Materials Outgassing Rate Decay in Vacuum at Isothermal Conditions

NASA Technical Reports Server (NTRS)

Huang, Alvin Y.; Kastanas, George N.; Kramer, Leonard; Soares, Carlos E.; Mikatarian, Ronald R.

2016-01-01

As a laboratory for scientific research, the International Space Station has been in Low Earth Orbit for nearly 20 years and is expected to be on-orbit for another 10 years. The ISS has been maintaining a relatively pristine contamination environment for science payloads. Materials outgassing induced contamination is currently the dominant source for sensitive surfaces on ISS and modeling the outgassing rate decay over a 20 to 30 year period is challenging. Materials outgassing is described herein as a diffusion-reaction process using ASTM E 1559 rate data. The observation of -1/2 (diffusion) or non-integers (reaction limited) as rate decay exponents for common ISS materials indicate classical reaction kinetics is unsatisfactory in modeling materials outgassing. Non-randomness of reactant concentrations at the interface is the source of this deviation from classical reaction kinetics. A diffusion limited decay was adopted as the result of the correlation of the contaminant layer thicknesses on returned ISS hardware, the existence of high outgassing silicone exhibiting near diffusion limited decay, and the confirmation of non-depleted material after ten years in the Low Earth Orbit.Keywords: Materials Outgassing, ASTM E 1559, Reaction Kinetics, Diffusion, Space Environments Effects, Contamination

Classical Molecular Dynamics with Mobile Protons.

PubMed

Lazaridis, Themis; Hummer, Gerhard

2017-11-27

An important limitation of standard classical molecular dynamics simulations is the inability to make or break chemical bonds. This restricts severely our ability to study processes that involve even the simplest of chemical reactions, the transfer of a proton. Existing approaches for allowing proton transfer in the context of classical mechanics are rather cumbersome and have not achieved widespread use and routine status. Here we reconsider the combination of molecular dynamics with periodic stochastic proton hops. To ensure computational efficiency, we propose a non-Boltzmann acceptance criterion that is heuristically adjusted to maintain the correct or desirable thermodynamic equilibria between different protonation states and proton transfer rates. Parameters are proposed for hydronium, Asp, Glu, and His. The algorithm is implemented in the program CHARMM and tested on proton diffusion in bulk water and carbon nanotubes and on proton conductance in the gramicidin A channel. Using hopping parameters determined from proton diffusion in bulk water, the model reproduces the enhanced proton diffusivity in carbon nanotubes and gives a reasonable estimate of the proton conductance in gramicidin A.

Unveiling the Interplay Between Diffusing CO2 and Ethanol Molecules in Champagne Wines by Classical Molecular Dynamics and (13)C NMR Spectroscopy.

PubMed

Bonhommeau, David A; Perret, Alexandre; Nuzillard, Jean-Marc; Cilindre, Clara; Cours, Thibaud; Alijah, Alexander; Liger-Belair, Gérard

2014-12-18

The diffusion coefficients of carbon dioxide (CO2) and ethanol (EtOH) in carbonated hydroalcoholic solutions and Champagne wines are evaluated as a function of temperature by classical molecular dynamics (MD) simulations and (13)C NMR spectroscopy measurements. The excellent agreement between theoretical and experimental diffusion coefficients suggest that ethanol is the main molecule, apart from water, responsible for the value of the CO2 diffusion coefficients in typical Champagne wines, a result that could likely be extended to most sparkling wines with alike ethanol concentrations. CO2 and EtOH hydrodynamical radii deduced from viscometry measurements by applying the Stokes-Einstein relationship are found to be mostly constant and in close agreement with MD predictions. The reliability of our approach should be of interest to physical chemists aiming to model transport phenomena in supersaturated aqueous solutions or water/alcohol mixtures.

Emergence of a Stern Layer from the Incorporation of Hydration Interactions into the Gouy-Chapman Model of the Electrical Double Layer.

PubMed

Brown, Matthew A; Bossa, Guilherme Volpe; May, Sylvio

2015-10-27

In one of the most commonly used phenomenological descriptions of the electrical double layer, a charged solid surface and a diffuse region of mobile ions are separated from each other by a thin charge-depleted Stern layer. The Stern layer acts as a capacitor that improves the classical Gouy-Chapman model by increasing the magnitude of the surface potential and limiting the maximal counterion concentration. We show that very similar Stern-like properties of the diffuse double layer emerge naturally from adding a nonelectrostatic hydration repulsion to the electrostatic Coulomb potential. The interplay of electrostatic attraction and hydration repulsion of the counterions and the surface leads to the formation of a diffuse counterion layer that remains well separated from the surface. In addition, hydration repulsions between the ions limit and control the maximal ion concentration and widen the width of the diffuse double layer. Our mean-field model, which we express in terms of electrostatic and hydration potentials, is physically consistent and conceptually similar to the classical Gouy-Chapman model. It allows the incorporation of ion specificity, accounts for hydration properties of charged surfaces, and predicts Stern layer properties, which we analyze in terms of the effective size of the hydrated counterions.

Instability of turing patterns in reaction-diffusion-ODE systems.

PubMed

Marciniak-Czochra, Anna; Karch, Grzegorz; Suzuki, Kanako

2017-02-01

The aim of this paper is to contribute to the understanding of the pattern formation phenomenon in reaction-diffusion equations coupled with ordinary differential equations. Such systems of equations arise, for example, from modeling of interactions between cellular processes such as cell growth, differentiation or transformation and diffusing signaling factors. We focus on stability analysis of solutions of a prototype model consisting of a single reaction-diffusion equation coupled to an ordinary differential equation. We show that such systems are very different from classical reaction-diffusion models. They exhibit diffusion-driven instability (turing instability) under a condition of autocatalysis of non-diffusing component. However, the same mechanism which destabilizes constant solutions of such models, destabilizes also all continuous spatially heterogeneous stationary solutions, and consequently, there exist no stable Turing patterns in such reaction-diffusion-ODE systems. We provide a rigorous result on the nonlinear instability, which involves the analysis of a continuous spectrum of a linear operator induced by the lack of diffusion in the destabilizing equation. These results are extended to discontinuous patterns for a class of nonlinearities.

Particle Transport through Scattering Regions with Clear Layers and Inclusions

NASA Astrophysics Data System (ADS)

Bal, Guillaume

2002-08-01

This paper introduces generalized diffusion models for the transport of particles in scattering media with nonscattering inclusions. Classical diffusion is known as a good approximation of transport only in scattering media. Based on asymptotic expansions and the coupling of transport and diffusion models, generalized diffusion equations with nonlocal interface conditions are proposed which offer a computationally cheap, yet accurate, alternative to solving the full phase-space transport equations. The paper shows which computational model should be used depending on the size and shape of the nonscattering inclusions in the simplified setting of two space dimensions. An important application is the treatment of clear layers in near-infrared (NIR) spectroscopy, an imaging technique based on the propagation of NIR photons in human tissues.

Advanced diffusion MRI and biomarkers in the central nervous system: a new approach.

PubMed

Martín Noguerol, T; Martínez Barbero, J P

The introduction of diffusion-weighted sequences has revolutionized the detection and characterization of central nervous system (CNS) disease. Nevertheless, the assessment of diffusion studies of the CNS is often limited to qualitative estimation. Moreover, the pathophysiological complexity of the different entities that affect the CNS cannot always be correctly explained through classical models. The development of new models for the analysis of diffusion sequences provides numerous parameters that enable a quantitative approach to both diagnosis and prognosis as well as to monitoring the response to treatment; these parameters can be considered potential biomarkers of health and disease. In this update, we review the physical bases underlying diffusion studies and diffusion tensor imaging, advanced models for their analysis (intravoxel coherent motion and kurtosis), and the biological significance of the parameters derived. Copyright © 2017 SERAM. Publicado por Elsevier España, S.L.U. All rights reserved.

Turing pattern dynamics and adaptive discretization for a super-diffusive Lotka-Volterra model.

PubMed

Bendahmane, Mostafa; Ruiz-Baier, Ricardo; Tian, Canrong

2016-05-01

In this paper we analyze the effects of introducing the fractional-in-space operator into a Lotka-Volterra competitive model describing population super-diffusion. First, we study how cross super-diffusion influences the formation of spatial patterns: a linear stability analysis is carried out, showing that cross super-diffusion triggers Turing instabilities, whereas classical (self) super-diffusion does not. In addition we perform a weakly nonlinear analysis yielding a system of amplitude equations, whose study shows the stability of Turing steady states. A second goal of this contribution is to propose a fully adaptive multiresolution finite volume method that employs shifted Grünwald gradient approximations, and which is tailored for a larger class of systems involving fractional diffusion operators. The scheme is aimed at efficient dynamic mesh adaptation and substantial savings in computational burden. A numerical simulation of the model was performed near the instability boundaries, confirming the behavior predicted by our analysis.

A Simulation Tool for Dynamic Contrast Enhanced MRI

PubMed Central

Mauconduit, Franck; Christen, Thomas; Barbier, Emmanuel Luc

2013-01-01

The quantification of bolus-tracking MRI techniques remains challenging. The acquisition usually relies on one contrast and the analysis on a simplified model of the various phenomena that arise within a voxel, leading to inaccurate perfusion estimates. To evaluate how simplifications in the interstitial model impact perfusion estimates, we propose a numerical tool to simulate the MR signal provided by a dynamic contrast enhanced (DCE) MRI experiment. Our model encompasses the intrinsic and relaxations, the magnetic field perturbations induced by susceptibility interfaces (vessels and cells), the diffusion of the water protons, the blood flow, the permeability of the vessel wall to the the contrast agent (CA) and the constrained diffusion of the CA within the voxel. The blood compartment is modeled as a uniform compartment. The different blocks of the simulation are validated and compared to classical models. The impact of the CA diffusivity on the permeability and blood volume estimates is evaluated. Simulations demonstrate that the CA diffusivity slightly impacts the permeability estimates ( for classical blood flow and CA diffusion). The effect of long echo times is investigated. Simulations show that DCE-MRI performed with an echo time may already lead to significant underestimation of the blood volume (up to 30% lower for brain tumor permeability values). The potential and the versatility of the proposed implementation are evaluated by running the simulation with realistic vascular geometry obtained from two photons microscopy and with impermeable cells in the extravascular environment. In conclusion, the proposed simulation tool describes DCE-MRI experiments and may be used to evaluate and optimize acquisition and processing strategies. PMID:23516414

Nucleation of Organic Molecules via a Hot Precursor State: Pentacene on Amorphous Mica

PubMed Central

2013-01-01

Organic thin films have attracted considerable interest due to their applicability in organic electronics. The classical scenario for thin film nucleation is the diffusion-limited aggregation (DLA). Recently, it has been shown that organic thin film growth is better described by attachment-limited aggregation (ALA). However, in both cases, an unusual relationship between the island density and the substrate temperature was observed. Here, we present an aggregation model that goes beyond the classical DLA or ALA models to explain this behavior. We propose that the (hot) molecules impinging on the surface cannot immediately equilibrate to the substrate temperature but remain in a hot precursor state. In this state, the molecules can migrate considerable distances before attaching to a stable or unstable island. This results in a significantly smaller island density than expected by assuming fast equilibration and random diffusion. We have applied our model to pentacene film growth on amorphous Muscovite mica. PMID:24340130

Exact Markov chain and approximate diffusion solution for haploid genetic drift with one-way mutation.

PubMed

Hössjer, Ola; Tyvand, Peder A; Miloh, Touvia

2016-02-01

The classical Kimura solution of the diffusion equation is investigated for a haploid random mating (Wright-Fisher) model, with one-way mutations and initial-value specified by the founder population. The validity of the transient diffusion solution is checked by exact Markov chain computations, using a Jordan decomposition of the transition matrix. The conclusion is that the one-way diffusion model mostly works well, although the rate of convergence depends on the initial allele frequency and the mutation rate. The diffusion approximation is poor for mutation rates so low that the non-fixation boundary is regular. When this happens we perturb the diffusion solution around the non-fixation boundary and obtain a more accurate approximation that takes quasi-fixation of the mutant allele into account. The main application is to quantify how fast a specific genetic variant of the infinite alleles model is lost. We also discuss extensions of the quasi-fixation approach to other models with small mutation rates. Copyright © 2015 Elsevier Inc. All rights reserved.

Including scattering within the room acoustics diffusion model: An analytical approach.

PubMed

Foy, Cédric; Picaut, Judicaël; Valeau, Vincent

2016-10-01

Over the last 20 years, a statistical acoustic model has been developed to predict the reverberant sound field in buildings. This model is based on the assumption that the propagation of the reverberant sound field follows a transport process and, as an approximation, a diffusion process that can be easily solved numerically. This model, initially designed and validated for rooms with purely diffuse reflections, is extended in the present study to mixed reflections, with a proportion of specular and diffuse reflections defined by a scattering coefficient. The proposed mathematical developments lead to an analytical expression of the diffusion constant that is a function of the scattering coefficient, but also on the absorption coefficient of the walls. The results obtained with this extended diffusion model are then compared with the classical diffusion model, as well as with a sound particles tracing approach considering mixed wall reflections. The comparison shows a good agreement for long rooms with uniform low absorption (α = 0.01) and uniform scattering. For a larger absorption (α = 0.1), the agreement is moderate, due to the fact that the proposed expression of the diffusion coefficient does not vary spatially. In addition, the proposed model is for now limited to uniform diffusion and should be extended in the future to more general cases.

Bounded diffusion impedance characterization of battery electrodes using fractional modeling

NASA Astrophysics Data System (ADS)

Gabano, Jean-Denis; Poinot, Thierry; Huard, Benoît

2017-06-01

This article deals with the ability of fractional modeling to describe the bounded diffusion behavior encountered in modern thin film and nanoparticles lithium battery electrodes. Indeed, the diffusion impedance of such batteries behaves as a half order integrator characterized by the Warburg impedance at high frequencies and becomes a classical integrator described by a capacitor at low frequencies. The transition between these two behaviors depends on the particles geometry. Three of them will be considered in this paper: planar, cylindrical and spherical ones. The fractional representation proposed is a gray box model able to perfectly fit the low and high frequency diffusive impedance behaviors while optimizing the frequency response transition. Identification results are provided using frequential simulation data considering the three electrochemical diffusion models based on the particles geometry. Furthermore, knowing this geometry allows to estimate the diffusion ionic resistance and time constant using the relationships linking these physical parameters to the structural fractional model parameters. Finally, other simulations using Randles impedance models including the charge transfer impedance and the external resistance demonstrate the interest of fractional modeling in order to identify properly not only the charge transfer impedance but also the diffusion physical parameters whatever the particles geometry.

[Diffusion and diffusion-osmosis models of the charged macromolecule transfer in barriers of biosystems].

PubMed

Varakin, A I; Mazur, V V; Arkhipova, N V; Serianov, Iu V

2009-01-01

Mathematical models of the transfer of charged macromolecules have been constructed on the basis of the classical equations of electromigration diffusion of Helmholtz-Smolukhovskii, Goldman, and Goldman-Hodgkin-Katz. It was shown that ion transfer in placental (mimicking lipid-protein barriers) and muscle barriers occurs by different mechanisms. In placental barriers, the electromigration diffusion occurs along lipid-protein channels formed due to the conformational deformation of phospholipid and protein molecules with the coefficients of diffusion D = (2.6-3.6) x 10(-8) cm2/s. The transfer in muscle barriers is due to the migration across charged interfibrillar channels with the negative diffusion activation energy, which is explained by changes in the structure of muscle fibers and expenditures of thermal energy for the extrusion of Cl- from channel walls with the diffusion coefficient D = (6.0-10.0) x 10(-6) cm2/s.

A Hele-Shaw-Cahn-Hilliard Model for Incompressible Two-Phase Flows with Different Densities

NASA Astrophysics Data System (ADS)

Dedè, Luca; Garcke, Harald; Lam, Kei Fong

2017-07-01

Topology changes in multi-phase fluid flows are difficult to model within a traditional sharp interface theory. Diffuse interface models turn out to be an attractive alternative to model two-phase flows. Based on a Cahn-Hilliard-Navier-Stokes model introduced by Abels et al. (Math Models Methods Appl Sci 22(3):1150013, 2012), which uses a volume-averaged velocity, we derive a diffuse interface model in a Hele-Shaw geometry, which in the case of non-matched densities, simplifies an earlier model of Lee et al. (Phys Fluids 14(2):514-545, 2002). We recover the classical Hele-Shaw model as a sharp interface limit of the diffuse interface model. Furthermore, we show the existence of weak solutions and present several numerical computations including situations with rising bubbles and fingering instabilities.

Explicit spatiotemporal simulation of receptor-G protein coupling in rod cell disk membranes.

PubMed

Schöneberg, Johannes; Heck, Martin; Hofmann, Klaus Peter; Noé, Frank

2014-09-02

Dim-light vision is mediated by retinal rod cells. Rhodopsin (R), a G-protein-coupled receptor, switches to its active form (R(∗)) in response to absorbing a single photon and activates multiple copies of the G-protein transducin (G) that trigger further downstream reactions of the phototransduction cascade. The classical assumption is that R and G are uniformly distributed and freely diffusing on disk membranes. Recent experimental findings have challenged this view by showing specific R architectures, including RG precomplexes, nonuniform R density, specific R arrangements, and immobile fractions of R. Here, we derive a physical model that describes the first steps of the photoactivation cascade in spatiotemporal detail and single-molecule resolution. The model was implemented in the ReaDDy software for particle-based reaction-diffusion simulations. Detailed kinetic in vitro experiments are used to parametrize the reaction rates and diffusion constants of R and G. Particle diffusion and G activation are then studied under different conditions of R-R interaction. It is found that the classical free-diffusion model is consistent with the available kinetic data. The existence of precomplexes between inactive R and G is only consistent with the data if these precomplexes are weak, with much larger dissociation rates than suggested elsewhere. Microarchitectures of R, such as dimer racks, would effectively immobilize R but have little impact on the diffusivity of G and on the overall amplification of the cascade at the level of the G protein. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Spike solutions in Gierer#x2013;Meinhardt model with a time dependent anomaly exponent

NASA Astrophysics Data System (ADS)

Nec, Yana

2018-01-01

Experimental evidence of complex dispersion regimes in natural systems, where the growth of the mean square displacement in time cannot be characterised by a single power, has been accruing for the past two decades. In such processes the exponent γ(t) in ⟨r2⟩ ∼ tγ(t) at times might be approximated by a piecewise constant function, or it can be a continuous function. Variable order differential equations are an emerging mathematical tool with a strong potential to model these systems. However, variable order differential equations are not tractable by the classic differential equations theory. This contribution illustrates how a classic method can be adapted to gain insight into a system of this type. Herein a variable order Gierer-Meinhardt model is posed, a generic reaction- diffusion system of a chemical origin. With a fixed order this system possesses a solution in the form of a constellation of arbitrarily situated localised pulses, when the components' diffusivity ratio is asymptotically small. The pattern was shown to exist subject to multiple step-like transitions between normal diffusion and sub-diffusion, as well as between distinct sub-diffusive regimes. The analytical approximation obtained permits qualitative analysis of the impact thereof. Numerical solution for typical cross-over scenarios revealed such features as earlier equilibration and non-monotonic excursions before attainment of equilibrium. The method is general and allows for an approximate numerical solution with any reasonably behaved γ(t).

Fractional Diffusion Analysis of the Electromagnetic Field In Fractured Media Part II: 2.5-D Approach

NASA Astrophysics Data System (ADS)

Ge, J.; Everett, M. E.; Weiss, C. J.

2012-12-01

A 2.5D finite difference (FD) frequency-domain modeling algorithm based on the theory of fractional diffusion of electromagnetic (EM) fields generated by a loop source lying above a fractured geological medium is addressed in this paper. The presence of fractures in the subsurface, usually containing highly conductive pore fluids, gives rise to spatially hierarchical flow paths of induced EM eddy currents. The diffusion of EM eddy currents in such formations is anomalous, generalizing the classical Gaussian process described by the conventional Maxwell equations. Based on the continuous time random walk (CTRW) theory, the diffusion of EM eddy currents in a rough medium is governed by the fractional Maxwell equations. Here, we model the EM response of a 2D subsurface containing fractured zones, with a 3D loop source, which results the so-called 2.5D model geometry. The governing equation in the frequency domain is converted using Fourier transform into k domain along the strike direction (along which the model conductivity doesn't vary). The resulting equation system is solved by the multifrontal massively parallel solver (MUMPS). The data obtained is then converted back to spatial domain and the time domain. We find excellent agreement between the FD and analytic solutions for a rough halfspace model. Then FD solutions are calculated for a 2D fault zone model with variable conductivity and roughness. We compare the results with responses from several classical models and explore the relationship between the roughness and the spatial density of the fracture distribution.

Diffusion and related transport mechanisms in brain tissue

NASA Astrophysics Data System (ADS)

Nicholson, Charles

2001-07-01

Diffusion plays a crucial role in brain function. The spaces between cells can be likened to the water phase of a foam and many substances move within this complicated region. Diffusion in this interstitial space can be accurately modelled with appropriate modifications of classical equations and quantified from measurements based on novel micro-techniques. Besides delivering glucose and oxygen from the vascular system to brain cells, diffusion also moves informational substances between cells, a process known as volume transmission. Deviations from expected results reveal how local uptake, degradation or bulk flow may modify the transport of molecules. Diffusion is also essential to many therapies that deliver drugs to the brain. The diffusion-generated concentration distributions of well-chosen molecules also reveal the structure of brain tissue. This structure is represented by the volume fraction (void space) and the tortuosity (hindrance to diffusion imposed by local boundaries or local viscosity). Analysis of these parameters also reveals how the local geometry of the brain changes with time or under pathological conditions. Theoretical and experimental approaches borrow from classical diffusion theory and from porous media concepts. Earlier studies were based on radiotracers but the recent methods use a point-source paradigm coupled with micro-sensors or optical imaging of macromolecules labelled with fluorescent tags. These concepts and methods are likely to be applicable elsewhere to measure diffusion properties in very small volumes of highly structured but delicate material.

Fractional derivatives in the diffusion process in heterogeneous systems: The case of transdermal patches.

PubMed

Caputo, Michele; Cametti, Cesare

2017-09-01

In this note, we present a simple mathematical model of drug delivery through transdermal patches by introducing a memory formalism in the classical Fick diffusion equation based on the fractional derivative. This approach is developed in the case of a medicated adhesive patch placed on the skin to deliver a time released dose of medication through the skin towards the bloodstream.The main resistance to drug transport across the skin resides in the diffusion through its outermost layer (the stratum corneum). Due to the complicated architecture of this region, a model based on a constant diffusivity in a steady-state condition results in too simplistic assumptions and more refined models are required.The introduction of a memory formalism in the diffusion process, where diffusion parameters depend at a certain time or position on what happens at preceeding times, meets this requirement and allows a significantly better description of the experimental results.The present model may be useful not only for analyzing the rate of skin permeation but also for predicting the drug concentration after transdermal drug delivery depending on the diffusion characteristics of the patch (its thickness and pseudo-diffusion coefficient). Copyright © 2017 Elsevier Inc. All rights reserved.

The Fisher-KPP problem with doubly nonlinear diffusion

NASA Astrophysics Data System (ADS)

Audrito, Alessandro; Vázquez, Juan Luis

2017-12-01

The famous Fisher-KPP reaction-diffusion model combines linear diffusion with the typical KPP reaction term, and appears in a number of relevant applications in biology and chemistry. It is remarkable as a mathematical model since it possesses a family of travelling waves that describe the asymptotic behaviour of a large class solutions 0 ≤ u (x , t) ≤ 1 of the problem posed in the real line. The existence of propagation waves with finite speed has been confirmed in some related models and disproved in others. We investigate here the corresponding theory when the linear diffusion is replaced by the "slow" doubly nonlinear diffusion and we find travelling waves that represent the wave propagation of more general solutions even when we extend the study to several space dimensions. A similar study is performed in the critical case that we call "pseudo-linear", i.e., when the operator is still nonlinear but has homogeneity one. With respect to the classical model and the "pseudo-linear" case, the "slow" travelling waves exhibit free boundaries.

Theory of Neutron Chain Reactions: Extracts from Volume I, Diffusion and Slowing Down of Neutrons: Chapter I. Elementary Theory of Neutron Diffusion. Chapter II. Second Order Diffusion Theory. Chapter III. Slowing Down of Neutrons

DOE R&D Accomplishments Database

Weinberg, Alvin M.; Noderer, L. C.

1951-05-15

The large scale release of nuclear energy in a uranium fission chain reaction involves two essentially distinct physical phenomena. On the one hand there are the individual nuclear processes such as fission, neutron capture, and neutron scattering. These are essentially quantum mechanical in character, and their theory is non-classical. On the other hand, there is the process of diffusion -- in particular, diffusion of neutrons, which is of fundamental importance in a nuclear chain reaction. This process is classical; insofar as the theory of the nuclear chain reaction depends on the theory of neutron diffusion, the mathematical study of chain reactions is an application of classical, not quantum mechanical, techniques.

Discovering the influential users oriented to viral marketing based on online social networks

NASA Astrophysics Data System (ADS)

Zhu, Zhiguo

2013-08-01

The target of viral marketing on the platform of popular online social networks is to rapidly propagate marketing information at lower cost and increase sales, in which a key problem is how to precisely discover the most influential users in the process of information diffusion. A novel method is proposed in this paper for helping companies to identify such users as seeds to maximize information diffusion in the viral marketing. Firstly, the user trust network oriented to viral marketing and users’ combined interest degree in the network including isolated users are extensively defined. Next, we construct a model considering the time factor to simulate the process of information diffusion in viral marketing and propose a dynamic algorithm description. Finally, experiments are conducted with a real dataset extracted from the famous SNS website Epinions. The experimental results indicate that the proposed algorithm has better scalability and is less time-consuming. Compared with the classical model, the proposed algorithm achieved a better performance than does the classical method on the two aspects of network coverage rate and time-consumption in our four sub-datasets.

Onset of fractional-order thermal convection in porous media

NASA Astrophysics Data System (ADS)

Karani, Hamid; Rashtbehesht, Majid; Huber, Christian; Magin, Richard L.

2017-12-01

The macroscopic description of buoyancy-driven thermal convection in porous media is governed by advection-diffusion processes, which in the presence of thermophysical heterogeneities fail to predict the onset of thermal convection and the average rate of heat transfer. This work extends the classical model of heat transfer in porous media by including a fractional-order advective-dispersive term to account for the role of thermophysical heterogeneities in shifting the thermal instability point. The proposed fractional-order model overcomes limitations of the common closure approaches for the thermal dispersion term by replacing the diffusive assumption with a fractional-order model. Through a linear stability analysis and Galerkin procedure, we derive an analytical formula for the critical Rayleigh number as a function of the fractional model parameters. The resulting critical Rayleigh number reduces to the classical value in the absence of thermophysical heterogeneities when solid and fluid phases have similar thermal conductivities. Numerical simulations of the coupled flow equation with the fractional-order energy model near the primary bifurcation point confirm our analytical results. Moreover, data from pore-scale simulations are used to examine the potential of the proposed fractional-order model in predicting the amount of heat transfer across the porous enclosure. The linear stability and numerical results show that, unlike the classical thermal advection-dispersion models, the fractional-order model captures the advance and delay in the onset of convection in porous media and provides correct scalings for the average heat transfer in a thermophysically heterogeneous medium.

On the anisotropic advection-diffusion equation with time dependent coefficients

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

Hernandez-Coronado, Hector; Coronado, Manuel; Del-Castillo-Negrete, Diego B.

The advection-diffusion equation with time dependent velocity and anisotropic time dependent diffusion tensor is examined in regard to its non-classical transport features and to the use of a non-orthogonal coordinate system. Although this equation appears in diverse physical problems, particularly in particle transport in stochastic velocity fields and in underground porous media, a detailed analysis of its solutions is lacking. In order to study the effects of the time-dependent coefficients and the anisotropic diffusion on transport, we solve analytically the equation for an initial Dirac delta pulse. Here, we discuss the solutions to three cases: one based on power-law correlationmore » functions where the pulse diffuses faster than the classical rate ~t, a second case specically designed to display slower rate of diffusion than the classical one, and a third case to describe hydrodynamic dispersion in porous media« less

On the anisotropic advection-diffusion equation with time dependent coefficients

DOE PAGES

Hernandez-Coronado, Hector; Coronado, Manuel; Del-Castillo-Negrete, Diego B.

2017-02-01

The advection-diffusion equation with time dependent velocity and anisotropic time dependent diffusion tensor is examined in regard to its non-classical transport features and to the use of a non-orthogonal coordinate system. Although this equation appears in diverse physical problems, particularly in particle transport in stochastic velocity fields and in underground porous media, a detailed analysis of its solutions is lacking. In order to study the effects of the time-dependent coefficients and the anisotropic diffusion on transport, we solve analytically the equation for an initial Dirac delta pulse. Here, we discuss the solutions to three cases: one based on power-law correlationmore » functions where the pulse diffuses faster than the classical rate ~t, a second case specically designed to display slower rate of diffusion than the classical one, and a third case to describe hydrodynamic dispersion in porous media« less

Second law of thermodynamics in volume diffusion hydrodynamics in multicomponent gas mixtures

NASA Astrophysics Data System (ADS)

Dadzie, S. Kokou

2012-10-01

We presented the thermodynamic structure of a new continuum flow model for multicomponent gas mixtures. The continuum model is based on a volume diffusion concept involving specific species. It is independent of the observer's reference frame and enables a straightforward tracking of a selected species within a mixture composed of a large number of constituents. A method to derive the second law and constitutive equations accompanying the model is presented. Using the configuration of a rotating fluid we illustrated an example of non-classical flow physics predicted by new contributions in the entropy and constitutive equations.

Macro and micro analysis of small molecule diffusion in amorphous polymers

NASA Astrophysics Data System (ADS)

Putta, Santosh Krishna

In this study, both macroscopic and microscopic numerical techniques have been explored, to model and understand the diffusion behavior of small molecules in amorphous polymers, which very often do not follow the classical Fickian law. It was attempted to understand the influence of various aspects of the molecular structure of a polymer on its macroscopic diffusion behavior. At the macroscopic level, a hybrid finite-element/finite-difference model is developed to implement the coupled diffusion and deformation constitutive equations. A viscoelasticity theory, combined with time-freevolume superposition is used to model the deformation processes. A freevolume-based model is used to model the diffusion processes. The freevolume in the polymer is used as a coupling factor between the deformation and the diffusion processes. The model is shown to qualitatively describe some of the typical non-Fickian diffusion behavior in polymers. However, it does not directly involve the microstructure of a polymer. Further, some of the input parameters to the model are difficult to obtain experimentally. A numerical microscopic approach is therefore adopted to study the molecular structure of polymers. A molecular mechanics and dynamics technique combined with a modified Rotational Isomeric State (RIS) approach, is followed to generate the molecular structure for two types of polycarbonates, and, two types of polyacrylates, starting only with their chemical structures. A new efficient 3-D algorithm for Delaunay Tessellation is developed, and, then applied to discretize the molecular structure into Delaunay Tetrahedra. By using the dicretized molecular structure, size, shape, and, connectivity of free-spaces for small molecule diffusion in the above mentioned polymers, are then studied in relation to their diffusion properties. The influence of polymer and side chain flexibility, and diffusant-diffusant and diffusant-polymer molecular interactions, is also discussed with respect to the diffusion properties.

Does the Sverdrup critical depth model explain bloom dynamics in estuaries?

USGS Publications Warehouse

Lucas, L.V.; Cloern, J.E.; Koseff, Jeffrey R.; Monismith, Stephen G.; Thompson, J.K.

1998-01-01

In this paper we use numerical models of coupled biological-hydrodynamic processes to search for general principles of bloom regulation in estuarine waters. We address three questions: what are the dynamics of stratification in coastal systems as influenced by variable freshwater input and tidal stirring? How does phytoplankton growth respond to these dynamics? Can the classical Sverdrup Critical Depth Model (SCDM) be used to predict the timing of bloom events in shallow coastal domains such as estuaries? We present results of simulation experiments which assume that vertical transport and net phytoplankton growth rates are horizontally homogeneous. In the present approach the temporally and spatially varying turbulent diffusivities for various stratification scenarios are calculated using a hydrodynamic code that includes the Mellor-Yamada 2.5 turbulence closure model. These diffusivities are then used in a time- and depth-dependent advection-diffusion equation, incorporating sources and sinks, for the phytoplankton biomass. Our modeling results show that, whereas persistent stratification greatly increases the probability of a bloom, semidiurnal periodic stratification does not increase the likelihood of a phytoplankton bloom over that of a constantly unstratified water column. Thus, for phytoplankton blooms, the physical regime of periodic stratification is closer to complete mixing than to persistent stratification. Furthermore, the details of persistent stratification are important: surface layer depth, thickness of the pycnocline, vertical density difference, and tidal current speed all weigh heavily in producing conditions which promote the onset of phytoplankton blooms. Our model results for shallow tidal systems do not conform to the classical concepts of stratification and blooms in deep pelagic systems. First, earlier studies (Riley, 1942, for example) suggest a monotonic increase in surface layer production as the surface layer shallows. Our model results suggest, however, a nonmonotonic relationship between phytoplankton population growth and surface layer depth, which results from a balance between several 'competing' processes, including the interaction of sinking with turbulent mixing and average net growth occurring within the surface layer. Second, we show that the traditional SCDM must be refined for application to energetic shallow systems or for systems in which surface layer mixing is not strong enough to counteract the sinking loss of phytoplankton. This need for refinement arises because of the leakage of phytoplankton from the surface layer by turbulent diffusion and sinking, processes not considered in the classical SCDM. Our model shows that, even for low sinking rates and small turbulent diffusivities, a significant % of the phytoplankton biomass produced in the surface layer can be lost by these processes.

Quantum fluctuations increase the self-diffusive motion of para-hydrogen in narrow carbon nanotubes.

PubMed

Kowalczyk, Piotr; Gauden, Piotr A; Terzyk, Artur P; Furmaniak, Sylwester

2011-05-28

Quantum fluctuations significantly increase the self-diffusive motion of para-hydrogen adsorbed in narrow carbon nanotubes at 30 K comparing to its classical counterpart. Rigorous Feynman's path integral calculations reveal that self-diffusive motion of para-hydrogen in a narrow (6,6) carbon nanotube at 30 K and pore densities below ∼29 mmol cm(-3) is one order of magnitude faster than the classical counterpart. We find that the zero-point energy and tunneling significantly smoothed out the free energy landscape of para-hydrogen molecules adsorbed in a narrow (6,6) carbon nanotube. This promotes a delocalization of the confined para-hydrogen at 30 K (i.e., population of unclassical paths due to quantum effects). Contrary the self-diffusive motion of classical para-hydrogen molecules in a narrow (6,6) carbon nanotube at 30 K is very slow. This is because classical para-hydrogen molecules undergo highly correlated movement when their collision diameter approached the carbon nanotube size (i.e., anomalous diffusion in quasi-one dimensional pores). On the basis of current results we predict that narrow single-walled carbon nanotubes are promising nanoporous molecular sieves being able to separate para-hydrogen molecules from mixtures of classical particles at cryogenic temperatures. This journal is © the Owner Societies 2011

A fast semi-discrete Kansa method to solve the two-dimensional spatiotemporal fractional diffusion equation

NASA Astrophysics Data System (ADS)

Sun, HongGuang; Liu, Xiaoting; Zhang, Yong; Pang, Guofei; Garrard, Rhiannon

2017-09-01

Fractional-order diffusion equations (FDEs) extend classical diffusion equations by quantifying anomalous diffusion frequently observed in heterogeneous media. Real-world diffusion can be multi-dimensional, requiring efficient numerical solvers that can handle long-term memory embedded in mass transport. To address this challenge, a semi-discrete Kansa method is developed to approximate the two-dimensional spatiotemporal FDE, where the Kansa approach first discretizes the FDE, then the Gauss-Jacobi quadrature rule solves the corresponding matrix, and finally the Mittag-Leffler function provides an analytical solution for the resultant time-fractional ordinary differential equation. Numerical experiments are then conducted to check how the accuracy and convergence rate of the numerical solution are affected by the distribution mode and number of spatial discretization nodes. Applications further show that the numerical method can efficiently solve two-dimensional spatiotemporal FDE models with either a continuous or discrete mixing measure. Hence this study provides an efficient and fast computational method for modeling super-diffusive, sub-diffusive, and mixed diffusive processes in large, two-dimensional domains with irregular shapes.

Mechanism of anisotropic surface self-diffusivity at the prismatic ice-vapor interface.

PubMed

Gladich, Ivan; Oswald, Amrei; Bowens, Natalie; Naatz, Sam; Rowe, Penny; Roeselova, Martina; Neshyba, Steven

2015-09-21

Predictive theoretical models for mesoscopic roughening of ice require improved understanding of attachment kinetics occurring at the ice-vapor interface. Here, we use classical molecular dynamics to explore the generality and mechanics of a transition from anisotropic to isotropic self-diffusivity on exposed prismatic surfaces. We find that self-diffusion parallel to the crystallographic a-axis is favored over the c-axis at sub-melt temperatures below about -35 °C, for three different representations of the water-water intermolecular potential. In the low-temperature anisotropic regime, diffusion results from interstitial admolecules encountering entropically distinct barriers to diffusion in the two in-plane directions. At higher temperatures, isotropic self-diffusion occurring deeper within the quasi-liquid layer becomes the dominant mechanism, owing to its larger energy of activation.

Materials outgassing rate decay in vacuum at isothermal conditions

NASA Astrophysics Data System (ADS)

Huang, Alvin Y.; Kastanas, George N.; Kramer, Leonard; Soares, Carlos E.; Mikatarian, Ronald R.

2016-09-01

As a laboratory for scientific research, the International Space Station has been in Low Earth Orbit for over 17 years and is planned to be on-orbit for another 10 years. The ISS has been maintaining a relatively pristine contamination environment for science payloads. Materials outgassing induced contamination is currently the dominant source for sensitive surfaces on ISS and modelling the outgassing rate decay over a 20 to 30 year period is challenging. Using ASTM E 1559 rate data, materials outgassing is described herein as a diffusion-reaction process with the interface playing a key role. The observation of -1/2 (diffusion) or non-integers (reaction limited) as rate decay exponents for common ISS materials indicate classical reaction kinetics is unsatisfactory in modelling materials outgassing. Nonrandomness of reactant concentrations at the interface is the source of this deviation from classical reaction kinetics. A t-1/2 decay is adopted as the result of the correlation of the contaminant layer thicknesses and composition on returned ISS hardware, the existence of high outgassing silicone exhibiting near diffusion limited decay, the confirmation of nondepleted material after ten years in Low Earth Orbit, and a potential slowdown of long term materials outgassing kinetics due to silicone contaminants at the interface.

Zubarev's Nonequilibrium Statistical Operator Method in the Generalized Statistics of Multiparticle Systems

NASA Astrophysics Data System (ADS)

Glushak, P. A.; Markiv, B. B.; Tokarchuk, M. V.

2018-01-01

We present a generalization of Zubarev's nonequilibrium statistical operator method based on the principle of maximum Renyi entropy. In the framework of this approach, we obtain transport equations for the basic set of parameters of the reduced description of nonequilibrium processes in a classical system of interacting particles using Liouville equations with fractional derivatives. For a classical systems of particles in a medium with a fractal structure, we obtain a non-Markovian diffusion equation with fractional spatial derivatives. For a concrete model of the frequency dependence of a memory function, we obtain generalized Kettano-type diffusion equation with the spatial and temporal fractality taken into account. We present a generalization of nonequilibrium thermofield dynamics in Zubarev's nonequilibrium statistical operator method in the framework of Renyi statistics.

Effects of degeneracy and response function in a diffusion predator-prey model

NASA Astrophysics Data System (ADS)

Li, Shanbing; Wu, Jianhua; Dong, Yaying

2018-04-01

In this paper, we consider positive solutions of a diffusion predator-prey model with a degeneracy under the Dirichlet boundary conditions. We first obtain sufficient conditions of the existence of positive solutions by the Leray-Schauder degree theory, and then analyze the limiting behavior of positive solutions as the growth rate of the predator goes to infinity and the conversion rates of the predator goes to zero, respectively. It is shown that these results for Holling II response function (i.e. m  >  0) reveal interesting contrast with that for the classical Lotka-Volterra predator-prey model (i.e. m  =  0).

Ab Initio Calculations of Transport in Titanium and Aluminum Mixtures

NASA Astrophysics Data System (ADS)

Walker, Nicholas; Novak, Brian; Tam, Ka Ming; Moldovan, Dorel; Jarrell, Mark

In classical molecular dynamics simulations, the self-diffusion and shear viscosity of titanium about the melting point have fallen within the ranges provided by experimental data. However, the experimental data is difficult to collect and has been rather scattered, making it of limited value for the validation of these calculations. By using ab initio molecular dynamics simulations within the density functional theory framework, the classical molecular dynamics data can be validated. The dynamical data from the ab initio molecular dynamics can also be used to calculate new potentials for use in classical molecular dynamics, allowing for more accurate classical dynamics simulations for the liquid phase. For metallic materials such as titanium and aluminum alloys, these calculations are very valuable due to an increasing demand for the knowledge of their thermophysical properties that drive the development of new materials. For example, alongside knowledge of the surface tension, viscosity is an important input for modeling the additive manufacturing process at the continuum level. We are developing calculations of the viscosity along with the self-diffusion for aluminum, titanium, and titanium-aluminum alloys with ab initio molecular dynamics. Supported by the National Science Foundation through cooperative agreement OIA-1541079 and the Louisiana Board of Regents.

Computing diffusivities from particle models out of equilibrium

NASA Astrophysics Data System (ADS)

Embacher, Peter; Dirr, Nicolas; Zimmer, Johannes; Reina, Celia

2018-04-01

A new method is proposed to numerically extract the diffusivity of a (typically nonlinear) diffusion equation from underlying stochastic particle systems. The proposed strategy requires the system to be in local equilibrium and have Gaussian fluctuations but it is otherwise allowed to undergo arbitrary out-of-equilibrium evolutions. This could be potentially relevant for particle data obtained from experimental applications. The key idea underlying the method is that finite, yet large, particle systems formally obey stochastic partial differential equations of gradient flow type satisfying a fluctuation-dissipation relation. The strategy is here applied to three classic particle models, namely independent random walkers, a zero-range process and a symmetric simple exclusion process in one space dimension, to allow the comparison with analytic solutions.

Using selection bias to explain the observed structure of Internet diffusions

PubMed Central

Golub, Benjamin; Jackson, Matthew O.

2010-01-01

Recently, large datasets stored on the Internet have enabled the analysis of processes, such as large-scale diffusions of information, at new levels of detail. In a recent study, Liben-Nowell and Kleinberg [(2008) Proc Natl Acad Sci USA 105:4633–4638] observed that the flow of information on the Internet exhibits surprising patterns whereby a chain letter reaches its typical recipient through long paths of hundreds of intermediaries. We show that a basic Galton–Watson epidemic model combined with the selection bias of observing only large diffusions suffices to explain these patterns. Thus, selection biases of which data we observe can radically change the estimation of classical diffusion processes. PMID:20534439

Modeling diffusion and reaction in soils: 9. The Buckingham-Burdine-Campbell equation for gas diffusivity in undisturbed soil

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

Moldrup, P.; Olesen, T.; Yamaguchi, T.

1999-08-01

Accurate description of gas diffusivity (ratio of gas diffusion coefficients in soil and free air, D{sub s}/D{sub 0}) in undisturbed soils is a prerequisite for predicting in situ transport and fate of volatile organic chemicals and greenhouse gases. Reference point gas diffusivities (R{sub p}) in completely dry soil were estimated for 20 undisturbed soils by assuming a power function relation between gas diffusivity and air-filled porosity ({epsilon}). Among the classical gas diffusivity models, the Buckingham (1904) expression, equal to the soil total porosity squared, best described R{sub p}. Inasmuch, as their previous works implied a soil-type dependency of D{sub s}/D{submore » 0}({epsilon}) in undisturbed soils, the Buckingham R{sub p} expression was inserted in two soil-type-dependent D{sub s}/D{sub 0}({epsilon}) models. One D{sub s}/D{sub 0}({epsilon}) model is a function of pore-size distribution (the Campbell water retention parameter used in a modified Burdine capillary tube model), and the other is a calibrated, empirical function of soil texture (silt + sand fraction). Both the Buckingham-Burdine-Campbell (BBC) and the Buckingham/soil texture-based D{sub s}/D{sub 0}({epsilon}) models described well the observed soil type effects on gas diffusivity and gave improved predictions compared with soil type independent models when tested against an independent data set for six undisturbed surface soils. This study emphasizes that simple but soil-type-dependent power function D{sub s}/D{sub 0}({epsilon}) models can adequately describe and predict gas diffusivity in undisturbed soil. The authors recommend the new BBC model as basis for modeling gas transport and reactions in undisturbed soil systems.« less

Molecular dynamics simulations of bubble nucleation in dark matter detectors.

PubMed

Denzel, Philipp; Diemand, Jürg; Angélil, Raymond

2016-01-01

Bubble chambers and droplet detectors used in dosimetry and dark matter particle search experiments use a superheated metastable liquid in which nuclear recoils trigger bubble nucleation. This process is described by the classical heat spike model of F. Seitz [Phys. Fluids (1958-1988) 1, 2 (1958)PFLDAS0031-917110.1063/1.1724333], which uses classical nucleation theory to estimate the amount and the localization of the deposited energy required for bubble formation. Here we report on direct molecular dynamics simulations of heat-spike-induced bubble formation. They allow us to test the nanoscale process described in the classical heat spike model. 40 simulations were performed, each containing about 20 million atoms, which interact by a truncated force-shifted Lennard-Jones potential. We find that the energy per length unit needed for bubble nucleation agrees quite well with theoretical predictions, but the allowed spike length and the required total energy are about twice as large as predicted. This could be explained by the rapid energy diffusion measured in the simulation: contrary to the assumption in the classical model, we observe significantly faster heat diffusion than the bubble formation time scale. Finally we examine α-particle tracks, which are much longer than those of neutrons and potential dark matter particles. Empirically, α events were recently found to result in louder acoustic signals than neutron events. This distinction is crucial for the background rejection in dark matter searches. We show that a large number of individual bubbles can form along an α track, which explains the observed larger acoustic amplitudes.

Brownian motion of electrons in time-dependent magnetic fields.

NASA Technical Reports Server (NTRS)

Iverson, G. J.; Williams, R. M.

1973-01-01

The behavior of a weakly ionized plasma in slowly varying time-dependent magnetic fields is studied through an extension of Williamson's stochastic theory. In particular, attention is focused on the properties of electron diffusion in the plane perpendicular to the direction of the magnetic field, when the field strength is large. It is shown that, in the strong field limit, the classical 1/B-squared dependence of the perpendicular diffusion coefficient is obtained for two models in which the field B(t) is monotonic in t and for two models in which B(t) possesses at least one turning point.

Coarse-grained molecular dynamics simulation of water diffusion in the presence of carbon nanotubes.

PubMed

Lado Touriño, Isabel; Naranjo, Arisbel Cerpa; Negri, Viviana; Cerdán, Sebastián; Ballesteros, Paloma

2015-11-01

Computational modeling of the translational diffusion of water molecules in anisotropic environments entails vital relevance to understand correctly the information contained in the magnetic resonance images weighted in diffusion (DWI) and of the diffusion tensor images (DTI). In the present work we investigated the validity, strengths and weaknesses of a coarse-grained (CG) model based on the MARTINI force field to simulate water diffusion in a medium containing carbon nanotubes (CNTs) as models of anisotropic water diffusion behavior. We show that water diffusion outside the nanotubes follows Ficḱs law, while water diffusion inside the nanotubes is not described by a Ficḱs behavior. We report on the influence on water diffusion of various parameters such as length and concentration of CNTs, comparing the CG results with those obtained from the more accurate classic force field calculation, like the all-atom approach. Calculated water diffusion coefficients decreased in the presence of nanotubes in a concentration dependent manner. We also observed smaller water diffusion coefficients for longer CNTs. Using the CG methodology we were able to demonstrate anisotropic diffusion of water inside the nanotube scaffold, but we could not prove anisotropy in the surrounding medium, suggesting that grouping several water molecules in a single diffusing unit may affect the diffusional anisotropy calculated. The methodologies investigated in this work represent a first step towards the study of more complex models, including anisotropic cohorts of CNTs or even neuronal axons, with reasonable savings in computation time. Copyright © 2015 Elsevier Inc. All rights reserved.

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

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

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

2015-10-15

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

Turbulent patterns in wall-bounded flows: A Turing instability?

NASA Astrophysics Data System (ADS)

Manneville, Paul

2012-06-01

In their way to/from turbulence, plane wall-bounded flows display an interesting transitional regime where laminar and turbulent oblique bands alternate, the origin of which is still mysterious. In line with Barkley's recent work about the pipe flow transition involving reaction-diffusion concepts, we consider plane Couette flow in the same perspective and transform Waleffe's classical four-variable model of self-sustaining process into a reaction-diffusion model. We show that, upon fulfillment of a condition on the relative diffusivities of its variables, the featureless turbulent regime becomes unstable against patterning as the result of a Turing instability. A reduced two-variable model helps us to delineate the appropriate region of parameter space. An intrinsic status is therefore given to the pattern's wavelength for the first time. Virtues and limitations of the model are discussed, calling for a microscopic support of the phenomenological approach.

Anomalous diffusion analysis of the lifting events in the event-chain Monte Carlo for the classical XY models

NASA Astrophysics Data System (ADS)

Kimura, Kenji; Higuchi, Saburo

2017-11-01

We introduce a novel random walk model that emerges in the event-chain Monte Carlo (ECMC) of spin systems. In the ECMC, the lifting variable specifying the spin to be updated changes its value to one of its interacting neighbor spins. This movement can be regarded as a random walk in a random environment with a feedback. We investigate this random walk numerically in the case of the classical XY model in 1, 2, and 3 dimensions to find that it is superdiffusive near the critical point of the underlying spin system. It is suggested that the performance improvement of the ECMC is related to this anomalous behavior.

Delay-induced Turing-like waves for one-species reaction-diffusion model on a network

NASA Astrophysics Data System (ADS)

Petit, Julien; Carletti, Timoteo; Asllani, Malbor; Fanelli, Duccio

2015-09-01

A one-species time-delay reaction-diffusion system defined on a complex network is studied. Traveling waves are predicted to occur following a symmetry-breaking instability of a homogeneous stationary stable solution, subject to an external nonhomogeneous perturbation. These are generalized Turing-like waves that materialize in a single-species populations dynamics model, as the unexpected byproduct of the imposed delay in the diffusion part. Sufficient conditions for the onset of the instability are mathematically provided by performing a linear stability analysis adapted to time-delayed differential equations. The method here developed exploits the properties of the Lambert W-function. The prediction of the theory are confirmed by direct numerical simulation carried out for a modified version of the classical Fisher model, defined on a Watts-Strogatz network and with the inclusion of the delay.

Pembrolizumab and Vorinostat in Treating Patients With Relapsed or Refractory Diffuse Large B-Cell Lymphoma, Follicular Lymphoma, or Hodgkin Lymphoma

ClinicalTrials.gov

2018-04-23

Grade 3a Follicular Lymphoma; Grade 3b Follicular Lymphoma; Recurrent Classical Hodgkin Lymphoma; Recurrent Diffuse Large B-Cell Lymphoma; Recurrent Follicular Lymphoma; Recurrent Grade 1 Follicular Lymphoma; Recurrent Grade 2 Follicular Lymphoma; Recurrent Mediastinal (Thymic) Large B-Cell Cell Lymphoma; Refractory Classical Hodgkin Lymphoma; Refractory Diffuse Large B-Cell Lymphoma; Refractory Follicular Lymphoma; Refractory Mediastinal (Thymic) Large B-Cell Cell Lymphoma

Energy diffusion controlled reaction rate of reacting particle driven by broad-band noise

NASA Astrophysics Data System (ADS)

Deng, M. L.; Zhu, W. Q.

2007-10-01

The energy diffusion controlled reaction rate of a reacting particle with linear weak damping and broad-band noise excitation is studied by using the stochastic averaging method. First, the stochastic averaging method for strongly nonlinear oscillators under broad-band noise excitation using generalized harmonic functions is briefly introduced. Then, the reaction rate of the classical Kramers' reacting model with linear weak damping and broad-band noise excitation is investigated by using the stochastic averaging method. The averaged Itô stochastic differential equation describing the energy diffusion and the Pontryagin equation governing the mean first-passage time (MFPT) are established. The energy diffusion controlled reaction rate is obtained as the inverse of the MFPT by solving the Pontryagin equation. The results of two special cases of broad-band noises, i.e. the harmonic noise and the exponentially corrected noise, are discussed in details. It is demonstrated that the general expression of reaction rate derived by the authors can be reduced to the classical ones via linear approximation and high potential barrier approximation. The good agreement with the results of the Monte Carlo simulation verifies that the reaction rate can be well predicted using the stochastic averaging method.

Double diffusivity model under stochastic forcing

NASA Astrophysics Data System (ADS)

Chattopadhyay, Amit K.; Aifantis, Elias C.

2017-05-01

The "double diffusivity" model was proposed in the late 1970s, and reworked in the early 1980s, as a continuum counterpart to existing discrete models of diffusion corresponding to high diffusivity paths, such as grain boundaries and dislocation lines. It was later rejuvenated in the 1990s to interpret experimental results on diffusion in polycrystalline and nanocrystalline specimens where grain boundaries and triple grain boundary junctions act as high diffusivity paths. Technically, the model pans out as a system of coupled Fick-type diffusion equations to represent "regular" and "high" diffusivity paths with "source terms" accounting for the mass exchange between the two paths. The model remit was extended by analogy to describe flow in porous media with double porosity, as well as to model heat conduction in media with two nonequilibrium local temperature baths, e.g., ion and electron baths. Uncoupling of the two partial differential equations leads to a higher-ordered diffusion equation, solutions of which could be obtained in terms of classical diffusion equation solutions. Similar equations could also be derived within an "internal length" gradient (ILG) mechanics formulation applied to diffusion problems, i.e., by introducing nonlocal effects, together with inertia and viscosity, in a mechanics based formulation of diffusion theory. While being remarkably successful in studies related to various aspects of transport in inhomogeneous media with deterministic microstructures and nanostructures, its implications in the presence of stochasticity have not yet been considered. This issue becomes particularly important in the case of diffusion in nanopolycrystals whose deterministic ILG-based theoretical calculations predict a relaxation time that is only about one-tenth of the actual experimentally verified time scale. This article provides the "missing link" in this estimation by adding a vital element in the ILG structure, that of stochasticity, that takes into account all boundary layer fluctuations. Our stochastic-ILG diffusion calculation confirms rapprochement between theory and experiment, thereby benchmarking a new generation of gradient-based continuum models that conform closer to real-life fluctuating environments.

Anomalous Diffusion of Single Particles in Cytoplasm

PubMed Central

Regner, Benjamin M.; Vučinić, Dejan; Domnisoru, Cristina; Bartol, Thomas M.; Hetzer, Martin W.; Tartakovsky, Daniel M.; Sejnowski, Terrence J.

2013-01-01

The crowded intracellular environment poses a formidable challenge to experimental and theoretical analyses of intracellular transport mechanisms. Our measurements of single-particle trajectories in cytoplasm and their random-walk interpretations elucidate two of these mechanisms: molecular diffusion in crowded environments and cytoskeletal transport along microtubules. We employed acousto-optic deflector microscopy to map out the three-dimensional trajectories of microspheres migrating in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM), continuous time random walk, and fractional BM were alternatively used to represent these trajectories. The comparison of the experimental and numerical data demonstrates that cytoskeletal transport along microtubules and diffusion in the cytosolic fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct signatures. Among the three random-walk models used, continuous time random walk provides the best representation of diffusion, whereas microtubular transport is accurately modeled with fractional BM. PMID:23601312

Definition of MYC genetic heteroclonality in diffuse large B-cell lymphoma with 8q24 rearrangement and its impact on protein expression.

PubMed

Valera, Alexandra; Epistolio, Samantha; Colomo, Lluis; Riva, Alice; Balagué, Olga; Dlouhy, Ivan; Tzankov, Alexandar; Bühler, Marco; Haralambieva, Eugenia; Campo, Elias; Soldini, Davide; Mazzucchelli, Luca; Martin, Vittoria

2016-08-01

MYC rearrangement can be detected in a subgroup of diffuse large B-cell lymphoma characterized by unfavorable prognosis. In contrast to Burkitt lymphoma, the correlation between MYC rearrangement and MYC protein expression in diffuse large B-cell lymphoma is less clear, as approximately one-third of rearranged cases show negative or low expression by immunohistochemistry. To better understand whether specific characteristics of the MYC rearrangement may influence its protein expression, we investigated 43 de novo diffuse large B-cell lymphoma positive for 8q24 rearrangement by FISH, using 14 Burkitt lymphoma for comparison. Different cell populations (clones), breakpoints (classical vs non-classical FISH patterns), partner genes (IGH vs non-IGH) and immunostaining were detected and analyzed using computerized image systems. In a subgroup of diffuse large B-cell lymphoma, we observed different clones within the same tumor distinguishing the founder clone with MYC rearrangement alone from other subclones, carrying MYC rearrangement coupled with loss/extra copies of derivatives/normal alleles. This picture, which we defined MYC genetic heteroclonality, was found in 42% of cases and correlated to negative MYC expression (P=0.026). Non-classical FISH breakpoints were detected in 16% of diffuse large B-cell lymphoma without affecting expression (P=0.040). Non-IGH gene was the preferential partner of rearrangement in those diffuse large B-cell lymphoma showing MYC heteroclonality (P=0.016) and/or non-classical FISH breakpoints (P=0.058). MYC heteroclonality was not observed in Burkitt lymphoma and all cases had positive MYC expression. Non-classical FISH MYC breakpoint and non-IGH partner were found in 29 and 20% of Burkitt lymphoma, respectively. In conclusion, MYC genetic heteroclonality is a frequent event in diffuse large B-cell lymphoma and may have a relevant role in modulating MYC expression.

A time fractional convection-diffusion equation to model gas transport through heterogeneous soil and gas reservoirs

NASA Astrophysics Data System (ADS)

Chang, Ailian; Sun, HongGuang; Zheng, Chunmiao; Lu, Bingqing; Lu, Chengpeng; Ma, Rui; Zhang, Yong

2018-07-01

Fractional-derivative models have been developed recently to interpret various hydrologic dynamics, such as dissolved contaminant transport in groundwater. However, they have not been applied to quantify other fluid dynamics, such as gas transport through complex geological media. This study reviewed previous gas transport experiments conducted in laboratory columns and real-world oil-gas reservoirs and found that gas dynamics exhibit typical sub-diffusive behavior characterized by heavy late-time tailing in the gas breakthrough curves (BTCs), which cannot be effectively captured by classical transport models. Numerical tests and field applications of the time fractional convection-diffusion equation (fCDE) have shown that the fCDE model can capture the observed gas BTCs including their apparent positive skewness. Sensitivity analysis further revealed that the three parameters used in the fCDE model, including the time index, the convection velocity, and the diffusion coefficient, play different roles in interpreting the delayed gas transport dynamics. In addition, the model comparison and analysis showed that the time fCDE model is efficient in application. Therefore, the time fractional-derivative models can be conveniently extended to quantify gas transport through natural geological media such as complex oil-gas reservoirs.

Role of oxygen diffusion at Ni/Cr2O3 interface in intergranular oxidation of Ni-Cr alloy

NASA Astrophysics Data System (ADS)

Medasani, Bharat; Sushko, Maria; Schreiber, Daniel; Rosso, Kevin; Bruemmer, Stephen

Certain Ni-Cr alloys used in nuclear systems experience intergranular oxidation and stress corrosion cracking when exposed to high-temperature water leading to their degradation and unexpected failure. To develop a mechanistic understanding of grain boundary oxidation processes, we proposed a mesoscale metal alloy oxidation model that combines quantum Density Functional Theory (DFT) with mesoscopic Poisson-Nernst-Planck/classical DFT. This framework encompasses the chemical specificity of elementary diffusion processes and mesoscale reactive dynamics, and allows modeling oxidation processes on experimentally relevant length scales from first principles. As a proof of concept, a preliminary model was previously employed that limited oxygen diffusion pathways to those through the oxide phase and did not allow oxygen diffusion in the alloy or across oxide/alloy interfaces. In this work, we expand the model to include oxygen diffusion pathways along Ni/Cr2O3 interfaces and demonstrate the increasing importance of such pathways for intergranular oxidation of Ni-Cr alloys with high Cr content. This work is supported by the U.S. Dept. of Energy, Office of Science, Basic Energy Sciences, Materials Sciences and Engineering Division. Simulations are performed using PNNL Institutional Computing facility.

Fractional order analysis of Sephadex gel structures: NMR measurements reflecting anomalous diffusion

NASA Astrophysics Data System (ADS)

Magin, Richard L.; Akpa, Belinda S.; Neuberger, Thomas; Webb, Andrew G.

2011-12-01

We report the appearance of anomalous water diffusion in hydrophilic Sephadex gels observed using pulse field gradient (PFG) nuclear magnetic resonance (NMR). The NMR diffusion data was collected using a Varian 14.1 Tesla imaging system with a home-built RF saddle coil. A fractional order analysis of the data was used to characterize heterogeneity in the gels for the dynamics of water diffusion in this restricted environment. Several recent studies of anomalous diffusion have used the stretched exponential function to model the decay of the NMR signal, i.e., exp[-( bD) α], where D is the apparent diffusion constant, b is determined the experimental conditions (gradient pulse separation, durations and strength), and α is a measure of structural complexity. In this work, we consider a different case where the spatial Laplacian in the Bloch-Torrey equation is generalized to a fractional order model of diffusivity via a complexity parameter, β, a space constant, μ, and a diffusion coefficient, D. This treatment reverts to the classical result for the integer order case. The fractional order decay model was fit to the diffusion-weighted signal attenuation for a range of b-values (0 < b < 4000 s mm -2). Throughout this range of b values, the parameters β, μ and D, were found to correlate with the porosity and tortuosity of the gel structure.

Continuum models of cohesive stochastic swarms: The effect of motility on aggregation patterns

NASA Astrophysics Data System (ADS)

Hughes, Barry D.; Fellner, Klemens

2013-10-01

Mathematical models of swarms of moving agents with non-local interactions have many applications and have been the subject of considerable recent interest. For modest numbers of agents, cellular automata or related algorithms can be used to study such systems, but in the present work, instead of considering discrete agents, we discuss a class of one-dimensional continuum models, in which the agents possess a density ρ(x,t) at location x at time t. The agents are subject to a stochastic motility mechanism and to a global cohesive inter-agent force. The motility mechanisms covered include classical diffusion, nonlinear diffusion (which may be used to model, in a phenomenological way, volume exclusion or other short-range local interactions), and a family of linear redistribution operators related to fractional diffusion equations. A variety of exact analytic results are discussed, including equilibrium solutions and criteria for unimodality of equilibrium distributions, full time-dependent solutions, and transitions between asymptotic collapse and asymptotic escape. We address the behaviour of the system for diffusive motility in the low-diffusivity limit for both smooth and singular interaction potentials and show how this elucidates puzzling behaviour in fully deterministic non-local particle interaction models. We conclude with speculative remarks about extensions and applications of the models.

Scaling of chaos in strongly nonlinear lattices.

PubMed

Mulansky, Mario

2014-06-01

Although it is now understood that chaos in complex classical systems is the foundation of thermodynamic behavior, the detailed relations between the microscopic properties of the chaotic dynamics and the macroscopic thermodynamic observations still remain mostly in the dark. In this work, we numerically analyze the probability of chaos in strongly nonlinear Hamiltonian systems and find different scaling properties depending on the nonlinear structure of the model. We argue that these different scaling laws of chaos have definite consequences for the macroscopic diffusive behavior, as chaos is the microscopic mechanism of diffusion. This is compared with previous results on chaotic diffusion [M. Mulansky and A. Pikovsky, New J. Phys. 15, 053015 (2013)], and a relation between microscopic chaos and macroscopic diffusion is established.

Communication: Modeling of concentration dependent water diffusivity in ionic solutions: Role of intermolecular charge transfer

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

Yao, Yi; Berkowitz, Max L., E-mail: maxb@unc.edu, E-mail: ykanai@unc.edu; Kanai, Yosuke, E-mail: maxb@unc.edu, E-mail: ykanai@unc.edu

2015-12-28

The translational diffusivity of water in solutions of alkali halide salts depends on the identity of ions, exhibiting dramatically different behavior even in solutions of similar salts of NaCl and KCl. The water diffusion coefficient decreases as the salt concentration increases in NaCl. Yet, in KCl solution, it slightly increases and remains above bulk value as salt concentration increases. Previous classical molecular dynamics simulations have failed to describe this important behavior even when polarizable models were used. Here, we show that inclusion of dynamical charge transfer among water molecules produces results in a quantitative agreement with experiments. Our results indicatemore » that the concentration-dependent diffusivity reflects the importance of many-body effects among the water molecules in aqueous ionic solutions. Comparison with quantum mechanical calculations shows that a heterogeneous and extended distribution of charges on water molecules around the ions due to ion-water and also water-water charge transfer plays a very important role in controlling water diffusivity. Explicit inclusion of the charge transfer allows us to model accurately the difference in the concentration-dependent water diffusivity between Na{sup +} and K{sup +} ions in simulations, and it is likely to impact modeling of a wide range of systems for medical and technological applications.« less

Calculation of Transport Coefficients in Dense Plasma Mixtures

NASA Astrophysics Data System (ADS)

Haxhimali, T.; Cabot, W. H.; Caspersen, K. J.; Greenough, J.; Miller, P. L.; Rudd, R. E.; Schwegler, E. R.

2011-10-01

We use classical molecular dynamics (MD) to estimate species diffusivity and viscosity in mixed dense plasmas. The Yukawa potential is used to describe the screened Coulomb interaction between the ions. This potential has been used widely, providing the basis for models of dense stellar materials, inertial confined plasmas, and colloidal particles in electrolytes. We calculate transport coefficients in equilibrium simulations using the Green- Kubo relation over a range of thermodynamic conditions including the viscosity and the self - diffusivity for each component of the mixture. The interdiffusivity (or mutual diffusivity) can then be related to the self-diffusivities by using a generalization of the Darken equation. We have also employed non-equilibrium MD to estimate interdiffusivity during the broadening of the interface between two regions each with a high concentration of either species. Here we present results for an asymmetric mixture between Ar and H. These can easily be extended to other plasma mixtures. A main motivation for this study is to develop accurate transport models that can be incorporated into the hydrodynamic codes to study hydrodynamic instabilities. We use classical molecular dynamics (MD) to estimate species diffusivity and viscosity in mixed dense plasmas. The Yukawa potential is used to describe the screened Coulomb interaction between the ions. This potential has been used widely, providing the basis for models of dense stellar materials, inertial confined plasmas, and colloidal particles in electrolytes. We calculate transport coefficients in equilibrium simulations using the Green- Kubo relation over a range of thermodynamic conditions including the viscosity and the self - diffusivity for each component of the mixture. The interdiffusivity (or mutual diffusivity) can then be related to the self-diffusivities by using a generalization of the Darken equation. We have also employed non-equilibrium MD to estimate interdiffusivity during the broadening of the interface between two regions each with a high concentration of either species. Here we present results for an asymmetric mixture between Ar and H. These can easily be extended to other plasma mixtures. A main motivation for this study is to develop accurate transport models that can be incorporated into the hydrodynamic codes to study hydrodynamic instabilities. This work was performed under the auspices of the US Dept. of Energy by Lawrence Livermore National Security, LLC under Contract DE-AC52-07NA27344.

Modeling viscosity and diffusion of plasma mixtures across coupling regimes

NASA Astrophysics Data System (ADS)

Arnault, Philippe

2014-10-01

Viscosity and diffusion of plasma for pure elements and multicomponent mixtures are modeled from the high-temperature low-density weakly coupled regime to the low-temperature high-density strongly coupled regime. Thanks to an atom in jellium modeling, the effect of electron screening on the ion-ion interaction is incorporated through a self-consistent definition of the ionization. This defines an effective One Component Plasma, or an effective Binary Ionic Mixture, that is representative of the strength of the interaction. For the viscosity and the interdiffusion of mixtures, approximate kinetic expressions are supplemented by mixing laws applied to the excess viscosity and self-diffusion of pure elements. The comparisons with classical and quantum molecular dynamics results reveal deviations in the range 20--40% on average with almost no predictions further than a factor of 2 over many decades of variation. Applications in the inertial confinement fusion context could help in predicting the growth of hydrodynamic instabilities.

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

Perriot, Romain; Uberuaga, Blas P.; Zamora, Richard J.

Diffusion in complex oxides is critical to ionic transport, radiation damage evolution, sintering, and aging. In complex oxides such as pyrochlores, anionic diffusion is dramatically affected by cation disorder. However, little is known about how disorder influences cation transport. Here, we report results from classical and accelerated molecular dynamics simulations of vacancy-mediated cation diffusion in Gd 2Ti 2O 7 pyrochlore, on the microsecond timescale. We find that diffusion is slow at low levels of disorder, while higher disorder allows for fast diffusion, which is then accompanied by antisite annihilation and reordering, and thus a slowing of cation transport. Cation diffusivitymore » is therefore not constant, but decreases as the material reorders. We also show that fast cation diffusion is triggered by the formation of a percolation network of antisites. This is in contrast with observations from other complex oxides and disordered media models, suggesting a fundamentally different relation between disorder and mass transport.« less

Diffusion and interactions of interstitials in hard-sphere interstitial solid solutions

NASA Astrophysics Data System (ADS)

van der Meer, Berend; Lathouwers, Emma; Smallenburg, Frank; Filion, Laura

2017-12-01

Using computer simulations, we study the dynamics and interactions of interstitial particles in hard-sphere interstitial solid solutions. We calculate the free-energy barriers associated with their diffusion for a range of size ratios and densities. By applying classical transition state theory to these free-energy barriers, we predict the diffusion coefficients, which we find to be in good agreement with diffusion coefficients as measured using event-driven molecular dynamics simulations. These results highlight that transition state theory can capture the interstitial dynamics in the hard-sphere model system. Additionally, we quantify the interactions between the interstitials. We find that, apart from excluded volume interactions, the interstitial-interstitial interactions are almost ideal in our system. Lastly, we show that the interstitial diffusivity can be inferred from the large-particle fluctuations alone, thus providing an empirical relationship between the large-particle fluctuations and the interstitial diffusivity.

Modeling of a Von Platen-Munters diffusion absorption refrigeration cycle

NASA Astrophysics Data System (ADS)

Agostini, Bruno; Agostini, Francesco; Habert, Mathieu

2016-09-01

This article presents a thermodynamical model of a Von-Platen diffusion absorption refrigeration cycle for power electronics applications. It is first validated by comparison with data available in the literature for the classical water-ammonia-helium cycle for commercial absorption fridges. Then new operating conditions corresponding to specific ABB applications, namely high ambient temperature and new organic fluids combinations compatible with aluminium are simulated and discussed. The target application is to cool power electronics converters in harsh environments with high ambient temperature by providing refrigeration without compressor, for passive components losses of about 500 W, with a compact and low cost solution.

Comparison and analysis of theoretical models for diffusion-controlled dissolution.

PubMed

Wang, Yanxing; Abrahamsson, Bertil; Lindfors, Lennart; Brasseur, James G

2012-05-07

Dissolution models require, at their core, an accurate diffusion model. The accuracy of the model for diffusion-dominated dissolution is particularly important with the trend toward micro- and nanoscale drug particles. Often such models are based on the concept of a "diffusion layer." Here a framework is developed for diffusion-dominated dissolution models, and we discuss the inadequacy of classical models that are based on an unphysical constant diffusion layer thickness assumption, or do not correctly modify dissolution rate due to "confinement effects": (1) the increase in bulk concentration from confinement of the dissolution process, (2) the modification of the flux model (the Sherwood number) by confinement. We derive the exact mathematical solution for a spherical particle in a confined fluid with impermeable boundaries. Using this solution, we analyze the accuracy of a time-dependent "infinite domain model" (IDM) and "quasi steady-state model" (QSM), both formally derived for infinite domains but which can be applied in approximate fashion to confined dissolution with proper adjustment of a concentration parameter. We show that dissolution rate is sensitive to the degree of confinement or, equivalently, to the total concentration C(tot). The most practical model, the QSM, is shown to be very accurate for most applications and, consequently, can be used with confidence in design-level dissolution models so long as confinement is accurately treated. The QSM predicts the ratio of diffusion layer thickness to particle radius (the Sherwood number) as a constant plus a correction that depends on the degree of confinement. The QSM also predicts that the time required for complete saturation or dissolution in diffusion-controlled dissolution experiments is singular (i.e., infinite) when total concentration equals the solubility. Using the QSM, we show that measured differences in dissolution rate in a diffusion-controlled dissolution experiment are a result of differences in the degree of confinement on the increase in bulk concentration independent of container geometry and polydisperse vs single particle dissolution. We conclude that the constant diffusion-layer thickness assumption is incorrect in principle and should be replaced by the QSM with accurate treatment of confinement in models of diffusion-controlled dissolution.

The Anderson localization problem, the Fermi-Pasta-Ulam paradox and the generalized diffusion approach

NASA Astrophysics Data System (ADS)

Kuzovkov, V. N.

2011-12-01

The goal of this paper is twofold. First, based on the interpretation of a quantum tight-binding model in terms of a classical Hamiltonian map, we consider the Anderson localization (AL) problem as the Fermi-Pasta-Ulam (FPU) effect in a modified dynamical system containing both stable and unstable (inverted) modes. Delocalized states in the AL are analogous to the stable quasi-periodic motion in FPU, whereas localized states are analogous to thermalization, respectively. The second aim is to use the classical Hamilton map for a simplified derivation of exact equations for the localization operator H(z). The latter was presented earlier (Kuzovkov et al 2002 J. Phys.: Condens. Matter 14 13777) treating the AL as a generalized diffusion in a dynamical system. We demonstrate that counter-intuitive results of our studies of the AL are similar to the FPU counter-intuitivity.

Lenalidomide and Blinatumomab in Treating Patients With Relapsed Non-Hodgkin Lymphoma

ClinicalTrials.gov

2018-06-11

CD19 Positive; Mediastinal Lymphoma; Recurrent B-Cell Lymphoma, Unclassifiable, With Features Intermediate Between Diffuse Large B-Cell Lymphoma and Classic Hodgkin Lymphoma; Recurrent Burkitt Lymphoma; Recurrent Diffuse Large B-Cell Lymphoma; Recurrent Grade 1 Follicular Lymphoma; Recurrent Grade 2 Follicular Lymphoma; Recurrent Grade 3 Follicular Lymphoma; Recurrent Mantle Cell Lymphoma; Recurrent Marginal Zone Lymphoma; Recurrent Non-Hodgkin Lymphoma; Recurrent Small Lymphocytic Lymphoma; Refractory B-Cell Lymphoma, Unclassifiable, With Features Intermediate Between Diffuse Large B-Cell Lymphoma and Classic Hodgkin Lymphoma; Refractory Burkitt Lymphoma; Refractory Diffuse Large B-Cell Lymphoma; Refractory Follicular Lymphoma; Refractory Mantle Cell Lymphoma; Refractory Small Lymphocytic Lymphoma

Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates.

PubMed

Cendagorta, Joseph R; Powers, Anna; Hele, Timothy J H; Marsalek, Ondrej; Bačić, Zlatko; Tuckerman, Mark E

2016-11-30

Clathrate hydrates hold considerable promise as safe and economical materials for hydrogen storage. Here we present a quantum mechanical study of H 2 and D 2 diffusion through a hexagonal face shared by two large cages of clathrate hydrates over a wide range of temperatures. Path integral molecular dynamics simulations are used to compute the free-energy profiles for the diffusion of H 2 and D 2 as a function of temperature. Ring polymer molecular dynamics rate theory, incorporating both exact quantum statistics and approximate quantum dynamical effects, is utilized in the calculations of the H 2 and D 2 diffusion rates in a broad temperature interval. We find that the shape of the quantum free-energy profiles and their height relative to the classical free energy barriers at a given temperature, as well as the rate of diffusion, are strongly affected by competing quantum effects: above 25 K, zero-point energy (ZPE) perpendicular to the reaction path for diffusion between cavities decreases the quantum rate compared to the classical rate, whereas at lower temperatures tunneling outcompetes the ZPE and as a result the quantum rate is greater than the classical rate.

Symmetry Reductions of Fourth-Order Nonlinear Diffusion Equations: Lubrication Model and Some Generalizations

NASA Astrophysics Data System (ADS)

Gandarias, M. L.; Medina, E.

Fourth-order nonlinear diffusion equations appear frequently in the description of physical processes, among these, the lubrication equation ut = (unuxxxx)x or the corresponding modified version ut = unuxxxx play an important role in the study of the interface movements. In this work we analyze the generalizations of the above equations given by ut = (f(u)uxxxx)x, ut = (f(u)uxxxx, and we find that if f(u) = un or f(u) = e-u the equations admit extra classical symmetries. The corresponding reductions are performed and some solutions are characterized.

Hydrodynamics of bacterial colonies: A model

NASA Astrophysics Data System (ADS)

Lega, J.; Passot, T.

2003-03-01

We propose a hydrodynamic model for the evolution of bacterial colonies growing on soft agar plates. This model consists of reaction-diffusion equations for the concentrations of nutrients, water, and bacteria, coupled to a single hydrodynamic equation for the velocity field of the bacteria-water mixture. It captures the dynamics inside the colony as well as on its boundary and allows us to identify a mechanism for collective motion towards fresh nutrients, which, in its modeling aspects, is similar to classical chemotaxis. As shown in numerical simulations, our model reproduces both usual colony shapes and typical hydrodynamic motions, such as the whirls and jets recently observed in wet colonies of Bacillus subtilis. The approach presented here could be extended to different experimental situations and provides a general framework for the use of advection-reaction-diffusion equations in modeling bacterial colonies.

Evolution of diffusion and dissemination theory.

PubMed

Dearing, James W

2008-01-01

The article provides a review and considers how the diffusion of innovations Research paradigm has changed, and offers suggestions for the further development of this theory of social change. Main emphases of diffusion Research studies are compared over time, with special attention to applications of diffusion theory-based concepts as types of dissemination science. A considerable degree of paradigmatic evolution is observed. The classical diffusion model focused on adopter innovativeness, individuals as the locus of decision, communication channels, and adoption as the primary outcome measures in post hoc observational study designs. The diffusion systems in question were centralized, with fidelity of implementation often assumed. Current dissemination Research and practice is better characterized by tests of interventions that operationalize one or more diffusion theory-based concepts and concepts from other change approaches, involve complex organizations as the units of adoption, and focus on implementation issues. Foment characterizes dissemination and implementation Research, Reflecting both its interdisciplinary Roots and the imperative of spreading evidence-based innovations as a basis for a new paradigm of translational studies of dissemination science.

Evidence for percolation diffusion of cations and reordering in disordered pyrochlore from accelerated molecular dynamics

DOE PAGES

Perriot, Romain; Uberuaga, Blas P.; Zamora, Richard J.; ...

2017-09-20

Diffusion in complex oxides is critical to ionic transport, radiation damage evolution, sintering, and aging. In complex oxides such as pyrochlores, anionic diffusion is dramatically affected by cation disorder. However, little is known about how disorder influences cation transport. Here, we report results from classical and accelerated molecular dynamics simulations of vacancy-mediated cation diffusion in Gd 2Ti 2O 7 pyrochlore, on the microsecond timescale. We find that diffusion is slow at low levels of disorder, while higher disorder allows for fast diffusion, which is then accompanied by antisite annihilation and reordering, and thus a slowing of cation transport. Cation diffusivitymore » is therefore not constant, but decreases as the material reorders. We also show that fast cation diffusion is triggered by the formation of a percolation network of antisites. This is in contrast with observations from other complex oxides and disordered media models, suggesting a fundamentally different relation between disorder and mass transport.« less

Detection of Buckminsterfullerene emission in the diffuse interstellar medium.

PubMed

Berné, O; Cox, N L J; Mulas, G; Joblin, C

2017-09-01

Emission of fullerenes in their infrared vibrational bands has been detected in space near hot stars. The proposed attribution of the diffuse interstellar bands at 9577 and 9632 Å to electronic transitions of the buckminsterfullerene cation (i.e. [Formula: see text]) was recently supported by new laboratory data, confirming the presence of this species in the diffuse interstellar medium (ISM). In this letter, we present the detection, also in the diffuse ISM, of the 17.4 and 18.9 μ m emission bands commonly attributed to vibrational bands of neutral C 60 . According to classical models that compute the charge state of large molecules in space, C 60 is expected to be mostly neutral in the diffuse ISM. This is in agreement with the abundances of diffuse C 60 we derive here from observations. We also find that C 60 is less abundant in the diffuse ISM than in star-forming regions, supporting the theory that C 60 can be formed in these regions.

Subdiffusion in Membrane Permeation of Small Molecules.

PubMed

Chipot, Christophe; Comer, Jeffrey

2016-11-02

Within the solubility-diffusion model of passive membrane permeation of small molecules, translocation of the permeant across the biological membrane is traditionally assumed to obey the Smoluchowski diffusion equation, which is germane for classical diffusion on an inhomogeneous free-energy and diffusivity landscape. This equation, however, cannot accommodate subdiffusive regimes, which have long been recognized in lipid bilayer dynamics, notably in the lateral diffusion of individual lipids. Through extensive biased and unbiased molecular dynamics simulations, we show that one-dimensional translocation of methanol across a pure lipid membrane remains subdiffusive on timescales approaching typical permeation times. Analysis of permeant motion within the lipid bilayer reveals that, in the absence of a net force, the mean squared displacement depends on time as t 0.7 , in stark contrast with the conventional model, which assumes a strictly linear dependence. We further show that an alternate model using a fractional-derivative generalization of the Smoluchowski equation provides a rigorous framework for describing the motion of the permeant molecule on the pico- to nanosecond timescale. The observed subdiffusive behavior appears to emerge from a crossover between small-scale rattling of the permeant around its present position in the membrane and larger-scale displacements precipitated by the formation of transient voids.

Knowledge diffusion in complex networks by considering time-varying information channels

NASA Astrophysics Data System (ADS)

Zhu, He; Ma, Jing

2018-03-01

In this article, based on a model of epidemic spreading, we explore the knowledge diffusion process with an innovative mechanism for complex networks by considering time-varying information channels. To cover the knowledge diffusion process in homogeneous and heterogeneous networks, two types of networks (the BA network and the ER network) are investigated. The mean-field theory is used to theoretically draw the knowledge diffusion threshold. Numerical simulation demonstrates that the knowledge diffusion threshold is almost linearly correlated with the mean of the activity rate. In addition, under the influence of the activity rate and distinct from the classic Susceptible-Infected-Susceptible (SIS) model, the density of knowers almost linearly grows with the spreading rate. Finally, in consideration of the ubiquitous mechanism of innovation, we further study the evolution of knowledge in our proposed model. The results suggest that compared with the effect of the spreading rate, the average knowledge version of the population is affected more by the innovation parameter and the mean of the activity rate. Furthermore, in the BA network, the average knowledge version of individuals with higher degree is always newer than those with lower degree.

How to Teach Recycling at an Advanced Phase of Diffusion

ERIC Educational Resources Information Center

Meneses, Gonzalo Diaz

2006-01-01

The author conducted an empirical study based on structural equation modeling with a convenience sample of 246 individuals with the goal of demonstrating that recycling behavior is a routine conduct and should be addressed as such in educational materials. Although the classic hierarchy of effects dominates the interpretation of recycling behavior…

Unifying models of dialect spread and extinction using surface tension dynamics

PubMed Central

2018-01-01

We provide a unified mathematical explanation of two classical forms of spatial linguistic spread. The wave model describes the radiation of linguistic change outwards from a central focus. Changes can also jump between population centres in a process known as hierarchical diffusion. It has recently been proposed that the spatial evolution of dialects can be understood using surface tension at linguistic boundaries. Here we show that the inclusion of long-range interactions in the surface tension model generates both wave-like spread, and hierarchical diffusion, and that it is surface tension that is the dominant effect in deciding the stable distribution of dialect patterns. We generalize the model to allow population mixing which can induce shrinkage of linguistic domains, or destroy dialect regions from within. PMID:29410847

Discriminating the effects of collapse models from environmental diffusion with levitated nanospheres

NASA Astrophysics Data System (ADS)

Li, Jie; Zippilli, Stefano; Zhang, Jing; Vitali, David

2016-05-01

Collapse models postulate the existence of intrinsic noise which modifies quantum mechanics and is responsible for the emergence of macroscopic classicality. Assessing the validity of these models is extremely challenging because it is nontrivial to discriminate unambiguously their presence in experiments where other hardly controllable sources of noise compete to the overall decoherence. Here we provide a simple procedure that is able to probe the hypothetical presence of the collapse noise with a levitated nanosphere in a Fabry-Pérot cavity. We show that the stationary state of the system is particularly sensitive, under specific experimental conditions, to the interplay between the trapping frequency, the cavity size, and the momentum diffusion induced by the collapse models, allowing one to detect them even in the presence of standard environmental noises.

Diffusive mixing and Tsallis entropy

DOE PAGES

O'Malley, Daniel; Vesselinov, Velimir V.; Cushman, John H.

2015-04-29

Brownian motion, the classical diffusive process, maximizes the Boltzmann-Gibbs entropy. The Tsallis q-entropy, which is non-additive, was developed as an alternative to the classical entropy for systems which are non-ergodic. A generalization of Brownian motion is provided that maximizes the Tsallis entropy rather than the Boltzmann-Gibbs entropy. This process is driven by a Brownian measure with a random diffusion coefficient. In addition, the distribution of this coefficient is derived as a function of q for 1 < q < 3. Applications to transport in porous media are considered.

Treatment of boundary conditions in through-diffusion: A case study of (85)Sr(2+) diffusion in compacted illite.

PubMed

Glaus, M A; Aertsens, M; Maes, N; Van Laer, L; Van Loon, L R

2015-01-01

Valuable techniques to measure effective diffusion coefficients in porous media are an indispensable prerequisite for a proper understanding of the migration of chemical-toxic and radioactive micropollutants in the subsurface and geosphere. The present article discusses possible pitfalls and difficulties in the classical through-diffusion technique applied to situations where large diffusive fluxes of cations in compacted clay minerals or clay rocks occur. The results obtained from a benchmark study, in which the diffusion of (85)Sr(2+) tracer in compacted illite has been studied using different experimental techniques, are presented. It is shown that these techniques may yield valuable results provided that an appropriate model is used for numerical simulations. It is further shown that effective diffusion coefficients may be systematically underestimated when the concentration at the downstream boundary is not taken adequately into account in modelling, even for very low concentrations. A criterion is derived for quasi steady-state situations, by which it can be decided whether the simplifying assumption of a zero-concentration at the downstream boundary in through-diffusion is justified or not. The application of the criterion requires, however, knowledge of the effective diffusion coefficient of the clay sample. Such knowledge is often absent or only approximately available during the planning phase of a diffusion experiment. Copyright © 2015 Elsevier B.V. All rights reserved.

Effects of lateral diffusion on morphology and dynamics of a microscopic lattice-gas model of pulsed electrodeposition.

PubMed

Frank, Stefan; Roberts, Daniel E; Rikvold, Per Arne

2005-02-08

The influence of nearest-neighbor diffusion on the decay of a metastable low-coverage phase (monolayer adsorption) in a square lattice-gas model of electrochemical metal deposition is investigated by kinetic Monte Carlo simulations. The phase-transformation dynamics are compared to the well-established Kolmogorov-Johnson-Mehl-Avrami theory. The phase transformation is accelerated by diffusion, but remains in accord with the theory for continuous nucleation up to moderate diffusion rates. At very high diffusion rates the phase-transformation kinetic shows a crossover to instantaneous nucleation. Then, the probability of medium-sized clusters is reduced in favor of large clusters. Upon reversal of the supersaturation, the adsorbate desorbs, but large clusters still tend to grow during the initial stages of desorption. Calculation of the free energy of subcritical clusters by enumeration of lattice animals yields a quasiequilibrium distribution which is in reasonable agreement with the simulation results. This is an improvement relative to classical droplet theory, which fails to describe the distributions, since the macroscopic surface tension is a bad approximation for small clusters.

Progress toward bridging from atomistic to continuum modeling to predict nuclear waste glass dissolution.

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

Zapol, Peter; Bourg, Ian; Criscenti, Louise Jacqueline

2011-10-01

This report summarizes research performed for the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Subcontinuum and Upscaling Task. The work conducted focused on developing a roadmap to include molecular scale, mechanistic information in continuum-scale models of nuclear waste glass dissolution. This information is derived from molecular-scale modeling efforts that are validated through comparison with experimental data. In addition to developing a master plan to incorporate a subcontinuum mechanistic understanding of glass dissolution into continuum models, methods were developed to generate constitutive dissolution rate expressions from quantum calculations, force field models were selected to generate multicomponent glass structures and gel layers,more » classical molecular modeling was used to study diffusion through nanopores analogous to those in the interfacial gel layer, and a micro-continuum model (K{mu}C) was developed to study coupled diffusion and reaction at the glass-gel-solution interface.« less

Multi-scale modeling of diffusion-controlled reactions in polymers: renormalisation of reactivity parameters.

PubMed

Everaers, Ralf; Rosa, Angelo

2012-01-07

The quantitative description of polymeric systems requires hierarchical modeling schemes, which bridge the gap between the atomic scale, relevant to chemical or biomolecular reactions, and the macromolecular scale, where the longest relaxation modes occur. Here, we use the formalism for diffusion-controlled reactions in polymers developed by Wilemski, Fixman, and Doi to discuss the renormalisation of the reactivity parameters in polymer models with varying spatial resolution. In particular, we show that the adjustments are independent of chain length. As a consequence, it is possible to match reactions times between descriptions with different resolution for relatively short reference chains and to use the coarse-grained model to make quantitative predictions for longer chains. We illustrate our results by a detailed discussion of the classical problem of chain cyclization in the Rouse model, which offers the simplest example of a multi-scale descriptions, if we consider differently discretized Rouse models for the same physical system. Moreover, we are able to explore different combinations of compact and non-compact diffusion in the local and large-scale dynamics by varying the embedding dimension.

The effect of multiplicity of stellar encounters and the diffusion coefficients in a locally homogeneous three-dimensional stellar medium: Removing the classical divergence

NASA Astrophysics Data System (ADS)

Rastorguev, A. S.; Utkin, N. D.; Chumak, O. V.

2017-08-01

Agekyan's λ-factor that allows for the effect of multiplicity of stellar encounters with large impact parameters has been used for the first time to directly calculate the diffusion coefficients in the phase space of a stellar system. Simple estimates show that the cumulative effect, i.e., the total contribution of distant encounters to the change in the velocity of a test star, given the multiplicity of stellar encounters, is finite, and the logarithmic divergence inherent in the classical description of diffusion is removed, as was shown previously byKandrup using a different, more complex approach. In this case, the expressions for the diffusion coefficients, as in the classical description, contain the logarithm of the ratio of two independent quantities: the mean interparticle distance and the impact parameter of a close encounter. However, the physical meaning of this logarithmic factor changes radically: it reflects not the divergence but the presence of two characteristic length scales inherent in the stellar medium.

Energy Models for One-Carrier Transport in Semiconductor Devices

NASA Technical Reports Server (NTRS)

Jerome, Joseph W.; Shu, Chi-Wang

1991-01-01

Moment models of carrier transport, derived from the Boltzmann equation, made possible the simulation of certain key effects through such realistic assumptions as energy dependent mobility functions. This type of global dependence permits the observation of velocity overshoot in the vicinity of device junctions, not discerned via classical drift-diffusion models, which are primarily local in nature. It was found that a critical role is played in the hydrodynamic model by the heat conduction term. When ignored, the overshoot is inappropriately damped. When the standard choice of the Wiedemann-Franz law is made for the conductivity, spurious overshoot is observed. Agreement with Monte-Carlo simulation in this regime required empirical modification of this law, or nonstandard choices. Simulations of the hydrodynamic model in one and two dimensions, as well as simulations of a newly developed energy model, the RT model, are presented. The RT model, intermediate between the hydrodynamic and drift-diffusion model, was developed to eliminate the parabolic energy band and Maxwellian distribution assumptions, and to reduce the spurious overshoot with physically consistent assumptions. The algorithms employed for both models are the essentially non-oscillatory shock capturing algorithms. Some mathematical results are presented and contrasted with the highly developed state of the drift-diffusion model.

Passive Membrane Permeability: Beyond the Standard Solubility-Diffusion Model.

PubMed

Parisio, Giulia; Stocchero, Matteo; Ferrarini, Alberta

2013-12-10

The spontaneous diffusion of solutes through lipid bilayers is still a challenge for theoretical predictions. Since permeation processes remain beyond the capabilities of unbiased molecular dynamics simulations, an alternative strategy is currently adopted to gain insight into their mechanism and time scale. This is based on a monodimensional description of the translocation process only in terms of the position of the solute along the normal to the lipid bilayer, which is formally expressed in the solubility-diffusion model. Actually, a role of orientational and conformational motions has been pointed out, and the use of advanced simulation techniques has been proposed to take into account their effect. Here, we discuss the limitations of the standard solubility-diffusion approach and propose a more general description of membrane translocation as a diffusion process on a free energy surface, which is a function of the translational and rotational degrees of freedom of the molecule. Simple expressions for the permeability coefficient are obtained under suitable conditions. For fast solute reorientation, the classical solubility-diffusion equation is recovered. Under the assumption that well-defined minima can be identified on the free energy landscape, a mechanistic interpretation of the permeability coefficient in terms of all possible permeation paths is given.

Long-time behavior and Turing instability induced by cross-diffusion in a three species food chain model with a Holling type-II functional response.

PubMed

Haile, Dawit; Xie, Zhifu

2015-09-01

In this paper, we study a strongly coupled reaction-diffusion system describing three interacting species in a food chain model, where the third species preys on the second one and simultaneously the second species preys on the first one. An intra-species competition b2 among the second predator is introduced to the food chain model. This parameter produces some very interesting result in linear stability and Turing instability. We first show that the unique positive equilibrium solution is locally asymptotically stable for the corresponding ODE system when the intra-species competition exists among the second predator. The positive equilibrium solution remains linearly stable for the reaction diffusion system without cross diffusion, hence it does not belong to the classical Turing instability scheme. But it becomes linearly unstable only when cross-diffusion also plays a role in the reaction-diffusion system, hence the instability is driven solely from the effect of cross diffusion. Our results also exhibit some interesting combining effects of cross-diffusion, intra-species competitions and inter-species interactions. Numerically, we conduct a one parameter analysis which illustrate how the interactions change the existence of stable equilibrium, limit cycle, and chaos. Some interesting dynamical phenomena occur when we perform analysis of interactions in terms of self-production of prey and intra-species competition of the middle predator. By numerical simulations, it illustrates the existence of nonuniform steady solutions and new patterns such as spot patterns, strip patterns and fluctuations due to the diffusion and cross diffusion in two-dimension. Published by Elsevier Inc.

Enhanced energy transport in genetically engineered excitonic networks.

PubMed

Park, Heechul; Heldman, Nimrod; Rebentrost, Patrick; Abbondanza, Luigi; Iagatti, Alessandro; Alessi, Andrea; Patrizi, Barbara; Salvalaggio, Mario; Bussotti, Laura; Mohseni, Masoud; Caruso, Filippo; Johnsen, Hannah C; Fusco, Roberto; Foggi, Paolo; Scudo, Petra F; Lloyd, Seth; Belcher, Angela M

2016-02-01

One of the challenges for achieving efficient exciton transport in solar energy conversion systems is precise structural control of the light-harvesting building blocks. Here, we create a tunable material consisting of a connected chromophore network on an ordered biological virus template. Using genetic engineering, we establish a link between the inter-chromophoric distances and emerging transport properties. The combination of spectroscopy measurements and dynamic modelling enables us to elucidate quantum coherent and classical incoherent energy transport at room temperature. Through genetic modifications, we obtain a significant enhancement of exciton diffusion length of about 68% in an intermediate quantum-classical regime.

Influence of cell shape, inhomogeneities and diffusion barriers in cell polarization models

NASA Astrophysics Data System (ADS)

Giese, Wolfgang; Eigel, Martin; Westerheide, Sebastian; Engwer, Christian; Klipp, Edda

2015-12-01

In silico experiments bear the potential for further understanding of biological transport processes by allowing a systematic modification of any spatial property and providing immediate simulation results. Cell polarization and spatial reorganization of membrane proteins are fundamental for cell division, chemotaxis and morphogenesis. We chose the yeast Saccharomyces cerevisiae as an exemplary model system which entails the shuttling of small Rho GTPases such as Cdc42 and Rho, between an active membrane-bound form and an inactive cytosolic form. We used partial differential equations to describe the membrane-cytosol shuttling of proteins. In this study, a consistent extension of a class of 1D reaction-diffusion systems into higher space dimensions is suggested. The membrane is modeled as a thin layer to allow for lateral diffusion and the cytosol is modeled as an enclosed volume. Two well-known polarization mechanisms were considered. One shows the classical Turing-instability patterns, the other exhibits wave-pinning dynamics. For both models, we investigated how cell shape and diffusion barriers like septin structures or bud scars influence the formation of signaling molecule clusters and subsequent polarization. An extensive set of in silico experiments with different modeling hypotheses illustrated the dependence of cell polarization models on local membrane curvature, cell size and inhomogeneities on the membrane and in the cytosol. In particular, the results of our computer simulations suggested that for both mechanisms, local diffusion barriers on the membrane facilitate Rho GTPase aggregation, while diffusion barriers in the cytosol and cell protrusions limit spontaneous molecule aggregations of active Rho GTPase locally.

Rule-based spatial modeling with diffusing, geometrically constrained molecules.

PubMed

Gruenert, Gerd; Ibrahim, Bashar; Lenser, Thorsten; Lohel, Maiko; Hinze, Thomas; Dittrich, Peter

2010-06-07

We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined. For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided. Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-type spatial stochastic simulation. We show, for example, that the combination of combinatorial complexity and geometric effects leads to the emergence of complex self-assemblies and transportation phenomena happening faster than diffusion (using a model of molecular walkers on microtubules). When the mentioned classical simulation approaches are applied, these aspects of modeled systems cannot be observed without very special treatment. Further more, we show that the geometric information can even change the organizational structure of the reaction system. That is, a set of chemical species that can in principle form a stationary state in a Differential Equation formalism, is potentially unstable when geometry is considered, and vice versa. We conclude that our approach provides a new general framework filling a gap in between approaches with no or rigid spatial representation like Partial Differential Equations and specialized coarse-grained spatial simulation systems like those for DNA or virus capsid self-assembly.

Rule-based spatial modeling with diffusing, geometrically constrained molecules

PubMed Central

2010-01-01

Background We suggest a new type of modeling approach for the coarse grained, particle-based spatial simulation of combinatorially complex chemical reaction systems. In our approach molecules possess a location in the reactor as well as an orientation and geometry, while the reactions are carried out according to a list of implicitly specified reaction rules. Because the reaction rules can contain patterns for molecules, a combinatorially complex or even infinitely sized reaction network can be defined. For our implementation (based on LAMMPS), we have chosen an already existing formalism (BioNetGen) for the implicit specification of the reaction network. This compatibility allows to import existing models easily, i.e., only additional geometry data files have to be provided. Results Our simulations show that the obtained dynamics can be fundamentally different from those simulations that use classical reaction-diffusion approaches like Partial Differential Equations or Gillespie-type spatial stochastic simulation. We show, for example, that the combination of combinatorial complexity and geometric effects leads to the emergence of complex self-assemblies and transportation phenomena happening faster than diffusion (using a model of molecular walkers on microtubules). When the mentioned classical simulation approaches are applied, these aspects of modeled systems cannot be observed without very special treatment. Further more, we show that the geometric information can even change the organizational structure of the reaction system. That is, a set of chemical species that can in principle form a stationary state in a Differential Equation formalism, is potentially unstable when geometry is considered, and vice versa. Conclusions We conclude that our approach provides a new general framework filling a gap in between approaches with no or rigid spatial representation like Partial Differential Equations and specialized coarse-grained spatial simulation systems like those for DNA or virus capsid self-assembly. PMID:20529264

SPIR: The potential spreaders involved SIR model for information diffusion in social networks

NASA Astrophysics Data System (ADS)

Rui, Xiaobin; Meng, Fanrong; Wang, Zhixiao; Yuan, Guan; Du, Changjiang

2018-09-01

The Susceptible-Infective-Removed (SIR) model is one of the most widely used models for the information diffusion research in social networks. Many researchers have devoted themselves to improving the classic SIR model in different aspects. However, on the one hand, the equations of these improved models are regarded as continuous functions, while the corresponding simulation experiments use discrete time, leading to the mismatch between numerical solutions got from mathematical method and experimental results obtained by simulating the spreading behaviour of each node. On the other hand, if the equations of these improved models are solved discretely, susceptible nodes will be calculated repeatedly, resulting in a big deviation from the actual value. In order to solve the above problem, this paper proposes a Susceptible-Potential-Infective-Removed (SPIR) model that analyses the diffusion process based on the discrete time according to simulation. Besides, this model also introduces a potential spreader set which solve the problem of repeated calculation effectively. To test the SPIR model, various experiments have been carried out from different angles on both artificial networks and real world networks. The Pearson correlation coefficient between numerical solutions of our SPIR equations and corresponding simulation results is mostly bigger than 0.95, which reveals that the proposed SPIR model is able to depict the information diffusion process with high accuracy.

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

NASA Astrophysics Data System (ADS)

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

2014-11-01

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

Underdamped scaled Brownian motion: (non-)existence of the overdamped limit in anomalous diffusion.

PubMed

Bodrova, Anna S; Chechkin, Aleksei V; Cherstvy, Andrey G; Safdari, Hadiseh; Sokolov, Igor M; Metzler, Ralf

2016-07-27

It is quite generally assumed that the overdamped Langevin equation provides a quantitative description of the dynamics of a classical Brownian particle in the long time limit. We establish and investigate a paradigm anomalous diffusion process governed by an underdamped Langevin equation with an explicit time dependence of the system temperature and thus the diffusion and damping coefficients. We show that for this underdamped scaled Brownian motion (UDSBM) the overdamped limit fails to describe the long time behaviour of the system and may practically even not exist at all for a certain range of the parameter values. Thus persistent inertial effects play a non-negligible role even at significantly long times. From this study a general questions on the applicability of the overdamped limit to describe the long time motion of an anomalously diffusing particle arises, with profound consequences for the relevance of overdamped anomalous diffusion models. We elucidate our results in view of analytical and simulations results for the anomalous diffusion of particles in free cooling granular gases.

Existence and uniqueness of steady state solutions of a nonlocal diffusive logistic equation

NASA Astrophysics Data System (ADS)

Sun, Linan; Shi, Junping; Wang, Yuwen

2013-08-01

In this paper, we consider a dynamical model of population biology which is of the classical Fisher type, but the competition interaction between individuals is nonlocal. The existence, uniqueness, and stability of the steady state solution of the nonlocal problem on a bounded interval with homogeneous Dirichlet boundary conditions are studied.

Communication in Development: Modifications in the Classical Diffusion Model for Family Planning.

ERIC Educational Resources Information Center

Rogers, Everett M.

The role of mass media and interpersonal communication in development in Latin America, Africa, and Asia is reviewed. Then, research and development program experience is synthesized to show (1) that the mass media at present play a major role in creating a "climate for modernization" among villagers, but are less important in diffusing…

THE SPATIO-TEMPORAL EVOLUTION OF SOLAR FLARES OBSERVED WITH AIA/SDO: FRACTAL DIFFUSION, SUB-DIFFUSION, OR LOGISTIC GROWTH?

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

Aschwanden, Markus J., E-mail: aschwanden@lmsal.com

2012-09-20

We explore the spatio-temporal evolution of solar flares by fitting a radial expansion model r(t) that consists of an exponentially growing acceleration phase, followed by a deceleration phase that is parameterized by the generalized diffusion function r(t){proportional_to}{kappa}(t - t{sub 1}){sup {beta}/2}, which includes the logistic growth limit ({beta} = 0), sub-diffusion ({beta} = 0-1), classical diffusion ({beta} = 1), super-diffusion ({beta} = 1-2), and the linear expansion limit ({beta} = 2). We analyze all M- and X-class flares observed with Geostationary Operational Environmental Satellite and Atmospheric Imaging Assembly/Solar Dynamics Observatory (SDO) during the first two years of the SDO mission,more » amounting to 155 events. We find that most flares operate in the sub-diffusive regime ({beta} = 0.53 {+-} 0.27), which we interpret in terms of anisotropic chain reactions of intermittent magnetic reconnection episodes in a low plasma-{beta} corona. We find a mean propagation speed of v = 15 {+-} 12 km s{sup -1}, with maximum speeds of v{sub max} = 80 {+-} 85 km s{sup -1} per flare, which is substantially slower than the sonic speeds expected for thermal diffusion of flare plasmas. The diffusive characteristics established here (for the first time for solar flares) is consistent with the fractal-diffusive self-organized criticality model, which predicted diffusive transport merely based on cellular automaton simulations.« less

Modelling uncertainties in the diffusion-advection equation for radon transport in soil using interval arithmetic.

PubMed

Chakraverty, S; Sahoo, B K; Rao, T D; Karunakar, P; Sapra, B K

2018-02-01

Modelling radon transport in the earth crust is a useful tool to investigate the changes in the geo-physical processes prior to earthquake event. Radon transport is modeled generally through the deterministic advection-diffusion equation. However, in order to determine the magnitudes of parameters governing these processes from experimental measurements, it is necessary to investigate the role of uncertainties in these parameters. Present paper investigates this aspect by combining the concept of interval uncertainties in transport parameters such as soil diffusivity, advection velocity etc, occurring in the radon transport equation as applied to soil matrix. The predictions made with interval arithmetic have been compared and discussed with the results of classical deterministic model. The practical applicability of the model is demonstrated through a case study involving radon flux measurements at the soil surface with an accumulator deployed in steady-state mode. It is possible to detect the presence of very low levels of advection processes by applying uncertainty bounds on the variations in the observed concentration data in the accumulator. The results are further discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dynamical influences on thermospheric composition: implications for semi-empirical models

NASA Astrophysics Data System (ADS)

Sutton, E. K.; Solomon, S. C.

2014-12-01

The TIE-GCM was recently augmented to include helium and argon, two approximately inert species that can be used as tracers of dynamics in the thermosphere. The former species is treated as a major species due to its large abundance near the upper boundary. The effects of exospheric transport are also included in order to simulate realistic seasonal and latitudinal helium distributions. The latter species is treated as a classical minor species, imparting absolutely no forces on the background atmosphere. In this study, we examine the interplay of the various dynamical terms - i.e. background circulation, molecular and Eddy diffusion - as they drive departures from the distributions that would be expected under the assumption of diffusive equilibrium. As this has implications on the formulation of all empirical thermospheric models, we use this understanding to address the following questions: (1) how do errors caused by the assumption of diffusive equilibrium manifest within empirical models of the thermosphere? and (2) where and when does an empirical model's output disagree with its underlying datasets due to the inherent limitations of said model's formulation?

Fractional Brownian motion run with a multi-scaling clock mimics diffusion of spherical colloids in microstructural fluids.

PubMed

Park, Moongyu; Cushman, John Howard; O'Malley, Dan

2014-09-30

The collective molecular reorientations within a nematic liquid crystal fluid bathing a spherical colloid cause the colloid to diffuse anomalously on a short time scale (i.e., as a non-Brownian particle). The deformations and fluctuations of long-range orientational order in the liquid crystal profoundly influence the transient diffusive regimes. Here we show that an anisotropic fractional Brownian process run with a nonlinear multiscaling clock effectively mimics this collective and transient phenomenon. This novel process has memory, Gaussian increments, and a multiscale mean square displacement that can be chosen independently from the fractal dimension of a particle trajectory. The process is capable of modeling multiscale sub-, super-, or classical diffusion. The finite-size Lyapunov exponents for this multiscaling process are defined for future analysis of related mixing processes.

Quantum State Diffusion

NASA Astrophysics Data System (ADS)

Percival, Ian

2005-10-01

1. Introduction; 2. Brownian motion and Itô calculus; 3. Open quantum systems; 4. Quantum state diffusion; 5. Localisation; 6. Numerical methods and examples; 7. Quantum foundations; 8. Primary state diffusion; 9. Classical dynamics of quantum localisation; 10. Semiclassical theory and linear dynamics.

New mechanism of spiral wave initiation in a reaction-diffusion-mechanics system.

PubMed

Weise, Louis D; Panfilov, Alexander V

2011-01-01

Spiral wave initiation in the heart muscle is a mechanism for the onset of dangerous cardiac arrhythmias. A standard protocol for spiral wave initiation is the application of a stimulus in the refractory tail of a propagating excitation wave, a region that we call the "classical vulnerable zone." Previous studies of vulnerability to spiral wave initiation did not take the influence of deformation into account, which has been shown to have a substantial effect on the excitation process of cardiomyocytes via the mechano-electrical feedback phenomenon. In this work we study the effect of deformation on the vulnerability of excitable media in a discrete reaction-diffusion-mechanics (dRDM) model. The dRDM model combines FitzHugh-Nagumo type equations for cardiac excitation with a discrete mechanical description of a finite-elastic isotropic material (Seth material) to model cardiac excitation-contraction coupling and stretch activated depolarizing current. We show that deformation alters the "classical," and forms a new vulnerable zone at longer coupling intervals. This mechanically caused vulnerable zone results in a new mechanism of spiral wave initiation, where unidirectional conduction block and rotation directions of the consequently initiated spiral waves are opposite compared to the mechanism of spiral wave initiation due to the "classical vulnerable zone." We show that this new mechanism of spiral wave initiation can naturally occur in situations that involve wave fronts with curvature, and discuss its relation to supernormal excitability of cardiac tissue. The concept of mechanically induced vulnerability may lead to a better understanding about the onset of dangerous heart arrhythmias via mechano-electrical feedback.

The Renaissance. Grade 7 Model Lesson for Standard 7.8. World History and Geography: Medieval and Early Modern Times. California History-Social Science Course Models.

ERIC Educational Resources Information Center

Zachlod, Michelle, Ed.

California State Standard 7.8 is delineated in the following manner: "Students analyze the origins, accomplishments, and diffusion of the Renaissance," in terms of the way in which the revival of classical learning and the arts affected a new interest in humanism; the importance of Florence in the early stages of the Renaissance and the…

Boundedness and global stability of the two-predator and one-prey models with nonlinear prey-taxis

NASA Astrophysics Data System (ADS)

Wang, Jianping; Wang, Mingxin

2018-06-01

This paper concerns the reaction-diffusion systems modeling the population dynamics of two predators and one prey with nonlinear prey-taxis. We first investigate the global existence and boundedness of the unique classical solution for the general model. Then, we study the global stabilities of nonnegative spatially homogeneous equilibria for an explicit system with type I functional responses and density-dependent death rates for the predators and logistic growth for the prey. Moreover, the convergence rates are also established.

A physically constrained classical description of the homogeneous nucleation of ice in water.

PubMed

Koop, Thomas; Murray, Benjamin J

2016-12-07

Liquid water can persist in a supercooled state to below 238 K in the Earth's atmosphere, a temperature range where homogeneous nucleation becomes increasingly probable. However, the rate of homogeneous ice nucleation in supercooled water is poorly constrained, in part, because supercooled water eludes experimental scrutiny in the region of the homogeneous nucleation regime where it can exist only fleetingly. Here we present a new parameterization of the rate of homogeneous ice nucleation based on classical nucleation theory. In our approach, we constrain the key terms in classical theory, i.e., the diffusion activation energy and the ice-liquid interfacial energy, with physically consistent parameterizations of the pertinent quantities. The diffusion activation energy is related to the translational self-diffusion coefficient of water for which we assess a range of descriptions and conclude that the most physically consistent fit is provided by a power law. The other key term is the interfacial energy between the ice embryo and supercooled water whose temperature dependence we constrain using the Turnbull correlation, which relates the interfacial energy to the difference in enthalpy between the solid and liquid phases. The only adjustable parameter in our model is the absolute value of the interfacial energy at one reference temperature. That value is determined by fitting this classical model to a selection of laboratory homogeneous ice nucleation data sets between 233.6 K and 238.5 K. On extrapolation to temperatures below 233 K, into a range not accessible to standard techniques, we predict that the homogeneous nucleation rate peaks between about 227 and 231 K at a maximum nucleation rate many orders of magnitude lower than previous parameterizations suggest. This extrapolation to temperatures below 233 K is consistent with the most recent measurement of the ice nucleation rate in micrometer-sized droplets at temperatures of 227-232 K on very short time scales using an X-ray laser technique. In summary, we present a new physically constrained parameterization for homogeneous ice nucleation which is consistent with the latest literature nucleation data and our physical understanding of the properties of supercooled water.

Spatially explicit control of invasive species using a reaction-diffusion model

USGS Publications Warehouse

Bonneau, Mathieu; Johnson, Fred A.; Romagosa, Christina M.

2016-01-01

Invasive species, which can be responsible for severe economic and environmental damages, must often be managed over a wide area with limited resources, and the optimal allocation of effort in space and time can be challenging. If the spatial range of the invasive species is large, control actions might be applied only on some parcels of land, for example because of property type, accessibility, or limited human resources. Selecting the locations for control is critical and can significantly impact management efficiency. To help make decisions concerning the spatial allocation of control actions, we propose a simulation based approach, where the spatial distribution of the invader is approximated by a reaction–diffusion model. We extend the classic Fisher equation to incorporate the effect of control both in the diffusion and local growth of the invader. The modified reaction–diffusion model that we propose accounts for the effect of control, not only on the controlled locations, but on neighboring locations, which are based on the theoretical speed of the invasion front. Based on simulated examples, we show the superiority of our model compared to the state-of-the-art approach. We illustrate the use of this model for the management of Burmese pythons in the Everglades (Florida, USA). Thanks to the generality of the modified reaction–diffusion model, this framework is potentially suitable for a wide class of management problems and provides a tool for managers to predict the effects of different management strategies.

Flame Shapes of Luminous NonBuoyant Laminar Coflowing Jet Diffusion Flames

NASA Technical Reports Server (NTRS)

Lin, K.-C.; Faeth, G. M.

1999-01-01

Laminar diffusion flames are of interest as model flame systems that are more tractable for analysis and experiments than practical turbulent diffusion flames. Certainly understanding laminar flames must precede understanding more complex turbulent flames while man'y laminar diffusion flame properties are directly relevant to turbulent diffusion flames using laminar flamelet concepts. Laminar diffusion flame shapes have been of interest since the classical study of Burke and Schumann because they involve a simple nonintrusive measurement that is convenient for evaluating flame structure predictions. Motivated by these observations, the shapes of laminar flames were considered during the present investigation. The present study was limited to nonbuoyant flames because most practical flames are not buoyant. Effects of buoyancy were minimized by observing flames having large flow velocities at small pressures. Present methods were based on the study of the shapes of nonbu,3yant round laminar jet diffusion flames of Lin et al. where it was found that a simple analysis due to Spalding yielded good predictions of the flame shapes reported by Urban et al. and Sunderland et al.

Study of the Fine-Scale Structure of Cumulus Clouds.

NASA Astrophysics Data System (ADS)

Rodi, Alfred R.

Small cumulus clouds are studied using data from an instrumented aircraft. Two aspects of the role of turbulence and mixing in these couds are examined: (1) the effect of mixing on the droplet size distribution, and (2) the effect of turbulence on the spread of ice crystal plumes artificially generated with cloud seeding agents. The data were collected in the course of the Bureau of Reclamation's High Plains Cooperative Experiment (HIPLEX) in Montana in the summers of 1978-80 by the University of Wyoming King Air aircraft. The shape of the cloud droplet spectrum as measured by the Particle Measuring Systems (PMS) Forward Scattering Spectrometer Probe (FSSP) is found to be very sensitive to entrainment of dry environmental air into the cloud. The narrowest cloud droplet spectra, the highest droplet concentrations, and the largest sized droplets are found in the cloud parcels which are least affected by entrainment. The most dilute regions of cloud exhibit the broadest spectra which are frequently bimodal. A procedure for measuring cloud inhomogeneity from FSSP is developed. The data shows that the clouds are extremely inhomogeneous in structure. Current models of inhomogeneous mixing are shown to be inadequate in explaining droplet spectrum effects. However, the inhomogeneous models characterize the data far better than classical models of droplet spectrum evolution. High resolution measurements of ice crystals from the PMS two dimensional imaging probe are used to characterize the spread of the ice crystal plume in seeded clouds. Plume spread is found to be a very complicated process which is in some cases dominated by organized motions in the cloud. As a result, classical diffusion theory is often inadequate to predict plume growth. The turbulent diffusion that occurs is shown to be best modeled using the relative diffusion concept of Richardson. Procedures for adapting aircraft data to the relative diffusion model are developed, including techniques for converting the aircraft Eulerian data into estimates of Lagrangian correlations. Predictions of the model are compared with observations of plume growth. A detailed analysis of errors in the air motion sensing system on the aircraft is presented. A procedure is developed to estimate the errors due to aircraft gyroscope sensitivity to horizontal accelerations.

Space-time models based on random fields with local interactions

NASA Astrophysics Data System (ADS)

Hristopulos, Dionissios T.; Tsantili, Ivi C.

2016-08-01

The analysis of space-time data from complex, real-life phenomena requires the use of flexible and physically motivated covariance functions. In most cases, it is not possible to explicitly solve the equations of motion for the fields or the respective covariance functions. In the statistical literature, covariance functions are often based on mathematical constructions. In this paper, we propose deriving space-time covariance functions by solving “effective equations of motion”, which can be used as statistical representations of systems with diffusive behavior. In particular, we propose to formulate space-time covariance functions based on an equilibrium effective Hamiltonian using the linear response theory. The effective space-time dynamics is then generated by a stochastic perturbation around the equilibrium point of the classical field Hamiltonian leading to an associated Langevin equation. We employ a Hamiltonian which extends the classical Gaussian field theory by including a curvature term and leads to a diffusive Langevin equation. Finally, we derive new forms of space-time covariance functions.

Multi-Scale Modeling and the Eddy-Diffusivity/Mass-Flux (EDMF) Parameterization

NASA Astrophysics Data System (ADS)

Teixeira, J.

2015-12-01

Turbulence and convection play a fundamental role in many key weather and climate science topics. Unfortunately, current atmospheric models cannot explicitly resolve most turbulent and convective flow. Because of this fact, turbulence and convection in the atmosphere has to be parameterized - i.e. equations describing the dynamical evolution of the statistical properties of turbulence and convection motions have to be devised. Recently a variety of different models have been developed that attempt at simulating the atmosphere using variable resolution. A key problem however is that parameterizations are in general not explicitly aware of the resolution - the scale awareness problem. In this context, we will present and discuss a specific approach, the Eddy-Diffusivity/Mass-Flux (EDMF) parameterization, that not only is in itself a multi-scale parameterization but it is also particularly well suited to deal with the scale-awareness problems that plague current variable-resolution models. It does so by representing small-scale turbulence using a classic Eddy-Diffusivity (ED) method, and the larger-scale (boundary layer and tropospheric-scale) eddies as a variety of plumes using the Mass-Flux (MF) concept.

Approximation of epidemic models by diffusion processes and their statistical inference.

PubMed

Guy, Romain; Larédo, Catherine; Vergu, Elisabeta

2015-02-01

Multidimensional continuous-time Markov jump processes [Formula: see text] on [Formula: see text] form a usual set-up for modeling [Formula: see text]-like epidemics. However, when facing incomplete epidemic data, inference based on [Formula: see text] is not easy to be achieved. Here, we start building a new framework for the estimation of key parameters of epidemic models based on statistics of diffusion processes approximating [Formula: see text]. First, previous results on the approximation of density-dependent [Formula: see text]-like models by diffusion processes with small diffusion coefficient [Formula: see text], where [Formula: see text] is the population size, are generalized to non-autonomous systems. Second, our previous inference results on discretely observed diffusion processes with small diffusion coefficient are extended to time-dependent diffusions. Consistent and asymptotically Gaussian estimates are obtained for a fixed number [Formula: see text] of observations, which corresponds to the epidemic context, and for [Formula: see text]. A correction term, which yields better estimates non asymptotically, is also included. Finally, performances and robustness of our estimators with respect to various parameters such as [Formula: see text] (the basic reproduction number), [Formula: see text], [Formula: see text] are investigated on simulations. Two models, [Formula: see text] and [Formula: see text], corresponding to single and recurrent outbreaks, respectively, are used to simulate data. The findings indicate that our estimators have good asymptotic properties and behave noticeably well for realistic numbers of observations and population sizes. This study lays the foundations of a generic inference method currently under extension to incompletely observed epidemic data. Indeed, contrary to the majority of current inference techniques for partially observed processes, which necessitates computer intensive simulations, our method being mostly an analytical approach requires only the classical optimization steps.

Computational approach to Thornley's problem by bivariate operational calculus

NASA Astrophysics Data System (ADS)

Bazhlekova, E.; Dimovski, I.

2012-10-01

Thornley's problem is an initial-boundary value problem with a nonlocal boundary condition for linear onedimensional reaction-diffusion equation, used as a mathematical model of spiral phyllotaxis in botany. Applying a bivariate operational calculus we find explicit representation of the solution, containing two convolution products of special solutions and the arbitrary initial and boundary functions. We use a non-classical convolution with respect to the space variable, extending in this way the classical Duhamel principle. The special solutions involved are represented in the form of fast convergent series. Numerical examples are considered to show the application of the present technique and to analyze the character of the solution.

Fractional-calculus diffusion equation

PubMed Central

2010-01-01

Background Sequel to the work on the quantization of nonconservative systems using fractional calculus and quantization of a system with Brownian motion, which aims to consider the dissipation effects in quantum-mechanical description of microscale systems. Results The canonical quantization of a system represented classically by one-dimensional Fick's law, and the diffusion equation is carried out according to the Dirac method. A suitable Lagrangian, and Hamiltonian, describing the diffusive system, are constructed and the Hamiltonian is transformed to Schrodinger's equation which is solved. An application regarding implementation of the developed mathematical method to the analysis of diffusion, osmosis, which is a biological application of the diffusion process, is carried out. Schrödinger's equation is solved. Conclusions The plot of the probability function represents clearly the dissipative and drift forces and hence the osmosis, which agrees totally with the macro-scale view, or the classical-version osmosis. PMID:20492677

Thermophysical properties of liquid Ni around the melting temperature from molecular dynamics simulation

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

Rozas, R. E.; Department of Physics, University of Bío-Bío, Av. Collao 1202, P.O. Box 5C, Concepción; Demiraǧ, A. D.

Thermophysical properties of liquid nickel (Ni) around the melting temperature are investigated by means of classical molecular dynamics (MD) simulation, using three different embedded atom method potentials to model the interactions between the Ni atoms. Melting temperature, enthalpy, static structure factor, self-diffusion coefficient, shear viscosity, and thermal diffusivity are compared to recent experimental results. Using ab initio MD simulation, we also determine the static structure factor and the mean-squared displacement at the experimental melting point. For most of the properties, excellent agreement is found between experiment and simulation, provided the comparison relative to the corresponding melting temperature. We discuss themore » validity of the Hansen-Verlet criterion for the static structure factor as well as the Stokes-Einstein relation between self-diffusion coefficient and shear viscosity. The thermal diffusivity is extracted from the autocorrelation function of a wavenumber-dependent temperature fluctuation variable.« less

First principles molecular dynamics of molten NaCl

NASA Astrophysics Data System (ADS)

Galamba, N.; Costa Cabral, B. J.

2007-03-01

First principles Hellmann-Feynman molecular dynamics (HFMD) results for molten NaCl at a single state point are reported. The effect of induction forces on the structure and dynamics of the system is studied by comparison of the partial radial distribution functions and the velocity and force autocorrelation functions with those calculated from classical MD based on rigid-ion and shell-model potentials. The first principles results reproduce the main structural features of the molten salt observed experimentally, whereas they are incorrectly described by both rigid-ion and shell-model potentials. Moreover, HFMD Green-Kubo self-diffusion coefficients are in closer agreement with experimental data than those predicted by classical MD. A comprehensive discussion of MD results for molten NaCl based on different ab initio parametrized polarizable interionic potentials is also given.

Vacancy–Vacancy Interaction Induced Oxygen Diffusivity Enhancement in Undoped Nonstoichiometric Ceria

DOE PAGES

Yuan, Fenglin; Zhang, Yanwen; Weber, William J.

2015-05-19

In this paper, molecular dynamics simulations and molecular static calculations have been used to systematically study oxygen vacancy transport in undoped nonstoichiometric ceria. A strong oxygen diffusivity enhancement appears in the vacancy concentration range of 2–4% over the temperature range from 1000 to 2000 K. An Arrhenius ion diffusion mechanism by vacancy hopping along the (100) direction is unambiguously identified, and an increasing trend of both the oxygen migration barrier and the prefactor with increasing vacancy concentration is observed. Within the framework of classical diffusion theory, a weak concentration dependence of the prefactor in oxygen vacancy migration is shown tomore » be crucial for explaining the unusual fast oxygen ion migration in the low concentration range and consequently the appearance of a maximum in oxygen diffusivity. Finally, a representative (100) direction interaction model is constructed to identify long-range vacancy–vacancy interaction as the structural origin of the positive correlation between oxygen migration barrier and vacancy concentration.« less

Validation of Potential Models for Li2O in Classical Molecular Dynamics Simulation

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

Oda, Takuji; Oya, Yasuhisa; Tanaka, Satoru

2007-08-01

Four Buckingham-type pairwise potential models for Li2O were assessed by molecular static and dynamics simulations. In the static simulation, all models afforded acceptable agreement with experimental values and ab initio calculation results for the crystalline properties. Moreover, the superionic phase transition was realized in the dynamics simulation. However, the Li diffusivity and the lattice expansion were not adequately reproduced at the same time by any model. When using these models in future radiation simulation, these features should be taken into account, in order to reduce the model dependency of the results.

Translucent Radiosity: Efficiently Combining Diffuse Inter-Reflection and Subsurface Scattering.

PubMed

Sheng, Yu; Shi, Yulong; Wang, Lili; Narasimhan, Srinivasa G

2014-07-01

It is hard to efficiently model the light transport in scenes with translucent objects for interactive applications. The inter-reflection between objects and their environments and the subsurface scattering through the materials intertwine to produce visual effects like color bleeding, light glows, and soft shading. Monte-Carlo based approaches have demonstrated impressive results but are computationally expensive, and faster approaches model either only inter-reflection or only subsurface scattering. In this paper, we present a simple analytic model that combines diffuse inter-reflection and isotropic subsurface scattering. Our approach extends the classical work in radiosity by including a subsurface scattering matrix that operates in conjunction with the traditional form factor matrix. This subsurface scattering matrix can be constructed using analytic, measurement-based or simulation-based models and can capture both homogeneous and heterogeneous translucencies. Using a fast iterative solution to radiosity, we demonstrate scene relighting and dynamically varying object translucencies at near interactive rates.

Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems

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

Zhen, Li; Yazdani, Alireza; Tartakovsky, Alexandre M.

2015-07-07

We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic DPD framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between particles, and an analytical formula is proposed to relate the mesoscopic concentration friction to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPDmore » simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.« less

The rate constant of a quantum-diffusion-controlled bimolecular reaction

NASA Astrophysics Data System (ADS)

Bondarev, B. V.

1986-04-01

A quantum-mechanical equation is derived in the tight-bond approximation which describes the motion and chemical interaction of a pair of species A and B when their displacement in the matrix is caused by tunnelling. Within the framework of the discrete model of random walks, definitions are given of the probability and rate constant of a reaction A + B → P (products) proceeding in a condensed medium. A method is suggested for calculating the rate constant of a quantum-diffusion-controlled bimolecular reaction. By this method, an expression is obtained for the rate constant in the stationary spherically symmetrical case. An equation for the density matrix is also proposed which describes the motion and chemical interaction of a pair of species when the quantum and classical diffusion are competitive.

Concentration-Encoded Subdiffusive Molecular Communication: Theory, Channel Characteristics, and Optimum Signal Detection.

PubMed

Mahfuz, Mohammad Upal; Makrakis, Dimitrios; Mouftah, Hussein T

2016-09-01

Unlike normal diffusion, in anomalous diffusion, the movement of a molecule is described by the correlated random walk model where the mean square displacement of a molecule depends on the power law of time. In molecular communication (MC), there are many scenarios when the propagation of molecules cannot be described by normal diffusion process, where anomalous diffusion is a better fit. In this paper, the effects of anomalous subdiffusion on concentration-encoded molecular communication (CEMC) are investigated. Although classical (i.e., normal) diffusion is a widely-used model of diffusion in molecular communication (MC) research, anomalous subdiffusion is quite common in biological media involving bio-nanomachines, yet inadequately addressed as a research issue so far. Using the fractional diffusion approach, the molecular propagation effects in the case of pure subdiffusion occurring in an unbounded three-dimensional propagation medium have been shown in detail in terms of temporal dispersion parameters of the impulse response of the subdiffusive channel. Correspondingly, the bit error rate (BER) performance of a CEMC system is investigated with sampling-based (SD) and strength (i.e., energy)-based (ED) signal detection methods. It is found that anomalous subdiffusion has distinctive time-dispersive properties that play a vital role in accurately designing a subdiffusive CEMC system. Unlike normal diffusion, to detect information symbols in subdiffusive CEMC, a receiver requires larger memory size to operate correctly and hence a more complex structure. An in-depth analysis has been made on the performances of SD and ED optimum receiver models under diffusion noise and intersymbol interference (ISI) scenarios when communication range, transmission data rate, and memory size vary. In subdiffusive CEMC, the SD method.

Effect of sharp maximum in ion diffusivity for liquid xenon

NASA Astrophysics Data System (ADS)

Lankin, A. V.; Orekhov, M. A.

2016-11-01

Ion diffusion in a liquid usually could be treated as a movement of an ion cluster in a viscous media. For small ions this leads to a special feature: diffusion coefficient is either independent of the ion size or increases with it. We find a different behavior for small ions in liquid xenon. Calculation of the dependence of an ion diffusion coefficient in liquid xenon on the ion size is carried out. Classical molecular dynamics method is applied. Calculated dependence of the ion diffusion coefficient on its radius has sharp maximums at the ion radiuses 1.75 and 2 Å. Every maximum is placed between two regions with different stable ion cluster configurations. This leads to the instability of these configurations in a small region between them. Consequently ion with radius near 1.75 or 2 Å could jump from one configuration to another. This increases the speed of the diffusion. A simple qualitative model for this effect is suggested. The decomposition of the ion movement into continuous and jump diffusion shows that continuous part of the diffusion is the same as for the ion cluster in the stable region.

Properties of grains derived from IRAS observations of dust

NASA Technical Reports Server (NTRS)

Wesselius, P. R.; Chlewicki, Grzegorz; Laureijs, Rene J.

1989-01-01

The authors used the results of Infrared Astronomy Satellite (IRAS) observations of diffuse medium dust to develop a theoretical model of the infrared properties of grains. Recent models based entirely on traditional observations of extinction and polarization include only particles whose equilibrium temperatures do not exceed 20 K in the diffuse interstellar medium. These classical grains, for which the authors have adopted the multipopulation model developed by Hong and Greenberg (1980), can explain only the emission in the IRAS 100 micron band. The measurements at shorter wavelengths (12, 25 and 60 microns) require two new particle populations. Vibrational fluorescence from aromatic molecules provides the most likely explanation for the emission observed at 12 microns, with polycyclic aeromatic hydrocarbons (PAHs) containing about 10 percent of cosmic carbon. A simplified model of the emission process shows that PAH molecules can also explain most of the emission measured by IRAS at 25 microns. The authors identified the warm particles responsible for the excess 60 microns emission with small (a approx. equals 0.01 microns) iron grains. A compilation of the available data on the optical properties of iron indicates that the diffuse medium temperature of small iron particles should be close to 50 K and implies that a large, possibly dominant, fraction of cosmic iron must be locked up in metallic particles in order to match the observed 60 microns intensities. The model matches the infrared fluxes typically observed by IRAS in the diffuse medium and can also reproduce the infrared surface brightness distribution in individual clouds. In particular, the combination of iron and classical cool grains can explain the surprising observations of the 60/100 microns flux ratio in clouds, which is either constant or increases slightly towards higher opacities. The presence of metallic grains has significant implications for the physics of the interstellar medium, including catalytic H2 formation, for which iron grains could be the main site; differences in depletion patterns between iron and other refractory elements (Mg, Si); and superparamagnetic behavior of large grains with embedded iron clusters giving rise to the observed high degree of alignment by the galactic magnetic field.

The effect of electric field geometry on the performance of electromembrane extraction systems: footprints of a third driving force along with migration and diffusion.

PubMed

Moazami, Hamid Reza; Hosseiny Davarani, Saied Saeed; Mohammadi, Jamil; Nojavan, Saeed; Abrari, Masoud

2015-09-03

The distribution of electric field vectors was first calculated for electromembrane extraction (EME) systems in classical and cylindrical electrode geometries. The results showed that supported liquid membrane (SLM) has a general field amplifying effect due to its lower dielectric constant in comparison with aqueous donor/acceptor solutions. The calculated norms of the electric field vector showed that a DC voltage of 50 V can create huge electric field strengths up to 64 kV m(-1) and 111 kV m(-1) in classical and cylindrical geometries respectively. In both cases, the electric field strength reached its peak value on the inner wall of the SLM. In the case of classical geometry, the field strength was a function of the polar position of the SLM whereas the field strength in cylindrical geometry was angularly uniform. In order to investigate the effect of the electrode geometry on the performance of real EME systems, the analysis was carried out in three different geometries including classical, helical and cylindrical arrangements using naproxen and sodium diclofenac as the model analytes. Despite higher field strength and extended cross sectional area, the helical and cylindrical geometries gave lower recoveries with respect to the classical EME. The observed decline of the signal was proved to be against the relations governing migration and diffusion processes, which means that a third driving force is involved in EME. The third driving force is the interaction between the radially inhomogeneous electric field and the analyte in its neutral form. Copyright © 2015 Elsevier B.V. All rights reserved.

Fluorescence Correlation Spectroscopy and Nonlinear Stochastic Reaction-Diffusion

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

Del Razo, Mauricio; Pan, Wenxiao; Qian, Hong

2014-05-30

The currently existing theory of fluorescence correlation spectroscopy (FCS) is based on the linear fluctuation theory originally developed by Einstein, Onsager, Lax, and others as a phenomenological approach to equilibrium fluctuations in bulk solutions. For mesoscopic reaction-diffusion systems with nonlinear chemical reactions among a small number of molecules, a situation often encountered in single-cell biochemistry, it is expected that FCS time correlation functions of a reaction-diffusion system can deviate from the classic results of Elson and Magde [Biopolymers (1974) 13:1-27]. We first discuss this nonlinear effect for reaction systems without diffusion. For nonlinear stochastic reaction-diffusion systems there are no closedmore » solutions; therefore, stochastic Monte-Carlo simulations are carried out. We show that the deviation is small for a simple bimolecular reaction; the most significant deviations occur when the number of molecules is small and of the same order. Extending Delbrück-Gillespie’s theory for stochastic nonlinear reactions with rapidly stirring to reaction-diffusion systems provides a mesoscopic model for chemical and biochemical reactions at nanometric and mesoscopic level such as a single biological cell.« less

Underdamped scaled Brownian motion: (non-)existence of the overdamped limit in anomalous diffusion

PubMed Central

Bodrova, Anna S.; Chechkin, Aleksei V.; Cherstvy, Andrey G.; Safdari, Hadiseh; Sokolov, Igor M.; Metzler, Ralf

2016-01-01

It is quite generally assumed that the overdamped Langevin equation provides a quantitative description of the dynamics of a classical Brownian particle in the long time limit. We establish and investigate a paradigm anomalous diffusion process governed by an underdamped Langevin equation with an explicit time dependence of the system temperature and thus the diffusion and damping coefficients. We show that for this underdamped scaled Brownian motion (UDSBM) the overdamped limit fails to describe the long time behaviour of the system and may practically even not exist at all for a certain range of the parameter values. Thus persistent inertial effects play a non-negligible role even at significantly long times. From this study a general questions on the applicability of the overdamped limit to describe the long time motion of an anomalously diffusing particle arises, with profound consequences for the relevance of overdamped anomalous diffusion models. We elucidate our results in view of analytical and simulations results for the anomalous diffusion of particles in free cooling granular gases. PMID:27462008

3D Time-lapse Imaging and Quantification of Mitochondrial Dynamics

NASA Astrophysics Data System (ADS)

Sison, Miguel; Chakrabortty, Sabyasachi; Extermann, Jérôme; Nahas, Amir; James Marchand, Paul; Lopez, Antonio; Weil, Tanja; Lasser, Theo

2017-02-01

We present a 3D time-lapse imaging method for monitoring mitochondrial dynamics in living HeLa cells based on photothermal optical coherence microscopy and using novel surface functionalization of gold nanoparticles. The biocompatible protein-based biopolymer coating contains multiple functional groups which impart better cellular uptake and mitochondria targeting efficiency. The high stability of the gold nanoparticles allows continuous imaging over an extended time up to 3000 seconds without significant cell damage. By combining temporal autocorrelation analysis with a classical diffusion model, we quantify mitochondrial dynamics and cast these results into 3D maps showing the heterogeneity of diffusion parameters across the whole cell volume.

Nivolumab With or Without Varlilumab in Treating Patients With Relapsed or Refractory Aggressive B-cell Lymphomas

ClinicalTrials.gov

2018-06-11

ALK-Positive Large B-Cell Lymphoma; Atypical Burkitt/Burkitt-Like Lymphoma; Burkitt-Like Lymphoma With 11q Aberration; Diffuse Large B-Cell Lymphoma Activated B-Cell Type; Diffuse Large B-Cell Lymphoma Associated With Chronic Inflammation; Diffuse Large B-Cell Lymphoma Germinal Center B-Cell Type; Diffuse Large B-Cell Lymphoma, Not Otherwise Specified; EBV-Positive Diffuse Large B-Cell Lymphoma, Not Otherwise Specified; EBV-Positive Mucocutaneous Ulcer; High-Grade B-Cell Lymphoma With MYC, BCL2, and BCL6 Rearrangements; Human Herpesvirus 8-Positive Neoplastic Cells Present; Intravascular Large B-Cell Lymphoma; Large B-Cell Lymphoma With IRF4 Rearrangement; Plasmablastic Lymphoma; Primary Cutaneous Diffuse Large B-Cell Lymphoma; Primary Cutaneous Diffuse Large B-Cell Lymphoma, Leg Type; Primary Diffuse Large B-Cell Lymphoma of the Central Nervous System; Primary Effusion Lymphoma; Recurrent B-Cell Lymphoma, Unclassifiable, With Features Intermediate Between Diffuse Large B-Cell Lymphoma and Classic Hodgkin Lymphoma; Recurrent Burkitt Lymphoma; Recurrent Diffuse Large B-Cell Lymphoma; Recurrent Lymphomatoid Granulomatosis; Recurrent Primary Mediastinal (Thymic) Large B-Cell Cell Lymphoma; Refractory B-Cell Lymphoma, Unclassifiable, With Features Intermediate Between Diffuse Large B-Cell Lymphoma and Classic Hodgkin Lymphoma; Refractory Burkitt Lymphoma; Refractory Diffuse Large B-Cell Lymphoma; Refractory Primary Mediastinal (Thymic) Large B-Cell Cell Lymphoma; Small Intestinal High Grade B-Cell Lymphoma, Not Otherwise Specified; T-Cell/Histiocyte-Rich Large B-Cell Lymphoma

Model for Ultrafast Carrier Scattering in Semiconductors

DTIC Science & Technology

2012-11-14

energy transfer between semi-classical carrier drift-diffusion under an electric field and quantum kinetics of interband /intersubband transitions...from an electron during each phonon-emission event. The net rate of phonon emission is determined by the Boltzmann scattering equation which depends ...energy-drift term under a strong dc field was demonstrated to reduce the field- dependent drift velocity and mobility. The Doppler shift in the energy

A space-fractional Monodomain model for cardiac electrophysiology combining anisotropy and heterogeneity on realistic geometries

NASA Astrophysics Data System (ADS)

Cusimano, N.; Gerardo-Giorda, L.

2018-06-01

Classical models of electrophysiology do not typically account for the effects of high structural heterogeneity in the spatio-temporal description of excitation waves propagation. We consider a modification of the Monodomain model obtained by replacing the diffusive term of the classical formulation with a fractional power of the operator, defined in the spectral sense. The resulting nonlocal model describes different levels of tissue heterogeneity as the fractional exponent is varied. The numerical method for the solution of the fractional Monodomain relies on an integral representation of the nonlocal operator combined with a finite element discretisation in space, allowing to handle in a natural way bounded domains in more than one spatial dimension. Numerical tests in two spatial dimensions illustrate the features of the model. Activation times, action potential duration and its dispersion throughout the domain are studied as a function of the fractional parameter: the expected peculiar behaviour driven by tissue heterogeneities is recovered.

A Model of Controlled Growth

NASA Astrophysics Data System (ADS)

Bressan, Alberto; Lewicka, Marta

2018-03-01

We consider a free boundary problem for a system of PDEs, modeling the growth of a biological tissue. A morphogen, controlling volume growth, is produced by specific cells and then diffused and absorbed throughout the domain. The geometric shape of the growing tissue is determined by the instantaneous minimization of an elastic deformation energy, subject to a constraint on the volumetric growth. For an initial domain with C}^{2,α boundary, our main result establishes the local existence and uniqueness of a classical solution, up to a rigid motion.

Anomalous transport regimes and asymptotic concentration distributions in the presence of advection and diffusion on a comb structure

NASA Astrophysics Data System (ADS)

Dvoretskaya, Olga A.; Kondratenko, Peter S.

2009-04-01

We study the transport of impurity particles on a comb structure in the presence of advection. The main body concentration and asymptotic concentration distributions are obtained. Seven different transport regimes occur on the comb structure with finite teeth: classical diffusion, advection, quasidiffusion, subdiffusion, slow classical diffusion, and two kinds of slow advection. Quasidiffusion deserves special attention. It is characterized by a linear growth of the mean-square displacement. However, quasidiffusion is an anomalous transport regime. We established that a change in transport regimes in time leads to a change in regimes in space. Concentration tails have a cascade structure, namely, consisting of several parts.

Generalized quantum Fokker-Planck, diffusion, and Smoluchowski equations with true probability distribution functions.

PubMed

Banik, Suman Kumar; Bag, Bidhan Chandra; Ray, Deb Shankar

2002-05-01

Traditionally, quantum Brownian motion is described by Fokker-Planck or diffusion equations in terms of quasiprobability distribution functions, e.g., Wigner functions. These often become singular or negative in the full quantum regime. In this paper a simple approach to non-Markovian theory of quantum Brownian motion using true probability distribution functions is presented. Based on an initial coherent state representation of the bath oscillators and an equilibrium canonical distribution of the quantum mechanical mean values of their coordinates and momenta, we derive a generalized quantum Langevin equation in c numbers and show that the latter is amenable to a theoretical analysis in terms of the classical theory of non-Markovian dynamics. The corresponding Fokker-Planck, diffusion, and Smoluchowski equations are the exact quantum analogs of their classical counterparts. The present work is independent of path integral techniques. The theory as developed here is a natural extension of its classical version and is valid for arbitrary temperature and friction (the Smoluchowski equation being considered in the overdamped limit).

Causal Diffusion and the Survival of Charge Fluctuations

NASA Astrophysics Data System (ADS)

Abdel-Aziz, Mohamed; Gavin, Sean

2004-10-01

Diffusion may obliterate fluctuation signals of the QCD phase transition in nuclear collisions at SPS and RHIC energies. We propose a hyperbolic diffusion equation to study the dissipation of net charge fluctuations [1]. This equation is needed in a relativistic context, because the classic parabolic diffusion equation violates causality. We find that causality substantially limits the extent to which diffusion can dissipate these fluctuations. [1] M. Abdel-Aziz and S. Gavin, nucl-th/0404058

Insight into He diffusion in apatite by ion beam experiments and quantum calculations: implication for the (U-Th)/He thermochronometer

NASA Astrophysics Data System (ADS)

Gautheron, C.; Mbongo-Djimbi, D.; Gerin, C.; Roques, J.; Bachelet, C.; Oliviero, E.; Tassan-Got, L.

2015-12-01

The apatite (U-Th)/He (AHe) system has rapidly become a very popular thermochronometer, however, interpretation of AHe age depends on a precise knowledge of He diffusion. Several studies suggest that He retention is function of the amount of damage that is controlled by U-Th concentration, grain chemistry and thermal history. Still, the models are not well constrained and do not fully explain the mechanism of He retention. In order to have a deeper insight into this issue, a multidisciplinary study on apatite combining physical methods such as multi-scale theoretical diffusion calculations based on Density Functional Theory (DFT) with diffusion experiments by ion beam Elastic Recoil Diffusion Analysis (ERDA) were performed. Quantum calculations permit to quantify He diffusivity base level for damage-free crystal and to estimate the additional energy cost to extract He atoms trapped in point defects (i.e. vacancies). On the other hand ion beam ERDA experiments allow to measure He diffusivity in artificially damaged crystals. We show that damage-free apatite crystals are characterized by low retention behavior and closure temperature of ~35°C for pure F-apatite to higher value for Cl rich apatite (up to 12°C higher), for typical grain size and cooling rate (Mbongo-Djimbi et al., 2015). Our computed closure temperature is slightly lower than previously reported experimental values (~50°C). Using ERDA and DFT modeling of damage, we show how He diffusivity is influenced by damage. Finally, we are able to propose a new modeling of He diffusion incorporating mechanisms not included in classical damage models, and taking into account the level of damage and apatite chemistry. We show that it could affect significantly AHe age interpretation. Mbongo-Djimbi D. et al. 2015. Apatite composition effect on (U-Th)/He thermochronometer: an atomistic point of view. Geohimica Cosmochim. Acta.

Reactive solid surface morphology variation via ionic diffusion.

PubMed

Sun, Zhenchao; Zhou, Qiang; Fan, Liang-Shih

2012-08-14

In gas-solid reactions, one of the most important factors that determine the overall reaction rate is the solid morphology, which can be characterized by a combination of smooth, convex and concave structures. Generally, the solid surface structure varies in the course of reactions, which is classically noted as being attributed to one or more of the following three mechanisms: mechanical interaction, molar volume change, and sintering. Here we show that if a gas-solid reaction involves the outward ionic diffusion of a solid-phase reactant then this outward ionic diffusion could eventually smooth the surface with an initial concave and/or convex structure. Specifically, the concave surface is filled via a larger outward diffusing surface pointing to the concave valley, whereas the height of the convex surface decreases via a lower outward diffusion flux in the vertical direction. A quantitative 2-D continuum diffusion model is established to analyze these two morphological variation processes, which shows consistent results with the experiments. This surface morphology variation by solid-phase ionic diffusion serves to provide a fourth mechanism that supplements the traditionally acknowledged solid morphology variation or, in general, porosity variation mechanisms in gas-solid reactions.

A novel model for the chaotic dynamics of superdiffusion

NASA Astrophysics Data System (ADS)

Cushman, J. H.; Park, M.; O'Malley, D.

2009-04-01

Previously we've shown that by modeling the convective velocity in a turbulent flow field as Brownian, one obtains Richardson super diffusion where the expected distance between pairs of particles scales with time cubed. By proving generalized central limit type theorems it's possible to show that modeling the velocity or the acceleration as α-stable Levy gives rise to more general scaling laws that can easily explain other super diffusive regimes. The problem with this latter approach is that the mean square displacement of a particle is infinite. Here we provide an alternate approach that gives a power law mean square displacement of any desired order. We do so by constructing compressed and stretched extensions to Brownian motion. The finite size Lyapunov exponent, the underlying stochastic differential equation and its corresponding Fokker-Planck equations are derived. The fractal dimension of these processes turns out to be the same as that of classical Brownian motion.

Decomposing task-switching costs with the diffusion model.

PubMed

Schmitz, Florian; Voss, Andreas

2012-02-01

In four experiments, task-switching processes were investigated with variants of the alternating runs paradigm and the explicit cueing paradigm. The classical diffusion model for binary decisions (Ratcliff, 1978) was used to dissociate different components of task-switching costs. Findings can be reconciled with the view that task-switching processes take place in successive phases as postulated by multiple-components models of task switching (e.g., Mayr & Kliegl, 2003; Ruthruff, Remington, & Johnston, 2001). At an earlier phase, task-set reconfiguration (Rogers & Monsell, 1995) or cue-encoding (Schneider & Logan, 2005) takes place, at a later phase, the response is selected in accord with constraints set in the first phase. Inertia effects (Allport, Styles, & Hsieh, 1994; Allport & Wylie, 2000) were shown to affect this later stage. Additionally, findings support the notion that response caution contributes to both global as well as to local switching costs when task switches are predictable.

Transverse Diffusivity of Cerebral Parenchyma Predicts Visual Tracking Performance in Relapsing-Remitting Multiple Sclerosis

ERIC Educational Resources Information Center

Warlop, Nele P.; Achten, Eric; Fieremans, Els; Debruyne, Jan; Vingerhoets, Guy

2009-01-01

This study investigated the relation between cerebral damage related to multiple sclerosis (MS) and cognitive decline as determined by two classical mental tracking tests. Cerebral damage in 15 relapsing-remitting MS patients was measured by diffusion tensor imaging (DTI). Fractional anisotropy, longitudinal and transverse diffusivity were defined…

On the transition between two-phase and single-phase interface dynamics in multicomponent fluids at supercritical pressures

NASA Astrophysics Data System (ADS)

Dahms, Rainer N.; Oefelein, Joseph C.

2013-09-01

A theory that explains the operating pressures where liquid injection processes transition from exhibiting classical two-phase spray atomization phenomena to single-phase diffusion-dominated mixing is presented. Imaging from a variety of experiments have long shown that under certain conditions, typically when the pressure of the working fluid exceeds the thermodynamic critical pressure of the liquid phase, the presence of discrete two-phase flow processes become diminished. Instead, the classical gas-liquid interface is replaced by diffusion-dominated mixing. When and how this transition occurs, however, is not well understood. Modern theory still lacks a physically based model to quantify this transition and the precise mechanisms that lead to it. In this paper, we derive a new model that explains how the transition occurs in multicomponent fluids and present a detailed analysis to quantify it. The model applies a detailed property evaluation scheme based on a modified 32-term Benedict-Webb-Rubin equation of state that accounts for the relevant real-fluid thermodynamic and transport properties of the multicomponent system. This framework is combined with Linear Gradient Theory, which describes the detailed molecular structure of the vapor-liquid interface region. Our analysis reveals that the two-phase interface breaks down not necessarily due to vanishing surface tension forces, but due to thickened interfaces at high subcritical temperatures coupled with an inherent reduction of the mean free molecular path. At a certain point, the combination of reduced surface tension, the thicker interface, and reduced mean free molecular path enter the continuum length scale regime. When this occurs, inter-molecular forces approach that of the multicomponent continuum where transport processes dominate across the interfacial region. This leads to a continuous phase transition from compressed liquid to supercritical mixture states. Based on this theory, a regime diagram for liquid injection is developed that quantifies the conditions under which classical sprays transition to dense-fluid jets. It is shown that the chamber pressure required to support diffusion-dominated mixing dynamics depends on the composition and temperature of the injected liquid and ambient gas. To illustrate the method and analysis, we use conditions typical of diesel engine injection. We also present a companion set of high-speed images to provide experimental validation of the presented theory. The basic theory is quite general and applies to a wide range of modern propulsion and power systems such as liquid rockets, gas turbines, and reciprocating engines. Interestingly, the regime diagram associated with diesel engine injection suggests that classical spray phenomena at typical injection conditions do not occur.

Quantum diffusion of H/D on Ni(111)—A partially adiabatic centroid MD study

NASA Astrophysics Data System (ADS)

Hopkinson, A. R.; Probert, M. I. J.

2018-03-01

We present the results of a theoretical study of H/D diffusion on a Ni(111) surface at a range of temperatures, from 250 K to 75 K. The diffusion is studied using both classical molecular dynamics and the partially adiabatic centroid molecular dynamics method. The calculations are performed with the hydrogen (or deuterium) moving in 3D across a static nickel surface using a novel Fourier interpolated potential energy surface which has been parameterized to density functional theory calculations. The results of the classical simulations are that the calculated diffusion coefficients are far too small and with too large a variation with temperature compared with experiment. By contrast, the quantum simulations are in much better agreement with experiment and show that quantum effects in the diffusion of hydrogen are significant at all temperatures studied. There is also a crossover to a quantum-dominated diffusive regime for temperatures below ˜150 K for hydrogen and ˜85 K for deuterium. The quantum diffusion coefficients are found to accurately reproduce the spread in values with temperature, but with an absolute value that is a little high compared with experiment.

A Rescorla-Wagner drift-diffusion model of conditioning and timing

PubMed Central

Alonso, Eduardo

2017-01-01

Computational models of classical conditioning have made significant contributions to the theoretic understanding of associative learning, yet they still struggle when the temporal aspects of conditioning are taken into account. Interval timing models have contributed a rich variety of time representations and provided accurate predictions for the timing of responses, but they usually have little to say about associative learning. In this article we present a unified model of conditioning and timing that is based on the influential Rescorla-Wagner conditioning model and the more recently developed Timing Drift-Diffusion model. We test the model by simulating 10 experimental phenomena and show that it can provide an adequate account for 8, and a partial account for the other 2. We argue that the model can account for more phenomena in the chosen set than these other similar in scope models: CSC-TD, MS-TD, Learning to Time and Modular Theory. A comparison and analysis of the mechanisms in these models is provided, with a focus on the types of time representation and associative learning rule used. PMID:29095819

Atomization and dense-fluid breakup regimes in liquid rocket engines

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

Oefelein, Joseph; Dahms, Rainer Norbert Uwe

Until recently, modern theory has lacked a fundamentally based model to predict the operating pressures where classical sprays transition to dense-fluid mixing with diminished surface tension. In this paper, such a model is presented to quantify this transition for liquid-oxygen–hydrogen and n-decane–gaseous-oxygen injection processes. The analysis reveals that respective molecular interfaces break down not necessarily because of vanishing surface tension forces but instead because of the combination of broadened interfaces and a reduction in mean free molecular path. When this occurs, the interfacial structure itself enters the continuum regime, where transport processes rather than intermolecular forces dominate. Using this model,more » regime diagrams for the respective systems are constructed that show the range of operating pressures and temperatures where this transition occurs. The analysis also reveals the conditions where classical spray dynamics persists even at high supercritical pressures. As a result, it demonstrates that, depending on the composition and temperature of the injected fluids, the injection process can exhibit either classical spray atomization, dense-fluid diffusion-dominated mixing, or supercritical mixing phenomena at chamber pressures encountered in state-of-the-art liquid rocket engines.« less

Atomization and dense-fluid breakup regimes in liquid rocket engines

DOE PAGES

Oefelein, Joseph; Dahms, Rainer Norbert Uwe

2015-04-20

Until recently, modern theory has lacked a fundamentally based model to predict the operating pressures where classical sprays transition to dense-fluid mixing with diminished surface tension. In this paper, such a model is presented to quantify this transition for liquid-oxygen–hydrogen and n-decane–gaseous-oxygen injection processes. The analysis reveals that respective molecular interfaces break down not necessarily because of vanishing surface tension forces but instead because of the combination of broadened interfaces and a reduction in mean free molecular path. When this occurs, the interfacial structure itself enters the continuum regime, where transport processes rather than intermolecular forces dominate. Using this model,more » regime diagrams for the respective systems are constructed that show the range of operating pressures and temperatures where this transition occurs. The analysis also reveals the conditions where classical spray dynamics persists even at high supercritical pressures. As a result, it demonstrates that, depending on the composition and temperature of the injected fluids, the injection process can exhibit either classical spray atomization, dense-fluid diffusion-dominated mixing, or supercritical mixing phenomena at chamber pressures encountered in state-of-the-art liquid rocket engines.« less

Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems

PubMed Central

Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em

2015-01-01

We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers. PMID:26156459

Quantum tunneling of oxygen atoms on very cold surfaces.

PubMed

Minissale, M; Congiu, E; Baouche, S; Chaabouni, H; Moudens, A; Dulieu, F; Accolla, M; Cazaux, S; Manicó, G; Pirronello, V

2013-08-02

Any evolving system can change state via thermal mechanisms (hopping a barrier) or via quantum tunneling. Most of the time, efficient classical mechanisms dominate at high temperatures. This is why an increase of the temperature can initiate the chemistry. We present here an experimental investigation of O-atom diffusion and reactivity on water ice. We explore the 6-25 K temperature range at submonolayer surface coverages. We derive the diffusion temperature law and observe the transition from quantum to classical diffusion. Despite the high mass of O, quantum tunneling is efficient even at 6 K. As a consequence, the solid-state astrochemistry of cold regions should be reconsidered and should include the possibility of forming larger organic molecules than previously expected.

From localization to anomalous diffusion in the dynamics of coupled kicked rotors

NASA Astrophysics Data System (ADS)

Notarnicola, Simone; Iemini, Fernando; Rossini, Davide; Fazio, Rosario; Silva, Alessandro; Russomanno, Angelo

2018-02-01

We study the effect of many-body quantum interference on the dynamics of coupled periodically kicked systems whose classical dynamics is chaotic and shows an unbounded energy increase. We specifically focus on an N -coupled kicked rotors model: We find that the interplay of quantumness and interactions dramatically modifies the system dynamics, inducing a transition between energy saturation and unbounded energy increase. We discuss this phenomenon both numerically and analytically through a mapping onto an N -dimensional Anderson model. The thermodynamic limit N →∞ , in particular, always shows unbounded energy growth. This dynamical delocalization is genuinely quantum and very different from the classical one: Using a mean-field approximation, we see that the system self-organizes so that the energy per site increases in time as a power law with exponent smaller than 1. This wealth of phenomena is a genuine effect of quantum interference: The classical system for N ≥2 always behaves ergodically with an energy per site linearly increasing in time. Our results show that quantum mechanics can deeply alter the regularity or ergodicity properties of a many-body-driven system.

Anomalous symmetry breaking in classical two-dimensional diffusion of coherent atoms

NASA Astrophysics Data System (ADS)

Pugatch, Rami; Bhattacharyya, Dipankar; Amir, Ariel; Sagi, Yoav; Davidson, Nir

2014-03-01

The electromagnetically induced transparency (EIT) spectrum of atoms diffusing in and out of a narrow beam is measured and shown to manifest the two-dimensional δ-function anomaly in a classical setting. In the limit of small-area beams, the EIT line shape is independent of power, and equal to the renormalized local density of states of a free particle Hamiltonian. The measured spectra for different powers and beam sizes collapses to a single universal curve with a characteristic logarithmic Van Hove singularity close to resonance.

An Artificial Intelligence Approach for Modeling and Prediction of Water Diffusion Inside a Carbon Nanotube

PubMed Central

2009-01-01

Modeling of water flow in carbon nanotubes is still a challenge for the classic models of fluid dynamics. In this investigation, an adaptive-network-based fuzzy inference system (ANFIS) is presented to solve this problem. The proposed ANFIS approach can construct an input–output mapping based on both human knowledge in the form of fuzzy if-then rules and stipulated input–output data pairs. Good performance of the designed ANFIS ensures its capability as a promising tool for modeling and prediction of fluid flow at nanoscale where the continuum models of fluid dynamics tend to break down. PMID:20596382

An Artificial Intelligence Approach for Modeling and Prediction of Water Diffusion Inside a Carbon Nanotube.

PubMed

Ahadian, Samad; Kawazoe, Yoshiyuki

2009-06-04

Modeling of water flow in carbon nanotubes is still a challenge for the classic models of fluid dynamics. In this investigation, an adaptive-network-based fuzzy inference system (ANFIS) is presented to solve this problem. The proposed ANFIS approach can construct an input-output mapping based on both human knowledge in the form of fuzzy if-then rules and stipulated input-output data pairs. Good performance of the designed ANFIS ensures its capability as a promising tool for modeling and prediction of fluid flow at nanoscale where the continuum models of fluid dynamics tend to break down.

Bayesian inference of radiation belt loss timescales.

NASA Astrophysics Data System (ADS)

Camporeale, E.; Chandorkar, M.

2017-12-01

Electron fluxes in the Earth's radiation belts are routinely studied using the classical quasi-linear radial diffusion model. Although this simplified linear equation has proven to be an indispensable tool in understanding the dynamics of the radiation belt, it requires specification of quantities such as the diffusion coefficient and electron loss timescales that are never directly measured. Researchers have so far assumed a-priori parameterisations for radiation belt quantities and derived the best fit using satellite data. The state of the art in this domain lacks a coherent formulation of this problem in a probabilistic framework. We present some recent progress that we have made in performing Bayesian inference of radial diffusion parameters. We achieve this by making extensive use of the theory connecting Gaussian Processes and linear partial differential equations, and performing Markov Chain Monte Carlo sampling of radial diffusion parameters. These results are important for understanding the role and the propagation of uncertainties in radiation belt simulations and, eventually, for providing a probabilistic forecast of energetic electron fluxes in a Space Weather context.

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

Morales, George J.; Maggs, James E.

The project expanded and developed mathematical descriptions, and corresponding numerical modeling, of non-diffusive transport to incorporate new perspectives derived from basic transport experiments performed in the LAPD device at UCLA, and at fusion devices throughout the world. By non-diffusive it is meant that the transport of fundamental macroscopic parameters of a system, such as temperature and density, does not follow the standard diffusive behavior predicted by a classical Fokker-Planck equation. The appearance of non-diffusive behavior is often related to underlying microscopic processes that cause the value of a system parameter, at one spatial position, to be linked to distant events,more » i.e., non-locality. In the LAPD experiments the underlying process was traced to large amplitude, coherent drift-waves that give rise to chaotic trajectories. Significant advances were made in this project. The results have lead to a new perspective about the fundamentals of edge transport in magnetically confined plasmas; the insight has important consequences for worldwide studies in fusion devices. Progress was also made in advancing the mathematical techniques used to describe fractional diffusion.« less

Stellar evolution with turbulent diffusion. I. A new formalism of mixing.

NASA Astrophysics Data System (ADS)

Deng, L.; Bressan, A.; Chiosi, C.

1996-09-01

In this paper we present a new formulation of diffusive mixing in stellar interiors aimed at casting light on the kind of mixing that should take place in the so-called overshoot regions surrounding fully convective zones. Key points of the analysis are the inclusion the concept of scale length most effective for mixing, by means of which the diffusion coefficient is formulated, and the inclusion of intermittence and stirring, two properties of turbulence known from laboratory fluid dynamics. The formalism is applied to follow the evolution of a 20Msun_ star with composition Z=0.008 and Y=0.25. Depending on the value of the diffusion coefficient holding in the overshoot region, the evolutionary behaviour of the test stars goes from the case of virtually no mixing (semiconvective like structures) to that of full mixing over there (standard overshoot models). Indeed, the efficiency of mixing in this region drives the extension of the intermediate fully convective shell developing at the onset of the the shell H-burning, and in turn the path in the HR Diagram (HRD). Models with low efficiency of mixing burn helium in the core at high effective temperatures, models with intermediate efficiency perform extended loops in the HRD, finally models with high efficiency spend the whole core He-burning phase at low effective temperatures. In order to cast light on this important point of stellar structure, we test whether or not in the regions of the H-burning shell a convective layer can develop. More precisely, we examine whether the Schwarzschild or the Ledoux criterion ought to be adopted in this region. Furthermore, we test the response of stellar models to the kind of mixing supposed to occur in the H-burning shell regions. Finally, comparing the time scale of thermal dissipation to the evolutionary time scale, we get the conclusion that no mixing in this region should occur. The models with intermediate efficiency of mixing and no mixing at all in the shell H-burning regions are of particular interest as they possess at the same time evolutionary characteristics that are separately typical of models calculated with different schemes of mixing. In other words, the new models share the same properties of models with standard overshoot, namely a wider main sequence band, higher luminosity, and longer lifetimes than classical models, but they also possess extended loops that are the main signature of the classical (semiconvective) description of convection at the border of the core.

Influence of surface wettability on transport mechanisms governing water droplet evaporation.

PubMed

Pan, Zhenhai; Weibel, Justin A; Garimella, Suresh V

2014-08-19

Prediction and manipulation of the evaporation of small droplets is a fundamental problem with importance in a variety of microfluidic, microfabrication, and biomedical applications. A vapor-diffusion-based model has been widely employed to predict the interfacial evaporation rate; however, its scope of applicability is limited due to incorporation of a number of simplifying assumptions of the physical behavior. Two key transport mechanisms besides vapor diffusion-evaporative cooling and natural convection in the surrounding gas-are investigated here as a function of the substrate wettability using an augmented droplet evaporation model. Three regimes are distinguished by the instantaneous contact angle (CA). In Regime I (CA ≲ 60°), the flat droplet shape results in a small thermal resistance between the liquid-vapor interface and substrate, which mitigates the effect of evaporative cooling; upward gas-phase natural convection enhances evaporation. In Regime II (60 ≲ CA ≲ 90°), evaporative cooling at the interface suppresses evaporation with increasing contact angle and counterbalances the gas-phase convection enhancement. Because effects of the evaporative cooling and gas-phase convection mechanisms largely neutralize each other, the vapor-diffusion-based model can predict the overall evaporation rates in this regime. In Regime III (CA ≳ 90°), evaporative cooling suppresses the evaporation rate significantly and reverses entirely the direction of natural convection induced by vapor concentration gradients in the gas phase. Delineation of these counteracting mechanisms reconciles previous debate (founded on single-surface experiments or models that consider only a subset of the governing transport mechanisms) regarding the applicability of the classic vapor-diffusion model. The vapor diffusion-based model cannot predict the local evaporation flux along the interface for high contact angle (CA ≥ 90°) when evaporative cooling is strong and the temperature gradient along the interface determines the peak local evaporation flux.

Controlled release of functional proteins through designer self-assembling peptide nanofiber hydrogel scaffold

PubMed Central

Koutsopoulos, Sotirios; Unsworth, Larry D.; Nagai, Yusuke; Zhang, Shuguang

2009-01-01

The release kinetics for a variety of proteins of a wide range of molecular mass, hydrodynamic radii, and isoelectric points through a nanofiber hydrogel scaffold consisting of designer self-assembling peptides were studied by using single-molecule fluorescence correlation spectroscopy (FCS). In contrast to classical diffusion experiments, the single-molecule approach allowed for the direct determination of diffusion coefficients for lysozyme, trypsin inhibitor, BSA, and IgG both inside the hydrogel and after being released into the solution. The results of the FCS analyses and the calculated pristine in-gel diffusion coefficients were compared with the values obtained from the Stokes–Einstein equation, Fickian diffusion models, and the literature. The release kinetics suggested that protein diffusion through nanofiber hydrogels depended primarily on the size of the protein. Protein diffusivities decreased, with increasing hydrogel nanofiber density providing a means of controlling the release kinetics. Secondary and tertiary structure analyses and biological assays of the released proteins showed that encapsulation and release did not affect the protein conformation and functionality. Our results show that this biocompatible and injectable designer self-assembling peptide hydrogel system may be useful as a carrier for therapeutic proteins for sustained release applications. PMID:19273853

Modeling fluid injection induced microseismicity in shales

NASA Astrophysics Data System (ADS)

Carcione, José M.; Currenti, Gilda; Johann, Lisa; Shapiro, Serge

2018-02-01

Hydraulic fracturing in shales generates a cloud of seismic—tensile and shear—events that can be used to evaluate the extent of the fracturing (event clouds) and obtain the hydraulic properties of the medium, such as the degree of anisotropy and the permeability. Firstly, we investigate the suitability of novel semi-analytical reference solutions for pore pressure evolution around a well after fluid injection in anisotropic media. To do so, we use cylindrical coordinates in the presence of a formation (a layer) and spherical coordinates for a homogeneous and unbounded medium. The involved differential equations are transformed to an isotropic diffusion equation by means of pseudo-spatial coordinates obtained from the spatial variables re-scaled by the permeability components. We consider pressure-dependent permeability components, which are independent of the spatial direction. The analytical solutions are compared to numerical solutions to verify their applicability. The comparison shows that the solutions are suitable for a limited permeability range and moderate to minor pressure dependences of the permeability. Once the pressure evolution around the well has been established, we can model the microseismic events. Induced seismicity by failure due to fluid injection in a porous rock depends on the properties of the hydraulic and elastic medium and in situ stress conditions. Here, we define a tensile threshold pressure above which there is tensile emission, while the shear threshold is obtained by using the octahedral stress criterion and the in situ rock properties and conditions. Subsequently, we generate event clouds for both cases and study the spatio-temporal features. The model considers anisotropic permeability and the results are spatially re-scaled to obtain an effective isotropic medium representation. For a 3D diffusion in spherical coordinates and exponential pressure dependence of the permeability, the results differ from those of the classical diffusion equation. Use of the classical front to fit cloud events spatially, provides good results but with a re-scaled value of these components. Modeling is required to evaluate the scaling constant in real cases.

On Facilitating the use of HARDI in population studies by creating Rotation-Invariant Markers

PubMed Central

Caruyer, Emmanuel; Verma, Ragini

2014-01-01

We design and evaluate a novel method to compute rotationally invariant features using High Angular Resolution Diffusion Imaging (HARDI) data. These measures quantify the complexity of the angular diffusion profile modeled using a higher order model, thereby giving more information than classical diffusion tensor-derived parameters. The method is based on the spherical harmonic (SH) representation of the angular diffusion information, and is generalizable to a range of HARDI reconstruction models. These scalars are obtained as homogeneous polynomials of the SH representation of a HARDI reconstruction model. We show that finding such polynomials is equivalent to solving a large linear system of equations, and present a numerical method based on sparse matrices to efficiently solve this system. Among the solutions, we only keep a subset of algebraically independent polynomials, using an algorithm based on a numerical implementation of the Jacobian criterion. We compute a set of 12 or 25 rotationally invariant measures representative of the underlying white matter for the rank-4 or rank-6 spherical harmonics (SH) representation of the apparent diffusion coefficient (ADC) profile, respectively. Synthetic data was used to investigate and quantify the difference in contrast. Real data acquired with multiple repetitions showed that within subject variation in the invariants was less than the difference across subjects - facilitating their use to study population differences. These results demonstrate that our measures are able to characterize white matter, especially complex white matter found in regions of fiber crossings and hence can be used to derive new biomarkers for HARDI and can be used for HARDI-based population analysis. PMID:25465846

Dynamic Partitioning of a GPI-Anchored Protein in Glycosphingolipid-Rich Microdomains Imaged by Single-Quantum Dot Tracking

PubMed Central

Pinaud, Fabien; Michalet, Xavier; Iyer, Gopal; Margeat, Emmanuel; Moore, Hsiao-Ping; Weiss, Shimon

2009-01-01

Recent experimental developments have led to a revision of the classical fluid mosaic model proposed by Singer and Nicholson 35 years ago. In particular, it is now well established that lipids and proteins diffuse heterogeneously in cell plasma membranes. Their complex motion patterns reflect the dynamic structure and composition of the membrane itself, as well as the presence of the underlying cytoskeleton scaffold and that of the extracellular matrix. How the structural organization of plasma membranes influences the diffusion of individual proteins remains a challenging, yet central question for cell signaling and its regulation. Here we have developed a raft-associated glycosylphosphatidyl Inositol-anchored avidin test probe (Av-GPI), whose diffusion patterns indirectly reports on the structure and dynamics of putative raft microdomains in the membrane of HeLa cells. Labeling with quantum dots (qdots) allowed high-resolution and long-term tracking of individual Av-GPI and the classification of their various diffusive behaviors. Using dual-color total internal reflection fluorescence (TIRF) microscopy, we studied the correlation between the diffusion of individual Av-GPI and the location of glycosphingolipid GM1-rich microdomains and caveolae. We show that Av-GPI exhibit a fast and a slow diffusion regime in different membrane regions, and that slowing down of their diffusion is correlated with entry in GM1-rich microdomains located in close proximity to, but distinct, from caveolae. We further show that Av-GPI dynamically partition in and out of these microdomains in a cholesterol-dependent manner. Our results provide direct evidence that cholesterol/sphingolipid-rich microdomains can compartmentalize the diffusion of GPI-anchored proteins in living cells and that the dynamic partitioning raft model appropriately describes the diffusive behavior of some raft-associated proteins across the plasma membrane. PMID:19416475

Suppression of Soot Formation and Shapes of Laminar Jet Diffusion Flames

NASA Technical Reports Server (NTRS)

Xu, F.; Dai, Z.; Faeth, G. M.

2001-01-01

Laminar nonpremixed (diffusion) flames are of interest because they provide model flame systems that are far more tractable for analysis and experiments than practical turbulent flames. In addition, many properties of laminar diffusion flames are directly relevant to turbulent diffusion flames using laminar flamelet concepts. Finally, laminar diffusion flame shapes have been of interest since the classical study of Burke and Schumann because they involve a simple nonintrusive measurement that is convenient for evaluating flame shape predictions. Motivated by these observations, the shapes of round hydrocarbon-fueled laminar jet diffusion flames were considered, emphasizing conditions where effects of buoyancy are small because most practical flames are not buoyant. Earlier studies of shapes of hydrocarbon-fueled nonbuoyant laminar jet diffusion flames considered combustion in still air and have shown that flames at the laminar smoke point are roughly twice as long as corresponding soot-free (blue) flames and have developed simple ways to estimate their shapes. Corresponding studies of hydrocarbon-fueled weakly-buoyant laminar jet diffusion flames in coflowing air have also been reported. These studies were limited to soot-containing flames at laminar smoke point conditions and also developed simple ways to estimate their shapes but the behavior of corresponding soot-free flames has not been addressed. This is unfortunate because ways of selecting flame flow properties to reduce soot concentrations are of great interest; in addition, soot-free flames are fundamentally important because they are much more computationally tractable than corresponding soot-containing flames. Thus, the objectives of the present investigation were to observe the shapes of weakly-buoyant laminar jet diffusion flames at both soot-free and smoke point conditions and to use the results to evaluate simplified flame shape models. The present discussion is brief.

Dynamic partitioning of a glycosyl-phosphatidylinositol-anchored protein in glycosphingolipid-rich microdomains imaged by single-quantum dot tracking.

PubMed

Pinaud, Fabien; Michalet, Xavier; Iyer, Gopal; Margeat, Emmanuel; Moore, Hsiao-Ping; Weiss, Shimon

2009-06-01

Recent experimental developments have led to a revision of the classical fluid mosaic model proposed by Singer and Nicholson more than 35 years ago. In particular, it is now well established that lipids and proteins diffuse heterogeneously in cell plasma membranes. Their complex motion patterns reflect the dynamic structure and composition of the membrane itself, as well as the presence of the underlying cytoskeleton scaffold and that of the extracellular matrix. How the structural organization of plasma membranes influences the diffusion of individual proteins remains a challenging, yet central, question for cell signaling and its regulation. Here we have developed a raft-associated glycosyl-phosphatidyl-inositol-anchored avidin test probe (Av-GPI), whose diffusion patterns indirectly report on the structure and dynamics of putative raft microdomains in the membrane of HeLa cells. Labeling with quantum dots (qdots) allowed high-resolution and long-term tracking of individual Av-GPI and the classification of their various diffusive behaviors. Using dual-color total internal reflection fluorescence (TIRF) microscopy, we studied the correlation between the diffusion of individual Av-GPI and the location of glycosphingolipid GM1-rich microdomains and caveolae. We show that Av-GPI exhibit a fast and a slow diffusion regime in different membrane regions, and that slowing down of their diffusion is correlated with entry in GM1-rich microdomains located in close proximity to, but distinct, from caveolae. We further show that Av-GPI dynamically partition in and out of these microdomains in a cholesterol-dependent manner. Our results provide direct evidence that cholesterol-/sphingolipid-rich microdomains can compartmentalize the diffusion of GPI-anchored proteins in living cells and that the dynamic partitioning raft model appropriately describes the diffusive behavior of some raft-associated proteins across the plasma membrane.

Permeability of a Fluid Lipid Bilayer to Short-Chain Alcohols from First Principles.

PubMed

Comer, Jeffrey; Schulten, Klaus; Chipot, Christophe

2017-06-13

Computational prediction of membrane permeability to small molecules requires accurate description of both the thermodynamics and kinetics underlying translocation across the lipid bilayer. In this contribution, well-converged, microsecond-long free-energy calculations are combined with a recently developed subdiffusive kinetics framework to describe the membrane permeation of a homologous series of short-tail alcohols, from methanol to 1-butanol, with unprecedented fidelity to the underlying molecular models. While the free-energy profiles exhibit barriers for passage through the center of the bilayer in all cases, the height of these barriers decreases with the length of the aliphatic chain of the alcohol, in quantitative agreement with experimentally determined differential solvation free energies in water and oil. A unique aspect of the subdiffusive model employed herein, which was developed in a previous article, is the determination of a position-dependent fractional order which quantifies the degree to which the motion of the alcohol deviates from classical diffusion along the thickness of the membrane. In the aqueous medium far from the bilayer, this quantity approaches 1.0, the asymptotic limit for purely classical diffusion, whereas it dips below 0.75 near the center of the membrane irrespective of the permeant. Remarkably, the fractional diffusivity near the center of membrane, where its influence on the permeability is the greatest, is similar among the four permeants despite the large difference in molecular weight and lipophilicity between methanol and 1-butanol. The relative permeabilities, which are estimated from the free-energy and fractional diffusivity profiles, are therefore determined predominantly by differences in the former rather than the latter. The predicted relative permeabilities are highly correlated with existing experimental results, albeit they do not agree quantitatively with them. On the other hand, quite unexpectedly, the reported experimental values for the short-tail alcohols are nearly three orders of magnitude lower than the available experimental measurement for water. Plausible explanations for this apparent disagreement between theory and experiment are considered in detail.

Modeling Dust in the Magellanic Clouds

NASA Astrophysics Data System (ADS)

Zonca, Alberto; Casu, Silvia; Mulas, Giacomo; Aresu, Giambattista; Cecchi-Pestellini, Cesare

2015-09-01

We model the extinction profiles observed in the Small and Large Magellanic clouds with a synthetic population of dust grains consisting of core-mantle particles and a collection of free-flying polycyclic aromatic hydrocarbons (PAHs). All different flavors of the extinction curves observed in the Magellanic Clouds (MCs) can be described by the present model, which has been previously (successfully) applied to a large sample of diffuse and translucent lines of sight in the Milky Way. We find that in the MCs the extinction produced by classical grains is generally larger than absorption by PAHs. Within this model, the nonlinear far-UV rise is accounted for by PAHs, whose presence in turn is always associated with a gap in the size distribution of classical particles. This hints either at a physical connection between (e.g., a common cause for) PAHs and the absence of middle-sized dust particles or the need for an additional component in the model that can account for the nonlinear far-UV rise without contributing to the UV bump at ∼217 nm such as, e.g., nanodiamonds.

Image model: new perspective for image processing and computer vision

NASA Astrophysics Data System (ADS)

Ziou, Djemel; Allili, Madjid

2004-05-01

We propose a new image model in which the image support and image quantities are modeled using algebraic topology concepts. The image support is viewed as a collection of chains encoding combination of pixels grouped by dimension and linking different dimensions with the boundary operators. Image quantities are encoded using the notion of cochain which associates values for pixels of given dimension that can be scalar, vector, or tensor depending on the problem that is considered. This allows obtaining algebraic equations directly from the physical laws. The coboundary and codual operators, which are generic operations on cochains allow to formulate the classical differential operators as applied for field functions and differential forms in both global and local forms. This image model makes the association between the image support and the image quantities explicit which results in several advantages: it allows the derivation of efficient algorithms that operate in any dimension and the unification of mathematics and physics to solve classical problems in image processing and computer vision. We show the effectiveness of this model by considering the isotropic diffusion.

Is cancer a pure growth curve or does it follow a kinetics of dynamical structural transformation?

PubMed

González, Maraelys Morales; Joa, Javier Antonio González; Cabrales, Luis Enrique Bergues; Pupo, Ana Elisa Bergues; Schneider, Baruch; Kondakci, Suleyman; Ciria, Héctor Manuel Camué; Reyes, Juan Bory; Jarque, Manuel Verdecia; Mateus, Miguel Angel O'Farril; González, Tamara Rubio; Brooks, Soraida Candida Acosta; Cáceres, José Luis Hernández; González, Gustavo Victoriano Sierra

2017-03-07

Unperturbed tumor growth kinetics is one of the more studied cancer topics; however, it is poorly understood. Mathematical modeling is a useful tool to elucidate new mechanisms involved in tumor growth kinetics, which can be relevant to understand cancer genesis and select the most suitable treatment. The classical Kolmogorov-Johnson-Mehl-Avrami as well as the modified Kolmogorov-Johnson-Mehl-Avrami models to describe unperturbed fibrosarcoma Sa-37 tumor growth are used and compared with the Gompertz modified and Logistic models. Viable tumor cells (1×10 5 ) are inoculated to 28 BALB/c male mice. Modified Gompertz, Logistic, Kolmogorov-Johnson-Mehl-Avrami classical and modified Kolmogorov-Johnson-Mehl-Avrami models fit well to the experimental data and agree with one another. A jump in the time behaviors of the instantaneous slopes of classical and modified Kolmogorov-Johnson-Mehl-Avrami models and high values of these instantaneous slopes at very early stages of tumor growth kinetics are observed. The modified Kolmogorov-Johnson-Mehl-Avrami equation can be used to describe unperturbed fibrosarcoma Sa-37 tumor growth. It reveals that diffusion-controlled nucleation/growth and impingement mechanisms are involved in tumor growth kinetics. On the other hand, tumor development kinetics reveals dynamical structural transformations rather than a pure growth curve. Tumor fractal property prevails during entire TGK.

Confinement regulates complex biochemical networks: initiation of blood clotting by "diffusion acting".

PubMed

Shen, Feng; Pompano, Rebecca R; Kastrup, Christian J; Ismagilov, Rustem F

2009-10-21

This study shows that environmental confinement strongly affects the activation of nonlinear reaction networks, such as blood coagulation (clotting), by small quantities of activators. Blood coagulation is sensitive to the local concentration of soluble activators, initiating only when the activators surpass a threshold concentration, and therefore is regulated by mass transport phenomena such as flow and diffusion. Here, diffusion was limited by decreasing the size of microfluidic chambers, and it was found that microparticles carrying either the classical stimulus, tissue factor, or a bacterial stimulus, Bacillus cereus, initiated coagulation of human platelet-poor plasma only when confined. A simple analytical argument and numerical model were used to describe the mechanism for this phenomenon: confinement causes diffusible activators to accumulate locally and surpass the threshold concentration. To interpret the results, a dimensionless confinement number, Cn, was used to describe whether a stimulus was confined, and a Damköhler number, Da(2), was used to describe whether a subthreshold stimulus could initiate coagulation. In the context of initiation of coagulation by bacteria, this mechanism can be thought of as "diffusion acting", which is distinct from "diffusion sensing". The ability of confinement and diffusion acting to change the outcome of coagulation suggests that confinement should also regulate other biological "on" and "off" processes that are controlled by thresholds.

A Stochastic Evolutionary Model for Protein Structure Alignment and Phylogeny

PubMed Central

Challis, Christopher J.; Schmidler, Scott C.

2012-01-01

We present a stochastic process model for the joint evolution of protein primary and tertiary structure, suitable for use in alignment and estimation of phylogeny. Indels arise from a classic Links model, and mutations follow a standard substitution matrix, whereas backbone atoms diffuse in three-dimensional space according to an Ornstein–Uhlenbeck process. The model allows for simultaneous estimation of evolutionary distances, indel rates, structural drift rates, and alignments, while fully accounting for uncertainty. The inclusion of structural information enables phylogenetic inference on time scales not previously attainable with sequence evolution models. The model also provides a tool for testing evolutionary hypotheses and improving our understanding of protein structural evolution. PMID:22723302

Robust three-body water simulation model

NASA Astrophysics Data System (ADS)

Tainter, C. J.; Pieniazek, P. A.; Lin, Y.-S.; Skinner, J. L.

2011-05-01

The most common potentials used in classical simulations of liquid water assume a pairwise additive form. Although these models have been very successful in reproducing many properties of liquid water at ambient conditions, none is able to describe accurately water throughout its complicated phase diagram. The primary reason for this is the neglect of many-body interactions. To this end, a simulation model with explicit three-body interactions was introduced recently [R. Kumar and J. L. Skinner, J. Phys. Chem. B 112, 8311 (2008), 10.1021/jp8009468]. This model was parameterized to fit the experimental O-O radial distribution function and diffusion constant. Herein we reparameterize the model, fitting to a wider range of experimental properties (diffusion constant, rotational correlation time, density for the liquid, liquid/vapor surface tension, melting point, and the ice Ih density). The robustness of the model is then verified by comparing simulation to experiment for a number of other quantities (enthalpy of vaporization, dielectric constant, Debye relaxation time, temperature of maximum density, and the temperature-dependent second and third virial coefficients), with good agreement.

A Diffusion Approximation Based on Renewal Processes with Applications to Strongly Biased Run-Tumble Motion.

PubMed

Thygesen, Uffe Høgsbro

2016-03-01

We consider organisms which use a renewal strategy such as run-tumble when moving in space, for example to perform chemotaxis in chemical gradients. We derive a diffusion approximation for the motion, applying a central limit theorem due to Anscombe for renewal-reward processes; this theorem has not previously been applied in this context. Our results extend previous work, which has established the mean drift but not the diffusivity. For a classical model of tumble rates applied to chemotaxis, we find that the resulting chemotactic drift saturates to the swimming velocity of the organism when the chemical gradients grow increasingly steep. The dispersal becomes anisotropic in steep gradients, with larger dispersal across the gradient than along the gradient. In contrast to one-dimensional settings, strong bias increases dispersal. We next include Brownian rotation in the model and find that, in limit of high chemotactic sensitivity, the chemotactic drift is 64% of the swimming velocity, independent of the magnitude of the Brownian rotation. We finally derive characteristic timescales of the motion that can be used to assess whether the diffusion limit is justified in a given situation. The proposed technique for obtaining diffusion approximations is conceptually and computationally simple, and applicable also when statistics of the motion is obtained empirically or through Monte Carlo simulation of the motion.

Diffusion in Deterministic Interacting Lattice Systems

NASA Astrophysics Data System (ADS)

Medenjak, Marko; Klobas, Katja; Prosen, Tomaž

2017-09-01

We study reversible deterministic dynamics of classical charged particles on a lattice with hard-core interaction. It is rigorously shown that the system exhibits three types of transport phenomena, ranging from ballistic, through diffusive to insulating. By obtaining an exact expressions for the current time-autocorrelation function we are able to calculate the linear response transport coefficients, such as the diffusion constant and the Drude weight. Additionally, we calculate the long-time charge profile after an inhomogeneous quench and obtain diffusive profilewith the Green-Kubo diffusion constant. Exact analytical results are corroborated by Monte Carlo simulations.

Report on the Implementation of Homogeneous Nucleation Scheme in MARMOT-based Phase Field Simulation

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

Li, Yulan; Hu, Shenyang Y.; Sun, Xin

2013-09-30

In this report, we summarized our effort in developing mesoscale phase field models for predicting precipitation kinetics in alloys during thermal aging and/or under irradiation in nuclear reactors. The first part focused on developing a method to predict the thermodynamic properties of critical nuclei such as the sizes and concentration profiles of critical nuclei, and nucleation barrier. These properties are crucial for quantitative simulations of precipitate evolution kinetics with phase field models. Fe-Cr alloy was chosen as a model alloy because it has valid thermodynamic and kinetic data as well as it is an important structural material in nuclear reactors.more » A constrained shrinking dimer dynamics (CSDD) method was developed to search for the energy minimum path during nucleation. With the method we are able to predict the concentration profiles of the critical nuclei of Cr-rich precipitates and nucleation energy barriers. Simulations showed that Cr concentration distribution in the critical nucleus strongly depends on the overall Cr concentration as well as temperature. The Cr concentration inside the critical nucleus is much smaller than the equilibrium concentration calculated by the equilibrium phase diagram. This implies that a non-classical nucleation theory should be used to deal with the nucleation of Cr precipitates in Fe-Cr alloys. The growth kinetics of both classical and non-classical nuclei was investigated by the phase field approach. A number of interesting phenomena were observed from the simulations: 1) a critical classical nucleus first shrinks toward its non-classical nucleus and then grows; 2) a non-classical nucleus has much slower growth kinetics at its earlier growth stage compared to the diffusion-controlled growth kinetics. 3) a critical classical nucleus grows faster at the earlier growth stage than the non-classical nucleus. All of these results demonstrated that it is critical to introduce the correct critical nuclei into phase field modeling in order to correctly capture the kinetics of precipitation. In most alloys the matrix phase and precipitate phase have different concentrations as well as different crystal structures. For example, Cu precipitates in FeCu alloys have fcc crystal structure while the matrix Fe-Cu solid solution has bcc structure at low temperature. The WBM model and KimS model, where both concentrations and order parameters are chosen to describe the microstructures, are commonly used to model precipitations in such alloys. The WBM and KimS models have not been implemented into Marmot yet. In the second part of this report, we focused on implementing the WBM and KimS models into Marmot. The Fe-Cu alloys, which are important structure materials in nuclear reactors, was taken as the model alloys to test the models.« less

A structured population model with diffusion in structure space.

PubMed

Pugliese, Andrea; Milner, Fabio

2018-05-09

A structured population model is described and analyzed, in which individual dynamics is stochastic. The model consists of a PDE of advection-diffusion type in the structure variable. The population may represent, for example, the density of infected individuals structured by pathogen density x, [Formula: see text]. The individuals with density [Formula: see text] are not infected, but rather susceptible or recovered. Their dynamics is described by an ODE with a source term that is the exact flux from the diffusion and advection as [Formula: see text]. Infection/reinfection is then modeled moving a fraction of these individuals into the infected class by distributing them in the structure variable through a probability density function. Existence of a global-in-time solution is proven, as well as a classical bifurcation result about equilibrium solutions: a net reproduction number [Formula: see text] is defined that separates the case of only the trivial equilibrium existing when [Formula: see text] from the existence of another-nontrivial-equilibrium when [Formula: see text]. Numerical simulation results are provided to show the stabilization towards the positive equilibrium when [Formula: see text] and towards the trivial one when [Formula: see text], result that is not proven analytically. Simulations are also provided to show the Allee effect that helps boost population sizes at low densities.

SHIR competitive information diffusion model for online social media

NASA Astrophysics Data System (ADS)

Liu, Yun; Diao, Su-Meng; Zhu, Yi-Xiang; Liu, Qing

2016-11-01

In online social media, opinion divergences and differentiations generally exist as a result of individuals' extensive participation and personalization. In this paper, a Susceptible-Hesitated-Infected-Removed (SHIR) model is proposed to study the dynamics of competitive dual information diffusion. The proposed model extends the classical SIR model by adding hesitators as a neutralized state of dual information competition. It is both hesitators and stable spreaders that facilitate information dissemination. Researching on the impacts of diffusion parameters, it is found that the final density of stiflers increases monotonically as infection rate increases and removal rate decreases. And the advantage information with larger stable transition rate takes control of whole influence of dual information. The density of disadvantage information spreaders slightly grows with the increase of its stable transition rate, while whole spreaders of dual information and the relaxation time remain almost unchanged. Moreover, simulations imply that the final result of competition is closely related to the ratio of stable transition rates of dual information. If the stable transition rates of dual information are nearly the same, a slightly reduction of the smaller one brings out a significant disadvantage in its propagation coverage. Additionally, the relationship of the ratio of final stiflers versus the ratio of stable transition rates presents power characteristic.

Distribution and Dynamic Properties of Xenon Dissolved in the Ionic Smectic Phase of [C16mim][NO3]: MD Simulation and Theoretical Model.

PubMed

Frezzato, Diego; Saielli, Giacomo

2016-03-10

We have investigated the structural and dynamic properties of Xe dissolved in the ionic liquid crystal (ILC) phase of 1-hexadecyl-3-methylimidazolium nitrate using classical molecular dynamics (MD) simulations. Xe is found to be preferentially dissolved within the hydrophobic environment of the alkyl chains rather than in the ionic layers of the smectic phase. The structural parameters and the estimated local diffusion coefficients concerning the short-time motion of Xe are used to parametrize a theoretical model based on the Smoluchowski equation for the macroscopic dynamics across the smectic layers, a feature which cannot be directly obtained from the relatively short MD simulations. This protocol represents an efficient combination of computational and theoretical tools to obtain information on slow processes concerning the permeability and diffusivity of the xenon in smectic ILCs.

Introduction of Shear-Based Transport Mechanisms in Radial-Axial Hybrid Hall Thruster Simulations

NASA Astrophysics Data System (ADS)

Scharfe, Michelle; Gascon, Nicolas; Scharfe, David; Cappelli, Mark; Fernandez, Eduardo

2007-11-01

Electron diffusion across magnetic field lines in Hall effect thrusters is experimentally observed to be higher than predicted by classical diffusion theory. Motivated by theoretical work for fusion applications and experimental measurements of Hall thrusters, numerical models for the electron transport are implemented in radial-axial hybrid simulations in order to compute the electron mobility using simulated plasma properties and fitting parameters. These models relate the cross-field transport to the imposed magnetic field distribution through shear suppression of turbulence-enhanced transport. While azimuthal waves likely enhance cross field mobility, axial shear in the electron fluid may reduce transport due to a reduction in turbulence amplitudes and modification of phase shifts between fluctuating properties. The sensitivity of the simulation results to the fitting parameters is evaluated and an examination is made of the transportability of these parameters to several Hall thruster devices.

Nonholonomic relativistic diffusion and exact solutions for stochastic Einstein spaces

NASA Astrophysics Data System (ADS)

Vacaru, S. I.

2012-03-01

We develop an approach to the theory of nonholonomic relativistic stochastic processes in curved spaces. The Itô and Stratonovich calculus are formulated for spaces with conventional horizontal (holonomic) and vertical (nonholonomic) splitting defined by nonlinear connection structures. Geometric models of the relativistic diffusion theory are elaborated for nonholonomic (pseudo) Riemannian manifolds and phase velocity spaces. Applying the anholonomic deformation method, the field equations in Einstein's gravity and various modifications are formally integrated in general forms, with generic off-diagonal metrics depending on some classes of generating and integration functions. Choosing random generating functions we can construct various classes of stochastic Einstein manifolds. We show how stochastic gravitational interactions with mixed holonomic/nonholonomic and random variables can be modelled in explicit form and study their main geometric and stochastic properties. Finally, the conditions when non-random classical gravitational processes transform into stochastic ones and inversely are analyzed.

Word diffusion and climate science.

PubMed

Bentley, R Alexander; Garnett, Philip; O'Brien, Michael J; Brock, William A

2012-01-01

As public and political debates often demonstrate, a substantial disjoint can exist between the findings of science and the impact it has on the public. Using climate-change science as a case example, we reconsider the role of scientists in the information-dissemination process, our hypothesis being that important keywords used in climate science follow "boom and bust" fashion cycles in public usage. Representing this public usage through extraordinary new data on word frequencies in books published up to the year 2008, we show that a classic two-parameter social-diffusion model closely fits the comings and goings of many keywords over generational or longer time scales. We suggest that the fashions of word usage contributes an empirical, possibly regular, correlate to the impact of climate science on society.

TU-F-CAMPUS-J-02: Evaluation of Textural Feature Extraction for Radiotherapy Response Assessment of Early Stage Breast Cancer Patients Using Diffusion Weighted MRI and Dynamic Contrast Enhanced MRI

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

Xie, Y; Wang, C; Horton, J

Purpose: To investigate the feasibility of using classic textural feature extraction in radiotherapy response assessment, we studied a unique cohort of early stage breast cancer patients with paired pre - and post-radiation Diffusion Weighted MRI (DWI-MRI) and Dynamic Contrast Enhanced MRI (DCE-MRI). Methods: 15 female patients from our prospective phase I trial evaluating preoperative radiotherapy were included in this retrospective study. Each patient received a single-fraction radiation treatment, and DWI and DCE scans were conducted before and after the radiotherapy. DWI scans were acquired using a spin-echo EPI sequence with diffusion weighting factors of b = 0 and b =more » 500 mm{sup 2} /s, and the apparent diffusion coefficient (ADC) maps were calculated. DCE-MRI scans were acquired using a T{sub 1}-weighted 3D SPGR sequence with a temporal resolution of about 1 minute. The contrast agent (CA) was intravenously injected with a 0.1 mmol/kg bodyweight dose at 2 ml/s. Two parameters, volume transfer constant (K{sup trans} ) and k{sub ep} were analyzed using the two-compartment Tofts kinetic model. For DCE parametric maps and ADC maps, 33 textural features were generated from the clinical target volume (CTV) in a 3D fashion using the classic gray level co-occurrence matrix (GLCOM) and gray level run length matrix (GLRLM). Wilcoxon signed-rank test was used to determine the significance of each texture feature’s change after the radiotherapy. The significance was set to 0.05 with Bonferroni correction. Results: For ADC maps calculated from DWI-MRI, 24 out of 33 CTV features changed significantly after the radiotherapy. For DCE-MRI pharmacokinetic parameters, all 33 CTV features of K{sup trans} and 33 features of k{sub ep} changed significantly. Conclusion: Initial results indicate that those significantly changed classic texture features are sensitive to radiation-induced changes and can be used for assessment of radiotherapy response in breast cancer.« less

Compression Freezing Kinetics of Water to Ice VII

DOE PAGES

Gleason, A. E.; Bolme, C. A.; Galtier, E.; ...

2017-07-11

Time-resolved x-ray diffraction (XRD) of compressed liquid water shows transformation to ice VII in 6 nsec, revealing crystallization rather than amorphous solidification during compression freezing. Application of classical nucleation theory indicates heterogeneous nucleation and one-dimensional (e.g., needlelike) growth. In conclusion, these first XRD data demonstrate rapid growth kinetics of ice VII with implications for fundamental physics of diffusion-mediated crystallization and thermodynamic modeling of collision or impact events on ice-rich planetary bodies.

Compression Freezing Kinetics of Water to Ice VII

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

Gleason, A. E.; Bolme, C. A.; Galtier, E.

Time-resolved x-ray diffraction (XRD) of compressed liquid water shows transformation to ice VII in 6 nsec, revealing crystallization rather than amorphous solidification during compression freezing. Application of classical nucleation theory indicates heterogeneous nucleation and one-dimensional (e.g., needlelike) growth. In conclusion, these first XRD data demonstrate rapid growth kinetics of ice VII with implications for fundamental physics of diffusion-mediated crystallization and thermodynamic modeling of collision or impact events on ice-rich planetary bodies.

Wright-Fisher diffusion bridges.

PubMed

Griffiths, Robert C; Jenkins, Paul A; Spanò, Dario

2017-10-06

The trajectory of the frequency of an allele which begins at x at time 0 and is known to have frequency z at time T can be modelled by the bridge process of the Wright-Fisher diffusion. Bridges when x=z=0 are particularly interesting because they model the trajectory of the frequency of an allele which appears at a time, then is lost by random drift or mutation after a time T. The coalescent genealogy back in time of a population in a neutral Wright-Fisher diffusion process is well understood. In this paper we obtain a new interpretation of the coalescent genealogy of the population in a bridge from a time t∈(0,T). In a bridge with allele frequencies of 0 at times 0 and T the coalescence structure is that the population coalesces in two directions from t to 0 and t to T such that there is just one lineage of the allele under consideration at times 0 and T. The genealogy in Wright-Fisher diffusion bridges with selection is more complex than in the neutral model, but still with the property of the population branching and coalescing in two directions from time t∈(0,T). The density of the frequency of an allele at time t is expressed in a way that shows coalescence in the two directions. A new algorithm for exact simulation of a neutral Wright-Fisher bridge is derived. This follows from knowing the density of the frequency in a bridge and exact simulation from the Wright-Fisher diffusion. The genealogy of the neutral Wright-Fisher bridge is also modelled by branching Pólya urns, extending a representation in a Wright-Fisher diffusion. This is a new very interesting representation that relates Wright-Fisher bridges to classical urn models in a Bayesian setting. Copyright © 2017 Elsevier Inc. All rights reserved.

Fixation Probability in a Haploid-Diploid Population

PubMed Central

Bessho, Kazuhiro; Otto, Sarah P.

2017-01-01

Classical population genetic theory generally assumes either a fully haploid or fully diploid life cycle. However, many organisms exhibit more complex life cycles, with both free-living haploid and diploid stages. Here we ask what the probability of fixation is for selected alleles in organisms with haploid-diploid life cycles. We develop a genetic model that considers the population dynamics using both the Moran model and Wright–Fisher model. Applying a branching process approximation, we obtain an accurate fixation probability assuming that the population is large and the net effect of the mutation is beneficial. We also find the diffusion approximation for the fixation probability, which is accurate even in small populations and for deleterious alleles, as long as selection is weak. These fixation probabilities from branching process and diffusion approximations are similar when selection is weak for beneficial mutations that are not fully recessive. In many cases, particularly when one phase predominates, the fixation probability differs substantially for haploid-diploid organisms compared to either fully haploid or diploid species. PMID:27866168

Magnetic monopole dynamics in spin ice.

PubMed

Jaubert, L D C; Holdsworth, P C W

2011-04-27

One of the most remarkable examples of emergent quasi-particles is that of the 'fractionalization' of magnetic dipoles in the low energy configurations of materials known as 'spin ice' into free and unconfined magnetic monopoles interacting via Coulomb's 1/r law (Castelnovo et al 2008 Nature 451 42-5). Recent experiments have shown that a Coulomb gas of magnetic charges really does exist at low temperature in these materials and this discovery provides a new perspective on otherwise largely inaccessible phenomenology. In this paper, after a review of the different spin ice models, we present detailed results describing the diffusive dynamics of monopole particles starting both from the dipolar spin ice model and directly from a Coulomb gas within the grand canonical ensemble. The diffusive quasi-particle dynamics of real spin ice materials within the 'quantum tunnelling' regime is modelled with Metropolis dynamics, with the particles constrained to move along an underlying network of oriented paths, which are classical analogues of the Dirac strings connecting pairs of Dirac monopoles.

Probability distribution of haplotype frequencies under the two-locus Wright-Fisher model by diffusion approximation.

PubMed

Boitard, Simon; Loisel, Patrice

2007-05-01

The probability distribution of haplotype frequencies in a population, and the way it is influenced by genetical forces such as recombination, selection, random drift ...is a question of fundamental interest in population genetics. For large populations, the distribution of haplotype frequencies for two linked loci under the classical Wright-Fisher model is almost impossible to compute because of numerical reasons. However the Wright-Fisher process can in such cases be approximated by a diffusion process and the transition density can then be deduced from the Kolmogorov equations. As no exact solution has been found for these equations, we developed a numerical method based on finite differences to solve them. It applies to transient states and models including selection or mutations. We show by several tests that this method is accurate for computing the conditional joint density of haplotype frequencies given that no haplotype has been lost. We also prove that it is far less time consuming than other methods such as Monte Carlo simulations.

Multilevel Preconditioners for Reaction-Diffusion Problems with Discontinuous Coefficients

DOE PAGES

Kolev, Tzanio V.; Xu, Jinchao; Zhu, Yunrong

2015-08-23

In this study, we extend some of the multilevel convergence results obtained by Xu and Zhu, to the case of second order linear reaction-diffusion equations. Specifically, we consider the multilevel preconditioners for solving the linear systems arising from the linear finite element approximation of the problem, where both diffusion and reaction coefficients are piecewise-constant functions. We discuss in detail the influence of both the discontinuous reaction and diffusion coefficients to the performance of the classical BPX and multigrid V-cycle preconditioner.

Transport dynamics -- one particle at a time

NASA Astrophysics Data System (ADS)

Granick, Steve

2010-03-01

By watching particles and molecules diffuse, one-by-one, the full displacement probability distribution can be measured, enabling one to see experimentally how, how fast, and with what fidelity to classical assumptions, particles and molecules diffuse through complex environments. This allows us to measuring the confining tube potential through which thin actin filaments reptate, and also some of the amazing differences in diffusion rate between colloidal particles and phospholipid vesicles of the same size. Pervasively, we find that Brownian diffusion can be non-Gaussian.

A theoretical model for the collective motion of proteins by means of principal component analysis

NASA Astrophysics Data System (ADS)

Kamberaj, Hiqmet

2011-02-01

A coarse grained model in the frame work of principal component analysis is presented. We used a bath of harmonic oscillators approach, based on classical mechanics, to derive the generalized Langevin equations of motion for the collective coordinates. The dynamics of the protein collective coordinates derived from molecular dynamics simulations have been studied for the Bovine Pancreatic Trypsin Inhibitor. We analyzed the stability of the method by studying structural fluctuations of the C a atoms obtained from a 20 ns molecular dynamics simulation. Subsequently, the dynamics of the collective coordinates of protein were characterized by calculating the dynamical friction coefficient and diffusion coefficients along with time-dependent correlation functions of collective coordinates. A dual diffusion behavior was observed with a fast relaxation time of short diffusion regime 0.2-0.4 ps and slow relaxation time of long diffusion about 1-2 ps. In addition, we observed a power law decay of dynamical friction coefficient with exponent for the first five collective coordinates varying from -0.746 to -0.938 for the real part and from -0.528 to -0.665 for its magnitude. It was found that only the first ten collective coordinates are responsible for configuration transitions occurring on time scale longer than 50 ps.

Multiple-tracer tests for contaminant transport process identification in saturated municipal solid waste

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

Woodman, N.D., E-mail: n.d.woodman@soton.ac.uk; Rees-White, T.C.; Stringfellow, A.M.

2015-04-15

Highlights: • Multiple tracers were applied to saturated MSW to test dual-porosity properties. • Lithium demonstrated to be non-conservative as a tracer. • 260 mm diameter column too small to test transport properties of MSW. • The classical advection-dispersion mode was rejected due to high dispersivity. • Characteristic diffusion times did not vary with the tracer. - Abstract: Two column tests were performed in conditions emulating vertical flow beneath the leachate table in a biologically active landfill to determine dominant transport mechanisms occurring in landfills. An improved understanding of contaminant transport process in wastes is required for developing better predictionsmore » about potential length of the long term aftercare of landfills, currently measured in timescales of centuries. Three tracers (lithium, bromide and deuterium) were used. Lithium did not behave conservatively. Given that lithium has been used extensively for tracing in landfill wastes, the tracer itself and the findings of previous tests which assume that it has behaved conservatively may need revisiting. The smaller column test could not be fitted with continuum models, probably because the volume of waste was below a representative elemental volume. Modelling compared advection-dispersion (AD), dual porosity (DP) and hybrid AD–DP models. Of these models, the DP model was found to be the most suitable. Although there is good evidence to suggest that diffusion is an important transport mechanism, the breakthrough curves of the different tracers did not differ from each other as would be predicted based on the free-water diffusion coefficients. This suggested that solute diffusion in wastes requires further study.« less

Quantum walks with tuneable self-avoidance in one dimension

PubMed Central

Camilleri, Elizabeth; Rohde, Peter P.; Twamley, Jason

2014-01-01

Quantum walks exhibit many unique characteristics compared to classical random walks. In the classical setting, self-avoiding random walks have been studied as a variation on the usual classical random walk. Here the walker has memory of its previous locations and preferentially avoids stepping back to locations where it has previously resided. Classical self-avoiding random walks have found numerous algorithmic applications, most notably in the modelling of protein folding. We consider the analogous problem in the quantum setting – a quantum walk in one dimension with tunable levels of self-avoidance. We complement a quantum walk with a memory register that records where the walker has previously resided. The walker is then able to avoid returning back to previously visited sites or apply more general memory conditioned operations to control the walk. We characterise this walk by examining the variance of the walker's distribution against time, the standard metric for quantifying how quantum or classical a walk is. We parameterise the strength of the memory recording and the strength of the memory back-action on the walker, and investigate their effect on the dynamics of the walk. We find that by manipulating these parameters, which dictate the degree of self-avoidance, the walk can be made to reproduce ideal quantum or classical random walk statistics, or a plethora of more elaborate diffusive phenomena. In some parameter regimes we observe a close correspondence between classical self-avoiding random walks and the quantum self-avoiding walk. PMID:24762398

A simple model for closure temperature of a trace element in cooling bi-mineralic systems

NASA Astrophysics Data System (ADS)

Liang, Yan

2015-09-01

Closure temperature is defined as the lower temperature limit at which the element of interest effectively ceases diffusive exchange with its surrounding medium during cooling. Here we generalize the classic equation of Dodson (1973) for cooling mono-mineralic systems to cooling bi-mineralic aggregates by considering diffusive exchange of a trace element between the two minerals in a closed system. We present a simple analytical model that includes key parameters affecting the closure temperature of a trace element in cooling bi-mineralic systems: cooling rate, temperature-dependent diffusion coefficients for the trace element in the two minerals, temperature-dependent partition coefficient of the trace element between the two minerals, effective grain sizes of the two minerals, and volume proportions of the minerals in the system. We show that closure temperatures of a trace element in cooling bi-mineralic systems are bounded by the closure temperatures of the trace element in the two mono-mineralic systems and that our generalized model reduces to Dodson's equation when one of the mineral serves as "an effective infinite" reservoir to the other mineral. Application to closure temperatures of REE in orthopyroxene and clinopyroxene bi-mineralic systems highlights the importance of REE diffusion and partitioning in the pyroxenes as well as clinopyroxene modal abundance and grain size in the systems. Closure temperatures for REE in two-pyroxene bearing equigranular rocks are controlled primarily by diffusion in orthopyroxene unless the modal abundance of clinopyroxene is very small. This has important bearings on the interpretation of temperatures derived from the REE-in-two-pyroxene thermometer.

Modeling pinchoff and reconnection in a Hele-Shaw cell. I. The models and their calibration

NASA Astrophysics Data System (ADS)

Lee, Hyeong-Gi; Lowengrub, J. S.; Goodman, J.

2002-02-01

This is the first paper in a two-part series in which we analyze two model systems to study pinchoff and reconnection in binary fluid flow in a Hele-Shaw cell with arbitrary density and viscosity contrast between the components. The systems stem from a simplification of a general system of equations governing the motion of a binary fluid (NSCH model [Lowengrub and Truskinovsky, Proc. R. Soc. London, Ser. A 454, 2617 (1998)]) to flow in a Hele-Shaw cell. The system takes into account the chemical diffusivity between different components of a fluid mixture and the reactive stresses induced by inhomogeneity. In one of the systems we consider (HSCH), the binary fluid may be compressible due to diffusion. In the other system (BHSCH), a Boussinesq approximation is used and the fluid is incompressible. In this paper, we motivate, present and calibrate the HSCH/BHSCH equations so as to yield the classical sharp interface model as a limiting case. We then analyze their equilibria, one dimensional evolution and linear stability. In the second paper [paper II, Phys. Fluids 14, 514 (2002)], we analyze the behavior of the models in the fully nonlinear regime. In the BHSCH system, the equilibrium concentration profile is obtained using the classical Maxwell construction [Rowlinson and Widom, Molecular Theory of Capillarity (Clarendon, Oxford, 1979)] and does not depend on the orientation of the gravitational field. We find that the equilibria in the HSCH model are somewhat surprising as the gravitational field actually affects the internal structure of an isolated interface by driving additional stratification of light and heavy fluids over that predicted in the Boussinesq case. A comparison of the linear growth rates indicates that the HSCH system is slightly more diffusive than the BHSCH system. In both, linear convergence to the sharp interface growth rates is observed in a parameter controlling the interface thickness. In addition, we identify the effect that each of the parameters, in the HSCH/BHSCH models, has on the linear growth rates. We then show how this analysis may be used to suggest a set of modified parameters which, when used in the HSCH/BHSCH systems, yield improved agreement with the sharp interface model at a finite interface thickness. Evidence of this improved agreement may be found in paper II.

Cross-diffusion-driven hydrodynamic instabilities in a double-layer system: General classification and nonlinear simulations

NASA Astrophysics Data System (ADS)

Budroni, M. A.

2015-12-01

Cross diffusion, whereby a flux of a given species entrains the diffusive transport of another species, can trigger buoyancy-driven hydrodynamic instabilities at the interface of initially stable stratifications. Starting from a simple three-component case, we introduce a theoretical framework to classify cross-diffusion-induced hydrodynamic phenomena in two-layer stratifications under the action of the gravitational field. A cross-diffusion-convection (CDC) model is derived by coupling the fickian diffusion formalism to Stokes equations. In order to isolate the effect of cross-diffusion in the convective destabilization of a double-layer system, we impose a starting concentration jump of one species in the bottom layer while the other one is homogeneously distributed over the spatial domain. This initial configuration avoids the concurrence of classic Rayleigh-Taylor or differential-diffusion convective instabilities, and it also allows us to activate selectively the cross-diffusion feedback by which the heterogeneously distributed species influences the diffusive transport of the other species. We identify two types of hydrodynamic modes [the negative cross-diffusion-driven convection (NCC) and the positive cross-diffusion-driven convection (PCC)], corresponding to the sign of this operational cross-diffusion term. By studying the space-time density profiles along the gravitational axis we obtain analytical conditions for the onset of convection in terms of two important parameters only: the operational cross-diffusivity and the buoyancy ratio, giving the relative contribution of the two species to the global density. The general classification of the NCC and PCC scenarios in such parameter space is supported by numerical simulations of the fully nonlinear CDC problem. The resulting convective patterns compare favorably with recent experimental results found in microemulsion systems.

A simple example of a classical gauge transformation

NASA Technical Reports Server (NTRS)

Whitten, R. C.

1983-01-01

Attention is given to the manner in which the interaction of a gravitational field with a diffusing gas is induced by a gauge transformation. Since the gas can be thought of as a field, the diffusion process may be represented by a Lagrangian density with the symmetry property of invariance under translation. While this property is lost when the field interacts with a static gravitational field, it is formally restored when an appropriate gauge transformation is performed. This ascription of field properties to a gas offers an illuminating illustration of the coupling of matter to a gauge field within the context of classical mechanics.

Test of electical resistivity and current diffusion modelling on MAST and JET

NASA Astrophysics Data System (ADS)

Keeling, D. L.; Challis, C. D.; Jenkins, I.; Hawkes, N. C.; Lupelli, I.; Michael, C.; de Bock, M. F. M.; the MAST Team; contributors, JET

2018-01-01

Experiments have been carried out on the MAST and JET tokamaks intended to compare the electrical resistivity of the plasma with theoretical formulations. The tests consist of obtaining motional stark effect (MSE) measurements in MHD-free plasmas during plasma current ramp-up (JET and MAST), ramp-down (MAST) and in stationary state (JET and MAST). Simulations of these plasmas are then performed in which the current profile evolution is calculated according to the poloidal field diffusion equation (PFDE) with classical or neoclassical resistivity. Synthetic MSE data are produced in the simulations for direct comparison with the experimental data. It is found that the toroidal current profile evolution modelled using neoclassical resistivity did not match the experimental observations on either device during current ramp-up or ramp-down as concluded from comparison of experimental and synthetic MSE profiles. In these phases, use of neoclassical resistivity in the modelling systematically overestimates the rate of current profile evolution. During the stationary state however, the modelled toroidal current profile matched experimental observations to a high degree of accuracy on both devices using neoclassical resistivity. Whilst no solution to the mismatch in the dynamic phases of the plasma is proposed, it is suggested that some physical process other than MHD which is not captured by the simple diffusive model of current profile evolution is responsible.

Modeling of the anode of a liquid-feed DMFC: Inhomogeneous compression effects and two-phase transport phenomena

NASA Astrophysics Data System (ADS)

García-Salaberri, Pablo A.; Vera, Marcos; Iglesias, Immaculada

2014-01-01

An isothermal two-phase 2D/1D across-the-channel model for the anode of a liquid-feed Direct Methanol Fuel Cell (DMFC) is presented. The model takes into account the effects of the inhomogeneous assembly compression of the Gas Diffusion Layer (GDL), including the spatial variations of porosity, diffusivity, permeability, capillary pressure, and electrical conductivity. The effective anisotropic properties of the GDL are evaluated from empirical data reported in the literature corresponding to Toray carbon paper TGP-H series. Multiphase transport is modeled according to the classical theory of porous media (two-fluid model), considering the effect of non-equilibrium evaporation and condensation of methanol and water. The numerical results evidence that the hydrophobic Leverett J-function approach is physically inconsistent to describe capillary transport in the anode of a DMFC when assembly compression effects are considered. In contrast, more realistic results are obtained when GDL-specific capillary pressure curves reflecting the mixed-wettability characteristics of GDLs are taken into account. The gas coverage factor at the GDL/channel interface also exhibits a strong influence on the gas-void fraction distribution in the GDL, which in turn depends on the relative importance between the capillary resistance induced by the inhomogeneous compression, Rc(∝ ∂pc / ∂ ε) , and the capillary diffusivity, Dbarc(∝ ∂pc / ∂ s) .

Modeling diffusion-governed solidification of ternary alloys - Part 2: Macroscopic transport phenomena and macrosegregation.

PubMed

Wu, M; Li, J; Ludwig, A; Kharicha, A

2014-09-01

Part 1 of this two-part investigation presented a multiphase solidification model incorporating the finite diffusion kinetics and ternary phase diagram with the macroscopic transport phenomena (Wu et al., 2013). In Part 2, the importance of proper treatment of the finite diffusion kinetics in the calculation of macrosegregation is addressed. Calculations for a two-dimensional (2D) square casting (50 × 50 mm 2 ) of Fe-0.45 wt.%C-1.06 wt.%Mn considering thermo-solutal convection and crystal sedimentation are performed. The modeling result indicates that the infinite liquid mixing kinetics as assumed by classical models (e.g., the Gulliver-Scheil or lever rule), which cannot properly consider the solute enrichment of the interdendritic or inter-granular melt at the early stage of solidification, might lead to an erroneous estimation of the macrosegregation. To confirm this statement, further theoretical and experimental evaluations are desired. The pattern and intensity of the flow and crystal sedimentation are dependent on the crystal morphologies (columnar or equiaxed); hence, the potential error of the calculated macrosegregation caused by the assumed growth kinetics depends on the crystal morphology. Finally, an illustrative simulation of an engineering 2.45-ton steel ingot is performed, and the results are compared with experimental results. This example demonstrates the model applicability for engineering castings regarding both the calculation efficiency and functionality.

SToRM: A Model for Unsteady Surface Hydraulics Over Complex Terrain

USGS Publications Warehouse

Simoes, Francisco J.

2014-01-01

A two-dimensional (depth-averaged) finite volume Godunov-type shallow water model developed for flow over complex topography is presented. The model is based on an unstructured cellcentered finite volume formulation and a nonlinear strong stability preserving Runge-Kutta time stepping scheme. The numerical discretization is founded on the classical and well established shallow water equations in hyperbolic conservative form, but the convective fluxes are calculated using auto-switching Riemann and diffusive numerical fluxes. The model’s implementation within a graphical user interface is discussed. Field application of the model is illustrated by utilizing it to estimate peak flow discharges in a flooding event of historic significance in Colorado, U.S.A., in 2013.

Corkscrew esophagus.

PubMed

Fonseca, Eduardo Kaiser Ururahy Nunes; Yamauchi, Fernando Ide; Tridente, Cassia Franco; Baroni, Ronaldo Hueb

2017-03-01

Corkscrew esophagus (also referred as rosary bead esophagus) is a classic finding of diffuse esophageal spasm (DES) in barium studies reflecting abnormal contractions, leading to compartmentalization and curling of the esophagus, ultimately giving an appearance similar to a corkscrew or rosary beads. We review the pathophysiology of this finding, correlating it to corkscrew and rosary images that originated this classic description.

On Entropy Production in the Madelung Fluid and the Role of Bohm's Potential in Classical Diffusion

NASA Astrophysics Data System (ADS)

Heifetz, Eyal; Tsekov, Roumen; Cohen, Eliahu; Nussinov, Zohar

2016-07-01

The Madelung equations map the non-relativistic time-dependent Schrödinger equation into hydrodynamic equations of a virtual fluid. While the von Neumann entropy remains constant, we demonstrate that an increase of the Shannon entropy, associated with this Madelung fluid, is proportional to the expectation value of its velocity divergence. Hence, the Shannon entropy may grow (or decrease) due to an expansion (or compression) of the Madelung fluid. These effects result from the interference between solutions of the Schrödinger equation. Growth of the Shannon entropy due to expansion is common in diffusive processes. However, in the latter the process is irreversible while the processes in the Madelung fluid are always reversible. The relations between interference, compressibility and variation of the Shannon entropy are then examined in several simple examples. Furthermore, we demonstrate that for classical diffusive processes, the "force" accelerating diffusion has the form of the positive gradient of the quantum Bohm potential. Expressing then the diffusion coefficient in terms of the Planck constant reveals the lower bound given by the Heisenberg uncertainty principle in terms of the product between the gas mean free path and the Brownian momentum.

Confinement Regulates Complex Biochemical Networks: Initiation of Blood Clotting by “Diffusion Acting”

PubMed Central

Shen, Feng; Pompano, Rebecca R.; Kastrup, Christian J.; Ismagilov, Rustem F.

2009-01-01

Abstract This study shows that environmental confinement strongly affects the activation of nonlinear reaction networks, such as blood coagulation (clotting), by small quantities of activators. Blood coagulation is sensitive to the local concentration of soluble activators, initiating only when the activators surpass a threshold concentration, and therefore is regulated by mass transport phenomena such as flow and diffusion. Here, diffusion was limited by decreasing the size of microfluidic chambers, and it was found that microparticles carrying either the classical stimulus, tissue factor, or a bacterial stimulus, Bacillus cereus, initiated coagulation of human platelet-poor plasma only when confined. A simple analytical argument and numerical model were used to describe the mechanism for this phenomenon: confinement causes diffusible activators to accumulate locally and surpass the threshold concentration. To interpret the results, a dimensionless confinement number, Cn, was used to describe whether a stimulus was confined, and a Damköhler number, Da2, was used to describe whether a subthreshold stimulus could initiate coagulation. In the context of initiation of coagulation by bacteria, this mechanism can be thought of as “diffusion acting”, which is distinct from “diffusion sensing”. The ability of confinement and diffusion acting to change the outcome of coagulation suggests that confinement should also regulate other biological “on” and “off” processes that are controlled by thresholds. PMID:19843446

Real time visualization of quantum walk

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

Miyazaki, Akihide; Hamada, Shinji; Sekino, Hideo

2014-02-20

Time evolution of quantum particles like electrons is described by time-dependent Schrödinger equation (TDSE). The TDSE is regarded as the diffusion equation of electrons with imaginary diffusion coefficients. And the TDSE is solved by quantum walk (QW) which is regarded as a quantum version of a classical random walk. The diffusion equation is solved in discretized space/time as in the case of classical random walk with additional unitary transformation of internal degree of freedom typical for quantum particles. We call the QW for solution of the TDSE a Schrödinger walk (SW). For observation of one quantum particle evolution under amore » given potential in atto-second scale, we attempt a successive computation and visualization of the SW. Using Pure Data programming, we observe the correct behavior of a probability distribution under the given potential in real time for observers of atto-second scale.« less

On the evolution of cured voxel in bulk photopolymerization upon focused Gaussian laser exposure

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

Bhole, Kiran, E-mail: kirandipali@gmail.com; Gandhi, Prasanna; Kundu, T.

Unconstrained depth photopolymerization is emerging as a promising technique for fabrication of several polymer microstructures such as self propagating waveguides, 3D freeform structures by bulk lithography, and polymer nanoparticles by flash exposure. Experimental observations reveal governing physics beyond Beer Lambert's law and scattering effects. This paper seeks to model unconstrained depth photopolymerization using classical nonlinear Schrödinger equation coupled with transient diffusion phenomenon. The beam propagation part of the proposed model considers scattering effects induced due to spatial variation of the refractive index as a function of the beam intensity. The critical curing energy model is used to further predict profilemore » of polymerized voxel. Profiles of photopolymerized voxel simulated using proposed model are compared with the corresponding experimental results for several cases of exposure dose and duration. The comparison shows close match leading to conclusion that the experimentally observed deviation from Beer Lambert's law is indeed due to combined effect of diffusion of photoinitiator and scattering of light because of change in the refractive index.« less

Quantum to classical transition in quantum field theory

NASA Astrophysics Data System (ADS)

Lombardo, Fernando C.

1998-12-01

We study the quatum to classical transition process in the context of quantum field theory. Extending the influence functional formalism of Feynman and Vernon, we study the decoherence process for self-interacting quantum fields in flat space. We also use this formalism for arbitrary geometries to analyze the quantum to classical transition in quantum gravity. After summarizing the main results known for the quantum Brownian motion, we consider a self-interacting field theory in Minkowski spacetime. We compute a coarse grained effective action by integrating out the field modes with wavelength shorter than a critical value. From this effective action we obtain the evolution equation for the reduced density matrix (master equation). We compute the diffusion coefficients for this equation and analyze the decoherence induced on the long-wavelength modes. We generalize the results to the case of a conformally coupled scalar field in de Sitter spacetime. We show that the decoherence is effective as long as the critical wavelength is taken to be not shorter than the Hubble radius. On the other hand, we study the classical limit for scalar-tensorial models in two dimensions. We consider different couplings between the dilaton and the scalar field. We discuss the Hawking radiation process and, from an exact evaluation of the influence functional, we study the conditions by which decoherence ensures the validity of the semiclassical approximation in cosmological metrics. Finally we consider four dimensional models with massive scalar fields, arbitrary coupled to the geometry. We compute the Einstein-Langevin equations in order to study the effect of the fluctuations induced by the quantum fields on the classical geometry.

Dipy, a library for the analysis of diffusion MRI data.

PubMed

Garyfallidis, Eleftherios; Brett, Matthew; Amirbekian, Bagrat; Rokem, Ariel; van der Walt, Stefan; Descoteaux, Maxime; Nimmo-Smith, Ian

2014-01-01

Diffusion Imaging in Python (Dipy) is a free and open source software project for the analysis of data from diffusion magnetic resonance imaging (dMRI) experiments. dMRI is an application of MRI that can be used to measure structural features of brain white matter. Many methods have been developed to use dMRI data to model the local configuration of white matter nerve fiber bundles and infer the trajectory of bundles connecting different parts of the brain. Dipy gathers implementations of many different methods in dMRI, including: diffusion signal pre-processing; reconstruction of diffusion distributions in individual voxels; fiber tractography and fiber track post-processing, analysis and visualization. Dipy aims to provide transparent implementations for all the different steps of dMRI analysis with a uniform programming interface. We have implemented classical signal reconstruction techniques, such as the diffusion tensor model and deterministic fiber tractography. In addition, cutting edge novel reconstruction techniques are implemented, such as constrained spherical deconvolution and diffusion spectrum imaging (DSI) with deconvolution, as well as methods for probabilistic tracking and original methods for tractography clustering. Many additional utility functions are provided to calculate various statistics, informative visualizations, as well as file-handling routines to assist in the development and use of novel techniques. In contrast to many other scientific software projects, Dipy is not being developed by a single research group. Rather, it is an open project that encourages contributions from any scientist/developer through GitHub and open discussions on the project mailing list. Consequently, Dipy today has an international team of contributors, spanning seven different academic institutions in five countries and three continents, which is still growing.

Coronal "wave": Magnetic Footprint Of A Cme?

NASA Astrophysics Data System (ADS)

Attrill, Gemma; Harra, L. K.; van Driel-Gesztelyi, L.; Demoulin, P.; Wuelser, J.

2007-05-01

We propose a new mechanism for the generation of "EUV coronal waves". This work is based on new analysis of data from SOHO/EIT, SOHO/MDI & STEREO/EUVI. Although first observed in 1997, the interpretation of coronal waves as flare-induced or CME-driven remains a debated topic. We investigate the properties of two "classical" SOHO/EIT coronal waves in detail. The source regions of the associated CMEs possess opposite helicities & the coronal waves display rotations in opposite senses. We observe deep dimmings near the flare site & also widespread diffuse dimming, accompanying the expansion of the EIT wave. We report a new property of these EIT waves, namely, that they display dual brightenings: persistent ones at the outermost edge of the core dimming regions & simultaneously diffuse brightenings constituting the leading edge of the coronal wave, surrounding the expanding diffuse dimmings. We show that such behaviour is consistent with a diffuse EIT wave being the magnetic footprint of a CME. We propose a new mechanism where driven magnetic reconnections between the skirt of the expanding CME & quiet-Sun magnetic loops generate the observed bright diffuse front. The dual brightenings & widespread diffuse dimming are identified as innate characteristics of this process. In addition we present some of the first analysis of a STEREO/EUVI limb coronal wave. We show how the evolution of the diffuse bright front & dimmings can be understood in terms of the model described above. We show that an apparently stationary part of the bright front can be understood in terms of magnetic interchange reconnections between the expanding CME & the "open" magnetic field of a low-latitude coronal hole. We use both the SOHO/EIT & STEREO/EUVI events to demonstrate that through successive reconnections, this new model provides a natural mechanism via which CMEs can become large-scale in the lower corona.

Dipy, a library for the analysis of diffusion MRI data

PubMed Central

Garyfallidis, Eleftherios; Brett, Matthew; Amirbekian, Bagrat; Rokem, Ariel; van der Walt, Stefan; Descoteaux, Maxime; Nimmo-Smith, Ian

2014-01-01

Diffusion Imaging in Python (Dipy) is a free and open source software project for the analysis of data from diffusion magnetic resonance imaging (dMRI) experiments. dMRI is an application of MRI that can be used to measure structural features of brain white matter. Many methods have been developed to use dMRI data to model the local configuration of white matter nerve fiber bundles and infer the trajectory of bundles connecting different parts of the brain. Dipy gathers implementations of many different methods in dMRI, including: diffusion signal pre-processing; reconstruction of diffusion distributions in individual voxels; fiber tractography and fiber track post-processing, analysis and visualization. Dipy aims to provide transparent implementations for all the different steps of dMRI analysis with a uniform programming interface. We have implemented classical signal reconstruction techniques, such as the diffusion tensor model and deterministic fiber tractography. In addition, cutting edge novel reconstruction techniques are implemented, such as constrained spherical deconvolution and diffusion spectrum imaging (DSI) with deconvolution, as well as methods for probabilistic tracking and original methods for tractography clustering. Many additional utility functions are provided to calculate various statistics, informative visualizations, as well as file-handling routines to assist in the development and use of novel techniques. In contrast to many other scientific software projects, Dipy is not being developed by a single research group. Rather, it is an open project that encourages contributions from any scientist/developer through GitHub and open discussions on the project mailing list. Consequently, Dipy today has an international team of contributors, spanning seven different academic institutions in five countries and three continents, which is still growing. PMID:24600385

Does ℏ play a role in multidimensional spectroscopy? Reduced hierarchy equations of motion approach to molecular vibrations.

PubMed

Sakurai, Atsunori; Tanimura, Yoshitaka

2011-04-28

To investigate the role of quantum effects in vibrational spectroscopies, we have carried out numerically exact calculations of linear and nonlinear response functions for an anharmonic potential system nonlinearly coupled to a harmonic oscillator bath. Although one cannot carry out the quantum calculations of the response functions with full molecular dynamics (MD) simulations for a realistic system which consists of many molecules, it is possible to grasp the essence of the quantum effects on the vibrational spectra by employing a model Hamiltonian that describes an intra- or intermolecular vibrational motion in a condensed phase. The present model fully includes vibrational relaxation, while the stochastic model often used to simulate infrared spectra does not. We have employed the reduced quantum hierarchy equations of motion approach in the Wigner space representation to deal with nonperturbative, non-Markovian, and nonsecular system-bath interactions. Taking the classical limit of the hierarchy equations of motion, we have obtained the classical equations of motion that describe the classical dynamics under the same physical conditions as in the quantum case. By comparing the classical and quantum mechanically calculated linear and multidimensional spectra, we found that the profiles of spectra for a fast modulation case were similar, but different for a slow modulation case. In both the classical and quantum cases, we identified the resonant oscillation peak in the spectra, but the quantum peak shifted to the red compared with the classical one if the potential is anharmonic. The prominent quantum effect is the 1-2 transition peak, which appears only in the quantum mechanically calculated spectra as a result of anharmonicity in the potential or nonlinearity of the system-bath coupling. While the contribution of the 1-2 transition is negligible in the fast modulation case, it becomes important in the slow modulation case as long as the amplitude of the frequency fluctuation is small. Thus, we observed a distinct difference between the classical and quantum mechanically calculated multidimensional spectra in the slow modulation case where spectral diffusion plays a role. This fact indicates that one may not reproduce the experimentally obtained multidimensional spectrum for high-frequency vibrational modes based on classical molecular dynamics simulations if the modulation that arises from surrounding molecules is weak and slow. A practical way to overcome the difference between the classical and quantum simulations was discussed.

Krogh-cylinder and infinite-domain models for washout of an inert diffusible solute from tissue.

PubMed

Secomb, Timothy W

2015-01-01

Models based on the Krogh-cylinder concept are developed to analyze the washout from tissue by blood flow of an inert diffusible solute that permeates blood vessel walls. During the late phase of washout, the outflowing solute concentration decays exponentially with time. This washout decay rate is predicted for a range of conditions. A single capillary is assumed to lie on the axis of a cylindrical tissue region. In the classic "Krogh-cylinder" approach, a no-flux boundary condition is applied on the outside of the cylinder. An alternative "infinite-domain" approach is proposed that allows for solute exchange across the boundary, but with zero net exchange. Both models are analyzed, using finite-element and analytical methods. The washout decay rate depends on blood flow rate, tissue diffusivity and vessel permeability of solute, and assumed boundary conditions. At low blood flow rates, the washout rate can exceed the value for a single well-mixed compartment. The infinite-domain approach predicts slower washout decay rates than the Krogh-cylinder approach. The infinite-domain approach overcomes a significant limitation of the Krogh-cylinder approach, while retaining its simplicity. It provides a basis for developing methods to deduce transport properties of inert solutes from observations of washout decay rates. © 2014 John Wiley & Sons Ltd.

A toxicity cost function approach to optimal CPA equilibration in tissues.

PubMed

Benson, James D; Higgins, Adam Z; Desai, Kunjan; Eroglu, Ali

2018-02-01

There is growing need for cryopreserved tissue samples that can be used in transplantation and regenerative medicine. While a number of specific tissue types have been successfully cryopreserved, this success is not general, and there is not a uniform approach to cryopreservation of arbitrary tissues. Additionally, while there are a number of long-established approaches towards optimizing cryoprotocols in single cell suspensions, and even plated cell monolayers, computational approaches in tissue cryopreservation have classically been limited to explanatory models. Here we develop a numerical approach to adapt cell-based CPA equilibration damage models for use in a classical tissue mass transport model. To implement this with real-world parameters, we measured CPA diffusivity in three human-sourced tissue types, skin, fibroid and myometrium, yielding propylene glycol diffusivities of 0.6 × 10 -6  cm 2 /s, 1.2 × 10 -6  cm 2 /s and 1.3 × 10 -6  cm 2 /s, respectively. Based on these results, we numerically predict and compare optimal multistep equilibration protocols that minimize the cell-based cumulative toxicity cost function and the damage due to excessive osmotic gradients at the tissue boundary. Our numerical results show that there are fundamental differences between protocols designed to minimize total CPA exposure time in tissues and protocols designed to minimize accumulated CPA toxicity, and that "one size fits all" stepwise approaches are predicted to be more toxic and take considerably longer than needed. Copyright © 2017 Elsevier Inc. All rights reserved.

Diffusion-weighted imaging and demyelinating diseases: new aspects of an old advanced sequence.

PubMed

Rueda-Lopes, Fernanda C; Hygino da Cruz, Luiz C; Doring, Thomas M; Gasparetto, Emerson L

2014-01-01

The purpose of this article is to discuss classic applications in diffusion-weighted imaging (DWI) in demyelinating disease and progression of DWI in the near future. DWI is an advanced technique used in the follow-up of demyelinating disease patients, focusing on the diagnosis of a new lesion before contrast enhancement. With technical advances, diffusion-tensor imaging; new postprocessing techniques, such as tract-based spatial statistics; new ways of calculating diffusion, such as kurtosis; and new applications for DWI and its spectrum are about to arise.

First passage times and asymmetry of DNA translocation

NASA Astrophysics Data System (ADS)

Lua, Rhonald C.; Grosberg, Alexander Y.

2005-12-01

Motivated by experiments in which single-stranded DNA with a short hairpin loop at one end undergoes unforced diffusion through a narrow pore, we study the first passage times for a particle, executing one-dimensional Brownian motion in an asymmetric sawtooth potential, to exit one of the boundaries. We consider the first passage times for the case of classical diffusion, characterized by a mean-square displacement of the form ⟨(Δx)2⟩˜t , and for the case of anomalous diffusion or subdiffusion, characterized by a mean-square displacement of the form ⟨(Δx)2⟩˜tγ with 0<γ<1 . In the context of classical diffusion, we obtain an expression for the mean first passage time and show that this quantity changes when the direction of the sawtooth is reversed or, equivalently, when the reflecting and absorbing boundaries are exchanged. We discuss at which numbers of “teeth” N (or number of DNA nucleotides) and at which heights of the sawtooth potential this difference becomes significant. For large N , it is well known that the mean first passage time scales as N2 . In the context of subdiffusion, the mean first passage time does not exist. Therefore, we obtain instead the distribution of first passage times in the limit of long times. We show that the prefactor in the power relation for this distribution is simply the expression for the mean first passage time in classical diffusion. We also describe a hypothetical experiment to calculate the average of the first passage times for a fraction of passage events that each end within some time t* . We show that this average first passage time scales as N2/γ in subdiffusion.

Effective temperatures and the breakdown of the Stokes-Einstein relation for particle suspensions.

PubMed

Mendoza, Carlos I; Santamaría-Holek, I; Pérez-Madrid, A

2015-09-14

The short- and long-time breakdown of the classical Stokes-Einstein relation for colloidal suspensions at arbitrary volume fractions is explained here by examining the role that confinement and attractive interactions play in the intra- and inter-cage dynamics executed by the colloidal particles. We show that the measured short-time diffusion coefficient is larger than the one predicted by the classical Stokes-Einstein relation due to a non-equilibrated energy transfer between kinetic and configuration degrees of freedom. This transfer can be incorporated in an effective kinetic temperature that is higher than the temperature of the heat bath. We propose a Generalized Stokes-Einstein relation (GSER) in which the effective temperature replaces the temperature of the heat bath. This relation then allows to obtain the diffusion coefficient once the viscosity and the effective temperature are known. On the other hand, the temporary cluster formation induced by confinement and attractive interactions of hydrodynamic nature makes the long-time diffusion coefficient to be smaller than the corresponding one obtained from the classical Stokes-Einstein relation. Then, the use of the GSER allows to obtain an effective temperature that is smaller than the temperature of the heat bath. Additionally, we provide a simple expression based on a differential effective medium theory that allows to calculate the diffusion coefficient at short and long times. Comparison of our results with experiments and simulations for suspensions of hard and porous spheres shows an excellent agreement in all cases.

Pre-Darcy flow in tight and shale formations

NASA Astrophysics Data System (ADS)

Dejam, Morteza; Hassanzadeh, Hassan; Chen, Zhangxin

2017-11-01

There are evidences that the fluid flow in tight and shale formations does not follow Darcy law, which is identified as pre-Darcy flow. Here, the unsteady linear flow of a slightly compressible fluid under the action of pre-Darcy flow is modeled and a generalized Boltzmann transformation technique is used to solve the corresponding highly nonlinear diffusivity equation analytically. The effect of pre-Darcy flow on the pressure diffusion in a homogenous formation is studied in terms of the nonlinear exponent, m, and the threshold pressure gradient, G1. In addition, the pressure gradient, flux, and cumulative production per unit area for different m and G1 are compared with the classical solution of the diffusivity equation based on Darcy flow. Department of Petroleum Engineering in College of Engineering and Applied Science at University of Wyoming and NSERC/AI-EES(AERI)/Foundation CMG and AITF (iCORE) Chairs in Department of Chemical and Petroleum Engineering at University of Calgary.

Prediction of competitive diffusion on complex networks

NASA Astrophysics Data System (ADS)

Zhao, Jiuhua; Liu, Qipeng; Wang, Lin; Wang, Xiaofan

2018-10-01

In this paper, we study the prediction problem of diffusion process on complex networks in competitive circumstances. With this problem solved, the competitors could timely intervene the diffusion process if needed such that an expected outcome might be obtained. We consider a model with two groups of competitors spreading opposite opinions on a network. A prediction method based on the mutual influences among the agents is proposed, called Influence Matrix (IM for short), and simulations on real-world networks show that the proposed IM method has quite high accuracy on predicting both the preference of any normal agent and the final competition result. For comparison purpose, classic centrality measures are also used to predict the competition result. It is shown that PageRank, Degree, Katz Centrality, and the IM method are suitable for predicting the competition result. More precisely, in undirected networks, the IM method performs better than these centrality measures when the competing group contains more than one agent; in directed networks, the IM method performs only second to PageRank.

Phase space effects on fast ion distribution function modeling in tokamaks

NASA Astrophysics Data System (ADS)

Podestà, M.; Gorelenkova, M.; Fredrickson, E. D.; Gorelenkov, N. N.; White, R. B.

2016-05-01

Integrated simulations of tokamak discharges typically rely on classical physics to model energetic particle (EP) dynamics. However, there are numerous cases in which energetic particles can suffer additional transport that is not classical in nature. Examples include transport by applied 3D magnetic perturbations and, more notably, by plasma instabilities. Focusing on the effects of instabilities, ad-hoc models can empirically reproduce increased transport, but the choice of transport coefficients is usually somehow arbitrary. New approaches based on physics-based reduced models are being developed to address those issues in a simplified way, while retaining a more correct treatment of resonant wave-particle interactions. The kick model implemented in the tokamak transport code TRANSP is an example of such reduced models. It includes modifications of the EP distribution by instabilities in real and velocity space, retaining correlations between transport in energy and space typical of resonant EP transport. The relevance of EP phase space modifications by instabilities is first discussed in terms of predicted fast ion distribution. Results are compared with those from a simple, ad-hoc diffusive model. It is then shown that the phase-space resolved model can also provide additional insight into important issues such as internal consistency of the simulations and mode stability through the analysis of the power exchanged between energetic particles and the instabilities.

Phase space effects on fast ion distribution function modeling in tokamaks

DOE Data Explorer

White, R. B. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Podesta, M. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Gorelenkova, M. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Fredrickson, E. D. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States); Gorelenkov, N. N. [Princeton Plasma Physics Lab. (PPPL), Princeton, NJ (United States)

2016-06-01

Integrated simulations of tokamak discharges typically rely on classical physics to model energetic particle (EP) dynamics. However, there are numerous cases in which energetic particles can suffer additional transport that is not classical in nature. Examples include transport by applied 3D magnetic perturbations and, more notably, by plasma instabilities. Focusing on the effects of instabilities, ad-hoc models can empirically reproduce increased transport, but the choice of transport coefficients is usually somehow arbitrary. New approaches based on physics-based reduced models are being developed to address those issues in a simplified way, while retaining a more correct treatment of resonant wave-particle interactions. The kick model implemented in the tokamak transport code TRANSP is an example of such reduced models. It includes modifications of the EP distribution by instabilities in real and velocity space, retaining correlations between transport in energy and space typical of resonant EP transport. The relevance of EP phase space modifications by instabilities is first discussed in terms of predicted fast ion distribution. Results are compared with those from a simple, ad-hoc diffusive model. It is then shown that the phase-space resolved model can also provide additional insight into important issues such as internal consistency of the simulations and mode stability through the analysis of the power exchanged between energetic particles and the instabilities.

A Web 2.0 Personal Learning Environment for Classical Chinese Poetry

NASA Astrophysics Data System (ADS)

Cao, Yiwei; Klamma, Ralf; Gao, Yan; Lau, Rynson W. H.; Jarke, Matthias

Classical Chinese Poetry (CCP) is a valuable but almost locked treasure chest of human wisdom and civilization since 2000 years. With the advent of the Web 2.0 a renaissance of CCP is possible even outside Chinese-speaking communities world-wide. With mobile technologies and educational games we can address new learning communities for CCP and open the chest again. In this paper, we introduce a Web 2.0 personal learning environment for CCP. We have developed a generic and interoperable data model for CCP we utilize not only for mobile learning scenarios but also for educational gaming with different levels of difficulty. Learners are empowered to learn Chinese poetry, language, history, and culture. This research work shows how modern information technologies assist users to diffuse knowledge across the borderlines of communities and societies.

Relationships between self-diffusivity, packing fraction, and excess entropy in simple bulk and confined fluids.

PubMed

Mittal, Jeetain; Errington, Jeffrey R; Truskett, Thomas M

2007-08-30

Static measures such as density and entropy, which are intimately connected to structure, have featured prominently in modern thinking about the dynamics of the liquid state. Here, we explore the connections between self-diffusivity, density, and excess entropy for two of the most widely used model "simple" liquids, the equilibrium Lennard-Jones and square-well fluids, in both bulk and confined environments. We find that the self-diffusivity data of the Lennard-Jones fluid can be approximately collapsed onto a single curve (i) versus effective packing fraction and (ii) in appropriately reduced form versus excess entropy, as suggested by two well-known scaling laws. Similar data collapse does not occur for the square-well fluid, a fact that can be understood on the basis of the nontrivial effects that temperature has on its static structure. Nonetheless, we show that the implications of confinement for the self-diffusivity of both of these model fluids, over a broad range of equilibrium conditions, can be predicted on the basis of knowledge of the bulk fluid behavior and either the effective packing fraction or the excess entropy of the confined fluid. Excess entropy is perhaps the most preferable route due to its superior predictive ability and because it is a standard, unambiguous thermodynamic quantity that can be readily predicted via classical density functional theories of inhomogeneous fluids.

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

Podestà, M., E-mail: mpodesta@pppl.gov; Gorelenkova, M.; Fredrickson, E. D.

Integrated simulations of tokamak discharges typically rely on classical physics to model energetic particle (EP) dynamics. However, there are numerous cases in which energetic particles can suffer additional transport that is not classical in nature. Examples include transport by applied 3D magnetic perturbations and, more notably, by plasma instabilities. Focusing on the effects of instabilities, ad-hoc models can empirically reproduce increased transport, but the choice of transport coefficients is usually somehow arbitrary. New approaches based on physics-based reduced models are being developed to address those issues in a simplified way, while retaining a more correct treatment of resonant wave-particle interactions.more » The kick model implemented in the tokamak transport code TRANSP is an example of such reduced models. It includes modifications of the EP distribution by instabilities in real and velocity space, retaining correlations between transport in energy and space typical of resonant EP transport. The relevance of EP phase space modifications by instabilities is first discussed in terms of predicted fast ion distribution. Results are compared with those from a simple, ad-hoc diffusive model. It is then shown that the phase-space resolved model can also provide additional insight into important issues such as internal consistency of the simulations and mode stability through the analysis of the power exchanged between energetic particles and the instabilities.« less

Critical analysis of partial discharge dynamics in air filled spherical voids

NASA Astrophysics Data System (ADS)

Callender, G.; Golosnoy, I. O.; Rapisarda, P.; Lewin, P. L.

2018-03-01

In this paper partial discharge (PD) is investigated inside a spherical air filled void at atmospheric pressure using a drift diffusion model. Discharge dynamics consisted of an electron avalanche transitioning into positive streamer, in agreement with earlier work on dielectric barrier discharges. Different model configurations were utilised to test many of the concepts employed in semi-analytical PD activity models, which use simplistic descriptions of the discharge dynamics. The results showed that many of these concepts may be erroneous, with significant discrepancies between the canonical reasoning and the simulation results. For example, the residual electric field, the electric field after a discharge, is significantly lower than the estimates used by classical PD activity models in the literature.

Dynamics of embedded curves by doubly-nonlocal reaction-diffusion systems

NASA Astrophysics Data System (ADS)

von Brecht, James H.; Blair, Ryan

2017-11-01

We study a class of nonlocal, energy-driven dynamical models that govern the motion of closed, embedded curves from both an energetic and dynamical perspective. Our energetic results provide a variety of ways to understand physically motivated energetic models in terms of more classical, combinatorial measures of complexity for embedded curves. This line of investigation culminates in a family of complexity bounds that relate a rather broad class of models to a generalized, or weighted, variant of the crossing number. Our dynamic results include global well-posedness of the associated partial differential equations, regularity of equilibria for these flows as well as a more detailed investigation of dynamics near such equilibria. Finally, we explore a few global dynamical properties of these models numerically.

Confined trapped alpha behaviour in TFTR deuterium-tritium plasmas

NASA Astrophysics Data System (ADS)

Medley, S. S.; Budny, R. V.; Duong, H. H.; Fisher, R. K.; Petrov, M. P.; Gorelenkov, N. N.; Redi, M. H.; Roquemore, A. L.; White, R. B.

1998-09-01

Confined trapped alpha energy spectra and differential radial density profiles in TFTR D-T plasmas were obtained with the pellet charge exchange (PCX) diagnostic, which measures high energy (Eα = 0.5-3.5 MeV) trapped alphas (v||/v = -0.048) at a single time slice (Δt approx 1 ms) with a spatial resolution of Δr approx 5 cm. Tritons produced in D-D plasmas and RF driven ion tails (H, 3He or T) were also observed and energetic tritium ion tail measurements are discussed. PCX alpha and triton energy spectra extending up to their birth energies were measured in the core of MHD quiescent discharges where the expected classical slowing down and pitch angle scattering effects are not complicated by stochastic ripple diffusion and sawtooth activity. Both the shape of the measured alpha and triton energy distributions and their density ratios are in good agreement with TRANSP predictions, indicating that the PCX measurements are consistent with classical thermalization of the fusion generated alphas and tritons. From calculations, these results set an upper limit on possible anomalous radial diffusion for trapped alphas of Dα <= 0.01 m2·s-1. Outside the core, where the trapped alphas are influenced by stochastic ripple diffusion effects, the PCX measurements are consistent with the functional dependence of the Goldston-White-Boozer stochastic ripple threshold on the alpha energy and the q profile. In the presence of strong sawtooth activity, the PCX diagnostic observes significant redistribution of the alpha signal radial profile wherein alphas are depleted in the core and redistributed to well outside the q = 1 radius, but apparently not beyond the energy dependent stochastic ripple loss boundary. The helical electric field produced during the sawtooth crash plays an essential role in modelling the sawtooth redistribution data. In sawtooth free discharge scenarios with reversed shear operation, the PCX diagnostic also observes radial profiles of the alpha signal that are significantly broader than those for supershots. ORBIT modelling of reversed shear and monotonic shear discharges is in agreement with the q dependent alpha profiles observed. Redistribution of trapped alpha particles in the presence of core localized toroidal Alfvén eigenmode (TAE) activity was observed and modelling of the PCX measurements based on a synergism involving the α-TAE resonance and the effect of stochastic ripple diffusion is in progress.

Tunneling-thermally activated vacancy diffusion mechanism in quantum crystals

NASA Astrophysics Data System (ADS)

Natsik, V. D.; Smirnov, S. N.

2017-10-01

We consider a quasiparticle model of a vacancy in a quantum crystal, with metastable quantum states localized at the lattice sites in potential wells of the crystal field. It is assumed that the quantum dynamics of such vacancies can be described in the semi-classical approximation, where its spectrum consists of a broad band with several split-off levels. The diffusive movement of the vacancy in the crystal volume is reduced to a sequence of tunneling and thermally activated hops between the lattice cites. The temperature dependence of the vacancy diffusion coefficient shows a monotonic decrease during cooling with a sharp transition from an exponential dependence that is characteristic of a high-temperature thermally activated diffusion, to a non-thermal tunneling process in the region of extremely low temperatures. Similar trends have been recently observed in an experimental study of mass-transfer in the 4He and 3He crystals [V. A. Zhuchkov et al., Low Temp. Phys. 41, 169 (2015); Low Temp. Phys. 42, 1075 (2016)]. This mechanism of vacancy diffusion and its analysis complement the concept of a diffusional flow of a defection-quasiparticle quantum gas with a band energy spectrum proposed by Andreev and Lifshitz [JETP 29, 1107 (1969)] and Andreev [Sov. Phys. Usp. 19, 137 (1976)].

Constitutive law for thermally-activated plasticity of recrystallized tungsten

NASA Astrophysics Data System (ADS)

Zinovev, Aleksandr; Terentyev, Dmitry; Dubinko, Andrii; Delannay, Laurent

2017-12-01

A physically-based constitutive law relevant for ITER-specification tungsten grade in as-recrystallized state is proposed. The material demonstrates stages III and IV of the plastic deformation, in which hardening rate does not drop to zero with the increase of applied stress. Despite the classical Kocks-Mecking model, valid at stage III, the strain hardening asymptotically decreases resembling a hyperbolic function. The material parameters are fitted by relying on tensile test data and by requiring that the strain and stress at the onset of diffuse necking (uniform elongation and ultimate tensile strength correspondingly) as well as the yield stress be reproduced. The model is then validated in the temperature range 300-600 °C with the help of finite element analysis of tensile tests which confirms the reproducibility of the experimental engineering curves up to the onset of diffuse necking, beyond which the development of ductile damage accelerates the material failure. This temperature range represents the low temperature application window for tungsten as divertor material in fusion reactor ITER.

Spectrum of the Nuclear Environment for GaAs Spin Qubits.

PubMed

Malinowski, Filip K; Martins, Frederico; Cywiński, Łukasz; Rudner, Mark S; Nissen, Peter D; Fallahi, Saeed; Gardner, Geoffrey C; Manfra, Michael J; Marcus, Charles M; Kuemmeth, Ferdinand

2017-04-28

Using a singlet-triplet spin qubit as a sensitive spectrometer of the GaAs nuclear spin bath, we demonstrate that the spectrum of Overhauser noise agrees with a classical spin diffusion model over 6 orders of magnitude in frequency, from 1 mHz to 1 kHz, is flat below 10 mHz, and falls as 1/f^{2} for frequency f≳1  Hz. Increasing the applied magnetic field from 0.1 to 0.75 T suppresses electron-mediated spin diffusion, which decreases the spectral content in the 1/f^{2} region and lowers the saturation frequency, each by an order of magnitude, consistent with a numerical model. Spectral content at megahertz frequencies is accessed using dynamical decoupling, which shows a crossover from the few-pulse regime (≲16π pulses), where transverse Overhauser fluctuations dominate dephasing, to the many-pulse regime (≳32 π pulses), where longitudinal Overhauser fluctuations with a 1/f spectrum dominate.

Fixation Probability in a Haploid-Diploid Population.

PubMed

Bessho, Kazuhiro; Otto, Sarah P

2017-01-01

Classical population genetic theory generally assumes either a fully haploid or fully diploid life cycle. However, many organisms exhibit more complex life cycles, with both free-living haploid and diploid stages. Here we ask what the probability of fixation is for selected alleles in organisms with haploid-diploid life cycles. We develop a genetic model that considers the population dynamics using both the Moran model and Wright-Fisher model. Applying a branching process approximation, we obtain an accurate fixation probability assuming that the population is large and the net effect of the mutation is beneficial. We also find the diffusion approximation for the fixation probability, which is accurate even in small populations and for deleterious alleles, as long as selection is weak. These fixation probabilities from branching process and diffusion approximations are similar when selection is weak for beneficial mutations that are not fully recessive. In many cases, particularly when one phase predominates, the fixation probability differs substantially for haploid-diploid organisms compared to either fully haploid or diploid species. Copyright © 2017 by the Genetics Society of America.

Homotopic solutions for unsteady second grade liquid utilizing non-Fourier double diffusion concept

NASA Astrophysics Data System (ADS)

Sohail, A.; Khan, W. A.; Khan, M.; Shah, S. I. A.

Main purpose of the current work is to investigate the features of unsteady Cattaneo-Christov heat and mass flux models on the second grade fluid over a stretching surface. The characteristics of unsteady Cattaneo-Christov heat and mass flux models are incorporated in the energy and concentration equations. The unsteady Cattaneo-Christov heat and mass flux models are the generalization of Fourier's and Fick's laws in which the time space upper-convected derivative are utilized to describe the heat conduction and mass diffusion phenomena. The suitable transformations are used to alter the governing partial differential equations into the ordinary differential equations. The resulting problem under consideration is solved analytically by using the homotopy analysis method (HAM). The effect of non-dimensional pertinent parameters on the temperature and concentration distribution are deliberated by using graphs and tables. Results show that the temperature and concentration profiles diminish for augmented values of the thermal and concentration relaxation parameters. Additionally, it is perceived that the temperature and concentration profiles are higher in case of classical Fourier's and Fick's laws as compared to non-Fourier's and non-Fick's laws.

Measurement of the Diffusion Coefficient of Water in RP-3 and RP-5 Jet Fuels Using Digital Holography Interferometry

NASA Astrophysics Data System (ADS)

Li, Chaoyue; Feng, Shiyu; Shao, Lei; Pan, Jun; Liu, Weihua

2018-04-01

The diffusion coefficient of water in jet fuel was measured employing double-exposure digital holographic interferometry to clarify the diffusion process and make the aircraft fuel system safe. The experimental method and apparatus are introduced in detail, and the digital image processing program is coded in MATLAB according to the theory of the Fourier transform. At temperatures ranging from 278.15 K to 333.15 K in intervals of 5 K, the diffusion coefficient of water in RP-3 and RP-5 jet fuels ranges from 2.6967 × 10 -10 m2·s-1 to 8.7332 × 10 -10 m2·s-1 and from 2.3517 × 10 -10 m2·s-1 to 8.0099 × 10-10 m2·s-1, respectively. The relationship between the measured diffusion coefficient and temperature can be well fitted by the Arrhenius law. The diffusion coefficient of water in RP-3 jet fuel is higher than that of water in RP-5 jet fuel at the same temperature. Furthermore, the viscosities of the two jet fuels were measured and found to be expressible in the form of the Arrhenius equation. The relationship among the diffusion coefficient, viscosity and temperature is analyzed according to the classic prediction model, namely the Stokes-Einstein correlation, and this correlation is further revised via experimental data to obtain a more accurate predication result.

Prioritization of candidate disease genes by topological similarity between disease and protein diffusion profiles.

PubMed

Zhu, Jie; Qin, Yufang; Liu, Taigang; Wang, Jun; Zheng, Xiaoqi

2013-01-01

Identification of gene-phenotype relationships is a fundamental challenge in human health clinic. Based on the observation that genes causing the same or similar phenotypes tend to correlate with each other in the protein-protein interaction network, a lot of network-based approaches were proposed based on different underlying models. A recent comparative study showed that diffusion-based methods achieve the state-of-the-art predictive performance. In this paper, a new diffusion-based method was proposed to prioritize candidate disease genes. Diffusion profile of a disease was defined as the stationary distribution of candidate genes given a random walk with restart where similarities between phenotypes are incorporated. Then, candidate disease genes are prioritized by comparing their diffusion profiles with that of the disease. Finally, the effectiveness of our method was demonstrated through the leave-one-out cross-validation against control genes from artificial linkage intervals and randomly chosen genes. Comparative study showed that our method achieves improved performance compared to some classical diffusion-based methods. To further illustrate our method, we used our algorithm to predict new causing genes of 16 multifactorial diseases including Prostate cancer and Alzheimer's disease, and the top predictions were in good consistent with literature reports. Our study indicates that integration of multiple information sources, especially the phenotype similarity profile data, and introduction of global similarity measure between disease and gene diffusion profiles are helpful for prioritizing candidate disease genes. Programs and data are available upon request.

Reverse-Selective Diffusion in Nanocomposite Membranes

NASA Astrophysics Data System (ADS)

Hill, Reghan J.

2006-06-01

The permeability of certain polymer membranes with impenetrable nanoinclusions increases with the particle volume fraction [T. C. Merkel , Science 296, 519 (2002)SCIEAS0036-807510.1126/science.1069580]. The discovery contradicts qualitative expectations based on Maxwell’s classical theory of conduction or diffusion in composites with homogeneous phases. This Letter presents a theory based on an hypothesis that polymer chains are repelled from the inclusions during membrane casting. The accompanying increase in free volume, and hence solute diffusivity, yields bulk transport properties that are in good agreement with experiments.

A Simple Mathematical Model Inspired by the Purkinje Cells: From Delayed Travelling Waves to Fractional Diffusion.

PubMed

Dipierro, Serena; Valdinoci, Enrico

2018-07-01

Recently, several experiments have demonstrated the existence of fractional diffusion in the neuronal transmission occurring in the Purkinje cells, whose malfunctioning is known to be related to the lack of voluntary coordination and the appearance of tremors. Also, a classical mathematical feature is that (fractional) parabolic equations possess smoothing effects, in contrast with the case of hyperbolic equations, which typically exhibit shocks and discontinuities. In this paper, we show how a simple toy-model of a highly ramified structure, somehow inspired by that of the Purkinje cells, may produce a fractional diffusion via the superposition of travelling waves that solve a hyperbolic equation. This could suggest that the high ramification of the Purkinje cells might have provided an evolutionary advantage of "smoothing" the transmission of signals and avoiding shock propagations (at the price of slowing a bit such transmission). Although an experimental confirmation of the possibility of such evolutionary advantage goes well beyond the goals of this paper, we think that it is intriguing, as a mathematical counterpart, to consider the time fractional diffusion as arising from the superposition of delayed travelling waves in highly ramified transmission media. The case of a travelling concave parabola with sufficiently small curvature is explicitly computed. The new link that we propose between time fractional diffusion and hyperbolic equation also provides a novelty with respect to the usual paradigm relating time fractional diffusion with parabolic equations in the limit. This paper is written in such a way as to be of interest to both biologists and mathematician alike. In order to accomplish this aim, both complete explanations of the objects considered and detailed lists of references are provided.

Spatial self-organization in hybrid models of multicellular adhesion

NASA Astrophysics Data System (ADS)

Bonforti, Adriano; Duran-Nebreda, Salva; Montañez, Raúl; Solé, Ricard

2016-10-01

Spatial self-organization emerges in distributed systems exhibiting local interactions when nonlinearities and the appropriate propagation of signals are at work. These kinds of phenomena can be modeled with different frameworks, typically cellular automata or reaction-diffusion systems. A different class of dynamical processes involves the correlated movement of agents over space, which can be mediated through chemotactic movement or minimization of cell-cell interaction energy. A classic example of the latter is given by the formation of spatially segregated assemblies when cells display differential adhesion. Here, we consider a new class of dynamical models, involving cell adhesion among two stochastically exchangeable cell states as a minimal model capable of exhibiting well-defined, ordered spatial patterns. Our results suggest that a whole space of pattern-forming rules is hosted by the combination of physical differential adhesion and the value of probabilities modulating cell phenotypic switching, showing that Turing-like patterns can be obtained without resorting to reaction-diffusion processes. If the model is expanded allowing cells to proliferate and die in an environment where diffusible nutrient and toxic waste are at play, different phases are observed, characterized by regularly spaced patterns. The analysis of the parameter space reveals that certain phases reach higher population levels than other modes of organization. A detailed exploration of the mean-field theory is also presented. Finally, we let populations of cells with different adhesion matrices compete for reproduction, showing that, in our model, structural organization can improve the fitness of a given cell population. The implications of these results for ecological and evolutionary models of pattern formation and the emergence of multicellularity are outlined.

Diffusion of two-dimensional epitaxial clusters on metal (100) surfaces: Facile versus nucleation-mediated behavior and their merging for larger sizes

NASA Astrophysics Data System (ADS)

Lai, King C.; Liu, Da-Jiang; Evans, James W.

2017-12-01

For diffusion of two-dimensional homoepitaxial clusters of N atoms on metal (100) surfaces mediated by edge atom hopping, macroscale continuum theory suggests that the diffusion coefficient scales like DN˜ N-β with β =3 /2 . However, we find quite different and diverse behavior in multiple size regimes. These include: (i) facile diffusion for small sizes N <9 ; (ii) slow nucleation-mediated diffusion with small β <1 for "perfect" sizes N = Np= L2 or L (L +1 ) , for L =3 ,4 , ... having unique ground-state shapes, for moderate sizes 9 ≤N ≤O (102) ; the same also applies for N =Np+3 , Np+ 4 , ... (iii) facile diffusion but with large β >2 for N =Np+1 and Np+2 also for moderate sizes 9 ≤N ≤O (102) ; (iv) merging of the above distinct branches and subsequent anomalous scaling with 1 ≲β <3 /2 , reflecting the quasifacetted structure of clusters, for larger N =O (102) to N =O (103) ; (v) classic scaling with β =3 /2 for very large N =O (103) and above. The specified size ranges apply for typical model parameters. We focus on the moderate size regime where we show that diffusivity cycles quasiperiodically from the slowest branch for Np+3 (not Np) to the fastest branch for Np+1 . Behavior is quantified by kinetic Monte Carlo simulation of an appropriate stochastic lattice-gas model. However, precise analysis must account for a strong enhancement of diffusivity for short time increments due to back correlation in the cluster motion. Further understanding of this enhancement, of anomalous size scaling behavior, and of the merging of various branches, is facilitated by combinatorial analysis of the number of the ground-state and low-lying excited state cluster configurations, and also of kink populations.

Diffusion of two-dimensional epitaxial clusters on metal (100) surfaces: Facile versus nucleation-mediated behavior and their merging for larger sizes

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

Lai, King C.; Liu, Da -Jiang; Evans, James W.

For diffusion of two-dimensional homoepitaxial clusters of N atoms on metal(100) surfaces mediated by edge atom hopping, macroscale continuum theory suggests that the diffusion coefficient scales like DN ~ N -β with β = 3/2. However, we find quite different and diverse behavior in multiple size regimes. These include: (i) facile diffusion for small sizes N < 9; (ii) slow nucleation-mediated diffusion with small β < 1 for “perfect” sizes N = N p = L 2 or L(L+1), for L = 3, 4,… having unique ground state shapes, for moderate sizes 9 ≤ N ≤ O(10 2); the samemore » also applies for N = N p +3, N p + 4,… (iii) facile diffusion but with large β > 2 for N = Np + 1 and N p + 2 also for moderate sizes 9 ≤ N ≤ O(10 2); (iv) merging of the above distinct branches and subsequent anomalous scaling with 1 ≲ β < 3/2, reflecting the quasi-facetted structure of clusters, for larger N = O(10 2) to N = O(10 3); and (v) classic scaling with β = 3/2 for very large N = O(103) and above. The specified size ranges apply for typical model parameters. We focus on the moderate size regime where show that diffusivity cycles quasi-periodically from the slowest branch for N p + 3 (not Np) to the fastest branch for Np + 1. Behavior is quantified by Kinetic Monte Carlo simulation of an appropriate stochastic lattice-gas model. However, precise analysis must account for a strong enhancement of diffusivity for short time increments due to back-correlation in the cluster motion. Further understanding of this enhancement, of anomalous size scaling behavior, and of the merging of various branches, is facilitated by combinatorial analysis of the number of the ground state and low-lying excited state cluster configurations, and also of kink populations.« less

Diffusion of two-dimensional epitaxial clusters on metal (100) surfaces: Facile versus nucleation-mediated behavior and their merging for larger sizes

DOE PAGES

Lai, King C.; Liu, Da -Jiang; Evans, James W.

2017-12-05

For diffusion of two-dimensional homoepitaxial clusters of N atoms on metal(100) surfaces mediated by edge atom hopping, macroscale continuum theory suggests that the diffusion coefficient scales like DN ~ N -β with β = 3/2. However, we find quite different and diverse behavior in multiple size regimes. These include: (i) facile diffusion for small sizes N < 9; (ii) slow nucleation-mediated diffusion with small β < 1 for “perfect” sizes N = N p = L 2 or L(L+1), for L = 3, 4,… having unique ground state shapes, for moderate sizes 9 ≤ N ≤ O(10 2); the samemore » also applies for N = N p +3, N p + 4,… (iii) facile diffusion but with large β > 2 for N = Np + 1 and N p + 2 also for moderate sizes 9 ≤ N ≤ O(10 2); (iv) merging of the above distinct branches and subsequent anomalous scaling with 1 ≲ β < 3/2, reflecting the quasi-facetted structure of clusters, for larger N = O(10 2) to N = O(10 3); and (v) classic scaling with β = 3/2 for very large N = O(103) and above. The specified size ranges apply for typical model parameters. We focus on the moderate size regime where show that diffusivity cycles quasi-periodically from the slowest branch for N p + 3 (not Np) to the fastest branch for Np + 1. Behavior is quantified by Kinetic Monte Carlo simulation of an appropriate stochastic lattice-gas model. However, precise analysis must account for a strong enhancement of diffusivity for short time increments due to back-correlation in the cluster motion. Further understanding of this enhancement, of anomalous size scaling behavior, and of the merging of various branches, is facilitated by combinatorial analysis of the number of the ground state and low-lying excited state cluster configurations, and also of kink populations.« less

Communication: Diffusion constant in supercooled water as the Widom line is crossed in no man's land

NASA Astrophysics Data System (ADS)

Ni, Yicun; Hestand, Nicholas J.; Skinner, J. L.

2018-05-01

According to the liquid-liquid critical point (LLCP) hypothesis, there are two distinct phases of supercooled liquid water, namely, high-density liquid and low-density liquid, separated by a coexistence line that terminates in an LLCP. If the LLCP is real, it is located within No Man's Land (NML), the region of the metastable phase diagram that is difficult to access using conventional experimental techniques due to rapid homogeneous nucleation to the crystal. However, a recent ingenious experiment has enabled measurement of the diffusion constant deep inside NML. In the current communication, these recent measurements are compared, with good agreement, to the diffusion constant of E3B3 water, a classical water model that explicitly includes three-body interactions. The behavior of the diffusion constant as the system crosses the Widom line (the extension of the liquid-liquid coexistence line into the one-phase region) is analyzed to derive information about the presence and location of the LLCP. Calculations over a wide range of temperatures and pressures show that the new experimental measurements are consistent with an LLCP having a critical pressure of over 0.6 kbar.

Multiple Scattering in Random Mechanical Systems and Diffusion Approximation

NASA Astrophysics Data System (ADS)

Feres, Renato; Ng, Jasmine; Zhang, Hong-Kun

2013-10-01

This paper is concerned with stochastic processes that model multiple (or iterated) scattering in classical mechanical systems of billiard type, defined below. From a given (deterministic) system of billiard type, a random process with transition probabilities operator P is introduced by assuming that some of the dynamical variables are random with prescribed probability distributions. Of particular interest are systems with weak scattering, which are associated to parametric families of operators P h , depending on a geometric or mechanical parameter h, that approaches the identity as h goes to 0. It is shown that ( P h - I)/ h converges for small h to a second order elliptic differential operator on compactly supported functions and that the Markov chain process associated to P h converges to a diffusion with infinitesimal generator . Both P h and are self-adjoint (densely) defined on the space of square-integrable functions over the (lower) half-space in , where η is a stationary measure. This measure's density is either (post-collision) Maxwell-Boltzmann distribution or Knudsen cosine law, and the random processes with infinitesimal generator respectively correspond to what we call MB diffusion and (generalized) Legendre diffusion. Concrete examples of simple mechanical systems are given and illustrated by numerically simulating the random processes.

Magnetic flux and heat losses by diffusive, advective, and Nernst effects in MagLIF-like plasma

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

Velikovich, A. L., E-mail: sasha.velikovich@nrl.navy.mil; Giuliani, J. L., E-mail: sasha.velikovich@nrl.navy.mil; Zalesak, S. T.

2014-12-15

The MagLIF approach to inertial confinement fusion involves subsonic/isobaric compression and heating of a DT plasma with frozen-in magnetic flux by a heavy cylindrical liner. The losses of heat and magnetic flux from the plasma to the liner are thereby determined by plasma advection and gradient-driven transport processes, such as thermal conductivity, magnetic field diffusion and thermomagnetic effects. Theoretical analysis based on obtaining exact self-similar solutions of the classical collisional Braginskii's plasma transport equations in one dimension demonstrates that the heat loss from the hot plasma to the cold liner is dominated by the transverse heat conduction and advection, andmore » the corresponding loss of magnetic flux is dominated by advection and the Nernst effect. For a large electron Hall parameter ω{sub e}τ{sub e} effective diffusion coefficients determining the losses of heat and magnetic flux are both shown to decrease with ω{sub e}τ{sub e} as does the Bohm diffusion coefficient, which is commonly associated with low collisionality and two-dimensional transport. This family of exact solutions can be used for verification of codes that model the MagLIF plasma dynamics.« less

A simple method for finding explicit analytic transition densities of diffusion processes with general diploid selection.

PubMed

Song, Yun S; Steinrücken, Matthias

2012-03-01

The transition density function of the Wright-Fisher diffusion describes the evolution of population-wide allele frequencies over time. This function has important practical applications in population genetics, but finding an explicit formula under a general diploid selection model has remained a difficult open problem. In this article, we develop a new computational method to tackle this classic problem. Specifically, our method explicitly finds the eigenvalues and eigenfunctions of the diffusion generator associated with the Wright-Fisher diffusion with recurrent mutation and arbitrary diploid selection, thus allowing one to obtain an accurate spectral representation of the transition density function. Simplicity is one of the appealing features of our approach. Although our derivation involves somewhat advanced mathematical concepts, the resulting algorithm is quite simple and efficient, only involving standard linear algebra. Furthermore, unlike previous approaches based on perturbation, which is applicable only when the population-scaled selection coefficient is small, our method is nonperturbative and is valid for a broad range of parameter values. As a by-product of our work, we obtain the rate of convergence to the stationary distribution under mutation-selection balance.

A Simple Method for Finding Explicit Analytic Transition Densities of Diffusion Processes with General Diploid Selection

PubMed Central

Song, Yun S.; Steinrücken, Matthias

2012-01-01

The transition density function of the Wright–Fisher diffusion describes the evolution of population-wide allele frequencies over time. This function has important practical applications in population genetics, but finding an explicit formula under a general diploid selection model has remained a difficult open problem. In this article, we develop a new computational method to tackle this classic problem. Specifically, our method explicitly finds the eigenvalues and eigenfunctions of the diffusion generator associated with the Wright–Fisher diffusion with recurrent mutation and arbitrary diploid selection, thus allowing one to obtain an accurate spectral representation of the transition density function. Simplicity is one of the appealing features of our approach. Although our derivation involves somewhat advanced mathematical concepts, the resulting algorithm is quite simple and efficient, only involving standard linear algebra. Furthermore, unlike previous approaches based on perturbation, which is applicable only when the population-scaled selection coefficient is small, our method is nonperturbative and is valid for a broad range of parameter values. As a by-product of our work, we obtain the rate of convergence to the stationary distribution under mutation–selection balance. PMID:22209899

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

Podesta, M.; Gorelenkova, M.; Fredrickson, E. D.

Here, integrated simulations of tokamak discharges typically rely on classical physics to model energetic particle (EP) dynamics. However, there are numerous cases in which energetic particles can suffer additional transport that is not classical in nature. Examples include transport by applied 3D magnetic perturbations and, more notably, by plasma instabilities. Focusing on the effects of instabilities,ad-hocmodels can empirically reproduce increased transport, but the choice of transport coefficients is usually somehow arbitrary. New approaches based on physics-based reduced models are being developed to address those issues in a simplified way, while retaining a more correct treatment of resonant wave-particle interactions. Themore » kick model implemented in the tokamaktransport code TRANSP is an example of such reduced models. It includes modifications of the EP distribution by instabilities in real and velocity space, retaining correlations between transport in energy and space typical of resonant EP transport. The relevance of EP phase space modifications by instabilities is first discussed in terms of predicted fast ion distribution. Results are compared with those from a simple, ad-hoc diffusive model. It is then shown that the phase-space resolved model can also provide additional insight into important issues such as internal consistency of the simulations and mode stability through the analysis of the power exchanged between energetic particles and the instabilities.« less

A multiscale quantum mechanics/electromagnetics method for device simulations.

PubMed

Yam, ChiYung; Meng, Lingyi; Zhang, Yu; Chen, GuanHua

2015-04-07

Multiscale modeling has become a popular tool for research applying to different areas including materials science, microelectronics, biology, chemistry, etc. In this tutorial review, we describe a newly developed multiscale computational method, incorporating quantum mechanics into electronic device modeling with the electromagnetic environment included through classical electrodynamics. In the quantum mechanics/electromagnetics (QM/EM) method, the regions of the system where active electron scattering processes take place are treated quantum mechanically, while the surroundings are described by Maxwell's equations and a semiclassical drift-diffusion model. The QM model and the EM model are solved, respectively, in different regions of the system in a self-consistent manner. Potential distributions and current densities at the interface between QM and EM regions are employed as the boundary conditions for the quantum mechanical and electromagnetic simulations, respectively. The method is illustrated in the simulation of several realistic systems. In the case of junctionless field-effect transistors, transfer characteristics are obtained and a good agreement between experiments and simulations is achieved. Optical properties of a tandem photovoltaic cell are studied and the simulations demonstrate that multiple QM regions are coupled through the classical EM model. Finally, the study of a carbon nanotube-based molecular device shows the accuracy and efficiency of the QM/EM method.

Analytical prediction of moisture absorption/desorption in resin matrix composites exposed to aircraft environments

NASA Technical Reports Server (NTRS)

Unnam, J.; Tenney, D. R.

1977-01-01

The moisture absorption/desorption behavior of resin matrix composites was mathematically modeled by classical diffusion theory using an effective diffusion coefficient. Good agreement was found between calculated moisture content and published data for T300/5208 graphite fiber reinforced epoxy matrix composite. Weather Bureau data for Langley Air Force Base and Norfolk, Va., were used to calculate the amount of moisture a T300/5208 composite panel would contain if exposed outdoors. Results obtained by using average monthly weather data for several high aircraft usage locations around the world suggest that, except for desert areas, geographical locations should have only minimal effect on the moisture absorption level reached in composites. Solar radiation data together with cloud and wind information were included in the analysis to estimate an effective temperature of the composite panel during ground exposure.

Phase-field modeling of isothermal quasi-incompressible multicomponent liquids

NASA Astrophysics Data System (ADS)

Tóth, Gyula I.

2016-09-01

In this paper general dynamic equations describing the time evolution of isothermal quasi-incompressible multicomponent liquids are derived in the framework of the classical Ginzburg-Landau theory of first order phase transformations. Based on the fundamental equations of continuum mechanics, a general convection-diffusion dynamics is set up first for compressible liquids. The constitutive relations for the diffusion fluxes and the capillary stress are determined in the framework of gradient theories. Next the general definition of incompressibility is given, which is taken into account in the derivation by using the Lagrange multiplier method. To validate the theory, the dynamic equations are solved numerically for the quaternary quasi-incompressible Cahn-Hilliard system. It is demonstrated that variable density (i) has no effect on equilibrium (in case of a suitably constructed free energy functional) and (ii) can influence nonequilibrium pattern formation significantly.

Understanding of flux-limited behaviors of heat transport in nonlinear regime

NASA Astrophysics Data System (ADS)

Guo, Yangyu; Jou, David; Wang, Moran

2016-01-01

The classical Fourier's law of heat transport breaks down in highly nonequilibrium situations as in nanoscale heat transport, where nonlinear effects become important. The present work is aimed at exploring the flux-limited behaviors based on a categorization of existing nonlinear heat transport models in terms of their theoretical foundations. Different saturation heat fluxes are obtained, whereas the same qualitative variation trend of heat flux versus exerted temperature gradient is got in diverse nonlinear models. The phonon hydrodynamic model is proposed to act as a standard to evaluate other heat flux limiters because of its more rigorous physical foundation. A deeper knowledge is thus achieved about the phenomenological generalized heat transport models. The present work provides deeper understanding and accurate modeling of nonlocal and nonlinear heat transport beyond the diffusive limit.

Frustration and correlations in stacked triangular-lattice Ising antiferromagnets

NASA Astrophysics Data System (ADS)

Burnell, F. J.; Chalker, J. T.

2015-12-01

We study multilayer triangular-lattice Ising antiferromagnets with interlayer interactions that are weak and frustrated in an abc stacking. By analyzing a coupled height model description of these systems, we show that they exhibit a classical spin liquid regime at low temperature, in which both intralayer and interlayer correlations are strong but there is no long-range order. Diffuse scattering in this regime is concentrated on a helix in reciprocal space, as observed for charge ordering in the materials LuFe2O4 and YbFe2O4 .

Molecular dynamics simulations of dense plasmas

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

Collins, L.A.; Kress, J.D.; Kwon, I.

1993-12-31

We have performed quantum molecular dynamics simulations of hot, dense plasmas of hydrogen over a range of temperatures(0.1-5eV) and densities(0.0625-5g/cc). We determine the forces quantum mechanically from density functional, extended Huckel, and tight binding techniques and move the nuclei according to the classical equations of motion. We determine pair-correlation functions, diffusion coefficients, and electrical conductivities. We find that many-body effects predominate in this regime. We begin to obtain agreement with the OCP and Thomas-Fermi models only at the higher temperatures and densities.

Constrained diffusion or immobile fraction on cell surfaces: a new interpretation.

PubMed Central

Feder, T J; Brust-Mascher, I; Slattery, J P; Baird, B; Webb, W W

1996-01-01

Protein lateral mobility in cell membranes is generally measured using fluorescence photobleaching recovery (FPR). Since the development of this technique, the data have been interpreted by assuming free Brownian diffusion of cell surface receptors in two dimensions, an interpretation that requires that a subset of the diffusing species remains immobile. The origin of this so-called immobile fraction remains a mystery. In FPR, the motions of thousands of particles are inherently averaged, inevitably masking the details of individual motions. Recently, tracking of individual cell surface receptors has identified several distinct types of motion (Gross and Webb, 1988; Ghosh and Webb, 1988, 1990, 1994; Kusumi et al. 1993; Qian et al. 1991; Slattery, 1995), thereby calling into question the classical interpretation of FPR data as free Brownian motion of a limited mobile fraction. We have measured the motion of fluorescently labeled immunoglobulin E complexed to high affinity receptors (Fc epsilon RI) on rat basophilic leukemia cells using both single particle tracking and FPR. As in previous studies, our tracking results show that individual receptors may diffuse freely, or may exhibit restricted, time-dependent (anomalous) diffusion. Accordingly, we have analyzed FPR data by a new model to take this varied motion into account, and we show that the immobile fraction may be due to particles moving with the anomalous subdiffusion associated with restricted lateral mobility. Anomalous subdiffusion denotes random molecular motion in which the mean square displacements grow as a power law in time with a fractional positive exponent less than one. These findings call for a new model of cell membrane structure. PMID:8744314

Numerical Determination of Critical Conditions for Thermal Ignition

NASA Technical Reports Server (NTRS)

Luo, W.; Wake, G. C.; Hawk, C. W.; Litchford, R. J.

2008-01-01

The determination of ignition or thermal explosion in an oxidizing porous body of material, as described by a dimensionless reaction-diffusion equation of the form .tu = .2u + .e-1/u over the bounded region O, is critically reexamined from a modern perspective using numerical methodologies. First, the classic stationary model is revisited to establish the proper reference frame for the steady-state solution space, and it is demonstrated how the resulting nonlinear two-point boundary value problem can be reexpressed as an initial value problem for a system of first-order differential equations, which may be readily solved using standard algorithms. Then, the numerical procedure is implemented and thoroughly validated against previous computational results based on sophisticated path-following techniques. Next, the transient nonstationary model is attacked, and the full nonlinear form of the reaction-diffusion equation, including a generalized convective boundary condition, is discretized and expressed as a system of linear algebraic equations. The numerical methodology is implemented as a computer algorithm, and validation computations are carried out as a prelude to a broad-ranging evaluation of the assembly problem and identification of the watershed critical initial temperature conditions for thermal ignition. This numerical methodology is then used as the basis for studying the relationship between the shape of the critical initial temperature distribution and the corresponding spatial moments of its energy content integral and an attempt to forge a fundamental conjecture governing this relation. Finally, the effects of dynamic boundary conditions on the classic storage problem are investigated and the groundwork is laid for the development of an approximate solution methodology based on adaptation of the standard stationary model.

Quantum Chaos

NASA Astrophysics Data System (ADS)

Casati, Giulio; Chirikov, Boris

2006-11-01

Preface; Acknowledgments; Introduction: 1. The legacy of chaos in quantum mechanics G. Casati and B. V. Chirikov; Part I. Classical Chaos and Quantum Localization: 2. Stochastic behaviour of a quantum pendulum under a periodic perturbation G. Casati, B. V. Chirikov, F. M. Izrailev and J. Ford; 3. Quantum dynamics of a nonintegrable system D. R. Grempel, R. E. Prange and S. E. Fishman; 4. Excitation of molecular rotation by periodic microwave pulses. A testing ground for Anderson localization R. Blümel, S. Fishman and U. Smilansky; 5. Localization of diffusive excitation in multi-level systems D. K. Shepelyansky; 6. Classical and quantum chaos for a kicked top F. Haake, M. Kus and R. Scharf; 7. Self-similarity in quantum dynamics L. E. Reichl and L. Haoming; 8. Time irreversibility of classically chaotic quantum dynamics K. Ikeda; 9. Effect of noise on time-dependent quantum chaos E. Ott, T. M. Antonsen Jr and J. D. Hanson; 10. Dynamical localization, dissipation and noise R. F. Graham; 11. Maximum entropy models and quantum transmission in disordered systems J.-L. Pichard and M. Sanquer; 12. Solid state 'atoms' in intense oscillating fields M. S. Sherwin; Part II. Atoms in Strong Fields: 13. Localization of classically chaotic diffusion for hydrogen atoms in microwave fields J. E. Bayfield, G. Casati, I. Guarneri and D. W. Sokol; 14. Inhibition of quantum transport due to 'scars' of unstable periodic orbits R. V. Jensen, M. M. Sanders, M. Saraceno and B. Sundaram; 15. Rubidium Rydberg atoms in strong fields G. Benson, G. Raithel and H. Walther; 16. Diamagnetic Rydberg atom: confrontation of calculated and observed spectra C.-H. Iu, G. R. Welch, M. M. Kash, D. Kleppner, D. Delande and J. C. Gay; 17. Semiclassical approximation for the quantum states of a hydrogen atom in a magnetic field near the ionization limit M. Y. Kuchiev and O. P. Sushkov; 18. The semiclassical helium atom D. Wintgen, K. Richter and G. Tanner; 19. Stretched helium: a model for quantum chaos in two-electron atoms R. Blümel and W. P. Reinhardt; Part III. Semiclassical Approximations: 20. Semiclassical theory of spectral rigidity M. V. Berry; 21. Semiclassical structure of trace formulas R. G. Littlejohn; 22. h-Expansion for quantum trace formulas P. Gaspard; 23. Pinball scattering B. Eckhardt, G. Russberg, P. Cvitanovic, P. E. Rosenqvist and P. Scherer; 24. Logarithm breaking time in quantum chaos G. P. Berman and G. M. Zaslavsky; 25. Semiclassical propagation: how long can it last? M. A. Sepulveda, S. Tomsovic and E. J. Heller; 26. The quantized Baker's transformation N. L. Balazs and A. Voros; 27. Classical structures in the quantized baker transformation M. Saraceno; 28. Quantum nodal points as fingerprints of classical chaos P. Leboeuf and A. Voros; 29. Chaology of action billiards A. M. Ozorio de Almeida and M. A. M. de Aguiar; Part IV. Level Statistics and Random Matrix Theory: 30. Characterization of chaotic quantum spectra and universality of level fluctuation laws O. Bohigas, M. J. Giannono, and C. Schmit; 31. Quantum chaos, localization and band random matrices F. M. Izrailev; 32. Structural invariance in channel space: a step toward understanding chaotic scattering in quantum mechanics T. H. Seligman; 33. Spectral properties of a Fermi accelerating disk R. Badrinarayanan and J. J. José; 34. Spectral properties of systems with dynamical localization T. Dittrich and U. Smilansky; 35. Unbound quantum diffusion and fractal spectra T. Geisel, R. Ketzmerick and G. Petschel; 36. Microwave studies in irregularly shaped billiards H.-J. Stöckmann, J. Stein and M. Kollman; Index.

Quantum Chaos

NASA Astrophysics Data System (ADS)

Casati, Giulio; Chirikov, Boris

1995-04-01

Preface; Acknowledgments; Introduction: 1. The legacy of chaos in quantum mechanics G. Casati and B. V. Chirikov; Part I. Classical Chaos and Quantum Localization: 2. Stochastic behaviour of a quantum pendulum under a periodic perturbation G. Casati, B. V. Chirikov, F. M. Izrailev and J. Ford; 3. Quantum dynamics of a nonintegrable system D. R. Grempel, R. E. Prange and S. E. Fishman; 4. Excitation of molecular rotation by periodic microwave pulses. A testing ground for Anderson localization R. Blümel, S. Fishman and U. Smilansky; 5. Localization of diffusive excitation in multi-level systems D. K. Shepelyansky; 6. Classical and quantum chaos for a kicked top F. Haake, M. Kus and R. Scharf; 7. Self-similarity in quantum dynamics L. E. Reichl and L. Haoming; 8. Time irreversibility of classically chaotic quantum dynamics K. Ikeda; 9. Effect of noise on time-dependent quantum chaos E. Ott, T. M. Antonsen Jr and J. D. Hanson; 10. Dynamical localization, dissipation and noise R. F. Graham; 11. Maximum entropy models and quantum transmission in disordered systems J.-L. Pichard and M. Sanquer; 12. Solid state 'atoms' in intense oscillating fields M. S. Sherwin; Part II. Atoms in Strong Fields: 13. Localization of classically chaotic diffusion for hydrogen atoms in microwave fields J. E. Bayfield, G. Casati, I. Guarneri and D. W. Sokol; 14. Inhibition of quantum transport due to 'scars' of unstable periodic orbits R. V. Jensen, M. M. Sanders, M. Saraceno and B. Sundaram; 15. Rubidium Rydberg atoms in strong fields G. Benson, G. Raithel and H. Walther; 16. Diamagnetic Rydberg atom: confrontation of calculated and observed spectra C.-H. Iu, G. R. Welch, M. M. Kash, D. Kleppner, D. Delande and J. C. Gay; 17. Semiclassical approximation for the quantum states of a hydrogen atom in a magnetic field near the ionization limit M. Y. Kuchiev and O. P. Sushkov; 18. The semiclassical helium atom D. Wintgen, K. Richter and G. Tanner; 19. Stretched helium: a model for quantum chaos in two-electron atoms R. Blümel and W. P. Reinhardt; Part III. Semiclassical Approximations: 20. Semiclassical theory of spectral rigidity M. V. Berry; 21. Semiclassical structure of trace formulas R. G. Littlejohn; 22. h-Expansion for quantum trace formulas P. Gaspard; 23. Pinball scattering B. Eckhardt, G. Russberg, P. Cvitanovic, P. E. Rosenqvist and P. Scherer; 24. Logarithm breaking time in quantum chaos G. P. Berman and G. M. Zaslavsky; 25. Semiclassical propagation: how long can it last? M. A. Sepulveda, S. Tomsovic and E. J. Heller; 26. The quantized Baker's transformation N. L. Balazs and A. Voros; 27. Classical structures in the quantized baker transformation M. Saraceno; 28. Quantum nodal points as fingerprints of classical chaos P. Leboeuf and A. Voros; 29. Chaology of action billiards A. M. Ozorio de Almeida and M. A. M. de Aguiar; Part IV. Level Statistics and Random Matrix Theory: 30. Characterization of chaotic quantum spectra and universality of level fluctuation laws O. Bohigas, M. J. Giannono, and C. Schmit; 31. Quantum chaos, localization and band random matrices F. M. Izrailev; 32. Structural invariance in channel space: a step toward understanding chaotic scattering in quantum mechanics T. H. Seligman; 33. Spectral properties of a Fermi accelerating disk R. Badrinarayanan and J. J. José; 34. Spectral properties of systems with dynamical localization T. Dittrich and U. Smilansky; 35. Unbound quantum diffusion and fractal spectra T. Geisel, R. Ketzmerick and G. Petschel; 36. Microwave studies in irregularly shaped billiards H.-J. Stöckmann, J. Stein and M. Kollman; Index.

Analytical Model for Diffusive Evaporation of Sessile Droplets Coupled with Interfacial Cooling Effect.

PubMed

Nguyen, Tuan A H; Biggs, Simon R; Nguyen, Anh V

2018-05-30

Current analytical models for sessile droplet evaporation do not consider the nonuniform temperature field within the droplet and can overpredict the evaporation by 20%. This deviation can be attributed to a significant temperature drop due to the release of the latent heat of evaporation along the air-liquid interface. We report, for the first time, an analytical solution of the sessile droplet evaporation coupled with this interfacial cooling effect. The two-way coupling model of the quasi-steady thermal diffusion within the droplet and the quasi-steady diffusion-controlled droplet evaporation is conveniently solved in the toroidal coordinate system by applying the method of separation of variables. Our new analytical model for the coupled vapor concentration and temperature fields is in the closed form and is applicable for a full range of spherical-cap shape droplets of different contact angles and types of fluids. Our analytical results are uniquely quantified by a dimensionless evaporative cooling number E o whose magnitude is determined only by the thermophysical properties of the liquid and the atmosphere. Accordingly, the larger the magnitude of E o , the more significant the effect of the evaporative cooling, which results in stronger suppression on the evaporation rate. The classical isothermal model is recovered if the temperature gradient along the air-liquid interface is negligible ( E o = 0). For substrates with very high thermal conductivities (isothermal substrates), our analytical model predicts a reversal of temperature gradient along the droplet-free surface at a contact angle of 119°. Our findings pose interesting challenges but also guidance for experimental investigations.

Thermal quantum time-correlation functions from classical-like dynamics

NASA Astrophysics Data System (ADS)

Hele, Timothy J. H.

2017-07-01

Thermal quantum time-correlation functions are of fundamental importance in quantum dynamics, allowing experimentally measurable properties such as reaction rates, diffusion constants and vibrational spectra to be computed from first principles. Since the exact quantum solution scales exponentially with system size, there has been considerable effort in formulating reliable linear-scaling methods involving exact quantum statistics and approximate quantum dynamics modelled with classical-like trajectories. Here, we review recent progress in the field with the development of methods including centroid molecular dynamics , ring polymer molecular dynamics (RPMD) and thermostatted RPMD (TRPMD). We show how these methods have recently been obtained from 'Matsubara dynamics', a form of semiclassical dynamics which conserves the quantum Boltzmann distribution. We also apply the Matsubara formalism to reaction rate theory, rederiving t → 0+ quantum transition-state theory (QTST) and showing that Matsubara-TST, like RPMD-TST, is equivalent to QTST. We end by surveying areas for future progress.

Numerical analysis of the diffusive mass transport in brain tissues with applications to optical sensors

NASA Astrophysics Data System (ADS)

Neculae, Adrian P.; Otte, Andreas; Curticapean, Dan

2013-03-01

In the brain-cell microenvironment, diffusion plays an important role: apart from delivering glucose and oxygen from the vascular system to brain cells, it also moves informational substances between cells. The brain is an extremely complex structure of interwoven, intercommunicating cells, but recent theoretical and experimental works showed that the classical laws of diffusion, cast in the framework of porous media theory, can deliver an accurate quantitative description of the way molecules are transported through this tissue. The mathematical modeling and the numerical simulations are successfully applied in the investigation of diffusion processes in tissues, replacing the costly laboratory investigations. Nevertheless, modeling must rely on highly accurate information regarding the main parameters (tortuosity, volume fraction) which characterize the tissue, obtained by structural and functional imaging. The usual techniques to measure the diffusion mechanism in brain tissue are the radiotracer method, the real time iontophoretic method and integrative optical imaging using fluorescence microscopy. A promising technique for obtaining the values for characteristic parameters of the transport equation is the direct optical investigation using optical fibers. The analysis of these parameters also reveals how the local geometry of the brain changes with time or under pathological conditions. This paper presents a set of computations concerning the mass transport inside the brain tissue, for different types of cells. By measuring the time evolution of the concentration profile of an injected substance and using suitable fitting procedures, the main parameters characterizing the tissue can be determined. This type of analysis could be an important tool in understanding the functional mechanisms of effective drug delivery in complex structures such as the brain tissue. It also offers possibilities to realize optical imaging methods for in vitro and in vivo measurements using optical fibers. The model also may help in radiotracer biomarker models for the understanding of the mechanism of action of new chemical entities.

A study of sound absorption by street canyon boundaries and asphalt rubber concrete pavement

NASA Astrophysics Data System (ADS)

Drysdale, Graeme Robert

A sound field model, based on a classical diffusion equation, is extended to account for sound absorption in a diffusion parameter used to model sound energy in a narrow street canyon. The model accounts for a single sound absorption coefficient, separate accommodation coefficients and a combination of separate absorption and accommodation coefficients from parallel canyon walls. The new expressions are compared to the original formula through numerical simulations to reveal the effect of absorption on sound diffusion. The newly established analytical formulae demonstrate satisfactory agreement with their predecessor under perfect reflection. As well, the influence of the extended diffusion parameter on normalized sound pressure levels in a narrow street canyon is in agreement with experimental data. The diffusion parameters are used to model sound energy density in a street canyon as a function of the sound absorption coefficient of the street canyon walls. The acoustic and material properties of conventional and asphalt rubber concrete (ARC) pavement are also studied to assess how the crumb rubber content influences sound absorption in street canyons. The porosity and absolute permeability of compacted specimens of asphalt rubber concrete are measured and compared to their normal and random incidence sound absorption coefficients as a function of crumb rubber content in the modified binder. Nonlinear trends are found between the sound absorption coefficients, porosity and absolute permeability of the compacted specimens and the percentage of crumb rubber in the modified binders. The cross-sectional areas of the air voids on the surfaces of the compacted specimens are measured using digital image processing techniques and a linear relationship is obtained between the average void area and crumb rubber content. The measured material properties are used to construct an empirical formula relating the average porosity, normal incidence noise reduction coefficients and percentage of crumb rubber in the modified binder of the compacted specimens.

Evidence for a Quantum-to-Classical Transition in a Pair of Coupled Quantum Rotors

NASA Astrophysics Data System (ADS)

Gadway, Bryce; Reeves, Jeremy; Krinner, Ludwig; Schneble, Dominik

2013-05-01

The understanding of how classical dynamics can emerge in closed quantum systems is a problem of fundamental importance. Remarkably, while classical behavior usually arises from coupling to thermal fluctuations or random spectral noise, it may also be an innate property of certain isolated, periodically driven quantum systems. Here, we experimentally realize the simplest such system, consisting of two coupled, kicked quantum rotors, by subjecting a coherent atomic matter wave to two periodically pulsed, incommensurate optical lattices. Momentum transport in this system is found to be radically different from that in a single kicked rotor, with a breakdown of dynamical localization and the emergence of classical diffusion. Our observation, which confirms a long-standing prediction for many-dimensional quantum-chaotic systems, sheds new light on the quantum-classical correspondence.

Diffusion of Charged Species in Liquids

NASA Astrophysics Data System (ADS)

Del Río, J. A.; Whitaker, S.

2016-11-01

In this study the laws of mechanics for multi-component systems are used to develop a theory for the diffusion of ions in the presence of an electrostatic field. The analysis begins with the governing equation for the species velocity and it leads to the governing equation for the species diffusion velocity. Simplification of this latter result provides a momentum equation containing three dominant forces: (a) the gradient of the partial pressure, (b) the electrostatic force, and (c) the diffusive drag force that is a central feature of the Maxwell-Stefan equations. For ideal gas mixtures we derive the classic Nernst-Planck equation. For liquid-phase diffusion we encounter a situation in which the Nernst-Planck contribution to diffusion differs by several orders of magnitude from that obtained for ideal gases.

Diffusion of Charged Species in Liquids.

PubMed

Del Río, J A; Whitaker, S

2016-11-04

In this study the laws of mechanics for multi-component systems are used to develop a theory for the diffusion of ions in the presence of an electrostatic field. The analysis begins with the governing equation for the species velocity and it leads to the governing equation for the species diffusion velocity. Simplification of this latter result provides a momentum equation containing three dominant forces: (a) the gradient of the partial pressure, (b) the electrostatic force, and (c) the diffusive drag force that is a central feature of the Maxwell-Stefan equations. For ideal gas mixtures we derive the classic Nernst-Planck equation. For liquid-phase diffusion we encounter a situation in which the Nernst-Planck contribution to diffusion differs by several orders of magnitude from that obtained for ideal gases.

Diffusion of Charged Species in Liquids

PubMed Central

del Río, J. A.; Whitaker, S.

2016-01-01

In this study the laws of mechanics for multi-component systems are used to develop a theory for the diffusion of ions in the presence of an electrostatic field. The analysis begins with the governing equation for the species velocity and it leads to the governing equation for the species diffusion velocity. Simplification of this latter result provides a momentum equation containing three dominant forces: (a) the gradient of the partial pressure, (b) the electrostatic force, and (c) the diffusive drag force that is a central feature of the Maxwell-Stefan equations. For ideal gas mixtures we derive the classic Nernst-Planck equation. For liquid-phase diffusion we encounter a situation in which the Nernst-Planck contribution to diffusion differs by several orders of magnitude from that obtained for ideal gases. PMID:27811959

Unified path integral approach to theories of diffusion-influenced reactions

NASA Astrophysics Data System (ADS)

Prüstel, Thorsten; Meier-Schellersheim, Martin

2017-08-01

Building on mathematical similarities between quantum mechanics and theories of diffusion-influenced reactions, we develop a general approach for computational modeling of diffusion-influenced reactions that is capable of capturing not only the classical Smoluchowski picture but also alternative theories, as is here exemplified by a volume reactivity model. In particular, we prove the path decomposition expansion of various Green's functions describing the irreversible and reversible reaction of an isolated pair of molecules. To this end, we exploit a connection between boundary value and interaction potential problems with δ - and δ'-function perturbation. We employ a known path-integral-based summation of a perturbation series to derive a number of exact identities relating propagators and survival probabilities satisfying different boundary conditions in a unified and systematic manner. Furthermore, we show how the path decomposition expansion represents the propagator as a product of three factors in the Laplace domain that correspond to quantities figuring prominently in stochastic spatially resolved simulation algorithms. This analysis will thus be useful for the interpretation of current and the design of future algorithms. Finally, we discuss the relation between the general approach and the theory of Brownian functionals and calculate the mean residence time for the case of irreversible and reversible reactions.

Zero point energy leakage in condensed phase dynamics: An assessment of quantum simulation methods for liquid water

NASA Astrophysics Data System (ADS)

Habershon, Scott; Manolopoulos, David E.

2009-12-01

The approximate quantum mechanical ring polymer molecular dynamics (RPMD) and linearized semiclassical initial value representation (LSC-IVR) methods are compared and contrasted in a study of the dynamics of the flexible q-TIP4P/F water model at room temperature. For this water model, a RPMD simulation gives a diffusion coefficient that is only a few percent larger than the classical diffusion coefficient, whereas a LSC-IVR simulation gives a diffusion coefficient that is three times larger. We attribute this discrepancy to the unphysical leakage of initially quantized zero point energy (ZPE) from the intramolecular to the intermolecular modes of the liquid as the LSC-IVR simulation progresses. In spite of this problem, which is avoided by construction in RPMD, the LSC-IVR may still provide a useful approximation to certain short-time dynamical properties which are not so strongly affected by the ZPE leakage. We illustrate this with an application to the liquid water dipole absorption spectrum, for which the RPMD approximation breaks down at frequencies in the O-H stretching region owing to contamination from the internal modes of the ring polymer. The LSC-IVR does not suffer from this difficulty and it appears to provide quite a promising way to calculate condensed phase vibrational spectra.

Zero point energy leakage in condensed phase dynamics: an assessment of quantum simulation methods for liquid water.

PubMed

Habershon, Scott; Manolopoulos, David E

2009-12-28

The approximate quantum mechanical ring polymer molecular dynamics (RPMD) and linearized semiclassical initial value representation (LSC-IVR) methods are compared and contrasted in a study of the dynamics of the flexible q-TIP4P/F water model at room temperature. For this water model, a RPMD simulation gives a diffusion coefficient that is only a few percent larger than the classical diffusion coefficient, whereas a LSC-IVR simulation gives a diffusion coefficient that is three times larger. We attribute this discrepancy to the unphysical leakage of initially quantized zero point energy (ZPE) from the intramolecular to the intermolecular modes of the liquid as the LSC-IVR simulation progresses. In spite of this problem, which is avoided by construction in RPMD, the LSC-IVR may still provide a useful approximation to certain short-time dynamical properties which are not so strongly affected by the ZPE leakage. We illustrate this with an application to the liquid water dipole absorption spectrum, for which the RPMD approximation breaks down at frequencies in the O-H stretching region owing to contamination from the internal modes of the ring polymer. The LSC-IVR does not suffer from this difficulty and it appears to provide quite a promising way to calculate condensed phase vibrational spectra.

Moving-Boundary Problems Associated with Lyopreservation

NASA Astrophysics Data System (ADS)

Gruber, Christopher Andrew

The work presented in this Dissertation is motivated by research into the preservation of biological specimens by way of vitrification, a technique known as lyopreservation. The operative principle behind lyopreservation is that a glassy material forms as a solution of sugar and water is desiccated. The microstructure of this glass impedes transport within the material, thereby slowing metabolism and effectively halting the aging processes in a biospecimen. This Dissertation is divided into two segments. The first concerns the nature of diffusive transport within a glassy state. Experimental studies suggest that diffusion within a glass is anomalously slow. Scaled Brownian motion (SBM) is proposed as a mathematical model which captures the qualitative features of anomalously slow diffusion while minimizing computational expense. This model is applied to several moving-boundary problems and the results are compared to a more well-established model, fractional anomalous diffusion (FAD). The virtues of SBM are based on the model's relative mathematical simplicity: the governing equation under FAD dynamics involves a fractional derivative operator, which precludes the use of analytical methods in almost all circumstances and also entails great computational expense. In some geometries, SBM allows similarity solutions, though computational methods are generally required. The use of SBM as an approximation to FAD when a system is "nearly classical'' is also explored. The second portion of this Dissertation concerns spin-drying, which is an experimental approach to biopreservation in a laboratory setting. A biospecimen is adhered to a glass wafer and this substrate is covered with sugar solution and rapidly spun on a turntable while water is evaporated from the film surface. The mathematical model for the spin-drying process includes diffusion, viscous fluid flow, and evaporation, among other contributions to the dynamics. Lubrication theory is applied to the model and an expansion in orthogonal polynomials is applied. The resulting system of equations is solved computationally. The influence of various experimental parameters upon the system dynamics is investigated, particularly the role of the spin rate. A convergence study of the solution verifies that the polynomial expansion method yields accurate results.

Self-energy-modified Poisson-Nernst-Planck equations: WKB approximation and finite-difference approaches.

PubMed

Xu, Zhenli; Ma, Manman; Liu, Pei

2014-07-01

We propose a modified Poisson-Nernst-Planck (PNP) model to investigate charge transport in electrolytes of inhomogeneous dielectric environment. The model includes the ionic polarization due to the dielectric inhomogeneity and the ion-ion correlation. This is achieved by the self energy of test ions through solving a generalized Debye-Hückel (DH) equation. We develop numerical methods for the system composed of the PNP and DH equations. Particularly, toward the numerical challenge of solving the high-dimensional DH equation, we developed an analytical WKB approximation and a numerical approach based on the selective inversion of sparse matrices. The model and numerical methods are validated by simulating the charge diffusion in electrolytes between two electrodes, for which effects of dielectrics and correlation are investigated by comparing the results with the prediction by the classical PNP theory. We find that, at the length scale of the interface separation comparable to the Bjerrum length, the results of the modified equations are significantly different from the classical PNP predictions mostly due to the dielectric effect. It is also shown that when the ion self energy is in weak or mediate strength, the WKB approximation presents a high accuracy, compared to precise finite-difference results.

A diffusion of innovations model of physician order entry.

PubMed

Ash, J S; Lyman, J; Carpenter, J; Fournier, L

2001-01-01

To interpret the results of a cross-site study of physician order entry (POE) in hospitals using a diffusion of innovations theory framework. Qualitative study using observation, focus groups, and interviews. Data were analyzed by an interdisciplinary team of researchers using a grounded approach to identify themes. Themes were then interpreted using classical Diffusion of Innovations (DOI) theory as described by Rogers [1]. Four high level themes were identified: organizational issues; clinical and professional issues; technology implementation issues; and issues related to the organization of information and knowledge. Further analysis using the DOI framework indicated that POE is an especially complex information technology innovation when one considers communication, time, and social system issues in addition to attributes of the innovation itself. Implementation strategies for POE should be designed to account for its complex nature. The ideal would be a system that is both customizable and integrated with other parts of the information system, is implemented with maximum involvement of users and high levels of support, and is surrounded by an atmosphere of trust and collaboration.

Adaptive distance metric learning for diffusion tensor image segmentation.

PubMed

Kong, Youyong; Wang, Defeng; Shi, Lin; Hui, Steve C N; Chu, Winnie C W

2014-01-01

High quality segmentation of diffusion tensor images (DTI) is of key interest in biomedical research and clinical application. In previous studies, most efforts have been made to construct predefined metrics for different DTI segmentation tasks. These methods require adequate prior knowledge and tuning parameters. To overcome these disadvantages, we proposed to automatically learn an adaptive distance metric by a graph based semi-supervised learning model for DTI segmentation. An original discriminative distance vector was first formulated by combining both geometry and orientation distances derived from diffusion tensors. The kernel metric over the original distance and labels of all voxels were then simultaneously optimized in a graph based semi-supervised learning approach. Finally, the optimization task was efficiently solved with an iterative gradient descent method to achieve the optimal solution. With our approach, an adaptive distance metric could be available for each specific segmentation task. Experiments on synthetic and real brain DTI datasets were performed to demonstrate the effectiveness and robustness of the proposed distance metric learning approach. The performance of our approach was compared with three classical metrics in the graph based semi-supervised learning framework.

Adaptive Distance Metric Learning for Diffusion Tensor Image Segmentation

PubMed Central

Kong, Youyong; Wang, Defeng; Shi, Lin; Hui, Steve C. N.; Chu, Winnie C. W.

2014-01-01

High quality segmentation of diffusion tensor images (DTI) is of key interest in biomedical research and clinical application. In previous studies, most efforts have been made to construct predefined metrics for different DTI segmentation tasks. These methods require adequate prior knowledge and tuning parameters. To overcome these disadvantages, we proposed to automatically learn an adaptive distance metric by a graph based semi-supervised learning model for DTI segmentation. An original discriminative distance vector was first formulated by combining both geometry and orientation distances derived from diffusion tensors. The kernel metric over the original distance and labels of all voxels were then simultaneously optimized in a graph based semi-supervised learning approach. Finally, the optimization task was efficiently solved with an iterative gradient descent method to achieve the optimal solution. With our approach, an adaptive distance metric could be available for each specific segmentation task. Experiments on synthetic and real brain DTI datasets were performed to demonstrate the effectiveness and robustness of the proposed distance metric learning approach. The performance of our approach was compared with three classical metrics in the graph based semi-supervised learning framework. PMID:24651858

Anomalous diffusion of water molecules at grain boundaries in ice Ih.

PubMed

Moreira, Pedro Augusto Franco Pinheiro; Veiga, Roberto Gomes de Aguiar; Ribeiro, Ingrid de Almeida; Freitas, Rodrigo; Helfferich, Julian; de Koning, Maurice

2018-05-23

Using ab initio and classical molecular dynamics simulations, we study pre-melting phenomena in pristine coincident-site-lattice grain boundaries (GBs) in proton-disordered hexagonal ice Ih at temperatures just below the melting point Tm. Concerning pre-melt-layer thicknesses, the results are consistent with the available experimental estimates for low-disorder impurity-free GBs. With regard to molecular mobility, the simulations provide a key new insight: the translational motion of the water molecules is found to be subdiffusive for time scales from ∼10 ns up to at least 0.1 μs. Moreover, the fact that the anomalous diffusion occurs even at temperatures just below Tm where the bulk supercooled liquid still diffuses normally suggests that it is related to the confinement of the GB pre-melt layers by the surrounding crystalline environment. Furthermore, we show that this behavior can be characterized by continuous-time random walk models in which the waiting-time distributions decay according to power-laws that are very similar to those describing dynamics in glass-forming systems.

A 2D multi-term time and space fractional Bloch-Torrey model based on bilinear rectangular finite elements

NASA Astrophysics Data System (ADS)

Qin, Shanlin; Liu, Fawang; Turner, Ian W.

2018-03-01

The consideration of diffusion processes in magnetic resonance imaging (MRI) signal attenuation is classically described by the Bloch-Torrey equation. However, many recent works highlight the distinct deviation in MRI signal decay due to anomalous diffusion, which motivates the fractional order generalization of the Bloch-Torrey equation. In this work, we study the two-dimensional multi-term time and space fractional diffusion equation generalized from the time and space fractional Bloch-Torrey equation. By using the Galerkin finite element method with a structured mesh consisting of rectangular elements to discretize in space and the L1 approximation of the Caputo fractional derivative in time, a fully discrete numerical scheme is derived. A rigorous analysis of stability and error estimation is provided. Numerical experiments in the square and L-shaped domains are performed to give an insight into the efficiency and reliability of our method. Then the scheme is applied to solve the multi-term time and space fractional Bloch-Torrey equation, which shows that the extra time derivative terms impact the relaxation process.

Can phoretic particles swim in two dimensions?

NASA Astrophysics Data System (ADS)

Sondak, David; Hawley, Cory; Heng, Siyu; Vinsonhaler, Rebecca; Lauga, Eric; Thiffeault, Jean-Luc

2016-12-01

Artificial phoretic particles swim using self-generated gradients in chemical species (self-diffusiophoresis) or charges and currents (self-electrophoresis). These particles can be used to study the physics of collective motion in active matter and might have promising applications in bioengineering. In the case of self-diffusiophoresis, the classical physical model relies on a steady solution of the diffusion equation, from which chemical gradients, phoretic flows, and ultimately the swimming velocity may be derived. Motivated by disk-shaped particles in thin films and under confinement, we examine the extension to two dimensions. Because the two-dimensional diffusion equation lacks a steady state with the correct boundary conditions, Laplace transforms must be used to study the long-time behavior of the problem and determine the swimming velocity. For fixed chemical fluxes on the particle surface, we find that the swimming velocity ultimately always decays logarithmically in time. In the case of finite Péclet numbers, we solve the full advection-diffusion equation numerically and show that this decay can be avoided by the particle moving to regions of unconsumed reactant. Finite advection thus regularizes the two-dimensional phoretic problem.

Peridynamic thermal diffusion

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

Oterkus, Selda; Madenci, Erdogan, E-mail: madenci@email.arizona.edu; Agwai, Abigail

This study presents the derivation of ordinary state-based peridynamic heat conduction equation based on the Lagrangian formalism. The peridynamic heat conduction parameters are related to those of the classical theory. An explicit time stepping scheme is adopted for numerical solution of various benchmark problems with known solutions. It paves the way for applying the peridynamic theory to other physical fields such as neutronic diffusion and electrical potential distribution.

Thermal conductance at atomically clean and disordered silicon/aluminum interfaces: A molecular dynamics simulation study

NASA Astrophysics Data System (ADS)

Ih Choi, Woon; Kim, Kwiseon; Narumanchi, Sreekant

2012-09-01

Thermal resistance between layers impedes effective heat dissipation in electronics packaging applications. Thermal conductance for clean and disordered interfaces between silicon (Si) and aluminum (Al) was computed using realistic Si/Al interfaces and classical molecular dynamics with the modified embedded atom method potential. These realistic interfaces, which include atomically clean as well as disordered interfaces, were obtained using density functional theory. At 300 K, the magnitude of interfacial conductance due to phonon-phonon scattering obtained from the classical molecular dynamics simulations was approximately five times higher than the conductance obtained using analytical elastic diffuse mismatch models. Interfacial disorder reduced the thermal conductance due to increased phonon scattering with respect to the atomically clean interface. Also, the interfacial conductance, due to electron-phonon scattering at the interface, was greater than the conductance due to phonon-phonon scattering. This indicates that phonon-phonon scattering is the bottleneck for interfacial transport at the semiconductor/metal interfaces. The molecular dynamics modeling predictions for interfacial thermal conductance for a 5-nm disordered interface between Si/Al were in-line with recent experimental data in the literature.

Quantum Hamilton equations of motion for bound states of one-dimensional quantum systems

NASA Astrophysics Data System (ADS)

Köppe, J.; Patzold, M.; Grecksch, W.; Paul, W.

2018-06-01

On the basis of Nelson's stochastic mechanics derivation of the Schrödinger equation, a formal mathematical structure of non-relativistic quantum mechanics equivalent to the one in classical analytical mechanics has been established in the literature. We recently were able to augment this structure by deriving quantum Hamilton equations of motion by finding the Nash equilibrium of a stochastic optimal control problem, which is the generalization of Hamilton's principle of classical mechanics to quantum systems. We showed that these equations allow a description and numerical determination of the ground state of quantum problems without using the Schrödinger equation. We extend this approach here to deliver the complete discrete energy spectrum and related eigenfunctions for bound states of one-dimensional stationary quantum systems. We exemplify this analytically for the one-dimensional harmonic oscillator and numerically by analyzing a quartic double-well potential, a model of broad importance in many areas of physics. We furthermore point out a relation between the tunnel splitting of such models and mean first passage time concepts applied to Nelson's diffusion paths in the ground state.

Computer simulation of liquid metals

NASA Astrophysics Data System (ADS)

Belashchenko, D. K.

2013-12-01

Methods for and the results of the computer simulation of liquid metals are reviewed. Two basic methods, classical molecular dynamics with known interparticle potentials and the ab initio method, are considered. Most attention is given to the simulated results obtained using the embedded atom model (EAM). The thermodynamic, structural, and diffusion properties of liquid metal models under normal and extreme (shock) pressure conditions are considered. Liquid-metal simulated results for the Groups I - IV elements, a number of transition metals, and some binary systems (Fe - C, Fe - S) are examined. Possibilities for the simulation to account for the thermal contribution of delocalized electrons to energy and pressure are considered. Solidification features of supercooled metals are also discussed.

Nano-swimmers in biological membranes and propulsion hydrodynamics in two dimensions.

PubMed

Huang, Mu-Jie; Chen, Hsuan-Yi; Mikhailov, Alexander S

2012-11-01

Active protein inclusions in biological membranes can represent nano-swimmers and propel themselves in lipid bilayers. A simple model of an active inclusion with three particles (domains) connected by variable elastic links is considered. First, the membrane is modeled as a two-dimensional viscous fluid and propulsion behavior in two dimensions is examined. After that, an example of a microscopic dynamical simulation is presented, where the lipid bilayer structure of the membrane is resolved and the solvent effects are included by multiparticle collision dynamics. Statistical analysis of data reveals ballistic motion of the swimmer, in contrast to the classical diffusion behavior found in the absence of active transitions between the states.

From nucleation to coalescence of Cu2O islands during in situ oxidation of Cu(001)

NASA Astrophysics Data System (ADS)

Yang, J. C.; Evan, D.; Tropia, L.

2002-07-01

The nucleation, growth, and coalescence of Cu2O islands due to oxidation of Cu(001) films were visualized by in situ ultrahigh-vacuum transmission electron microscopy. We have previously demonstrated that the nucleation and initial growth of copper oxides is dominated by oxygen surface diffusion. These surface models have been extended to quantitatively represent the coalescence behavior of copper oxidation in the framework of the Johnson-Mehl-Avrami-Kolmogorov theory. An excellent agreement exists between the experimental data of nucleation to coalescence with the surface model. The implication could be an alternate paradigm for passivation and oxidation, since classic theories assume uniform film growth.

Nanostructure control: Nucleation and diffusion studies for predictable ultra thin film morphologies

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

Hershberger, Matthew

This thesis covers PhD research on two systems with unique and interesting physics. The first system is lead (Pb) deposited on the silicon (111) surface with the 7x7 reconstruction. Pb and Si are mutually bulk insoluble resulting in this system being an ideal case for studying metal and semiconductor interactions. Initial Pb deposition causes an amorphous wetting layer to form across to surface. Continued deposition results in Pb(111) island growth. Classic literature has classified this system as the Stranski-Krastanov growth mode although the system is not near equilibrium conditions. Our research shows a growth mode distinctly different than classical expectationsmore » and begins a discussion of reclassifying diffusion and nucleation for systems far away from the well-studied equilibrium cases.« less

Phase space effects on fast ion distribution function modeling in tokamaks

DOE PAGES

Podesta, M.; Gorelenkova, M.; Fredrickson, E. D.; ...

2016-04-14

Here, integrated simulations of tokamak discharges typically rely on classical physics to model energetic particle (EP) dynamics. However, there are numerous cases in which energetic particles can suffer additional transport that is not classical in nature. Examples include transport by applied 3D magnetic perturbations and, more notably, by plasma instabilities. Focusing on the effects of instabilities,ad-hocmodels can empirically reproduce increased transport, but the choice of transport coefficients is usually somehow arbitrary. New approaches based on physics-based reduced models are being developed to address those issues in a simplified way, while retaining a more correct treatment of resonant wave-particle interactions. Themore » kick model implemented in the tokamaktransport code TRANSP is an example of such reduced models. It includes modifications of the EP distribution by instabilities in real and velocity space, retaining correlations between transport in energy and space typical of resonant EP transport. The relevance of EP phase space modifications by instabilities is first discussed in terms of predicted fast ion distribution. Results are compared with those from a simple, ad-hoc diffusive model. It is then shown that the phase-space resolved model can also provide additional insight into important issues such as internal consistency of the simulations and mode stability through the analysis of the power exchanged between energetic particles and the instabilities.« less

Novel surface diffusion characteristics for a robust pentacene derivative on Au(1 1 1) surfaces

NASA Astrophysics Data System (ADS)

Miller, Ryan A.; Larson, Amanda; Pohl, Karsten

2017-06-01

Molecular dynamics simulations have been performed in both the ab initio and classical mechanics frameworks of 5,6,7-trithiapentacene-13-one (TTPO) molecules on flat Au(1 1 1) surfaces. Results show new surface diffusion characteristics including a strong preference for the molecule to align its long axis parallel to the sixfold Au(1 1 1) symmetry directions and subsequently diffuse along these close-packed directions, and a calculated activation energy for diffusion of 0.142 eV, about four times larger than that for pure pentacene on Au. The temperature-dependent diffusion coefficients were calculated to help quantify the molecular mobility during the experimentally observed process of forming self-assembled monolayers on gold electrodes.

Transient chaos - a resolution of breakdown of quantum-classical correspondence in optomechanics.

PubMed

Wang, Guanglei; Lai, Ying-Cheng; Grebogi, Celso

2016-10-17

Recently, the phenomenon of quantum-classical correspondence breakdown was uncovered in optomechanics, where in the classical regime the system exhibits chaos but in the corresponding quantum regime the motion is regular - there appears to be no signature of classical chaos whatsoever in the corresponding quantum system, generating a paradox. We find that transient chaos, besides being a physically meaningful phenomenon by itself, provides a resolution. Using the method of quantum state diffusion to simulate the system dynamics subject to continuous homodyne detection, we uncover transient chaos associated with quantum trajectories. The transient behavior is consistent with chaos in the classical limit, while the long term evolution of the quantum system is regular. Transient chaos thus serves as a bridge for the quantum-classical transition (QCT). Strikingly, as the system transitions from the quantum to the classical regime, the average chaotic transient lifetime increases dramatically (faster than the Ehrenfest time characterizing the QCT for isolated quantum systems). We develop a physical theory to explain the scaling law.

Transient chaos - a resolution of breakdown of quantum-classical correspondence in optomechanics

PubMed Central

Wang, Guanglei; Lai, Ying-Cheng; Grebogi, Celso

2016-01-01

Recently, the phenomenon of quantum-classical correspondence breakdown was uncovered in optomechanics, where in the classical regime the system exhibits chaos but in the corresponding quantum regime the motion is regular - there appears to be no signature of classical chaos whatsoever in the corresponding quantum system, generating a paradox. We find that transient chaos, besides being a physically meaningful phenomenon by itself, provides a resolution. Using the method of quantum state diffusion to simulate the system dynamics subject to continuous homodyne detection, we uncover transient chaos associated with quantum trajectories. The transient behavior is consistent with chaos in the classical limit, while the long term evolution of the quantum system is regular. Transient chaos thus serves as a bridge for the quantum-classical transition (QCT). Strikingly, as the system transitions from the quantum to the classical regime, the average chaotic transient lifetime increases dramatically (faster than the Ehrenfest time characterizing the QCT for isolated quantum systems). We develop a physical theory to explain the scaling law. PMID:27748418

The {sech}( {\\hat{ξ }} ) -Type Profiles: A Swiss-Army Knife for Exact Analytical Modeling of Thermal Diffusion and Wave Propagation in Graded Media

NASA Astrophysics Data System (ADS)

Krapez, J.-C.

2018-07-01

This work deals with the exact analytical modeling of transfer phenomena in heterogeneous materials exhibiting one-dimensional continuous variations of their properties. Regarding heat transfer, it has recently been shown that by applying a Liouville transformation and multiple Darboux transformations, infinite sequences of solvable profiles of thermal effusivity can be constructed together with the associated temperature (exact) solutions, all in closed-form expressions (vs. the diffusion-time variable and with a growing number of parameters). In addition, a particular class of profiles, the so-called {sech}( {\\hat{ξ }} ) -type profiles, exhibit high agility and at the same time parsimony. In this paper we delve further into the description of these solvable profiles and their properties. Most importantly, their quadrupole formulation is provided, enabling smooth synthetic profiles of effusivity of arbitrary complexity to be built, and allowing the corresponding temperature dynamic response to be obtained very easily thereafter. Examples are given with increasing variability of the effusivity and an increasing number of elementary profiles. These highly flexible profiles are equally relevant to providing an exact analytical solution to wave propagation problems in 1D graded media (i.e., Maxwell's equations, the acoustic equation, the telegraph equation, etc.). From now on, whether it be for diffusion-like or wave-like problems, when the leading properties present (possibly piecewise-) continuously heterogeneous profiles, the classical staircase model can be advantageously replaced by a "high-level" quadrupole model consisting of one or more {sech}( {\\hat{ξ }} ) -type profiles, which makes the latter a true Swiss-Army knife for analytical modeling.

Exposure, hazard, and survival analysis of diffusion on social networks.

PubMed

Wu, Jiacheng; Crawford, Forrest W; Kim, David A; Stafford, Derek; Christakis, Nicholas A

2018-04-29

Sociologists, economists, epidemiologists, and others recognize the importance of social networks in the diffusion of ideas and behaviors through human societies. To measure the flow of information on real-world networks, researchers often conduct comprehensive sociometric mapping of social links between individuals and then follow the spread of an "innovation" from reports of adoption or change in behavior over time. The innovation is introduced to a small number of individuals who may also be encouraged to spread it to their network contacts. In conjunction with the known social network, the pattern of adoptions gives researchers insight into the spread of the innovation in the population and factors associated with successful diffusion. Researchers have used widely varying statistical tools to estimate these quantities, and there is disagreement about how to analyze diffusion on fully observed networks. Here, we describe a framework for measuring features of diffusion processes on social networks using the epidemiological concepts of exposure and competing risks. Given a realization of a diffusion process on a fully observed network, we show that classical survival regression models can be adapted to estimate the rate of diffusion, and actor/edge attributes associated with successful transmission or adoption, while accounting for the topology of the social network. We illustrate these tools by applying them to a randomized network intervention trial conducted in Honduras to estimate the rate of adoption of 2 health-related interventions-multivitamins and chlorine bleach for water purification-and determine factors associated with successful social transmission. Copyright © 2018 John Wiley & Sons, Ltd.

An Advection-Diffusion Concept for Solute Transport in Heterogeneous Unconsolidated Geological Deposits

NASA Astrophysics Data System (ADS)

Gillham, R. W.; Sudicky, E. A.; Cherry, J. A.; Frind, E. O.

1984-03-01

In layered permeable deposits with flow predominately parallel to the bedding, advection causes rapid solute transport in the more permeable layers. As the solute advances more rapidly in these layers, solute mass is continually transferred to the less permeable layers as a result of molecular diffusion due to the concentration gradient between the layers. The interlayer solute transfer causes the concentration to decline along the permeable layers at the expense of increasing the concentration in the less permeable layers, which produces strongly dispersed concentration profiles in the direction of flow. The key parameters affecting the dispersive capability of the layered system are the diffusion coefficients for the less permeable layers, the thicknesses of the layers, and the hydraulic conductivity contrasts between the layers. Because interlayer solute transfer by transverse molecular diffusion is a time-dependent process, the advection-diffusion concept predicts a rate of longitudinal spreading during the development of the dispersion process that is inconsistent with the classical Fickian dispersion model. A second consequence of the solute-storage effect offered by transverse diffusion into low-permeability layers is a rate of migration of the frontal portion of a contaminant in the permeable layers that is less than the groundwater velocity. Although various lines of evidence are presented in support of the advection-diffusion concept, more work is required to determine the range of geological materials for which it is applicable and to develop mathematical expressions that will make it useful as a predictive tool for application to field cases of contaminant migration.

The Dynamics of Helium and its Impact on the Upper Thermosphere

NASA Astrophysics Data System (ADS)

Sutton, E. K.; Thayer, J. P.; Wang, W.; Solomon, S. C.; Schmidt, F.

2015-12-01

The TIE-GCM was recently augmented to include helium and argon, two approximately inert species that can be used as tracers of dynamics in the thermosphere. The former species is treated as a major species due to its large abundance near the upper boundary. The effects of exospheric transport are also included in order to simulate realistic seasonal and latitudinal helium distributions. The latter species is treated as a classical minor species, imparting absolutely no forces on the background atmosphere. In this study, we examine the interplay of the various dynamical terms - i.e. background circulation, molecular and Eddy diffusion - as they drive departures from the distributions that would be expected under assumptions of diffusive equilibrium. As this has implications on the formulation of all semi-empirical thermospheric models, we use this understanding to identify the conditions under which helium can significantly affect nowcasts and forecasts of neutral density.

Application of various FLD modelling approaches

NASA Astrophysics Data System (ADS)

Banabic, D.; Aretz, H.; Paraianu, L.; Jurco, P.

2005-07-01

This paper focuses on a comparison between different modelling approaches to predict the forming limit diagram (FLD) for sheet metal forming under a linear strain path using the recently introduced orthotropic yield criterion BBC2003 (Banabic D et al 2005 Int. J. Plasticity 21 493-512). The FLD models considered here are a finite element based approach, the well known Marciniak-Kuczynski model, the modified maximum force criterion according to Hora et al (1996 Proc. Numisheet'96 Conf. (Dearborn/Michigan) pp 252-6), Swift's diffuse (Swift H W 1952 J. Mech. Phys. Solids 1 1-18) and Hill's classical localized necking approach (Hill R 1952 J. Mech. Phys. Solids 1 19-30). The FLD of an AA5182-O aluminium sheet alloy has been determined experimentally in order to quantify the predictive capabilities of the models mentioned above.

Diagnosis of breast masses from dynamic contrast-enhanced and diffusion-weighted MR: a machine learning approach.

PubMed

Cai, Hongmin; Peng, Yanxia; Ou, Caiwen; Chen, Minsheng; Li, Li

2014-01-01

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) is increasingly used for breast cancer diagnosis as supplementary to conventional imaging techniques. Combining of diffusion-weighted imaging (DWI) of morphology and kinetic features from DCE-MRI to improve the discrimination power of malignant from benign breast masses is rarely reported. The study comprised of 234 female patients with 85 benign and 149 malignant lesions. Four distinct groups of features, coupling with pathological tests, were estimated to comprehensively characterize the pictorial properties of each lesion, which was obtained by a semi-automated segmentation method. Classical machine learning scheme including feature subset selection and various classification schemes were employed to build prognostic model, which served as a foundation for evaluating the combined effects of the multi-sided features for predicting of the types of lesions. Various measurements including cross validation and receiver operating characteristics were used to quantify the diagnostic performances of each feature as well as their combination. Seven features were all found to be statistically different between the malignant and the benign groups and their combination has achieved the highest classification accuracy. The seven features include one pathological variable of age, one morphological variable of slope, three texture features of entropy, inverse difference and information correlation, one kinetic feature of SER and one DWI feature of apparent diffusion coefficient (ADC). Together with the selected diagnostic features, various classical classification schemes were used to test their discrimination power through cross validation scheme. The averaged measurements of sensitivity, specificity, AUC and accuracy are 0.85, 0.89, 90.9% and 0.93, respectively. Multi-sided variables which characterize the morphological, kinetic, pathological properties and DWI measurement of ADC can dramatically improve the discriminatory power of breast lesions.

MRI and clinical features of maple syrup urine disease: preliminary results in 10 cases.

PubMed

Cheng, Ailan; Han, Lianshu; Feng, Yun; Li, Huimin; Yao, Rong; Wang, Dengbin; Jin, Biao

2017-01-01

We aimed to evaluate the magnetic resonance imaging (MRI) and clinical features of maple syrup urine disease (MSUD). This retrospective study consisted of 10 MSUD patients confirmed by genetic testing. All patients underwent brain MRI. Phenotype, genotype, and areas of brain injury on MRI were retrospectively reviewed. Six patients (60%) had the classic form of MSUD with BCKDHB mutation, three patients (30%) had the intermittent form (two with BCKDHA mutations and one with DBT mutation), and one patient (10%) had the thiamine-responsive form with DBT mutation. On diffusion-weighted imaging, nine cases presented restricted diffusion in myelinated areas, and one intermittent case with DBT mutation was normal. The classic form of MSUD involved the basal ganglia in six cases; the cerebellum, mesencephalon, pons, and supratentorial area in five cases; and the thalamus in four cases, respectively. The intermittent form involved the cerebellum, pons, and supratentorial area in two cases. The thiamine-responsive form involved the basal ganglia and supratentorial area. Our preliminary results indicate that patients with MSUD presented more commonly in classic form with BCKDHB mutation and displayed extensive brain injury on MRI.

Thermodynamics and Kinetics of Prenucleation Clusters, Classical and Non-Classical Nucleation

PubMed Central

Zahn, Dirk

2015-01-01

Recent observations of prenucleation species and multi-stage crystal nucleation processes challenge the long-established view on the thermodynamics of crystal formation. Here, we review and generalize extensions to classical nucleation theory. Going beyond the conventional implementation as has been used for more than a century now, nucleation inhibitors, precursor clusters and non-classical nucleation processes are rationalized as well by analogous concepts based on competing interface and bulk energy terms. This is illustrated by recent examples of species formed prior to/instead of crystal nucleation and multi-step nucleation processes. Much of the discussed insights were obtained from molecular simulation using advanced sampling techniques, briefly summarized herein for both nucleation-controlled and diffusion-controlled aggregate formation. PMID:25914369

Computational approach to integrate 3D X-ray microtomography and NMR data

NASA Astrophysics Data System (ADS)

Lucas-Oliveira, Everton; Araujo-Ferreira, Arthur G.; Trevizan, Willian A.; Fortulan, Carlos A.; Bonagamba, Tito J.

2018-07-01

Nowadays, most of the efforts in NMR applied to porous media are dedicated to studying the molecular fluid dynamics within and among the pores. These analyses have a higher complexity due to morphology and chemical composition of rocks, besides dynamic effects as restricted diffusion, diffusional coupling, and exchange processes. Since the translational nuclear spin diffusion in a confined geometry (e.g. pores and fractures) requires specific boundary conditions, the theoretical solutions are restricted to some special problems and, in many cases, computational methods are required. The Random Walk Method is a classic way to simulate self-diffusion along a Digital Porous Medium. Bergman model considers the magnetic relaxation process of the fluid molecules by including a probability rate of magnetization survival under surface interactions. Here we propose a statistical approach to correlate surface magnetic relaxivity with the computational method applied to the NMR relaxation in order to elucidate the relationship between simulated relaxation time and pore size of the Digital Porous Medium. The proposed computational method simulates one- and two-dimensional NMR techniques reproducing, for example, longitudinal and transverse relaxation times (T1 and T2, respectively), diffusion coefficients (D), as well as their correlations. For a good approximation between the numerical and experimental results, it is necessary to preserve the complexity of translational diffusion through the microstructures in the digital rocks. Therefore, we use Digital Porous Media obtained by 3D X-ray microtomography. To validate the method, relaxation times of ideal spherical pores were obtained and compared with the previous determinations by the Brownstein-Tarr model, as well as the computational approach proposed by Bergman. Furthermore, simulated and experimental results of synthetic porous media are compared. These results make evident the potential of computational physics in the analysis of the NMR data for complex porous materials.

Density-Gradient Theory: A Macroscopic Approach to Quantum Confinement and Tunneling in Semiconductor Devices

DTIC Science & Technology

2011-01-01

that are attractive as luminescent biolabels, and possibly also for optoelectronic devices and solar cells . The equilibrium nature of such situations...The boundary layers as- sociated with the diffusion and Debye lengths are familiar, while that of LQ defines the layer in which the quantum in...circuits, transmission lines Diffusion -drift, density-gradient Semi-classical electron dynamics, Boltzmann transport Schrödinger, density- matrix, Wigner

N vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in TiN studied by ab-initio and classical molecular dynamics

NASA Astrophysics Data System (ADS)

Sangiovanni, Davide G.; Alling, Björn; Hultman, Lars; Abrikosov, Igor A.

2015-03-01

We use ab-initio and classical molecular dynamics (AIMD, CMD) to simulate diffusion of N vacancy and N self-interstitial point-defects in B1 TiN. The physical properties of TiN, important material system for thin film and coatings applications, are largely dictated by concentration and mobility of point defects. We determine N dilute-point-defect diffusion pathways, activation energies, attempt frequencies, and diffusion coefficients as a function of temperature. In addition, MD simulations reveal an unanticipated atomistic process, which controls the spontaneous formation of N-self-interstitial/N-vacancy pairs (Frenkel pairs) in defect-free TiN. This entails that a N lattice atom leaves its bulk position and bonds to a neighboring N lattice atom. In most cases, Frenkel-pair NI and NV recombine within a fraction of ns; 50% of these processes result in the exchange of two nitrogen lattice atoms. Occasionally, however, Frenkel-pair N-interstitial atoms permanently escape from the anion vacancy site, thus producing unpaired NI and NV point defects. The Knut and Alice Wallenberg foundation (Isotope Project, 2011.0094), the Swedish Research Council (VR) Linköping Linnaeus Initiative LiLi-NFM (Grant 2008-6572), and the Swedish Government Strategic Research (Grant MatLiU 2009-00971).

Selectivity and self-diffusion of CO2 and H2 in a mixture on a graphite surface

PubMed Central

Trinh, Thuat T.; Vlugt, Thijs J. H.; Hägg, May-Britt; Bedeaux, Dick; Kjelstrup, Signe

2013-01-01

We performed classical molecular dynamics (MD) simulations to understand the mechanism of adsorption from a gas mixture of CO2 and H2 (mole fraction of CO2 = 0.30) and diffusion along a graphite surface, with the aim to help enrich industrial off-gases in CO2, separating out H2. The temperature of the system in the simulation covered typical industrial conditions for off-gas treatment (250–550 K). The interaction energy of single molecules CO2 or H2 on graphite surface was calculated with classical force fields (FFs) and with Density Functional Theory (DFT). The results were in good agreement. The binding energy of CO2 on graphite surface is three times larger than that of H2. At lower temperatures, the selectivity of CO2 over H2 is five times larger than at higher temperatures. The position of the dividing surface was used to explain how the adsorption varies with pore size. In the temperature range studied, the self-diffusion coefficient of CO2 is always smaller than of H2. The temperature variation of the selectivities and the self-diffusion coefficient imply that the carbon molecular sieve membrane can be used for gas enrichment of CO2. PMID:24790965

Nitrogen vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in B 1 TiN studied by ab initio and classical molecular dynamics with optimized potentials

NASA Astrophysics Data System (ADS)

Sangiovanni, D. G.; Alling, B.; Steneteg, P.; Hultman, L.; Abrikosov, I. A.

2015-02-01

We use ab initio and classical molecular dynamics (AIMD and CMD) based on the modified embedded-atom method (MEAM) potential to simulate diffusion of N vacancy and N self-interstitial point defects in B 1 TiN. TiN MEAM parameters are optimized to obtain CMD nitrogen point-defect jump rates in agreement with AIMD predictions, as well as an excellent description of Ti Nx(˜0.7

A novel information cascade model in online social networks

NASA Astrophysics Data System (ADS)

Tong, Chao; He, Wenbo; Niu, Jianwei; Xie, Zhongyu

2016-02-01

The spread and diffusion of information has become one of the hot issues in today's social network analysis. To analyze the spread of online social network information and the attribute of cascade, in this paper, we discuss the spread of two kinds of users' decisions for city-wide activities, namely the "want to take part in the activity" and "be interested in the activity", based on the users' attention in "DouBan" and the data of the city-wide activities. We analyze the characteristics of the activity-decision's spread in these aspects: the scale and scope of the cascade subgraph, the structure characteristic of the cascade subgraph, the topological attribute of spread tree, and the occurrence frequency of cascade subgraph. On this basis, we propose a new information spread model. Based on the classical independent diffusion model, we introduce three mechanisms, equal probability, similarity of nodes, and popularity of nodes, which can generate and affect the spread of information. Besides, by conducting the experiments in six different kinds of network data set, we compare the effects of three mechanisms above mentioned, totally six specific factors, on the spread of information, and put forward that the node's popularity plays an important role in the information spread.

Fractal pharmacokinetics.

PubMed

Pereira, Luis M

2010-06-01

Pharmacokinetics (PK) has been traditionally dealt with under the homogeneity assumption. However, biological systems are nowadays comprehensively understood as being inherently fractal. Specifically, the microenvironments where drug molecules interact with membrane interfaces, metabolic enzymes or pharmacological receptors, are unanimously recognized as unstirred, space-restricted, heterogeneous and geometrically fractal. Therefore, classical Fickean diffusion and the notion of the compartment as a homogeneous kinetic space must be revisited. Diffusion in fractal spaces has been studied for a long time making use of fractional calculus and expanding on the notion of dimension. Combining this new paradigm with the need to describe and explain experimental data results in defining time-dependent rate constants with a characteristic fractal exponent. Under the one-compartment simplification this strategy is straightforward. However, precisely due to the heterogeneity of the underlying biology, often at least a two-compartment model is required to address macroscopic data such as drug concentrations. This simple modelling step-up implies significant analytical and numerical complications. However, a few methods are available that make possible the original desideratum. In fact, exploring the full range of parametric possibilities and looking at different drugs and respective biological concentrations, it may be concluded that all PK modelling approaches are indeed particular cases of the fractal PK theory.

Fire suppression as a thermal implosion

NASA Astrophysics Data System (ADS)

Novozhilov, Vasily

2017-01-01

The present paper discusses the possibility of the thermal implosion scenario. This process would be a reverse of the well known thermal explosion (autoignition) phenomenon. The mechanism for thermal implosion scenario is proposed which involves quick suppression of the turbulent diffusion flame. Classical concept of the thermal explosion is discussed first. Then a possible scenario for the reverse process (thermal implosion) is discussed and illustrated by a relevant mathematical model. Based on the arguments presented in the paper, thermal implosion may be observed as an unstable equilibrium point on the generalized Semenov diagram for turbulent flame, however this hypothesis requires ultimate experimental confirmation.

Sound, infrasound, and sonic boom absorption by atmospheric clouds.

PubMed

Baudoin, Michaël; Coulouvrat, François; Thomas, Jean-Louis

2011-09-01

This study quantifies the influence of atmospheric clouds on propagation of sound and infrasound, based on an existing model [Gubaidulin and Nigmatulin, Int. J. Multiphase Flow 26, 207-228 (2000)]. Clouds are considered as a dilute and polydisperse suspension of liquid water droplets within a mixture of dry air and water vapor, both considered as perfect gases. The model is limited to low and medium altitude clouds, with a small ice content. Four physical mechanisms are taken into account: viscoinertial effects, heat transfer, water phase changes (evaporation and condensation), and vapor diffusion. Physical properties of atmospheric clouds (altitude, thickness, water content and droplet size distribution) are collected, along with values of the thermodynamical coefficients. Different types of clouds have been selected. Quantitative evaluation shows that, for low audible and infrasound frequencies, absorption within clouds is several orders of magnitude larger than classical absorption. The importance of phase changes and vapor diffusion is outlined. Finally, numerical simulations for nonlinear propagation of sonic booms indicate that, for thick clouds, attenuation can lead to a very large decay of the boom at the ground level. © 2011 Acoustical Society of America

On the long time behavior of non-autonomous Lotka-Volterra models with diffusion via the sub-supertrajectory method

NASA Astrophysics Data System (ADS)

Langa, José A.; Rodríguez-Bernal, Aníbal; Suárez, Antonio

In this paper we study in detail the geometrical structure of global pullback and forwards attractors associated to non-autonomous Lotka-Volterra systems in all the three cases of competition, symbiosis or prey-predator. In particular, under some conditions on the parameters, we prove the existence of a unique nondegenerate global solution for these models, which attracts any other complete bounded trajectory. Thus, we generalize the existence of a unique strictly positive stable (stationary) solution from the autonomous case and we extend to Lotka-Volterra systems the result for scalar logistic equations. To this end we present the sub-supertrajectory tool as a generalization of the now classical sub-supersolution method. In particular, we also conclude pullback and forwards permanence for the above models.

Broken symmetry and critical transport properties of random metals

PubMed Central

Phillips, J. C.

1997-01-01

Recent experimental data on the conductivity σ+(T), T → 0, on the metallic side of the metal–insulator transition in ideally random (neutron transmutation-doped) 70Ge:Ga have shown that σ+(0) ∝ (N − Nc)μ with μ = ½, confirming earlier ultra-low-temperature results for Si:P. This value is inconsistent with theoretical predictions based on diffusive classical scaling models, but it can be understood by a quantum-directed percolative filamentary amplitude model in which electronic basis states exist which have a well-defined momentum parallel but not normal to the applied electric field. The model, which is based on a new kind of broken symmetry, also explains the anomalous sign reversal of the derivative of the temperature dependence in the critical regime. PMID:11038579

Diffusion of innovations in Axelrod’s model

NASA Astrophysics Data System (ADS)

Tilles, Paulo F. C.; Fontanari, José F.

2015-11-01

Axelrod's model for the dissemination of culture contains two key factors required to model the process of diffusion of innovations, namely, social influence (i.e., individuals become more similar when they interact) and homophily (i.e., individuals interact preferentially with similar others). The strength of these social influences are controlled by two parameters: $F$, the number of features that characterizes the cultures and $q$, the common number of states each feature can assume. Here we assume that the innovation is a new state of a cultural feature of a single individual -- the innovator -- and study how the innovation spreads through the networks among the individuals. For infinite regular lattices in one (1D) and two dimensions (2D), we find that initially the successful innovation spreads linearly with the time $t$, but in the long-time limit it spreads diffusively ($\\sim t^{1/2}$) in 1D and sub-diffusively ($\\sim t/\\ln t$) in 2D. For finite lattices, the growth curves for the number of adopters are typically concave functions of $t$. For random graphs with a finite number of nodes $N$, we argue that the classical S-shaped growth curves result from a trade-off between the average connectivity $K$ of the graph and the per feature diversity $q$. A large $q$ is needed to reduce the pace of the initial spreading of the innovation and thus delimit the early-adopters stage, whereas a large $K$ is necessary to ensure the onset of the take-off stage at which the number of adopters grows superlinearly with $t$. In an infinite random graph we find that the number of adopters of a successful innovation scales with $t^\\gamma$ with $\\gamma =1$ for $K> 2$ and $1/2 < \\gamma < 1$ for $K=2$. We suggest that the exponent $\\gamma$ may be a useful index to characterize the process of diffusion of successful innovations in diverse scenarios.

Serial vs. parallel models of attention in visual search: accounting for benchmark RT-distributions.

PubMed

Moran, Rani; Zehetleitner, Michael; Liesefeld, Heinrich René; Müller, Hermann J; Usher, Marius

2016-10-01

Visual search is central to the investigation of selective visual attention. Classical theories propose that items are identified by serially deploying focal attention to their locations. While this accounts for set-size effects over a continuum of task difficulties, it has been suggested that parallel models can account for such effects equally well. We compared the serial Competitive Guided Search model with a parallel model in their ability to account for RT distributions and error rates from a large visual search data-set featuring three classical search tasks: 1) a spatial configuration search (2 vs. 5); 2) a feature-conjunction search; and 3) a unique feature search (Wolfe, Palmer & Horowitz Vision Research, 50(14), 1304-1311, 2010). In the parallel model, each item is represented by a diffusion to two boundaries (target-present/absent); the search corresponds to a parallel race between these diffusors. The parallel model was highly flexible in that it allowed both for a parametric range of capacity-limitation and for set-size adjustments of identification boundaries. Furthermore, a quit unit allowed for a continuum of search-quitting policies when the target is not found, with "single-item inspection" and exhaustive searches comprising its extremes. The serial model was found to be superior to the parallel model, even before penalizing the parallel model for its increased complexity. We discuss the implications of the results and the need for future studies to resolve the debate.

An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data.

PubMed

Ferrer-Admetlla, Anna; Leuenberger, Christoph; Jensen, Jeffrey D; Wegmann, Daniel

2016-06-01

The joint and accurate inference of selection and demography from genetic data is considered a particularly challenging question in population genetics, since both process may lead to very similar patterns of genetic diversity. However, additional information for disentangling these effects may be obtained by observing changes in allele frequencies over multiple time points. Such data are common in experimental evolution studies, as well as in the comparison of ancient and contemporary samples. Leveraging this information, however, has been computationally challenging, particularly when considering multilocus data sets. To overcome these issues, we introduce a novel, discrete approximation for diffusion processes, termed mean transition time approximation, which preserves the long-term behavior of the underlying continuous diffusion process. We then derive this approximation for the particular case of inferring selection and demography from time series data under the classic Wright-Fisher model and demonstrate that our approximation is well suited to describe allele trajectories through time, even when only a few states are used. We then develop a Bayesian inference approach to jointly infer the population size and locus-specific selection coefficients with high accuracy and further extend this model to also infer the rates of sequencing errors and mutations. We finally apply our approach to recent experimental data on the evolution of drug resistance in influenza virus, identifying likely targets of selection and finding evidence for much larger viral population sizes than previously reported. Copyright © 2016 by the Genetics Society of America.

Impact of solvent granularity and layering on tracer hydrodynamics in confinement.

PubMed

Bollinger, Jonathan A; Carmer, James; Jain, Avni; Truskett, Thomas M

2016-11-28

Classic hydrodynamic arguments establish that when a spherical tracer particle is suspended between parallel walls, tracer-wall coupling mediated by the solvent will cause the tracer to exhibit position-dependent diffusivity. We investigate how the diffusivity profiles of confined tracers are impacted by the diameter size-ratio of the tracer to solvent: starting from the classic limit of infinite size-ratio (i.e., continuum solvent), we consider size-ratios of four or less to examine how hydrodynamic predictions are disrupted for systems where the tracer and solvent are of similar scale. We use computer simulations and techniques based on the Fokker-Planck formalism to calculate the diffusivity profiles of hard-sphere tracer particles in hard-sphere solvents, focusing on the dynamics perpendicular to the walls. Given wall separations of several tracer diameters, we first consider confinement between hard walls, where anisotropic structuring at the solvent lengthscale generates inhomogeneity in the tracer free-energy landscape and undermines hydrodynamic predictions locally. We then introduce confining planes that we term transparent walls, which restrict tracer and solvent center-accessibilities while completely eliminating static anisotropy, and reveal position-dependent signatures in tracer diffusivity solely attributable to confinement. With or without suppressing static heterogeneity, we find that tracer diffusivity increasingly deviates on a local basis from hydrodynamic predictions at smaller size-ratios. However, hydrodynamic theory still approximately captures spatially-averaged dynamics across the pores even for very small tracer-solvent size-ratios over a wide range of solvent densities and wall separations.

Molecular dynamics simulation of metallic impurity diffusion in liquid lead-bismuth eutectic (LBE)

NASA Astrophysics Data System (ADS)

Gao, Yun; Takahashi, Minoru; Cavallotti, Carlo; Raos, Guido

2018-04-01

Corrosion of stainless steels by lead-bismuth eutectic (LBE) is an important problem which depends, amongst other things, on the diffusion of the steel components inside this liquid alloy. Here we present the results of classical molecular dynamics simulations of the diffusion of Fe and Ni within LBE. The simulations complement experimental studies of impurity diffusion by our group and provide an atomic-level understanding of the relevant diffusion phenomena. They are based on the embedded atom method (EAM) to represent many-body interactions among atoms. The EAM potentials employed in our simulations have been validated against ab initio density functional calculations. We show that the experimental and simulation results for the temperature-dependent viscosity of LBE and the impurity diffusion coefficients can be reconciled by assuming that the Ni and Fe diffuse mainly as nanoscopic clusters below 1300 K. The average Fe and Ni cluster sizes decrease with increasing the temperature and there is essentially single-atom diffusion at higher temperatures.

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

Duncan, Andrew, E-mail: a.duncan@imperial.ac.uk; Erban, Radek, E-mail: erban@maths.ox.ac.uk; Zygalakis, Konstantinos, E-mail: k.zygalakis@ed.ac.uk

Stochasticity plays a fundamental role in various biochemical processes, such as cell regulatory networks and enzyme cascades. Isothermal, well-mixed systems can be modelled as Markov processes, typically simulated using the Gillespie Stochastic Simulation Algorithm (SSA) [25]. While easy to implement and exact, the computational cost of using the Gillespie SSA to simulate such systems can become prohibitive as the frequency of reaction events increases. This has motivated numerous coarse-grained schemes, where the “fast” reactions are approximated either using Langevin dynamics or deterministically. While such approaches provide a good approximation when all reactants are abundant, the approximation breaks down when onemore » or more species exist only in small concentrations and the fluctuations arising from the discrete nature of the reactions become significant. This is particularly problematic when using such methods to compute statistics of extinction times for chemical species, as well as simulating non-equilibrium systems such as cell-cycle models in which a single species can cycle between abundance and scarcity. In this paper, a hybrid jump-diffusion model for simulating well-mixed stochastic kinetics is derived. It acts as a bridge between the Gillespie SSA and the chemical Langevin equation. For low reactant reactions the underlying behaviour is purely discrete, while purely diffusive when the concentrations of all species are large, with the two different behaviours coexisting in the intermediate region. A bound on the weak error in the classical large volume scaling limit is obtained, and three different numerical discretisations of the jump-diffusion model are described. The benefits of such a formalism are illustrated using computational examples.« less

Cellular Immunotherapy Following Chemotherapy in Treating Patients With Recurrent Non-Hodgkin Lymphomas, Chronic Lymphocytic Leukemia or B-Cell Prolymphocytic Leukemia

ClinicalTrials.gov

2018-04-20

Post-transplant Lymphoproliferative Disorder; B-Cell Prolymphocytic Leukemia; Recurrent Adult Burkitt Lymphoma; Recurrent Adult Diffuse Large Cell Lymphoma; Recurrent Grade 1 Follicular Lymphoma; Recurrent Grade 2 Follicular Lymphoma; Recurrent Grade 3 Follicular Lymphoma; Recurrent Mantle Cell Lymphoma; Recurrent Marginal Zone Lymphoma; Recurrent Small Lymphocytic Lymphoma; Refractory Chronic Lymphocytic Leukemia; Refractory Hairy Cell Leukemia; B-Cell Lymphoma, Unclassifiable, With Features Intermediate Between Diffuse Large B-Cell Lymphoma and Burkitt Lymphoma; B-Cell Lymphoma, Unclassifiable, With Features Intermediate Between Diffuse Large B-Cell Lymphoma and Classical Hodgkin Lymphoma; Recurrent Lymphoplasmacytic Lymphoma

UO(2) Oxidative Corrosion by Nonclassical Diffusion.

PubMed

Stubbs, Joanne E; Chaka, Anne M; Ilton, Eugene S; Biwer, Craig A; Engelhard, Mark H; Bargar, John R; Eng, Peter J

2015-06-19

Using x-ray scattering, spectroscopy, and density-functional theory, we determine the structure of the oxidation front when a UO(2) (111) surface is exposed to oxygen at ambient conditions. In contrast to classical diffusion and previously reported bulk UO(2+x) structures, we find oxygen interstitials order into a nanoscale superlattice with three-layer periodicity and uranium in three oxidation states: IV, V, and VI. This oscillatory diffusion profile is driven by the nature of the electron transfer process, and has implications for understanding the initial stages of oxidative corrosion in materials at the atomistic level.

Thermal Expansion and Diffusion Coefficients of Carbon Nanotube-Polymer Composites

NASA Technical Reports Server (NTRS)

Wei, Chengyu; Srivastava, Deepak; Cho, Kyeongjae; Biegel, Bryan (Technical Monitor)

2001-01-01

Classical molecular dynamics (MD) simulations employing Brenner potential for intra-nanotube interactions and van der Waals forces for polymer-nanotube interface have been used to investigate thermal expansion and diffusion characteristics of carbon nanotube-polyethylene composites. Addition of carbon nanotubes to polymer matrix is found to significantly increase the glass transition temperature Tg, and thermal expansion and diffusion coefficients in the composite above Tg. The increase has been attributed to the temperature dependent increase of the excluded volume for the polymer chains, and the findings could have implications in the composite processing, coating and painting applications.

On the Origin of Quantum Diffusion Coefficient and Quantum Potential

NASA Astrophysics Data System (ADS)

Gupta, Aseem

2016-03-01

Synchronizability of space and time experiences between different inhabitants of a spacetime is abstracted as a fundamental premise of Classical physics. Absence thereof i.e. desynchronization between space and time experiences of a system under study and the observer is then studied for a single dimension single particle system. Desynchronization fundamentally makes probability concepts enter physics ab-initio and not as secondary tools to deal with situations wherein incomplete information in situation following perfectly deterministic dynamics demands its introduction. Desynchronization model based on Poisson distribution of events vis-à-vis an observer, leads to expectation of particle's motion as a Brownian motion deriving Nelson's quantum diffusion coefficient naturally, without needing to postulate it. This model also incorporates physical effects akin to those of Bohm's Quantum Potential, again without needing any sub-quantum medium. Schrodinger's equation is shown to be derivable incorporating desynchronization only of space while Quantum Field Theory is shown to model desynchronization of time as well. Fundamental suggestion of the study is that it is desynchronization that is at the root of quantum phenomena rather than sub-micro scales of spacetime. Absence of possibility of synchronization between system's space and time and those of observer is studied. Mathematical modeling of desynchronized evolution explains some intriguing aspects of Quantum Mechanical theory.

Causal implications of viscous damping in compressible fluid flows

PubMed

Jordan; Meyer; Puri

2000-12-01

Classically, a compressible, isothermal, viscous fluid is regarded as a mathematical continuum and its motion is governed by the linearized continuity, Navier-Stokes, and state equations. Unfortunately, solutions of this system are of a diffusive nature and hence do not satisfy causality. However, in the case of a half-space of fluid set to motion by a harmonically vibrating plate the classical equation of motion can, under suitable conditions, be approximated by the damped wave equation. Since this equation is hyperbolic, the resulting solutions satisfy causal requirements. In this work the Laplace transform and other analytical and numerical tools are used to investigate this apparent contradiction. To this end the exact solutions, as well as their special and limiting cases, are found and compared for the two models. The effects of the physical parameters on the solutions and associated quantities are also studied. It is shown that propagating wave fronts are only possible under the hyperbolic model and that the concept of phase speed has different meanings in the two formulations. In addition, discontinuities and shock waves are noted and a physical system is modeled under both formulations. Overall, it is shown that the hyperbolic form gives a more realistic description of the physical problem than does the classical theory. Lastly, a simple mechanical analog is given and connections to viscoelastic fluids are noted. In particular, the research presented here supports the notion that linear compressible, isothermal, viscous fluids can, at least in terms of causality, be better characterized as a type of viscoelastic fluid.

Stochastic inflation in phase space: is slow roll a stochastic attractor?

NASA Astrophysics Data System (ADS)

Grain, Julien; Vennin, Vincent

2017-05-01

An appealing feature of inflationary cosmology is the presence of a phase-space attractor, ``slow roll'', which washes out the dependence on initial field velocities. We investigate the robustness of this property under backreaction from quantum fluctuations using the stochastic inflation formalism in the phase-space approach. A Hamiltonian formulation of stochastic inflation is presented, where it is shown that the coarse-graining procedure—where wavelengths smaller than the Hubble radius are integrated out—preserves the canonical structure of free fields. This means that different sets of canonical variables give rise to the same probability distribution which clarifies the literature with respect to this issue. The role played by the quantum-to-classical transition is also analysed and is shown to constrain the coarse-graining scale. In the case of free fields, we find that quantum diffusion is aligned in phase space with the slow-roll direction. This implies that the classical slow-roll attractor is immune to stochastic effects and thus generalises to a stochastic attractor regardless of initial conditions, with a relaxation time at least as short as in the classical system. For non-test fields or for test fields with non-linear self interactions however, quantum diffusion and the classical slow-roll flow are misaligned. We derive a condition on the coarse-graining scale so that observational corrections from this misalignment are negligible at leading order in slow roll.

Ionization of the diffuse gas in galaxies: Hot low-mass evolved stars at work

NASA Astrophysics Data System (ADS)

Flores-Fajardo, N.; Morisset, C.; Stasinska, G.; Binette, L.

2011-10-01

The Diffuse Ionized Medium (DIG) is visible through its faint optical line emission outside classical HII regions (Reynolds 1971) and turns out to be a major component of the interstellar medium in galaxies. OB stars in galaxies likely represent the main source of ionizing photons for the DIG. However, an additional source is needed to explain the increase of [NII]/Hα, [SII]/Hα with galactic height.

Diffusion Monte Carlo approach versus adiabatic computation for local Hamiltonians

NASA Astrophysics Data System (ADS)

Bringewatt, Jacob; Dorland, William; Jordan, Stephen P.; Mink, Alan

2018-02-01

Most research regarding quantum adiabatic optimization has focused on stoquastic Hamiltonians, whose ground states can be expressed with only real non-negative amplitudes and thus for whom destructive interference is not manifest. This raises the question of whether classical Monte Carlo algorithms can efficiently simulate quantum adiabatic optimization with stoquastic Hamiltonians. Recent results have given counterexamples in which path-integral and diffusion Monte Carlo fail to do so. However, most adiabatic optimization algorithms, such as for solving MAX-k -SAT problems, use k -local Hamiltonians, whereas our previous counterexample for diffusion Monte Carlo involved n -body interactions. Here we present a 6-local counterexample which demonstrates that even for these local Hamiltonians there are cases where diffusion Monte Carlo cannot efficiently simulate quantum adiabatic optimization. Furthermore, we perform empirical testing of diffusion Monte Carlo on a standard well-studied class of permutation-symmetric tunneling problems and similarly find large advantages for quantum optimization over diffusion Monte Carlo.

Molecular dynamics simulation of self-diffusion processes in titanium in bulk material, on grain junctions and on surface.

PubMed

Sushko, Gennady B; Verkhovtsev, Alexey V; Yakubovich, Alexander V; Schramm, Stefan; Solov'yov, Andrey V

2014-08-21

The process of self-diffusion of titanium atoms in a bulk material, on grain junctions and on surface is explored numerically in a broad temperature range by means of classical molecular dynamics simulation. The analysis is carried out for a nanoscale cylindrical sample consisting of three adjacent sectors and various junctions between nanocrystals. The calculated diffusion coefficient varies by several orders of magnitude for different regions of the sample. The calculated values of the bulk diffusion coefficient correspond reasonably well to the experimental data obtained for solid and molten states of titanium. Investigation of diffusion in the nanocrystalline titanium is of a significant importance because of its numerous technological applications. This paper aims to reduce the lack of data on diffusion in titanium and describe the processes occurring in bulk, at different interfaces and on surface of the crystalline titanium.

A Novel Richardson-Lucy Model with Dictionary Basis and Spatial Regularization for Isolating Isotropic Signals.

PubMed

Xu, Tiantian; Feng, Yuanjing; Wu, Ye; Zeng, Qingrun; Zhang, Jun; He, Jianzhong; Zhuge, Qichuan

2017-01-01

Diffusion-weighted magnetic resonance imaging is a non-invasive imaging method that has been increasingly used in neuroscience imaging over the last decade. Partial volume effects (PVEs) exist in sampling signal for many physical and actual reasons, which lead to inaccurate fiber imaging. We overcome the influence of PVEs by separating isotropic signal from diffusion-weighted signal, which can provide more accurate estimation of fiber orientations. In this work, we use a novel response function (RF) and the correspondent fiber orientation distribution function (fODF) to construct different signal models, in which case the fODF is represented using dictionary basis function. We then put forward a new index Piso, which is a part of fODF to quantify white and gray matter. The classic Richardson-Lucy (RL) model is usually used in the field of digital image processing to solve the problem of spherical deconvolution caused by highly ill-posed least-squares algorithm. In this case, we propose an innovative model integrating RL model with spatial regularization to settle the suggested double-models, which improve noise resistance and accuracy of imaging. Experimental results of simulated and real data show that the proposal method, which we call iRL, can robustly reconstruct a more accurate fODF and the quantitative index Piso performs better than fractional anisotropy and general fractional anisotropy.

A Novel Richardson-Lucy Model with Dictionary Basis and Spatial Regularization for Isolating Isotropic Signals

PubMed Central

Feng, Yuanjing; Wu, Ye; Zeng, Qingrun; Zhang, Jun; He, Jianzhong; Zhuge, Qichuan

2017-01-01

Diffusion-weighted magnetic resonance imaging is a non-invasive imaging method that has been increasingly used in neuroscience imaging over the last decade. Partial volume effects (PVEs) exist in sampling signal for many physical and actual reasons, which lead to inaccurate fiber imaging. We overcome the influence of PVEs by separating isotropic signal from diffusion-weighted signal, which can provide more accurate estimation of fiber orientations. In this work, we use a novel response function (RF) and the correspondent fiber orientation distribution function (fODF) to construct different signal models, in which case the fODF is represented using dictionary basis function. We then put forward a new index Piso, which is a part of fODF to quantify white and gray matter. The classic Richardson-Lucy (RL) model is usually used in the field of digital image processing to solve the problem of spherical deconvolution caused by highly ill-posed least-squares algorithm. In this case, we propose an innovative model integrating RL model with spatial regularization to settle the suggested double-models, which improve noise resistance and accuracy of imaging. Experimental results of simulated and real data show that the proposal method, which we call iRL, can robustly reconstruct a more accurate fODF and the quantitative index Piso performs better than fractional anisotropy and general fractional anisotropy. PMID:28081561

Nuclear physics: Macroscopic aspects

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

Swiatecki, W.J.

1993-12-01

A systematic macroscopic, leptodermous approach to nuclear statics and dynamics is described, based formally on the assumptions {h_bar} {yields} 0 and b/R << 1, where b is the surface diffuseness and R the nuclear radius. The resulting static model of shell-corrected nuclear binding energies and deformabilities is accurate to better than 1 part in a thousand and yields a firm determination of the principal properties of the nuclear fluid. As regards dynamics, the above approach suggests that nuclear shape evolutions will often be dominated by dissipation, but quantitative comparisons with experimental data are more difficult than in the case ofmore » statics. In its simplest liquid drop version the model exhibits interesting formal connections to the classic astronomical problem of rotating gravitating masses.« less

Modelling information dissemination under privacy concerns in social media

NASA Astrophysics Data System (ADS)

Zhu, Hui; Huang, Cheng; Lu, Rongxing; Li, Hui

2016-05-01

Social media has recently become an important platform for users to share news, express views, and post messages. However, due to user privacy preservation in social media, many privacy setting tools are employed, which inevitably change the patterns and dynamics of information dissemination. In this study, a general stochastic model using dynamic evolution equations was introduced to illustrate how privacy concerns impact the process of information dissemination. Extensive simulations and analyzes involving the privacy settings of general users, privileged users, and pure observers were conducted on real-world networks, and the results demonstrated that user privacy settings affect information differently. Finally, we also studied the process of information diffusion analytically and numerically with different privacy settings using two classic networks.

Developing a model of plant hormone interactions

PubMed Central

Wang, Yu Hua

2011-01-01

Plant growth and development is influenced by mutual interactions among plant hormones. The five classical plant hormones are auxins, cytokinins, gibberellins, abscisic acid and ethylene. They are small diffusible molecules that easily penetrate between cells. In addition, newer classes of plant hormones have been identified such as brassinosteroids, jasmonic acid, salicylic acid and various small proteins or peptides. These hormones also play important roles in the regulation of plant growth and development. This review begins with a brief summary of the current findings on plant hormones. Based on this knowledge, a conceptual model about interactions among plant hormones is built so as to link and develop an understanding of the diverse functions of different plant hormones as a whole in plants. PMID:21406974

Analytical modeling of drug dynamics induced by eluting stents in the coronary multi-layered curved domain.

PubMed

d'Errico, Michele; Sammarco, Paolo; Vairo, Giuseppe

2015-09-01

Pharmacokinetics induced by drug eluting stents (DES) in coronary walls is modeled by means of a one-dimensional multi-layered model, accounting for vessel curvature and non-homogeneous properties of the arterial tissues. The model includes diffusion mechanisms, advection effects related to plasma filtration through the walls, and bio-chemical drug reactions. A non-classical Sturm-Liouville problem with discontinuous coefficients is derived, whose closed-form analytical solution is obtained via an eigenfunction expansion. Soundness and consistency of the proposed approach are shown by numerical computations based on possible clinical treatments involving both hydrophilic and hydrophobic drugs. The influence of the main model parameters on drug delivery mechanisms is analyzed, highlighting the effects induced by vessel curvature and yielding comparative indications and useful insights into the concurring mechanisms governing the pharmacokinetics. Copyright © 2015. Published by Elsevier Inc.

A multi-scale Lattice Boltzmann model for simulating solute transport in 3D X-ray micro-tomography images of aggregated porous materials

NASA Astrophysics Data System (ADS)

Zhang, Xiaoxian; Crawford, John W.; Flavel, Richard J.; Young, Iain M.

2016-10-01

The Lattice Boltzmann (LB) model and X-ray computed tomography (CT) have been increasingly used in combination over the past decade to simulate water flow and chemical transport at pore scale in porous materials. Because of its limitation in resolution and the hierarchical structure of most natural soils, the X-ray CT tomography can only identify pores that are greater than its resolution and treats other pores as solid. As a result, the so-called solid phase in X-ray images may in reality be a grey phase, containing substantial connected pores capable of conducing fluids and solute. Although modified LB models have been developed to simulate fluid flow in such media, models for solute transport are relatively limited. In this paper, we propose a LB model for simulating solute transport in binary soil images containing permeable solid phase. The model is based on the single-relaxation time approach and uses a modified partial bounce-back method to describe the resistance caused by the permeable solid phase to chemical transport. We derive the relationship between the diffusion coefficient and the parameter introduced in the partial bounce-back method, and test the model against analytical solution for movement of a pulse of tracer. We also validate it against classical finite volume method for solute diffusion in a simple 2D image, and then apply the model to a soil image acquired using X-ray tomography at resolution of 30 μm in attempts to analyse how the ability of the solid phase to diffuse solute at micron-scale affects the behaviour of the solute at macro-scale after a volumetric average. Based on the simulated results, we discuss briefly the danger in interpreting experimental results using the continuum model without fully understanding the pore-scale processes, as well as the potential of using pore-scale modelling and tomography to help improve the continuum models.

Basis for a neuronal version of Grover's quantum algorithm

PubMed Central

Clark, Kevin B.

2014-01-01

Grover's quantum (search) algorithm exploits principles of quantum information theory and computation to surpass the strong Church–Turing limit governing classical computers. The algorithm initializes a search field into superposed N (eigen)states to later execute nonclassical “subroutines” involving unitary phase shifts of measured states and to produce root-rate or quadratic gain in the algorithmic time (O(N1/2)) needed to find some “target” solution m. Akin to this fast technological search algorithm, single eukaryotic cells, such as differentiated neurons, perform natural quadratic speed-up in the search for appropriate store-operated Ca2+ response regulation of, among other processes, protein and lipid biosynthesis, cell energetics, stress responses, cell fate and death, synaptic plasticity, and immunoprotection. Such speed-up in cellular decision making results from spatiotemporal dynamics of networked intracellular Ca2+-induced Ca2+ release and the search (or signaling) velocity of Ca2+ wave propagation. As chemical processes, such as the duration of Ca2+ mobilization, become rate-limiting over interstore distances, Ca2+ waves quadratically decrease interstore-travel time from slow saltatory to fast continuous gradients proportional to the square-root of the classical Ca2+ diffusion coefficient, D1/2, matching the computing efficiency of Grover's quantum algorithm. In this Hypothesis and Theory article, I elaborate on these traits using a fire-diffuse-fire model of store-operated cytosolic Ca2+ signaling valid for glutamatergic neurons. Salient model features corresponding to Grover's quantum algorithm are parameterized to meet requirements for the Oracle Hadamard transform and Grover's iteration. A neuronal version of Grover's quantum algorithm figures to benefit signal coincidence detection and integration, bidirectional synaptic plasticity, and other vital cell functions by rapidly selecting, ordering, and/or counting optional response regulation choices. PMID:24860419

Charge heterogeneity of surfaces: mapping and effects on surface forces.

PubMed

Drelich, Jaroslaw; Wang, Yu U

2011-07-11

The DLVO theory treats the total interaction force between two surfaces in a liquid medium as an arithmetic sum of two components: Lifshitz-van der Waals and electric double layer forces. Despite the success of the DLVO model developed for homogeneous surfaces, a vast majority of surfaces of particles and materials in technological systems are of a heterogeneous nature with a mosaic structure composed of microscopic and sub-microscopic domains of different surface characteristics. In such systems, the heterogeneity of the surface can be more important than the average surface character. Attractions can be stronger, by orders of magnitude, than would be expected from the classical mean-field DLVO model when area-averaged surface charge or potential is employed. Heterogeneity also introduces anisotropy of interactions into colloidal systems, vastly ignored in the past. To detect surface heterogeneities, analytical tools which provide accurate and spatially resolved information about material surface chemistry and potential - particularly at microscopic and sub-microscopic resolutions - are needed. Atomic force microscopy (AFM) offers the opportunity to locally probe not only changes in material surface characteristic but also charges of heterogeneous surfaces through measurements of force-distance curves in electrolyte solutions. Both diffuse-layer charge densities and potentials can be calculated by fitting the experimental data with a DLVO theoretical model. The surface charge characteristics of the heterogeneous substrate as recorded by AFM allow the charge variation to be mapped. Based on the obtained information, computer modeling and simulation can be performed to study the interactions among an ensemble of heterogeneous particles and their collective motions. In this paper, the diffuse-layer charge mapping by the AFM technique is briefly reviewed, and a new Diffuse Interface Field Approach to colloid modeling and simulation is briefly discussed. Copyright © 2011 Elsevier B.V. All rights reserved.

Osmotic pressure beyond concentration restrictions.

PubMed

Grattoni, Alessandro; Merlo, Manuele; Ferrari, Mauro

2007-10-11

Osmosis is a fundamental physical process that involves the transit of solvent molecules across a membrane separating two liquid solutions. Osmosis plays a role in many biological processes such as fluid exchange in animal cells (Cell Biochem. Biophys. 2005, 42, 277-345;1 J. Periodontol. 2007, 78, 757-7632) and water transport in plants. It is also involved in many technological applications such as drug delivery systems (Crit. Rev. Ther. Drug. 2004, 21, 477-520;3 J. Micro-Electromech. Syst. 2004, 13, 75-824) and water purification. Extensive attention has been dedicated in the past to the modeling of osmosis, starting with the classical theories of van't Hoff and Morse. These are predictive, in the sense that they do not involve adjustable parameters; however, they are directly applicable only to limited regimes of dilute solute concentrations. Extensions beyond the domains of validity of these classical theories have required recourse to fitting parameters, transitioning therefore to semiempirical, or nonpredictive models. A novel approach was presented by Granik et al., which is not a priori restricted in concentration domains, presents no adjustable parameters, and is mechanistic, in the sense that it is based on a coupled diffusion model. In this work, we examine the validity of predictive theories of osmosis, by comparison with our new experimental results, and a meta-analysis of literature data.

MRI and clinical features of maple syrup urine disease: preliminary results in 10 cases

PubMed Central

Cheng, Ailan; Han, Lianshu; Feng, Yun; Li, Huimin; Yao, Rong; Wang, Dengbin; Jin, Biao

2017-01-01

PURPOSE We aimed to evaluate the magnetic resonance imaging (MRI) and clinical features of maple syrup urine disease (MSUD). METHODS This retrospective study consisted of 10 MSUD patients confirmed by genetic testing. All patients underwent brain MRI. Phenotype, genotype, and areas of brain injury on MRI were retrospectively reviewed. RESULTS Six patients (60%) had the classic form of MSUD with BCKDHB mutation, three patients (30%) had the intermittent form (two with BCKDHA mutations and one with DBT mutation), and one patient (10%) had the thiamine-responsive form with DBT mutation. On diffusion-weighted imaging, nine cases presented restricted diffusion in myelinated areas, and one intermittent case with DBT mutation was normal. The classic form of MSUD involved the basal ganglia in six cases; the cerebellum, mesencephalon, pons, and supratentorial area in five cases; and the thalamus in four cases, respectively. The intermittent form involved the cerebellum, pons, and supratentorial area in two cases. The thiamine-responsive form involved the basal ganglia and supratentorial area. CONCLUSION Our preliminary results indicate that patients with MSUD presented more commonly in classic form with BCKDHB mutation and displayed extensive brain injury on MRI. PMID:28830848

Stochastic collective dynamics of charged-particle beams in the stability regime

NASA Astrophysics Data System (ADS)

Petroni, Nicola Cufaro; de Martino, Salvatore; de Siena, Silvio; Illuminati, Fabrizio

2001-01-01

We introduce a description of the collective transverse dynamics of charged (proton) beams in the stability regime by suitable classical stochastic fluctuations. In this scheme, the collective beam dynamics is described by time-reversal invariant diffusion processes deduced by stochastic variational principles (Nelson processes). By general arguments, we show that the diffusion coefficient, expressed in units of length, is given by λcN, where N is the number of particles in the beam and λc the Compton wavelength of a single constituent. This diffusion coefficient represents an effective unit of beam emittance. The hydrodynamic equations of the stochastic dynamics can be easily recast in the form of a Schrödinger equation, with the unit of emittance replacing the Planck action constant. This fact provides a natural connection to the so-called ``quantum-like approaches'' to beam dynamics. The transition probabilities associated to Nelson processes can be exploited to model evolutions suitable to control the transverse beam dynamics. In particular we show how to control, in the quadrupole approximation to the beam-field interaction, both the focusing and the transverse oscillations of the beam, either together or independently.

Morse-Smale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations

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

Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun

Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrödinger’s equation, they generate the electronic structure of the simulated atoms as a scalar field. However, methods for analyzing these volume data are not yet common in molecular visualization. The Morse-Smale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete Morse-Smale complex to analysis of first-principles battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ Morse-Smale decomposition to determine the possible lithium ionmore » diffusion paths within that structure. Our approach is novel in that it uses the wavefunction itself as opposed distance fields, and that we analyze the 1-skeleton of the Morse-Smale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1-skeleton define features, namely carbon rings with specific valence. We compare our analysis of DFT data with that of a distance field approximation, and discuss implications on larger classical molecular dynamics simulations.« less

Pre-Darcy Flow in Porous Media

NASA Astrophysics Data System (ADS)

Dejam, Morteza; Hassanzadeh, Hassan; Chen, Zhangxin

2017-10-01

Fluid flow in porous media is very important in a wide range of science and engineering applications. The entire establishment of fluid flow application in porous media is based on the use of an experimental law proposed by Darcy (1856). There are evidences in the literature that the flow of a fluid in consolidated and unconsolidated porous media does not follow Darcy law at very low fluxes, which is called pre-Darcy flow. In this paper, the unsteady flow regimes of a slightly compressible fluid under the linear and radial pre-Darcy flow conditions are modeled and the corresponding highly nonlinear diffusivity equations are solved analytically by aid of a generalized Boltzmann transformation technique. The influence of pre-Darcy flow on the pressure diffusion for homogeneous porous media is studied in terms of the nonlinear exponent and the threshold pressure gradient. In addition, the pressure gradient, flux, and cumulative production per unit area are compared with the classical solution of the diffusivity equation based on Darcy flow. The presented results advance our understanding of fluid flow in low-permeability media such as shale and tight formations, where pre-Darcy is the dominant flow regime.

Nucleation of rotating crystals by Thiovulum majus bacteria

NASA Astrophysics Data System (ADS)

Petroff, A. P.; Libchaber, A.

2018-01-01

Thiovulum majus self-organize on glass surfaces into active two-dimensional crystals of rotating cells. Unlike classical crystals, these bacterial crystallites continuously rotate and reorganize as the power of rotating cells is dissipated by the surrounding flow. In this article, we describe the earliest stage of crystallization, the attraction of two bacteria into a hydrodynamically-bound dimer. This process occurs in three steps. First a free-swimming cell collides with the wall and becomes hydrodynamically bound to the two-dimensional surface. We present a simple model to understand how viscous forces localize cells near the chamber walls. Next, the cell diffuses over the surface for an average of 63+/- 6 s before escaping to the bulk fluid. The diffusion coefficient {D}{{eff}}=7.98 +/- 0.1 μ {{{m}}}2 {{{s}}}-1 of these 8.5 μ {{m}} diameter cells corresponds to a temperature of (4.16+/- 0.05)× {10}4 K, and thus cannot be explained by equilibrium fluctuations. Finally, two cells coalesce into a rotating dimer when the convergent flow created by each cell overwhelms their active Brownian motion. This occurs when cells diffuse to within a distance of 13.3 ± 0.2 μm of each other.

Absorption Kinetics of Phage Lambda on Its Host Under Shear Flow

NASA Astrophysics Data System (ADS)

Yip, C. W.; Wu, X. L.

2000-03-01

Classical blender experiment by Hershey and Chase played a seminal role in illustrating the infectious process of bacteriophage to its host, and showed unequivocally that DNA is responsible for the transmission of heredity. Subsequent works by others have established that interaction between phage particles and bacterial cells is a diffusion-limited process in that, statistically speaking, each collision results in an irreversible infection. However, such a result is hard to reconcile with the fact that the infection appears to be independent of the density of phage receptors on the bacterial cell membrane. Thus, quantitative experiments showing how a phage finds its receptor and how long does it take would be valuable to this paradoxical view. Simple calculations based on Brownian motion of the phage particles show that the interaction time between the receptor and the phage is given by tau=b^2/(5D), where b is the length of the phage and D is its diffusion coefficient. Using a shear flow apparatus we study absorption kinetics of lambda phage on E. Coli (strain YMEL) under different flow conditions, and the results are compared with a simple diffusion model taking into account the hydrodynamic convection and the interaction time tau.

Solitary Pulmonary Nodule

DTIC Science & Technology

2010-05-01

also classically has “ popcorn ” calcifications.1 Another benign albeit rarer diagnosis that can be considered in patients from the southern...spiculated border 95% with corona radiata3 Calcifications Diffuse homogenous Central Laminated “ Popcorn ” Any other pattern Density *seldom

Ultrastructural localization of acetylcholinesterase in neurofibrillary tangles, neuropil threads and senile plaques in aged and Alzheimer's brain.

PubMed

Gomez-Ramos, P; Mufson, E J; Moran, M A

1992-01-13

Acetylcholinesterase (AChE) histochemistry was used to evaluate the accumulation of this enzyme in senile plaques, neurofibrillary tangles and neuropil threads using light and electron microscopy in Alzheimer's disease as well as non-demented aged brains. Under the electron microscope, a crystalline-like AChE precipitate was localized over paired helical filaments and straight filaments in both neurofibrillary tangles and neuropil threads. AChE reaction product also decorated the amyloid fibrils in diffuse plaques as well as the halo and the heavy accumulation of amyloid which forms the core of classical plaques. In both diffuse plaques and the halo of classical plaques, we found AChE-positive structures resembling cell processes, which in some cases appeared to contain amyloid fibrils. The possible origin and significance of AChE localized over paired helical filaments, straight filaments and amyloid is discussed.

Local multiplicative Schwarz algorithms for convection-diffusion equations

NASA Technical Reports Server (NTRS)

Cai, Xiao-Chuan; Sarkis, Marcus

1995-01-01

We develop a new class of overlapping Schwarz type algorithms for solving scalar convection-diffusion equations discretized by finite element or finite difference methods. The preconditioners consist of two components, namely, the usual two-level additive Schwarz preconditioner and the sum of some quadratic terms constructed by using products of ordered neighboring subdomain preconditioners. The ordering of the subdomain preconditioners is determined by considering the direction of the flow. We prove that the algorithms are optimal in the sense that the convergence rates are independent of the mesh size, as well as the number of subdomains. We show by numerical examples that the new algorithms are less sensitive to the direction of the flow than either the classical multiplicative Schwarz algorithms, and converge faster than the additive Schwarz algorithms. Thus, the new algorithms are more suitable for fluid flow applications than the classical additive or multiplicative Schwarz algorithms.

Ratchet effect in the quantum kicked rotor and its destruction by dynamical localization

NASA Astrophysics Data System (ADS)

Hainaut, Clément; Rançon, Adam; Clément, Jean-François; Garreau, Jean Claude; Szriftgiser, Pascal; Chicireanu, Radu; Delande, Dominique

2018-06-01

We study experimentally a quantum kicked rotor with broken parity symmetry, supporting a ratchet effect due to the presence of a classical accelerator mode. We show that the short-time dynamics is very well described by the classical dynamics, characterized by a strongly asymmetric momentum distribution with directed motion on one side, and an anomalous diffusion on the other. At longer times, quantum effects lead to dynamical localization, causing an asymptotic resymmetrization of the wave function.

One-electron propagation in Fermi, Pasta, Ulam disordered chains with Gaussian acoustic pulse pumping

NASA Astrophysics Data System (ADS)

Silva, L. D. Da; Dos Santos, J. L. L.; Ranciaro Neto, A.; Sales, M. O.; de Moura, F. A. B. F.

In this work, we consider a one-electron moving on a Fermi, Pasta, Ulam disordered chain under effect of electron-phonon interaction and a Gaussian acoustic pulse pumping. We describe electronic dynamics using quantum mechanics formalism and the nonlinear atomic vibrations using standard classical physics. Solving numerical equations related to coupled quantum/classical behavior of this system, we study electronic propagation properties. Our calculations suggest that the acoustic pumping associated with the electron-lattice interaction promote a sub-diffusive electronic dynamics.

Hypertensive brain stem encephalopathy.

PubMed

Liao, Pen-Yuan; Lee, Chien-Chang; Chen, Cheng-Yu

2015-01-01

A 48-year-old man presented with headache and extreme hypertension. Computed tomography showed diffuse brain stem hypodensity. Magnetic resonance imaging revealed diffuse brain stem vasogenic edema. Hypertensive brain stem encephalopathy is an uncommon manifestation of hypertensive encephalopathy, which classically occurs at parietooccipital white matter. Because of its atypical location, the diagnosis can be challenging. Moreover, the coexistence of hypertension and brain stem edema could also direct clinicians toward a diagnosis of ischemic infarction, leading to a completely contradictory treatment goal.

Analysis of Recent Agile Mirror Data

DTIC Science & Technology

1994-03-28

pressures, the positive column in the agile mirror discharges is beam dominated. To investigate this more fully, a retarding field analyzer is being...perpendicular to the magnetic field has been observed.) Bohm postulated a diffusion coefficient 7 scaling as 1/B (instead of the classical 1B 2 scaling) to...mTorr and a current 9 of 1.5 A was obtained at a voltage of 150 V. The axial magnetic field strength was 3000 Gauss. The Bohm diffusion coefficient

Mechanism of Urea Crystal Dissolution in Water from Molecular Dynamics Simulation.

PubMed

Anand, Abhinav; Patey, G N

2018-01-25

Molecular dynamics simulations are used to determine the mechanism of urea crystal dissolution in water under sink conditions. Crystals of cubic and tablet shapes are considered, and results are reported for four commonly used water models. The dissolution rates for different water models can differ considerably, but the overall dissolution mechanism remains the same. Urea dissolution occurs in three stages: a relatively fast initial stage, a slower intermediate stage, and a final stage. We show that the long intermediate stage is well described by classical rate laws, which assume that the dissolution rate is proportional to the active surface area. By carrying out simulations at different temperatures, we show that urea dissolution is an activated process, with an activation energy of ∼32 kJ mol -1 . Our simulations give no indication of a significant diffusion layer, and we conclude that the detachment of molecules from the crystal is the rate-determining step for dissolution. The results we report for urea are consistent with earlier observations for the dissolution of NaCl crystals. This suggests that the three-stage mechanism and classical rate laws might apply to the dissolution of other ionic and molecular crystals.

Modeling the Gross-Pitaevskii Equation Using the Quantum Lattice Gas Method

NASA Astrophysics Data System (ADS)

Oganesov, Armen

We present an improved Quantum Lattice Gas (QLG) algorithm as a mesoscopic unitary perturbative representation of the mean field Gross Pitaevskii (GP) equation for Bose-Einstein Condensates (BECs). The method employs an interleaved sequence of unitary collide and stream operators. QLG is applicable to many different scalar potentials in the weak interaction regime and has been used to model the Korteweg-de Vries (KdV), Burgers and GP equations. It can be implemented on both quantum and classical computers and is extremely scalable. We present results for 1D soliton solutions with positive and negative internal interactions, as well as vector solitons with inelastic scattering. In higher dimensions we look at the behavior of vortex ring reconnection. A further improvement is considered with a proper operator splitting technique via a Fourier transformation. This is great for quantum computers since the quantum FFT is exponentially faster than its classical counterpart which involves non-local data on the entire lattice (Quantum FFT is the backbone of the Shor algorithm for quantum factorization). We also present an imaginary time method in which we transform the Schrodinger equation into a diffusion equation for recovering ground state initial conditions of a quantum system suitable for the QLG algorithm.

Mathematical models for the diffusion magnetic resonance signal abnormality in patients with prion diseases.

PubMed

Figini, Matteo; Alexander, Daniel C; Redaelli, Veronica; Fasano, Fabrizio; Grisoli, Marina; Baselli, Giuseppe; Gambetti, Pierluigi; Tagliavini, Fabrizio; Bizzi, Alberto

2015-01-01

In clinical practice signal hyperintensity in the cortex and/or in the striatum on magnetic resonance (MR) diffusion-weighted images (DWIs) is a marker of sporadic Creutzfeldt-Jakob Disease (sCJD). MR diagnostic accuracy is greater than 90%, but the biophysical mechanisms underpinning the signal abnormality are unknown. The aim of this prospective study is to combine an advanced DWI protocol with new mathematical models of the microstructural changes occurring in prion disease patients to investigate the cause of MR signal alterations. This underpins the later development of more sensitive and specific image-based biomarkers. DWI data with a wide a range of echo times and diffusion weightings were acquired in 15 patients with suspected diagnosis of prion disease and in 4 healthy age-matched subjects. Clinical diagnosis of sCJD was made in nine patients, genetic CJD in one, rapidly progressive encephalopathy in three, and Gerstmann-Sträussler-Scheinker syndrome in two. Data were analysed with two bi-compartment models that represent different hypotheses about the histopathological alterations responsible for the DWI signal hyperintensity. A ROI-based analysis was performed in 13 grey matter areas located in affected and apparently unaffected regions from patients and healthy subjects. We provide for the first time non-invasive estimate of the restricted compartment radius, designed to reflect vacuole size, which is a key discriminator of sCJD subtypes. The estimated vacuole size in DWI hyperintense cortex was in the range between 3 and 10 µm that is compatible with neuropathology measurements. In DWI hyperintense grey matter of sCJD patients the two bi-compartment models outperform the classic mono-exponential ADC model. Both new models show that T2 relaxation times significantly increase, fast and slow diffusivities reduce, and the fraction of the compartment with slow/restricted diffusion increases compared to unaffected grey matter of patients and healthy subjects. Analysis of the raw DWI signal allows us to suggest the following acquisition parameters for optimized detection of CJD lesions: b = 3000 s/mm(2) and TE = 103 ms. In conclusion, these results provide the first in vivo estimate of mean vacuole size, new insight on the mechanisms of DWI signal changes in prionopathies and open the way to designing an optimized acquisition protocol to improve early clinical diagnosis and subtyping of sCJD.

Non-classical nuclei and growth kinetics of Cr precipitates in FeCr alloys during ageing

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

Li, Yulan; Hu, Shenyang Y.; Zhang, Lei

2014-01-10

In this manuscript, we quantitatively calculated the thermodynamic properties of critical nuclei of Cr precipitates in FeCr alloys. The concentration profiles of the critical nuclei and nucleation energy barriers were predicted by the constrained shrinking dimer dynamics (CSDD) method. It is found that Cr concentration distribution in the critical nuclei strongly depend on the overall Cr concentration as well as temperature. The critical nuclei are non-classical because the concentration in the nuclei is smaller than the thermodynamic equilibrium value. These results are in agreement with atomic probe observation. The growth kinetics of both classical and non-classical nuclei was investigated bymore » the phase field approach. The simulations of critical nucleus evolution showed a number of interesting phenomena: 1) a critical classical nucleus first shrinks toward its non-classical nucleus and then grows; 2) a non-classical nucleus has much slower growth kinetics at its earlier growth stage compared to the diffusion-controlled growth kinetics. 3) a critical classical nucleus grows faster at the earlier growth stage than the non-classical nucleus. All of these results demonstrate that it is critical to introduce the correct critical nuclei in order to correctly capture the kinetics of precipitation.« less

Structure and dynamics of propylammonium nitrate-acetonitrile mixtures: An intricate multi-scale system probed with experimental and theoretical techniques.

PubMed

Campetella, Marco; Mariani, Alessandro; Sadun, Claudia; Wu, Boning; Castner, Edward W; Gontrani, Lorenzo

2018-04-07

In this article, we report the study of structural and dynamical properties for a series of acetonitrile/propylammonium nitrate mixtures as a function of their composition. These systems display an unusual increase in intensity in their X-ray diffraction patterns in the low-q regime, and their 1 H-NMR diffusion-ordered NMR spectroscopy (DOSY) spectra display unusual diffusivities. However, the magnitude of both phenomena for mixtures of propylammonium nitrate is smaller than those observed for ethylammonium nitrate mixtures with the same cosolvent, suggesting that the cation alkyl tail plays an important role in these observations. The experimental X-ray scattering data are compared with the results of molecular dynamics simulations, including both ab initio studies used to interpret short-range interactions and classical simulations to describe longer range interactions. The higher level calculations highlight the presence of a strong hydrogen bond network within the ionic liquid, only slightly perturbed even at high acetonitrile concentration. These strong interactions lead to the symmetry breaking of the NO 3 - vibrations, with a splitting of about 88 cm -1 in the ν 3 antisymmetric stretch. The classical force field simulations use a greater number of ion pairs, but are not capable of fully describing the longest range interactions, although they do successfully account for the observed concentration trend, and the analysis of the models confirms the nano-inhomogeneity of these kinds of samples.

Structure and dynamics of propylammonium nitrate-acetonitrile mixtures: An intricate multi-scale system probed with experimental and theoretical techniques

NASA Astrophysics Data System (ADS)

Campetella, Marco; Mariani, Alessandro; Sadun, Claudia; Wu, Boning; Castner, Edward W.; Gontrani, Lorenzo

2018-04-01

In this article, we report the study of structural and dynamical properties for a series of acetonitrile/propylammonium nitrate mixtures as a function of their composition. These systems display an unusual increase in intensity in their X-ray diffraction patterns in the low-q regime, and their 1H-NMR diffusion-ordered NMR spectroscopy (DOSY) spectra display unusual diffusivities. However, the magnitude of both phenomena for mixtures of propylammonium nitrate is smaller than those observed for ethylammonium nitrate mixtures with the same cosolvent, suggesting that the cation alkyl tail plays an important role in these observations. The experimental X-ray scattering data are compared with the results of molecular dynamics simulations, including both ab initio studies used to interpret short-range interactions and classical simulations to describe longer range interactions. The higher level calculations highlight the presence of a strong hydrogen bond network within the ionic liquid, only slightly perturbed even at high acetonitrile concentration. These strong interactions lead to the symmetry breaking of the NO3 - vibrations, with a splitting of about 88 cm-1 in the ν3 antisymmetric stretch. The classical force field simulations use a greater number of ion pairs, but are not capable of fully describing the longest range interactions, although they do successfully account for the observed concentration trend, and the analysis of the models confirms the nano-inhomogeneity of these kinds of samples.

Fundamentals and techniques of nonimaging optics for solar energy concentration

NASA Astrophysics Data System (ADS)

Winston, R.; Gallagher, J. J.

1980-05-01

The properties of a variety of new and previously known nonimaging optical configurations were investigated. A thermodynamic model which explains quantitatively the enhancement of effective absorptance of gray body receivers through cavity effects was developed. The classic method of Liu and Jordan, which allows one to predict the diffuse sunlight levels through correlation with the total and direct fraction was revised and updated and applied to predict the performance of nonimaging solar collectors. The conceptual design for an optimized solar collector which integrates the techniques of nonimaging concentration with evacuated tube collector technology was carried out and is presently the basis for a separately funded hardware development project.

Stochastic effects in hybrid inflation

NASA Astrophysics Data System (ADS)

Martin, Jérôme; Vennin, Vincent

2012-02-01

Hybrid inflation is a two-field model where inflation ends due to an instability. In the neighborhood of the instability point, the potential is very flat and the quantum fluctuations dominate over the classical motion of the inflaton and waterfall fields. In this article, we study this regime in the framework of stochastic inflation. We numerically solve the two coupled Langevin equations controlling the evolution of the fields and compute the probability distributions of the total number of e-folds and of the inflation exit point. Then, we discuss the physical consequences of our results, in particular, the question of how the quantum diffusion can affect the observable predictions of hybrid inflation.

Locally enhanced sampling molecular dynamics study of the dioxygen transport in human cytoglobin.

PubMed

Orlowski, Slawomir; Nowak, Wieslaw

2007-07-01

Cytoglobin (Cyg)--a new member of the vertebrate heme globin family--is expressed in many tissues of the human body but its physiological role is still unclear. It may deliver oxygen under hypoxia, serve as a scavenger of reactive species or be involved in collagen synthesis. This protein is usually six-coordinated and binds oxygen by a displacement of the distal HisE7 imidazole. In this paper, the results of 60 ns molecular dynamics (MD) simulations of dioxygen diffusion inside Cyg matrix are discussed. In addition to a classical MD trajectory, an approximate Locally Enhanced Sampling (LES) method has been employed. Classical diffusion paths were carefully analyzed, five cavities in dynamical structures were determined and at least four distinct ligand exit paths were identified. The most probable exit/entry path is connected with a large tunnel present in Cyg. Several residues that are perhaps critical for kinetics of small gaseous diffusion were discovered. A comparison of gaseous ligand transport in Cyg and in the most studied heme protein myoglobin is presented. Implications of efficient oxygen transport found in Cyg to its possible physiological role are discussed.

Structural white matter changes in adolescents and young adults with maple syrup urine disease.

PubMed

Klee, D; Thimm, E; Wittsack, H J; Schubert, D; Primke, R; Pentang, G; Schaper, J; Mödder, U; Antoch, A; Wendel, U; Cohnen, M

2013-11-01

To get insight into the nature of magnetic resonance (MR) white matter abnormalities of patients with classic maple syrup urine disease (MSUD) under diet control. Ten patients with classic MSUD and one with a severe MSUD variant (mean age 21.5 ± 5.1 years) on diet and 11 age and sex-matched healthy subjects were enrolled. Apart from standard MR sequences, diffusion weighted images (DWI), diffusion tensor images (DTI), and magnetization transfer images (MT) were obtained and comparatively analyzed for apparent diffusion coefficient (ADC), tensor fractional anisotropy (FA) and MT maps in 11 regions of interest (ROI) within the white matter. In MSUD patients DWI, DTI and FA showed distinct signal changes in the cerebral hemispheres, the dorsal limb of internal capsule, the brain stem and the central cerebellum. Signal intensity was increased in DWI with a reduced ADC and decreased values for FA. MT did not reveal differences between patients and control subjects. Signal abnormalities in the white matter of adolescents and young adults under diet control may be interpreted as consequence of structural alterations like dysmyelination. The reduced ADC and FA in the white matter with preserved MT indicate a reduction in fiber tracks.

Comparison of different bioheat transfer models for assessment of burns injuries

NASA Astrophysics Data System (ADS)

Łapka, Piotr; Furmański, Piotr; Wiśniewski, Tomasz S.

2016-12-01

Two bioheat transfer models i.e.: the classical Pennes model and a more realistic two-equation model which accounted for blood vessel structure in the skin as well as heat transfer in the tissue and arteria blood were coupled with heat and mass transfer model in the protective multilayer garment. The clothing model included conductive-radiative heat transfer with water vapor diffusion in pores and air gaps as well as sorption and desorption of water in fibers. Thermal radiation was modeled rigorously e.g.: both the tissue and fabrics were assumed non-gray, absorbing, emitting and anisotropically scattering. Additionally different refractive indices of fabrics, air and tissue and resulting optical phenomena at separating interfaces were accounted for. Both bioheat models were applied for predicting skin temperature distributions and possibility of burns for different exposition times and radiative heat fluxes incident on external surface of the protective garment. Performed analyses revealed that heat transfer in the skin subjected to high heat flux is independent of the blood vessel structure.

Modelling and testing the x-ray performance of CCD and CMOS APS detectors using numerical finite element simulations

NASA Astrophysics Data System (ADS)

Weatherill, Daniel P.; Stefanov, Konstantin D.; Greig, Thomas A.; Holland, Andrew D.

2014-07-01

Pixellated monolithic silicon detectors operated in a photon-counting regime are useful in spectroscopic imaging applications. Since a high energy incident photon may produce many excess free carriers upon absorption, both energy and spatial information can be recovered by resolving each interaction event. The performance of these devices in terms of both the energy and spatial resolution is in large part determined by the amount of diffusion which occurs during the collection of the charge cloud by the pixels. Past efforts to predict the X-ray performance of imaging sensors have used either analytical solutions to the diffusion equation or simplified monte carlo electron transport models. These methods are computationally attractive and highly useful but may be complemented using more physically detailed models based on TCAD simulations of the devices. Here we present initial results from a model which employs a full transient numerical solution of the classical semiconductor equations to model charge collection in device pixels under stimulation from initially Gaussian photogenerated charge clouds, using commercial TCAD software. Realistic device geometries and doping are included. By mapping the pixel response to different initial interaction positions and charge cloud sizes, the charge splitting behaviour of the model sensor under various illuminations and operating conditions is investigated. Experimental validation of the model is presented from an e2v CCD30-11 device under varying substrate bias, illuminated using an Fe-55 source.

Backtracking dynamics of RNA polymerase: pausing and error correction.

PubMed

Sahoo, Mamata; Klumpp, Stefan

2013-09-18

Transcription by RNA polymerases is frequently interrupted by pauses. One mechanism of such pauses is backtracking, where the RNA polymerase translocates backward with respect to both the DNA template and the RNA transcript, without shortening the transcript. Backtracked RNA polymerases move in a diffusive fashion and can return to active transcription either by diffusive return to the position where backtracking was initiated or by cleaving the transcript. The latter process also provides a mechanism for proofreading. Here we present some exact results for a kinetic model of backtracking and analyse its impact on the speed and the accuracy of transcription. We show that proofreading through backtracking is different from the classical (Hopfield-Ninio) scheme of kinetic proofreading. Our analysis also suggests that, in addition to contributing to the accuracy of transcription, backtracking may have a second effect: it attenuates the slow down of transcription that arises as a side effect of discriminating between correct and incorrect nucleotides based on the stepping rates.

Backtracking dynamics of RNA polymerase: pausing and error correction

NASA Astrophysics Data System (ADS)

Sahoo, Mamata; Klumpp, Stefan

2013-09-01

Transcription by RNA polymerases is frequently interrupted by pauses. One mechanism of such pauses is backtracking, where the RNA polymerase translocates backward with respect to both the DNA template and the RNA transcript, without shortening the transcript. Backtracked RNA polymerases move in a diffusive fashion and can return to active transcription either by diffusive return to the position where backtracking was initiated or by cleaving the transcript. The latter process also provides a mechanism for proofreading. Here we present some exact results for a kinetic model of backtracking and analyse its impact on the speed and the accuracy of transcription. We show that proofreading through backtracking is different from the classical (Hopfield-Ninio) scheme of kinetic proofreading. Our analysis also suggests that, in addition to contributing to the accuracy of transcription, backtracking may have a second effect: it attenuates the slow down of transcription that arises as a side effect of discriminating between correct and incorrect nucleotides based on the stepping rates.

Ameba-like diffusion in two-dimensional polymer melts: how critical exponents determine the structural relaxation

NASA Astrophysics Data System (ADS)

Kreer, Torsten; Meyer, Hendrik; Baschnagel, Joerg

2008-03-01

By means of numerical investigations we demonstrate that the structural relaxation of linear polymers in two dimensional (space-filling) melts is characterized by ameba-like diffusion, where the chains relax via frictional dissipation at their interfacial contact lines. The perimeter length of the contact line determines a new length scale, which does not exist in three dimensions. We show how this length scale follows from the critical exponents, which hence characterize not only the static but also the dynamic properties of the melt. Our data is in agreement with recent theoretical predictions, concerning the time-dependence of single-monomer mean-square displacements and the scaling of concomitant relaxation times with the degree of polymerization. For the latter we demonstrate a density crossover-scaling as an additional test for ameba-like relaxation. We compare our results to the conceptually different Rouse model, which predicts numerically close exponents. Our data can clearly rule out the classical picture as the relevant relaxation mechanism in two-dimensional polymer melts.

Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations.

PubMed

Ollila, O H Samuli; Heikkinen, Harri A; Iwaï, Hideo

2018-06-14

Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the experimental data is often complicated, especially for molecules with anisotropic shape. Here, we apply classical molecular dynamics simulations to interpret the conformational fluctuations and rotational tumbling of proteins with arbitrarily anisotropic shape. The direct calculation of spin relaxation times from simulation data did not reproduce the experimental data. This was successfully corrected by scaling the overall rotational diffusion coefficients around the protein inertia axes with a constant factor. The achieved good agreement with experiments allowed the interpretation of the internal and overall dynamics of proteins with significantly anisotropic shape. The overall rotational diffusion was found to be Brownian, having only a short subdiffusive region below 0.12 ns. The presented methodology can be applied to interpret rotational dynamics and conformation fluctuations of proteins with arbitrary anisotropic shape. However, a water model with more realistic dynamical properties is probably required for intrinsically disordered proteins.

Accelerated and Airy-Bloch oscillations

NASA Astrophysics Data System (ADS)

Longhi, Stefano

2016-09-01

A quantum particle subjected to a constant force undergoes an accelerated motion following a parabolic path, which differs from the classical motion just because of wave packet spreading (quantum diffusion). However, when a periodic potential is added (such as in a crystal) the particle undergoes Bragg scattering and an oscillatory (rather than accelerated) motion is found, corresponding to the famous Bloch oscillations (BOs). Here, we introduce an exactly-solvable quantum Hamiltonian model, corresponding to a generalized Wannier-Stark Hamiltonian Ĥ, in which a quantum particle shows an intermediate dynamical behavior, namely an oscillatory motion superimposed to an accelerated one. Such a novel dynamical behavior is referred to as accelerated BOs. Analytical expressions of the spectrum, improper eigenfunctions and propagator of the generalized Wannier-Stark Hamiltonian Ĥ are derived. Finally, it is shown that acceleration and quantum diffusion in the generalized Wannier-Stark Hamiltonian are prevented for Airy wave packets, which undergo a periodic breathing dynamics that can be referred to as Airy-Bloch oscillations.

On the Small Mass Limit of Quantum Brownian Motion with Inhomogeneous Damping and Diffusion

NASA Astrophysics Data System (ADS)

Lim, Soon Hoe; Wehr, Jan; Lampo, Aniello; García-March, Miguel Ángel; Lewenstein, Maciej

2018-01-01

We study the small mass limit (or: the Smoluchowski-Kramers limit) of a class of quantum Brownian motions with inhomogeneous damping and diffusion. For Ohmic bath spectral density with a Lorentz-Drude cutoff, we derive the Heisenberg-Langevin equations for the particle's observables using a quantum stochastic calculus approach. We set the mass of the particle to equal m = m0 ɛ , the reduced Planck constant to equal \\hbar = ɛ and the cutoff frequency to equal Λ = E_{Λ}/ɛ , where m_0 and E_{Λ} are positive constants, so that the particle's de Broglie wavelength and the largest energy scale of the bath are fixed as ɛ → 0. We study the limit as ɛ → 0 of the rescaled model and derive a limiting equation for the (slow) particle's position variable. We find that the limiting equation contains several drift correction terms, the quantum noise-induced drifts, including terms of purely quantum nature, with no classical counterparts.

Native oxide formation on pentagonal copper nanowires: A TEM study

NASA Astrophysics Data System (ADS)

Hajimammadov, Rashad; Mohl, Melinda; Kordas, Krisztian

2018-06-01

Hydrothermally synthesized copper nanowires were allowed to oxidize in air at room temperature and 30% constant humidity for the period of 22 days. The growth of native oxide layer was followed up by high-resolution transmission electron microscopy and diffraction to reveal and understand the kinetics of the oxidation process. Copper oxides appear in the form of differently oriented crystalline phases around the metallic core as a shell-like layer (Cu2O) and as nanoscopic islands (CuO) on the top of that. Time dependent oxide thickness data suggests that oxidation follows the field-assisted growth model at the beginning of the process, as practically immediately an oxide layer of ∼2.8 nm thickness develops on the surface. However, after this initial rapid growth, the local field attenuates and the classical parabolic diffusion limited growth plays the main role in the oxidation. Because of the single crystal facets on the side surface of penta-twinned Cu nanowires, the oxidation rate in the diffusion limited regime is lower than in polycrystalline films.

Multiscale framework for predicting the coupling between deformation and fluid diffusion in porous rocks

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

Andrade, José E; Rudnicki, John W

2012-12-14

In this project, a predictive multiscale framework will be developed to simulate the strong coupling between solid deformations and fluid diffusion in porous rocks. We intend to improve macroscale modeling by incorporating fundamental physical modeling at the microscale in a computationally efficient way. This is an essential step toward further developments in multiphysics modeling, linking hydraulic, thermal, chemical, and geomechanical processes. This research will focus on areas where severe deformations are observed, such as deformation bands, where classical phenomenology breaks down. Multiscale geometric complexities and key geomechanical and hydraulic attributes of deformation bands (e.g., grain sliding and crushing, and poremore » collapse, causing interstitial fluid expulsion under saturated conditions), can significantly affect the constitutive response of the skeleton and the intrinsic permeability. Discrete mechanics (DEM) and the lattice Boltzmann method (LBM) will be used to probe the microstructure---under the current state---to extract the evolution of macroscopic constitutive parameters and the permeability tensor. These evolving macroscopic constitutive parameters are then directly used in continuum scale predictions using the finite element method (FEM) accounting for the coupled solid deformation and fluid diffusion. A particularly valuable aspect of this research is the thorough quantitative verification and validation program at different scales. The multiscale homogenization framework will be validated using X-ray computed tomography and 3D digital image correlation in situ at the Advanced Photon Source in Argonne National Laboratories. Also, the hierarchical computations at the specimen level will be validated using the aforementioned techniques in samples of sandstone undergoing deformation bands.« less

White matter pathology in ALS and lower motor neuron ALS variants: a diffusion tensor imaging study using tract-based spatial statistics.

PubMed

Prudlo, Johannes; Bißbort, Charlotte; Glass, Aenne; Grossmann, Annette; Hauenstein, Karlheinz; Benecke, Reiner; Teipel, Stefan J

2012-09-01

The aim of this work was to investigate white-matter microstructural changes within and outside the corticospinal tract in classical amyotrophic lateral sclerosis (ALS) and in lower motor neuron (LMN) ALS variants by means of diffusion tensor imaging (DTI). We investigated 22 ALS patients and 21 age-matched controls utilizing a whole-brain approach with a 1.5-T scanner for DTI. The patient group was comprised of 15 classical ALS- and seven LMN ALS-variant patients (progressive muscular atrophy, flail arm and flail leg syndrome). Disease severity was measured by the revised version of the functional rating scale. White matter fractional anisotropy (FA) was assessed using tract-based spatial statistics (TBSS) and a region of interest (ROI) approach. We found significant FA reductions in motor and extra-motor cerebral fiber tracts in classical ALS and in the LMN ALS-variant patients compared to controls. The voxel-based TBSS results were confirmed by the ROI findings. The white matter damage correlated with the disease severity in the patient group and was found in a similar distribution, but to a lesser extent, among the LMN ALS-variant subgroup. ALS and LMN ALS variants are multisystem degenerations. DTI shows the potential to determine an earlier diagnosis, particularly in LMN ALS variants. The statistically identical findings of white matter lesions in classical ALS and LMN variants as ascertained by DTI further underline that these variants should be regarded as part of the ALS spectrum.

Stochastic inflation in phase space: is slow roll a stochastic attractor?

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

Grain, Julien; Vennin, Vincent, E-mail: julien.grain@ias.u-psud.fr, E-mail: vincent.vennin@port.ac.uk

An appealing feature of inflationary cosmology is the presence of a phase-space attractor, ''slow roll'', which washes out the dependence on initial field velocities. We investigate the robustness of this property under backreaction from quantum fluctuations using the stochastic inflation formalism in the phase-space approach. A Hamiltonian formulation of stochastic inflation is presented, where it is shown that the coarse-graining procedure—where wavelengths smaller than the Hubble radius are integrated out—preserves the canonical structure of free fields. This means that different sets of canonical variables give rise to the same probability distribution which clarifies the literature with respect to this issue.more » The role played by the quantum-to-classical transition is also analysed and is shown to constrain the coarse-graining scale. In the case of free fields, we find that quantum diffusion is aligned in phase space with the slow-roll direction. This implies that the classical slow-roll attractor is immune to stochastic effects and thus generalises to a stochastic attractor regardless of initial conditions, with a relaxation time at least as short as in the classical system. For non-test fields or for test fields with non-linear self interactions however, quantum diffusion and the classical slow-roll flow are misaligned. We derive a condition on the coarse-graining scale so that observational corrections from this misalignment are negligible at leading order in slow roll.« less

FAST TRACK COMMUNICATION: Quantum anomalies and linear response theory

NASA Astrophysics Data System (ADS)

Sela, Itamar; Aisenberg, James; Kottos, Tsampikos; Cohen, Doron

2010-08-01

The analysis of diffusive energy spreading in quantized chaotic driven systems leads to a universal paradigm for the emergence of a quantum anomaly. In the classical approximation, a driven chaotic system exhibits stochastic-like diffusion in energy space with a coefficient D that is proportional to the intensity ɛ2 of the driving. In the corresponding quantized problem the coherent transitions are characterized by a generalized Wigner time tɛ, and a self-generated (intrinsic) dephasing process leads to nonlinear dependence of D on ɛ2.

Inter-cusp Ion and Electron Transport in a Nstar-derivative Ion Thruster

NASA Technical Reports Server (NTRS)

Foster, John E.

2001-01-01

Diffusion of electrons and ions to anode surfaces between the magnetic cusps of a NASA Solar Electric Propulsion Technology Application Readiness ion thruster has been characterized. Ion flux measurements were made at the anode and at the screen grid electrode. The measurements indicated that the average ion current density at the anode and at the screen grid were approximately equal. Additionally, it was found that the electron flux to the anode between cusps is best described by the classical cross-field diffusion coefficient.

Ion and Electron Transport in an Nstar-derivative Ion Thruster. Revised

NASA Technical Reports Server (NTRS)

Foster, John E.

2001-01-01

Diffusion of electrons and ions to anode surfaces between the magnetic cusps of a NASA Solar Electric Propulsion Technology Application Readiness ion thruster has been characterized. Ion flux measurements were made at the anode and at the screen grid electrode. The measurements indicated that the average ion current density at the anode and at the screen grid were approximately equal. Additionally, it was found that the electron flux to the anode between cusps is best described by the classical cross-field diffusion coefficient.

Investigation of the expansion rate scaling of plasmas in the Electron Diffusion Gauge experiment

NASA Astrophysics Data System (ADS)

Morrison, Kyle A.; Davidson, Ronald C.; Paul, Stephen F.; Jenkins, Thomas G.

2002-01-01

The expansion of the Electron Diffusion Gauge (EDG) pure electron plasma due to collisions with background neutral gas atoms is characterized by the pressure and magnetic field scaling of the profile expansion rate (d/dt). Data obtained at higher background gas pressures [1] than previously studied [2] is presented. The measured expansion rate in the higher pressure regime is found to be in good agreement with the classical estimate of the expansion rate [3].

On asymptotic behavior and energy distribution for some one-dimensional non-parabolic diffusion problems

NASA Astrophysics Data System (ADS)

Kim, Seonghak; Yan, Baisheng

2018-06-01

We study some non-parabolic diffusion problems in one space dimension, where the diffusion flux exhibits forward and backward nature of the Perona–Malik, Höllig or non-Fourier type. Classical weak solutions to such problems are constructed in a way to capture some expected and unexpected properties, including anomalous asymptotic behaviors and energy dissipation or allocation. Specific properties of solutions will depend on the type of the diffusion flux, but the primary method of our study relies on reformulating diffusion equations involved as an inhomogeneous partial differential inclusion and on constructing solutions from the differential inclusion by a combination of the convex integration and Baire’s category methods. In doing so, we introduce the appropriate notion of subsolutions of the partial differential inclusion and their transition gauge, which plays a pivotal role in dealing with some specific features of the constructed weak solutions.

Posterior reversible encephalopathy syndrome: a case of unusual diffusion-weighted MR images.

PubMed

Benziada-Boudour, A; Schmitt, E; Kremer, S; Foscolo, S; Rivière, A-S; Tisserand, M; Boudour, A; Bracard, S

2009-05-01

Posterior reversible encephalopathy (PRES) represents an uncommon entity related to multiple pathologies, the most common of which is hypertensive crisis. PRES is classically characterized as symmetrical parieto-occipital edema, but may affect other areas of the brain. Diffusion-weighted magnetic resonance imaging (DWI) is important for differentiating between vasogenic and cytotoxic edema. We present here the case of a 43-year-old woman, known to suffer from arterial hypertension and severe renal failure, who developed PRES with restricted apparent diffusion coefficients (ADC) in various cerebral areas, suggesting irreversible tissue damage. Nevertheless, follow-up cranial MRI revealed complete remission, indicating that restricted diffusion does not always lead to cell death in this pathology. The underlying pathophysiological mechanism is not well understood. Such reversibility of diffusion anomalies has already been reported with transient ischemia, vasospasm after subarachnoid hemorrhage and epilepsy but, to our knowledge, never before in PRES.

Overview of transport, fast particle and heating and current drive physics using tritium in JET plasmas

NASA Astrophysics Data System (ADS)

Stork, D.; Baranov, Yu.; Belo, P.; Bertalot, L.; Borba, D.; Brzozowski, J. H.; Challis, C. D.; Ciric, D.; Conroy, S.; de Baar, M.; de Vries, P.; Dumortier, P.; Garzotti, L.; Hawkes, N. C.; Hender, T. C.; Joffrin, E.; Jones, T. T. C.; Kiptily, V.; Lamalle, P.; Mailloux, J.; Mantsinen, M.; McDonald, D. C.; Nave, M. F. F.; Neu, R.; O'Mullane, M.; Ongena, J.; Pearce, R. J.; Popovichev, S.; Sharapov, S. E.; Stamp, M.; Stober, J.; Surrey, E.; Valovic, M.; Voitsekhovitch, I.; Weisen, H.; Whiteford, A. D.; Worth, L.; Yavorskij, V.; Zastrow, K.-D.; EFDA contributors, JET

2005-10-01

Results are presented from the JET Trace Tritium Experimental (TTE) campaign using minority tritium (T) plasmas (nT/nD < 3%). Thermal tritium particle transport coefficients (DT, vT) are found to exceed neo-classical values in all regimes, except in ELMy H-modes at high densities and in the region of internal transport barriers (ITBs) in reversed shear plasmas. In ELMy H-mode dimensionless parameter scans, at q95 ~ 2.8 and triangularity δ = 0.2, the T particle transport scales in a gyro-Bohm manner in the inner plasma (r/a < 0.4), whilst the outer plasma particle transport scaling is more Bohm-like. Dimensionless parameter scans show contrasting behaviour for the trace particle confinement (increases with collisionality, ν* and β) and bulk energy confinement (decreases with ν* and is independent of β). In an extended ELMy H-mode data set, with ρ*, ν*, β and q varied but with neo-classical tearing modes (NTMs) either absent or limited to weak, benign core modes (4/3 or above), the multiparameter fit to the normalized diffusion coefficient in the outer plasma (0.65 < r/a < 0.8) gives DT/Bphi ~ ρ*2.46ν*-0.23β-1.01q2.03. In hybrid scenarios (qmin ~ 1, low positive shear, no sawteeth), the T particle confinement is found to scale with increasing triangularity and plasma current. Comparing regimes (ELMy H-mode, ITB plasma and hybrid scenarios) in the outer plasma region, a correlation of high values of DT with high values of vT is seen. The normalized diffusion coefficients for the hybrid and ITB scenarios do not fit the scaling derived for ELMy H-modes. The normalized tritium diffusion scales with normalized poloidal Larmor radius (\\rho_{\\theta}^\\ast=q\\rho^{\\ast}) in a manner close to gyro-Bohm ({\\sim}\\rho_{\\theta}^{\\ast 3}) , with an added inverse β dependence. The effects of ELMs, sawteeth and NTMs on the T particle transport are described. Fast-ion confinement in current-hole (CH) plasmas was tested in TTE by tritium neutral beam injection into JET CH plasmas. γ-rays from the reactions of fusion alpha and beryllium impurities (9Be(α, nγ)12C) characterized the fast fusion-alpha population evolution. The γ-decay times are consistent with classical alpha plus parent fast triton slowing down times (τTs + ταs) for high plasma currents (Ip > 2 MA) and monotonic q-profiles. In CH discharges the γ-ray emission decay times are much lower than classical (τTs+ταs), indicating alpha confinement degradation, due to the orbit losses and particle orbit drift predicted by a 3-D Fokker-Planck numerical code and modelled using TRANSP.

Study on plasma sheath and plasma transport properties in the azimuthator

NASA Astrophysics Data System (ADS)

Zhenyu, WANG; Binhao, JIANG; N, A. STROKIN; A, N. STUPIN

2018-04-01

A physical model of transport in an azimuthator channel with the sheath effect resulting from the interaction between the plasma and insulation wall is established in this paper. Particle in cell simulation is carried out by the model and results show that, besides the transport due to classical and Bohm diffusions, the sheath effect can significantly influences the transport in the channel. As a result, the ion density is larger than the electron density at the exit of azimuthator, and the non-neutral plasma jet is divergent, which is unfavorable for mass separation. Then, in order to improve performance of the azimuthator, a cathode is designed to emit electrons. Experiment results have demonstrated that the auxiliary cathode can obviously compensate the space charge in the plasma.

Molecular finite-size effects in stochastic models of equilibrium chemical systems.

PubMed

Cianci, Claudia; Smith, Stephen; Grima, Ramon

2016-02-28

The reaction-diffusion master equation (RDME) is a standard modelling approach for understanding stochastic and spatial chemical kinetics. An inherent assumption is that molecules are point-like. Here, we introduce the excluded volume reaction-diffusion master equation (vRDME) which takes into account volume exclusion effects on stochastic kinetics due to a finite molecular radius. We obtain an exact closed form solution of the RDME and of the vRDME for a general chemical system in equilibrium conditions. The difference between the two solutions increases with the ratio of molecular diameter to the compartment length scale. We show that an increase in the fraction of excluded space can (i) lead to deviations from the classical inverse square root law for the noise-strength, (ii) flip the skewness of the probability distribution from right to left-skewed, (iii) shift the equilibrium of bimolecular reactions so that more product molecules are formed, and (iv) strongly modulate the Fano factors and coefficients of variation. These volume exclusion effects are found to be particularly pronounced for chemical species not involved in chemical conservation laws. Finally, we show that statistics obtained using the vRDME are in good agreement with those obtained from Brownian dynamics with excluded volume interactions.

Transport Mechanism of Guest Methane in Water-Filled Nanopores

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

Bui, Tai; Phan, Anh; Cole, David R.

We computed the transport of methane through 1 nm wide slit-shaped pores carved out of selected solid substrates using classical molecular dynamics simulations. The transport mechanism was elucidated via the implementation of the well-tempered metadynamics algorithm, which allowed for the quantification and visualization of the free energy landscape sampled by the guest molecule. Models for silica, magnesium oxide, alumina, muscovite, and calcite were used as solid substrates. Slit-shaped pores of width 1 nm were carved out of these materials and filled with liquid water. Methane was then inserted at low concentration. The results show that the diffusion of methane throughmore » the hydrated pores is strongly dependent on the solid substrate. While methane molecules diffuse isotropically along the directions parallel to the pore surfaces in most of the pores considered, anisotropic diffusion was observed in the hydrated calcite pore. The differences observed in the various pores are due to local molecular properties of confined water, including molecular structure and solvation free energy. The transport mechanism and the diffusion coefficients are dependent on the free energy barriers encountered by one methane molecule as it migrates from one preferential adsorption site to a neighboring one. It was found that the heterogeneous water distribution in different hydration layers and the low free energy pathways in the plane parallel to the pore surfaces yield the anisotropic diffusion of methane molecules in the hydrated calcite pore. Our observations contribute to an ongoing debate on the relation between local free energy profiles and diffusion coefficients and could have important practical consequences in various applications, ranging from the design of selective membranes for gas separations to the sustainable deployment of shale gas.« less

Transport Mechanism of Guest Methane in Water-Filled Nanopores

DOE PAGES

Bui, Tai; Phan, Anh; Cole, David R.; ...

2017-05-11

We computed the transport of methane through 1 nm wide slit-shaped pores carved out of selected solid substrates using classical molecular dynamics simulations. The transport mechanism was elucidated via the implementation of the well-tempered metadynamics algorithm, which allowed for the quantification and visualization of the free energy landscape sampled by the guest molecule. Models for silica, magnesium oxide, alumina, muscovite, and calcite were used as solid substrates. Slit-shaped pores of width 1 nm were carved out of these materials and filled with liquid water. Methane was then inserted at low concentration. The results show that the diffusion of methane throughmore » the hydrated pores is strongly dependent on the solid substrate. While methane molecules diffuse isotropically along the directions parallel to the pore surfaces in most of the pores considered, anisotropic diffusion was observed in the hydrated calcite pore. The differences observed in the various pores are due to local molecular properties of confined water, including molecular structure and solvation free energy. The transport mechanism and the diffusion coefficients are dependent on the free energy barriers encountered by one methane molecule as it migrates from one preferential adsorption site to a neighboring one. It was found that the heterogeneous water distribution in different hydration layers and the low free energy pathways in the plane parallel to the pore surfaces yield the anisotropic diffusion of methane molecules in the hydrated calcite pore. Our observations contribute to an ongoing debate on the relation between local free energy profiles and diffusion coefficients and could have important practical consequences in various applications, ranging from the design of selective membranes for gas separations to the sustainable deployment of shale gas.« less

Growth of bacteria in 3-d colonies

PubMed Central

Mugler, Andrew; Kim, Justin

2017-01-01

The dynamics of growth of bacterial populations has been extensively studied for planktonic cells in well-agitated liquid culture, in which all cells have equal access to nutrients. In the real world, bacteria are more likely to live in physically structured habitats as colonies, within which individual cells vary in their access to nutrients. The dynamics of bacterial growth in such conditions is poorly understood, and, unlike that for liquid culture, there is not a standard broadly used mathematical model for bacterial populations growing in colonies in three dimensions (3-d). By extending the classic Monod model of resource-limited population growth to allow for spatial heterogeneity in the bacterial access to nutrients, we develop a 3-d model of colonies, in which bacteria consume diffusing nutrients in their vicinity. By following the changes in density of E. coli in liquid and embedded in glucose-limited soft agar, we evaluate the fit of this model to experimental data. The model accounts for the experimentally observed presence of a sub-exponential, diffusion-limited growth regime in colonies, which is absent in liquid cultures. The model predicts and our experiments confirm that, as a consequence of inter-colony competition for the diffusing nutrients and of cell death, there is a non-monotonic relationship between total number of colonies within the habitat and the total number of individual cells in all of these colonies. This combined theoretical-experimental study reveals that, within 3-d colonies, E. coli cells are loosely packed, and colonies produce about 2.5 times as many cells as the liquid culture from the same amount of nutrients. We verify that this is because cells in liquid culture are larger than in colonies. Our model provides a baseline description of bacterial growth in 3-d, deviations from which can be used to identify phenotypic heterogeneities and inter-cellular interactions that further contribute to the structure of bacterial communities. PMID:28749935

Coronal ``Wave'': Magnetic Footprint of a Coronal Mass Ejection?

NASA Astrophysics Data System (ADS)

Attrill, Gemma D. R.; Harra, Louise K.; van Driel-Gesztelyi, Lidia; Démoulin, Pascal

2007-02-01

We investigate the properties of two ``classical'' EUV Imaging Telescope (EIT) coronal waves. The two source regions of the associated coronal mass ejections (CMEs) possess opposite helicities, and the coronal waves display rotations in opposite senses. We observe deep core dimmings near the flare site and also widespread diffuse dimming, accompanying the expansion of the EIT wave. We also report a new property of these EIT waves, namely, that they display dual brightenings: persistent ones at the outermost edge of the core dimming regions and simultaneously diffuse brightenings constituting the leading edge of the coronal wave, surrounding the expanding diffuse dimmings. We show that such behavior is consistent with a diffuse EIT wave being the magnetic footprint of a CME. We propose a new mechanism where driven magnetic reconnections between the skirt of the expanding CME magnetic field and quiet-Sun magnetic loops generate the observed bright diffuse front. The dual brightenings and the widespread diffuse dimming are identified as innate characteristics of this process.

MULTI-WAVELENGTH OBSERVATIONS OF THE SPATIO-TEMPORAL EVOLUTION OF SOLAR FLARES WITH AIA/SDO. I. UNIVERSAL SCALING LAWS OF SPACE AND TIME PARAMETERS

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

Aschwanden, Markus J.; Zhang, Jie; Liu, Kai, E-mail: aschwanden@lmsal.com, E-mail: jzhang7@gmu.edu

2013-09-20

We extend a previous statistical solar flare study of 155 GOES M- and X-class flares observed with AIA/SDO to all seven coronal wavelengths (94, 131, 171, 193, 211, 304, and 335 Å) to test the wavelength dependence of scaling laws and statistical distributions. Except for the 171 and 193 Å wavelengths, which are affected by EUV dimming caused by coronal mass ejections (CMEs), we find near-identical size distributions of geometric (lengths L, flare areas A, volumes V, and fractal dimension D{sub 2}), temporal (flare durations T), and spatio-temporal parameters (diffusion coefficient κ, spreading exponent β, and maximum expansion velocities v{submore » max}) in different wavelengths, which are consistent with the universal predictions of the fractal-diffusive avalanche model of a slowly driven, self-organized criticality (FD-SOC) system, i.e., N(L)∝L {sup –3}, N(A)∝A {sup –2}, N(V)∝V {sup –5/3}, N(T)∝T {sup –2}, and D{sub 2} = 3/2, for a Euclidean dimension d = 3. Empirically, we find also a new strong correlation κ∝L {sup 0.94±0.01} and the three-parameter scaling law L∝κ T {sup 0.1}, which is more consistent with the logistic-growth model than with classical diffusion. The findings suggest long-range correlation lengths in the FD-SOC system that operate in the vicinity of a critical state, which could be used for predictions of individual extreme events. We find also that eruptive flares (with accompanying CMEs) have larger volumes V, longer flare durations T, higher EUV and soft X-ray fluxes, and somewhat larger diffusion coefficients κ than confined flares (without CMEs)« less

Laminar Diffusion Flame Studies (Ground- and Space-Based Studies)

NASA Technical Reports Server (NTRS)

Dai, Z.; El-Leathy, A. M.; Lin, K.-C.; Sunderland, P. B.; Xu, F.; Faeth, G. M.; Urban, D. L. (Technical Monitor); Yuan, Z.-G. (Technical Monitor)

2000-01-01

Laminar diffusion flames are of interest because they provide model flame systems that are far more tractable for analysis and experiments than more practical turbulent diffusion flames. Certainly, understanding flame processes within laminar diffusion flames must precede understanding these processes in more complex turbulent diffusion flames. In addition, many properties of laminar diffusion flames are directly relevant to turbulent diffusion flames using laminar flamelet concepts. Laminar jet diffusion flame shapes (luminous flame boundaries) have been of particular interest since the classical study of Burke and Schumann because they are a simple nonintrusive measurement that is convenient for evaluating flame structure predictions. Thus, consideration of laminar flame shapes is undertaken in the following, emphasizing conditions where effects of gravity are small, due to the importance of such conditions to practical applications. Another class of interesting properties of laminar diffusion flames are their laminar soot and smoke point properties (i.e., the flame length, fuel flow rate, characteristic residence time, etc., at the onset of soot appearance in the flame (the soot point) and the onset of soot emissions from the flame (the smoke point)). These are useful observable soot properties of nonpremixed flames because they provide a convenient means to rate several aspects of flame sooting properties: the relative propensity of various fuels to produce soot in flames; the relative effects of fuel structure, fuel dilution, flame temperature and ambient pressure on the soot appearance and emission properties of flames; the relative levels of continuum radiation from soot in flames; and effects of the intrusion of gravity (or buoyant motion) on emissions of soot from flames. An important motivation to define conditions for soot emissions is that observations of laminar jet diffusion flames in critical environments, e.g., space shuttle and space station facilities, cannot involve soot emitting flames in order to ensure that test chamber windows used for experimental observations are not blocked by soot deposits, thereby compromising unusually valuable experimental results. Another important motivation to define conditions where soot is present in diffusion flames is that flame chemistry, transport and radiation properties are vastly simplified when soot is absent, making such flames far more tractable for detailed numerical simulations than corresponding soot-containing flames. Motivated by these observations, the objectives of this phase of the investigation were as follows: (1) Observe flame-sheet shapes (the location of the reaction zone near phi=1) of nonluminous (soot free) laminar jet diffusion flames in both still and coflowing air and use these results to develop simplified models of flame-sheet shapes for these conditions; (2) Observe luminous flame boundaries of luminous (soot-containing) laminar jet diffusion flames in both still and coflowing air and use these results to develop simplified models of luminous flame boundaries for these conditions. In order to fix ideas here, maximum luminous flame boundaries at the laminar smoke point conditions were sought, i.e., luminous flame boundaries at the laminar smoke point; (3) Observe effects of coflow on laminar soot- and smoke-point conditions because coflow has been proposed as a means to control soot emissions and minimize the presence of soot in diffusion flames.

Congested Aggregation via Newtonian Interaction

NASA Astrophysics Data System (ADS)

Craig, Katy; Kim, Inwon; Yao, Yao

2018-01-01

We consider a congested aggregation model that describes the evolution of a density through the competing effects of nonlocal Newtonian attraction and a hard height constraint. This provides a counterpoint to existing literature on repulsive-attractive nonlocal interaction models, where the repulsive effects instead arise from an interaction kernel or the addition of diffusion. We formulate our model as the Wasserstein gradient flow of an interaction energy, with a penalization to enforce the constraint on the height of the density. From this perspective, the problem can be seen as a singular limit of the Keller-Segel equation with degenerate diffusion. Two key properties distinguish our problem from previous work on height constrained equations: nonconvexity of the interaction kernel (which places the model outside the scope of classical gradient flow theory) and nonlocal dependence of the velocity field on the density (which causes the problem to lack a comparison principle). To overcome these obstacles, we combine recent results on gradient flows of nonconvex energies with viscosity solution theory. We characterize the dynamics of patch solutions in terms of a Hele-Shaw type free boundary problem and, using this characterization, show that in two dimensions patch solutions converge to a characteristic function of a disk in the long-time limit, with an explicit rate on the decay of the energy. We believe that a key contribution of the present work is our blended approach, combining energy methods with viscosity solution theory.

Diffusion of Sticky Nanoparticles in a Polymer Melt: Crossover from Suppressed to Enhanced Transport

DOE PAGES

Carroll, Bobby; Bocharova, Vera; Carrillo, Jan-Michael Y.; ...

2018-03-09

The self-diffusion of a single large particle in a fluid is usually described by the classic Stokes–Einstein (SE) hydrodynamic relation. However, there are many fluids where the SE prediction for nanoparticles diffusion fails. These systems include diffusion of nanoparticles in porous media, in entangled and unentangled polymer melts and solutions, and protein diffusion in biological environments. A fundamental understanding of the microscopic parameters that govern nanoparticle diffusion is relevant to a wide range of applications. Here in this work, we present experimental measurements of the tracer diffusion coefficient of small and large nanoparticles that experience strong attractions with unentangled andmore » entangled polymer melt matrices. For the small nanoparticle system, a crossover from suppressed to enhanced diffusion is observed with increasing polymer molecular weight. We interpret these observations based on our theoretical and simulation insights of the preceding article (paper 1) as a result of a crossover from an effective hydrodynamic core–shell to a nonhydrodynamic vehicle mechanism of transport, with the latter strongly dependent on polymer–nanoparticle desorption time. In conclusion, a general zeroth-order qualitative picture for small sticky nanoparticle diffusion in polymer melts is proposed.« less

Diffusion of Sticky Nanoparticles in a Polymer Melt: Crossover from Suppressed to Enhanced Transport

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

Carroll, Bobby; Bocharova, Vera; Carrillo, Jan-Michael Y.

The self-diffusion of a single large particle in a fluid is usually described by the classic Stokes–Einstein (SE) hydrodynamic relation. However, there are many fluids where the SE prediction for nanoparticles diffusion fails. These systems include diffusion of nanoparticles in porous media, in entangled and unentangled polymer melts and solutions, and protein diffusion in biological environments. A fundamental understanding of the microscopic parameters that govern nanoparticle diffusion is relevant to a wide range of applications. Here in this work, we present experimental measurements of the tracer diffusion coefficient of small and large nanoparticles that experience strong attractions with unentangled andmore » entangled polymer melt matrices. For the small nanoparticle system, a crossover from suppressed to enhanced diffusion is observed with increasing polymer molecular weight. We interpret these observations based on our theoretical and simulation insights of the preceding article (paper 1) as a result of a crossover from an effective hydrodynamic core–shell to a nonhydrodynamic vehicle mechanism of transport, with the latter strongly dependent on polymer–nanoparticle desorption time. In conclusion, a general zeroth-order qualitative picture for small sticky nanoparticle diffusion in polymer melts is proposed.« less

Phase-field model for isothermal phase transitions in binary alloys

NASA Technical Reports Server (NTRS)

Wheeler, A. A.; Boettinger, W. J.; Mcfadden, G. B.

1992-01-01

A new phase field model is described which models isothermal phase transitions between ideal binary alloy solution phases. Equations are developed for the temporal and spatial variation of the phase field, which describes the identity of the phase, and of the composition. An asymptotic analysis, as the gradient energy coefficient of the phase field becomes small, was conducted. From the analysis, it is shown that the model recovers classical sharp interface models of this situation when the interfacial layers are thin, and they show how to relate the parameters appearing in the phase field model to material and growth parameters in real systems. Further, three stages of temporal evolution are identified: the first corresponding to interfacial genesis which occurs very rapidly; the second to interfacial motion controlled by the local energy difference across the interface and diffusion; the last taking place on a long time scale in which curvature effects are important and which correspond to Ostwald ripening. The results of the numerical calculations are presented.

Liquid li structure and dynamics: A comparison between OFDFT and second nearest-neighbor embedded-atom method

DOE PAGES

Chen, Mohan; Vella, Joseph R.; Panagiotopoulos, Athanassios Z.; ...

2015-04-08

The structure and dynamics of liquid lithium are studied using two simulation methods: orbital-free (OF) first-principles molecular dynamics (MD), which employs OF density functional theory (DFT), and classical MD utilizing a second nearest-neighbor embedded-atom method potential. The properties we studied include the dynamic structure factor, the self-diffusion coefficient, the dispersion relation, the viscosity, and the bond angle distribution function. Our simulation results were compared to available experimental data when possible. Each method has distinct advantages and disadvantages. For example, OFDFT gives better agreement with experimental dynamic structure factors, yet is more computationally demanding than classical simulations. Classical simulations can accessmore » a broader temperature range and longer time scales. The combination of first-principles and classical simulations is a powerful tool for studying properties of liquid lithium.« less

Extending Bell's beables to encompass dissipation, decoherence, and the quantum-to-classical transition through quantum trajectories

NASA Astrophysics Data System (ADS)

Lorenzen, F.; de Ponte, M. A.; Moussa, M. H. Y.

2009-09-01

In this paper, employing the Itô stochastic Schrödinger equation, we extend Bell’s beable interpretation of quantum mechanics to encompass dissipation, decoherence, and the quantum-to-classical transition through quantum trajectories. For a particular choice of the source of stochasticity, the one leading to a dissipative Lindblad-type correction to the Hamiltonian dynamics, we find that the diffusive terms in Nelsons stochastic trajectories are naturally incorporated into Bohm’s causal dynamics, yielding a unified Bohm-Nelson theory. In particular, by analyzing the interference between quantum trajectories, we clearly identify the decoherence time, as estimated from the quantum formalism. We also observe the quantum-to-classical transition in the convergence of the infinite ensemble of quantum trajectories to their classical counterparts. Finally, we show that our extended beables circumvent the problems in Bohm’s causal dynamics regarding stationary states in quantum mechanics.

Classical electromagnetic fields from quantum sources in heavy-ion collisions

NASA Astrophysics Data System (ADS)

Holliday, Robert; McCarty, Ryan; Peroutka, Balthazar; Tuchin, Kirill

2017-01-01

Electromagnetic fields are generated in high energy nuclear collisions by spectator valence protons. These fields are traditionally computed by integrating the Maxwell equations with point sources. One might expect that such an approach is valid at distances much larger than the proton size and thus such a classical approach should work well for almost the entire interaction region in the case of heavy nuclei. We argue that, in fact, the contrary is true: due to the quantum diffusion of the proton wave function, the classical approximation breaks down at distances of the order of the system size. We compute the electromagnetic field created by a charged particle described initially as a Gaussian wave packet of width 1 fm and evolving in vacuum according to the Klein-Gordon equation. We completely neglect the medium effects. We show that the dynamics, magnitude and even sign of the electromagnetic field created by classical and quantum sources are different.

Transport of carbon ion test particles and hydrogen recycling in the plasma of the Columbia tokamak HBT'' (High Beta Tokamak)

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

Wang, Jian-Hua.

Carbon impurity ion transport is studied in the Columbia High Beta Tokamak (HBT), using a carbon tipped probe which is inserted into the plasma (n{sub e} {approx} 1 {minus} 5 {times} 10{sup 14} (cm{sup {minus}3}), T{sub e} {approx} 4 {minus} 10 (eV), B{sub t} {approx} 0.2 {minus} 0.4(T)). Carbon impurity light, mainly the strong lines of C{sub II}(4267A, emitted by the C{sup +} ions) and C{sub III} (4647A, emitted by the C{sup ++} ions), is formed by the ablation or sputtering of plasma ions and by the discharge of the carbon probe itself. The diffusion transport of the carbon ionsmore » is modeled by measuring the space-and-time dependent spectral light emission of the carbon ions with a collimated optical beam and photomultiplier. The point of emission can be observed in such a way as to sample regions along and transverse to the toroidal magnetic field. The carbon ion diffusion coefficients are obtained by fitting the data to a diffusion transport model. It is found that the diffusion of the carbon ions is classical'' and is controlled by the high collisionality of the HBT plasma; the diffusion is a two-dimensional problem and the expected dependence on the charge of the impurity ion is observed. The measurement of the spatial distribution of the H{sub {alpha}} emissivity was obtained by inverting the light signals from a 4-channel polychromator, the data were used to calculate the minor-radial influx, the density, and the recycling time of neutral hydrogen atoms or molecules. The calculation shows that the particle recycling time {tau}{sub p} is comparable with the plasma energy confinement time {tau}{sub E}; therefore, the recycling of the hot plasma ions with the cold neutrals from the walls is one of the main mechanisms for loss of plasma energy.« less

Computational approach to integrate 3D X-ray microtomography and NMR data.

PubMed

Lucas-Oliveira, Everton; Araujo-Ferreira, Arthur G; Trevizan, Willian A; Fortulan, Carlos A; Bonagamba, Tito J

2018-05-04

Nowadays, most of the efforts in NMR applied to porous media are dedicated to studying the molecular fluid dynamics within and among the pores. These analyses have a higher complexity due to morphology and chemical composition of rocks, besides dynamic effects as restricted diffusion, diffusional coupling, and exchange processes. Since the translational nuclear spin diffusion in a confined geometry (e.g. pores and fractures) requires specific boundary conditions, the theoretical solutions are restricted to some special problems and, in many cases, computational methods are required. The Random Walk Method is a classic way to simulate self-diffusion along a Digital Porous Medium. Bergman model considers the magnetic relaxation process of the fluid molecules by including a probability rate of magnetization survival under surface interactions. Here we propose a statistical approach to correlate surface magnetic relaxivity with the computational method applied to the NMR relaxation in order to elucidate the relationship between simulated relaxation time and pore size of the Digital Porous Medium. The proposed computational method simulates one- and two-dimensional NMR techniques reproducing, for example, longitudinal and transverse relaxation times (T 1 and T 2 , respectively), diffusion coefficients (D), as well as their correlations. For a good approximation between the numerical and experimental results, it is necessary to preserve the complexity of translational diffusion through the microstructures in the digital rocks. Therefore, we use Digital Porous Media obtained by 3D X-ray microtomography. To validate the method, relaxation times of ideal spherical pores were obtained and compared with the previous determinations by the Brownstein-Tarr model, as well as the computational approach proposed by Bergman. Furthermore, simulated and experimental results of synthetic porous media are compared. These results make evident the potential of computational physics in the analysis of the NMR data for complex porous materials. Copyright © 2018 Elsevier Inc. All rights reserved.

Correction of terrestrial LiDAR intensity channel using Oren-Nayar reflectance model: An application to lithological differentiation

NASA Astrophysics Data System (ADS)

Carrea, Dario; Abellan, Antonio; Humair, Florian; Matasci, Battista; Derron, Marc-Henri; Jaboyedoff, Michel

2016-03-01

Ground-based LiDAR has been traditionally used for surveying purposes via 3D point clouds. In addition to XYZ coordinates, an intensity value is also recorded by LiDAR devices. The intensity of the backscattered signal can be a significant source of information for various applications in geosciences. Previous attempts to account for the scattering of the laser signal are usually modelled using a perfect diffuse reflection. Nevertheless, experience on natural outcrops shows that rock surfaces do not behave as perfect diffuse reflectors. The geometry (or relief) of the scanned surfaces plays a major role in the recorded intensity values. Our study proposes a new terrestrial LiDAR intensity correction, which takes into consideration the range, the incidence angle and the geometry of the scanned surfaces. The proposed correction equation combines the classical radar equation for LiDAR with the bidirectional reflectance distribution function of the Oren-Nayar model. It is based on the idea that the surface geometry can be modelled by a relief of multiple micro-facets. This model is constrained by only one tuning parameter: the standard deviation of the slope angle distribution (σslope) of micro-facets. Firstly, a series of tests have been carried out in laboratory conditions on a 2 m2 board covered by black/white matte paper (perfect diffuse reflector) and scanned at different ranges and incidence angles. Secondly, other tests were carried out on rock blocks of different lithologies and surface conditions. Those tests demonstrated that the non-perfect diffuse reflectance of rock surfaces can be practically handled by the proposed correction method. Finally, the intensity correction method was applied to a real case study, with two scans of the carbonate rock outcrop of the Dents-du-Midi (Swiss Alps), to improve the lithological identification for geological mapping purposes. After correction, the intensity values are proportional to the intrinsic material reflectance and are independent from range, incidence angle and scanned surface geometry. The corrected intensity values significantly improve the material differentiation.

Group-based strategy diffusion in multiplex networks with weighted values

NASA Astrophysics Data System (ADS)

Yu, Jianyong; Jiang, J. C.; Xiang, Leijun

2017-03-01

The information diffusion of multiplex social networks has received increasing interests in recent years. Actually, the multiplex networks are made of many communities, and it should be gotten more attention for the influences of community level diffusion, besides of individual level interactions. In view of this, this work explores strategy interactions and diffusion processes in multiplex networks with weighted values from a new perspective. Two different groups consisting of some agents with different influential strength are firstly built in each layer network, the authority and non-authority groups. The strategy interactions between different groups in intralayer and interlayer networks are performed to explore community level diffusion, by playing two classical strategy games, Prisoner's Dilemma and Snowdrift Game. The impact forces from the different groups and the reactive forces from individual agents are simultaneously taken into account in intralayer and interlayer interactions. This paper reveals and explains the evolutions of cooperation diffusion and the influences of interlayer interaction tight degrees in multiplex networks with weighted values. Some thresholds of critical parameters of interaction degrees and games parameters settings are also discussed in group-based strategy diffusion.

Double-diffusive layers in the Adriatic Sea

NASA Astrophysics Data System (ADS)

Carniel, Sandro; Sclavo, Mauro; Kantha, Lakshmi; Prandke, Hartmut

2008-01-01

A microstructure profiler was deployed to make turbulence measurements in the upper layers of the southern Adriatic Sea in the Mediterranean during the Naval Research Laboratory (NRL) DART06A (Dynamics of the Adriatic in Real Time) winter cruise in March 2006. Measurements in the Po river plume along the Italian coast near the Gargano promontory displayed classic double-diffusive layers and staircase structures resulting from the relatively colder and fresher wintertime Po river outflow water masses overlying warmer and more saline water masses from the Adriatic Sea. We report here on the water mass and turbulence structure measurements made both in the double-diffusive interfaces and the adjoining mixed layers in the water columns undergoing double-diffusive convection (DDC). This dataset augments the relatively sparse observations available hitherto on the diffusive layer type of DDC. Measured turbulence diffusivities are consistent with those from earlier theoretical and experimental formulations, suggesting that the wintertime Po river plume is a convenient and easily accessible place to study double diffusive convective processes of importance to mixing in the interior of many regions of the global oceans.

Superdiffusion revisited in view of collisionless reconnection

NASA Astrophysics Data System (ADS)

Treumann, R. A.; Baumjohann, W.

2014-06-01

The concept of diffusion in collisionless space plasmas like those near the magnetopause and in the geomagnetic tail during reconnection is reexamined making use of the division of particle orbits into waiting orbits and break-outs into ballistic motion lying at the bottom, for instance, of Lévy flights. The rms average displacement in this case increases with time, describing superdiffusion, though faster than classical, is still a weak process, being however strong enough to support fast reconnection. Referring to two kinds of numerical particle-in-cell simulations we determine the anomalous diffusion coefficient, the anomalous collision frequency on which the diffusion process is based, and construct a relation between the diffusion coefficients and the resistive scale. The anomalous collision frequency from electron pseudo-viscosity in reconnection turns out to be of the order of the lower-hybrid frequency with the latter providing a lower limit, thus making similar assumptions physically meaningful. Tentative though not completely justified use of the κ distribution yields κ ≈ 6 in the reconnection diffusion region and, for the anomalous diffusion coefficient, the order of several times Bohm diffusivity.

Analysis of single quantum-dot mobility inside 1D nanochannel devices

NASA Astrophysics Data System (ADS)

Hoang, H. T.; Segers-Nolten, I. M.; Tas, N. R.; van Honschoten, J. W.; Subramaniam, V.; Elwenspoek, M. C.

2011-07-01

We visualized individual quantum dots using a combination of a confining nanochannel and an ultra-sensitive microscope system, equipped with a high numerical aperture lens and a highly sensitive camera. The diffusion coefficients of the confined quantum dots were determined from the experimentally recorded trajectories according to the classical diffusion theory for Brownian motion in two dimensions. The calculated diffusion coefficients were three times smaller than those in bulk solution. These observations confirm and extend the results of Eichmann et al (2008 Langmuir 24 714-21) to smaller particle diameters and more narrow confinement. A detailed analysis shows that the observed reduction in mobility cannot be explained by conventional hydrodynamic theory.

Follicular patterned lesions of the thyroid gland: a practical algorithmic approach.

PubMed

Chetty, Runjan

2011-09-01

Follicular patterned lesions of the thyroid are problematic and interpretation is often subjective. While thyroid experts are comfortable with their own criteria and thresholds, those encountering these lesions sporadically have a degree of uncertainty with a proportion of cases. The purpose of this review is to highlight the importance of proper diligent sampling of an encapsulated thyroid lesion (in totality in many cases), examination for capsular and vascular invasion, and finally the assessment of nuclear changes that are pathognomonic of papillary thyroid carcinoma (PTC). Based on these established criteria, an algorithmic approach is suggested using known, accepted terminology. The importance of unequivocal, clear-cut nuclear features of PTC as opposed to inconclusive features is stressed. If the nuclear features in an encapsulated, non-invasive follicular patterned lesion fall short of those encountered in classical PTC, but nonetheless are still worrying or concerning, the term 'uncertain malignant potential or behaviour, most likely benign' is suggested. Indubitable, classical PTC nuclei (whether diffuse or restricted to a single high-power field) are diagnostic of a PTC be it classical, non-invasive or invasive follicular variant PTC. Capsular and vascular invasion remain the only reliable predictors of outcome, as non-invasive, encapsulated follicular variant PTC, even with diffuse PTC nuclear change, behaves in an indolent fashion.

SToRM: A Model for 2D environmental hydraulics

USGS Publications Warehouse

Simões, Francisco J. M.

2017-01-01

A two-dimensional (depth-averaged) finite volume Godunov-type shallow water model developed for flow over complex topography is presented. The model, SToRM, is based on an unstructured cell-centered finite volume formulation and on nonlinear strong stability preserving Runge-Kutta time stepping schemes. The numerical discretization is founded on the classical and well established shallow water equations in hyperbolic conservative form, but the convective fluxes are calculated using auto-switching Riemann and diffusive numerical fluxes. Computational efficiency is achieved through a parallel implementation based on the OpenMP standard and the Fortran programming language. SToRM’s implementation within a graphical user interface is discussed. Field application of SToRM is illustrated by utilizing it to estimate peak flow discharges in a flooding event of the St. Vrain Creek in Colorado, U.S.A., in 2013, which reached 850 m3/s (~30,000 f3 /s) at the location of this study.

Heat and Mass Transfer with Condensation in Capillary Porous Bodies

PubMed Central

2014-01-01

The purpose of this present work is related to wetting process analysis caused by condensation phenomena in capillary porous material by using a numerical simulation. Special emphasis is given to the study of the mechanism involved and the evaluation of classical theoretical models used as a predictive tool. A further discussion will be given for the distribution of the liquid phase for both its pendular and its funicular state and its consequence on diffusion coefficients of the mathematical model used. Beyond the complexity of the interaction effects between vaporisation-condensation processes on the gas-liquid interfaces, the comparison between experimental and numerical simulations permits to identify the specific contribution and the relative part of mass and energy transport parameters. This analysis allows us to understand the contribution of each part of the mathematical model used and to simplify the study. PMID:24688366

A diatom record of CO2 decline since the late Miocene

NASA Astrophysics Data System (ADS)

Mejía, Luz María; Méndez-Vicente, Ana; Abrevaya, Lorena; Lawrence, Kira T.; Ladlow, Caroline; Bolton, Clara; Cacho, Isabel; Stoll, Heather

2017-12-01

Extratropical sea surface temperature records from alkenones record a dramatic cooling of up to 17 °C over the last ∼14 Ma, but the relationship between this cooling and greenhouse gas forcing has been elusive due to sparse and contrasting reconstructions of atmospheric CO2 for the time period. Alkenone carbon isotopic fractionation during photosynthesis has previously been used to estimate changes in pCO2 over this interval, but is complicated by significant changes in cell size of the alkenone-producing coccolithophorids over this time period. In this study, we reconstruct carbon isotopic fractionation during photosynthesis (εp) using organic compounds trapped within the frustules of pennate diatoms in sediments from the Eastern Equatorial Pacific Ocean at Ocean Drilling Program Site 846 over the last ∼13 Ma. Physical separation of pennate diatoms prior to measuring carbon isotopic fractionation enables us to obtain a record with constant cell geometry, eliminating this factor of uncertainty in our pCO2 reconstruction. In the past ∼11 Ma, εp declines from 15.5 to 10.3‰. Using the classic diffusive model and taking into account variations in opal content, alkenone concentration and coccolith Sr/Ca as indicators of past productivity and growth rate, and sea surface temperature records from the site, we estimate a decline in pCO2 from 454 (+ / - 41) to 250 (+ / - 15) ppmv between ∼11 and 6 Ma. Models accounting for changing the significance of active carbon uptake for photosynthesis, which likely produce more accurate CO2 estimates, suggest a significant larger pCO2 decline of up to twice that shown by the classic diffusive model (in average from 794 (+ / - 233) ppmv at ∼11 Ma to 288 (+/-25) ppmv at ∼6 Ma, considering growth rates varying between 0.5 and 1.7 day-1). Large uncertainties in the pCO2 estimated between ∼8 and 11 Ma using the active uptake model are related to the growth rate used for calculations. Together, these results suggest CO2 forcing for this period of steep decline in temperatures.

Segregating gas from melt: an experimental study of the Ostwald ripening of vapor bubbles in magmas

USGS Publications Warehouse

Lautze, Nicole C.; Sisson, Thomas W.; Mangan, Margaret T.; Grove, Timothy L.

2011-01-01

Diffusive coarsening (Ostwald ripening) of H2O and H2O-CO2 bubbles in rhyolite and basaltic andesite melts was studied with elevated temperature–pressure experiments to investigate the rates and time spans over which vapor bubbles may enlarge and attain sufficient buoyancy to segregate in magmatic systems. Bubble growth and segregation are also considered in terms of classical steady-state and transient (non-steady-state) ripening theory. Experimental results are consistent with diffusive coarsening as the dominant mechanism of bubble growth. Ripening is faster in experiments saturated with pure H2O than in those with a CO2-rich mixed vapor probably due to faster diffusion of H2O than CO2 through the melt. None of the experimental series followed the time1/3 increase in mean bubble radius and time-1 decrease in bubble number density predicted by classical steady-state ripening theory. Instead, products are interpreted as resulting from transient regime ripening. Application of transient regime theory suggests that bubbly magmas may require from days to 100 years to reach steady-state ripening conditions. Experimental results, as well as theory for steady-state ripening of bubbles that are immobile or undergoing buoyant ascent, indicate that diffusive coarsening efficiently eliminates micron-sized bubbles and would produce mm-sized bubbles in 102–104 years in crustal magma bodies. Once bubbles attain mm-sizes, their calculated ascent rates are sufficient that they could transit multiple kilometers over hundreds to thousands of years through mafic and silicic melt, respectively. These results show that diffusive coarsening can facilitate transfer of volatiles through, and from, magmatic systems by creating bubbles sufficiently large for rapid ascent.

Dual view FIDA measurements on MAST

NASA Astrophysics Data System (ADS)

Michael, C. A.; Conway, N.; Crowley, B.; Jones, O.; Heidbrink, W. W.; Pinches, S.; Braeken, E.; Akers, R.; Challis, C.; Turnyanskiy, M.; Patel, A.; Muir, D.; Gaffka, R.; Bailey, S.

2013-09-01

A fast-ion deuterium alpha (FIDA) spectrometer was installed on MAST to measure radially resolved information about the fast-ion density and its distribution in energy and pitch angle. Toroidally and vertically directed collection lenses are employed, to detect both passing and trapped particle dynamics, and reference views are installed to subtract the background. This background is found to contain a substantial amount of passive FIDA emission driven by edge neutrals, and to depend delicately on viewing geometry. Results are compared with theoretical expectations based on the codes NUBEAM (for fast-ion distributions) and FIDASIM. Calibrating via the measured beam emission peaks, the toroidal FIDA signal profile agrees with classical simulations in magnetohydrodynamic quiescent discharges where the neutron rate is also classical. Long-lived modes (LLMs) and chirping modes decrease the core FIDA signal significantly, and the profile can be matched closely to simulations using anomalous diffusive transport; a spatially uniform diffusion coefficient is sufficient for chirping modes, while a core localized diffusion is better for a LLM. Analysis of a discharge with chirping mode activity shows a dramatic drop in the core FIDA signal and rapid increase in the edge passive signal at the onset of the burst indicating a very rapid redistribution towards the edge. Vertical-viewing measurements show a discrepancy with simulations at higher Doppler shifts when the neutron rate is classical, which, combined with the fact that the toroidal signals agree, means that the difference must be occurring for pitch angles near the trapped-passing boundary, although uncertainties in the background subtraction, which are difficult to assess, may contribute to this. Further evidence of an anomalous transport mechanism for these particles is provided by the fact that an increase of beam power does not increase the higher energy vertical FIDA signals, while the toroidal signals do increase.

Spectra of turbulently advected scalars that have small Schmidt number

NASA Astrophysics Data System (ADS)

Hill, Reginald J.

2017-09-01

Exact statistical equations are derived for turbulent advection of a passive scalar having diffusivity much larger than the kinematic viscosity, i.e., small Schmidt number. The equations contain all terms needed for precise direct numerical simulation (DNS) quantification. In the appropriate limit, the equations reduce to the classical theory for which the scalar spectrum is proportional to the energy spectrum multiplied by k-4, which, in turn, results in the inertial-diffusive range power law, k-17 /3. The classical theory was derived for the case of isotropic velocity and scalar fields. The exact equations are simplified for less restrictive cases: (1) locally isotropic scalar fluctuations at dissipation scales with no restriction on symmetry of the velocity field, (2) isotropic velocity field with averaging over all wave-vector directions with no restriction on the symmetry of the scalar, motivated by that average being used for DNS, and (3) isotropic velocity field with axisymmetric scalar fluctuations, motivated by the mean-scalar-gradient-source case. The equations are applied to recently published DNSs of passive scalars for the cases of a freely decaying scalar and a mean-scalar-gradient source. New terms in the exact equations are estimated for those cases and are found to be significant; those terms cause the deviations from the classical theory found by the DNS studies. A new formula for the mean-scalar-gradient case explains the variation of the scalar spectra for the DNS of the smallest Schmidt-number cases. Expansion in Legendre polynomials reveals the effect of axisymmetry. Inertial-diffusive-range formulas for both the zero- and second-order Legendre contributions are given. Exact statistical equations reveal what must be quantified using DNS to determine what causes deviations from asymptotic relationships.

Investigation of a Mercury-Argon Hot Cathode Discharge

NASA Astrophysics Data System (ADS)

Wamsley, Robert Charles

Classical absorption and laser induced fluorescence (LIF) experiments are used to investigate processes in the cathode region of a Hg-Ar hot cathode discharge. The absorption and LIF measurements are used to test the qualitative understanding and develop a quantitative model of a hot cathode discharge. The main contribution of this thesis is a model of the negative glow region that demonstrates the importance of Penning ionization to the ionization balance in the negative glow. We modeled the excited argon balance equation using a Monte Carlo simulation. In this simulation we used the trapped radiative decay rate of the resonance levels and the Penning ionization rate as the dominant loss terms in the balance equation. The simulated data is compared to and found to agree with absolute excited argon densities measured in a classical absorption experiment. We found the primary production rate per unit volume of excited Ar atoms in the simulation is sharply peaked near the cathode hot spot. We used the ion production rate from this simulation and a Green's function solution to the ambipolar diffusion equation to calculate the contribution of Penning ionization to the total ion density. We compared the results of this calculation to our experimental values of the Hg ^+ densities in the negative glow. We found that Penning ionization is an important and possibly the dominant ionization process in the negative glow.

Diffuse idiopathic pulmonary neuroendocrine cell hyperplasia: Report of two cases.

PubMed

García-Fontán, Eva; Blanco Ramos, Montserrat; García, Jose Soro; Carrasco, Rommel; Cañizares, Miguel Ángel; González Piñeiro, Ana

2018-05-19

Diffuse idiopathic pulmonary neuroendocrine cell hyperplasia (DIPNECH) is a rare disorder characterized by a proliferation of neuroendocrine cells within the lung. It is classically described as a disease with persistent cough, dyspnea and wheezing in non-smoker middle aged females. CT of the chest reveals diffuse air trapping with mosaic pattern. We present two cases of DIPNECH that were sent to our department to perform a lung biopsy with the diagnostic suspicion of diffuse interstitial disease. Both cases were women with a history of chronic cough and moderate effort dyspnea. The aim of this paper is that physicians take into account this diagnostic entity before treating as an asthmatic a patient with these characteristics, not forgetting that they are prenoplastic lesions. Copyright © 2018 Elsevier España, S.L.U. All rights reserved.

Size quantization in high-temperature superconducting cuprates and a link to Einstein's diffusion law

NASA Astrophysics Data System (ADS)

Roeser, H. P.; Bohr, A.; Haslam, D. T.; López, J. S.; Stepper, M.; Nikoghosyan, A. S.

2012-07-01

Optimum doping of high-temperature superconductors (HTSC) defines a superconducting unit volume for each HTSC. For a single-mode HTSC, e.g., a cuprate with one CuO2 plane, the volume is given by Vsc=cx2, where c is the unit cell height and x the doping distance. The experimental resistivity at Tc is connected to the structure by ρ(exp)≈c×h/(2e2). Combining this result with the classical definition of resistivity leads to an equation similar to Einstein's diffusion law x2/(2τ)=h/(2Meff)=D, where τ is the relaxation time, Meff=2me and D the diffusion constant. It has also been shown that the mean free path d=x. The Einstein-Smoluchowski diffusion relation D=μkBTc provides a connection to Tc.

Ion Diffusivity through the Solid Electrolyte Interphase in Lithium-Ion Batteries

DOE PAGES

Benitez, Laura; Seminario, Jorge M.

2017-05-17

Understanding the transport properties of the solid electrolyte interface (SEI) is a critical piece in the development of lithium ion batteries (LIB) with better performance. We studied the lithium ion diffusivity in the main components of the SEI found in LIB with silicon anodes and performed classical molecular dynamics (MD) simulations on lithium fluoride (LiF), lithium oxide (Li 2O) and lithium carbonate (Li 2CO 3) in order to provide insights and to calculate the diffusion coefficients of Li-ions at temperatures in the range of 250 K to 400 K, which is within the LIB operating temperature range. We find amore » slight increase in the diffusivity as the temperature increases and since diffusion is noticeable at high temperatures, Li-ion diffusion in the range of 130 to 1800 K was also studied and the diffusion mechanisms involved in each SEI compound were analyzed. We observed that the predominant mechanisms of Li-ion diffusion included vacancy assisted and knock-off diffusion in LiF, direct exchange in Li 2O, and vacancy and knock-off in Li 2CO 3. Moreover, we also evaluated the effect of applied electric fields in the diffusion of Li-ions at room temperature.« less

Ion Diffusivity through the Solid Electrolyte Interphase in Lithium-Ion Batteries

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

Benitez, Laura; Seminario, Jorge M.

Understanding the transport properties of the solid electrolyte interface (SEI) is a critical piece in the development of lithium ion batteries (LIB) with better performance. We studied the lithium ion diffusivity in the main components of the SEI found in LIB with silicon anodes and performed classical molecular dynamics (MD) simulations on lithium fluoride (LiF), lithium oxide (Li 2O) and lithium carbonate (Li 2CO 3) in order to provide insights and to calculate the diffusion coefficients of Li-ions at temperatures in the range of 250 K to 400 K, which is within the LIB operating temperature range. We find amore » slight increase in the diffusivity as the temperature increases and since diffusion is noticeable at high temperatures, Li-ion diffusion in the range of 130 to 1800 K was also studied and the diffusion mechanisms involved in each SEI compound were analyzed. We observed that the predominant mechanisms of Li-ion diffusion included vacancy assisted and knock-off diffusion in LiF, direct exchange in Li 2O, and vacancy and knock-off in Li 2CO 3. Moreover, we also evaluated the effect of applied electric fields in the diffusion of Li-ions at room temperature.« less

Implementation of two-phase tritium models for helium bubbles in HCLL breeding blanket modules

NASA Astrophysics Data System (ADS)

Fradera, J.; Sedano, L.; Mas de les Valls, E.; Batet, L.

2011-10-01

Tritium self-sufficiency requirement of future DT fusion reactors involves large helium production rates in the breeding blankets; this might impact on the conceptual design of diverse fusion power reactor units, such as Liquid Metal (LM) blankets. Low solubility, long residence-times and high production rates create the conditions for Helium nucleation, which could mean effective T sinks in LM channels. A model for helium nano-bubble formation and tritium conjugate transport phenomena in liquid Pb17.5Li and EUROFER is proposed. In a first approximation, it has been considered that He bubbles can be represented as a passive scalar. The nucleation model is based on the classical theory and includes a simplified bubble growth model. The model captures the interaction of tritium with bubbles and tritium diffusion through walls. Results show the influence of helium cavitation on tritium inventory and the importance of simulating the system walls instead of imposing fixed boundary conditions.

Quantitative Microplate-Based Respirometry with Correction for Oxygen Diffusion

PubMed Central

2009-01-01

Respirometry using modified cell culture microplates offers an increase in throughput and a decrease in biological material required for each assay. Plate based respirometers are susceptible to a range of diffusion phenomena; as O2 is consumed by the specimen, atmospheric O2 leaks into the measurement volume. Oxygen also dissolves in and diffuses passively through the polystyrene commonly used as a microplate material. Consequently the walls of such respirometer chambers are not just permeable to O2 but also store substantial amounts of gas. O2 flux between the walls and the measurement volume biases the measured oxygen consumption rate depending on the actual [O2] gradient. We describe a compartment model-based correction algorithm to deconvolute the biological oxygen consumption rate from the measured [O2]. We optimize the algorithm to work with the Seahorse XF24 extracellular flux analyzer. The correction algorithm is biologically validated using mouse cortical synaptosomes and liver mitochondria attached to XF24 V7 cell culture microplates, and by comparison to classical Clark electrode oxygraph measurements. The algorithm increases the useful range of oxygen consumption rates, the temporal resolution, and durations of measurements. The algorithm is presented in a general format and is therefore applicable to other respirometer systems. PMID:19555051

DANGEROUS LIAISONS? DATING AND DRINKING DIFFUSION IN ADOLESCENT PEER NETWORKS*

PubMed Central

Kreager, Derek A.; Haynie, Dana L.

2014-01-01

The onset and escalation of alcohol consumption and romantic relationships are hallmarks of adolescence, yet only recently have these domains jointly been the focus of sociological inquiry. We extend this literature by connecting alcohol use, dating and peers to understand the diffusion of drinking behavior in school-based friendship networks. Drawing on Granovetter’s classic concept of weak ties, we argue that adolescent romantic partners are likely to be network bridges, or liaisons, connecting daters to new peer contexts which, in turn, promote changes in individual drinking behaviors and allow these behaviors to spread across peer networks. Using longitudinal data of 459 couples from the National Longitudinal Study of Adolescent Health, we estimate Actor-Partner Interdependence Models and identify the unique contributions of partners’ drinking, friends’ drinking, and friends-of-partners’ drinking to daters’ own future binge drinking and drinking frequency. Findings support the liaison hypothesis and suggest that friends-of-partners’ drinking have net associations with adolescent drinking patterns. Moreover, the coefficient for friends-of-partners drinking is larger than the coefficient for one’s own peers and generally immune to prior selection. Our findings suggest that romantic relationships are important mechanisms for understanding the diffusion of emergent problem behaviors in adolescent peer networks. PMID:25328162

A Method for Molecular Dynamics on Curved Surfaces

PubMed Central

Paquay, Stefan; Kusters, Remy

2016-01-01

Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in the field of diffusive transport have focused on solving the diffusion equation on curved surfaces, for which it is not tractable to incorporate particle interactions even though these play a crucial role in crowded systems. We show here that it is possible to take such interactions into account by combining standard constraint algorithms with the classical velocity Verlet scheme to perform molecular dynamics simulations of particles constrained to an arbitrarily curved surface. Furthermore, unlike Brownian dynamics schemes in local coordinates, our method is based on Cartesian coordinates, allowing for the reuse of many other standard tools without modifications, including parallelization through domain decomposition. We show that by applying the schemes to the Langevin equation for various surfaces, we obtain confined Brownian motion, which has direct applications to many biological and physical problems. Finally we present two practical examples that highlight the applicability of the method: 1) the influence of crowding and shape on the lateral diffusion of proteins in curved membranes; and 2) the self-assembly of a coarse-grained virus capsid protein model. PMID:27028633

A Method for Molecular Dynamics on Curved Surfaces

NASA Astrophysics Data System (ADS)

Paquay, Stefan; Kusters, Remy

2016-03-01

Dynamics simulations of constrained particles can greatly aid in understanding the temporal and spatial evolution of biological processes such as lateral transport along membranes and self-assembly of viruses. Most theoretical efforts in the field of diffusive transport have focussed on solving the diffusion equation on curved surfaces, for which it is not tractable to incorporate particle interactions even though these play a crucial role in crowded systems. We show here that it is possible to combine standard constraint algorithms with the classical velocity Verlet scheme to perform molecular dynamics simulations of particles constrained to an arbitrarily curved surface, in which such interactions can be taken into account. Furthermore, unlike Brownian dynamics schemes in local coordinates, our method is based on Cartesian coordinates allowing for the reuse of many other standard tools without modifications, including parallelisation through domain decomposition. We show that by applying the schemes to the Langevin equation for various surfaces, confined Brownian motion is obtained, which has direct applications to many biological and physical problems. Finally we present two practical examples that highlight the applicability of the method: (i) the influence of crowding and shape on the lateral diffusion of proteins in curved membranes and (ii) the self-assembly of a coarse-grained virus capsid protein model.

Defect chemistry and lithium transport in Li3OCl anti-perovskite superionic conductors.

PubMed

Lu, Ziheng; Chen, Chi; Baiyee, Zarah Medina; Chen, Xin; Niu, Chunming; Ciucci, Francesco

2015-12-28

Lithium-rich anti-perovskites (LiRAPs) are a promising family of solid electrolytes, which exhibit ionic conductivities above 10(-3) S cm(-1) at room temperature, among the highest reported values to date. In this work, we investigate the defect chemistry and the associated lithium transport in Li3OCl, a prototypical LiRAP, using ab initio density functional theory (DFT) calculations and classical molecular dynamics (MD) simulations. We studied three types of charge neutral defect pairs, namely the LiCl Schottky pair, the Li2O Schottky pair, and the Li interstitial with a substitutional defect of O on the Cl site. Among them the LiCl Schottky pair has the lowest binding energy and is the most energetically favorable for diffusion as computed by DFT. This is confirmed by classical MD simulations, where the computed Li ion diffusion coefficients for LiCl Schottky systems are significantly higher than those for the other two defects considered and the activation energy in LiCl deficient Li3OCl is comparable to experimental values. The high conductivities and low activation energies of LiCl Schottky systems are explained by the low energy pathways of Li between the Cl vacancies. We propose that Li vacancy hopping is the main diffusion mechanism in highly conductive Li3OCl.

Transport of gases between the environment and alveoli – theoretical foundations

PubMed Central

Butler, James P.; Tsuda, Akira

2015-01-01

The transport of oxygen and carbon dioxide in the gas phase from the ambient environment to and from the alveolar gas/blood interface is accomplished through the tracheobronchial tree, and involves mechanisms of bulk or convective transport and diffusive net transport. The geometry of the airway tree and the fluid dynamics of these two transport processes combine in such a way that promotes a classical fractionation of ventilation into dead space and alveolar ventilation respectively. This simple picture continues to capture much of the essence of gas phase transport. On the other hand, a more detailed look at the interaction of convection and diffusion leads to significant new issues, many of which remain open questions. These are associated with parallel and serial inhomogeneities especially within the distal acinar units, velocity profiles in distal airways and terminal spaces subject to moving boundary conditions, and the serial transport of respiratory gases within the complex acinar architecture. This chapter focuses specifically on the theoretical foundations of gas transport, addressing two broad areas. The first deals with the reasons why the classical picture of alveolar and dead space ventilation is so successful; the second examines the underlying assumptions within current approximations to convective and diffusive transport, and how they interact to effect net gas exchange. PMID:23733643

A Mechanical Model of Brownian Motion for One Massive Particle Including Slow Light Particles

NASA Astrophysics Data System (ADS)

Liang, Song

2018-01-01

We provide a connection between Brownian motion and a classical mechanical system. Precisely, we consider a system of one massive particle interacting with an ideal gas, evolved according to non-random mechanical principles, via interaction potentials, without any assumption requiring that the initial velocities of the environmental particles should be restricted to be "fast enough". We prove the convergence of the (position, velocity)-process of the massive particle under a certain scaling limit, such that the mass of the environmental particles converges to 0 while the density and the velocities of them go to infinity, and give the precise expression of the limiting process, a diffusion process.

Fractional flow in fractured chalk; a flow and tracer test revisited.

PubMed

Odling, N E; West, L J; Hartmann, S; Kilpatrick, A

2013-04-01

A multi-borehole pumping and tracer test in fractured chalk is revisited and reinterpreted in the light of fractional flow. Pumping test data analyzed using a fractional flow model gives sub-spherical flow dimensions of 2.2-2.4 which are interpreted as due to the partially penetrating nature of the pumped borehole. The fractional flow model offers greater versatility than classical methods for interpreting pumping tests in fractured aquifers but its use has been hampered because the hydraulic parameters derived are hard to interpret. A method is developed to convert apparent transmissivity and storativity (L(4-n)/T and S(2-n)) to conventional transmissivity and storativity (L2/T and dimensionless) for the case where flow dimension, 2

Integrated water system simulation by considering hydrological and biogeochemical processes: model development, with parameter sensitivity and autocalibration

NASA Astrophysics Data System (ADS)

Zhang, Y. Y.; Shao, Q. X.; Ye, A. Z.; Xing, H. T.; Xia, J.

2016-02-01

Integrated water system modeling is a feasible approach to understanding severe water crises in the world and promoting the implementation of integrated river basin management. In this study, a classic hydrological model (the time variant gain model: TVGM) was extended to an integrated water system model by coupling multiple water-related processes in hydrology, biogeochemistry, water quality, and ecology, and considering the interference of human activities. A parameter analysis tool, which included sensitivity analysis, autocalibration and model performance evaluation, was developed to improve modeling efficiency. To demonstrate the model performances, the Shaying River catchment, which is the largest highly regulated and heavily polluted tributary of the Huai River basin in China, was selected as the case study area. The model performances were evaluated on the key water-related components including runoff, water quality, diffuse pollution load (or nonpoint sources) and crop yield. Results showed that our proposed model simulated most components reasonably well. The simulated daily runoff at most regulated and less-regulated stations matched well with the observations. The average correlation coefficient and Nash-Sutcliffe efficiency were 0.85 and 0.70, respectively. Both the simulated low and high flows at most stations were improved when the dam regulation was considered. The daily ammonium-nitrogen (NH4-N) concentration was also well captured with the average correlation coefficient of 0.67. Furthermore, the diffuse source load of NH4-N and the corn yield were reasonably simulated at the administrative region scale. This integrated water system model is expected to improve the simulation performances with extension to more model functionalities, and to provide a scientific basis for the implementation in integrated river basin managements.

The strengths and limitations of effective centroid force models explored by studying isotopic effects in liquid water

NASA Astrophysics Data System (ADS)

Yuan, Ying; Li, Jicun; Li, Xin-Zheng; Wang, Feng

2018-05-01

The development of effective centroid potentials (ECPs) is explored with both the constrained-centroid and quasi-adiabatic force matching using liquid water as a test system. A trajectory integrated with the ECP is free of statistical noises that would be introduced when the centroid potential is approximated on the fly with a finite number of beads. With the reduced cost of ECP, challenging experimental properties can be studied in the spirit of centroid molecular dynamics. The experimental number density of H2O is 0.38% higher than that of D2O. With the ECP, the H2O number density is predicted to be 0.42% higher, when the dispersion term is not refit. After correction of finite size effects, the diffusion constant of H2O is found to be 21% higher than that of D2O, which is in good agreement with the 29.9% higher diffusivity for H2O observed experimentally. Although the ECP is also able to capture the redshifts of both the OH and OD stretching modes in liquid water, there are a number of properties that a classical simulation with the ECP will not be able to recover. For example, the heat capacities of H2O and D2O are predicted to be almost identical and higher than the experimental values. Such a failure is simply a result of not properly treating quantized vibrational energy levels when the trajectory is propagated with classical mechanics. Several limitations of the ECP based approach without bead population reconstruction are discussed.

The transboundary non-renewable Nubian Aquifer System of Chad, Egypt, Libya and Sudan: classical groundwater questions and parsimonious hydrogeologic analysis and modeling

NASA Astrophysics Data System (ADS)

Voss, Clifford I.; Soliman, Safaa M.

2014-03-01

Parsimonious groundwater modeling provides insight into hydrogeologic functioning of the Nubian Aquifer System (NAS), the world's largest non-renewable groundwater system (belonging to Chad, Egypt, Libya, and Sudan). Classical groundwater-resource issues exist (magnitude and lateral extent of drawdown near pumping centers) with joint international management questions regarding transboundary drawdown. Much of NAS is thick, containing a large volume of high-quality groundwater, but receives insignificant recharge, so water-resource availability is time-limited. Informative aquifer data are lacking regarding large-scale response, providing only local-scale information near pumps. Proxy data provide primary underpinning for understanding regional response: Holocene water-table decline from the previous pluvial period, after thousands of years, results in current oasis/sabkha locations where the water table still intersects the ground. Depletion is found to be controlled by two regional parameters, hydraulic diffusivity and vertical anisotropy of permeability. Secondary data that provide insight are drawdowns near pumps and isotope-groundwater ages (million-year-old groundwaters in Egypt). The resultant strong simply structured three-dimensional model representation captures the essence of NAS regional groundwater-flow behavior. Model forecasts inform resource management that transboundary drawdown will likely be minimal—a nonissue—whereas drawdown within pumping centers may become excessive, requiring alternative extraction schemes; correspondingly, significant water-table drawdown may occur in pumping centers co-located with oases, causing oasis loss and environmental impacts.

Non-Arrhenius temperature dependence of the island density of one-dimensional Al chains on Si(100): A kinetic Monte Carlo study

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

Albia, Jason R.; Albao, Marvin A., E-mail: maalbao@uplb.edu.ph

Classical nucleation theory predicts that the evolution of mean island density with temperature during growth in one-dimensional systems obeys the Arrhenius relation. In this study, kinetic Monte Carlo simulations of a suitable atomistic lattice-gas model were performed to investigate the experimentally observed non-Arrhenius scaling behavior of island density in the case of one-dimensional Al islands grown on Si(100). Previously, it was proposed that adatom desorption resulted in a transition temperature signaling the departure from classical predictions. Here, the authors demonstrate that desorption above the transition temperature is not possible. Instead, the authors posit that the existence of a transition temperaturemore » is due to a combination of factors such as reversibility of island growth, presence of C-defects, adatom diffusion rates, as well as detachment rates at island ends. In addition, the authors show that the anomalous non-Arrhenius behavior vanishes when adatom binds irreversibly with C-defects as observed in In on Si(100) studies.« less

Reversible geminate recombination of hydrogen-bonded water molecule pair

NASA Astrophysics Data System (ADS)

Markovitch, Omer; Agmon, Noam

2008-08-01

The (history independent) autocorrelation function for a hydrogen-bonded water molecule pair, calculated from classical molecular dynamics trajectories of liquid water, exhibits a t-3/2 asymptotic tail. Its whole time dependence agrees quantitatively with the solution for reversible diffusion-influenced geminate recombination derived by Agmon and Weiss [J. Chem. Phys. 91, 6937 (1989)]. Agreement with diffusion theory is independent of the precise definition of the bound state. Given the water self-diffusion constant, this theory enables us to determine the dissociation and bimolecular recombination rate parameters for a water dimer. (The theory is indispensable for obtaining the bimolecular rate coefficient.) Interestingly, the activation energies obtained from the temperature dependence of these rate coefficients are similar, rather than differing by the hydrogen-bond (HB) strength. This suggests that recombination requires displacing another water molecule, which meanwhile occupied the binding site. Because these activation energies are about twice the HB strength, cleavage of two HBs may be required to allow pair separation. The autocorrelation function without the HB angular restriction yields a recombination rate coefficient that is larger than that for rebinding to all four tetrahedral water sites (with angular restrictions), suggesting the additional participation of interstitial sites. Following dissociation, the probability of the pair to be unbound but within the reaction sphere rises more slowly than expected, possibly because binding to the interstitial sites delays pair separation. An extended diffusion model, which includes an additional binding site, can account for this behavior.

Zonal flow evolution and overstability in accretion discs

NASA Astrophysics Data System (ADS)

Vanon, R.; Ogilvie, G. I.

2017-04-01

This work presents a linear analytical calculation on the stability and evolution of a compressible, viscous self-gravitating (SG) Keplerian disc with both horizontal thermal diffusion and a constant cooling time-scale when an axisymmetric structure is present and freely evolving. The calculation makes use of the shearing sheet model and is carried out for a range of cooling times. Although the solutions to the inviscid problem with no cooling or diffusion are well known, it is non-trivial to predict the effect caused by the introduction of cooling and of small diffusivities; this work focuses on perturbations of intermediate wavelengths, therefore representing an extension to the classical stability analysis on thermal and viscous instabilities. For density wave modes, the analysis can be simplified by means of a regular perturbation analysis; considering both shear and thermal diffusivities, the system is found to be overstable for intermediate and long wavelengths for values of the Toomre parameter Q ≲ 2; a non-SG instability is also detected for wavelengths ≳18H, where H is the disc scale-height, as long as γ ≲ 1.305. The regular perturbation analysis does not, however, hold for the entropy and potential vorticity slow modes as their ideal growth rates are degenerate. To understand their evolution, equations for the axisymmetric structure's amplitudes in these two quantities are analytically derived and their instability regions obtained. The instability appears boosted by increasing the value of the adiabatic index and of the Prandtl number, while it is quenched by efficient cooling.

Magnetic flux and heat losses by diffusive, advective, and Nernst effects in magnetized liner inertial fusion-like plasma

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

Velikovich, A. L.; Giuliani, J. L.; Zalesak, S. T.

The magnetized liner inertial fusion (MagLIF) approach to inertial confinement fusion [Slutz et al., Phys. Plasmas 17, 056303 (2010); Cuneo et al., IEEE Trans. Plasma Sci. 40, 3222 (2012)] involves subsonic/isobaric compression and heating of a deuterium-tritium plasma with frozen-in magnetic flux by a heavy cylindrical liner. The losses of heat and magnetic flux from the plasma to the liner are thereby determined by plasma advection and gradient-driven transport processes, such as thermal conductivity, magnetic field diffusion, and thermomagnetic effects. Theoretical analysis based on obtaining exact self-similar solutions of the classical collisional Braginskii's plasma transport equations in one dimension demonstratesmore » that the heat loss from the hot compressed magnetized plasma to the cold liner is dominated by transverse heat conduction and advection, and the corresponding loss of magnetic flux is dominated by advection and the Nernst effect. For a large electron Hall parameter (ω{sub e}τ{sub e}≫1), the effective diffusion coefficients determining the losses of heat and magnetic flux to the liner wall are both shown to decrease with ω{sub e}τ{sub e} as does the Bohm diffusion coefficient cT/(16eB), which is commonly associated with low collisionality and two-dimensional transport. We demonstrate how this family of exact solutions can be used for verification of codes that model the MagLIF plasma dynamics.« less

Pressure and Chemical Potential: Effects Hydrophilic Soils Have on Adsorption and Transport

NASA Astrophysics Data System (ADS)

Bennethum, L. S.; Weinstein, T.

2003-12-01

Using the assumption that thermodynamic properties of fluid is affected by its proximity to the solid phase, a theoretical model has been developed based on upscaling and fundamental thermodynamic principles (termed Hybrid Mixture Theory). The theory indicates that Darcy's law and the Darcy-scale chemical potential (which determines the rate of adsorption and diffusion) need to be modified in order to apply to soils containing hydrophilic soils. In this talk we examine the Darcy-scale definition of pressure and chemical potential, especially as it applies to hydrophilic soils. To arrive at our model, we used hybrid mixture theory - first pioneered by Hassanizadeh and Gray in 1979. The technique involves averaging the field equations (i.e. conservation of mass, momentum balance, energy balance, etc.) to obtain macroscopic field equations, where each field variable is defined precisely in terms of its microscale counterpart. To close the system consistently with classical thermodynamics, the entropy inequality is exploited in the sense of Coleman and Noll. With the exceptions that the macroscale field variables are defined precisely in terms of their microscale counterparts and that microscopic interfacial equations can also be treated in a similar manner, the resulting system of equations is consistent with those derived using classical mixture theory. Hence the terminology, Hybrid Mixture Theory.

Capturing the 3D Motion of an Infalling Galaxy via Fluid Dynamics

NASA Astrophysics Data System (ADS)

Su, Yuanyuan; Kraft, Ralph P.; Nulsen, Paul E. J.; Roediger, Elke; Forman, William R.; Churazov, Eugene; Randall, Scott W.; Jones, Christine; Machacek, Marie E.

2017-01-01

The Fornax Cluster is the nearest (≤slant 20 Mpc) galaxy cluster in the southern sky. NGC 1404 is a bright elliptical galaxy falling through the intracluster medium (ICM) of the Fornax Cluster. The sharp leading edge of NGC 1404 forms a classical “cold front” that separates 0.6 keV dense interstellar medium and 1.5 keV diffuse ICM. We measure the angular pressure variation along the cold front using a very deep (670 ks) Chandra X-ray observation. We are taking the classical approach—using stagnation pressure to determine a substructure’s speed—to the next level by not only deriving a general speed but also directionality, which yields the complete velocity field as well as the distance of the substructure directly from the pressure distribution. We find a hydrodynamic model consistent with the pressure jump along NGC 1404's atmosphere measured in multiple directions. The best-fit model gives an inclination of 33° and a Mach number of 1.3 for the infall of NGC 1404, in agreement with complementary measurements of the motion of NGC 1404. Our study demonstrates the successful treatment of a highly ionized ICM as ideal fluid flow, in support of the hypothesis that magnetic pressure is not dynamically important over most of the virial region of galaxy clusters.

Hemiconvulsion-hemiplegia-epilepsy syndrome: characteristic early magnetic resonance imaging findings.

PubMed

Freeman, Jeremy L; Coleman, Lee T; Smith, Lindsay J; Shield, Lloyd K

2002-01-01

We report three patients with hemiconvulsion-hemiplegia-epilepsy syndrome who presented acutely and were shown to have striking neuroimaging findings suggestive of diffuse cytotoxic edema confined to one hemisphere, including extensive diffusion-weighted imaging abnormalities in two cases. Two patients subsequently developed progressive and extensive atrophy of the involved hemisphere. These findings are consistent with earlier descriptions of the classic neuroradiologic features of this syndrome and are helpful in the differential diagnosis of acute infantile hemiplegia. Further, the findings support the previously proposed pathogenetic mechanism of neuronal injury caused by status epilepticus.

Properties of water along the liquid-vapor coexistence curve via molecular dynamics simulations using the polarizable TIP4P-QDP-LJ water model

PubMed Central

Bauer, Brad A.; Patel, Sandeep

2009-01-01

We present an extension of the TIP4P-QDP model, TIP4P-QDP-LJ, that is designed to couple changes in repulsive and dispersive nonbond interactions to changes in polarizability. Polarizability is intimately related to the dispersion component of classical force field models of interactions, and we explore the effect of incorporating this connection explicitly on properties along the liquid-vapor coexistence curve of pure water. Parametrized to reproduce condensed-phase liquid water properties at 298 K, the TIP4P-QDP-LJ model predicts density, enthalpy of vaporization, self-diffusion constant, and the dielectric constant at ambient conditions to about the same accuracy as TIP4P-QDP but shows remarkable improvement in reproducing the liquid-vapor coexistence curve. TIP4P-QDP-LJ predicts critical constants of Tc=623 K, ρc=0.351 g∕cm3, and Pc=250.9 atm, which are in good agreement with experimental values of Tc=647.1 K, ρc=0.322 g∕cm3, and Pc=218 atm, respectively. Applying a scaling factor correction (obtained by fitting the experimental vapor-liquid equilibrium data to the law of rectilinear diameters using a three-term Wegner expansion) the model predicts critical constants (Tc=631 K and ρc=0.308 g∕cm3). Dependence of enthalpy of vaporization, self-diffusion constant, surface tension, and dielectric constant on temperature are shown to reproduce experimental trends. We also explore the interfacial potential drop across the liquid-vapor interface for the temperatures studied. The interfacial potential demonstrates little temperature dependence at lower temperatures (300–450 K) and significantly enhanced (exponential) dependence at elevated temperatures. Terms arising from the decomposition of the interfacial potential into dipole and quadrupole contributions are shown to monotonically approach zero as the temperature approaches the critical temperature. Results of this study suggest that self-consistently treating the coupling of phase-dependent polarizability with dispersion interactions in classical water force fields may be an important effect for the extension of polarizable water force fields to reproduce properties along the liquid-vapor coexistence envelope as well as near critical conditions. More importantly, the present study demonstrates the rather remarkable transferability of a water model parametrized to a single state point to other thermodynamic states. Further studies are recommended. PMID:19725623

Properties of water along the liquid-vapor coexistence curve via molecular dynamics simulations using the polarizable TIP4P-QDP-LJ water model.

PubMed

Bauer, Brad A; Patel, Sandeep

2009-08-28

We present an extension of the TIP4P-QDP model, TIP4P-QDP-LJ, that is designed to couple changes in repulsive and dispersive nonbond interactions to changes in polarizability. Polarizability is intimately related to the dispersion component of classical force field models of interactions, and we explore the effect of incorporating this connection explicitly on properties along the liquid-vapor coexistence curve of pure water. Parametrized to reproduce condensed-phase liquid water properties at 298 K, the TIP4P-QDP-LJ model predicts density, enthalpy of vaporization, self-diffusion constant, and the dielectric constant at ambient conditions to about the same accuracy as TIP4P-QDP but shows remarkable improvement in reproducing the liquid-vapor coexistence curve. TIP4P-QDP-LJ predicts critical constants of T(c)=623 K, rho(c)=0.351 g/cm(3), and P(c)=250.9 atm, which are in good agreement with experimental values of T(c)=647.1 K, rho(c)=0.322 g/cm(3), and P(c)=218 atm, respectively. Applying a scaling factor correction (obtained by fitting the experimental vapor-liquid equilibrium data to the law of rectilinear diameters using a three-term Wegner expansion) the model predicts critical constants (T(c)=631 K and rho(c)=0.308 g/cm(3)). Dependence of enthalpy of vaporization, self-diffusion constant, surface tension, and dielectric constant on temperature are shown to reproduce experimental trends. We also explore the interfacial potential drop across the liquid-vapor interface for the temperatures studied. The interfacial potential demonstrates little temperature dependence at lower temperatures (300-450 K) and significantly enhanced (exponential) dependence at elevated temperatures. Terms arising from the decomposition of the interfacial potential into dipole and quadrupole contributions are shown to monotonically approach zero as the temperature approaches the critical temperature. Results of this study suggest that self-consistently treating the coupling of phase-dependent polarizability with dispersion interactions in classical water force fields may be an important effect for the extension of polarizable water force fields to reproduce properties along the liquid-vapor coexistence envelope as well as near critical conditions. More importantly, the present study demonstrates the rather remarkable transferability of a water model parametrized to a single state point to other thermodynamic states. Further studies are recommended.

A new interpretation of the Keller-Segel model based on multiphase modelling.

PubMed

Byrne, Helen M; Owen, Markus R

2004-12-01

In this paper an alternative derivation and interpretation are presented of the classical Keller-Segel model of cell migration due to random motion and chemotaxis. A multiphase modelling approach is used to describe how a population of cells moves through a fluid containing a diffusible chemical to which the cells are attracted. The cells and fluid are viewed as distinct components of a two-phase mixture. The principles of mass and momentum balance are applied to each phase, and appropriate constitutive laws imposed to close the resulting equations. A key assumption here is that the stress in the cell phase is influenced by the concentration of the diffusible chemical. By restricting attention to one-dimensional cartesian geometry we show how the model reduces to a pair of nonlinear coupled partial differential equations for the cell density and the chemical concentration. These equations may be written in the form of the Patlak-Keller-Segel model, naturally including density-dependent nonlinearities in the cell motility coefficients. There is a direct relationship between the random motility and chemotaxis coefficients, both depending in an inter-related manner on the chemical concentration. We suggest that this may explain why many chemicals appear to stimulate both chemotactic and chemokinetic responses in cell populations. After specialising our model to describe slime mold we then show how the functional form of the chemical potential that drives cell locomotion influences the ability of the system to generate spatial patterns. The paper concludes with a summary of the key results and a discussion of avenues for future research.

Numerical modeling of physical vapor transport under microgravity conditions: Effect of thermal creep and stress

NASA Technical Reports Server (NTRS)

Mackowski, Daniel W.; Knight, Roy W.

1993-01-01

One of the most promising applications of microgravity (micro-g) environments is the manufacture of exotic and high-quality crystals in closed cylindrical ampoules using physical vapor transport (PVT) processes. The quality enhancements are believed to be due to the absence of buoyant convection in the weightless environment - resulting in diffusion-limited transport of the vapor. In a typical experiment, solid-phase sample material is initially contained at one end of the ampoule. The sample is made to sublime into the vapor phase and deposit onto the opposite end by maintaining the source at an elevated temperature with respect to the deposit. Identification of the physical factors governing both the rates and uniformity of crystal growth, and the optimization of the micro-g technology, will require an accurate modeling of the vapor transport within the ampoule. Previous micro-g modeling efforts have approached the problem from a 'classical' convective/diffusion formulation, in which convection is driven by the action of buoyancy on thermal and solutal density differences. The general conclusion of these works have been that in low gravity environments the effect of buoyancy on vapor transport is negligible, and vapor transport occurs in a diffusion-limited mode. However, it has been recently recognized than in the non-isothermal (and often low total pressure) conditions encountered in ampoules, the commonly-assumed no-slip boundary condition to the differential equations governing fluid motion can be grossly unrepresentative of the actual situation. Specifically, the temperature gradients can give rise to thermal creep flows at the ampoule side walls. In addition, temperature gradients in the vapor itself can, through the action of thermal stress, lead to bulk fluid convection.

Diffusion of a new intermediate product in a simple 'classical-Schumpeterian' model.

PubMed

Haas, David

2018-05-01

This paper deals with the problem of new intermediate products within a simple model, where production is circular and goods enter into the production of other goods. It studies the process by which the new good is absorbed into the economy and the structural transformation that goes with it. By means of a long-period method the forces of structural transformation are examined, in particular the shift of existing means of production towards the innovation and the mechanism of differential growth in terms of alternative techniques and their associated systems of production. We treat two important Schumpeterian topics: the question of technological unemployment and the problem of 'forced saving' and the related problem of an involuntary reduction of real consumption per capita. It is shown that both phenomena are potential by-products of the transformation process.

Crystallization tendencies of modelled Lennard-Jones liquids with different attractions

NASA Astrophysics Data System (ADS)

Valdès, L.-C.; Gerges, J.; Mizuguchi, T.; Affouard, F.

2018-01-01

Molecular dynamics simulations are performed on simple models composed of monoatomic Lennard-Jones atoms for which the repulsive interaction is the same but the attractive part is tuned. We investigate the precise role of the attractive part of the interaction potential on different structural, dynamical, and thermodynamical properties of these systems in the liquid and crystalline states. It includes crystallization trends for which the main physical ingredients involved have been computed: the diffusion coefficient, the Gibbs energy difference between the liquid and the crystalline state, and the crystal-liquid interfacial free energy. Results are compared with predictions from the classical nucleation theory including transient and steady-state regimes at moderate and deeper undercooling. The question of the energetic and entropic impact of the repulsive and attractive part of the interaction potential towards crystallization is also addressed.

Transport studies in high-performance field reversed configuration plasmas

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

Gupta, S., E-mail: sgupta@trialphaenergy.com; Barnes, D. C.; Dettrick, S. A.

2016-05-15

A significant improvement of field reversed configuration (FRC) lifetime and plasma confinement times in the C-2 plasma, called High Performance FRC regime, has been observed with neutral beam injection (NBI), improved edge stability, and better wall conditioning [Binderbauer et al., Phys. Plasmas 22, 056110 (2015)]. A Quasi-1D (Q1D) fluid transport code has been developed and employed to carry out transport analysis of such C-2 plasma conditions. The Q1D code is coupled to a Monte-Carlo code to incorporate the effect of fast ions, due to NBI, on the background FRC plasma. Numerically, the Q1D transport behavior with enhanced transport coefficients (butmore » with otherwise classical parametric dependencies) such as 5 times classical resistive diffusion, classical thermal ion conductivity, 20 times classical electron thermal conductivity, and classical fast ion behavior fit with the experimentally measured time evolution of the excluded flux radius, line-integrated density, and electron/ion temperature. The numerical study shows near sustainment of poloidal flux for nearly 1 ms in the presence of NBI.« less

Analytical solution for the advection-dispersion transport equation in layered media

USDA-ARS?s Scientific Manuscript database

The advection-dispersion transport equation with first-order decay was solved analytically for multi-layered media using the classic integral transform technique (CITT). The solution procedure used an associated non-self-adjoint advection-diffusion eigenvalue problem that had the same form and coef...

A nonlinear equation for ionic diffusion in a strong binary electrolyte

PubMed Central

Ghosal, Sandip; Chen, Zhen

2010-01-01

The problem of the one-dimensional electro-diffusion of ions in a strong binary electrolyte is considered. The mathematical description, known as the Poisson–Nernst–Planck (PNP) system, consists of a diffusion equation for each species augmented by transport owing to a self-consistent electrostatic field determined by the Poisson equation. This description is also relevant to other important problems in physics, such as electron and hole diffusion across semiconductor junctions and the diffusion of ions in plasmas. If concentrations do not vary appreciably over distances of the order of the Debye length, the Poisson equation can be replaced by the condition of local charge neutrality first introduced by Planck. It can then be shown that both species diffuse at the same rate with a common diffusivity that is intermediate between that of the slow and fast species (ambipolar diffusion). Here, we derive a more general theory by exploiting the ratio of the Debye length to a characteristic length scale as a small asymptotic parameter. It is shown that the concentration of either species may be described by a nonlinear partial differential equation that provides a better approximation than the classical linear equation for ambipolar diffusion, but reduces to it in the appropriate limit. PMID:21818176

Global Regularity and Time Decay for the 2D Magnetohydrodynamic Equations with Fractional Dissipation and Partial Magnetic Diffusion

NASA Astrophysics Data System (ADS)

Dong, Bo-Qing; Jia, Yan; Li, Jingna; Wu, Jiahong

2018-05-01

This paper focuses on a system of the 2D magnetohydrodynamic (MHD) equations with the kinematic dissipation given by the fractional operator (-Δ )^α and the magnetic diffusion by partial Laplacian. We are able to show that this system with any α >0 always possesses a unique global smooth solution when the initial data is sufficiently smooth. In addition, we make a detailed study on the large-time behavior of these smooth solutions and obtain optimal large-time decay rates. Since the magnetic diffusion is only partial here, some classical tools such as the maximal regularity property for the 2D heat operator can no longer be applied. A key observation on the structure of the MHD equations allows us to get around the difficulties due to the lack of full Laplacian magnetic diffusion. The results presented here are the sharpest on the global regularity problem for the 2D MHD equations with only partial magnetic diffusion.

Determination of diffusion coefficient in disordered organic semiconductors

NASA Astrophysics Data System (ADS)

Rani, Varsha; Sharma, Akanksha; Ghosh, Subhasis

2016-05-01

Charge carrier transport in organic semiconductors is dominated by positional and energetic disorder in Gaussian density of states (GDOS) and is characterized by hopping through localized states. Due to the immobilization of charge carriers in these localized states, significant non-uniform carrier distribution exists, resulting diffusive transport. A simple, nevertheless powerful technique to determine diffusion coefficient D in disordered organic semiconductors has been presented. Diffusion coefficients of charge carriers in two technologically important organic molecular semiconductors, Pentacene and copper phthalocyanine (CuPc) have been measured from current-voltage (J-V) characteristics of Al/Pentacene/Au and Al/CuPc/Au based Schottky diodes. Ideality factor g and carrier mobility μ have been calculated from the exponential and space charge limited region respectively of J-V characteristics. Classical Einstein relation is not valid in organic semiconductors due to energetic disorders in DOS. Using generalized Einstein relation, diffusion coefficients have been obtained to be 1.31×10-6 and 1.73×10-7 cm2/s for Pentacene and CuPc respectively.

Quantitative characterization of non-classic polarization of cations on clay aggregate stability.

PubMed

Hu, Feinan; Li, Hang; Liu, Xinmin; Li, Song; Ding, Wuquan; Xu, Chenyang; Li, Yue; Zhu, Longhui

2015-01-01

Soil particle interactions are strongly influenced by the concentration, valence and ion species and the pH of the bulk solution, which will also affect aggregate stability and particle transport. In this study, we investigated clay aggregate stability in the presence of different alkali ions (Li+, Na+, K+, and Cs+) at concentrations from10-5 to 10-1 mol L-1. Strong specific ion effects on clay aggregate stability were observed, and showed the order Cs+>K+>Na+>Li+. We found that it was not the effects of ion size, hydration, and dispersion forces in the cation-surface interactions but strong non-classic polarization of adsorbed cations that resulted in these specific effects. In this study, the non-classic dipole moments of each cation species resulting from the non-classic polarization were estimated. By comparing non-classic dipole moments with classic values, the observed dipole moments of adsorbed cations were up to 104 times larger than the classic values for the same cation. The observed non-classic dipole moments sharply increased with decreasing electrolyte concentration. We conclude that strong non-classic polarization could significantly suppress the thickness of the diffuse layer, thereby weakening the electric field near the clay surface and resulting in improved clay aggregate stability. Even though we only demonstrated specific ion effects on aggregate stability with several alkali ions, our results indicate that these effects could be universally important in soil aggregate stability.

Quantitative Characterization of Non-Classic Polarization of Cations on Clay Aggregate Stability

PubMed Central

Hu, Feinan; Li, Hang; Liu, Xinmin; Li, Song; Ding, Wuquan; Xu, Chenyang; Li, Yue; Zhu, Longhui

2015-01-01

Soil particle interactions are strongly influenced by the concentration, valence and ion species and the pH of the bulk solution, which will also affect aggregate stability and particle transport. In this study, we investigated clay aggregate stability in the presence of different alkali ions (Li+, Na+, K+, and Cs+) at concentrations from10−5 to 10−1 mol L−1. Strong specific ion effects on clay aggregate stability were observed, and showed the order Cs+>K+>Na+>Li+. We found that it was not the effects of ion size, hydration, and dispersion forces in the cation–surface interactions but strong non-classic polarization of adsorbed cations that resulted in these specific effects. In this study, the non-classic dipole moments of each cation species resulting from the non-classic polarization were estimated. By comparing non-classic dipole moments with classic values, the observed dipole moments of adsorbed cations were up to 104 times larger than the classic values for the same cation. The observed non-classic dipole moments sharply increased with decreasing electrolyte concentration. We conclude that strong non-classic polarization could significantly suppress the thickness of the diffuse layer, thereby weakening the electric field near the clay surface and resulting in improved clay aggregate stability. Even though we only demonstrated specific ion effects on aggregate stability with several alkali ions, our results indicate that these effects could be universally important in soil aggregate stability. PMID:25874864

Product interactions and feedback in diffusion-controlled reactions

NASA Astrophysics Data System (ADS)

Roa, Rafael; Siegl, Toni; Kim, Won Kyu; Dzubiella, Joachim

2018-02-01

Steric or attractive interactions among reactants or between reactants and inert crowders can substantially influence the total rate of a diffusion-influenced reaction in the liquid phase. However, the role of the product species, which has typically different physical properties than the reactant species, has been disregarded so far. Here we study the effects of reactant-product and product-product interactions as well as asymmetric diffusion properties on the rate of diffusion-controlled reactions in the classical Smoluchowski-setup for chemical transformations at a perfect catalytic sphere. For this, we solve the diffusion equation with appropriate boundary conditions coupled by a mean-field approach on the second virial level to account for the particle interactions. We find that all particle spatial distributions and the total rate can change significantly, depending on the diffusion and interaction properties of the accumulated products. Complex competing and self-regulating (homeostatic) or self-amplifying effects are observed for the system, leading to both decrease and increase in the rates, as the presence of interacting products feeds back to the reactant flux and thus the rate with which the products are generated.

Nuclear Quantum Effects in H+ and OH- Diffusion Along Confined Water Wires from Ab Initio Path Integral Molecular Dyanmics

NASA Astrophysics Data System (ADS)

Rossi, Mariana; Ceriotti, Michele; Manolopoulos, David

Diffusion of H+ and OH- along water wires provides an efficient mechanism for charge transport that is exploited by biological systems and shows promise in technological applications. However, what is lacking for a better control and design of these systems is a thorough theoretical understanding of the diffusion process at the atomic scale. Here we consider H+ and OH- in finite water wires using density functional theory. We employ machine learning techniques to identify the charged species, thus obtaining an agnostic definition of the charge. We employ thermostated ring polymer molecular dynamics and extract a ``universal'' diffusion coefficient from simulations with different wire sizes by considering Langevin dynamics on the potential of mean force of the charged species. In the classical case, diffusion coefficients depend significantly on the potential energy surface, in particular on how dispersion forces modulate O-O distances. NQEs, however, make the diffusion less sensitive to the underlying potential and geometry of the wire, presumably making them more robust to environment fluctuations.

Comment on "A centroid molecular dynamics study of liquid para hydrogen and ortho deuterium" [J. Chem. Phys. 121, 6412 (2004)].

PubMed

Miller, Thomas F; Manolopoulos, David E; Madden, Paul A; Konieczny, Martin; Oberhofer, Harald

2005-02-01

We show that the two phase points considered in the recent simulations of liquid para hydrogen by Hone and Voth lie in the liquid-vapor coexistence region of a purely classical molecular dynamics simulation. By contrast, their phase point for ortho deuterium was in the one-phase liquid region for both classical and quantum simulations. These observations are used to account for their report that quantum mechanical effects enhance the diffusion in liquid para hydrogen and decrease it in ortho deuterium.(c) 2005 American Institute of Physics.

Diurnal cycle of precipitation at Dakar in the model LMDZ

NASA Astrophysics Data System (ADS)

Sane, Y.; Bonazzola, M.; Hourdin, F.; Diongue-Niang, A.

2009-04-01

Most diurnal cycles of precipitation are not well represented in general circulation models (GCMs). It is a concern for climate modeling because of the key role of clouds in the radiative and water budgets. The diurnal phasing of deep convection is a challenge, the pact of deep convection being generally simulated too early in the day (Guichard et al., 2004). Thus a "thermal plume model" - a mass flux scheme combined with a classical diffusive approach - originally developed to represent turbulent transport in the dry convective boundary layer, is extented to the representation of cloud processes. The modified parametrization was validated in a 1D configuration against results of large eddy simulations (Rio, 2008). It is here validated in a 3D configuration against in situ precipitation measurements of the AMMA campaign. A data analysis of the diurnal cycle of precipitation as measured by the pluviometers net in the Dakar area is performed. The improvement of the diurnal cyle of convection in the GCM is demonstrated, and the involved processes are analysed.

Three-dimensional kinetic and fluid dynamic modeling and three iterative algorithms for side-pumped alkali vapor lasers

NASA Astrophysics Data System (ADS)

Shen, Binglin; Xu, Xingqi; Xia, Chunsheng; Pan, Bailiang

2017-11-01

Combining the kinetic and fluid dynamic processes in static and flowing-gas diode-pumped alkali vapor lasers, a comprehensive physical model with three cyclically iterative algorithms for simulating the three-dimensional pump and laser intensities as well as temperature distribution in the vapor cell of side-pumped alkali vapor lasers is established. Comparison with measurement of a static side-pumped cesium vapor laser with a diffuse type hollow cylinder cavity, and with classical and modified models is made. Influences of flowed velocity and pump power on laser power are calculated and analyzed. The results have demonstrated that for high-power side-pumped alkali vapor lasers, it is necessary to take into account the three-dimensional distributions of pump energy, laser energy and temperature in the cell to simultaneously obtain the thermal features and output characteristics. Therefore, the model can deepen the understanding of the complete kinetic and fluid dynamic mechanisms of a side-pumped alkali vapor laser, and help with its further experimental design.

High-Pressure Transport Properties Of Fluids: Theory And Data From Levitated Drops At Combustion-Relevant Temperatures

NASA Technical Reports Server (NTRS)

Bellan, Josette; Harstad, Kenneth; Ohsaka, Kenichi

2003-01-01

Although the high pressure multicomponent fluid conservation equations have already been derived and approximately validated for binary mixtures by this PI, the validation of the multicomponent theory is hampered by the lack of existing mixing rules for property calculations. Classical gas dynamics theory can provide property mixing-rules at low pressures exclusively. While thermal conductivity and viscosity high-pressure mixing rules have been documented in the literature, there is no such equivalent for the diffusion coefficients and the thermal diffusion factors. The primary goal of this investigation is to extend the low pressure mixing rule theory to high pressures and validate the new theory with experimental data from levitated single drops. The two properties that will be addressed are the diffusion coefficients and the thermal diffusion factors. To validate/determine the property calculations, ground-based experiments from levitated drops are being conducted.

Laminar and Turbulent Gaseous Diffusion Flames. Appendix C

NASA Technical Reports Server (NTRS)

Faeth, G. M.; Urban, D. L. (Technical Monitor); Yuan, Z.-G. (Technical Monitor)

2001-01-01

Recent measurements and predictions of the properties of homogeneous (gaseous) laminar and turbulent non-premixed (diffusion) flames are discussed, emphasizing results from both ground- and space-based studies at microgravity conditions. Initial considerations show that effects of buoyancy not only complicate the interpretation of observations of diffusion flames but at times mislead when such results are applied to the non-buoyant diffusion flame conditions of greatest practical interest. This behavior motivates consideration of experiments where effects of buoyancy are minimized; therefore, methods of controlling the intrusion of buoyancy during observations of non-premixed flames are described, considering approaches suitable for both normal laboratory conditions as well as classical microgravity techniques. Studies of laminar flames at low-gravity and microgravity conditions are emphasized in view of the computational tractability of such flames for developing methods of predicting flame structure as well as the relevance of such flames to more practical turbulent flames by exploiting laminar flamelet concepts.

Multiband corrections for the semi-classical simulation of interband tunneling in GaAs tunnel junctions

NASA Astrophysics Data System (ADS)

Louarn, K.; Claveau, Y.; Hapiuk, D.; Fontaine, C.; Arnoult, A.; Taliercio, T.; Licitra, C.; Piquemal, F.; Bounouh, A.; Cavassilas, N.; Almuneau, G.

2017-09-01

The aim of this study is to investigate the impact of multiband corrections on the current density in GaAs tunnel junctions (TJs) calculated with a refined yet simple semi-classical interband tunneling model (SCITM). The non-parabolicity of the considered bands and the spin-orbit effects are considered by using a recently revisited SCITM available in the literature. The model is confronted to experimental results from a series of molecular beam epitaxy grown GaAs TJs and to numerical results obtained with a full quantum model based on the non-equilibrium Green’s function formalism and a 6-band k.p Hamiltonian. We emphasize the importance of considering the non-parabolicity of the conduction band by two different measurements of the energy-dependent electron effective mass in N-doped GaAs. We also propose an innovative method to compute the non-uniform electric field in the TJ for the SCITM simulations, which is of prime importance for a successful operation of the model. We demonstrate that, when considering the multiband corrections and this new computation of the non-uniform electric field, the SCITM succeeds in predicting the electrical characteristics of GaAs TJs, and are also in agreement with the quantum model. Besides the fundamental study of the tunneling phenomenon in TJs, the main benefit of this SCITM is that it can be easily embedded into drift-diffusion software, which are the most widely-used simulation tools for electronic and opto-electronic devices such as multi-junction solar cells, tunnel field-effect transistors, or vertical-cavity surface-emitting lasers.

ADHD performance reflects inefficient but not impulsive information processing: a diffusion model analysis.

PubMed

Metin, Baris; Roeyers, Herbert; Wiersema, Jan R; van der Meere, Jaap J; Thompson, Margaret; Sonuga-Barke, Edmund

2013-03-01

Attention-deficit/hyperactivity disorder (ADHD) is associated with performance deficits across a broad range of tasks. Although individual tasks are designed to tap specific cognitive functions (e.g., memory, inhibition, planning, etc.), these deficits could also reflect general effects related to either inefficient or impulsive information processing or both. These two components cannot be isolated from each other on the basis of classical analysis in which mean reaction time (RT) and mean accuracy are handled separately. Seventy children with a diagnosis of combined type ADHD and 50 healthy controls (between 6 and 17 years) performed two tasks: a simple two-choice RT (2-CRT) task and a conflict control task (CCT) that required higher levels of executive control. RT and errors were analyzed using the Ratcliff diffusion model, which divides decisional time into separate estimates of information processing efficiency (called "drift rate") and speed-accuracy tradeoff (SATO, called "boundary"). The model also provides an estimate of general nondecisional time. Results were the same for both tasks independent of executive load. ADHD was associated with lower drift rate and less nondecisional time. The groups did not differ in terms of boundary parameter estimates. RT and accuracy performance in ADHD appears to reflect inefficient rather than impulsive information processing, an effect independent of executive function load. The results are consistent with models in which basic information processing deficits make an important contribution to the ADHD cognitive phenotype. PsycINFO Database Record (c) 2013 APA, all rights reserved.

A discrete model of Ostwald ripening based on multiple pairwise interactions

NASA Astrophysics Data System (ADS)

Di Nunzio, Paolo Emilio

2018-06-01

A discrete multi-particle model of Ostwald ripening based on direct pairwise interactions is developed for particles with incoherent interfaces as an alternative to the classical LSW mean field theory. The rate of matter exchange depends on the average surface-to-surface interparticle distance, a characteristic feature of the system which naturally incorporates the effect of volume fraction of second phase. The multi-particle diffusion is described through the definition of an interaction volume containing all the particles involved in the exchange of solute. At small volume fractions this is proportional to the size of the central particle, at higher volume fractions it gradually reduces as a consequence of diffusion screening described on a geometrical basis. The topological noise present in real systems is also included. For volume fractions below about 0.1 the model predicts broad and right-skewed stationary size distributions resembling a lognormal function. Above this value, a transition to sharper, more symmetrical but still right-skewed shapes occurs. An excellent agreement with experiments is obtained for 3D particle size distributions of solid-solid and solid-liquid systems with volume fraction 0.07, 0.30, 0.52 and 0.74. The kinetic constant of the model depends on the cube root of volume fraction up to about 0.1, then increases rapidly with an upward concavity. It is in good agreement with the available literature data on solid-liquid mixtures in the volume fraction range from 0.20 to about 0.75.

Physical properties of asteroids derived from a novel approach to modeling of optical lightcurves and WISE thermalinfrared data

NASA Astrophysics Data System (ADS)

Durech, Josef; Hanus, Josef; Delbo, Marco; Ali-Lagoa, Victor; Carry, Benoit

2014-11-01

Convex shape models and spin vectors of asteroids are now routinely derived from their disk-integrated lightcurves by the lightcurve inversion method of Kaasalainen et al. (2001, Icarus 153, 37). These shape models can be then used in combination with thermal infrared data and a thermophysical model to derive other physical parameters - size, albedo, macroscopic roughness and thermal inertia of the surface. In this classical two-step approach, the shape and spin parameters are kept fixed during the thermophysical modeling when the emitted thermal flux is computed from the surface temperature, which is computed by solving a 1-D heat diffusion equation in sub-surface layers. A novel method of simultaneous inversion of optical and infrared data was presented by Durech et al. (2012, LPI Contribution No. 1667, id.6118). The new algorithm uses the same convex shape representation as the lightcurve inversion but optimizes all relevant physical parameters simultaneously (including the shape, size, rotation vector, thermal inertia, albedo, surface roughness, etc.), which leads to a better fit to the thermal data and a reliable estimation of model uncertainties. We applied this method to selected asteroids using their optical lightcurves from archives and thermal infrared data observed by the Wide-field Infrared Survey Explorer (WISE) satellite. We will (i) show several examples of how well our model fits both optical and infrared data, (ii) discuss the uncertainty of derived parameters (namely the thermal inertia), (iii) compare results obtained with the two-step approach with those obtained by our method, (iv) discuss the advantages of this simultaneous approach with respect to the classical two-step approach, and (v) advertise the possibility to use this approach to tens of thousands asteroids for which enough WISE and optical data exist.

Constitutive activation of alternative nuclear factor kappa B pathway in canine diffuse large B-cell lymphoma contributes to tumor cell survival and is a target of new adjuvant therapies.

PubMed

Seelig, Davis M; Ito, Daisuke; Forster, Colleen L; Yoon, Una A; Breen, Matthew; Burns, Linda J; Bachanova, Veronika; Lindblad-Toh, Kerstin; O'Brien, Timothy D; Schmechel, Stephen C; Rizzardi, Anthony E; Modiano, Jaime F; Linden, Michael A

2017-07-01

Activation of the classical nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) pathway is a common molecular event observed in both human and canine diffuse large B-cell lymphoma (DLBCL). Although the oncogenic potential of the alternative NFκB pathway (ANFκBP) has also been recently identified in DLBCL, its precise role in tumor pathogenesis and potential as a treatment target is understudied. We hypothesized that up-regulation of the ANFκBP plays an important role in the proliferation and survival of canine DLBCL cells, and we demonstrate that the ANFκBP is constitutively active in primary canine DLBCL samples and a cell line (CLBL1). We further demonstrate that a small interfering RNA inhibits the activation of the NFκB pathway and induces apoptosis in canine DLBCL cells. In conclusion, the ANFκBP facilitates survival of canine DLBCL cells, and thus, dogs with spontaneous DLBCL can provide a useful large animal model to study therapies targeting the ANFκBP.

Quantification of ionic transport within thermally-activated batteries using electron probe micro-analysis

DOE PAGES

Humplik, Thomas; Stirrup, Emily K.; Grillet, Anne M.; ...

2016-04-30

The transient transport of electrolytes in thermally-activated batteries is studied in this paper using electron probe micro-analysis (EPMA), demonstrating the robust capability of EPMA as a useful tool for studying and quantifying mass transport within porous materials, particularly in difficult environments where classical flow measurements are challenging. By tracking the mobility of bromine and potassium ions from the electrolyte stored within the separator into the lithium silicon anode and iron disulfide cathode, we are able to quantify the transport mechanisms and physical properties of the electrodes including permeability and tortuosity. Due to the micron to submicron scale porous structure ofmore » the initially dry anode, a fast capillary pressure driven flow is observed into the anode from which we are able to set a lower bound on the permeability of 10 -1 mDarcy. The transport into the cathode is diffusion-limited because the cathode originally contained some electrolyte before activation. Finally, using a transient one-dimensional diffusion model, we estimate the tortuosity of the cathode electrode to be 2.8 ± 0.8.« less

Transient Ejector Analysis (TEA) code user's guide

NASA Technical Reports Server (NTRS)

Drummond, Colin K.

1993-01-01

A FORTRAN computer program for the semi analytic prediction of unsteady thrust augmenting ejector performance has been developed, based on a theoretical analysis for ejectors. That analysis blends classic self-similar turbulent jet descriptions with control-volume mixing region elements. Division of the ejector into an inlet, diffuser, and mixing region allowed flexibility in the modeling of the physics for each region. In particular, the inlet and diffuser analyses are simplified by a quasi-steady-analysis, justified by the assumption that pressure is the forcing function in those regions. Only the mixing region is assumed to be dominated by viscous effects. The present work provides an overview of the code structure, a description of the required input and output data file formats, and the results for a test case. Since there are limitations to the code for applications outside the bounds of the test case, the user should consider TEA as a research code (not as a production code), designed specifically as an implementation of the proposed ejector theory. Program error flags are discussed, and some diagnostic routines are presented.

Superdiffusive gas recovery from nanopores

NASA Astrophysics Data System (ADS)

Wu, Haiyi; He, Yadong; Qiao, Rui

2016-11-01

Understanding the recovery of gas from reservoirs featuring pervasive nanopores is essential for effective shale gas extraction. Classical theories cannot accurately predict such gas recovery and many experimental observations are not well understood. Here we report molecular simulations of the recovery of gas from single nanopores, explicitly taking into account molecular gas-wall interactions. We show that, in very narrow pores, the strong gas-wall interactions are essential in determining the gas recovery behavior both quantitatively and qualitatively. These interactions cause the total diffusion coefficients of the gas molecules in nanopores to be smaller than those predicted by kinetic theories, hence slowing down the rate of gas recovery. These interactions also lead to significant adsorption of gas molecules on the pore walls. Because of the desorption of these gas molecules during gas recovery, the gas recovery from the nanopore does not exhibit the usual diffusive scaling law (i.e., the accumulative recovery scales as R ˜t1 /2 ) but follows a superdiffusive scaling law R ˜tn (n >0.5 ), which is similar to that observed in some field experiments. For the system studied here, the superdiffusive gas recovery scaling law can be captured well by continuum models in which the gas adsorption and desorption from pore walls are taken into account using the Langmuir model.

Multimodal brain-tumor segmentation based on Dirichlet process mixture model with anisotropic diffusion and Markov random field prior.

PubMed

Lu, Yisu; Jiang, Jun; Yang, Wei; Feng, Qianjin; Chen, Wufan

2014-01-01

Brain-tumor segmentation is an important clinical requirement for brain-tumor diagnosis and radiotherapy planning. It is well-known that the number of clusters is one of the most important parameters for automatic segmentation. However, it is difficult to define owing to the high diversity in appearance of tumor tissue among different patients and the ambiguous boundaries of lesions. In this study, a nonparametric mixture of Dirichlet process (MDP) model is applied to segment the tumor images, and the MDP segmentation can be performed without the initialization of the number of clusters. Because the classical MDP segmentation cannot be applied for real-time diagnosis, a new nonparametric segmentation algorithm combined with anisotropic diffusion and a Markov random field (MRF) smooth constraint is proposed in this study. Besides the segmentation of single modal brain-tumor images, we developed the algorithm to segment multimodal brain-tumor images by the magnetic resonance (MR) multimodal features and obtain the active tumor and edema in the same time. The proposed algorithm is evaluated using 32 multimodal MR glioma image sequences, and the segmentation results are compared with other approaches. The accuracy and computation time of our algorithm demonstrates very impressive performance and has a great potential for practical real-time clinical use.

Multimodal Brain-Tumor Segmentation Based on Dirichlet Process Mixture Model with Anisotropic Diffusion and Markov Random Field Prior

PubMed Central

Lu, Yisu; Jiang, Jun; Chen, Wufan

2014-01-01

Brain-tumor segmentation is an important clinical requirement for brain-tumor diagnosis and radiotherapy planning. It is well-known that the number of clusters is one of the most important parameters for automatic segmentation. However, it is difficult to define owing to the high diversity in appearance of tumor tissue among different patients and the ambiguous boundaries of lesions. In this study, a nonparametric mixture of Dirichlet process (MDP) model is applied to segment the tumor images, and the MDP segmentation can be performed without the initialization of the number of clusters. Because the classical MDP segmentation cannot be applied for real-time diagnosis, a new nonparametric segmentation algorithm combined with anisotropic diffusion and a Markov random field (MRF) smooth constraint is proposed in this study. Besides the segmentation of single modal brain-tumor images, we developed the algorithm to segment multimodal brain-tumor images by the magnetic resonance (MR) multimodal features and obtain the active tumor and edema in the same time. The proposed algorithm is evaluated using 32 multimodal MR glioma image sequences, and the segmentation results are compared with other approaches. The accuracy and computation time of our algorithm demonstrates very impressive performance and has a great potential for practical real-time clinical use. PMID:25254064

Collision cross sections and transport coefficients of O-, O2 -, O3 - and O4 - negative ions in O2, N2 and dry air for non-thermal plasmas modelling

NASA Astrophysics Data System (ADS)

Hennad, Ali; Yousfi, Mohammed

2018-02-01

The ions interaction data such as interaction potential parameters, elastic and inelastic collision cross sections and the transport coefficients (reduced mobility and diffusion coefficients) have been determined and analyzed in the case of the main negative oxygen ions (O-, O2 -, O3 - and O4 -) present in low temperature plasma at atmospheric pressure when colliding O2, N2 and dry air. The ion transport has been determined from an optimized Monte Carlo simulation using calculated elastic and experimentally fitted inelastic collision cross sections. The elastic momentum transfer collision cross sections have been calculated from a semi-classical JWKB approximation based on a ( n-4) rigid core interaction potential model. The cross sections sets involving elastic and inelastic processes were then validated using measured reduced mobility data and also diffusion coefficient whenever available in the literature. From the sets of elastic and inelastic collision cross sections thus obtained for the first time for O3-/O2, O2 -/N2, O3 -/N2, and O4 -/N2 systems, the ion transport coefficients were calculated in pure gases and dry air over a wide range of the density reduced electric field E/N.

Capillary transit time heterogeneity and flow-metabolism coupling after traumatic brain injury

PubMed Central

Østergaard, Leif; Engedal, Thorbjørn S; Aamand, Rasmus; Mikkelsen, Ronni; Iversen, Nina K; Anzabi, Maryam; Næss-Schmidt, Erhard T; Drasbek, Kim R; Bay, Vibeke; Blicher, Jakob U; Tietze, Anna; Mikkelsen, Irene K; Hansen, Brian; Jespersen, Sune N; Juul, Niels; Sørensen, Jens CH; Rasmussen, Mads

2014-01-01

Most patients who die after traumatic brain injury (TBI) show evidence of ischemic brain damage. Nevertheless, it has proven difficult to demonstrate cerebral ischemia in TBI patients. After TBI, both global and localized changes in cerebral blood flow (CBF) are observed, depending on the extent of diffuse brain swelling and the size and location of contusions and hematoma. These changes vary considerably over time, with most TBI patients showing reduced CBF during the first 12 hours after injury, then hyperperfusion, and in some patients vasospasms before CBF eventually normalizes. This apparent neurovascular uncoupling has been ascribed to mitochondrial dysfunction, hindered oxygen diffusion into tissue, or microthrombosis. Capillary compression by astrocytic endfeet swelling is observed in biopsies acquired from TBI patients. In animal models, elevated intracranial pressure compresses capillaries, causing redistribution of capillary flows into patterns argued to cause functional shunting of oxygenated blood through the capillary bed. We used a biophysical model of oxygen transport in tissue to examine how capillary flow disturbances may contribute to the profound changes in CBF after TBI. The analysis suggests that elevated capillary transit time heterogeneity can cause critical reductions in oxygen availability in the absence of ‘classic' ischemia. We discuss diagnostic and therapeutic consequences of these predictions. PMID:25052556

In Situ FTIR Microspectroscopy of Brain Tissue from a Transgenic Mouse Model of Alzheimer Disease

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

Rak,M.; Del Bigio, M.; Mai, S.

2007-01-01

Plaques composed of the A{beta} peptide are the main pathological feature of Alzheimer's disease. Dense-core plaques are fibrillar deposits of A{beta}, showing all the classical properties of amyloid including {beta}-sheet secondary structure, while diffuse plaques are amorphous deposits. We studied both plaque types, using synchrotron infrared (IR) microspectroscopy, a technique that allows the chemical composition and average protein secondary structure to be investigated in situ. We examined plaques in hippocampal, cortical and caudal tissue from 5- to 21-month-old TgCRND8 mice, a transgenic model expressing doubly mutant amyloid precursor protein, and displaying impaired hippocampal function and robust pathology from an earlymore » age. Spectral analysis confirmed that the congophilic plaque cores were composed of protein in a {beta}-sheet conformation. The amide I maximum of plaque cores was at 1623 cm-1, and unlike for in vitro A{beta} fibrils, the high-frequency (1680-1690 cm-1) component attributed to antiparallel {beta}-sheet was not observed. A significant elevation in phospholipids was found around dense-core plaques in TgCRND8 mice ranging in age from 5 to 21 months. In contrast, diffuse plaques were not associated with IR detectable changes in protein secondary structure or relative concentrations of any other tissue components.« less

Numerical simulation of the geodynamo reaches Earth's core dynamical regime

NASA Astrophysics Data System (ADS)

Aubert, J.; Gastine, T.; Fournier, A.

2016-12-01

Numerical simulations of the geodynamo have been successful at reproducing a number of static (field morphology) and kinematic (secular variation patterns, core surface flows and westward drift) features of Earth's magnetic field, making them a tool of choice for the analysis and retrieval of geophysical information on Earth's core. However, classical numerical models have been run in a parameter regime far from that of the real system, prompting the question of whether we do get "the right answers for the wrong reasons", i.e. whether the agreement between models and nature simply occurs by chance and without physical relevance in the dynamics. In this presentation, we show that classical models succeed in describing the geodynamo because their large-scale spatial structure is essentially invariant as one progresses along a well-chosen path in parameter space to Earth's core conditions. This path is constrained by the need to enforce the relevant force balance (MAC or Magneto-Archimedes-Coriolis) and preserve the ratio of the convective overturn and magnetic diffusion times. Numerical simulations performed along this path are shown to be spatially invariant at scales larger than that where the magnetic energy is ohmically dissipated. This property enables the definition of large-eddy simulations that show good agreement with direct numerical simulations in the range where both are feasible, and that can be computed at unprecedented values of the control parameters, such as an Ekman number E=10-8. Combining direct and large-eddy simulations, large-scale invariance is observed over half the logarithmic distance in parameter space between classical models and Earth. The conditions reached at this mid-point of the path are furthermore shown to be representative of the rapidly-rotating, asymptotic dynamical regime in which Earth's core resides, with a MAC force balance undisturbed by viscosity or inertia, the enforcement of a Taylor state and strong-field dynamo action. We conclude that numerical modelling has advanced to a stage where it is possible to use models correctly representing the statics, kinematics and now the dynamics of the geodynamo. This opens the way to a better analysis of the geomagnetic field in the time and space domains.

Diffusion-driven fluid dynamics in ideal gases and plasmas

NASA Astrophysics Data System (ADS)

Vold, E. L.; Yin, L.; Taitano, W.; Molvig, K.; Albright, B. J.

2018-06-01

The classical transport theory based on Chapman-Enskog methods provides self-consistent approximations for the kinetic flux of mass, heat, and momentum in a fluid limit characterized with a small Knudsen number. The species mass fluxes relative to the center of mass, or "diffusive fluxes," are expressed as functions of known gradient quantities with kinetic coefficients evaluated using similar analyses for mixtures of gases or plasma components. The sum over species of the diffusive mass fluxes is constrained to be zero in the Lagrange frame, and thus results in a non-zero molar flux leading to a pressure perturbation. At an interface between two species initially in pressure equilibrium, the pressure perturbation driven by the diffusive molar flux induces a center of mass velocity directed from the species of greater atomic mass towards the lighter atomic mass species. As the ratio of the species particle masses increases, this center of mass velocity carries an increasingly greater portion of the mass across the interface and for a particle mass ratio greater than about two, the center of mass velocity carries more mass than the gradient driven diffusion flux. Early time transients across an interface between two species in a 1D plasma regime and initially in equilibrium are compared using three methods; a fluid code with closure in a classical transport approximation, a particle in cell simulation, and an implicit Fokker-Planck solver for the particle distribution functions. The early time transient phenomenology is shown to be similar in each of the computational simulation methods, including a pressure perturbation associated with the stationary "induced" component of the center of mass velocity which decays to pressure equilibrium during diffusion. At early times, the diffusive process generates pressure and velocity waves which propagate outward from the interface and are required to maintain momentum conservation. The energy in the outgoing waves dissipates as heat in viscous regions, and it is hypothesized that these diffusion driven waves may sustain fluctuations in less viscid finite domains after reflections from the boundaries. These fluid dynamic phenomena are similar in gases or plasmas and occur in flow transients with a moderate Knudsen number. The analysis and simulation results show how the kinetic flux, represented in the fluid transport closure, directly modifies the mass averaged flow described with the Euler equations.

White matter changes in an untreated, newly diagnosed case of classical homocystinuria.

PubMed

Brenton, J Nicholas; Matsumoto, Julie A; Rust, Robert S; Wilson, William G

2014-01-01

The authors report the case of a 4-year-old boy who developed progressive unilateral weakness and developmental delays prior to his diagnosis of classical homocystinuria. Magnetic resonance imaging (MRI) of the brain demonstrated diffuse white matter changes, raising the concern for a secondary diagnosis causing leukoencephalopathy, since classical homocystinuria is not typically associated with these changes. Other inborn errors of the transsulfuration pathway have been reported as causing these changes. Once begun on therapy for his homocystinuria, his neurologic deficits resolved and his delays rapidly improved. Repeat MRI performed one year after instating therapy showed resolution of his white matter abnormalities. This case illustrates the need to consider homocystinuria and other amino acidopathies in the differential diagnosis of childhood white matter diseases and lends weight to the hypothesis that hypermethioninemia may induce white matter changes.

Multiphysics modeling of non-linear laser-matter interactions for optically active semiconductors

NASA Astrophysics Data System (ADS)

Kraczek, Brent; Kanp, Jaroslaw

Development of photonic devices for sensors and communications devices has been significantly enhanced by computational modeling. We present a new computational method for modelling laser propagation in optically-active semiconductors within the paraxial wave approximation (PWA). Light propagation is modeled using the Streamline-upwind/Petrov-Galerkin finite element method (FEM). Material response enters through the non-linear polarization, which serves as the right-hand side of the FEM calculation. Maxwell's equations for classical light propagation within the PWA can be written solely in terms of the electric field, producing a wave equation that is a form of the advection-diffusion-reaction equations (ADREs). This allows adaptation of the computational machinery developed for solving ADREs in fluid dynamics to light-propagation modeling. The non-linear polarization is incorporated using a flexible framework to enable the use of multiple methods for carrier-carrier interactions (e.g. relaxation-time-based or Monte Carlo) to enter through the non-linear polarization, as appropriate to the material type. We demonstrate using a simple carrier-carrier model approximating the response of GaN. Supported by ARL Materials Enterprise.

A control-volume method for analysis of unsteady thrust augmenting ejector flows

NASA Technical Reports Server (NTRS)

Drummond, Colin K.

1988-01-01

A method for predicting transient thrust augmenting ejector characteristics is presented. The analysis blends classic self-similar turbulent jet descriptions with a control volume mixing region discretization to solicit transient effects in a new way. Division of the ejector into an inlet, diffuser, and mixing region corresponds with the assumption of viscous-dominated phenomenon in the latter. Inlet and diffuser analyses are simplified by a quasi-steady analysis, justified by the assumptions that pressure is the forcing function in those regions. Details of the theoretical foundation, the solution algorithm, and sample calculations are given.

Breathing pulses in singularly perturbed reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Veerman, Frits

2015-07-01

The weakly nonlinear stability of pulses in general singularly perturbed reaction-diffusion systems near a Hopf bifurcation is determined using a centre manifold expansion. A general framework to obtain leading order expressions for the (Hopf) centre manifold expansion for scale separated, localised structures is presented. Using the scale separated structure of the underlying pulse, directly calculable expressions for the Hopf normal form coefficients are obtained in terms of solutions to classical Sturm-Liouville problems. The developed theory is used to establish the existence of breathing pulses in a slowly nonlinear Gierer-Meinhardt system, and is confirmed by direct numerical simulation.

On solutions of the fifth-order dispersive equations with porous medium type non-linearity

NASA Astrophysics Data System (ADS)

Kocak, Huseyin; Pinar, Zehra

2018-07-01

In this work, we focus on obtaining the exact solutions of the fifth-order semi-linear and non-linear dispersive partial differential equations, which have the second-order diffusion-like (porous-type) non-linearity. The proposed equations were not studied in the literature in the sense of the exact solutions. We reveal solutions of the proposed equations using the classical Riccati equations method. The obtained exact solutions, which can play a key role to simulate non-linear waves in the medium with dispersion and diffusion, are illustrated and discussed in details.

Enhanced Thermal Diffusion of Li in Graphite by Alternating Vertical Electric Field: A Hybrid Quantum-Classical Simulation Study

NASA Astrophysics Data System (ADS)

Ohba, Nobuko; Ogata, Shuji; Tamura, Tomoyuki; Kobayashi, Ryo; Yamakawa, Shunsuke; Asahi, Ryoji

2012-02-01

Enhancing the diffusivity of the Li ion in a Li-graphite intercalation compound that has been used as a negative electrode in the Li-ion rechargeable battery, is important in improving both the recharging speed and power of the battery. In the compound, the Li ion creates a long-range stress field around itself by expanding the interlayer spacing of graphite. We advance the hybrid quantum-classical simulation code to include the external electric field in addition to the long-range stress field by first-principles simulation. In the hybrid code, the quantum region selected adaptively around the Li ion is treated using the real-space density-functional theory for electrons. The rest of the system is described with an empirical interatomic potential that includes the term relating to the dispersion force between the C atoms in different layers. Hybrid simulation runs for Li dynamics in graphite are performed at 423 K under various settings of the amplitude and frequency of alternating electric fields perpendicular to C-layers. We find that the in-plane diffusivity of the Li ion is enhanced significantly by the electric field if the amplitude is larger than 0.2 V/Å within its order and the frequency is as high as 1.7 THz. The microscopic mechanisms of the enhancement are explained.

Fractional calculus in hydrologic modeling: A numerical perspective

PubMed Central

Benson, David A.; Meerschaert, Mark M.; Revielle, Jordan

2013-01-01

Fractional derivatives can be viewed either as handy extensions of classical calculus or, more deeply, as mathematical operators defined by natural phenomena. This follows the view that the diffusion equation is defined as the governing equation of a Brownian motion. In this paper, we emphasize that fractional derivatives come from the governing equations of stable Lévy motion, and that fractional integration is the corresponding inverse operator. Fractional integration, and its multi-dimensional extensions derived in this way, are intimately tied to fractional Brownian (and Lévy) motions and noises. By following these general principles, we discuss the Eulerian and Lagrangian numerical solutions to fractional partial differential equations, and Eulerian methods for stochastic integrals. These numerical approximations illuminate the essential nature of the fractional calculus. PMID:23524449

Structural and diffusion characterizations of steam-stable mesostructured zeolitic UL-ZSM-5 materials.

PubMed

Vinh-Thang, Hoang; Huang, Qinglin; Ungureanu, Adrian; Eić, Mladen; Trong-On, Do; Kaliaguine, Serge

2006-05-09

A series of mesoporous UL-ZSM-5 materials (Si/Al = 50) with different micro- and mesoporosity as well as crystallinity was prepared following the procedure proposed in one of our recent studies (Trong-On, D.; Kaliaguine, S. Angew. Chem. Int. Ed. 2001, 40, 3248-3251. Trong-On, D.; Kaliaguine, S. U.S. Patent 6,669,924, B1, 2003). These materials have zeolitic structure in the form of nanoparticles intergrown in the walls of the amorphous wormhole-like aluminosilicate mesopores of Al-Meso-50, which was used as a precursor in the synthesis. The structure, crystallinity, and textural properties of the synthesized materials, as well as a reference ZSM-5 zeolite sample, were determined by X-ray diffraction (XRD), transmission electron microscopy (TEM)/scanning electron microscoy (SEM) analyses, Fourier transform infrared spectroscopy (FTIR), 27Al magic angle spinning (MAS) nuclear magnetic resonance (NMR), and nitrogen adsorption/desorption techniques. The acid properties were examined by FTIR of adsorbed pyridine. UL-ZSM-5 materials were shown to be highly hydrothermally stable. The diffusion of two C7 hydrocarbons, i.e., n-heptane and toluene, in four UL-ZSM-5 materials with different microporosities, related acidities, and crystallinities were investigated using the zero-length column (ZLC) method. Furthermore, the wormhole-like mesostructured aluminosilicate precursor (Al-Meso-50) and a reference MFI zeolite sample were also investigated using the same technique. A theoretical model considering a combination of mesopore diffusion (with surface slip in the main channels) with an activated, mainly surface diffusion mechanism in the intrawall biporous structure, was proposed and employed to interpret the experimental ZLC results. A classical Knudsen type of diffusion was replaced by an activated surface slip type of diffusion mechanism in the mesopores. The transport of n-heptane in UL-ZSM-5 materials was found to be mainly controlled by mesopore diffusion in the main-channel structure, while that of toluene was dominated by the intrawall diffusion process. Diffusion activation energies of n-heptane are about 2 times higher in comparison to toluene, which has a larger kinetic diameter. The main mesopore channel structure seems to appreciably contribute to the overall mass transport. Furthermore, the effect of hydrothermal treatment (20% steam at 800 degrees C for 24 h) on the diffusion of these two sorbates on UL-ZSM-5 materials was also evaluated.

The transboundary non-renewable Nubian Aquifer System of Chad, Egypt, Libya and Sudan: classical groundwater questions and parsimonious hydrogeologic analysis and modelin

USGS Publications Warehouse

Voss, Clifford I.; Soliman, Safaa M.

2014-01-01

Parsimonious groundwater modeling provides insight into hydrogeologic functioning of the Nubian Aquifer System (NAS), the world’s largest non-renewable groundwater system (belonging to Chad, Egypt, Libya, and Sudan). Classical groundwater-resource issues exist (magnitude and lateral extent of drawdown near pumping centers) with joint international management questions regarding transboundary drawdown. Much of NAS is thick, containing a large volume of high-quality groundwater, but receives insignificant recharge, so water-resource availability is time-limited. Informative aquifer data are lacking regarding large-scale response, providing only local-scale information near pumps. Proxy data provide primary underpinning for understanding regional response: Holocene water-table decline from the previous pluvial period, after thousands of years, results in current oasis/sabkha locations where the water table still intersects the ground. Depletion is found to be controlled by two regional parameters, hydraulic diffusivity and vertical anisotropy of permeability. Secondary data that provide insight are drawdowns near pumps and isotope-groundwater ages (million-year-old groundwaters in Egypt). The resultant strong simply structured three-dimensional model representation captures the essence of NAS regional groundwater-flow behavior. Model forecasts inform resource management that transboundary drawdown will likely be minimal—a nonissue—whereas drawdown within pumping centers may become excessive, requiring alternative extraction schemes; correspondingly, significant water-table drawdown may occur in pumping centers co-located with oases, causing oasis loss and environmental impacts.

Fluorescence Correlation Spectroscopy to Study Diffusion of Polymer Chains within Layered Hydrogen-Bonded Polymer Films

NASA Astrophysics Data System (ADS)

Pristinski, Denis; Kharlampieva, Evguenia; Sukhishvili, Svetlana

2002-03-01

Fluorescence Correlation Spectroscopy (FCS) has been used to probe molecular motions within polymer multilayers formed by hydrogen-bonding sequential self-assembly. Polyethylene glycol (PEG) molecules were end-labeled with the fluorescent tags, and self-assembled with polymethacrylic acid (PMAA) using layer-by-layer deposition. We have found that molecules included in the top adsorbed layer have significant mobility at the millisecond time scale, probably due to translational diffusion. However, their dynamics deviate from classical Brownian motion with a single diffusion time. Possible reasons for the deviation are discussed. We found that motions were significantly slowed with increasing depth within the PEG/PMAA multilayer. This phenomena occured in a narrow pH range around 4.0 in which intermolecular interactions were relatively weak.

Effective stochastic generator with site-dependent interactions

NASA Astrophysics Data System (ADS)

Khamehchi, Masoumeh; Jafarpour, Farhad H.

2017-11-01

It is known that the stochastic generators of effective processes associated with the unconditioned dynamics of rare events might consist of non-local interactions; however, it can be shown that there are special cases for which these generators can include local interactions. In this paper, we investigate this possibility by considering systems of classical particles moving on a one-dimensional lattice with open boundaries. The particles might have hard-core interactions similar to the particles in an exclusion process, or there can be many arbitrary particles at a single site in a zero-range process. Assuming that the interactions in the original process are local and site-independent, we will show that under certain constraints on the microscopic reaction rules, the stochastic generator of an unconditioned process can be local but site-dependent. As two examples, the asymmetric zero-temperature Glauber model and the A-model with diffusion are presented and studied under the above-mentioned constraints.

Stable time filtering of strongly unstable spatially extended systems

PubMed Central

Grote, Marcus J.; Majda, Andrew J.

2006-01-01

Many contemporary problems in science involve making predictions based on partial observation of extremely complicated spatially extended systems with many degrees of freedom and with physical instabilities on both large and small scale. Various new ensemble filtering strategies have been developed recently for these applications, and new mathematical issues arise. Because ensembles are extremely expensive to generate, one such issue is whether it is possible under appropriate circumstances to take long time steps in an explicit difference scheme and violate the classical Courant–Friedrichs–Lewy (CFL)-stability condition yet obtain stable accurate filtering by using the observations. These issues are explored here both through elementary mathematical theory, which provides simple guidelines, and the detailed study of a prototype model. The prototype model involves an unstable finite difference scheme for a convection–diffusion equation, and it is demonstrated below that appropriate observations can result in stable accurate filtering of this strongly unstable spatially extended system. PMID:16682626

Stable time filtering of strongly unstable spatially extended systems.

PubMed

Grote, Marcus J; Majda, Andrew J

2006-05-16

Many contemporary problems in science involve making predictions based on partial observation of extremely complicated spatially extended systems with many degrees of freedom and with physical instabilities on both large and small scale. Various new ensemble filtering strategies have been developed recently for these applications, and new mathematical issues arise. Because ensembles are extremely expensive to generate, one such issue is whether it is possible under appropriate circumstances to take long time steps in an explicit difference scheme and violate the classical Courant-Friedrichs-Lewy (CFL)-stability condition yet obtain stable accurate filtering by using the observations. These issues are explored here both through elementary mathematical theory, which provides simple guidelines, and the detailed study of a prototype model. The prototype model involves an unstable finite difference scheme for a convection-diffusion equation, and it is demonstrated below that appropriate observations can result in stable accurate filtering of this strongly unstable spatially extended system.

Continuum theories for fluid-particle flows: Some aspects of lift forces and turbulence

NASA Technical Reports Server (NTRS)

Mctigue, David F.; Givler, Richard C.; Nunziato, Jace W.

1988-01-01

A general framework is outlined for the modeling of fluid particle flows. The momentum exchange between the constituents embodies both lift and drag forces, constitutive equations for which can be made explicit with reference to known single particle analysis. Relevant results for lift are reviewed, and invariant representations are posed. The fluid and particle velocities and the particle volume fraction are then decomposed into mean and fluctuating parts to characterize turbulent motions, and the equations of motion are averaged. In addition to the Reynolds stresses, further correlations between concentration and velocity fluctuations appear. These can be identified with turbulent transport processes such as eddy diffusion of the particles. When the drag force is dominant, the classical convection dispersion model for turbulent transport of particles is recovered. When other interaction forces enter, particle segregation effects can arise. This is illustrated qualitatively by consideration of turbulent channel flow with lift effects included.

Darcy-Forchheimer flow with Cattaneo-Christov heat flux and homogeneous-heterogeneous reactions

PubMed Central

Hayat, Tasawar; Haider, Farwa; Alsaedi, Ahmed

2017-01-01

Here Darcy-Forchheimer flow of viscoelastic fluids has been analyzed in the presence of Cattaneo-Christov heat flux and homogeneous-heterogeneous reactions. Results for two viscoelastic fluids are obtained and compared. A linear stretching surface has been used to generate the flow. Flow in porous media is characterized by considering the Darcy-Forchheimer model. Modified version of Fourier's law through Cattaneo-Christov heat flux is employed. Equal diffusion coefficients are employed for both reactants and auto catalyst. Optimal homotopy scheme is employed for solutions development of nonlinear problems. Solutions expressions of velocity, temperature and concentration fields are provided. Skin friction coefficient and heat transfer rate are computed and analyzed. Here the temperature and thermal boundary layer thickness are lower for Cattaneo-Christov heat flux model in comparison to classical Fourier's law of heat conduction. Moreover, the homogeneous and heterogeneous reactions parameters have opposite behaviors for concentration field. PMID:28380014

Anomalous transport in cellular flows: The role of initial conditions and aging

NASA Astrophysics Data System (ADS)

Pöschke, Patrick; Sokolov, Igor M.; Nepomnyashchy, Alexander A.; Zaks, Michael A.

2016-09-01

We consider the diffusion-advection problem in two simple cellular flow models (often invoked as examples of subdiffusive tracer motion) and concentrate on the intermediate time range, in which the tracer motion indeed may show subdiffusion. We perform extensive numerical simulations of the systems under different initial conditions and show that the pure intermediate-time subdiffusion regime is only evident when the particles start at the border between different cells, i.e., at the separatrix, and is less pronounced or absent for other initial conditions. The motion moreover shows quite peculiar aging properties, which are also mirrored in the behavior of the time-averaged mean squared displacement for single trajectories. This kind of behavior is due to the complex motion of tracers trapped inside the cell and is absent in classical models based on continuous-time random walks with no dynamics in the trapped state.

Determination of the diffusivity, dispersion, skewness and kurtosis in heterogeneous porous flow. Part I: Analytical solutions with the extended method of moments.

NASA Astrophysics Data System (ADS)

Ginzburg, Irina; Vikhansky, Alexander

2018-05-01

The extended method of moments (EMM) is elaborated in recursive algorithmic form for the prediction of the effective diffusivity, the Taylor dispersion dyadic and the associated longitudinal high-order coefficients in mean-concentration profiles and residence-time distributions. The method applies in any streamwise-periodic stationary d-dimensional velocity field resolved in the piecewise continuous heterogeneous porosity field. It is demonstrated that EMM reduces to the method of moments and the volume-averaging formulation in microscopic velocity field and homogeneous soil, respectively. The EMM simultaneously constructs two systems of moments, the spatial and the temporal, without resorting to solving of the high-order upscaled PDE. At the same time, the EMM is supported with the reconstruction of distribution from its moments, allowing to visualize the deviation from the classical ADE solution. The EMM can be handled by any linear advection-diffusion solver with explicit mass-source and diffusive-flux jump condition on the solid boundary and permeable interface. The prediction of the first four moments is decisive in the optimization of the dispersion, asymmetry, peakedness and heavy-tails of the solute distributions, through an adequate design of the composite materials, wetlands, chemical devices or oil recovery. The symbolic solutions for dispersion, skewness and kurtosis are constructed in basic configurations: diffusion process and Darcy flow through two porous blocks in "series", straight and radial Poiseuille flow, porous flow governed by the Stokes-Brinkman-Darcy channel equation and a fracture surrounded by penetrable diffusive matrix or embedded in porous flow. We examine the moments dependency upon porosity contrast, aspect ratio, Péclet and Darcy numbers, but also for their response on the effective Brinkman viscosity applied in flow modeling. Two numerical Lattice Boltzmann algorithms, a direct solver of the microscopic ADE in heterogeneous structure and a novel scheme for EMM numerical formulation, are called for validation of the constructed analytical predictions.

Anomalous Surface Diffusion of Protons on Lipid Membranes

PubMed Central

Wolf, Maarten G.; Grubmüller, Helmut; Groenhof, Gerrit

2014-01-01

The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of −13.0 ± 0.5 kJ mol−1. The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery. PMID:24988343

Nuclear magnetic resonance diffusion pore imaging: Experimental phase detection by double diffusion encoding

NASA Astrophysics Data System (ADS)

Demberg, Kerstin; Laun, Frederik Bernd; Windschuh, Johannes; Umathum, Reiner; Bachert, Peter; Kuder, Tristan Anselm

2017-02-01

Diffusion pore imaging is an extension of diffusion-weighted nuclear magnetic resonance imaging enabling the direct measurement of the shape of arbitrarily formed, closed pores by probing diffusion restrictions using the motion of spin-bearing particles. Examples of such pores comprise cells in biological tissue or oil containing cavities in porous rocks. All pores contained in the measurement volume contribute to one reconstructed image, which reduces the problem of vanishing signal at increasing resolution present in conventional magnetic resonance imaging. It has been previously experimentally demonstrated that pore imaging using a combination of a long and a narrow magnetic field gradient pulse is feasible. In this work, an experimental verification is presented showing that pores can be imaged using short gradient pulses only. Experiments were carried out using hyperpolarized xenon gas in well-defined pores. The phase required for pore image reconstruction was retrieved from double diffusion encoded (DDE) measurements, while the magnitude could either be obtained from DDE signals or classical diffusion measurements with single encoding. The occurring image artifacts caused by restrictions of the gradient system, insufficient diffusion time, and by the phase reconstruction approach were investigated. Employing short gradient pulses only is advantageous compared to the initial long-narrow approach due to a more flexible sequence design when omitting the long gradient and due to faster convergence to the diffusion long-time limit, which may enable application to larger pores.

Anomalous surface diffusion of protons on lipid membranes.

PubMed

Wolf, Maarten G; Grubmüller, Helmut; Groenhof, Gerrit

2014-07-01

The cellular energy machinery depends on the presence and properties of protons at or in the vicinity of lipid membranes. To asses the energetics and mobility of a proton near a membrane, we simulated an excess proton near a solvated DMPC bilayer at 323 K, using a recently developed method to include the Grotthuss proton shuttling mechanism in classical molecular dynamics simulations. We obtained a proton surface affinity of -13.0 ± 0.5 kJ mol(-1). The proton interacted strongly with both lipid headgroup and linker carbonyl oxygens. Furthermore, the surface diffusion of the proton was anomalous, with a subdiffusive regime over the first few nanoseconds, followed by a superdiffusive regime. The time- and distance dependence of the proton surface diffusion coefficient within these regimes may also resolve discrepancies between previously reported diffusion coefficients. Our simulations show that the proton anomalous surface diffusion originates from restricted diffusion in two different surface-bound states, interrupted by the occasional bulk-mediated long-range surface diffusion. Although only a DMPC membrane was considered in this work, we speculate that the restrictive character of the on-surface diffusion is highly sensitive to the specific membrane conditions, which can alter the relative contributions of the surface and bulk pathways to the overall diffusion process. Finally, we discuss the implications of our findings for the energy machinery. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Stochastic Physicochemical Dynamics

NASA Astrophysics Data System (ADS)

Tsekov, R.

2001-02-01

Thermodynamic Relaxation in Quantum Systems: A new approach to quantum Markov processes is developed and the corresponding Fokker-Planck equation is derived. The latter is examined to reproduce known results from classical and quantum physics. It was also applied to the phase-space description of a mechanical system thus leading to a new treatment of this problem different from the Wigner presentation. The equilibrium probability density obtained in the mixed coordinate-momentum space is a reasonable extension of the Gibbs canonical distribution. The validity of the Einstein fluctuation-dissipation relation is discussed in respect to the type of relaxation in an isothermal system. The first model, presuming isothermic fluctuations, leads to the Einstein formula. The second model supposes adiabatic fluctuations and yields another relation between the diffusion coefficient and mobility of a Brownian particle. A new approach to relaxations in quantum systems is also proposed that demonstrates applicability only of the adiabatic model for description of the quantum Brownian dynamics. Stochastic Dynamics of Gas Molecules: A stochastic Langevin equation is derived, describing the thermal motion of a molecule immersed in a rested fluid of identical molecules. The fluctuation-dissipation theorem is proved and a number of correlation characteristics of the molecular Brownian motion are obtained. A short review of the classical theory of Brownian motion is presented. A new method is proposed for derivation of the Fokker-Planck equations, describing the probability density evolution, from stochastic differential equations. It is also proven via the central limit theorem that the white noise is only Gaussian. The applicability of stochastic differential equations to thermodynamics is considered and a new form, different from the classical Ito and Stratonovich forms, is introduced. It is shown that the new presentation is more appropriate for the description of thermodynamic fluctuations. The range of validity of the Boltzmann-Einstein principle is also discussed and a generalized alternative is proposed. Both expressions coincide in the small fluctuation limit, providing a normal distribution density. Fluctuation Stability of Thin Liquid Films: Memory effect of Brownian motion in an incompressible fluid is studied. The reasoning is based on the Mori-Zwanzig formalism and a new formulation of the Langevin force as a result of collisions between an effective and the Brownian particles. Thus, the stochastic force autocorrelation function with finite dispersion and the corresponding Brownian particle velocity autocorrelation function are obtained. It is demonstrated that the dynamic structure is very important for the rate of drainage of a thin liquid film and it can be effectively taken into account by a dynamic fractal dimension. It is shown that the latter is a powerful tool for description of the film drainage and classifies all the known results from the literature. The obtained general expression for the thinning rate is a heuristic one and predicts variety of drainage models, which are even difficult to simulate in practice. It is a typical example of a scaling law, which explains the origin of the complicate dependence of the thinning rate on the film radius. On the basis of the theory of stochastic processes the evolution of the spatial correlation function of the surface waves on a thin liquid film as well as the corresponding root mean square amplitude A(t) and number of uncorrelated subdomains N(t) are obtained. A formulation of the life time of unstable nonthinning films is proposed, based on the evolution of A and N. It is shown that the presence of uncorrelated subdomains shortens the life time of the film. Some numerical results for A(t) and N(t) at different film thicknesses h and areas S, are demonstrated, taking into account only van der Waals and capillary forces. Resonant Diffusion in Molecular Solid Structures: A new approach to Brownian motion of atomic clusters on solid surfaces is developed. The main topic discussed is the dependence of the diffusion coefficient on the fit between the surface static potential and the internal cluster configuration. It is shown this dependence is non-monotonous, which is the essence of the so-called resonant diffusion. Assuming quicker inner motion of the cluster than its translation, adiabatic separation of these variables is possible and a relatively simple expression for the diffusion coefficient is obtained. In this way, the role of cluster vibrations is accounted for, thus leading to a more complex resonance in the cluster surface mobility. Diffusion of normal alkanes in one-dimensional zeolites is theoretically studied on the basis of the stochastic equation formalism. The calculated diffusion coefficient accounts for the vibrations of the diffusing molecule and zeolite framework, molecule-zeolite interaction, and specific structure of the zeolite. It is shown that when the interaction potential is predominantly determined by the zeolite pore structure, the diffusion coefficient varies periodically with the number of carbon atoms of the alkane molecule, a phenomenon called resonant diffusion. A criterion for observable resonance is obtained from the balance between the interaction potentials of the molecule due to the atomic and pore structures of the zeolite. It shows that the diffusion is not resonant in zeolites without pore structure, such as ZSM-12. Moreover, even in zeolites with developed pore structure no resonant dependence of the diffusion constant can be detected if the pore structure energy barriers are not at least three times higher than the atomic structure energy barriers. The role of the alkane molecule vibrations is examined as well and a surprising effect of suppression of the diffusion in comparison with the case of a rigid molecule is observed. This effect is explained with the balance between the static and dynamic interaction of the molecule and zeolite. Catalytic Kinetics of Chemical Dissociation: A unified description of the catalytic effect of Cu-exchanged zeolites is proposed for the decomposition of NO. A general expression for the rate constant of NO decomposition is obtained by assuming that the rate-determining step consists of the transferring of a single atom associated with breaking of the N-O bond. The analysis is performed on the base of the generalized Langevin equation and takes into account both the potential interactions in the system and the memory effects due to the zeolite vibrations. Two different mechanisms corresponding to monomolecular and bimolecular NO decomposition are discussed. The catalytic effect in the monomolecular mechanism is related to both the Cu+ ions and zeolite O-vacancies, while in the case of the bimolecular mechanism the zeolite contributes through dissipation only. The comparison of the theoretically calculated rate constants with experimental results reveals additional information about the geometric and energetic characteristics of the active centers and confirms the logic of the proposed models.

Studies on Aspirin Crystals Generated by a Modified Vapor Diffusion Method.

PubMed

Mittal, Amit; Malhotra, Deepak; Jain, Preeti; Kalia, Anupama; Shunmugaperumal, Tamilvanan

2016-08-01

The objectives of the current investigation were (1) to study the influence of selected two different non-solvents (diethylether and dichloromethane) on the drug crystal formation of a model drug, aspirin (ASP-I) by the modified vapor diffusion method and (2) to characterize and compare the generated crystals (ASP-II and ASP-III) using different analytical techniques with that of unprocessed ASP-I. When compared to the classical vapor diffusion method which consumes about 15 days to generate drug crystals, the modified method needs only 12 h to get the same. Fourier transform-infrared spectroscopy (FT-IR) reveals that the internal structures of ASP-II and ASP-III crystals were identical when compared with ASP-I. Although the drug crystals showed a close similarity in X-ray diffraction patterns, the difference in the relative intensities of some of the diffraction peaks (especially at 2θ values of around 7.7 and 15.5) could be attributed to the crystal habit or crystal size modification. Similarly, the differential scanning calorimetry (DSC) study speculates that only the crystal habit modifications might occur but without involving any change in internal structure of the generated drug polymorphic form I. This is further substantiated from the scanning electron microscopy (SEM) pictures that indicated the formation of platy shape for the ASP-II crystals and needle shape for the ASP-III crystals. In addition, the observed slow dissolution of ASP crystals should indicate polymorph form I formation. Thus, the modified vapor diffusion method could routinely be used to screen and legally secure all possible forms of other drug entities too.

E-Learning and Knowledge Management: The MEMORAe Project.

ERIC Educational Resources Information Center

Abel, Marie-Helene; Lenne, Dominique; Cisse, Omar

E-learning leads to changes in the way courses are conceived. Diffused through the Web, course content cannot be the pure transcription of a "classical" course. The students need to personalize it and to access it when they need it (just-in-time). The MEMORAe project aims at applying knowledge management techniques to improve the…

The Reflexive Producer: The Influence of Farmer Knowledge upon the Use of Bt Corn

ERIC Educational Resources Information Center

Kaup, Brent Z.

2008-01-01

This paper examines the influence of farmer knowledge upon decision making processes. Drawing upon the sociological debates around the ideas of reflexive modernity and biotechnology as well as from classic adoption and diffusion studies, I explore the influences upon farmers' use of "Bacillus thuringiensis" (Bt) corn. Utilizing survey data…

On the relationship between the classical Dicke-Jaynes-Cummings-Gaudin model and the nonlinear Schroedinger equation

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

Du, Dianlou; Geng, Xue

2013-05-15

In this paper, the relationship between the classical Dicke-Jaynes-Cummings-Gaudin (DJCG) model and the nonlinear Schroedinger (NLS) equation is studied. It is shown that the classical DJCG model is equivalent to a stationary NLS equation. Moreover, the standard NLS equation can be solved by the classical DJCG model and a suitably chosen higher order flow. Further, it is also shown that classical DJCG model can be transformed into the classical Gaudin spin model in an external magnetic field through a deformation of Lax matrix. Finally, the separated variables are constructed on the common level sets of Casimir functions and the generalizedmore » action-angle coordinates are introduced via the Hamilton-Jacobi equation.« less

A numerical method for solving a nonlinear 2-D optimal control problem with the classical diffusion equation

NASA Astrophysics Data System (ADS)

Mamehrashi, K.; Yousefi, S. A.

2017-02-01

This paper presents a numerical solution for solving a nonlinear 2-D optimal control problem (2DOP). The performance index of a nonlinear 2DOP is described with a state and a control function. Furthermore, dynamic constraint of the system is given by a classical diffusion equation. It is preferred to use the Ritz method for finding the numerical solution of the problem. The method is based upon the Legendre polynomial basis. By using this method, the given optimisation nonlinear 2DOP reduces to the problem of solving a system of algebraic equations. The benefit of the method is that it provides greater flexibility in which the given initial and boundary conditions of the problem are imposed. Moreover, compared with the eigenfunction method, the satisfactory results are obtained only in a small number of polynomials order. This numerical approach is applicable and effective for such a kind of nonlinear 2DOP. The convergence of the method is extensively discussed and finally two illustrative examples are included to observe the validity and applicability of the new technique developed in the current work.

On observation of position in quantum theory

NASA Astrophysics Data System (ADS)

Kryukov, A.

2018-05-01

Newtonian and Schrödinger dynamics can be formulated in a physically meaningful way within the same Hilbert space framework. This fact was recently used to discover an unexpected relation between classical and quantum motions that goes beyond the results provided by the Ehrenfest theorem. A formula relating the normal probability distribution and the Born rule was also found. Here the dynamical mechanism responsible for the latter formula is proposed and applied to measurements of macroscopic and microscopic systems. A relationship between the classical Brownian motion and the diffusion of state on the space of states is discovered. The role of measuring devices in quantum theory is investigated in the new framework. It is shown that the so-called collapse of the wave function is not measurement specific and does not require a "concentration" near the eigenstates of the measured observable. Instead, it is explained by the common diffusion of a state over the space of states under interaction with the apparatus and the environment. This in turn provides us with a basic reason for the definite position of macroscopic bodies in space.

A Binomial Modeling Approach for Upscaling Colloid Transport Under Unfavorable Attachment Conditions: Emergent Prediction of Nonmonotonic Retention Profiles

NASA Astrophysics Data System (ADS)

Hilpert, Markus; Johnson, William P.

2018-01-01

We used a recently developed simple mathematical network model to upscale pore-scale colloid transport information determined under unfavorable attachment conditions. Classical log-linear and nonmonotonic retention profiles, both well-reported under favorable and unfavorable attachment conditions, respectively, emerged from our upscaling. The primary attribute of the network is colloid transfer between bulk pore fluid, the near-surface fluid domain (NSFD), and attachment (treated as irreversible). The network model accounts for colloid transfer to the NSFD of downgradient grains and for reentrainment to bulk pore fluid via diffusion or via expulsion at rear flow stagnation zones (RFSZs). The model describes colloid transport by a sequence of random trials in a one-dimensional (1-D) network of Happel cells, which contain a grain and a pore. Using combinatorial analysis that capitalizes on the binomial coefficient, we derived from the pore-scale information the theoretical residence time distribution of colloids in the network. The transition from log-linear to nonmonotonic retention profiles occurs when the conditions underlying classical filtration theory are not fulfilled, i.e., when an NSFD colloid population is maintained. Then, nonmonotonic retention profiles result potentially both for attached and NSFD colloids. The concentration maxima shift downgradient depending on specific parameter choice. The concentration maxima were also shown to shift downgradient temporally (with continued elution) under conditions where attachment is negligible, explaining experimentally observed downgradient transport of retained concentration maxima of adhesion-deficient bacteria. For the case of zero reentrainment, we develop closed-form, analytical expressions for the shape, and the maximum of the colloid retention profile.