history of telluric interiors and atmospheres during the ocean magma stage, a coupled interior-atmosphere-escape model is being developed. This paper describes the atmospheric part and its first preliminary results. A unidimensional, radiative-convective, H2O-CO2 atmosphere is modeled following a vertical T(z) profile similar to Kasting (1988) and Abe and Matsui (1988). Opacities in the thermal IR are then computed using a k-correlated code (KSPECTRUM), tabulated continuum opacities for H2O-H2O and CO2-CO2 absorption, and water or sulphuric acid clouds in the moist convective zone (whenever present). The first results show the existence of two regimes depending on the relative value of the surface temperature Ts compared to a threshold temperature Tc depending on the total gaseous inventory. For Ts < Tc, efficient blanketing results in a cool upper atmosphere, a cloud cover, and a long lifetime for the underneath magma ocean with a net thermal IR flux between 160 and 200 Wm-2. For Ts > Tc, the blanketing is not efficient enough to prevent large radiative heat loss to space through a hot, cloudless atmosphere. Our current calculations may underestimate the thermal flux in the case of hot surfaces with little gaseous content in the atmosphere.
NASA Astrophysics Data System (ADS)
Zulkoffli, Zuliani; Abu Bakar, Elmi
2016-02-01
This paper present pose estimation relation of CAD model object and Projection Real Object (PRI). Image sequence of PRI and CAD model rotate on z axis at 10 degree interval in simulation and real scene used in this experiment. All this image is go through preprocessing stage to rescale object size and image size and transform all the image into silhouette. Correlation of CAD and PRI image is going through in this stage. Magnitude spectrum shows a reliable value in range 0.99 to 1.00 and Phase spectrum correlation shows a fluctuate graph in range 0.56 - 0.97. Euclidean distance correlation graph for CAD and PRI shows 2 zone of similar value due to almost symmetrical object shape. Processing stage of retrieval inspected PRI image in CAD database was carried out using range phase spectrum and maximum magnitude spectrum value within ±10% tolerance. Additional processing stage of retrieval inspected PRI image using Euclidean distance within ±5% tolerance also carried out. Euclidean matching shows a reliable result compared to range phase spectrum and maximum magnitude spectrum value by sacrificing more than 5 times processing time.
NASA Astrophysics Data System (ADS)
Kirkby, A.; Heinson, G.; Holford, S.; Thiel, S.
2015-06-01
We present 1D anisotropic inversion of magnetotelluric (MT) data as a potential tool for mapping structural permeability in sedimentary basins. Using 1D inversions of a 171 site, broadband MT data set from the Koroit region of the Otway Basin, Victoria, Australia, we have delineated an electrically anisotropic layer at approximately 2.5 to 3.5 km depth. The anisotropy strike is consistent between stations at approximately 160° east of north. The depth of anisotropy corresponds to the top depth of the Lower Cretaceous Crayfish Group, and the anisotropy factor increases from west to east. We interpret the anisotropy as resulting from north-northwest oriented, fluid-filled fractures resulting in enhanced electrical and hydraulic conductivity. This interpretation is consistent with permeability data from well formation tests. It is also consistent with the orientation of mapped faults in the area, which are optimally oriented for reactivation in the current stress field.
NASA Astrophysics Data System (ADS)
Bernardie, S.; Desramaut, N.; Russo, G.; Grandjean, G.
2012-04-01
Predicting landslide surface displacements is a challenge for scientists, as it may help save human lives and protect individual housing or transport, energetic facilities. One of the main challenges in active landslide monitoring concerns the prediction of slope's movements in the near future. This study focuses on an innovative methodology to predict landslide surface accelerations, based on a black box tool coupled to a 1D mechanical model. These models are able to predict the evolution of the daily displacements according to the variations of precipitation. More specifically, the impulse response model allows predicting the changes in the landslide movements by computing the transfer function between the input signal (precipitation in this case) and the output signal (the displacements). The second model is based on a simple 1D mechanical assumption, with considering a viscoplastic behavior of the landslide's material, and with taking into account the evolution of the pore water pressure in time. These methods have been applied to the Super-Sauze landslide, located in the Southern French Alps, mountainous region. This site is controlled by complex hydrologic processes leading to active movements within black marls, with velocities ranging between 0.002 and 0.4 m per day. After preliminary tests, results show that the snowmelt has to be taken into account in the models, since the phenomena of freezing /thawing has an influence on the water refills, leading to movement changes. Different approaches to integrate rainfall and/or snow-melting inputs are compared and their complementarity is demonstrated. Finally, a validated methodology for predicting movement changes within landslide based on criteria of comparison between the observed and calculated velocities can be proposed. The results suggest that the impulse response model reproduces the observed data with very good accuracy, whereas the mechanical model seems to be more adapted to predict the movements
A generalized kinetic model for heterogeneous gas-solid reactions.
Xu, Zhijie; Sun, Xin; Khaleel, Mohammad A
2012-08-21
We present a generalized kinetic model for gas-solid heterogeneous reactions taking place at the interface between two phases. The model studies the reaction kinetics by taking into account the reactions at the interface, as well as the transport process within the product layer. The standard unreacted shrinking core model relies on the assumption of quasi-static diffusion that results in a steady-state concentration profile of gas reactant in the product layer. By relaxing this assumption and resolving the entire problem, general solutions can be obtained for reaction kinetics, including the reaction front velocity and the conversion (volume fraction of reacted solid). The unreacted shrinking core model is shown to be accurate and in agreement with the generalized model for slow reaction (or fast diffusion), low concentration of gas reactant, and small solid size. Otherwise, a generalized kinetic model should be used. PMID:22920132
A generalized kinetic model for heterogeneous gas-solid reactions
NASA Astrophysics Data System (ADS)
Xu, Zhijie; Sun, Xin; Khaleel, Mohammad A.
2012-08-01
We present a generalized kinetic model for gas-solid heterogeneous reactions taking place at the interface between two phases. The model studies the reaction kinetics by taking into account the reactions at the interface, as well as the transport process within the product layer. The standard unreacted shrinking core model relies on the assumption of quasi-static diffusion that results in a steady-state concentration profile of gas reactant in the product layer. By relaxing this assumption and resolving the entire problem, general solutions can be obtained for reaction kinetics, including the reaction front velocity and the conversion (volume fraction of reacted solid). The unreacted shrinking core model is shown to be accurate and in agreement with the generalized model for slow reaction (or fast diffusion), low concentration of gas reactant, and small solid size. Otherwise, a generalized kinetic model should be used.
Dynamics and kinetics of model biological systems
NASA Astrophysics Data System (ADS)
Mirigian, Stephen
In this work we study three systems of biological interest: the translocation of a heterogeneously charged polymer through an infinitely thin pore, the wrapped of a rigid particle by a soft vesicle and the modification of the dynamical properties of a gel due to the presence of rigid inclusions. We study the kinetics of translocation for a heterogeneously charged polyelectrolyte through an infinitely narrow pore using the Fokker-Planck formalism to compute mean first passage times, the probability of successful translocation, and the mean successful translocation time for a diblock copolymer. We find, in contrast to the homopolymer result, that details of the boundary conditions lead to qualitatively different behavior. Under experimentally relevant conditions for a diblock copolymer we find that there is a threshold length of the charged block, beyond which the probability of successful translocation is independent of charge fraction. Additionally, we find that mean successful translocation time exhibits non-monotonic behavior with increasing length of the charged fraction; there is an optimum length of the charged block where the mean successful translocation time is slowest and there can be a substantial range of charge fraction where it is slower than a minimally charged chain. For a fixed total charge on the chain, we find that finer distributions of the charge along the chain leads to a significant reduction in mean translocation time compared to the diblock distribution. Endocytosis is modeled using a simple geometrical model from the literature. We map the process of wrapping a rigid spherical bead onto a one-dimensional stochastic process described by the Fokker-Planck equation to compute uptake rates as a function of membrane properties and system geometry. We find that simple geometrical considerations pick an optimal particle size for uptake and a corresponding maximal uptake rate, which can be controlled by altering the material properties of the
Biomass torrefaction: modeling of volatile and solid product evolution kinetics.
Bates, Richard B; Ghoniem, Ahmed F
2012-11-01
The aim of this work is the development of a kinetics model for the evolution of the volatile and solid product composition during torrefaction conditions between 200 and 300°C. Coupled to an existing two step solid mass loss kinetics mechanism, this model describes the volatile release kinetics in terms of a set of identifiable chemical components, permitting the solid product composition to be estimated by mass conservation. Results show that most of the volatiles released during the first stage include highly oxygenated species such as water, acetic acid, and carbon dioxide, while volatiles released during the second step are composed primarily of lactic acid, methanol, and acetic acid. This kinetics model will be used in the development of a model to describe reaction energy balance and heat release dynamics. PMID:23026268
An integral representation of functions in gas-kinetic models
NASA Astrophysics Data System (ADS)
Perepelitsa, Misha
2016-08-01
Motivated by the theory of kinetic models in gas dynamics, we obtain an integral representation of lower semicontinuous functions on {{{R}}^d,} {d≥1}. We use the representation to study the problem of compactness of a family of the solutions of the discrete time BGK model for the compressible Euler equations. We determine sufficient conditions for strong compactness of moments of kinetic densities, in terms of the measures from their integral representations.
HCCI in a CFR engine: experiments and detailed kinetic modeling
Flowers, D; Aceves, S; Smith, R; Torres, J; Girard, J; Dibble, R
1999-11-05
Single cylinder engine experiments and chemical kinetic modeling have been performed to study the effect of variations in fuel, equivalence ratio, and intake charge temperature on the start of combustion and the heat release rate. Neat propane and a fuel blend of 15% dimethyl-ether in methane have been studied. The results demonstrate the role of these parameters on the start of combustion, efficiency, imep, and emissions. Single zone kinetic modeling results show the trends consistent with the experimental results.
Shen, Guang-Bin; Xia, Ke; Li, Xiu-Tao; Li, Jun-Ling; Fu, Yan-Hua; Yuan, Lin; Zhu, Xiao-Qing
2016-03-24
In this work, kinetic isotope effect (KIEself) values of 68 hydride self-exchange reactions, XH(D) + X(+) → X(+) + XH(D), in acetonitrile at 298 K were determined using a new experimental method. KIE values of 4556 hydride cross transfer reactions, XH(D) + Y(+) → X(+) + YH(D), in acetonitrile were estimated from the 68 determined KIEself values of hydride self-exchange reactions using a new KIE relation formula derived from Zhu's kinetic equation and the reliability of the estimations was verified using different experimental methods. A new KIE kinetic model to explain and predict KIE values was developed according to Zhu's kinetic model using two different Morse free energy curves instead of one Morse free energy curve in the traditional KIE theories to describe the free energy changes of X-H bond and X-D bond dissociation in chemical reactions. The most significant contribution of this paper to KIE theory is to build a new KIE kinetic model, which can be used to not only uniformly explain the various (normal, enormous and inverse) KIE values but also safely prodict KIE values of various chemical reactions. PMID:26938149
Detailed Chemical Kinetic Modeling of Cyclohexane Oxidation
Silke, E J; Pitz, W J; Westbrook, C K; Ribaucour, M
2006-11-10
A detailed chemical kinetic mechanism has been developed and used to study the oxidation of cyclohexane at both low and high temperatures. Reaction rate constant rules are developed for the low temperature combustion of cyclohexane. These rules can be used for in chemical kinetic mechanisms for other cycloalkanes. Since cyclohexane produces only one type of cyclohexyl radical, much of the low temperature chemistry of cyclohexane is described in terms of one potential energy diagram showing the reaction of cyclohexyl radical + O{sub 2} through five, six and seven membered ring transition states. The direct elimination of cyclohexene and HO{sub 2} from RO{sub 2} is included in the treatment using a modified rate constant of Cavallotti et al. Published and unpublished data from the Lille rapid compression machine, as well as jet-stirred reactor data are used to validate the mechanism. The effect of heat loss is included in the simulations, an improvement on previous studies on cyclohexane. Calculations indicated that the production of 1,2-epoxycyclohexane observed in the experiments can not be simulated based on the current understanding of low temperature chemistry. Possible 'alternative' H-atom isomerizations leading to different products from the parent O{sub 2}QOOH radical were included in the low temperature chemical kinetic mechanism and were found to play a significant role.
Zhang, Damao; Wang, Zhien; Heymsfield, Andrew J.; Fan, Jiwen; Luo, Tao
2014-10-01
Measurement of ice number concentration in clouds is important but still challenging. Stratiform mixed-phase clouds (SMCs) provide a simple scenario for retrieving ice number concentration from remote sensing measurements. The simple ice generation and growth pattern in SMCs offers opportunities to use cloud radar reflectivity (Ze) measurements and other cloud properties to infer ice number concentration quantitatively. To understand the strong temperature dependency of ice habit and growth rate quantitatively, we develop a 1-D ice growth model to calculate the ice diffusional growth along its falling trajectory in SMCs. The radar reflectivity and fall velocity profiles of ice crystals calculated from the 1-D ice growth model are evaluated with the Atmospheric Radiation Measurements (ARM) Climate Research Facility (ACRF) ground-based high vertical resolution radar measurements. Combining Ze measurements and 1-D ice growth model simulations, we develop a method to retrieve the ice number concentrations in SMCs at given cloud top temperature (CTT) and liquid water path (LWP). The retrieved ice concentrations in SMCs are evaluated with in situ measurements and with a three-dimensional cloud-resolving model simulation with a bin microphysical scheme. These comparisons show that the retrieved ice number concentrations are within an uncertainty of a factor of 2, statistically.
Information cascade, Kirman's ant colony model, and kinetic Ising model
NASA Astrophysics Data System (ADS)
Hisakado, Masato; Mori, Shintaro
2015-01-01
In this paper, we discuss a voting model in which voters can obtain information from a finite number of previous voters. There exist three groups of voters: (i) digital herders and independent voters, (ii) analog herders and independent voters, and (iii) tanh-type herders. In our previous paper Hisakado and Mori (2011), we used the mean field approximation for case (i). In that study, if the reference number r is above three, phase transition occurs and the solution converges to one of the equilibria. However, the conclusion is different from mean field approximation. In this paper, we show that the solution oscillates between the two states. A good (bad) equilibrium is where a majority of r select the correct (wrong) candidate. In this paper, we show that there is no phase transition when r is finite. If the annealing schedule is adequately slow from finite r to infinite r, the voting rate converges only to the good equilibrium. In case (ii), the state of reference votes is equivalent to that of Kirman's ant colony model, and it follows beta binomial distribution. In case (iii), we show that the model is equivalent to the finite-size kinetic Ising model. If the voters are rational, a simple herding experiment of information cascade is conducted. Information cascade results from the quenching of the kinetic Ising model. As case (i) is the limit of case (iii) when tanh function becomes a step function, the phase transition can be observed in infinite size limit. We can confirm that there is no phase transition when the reference number r is finite.
Elimination kinetic model for organic chemicals in earthworms.
Dimitrova, N; Dimitrov, S; Georgieva, D; Van Gestel, C A M; Hankard, P; Spurgeon, D; Li, H; Mekenyan, O
2010-08-15
Mechanistic understanding of bioaccumulation in different organisms and environments should take into account the influence of organism and chemical depending factors on the uptake and elimination kinetics of chemicals. Lipophilicity, metabolism, sorption (bioavailability) and biodegradation of chemicals are among the important factors that may significantly affect the bioaccumulation process in soil organisms. This study attempts to model elimination kinetics of organic chemicals in earthworms by accounting for the effects of both chemical and biological properties, including metabolism. The modeling approach that has been developed is based on the concept for simulating metabolism used in the BCF base-line model developed for predicting bioaccumulation in fish. Metabolism was explicitly accounted for by making use of the TIMES engine for simulation of metabolism and a set of principal transformations. Kinetic characteristics of transformations were estimated on the basis of observed kinetics data for the elimination of organic chemicals from earthworms. PMID:20185163
NASA Astrophysics Data System (ADS)
Wittkowski, M.; Chiavassa, A.; Freytag, B.; Scholz, M.; Höfner, S.; Karovicova, I.; Whitelock, P. A.
2016-03-01
Aims: We aim at comparing spectro-interferometric observations of Mira variable asymptotic giant branch (AGB) stars with the latest 1D dynamic model atmospheres based on self-excited pulsation models (CODEX models) and with 3D dynamic model atmospheres including pulsation and convection (CO5BOLD models) to better understand the processes that extend the molecular atmosphere to radii where dust can form. Methods: We obtained a total of 20 near-infrared K-band spectro-interferometric snapshot observations of the Mira variables o Cet, R Leo, R Aqr, X Hya, W Vel, and R Cnc with a spectral resolution of about 1500. We compared observed flux and visibility spectra with predictions by CODEX 1D dynamic model atmospheres and with azimuthally averaged intensities based on CO5BOLD 3D dynamic model atmospheres. Results: Our visibility data confirm the presence of spatially extended molecular atmospheres located above the continuum radii with large-scale inhomogeneities or clumps that contribute a few percent of the total flux. The detailed structure of the inhomogeneities or clumps show a variability on time scales of 3 months and above. Both modeling attempts provided satisfactory fits to our data. In particular, they are both consistent with the observed decrease in the visibility function at molecular bands of water vapor and CO, indicating a spatially extended molecular atmosphere. Observational variability phases are mostly consistent with those of the best-fit CODEX models, except for near-maximum phases, where data are better described by near-minimum models. Rosseland angular diameters derived from the model fits are broadly consistent between those based on the 1D and the 3D models and with earlier observations. We derived fundamental parameters including absolute radii, effective temperatures, and luminosities for our sources. Conclusions: Our results provide a first observational support for theoretical results that shocks induced by convection and pulsation in the
Chemical Kinetic Models for HCCI and Diesel Combustion
Pitz, W J; Westbrook, C K; Mehl, M; Sarathy, S M
2010-11-15
Predictive engine simulation models are needed to make rapid progress towards DOE's goals of increasing combustion engine efficiency and reducing pollutant emissions. These engine simulation models require chemical kinetic submodels to allow the prediction of the effect of fuel composition on engine performance and emissions. Chemical kinetic models for conventional and next-generation transportation fuels need to be developed so that engine simulation tools can predict fuel effects. The objectives are to: (1) Develop detailed chemical kinetic models for fuel components used in surrogate fuels for diesel and HCCI engines; (2) Develop surrogate fuel models to represent real fuels and model low temperature combustion strategies in HCCI and diesel engines that lead to low emissions and high efficiency; and (3) Characterize the role of fuel composition on low temperature combustion modes of advanced combustion engines.
Kinetic modeling of hyperpolarized 13C 1-pyruvate metabolism in normal rats and TRAMP mice
NASA Astrophysics Data System (ADS)
Zierhut, Matthew L.; Yen, Yi-Fen; Chen, Albert P.; Bok, Robert; Albers, Mark J.; Zhang, Vickie; Tropp, Jim; Park, Ilwoo; Vigneron, Daniel B.; Kurhanewicz, John; Hurd, Ralph E.; Nelson, Sarah J.
2010-01-01
PurposeTo investigate metabolic exchange between 13C 1-pyruvate, 13C 1-lactate, and 13C 1-alanine in pre-clinical model systems using kinetic modeling of dynamic hyperpolarized 13C spectroscopic data and to examine the relationship between fitted parameters and dose-response. Materials and methodsDynamic 13C spectroscopy data were acquired in normal rats, wild type mice, and mice with transgenic prostate tumors (TRAMP) either within a single slice or using a one-dimensional echo-planar spectroscopic imaging (1D-EPSI) encoding technique. Rate constants were estimated by fitting a set of exponential equations to the dynamic data. Variations in fitted parameters were used to determine model robustness in 15 mm slices centered on normal rat kidneys. Parameter values were used to investigate differences in metabolism between and within TRAMP and wild type mice. ResultsThe kinetic model was shown here to be robust when fitting data from a rat given similar doses. In normal rats, Michaelis-Menten kinetics were able to describe the dose-response of the fitted exchange rate constants with a 13.65% and 16.75% scaled fitting error (SFE) for kpyr→lac and kpyr→ala, respectively. In TRAMP mice, kpyr→lac increased an average of 94% after up to 23 days of disease progression, whether the mice were untreated or treated with casodex. Parameters estimated from dynamic 13C 1D-EPSI data were able to differentiate anatomical structures within both wild type and TRAMP mice. ConclusionsThe metabolic parameters estimated using this approach may be useful for in vivo monitoring of tumor progression and treatment efficacy, as well as to distinguish between various tissues based on metabolic activity.
Hybrid fluid/kinetic model for parallel heat conduction
Callen, J.D.; Hegna, C.C.; Held, E.D.
1998-12-31
It is argued that in order to use fluid-like equations to model low frequency ({omega} < {nu}) phenomena such as neoclassical tearing modes in low collisionality ({nu} < {omega}{sub b}) tokamak plasmas, a Chapman-Enskog-like approach is most appropriate for developing an equation for the kinetic distortion (F) of the distribution function whose velocity-space moments lead to the needed fluid moment closure relations. Further, parallel heat conduction in a long collision mean free path regime can be described through a combination of a reduced phase space Chapman-Enskog-like approach for the kinetics and a multiple-time-scale analysis for the fluid and kinetic equations.
Li, Yulan; Hu, Shenyang Y.; Sun, Xin; Khaleel, Mohammad A.
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 bubble 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
Kinetic Modelling of Macroscopic Properties Changes during Crosslinked Polybutadiene Oxidation
NASA Astrophysics Data System (ADS)
Audouin, Ludmila; Coquillat, Marie; Colin, Xavier; Verdu, Jacques; Nevière, Robert
2008-08-01
The thermal oxidation of additive free hydroxyl-terminated polybutadiene (HTPB) isocyanate crosslinked rubber bulk samples has been studied at 80, 100 and 120 °C in air. The oxidation kinetics has been monitored by gravimetry and thickness distribution of oxidation products was determined by FTIR mapping. Changes of elastic shear modulus G' during oxidation were followed during oxidation at the same temperatures. The kinetic model established previously for HTPB has been adapted for bulk sample oxidation using previously determined set of kinetic parameters. Oxygen diffusion control of oxidation has been introduced into the model. The mass changes kinetic curves and oxidation products profiles were simulated and adequate fit was obtained. Using the rubber elasticity theory the elastic modulus changes were simulated taking into account the elastically active chains concentration changes due to chain scission and crosslinking reactions. The reasonable fit of G' as a function of oxidation time experimental curves was obtained.
Breakdown parameter for kinetic modeling of multiscale gas flows.
Meng, Jianping; Dongari, Nishanth; Reese, Jason M; Zhang, Yonghao
2014-06-01
Multiscale methods built purely on the kinetic theory of gases provide information about the molecular velocity distribution function. It is therefore both important and feasible to establish new breakdown parameters for assessing the appropriateness of a fluid description at the continuum level by utilizing kinetic information rather than macroscopic flow quantities alone. We propose a new kinetic criterion to indirectly assess the errors introduced by a continuum-level description of the gas flow. The analysis, which includes numerical demonstrations, focuses on the validity of the Navier-Stokes-Fourier equations and corresponding kinetic models and reveals that the new criterion can consistently indicate the validity of continuum-level modeling in both low-speed and high-speed flows at different Knudsen numbers. PMID:25019910
Kinetic exchange models: From molecular physics to social science
NASA Astrophysics Data System (ADS)
Patriarca, Marco; Chakraborti, Anirban
2013-08-01
We discuss several multi-agent models that have their origin in the kinetic exchange theory of statistical mechanics and have been recently applied to a variety of problems in the social sciences. This class of models can be easily adapted for simulations in areas other than physics, such as the modeling of income and wealth distributions in economics and opinion dynamics in sociology.
EFFECTS OF PHOTOCHEMICAL KINETIC MECHANISMS ON OXIDANT MODEL PREDICTIONS
The comparative effects of kinetic mechanisms on oxidant model predictions have been tested using two different mechanisms (the Carbon-Bond Mechanism II (CBM-II) and the Demerjian Photochemical Box Model (DPBM) mechanism) in three air quality models (the OZIPM/EKMA, the Urban Air...
Detailed Chemical Kinetic Modeling of Hydrazine Decomposition
NASA Technical Reports Server (NTRS)
Meagher, Nancy E.; Bates, Kami R.
2000-01-01
The purpose of this research project is to develop and validate a detailed chemical kinetic mechanism for gas-phase hydrazine decomposition. Hydrazine is used extensively in aerospace propulsion, and although liquid hydrazine is not considered detonable, many fuel handling systems create multiphase mixtures of fuels and fuel vapors during their operation. Therefore, a thorough knowledge of the decomposition chemistry of hydrazine under a variety of conditions can be of value in assessing potential operational hazards in hydrazine fuel systems. To gain such knowledge, a reasonable starting point is the development and validation of a detailed chemical kinetic mechanism for gas-phase hydrazine decomposition. A reasonably complete mechanism was published in 1996, however, many of the elementary steps included had outdated rate expressions and a thorough investigation of the behavior of the mechanism under a variety of conditions was not presented. The current work has included substantial revision of the previously published mechanism, along with a more extensive examination of the decomposition behavior of hydrazine. An attempt to validate the mechanism against the limited experimental data available has been made and was moderately successful. Further computational and experimental research into the chemistry of this fuel needs to be completed.
Chemical kinetic modeling of H{sub 2} applications
Marinov, N.M.; Westbrook, C.K.; Cloutman, L.D.
1995-09-01
Work being carried out at LLNL has concentrated on studies of the role of chemical kinetics in a variety of problems related to hydrogen combustion in practical combustion systems, with an emphasis on vehicle propulsion. Use of hydrogen offers significant advantages over fossil fuels, and computer modeling provides advantages when used in concert with experimental studies. Many numerical {open_quotes}experiments{close_quotes} can be carried out quickly and efficiently, reducing the cost and time of system development, and many new and speculative concepts can be screened to identify those with sufficient promise to pursue experimentally. This project uses chemical kinetic and fluid dynamic computational modeling to examine the combustion characteristics of systems burning hydrogen, either as the only fuel or mixed with natural gas. Oxidation kinetics are combined with pollutant formation kinetics, including formation of oxides of nitrogen but also including air toxics in natural gas combustion. We have refined many of the elementary kinetic reaction steps in the detailed reaction mechanism for hydrogen oxidation. To extend the model to pressures characteristic of internal combustion engines, it was necessary to apply theoretical pressure falloff formalisms for several key steps in the reaction mechanism. We have continued development of simplified reaction mechanisms for hydrogen oxidation, we have implemented those mechanisms into multidimensional computational fluid dynamics models, and we have used models of chemistry and fluid dynamics to address selected application problems. At the present time, we are using computed high pressure flame, and auto-ignition data to further refine the simplified kinetics models that are then to be used in multidimensional fluid mechanics models. Detailed kinetics studies have investigated hydrogen flames and ignition of hydrogen behind shock waves, intended to refine the detailed reactions mechanisms.
NASA Astrophysics Data System (ADS)
Kirkegaard, Casper; Foged, Nikolaj; Auken, Esben; Christiansen, Anders Vest; Sørensen, Kurt
2012-09-01
Helicopter borne time domain EM systems historically measure only the Z-component of the secondary field, whereas fixed wing systems often measure all field components. For the latter systems the X-component is often used to map discrete conductors, whereas it finds little use in the mapping of layered settings. Measuring the horizontal X-component with an offset loop helicopter system probes the earth with a complementary sensitivity function that is very different from that of the Z-component, and could potentially be used for improving resolution of layered structures in one dimensional modeling. This area is largely unexplored in terms of quantitative results in the literature, since measuring and inverting X-component data from a helicopter system is not straightforward: The signal strength is low, the noise level is high, the signal is very sensitive to the instrument pitch and the sensitivity function also has a complex lateral behavior. The basis of our study is a state of the art inversion scheme, using a local 1D forward model description, in combination with experiences gathered from extending the SkyTEM system to measure the X component. By means of a 1D sensitivity analysis we motivate that in principle resolution of layered structures can be improved by including an X-component signal in a 1D inversion, given the prerequisite that a low-pass filter of suitably low cut-off frequency can be employed. In presenting our practical experiences with modifying the SkyTEM system we discuss why this prerequisite unfortunately can be very difficult to fulfill in practice. Having discussed instrumental limitations we show what can be obtained in practice using actual field data. Here, we demonstrate how the issue of high sensitivity towards instrument pitch can be overcome by including the pitch angle as an inversion parameter and how joint inversion of the Z- and X-components produces virtually the same model result as for the Z-component alone. We conclude that
Kinetic model for the collisionless sheath of a collisional plasma
NASA Astrophysics Data System (ADS)
Tang, Xian-Zhu; Guo, Zehua
2016-08-01
Collisional plasmas typically have mean-free-path still much greater than the Debye length, so the sheath is mostly collisionless. Once the plasma density, temperature, and flow are specified at the sheath entrance, the profile variation of electron and ion density, temperature, flow speed, and conductive heat fluxes inside the sheath is set by collisionless dynamics, and can be predicted by an analytical kinetic model distribution. These predictions are contrasted here with direct kinetic simulations, showing good agreement.
The Nonlinear Magnetosphere: Expressions in MHD and in Kinetic Models
NASA Technical Reports Server (NTRS)
Hesse, Michael; Birn, Joachim
2011-01-01
Like most plasma systems, the magnetosphere of the Earth is governed by nonlinear dynamic evolution equations. The impact of nonlinearities ranges from large scales, where overall dynamics features are exhibiting nonlinear behavior, to small scale, kinetic, processes, where nonlinear behavior governs, among others, energy conversion and dissipation. In this talk we present a select set of examples of such behavior, with a specific emphasis on how nonlinear effects manifest themselves in MHD and in kinetic models of magnetospheric plasma dynamics.
Kinetic model of continuous-wave flow chemical lasers
NASA Astrophysics Data System (ADS)
Gao, Z.; X., E.
1982-02-01
A kinetic approach to modeling the gain in a chemical wave continuous laser when the lasing frequency is coincident with the center of the line shape is presented. Governing equations are defined for the relaxing behavior of an initially nonequilibrium distribution toward the local equilibrium Boltzmann-Maxwellian distribution. A new gain is introduced which is related to the thermal motion of the molecules and cold-reaction and premixed CW models are discussed. Coincidence of the lasing frequency with the line shape is demonstrated to result in a radiative intensity within the homogeneous broadening limit. The rate model predictions are compared with those of the kinetic model. It is found that when the broadening parameter is less than 0.2 the kinetic model more accurately describes the behavior of the CW chemical laser.
NASA Astrophysics Data System (ADS)
Van Eester, Dirk; Lerche, Ernesto
2013-05-01
Both at low and higher cyclotron harmonics, properly accounting for finite Larmor radius effects is crucial in many ion cyclotron resonance frequency heating scenario's creating high energy tails. This paper discusses an extension TOMCAT-U of the 1D TOMCAT tokamak plasma wave equation solver (Van Eester and Koch 1998 Plasma Phys. Control. Fusion 40 1949) to arbitrary harmonics and arbitrary wavelengths while only keeping leading order terms in equilibrium variation terms. Rather than adopting the particle position, the guiding center position is used as the independent variable when writing down an expression for the dielectric response that is suitable for numerical application. This choice of independent variable yields intuitive expressions involving the Kennel-Engelmann operator which can directly be linked to the corresponding expressions in the RF diffusion operator appearing in the Fokker-Planck equation. It also guarantees that a positive definite power transfer from waves to particles is ensured for any of the wave modes in a plasma in which all populations have a Maxwellian distribution, as is expected from first principles. Rather than relying on a truncated Taylor series expansion of the dielectric response, an integrodifferential approach that retains all finite Larmor radius effects is proposed. To keep the required computation time for this generalized description reasonable, tabulation of integrals is intensively used. Although the accent is on the presentation of the upgraded formalism as well as the adopted recursions and tabulations, a few examples are provided to illustrate the potential of the new wave code that relies on these tabulations.
A coke oven model including thermal decomposition kinetics of tar
Munekane, Fuminori; Yamaguchi, Yukio; Tanioka, Seiichi
1997-12-31
A new one-dimensional coke oven model has been developed for simulating the amount and the characteristics of by-products such as tar and gas as well as coke. This model consists of both heat transfer and chemical kinetics including thermal decomposition of coal and tar. The chemical kinetics constants are obtained by estimation based on the results of experiments conducted to investigate the thermal decomposition of both coal and tar. The calculation results using the new model are in good agreement with experimental ones.
Kinetic modeling of the Townsend breakdown in argon
NASA Astrophysics Data System (ADS)
Macheret, S. O.; Shneider, M. N.
2013-10-01
Kinetic modeling of the Townsend breakdown in argon was performed in the "forward-back" approximation. The kinetic model was found to adequately describe the left branch of the Paschen curve, and the important role of ionization by fast ions and atoms near the cathode, as well as the increase in secondary emission coefficient in strong electric fields described in the literature, was confirmed. The modeling also showed that the electron energy distribution function develops a beam of high-energy electrons and that the runaway effect, i.e., the monotonic increase of the mean electron energy with the distance from the cathode, occurs at the left branch of the Paschen curve.
Alastruey, Jordi; Khir, Ashraf W.; Matthys, Koen S.; Segers, Patrick; Sherwin, Spencer J.; Verdonck, Pascal R.; Parker, Kim H.; Peiró, Joaquim
2011-01-01
The accuracy of the nonlinear one-dimensional (1-D) equations of pressure and flow wave propagation in Voigt-type visco-elastic arteries was tested against measurements in a well-defined experimental 1:1 replica of the 37 largest conduit arteries in the human systemic circulation. The parameters required by the numerical algorithm were directly measured in the in vitro setup and no data fitting was involved. The inclusion of wall visco-elasticity in the numerical model reduced the underdamped high-frequency oscillations obtained using a purely elastic tube law, especially in peripheral vessels, which was previously reported in this paper [Matthys et al., 2007. Pulse wave propagation in a model human arterial network: Assessment of 1-D numerical simulations against in vitro measurements. J. Biomech. 40, 3476–3486]. In comparison to the purely elastic model, visco-elasticity significantly reduced the average relative root-mean-square errors between numerical and experimental waveforms over the 70 locations measured in the in vitro model: from 3.0% to 2.5% (p<0.012) for pressure and from 15.7% to 10.8% (p<0.002) for the flow rate. In the frequency domain, average relative errors between numerical and experimental amplitudes from the 5th to the 20th harmonic decreased from 0.7% to 0.5% (p<0.107) for pressure and from 7.0% to 3.3% (p<10−6) for the flow rate. These results provide additional support for the use of 1-D reduced modelling to accurately simulate clinically relevant problems at a reasonable computational cost. PMID:21724188
Verley, Jason C.; Axness, Carl L.; Hembree, Charles Edward; Keiter, Eric Richard; Kerr, Bert
2012-04-01
Photocurrent generated by ionizing radiation represents a threat to microelectronics in radiation environments. Circuit simulation tools such as SPICE [1] can be used to analyze these threats, and typically rely on compact models for individual electrical components such as transistors and diodes. Compact models consist of a handful of differential and/or algebraic equations, and are derived by making simplifying assumptions to any of the many semiconductor transport equations. Historically, many photocurrent compact models have suffered from accuracy issues due to the use of qualitative approximation, rather than mathematically correct solutions to the ambipolar diffusion equation. A practical consequence of this inaccuracy is that a given model calibration is trustworthy over only a narrow range of operating conditions. This report describes work to produce improved compact models for photocurrent. Specifically, an analytic model is developed for epitaxial diode structures that have a highly doped subcollector. The analytic model is compared with both numerical TCAD calculations, as well as the compact model described in reference [2]. The new analytic model compares well against TCAD over a wide range of operating conditions, and is shown to be superior to the compact model from reference [2].
Hard-sphere kinetic models for inert and reactive mixtures.
Polewczak, Jacek
2016-10-19
I consider stochastic variants of a simple reacting sphere (SRS) kinetic model (Xystris and Dahler 1978 J. Chem. Phys. 68 387-401, Qin and Dahler 1995 J. Chem. Phys. 103 725-50, Dahler and Qin 2003 J. Chem. Phys. 118 8396-404) for dense reacting mixtures. In contrast to the line-of-center models of chemical reactive models, in the SRS kinetic model, the microscopic reversibility (detailed balance) can be easily shown to be satisfied, and thus all mathematical aspects of the model can be fully justified. In the SRS model, the molecules behave as if they were single mass points with two internal states. Collisions may alter the internal states of the molecules, and this occurs when the kinetic energy associated with the reactive motion exceeds the activation energy. Reactive and non-reactive collision events are considered to be hard sphere-like. I consider a four component mixture A, B, A (*), B (*), in which the chemical reactions are of the type [Formula: see text], with A (*) and B (*) being distinct species from A and B. This work extends the joined works with George Stell to the kinetic models of dense inert and reactive mixtures. The idea of introducing smearing-type effect in the collisional process results in a new class of stochastic kinetic models for both inert and reactive mixtures. In this paper the important new mathematical properties of such systems of kinetic equations are proven. The new results for stochastic revised Enskog system for inert mixtures are also provided. PMID:27545341
Korrodi-Gregório, Luís; Margarida Lopes, Ana; Esteves, Sara L. C.; Afonso, Sandra; Lemos de Matos, Ana; Lissovsky, Andrey A.; da Cruz e Silva, Odete A. B.; Esteves, Pedro José; Fardilha, Margarida
2013-01-01
T-complex testis expressed protein 1 domain containing 4 (TCTEX1D4) contains the canonical phosphoprotein phosphatase 1 (PPP1) binding motif, composed by the amino acid sequence RVSF. We identified and validated the binding of TCTEX1D4 to PPP1 and demonstrated that indeed this protein is a novel PPP1 interacting protein. Analyses of twenty-one mammalian species available in public databases and seven Lagomorpha sequences obtained in this work showed that the PPP1 binding motif 90RVSF93 is present in all of them and is flanked by a palindromic sequence, PLGS, except in three species of pikas (Ochotona princeps, O. dauurica and O. pusilla). Furthermore, for the Ochotona species an extra glycosylation site, motif 96NLS98, and the loss of the palindromic sequence were observed. Comparison with other lagomorphs suggests that this event happened before the Ochotona radiation. The dN/dS for the sequence region comprising the PPP1 binding motif and the flanking palindrome highly supports the hypothesis that for Ochotona species this region has been evolving under positive selection. In addition, mutational screening shows that the ability of pikas TCTEX1D4 to bind to PPP1 is maintained, although the PPP1 binding motif is disrupted, and the N- and C-terminal surrounding residues are also abrogated. These observations suggest pika as an ideal model to study novel PPP1 complexes regulatory mechanisms. PMID:24130861
Kinetic Modeling of the Moon-Solar Wind Plasma Interaction
NASA Astrophysics Data System (ADS)
Fatemi, S.; Poppe, A. R.; Halekas, J. S.; Delory, G. T.; Holmstrom, M.; Farrell, W. M.
2016-05-01
We use a three-dimensional self-consistent hybrid model of plasma (kinetic ions, fluid electrons) to study solar wind plasma interaction with the Moon. We have studied lunar wake, interaction with crustal fields, and lunar interior with our model.
Technology Transfer Automated Retrieval System (TEKTRAN)
Watershed modeling is a key component of watershed management that involves the simulation of hydrological and fluvial processes for predicting flow and sediment transport within a watershed. For practical purposes, most numerical models have been developed to simulate either runoff and soil erosion...
Computer-Aided Construction of Chemical Kinetic Models
Green, William H.
2014-12-31
The combustion chemistry of even simple fuels can be extremely complex, involving hundreds or thousands of kinetically significant species. The most reasonable way to deal with this complexity is to use a computer not only to numerically solve the kinetic model, but also to construct the kinetic model in the first place. Because these large models contain so many numerical parameters (e.g. rate coefficients, thermochemistry) one never has sufficient data to uniquely determine them all experimentally. Instead one must work in “predictive” mode, using theoretical rather than experimental values for many of the numbers in the model, and as appropriate refining the most sensitive numbers through experiments. Predictive chemical kinetics is exactly what is needed for computer-aided design of combustion systems based on proposed alternative fuels, particularly for early assessment of the value and viability of proposed new fuels before those fuels are commercially available. This project was aimed at making accurate predictive chemical kinetics practical; this is a challenging goal which requires a range of science advances. The project spanned a wide range from quantum chemical calculations on individual molecules and elementary-step reactions, through the development of improved rate/thermo calculation procedures, the creation of algorithms and software for constructing and solving kinetic simulations, the invention of methods for model-reduction while maintaining error control, and finally comparisons with experiment. Many of the parameters in the models were derived from quantum chemistry calculations, and the models were compared with experimental data measured in our lab or in collaboration with others.
Model reduction for chemical kinetics: An optimization approach
Petzold, L.; Zhu, W.
1999-04-01
The kinetics of a detailed chemically reacting system can potentially be very complex. Although the chemist may be interested in only a few species, the reaction model almost always involves a much larger number of species. Some of those species are radicals, which are very reactive species and can be important intermediaries in the reaction scheme. A large number of elementary reactions can occur among the species; some of these reactions are fast and some are slow. The aim of simplified kinetics modeling is to derive the simplest reaction system which retains the essential features of the full system. An optimization-based method for reduction of the number of species and reactions in chemical kinetics model is described. Numerical results for several reaction mechanisms illustrate the potential of this approach.
Kinetic modelling for zinc (II) ions biosorption onto Luffa cylindrica
NASA Astrophysics Data System (ADS)
Oboh, I.; Aluyor, E.; Audu, T.
2015-03-01
The biosorption of Zinc (II) ions onto a biomaterial - Luffa cylindrica has been studied. This biomaterial was characterized by elemental analysis, surface area, pore size distribution, scanning electron microscopy, and the biomaterial before and after sorption, was characterized by Fourier Transform Infra Red (FTIR) spectrometer. The kinetic nonlinear models fitted were Pseudo-first order, Pseudo-second order and Intra-particle diffusion. A comparison of non-linear regression method in selecting the kinetic model was made. Four error functions, namely coefficient of determination (R2), hybrid fractional error function (HYBRID), average relative error (ARE), and sum of the errors squared (ERRSQ), were used to predict the parameters of the kinetic models. The strength of this study is that a biomaterial with wide distribution particularly in the tropical world and which occurs as waste material could be put into effective utilization as a biosorbent to address a crucial environmental problem.
Kinetic modelling for zinc (II) ions biosorption onto Luffa cylindrica
Oboh, I.; Aluyor, E.; Audu, T.
2015-03-30
The biosorption of Zinc (II) ions onto a biomaterial - Luffa cylindrica has been studied. This biomaterial was characterized by elemental analysis, surface area, pore size distribution, scanning electron microscopy, and the biomaterial before and after sorption, was characterized by Fourier Transform Infra Red (FTIR) spectrometer. The kinetic nonlinear models fitted were Pseudo-first order, Pseudo-second order and Intra-particle diffusion. A comparison of non-linear regression method in selecting the kinetic model was made. Four error functions, namely coefficient of determination (R{sup 2}), hybrid fractional error function (HYBRID), average relative error (ARE), and sum of the errors squared (ERRSQ), were used to predict the parameters of the kinetic models. The strength of this study is that a biomaterial with wide distribution particularly in the tropical world and which occurs as waste material could be put into effective utilization as a biosorbent to address a crucial environmental problem.
Simulations of plasma sheaths using continuum kinetic models
NASA Astrophysics Data System (ADS)
Srinivasan, Bhuvana; Hakim, Ammar
2015-11-01
Understanding plasma sheath physics is important for the performance of devices such as Hall thrusters due to the effect of energetic particles on electrode erosion. Plasma sheath physics is studied using kinetic and multi-fluid models with relevance to secondary electron emissions and plasma-surface interactions. Continuum kinetic models are developed to directly solve the Vlasov-Poisson equation using the discontinuous Galerkin method for each of the ion and electron species. A steady-state sheath is simulated by including a simple model for a neutral fluid. Multi-fluid simulations for the plasma sheath are also performed using the discontinuous Galerkin method to solve a complete set of fluid equations for each of the ion and electron species. The kinetic plasma sheath is compared to a multi-fluid plasma sheath. Supported by Air Force Office of Scientific Research.
Microscopic kinetic model for polymer crystal growth
NASA Astrophysics Data System (ADS)
Hu, Wenbing
2011-03-01
Linear crystal growth rates characterize the net result of competition between growth and melting at the liquid-solid interfaces. The rate equation for polymer crystal growth can be derived with a barrier term for crystal growth and with a driving force term of excess lamellar thickness, provided that growth and melting share the same rate-determining steps at the growth front. Such an ansatz can be verified by the kinetic symmetry between growth and melting around the melting point of lamellar crystals, as made in our recent dynamic Monte Carlo simulations. The profile of the growth/melting front appears as wedge-shaped, with the free energy barrier for intramolecular secondary crystal nucleation at its top, and with the driving force gained via instant thickening at its bottom. Such a scenario explains unique phenomena on polymer crystal growth, such as chain folding, regime transitions, molecular segregation of polydisperse polymers, self-poisoning with integer-number chain-folding of short chains, and colligative growth rates of binary mixtures of two chain lengths. Financial support from NNSFC No. 20825415 and NBRPC No. 2011CB606100 is acknowledged.
A Detailed Chemical Kinetic Model for TNT
Pitz, W J; Westbrook, C K
2005-01-13
A detailed chemical kinetic mechanism for 2,4,6-tri-nitrotoluene (TNT) has been developed to explore problems of explosive performance and soot formation during the destruction of munitions. The TNT mechanism treats only gas-phase reactions. Reactions for the decomposition of TNT and for the consumption of intermediate products formed from TNT are assembled based on information from the literature and on current understanding of aromatic chemistry. Thermodynamic properties of intermediate and radical species are estimated by group additivity. Reaction paths are developed based on similar paths for aromatic hydrocarbons. Reaction-rate constant expressions are estimated from the literature and from analogous reactions where the rate constants are available. The detailed reaction mechanism for TNT is added to existing reaction mechanisms for RDX and for hydrocarbons. Computed results show the effect of oxygen concentration on the amount of soot precursors that are formed in the combustion of RDX and TNT mixtures in N{sub 2}/O{sub 2} mixtures.
Kinetic model for dilute traffic flow
NASA Astrophysics Data System (ADS)
Balouchi, Ashkan; Browne, Dana A.
The flow of traffic represents a many-particle non-equilibrium problem with important practical consequences. Traffic behavior has been studied using a variety of approaches, including fluid dynamics models, Boltzmann equation, and recently cellular automata (CA). The CA model for traffic flow that Nagel and Schreckenberg (NS) introduced can successfully mimic many of the known features of the traffic flow. We show that in the dilute limit of the NS model, where vehicles exhibit free flow, cars show significant nearest neighbor correlation primarily via a short-range repulsion. introduce an approximate analytic model to describe this dilute limit. We show that the distribution of the distance between consecutive vehicles obeys a drift-diffusion equation. We compared this model with direct simulations. The steady state solution and relaxation of this model agrees well with direct simulations. We explore how this model breaks down as the transition to jams occurs.
NASA Astrophysics Data System (ADS)
Yang, Jun; Leconte, Jérémy; Wolf, Eric T.; Goldblatt, Colin; Feldl, Nicole; Merlis, Timothy; Wang, Yuwei; Koll, Daniel D. B.; Ding, Feng; Forget, François; Abbot, Dorian S.
2016-08-01
An accurate estimate of the inner edge of the habitable zone is critical for determining which exoplanets are potentially habitable and for designing future telescopes to observe them. Here, we explore differences in estimating the inner edge among seven one-dimensional radiative transfer models: two line-by-line codes (SMART and LBLRTM) as well as five band codes (CAM3, CAM4_Wolf, LMDG, SBDART, and AM2) that are currently being used in global climate models. We compare radiative fluxes and spectra in clear-sky conditions around G and M stars, with fixed moist adiabatic profiles for surface temperatures from 250 to 360 K. We find that divergences among the models arise mainly from large uncertainties in water vapor absorption in the window region (10 μm) and in the region between 0.2 and 1.5 μm. Differences in outgoing longwave radiation increase with surface temperature and reach 10–20 W m‑2 differences in shortwave reach up to 60 W m‑2, especially at the surface and in the troposphere, and are larger for an M-dwarf spectrum than a solar spectrum. Differences between the two line-by-line models are significant, although smaller than among the band models. Our results imply that the uncertainty in estimating the insolation threshold of the inner edge (the runaway greenhouse limit) due only to clear-sky radiative transfer is ≈10% of modern Earth’s solar constant (i.e., ≈34 W m‑2 in global mean) among band models and ≈3% between the two line-by-line models. These comparisons show that future work is needed that focuses on improving water vapor absorption coefficients in both shortwave and longwave, as well as on increasing the resolution of stellar spectra in broadband models.
Grant, K.E.; Taylor, K.E.; Ellis, J.S.; Wuebbles, D.J.
1987-07-01
The authors have implemented a series of state of the art radiation transport submodels in previously developed one dimensional and two dimensional chemical transport models of the troposphere and stratosphere. These submodels provide the capability of calculating accurate solar and infrared heating rates. They are a firm basis for further radiation submodel development as well as for studying interactions between radiation and model dynamics under varying conditions of clear sky, clouds, and aerosols. 37 refs., 3 figs.
NASA Astrophysics Data System (ADS)
Ryu, Jaiyoung; Hu, Xiao; Shadden, Shawn C.
2014-11-01
The cerebral circulation is unique in its ability to maintain blood flow to the brain under widely varying physiologic conditions. Incorporating this autoregulatory response is critical to cerebral blood flow modeling, as well as investigations into pathological conditions. We discuss a one-dimensional nonlinear model of blood flow in the cerebral arteries that includes coupling of autoregulatory lumped parameter networks. The model is tested to reproduce a common clinical test to assess autoregulatory function - the carotid artery compression test. The change in the flow velocity at the middle cerebral artery (MCA) during carotid compression and release demonstrated strong agreement with published measurements. The model is then used to investigate vasospasm of the MCA, a common clinical concern following subarachnoid hemorrhage. Vasospasm was modeled by prescribing vessel area reduction in the middle portion of the MCA. Our model showed similar increases in velocity for moderate vasospasms, however, for serious vasospasm (~ 90% area reduction), the blood flow velocity demonstrated decrease due to blood flow rerouting. This demonstrates a potentially important phenomenon, which otherwise would lead to false-negative decisions on clinical vasospasm if not properly anticipated.
Molecular mechanisms of protein aggregation from global fitting of kinetic models.
Meisl, Georg; Kirkegaard, Julius B; Arosio, Paolo; Michaels, Thomas C T; Vendruscolo, Michele; Dobson, Christopher M; Linse, Sara; Knowles, Tuomas P J
2016-02-01
fitting the chosen models using an advanced minimization algorithm to yield the reaction orders and rate constants. Finally, we outline how to use this approach to investigate which targets potential inhibitors of amyloid formation bind to and where in the reaction mechanism they act. The protocol, from processing data to determining mechanisms, can be completed in <1 d. PMID:26741409
NASA Astrophysics Data System (ADS)
Khonde, Ruta Dhanram; Chaurasia, Ashish Subhash
2015-04-01
The present study provides the kinetic model to describe the pyrolysis of sawdust, rice-husk and sugarcane bagasse as biomass. The kinetic scheme used for modelling of primary pyrolysis consisting of the two parallel reactions giving gaseous volatiles and solid char. Estimation of kinetic parameters for pyrolysis process has been carried out for temperature range of 773-1,173 K. As there are serious issues regarding non-convergence of some of the methods or solutions converging to local-optima, the proposed kinetic model is optimized to predict the best values of kinetic parameters for the system using three approaches—Two-dimensional surface fitting non-linear regression technique, MS-Excel Solver Tool and COMSOL software. The model predictions are in agreement with experimental data over a wide range of pyrolysis conditions. The estimated value of kinetic parameters are compared with earlier researchers and found to be matching well.
NASA Astrophysics Data System (ADS)
Hoch, J. M.; Bierkens, M. F.; Van Beek, R.; Winsemius, H.; Haag, A.
2015-12-01
Understanding the dynamics of fluvial floods is paramount to accurate flood hazard and risk modeling. Currently, economic losses due to flooding constitute about one third of all damage resulting from natural hazards. Given future projections of climate change, the anticipated increase in the World's population and the associated implications, sound knowledge of flood hazard and related risk is crucial. Fluvial floods are cross-border phenomena that need to be addressed accordingly. Yet, only few studies model floods at the large-scale which is preferable to tiling the output of small-scale models. Most models cannot realistically model flood wave propagation due to a lack of either detailed channel and floodplain geometry or the absence of hydrologic processes. This study aims to develop a large-scale modeling tool that accounts for both hydrologic and hydrodynamic processes, to find and understand possible sources of errors and improvements and to assess how the added hydrodynamics affect flood wave propagation. Flood wave propagation is simulated by DELFT3D-FM (FM), a hydrodynamic model using a flexible mesh to schematize the study area. It is coupled to PCR-GLOBWB (PCR), a macro-scale hydrological model, that has its own simpler 1D routing scheme (DynRout) which has already been used for global inundation modeling and flood risk assessments (GLOFRIS; Winsemius et al., 2013). A number of model set-ups are compared and benchmarked for the simulation period 1986-1996: (0) PCR with DynRout; (1) using a FM 2D flexible mesh forced with PCR output and (2) as in (1) but discriminating between 1D channels and 2D floodplains, and, for comparison, (3) and (4) the same set-ups as (1) and (2) but forced with observed GRDC discharge values. Outputs are subsequently validated against observed GRDC data at Óbidos and flood extent maps from the Dartmouth Flood Observatory. The present research constitutes a first step into a globally applicable approach to fully couple
Effects of a space modulation on the behavior of a 1D alternating Heisenberg spin-1/2 model.
Mahdavifar, Saeed; Abouie, Jahanfar
2011-06-22
The effects of a magnetic field (h) and a space modulation (δ) on the magnetic properties of a one-dimensional antiferromagnetic-ferromagnetic Heisenberg spin-1/2 model have been studied by means of numerical exact diagonalization of finite size systems, the nonlinear σ model, and a bosonization approach. The space modulation is considered on the antiferromagnetic couplings. At δ = 0, the model is mapped to a gapless Lüttinger liquid phase by increasing the magnetic field. However, the space modulation induces a new gap in the spectrum of the system and the system experiences different quantum phases which are separated by four critical fields. By opening the new gap, a magnetization plateau appears at ½M(sat). The effects of the space modulation are reflected in the emergence of a plateau in other physical functions such as the F-dimer and the bond-dimer order parameters, and the pair-wise entanglement. PMID:21613724
NASA Technical Reports Server (NTRS)
Schmitt, G. A.; Abreu, V. J.; Hays, P. B.
1981-01-01
Thermal and nonthermal O(1D) number density profiles are calculated. The two populations are assumed to be coupled by a thermalization cross-section which determines the loss and production in the nonthermal and thermal populations, respectively. The sources, sinks and transport of the two populations are used to model volume emission rate profiles at 6300 A. The 6300 A brightness measured by the Visible Airglow Experiment is then used to establish the presence of the nonthermal population and to determine the thermalization cross-section.
NASA Astrophysics Data System (ADS)
Ireland, Gareth; Petropoulos, George P.; Carlson, Toby N.; Purdy, Sarah
2015-04-01
Sensitivity analysis (SA) consists of an integral and important validatory check of a computer simulation model before it is used to perform any kind of analysis. In the present work, we present the results from a SA performed on the SimSphere Soil Vegetation Atmosphere Transfer (SVAT) model utilising a cutting edge and robust Global Sensitivity Analysis (GSA) approach, based on the use of the Gaussian Emulation Machine for Sensitivity Analysis (GEM-SA) tool. The sensitivity of the following model outputs was evaluated: the ambient CO2 concentration and the rate of CO2 uptake by the plant, the ambient O3 concentration, the flux of O3 from the air to the plant/soil boundary, and the flux of O3 taken up by the plant alone. The most sensitive model inputs for the majority of model outputs were related to the structural properties of vegetation, namely, the Leaf Area Index, Fractional Vegetation Cover, Cuticle Resistance and Vegetation Height. External CO2 in the leaf and the O3 concentration in the air input parameters also exhibited significant influence on model outputs. This work presents a very important step towards an all-inclusive evaluation of SimSphere. Indeed, results from this study contribute decisively towards establishing its capability as a useful teaching and research tool in modelling Earth's land surface interactions. This is of considerable importance in the light of the rapidly expanding use of this model worldwide, which also includes research conducted by various Space Agencies examining its synergistic use with Earth Observation data towards the development of operational products at a global scale. This research was supported by the European Commission Marie Curie Re-Integration Grant "TRANSFORM-EO". SimSphere is currently maintained and freely distributed by the Department of Geography and Earth Sciences at Aberystwyth University (http://www.aber.ac.uk/simsphere). Keywords: CO2 flux, ambient CO2, O3 flux, SimSphere, Gaussian process emulators
NASA Astrophysics Data System (ADS)
Valstar, Johan; Rowe, Ed; Konstantina, Moirogiorgou; Giannakis, Giorgos; Nikolaidis, Nikolaos
2014-05-01
explore the complex interactions involved in soil development and change. We were unable to identify appropriately-detailed existing models for plant productivity and for the dynamics of soil aggregation and porosity, and so developed the PROSUM and CAST models, respectively, to simulate these subsystems. Moreover, we applied the BRNS generator to obtain a chemical equilibrium model. These were combined with HYDRUS-1D (water and solute transport), a weathering model (derived from the SAFE model) and a simple bioturbation model. The model includes several feedbacks, such as the effect of soil organic matter on water retention and hydraulic conductivity. We encountered several important challenges when building the integrated model. First, a mechanism was developed that initiates the execution of a single time step for an individual sub-model and accounts for the relevant mass transfers between sub-models. This allows for different and sometimes variable time step duration in the submodels. Secondly, we removed duplicated processes and identified and included relevant solute production terms that had been neglected. The model is being tested against datasets obtained from several Soil Critical Zone Observatories in Europe. This contribution focuses on the design strategy for the model.
NASA Astrophysics Data System (ADS)
Kim, W.; Yum, S. S.
2015-12-01
Visibility degradation due to fog can be very hazardous both to ground transportation and aviation traffic. However, prediction of fog using numerical models is difficult because fog formation is usually determined by local meteorological conditions that are hard to be measured and modeled with sufficient resolution. For this reason, there have been several attempts to build a coupled system of a fine resolution 1D model and a 3D mesoscale model with a usual grid resolution. In this study we uses the coupled system of the 1D PAFOG model and the 3D WRF model to simulate fogs formed at a southern coastal region of Korea, where the National Center for Intensive Observation of Severe Weather (NCIO) is located. Unique to NCIO is that it has a 300 m meteorological tower on which some basic meteorological variables (temperature, dew point temperature and winds) are measured at eleven different altitudes. In addition comprehensive cloud physics measurements are made with various remote sensing instruments such as cloud radar, wind profiler, microwave radiometer, micro rain radar. Several fog cases are identified during 2015 and will be simulated by the coupled system. The comprehensive set of measurement data from NCIO will be utilized as input to the model system and for evaluating the results. Particularly the data for initial and boundary conditions, which are tightly connected to the coupled model predictability, are extracted from the tower measurement. Furthermore, various sensitivity experiments will be done to enhance our understanding of the coastal fog formation mechanism. Detailed results will be discussed at the conference.
VizieR Online Data Catalog: Grid of 1D models for Mg line formation (Osorio+, 2016)
NASA Astrophysics Data System (ADS)
Osorio, Y.; Barklem, P. S.
2015-11-01
Table mgnlte.dat provides equivalent widths in LTE and non-LTE for 19 MgI spectral lines calculated in 3859 stellar atmospheres and using 21 Mg abundance per star. These data can be used to calculate abundance corrections in a broad variety of stellar models and Mg enhancements in a consistent way. The tables in data/* provides departure coefficients of the LEVEL in 10563 stellar atmospheres at 56 depth points in the atmosphere and using 21 Mg abundance values per star. These data can be used to calculate abundance corrections in a broad variety of stellar models and Mg enhancements in a consistent way. The format of the departure coefficients is the unit-less value of the ratio between the nlte and lte population of the level LEVEL of Mg. (3 data files).
Solid-liquid interdiffusion (SLID) bonding in the Au-In system: experimental study and 1D modelling
NASA Astrophysics Data System (ADS)
Deillon, Léa; Hessler-Wyser, Aïcha; Hessler, Thierry; Rappaz, Michel
2015-12-01
Au-In bonds with a nominal composition of about 60 at.% In were fabricated for use in wafer-level packaging of MEMS. The microstructure of the bonds was studied by scanning electron microscopy. The bond hermeticity was then assessed using oxidation of Cu thin discs predeposited within the sealed packages. The three intermetallic compounds AuIn2, AuIn and Au7In3 were observed. Their thickness evolution during bonding and after subsequent heat treatment was successfully modelled using a finite difference model of diffusion, thermodynamic data and diffusion coefficients calibrated from isothermal diffusion couples. 17% of the packages were hermetic and, although the origin of the leaks could not be clearly identified, it appeared that hermeticity was correlated with the unevenness of the metallisation and/or wafer and the fact that the bonds shrink due to density differences as the relative fractions of the various phases gradually evolve.
NASA Technical Reports Server (NTRS)
Reinarts, Thomas R.; Crain, William K.; Stuckey, C. Irvin; Palko, Richard L.
1998-01-01
The purpose of the work is to demonstrate that the flat test panel substrate temperatures are consistent with analysis predictions for MCC-1 applied to a aluminum substrate. The testing was performed in an aerothermal facility on samples of three different thicknesses of MCC-1 on an aluminum substrate. The results of the test were compared with a Transient Thermal model. The key assumptions of the Transient Thermal model were: (1) a one-dimensional heat transfer; (2) a constant ablation recession rate (determined from pre and post-test measurements); (3) ablation temperature of 540 degrees F; (4) Char left behind the ablation front; and (5) temperature jump correction for incident heat transfer coefficient. Two methods were used to model the heating of bare MCC-1: (1) Directly input surface temperature as a function of time; and (2) Aerothermal heating using calibration plate data and subtracting the radiation losses to tunnel walls. The results are presented as graphs. This article is presented in Viewgraph format.
The (O1D) 630.0 nm thermospheric dayglow measured by WINDII and modeled by TRANSCAR
NASA Astrophysics Data System (ADS)
Culot, F.; Lathuillère, C.; Lilensten, J.; Witasse, O.
2003-04-01
A key problem in aeronomic research is the study of airglow emissions. They are observed by a large range of techniques such as rockets, ground-based and space instruments. They provide a better understanding of the processes controling the state of the upper mesosphere and thermosphere. The modeling of those emissions is a complementary approach. It involves a wide variety of quantities : EUV &UV solar fluxes, photoelectron fluxes, neutral, ion, and electron densities and temperatures, and also chemical reactions rates. In this work we focus on the 630.0 nm emission (red line), using all of the Wind Imaging Interferometer (WINDII) available data from February 1992 to June 1995, in order to obtain the Volume Emission Rate profiles. Thus, we analyse the links between the altitude and intensity of the measured profiles peaks and various geophysical parameters, among them the Solar Zenith Angle and the solar activity. Finally, we compare our results with those given by the TRANSCAR model which allows us to adjust our modeling of the upper atmosphere and gives rise to a better understanding of the dayglow emissions.
An efficient chemical kinetics solver using high dimensional model representation
Shorter, J.A.; Ip, P.C.; Rabitz, H.A.
1999-09-09
A high dimensional model representation (HDMR) technique is introduced to capture the input-output behavior of chemical kinetic models. The HDMR expresses the output chemical species concentrations as a rapidly convergent hierarchical correlated function expansion in the input variables. In this paper, the input variables are taken as the species concentrations at time t{sub i} and the output is the concentrations at time t{sub i} + {delta}, where {delta} can be much larger than conventional integration time steps. A specially designed set of model runs is performed to determine the correlated functions making up the HDMR. The resultant HDMR can be used to (1) identify the key input variables acting independently or cooperatively on the output, and (2) create a high speed fully equivalent operational model (FEOM) serving to replace the original kinetic model and its differential equation solver. A demonstration of the HDMR technique is presented for stratospheric chemical kinetics. The FEOM proved to give accurate and stable chemical concentrations out to long times of many years. In addition, the FEOM was found to be orders of magnitude faster than a conventional stiff equation solver. This computational acceleration should have significance in many chemical kinetic applications.
Towards a principled way of making kinetic models from data
NASA Astrophysics Data System (ADS)
Presse, Steve
2012-02-01
Kinetic model extraction from noisy data is the basic route to mechanistic insight in biology. I will show how the tools of Maximum Caliber (the dynamical analog of Maximum Entropy) can be used to infer -and not fit- models in a way which is driven by the structure and limitations of the data. For instance, the typical output of an experiment in systems biology is the stochastic expression of one reporter gene. Master equations used to model the regulatory process underlying the stochastic gene expression require knowledge of a circuit topology and rates. However rates and topology are often fit as these are rarely all independently determinable from the limited data. Our goal is to build a kinetic model from the data available with no adjustable parameter using the tools of Maximum Caliber. We apply our method to infer the statistics of rare stochastic switching events in the genetic toggle switch from fluctuations on shorter measurable timescales. In addition, we discuss how these tools can be used to infer kinetic models from real single molecule data drawn from anomalous folding kinetics of phosphoglycerate kinase and RNA hairpin zipping-unzipping time traces.
Kinetics of steel slag leaching: Batch tests and modeling.
De Windt, Laurent; Chaurand, Perrine; Rose, Jerome
2011-02-01
Reusing steel slag as an aggregate for road construction requires to characterize the leaching kinetics and metal releases. In this study, basic oxygen furnace (BOF) steel slag were subjected to batch leaching tests at liquid to solid ratios (L/S) of 10 and 100 over 30 days; the leachate chemistry being regularly sampled in time. A geochemical model of the steel slag is developed and validated from experimental data, particularly the evolution with leaching of mineralogical composition of the slag and trace element speciation. Kinetics is necessary for modeling the primary phase leaching, whereas a simple thermodynamic equilibrium approach can be used for secondary phase precipitation. The proposed model simulates the kinetically-controlled dissolution (hydrolysis) of primary phases, the precipitation of secondary phases (C-S-H, hydroxide and spinel), the pH and redox conditions, and the progressive release of major elements as well as the metals Cr and V. Modeling indicates that the dilution effect of the L/S ratio is often coupled to solubility-controlled processes, which are sensitive to both the pH and the redox potential. A sensitivity analysis of kinetic uncertainties on the modeling of element releases is performed. PMID:20646922
Kinetic theory and models of the global heliosphere
NASA Astrophysics Data System (ADS)
Izmodenov, Vladislav
2016-07-01
Current state of art in the kinetic-MHD modeling of the solar/stellar wind interaction with the local interstellar medium (LISM) will be reviewed. New model results will be presented as well as compared with currently available observations from both Voyagers and Interstellar Boundary Explorer (IBEX). Differences between model and observations will be discussed. Especial discussion will be on the recently suggested (by M. Opher and J. Drake) two-jet structure of the heliosphere.
NASA Astrophysics Data System (ADS)
Yu, Chih-Peng; Cheng, Chia-Chi; Lai, Jiunnren; Chiang, Chih-Hung
2012-04-01
In this study, a linear model with frequency dependent structural property was used to generate the corresponding frequency response function and dynamic stiffness for selected dynamic problems where certain nonlinearity can be resulted from time/space varying characteristics of the bridge vibrations. Derivation of the proposed formula is based on the vibration theory of the elementary member with frequency dependent elastic properties, in which Modulus of Elasticity can be interpreted as serial and parallel connections of springs and dashpots. This paper first describes the use of the proposed formulation to reasonably depict the nonlinear cable vibration associated with the varying tension forces over time. The proposed formulation can also be used to simulate flexural vibration of damage beams in which the elastic property involves certain space varying or time varying characteristics. Simple numerical/experimental data were next used to demonstrate and confirm the potential application of such simulation idea. Consequently, it is concluded that such assessment model with frequency dependent parameters can be practically feasible and serve as a useful tool in the spectral analysis regarding dynamic problems of slender bridge members.
Floodplain mapping via 1D and quasi-2D numerical models in the valley of Thessaly, Greece
NASA Astrophysics Data System (ADS)
Oikonomou, Athanasios; Dimitriadis, Panayiotis; Koukouvinos, Antonis; Tegos, Aristoteles; Pagana, Vasiliki; Panagopoulos, Panayiotis-Dionisios; Mamassis, Nikolaos; Koutsoyiannis, Demetris
2013-04-01
The European Union Floods Directive defines a flood as 'a covering by water of land not normally covered by water'. Human activities, such as agriculture, urban development, industry and tourism, contribute to an increase in the likelihood and adverse impacts of flood events. The study of the hydraulic behaviour of a river is important in flood risk management. Here, we investigate the behaviour of three hydraulic models, with different theoretical frameworks, in a real case scenario. The area is located in the Penios river basin, in the plain of Thessaly (Greece). The three models used are the one-dimensional HEC-RAS and the quasi two-dimensional LISFLOOD-FP and FLO-2D which are compared to each other, in terms of simulated maximum water depth as well as maximum flow velocity, and to a real flood event. Moreover, a sensitivity analysis is performed to determine how each simulation is affected by the river and floodplain roughness coefficient, in terms of flood inundation.
NASA Astrophysics Data System (ADS)
Harel, Marie-Alice; Mouche, Emmanuel
2015-04-01
Despite the recent research focused on runoff pattern connectivity in hydrology, there is a surprising lack of theoretical knowledge regarding hillslope runoff generation and dynamics during a rainfall event. The transient problem is especially unaddressed. In this paper we propose a model based on queueing theory formalism for the infiltration-excess overland flow generation on soils with random infiltration properties. The influence of rainfall intensity and duration on runoff dynamics and connectivity is studied thanks to this model, numerical simulation and available steady-state results. We limit our study to a rainfall intensity that is a rectangular function of time. Exact solutions for the case of spatially random exponential distributions of soil infiltrability and rainfall intensity are developed. Simulations validate these analytical results and allow for the study the rising and recession limbs of the hydrograph for different rainfall characteristics. The case of a deterministic uniform rainfall rate and different infiltrability distributions is also discussed in light of runoff connectivity. We show that the connectivity framework contributes to a better understanding and prediction of runoff pattern formation and evolution with time. A fragmented overland flow is shown to have shorter charge and discharge periods after the onset and offset of rainfall compared to well connected runoff fields. These results demonstrate that the transient regime characteristics are linked with connectivity parameters, rainstorm properties and scale issues.
NASA Technical Reports Server (NTRS)
Minow, Joseph I.; Coffey, Victoria N.; Parker, Linda N.; Blackwell, William C., Jr.; Jun, Insoo; Garrett, Henry B.
2007-01-01
The NUMIT 1-dimensional bulk charging model is used as a screening to ol for evaluating time-dependent bulk internal or deep dielectric) ch arging of dielectrics exposed to penetrating electron environments. T he code is modified to accept time dependent electron flux time serie s along satellite orbits for the electron environment inputs instead of using the static electron flux environment input originally used b y the code and widely adopted in bulk charging models. Application of the screening technique ts demonstrated for three cases of spacecraf t exposure within the Earth's radiation belts including a geostationa ry transfer orbit and an Earth-Moon transit trajectory for a range of orbit inclinations. Electric fields and charge densities are compute d for dielectric materials with varying electrical properties exposed to relativistic electron environments along the orbits. Our objectiv e is to demonstrate a preliminary application of the time-dependent e nvironments input to the NUMIT code for evaluating charging risks to exposed dielectrics used on spacecraft when exposed to the Earth's ra diation belts. The results demonstrate that the NUMIT electric field values in GTO orbits with multiple encounters with the Earth's radiat ion belts are consistent with previous studies of charging in GTO orb its and that potential threat conditions for electrostatic discharge exist on lunar transit trajectories depending on the electrical proper ties of the materials exposed to the radiation environment.
Gyrofluid turbulence models with kinetic effects
Dorland, W.; Hammett, G.W.
1992-12-01
Nonlinear gyrofluid equations are derived by taking moments of the nonlinear, electrostatic gyrokinetic equation. The principal model presented includes evolution equations for the guiding center n, u[parallel], T[parallel], and T[perpendicular] along with an equation expressing the quasineutrality constraint. Additional evolution equations for higher moments are derived which may be used if greater accuracy is desired. The moment hierarchy is closed with a Landau-damping model which is equivalent to a multi-pole approximation to the plasma dispersion function, extended to include finite Larmor radius effects. In particular, new dissipative, nonlinear terms are found which model the perpendicular phase-mixing of the distribution function along contours of constant electrostatic potential. These FLR phase-mixing'' terms introduce a hyperviscosity-like damping [proportional to] k[sub [perpendicular
NASA Astrophysics Data System (ADS)
Sakaris, C. S.; Sakellariou, J. S.; Fassois, S. D.
2016-06-01
This study focuses on the problem of vibration-based damage precise localization via data-based, time series type, methods for structures consisting of 1D, 2D, or 3D elements. A Generalized Functional Model Based method is postulated based on an expanded Vector-dependent Functionally Pooled ARX (VFP-ARX) model form, capable of accounting for an arbitrary structural topology. The FP model's operating parameter vector elements are properly constrained to reflect any given topology. Damage localization is based on operating parameter vector estimation within the specified topology, so that the location estimate and its uncertainty bounds are statistically optimal. The method's effectiveness is experimentally demonstrated through damage precise localization on a laboratory spatial truss structure using various damage scenarios and a single pair of random excitation - vibration response signals in a low and limited frequency bandwidth.
Kinetic model of particle-inhibited grain growth
NASA Astrophysics Data System (ADS)
Thompson, Gary Scott
The effects of second phase particles on matrix grain growth kinetics were investigated using Al2O3-SiC as a model system. In particular, the validity of the conclusion drawn from a previous kinetic analysis that the kinetics of particle-inhibited grain growth in Al2 O3-SiC samples with an intermediate volume fraction of second phase could be well quantified by a modified-Zener model was investigated. A critical analysis of assumptions made during the previous kinetic analysis revealed oversimplifications which affect the validity of the conclusion. Specifically, the degree of interaction between particles and grain boundaries was assumed to be independent of the mean second phase particle size and size distribution. In contrast, current measurements indicate that the degree of interaction in Al2O3-SiC is dependent on these parameters. An improved kinetic model for particle-inhibited grain growth in Al 2O3-SiC was developed using a modified-Zener approach. The comparison of model predictions with experimental grain growth data indicated that significant discrepancies (as much as 4--5 orders of magnitude) existed. Based on this, it was concluded that particles had a much more significant effect on grain growth kinetics than that caused by a simple reduction of the boundary driving force due to the removal of boundary area. Consequently, it was also concluded that the conclusion drawn from the earlier kinetic analysis regarding the validity of a modified-Zener model was incorrect. Discrepancies between model and experiment were found to be the result of a significant decrease in experimental growth rate constant not predicted by the model. Possible physical mechanisms for such a decrease were investigated. The investigation of a small amount of SiO2 on grain growth in Al2O3 indicated that the decrease was not the result of a decrease in grain boundary mobility due to impurity contamination by particles. By process of elimination and based on previous observations
NASA Astrophysics Data System (ADS)
Ghorbani, Ahmad; Camerlynck, Christian; Florsch, Nicolas
2009-02-01
An inversion code has been constructed using Matlab, to recover 1D parameters of the Cole-Cole model from spectral induced polarization data. In a spectral induced polarization survey, impedances are recorded at various frequencies. Both induced polarization and electromagnetic coupling effects occur simultaneously over the experimental frequency bandwidth, and these become progressively more dominant when the frequency increases. We used the CR1Dmod code published by Ingeman-Nielsen and Baumgartner [2006]. This code solves for electromagnetic responses, in the presence of complex resistivity effects in a 1D Earth. In this paper, a homotopy method has been designed by the authors to overcome the local convergence problem of normal iterative methods. In addition, in order to further condition the inverse problem, we incorporated standard Gauss-Newton (or quasi-Newton) methods. Graphical user interfaces enable straightforward entering of the data and the a priori model, as well as the cable configuration. Two synthetic examples are presented, showing that the spectral parameters can be recovered from multifrequency, complex resistivity data.
NASA Astrophysics Data System (ADS)
Laginha Silva, Patricia; Martins, Flávio A.; Boski, Tomász; Sampath, Dissanayake M. R.
2010-05-01
processes. In this viewpoint the system is broken down into its fundamental components and processes and the model is build up by selecting the important processes regardless of its time and space scale. This viewpoint was only possible to pursue in the recent years due to improvement in system knowledge and computer power (Paola, 2000). The primary aim of this paper is to demonstrate that it is possible to simulate the evolution of the sediment river bed, traditionally studied with synthetic models, with a process-based hydrodynamic, sediment transport and morphodynamic model, solving explicitly the mass and momentum conservation equations. With this objective, a comparison between two mathematical models for alluvial rivers is made to simulate the evolution of the sediment river bed of a conceptual 1D embayment for periods in the order of a thousand years: the traditional synthetic basin infilling aggregate diffusive type model based on the diffusion equation (Paola, 2000), used in the "synthesist" viewpoint and the process-based model MOHID (Miranda et al., 2000). The simulation of the sediment river bed evolution achieved by the process-based model MOHID is very similar to those obtained by the diffusive type model, but more complete due to the complexity of the process-based model. In the MOHID results it is possible to observe a more comprehensive and realistic results because this type of model include processes that is impossible to a synthetic model to describe. At last the combined effect of tide, sea level rise and river discharges was investigated in the process based model. These effects cannot be simulated using the diffusive type model. The results demonstrate the feasibility of using process based models to perform studies in scales of 10000 years. This is an advance relative to the use of synthetic models, enabling the use of variable forcing. REFERENCES • Briggs, L.I. and Pollack, H.N., 1967. Digital model of evaporate sedimentation. Science, 155, 453
Kinetic modeling of kraft delignification of Eucalyptus globulus
Santos, A.; Rodriguez, F.; Gilarranz, M.A.; Moreno, D.; Garcia-Ochoa, F.
1997-10-01
A kinetic model for the kraft pulping delignification of Eucalyptus globulus is proposed. This model is discriminated among some kinetic expressions often used in the literature, and the kinetic parameters are determined by fitting of experimental results. A total of 25 isothermal experiments at liquor-to-wood ratios of 50 and 5 L/kg have been carried out. Initial, bulk, and residual delignification stages have been observed during the lignin removal, the transitions being, referring to the lignin initial content, about 82 and 3%. Carbohydrate removal and effective alkali-metal and hydrosulfide consumption have been related with the lignin removal by means of effective stoichiometric coefficients for each stage, coefficients also being calculated by fitting of the experimental data. The kinetic model chosen has been used to simulate typical kraft pulping experiments carried out at nonisothermal conditions, using a temperature ramp. The model yields simulated values close to those obtained experimentally for the wood studied and also ably reproduces the trends of the literature data.
Spin Kinetic Models of Plasmas - Semiclassical and Quantum Mechanical Theory
Brodin, Gert; Marklund, Mattias; Zamanian, Jens
2009-11-10
In this work a recently published semiclassical spin kinetic model, generalizing those of previous authors are discussed. Some previously described properties are reviewed, and a new example illustrating the theory is presented. The generalization to a fully quantum mechanical description is discussed, and the main features of such a theory is outlined. Finally, the main conclusions are presented.
Paradigms of Complexity in Modelling of Fluid and Kinetic Processes
NASA Astrophysics Data System (ADS)
Diamond, P. H.
2006-10-01
The need to discuss and compare a wide variety of models of fluid and kinetic processes is motivated by the astonishing wide variety of complex physical phenomena which occur in plasmas in nature. Such phenomena include, but are not limited to: turbulence, turbulent transport and mixing, reconnection and structure formation. In this talk, I will review how various fluid and kinetic models come to grips with the essential physics of these phenomena. For example, I will discuss how the idea of a turbulent cascade and the concept of an ``eddy'' are realized quite differently in fluid and Vlasov models. Attention will be placed primarily on physical processes, the physics content of various models, and the consequences of choices in model construction, rather than on the intrinsic mathematical structure of the theories. Examples will be chosen from fusion, laboratory, space and astrophysical plasmas.
Towards cleaner combustion engines through groundbreaking detailed chemical kinetic models
Battin-Leclerc, Frédérique; Blurock, Edward; Bounaceur, Roda; Fournet, René; Glaude, Pierre-Alexandre; Herbinet, Olivier; Sirjean, Baptiste; Warth, V.
2013-01-01
In the context of limiting the environmental impact of transportation, this paper reviews new directions which are being followed in the development of more predictive and more accurate detailed chemical kinetic models for the combustion of fuels. In the first part, the performance of current models, especially in terms of the prediction of pollutant formation, is evaluated. In the next parts, recent methods and ways to improve these models are described. An emphasis is given on the development of detailed models based on elementary reactions, on the production of the related thermochemical and kinetic parameters, and on the experimental techniques available to produce the data necessary to evaluate model predictions under well defined conditions. PMID:21597604
Second-order kinetic Kohn-Sham lattice model
NASA Astrophysics Data System (ADS)
Solórzano, S.; Mendoza, M.; Herrmann, H. J.
2016-06-01
In this work, we introduce a semi-implicit second-order correction scheme to the kinetic Kohn-Sham lattice model. This approach is validated by performing realistic exchange-correlation energy calculations of atoms and dimers of the first two rows of the Periodic Table, finding good agreement with the expected values. Additionally, we simulate the ethane molecule, where we recover the bond lengths and compare the results with standard methods. Finally, we discuss the current applicability of pseudopotentials within the lattice kinetic Kohn-Sham approach.
Shuai, Z.; Bredas, J.L.; Saxena, A.; Gammel, J.T.; Bishop, A.R.
1994-10-01
Within a two-band model, the authors investigate the electroabsorption (EA) and third-harmonic generation (THG) processes in halogen-bridged mixed-valence Pt complexes: PtCl, PtBr and Ptl. For PtCl, the theoretical THG spectrum shows three peaks, corresponding to (i) a three-photon resonance at 0.83 eV originating in a M(etal)-M(etal) transition; (ii) a two-photon resonance at 1.5 eV from an M-M band-edge transition; and (iii) a three-photon resonance at 1.6 eV from an M-X transition. The latter two peaks account well for the twin-peak structure seen experimentally. They show that the twin-peak intensity strongly decreases from PtCl to PtBr and disappears for PtI. They also discuss the theoretical EA spectra due to localized defects (polarons, bipolarons, kinks, and excitons).
Gyrofluid turbulence models with kinetic effects
Dorland, W.; Hammett, G.W.
1992-12-01
Nonlinear gyrofluid equations are derived by taking moments of the nonlinear, electrostatic gyrokinetic equation. The principal model presented includes evolution equations for the guiding center n, u{parallel}, T{parallel}, and T{perpendicular} along with an equation expressing the quasineutrality constraint. Additional evolution equations for higher moments are derived which may be used if greater accuracy is desired. The moment hierarchy is closed with a Landau-damping model which is equivalent to a multi-pole approximation to the plasma dispersion function, extended to include finite Larmor radius effects. In particular, new dissipative, nonlinear terms are found which model the perpendicular phase-mixing of the distribution function along contours of constant electrostatic potential. These ``FLR phase-mixing`` terms introduce a hyperviscosity-like damping {proportional_to} k{sub {perpendicular}}{sup 2}{vert_bar}{Phi}{sub {rvec k}}{rvec k} {times}{rvec k}{prime}{vert_bar} which should provide a physics-based damping mechanism at high k{perpendicular}{rho} which is potentially as important as the usual polarization drift nonlinearity. The moments are taken in guiding center space to pick up the correct nonlinear FLR terms and the gyroaveraging of the shear. The equations are solved with a nonlinear, three dimensional initial value code. Linear results are presented, showing excellent agreement with linear gyrokinetic theory.
Modeling the Kinetics of Open Self-Assembly.
Verdier, Timothée; Foret, Lionel; Castelnovo, Martin
2016-07-01
In this work, we explore theoretically the kinetics of molecular self-assembly in the presence of constant monomer flux as an input, and a maximal size. The proposed model is supposed to reproduce the dynamics of viral self-assembly for enveloped virus. It turns out that the kinetics of open self-assembly is rather quantitatively different from the kinetics of similar closed assembly. In particular, our results show that the convergence toward the stationary state is reached through assembly waves. Interestingly, we show that the production of complete clusters is much more efficient in the presence of a constant input flux, rather than providing all monomers at the beginning of the self-assembly. PMID:27295398
Non isothermal model free kinetics for pyrolysis of rice straw.
Mishra, Garima; Bhaskar, Thallada
2014-10-01
The kinetics of thermal decomposition of rice straw was studied by thermogravimetry. Non-isothermal thermogravimetric data of rice straw decomposition in nitrogen atmosphere at six different heating rates of 5-40 °C/min was used for evaluating kinetics using several model free kinetic methods. The results showed that the decomposition process exhibited two zones of constant apparent activation energies. The values ranged from 142 to 170 kJ/mol (E(avg) = 155.787 kJ/mol), and 170 to 270 kJ/mol (E(avg) = 236.743 kJ/mol) in the conversion range of 5-60% and 61-90% respectively. These values were used to determine the reaction mechanism of process using master plots and compensation parameters. The results show that the reaction mechanism of whole process can be kinetically characterized by two successive reactions, a diffusion reaction followed by a third order rate equation. The kinetic results were validated using isothermal predictions. The results derived are useful for development and optimization of biomass thermochemical conversion systems. PMID:25105267
Boukazouha, F; Poulin-Vittrant, G; Tran-Huu-Hue, L P; Bavencoffe, M; Boubenider, F; Rguiti, M; Lethiecq, M
2015-07-01
This article is dedicated to the study of Piezoelectric Transformers (PTs), which offer promising solutions to the increasing need for integrated power electronics modules within autonomous systems. The advantages offered by such transformers include: immunity to electromagnetic disturbances; ease of miniaturisation for example, using conventional micro fabrication processes; and enhanced performance in terms of voltage gain and power efficiency. Central to the adequate description of such transformers is the need for complex analytical modeling tools, especially if one is attempting to include combined contributions due to (i) mechanical phenomena owing to the different propagation modes which differ at the primary and secondary sides of the PT; and (ii) electrical phenomena such as the voltage gain and power efficiency, which depend on the electrical load. The present work demonstrates an original one-dimensional (1D) analytical model, dedicated to a Rosen-type PT and simulation results are successively compared against that of a three-dimensional (3D) Finite Element Analysis (COMSOL Multiphysics software) and experimental results. The Rosen-type PT studied here is based on a single layer soft PZT (P191) with corresponding dimensions 18 mm × 3 mm × 1.5 mm, which operated at the second harmonic of 176 kHz. Detailed simulational and experimental results show that the presented 1D model predicts experimental measurements to within less than 10% error of the voltage gain at the second and third resonance frequency modes. Adjustment of the analytical model parameters is found to decrease errors relative to experimental voltage gain to within 1%, whilst a 2.5% error on the output admittance magnitude at the second resonance mode were obtained. Relying on the unique assumption of one-dimensionality, the present analytical model appears as a useful tool for Rosen-type PT design and behavior understanding. PMID:25753623
A spatially resolved surface kinetic model for forsterite dissolution
NASA Astrophysics Data System (ADS)
Maher, Kate; Johnson, Natalie C.; Jackson, Ariel; Lammers, Laura N.; Torchinsky, Abe B.; Weaver, Karrie L.; Bird, Dennis K.; Brown, Gordon E.
2016-02-01
The development of complex alteration layers on silicate mineral surfaces undergoing dissolution is a widely observed phenomenon. Given the complexity of these layers, most kinetic models used to predict rates of mineral-fluid interactions do not explicitly consider their formation. As a result, the relationship between the development of the altered layers and the final dissolution rate is poorly understood. To improve our understanding of the relationship between the alteration layer and the dissolution rate, we developed a spatially resolved surface kinetic model for olivine dissolution and applied it to a series of closed-system experiments consisting of three-phases (water (±NaCl), olivine, and supercritical CO2) at conditions relevant to in situ mineral carbonation (i.e. 60 °C, 100 bar CO2). We also measured the corresponding δ26/24Mg of the dissolved Mg during early stages of dissolution. Analysis of the solid reaction products indicates the formation of Mg-depleted layers on the olivine surface as quickly as 2 days after the experiment was started and before the bulk solution reached saturation with respect to amorphous silica. The δ26/24Mg of the dissolved Mg decreased by approximately 0.4‰ in the first stages of the experiment and then approached the value of the initial olivine (-0.35‰) as the steady-state dissolution rate was approached. We attribute the preferential release of 24Mg to a kinetic effect associated with the formation of a Mg-depleted layer that develops as protons exchange for Mg2+. We used experimental data to calibrate a surface kinetic model for olivine dissolution that includes crystalline olivine, a distinct "active layer" from which Mg can be preferentially removed, and secondary amorphous silica precipitation. By coupling the spatial arrangement of ions with the kinetics, this model is able to reproduce both the early and steady-state long-term dissolution rates, and the kinetic isotope fractionation. In the early stages of
Enhanced NLTE Atomic Kinetics Modeling Capabilities in HYDRA
NASA Astrophysics Data System (ADS)
Patel, Mehul V.; Scott, Howard A.; Marinak, Michael M.
2014-10-01
In radiation hydrodynamics modeling of ICF targets, an NLTE treatment of atomic kinetics is necessary for modeling high-Z hohlraum wall materials, high-Z dopants mixed in the central gas hotspot, and is potentially needed for accurate modeling of outer layers of the capsule ablator. Over the past several years, the NLTE DCA atomic physics capabilities in the 3D ICF radiation hydrodynamics code HYDRA have been significantly enhanced. The underlying atomic models have been improved, additional kinetics options including the ability to run DCA in cells with dynamic mixing of species has been added, and the computational costs have been significantly reduced using OpenMP threading. To illustrate the improved capabilities, we will show higher fidelity results from simulations of ICF hohlraum energetics, laser irradiated sphere experiments, and ICF capsule implosions. Prepared by LLNL under Contract DE-AC52-07NA27344.
A Structural, Kinetic Model of Soft Tissue Thermomechanics☆
Stylianopoulos, Triantafyllos; Aksan, Alptekin; Barocas, Victor H.
2008-01-01
Abstract A structure-based kinetic model was developed to predict the thermomechanical response of collagenous soft tissues. The collagen fibril was represented as an ensemble of molecular arrays with cross-links connecting the collagen molecules within the same array. A two-state kinetic model for protein folding was employed to represent the native and the denatured states of the collagen molecule. The Monte Carlo method was used to determine the state of the collagen molecule when subjected to thermal and mechanical loads. The model predictions were compared to existing experimental data for New Zealand white rabbit patellar tendons. The model predictions for one-dimensional tissue shrinkage and the corresponding mechanical property degradation agreed well with the experimental data, showing that the gross tissue behavior is dictated by molecular-level phenomena. PMID:17890379
Chemistry Resolved Kinetic Flow Modeling of TATB Based Explosives
Vitello, P A; Fried, L E; Howard, W M; Levesque, G; Souers, P C
2011-07-21
Detonation waves in insensitive, TATB based explosives are believed to have multi-time scale regimes. The initial burn rate of such explosives has a sub-microsecond time scale. However, significant late-time slow release in energy is believed to occur due to diffusion limited growth of carbon. In the intermediate time scale concentrations of product species likely change from being in equilibrium to being kinetic rate controlled. They use the thermo-chemical code CHEETAH linked to an ALE hydrodynamics code to model detonations. They term their model chemistry resolved kinetic flow as CHEETAH tracks the time dependent concentrations of individual species in the detonation wave and calculates EOS values based on the concentrations. A HE-validation suite of model simulations compared to experiments at ambient, hot, and cold temperatures has been developed. They present here a new rate model and comparison with experimental data.
Chemical Kinetic Modeling of Combustion of Automotive Fuels
Pitz, W J; Westbrook, C K; Silke, E J
2006-11-10
The objectives of this report are to: (1) Develop detailed chemical kinetic reaction models for components of fuels, including olefins and cycloalkanes used in diesel, spark-ignition and HCCI engines; (2) Develop surrogate mixtures of hydrocarbon components to represent real fuels and lead to efficient reduced combustion models; and (3) Characterize the role of fuel composition on production of emissions from practical automotive engines.
Kasinathan, N.; Rajakumar, A.; Vaidyanathan, G.; Chetal, S.C.
1995-09-01
Post shutdown decay heat removal is an important safety requirement in any nuclear system. In order to improve the reliability of this function, Liquid metal (sodium) cooled fast breeder reactors (LMFBR) are equipped with redundant hot pool dipped immersion coolers connected to natural draught air cooled heat exchangers through intermediate sodium circuits. During decay heat removal, flow through the core, immersion cooler primary side and in the intermediate sodium circuits are also through natural convection. In order to establish the viability and validate computer codes used in making predictions, a 1:20 scale experimental model called RAMONA with water as coolant has been built and experimental simulation of decay heat removal situation has been performed at KfK Karlsruhe. Results of two such experiments have been compiled and published as benchmarks. This paper brings out the results of the numerical simulation of one of the benchmark case through a 1D/2D coupled code system, DHDYN-1D/THYC-2D and the salient features of the comparisons. Brief description of the formulations of the codes are also included.
NASA Astrophysics Data System (ADS)
Carmelo, J. M. P.; Gu, Shi-Jian; Sampaio, M. J.
2014-06-01
Finite-temperature T > 0 transport properties of integrable and nonintegrable one-dimensional (1D) many-particle quantum systems are rather different, showing ballistic and diffusive behavior, respectively. The repulsive 1D Hubbard model is a prominent example of an integrable correlated system. For electronic densities n ≠ 1 (and spin densities m ≠ 0) it is an ideal charge (and spin) conductor, with ballistic charge (and spin) transport for T ⩾ 0. In spite of the fact that it is solvable by the Bethe ansatz, at n = 1 (and m = 0) its T > 0 charge (and spin) transport properties are an issue that remains poorly understood. Here we combine this solution with symmetry and the explicit calculation of current-operator matrix elements between energy eigenstates to show that for on-site repulsion U > 0 and at n = 1 the charge stiffness Dη(T) vanishes for T > 0 in the thermodynamic limit. A similar behavior is found by such methods for the spin stiffness Ds(T) for U > 0 and T > 0, which vanishes at m = 0. This absence of finite temperature n = 1 ballistic charge transport and m = 0 ballistic spin transport are exact results that clarify long-standing open problems.
Kinetic modelling of molecular hydrogen transport in microporous carbon materials.
Hankel, M.; Zhang, H.; Nguyen, T. X.; Bhatia, S. K.; Gray, S. K.; Smith, S. C.
2011-01-01
The proposal of kinetic molecular sieving of hydrogen isotopes is explored by employing statistical rate theory methods to describe the kinetics of molecular hydrogen transport in model microporous carbon structures. A Lennard-Jones atom-atom interaction potential is utilized for the description of the interactions between H{sub 2}/D{sub 2} and the carbon framework, while the requisite partition functions describing the thermal flux of molecules through the transition state are calculated quantum mechanically in view of the low temperatures involved in the proposed kinetic molecular sieving application. Predicted kinetic isotope effects for initial passage from the gas phase into the first pore mouth are consistent with expectations from previous modeling studies, namely, that at sufficiently low temperatures and for sufficiently narrow pore mouths D{sub 2} transport is dramatically favored over H{sub 2}. However, in contrast to expectations from previous modeling, the absence of any potential barrier along the minimum energy pathway from the gas phase into the first pore mouth yields a negative temperature dependence in the predicted absolute rate coefficients - implying a negative activation energy. In pursuit of the effective activation barrier, we find that the minimum potential in the cavity is significantly higher than in the pore mouth for nanotube-shaped models, throwing into question the common assumption that passage through the pore mouths should be the rate-determining step. Our results suggest a new mechanism that, depending on the size and shape of the cavity, the thermal activation barrier may lie in the cavity rather than at the pore mouth. As a consequence, design strategies for achieving quantum-mediated kinetic molecular sieving of H{sub 2}/D{sub 2} in a microporous membrane will need, at the very least, to take careful account of cavity shape and size in addition to pore-mouth size in order to ensure that the selective step, namely passage
A simplified model for average kinetic energy flux within large wind turbine arrays
NASA Astrophysics Data System (ADS)
Markfort, Corey; Zhang, Wei; Porte-Agel, Fernando
2015-11-01
We investigate the kinetic energy distribution within an array of wind turbines using a 1-D model for the interactions between large-scale wind farms and the atmospheric boundary layer (ABL). Obstructed shear flow scaling is used to predict the development length of the wind farm flow as well as vertical momentum flux. Within the region of flow development, momentum and energy is advected into the wind farm and wake turbulence draws excess momentum in from between turbines. This is characterized by large dispersive fluxes. Once the flow within the farm is developed, the area - averaged velocity profile exhibits an inflection point, characteristic of obstructed shear flows. The inflected velocity profile is responsible for a characteristic turbulence eddy scale, which may be responsible for a significant amount of the vertical momentum and energy flux. Prediction of this scale is useful for determining the amount of available power for harvesting. The model result for kinetic energy flux is compared to wind tunnel measurements. The model is useful for optimizing wind turbine spacing and layout, and for assessing the impacts of wind farms on nearby wind resources and the environment.
Kinetic Model Development for Lignin Pyrolysis
Clark, J.; Robichaud, D.; Nimlos, M.
2012-01-01
Lignin pyrolysis poses a significant barrier to the formation of liquid fuel products from biomass. Lignin pyrolyzes at higher temperatures than other biomass components (e.g. cellulose and hemi-cellulose) and tends to form radicals species that lead to cross-linking and ultimately char formation. A first step in the advancement of biomass-to-fuel technology is to discover the underlying mechanisms that lead to the breakdown of lignin at lower temperatures into more stable and usable products. We have investigated the thermochemistry of the various inter-linkage units found in lignin (B-O4, a-O4, B-B, B-O5, etc) using electronic structure calculations at the M06-2x/6-311++G(d,p) on a series of dimer model compounds. In addition to bond homolysis reactions, a variety of concerted elimination pathways are under investigation that tend to produce closed-shell stable products. Such a bottom-up approach could aid in the targeted development of catalysts that produce more desirable products under less severe reactor conditions.
Kinetic model of the Buyers’ market
NASA Astrophysics Data System (ADS)
Zhykharsky, Alexander V.
2013-09-01
In this work the following results are received. The closed mathematical apparatus describing the process of interaction of the Buyers’ market with retail Shop is created. The “statistical analogy” between the vacuum electrostatic diode and the Buyers’ market co-operating with retail Shop is considered. On the basis of the spent analysis the closed mathematical apparatus describing process of interaction of the Buyers’ market with retail Shop is created. The analytical expressions connecting a stream of Buyers, come to Shop, and a stream of the gain of Shop, with parameters of the Buyers’ market are received. For check of adequacy of the received model it is solved of some real “market” problems. On the basis of the spent researches principles of construction of Information-analytical Systems of new type which provide direct measurements of parameters of the Buyers’ market are developed. Actually these Systems are devices for measurement of parameters of this market. In this work it is shown that by means of the device developed for measurement of parameters of the Buyers’ market, creation of a new science-“demandodynamics” the Buyers’ market, is possible. Here the term “demandodynamics the Buyers’ market” is accepted by analogy to the term “thermodynamics” in physics. (In this work it is shown that for the Buyers’ market concept “demand” is similar to concept “temperature” in physics.) The construction methodology “demandodynamics” the Buyers’ market is defined and is shown that within the limits of this science working out of a technique of a direct control by a condition of the Buyers’ market is possible.
A kinetic-MHD model for low frequency phenomena
Cheng, C.Z.
1991-07-01
A hybrid kinetic-MHD model for describing low-frequency phenomena in high beta anisotropic plasmas that consist of two components: a low energy core component and an energetic component with low density. The kinetic-MHD model treats the low energy core component by magnetohydrodynamic (MHD) description, the energetic component by kinetic approach such as the gyrokinetic equation, and the coupling between the dynamics of these two components through plasma pressure in the momentum equation. The kinetic-MHD model optimizes both the physics contents and the theoretical efforts in studying low frequency MHD waves and transport phenomena in general magnetic field geometries, and can be easily modified to include the core plasma kinetic effects if necessary. It is applicable to any magnetized collisionless plasma system where the parallel electric field effects are negligibly small. In the linearized limit two coupled eigenmode equations for describing the coupling between the transverse Alfven type and the compressional Alfven type waves are derived. The eigenmode equations are identical to those derived from the full gyrokinetic equation in the low frequency limit and were previously analyzed both analytically nd numerically to obtain the eigenmode structure of the drift mirror instability which explains successfully the multi-satellite observation of antisymmetric field-aligned structure of the compressional magnetic field of Pc 5 waves in the magnetospheric ring current plasma. Finally, a quadratic form is derived to demonstrate the stability of the low-frequency transverse and compressional Alfven type instabilities in terms of the pressure anisotropy parameter {tau} and the magnetic field curvature-pressure gradient parameter. A procedure for determining the stability of a marginally stable MHD wave due to wave-particle resonances is also presented.
Kinetic model of DNA replication in eukaryotic organisms
NASA Astrophysics Data System (ADS)
Bechhoefer, John; Herrick, John; Bensimon, Aaron
2001-03-01
We introduce an analogy between DNA replication in eukaryotic organisms and crystal growth in one dimension. Drawing on models of crystallization kinetics developed in the 1930s to describe the freezing of metals, we formulate a kinetic model of DNA replication that quantitatively describes recent results on DNA replication in the in vitro system of Xenopus laevis prior to the mid-blastula transition. It allows one, for the first time, to determine the parameters governing the DNA replication program in a eukaryote on a genome-wide basis. In particular, we have determined the frequency of origin activation in time and space during the cell cycle. Although we focus on a specific stage of development, this model can easily be adapted to describe replication in many other organisms, including budding yeast.
Kinetic models for historical processes of fast invasion and aggression
NASA Astrophysics Data System (ADS)
Aristov, Vladimir V.; Ilyin, Oleg V.
2015-04-01
In the last few decades many investigations have been devoted to theoretical models in new areas concerning description of different biological, sociological, and historical processes. In the present paper we suggest a model of the Nazi Germany invasion of Poland, France, and the USSR based on kinetic theory. We simulate this process with the Cauchy boundary problem for two-element kinetic equations. The solution of the problem is given in the form of a traveling wave. The propagation velocity of a front line depends on the quotient between initial forces concentrations. Moreover it is obtained that the general solution of the model can be expressed in terms of quadratures and elementary functions. Finally it is shown that the front-line velocities agree with the historical data.
A chemical kinetic modeling study of chlorinated hydrocarbon combustion
Pitz, W.J.; Westbrook, C.K.
1990-09-05
The combustion of chloroethane is modeled as a stirred reactor so that we can study critical emission characteristics of the reactor as a function of residence time. We examine important operating conditions such as pressure, temperature, and equivalence ratio and their influence on destructive efficiency of chloroethane. The model uses a detailed chemical kinetic mechanism that we have developed previously for C{sub 3} hydrocarbons. We have added to this mechanism the chemical kinetic mechanism for C{sub 2} chlorinated hydrocarbons developed by Senkan and coworkers. In the modeling calculations, sensitivity coefficients are determined to find which reaction-rate constants have the largest effect on destructive efficiency. 24 refs., 6 figs., 1 tab.
Kinetic modeling of Nernst effect in magnetized hohlraums
NASA Astrophysics Data System (ADS)
Joglekar, A. S.; Ridgers, C. P.; Kingham, R. J.; Thomas, A. G. R.
2016-04-01
We present nanosecond time-scale Vlasov-Fokker-Planck-Maxwell modeling of magnetized plasma transport and dynamics in a hohlraum with an applied external magnetic field, under conditions similar to recent experiments. Self-consistent modeling of the kinetic electron momentum equation allows for a complete treatment of the heat flow equation and Ohm's law, including Nernst advection of magnetic fields. In addition to showing the prevalence of nonlocal behavior, we demonstrate that effects such as anomalous heat flow are induced by inverse bremsstrahlung heating. We show magnetic field amplification up to a factor of 3 from Nernst compression into the hohlraum wall. The magnetic field is also expelled towards the hohlraum axis due to Nernst advection faster than frozen-in flux would suggest. Nonlocality contributes to the heat flow towards the hohlraum axis and results in an augmented Nernst advection mechanism that is included self-consistently through kinetic modeling.
Chemistry resolved kinetic flow modeling of TATB based explosives
NASA Astrophysics Data System (ADS)
Vitello, Peter; Fried, Laurence E.; William, Howard; Levesque, George; Souers, P. Clark
2012-03-01
Detonation waves in insensitive, TATB-based explosives are believed to have multiple time scale regimes. The initial burn rate of such explosives has a sub-microsecond time scale. However, significant late-time slow release in energy is believed to occur due to diffusion limited growth of carbon. In the intermediate time scale concentrations of product species likely change from being in equilibrium to being kinetic rate controlled. We use the thermo-chemical code CHEETAH linked to an ALE hydrodynamics code to model detonations. We term our model chemistry resolved kinetic flow, since CHEETAH tracks the time dependent concentrations of individual species in the detonation wave and calculates EOS values based on the concentrations. We present here two variants of our new rate model and comparison with hot, ambient, and cold experimental data for PBX 9502.
Reproducing Phenomenology of Peroxidation Kinetics via Model Optimization
NASA Astrophysics Data System (ADS)
Ruslanov, Anatole D.; Bashylau, Anton V.
2010-06-01
We studied mathematical modeling of lipid peroxidation using a biochemical model system of iron (II)-ascorbate-dependent lipid peroxidation of rat hepatocyte mitochondrial fractions. We found that antioxidants extracted from plants demonstrate a high intensity of peroxidation inhibition. We simplified the system of differential equations that describes the kinetics of the mathematical model to a first order equation, which can be solved analytically. Moreover, we endeavor to algorithmically and heuristically recreate the processes and construct an environment that closely resembles the corresponding natural system. Our results demonstrate that it is possible to theoretically predict both the kinetics of oxidation and the intensity of inhibition without resorting to analytical and biochemical research, which is important for cost-effective discovery and development of medical agents with antioxidant action from the medicinal plants.
Kinetic models for historical processes of fast invasion and aggression.
Aristov, Vladimir V; Ilyin, Oleg V
2015-04-01
In the last few decades many investigations have been devoted to theoretical models in new areas concerning description of different biological, sociological, and historical processes. In the present paper we suggest a model of the Nazi Germany invasion of Poland, France, and the USSR based on kinetic theory. We simulate this process with the Cauchy boundary problem for two-element kinetic equations. The solution of the problem is given in the form of a traveling wave. The propagation velocity of a front line depends on the quotient between initial forces concentrations. Moreover it is obtained that the general solution of the model can be expressed in terms of quadratures and elementary functions. Finally it is shown that the front-line velocities agree with the historical data. PMID:25974546
Kinetic modelling of laccase mediated delignification of Lantana camara.
Gujjala, Lohit K S; Bandyopadhyay, Tapas K; Banerjee, Rintu
2016-07-01
Enzymatic delignification is seen as a green step in biofuels production owing to its specificity towards lignin and its proper understanding requires a kinetic study to decipher intricate details of the process such as thermodynamic parameters viz., activation energy, entropy change and enthalpy change. A system of two coupled kinetic models has been constructed to model laccase mediated delignification of Lantana camara. From the simulated output, activation energy was predicted to be 45.56 and 56.06 kJ/mol, entropy change was observed to be 1.08 × 10(2) and 1.05 × 10(2)cal/mol-K and enthalpy change was determined to be 3.33 × 10(4) and 3.20 × 10(4)cal/mol, respectively from Tessier's and Michaelis Menten model. While comparing the prediction efficiency, it was noticed that Tessier's model gave better performance. Sensitivity analysis was also conducted and it was observed that the model was most sensitive towards temperature dependent kinetic constants. PMID:27082268
Kinetic Modeling of Oxidative Coagulation for Arsenic Removal
Kim, Jin-Wook; Kramer, Timothy A.
2004-03-31
A model of oxidative coagulation consisting of Fenton's reagent (Fe(II)/H2O2 at pH 7.0) was established. The optimum condition was found when the mole ratio of As(III):H2O2:Fe(II)=1:15:20. In this optimum condition, all of Fe(II) was converted to HFO (am-Fe(OH)3) and precipitated to be used as the oxidized arsenic(V) adsorbent and particle coagulant. Two sorption models consisting of a surface complexation model and a kinetic model were developed and coupled. Using the coupled sorption model, the kinetics of HFO surface charge/potential during As(V) sorption was calculated. Further, during arsenic sorption, the colloid stability kinetics resulting from the perikinetic coagulation mechanism was calculated by considering interparticle forces. Colloid surface potential was decreased from 60 mv to 12 mv in proportion to the amount of arsenic adsorbed onto HFO and this surface potential directly affected the colloid stability (collision efficiency).
NASA Astrophysics Data System (ADS)
Hurlbatt, A.; O’Connell, D.; Gans, T.
2016-08-01
Analytical and numerical models allow investigation of complicated discharge phenomena and the interplay that makes plasmas such a complex environment. Global models are quick to implement and can have almost negligible computation cost, but provide only bulk or spatially averaged values. Full fluid models take longer to develop, and can take days to solve, but provide accurate spatio-temporal profiles of the whole plasma. The work presented here details a different type of model, analytically similar to fluid models, but computationally closer to a global model, and able to give spatially resolved solutions for the challenging environment of electronegative plasmas. Included are non-isothermal electrons, gas heating, and coupled neutral dynamics. Solutions are reached in seconds to minutes, and spatial profiles are given for densities, fluxes, and temperatures. This allows the semi-analytical model to fill the gap that exists between global and full fluid models, extending the tools available to researchers. The semi-analytical model can perform broad parameter sweeps that are not practical with more computationally expensive models, as well as exposing non-trivial trends that global models cannot capture. Examples are given for a low pressure oxygen CCP. Excellent agreement is shown with a full fluid model, and comparisons are drawn with the corresponding global model.
A review of the kinetic statistical strength model
Attia, A.V.
1996-03-11
This is a review of the Kinetic-Statistical Strength (KSS) model described in the report ``Models of Material Strength, Fracture and Failure`` by V. Kuropatenko and V. Bychenkov. The models for metals subjected to high strain rates (explosions) are focussed on. Model implementation appears possible in a hydrocode. Applying the model to the shock response of metals will require a data source for the Weibull parameter {alpha}{sub u}, short of measuing the strength of specimens of various sizes. Model validation will require more detail on the experiments successfully calculated by SPRUT. Evaluation of the KSS model is needed against other existing rate-dependent models for metals such as the Steinberg-Lund or MTS model on other shock experiments.
Progress in Chemical Kinetic Modeling for Surrogate Fuels
Pitz, W J; Westbrook, C K; Herbinet, O; Silke, E J
2008-06-06
Gasoline, diesel, and other alternative transportation fuels contain hundreds to thousands of compounds. It is currently not possible to represent all these compounds in detailed chemical kinetic models. Instead, these fuels are represented by surrogate fuel models which contain a limited number of representative compounds. We have been extending the list of compounds for detailed chemical models that are available for use in fuel surrogate models. Detailed models for components with larger and more complicated fuel molecular structures are now available. These advancements are allowing a more accurate representation of practical and alternative fuels. We have developed detailed chemical kinetic models for fuels with higher molecular weight fuel molecules such as n-hexadecane (C16). Also, we can consider more complicated fuel molecular structures like cyclic alkanes and aromatics that are found in practical fuels. For alternative fuels, the capability to model large biodiesel fuels that have ester structures is becoming available. These newly addressed cyclic and ester structures in fuels profoundly affect the reaction rate of the fuel predicted by the model. Finally, these surrogate fuel models contain large numbers of species and reactions and must be reduced for use in multi-dimensional models for spark-ignition, HCCI and diesel engines.
Development of Detailed Kinetic Models for Fischer-Tropsch Fuels
Westbrook, C K; Pitz, W J; Carstensen, H; Dean, A M
2008-10-28
Fischer-Tropsch (FT) fuels can be synthesized from a syngas stream generated by the gasification of biomass. As such they have the potential to be a renewable hydrocarbon fuel with many desirable properties. However, both the chemical and physical properties are somewhat different from the petroleum-based hydrocarbons that they might replace, and it is important to account for such differences when considering using them as replacements for conventional fuels in devices such as diesel engines and gas turbines. FT fuels generally contain iso-alkanes with one or two substituted methyl groups to meet the pour-point specifications. Although models have been developed for smaller branched alkanes such as isooctane, additional efforts are required to properly capture the kinetics of the larger branched alkanes. Recently, Westbrook et al. developed a chemical kinetic model that can be used to represent the entire series of n-alkanes from C{sub 1} to C{sub 16} (Figure 1). In the current work, the model is extended to treat 2,2,4,4,6,8,8-heptamethylnonane (HMN), a large iso-alkane. The same reaction rate rules used in the iso-octane mechanism were incorporated in the HMN mechanism. Both high and low temperature chemistry was included so that the chemical kinetic model would be applicable to advanced internal combustion engines using low temperature combustion strategies. The chemical kinetic model consists of 1114 species and 4468 reactions. Concurrently with this effort, work is underway to improve the details of specific reaction classes in the mechanism, guided by high-level electronic structure calculations. Attention is focused upon development of accurate rate rules for abstraction of the tertiary hydrogens present in branched alkanes and properly accounting for the pressure dependence of the ?-scission, isomerization, and R + O{sub 2} reactions.
Modelling couplings between reaction, fluid flow and deformation: Kinetics
NASA Astrophysics Data System (ADS)
Malvoisin, Benjamin; Podladchikov, Yury Y.; Connolly, James A. D.
2016-04-01
Mineral assemblages out of equilibrium are commonly found in metamorphic rocks testifying of the critical role of kinetics for metamorphic reactions. As experimentally determined reaction rates in fluid-saturated systems generally indicate complete reaction in less than several years, i.e. several orders of magnitude faster than field-based estimates, metamorphic reaction kinetics are generally thought to be controlled by transport rather than by processes at the mineral surface. However, some geological processes like earthquakes or slow-slip events have shorter characteristic timescales, and transport processes can be intimately related to mineral surface processes. Therefore, it is important to take into account the kinetics of mineral surface processes for modelling fluid/rock interactions. Here, a model coupling reaction, fluid flow and deformation was improved by introducing a delay in the achievement of equilibrium. The classical formalism for dissolution/precipitation reactions was used to consider the influence of the distance from equilibrium and of temperature on the reaction rate, and a dependence on porosity was introduced to model evolution of reacting surface area during reaction. The fitting of experimental data for three reactions typically occurring in metamorphic systems (serpentine dehydration, muscovite dehydration and calcite decarbonation) indicates a systematic faster kinetics close from equilibrium on the dehydration side than on the hydration side. This effect is amplified through the porosity term in the reaction rate since porosity is formed during dehydration. Numerical modelling indicates that this difference in reaction rate close from equilibrium plays a key role in microtextures formation. The developed model can be used in a wide variety of geological systems where couplings between reaction, deformation and fluid flow have to be considered.
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.
Kinetic model of metabolic network for xiamenmycin biosynthetic optimisation.
Xu, Min-juan; Chen, Yong-cong; Xu, Jun; Ao, Ping; Zhu, Xiao-mei
2016-02-01
Xiamenmycins, a series of prenylated benzopyran compounds with anti-fibrotic bioactivities, were isolated from a mangrove-derived Streptomyces xiamenensis. To fulfil the requirements of pharmaceutical investigations, a high production of xiamenmycin is needed. In this study, the authors present a kinetic metabolic model to evaluate fluxes in an engineered Streptomyces lividans with xiamenmycin-oriented genetic modification based on generic enzymatic rate equations and stability constraints. Lyapunov function was used for a viability optimisation. From their kinetic model, the flux distributions for the engineered S. lividans fed on glucose and glycerol as carbon sources were calculated. They found that if the bacterium can utilise glucose simultaneously with glycerol, xiamenmycin production can be enhanced by 40% theoretically, while maintaining the same growth rate. Glycerol may increase the flux for phosphoenolpyruvate synthesis without interfering citric acid cycle. They therefore believe this study demonstrates a possible new direction for bioengineering of S. lividans. PMID:26816395
Polar Coordinate Lattice Boltzmann Kinetic Modeling of Detonation Phenomena
NASA Astrophysics Data System (ADS)
Lin, Chuan-Dong; Xu, Ai-Guo; Zhang, Guang-Cai; Li, Ying-Jun
2014-11-01
A novel polar coordinate lattice Boltzmann kinetic model for detonation phenomena is presented and applied to investigate typical implosion and explosion processes. In this model, the change of discrete distribution function due to local chemical reaction is dynamically coupled into the modified lattice Boltzmann equation which could recover the Navier—Stokes equations, including contribution of chemical reaction, via the Chapman—Enskog expansion. For the numerical investigations, the main focuses are the nonequilibrium behaviors in these processes. The system at the disc center is always in its thermodynamic equilibrium in the highly symmetric case. The internal kinetic energies in different degrees of freedom around the detonation front do not coincide. The dependence of the reaction rate on the pressure, influences of the shock strength and reaction rate on the departure amplitude of the system from its local thermodynamic equilibrium are probed.
Urban multitarget tracking via gas-kinetic dynamics models
NASA Astrophysics Data System (ADS)
Mahler, Ronald
2013-05-01
Multitarget tracking in urban environments presents a major theoretical and practical challenge. A recently suggested approach is that of modeling traffic dynamics using the fluid-kinetic methods of traffic-flow theory (TFT). I propose use of the newer, more general, gas-kinetic (GK) approach to TFT. In GK, traffic flow is modeled as a one- or two-dimensional constrained gas. The paper demonstrates the following. (1) The foundational concept in GK--the "phase-space density"--is the same thing as the probability hypothesis density (PHD) of multitarget tracking theory. (2) The theoretically best-that-one-can do approach to TFT-based tracking is a PHD filter. (3) Better performance can be obtained by augmenting this PHD filter as a cardinalized PHD (CPHD) filter. A simple example is presented to illustrate how PHD/CPHD filters can be integrated with conventional macroscopic, mesoscopic, and microscopic TFT.
NASA Astrophysics Data System (ADS)
Persson, O. P.; Solomon, A.
2013-12-01
Though leads only represent a small portion of the Arctic sea-ice area, their contribution to the surface turbulent energy and momentum fluxes can be significant. Numerous modeling studies presented in the literature have been conducted examining these effects. The results of such studies have indicated the importance of the environmental large-scale stability, the environmental humidity, the lead width, the ice (lead) concentration, the lead size distribution, the character of the leads (open water, refrozen), etc. Because global climate models (GCMs) show significant sensitivity to the large-scale net energy flux from the heterogeneous sea-ice surface, and because thinner ice in the projected future Arctic climate will likely result in increasing lead fractions, the appropriate GCM representation of this complex system is important. This study presents modeling results based on observations from the Surface Heat Budget of the Arctic Ocean (SHEBA) experiment, for which the mid-winter sea-ice was greatly heterogeneous. In mid-January, the 100x100 km region surrounding the SHEBA ice camp consisted of a lead fraction of ~16-33% as revealed by SAR data. This included primarily older refrozen lead areas that were generated at least a month earlier (~16-25% areal coverage), with a smaller fraction of newly opened leads (~4-9% areal coverage). Utilizing the sequence of SAR images, the atmospheric observations at the SHEBA site, and a 1-D snow and ice model, the spatial distribution of sea-ice thickness, snow depth, and surface temperatures within this domain were estimated over a 6-week period, revealing the significant impact of leads in all stages on GCM-scale temperatures and fluxes. This combined observational/model data series is used to evaluate a variety of one-dimensional turbulent flux aggregation techniques (e.g., mosaic) that use different assumptions. Furthermore, by using the spatial distribution of these surface characteristics, three-dimensional large eddy
Kinetic modelling of pressure filtration of ceramic powder suspensions
Correia, L.A.; Salomoni, A.; Hey, A.W.
1995-09-01
A kinetic model developed for radial pressure filtration is described and used to study the casting behaviour of an Alumina (Al6SG) and a Zirconia (TZ3Ys) slip stabilized with Dolapix CE64. For the Zirconia slip no influence of pressure and curvature is found. The casting behaviour of the Alumina slip seems to be influenced by both the pressure and the curvature of the filtrating surface.
Kinetic models for socio-economic dynamics of speculative markets
NASA Astrophysics Data System (ADS)
Maldarella, Dario; Pareschi, Lorenzo
2012-02-01
In this paper we introduce a simple model for a financial market characterized by a single stock or good and an interplay between two different trader populations, chartists and fundamentalists, which determine the price dynamics of the stock. The model has been inspired by the microscopic Lux-Marchesi model (Lux and Marchesi (2000, 1999) [3,25]). The introduction of kinetic equations permits to study the asymptotic behavior of the investments and the price distributions and to characterize the regimes of lognormal behavior and the formation of power law tails.
NASA Astrophysics Data System (ADS)
Szilagyi, John; Parchamy, Homaira; Masnavi, Majid; Richardson, Martin; One Team
2013-10-01
The VUV light sources have applications in various scientific and engineering fields, such as semiconductor industry, nanometer processing, and photochemistry. A detailed multilevel non-LTE atomic model is developed to investigate emissivity and absorption properties of low temperature Nobel gas plasmas around 80 nm based on the Yb/Al multilayer mirrors. We will present the optimum regions for conversion efficiency of Nobel gas targets against target density and laser parameters by means of 1D hydrodynamic coupled to a developed population kinetics codes. We discuss in detailed predictions by comparing calculations to our experimental results.
Allué, José Antonio; Sarasa, Leticia; Izco, María; Pérez-Grijalba, Virginia; Fandos, Noelia; Pascual-Lucas, María; Ogueta, Samuel; Pesini, Pedro; Sarasa, Manuel
2016-05-30
APPswe/PS1dE9 and Tg2576 are very common transgenic mouse models of Alzheimer's disease (AD), used in many laboratories as tools to research the mechanistic process leading to the disease. In order to augment our knowledge about the amyloid-β (Aβ) isoforms present in both transgenic mouse models, we have developed two chromatographic methods, one acidic and the other basic, for the characterization of the Aβ species produced in the brains of the two transgenic mouse models. After immunoprecipitation and micro-liquid chromatography-electrospray ionization mass spectrometry/mass spectrometry, 10 species of Aβ, surprisingly all of human origin, were detected in the brain of Tg2576 mouse, whereas 39 species, of both murine and human origin, were detected in the brain of the APP/PS1 mouse. To the best of our knowledge, this is the first study showing the identification of such a high number of Aβ species in the brain of the APP/PS1 transgenic mouse, whereas, in contrast, a much lower number of Aβ species were identified in the Tg2576 mouse. Therefore, this study brings to light a relevant phenotypic difference between these two popular mice models of AD. PMID:27258422
Kinetic Modeling of Sunflower Grain Filling and Fatty Acid Biosynthesis.
Durruty, Ignacio; Aguirrezábal, Luis A N; Echarte, María M
2016-01-01
Grain growth and oil biosynthesis are complex processes that involve various enzymes placed in different sub-cellular compartments of the grain. In order to understand the mechanisms controlling grain weight and composition, we need mathematical models capable of simulating the dynamic behavior of the main components of the grain during the grain filling stage. In this paper, we present a non-structured mechanistic kinetic model developed for sunflower grains. The model was first calibrated for sunflower hybrid ACA855. The calibrated model was able to predict the theoretical amount of carbohydrate equivalents allocated to the grain, grain growth and the dynamics of the oil and non-oil fraction, while considering maintenance requirements and leaf senescence. Incorporating into the model the serial-parallel nature of fatty acid biosynthesis permitted a good representation of the kinetics of palmitic, stearic, oleic, and linoleic acids production. A sensitivity analysis showed that the relative influence of input parameters changed along grain development. Grain growth was mostly affected by the specific growth parameter (μ') while fatty acid composition strongly depended on their own maximum specific rate parameters. The model was successfully applied to two additional hybrids (MG2 and DK3820). The proposed model can be the first building block toward the development of a more sophisticated model, capable of predicting the effects of environmental conditions on grain weight and composition, in a comprehensive and quantitative way. PMID:27242809
Kinetic Modeling of Sunflower Grain Filling and Fatty Acid Biosynthesis
Durruty, Ignacio; Aguirrezábal, Luis A. N.; Echarte, María M.
2016-01-01
Grain growth and oil biosynthesis are complex processes that involve various enzymes placed in different sub-cellular compartments of the grain. In order to understand the mechanisms controlling grain weight and composition, we need mathematical models capable of simulating the dynamic behavior of the main components of the grain during the grain filling stage. In this paper, we present a non-structured mechanistic kinetic model developed for sunflower grains. The model was first calibrated for sunflower hybrid ACA855. The calibrated model was able to predict the theoretical amount of carbohydrate equivalents allocated to the grain, grain growth and the dynamics of the oil and non-oil fraction, while considering maintenance requirements and leaf senescence. Incorporating into the model the serial-parallel nature of fatty acid biosynthesis permitted a good representation of the kinetics of palmitic, stearic, oleic, and linoleic acids production. A sensitivity analysis showed that the relative influence of input parameters changed along grain development. Grain growth was mostly affected by the specific growth parameter (μ′) while fatty acid composition strongly depended on their own maximum specific rate parameters. The model was successfully applied to two additional hybrids (MG2 and DK3820). The proposed model can be the first building block toward the development of a more sophisticated model, capable of predicting the effects of environmental conditions on grain weight and composition, in a comprehensive and quantitative way. PMID:27242809
Modeling solute advection coupled with sorption kinetics in heterogeneous formations
NASA Astrophysics Data System (ADS)
Selroos, Jan-Olof; Cvetkovic, Vladimir
1992-05-01
A method for coupling sorption kinetics and solute advection in particle-tracking models is proposed; this method is efficient for the case where sorption rate coefficients can be assumed constant field scale parameters. A simulation example of reactive solute advection in two-dimensional heterogeneous porous media is presented. The effect of sorption kinetics on solute advection is investigated. Nonequilibrium effects are exhibited as enhanced tailing in the solute breakthrough. Because high variability in the hydraulic conductivity also yields enhanced tailing, the nonequilibrium effect is more pronounced for the case of low variability. Moreover, it may be difficult to distinguish cases of low variability with nonequilibrium sorption from cases of high variability with equilibrium sorption. A comparison of Monte Carlo ensemble results is made with an analytical model for the mass arrival of kinetically sorbing solute in heterogeneous porous media obtained using first-order perturbation. The comparison indicates that the analytical model provides reasonable approximations of the expected solute breakthrough if the variance of the natural logarithm of the hydraulic conductivity is smaller than 1.
Chemistry Resolved Kinetic Flow Modeling of TATB Based Explosives
NASA Astrophysics Data System (ADS)
Vitello, Peter; Fried, Lawrence; Howard, Mike; Levesque, George; Souers, Clark
2011-06-01
Detonation waves in insensitive, TATB based explosives are believed to have multi-time scale regimes. The initial burn rate of such explosives has a sub-microsecond time scale. However, significant late-time slow release in energy is believed to occur due to diffusion limited growth of carbon. In the intermediate time scale concentrations of product species likely change from being in equilibrium to being kinetic rate controlled. We use the thermo-chemical code CHEETAH linked to ALE hydrodynamics codes to model detonations. We term our model chemistry resolved kinetic flow as CHEETAH tracks the time dependent concentrations of individual species in the detonation wave and calculate EOS values based on the concentrations. A validation suite of model simulations compared to recent high fidelity metal push experiments at ambient and cold temperatures has been developed. We present here a study of multi-time scale kinetic rate effects for these experiments. Prepared by LLNL under Contract DE-AC52-07NA27344.
Computation Molecular Kinetics Model of HZE Induced Cell Cycle Arrest
NASA Technical Reports Server (NTRS)
Cucinotta, Francis A.; Ren, Lei
2004-01-01
Cell culture models play an important role in understanding the biological effectiveness of space radiation. High energy and charge (HZE) ions produce prolonged cell cycle arrests at the G1/S and G2/M transition points in the cell cycle. A detailed description of these phenomena is needed to integrate knowledge of the expression of DNA damage in surviving cells, including the determination of relative effectiveness factors between different types of radiation that produce differential types of DNA damage and arrest durations. We have developed a hierarchical kinetics model that tracks the distribution of cells in various cell phase compartments (early G1, late G1, S, G2, and M), however with transition rates that are controlled by rate-limiting steps in the kinetics of cyclin-cdk's interactions with their families of transcription factors and inhibitor molecules. The coupling of damaged DNA molecules to the downstream cyclin-cdk inhibitors is achieved through a description of the DNA-PK and ATM signaling pathways. For HZE irradiations we describe preliminary results, which introduce simulation of the stochastic nature of the number of direct particle traversals per cell in the modulation of cyclin-cdk and cell cycle population kinetics. Comparison of the model to data for fibroblast cells irradiated photons or HZE ions are described.
NASA Astrophysics Data System (ADS)
Muench, Thomas; Koch, Manfred; Schlittenhard, Jörg
2010-05-01
On December 5, 2004 a strong earthquake occurred near the city of Waldkirch, about 30 km's north of Freiburg, with a local magnitude of ML = 5.4. This seismic event was one of the strongest observed since the ML = 5.7 'Schwäbische Alb' event of September 3, 1978, 30 years before. In the aftermath of the event several institutions (Bens, BGR, LGBR, LED, SED and NEIC) have attempted to relocate this earthquake that came up with a hypocentral depth range of 9 - 12 km which. In fact, as the exact hypocentral location of the Waldkirch - and other events in the area - namely, the seismic depths, are of utmost importance for the further understanding of the seismotectonics as well as of the seismic hazard in the upper Rhinegraben area, one cannot over stress the necessity for a hypocenter relocation as best as possible. This requires a careful analysis of all factors that may impede an unbiased relocation of such an event. In the present talk we put forward the question whether the Waldkirch seismic event can be relocated with sufficient accuracy by a regional network when, additionally, improved regional 1D- and 3D seismic velocity models for the crust and upper mantle that take into consideration Pn-anisotropy of the upper mantle beneath Germany are employed in the hypocentral determination process. The seismological work starts with a comprehensive analysis of the dataset available for the relocation of the event. By means of traveltime curves a reevaluation of the observed phases is done and it is shown that some of the big observed traveltime residuals are most likely the consequence of wrongly associated phases as well as of the neglect of the anisotropic Pn traveltime correction for the region. Then hypcocenter relocations are done for 1D vertically inhomogeneous and 3D laterally inhomogeneous seismic velocity models, without and with the anisotropic Pn-traveltime correction included. The effects of the - often not well-known - Moho depth and of the VP
Multiensemble Markov models of molecular thermodynamics and kinetics.
Wu, Hao; Paul, Fabian; Wehmeyer, Christoph; Noé, Frank
2016-06-01
We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models-clustering of high-dimensional spaces and modeling of complex many-state systems-with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein-ligand binding model. PMID:27226302
NASA Astrophysics Data System (ADS)
Brown, A.; Dahlke, H. E.
2015-12-01
The ability of soil to infiltrate large volumes of water is fundamental to managed aquifer recharge (MAR) when using infiltration basins or agricultural fields. In order to investigate the feasibility of using agricultural fields for MAR we conducted a field experiment designed to not only assess the resilience of alfalfa (Medicago sativa) to large ( 300 mm ), short duration (1.5 hour), repeated irrigation events during the winter but also how crop resilience was influenced by soil water movement. We hypothesized that large irrigation amounts designed for groundwater recharge could cause prolonged saturated conditions in the root-zone and yield loss. Tensiometers were installed at two depths (60 and 150 cm) in a loam soil to monitor the changes in soil matric potential within and below the root-zone following irrigation events in each of five experimental plots (8 x 16 m2). To simulate the individual infiltration events we employed the HYDRUS-1D computational module (Simunek et al., 2005) and compared the finite-water content vadose zone flow method (Ogden et al. 2015) with numerical solutions to the Richards' equation. For both models we assumed a homogenous and isotropic root zone that is initially unsaturated with no water flow. Here we assess the ability of these two models to account for the control volume applied to the plots and to capture sharp changes in matric potential that were observed in the early time after an irrigation pulse. The goodness-of-fit of the models was evaluated using the root mean square error (RMSE) for observed and predicted values of cumulative infiltration over time, wetting front depth over time and water content at observation nodes. For the finite-water content method, the RMSE values and output for observation nodes were similar to that from the HYDRUS-1D solution. This indicates that the finite-water content method may be useful for predicting the fate of large volumes of water applied for MAR. Moreover, both models suggest a
NASA Astrophysics Data System (ADS)
Brown, A.; Dahlke, H. E.
2015-12-01
The ability of soil to infiltrate large volumes of water is fundamental to managed aquifer recharge (MAR) when using infiltration basins or agricultural fields. In order to investigate the feasibility of using agricultural fields for MAR we conducted a field experiment designed to not only assess the resilience of alfalfa (Medicago sativa) to large (300 mm), short duration (1.5 hour), repeated irrigation events during the winter but also how crop resilience was influenced by soil water movement. We hypothesized that large irrigation amounts designed for groundwater recharge could cause prolonged saturated conditions in the root-zone and yield loss. Tensiometers were installed at two depths (60 and 150 cm) in a loam soil to monitor the changes in soil matric potential within and below the root-zone following irrigation events in each of five experimental plots (8 x 16 m2). To simulate the individual infiltration events we employed the HYDRUS-1D computational module (Simunek et al., 2005) and compared the finite-water content vadose zone flow method (Ogden et al. 2015) with numerical solutions to the Richards' equation. For both models we assumed a homogenous and isotropic root zone that is initially unsaturated with no water flow. Here we assess the ability of these two models to account for the control volume applied to the plots and to capture sharp changes in matric potential that were observed in the early time after an irrigation pulse. The goodness-of-fit of the models was evaluated using the root mean square error (RMSE) for observed and predicted values of cumulative infiltration over time, wetting front depth over time and water content at observation nodes. For the finite-water content method, the RMSE values and output for observation nodes were similar to that from the HYDRUS-1D solution. This indicates that the finite-water content method may be useful for predicting the fate of large volumes of water applied for MAR. Moreover, both models suggest a
NASA Astrophysics Data System (ADS)
Delettrez, J. A.; Myatt, J. F.; Yaakobi, B.
2015-11-01
The modeling of the fast-electron transport in the 1-D hydrodynamic code LILAC was modified because of the addition of cross-beam-energy-transfer (CBET) in implosion simulations. Using the old fast-electron with source model CBET results in a shift of the peak of the hard x-ray (HXR) production from the end of the laser pulse, as observed in experiments, to earlier in the pulse. This is caused by a drop in the laser intensity of the quarter-critical surface from CBET interaction at lower densities. Data from simulations with the laser plasma simulation environment (LPSE) code will be used to modify the source algorithm in LILAC. In addition, the transport model in LILAC has been modified to include deviations from the straight-line algorithm and non-specular reflection at the sheath to take into account the scattering from collisions and magnetic fields in the corona. Simulation results will be compared with HXR emissions from both room-temperature plastic and cryogenic target experiments. This material is based upon work supported by the Department of Energy National Nuclear Security Administration under Award Number DE-NA0001944.
Sénégond, Nicolas; Boulmé, Audren; Plag, Camille; Teston, Franck; Certon, Dominique
2013-07-01
We report a fast time-domain model of fluid-coupled cMUTs developed to predict the transient response-i.e., the impulse pressure response--of an element of a linear 1-D array. Mechanical equations of the cMUT diaphragm are solved with 2-D finite-difference schemes. The time-domain solving method is a fourth--order Runge-Kutta algorithm. The model takes into account the electrostatic nonlinearity and the contact with the bottom electrode when the membrane is collapsed. Mutual acoustic coupling between cells is introduced through the numerical implementation of analytical solutions of the impulse diffraction theory established in the case of acoustic sources with rectangular geometry. Processing times are very short: they vary from a few minutes for a single cell to a maximum of 30 min for one element of an array. After a description of the model, the impact of the nonlinearity and the pull-in/pull-out phenomena on the dynamic behavior of the cMUT diaphragm is discussed. Experimental results of mechanical displacements obtained by interferometric measurements and the acoustic pressure field are compared with simulations. Different excitation signals-high-frequency bandwidth pulses and toneburst excitations of varying central frequency-were chosen to compare theory with experimental results. PMID:25004518
NASA Astrophysics Data System (ADS)
Kristensen, Tom; Simoni, Andrea; Launay, Jean-Michel
2016-05-01
We compute scattering and bound state properties for two ultracold molecules in a pure 1D optical lattice. We introduce reference functions with complex quasi-momentum that naturally account for the effect of excited energy bands. Our exact results for a short-range interaction are first compared with the simplest version of the standard Bose-Hubbard (BH) model. Such comparison allows us to highlight the effect of the excited bands, of the non-on-site interaction and of tunneling with distant neighbor, that are not taken into account in the BH model. The effective interaction can depend strongly on the particle quasi-momenta and can present a resonant behavior even in a deep lattice. As a second step, we study scattering of two polar particles in the optical lattice. Peculiar Wigner threshold laws stem from the interplay of the long range dipolar interaction and the presence of the energy bands. We finally assess the validity of an extended Bose-Hubbard model for dipolar gases based on our exact two-body calculations. This work was supported by the Agence Nationale de la Recherche (Contract No. ANR-12-BS04-0020-01).
NASA Astrophysics Data System (ADS)
Guo, Leicheng; Wegen, Mick; Wang, Zheng Bing; Roelvink, Dano; He, Qing
2016-05-01
Tidal asymmetry is an important mechanism generating tidal residual sediment transport (TRST) in tidal environments. So far, it is known that a number of tidal interactions (e.g., M2-M4 and M2-O1-K1) can induce tidal asymmetry and associated TRST; however, their variability and morphodynamic impacts are insufficiently explored. Inspired by the river and tidal forcing conditions in the Yangtze River Estuary, we explore the morphodynamic development of a 560 km long estuary under the boundary forcing conditions of varyingly combined tidal constituents and river discharges using a schematized 1-D morphodynamic model for long-term (millennial) simulations. We then employ an analytical scheme which integrates sediment transport as a function of flow velocities to decompose the contribution of different tidal interactions on TRST and to explain how the river and tidal interactions control TRST and associated morphodynamics. Model results display varying equilibrium bed profiles. Analytical results suggest that (1) a series of tidal interactions creates multiple tidal asymmetries and associated TRST, (2) river flow modulates tidal asymmetry nonlinearly in space, and (3) more tidal constituents at the sea boundary persistently enhance the seaward TRST through river-tide interactions. It is the combined effects of multiple tidal asymmetries and river-tide interactions that determine the net TRST and consequent morphodynamic development. It thus suggests that tidal harmonics of significant amplitudes need to be considered properly as boundary conditions for long-term, large-scale morphodynamic modeling.
Toba, Junya; Nikkuni, Miyu; Ishizeki, Masato; Yoshii, Aya; Watamura, Naoto; Inoue, Takafumi; Ohshima, Toshio
2016-05-13
Alzheimer's disease (AD) is one of the best known neurodegenerative diseases; it causes dementia and its pathological features include accumulation of amyloid β (Aβ) and neurofibrillary tangles (NFTs) in the brain. Elevated Cdk5 activity and CRMP2 phosphorylation have been reported in the brains of AD model mice at the early stage of the disease, but the significance thereof in human AD remains unelucidated. We have recently reported that Aβ accumulation in the cerebellum of AD model APPswe/PS1dE9 (APP/PS1) mice, and cerebellar dysfunctions, such as impairment of motor coordination ability and long-term depression (LTD) induction, at the pre-Aβ accumulation stage. In the present study, we found increased phosphorylation levels of CRMP2 as well as increased p35 protein levels in the cerebellum of APP/PS1 mice. Interestingly, we show that pioglitazone, an agonist of peroxisome proliferator-activated receptor γ, normalized the p35 protein and CRMP2 phosphorylation levels in the cerebellum. Impaired motor coordination ability and LTD in APP/PS1 mice were ameliorated by pioglitazone treatment at the pre-Aβ accumulation stage. These results suggest a correlation between CRMP2 phosphorylation and AD pathophysiology, and indicate the effectiveness of pioglitazone treatment at the pre-Aβ accumulation stage in AD model mice. PMID:27059136
Study on kinetic model of microwave thermocatalytic treatment of biomass tar model compound.
Anis, Samsudin; Zainal, Z A
2014-01-01
Kinetic model parameters for toluene conversion under microwave thermocatalytic treatment were evaluated. The kinetic rate constants were determined using integral method based on experimental data and coupled with Arrhenius equation for obtaining the activation energies and pre-exponential factors. The model provides a good agreement with the experimental data. The kinetic model was also validated with standard error of 3% on average. The extrapolation of the model showed a reasonable trend to predict toluene conversion and product yield both in thermal and catalytic treatments. Under microwave irradiation, activation energy of toluene conversion was lower in the range of 3-27 kJ mol(-1) compared to those of conventional heating reported in the literatures. The overall reaction rate was six times higher compared to conventional heating. As a whole, the kinetic model works better for tar model removal in the absence of gas reforming within a level of reliability demonstrated in this study. PMID:24231266
Kinetic and reactor models for HDT of middle distillates
Cotta, R.M.; Filho, R.M.
1996-12-31
Hydrodesulfurization (HDS) and hydrodenitrogenation (HDN) of middle distillates over a commercial Ni-Mo/y-Al{sub 2}O{sub 3} has been studied under wide operating conditions just as 340 to 380{degrees}C and 38 to 98 atm. A Power Law model was presented to each one of those reactions. The parameters of kinetic equations were estimated solving the ordinary differential equations by the 4 order Runge-Kutta-Gill algorithm and Marquardt method for searching of set of kinetic parameters (kinetic constants as well as the orders of reactions). An adiabatic diesel hydrotreating trickle-bed reactor packed with the same catalyst was simulated numerically in order to check up the behavior of this specific reaction system. One dimensional pseudo-homogeneous model was used in this work. For each feed, the mass and energy balance equations were integrated along the length of the catalytic bed using the 4th Runge-Kutta-Gill method. The performance of two industrial reactors was checked. 5 refs., 2 tabs.
Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism
Fleming, R.M.T.; Thiele, I.; Provan, G.; Nasheuer, H.P.
2010-01-01
The quantitative analysis of biochemical reactions and metabolites is at frontier of biological sciences. The recent availability of high-throughput technology data sets in biology has paved the way for new modelling approaches at various levels of complexity including the metabolome of a cell or an organism. Understanding the metabolism of a single cell and multi-cell organism will provide the knowledge for the rational design of growth conditions to produce commercially valuable reagents in biotechnology. Here, we demonstrate how equations representing steady state mass conservation, energy conservation, the second law of thermodynamics, and reversible enzyme kinetics can be formulated as a single system of linear equalities and inequalities, in addition to linear equalities on exponential variables. Even though the feasible set is non-convex, the reformulation is exact and amenable to large-scale numerical analysis, a prerequisite for computationally feasible genome scale modelling. Integrating flux, concentration and kinetic variables in a unified constraint-based formulation is aimed at increasing the quantitative predictive capacity of flux balance analysis. Incorporation of experimental and theoretical bounds on thermodynamic and kinetic variables ensures that the predicted steady state fluxes are both thermodynamically and biochemically feasible. The resulting in silico predictions are tested against fluxomic data for central metabolism in E. coli and compare favourably with in silico prediction by flux balance analysis. PMID:20230840
Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.
Fleming, R M T; Thiele, I; Provan, G; Nasheuer, H P
2010-06-01
The quantitative analysis of biochemical reactions and metabolites is at frontier of biological sciences. The recent availability of high-throughput technology data sets in biology has paved the way for new modelling approaches at various levels of complexity including the metabolome of a cell or an organism. Understanding the metabolism of a single cell and multi-cell organism will provide the knowledge for the rational design of growth conditions to produce commercially valuable reagents in biotechnology. Here, we demonstrate how equations representing steady state mass conservation, energy conservation, the second law of thermodynamics, and reversible enzyme kinetics can be formulated as a single system of linear equalities and inequalities, in addition to linear equalities on exponential variables. Even though the feasible set is non-convex, the reformulation is exact and amenable to large-scale numerical analysis, a prerequisite for computationally feasible genome scale modelling. Integrating flux, concentration and kinetic variables in a unified constraint-based formulation is aimed at increasing the quantitative predictive capacity of flux balance analysis. Incorporation of experimental and theoretical bounds on thermodynamic and kinetic variables ensures that the predicted steady state fluxes are both thermodynamically and biochemically feasible. The resulting in silico predictions are tested against fluxomic data for central metabolism in Escherichia coli and compare favourably with in silico prediction by flux balance analysis. PMID:20230840
Magnetic-sublevel atomic kinetics modeling for line polarization spectroscopy
Hakel, P.; Mancini, R. C.
2004-01-01
We discuss the mechanism of polarized X-ray line emission in plasmas, its connection to plasma anisotropy, and introduce an atomic kinetics model and code (POLAR) based on the population kinetics of magnetic sublevels. POLAR represents a multi-level, multi-process approach to the problem of polarized spectra in plasmas, and hence it is well suited for plasma applications where cascade effects and alignment transfer can become important. Polarization degrees of X-ray spectral lines computed with POLAR were successfully benchmarked against calculations done with other formalisms, and experimental results obtained at the EBIT facility of Lawrence Livermore National Laboratory. We also investigated the polarization of He-like Si X-ray satellite lines as spectral signatures of anisotropy in the electron distribution function. A comprehensive modeling study was performed taking into account hydrodynamics and electron kinetics. We find that two satellite lines connecting singlet states develop a noticeable polarization while the triplet lines remain unpolarized. These results suggest a scenario where triplet lines could be used as a reference while the singlets could be used as polarized markers of plasma anisotropy.
Kinetic models for in vivo interaction of radioligand and neuroreceptors
Holland, M.J.C. )
1990-02-26
Estimating the amount of nonspecifically bound ligand is required for the analysis of kinetic data derived from in vivo studies of radioligand-neuroreceptor interactions. Most models assume that nonspecific binding is nonsaturable and rapidly reversible and, therefore, represent nonspecific binding as a constant fraction of the radioligand present in a given tissue compartment. This treatment of nonspecific binding predicts that all brain regions will exhibit similar levels of nonspecific binding subject only to differences in blood flow, and is used to justify the practice of estimating specific binding in receptor-rich regions by subtracting the total radioligand in receptor-poor regions from that found in the receptor-rich region. In reality, however, nonspecific binding is probably heterogeneous in character. Some of it may not exhibit very rapid kinetics relative to specific binding to receptors; some of it may be irreversible. When computer simulations are performed using a model which treats nonspecific binding as a separate compartment with its own kinetic parameters rather than as a constant fraction of the radioligand in extracellular fluid, predicted levels of nonspecific binding differ in receptor-rich and receptor-poor regions, suggesting that using receptor-poor regions to estimate nonspecific binding may not be justified.
Kinetic model of impurity poisoning during growth of calcite
DeYoreo, J; Wasylenki, L; Dove, P; Wilson, D; Han, N
2004-05-18
The central role of the organic component in biologically controlled mineralization is widely recognized. These proteins are characterized by a high proportion of acidic amino acid residues, especially aspartate, Asp. At the same time, biomineralization takes place in the presence of a number of naturally-occurring, inorganic impurities, particularly Mg and Sr. In an attempt to decipher the controls on calcite growth imposed by both classes of modifiers, we have used in situ AFM to investigate the dependence of growth morphology and step kinetics on calcite in the presence of Sr{sup 2+}, as well as a wide suite of Aspartic acid-bearing polypeptides. In each case, we observe a distinct and step-specific modification. Most importantly, we find that the step speed exhibits a characteristic dependence on impurity concentration not predicted by existing crystal growth models. While all of the impurities clearly induce appearance of a 'dead zone,' neither the width of that dead zone nor the dependence of step speed on activity or impurity content can be explained by invoking the Gibbs-Thomson effect, which is the basis for the Cabrera-Vermilyea model of impurity poisoning. Common kink-blocking models also fail to explain the observed dependencies. Here we propose a kinetic model of inhibition based on a 'cooperative' effect of impurity adsorption at adjacent kink sites. The model is in qualitative agreement with the experimental results in that it predicts a non-linear dependence of dead zone width on impurity concentration, as well as a sharp drop in step speed above a certain impurity content. However, a detailed model of impurity adsorption kinetics that give quantitative agreement with the data has yet to be developed.
Kinetic measurements of hydrocarbon conversion reactions on model metal surfaces.
Wilson, Jarod; Guo, Hansheng; Morales, Ricardo; Podgornov, Egor; Lee, Ilkeun; Zaera, Francisco
2007-08-01
Examples from recent studies in our laboratory are presented to illustrate the main tools available to surface scientists for the determination of the kinetics of surface reactions. Emphasis is given here to hydrocarbon conversions and studies that rely on the use of model systems, typically single crystals and controlled (ultrahigh vacuum) environments. A detailed discussion is provided on the use of temperature-programmed desorption for the determination of activation energies as well as for product identification and yield estimations. Isothermal kinetic measurements are addressed next by focusing on studies under vacuum using molecular beams and surface-sensitive spectroscopies. That is followed by a review of the usefulness of high-pressure cells and other reactor designs for the emulation of realistic catalytic conditions. Finally, an analysis of the power of isotope labeling and chemical substitutions in mechanistic research on surface reactions is presented. PMID:17637975
Modeling interface-controlled phase transformation kinetics in thin films
NASA Astrophysics Data System (ADS)
Pang, E. L.; Vo, N. Q.; Philippe, T.; Voorhees, P. W.
2015-05-01
The Johnson-Mehl-Avrami-Kolmogorov (JMAK) equation is widely used to describe phase transformation kinetics. This description, however, is not valid in finite size domains, in particular, thin films. A new computational model incorporating the level-set method is employed to study phase evolution in thin film systems. For both homogeneous (bulk) and heterogeneous (surface) nucleation, nucleation density and film thickness were systematically adjusted to study finite-thickness effects on the Avrami exponent during the transformation process. Only site-saturated nucleation with isotropic interface-kinetics controlled growth is considered in this paper. We show that the observed Avrami exponent is not constant throughout the phase transformation process in thin films with a value that is not consistent with the dimensionality of the transformation. Finite-thickness effects are shown to result in reduced time-dependent Avrami exponents when bulk nucleation is present, but not necessarily when surface nucleation is present.
Modeling transport kinetics in clinoptilolite-phosphate rock systems
NASA Technical Reports Server (NTRS)
Allen, E. R.; Ming, D. W.; Hossner, L. R.; Henninger, D. L.
1995-01-01
Nutrient release in clinoptilolite-phosphate rock (Cp-PR) systems occurs through dissolution and cation-exchange reactions. Investigating the kinetics of these reactions expands our understanding of nutrient release processes. Research was conducted to model transport kinetics of nutrient release in Cp-PR systems. The objectives were to identify empirical models that best describe NH4, K, and P release and define diffusion-controlling processes. Materials included a Texas clinoptilolite (Cp) and North Carolina phosphate rock (PR). A continuous-flow thin-disk technique was used. Models evaluated included zero order, first order, second order, parabolic diffusion, simplified Elovich, Elovich, and power function. The power-function, Elovich, and parabolic-diffusion models adequately described NH4, K, and P release. The power-function model was preferred because of its simplicity. Models indicated nutrient release was diffusion controlled. Primary transport processes controlling nutrient release for the time span observed were probably the result of a combination of several interacting transport mechanisms.
Multiensemble Markov models of molecular thermodynamics and kinetics
Wu, Hao; Paul, Fabian; Noé, Frank
2016-01-01
We introduce the general transition-based reweighting analysis method (TRAM), a statistically optimal approach to integrate both unbiased and biased molecular dynamics simulations, such as umbrella sampling or replica exchange. TRAM estimates a multiensemble Markov model (MEMM) with full thermodynamic and kinetic information at all ensembles. The approach combines the benefits of Markov state models—clustering of high-dimensional spaces and modeling of complex many-state systems—with those of the multistate Bennett acceptance ratio of exploiting biased or high-temperature ensembles to accelerate rare-event sampling. TRAM does not depend on any rate model in addition to the widely used Markov state model approximation, but uses only fundamental relations such as detailed balance and binless reweighting of configurations between ensembles. Previous methods, including the multistate Bennett acceptance ratio, discrete TRAM, and Markov state models are special cases and can be derived from the TRAM equations. TRAM is demonstrated by efficiently computing MEMMs in cases where other estimators break down, including the full thermodynamics and rare-event kinetics from high-dimensional simulation data of an all-atom protein–ligand binding model. PMID:27226302
Isothermal crystallization kinetic modeling of poly(etherketoneketone) (PEKK)
NASA Astrophysics Data System (ADS)
Choupin, T.; Paris, C.; Cinquin, J.; Fayolle, B.; Régnier, G.
2016-05-01
Isothermal melt and cold crystallization kinetics of poly(etherketoneketone) (PEKK) have been investigated by differential scanning calorimetry. A modified Avrami model has been used to describe the two-stage crystallization of PEKK. The primary crystallization stage is assumed to be a two dimensional nucleation growth with an Avrami exponent of 2 whereas the secondary stage is assumed to be a one dimensional nucleation growth with an Avrami exponent of 1. The evolution of the crystallization constant rates depending on temperature has been modeled with the Hoffman and Lauritzen growth equation. The activation energy of nucleation constants Kg for both crystallizations are presented.
Kinetic modeling of non-ideal explosives with CHEETAH
Fried, L E; Howard, W M; Souers, P C
1998-08-06
We report an implementation of the Wood-Kirkwood kinetic detonation model based on multi-species equations of state and multiple reaction rate laws. Finite rate laws are used for the slowest chemical reactions. Other reactions are given infinite rates and are kept in constant thermodynamic equilibrium. We model a wide range of ideal and non-ideal composite energetic materials. We find that we can replicate experimental detonation velocities to within a few per cent, while obtaining good agreement with estimated reaction zone lengths. The detonation velocity as a function of charge radius is also correctly reproduced.
NASA Astrophysics Data System (ADS)
Borbon, A.; Ruiz, M.; Bechara, J.; Afif, C.; Huntrieser, H.; Mills, G.; Mari, C.; Reeves, C.; Schlager, H.
2010-12-01
Deep convection plays a key role in determining global atmospheric composition of the upper troposphere by the fast uplift of HOx radical and ozone precursors to the upper troposphere. Formaldehyde (HCHO) is one important gas precursor. It is the most abundant carbonyl compound originating from both primary processes and photooxidation of volatile organic compounds. Thus, determining its source strength to the upper troposphere is important for estimating ozone production. However processes governing its fate are multiple and complex including dynamics (entrainment and detrainment), multiphase chemistry and cloud microphysics. As a result, the flux of formaldehyde to the upper troposphere is still uncertain. The goal of this study is to examine the redistribution of formaldehyde in tropical mesoscale convective systems (MSC) and to estimate its sources and sinks during convective transport to the upper troposphere. The novelty here is to combine 1D modelling (Meso NH model) and formaldehyde aircraft observations. Observations were collected over West Africa during the monsoon period (July-August 2006) of the AMMA experiment. Four aircrafts (English BAe-146, French ATR-42 and Falcon-20 and German Falcon-20) were deployed over a large domain (long.: -8°E-5°W, lat. 4°N-20°N, alt.: 0 12 km) with formaldehyde measuring instruments on board. First, this presentation will point out the construction of a comprehensive and consistent data set of formaldehyde by ensuring data comparability thanks to aircraft intercomparison flights, multiple chemical tracer approach (CO, O3 and relative humidity) and a spatial gridding of the domain. Then formaldehyde spatial variability will be examined under background and convective conditions. Finally, the relative importance of transport (entrainment) and wet scavenging will be discussed from selected AMMA flights. For that purpose, the following equation system has been resolved [HCHO]transported to UT=[HCHO]measured - [HCHO
Darvesh, Sultan; Cash, Meghan K.; Reid, G. Andrew; Martin, Earl; Mitnitski, Arnold; Geula, Changiz
2011-01-01
Histochemical analysis of Alzheimer disease (AD) brain tissues indicates that butyrylcholinesterase (BuChE) is present in β-amyloid (Aβ) plaques. The role of BuChE in AD pathology is unknown but an animal model developing similar BuChE-associated Aβ plaques could provide insights. The APPSWE/PSEN1dE9 mouse (ADTg), which develops Aβ plaques, was examined to determine if BuChE associates with these plaques, as in AD. We found that in mature ADTg mice, BuChE activity associated with Aβ plaques. Aβ-, thioflavin-S- and BuChE-positive plaques mainly accumulated in olfactory structures, cerebral cortex, hippocampal formation, amygdala and cerebellum. No plaques were stained for acetylcholinesterase activity. The distribution and abundance of plaque staining in ADTg closely resembled many aspects of plaque staining in AD. BuChE staining consistently showed fewer plaques than were detected with Aβ immunostaining but a greater number of plaques than were visualized with thioflavin-S. Double-labelling experiments demonstrated that all BuChE-positive plaques were Aβ-positive while only some BuChE-positive plaques were thioflavin-S-positive. These observations suggest that BuChE is associated with a subpopulation of Aβ plaques and may play a role in AD plaque maturation. Further study of this animal model could clarify the role of BuChE in AD pathology. PMID:22157615
NASA Astrophysics Data System (ADS)
Bryan, Alexander M.; Cheng, Susan J.; Ashworth, Kirsti; Guenther, Alex B.; Hardiman, Brady S.; Bohrer, Gil; Steiner, Allison L.
2015-11-01
Foliar emissions of biogenic volatile organic compounds (BVOC)-important precursors of tropospheric ozone and secondary organic aerosols-vary widely by vegetation type. Modeling studies to date typically represent the canopy as a single dominant tree type or a blend of tree types, yet many forests are diverse with trees of varying height. To assess the sensitivity of biogenic emissions to tree height variation, we compare two 1-D canopy model simulations in which BVOC emission potentials are homogeneous or heterogeneous with canopy depth. The heterogeneous canopy emulates the mid-successional forest at the University of Michigan Biological Station (UMBS). In this case, high-isoprene-emitting foliage (e.g., aspen and oak) is constrained to the upper canopy, where higher sunlight availability increases the light-dependent isoprene emission, leading to 34% more isoprene and its oxidation products as compared to the homogeneous simulation. Isoprene declines from aspen mortality are 10% larger when heterogeneity is considered. Overall, our results highlight the importance of adequately representing complexities of forest canopy structure when simulating light-dependent BVOC emissions and chemistry.
Bryan, Alexander M.; Cheng, Susan J.; Ashworth, Kirsti; Guenther, Alex B.; Hardiman, Brady; Bohrer, Gil; Steiner, A. L.
2015-11-01
Foliar emissions of biogenic volatile organic compounds (BVOC)dimportant precursors of tropospheric ozone and secondary organic aerosolsdvary widely by vegetation type. Modeling studies to date typi-cally represent the canopy as a single dominant tree type or a blend of tree types, yet many forests are diverse with trees of varying height. To assess the sensitivity of biogenic emissions to tree height vari-ation, we compare two 1-D canopy model simulations in which BVOC emission potentials are homo-geneous or heterogeneous with canopy depth. The heterogeneous canopy emulates the mid-successional forest at the University of Michigan Biological Station (UMBS). In this case, high-isoprene-emitting fo-liage (e.g., aspen and oak) is constrained to the upper canopy, where higher sunlight availability increases the light-dependent isoprene emission, leading to 34% more isoprene and its oxidation products as compared to the homogeneous simulation. Isoprene declines from aspen mortality are 10% larger when heterogeneity is considered. Overall, our results highlight the importance of adequately representing complexities of forest canopy structure when simulating light-dependent BVOC emissions and chemistry.
Kinetic energy for the nuclear Yang-Mills collective model
NASA Astrophysics Data System (ADS)
Rosensteel, George; Sparks, Nick
2015-10-01
The Bohr-Mottelson-Frankfurt model of nuclear rotations and quadrupole vibrations is a foundational model in nuclear structure physics. The model, also called the geometrical collective model or simply GCM, has two hidden mathematical structures, one Lie group theoretic and the other differential geometric. Although the group structure has been understood for some time, the geometric structure is a new unexplored feature that shares the same mathematical origin as Yang-Mills, viz., a vector bundle with a non-abelian structure group and a connection. Using the de Rham Laplacian ▵ = * d * d from differential geometry for the kinetic energy extends significantly the physical scope of the GCM model. This Laplacian contains a ``magnetic'' term due to the coupling between base manifold rotational and fiber vorticity degrees of freedom. When the connection specializes to irrotational flow, the Laplacian reduces to the Bohr-Mottelson kinetic energy operator. More generally, the connection yields a moment of inertia that is intermediate between the extremes of irrotational flow and rigid body motion.
A Detailed Level Kinetics Model of NO Vibrational Energy Distributions
NASA Technical Reports Server (NTRS)
Sharma, Surendra P.; Gilmore, John; Cavolowsky, John A. (Technical Monitor)
1996-01-01
Several contemporary problems have pointed to the desirability of a detailed level kinetics approach to modeling the distribution of vibrational energy in NO. Such a model is necessary when vibrational redistribution reactions are insufficient to maintain a Boltzmann distribution over the vibrational energy states. Recent calculations of the rate constant for the first reaction of the Zeldovich mechanism (N2 + O (goes to) NO + N) have suggested that the product NO is formed in high vibrational states. In shock layer flowfields, the product NO molecules may experience an insufficient number of collisions to establish a Boltzmann distribution over vibrational states, thus necessitating a level kinetics model. In other flows, such as expansions of high temperature air, fast, near-resonance vibrational energy exchanges with N2 and O2 may also require a level specific model for NO because of the relative rates of vibrational exchange and redistribution. The proposed report will integrate computational and experimental components to construct such a model for the NO molecule.
Langrangian model of nitrogen kinetics in the Chattahoochee river
Jobson, H.E.
1987-01-01
A Lagrangian reference frame is used to solve the convection-dispersion equation and interpret water-quality obtained from the Chattahoochee River. The model was calibrated using unsteady concentrations of organic nitrogen, ammonia, and nitrite plus nitrate obtained during June 1977 and verified using data obtained during August 1976. Reaction kinetics of the cascade type are shown to provide a reasonable description of the nitrogen-species processes in the Chattahoochee River. The conceptual model is easy to visualize in the physical sense and the output includes information that is not easily determined from an Eulerian approach, but which is very helpful in model calibration and data interpretation. For example, the model output allows one to determine which data are of most value in model calibration or verification.
Tholeti, Siva Sashank; Alexeenko, Alina A.; Shneider, Mikhail N.
2014-06-15
We present numerical kinetic modeling of generation and evolution of the plasma produced as a result of resonance enhanced multiphoton ionization (REMPI) in Argon gas. The particle-in-cell/Monte Carlo collision (PIC/MCC) simulations capture non-equilibrium effects in REMPI plasma expansion by considering the major collisional processes at the microscopic level: elastic scattering, electron impact ionization, ion charge exchange, and recombination and quenching for metastable excited atoms. The conditions in one-dimensional (1D) and two-dimensional (2D) formulations correspond to known experiments in Argon at a pressure of 5 Torr. The 1D PIC/MCC calculations are compared with the published results of local drift-diffusion model, obtained for the same conditions. It is shown that the PIC/MCC and diffusion-drift models are in qualitative and in reasonable quantitative agreement during the ambipolar expansion stage, whereas significant non-equilibrium exists during the first few 10 s of nanoseconds. 2D effects are important in the REMPI plasma expansion. The 2D PIC/MCC calculations produce significantly lower peak electron densities as compared to 1D and show a better agreement with experimentally measured microwave radiation scattering.
Kinetic model for astaxanthin aggregation in water-methanol mixtures
NASA Astrophysics Data System (ADS)
Giovannetti, Rita; Alibabaei, Leila; Pucciarelli, Filippo
2009-07-01
The aggregation of astaxanthin in hydrated methanol was kinetically studied in the temperature range from 10 °C to 50 °C, at different astaxanthin concentrations and solvent composition. A kinetic model for the formation and transformation of astaxanthin aggregated has been proposed. Spectrophotometric studies showed that monomeric astaxanthin decayed to H-aggregates that after-wards formed J-aggregates when water content was 50% and the temperature lower than 20 °C; at higher temperatures, very stable J-aggregates were formed directly. Monomer formed very stable H-aggregates when the water content was greater than 60%; in these conditions H-aggregates decayed into J-aggregates only when the temperature was at least 50 °C. Through these findings it was possible to establish that the aggregation reactions took place through a two steps consecutive reaction with first order kinetic constants and that the values of these depended on the solvent composition and temperature.
Iwamoto, Masami; Nakahira, Yuko
2015-11-01
Accurate prediction of occupant head kinematics is critical for better understanding of head/face injury mechanisms in side impacts, especially far-side occupants. In light of the fact that researchers have demonstrated that muscle activations, especially in neck muscles, can affect occupant head kinematics, a human body finite element (FE) model that considers muscle activation is useful for predicting occupant head kinematics in real-world automotive accidents. In this study, we developed a human body FE model called the THUMS (Total HUman Model for Safety) Version 5 that contains 262 one-dimensional (1D) Hill-type muscle models over the entire body. The THUMS was validated against 36 series of PMHS (Post Mortem Human Surrogate) and volunteer test data in this study, and 16 series of PMHS and volunteer test data on side impacts are presented. Validation results with force-time curves were also evaluated quantitatively using the CORA (CORrelation and Analysis) method. The validation results suggest that the THUMS has good biofidelity in the responses of the regional or full body for side impacts, but relatively poor biofidelity in its local level of responses such as brain displacements. Occupant kinematics predicted by the THUMS with a muscle controller using 22 PID (Proportional-Integral- Derivative) controllers were compared with those of volunteer test data on low-speed lateral impacts. The THUMS with muscle controller reproduced the head kinematics of the volunteer data more accurately than that without muscle activation, although further studies on validation of torso kinematics are needed for more accurate predictions of occupant head kinematics. PMID:26660740
A hybrid model describing ion induced kinetic electron emission
NASA Astrophysics Data System (ADS)
Hanke, S.; Duvenbeck, A.; Heuser, C.; Weidtmann, B.; Wucher, A.
2015-06-01
We present a model to describe the kinetic internal and external electron emission from an ion bombarded metal target. The model is based upon a molecular dynamics treatment of the nuclear degree of freedom, the electronic system is assumed as a quasi-free electron gas characterized by its Fermi energy, electron temperature and a characteristic attenuation length. In a series of previous works we have employed this model, which includes the local kinetic excitation as well as the rapid spread of the generated excitation energy, in order to calculate internal and external electron emission yields within the framework of a Richardson-Dushman-like thermionic emission model. However, this kind of treatment turned out to fail in the realistic prediction of experimentally measured internal electron yields mainly due to the restriction of the treatment of electronic transport to a diffusive manner. Here, we propose a slightly modified approach additionally incorporating the contribution of hot electrons which are generated in the bulk material and undergo ballistic transport towards the emitting interface.
NASA Astrophysics Data System (ADS)
McCarthy, M. C.; Boering, K. A.; Rice, A. L.; Tyler, S. C.; Connell, P.; Atlas, E.
2003-08-01
New high-precision measurements of the carbon and hydrogen isotopic compositions of stratospheric CH4 made on whole air samples collected aboard the NASA ER-2 aircraft are compared with results from the Lawrence Livermore National Laboratory 2-D model. Model runs incorporating sets of experimentally determined kinetic isotope effects (KIEs) for the reactions of CH4 with each of the oxidants OH, O(1D), and Cl are examined with the goals of determining (1) how well the 2-D model can reproduce the observations for both the carbon and hydrogen isotopic compositions, (2) what factors are responsible for the observed increase in the apparent isotopic fractionation factors with decreasing methane mixing ratios, and (3) how sensitive the modeled isotopic compositions are to various experimentally determined KIEs. Bound by estimates of the effects of uncertainties in model chemistry and transport on isotopic compositions, we then examine the constraints the ER-2 observations place on values for the KIEs. For the carbon KIE for reaction of CH4 with O(1D), for example, the analysis of model results and observations favors the larger of the experimental values, 1.013, over a value of 1.001. These analyses also suggest that intercomparisons of results from different models using a given set of KIEs may be useful as a new diagnostic of model-model differences in integrated chemistry and transport.
Modeling anomalous radial transport in kinetic transport codes
NASA Astrophysics Data System (ADS)
Bodi, K.; Krasheninnikov, S. I.; Cohen, R. H.; Rognlien, T. D.
2009-11-01
Anomalous transport is typically the dominant component of the radial transport in magnetically confined plasmas, where the physical origin of this transport is believed to be plasma turbulence. A model is presented for anomalous transport that can be used in continuum kinetic edge codes like TEMPEST, NEO and the next-generation code being developed by the Edge Simulation Laboratory. The model can also be adapted to particle-based codes. It is demonstrated that the model with a velocity-dependent diffusion and convection terms can match a diagonal gradient-driven transport matrix as found in contemporary fluid codes, but can also include off-diagonal effects. The anomalous transport model is also combined with particle drifts and a particle/energy-conserving Krook collision operator to study possible synergistic effects with neoclassical transport. For the latter study, a velocity-independent anomalous diffusion coefficient is used to mimic the effect of long-wavelength ExB turbulence.
Tracer kinetic modelling in MRI: estimating perfusion and capillary permeability
NASA Astrophysics Data System (ADS)
Sourbron, S. P.; Buckley, D. L.
2012-01-01
The tracer-kinetic models developed in the early 1990s for dynamic contrast-enhanced MRI (DCE-MRI) have since become a standard in numerous applications. At the same time, the development of MRI hardware has led to increases in image quality and temporal resolution that reveal the limitations of the early models. This in turn has stimulated an interest in the development and application of a second generation of modelling approaches. They are designed to overcome these limitations and produce additional and more accurate information on tissue status. In particular, models of the second generation enable separate estimates of perfusion and capillary permeability rather than a single parameter Ktrans that represents a combination of the two. A variety of such models has been proposed in the literature, and development in the field has been constrained by a lack of transparency regarding terminology, notations and physiological assumptions. In this review, we provide an overview of these models in a manner that is both physically intuitive and mathematically rigourous. All are derived from common first principles, using concepts and notations from general tracer-kinetic theory. Explicit links to their historical origins are included to allow for a transfer of experience obtained in other fields (PET, SPECT, CT). A classification is presented that reveals the links between all models, and with the models of the first generation. Detailed formulae for all solutions are provided to facilitate implementation. Our aim is to encourage the application of these tools to DCE-MRI by offering researchers a clearer understanding of their assumptions and requirements.
Gurevicius, Kestutis; Lipponen, Arto; Tanila, Heikki
2013-05-01
Amyloid precursor protein transgenic mice modeling Alzheimer's disease display frequent occurrence of seizures peaking at an age when amyloid plaques start to form in the cortex and hippocampus. We tested the hypothesis that numerous reported interactions of amyloid-β with cell surface molecules result in altered excitation-inhibition balance in brain-wide neural networks, eventually leading to epileptogenesis. We examined electroencephalograms (EEGs) and auditory-evoked potentials (AEPs) in freely moving 4-month-old APPswe/PS1dE9 (APdE9) and wild-type (WT) control mice in the hippocampus, cerebral cortex, and thalamus during movement, quiet waking, non-rapid eye movement sleep, and rapid eye movement (REM) sleep. Cortical EEG power was higher in APdE9 mice than in WT mice over a broad frequency range (5-100 Hz) and during all 4 behavioral states. Thalamic EEG power was also increased but in a narrower range (10-80 Hz). Furthermore, APdE9 mice displayed augmented cortical and thalamic AEPs. While power and theta-gamma modulation were preserved in the APdE9 hippocampus, REM sleep-related phase shift of theta-gamma modulation was altered. Our data suggest that at the early stage of amyloid pathology, cortical principal cells become hyperexcitable and via extensive cortico-thalamic connection drive thalamic cells. Minor hippocampal changes are most likely secondary to abnormal entorhinal input. PMID:22581851
A 1D radiative-convective model of H2O-CO2 atmospheres around young telluric planets: an update
NASA Astrophysics Data System (ADS)
Marcq, Emmanuel; Salvador, Arnaud; Massol, Hélène; Chassefière, Éric
2016-04-01
The study of the early phases of the evolution of terrestrial planets has recently known significant progress [1,2]. It appears that their cooling phase during the magma ocean stage is first dominated by a radiative cooling stage through its atmosphere. If the planet is able to reach radiative balance during this stage, then its further evolution is dominated by the escape flux, and no large scale condensation of water occurs (Hamano-type II planets). On the other hand, if the planet is far enough from the sun, then radiative equilibrium cannot be reached until the outgoing flux has fallen below the runaway greenhouse limit, implying the condensation of most atmospheric water vapor into a global water ocean, thus sheltering most water from atmospheric escape (Hamano-type I planet). In the solar system, Earth is clearly a type-I planet, whereas Venus was most likely a type-II planet from quite early on in its history [1,2]. In this presentation, we will deal with the atmospheric radiative model used by [2] and first described in [3]. After describing its recent improvements since [3] (pressure grid enabling an arbitrary total volatile amount, correction of the k-correlated radiative transfer in the thermal radiation, improvement of the numerical stability and integration scheme) and their consequences on the detectability of extrasolar type-I or type-II planets, we will deal with the possible improvements and extensions to such models, such as but not limited to: (1) adopting a 1D-spherical geometry suited for larger atmospheres around smaller planets, (2) improvement of the visible albedo parameterization based on recent 3D-modelling GCM [4]. [1] : K. Hamano et al., Nature (2013) [2] : T. Lebrun et al. JGR (2013) [3] : E. Marcq, JGR (2012) [4] : J. Leconte et al. (2015)
Jiang, Shuang; Pang, Liping; Buchan, Graeme D; Simůnek, Jirí; Noonan, Mike J; Close, Murray E
2010-02-01
HYDRUS-1D was used to simulate water flow and leaching of fecal coliforms and bromide (Br) through six undisturbed soil lysimeters (70 cm depth by 50 cm diameter) under field conditions. Dairy shed effluent (DSE) spiked with Br was applied to the lysimeters, which contained fine sandy loam layers. This application was followed by fortnightly spray or flood water irrigation. Soil water contents were measured at four soil depths over 171 days, and leachate was collected from the bottom. The post-DSE period simulations yielded a generally decreased saturated water content compared to the pre-DSE period, and an increased saturated hydraulic conductivity and air-entry index, suggesting that changes in soil hydraulic properties (e.g. via changes in structure) can be induced by irrigation and seasonal effects. The single-porosity flow model was successful in simulating water flow under natural climatic conditions and spray irrigation. However, for lysimeters under flood irrigation, when the effect of preferential flow paths becomes more significant, the good agreement between predicted and observed water contents could only be achieved by using a dual-porosity flow model. Results derived from a mobile-immobile transport model suggest that compared to Br, bacteria were transported through a narrower pore-network with less mass exchange between mobile and immobile water zones. Our study suggests that soils with higher topsoil clay content and soils under flood irrigation are at a high risk of bacteria leaching through preferential flow paths. Irrigation management strategies must minimize the effect of preferential flow to reduce bacterial leaching from land applications of effluent. PMID:19775719
Quantitative description of realistic wealth distributions by kinetic trading models.
Lammoglia, Nelson; Muñoz, Víctor; Rogan, José; Toledo, Benjamín; Zarama, Roberto; Valdivia, Juan Alejandro
2008-10-01
Data on wealth distributions in trading markets show a power law behavior x(-)(1+alpha) at the high end, where, in general, alpha is greater than 1 (Pareto's law). Models based on kinetic theory, where a set of interacting agents trade money, yield power law tails if agents are assigned a saving propensity. In this paper we are solving the inverse problem, that is, in finding the saving propensity distribution which yields a given wealth distribution for all wealth ranges. This is done explicitly for two recently published and comprehensive wealth datasets. PMID:18999570
Kinetic mixing effect in the 3 -3 -1 -1 model
NASA Astrophysics Data System (ADS)
Dong, P. V.; Si, D. T.
2016-06-01
We show that the mixing effect of the neutral gauge bosons in the 3 -3 -1 -1 model comes from two sources. The first one is due to the 3 -3 -1 -1 gauge symmetry breaking as usual, whereas the second one results from the kinetic mixing between the gauge bosons of U (1 )X and U (1 )N groups, which are used to determine the electric charge and baryon minus lepton numbers, respectively. Such mixings modify the ρ -parameter and the known couplings of Z with fermions. The constraints that arise from flavor-changing neutral currents due to the gauge boson mixings and nonuniversal fermion generations are also given.
Quantitative description of realistic wealth distributions by kinetic trading models
NASA Astrophysics Data System (ADS)
Lammoglia, Nelson; Muñoz, Víctor; Rogan, José; Toledo, Benjamín; Zarama, Roberto; Valdivia, Juan Alejandro
2008-10-01
Data on wealth distributions in trading markets show a power law behavior x-(1+α) at the high end, where, in general, α is greater than 1 (Pareto’s law). Models based on kinetic theory, where a set of interacting agents trade money, yield power law tails if agents are assigned a saving propensity. In this paper we are solving the inverse problem, that is, in finding the saving propensity distribution which yields a given wealth distribution for all wealth ranges. This is done explicitly for two recently published and comprehensive wealth datasets.
A generic 3D kinetic model of gene expression
NASA Astrophysics Data System (ADS)
Zhdanov, Vladimir P.
2012-04-01
Recent experiments show that mRNAs and proteins can be localized both in prokaryotic and eukaryotic cells. To describe such situations, I present a 3D mean-field kinetic model aimed primarily at gene expression in prokaryotic cells, including the formation of mRNA, its translation into protein, and slow diffusion of these species. Under steady-state conditions, the mRNA and protein spatial distribution is described by simple exponential functions. The protein concentration near the gene transcribed into mRNA is shown to depend on the protein and mRNA diffusion coefficients and degradation rate constants.
Bio-butanol: Combustion properties and detailed chemical kinetic model
Black, G.; Curran, H.J.; Pichon, S.; Simmie, J.M.; Zhukov, V.
2010-02-15
Autoignition delay time measurements were performed at equivalence ratios of 0.5, 1 and 2 for butan-1-ol at reflected shock pressures of 1, 2.6 and 8 atm at temperatures from 1100 to 1800 K. High-level ab initio calculations were used to determine enthalpies of formation and consequently bond dissociation energies for each bond in the alcohol. A detailed chemical kinetic model consisting of 1399 reactions involving 234 species was constructed and tested against the delay times and also against recent jet-stirred reactor speciation data with encouraging results. The importance of enol chemistry is highlighted. (author)
NASA Astrophysics Data System (ADS)
Bozza, Andrea; Durand, Arnaud; Allenbach, Bernard; Confortola, Gabriele; Bocchiola, Daniele
2013-04-01
We present a feasibility study to explore potential of high-resolution imagery, coupled with hydraulic flood modeling to predict flooding risks, applied to the case study of Gonaives basins (585 km²), Haiti. We propose a methodology working at different scales, providing accurate results and a faster intervention during extreme flood events. The 'Hispaniola' island, in the Caribbean tropical zone, is often affected by extreme floods events. Floods are caused by tropical springs and hurricanes, and may lead to several damages, including cholera epidemics, as recently occurred, in the wake of the earthquake upon January 12th 2010 (magnitude 7.0). Floods studies based upon hydrological and hydraulic modeling are hampered by almost complete lack of ground data. Thenceforth, and given the noticeable cost involved in the organization of field measurement campaigns, the need for exploitation of remote sensing images data. HEC-RAS 1D modeling is carried out under different scenarios of available Digital Elevation Models. The DEMs are generated using optical remote sensing satellite (WorldView-1) and SRTM, combined with information from an open source database (Open Street Map). We study two recent flood episodes, where flood maps from remote sensing were available. Flood extent and land use have been assessed by way of data from SPOT-5 satellite, after hurricane Jeanne in 2004 and hurricane Hanna in 2008. A semi-distributed, DEM based hydrological model is used to simulate flood flows during the hurricanes. Precipitation input is taken from daily rainfall data derived from TRMM satellite, plus proper downscaling. The hydraulic model is calibrated using floodplain friction as tuning parameters against the observed flooded area. We compare different scenarios of flood simulation, and the predictive power of model calibration. The method provide acceptable results in depicting flooded areas, especially considering the tremendous lack of ground data, and show the potential of
A new kinetic model for human iodine metabolism
Ficken, V.J.; Allen, E.W.; Adams, G.D.
1985-05-01
A new kinetic model of iodine metabolism incorporating preferential organification of tyrosil (TYR) residues of thyroglobulin is developed and evaluated for euthyroid (n=5) and hyperthyroid (n=11) subjects. Iodine and peripheral T4 metabolims were measured with oral /sup 131/I-NaI and intravenous /sup 125/I-74 respectively. Data (obtained over 10 days) and kinetic model are analyzed using the SAAM27 program developed by Berman (1978). Compartment rate constants (mean rate per hour +- ISD) are tabulated in this paper. Thyroid and renal iodide clearance compare favorably with values reported in the literature. TYR rate constants were not unique; however, values obtained are within the range of rate constants determined from the invitro data reported by others. Intraluminal iodine as coupled TYR is predicted to be 21% for euthyroid and 59% for hyperthyroid subjects compared to analytical chemical methods of 30% and 51% respectively determined elsewhere. The authors plan to evaluate this model as a method of predicting the thyroid radiation dose from orally administered I/sup 131/.
NASA Astrophysics Data System (ADS)
Khosravi, M.; Baron, P.; Urban, J.; Froidevaux, L.; Jonsson, A. I.; Kasai, Y.; Kuribayashi, K.; Mitsuda, C.; Murtagh, D. P.; Sagawa, H.; Santee, M. L.; Sato, T. O.; Shiotani, M.; Suzuki, M.; von Clarmann, T.; Walker, K. A.; Wang, S.
2012-08-01
The diurnal variation of HOCl and the related species ClO, HO2 and HCl measured by satellites has been compared with the results of a one-dimensional photochemical model. The study compares the data from various limb-viewing instruments with model simulations from the middle stratosphere to the lower mesosphere. Data from three sub-millimeter instruments and two infrared spectrometers are used, namely from the Sub-Millimeter Radiometer (SMR) on board Odin, the Microwave Limb Sounder (MLS) on board Aura, the Superconducting Submillimeter-wave Limb-Emission Sounder (SMILES) on the International Space Station, the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) on board ENVISAT, and the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS) on board SCISAT. Inter-comparison of the measurements from instruments on sun-synchronous satellites (SMR, MLS, MIPAS) and measurements from solar occultation instruments (ACE-FTS) is challenging since the measurements correspond to different solar zenith angles (or local times). However, using a model which covers all solar zenith angles and the new SMILES instrument which measures at all local times over a period of several months provides the possibility to indirectly compare the diurnally variable species. The satellite data were averaged for latitudes of 20° S to 20° N for the SMILES observation period from November 2009 to April 2010 and were compared at three altitudes: 35, 45 and 55 km. This study presents the first evaluation of HO2 Odin/SMR data and also the first comparison of the new SMILES data and the latest version of MLS (version 3.3) with other satellite observations. The MISU-1D model has been run for conditions and locations of the observations. The diurnal cycle features for the species investigated here are generally well reproduced by the model. The satellite observations and the model generally agree well in terms of absolute mixing ratios as well as differences between
PLUME-MoM 1.0: a new 1-D model of volcanic plumes based on the method of moments
NASA Astrophysics Data System (ADS)
de'Michieli Vitturi, M.; Neri, A.; Barsotti, S.
2015-05-01
In this paper a new mathematical model for volcanic plumes, named PlumeMoM, is presented. The model describes the steady-state 1-D dynamics of the plume in a 3-D coordinate system, accounting for continuous variability in particle distribution of the pyroclastic mixture ejected at the vent. Volcanic plumes are composed of pyroclastic particles of many different sizes ranging from a few microns up to several centimeters and more. Proper description of such a multiparticle nature is crucial when quantifying changes in grain-size distribution along the plume and, therefore, for better characterization of source conditions of ash dispersal models. The new model is based on the method of moments, which allows description of the pyroclastic mixture dynamics not only in the spatial domain but also in the space of properties of the continuous size-distribution of the particles. This is achieved by formulation of fundamental transport equations for the multiparticle mixture with respect to the different moments of the grain-size distribution. Different formulations, in terms of the distribution of the particle number, as well as of the mass distribution expressed in terms of the Krumbein log scale, are also derived. Comparison between the new moments-based formulation and the classical approach, based on the discretization of the mixture in N discrete phases, shows that the new model allows the same results to be obtained with a significantly lower computational cost (particularly when a large number of discrete phases is adopted). Application of the new model, coupled with uncertainty quantification and global sensitivity analyses, enables investigation of the response of four key output variables (mean and standard deviation (SD) of the grain-size distribution at the top of the plume, plume height and amount of mass lost by the plume during the ascent) to changes in the main input parameters (mean and SD) characterizing the pyroclastic mixture at the base of the plume
NASA Astrophysics Data System (ADS)
Driba, D. L.; De Lucia, M.; Peiffer, S.
2014-12-01
Fluid-rock interactions in geothermal reservoirs are driven by the state of disequilibrium that persists among solid and solutes due to changing temperature and pressure. During operation of enhanced geothermal systems, injection of cooled water back into the reservoir disturbs the initial thermodynamic equilibrium between the reservoir and its geothermal fluid, which may induce modifications in permeability through changes in porosity and pore space geometry, consequently bringing about several impairments to the overall system.Modeling of fluid-rock interactions induced by injection of cold brine into Groß Schönebeck geothermal reservoir system situated in the Rotliegend sandstone at 4200m depth have been done by coupling geochemical modeling Code Phreeqc with OpenGeoSys. Through batch modeling the re-evaluation of the measured hydrochemical composition of the brine has been done using Quintessa databases, the results from the calculation indicate that a mineral phases comprising of K-feldspar, hematite, Barite, Calcite and Dolomite was found to match the hypothesis of equilibrium with the formation fluid, Reducing conditions are presumed in the model (pe = -3.5) in order to match the amount of observed dissolved Fe and thus considered as initial state for the reactive transport modeling. based on a measured composition of formation fluids and the predominant mineralogical assemblage of the host rock, a preliminary 1D Reactive transport modeling (RTM) was run with total time set to 30 years; results obtained for the initial simulation revealed that during this period, no significant change is evident for K-feldspar. Furthermore, the precipitation of calcite along the flow path in the brine results in a drop of pH from 6.2 to a value of 5.2 noticed over the simulated period. The circulation of cooled fluid in the reservoir is predicted to affect the temperature of the reservoir within the first 100 -150m from the injection well. Examination of porosity change in
Chemical Kinetic Models for HCCI and Diesel Combustion
Pitz, W J; Westbook, C K; Mehl, M
2008-10-30
Hydrocarbon fuels for advanced combustion engines consist of complex mixtures of hundreds or even thousands of different components. These components can be grouped into a number of chemically distinct classes, consisting of n-paraffins, branched paraffins, cyclic paraffins, olefins, oxygenates, and aromatics. Biodiesel contains its own unique chemical class called methyl esters. The fractional amounts of these chemical classes are quite different in gasoline, diesel fuel, oil-sand derived fuels and bio-derived fuels, which contributes to the very different combustion characteristics of each of these types of combustion systems. The objectives of this project are: (1) Develop detailed chemical kinetic models for fuel components used in surrogate fuels for diesel and HCCI engines; (2) Develop surrogate fuel models to represent real fuels and model low temperature combustion strategies in HCCI and diesel engines that lead to low emissions and high efficiency; and (3) Characterize the role of fuel composition on low temperature combustion modes of advanced combustion engines.
Upper D region chemical kinetic modeling of LORE relaxation times
NASA Astrophysics Data System (ADS)
Gordillo-Vázquez, F. J.; Luque, A.; Haldoupis, C.
2016-04-01
The recovery times of upper D region electron density elevations, caused by lightning-induced electromagnetic pulses (EMP), are modeled. The work was motivated from the need to understand a recently identified narrowband VLF perturbation named LOREs, an acronym for LOng Recovery Early VLF events. LOREs associate with long-living electron density perturbations in the upper D region ionosphere; they are generated by strong EMP radiated from large peak current intensities of ±CG (cloud to ground) lightning discharges, known also to be capable of producing elves. Relaxation model scenarios are considered first for a weak enhancement in electron density and then for a much stronger one caused by an intense lightning EMP acting as an impulsive ionization source. The full nonequilibrium kinetic modeling of the perturbed mesosphere in the 76 to 92 km range during LORE-occurring conditions predicts that the electron density relaxation time is controlled by electron attachment at lower altitudes, whereas above 79 km attachment is balanced totally by associative electron detachment so that electron loss at these higher altitudes is controlled mainly by electron recombination with hydrated positive clusters H+(H2O)n and secondarily by dissociative recombination with NO+ ions, a process which gradually dominates at altitudes >88 km. The calculated recovery times agree fairly well with LORE observations. In addition, a simplified (quasi-analytic) model build for the key charged species and chemical reactions is applied, which arrives at similar results with those of the full kinetic model. Finally, the modeled recovery estimates for lower altitudes, that is <79 km, are in good agreement with the observed short recovery times of typical early VLF events, which are known to be associated with sprites.
Kinetic model of sucrose accumulation in maturing sugarcane culm tissue.
Uys, Lafras; Botha, Frederik C; Hofmeyr, Jan-Hendrik S; Rohwer, Johann M
2007-01-01
Biochemically, it is not completely understood why or how commercial varieties of sugarcane (Saccharum officinarum) are able to accumulate sucrose in high concentrations. Such concentrations are obtained despite the presence of sucrose synthesis/breakdown cycles (futile cycling) in the culm of the storage parenchyma. Given the complexity of the process, kinetic modelling may help to elucidate the factors governing sucrose accumulation or direct the design of experimental optimisation strategies. This paper describes the extension of an existing model of sucrose accumulation (Rohwer, J.M., Botha, F.C., 2001. Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem. J. 358, 437-445) to account for isoforms of sucrose synthase and fructokinase, carbon partitioning towards fibre formation, and the glycolytic enzymes phosphofructokinase (PFK), pyrophosphate-dependent PFK and aldolase. Moreover, by including data on the maximal activity of the enzymes as measured in different internodes, a growth model was constructed that describes the metabolic behaviour as sugarcane parenchymal tissue matures from internodes 3-10. While there was some discrepancy between modelled and experimentally determined steady-state sucrose concentrations in the cytoplasm, steady-state fluxes showed a better fit. The model supports a hypothesis of vacuolar sucrose accumulation against a concentration gradient. A detailed metabolic control analysis of sucrose synthase showed that each isoform has a unique control profile. Fructose uptake by the cell and sucrose uptake by the vacuole had a negative control on the futile cycling of sucrose and a positive control on sucrose accumulation, while the control profile for neutral invertase was reversed. When the activities of these three enzymes were changed from their reference values, the effects on futile cycling and sucrose accumulation were amplified. The model can be run online at the JWS Online
NASA Astrophysics Data System (ADS)
Janssen, Ruud H. H.; Tsimpidi, Alexandra P.; Karydis, Vlassis A.; Lelieveld, Jos
2014-05-01
In spite of rapid developments in our understanding of organic aerosol (OA) physicochemical properties, representing the OA composition and evolution over urban areas remains a challenge. This study addresses the diurnal evolution of OA over Paris during the MEGAPOLI campaign. We analyze the observations with a model that aims at a balanced representation of the various processes that contribute to the diurnal variation of the organic aerosol budget. It is a 1D Eulerian model of the atmospheric boundary layer that contains advanced modules for gas-phase chemistry, gas/particle partitioning, and dry deposition. The model represents a computationally efficient framework for the accurate description of OA formation and photochemical evolution in the boundary layer. Semi-volatile organic components are distributed into volatility bins based on their saturation concentration and are allowed to partition into the aerosol phase. Furthermore, the semi-volatile organics in the gas phase continue to react with OH radical leading to compounds with lower volatility and hence continued OA formation. Model results are evaluated against available observations of OA, gas-phase chemistry and boundary layer dynamics. The model results are used along with the Aerosol Mass Spectrometer (AMS) dataset from the MEGAPOLI campaign to give new insights into the sources and diurnal production of OA over Paris. Furthermore, budget calculations are performed to show the contribution of the various processes (i.e., photochemistry, aerosol thermodynamics, boundary layer dynamics, etc.) to the calculated OA mass. Finally, the influence of uncertainties in several processes that determine the OA budget on the calculated OA properties is systematically analyzed through a series of sensitivity analyses. These include emission fractions of semivolatile and intermediate volatile compounds (SVOC/IVOC), secondary OA yields for the various gas-phase precursors, gas-phase aging of SVOC and IVOC during
Kinetic modeling and design of colloidal lock and key assembly.
Beltran-Villegas, Daniel J; Colón-Meléndez, Laura; Solomon, Michael J; Larson, Ronald G
2016-02-01
We investigate the kinetics of colloidal lock and key particle assembly by modeling transitions between free, non-specifically and specifically (dumbbells) bound pairs to enable the rapid formation of specific pairs. We expand on a model introduced in a previous publication (Colón-Meléndez et al., 2015) to account for the shape complementarity between the lock and the key particle. Specifically we develop a theory to predict free energy differences between specific and non-specific states based on the interaction potential between arbitrary surfaces and apply this to the interaction of a spherical key particle with the concave dimple surface. Our results show that a lock particle dimple slightly wider than the key particle radius results in optimal binding, but also show escape rates much smaller than those observed in experimental measurements described in the paper cited above. We assess the possible sources of error in experiments and in analysis, including spatial and temporal resolution of the confocal microscopy method used to measure kinetic coefficients, the polydispersity of the lock dimple size, and the sedimentation of the particles in a quasi-two-dimensional layer. We find that the largest sources of variation are in the limited temporal resolution of the experiments, which we account for in our theory, and in the quasi-two-dimensional nature of the experiment that leads to misidentification of non-specific pairs as specific ones. Accounting for these sources of variation results in very good quantitative agreement with experimental data. PMID:26550782
Modeling and Computer Simulation: Molecular Dynamics and Kinetic Monte Carlo
Wirth, B.D.; Caturla, M.J.; Diaz de la Rubia, T.
2000-10-10
Recent years have witnessed tremendous advances in the realistic multiscale simulation of complex physical phenomena, such as irradiation and aging effects of materials, made possible by the enormous progress achieved in computational physics for calculating reliable, yet tractable interatomic potentials and the vast improvements in computational power and parallel computing. As a result, computational materials science is emerging as an important complement to theory and experiment to provide fundamental materials science insight. This article describes the atomistic modeling techniques of molecular dynamics (MD) and kinetic Monte Carlo (KMC), and an example of their application to radiation damage production and accumulation in metals. It is important to note at the outset that the primary objective of atomistic computer simulation should be obtaining physical insight into atomic-level processes. Classical molecular dynamics is a powerful method for obtaining insight about the dynamics of physical processes that occur on relatively short time scales. Current computational capability allows treatment of atomic systems containing as many as 10{sup 9} atoms for times on the order of 100 ns (10{sup -7}s). The main limitation of classical MD simulation is the relatively short times accessible. Kinetic Monte Carlo provides the ability to reach macroscopic times by modeling diffusional processes and time-scales rather than individual atomic vibrations. Coupling MD and KMC has developed into a powerful, multiscale tool for the simulation of radiation damage in metals.
Growth kinetics in a phase field model with continuous symmetry
NASA Astrophysics Data System (ADS)
Marini Bettolo Marconi, Umberto; Crisanti, Andrea
1996-07-01
We discuss the static and kinetic properties of a Ginzburg-Landau spherically symmetric O(N) model recently introduced [U. Marini Bettolo Marconi and A. Crisanti, Phys. Rev. Lett. 75, 2168 (1995)] in order to generalize the so-called phase field model of Langer [Rev. Mod. Phys. 52, 1 (1980); Science 243, 1150 (1989)]. The Hamiltonian contains two O(N) invariant fields φ and U bilinearly coupled. The order parameter field φ evolves according to a nonconserved dynamics, whereas the diffusive field U follows a conserved dynamics. In the limit N-->∞ we obtain an exact solution, which displays an interesting kinetic behavior characterized by three different growth regimes. In the early regime the system displays normal scaling and the average domain size grows as t1/2; in the intermediate regime one observes a finite wave-vector instability, which is related to the Mullins-Sekerka instability; finally, in the late stage the structure function has a multiscaling behavior, while the domain size grows as t1/4.
NASA Astrophysics Data System (ADS)
Habert, J.; Ricci, S.; Le Pape, E.; Thual, O.; Piacentini, A.; Goutal, N.; Jonville, G.; Rochoux, M.
2016-01-01
This paper presents a data-driven hydrodynamic simulator based on the 1-D hydraulic solver dedicated to flood forecasting with lead time of an hour up to 24 h. The goal of the study is to reduce uncertainties in the hydraulic model and thus provide more reliable simulations and forecasts in real time for operational use by the national hydrometeorological flood forecasting center in France. Previous studies have shown that sequential assimilation of water level or discharge data allows to adjust the inflows to the hydraulic network resulting in a significant improvement of the discharge while leaving the water level state imperfect. Two strategies are proposed here to improve the water level-discharge relation in the model. At first, a modeling strategy consists in improving the description of the river bed geometry using topographic and bathymetric measurements. Secondly, an inverse modeling strategy proposes to locally correct friction coefficients in the river bed and the flood plain through the assimilation of in situ water level measurements. This approach is based on an Extended Kalman filter algorithm that sequentially assimilates data to infer the upstream and lateral inflows at first and then the friction coefficients. It provides a time varying correction of the hydrological boundary conditions and hydraulic parameters. The merits of both strategies are demonstrated on the Marne catchment in France for eight validation flood events and the January 2004 flood event is used as an illustrative example throughout the paper. The Nash-Sutcliffe criterion for water level is improved from 0.135 to 0.832 for a 12-h forecast lead time with the data assimilation strategy. These developments have been implemented at the SAMA SPC (local flood forecasting service in the Haute-Marne French department) and used for operational forecast since 2013. They were shown to provide an efficient tool for evaluating flood risk and to improve the flood early warning system
A general moment expansion method for stochastic kinetic models
NASA Astrophysics Data System (ADS)
Ale, Angelique; Kirk, Paul; Stumpf, Michael P. H.
2013-05-01
Moment approximation methods are gaining increasing attention for their use in the approximation of the stochastic kinetics of chemical reaction systems. In this paper we derive a general moment expansion method for any type of propensities and which allows expansion up to any number of moments. For some chemical reaction systems, more than two moments are necessary to describe the dynamic properties of the system, which the linear noise approximation is unable to provide. Moreover, also for systems for which the mean does not have a strong dependence on higher order moments, moment approximation methods give information about higher order moments of the underlying probability distribution. We demonstrate the method using a dimerisation reaction, Michaelis-Menten kinetics and a model of an oscillating p53 system. We show that for the dimerisation reaction and Michaelis-Menten enzyme kinetics system higher order moments have limited influence on the estimation of the mean, while for the p53 system, the solution for the mean can require several moments to converge to the average obtained from many stochastic simulations. We also find that agreement between lower order moments does not guarantee that higher moments will agree. Compared to stochastic simulations, our approach is numerically highly efficient at capturing the behaviour of stochastic systems in terms of the average and higher moments, and we provide expressions for the computational cost for different system sizes and orders of approximation. We show how the moment expansion method can be employed to efficiently quantify parameter sensitivity. Finally we investigate the effects of using too few moments on parameter estimation, and provide guidance on how to estimate if the distribution can be accurately approximated using only a few moments.
Simulation of carbon gasification kinetics using an edge recession model
Takashi Kyotani; Leon y Leon, C.A.L.; Radovic, L.R. )
1993-07-01
An edge recession modeling method is proposed as a new approach to the prediction of carbon gasification kinetics. Using this method, the variations in reactive surface area (RSA) and specific reactivity (R) with conversion were simulated for several polynuclear aromatic molecules adopted as models of carbon crystallites. The effects of crystallite size and shape, edge site reactivity and vacancies on the changes in RSA and R with conversion were investigated. As a result, RSA and R were found to be essentially independent of crystallite shape, but to depend on crystallite size and the presence of vacancies. Good agreement was obtained between model predictions and experimental data for several kinds of model carbon crystallites. In the case of structurally disordered carbons (such as chars), simultaneous gasification of model crystallites of two different sizes gave better predictions than that of single-size crystallites. The edge recession model is proposed as an alternative, or at least complementary, approach to the more conventional (and, arguably, less physically meaningful) pore structure development models.
Developing a computational model of human hand kinetics using AVS
Abramowitz, Mark S.
1996-05-01
As part of an ongoing effort to develop a finite element model of the human hand at the Institute for Scientific Computing Research (ISCR), this project extended existing computational tools for analyzing and visualizing hand kinetics. These tools employ a commercial, scientific visualization package called AVS. FORTRAN and C code, originally written by David Giurintano of the Gillis W. Long Hansen`s Disease Center, was ported to a different computing platform, debugged, and documented. Usability features were added and the code was made more modular and readable. When the code is used to visualize bone movement and tendon paths for the thumb, graphical output is consistent with expected results. However, numerical values for forces and moments at the thumb joints do not yet appear to be accurate enough to be included in ISCR`s finite element model. Future work includes debugging the parts of the code that calculate forces and moments and verifying the correctness of these values.
Kinetic model for colchicine inhibition of microtubule assembly
Sternlicht, H.; Ringel, I.; Szasz, J.
1980-10-01
Colchicine is a potent drug used to probe microtubule dependent processes. We have recently shown that substoichiometric concentrations of colchicine-tubulin complex (CD), a 1:1 tight binding complex of drug with tubulin, copolymerizes with tubulin to form microtubule copolymers. The affinity of the microtubule ends for tublin decreased as the CD mole fraction in the microtubule increased. Mole fraction ratios as small as 1 CD to approx. 50 to 100 tubulins in the copolymers were accompanied by a significant change in binding affinities and polymerization rates. We have further extended our investigation of the CD-tubulin copolymerization reaction. A kinetic model was derived which relates the composition of the microtubule copolymer to the composition of the reaction mixture. This model allowed a predictive correlation to be made between copolymer composition and the extent of assembly inhibition.
Fluid catalytic cracking catalyst for reformulated gasolines: Kinetic modeling
Gianetto, A. ); Farag, H.I. . Dept. of Chemical Engineering); Blasetti, A.P. . Dept. de Procesos); Lasa, H.I. de . Faculty of Engineering Science)
1994-12-01
Changes of the relative importance of intradiffusion on USY zeolite crystals were studied as a way of affecting selectivity of catalytic cracking reactions. Zeolite crystals were synthesized (Si/Al = 2.4), activated and stabilized using ion exchange and steam calcination to obtain USSY (Ultra Stable Submicron Y) zeolites. After the activation the zeolites were pelletized (45--60 [mu]m particles). USSYs were tested in a novel Riser Simulator. Results obtained show that total aromatics (BTX), benzene, C[sub 4] olefins, and coke were significantly affected with the change of zeolite crystal sizes. Gasolines produced with USSY zeolites contain less aromatics and particularly lower benzene levels. Experimental results were analyzed with a model including several lumps: unconverted gas oil, gasoline, light gases, and coke. This model also accounts for catalyst deactivation as a function of coke on catalyst. Various kinetic parameters were determined with their corresponding spans for the 95% level of confidence.
High Temperature Chemical Kinetic Combustion Modeling of Lightly Methylated Alkanes
Sarathy, S M; Westbrook, C K; Pitz, W J; Mehl, M
2011-03-01
Conventional petroleum jet and diesel fuels, as well as alternative Fischer-Tropsch (FT) fuels and hydrotreated renewable jet (HRJ) fuels, contain high molecular weight lightly branched alkanes (i.e., methylalkanes) and straight chain alkanes (n-alkanes). Improving the combustion of these fuels in practical applications requires a fundamental understanding of large hydrocarbon combustion chemistry. This research project presents a detailed high temperature chemical kinetic mechanism for n-octane and three lightly branched isomers octane (i.e., 2-methylheptane, 3-methylheptane, and 2,5-dimethylhexane). The model is validated against experimental data from a variety of fundamental combustion devices. This new model is used to show how the location and number of methyl branches affects fuel reactivity including laminar flame speed and species formation.
Chemical kinetic modeling of component mixtures relevant to gasoline
Mehl, M; Curran, H J; Pitz, W J; Westbrook, C K
2009-02-13
Real fuels are complex mixtures of thousands of hydrocarbon compounds including linear and branched paraffins, naphthenes, olefins and aromatics. It is generally agreed that their behavior can be effectively reproduced by simpler fuel surrogates containing a limited number of components. In this work, a recently revised version of the kinetic model by the authors is used to analyze the combustion behavior of several components relevant to gasoline surrogate formulation. Particular attention is devoted to linear and branched saturated hydrocarbons (PRF mixtures), olefins (1-hexene) and aromatics (toluene). Model predictions for pure components, binary mixtures and multi-component gasoline surrogates are compared with recent experimental information collected in rapid compression machine, shock tube and jet stirred reactors covering a wide range of conditions pertinent to internal combustion engines. Simulation results are discussed focusing attention on the mixing effects of the fuel components.
NASA Astrophysics Data System (ADS)
Mogensen, Ditte; Aaltonen, Hermanni; Aalto, Juho; Bäck, Jaana; Kieloaho, Antti-Jussi; Gierens, Rosa; Smolander, Sampo; Kulmala, Markku; Boy, Michael
2015-04-01
Volatile organic compounds (VOCs) are emitted from the biosphere and can work as precursor gases for aerosol particles that can affect the climate (e.g. Makkonen et al., ACP, 2012). VOC emissions from needles and leaves have gained the most attention, however other parts of the ecosystem also have the ability to emit a vast amount of VOCs. This, often neglected, source can be important e.g. at periods where leaves are absent. Both sources and drivers related to forest floor emission of VOCs are currently limited. It is thought that the sources are mainly due to degradation of organic matter (Isidorov and Jdanova, Chemosphere, 2002), living roots (Asensio et al., Soil Biol. Biochem., 2008) and ground vegetation. The drivers are biotic (e.g. microbes) and abiotic (e.g. temperature and moisture). However, the relative importance of the sources and the drivers individually are currently poorly understood. Further, the relative importance of these factors is highly dependent on the tree species occupying the area of interest. The emission of isoprene and monoterpenes where measured from the boreal forest floor at the SMEAR II station in Southern Finland (Hari and Kulmala, Boreal Env. Res., 2005) during the snow-free period in 2010-2012. We used a dynamic method with 3 automated chambers analyzed by Proton Transfer Reaction - Mass Spectrometer (Aaltonen et al., Plant Soil, 2013). Using this data, we have developed empirical parameterizations for the emission of isoprene and monoterpenes from the forest floor. These parameterizations depends on abiotic factors, however, since the parameterizations are based on field measurements, biotic features are captured. Further, we have used the 1D chemistry-transport model SOSAA (Boy et al., ACP, 2011) to test the seasonal relative importance of inclusion of these parameterizations of the forest floor compared to the canopy crown emissions, on the atmospheric reactivity throughout the canopy.
Ultralocal models of modified gravity without kinetic term
NASA Astrophysics Data System (ADS)
Brax, Philippe; Rizzo, Luca Alberto; Valageas, Patrick
2016-08-01
We present a class of modified-gravity theories which we call ultralocal models. We add a scalar field, with negligible kinetic terms, to the Einstein-Hilbert action. We also introduce a conformal coupling to matter. This gives rise to a new screening mechanism which is not entirely due to the nonlinearity of the scalar-field potential or the coupling function but to the absence of the kinetic term. As a result this removes any fifth force between isolated objects in vacuum. It turns out that these models are similar to chameleon-type theories with a large mass when considered outside the Compton wavelength but differ on shorter scales. The predictions of these models only depend on a single free function, as the potential and the coupling function are degenerate, with an amplitude given by a parameter α ≲10-6 , whose magnitude springs from requiring a small modification of Newton's potential astrophysically and cosmologically. This singles out a redshift zα˜α-1 /3≳100 where the fifth force is the greatest. The cosmological background follows the Λ cold dark matter (Λ CDM ) history within a 10-6 accuracy, while cosmological perturbations are significantly enhanced (or damped) on small scales, k ≳2 h Mpc-1 at z =0 . The spherical collapse and the halo mass function are modified in the same manner. We find that the modifications of gravity are greater for galactic or subgalactic structures. We also present a thermodynamic analysis of the nonlinear and inhomogeneous fifth-force regime where we find that the Universe is not made more inhomogeneous before zα when the fifth force dominates, and does not lead to the existence of clumped matter on extra small scales inside halos for large masses while this possibility exists for masses M ≲1 011M⊙ where the phenomenology of ultralocal models would be most different from Λ CDM .
Parameter estimation for models of ligninolytic and cellulolytic enzyme kinetics
Wang, Gangsheng; Post, Wilfred M; Mayes, Melanie; Frerichs, Joshua T; Jagadamma, Sindhu
2012-01-01
While soil enzymes have been explicitly included in the soil organic carbon (SOC) decomposition models, there is a serious lack of suitable data for model parameterization. This study provides well-documented enzymatic parameters for application in enzyme-driven SOC decomposition models from a compilation and analysis of published measurements. In particular, we developed appropriate kinetic parameters for five typical ligninolytic and cellulolytic enzymes ( -glucosidase, cellobiohydrolase, endo-glucanase, peroxidase, and phenol oxidase). The kinetic parameters included the maximum specific enzyme activity (Vmax) and half-saturation constant (Km) in the Michaelis-Menten equation. The activation energy (Ea) and the pH optimum and sensitivity (pHopt and pHsen) were also analyzed. pHsen was estimated by fitting an exponential-quadratic function. The Vmax values, often presented in different units under various measurement conditions, were converted into the same units at a reference temperature (20 C) and pHopt. Major conclusions are: (i) Both Vmax and Km were log-normal distributed, with no significant difference in Vmax exhibited between enzymes originating from bacteria or fungi. (ii) No significant difference in Vmax was found between cellulases and ligninases; however, there was significant difference in Km between them. (iii) Ligninases had higher Ea values and lower pHopt than cellulases; average ratio of pHsen to pHopt ranged 0.3 0.4 for the five enzymes, which means that an increase or decrease of 1.1 1.7 pH units from pHopt would reduce Vmax by 50%. (iv) Our analysis indicated that the Vmax values from lab measurements with purified enzymes were 1 2 orders of magnitude higher than those for use in SOC decomposition models under field conditions.
NASA Astrophysics Data System (ADS)
Khosravi, M.; Baron, P.; Urban, J.; Froidevaux, L.; Jonsson, A. I.; Kasai, Y.; Kuribayashi, K.; Mitsuda, C.; Murtagh, D. P.; Sagawa, H.; Santee, M. L.; Sato, T. O.; Shiotani, M.; Suzuki, M.; von Clarmann, T.; Walker, K. A.; Wang, S.
2013-08-01
The diurnal variation of HOCl and the related species ClO, HO2 and HCl measured by satellites has been compared with the results of a one-dimensional photochemical model. The study compares the data from various limb-viewing instruments with model simulations from the middle stratosphere to the lower mesosphere. Data from three sub-millimetre instruments and two infrared spectrometers are used, namely from the Sub-Millimetre Radiometer (SMR) on board Odin, the Microwave Limb Sounder (MLS) on board Aura, the Superconducting Submillimeter-wave Limb-Emission Sounder (SMILES) on the International Space Station, the Michelson Interferometer for Passive Atmospheric Sounding (MIPAS) on board ENVISAT, and the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS) on board SCISAT. Inter-comparison of the measurements from instruments on sun-synchronous satellites (SMR, MLS, MIPAS) and measurements from solar occultation instruments (ACE-FTS) is challenging since the measurements correspond to different solar zenith angles (or local times). However, using a model which covers all solar zenith angles and data from the SMILES instrument which measured at all local times over a period of several months provides the possibility to verify the model and to indirectly compare the diurnally variable species. The satellite data were averaged for latitudes of 20° S to 20° N for the SMILES observation period from November 2009 to April 2010 and were compared at three altitudes: 35, 45 and 55 km. Besides presenting the SMILES data, the study also shows a first comparison of the latest MLS data (version 3.3) of HOCl, ClO, and HO2 with other satellite observations, as well as a first evaluation of HO2 observations made by Odin/SMR. The MISU-1D model has been carefully initialised and run for conditions and locations of the observations. The diurnal cycle features for the species investigated here are generally well reproduced by the model. The satellite observations
Integration Strategies for Efficient Multizone Chemical Kinetics Models
McNenly, M J; Havstad, M A; Aceves, S M; Pitz, W J
2009-10-15
Three integration strategies are developed and tested for the stiff, ordinary differential equation (ODE) integrators used to solve the fully coupled multizone chemical kinetics model. Two of the strategies tested are found to provide more than an order of magnitude of improvement over the original, basic level of usage for the stiff ODE solver. One of the faster strategies uses a decoupled, or segregated, multizone model to generate an approximate Jacobian. This approach yields a 35-fold reduction in the computational cost for a 20 zone model. Using the same approximate Jacobian as a preconditioner for an iterative Krylov-type linear system solver, the second improved strategy achieves a 75-fold reduction in the computational cost for a 20 zone model. The faster strategies achieve their cost savings with no significant loss of accuracy. The pressure, temperature and major species mass fractions agree with the solution from the original integration approach to within six significant digits; and the radical mass fractions agree with the original solution to within four significant digits. The faster strategies effectively change the cost scaling of the multizone model from cubic to quadratic, with respect to the number of zones. As a consequence of the improved scaling, the 40 zone model offers more than a 250-fold cost savings over the basic calculation.
Discrete Kinetic Models from Funneled Energy Landscape Simulations
Burger, Anat; Craig, Patricio O.; Komives, Elizabeth A.; Wolynes, Peter G.
2012-01-01
A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an “inside-out”, nucleation-propagation like character. PMID:23251375
Constraining kinetic rates of mineral reactions using reactive transport models
NASA Astrophysics Data System (ADS)
Bolton, E. W.; Wang, Z.; Ague, J.; Bercovici, D.; Cai, Z.; Karato, S.; Oristaglio, M. L.; Qiu, L.
2012-12-01
We use a reactive transport model to better understand results of experiments to obtain kinetic rates of mineral reactions in closed systems. Closed system experiments pose special challenges in that secondary minerals may form that modify the fluid composition evolution and may grow on the dissolving minerals thus armoring the surface. Even so, such closed system experiments provide critical data for what minerals would actually form in field applications and how coupled dissolution and precipitation mineral reactions are strongly linked. Comparing to experimental observations can test the reactive transport model, and the experimental observations can be better understood by comparing the results to the modeling. We apply a 0D end member of the model to understand the dissolution of single crystals of forsterite in a variety of settings (low pH, high pH, or NaHCO3 initial fluids, at 100 C and 1 bar, or 200 C and 150 bar). Depending on the initial conditions, we observe the precipitation of talc, brucite, amorphous silica, chrysotile, or magnesite, in various combinations. We compare simulation results to fluid compositions and the presence of secondary minerals experimentally sampled at various times. Insight from the simulations helped create an inverse model to extract the rates of forsterite dissolution and to create a simple forward model useful for exploring the influence of system size, secondary mineral surface areas, etc. Our reactive transport model allows secondary minerals to armor the forsterite surface, which can strongly decrease the dissolution rate as the system evolves. Tuning our model with experimentally derived rates and assuring relevant processes are included so as to reproduce experimental observations is necessary before upscaling to heterogeneous field conditions. The reactive transport model will be used for field-scale sequestration simulations and coupled with a geomechanical model that includes the influence of deformation.
[Kinetics model for batch culture of white rot fungus].
Xiong, Xiao-ping; Wen, Xiang-hua; Xu, Kang-ning; Bian, Bing-hui
2008-02-01
In order to understand ligninolytic enzymes production process during culture of white rot fungus, accordingly to direct the design of fermentation process, a kinetics model was built for the batch culture of Phanerochaete chrysosporium. The parameters in the model were calibrated based on the experimental data from free and immobilized culture separately. The difference between each variable's values calculated based on kinetics model and experimental data is within 15%. Comparing parameters for the free and the immobilized culture, it is found that maximum biomass concentrations are both 1.78 g/L; growth rate ratio of immobilized culture (0.6683 d(-1)) is larger than that of free culture (0.5144 d(-1)); very little glucose is consumed for biomass growth in free culture while in immobilized culture much glucose is used and ammonium nitrogen is consumed at a greater rate. Ligninolytic enzymes production process is non-growth related; fungal pellets can produce MnP (231 U/L) in free culture with a production rate of 115.8 U x (g x d)(-1) before peak and 26.1 U x (g x d)(-1) after peak, thus fed-batch is a possible mode to improve MnP production and fermentation efficiency. MnP (410 U/L) and LiP (721 U/L) can be produced in immobilized culture, but MnP and LiP production rate decrease from 80.1 U x (g x d)(-1) and 248.9 U x (g x d)(-1) to 6.04 U x (g x d)(-1) and 0 U x (g x d)(-1), respectively, indicating a proper feed moment is before the enzymes peak during fed-batch culture. PMID:18613526
Photon kinetic modeling of laser pulse propagation in underdense plasma
Reitsma, A. J. W.; Trines, R. M. G. M.; Bingham, R.; Cairns, R. A.; Mendonca, J. T.; Jaroszynski, D. A.
2006-11-15
This paper discusses photon kinetic theory, which is a description of the electromagnetic field in terms of classical particles in coordinate and wave number phase space. Photon kinetic theory is applied to the interaction of laser pulses with underdense plasma and the transfer of energy and momentum between the laser pulse and the plasma is described in photon kinetic terms. A comparison is made between a one-dimensional full wave and a photon kinetic code for the same laser and plasma parameters. This shows that the photon kinetic simulations accurately reproduce the pulse envelope evolution for photon frequencies down to the plasma frequency.
Kinetic modeling of sodium in the exosphere of Mercury
NASA Astrophysics Data System (ADS)
Tenishev, V.; Rubin, M.; Combi, M. R.; Slavin, J. A.; Raines, J. M.
2012-12-01
Discovered more that 20 years ago Mercury's sodium exosphere is characterized by rapid variations determined by planet's orbital motion and rotation. Because collisions are rare, the sodium atom velocity distribution is determined by a unique combination of radiation pressure, source and loss processes, and the interaction with the surface. Neutral sodium atoms injected into the exosphere can be photo-ionized by solar radiation. These ions have been recently observed by FIPS instrument onboard of MESSENGER, and can help in a better understanding of the nature of the source processes as well as the structure of the neutral exosphere itself. A detailed theoretical study of the sodium distribution in the exosphere requires numerical modeling. Having kinetic theory as a physical basis, our exospheric Monte Carlo model preserves the kinetic nature of these exospheric processes. The distinctive features of the model include accounting for the planet's rotation and motion along its orbit, the realistic distribution of the sources, an accurate calculation of the g-factor, and simulation of the photolytic reactions in the exosphere and tail. Here we describe the results of our numerical study of the neutral sodium environment around Mercury. The primary goal of this work was to combine, in a self-consistent manner, models of different surface processes, the planet's orbital motion and rotation, and time-dependent dynamics of sodium atoms in the exosphere. Using ground based and in situ observations obtained at different times to constrain our model allows us to get a more comprehensive picture of Mercury's exosphere including the source and loss rates of sodium. We discuss relative importance of the source processes in the sodium exosphere, the effect of solar radiation pressure on the structure of the tail, and the effect of the surface sticking as well as of the planetary rotation and orbital motion on the sodium surface abundance. Presented simulations cover a domain
Kinetic Modeling of Toluene Oxidation for Surrogate Fuel Applications
Frassoldati, A; Mehl, M; Fietzek, R; Faravelli, T; Pitz, W J; Ranzi, E
2009-04-21
New environmental issues, like the effect of combustion-generated greenhouse gases, provide motivation to better characterize oxidation of hydrocarbons. Transportation, in particular, significantly contributes to energy consumption and CO{sub 2} emissions. Kinetic studies about the combustion of fuels under conditions typical of internal combustion engines provides important support to improve mechanism formulation and to eventually provide better computational tools that can be used to increase the engine performance. It is foreseeable that at least in the next 30 years the main transportation fuels will be either gasoline or diesel. Unfortunately, these fuels are very complex mixtures of many components. Moreover, their specifications and performance requirements significantly change the composition of these fuels: gasoline and diesel mixtures are different if coming from different refineries or they are different from winter to summer. At the same time a fuel with a well defined and reproducible composition is needed for both experimental and modeling work. In response to these issues, surrogate fuels are proposed. Surrogate fuels are defined as mixtures of a small number of hydrocarbons whose relative concentrations is adjusted in order to approximate the chemical and physical properties of a real fuel. Surrogate fuels are then very useful both for the design of reproducible experimental tests and also for the development of reliable kinetic models. The primary reference fuels (PRF) are a typical and old example of surrogate fuel: n-heptane and iso-octane mixtures are used to reproduce antiknock propensity of complex mixtures contained in a gasoline. PRFs are not able to surrogate gasoline in operating conditions different from standard ones and new surrogates have been recently proposed. Toluene is included in all of them as a species able to represent the behavior of aromatic compounds. On the other side, the toluene oxidation chemistry is not so well
Chalise, Roshan Khanal, Raju
2015-11-15
We have developed a self-consistent 1d3v (one dimension in space and three dimension in velocity) Kinetic Trajectory Simulation (KTS) model, which can be used for modeling various situations of interest and yields results of high accuracy. Exact ion trajectories are followed, to calculate along them the ion distribution function, assuming an arbitrary injection ion distribution. The electrons, on the other hand, are assumed to have a cut-off Maxwellian velocity distribution at injection and their density distribution is obtained analytically. Starting from an initial guess, the potential profile is iterated towards the final time-independent self-consistent state. We have used it to study plasma sheath region formed in presence of an oblique magnetic field. Our results agree well with previous works from other models, and hence, we expect our 1d3v KTS model to provide a basis for the studying of all types of magnetized plasmas, yielding more accurate results.
NASA Astrophysics Data System (ADS)
Murray, Keenan A.; Kramer, Louisa J.; Doskey, Paul V.; Ganzeveld, Laurens; Seok, Brian; Van Dam, Brie; Helmig, Detlev
2015-09-01
Observed depth profiles of nitric oxide (NO), nitrogen dioxide (NO2), and ozone (O3) in snowpack interstitial air at Summit, Greenland were best replicated by a 1-D process-scale model, which included (1) geometrical representation of snow grains as spheres, (2) aqueous-phase chemistry confined to a quasi-liquid layer (QLL) on the surface of snow grains, and (3) initialization of the species concentrations in the QLL through equilibrium partitioning with mixing ratios in snowpack interstitial air. A comprehensive suite of measurements in and above snowpack during a high O3 event facilitated analysis of the relationship between the chemistry of snowpack and the overlying atmosphere. The model successfully reproduced 2 maxima (i.e., a peak near the surface of the snowpack at solar noon and a larger peak occurring in the evening that extended down from 0.5 to 2 m) in the diurnal profile of NO2 within snowpack interstitial air. The maximum production rate of NO2 by photolysis of nitrate (NO3-) was approximately 108 molec cm-3 s-1, which explained daily observations of maxima in NO2 mixing ratios near solar noon. Mixing ratios of NO2 in snowpack interstitial air were greatest in the deepest layers of the snowpack at night and were attributed to thermal decomposition of peroxynitric acid, which produced up to 106 molec NO2 cm-3 s-1. Highest levels of NO in snowpack interstitial air were confined to upper layers of the snowpack and observed profiles were consistent with photolysis of NO2. Production of nitrogen oxides (NOx) from NO3- photolysis was estimated to be two orders of magnitude larger than NO production and supports the hypothesis that NO3- photolysis is the primary source of NOx within sunlit snowpack in the Arctic. Aqueous-phase oxidation of formic acid by O3 resulted in a maximum consumption rate of ∼106-107 molec cm-3 s-1 and was the primary removal mechanism for O3.
Pedrós, Ignacio; Petrov, Dmitry; Allgaier, Michael; Sureda, Francesc; Barroso, Emma; Beas-Zarate, Carlos; Auladell, Carme; Pallàs, Mercè; Vázquez-Carrera, Manuel; Casadesús, Gemma; Folch, Jaume; Camins, Antoni
2014-09-01
The present study had focused on the behavioral phenotype and gene expression profile of molecules related to insulin receptor signaling in the hippocampus of 3 and 6 month-old APPswe/PS1dE9 (APP/PS1) transgenic mouse model of Alzheimer's disease (AD). Elevated levels of the insoluble Aβ (1-42) were detected in the brain extracts of the transgenic animals as early as 3 months of age, prior to the Aβ plaque formation (pre-plaque stage). By the early plaque stage (6 months) both the soluble and insoluble Aβ (1-40) and Aβ (1-42) peptides were detectable. We studied the expression of genes related to memory function (Arc, Fos), insulin signaling, including insulin receptor (Insr), Irs1 and Irs2, as well as genes involved in insulin growth factor pathways, such as Igf1, Igf2, Igfr and Igfbp2. We also examined the expression and protein levels of key molecules related to energy metabolism (PGC1-α, and AMPK) and mitochondrial functionality (OXPHOS, TFAM, NRF1 and NRF2). 6 month-old APP/PS1 mice demonstrated impaired cognitive ability, were glucose intolerant and showed a significant reduction in hippocampal Insr and Irs2 transcripts. Further observations also suggest alterations in key cellular energy sensors that regulate the activities of a number of metabolic enzymes through phosphorylation, such as a decrease in the Prkaa2 mRNA levels and in the pAMPK (Thr172)/Total APMK ratio. Moreover, mRNA and protein analysis reveals a significant downregulation of genes essential for mitochondrial replication and respiratory function, including PGC-1α in hippocampal extracts of APP/PS1 mice, compared to age-matched wild-type controls at 3 and 6 months of age. Overall, the findings of this study show early alterations in genes involved in insulin and energy metabolism pathways in an APP/PS1 model of AD. These changes affect the activity of key molecules like NRF1 and PGC-1α, which are involved in mitochondrial biogenesis. Our results reinforce the hypothesis that the
Calcite growth kinetics: Modeling the effect of solution stoichiometry
NASA Astrophysics Data System (ADS)
Wolthers, Mariëtte; Nehrke, Gernot; Gustafsson, Jon Petter; Van Cappellen, Philippe
2012-01-01
Until recently the influence of solution stoichiometry on calcite crystal growth kinetics has attracted little attention, despite the fact that in most aqueous environments calcite precipitates from non-stoichiometric solution. In order to account for the dependence of the calcite crystal growth rate on the cation to anion ratio in solution, we extend the growth model for binary symmetrical electrolyte crystals of Zhang and Nancollas (1998) by combining it with the surface complexation model for the chemical structure of the calcite-aqueous solution interface of Wolthers et al. (2008). To maintain crystal stoichiometry, the rate of attachment of calcium ions to step edges is assumed to equal the rate of attachment of carbonate plus bicarbonate ions. The model parameters are optimized by fitting the model to the step velocities obtained previously by atomic force microscopy (AFM, Teng et al., 2000; Stack and Grantham, 2010). A variable surface roughness factor is introduced in order to reconcile the new process-based growth model with bulk precipitation rates measured in seeded calcite growth experiments. For practical applications, we further present empirical parabolic rate equations fitted to bulk growth rates of calcite in common background electrolytes and in artificial seawater-type solutions. Both the process-based and empirical growth rate equations agree with measured calcite growth rates over broad ranges of ionic strength, pH, solution stoichiometry and degree of supersaturation.
Kinetic Modelling of Parallel Electron Transport in TdeV.
NASA Astrophysics Data System (ADS)
Shoucri, M.; Shkarofsky, I.; Stansfield, B.; Batishchev, O.; Batishcheva, A.; Krasheninnikov, S.; Sigmar
1996-11-01
The 1D2V Fokker-Planck code ALLA [1] is used to model parallel electron transport in the SOL of TdeV. Our model uses detached and attached experimental data [2] given by Langmuir probes, Li ablation and He spectroscopy. We obtain the electron distribution function on a precise 257x65x60 non-uniform grid. Strong deviations of hydrogen and carbon excitation rates, and heat conduction coefficient from their Maxwellian values are shown. We compare the calculated variation of the effective temperature at the reciprocating probe position with experimental measurements. We also explain by non-local effects why different experimental techniques show differences in the electron temperature. altaffiltext [1] A.A.Batishcheva et al., Physics of Plasmas 3 (1996) 1634 altaffiltext [2] B.L.Stansfield et al., Proc. 22 Eur.Conf., Bornemouth, 19C pIII-101. *Supported by Government of Canada, Hydro-Québec and INRS. Work performed under USDoE contracts DE-FG02-91-ER-54109 at MIT and DE-FG02-88-ER-53263 at Lodestar.
A general kinetic-flow coupling model for FCC riser flow simulation.
Chang, S. L.
1998-05-18
A computational fluid dynamic (CFD) code has been developed for fluid catalytic cracking (FCC) riser flow simulation. Depending on the application of interest, a specific kinetic model is needed for the FCC flow simulation. This paper describes a method to determine a kinetic model based on limited pilot-scale test data. The kinetic model can then be used with the CFD code as a tool to investigate optimum operating condition ranges for a specific FCC unit.
Incorporation of chemical kinetic models into process control
Herget, C.J.; Frazer, J.W.
1981-07-08
An important consideration in chemical process control is to determine the precise rationing of reactant streams, particularly when a large time delay exists between the mixing of the reactants and the measurement of the product. In this paper, a method is described for incorporating chemical kinetic models into the control strategy in order to achieve optimum operating conditions. The system is first characterized by determining a reaction rate surface as a function of all input reactant concentrations over a feasible range. A nonlinear constrained optimization program is then used to determine the combination of reactants which produces the specified yield at minimum cost. This operating condition is then used to establish the nominal concentrations of the reactants. The actual operation is determined through a feedback control system employing a Smith predictor. The method is demonstrated on a laboratory bench scale enzyme reactor.
Low pressure microplasmas enabled by field ionization: Kinetic modeling
NASA Astrophysics Data System (ADS)
Macheret, Sergey O.; Tholeti, Siva Sashank; Alexeenko, Alina A.
2016-05-01
A principle of microplasma generation that utilizes field emission of electrons at the cathode and field ionization producing ions at the anode, both processes relying on nanorods or nanotubes, is explored theoretically. In this plasma generation concept, collisional ionization of atoms and molecules by electron impact would play a negligible role. Analytical estimates as well as plasma kinetic modeling by particle-in-cell method with Monte Carlo collisions in argon confirm that this principle can enable substantial plasma densities at near-collisionless microgaps, while requiring relatively low voltages, less than 100 V. An order of magnitude increase in electron number density can be achieved due to enhancement of field emission at the cathode by positive space charge at high field ionization ion current densities.
A phase-separation kinetic model for coke formation
Wiehe, I.A. . Corporate Research Lab.)
1993-11-01
Coke formation during the thermolysis of petroleum residua is postulated to occur by a mechanism that involves the liquid-liquid phase separation of reacted asphaltenes to form a phase that is lean in abstractable hydrogen. This mechanism provides the basis of a model that quantitatively describes the kinetics for the thermolysis of Cold Lake vacuum residuum and its deasphalted oil in an open-tube reactor at 400 C. The previously unreacted asphaltenes were found to be the fraction with the highest rate of thermal reaction but with the least extent of reaction. This not only described the appearance and disappearance of asphaltenes but also quantitatively described the variation in molecular weight and hydrogen content of the asphaltenes with reaction time. Further evidence of the liquid-liquid phase separation was the observation of spherical particles of liquid crystalline coke and the preferential conversion of the most associated asphaltenes to coke.
A phase separation kinetic model for coke formation
Wiehe, I.A.
1993-12-31
Coke formation during the thermolysis of petroleum residua is postulated to occur by a mechanism that involves the liquid-liquid phase separation of reacted asphaltenes to form a phase that is lean in abstractable hydrogen. This mechanism provides the basis of a model the quantitatively describes the kinetics for the thermolysis of Cold Lake vacuum residuum and its deasphalted oil in an open tube reactor at 400{degrees}C. The previously unreacted asphaltenes were found to be the fraction with the highest rate of thermal reaction but with the least extent of reaction. Further evidence of the liquid-liquid phase separation was the observation of spherical particles of liquid crystalline coke and the preferential conversion of the most associated asphaltenes to coke.
An Experimental and Kinetic Modeling Study of Methyl Decanoate Combustion
Sarathy, S M; Thomson, M J; Pitz, W J; Lu, T
2010-02-19
Biodiesel is typically a mixture of long chain fatty acid methyl esters for use in compression ignition engines. Improving biofuel engine performance requires understanding its fundamental combustion properties and the pathways of combustion. This research study presents new combustion data for methyl decanoate in an opposed-flow diffusion flame. An improved detailed chemical kinetic model for methyl decanoate combustion is developed, which serves as the basis for deriving a skeletal mechanism via the direct relation graph method. The novel skeletal mechanism consists of 648 species and 2998 reactions. This mechanism well predicts the methyl decanoate opposed-flow diffusion flame data. The results from the flame simulations indicate that methyl decanoate is consumed via abstraction of hydrogen atoms to produce fuel radicals, which lead to the production of alkenes. The ester moiety in methyl decanoate leads to the formation of low molecular weight oxygenated compounds such as carbon monoxide, formaldehyde, and ketene.
Kinetic modeling of an IBr solar pumped laser
NASA Technical Reports Server (NTRS)
Harries, W. L.; Meador, W. E.
1983-01-01
The possibility of using an IBr laser as a solar-energy converter is examined theoretically, and reasons for its choice are given. Broadband absorption results in dissociation with the formation of excited metastable Br atoms, some of which then lase to the ground state Br. The ground state is depopulated by three-body recombination and, more importantly, by exchange reactions which more than compensate for the high quenching in heteronuclear halogen systems. Kinetic modeling indicates lasing is possible in the pulsed mode and possibly in the steady state with a cooled gas flow system. Temperature effects are discussed. The efficiency of the laser approaches 1.2 percent at optical thicknesses large enough for complete absorption of the photons.
Effects of turbulence on a kinetic auroral arc model
NASA Technical Reports Server (NTRS)
Cornwall, J. M.; Chiu, Y. T.
1981-01-01
A plasma kinetic model of an inverted-V auroral arc structure which includes the effects of electrostatic turbulence is proposed. In the absence of turbulence, a parallel potential drop is supported by magnetic mirror forces and charge quasi neutrality, with energetic auroral ions penetrating to low altitudes; relative to the electrons, the ions' pitch angle distribution is skewed toward smaller pitch angles. The electrons energized by the potential drop form a current which excites electrostatic turbulence. In equilibrium the plasma is marginally stable. The conventional anomalous resistivity contribution to the potential drop is very small. Anomalous resistivity processes are far too dissipative to be powered by auroral particles. It is concluded that under certain circumstances equilibrium may be impossible and relaxation oscillations set in.
A Model of the Kinetics of Insulin in Man
Sherwin, Robert S.; Kramer, Karl J.; Tobin, Jordan D.; Insel, Paul A.; Liljenquist, John E.; Berman, Mones; Andres, Reubin
1974-01-01
The design of the present study of the kinetics of insulin in man combines experimental features which obviate two of the major problems in previous insulin studies. (a) The use of radioiodinated insulin as a tracer has been shown to be inappropriate since its metabolism differs markedly from that of the native hormone. Therefore porcine insulin was administered by procedures which raised insulin levels in arterial plasma into the upper physiologic range. Hypoglycemia was prevented by adjusting the rate of an intravenous infusion of glucose in order to control the blood glucose concentration (the glucose-clamp technique). (b) Estimation of a single biological half-time of insulin after pulse injection of the hormone has been shown to be inappropriate since plasma insulin disappearance curves are multiexponential. Therefore the SAAM 25 computer program was used in order to define the parameters of a three compartment insulin model. The combined insulin mass of the three compartments (expressed as plasma equivalent volume) is equal to inulin space (15.7% body wt). Compartment 1 is apparently the plasma space (4.5%). The other two compartments are extra-vascular; compartment 2 is small (1.7%) and equilibrates rapidly with plasma, and compartment 3 is large (9.5%) and equilibrates slowly with plasma. The SAAM 25 program can simulate the buildup and decay of insulin in compartments 2 and 3 which cannot be assayed directly. Insulin in compartment 3 was found to correlate remarkably with the time-course of the servo-controlled glucose infusion. Under conditions of a steady-state arterial glucose level, glucose infusion is a measure of glucose utilization. We conclude that compartment 3 insulin (rather than plasma insulin) is a more direct determinant of glucose utilization. We suggest that the combined use of glucose-clamp and kinetic-modeling techniques should aid in the delineation of pathophysiologic states affecting glucose and insulin metabolism. Images PMID:4856884
Dayglow on Mars: Kinetic modelling with SPICAM UV limb data
NASA Astrophysics Data System (ADS)
Simon, C.; Witasse, O.; Leblanc, F.; Gronoff, G.; Bertaux, J.-L.
2009-07-01
The UV spectrometer experiment SPICAM onboard ESA Mars Express has been orbiting Mars since December 2003. We present here some comparisons between airglow data that have been newly interpreted with the advanced kinetic model Trans-Mars. A series of numerical one-dimensional kinetic models, in the Trans-* family [Lilensten, J., Blelly. P.L., 2002. The TEC and F2 parameters as tracers of the ionosphere and thermosphere. J. Atmos. Solar-Terrestrial Phys. 64, 775-793] has been developed over the last years to take into account of airglow processes and yield altitude line profiles in planetary upper atmospheres (Earth, Venus, Titan and Mars). Trans-Mars is the last evolution of these simulations, applied to Mars. Electron and photon cross sections have been recently updated. The computed model line profiles are comparable to those of Fox and Dalgarno [1979b. Ionization, luminosity, and heating of the upper atmosphere of Mars. J. Geophys. Res. 84, 7315-7333] and Shematovich et al. [2008. Monte Carlo model of electron transport for the calculation of Mars dayglow emissions. J. Geophys. Res. (Planets) 113(E12), 2011]. Nearly 70000 limb UV spectra recorded by SPICAM between October 2004 and May 2006 are analysed in order to obtain altitude emission profiles on the main dayglow emissions. A variable point spread function (PSF) determined statistically throughout the wavelength range is used to estimate precisely the intensity of the airglow. This includes the Cameron bands ( a3Π-X1Σ) of CO, the CO2+ ultraviolet doublet ( B2Σu+-X2Πg) at 289.0 nm and the oxygen emission at 297.2 nm. Instrumental uncertainties of the emissions remain under 15%. Five groups of comparable orbits are selected to prepare for the data interpretation. The seasonal and solar activity effects on the dayside CO 'Cameron Bands', CO2+ and OI(2972 Å) emissions are discussed in light of previous studies. These emissions exhibit for equatorial latitudes two maxima of intensity for LS=140∘ and 290
Kinetic modeling of the Saturn ring-ionosphere plasma environment
NASA Technical Reports Server (NTRS)
Wilson, G. R.; Waite, J. H., Jr.
1989-01-01
A time-independent kinetic plasma model was developed on the basis of the Li et al. (1988) semikinetic plasma model and was used to study the interaction of the Saturnian ionosphere and ring plasma. The model includes the gravitational magnetic mirror and centripetal and ambipolar electric forces, and the effect of the mixing of two plasma populations. The results obtained indicate that the density, temperature, and composition of plasma near the rings changing in the direction from the inner C ring to the outer A ring, due to the fact that the predominant source of plasma changes from the ionosphere to the rings. The model results also suggest that the outflow of hydrogen from the ionosphere to the rings may be shut off for field lines passing through the outer B and A ring, due to the ambipolar electric field set up by the warm ring plasma trapped near the ring plane by the centipetal force. In these regions, there will be a net flux of O(+) ions from the rings to the ionosphere.
Modeling Momentum Transfer from Kinetic Impacts: Implications for Redirecting Asteroids
Stickle, A. M.; Atchison, J. A.; Barnouin, O. S.; Cheng, A. F.; Crawford, D. A.; Ernst, C. M.; Fletcher, Z.; Rivkin, A. 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 of 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.
Modeling Momentum Transfer from Kinetic Impacts: Implications for Redirecting Asteroids
Stickle, A. M.; Atchison, J. A.; Barnouin, O. S.; Cheng, A. F.; Crawford, D. A.; Ernst, C. M.; Fletcher, Z.; Rivkin, A. 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
Metabolic engineering with multi-objective optimization of kinetic models.
Villaverde, Alejandro F; Bongard, Sophia; Mauch, Klaus; Balsa-Canto, Eva; Banga, Julio R
2016-03-20
Kinetic models have a great potential for metabolic engineering applications. They can be used for testing which genetic and regulatory modifications can increase the production of metabolites of interest, while simultaneously monitoring other key functions of the host organism. This work presents a methodology for increasing productivity in biotechnological processes exploiting dynamic models. It uses multi-objective dynamic optimization to identify the combination of targets (enzymatic modifications) and the degree of up- or down-regulation that must be performed in order to optimize a set of pre-defined performance metrics subject to process constraints. The capabilities of the approach are demonstrated on a realistic and computationally challenging application: a large-scale metabolic model of Chinese Hamster Ovary cells (CHO), which are used for antibody production in a fed-batch process. The proposed methodology manages to provide a sustained and robust growth in CHO cells, increasing productivity while simultaneously increasing biomass production, product titer, and keeping the concentrations of lactate and ammonia at low values. The approach presented here can be used for optimizing metabolic models by finding the best combination of targets and their optimal level of up/down-regulation. Furthermore, it can accommodate additional trade-offs and constraints with great flexibility. PMID:26826510
A computational kinetic model of diffusion for molecular systems
Teo, Ivan; Schulten, Klaus
2013-01-01
Regulation of biomolecular transport in cells involves intra-protein steps like gating and passage through channels, but these steps are preceded by extra-protein steps, namely, diffusive approach and admittance of solutes. The extra-protein steps develop over a 10–100 nm length scale typically in a highly particular environment, characterized through the protein's geometry, surrounding electrostatic field, and location. In order to account for solute energetics and mobility of solutes in this environment at a relevant resolution, we propose a particle-based kinetic model of diffusion based on a Markov State Model framework. Prerequisite input data consist of diffusion coefficient and potential of mean force maps generated from extensive molecular dynamics simulations of proteins and their environment that sample multi-nanosecond durations. The suggested diffusion model can describe transport processes beyond microsecond duration, relevant for biological function and beyond the realm of molecular dynamics simulation. For this purpose the systems are represented by a discrete set of states specified by the positions, volumes, and surface elements of Voronoi grid cells distributed according to a density function resolving the often intricate relevant diffusion space. Validation tests carried out for generic diffusion spaces show that the model and the associated Brownian motion algorithm are viable over a large range of parameter values such as time step, diffusion coefficient, and grid density. A concrete application of the method is demonstrated for ion diffusion around and through the Eschericia coli mechanosensitive channel of small conductance ecMscS. PMID:24089741
A computational kinetic model of diffusion for molecular systems
NASA Astrophysics Data System (ADS)
Teo, Ivan; Schulten, Klaus
2013-09-01
Regulation of biomolecular transport in cells involves intra-protein steps like gating and passage through channels, but these steps are preceded by extra-protein steps, namely, diffusive approach and admittance of solutes. The extra-protein steps develop over a 10-100 nm length scale typically in a highly particular environment, characterized through the protein's geometry, surrounding electrostatic field, and location. In order to account for solute energetics and mobility of solutes in this environment at a relevant resolution, we propose a particle-based kinetic model of diffusion based on a Markov State Model framework. Prerequisite input data consist of diffusion coefficient and potential of mean force maps generated from extensive molecular dynamics simulations of proteins and their environment that sample multi-nanosecond durations. The suggested diffusion model can describe transport processes beyond microsecond duration, relevant for biological function and beyond the realm of molecular dynamics simulation. For this purpose the systems are represented by a discrete set of states specified by the positions, volumes, and surface elements of Voronoi grid cells distributed according to a density function resolving the often intricate relevant diffusion space. Validation tests carried out for generic diffusion spaces show that the model and the associated Brownian motion algorithm are viable over a large range of parameter values such as time step, diffusion coefficient, and grid density. A concrete application of the method is demonstrated for ion diffusion around and through the Eschericia coli mechanosensitive channel of small conductance ecMscS.
Detailed kinetic modeling study of n-pentanol oxidation
Heufer, K. Alexander; Sarathy, S. Mani; Curran, Henry J.; Davis, Alexander C.; Westbrook, Charles K.; Pitz, William J.
2012-09-28
To help overcome the world’s dependence upon fossil fuels, suitable biofuels are promising alternatives that can be used in the transportation sector. Recent research on internal combustion engines shows that short alcoholic fuels (e.g., ethanol or n-butanol) have reduced pollutant emissions and increased knock resistance compared to fossil fuels. Although higher molecular weight alcohols (e.g., n-pentanol and n-hexanol) exhibit higher reactivity that lowers their knock resistance, they are suitable for diesel engines or advanced engine concepts, such as homogeneous charge compression ignition (HCCI), where higher reactivity at lower temperatures is necessary for engine operation. The present study presents a detailedmore » kinetic model for n-pentanol based on modeling rules previously presented for n-butanol. This approach was initially validated using quantum chemistry calculations to verify the most stable n-pentanol conformation and to obtain C–H and C–C bond dissociation energies. In addition, the proposed model has been validated against ignition delay time data, speciation data from a jet-stirred reactor, and laminar flame velocity measurements. Overall, the model shows good agreement with the experiments and permits a detailed discussion of the differences between alcohols and alkanes.« less
NASA Astrophysics Data System (ADS)
Maher Abourabia, Aly; Hassan, Kawsar Mohammad; Abo-Elghar, Eman Mohammad
2015-02-01
We investigate a bio-system composed of a shape memory alloy (SMA) immersed and subjected to heat convection in a blood vessel, affected by heart beats that create a wave motion of long wavelength. The tackled model in (2+1)-D is based on the continuity and momentum equations for the fluid phase, besides; the state of the SMA are described via previous works in the form of statistical distributions of energy for both Martensite and Austenite phases. The solution based on the reductive perturbation technique gives a thermal diffusion-like equation as a key for expressing the temperature and velocity components of the blood. In terms of two cases concerning the difference between the wave numbers in the perpendicular directions, it is found that the system's temperature increases nonlinearly from a minimum initial temperature 293 K (20 °C) up to a maximum value about 316.68 K (43.68 °C), then tends to decrease along the blood flow (anisotropy of K and L) direction. In both cases it is observed that the SMA acquires most of this temperature raising not the blood because of its conventional biological limits (37-40 °C). The range of the heart beats wave numbers characteristic for each person plays an important role in realizing phase changes in the anisotropic case leading to the formation of the hysteresis loops Martensite-Austenite-Martensite or vice versa, according to the energy variation. The entropy generation σ is investigated for the system (Blood + SMA), it predicts that along the flow direction the system gains energy convectively up to a maximum value, then reverses his tendency to gradually loosing energy passing by the equilibrium state, then the system looses energy to the surroundings by the same amount which was gained beforehand. The loss diminishes but stops before arriving to equilibrium again. For certain differences in wave numbers the system starts to store energy again after it passes by the state of equilibrium for the second time. In the
O'Leary, Timothy P; Brown, Richard E
2009-07-19
The APPswe/PS1dE9 mouse is a double transgenic model of Alzheimer's disease, which harbors mutant mouse/human amyloid precursor protein (Swedish K594N/M595L) and presenilin-1 genes (PS1-dE9). These mice develop beta-amyloid plaques and exhibit visuo-spatial learning and memory impairment in the Morris water maze (MWM) at 8-12 and 16-18 months of age. To extend these findings, we tested visuo-spatial learning and memory of male and female APPswe/PS1dE9 mice at 16 months of age on the Barnes maze. APPswe/PS1dE9 mice showed impaired acquisition learning using measures of latency, distance traveled, errors and hole deviation scores, and were less likely to use the spatial search strategy to locate the escape hole than wild-type mice. APPswe/PS1dE9 mice also showed a deficit in memory in probe tests on the Barnes maze relative to wild-type mice. Learning and memory deficits, however, were not found during reversal training and reversal probe tests. Sex differences were observed, as male APPswe/PS1dE9 mice had smaller reversal effects than male wild-type mice, but females of each genotype did not differ. Overall, these results replicate previous findings using the MWM, and indicate that APPswe/PS1dE9 mice have impaired visuo-spatial learning and memory at 16 months of age. PMID:19428625
1D ferrimagnetism in homometallic chains
NASA Astrophysics Data System (ADS)
Coronado, E.; Gómez-García, C. J.; Borrás-Almenar, J. J.
1990-05-01
The magnetic properties of the cobalt zigzag chain Co(bpy)(NCS)2 (bpy=2,2'-bipyridine) are discussed on the basis of an Ising-chain model that takes into account alternating Landé factors. It is emphasized, for the first time, that a homometallic chain containing only one type of site can give rise to a 1D ferrimagneticlike behavior.
The use of automated parameter searches to improve ion channel kinetics for neural modeling.
Hendrickson, Eric B; Edgerton, Jeremy R; Jaeger, Dieter
2011-10-01
The voltage and time dependence of ion channels can be regulated, notably by phosphorylation, interaction with phospholipids, and binding to auxiliary subunits. Many parameter variation studies have set conductance densities free while leaving kinetic channel properties fixed as the experimental constraints on the latter are usually better than on the former. Because individual cells can tightly regulate their ion channel properties, we suggest that kinetic parameters may be profitably set free during model optimization in order to both improve matches to data and refine kinetic parameters. To this end, we analyzed the parameter optimization of reduced models of three electrophysiologically characterized and morphologically reconstructed globus pallidus neurons. We performed two automated searches with different types of free parameters. First, conductance density parameters were set free. Even the best resulting models exhibited unavoidable problems which were due to limitations in our channel kinetics. We next set channel kinetics free for the optimized density matches and obtained significantly improved model performance. Some kinetic parameters consistently shifted to similar new values in multiple runs across three models, suggesting the possibility for tailored improvements to channel models. These results suggest that optimized channel kinetics can improve model matches to experimental voltage traces, particularly for channels characterized under different experimental conditions than recorded data to be matched by a model. The resulting shifts in channel kinetics from the original template provide valuable guidance for future experimental efforts to determine the detailed kinetics of channel isoforms and possible modulated states in particular types of neurons. PMID:21243419
NASA Astrophysics Data System (ADS)
Mastin, L. G.; Sherrod, D. R.; Vallance, J. W.; Thornber, C. T.; Ewert, J. W.
2005-12-01
The dome-building eruption at Mount St. Helens has occurred through glacial ice and snow that would be expected to substantially affect the character of the eruption. Nevertheless, the role of water in the eruption to date has not always been clear. For example, on March 8, 2005, a half-hour-long tephra blast sent a plume to a maximum of ~9 km above the vent (based on pilot reports); seismicity and plume heights were greatest during the first ~10 minutes, then persisted for another ~15 minutes at a lower level before the eruption stopped. Tephra volume within 5 km2 downwind of the vent was ~5x104 m3 DRE, but trace amounts were reported at least to Ellensburg, WA (150 km NE), suggesting a total areal coverage >5,000 km2 and total volume >1x105 m3. Assuming that most of this material was expelled in the first ten minutes and had a density of 2500 kg/m3, the mass flow rate (M) during the vigorous phase was >~4x105 kg/s. The tephra, composed primarily of non-pumiceous broken and decrepitated dome rock, could have been expelled either by groundwater and steam at relatively modest (boiling-point) temperatures, or by magmatic gas at much higher temperatures. The high plume, however, suggested significant buoyancy, perhaps driven by temperatures closer to magmatic. To assess the effect of magmatic heat on plume height, we employ a 1-D steady volcanic plume model that uses specified vent diameter, exit velocity, eruption temperature, mass fractions of gas and added external water, and profiles of atmospheric temperature and humidity, to calculate plume height and plume properties as a function of elevation. The model considers the enthalpy of equilibrium water condensation and of ice formation. Model results show that, under atmospheric temperature and humidity profiles measured near Mount St. Helens on the afternoon of March 8, 2005, a plume height (h) of 7-9 km could have developed with eruption temperatures (T) as low as 100° C, provided the mass fraction of water vapor
Global Kinetic Modeling of Banded Electron Structures in the Plasmasphere
NASA Technical Reports Server (NTRS)
Liemohn, M. W.; Khazanov, G. V.
1997-01-01
Significant fluxes of 10 eV to 30 keV electrons have been detected in the plasmasphere, appearing as banded structures in energy with broad spatial extents and slowly evolving over several days. It is thought that these populations are decaying plasma sheet electrons injected into the corotating region of near-Earth space. This capture can occur when the convective electric field drops rapidly and the Alfven boundary suddenly outward, trapping the inner edge of the plasma sheet along closed drift paths. Our bounce-averaged kinetic model of superthermal electron transport is able to simulate this capture and the subsequent drift, diffusion, and decay of the plasma cloud. Results of this simulation will be shown and discussed, from the initial injection during the elevated convection to the final loss of the particles. It is thought that not only Coulomb collisions but also wave-particle interactions play a significant role in altering the plasma cloud. Quasilinear diffusion is currently being incorporated into the model and the importance of this mechanism will be examined. Also, the high anisotropy of the trapped population could be unstable and generate plasma waves. These and other processes will be investigated to determine the final fate of the cloud and to quantify where, how, and when the energy of the plasma cloud is deposited. Comparisons with CRRES observations of these events are shown to verify the model and explain the data.
Chemical Kinetic Modeling of HMX and TATB Laser Ignition Tests
Tarver, C M
2004-03-02
Recent laser ignition experiments on octahydro-1,3,5,7-tetranitro-1,3,5,7-terrazocine (HMX) and 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) subjected to laser fluxes ranging from 10 to 800 W/cm{sup 2} produced ignition times from seconds to milliseconds. Global chemical kinetic thermal decomposition models for HMX and TATB have been developed to calculate times to thermal explosion for experiments in the seconds to days time frame. These models are applied to the laser ignition experimental data in this paper. Excellent agreement was obtained for TATB, while the calculated ignition times were longer than experiment for HMX at lower laser fluxes. At the temperatures produced in the laser experiments, HMX melts. Melting generally increases condensed phase reaction rates so faster rates were used for three of the HMX reaction rates. This improved agreement with experiments at the lower laser fluxes but yielded very fast ignition at high fluxes. The calculated times to ignition are in reasonable agreement with the laser ignition experiments, and this justifies the use of these models for estimating reaction times at impact and shock ''hot spot'' temperatures.
Kinetic Modeling of Damage Repair, Genome Instability, and Neoplastic Transformation
Stewart, Robert D
2007-03-17
Inducible repair and pathway interactions may fundamentally alter the shape of dose-response curves because different mechanisms may be important under low- and high-dose exposure conditions. However, the significance of these phenomena for risk assessment purposes is an open question. This project developed new modeling tools to study the putative effects of DNA damage induction and repair on higher-level biological endpoints, including cell killing, neoplastic transformation and cancer. The project scope included (1) the development of new approaches to simulate the induction and base excision repair (BER) of DNA damage using Monte Carlo methods and (2) the integration of data from the Monte Carlo simulations with kinetic models for higher-level biological endpoints. Methods of calibrating and testing such multiscale biological simulations were developed. We also developed models to aid in the analysis and interpretation of data from experimental assays, such as the pulsed-field gel electrophoresis (PFGE) assay used to quantity the amount of DNA damage caused by ionizing radiation.
A kinetic model of rapidly reversible nonphotochemical quenching
Zaks, Julia; Amarnath, Kapil; Kramer, David M.; Niyogi, Krishna K.; Fleming, Graham R.
2012-01-01
Oxygen-evolving photosynthetic organisms possess nonphotochemical quenching (NPQ) pathways that protect against photo-induced damage. The majority of NPQ in plants is regulated on a rapid timescale by changes in the pH of the thylakoid lumen. In order to quantify the rapidly reversible component of NPQ, called qE, we developed a mathematical model of pH-dependent quenching of chlorophyll excitations in Photosystem II. Our expression for qE depends on the protonation of PsbS and the deepoxidation of violaxanthin by violaxanthin deepoxidase. The model is able to simulate the kinetics of qE at low and high light intensities. The simulations suggest that the pH of the lumen, which activates qE, is not itself affected by qE. Our model provides a framework for testing hypothesized qE mechanisms and for assessing the role of qE in improving plant fitness in variable light intensity. PMID:22891305
Chemical kinetic modeling of component mixtures relevant to gasoline
Mehl, M; Curran, H J; Pitz, W J; Dooley, S; Westbrook, C K
2008-05-29
Detailed kinetic models of pyrolysis and combustion of hydrocarbon fuels are nowadays widely used in the design of internal combustion engines and these models are effectively applied to help meet the increasingly stringent environmental and energetic standards. In previous studies by the combustion community, such models not only contributed to the understanding of pure component combustion, but also provided a deeper insight into the combustion behavior of complex mixtures. One of the major challenges in this field is now the definition and the development of appropriate surrogate models able to mimic the actual features of real fuels. Real fuels are complex mixtures of thousands of hydrocarbon compounds including linear and branched paraffins, naphthenes, olefins and aromatics. Their behavior can be effectively reproduced by simpler fuel surrogates containing a limited number of components. Aside the most commonly used surrogates containing iso-octane and n-heptane only, the so called Primary Reference Fuels (PRF), new mixtures have recently been suggested to extend the reference components in surrogate mixtures to also include alkenes and aromatics. It is generally agreed that, including representative species for all the main classes of hydrocarbons which can be found in real fuels, it is possible to reproduce very effectively in a wide range of operating conditions not just the auto-ignition propensity of gasoline or Diesel fuels, but also their physical properties and their combustion residuals [1]. In this work, the combustion behavior of several components relevant to gasoline surrogate formulation is computationally examined. The attention is focused on the autoignition of iso-octane, hexene and their mixtures. Some important issues relevant to the experimental and modeling investigation of such fuels are discussed with the help of rapid compression machine data and calculations. Following the model validation, the behavior of mixtures is discussed on the
A kinetic model for RNA-interference of focal adhesions
2013-01-01
Background Focal adhesions are integrin-based cell-matrix contacts that transduce and integrate mechanical and biochemical cues from the environment. They develop from smaller and more numerous focal complexes under the influence of mechanical force and are key elements for many physiological and disease-related processes, including wound healing and metastasis. More than 150 different proteins localize to focal adhesions and have been systematically classified in the adhesome project (http://www.adhesome.org). First RNAi-screens have been performed for focal adhesions and the effect of knockdown of many of these components on the number, size, shape and location of focal adhesions has been reported. Results We have developed a kinetic model for RNA interference of focal adhesions which represents some of its main elements: a spatially layered structure, signaling through the small GTPases Rac and Rho, and maturation from focal complexes to focal adhesions under force. The response to force is described by two complementary scenarios corresponding to slip and catch bond behavior, respectively. Using estimated and literature values for the model parameters, three time scales of the dynamics of RNAi-influenced focal adhesions are identified: a sub-minute time scale for the assembly of focal complexes, a sub-hour time scale for the maturation to focal adhesions, and a time scale of days that controls the siRNA-mediated knockdown. Our model shows bistability between states dominated by focal complexes and focal adhesions, respectively. Catch bonding strongly extends the range of stability of the state dominated by focal adhesions. A sensitivity analysis predicts that knockdown of focal adhesion components is more efficient for focal adhesions with slip bonds or if the system is in a state dominated by focal complexes. Knockdown of Rho leads to an increase of focal complexes. Conclusions The suggested model provides a kinetic description of the effect of RNA
NASA Astrophysics Data System (ADS)
Jones, Alan G.; Afonso, Juan Carlos; Fullea, Javier; Salajegheh, Farshad
2014-02-01
Modeling the continental lithosphere's physical properties, especially its depth extent, must be done within a self-consistent petrological-geophysical framework; modeling using only one or two data types may easily lead to inconsistencies and erroneous interpretations. Using the LitMod approach for hypothesis testing and first-order modeling, we show how assumptions made about crustal information and the probable compositions of the lithospheric and sub-lithospheric mantle affect particular observables, particularly especially surface topographic elevation. The critical crustal parameter is density, leading to ca. 600 m error in topography for 50 kg m- 3 imprecision. The next key parameter is crustal thickness, and uncertainties in its definition lead to around ca. 4 km uncertainty in LAB for every 1 km of variation in Moho depth. Possible errors in the other assumed crustal parameters introduce a few kilometers of uncertainty in the depth to the LAB. We use Ireland as a natural laboratory to demonstrate the approach. From first-order arguments and given reasonable assumptions, a topographic elevation in the range of 50-100 m, which is the average across Ireland, requires that the lithosphere-asthenosphere boundary (LAB) beneath most of Ireland must lie in the range 90-115 km. A somewhat shallower (to 85 km) LAB is permitted, but the crust must be thinned (< 29 km) to compensate. The observations, especially topography, are inconsistent with suggestions, based on interpretation of S-to-P receiver functions, that the LAB thins from 85 km in southern Ireland to 55 km in central northern Ireland over a distance of < 150 km. Such a thin lithosphere would result in over 1000 m of uplift, and such rapid thinning by 30 km over less than 150 km would yield significant north-south variations in topographic elevation, Bouguer anomaly, and geoid height, none of which are observed. Even juxtaposing the most extreme probable depleted composition for the lithospheric mantle
Heterogeneous kinetic modeling of the catalytic conversion of cycloparaffins
NASA Astrophysics Data System (ADS)
Al-Sabawi, Mustafa N.
catalytic conversions respectively, are reported. Using these data, heterogeneous kinetic models accounting for intracrystallite molecular transport, adsorption and thermal and catalytic cracking of both cycloparaffin reactants are established. Results show that undesirable hydrogen transfer reactions are more pronounced and selectively favoured against other reactions at lower reaction temperatures, while the desirable ring-opening and cracking reactions predominate at the higher reaction temperatures. Moreover, results of the present work show that while crystallite size may have an effect on the overall conversion in some situations, there is a definite effect on the selectivity of products obtained during the cracking of MCH and decalin and the cracking of MCH in a mixture with co-reactants such as 1,3,5-triisopropylbenzene. Keywords. cycloparaffins, naphthenes, fluid catalytic cracking, kinetic modeling, Y-zeolites, diffusion, adsorption, ring-opening, hydrogen transfer, catalyst selectivity.
Numerical modeling of radiation physics in kinetic plasmas [II
NASA Astrophysics Data System (ADS)
Paraschiv, Ioana; Sentoku, Yasuhiko; Mancini, Roberto
2014-10-01
X-ray radiation is an important feature of ultra-intense laser interactions with high Z materials. In order to take into account the radiation effects in the high energy density plasmas created by such interactions, we have modified the collisional particle-in-cell code PICLS to self-consistently model the x-ray radiation transport (RT). Solving the equation of radiation transport requires the creation of a non-LTE database of emissivities and opacities as functions of photon frequency for given densities, bulk electron temperatures, hot electron temperatures, and hot electron fractions. The database was generated using results computed by a non-equilibrium, collisional-radiative atomic kinetics code. Using the two-dimensional RT-PICLS code we have studied the X-ray transport in an ultrafast heated target and the dependence of the emitted K- α radiation on the fast electron dynamics in the solid target. The details of these results obtained from the implementation of the radiation transport model into the PICLS calculations will be reported in this presentation. Work supported by the DOE Office of Science Grant No. DE-SC0008827 and by the NNSA/DOE Grants No. DE-FC52-06NA27616 and DE-NA0002075.
Kinetic modeling of copper biosorption by immobilized biomass
Veglio, F.; Beolchini, F.; Toro, L.
1998-03-01
Biosorption of heavy metals is one of the most promising technologies involved in the removal of toxic metals from industrial waste streams and natural waters. The kinetic modeling of copper biosorption by Arthrobacter sp. immobilized in a hydroxyethyl methacrylate-based matrix is reported in this work. The resin-biomass complex (RBC) has been used for copper biosorption in different conditions according to a factorial experiment. Factors investigated were cross-linker (trimethylolpropane trimethacrylate) concentration, biomass concentration in the solid, and particles` granulometry. A maximum copper specific uptake of abut 7 mg of Cu/g of biomass (dry weight) has been observed, in the case of a RBC with the following characteristics: 2% (w/w) cross-linker concentration, 8% (w/w) biomass concentration, and 425--750 {micro}m granulometry. The shrinking core model has been used for the fitting of experimental data. A good fit has been found in the case of controlling intraparticle diffusion in all experimental trials. The copper diffusion coefficient in RBC has been estimated from the slope of the regression lines. Values obtained for the diffusion coefficients do not differ from one another with respect to the estimated standard error. An average apparent copper diffusion coefficient of about 3 {times} 10{sup {minus}6} cm{sup 2}/s has been found.
Kinetic Modeling of Combustion Characteristics of Real Biodiesel Fuels
Naik, C V; Westbrook, C K
2009-04-08
Biodiesel fuels are of much interest today either for replacing or blending with conventional fuels for automotive applications. Predicting engine effects of using biodiesel fuel requires accurate understanding of the combustion characteristics of the fuel, which can be acquired through analysis using reliable detailed reaction mechanisms. Unlike gasoline or diesel that consists of hundreds of chemical compounds, biodiesel fuels contain only a limited number of compounds. Over 90% of the biodiesel fraction is composed of 5 unique long-chain C{sub 18} and C{sub 16} saturated and unsaturated methyl esters. This makes modeling of real biodiesel fuel possible without the need for a fuel surrogate. To this end, a detailed chemical kinetic mechanism has been developed for determining the combustion characteristics of a pure biodiesel (B100) fuel, applicable from low- to high-temperature oxidation regimes. This model has been built based on reaction rate rules established in previous studies at Lawrence Livermore National Laboratory. Computed results are compared with the few fundamental experimental data that exist for biodiesel fuel and its components. In addition, computed results have been compared with experimental data for other long-chain hydrocarbons that are similar in structure to the biodiesel components.
Kinetic Modeling of a Heterogeneous Fenton Oxidative Treatment of Petroleum Refining Wastewater
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 (k2′), their final oxidation step (k1′), and the direct conversion to endproducts step (k3′) 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
Rites of passage: requirements and standards for building kinetic models of metabolic phenotypes.
Miskovic, Ljubisa; Tokic, Milenko; Fengos, Georgios; Hatzimanikatis, Vassily
2015-12-01
The overarching ambition of kinetic metabolic modeling is to capture the dynamic behavior of metabolism to such an extent that systems and synthetic biology strategies can reliably be tested in silico. The lack of kinetic data hampers the development of kinetic models, and most of the current models use ad hoc reduced stoichiometry or oversimplified kinetic rate expressions, which may limit their predictive strength. There is a need to introduce the community-level standards that will organize and accelerate the future developments in this area. We introduce here a set of requirements that will ensure the model quality, we examine the current kinetic models with respect to these requirements, and we propose a general workflow for constructing models that satisfy these requirements. PMID:26342586
Nyman, Jeffry S; Merkel, Alyssa R; Uppuganti, Sasidhar; Nayak, Bijaya; Rowland, Barbara; Makowski, Alexander J; Oyajobi, Babatunde O; Sterling, Julie A
2016-10-01
Multiple myeloma (MM) patients frequently develop tumor-induced bone destruction, yet no therapy completely eliminates the tumor or fully reverses bone loss. Transforming growth factor-β (TGF-β) activity often contributes to tumor-induced bone disease, and pre-clinical studies have indicated that TGF-β inhibition improves bone volume and reduces tumor growth in bone metastatic breast cancer. We hypothesized that inhibition of TGF-β signaling also reduces tumor growth, increases bone volume, and improves vertebral body strength in MM-bearing mice. We treated myeloma tumor-bearing (immunocompetent KaLwRij and immunocompromised Rag2-/-) mice with a TGF-β inhibitory (1D11) or control (13C4) antibody, with or without the anti-myeloma drug bortezomib, for 4weeks after inoculation of murine 5TGM1 MM cells. TGF-β inhibition increased trabecular bone volume, improved trabecular architecture, increased tissue mineral density of the trabeculae as assessed by ex vivo micro-computed tomography, and was associated with significantly greater vertebral body strength in biomechanical compression tests. Serum monoclonal paraprotein titers and spleen weights showed that 1D11 monotherapy did not reduce overall MM tumor burden. Combination therapy with 1D11 and bortezomib increased vertebral body strength, reduced tumor burden, and reduced cortical lesions in the femoral metaphysis, although it did not significantly improve cortical bone strength in three-point bending tests of the mid-shaft femur. Overall, our data provides rationale for evaluating inhibition of TGF-β signaling in combination with existing anti-myeloma agents as a potential therapeutic strategy to improve outcomes in patients with myeloma bone disease. PMID:27423464
Microbial Kinetic Model for the Degradation of Poorly Soluble Organic Materials
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 ...
Zhang, Wei; Hao, Jian; Liu, Rui; Zhang, Zhuo; Lei, Gesheng; Su, Changjun; Miao, Jianting; Li, Zhuyi
2011-09-23
Amyloid-beta peptide (Aβ) is believed to be central in the pathogenesis of Alzheimer's disease (AD) characterized by cognitive deficits. However, it remains uncertain which form(s) of Aβ pathology is responsible for the cognitive deficits in AD. In the present study, the cognitive deficits and the profiles of Aβ pathology were characterized in the 12-month-old APPswe/PS1dE9 double transgenic mice, and their correlations were examined. Compared with non-transgenic littermates, the middle-aged APPswe/PS1dE9 mice exhibited spatial learning and memory deficits in the water maze test and long-term contextual memory deficits in the step-down passive avoidance test. Among the middle-aged APPswe/PS1dE9 mice, hippocampal soluble Aβ1-40 and Aβ1-42 levels were highly correlated with spatial learning deficits and long-term contextual memory deficits, as well as cortical and hippocampal soluble Aβ1-40 and Aβ1-42 levels were strongly correlated with spatial memory deficits. By contrast, no significant correlations were observed between three measures of cognitive functions and amyloid plaque burden (total Aβ plaque load and fibrillar Aβ plaque load), total Aβ levels (Aβ1-40 and Aβ1-42), as well as insoluble Aβ levels (Aβ1-40 and Aβ1-42). Stepwise multiple regression analysis identified hippocampal soluble Aβ1-40 and Aβ1-42 levels as independent factors for predicting the spatial learning deficits and the long-term contextual memory deficits, as well as hippocampal and cortical soluble Aβ1-40 and Aβ1-42 levels as independent factors for predicting the spatial memory deficits in transgenic mice. These results demonstrate that cognitive deficits are highly related to the levels of soluble Aβ in middle-aged APPswe/PS1dE9 mice, in which soluble Aβ levels are only a tiny fraction of the amount of total Aβ levels. Consequently, our findings provide further evidence that soluble Aβ might primarily contribute to cognitive deficits in AD, suggesting that reducing
Kinetics and fixed-bed reactor modeling of butane oxidation to maleic anhydride
Sharma, R.K.; Cresswell, D.L. ); Newson, E.J. )
1991-01-01
This paper reports on selective oxidation kinetics of n-butane to maleic anhydride in air studied over a commercial, fixed-bed vanadium-phosphor oxide catalyst. The temperature range was 573-653 K with butane concentrations up to 3 mol % in the feed, which is within flammability limits but below ignition temperatures. The rate data were modeled using power law kinetics with product inhibition and included total oxidation and decomposition reactions. Kinetic parameters were estimated using a multiresponse, nonlinear regression algorithm showing intercorrelation effects. The kinetics were combined with independent measurements of catalyst diffusivity and reactor heat transfer using a one- dimensional heterogeneous reactor model.
Multiscale Model for the Assembly Kinetics of Protein Complexes.
Xie, Zhong-Ru; Chen, Jiawen; Wu, Yinghao
2016-02-01
The assembly of proteins into high-order complexes is a general mechanism for these biomolecules to implement their versatile functions in cells. Natural evolution has developed various assembling pathways for specific protein complexes to maintain their stability and proper activities. Previous studies have provided numerous examples of the misassembly of protein complexes leading to severe biological consequences. Although the research focusing on protein complexes has started to move beyond the static representation of quaternary structures to the dynamic aspect of their assembly, the current understanding of the assembly mechanism of protein complexes is still largely limited. To tackle this problem, we developed a new multiscale modeling framework. This framework combines a lower-resolution rigid-body-based simulation with a higher-resolution Cα-based simulation method so that protein complexes can be assembled with both structural details and computational efficiency. We applied this model to a homotrimer and a heterotetramer as simple test systems. Consistent with experimental observations, our simulations indicated very different kinetics between protein oligomerization and dimerization. The formation of protein oligomers is a multistep process that is much slower than dimerization but thermodynamically more stable. Moreover, we showed that even the same protein quaternary structure can have very diverse assembly pathways under different binding constants between subunits, which is important for regulating the functions of protein complexes. Finally, we revealed that the binding between subunits in a complex can be synergistically strengthened during assembly without considering allosteric regulation or conformational changes. Therefore, our model provides a useful tool to understand the general principles of protein complex assembly. PMID:26738810
Freed by interaction kinetic states in the Harper model
NASA Astrophysics Data System (ADS)
Frahm, Klaus M.; Shepelyansky, Dima L.
2015-12-01
We study the problem of two interacting particles in a one-dimensional quasiperiodic lattice of the Harper model. We show that a short or long range interaction between particles leads to emergence of delocalized pairs in the non-interacting localized phase. The properties of these freed by interaction kinetic states (FIKS) are analyzed numerically including the advanced Arnoldi method. We find that the number of sites populated by FIKS pairs grows algebraically with the system size with the maximal exponent b = 1, up to a largest lattice size N = 10 946 reached in our numerical simulations, thus corresponding to a complete delocalization of pairs. For delocalized FIKS pairs the spectral properties of such quasiperiodic operators represent a deep mathematical problem. We argue that FIKS pairs can be detected in the framework of recent cold atom experiments [M. Schreiber et al., Science 349, 842 (2015)] by a simple setup modification. We also discuss possible implications of FIKS pairs for electron transport in the regime of charge-density wave and high T c superconductivity.
Kinetic modeling of spectra of flames with suppressants
Green, A.E.S.; Xue, Hui
1995-12-31
The phase out of halons in response to the Montreal Protocol and the quest for alternative fire suppressants has focused attention on the current lack of understanding of mechanisms of flame extinction. Challenges to the free-radical scavenging mechanism in which chemical chains in combustion are interrupted have raised serious questions as to why the halons are effective. Low-resolution ultraviolet computer spectroscopy can be used to observe the OH radical and other simple molecules when acted upon by halon or alternative suppressants. However, the physical and chemical interpretation of such observations requires reaction rates leading to the OH radical and other observable molecules in 3-6 eV electronic states. Using a simple kinetics model, the authors illustrate where major reaction rates to excited states would be helpful to the interpretation of the interaction of suppressants with flames. Quantum chemists could provide a valuable service by providing such rates and helping to assess whether or not flame suppression by free-radical scavenging is a significant mechanism. 29 refs., 5 figs.
NASA Astrophysics Data System (ADS)
Toyota, K.; Dastoor, A. P.; Ryzhkov, A.
2014-04-01
Atmospheric mercury depletion events (AMDEs) refer to a recurring depletion of mercury occurring in the springtime Arctic (and Antarctic) boundary layer, in general, concurrently with ozone depletion events (ODEs). To close some of the knowledge gaps in the physical and chemical mechanisms of AMDEs and ODEs, we have developed a one-dimensional model that simulates multiphase chemistry and transport of trace constituents throughout porous snowpack and in the overlying atmospheric boundary layer (ABL). This paper constitutes Part 2 of the study, describing the mercury component of the model and its application to the simulation of AMDEs. Building on model components reported in Part 1 ("In-snow bromine activation and its impact on ozone"), we have developed a chemical mechanism for the redox reactions of mercury in the gas and aqueous phases with temperature dependent reaction rates and equilibrium constants accounted for wherever possible. Thus the model allows us to study the chemical and physical processes taking place during ODEs and AMDEs within a single framework where two-way interactions between the snowpack and the atmosphere are simulated in a detailed, process-oriented manner. Model runs are conducted for meteorological and chemical conditions that represent the springtime Arctic ABL characterized by the presence of "haze" (sulfate aerosols) and the saline snowpack on sea ice. The oxidation of gaseous elemental mercury (GEM) is initiated via reaction with Br-atom to form HgBr, followed by competitions between its thermal decomposition and further reactions to give thermally stable Hg(II) products. To shed light on uncertain kinetics and mechanisms of this multi-step oxidation process, we have tested different combinations of their rate constants based on published laboratory and quantum mechanical studies. For some combinations of the rate constants, the model simulates roughly linear relationships between the gaseous mercury and ozone concentrations as
Kinetic modelling of runaway electron avalanches in tokamak plasmas
NASA Astrophysics Data System (ADS)
Nilsson, E.; Decker, J.; Peysson, Y.; Granetz, R. S.; Saint-Laurent, F.; Vlainic, M.
2015-09-01
Runaway electrons can be generated in tokamak plasmas if the accelerating force from the toroidal electric field exceeds the collisional drag force owing to Coulomb collisions with the background plasma. In ITER, disruptions are expected to generate runaway electrons mainly through knock-on collisions (Hender et al 2007 Nucl. Fusion 47 S128-202), where enough momentum can be transferred from existing runaways to slow electrons to transport the latter beyond a critical momentum, setting off an avalanche of runaway electrons. Since knock-on runaways are usually scattered off with a significant perpendicular component of the momentum with respect to the local magnetic field direction, these particles are highly magnetized. Consequently, the momentum dynamics require a full 3D kinetic description, since these electrons are highly sensitive to the magnetic non-uniformity of a toroidal configuration. For this purpose, a bounce-averaged knock-on source term is derived. The generation of runaway electrons from the combined effect of Dreicer mechanism and knock-on collision process is studied with the code LUKE, a solver of the 3D linearized bounce-averaged relativistic electron Fokker-Planck equation (Decker and Peysson 2004 DKE: a fast numerical solver for the 3D drift kinetic equation Report EUR-CEA-FC-1736, Euratom-CEA), through the calculation of the response of the electron distribution function to a constant parallel electric field. The model, which has been successfully benchmarked against the standard Dreicer runaway theory now describes the runaway generation by knock-on collisions as proposed by Rosenbluth (Rosenbluth and Putvinski 1997 Nucl. Fusion 37 1355-62). This paper shows that the avalanche effect can be important even in non-disruptive scenarios. Runaway formation through knock-on collisions is found to be strongly reduced when taking place off the magnetic axis, since trapped electrons can not contribute to the runaway electron population. Finally, the
NASA Astrophysics Data System (ADS)
Toyota, K.; Dastoor, A. P.; Ryzhkov, A.
2013-08-01
Atmospheric mercury depletion events (AMDEs) refer to a recurring depletion of mercury in the springtime Arctic (and Antarctic) boundary layer, occurring, in general, concurrently with ozone depletion events (ODEs). To close some of the knowledge gaps in the physical and chemical mechanisms of AMDEs and ODEs, we have developed a one-dimensional model that simulates multiphase chemistry and transport of trace constituents throughout porous snowpack and in the overlying atmospheric boundary layer (ABL). Building on the model reported in a companion paper (Part 1: In-snow bromine activation and its impact on ozone), we have expanded the chemical mechanism to include the reactions of mercury in the gas- and aqueous-phases with temperature dependence of rate and equilibrium constants accounted for wherever possible. Thus the model allows us to study the chemical and physical processes taking place during ODEs and AMDEs within a single framework where two-way interactions between the snowpack and the atmosphere are simulated in a detailed, process-oriented manner. Model runs are conducted for meteorological and chemical conditions representing the springtime Arctic ABL loaded with "haze" sulfate aerosols and the underlying saline snowpack laid on sea ice. Using recent updates for the Hg + Br \\rightleftarrows HgBr reaction kinetics, we show that the rate and magnitude of photochemical loss of gaseous elemental mercury (GEM) during AMDEs exhibit a strong dependence on the choice of reaction(s) of HgBr subsequent to its formation. At 253 K, the temperature that is presumably low enough for bromine radical chemistry to cause prominent AMDEs as indicated from field observations, the parallel occurrence of AMDEs and ODEs is simulated if the reaction HgBr + BrO is assumed to produce a thermally stable intermediate, Hg(OBr)Br, at the same rate constant as the reaction HgBr + Br. On the contrary, the simulated depletion of atmospheric mercury is notably diminished by not
Sol-gel kinetics: /sup 29/SI NMR and a statistical reaction model
Assink, R.A.; Kay, B.D.
1988-01-01
Sol-gel processes allow one to prepare novel materials at low processing temperatures. A detailed understanding of the chemical kinetics of such systems is important to fully exploit the unique features of sol-gel processing. This paper describes a systematic approach to the study of sol-gel kinetics which employs /sup 29/Si NMR spectroscopy and kinetic modelling techniques. 2 figs., 1 tab.
Holod, I.; Lin, Z.
2013-03-15
The fluid-kinetic hybrid electron model is verified in global gyrokinetic particle simulation of linear electromagnetic drift-Alfvenic instabilities in tokamak. In particular, we have recovered the {beta}-stabilization of the ion temperature gradient mode, transition to collisionless trapped electron mode, and the onset of kinetic ballooning mode as {beta}{sub e} (ratio of electron kinetic pressure to magnetic pressure) increases.
Kinetic model of carbonate dissolution in Martian meteorite ALH84001
NASA Astrophysics Data System (ADS)
Kopp, R. E.; Humayun, M.
2003-09-01
The magnetites and sulfides located in the rims of carbonate globules in the Martian meteorite ALH84001 have been claimed as evidence of past life on Mars. Here, we consider the possibility that the rims were formed by dissolution and reprecipitation of the primary carbonate by the action of water. To estimate the rate of these solution-precipitation reactions, a kinetic model of magnesite-siderite carbonate dissolution was applied and used to examine the physicochemical conditions under which these rims might have formed. The results indicate that the formation of the rims could have taken place in < 50 yr of exposure to small amounts of aqueous fluids at ambient temperatures. Plausible conditions pertaining to reactions under a hypothetical ancient Martian atmosphere (1 bar CO 2), the modern Martian atmosphere (8 mbar CO 2), and the present terrestrial atmosphere (0.35 mbar CO 2) were explored to constrain the site of the process. The results indicated that such reactions likely occurred under the latter two conditions. The possibility of Antarctic weathering must be entertained, which, if correct, would imply that the plausibly biogenic minerals (single-domain magnetite of characteristic morphology and sulfide) reported from the rims may be the products of terrestrial microbial activity. This model is discussed in terms of the available isotope data and found to be compatible with the formation of ALH84001 rims. Particularly, anticorrelated variations of radiocarbon with δ 13C indicate that carbonate in ALH84001 was affected by solution-precipitation reactions immediately after its initial fall (˜13,000 yr ago) and then again during its recent exposure prior to collection.
Decarboxylation of Δ 9-tetrahydrocannabinol: Kinetics and molecular modeling
NASA Astrophysics Data System (ADS)
Perrotin-Brunel, Helene; Buijs, Wim; van Spronsen, Jaap; van Roosmalen, Maaike J. E.; Peters, Cor J.; Verpoorte, Rob; Witkamp, Geert-Jan
2011-02-01
Efficient tetrahydrocannabinol (Δ 9-THC) production from cannabis is important for its medical application and as basis for the development of production routes of other drugs from plants. This work presents one of the steps of Δ 9-THC production from cannabis plant material, the decarboxylation reaction, transforming the Δ 9-THC-acid naturally present in the plant into the psychoactive Δ 9-THC. Results of experiments showed pseudo-first order reaction kinetics, with an activation barrier of 85 kJ mol -1 and a pre-exponential factor of 3.7 × 10 8 s -1. Using molecular modeling, two options were identified for an acid catalyzed β-keto acid type mechanism for the decarboxylation of Δ 9-THC-acid. Each of these mechanisms might play a role, depending on the actual process conditions. Formic acid proved to be a good model for a catalyst of such a reaction. Also, the computational idea of catalysis by water to catalysis by an acid, put forward by Li and Brill, and Churchev and Belbruno was extended, and a new direct keto-enol route was found. A direct keto-enol mechanism catalyzed by formic acid seems to be the best explanation for the observed activation barrier and the pre-exponential factor of the decarboxylation of Δ 9-THC-acid. Evidence for this was found by performing an extraction experiment with Cannabis Flos. It revealed the presence of short chain carboxylic acids supporting this hypothesis. The presented approach is important for the development of a sustainable production of Δ 9-THC from the plant.
Electrical and kinetic model of an atmospheric rf device for plasma aerodynamics applications
Pinheiro, Mario J.; Martins, Alexandre A.
2010-08-15
The asymmetrically mounted flat plasma actuator is investigated using a self-consistent two-dimensional fluid model at atmospheric pressure. The computational model assumes the drift-diffusion approximation and uses a simple plasma kinetic model. It investigated the electrical and kinetic properties of the plasma, calculated the charged species concentrations, surface charge density, electrohydrodynamic forces, and gas speed. The present computational model contributes to understand the main physical mechanisms, and suggests ways to improve its performance.
NASA Astrophysics Data System (ADS)
Haustein, Karsten; King, James; Wiggs, Giles; Washington, Richard
2013-04-01
Dust emission schemes in climate models are relatively simple and are often tuned to represent observed background aerosol concentrations many of which are thousands of kilometres from source regions. Parameterisations of dust emission in numerical models were developed from idealised experiments such as those conducted in wind tunnels. Improvement of current model dust emission schemes has been difficult to achieve because of the paucity of observations from key dust sources. The Dust Observations for Models project (DO4Models) aims to gather data from source regions at a scale appropriate to climate model grid box resolution. Here we present the results of 1D box model simulations in which three commonly used parameterisations for the horizontal and vertical dust emission flux (Marticorena and Bergametti 1995, Alfaro and Gomez 2001, Shao et al. 2004) are applied and compared with Do4Models field campaign data retrieved over a typical salt pan dust source (Sua Pan, Botswana). The sensitivity of the schemes to input parameters such as soil moisture content, aerodynamic surface roughness length, shear velocity, soil texture class, and particle size is tested with particular regard to the representation of horizontal-to-vertical-mass-flux ratio. The effects of spatial averaging over 11 field sites is evaluated as is the average dust emission flux of a typical 12x12km model grid box. It is analysed whether the full range of surface processes (temporal changes in roughness, moisture, and soil conditions) is represented sufficiently well after averaging yet. Furthermore, the application of the dispersed soil size distribution on the performance of the emission schemes compared to the typically used undisturbed soil size distribution provided from soil databases is examined. Preliminary results suggest that the current schemes do not describe the observed emission process well. The scheme after Shao et al. (2004) provides the most accurate horizontal flux estimate so far
Modeling of hydrogen production methods: Single particle model and kinetics assessment
Miller, R.S.; Bellan, J.
1996-10-01
The investigation carried out by the Jet Propulsion Laboratory (JPL) is devoted to the modeling of biomass pyrolysis reactors producing an oil vapor (tar) which is a precursor to hydrogen. This is an informal collaboration with NREL whereby JPL uses the experimentally-generated NREL data both as initial and boundary conditions for the calculations, and as a benchmark for model validation. The goal of this investigation is to find drivers of biomass fast-pyrolysis in the low temperature regime. The rationale is that experimental observations produce sparse discrete conditions for model validation, and that numerical simulations produced with a validated model are an economic way to find control parameters and an optimal operation regime, thereby circumventing costly changes in hardware and tests. During this first year of the investigation, a detailed mathematical model has been formulated for the temporal and spatial accurate modeling of solid-fluid reactions in biomass particles. These are porous particles for which volumetric reaction rate data is known a priori and both the porosity and the permeability of the particle are large enough to allow for continuous gas phase flow. The methodology has been applied to the pyrolysis of spherically symmetric biomass particles by considering previously published kinetics schemes for both cellulose and wood. The results show that models which neglect the thermal and species boundary layers exterior to the particle will generally over predict both the pyrolysis rates and experimentally obtainable tar yields. An evaluation of the simulation results through comparisons with experimental data indicates that while the cellulose kinetics is reasonably accurate, the wood pyrolysis kinetics is not accurate; particularly at high reactor temperatures. Current effort in collaboration with NREL is aimed at finding accurate wood kinetics.
Kinetic modelling of RDF pyrolysis: Model-fitting and model-free approaches.
Çepelioğullar, Özge; Haykırı-Açma, Hanzade; Yaman, Serdar
2016-02-01
In this study, refuse derived fuel (RDF) was selected as solid fuel and it was pyrolyzed in a thermal analyzer from room temperature to 900°C at heating rates of 5, 10, 20, and 50°C/min in N2 atmosphere. The obtained thermal data was used to calculate the kinetic parameters using Coats-Redfern, Friedman, Flylnn-Wall-Ozawa (FWO) and Kissinger-Akahira-Sunose (KAS) methods. As a result of Coats-Redfern model, decomposition process was assumed to be four independent reactions with different reaction orders. On the other hand, model free methods demonstrated that activation energy trend had similarities for the reaction progresses of 0.1, 0.2-0.7 and 0.8-0.9. The average activation energies were found between 73-161kJ/mol and it is possible to say that FWO and KAS models produced closer results to the average activation energies compared to Friedman model. Experimental studies showed that RDF may be a sustainable and promising feedstock for alternative processes in terms of waste management strategies. PMID:26613830
Ryll, A; Bucher, J; Bonin, A; Bongard, S; Gonçalves, E; Saez-Rodriguez, J; Niklas, J; Klamt, S
2014-10-01
Systems biology has to increasingly cope with large- and multi-scale biological systems. Many successful in silico representations and simulations of various cellular modules proved mathematical modelling to be an important tool in gaining a solid understanding of biological phenomena. However, models spanning different functional layers (e.g. metabolism, signalling and gene regulation) are still scarce. Consequently, model integration methods capable of fusing different types of biological networks and various model formalisms become a key methodology to increase the scope of cellular processes covered by mathematical models. Here we propose a new integration approach to couple logical models of signalling or/and gene-regulatory networks with kinetic models of metabolic processes. The procedure ends up with an integrated dynamic mod