Mahakrishnan, Sathiya; Chakraborty, Subrata; Vijay, Amrendra
2016-09-15
Diffusion, an emergent nonequilibrium transport phenomenon, is a nontrivial manifestation of the correlation between the microscopic dynamics of individual molecules and their statistical behavior observed in experiments. We present a thorough investigation of this viewpoint using the mathematical tools of quantum scattering, within the framework of Boltzmann transport theory. In particular, we ask: (a) How and when does a normal diffusive transport become anomalous? (b) What physical attribute of the system is conceptually useful to faithfully rationalize large variations in the coefficient of normal diffusion, observed particularly within the dynamical environment of biological cells? To characterize the diffusive transport, we introduce, analogous to continuous phase transitions, the curvature of the mean square displacement as an order parameter and use the notion of quantum scattering length, which measures the effective interactions between the diffusing molecules and the surrounding, to define a tuning variable, η. We show that the curvature signature conveniently differentiates the normal diffusion regime from the superdiffusion and subdiffusion regimes and the critical point, η = ηc, unambiguously determines the coefficient of normal diffusion. To solve the Boltzmann equation analytically, we use a quantum mechanical expression for the scattering amplitude in the Boltzmann collision term and obtain a general expression for the effective linear collision operator, useful for a variety of transport studies. We also demonstrate that the scattering length is a useful dynamical characteristic to rationalize experimental observations on diffusive transport in complex systems. We assess the numerical accuracy of the present work with representative experimental results on diffusion processes in biological systems. Furthermore, we advance the idea of temperature-dependent effective voltage (of the order of 1 μV or less in a biological environment, for example
Fractal Location and Anomalous Diffusion Dynamics for Oil Wells from the KY Geological Survey
Andrew, Keith; Andrew, Kevin A
2009-01-01
Utilizing data available from the Kentucky Geonet (KYGeonet.ky.gov) the fossil fuel mining locations created by the Kentucky Geological Survey geo-locating oil and gas wells are mapped using ESRI ArcGIS in Kentucky single plain 1602 ft projection. This data was then exported into a spreadsheet showing latitude and longitude for each point to be used for modeling at different scales to determine the fractal dimension of the set. Following the porosity and diffusivity studies of Tarafdar and Roy1 we extract fractal dimensions of the fossil fuel mining locations and search for evidence of scaling laws for the set of deposits. The Levy index is used to determine a match to a statistical mechanically motivated generalized probability function for the wells. This probability distribution corresponds to a solution of a dynamical anomalous diffusion equation of fractional order that describes the Levy paths which can be solved in the diffusion limit by the Fox H function ansatz.
Anomalous diffusion of epicentres
Sotolongo-Costa, Oscar; Posadas, A; Luzon, F
2007-01-01
The classification of earthquakes in main shocks and aftershocks by a method recently proposed by M. Baiesi and M. Paczuski allows to the generation of a complex network composed of clusters that group the most correlated events. The spatial distribution of epicentres inside these structures corresponding to the catalogue of earthquakes in the eastern region of Cuba shows anomalous anti-diffusive behaviour evidencing the attractive nature of the main shock and the possible description in terms of fractional kinetics.
Fractal model of anomalous diffusion.
Gmachowski, Lech
2015-12-01
An equation of motion is derived from fractal analysis of the Brownian particle trajectory in which the asymptotic fractal dimension of the trajectory has a required value. The formula makes it possible to calculate the time dependence of the mean square displacement for both short and long periods when the molecule diffuses anomalously. The anomalous diffusion which occurs after long periods is characterized by two variables, the transport coefficient and the anomalous diffusion exponent. An explicit formula is derived for the transport coefficient, which is related to the diffusion constant, as dependent on the Brownian step time, and the anomalous diffusion exponent. The model makes it possible to deduce anomalous diffusion properties from experimental data obtained even for short time periods and to estimate the transport coefficient in systems for which the diffusion behavior has been investigated. The results were confirmed for both sub and super-diffusion.
Martelloni, Gianluca; Bagnoli, Franco
2016-04-01
Richardson's treatise on turbulent diffusion in 1926 [24] and today, the list of system displaying anomalous dynamical behavior is quite extensive. We only report some examples: charge carrier transport in amorphous semiconductors [25], porous systems [26], reptation dynamics in polymeric systems [27, 28], transport on fractal geometries [29], the long-time dynamics of DNA sequences [30]. In this scenario, the fractional calculus is used to generalized the Fokker-Planck linear equation -∂P (x,t)=D ∇2P (x,t), ∂t (3) where P (x,t) is the density of probability in the space x=[x1, x2, x3] and time t, while D >0 is the diffusion coefficient. Such processes are characterized by Eq. (1). An example of Eq. (3) generalization is ∂∂tP (x,t)=D∇ αP β(x,t) - ∞ - 1 , (4) where the fractional based-derivatives Laplacian Σ(∂α/∂xα)i, (i = 1, 2, 3), of non-linear term Pβ(x,t) is taken into account [31]. Another generalized form is represented by equation ∂∂tδδP(x,t)=D ∇ αP(x,t) δ > 0 α ≤ 2 , (5) that considers also the fractional time-derivative [32]. These fractional-described processes exhibit a power law patters as expressed by Eq. (2). This general introduction introduces the presented work, whose aim is to develop a theoretical model in order to forecast the triggering and propagation of landslides, using the techniques of fractional calculus. The latter is suitable for modeling the water infiltration (i.e., the pore water pressure diffusion in the soil) and the dynamical processes in the fractal media [33]. Alternatively the fractal representation of temporal and spatial derivative (the fractal order only appears in the denominator of the derivative) is considered and the results are compared to the fractional one. The prediction of landslides and the discovering of the triggering mechanism, is one of the challenging problems in earth science. Landslides can be triggered by different factors but in most cases the trigger is an intense or long rain
Anomalous Fractional Diffusion Equation for Transport Phenomena
Institute of Scientific and Technical Information of China (English)
QiuhuaZENG; HouqiangLI; 等
1999-01-01
We derive the standard diffusion equation from the continuity equation and by discussing the defectiveness of earlier proposed equations,we get the generalized fractional diffusion equation for anomalous diffusion.
Communication: Probing anomalous diffusion in frequency space
Energy Technology Data Exchange (ETDEWEB)
Stachura, Sławomir [Centre de Biophys. Moléculaire, CNRS, Rue Charles Sadron, 45071 Orléans (France); Synchrotron Soleil, L’Orme de Merisiers, 91192 Gif-sur-Yvette (France); Kneller, Gerald R., E-mail: gerald.kneller@cnrs-orleans.fr [Centre de Biophys. Moléculaire, CNRS, Rue Charles Sadron, 45071 Orléans (France); Synchrotron Soleil, L’Orme de Merisiers, 91192 Gif-sur-Yvette (France); Université d’Orléans, Chateau de la Source-Av. du Parc Floral, 45067 Orléans (France)
2015-11-21
Anomalous diffusion processes are usually detected by analyzing the time-dependent mean square displacement of the diffusing particles. The latter evolves asymptotically as W(t) ∼ 2D{sub α}t{sup α}, where D{sub α} is the fractional diffusion constant and 0 < α < 2. In this article we show that both D{sub α} and α can also be extracted from the low-frequency Fourier spectrum of the corresponding velocity autocorrelation function. This offers a simple method for the interpretation of quasielastic neutron scattering spectra from complex (bio)molecular systems, in which subdiffusive transport is frequently encountered. The approach is illustrated and validated by analyzing molecular dynamics simulations of molecular diffusion in a lipid POPC bilayer.
Anomalous diffusion in fractal globules.
Tamm, M V; Nazarov, L I; Gavrilov, A A; Chertovich, A V
2015-05-01
The fractal globule state is a popular model for describing chromatin packing in eukaryotic nuclei. Here we provide a scaling theory and dissipative particle dynamics computer simulation for the thermal motion of monomers in the fractal globule state. Simulations starting from different entanglement-free initial states show good convergence which provides evidence supporting the existence of a unique metastable fractal globule state. We show monomer motion in this state to be subdiffusive described by ⟨X(2)(t)⟩∼t(αF) with αF close to 0.4. This result is in good agreement with existing experimental data on the chromatin dynamics, which makes an additional argument in support of the fractal globule model of chromatin packing.
Violation of Fourier's Law and Anomalous Heat Diffusion in Silicon
2010-01-01
We study heat conduction and diffusion in silicon nanowires (SiNWs) systematically by using non-equilibrium molecular dynamics. It is found that the thermal conductivity of SiNWs diverges with the length, even when the length is up to 1,100 nm which is much longer than the phonon mean free path. Moreover, an anomalous heat diffusion is observed which is believed to be responsible for the length dependent thermal conductivity. Our results provide strong evidence that Fourier's law of heat cond...
Anomalous Dynamical Responses in a Driven System
Dutta, Suman
2016-01-01
The interplay between structure and dynamics in non-equilibrium steady-state is far from understood. We address this interplay by tracking Brownian Dynamics trajectories of particles in a binary colloid of opposite charges in an external electric field, undergoing cross-over from homogeneous to lane state, a prototype of heterogeneous structure formation in non-equilibrium systems. We show that the length scale of structural correlations controls heterogeneity in diffusion and consequent anomalous dynamic responses, like the exponential tail in probability distributions of particle displacements and stretched exponential structural relaxation. We generalise our observations using equations for steady state density which may aid to understand microscopic basis of heterogeneous diffusion in condensed matter systems.
Anomalous diffusion and scaling in coupled stochastic processes
Energy Technology Data Exchange (ETDEWEB)
Bel, Golan [Los Alamos National Laboratory; Nemenman, Ilya [Los Alamos National Laboratory
2009-01-01
Inspired by problems in biochemical kinetics, we study statistical properties of an overdamped Langevin processes with the friction coefficient depending on the state of a similar, unobserved, process. Integrating out the latter, we derive the Pocker-Planck the friction coefficient of the first depends on the state of the second. Integrating out the latter, we derive the Focker-Planck equation for the probability distribution of the former. This has the fonn of diffusion equation with time-dependent diffusion coefficient, resulting in an anomalous diffusion. The diffusion exponent can not be predicted using a simple scaling argument, and anomalous scaling appears as well. The diffusion exponent of the Weiss-Havlin comb model is derived as a special case, and the same exponent holds even for weakly coupled processes. We compare our theoretical predictions with numerical simulations and find an excellent agreement. The findings caution against treating biochemical systems with unobserved dynamical degrees of freedom by means of standandard, diffusive Langevin descritpion.
Anomalous diffusion in geophysical and laboratory turbulence
Directory of Open Access Journals (Sweden)
A. Tsinober
1994-01-01
Full Text Available We present an overview and some new results on anomalous diffusion of passive scalar in turbulent flows (including those used by Richardson in his famous paper in 1926. The obtained results are based on the analysis of the properties of invariant quantities (energy, enstrophy, dissipation, enstrophy generation, helicity density, etc. - i.e. independent of the choice of the system of reference as the most appropriate to describe physical processes - in three different turbulent laboratory flows (grid-flow, jet and boundary layer, see Tsinober et al. (1992 and Kit et al. (1993. The emphasis is made on the relations between the asymptotic properties of the intermittency exponents of higher order moments of different turbulent fields (energy, dissipation, helicity, spontaneous breaking of isotropy and reflexional symmetry and the variability of turbulent diffusion in the atmospheric boundary layer, in the troposphere and in the stratosphere. It is argued that local spontaneous breaking of isotropy of turbulent flow results in anomalous scaling laws for turbulent diffusion (as compared to the scaling law of Richardson which are observed, as a rule, in different atmospheric layers from the atmospheric boundary layer (ABL to the stratosphere. Breaking of rotational symmetry is important in the ABL, whereas reflexional symmetry breaking is dominating in the troposphere locally and in the stratosphere globally. The results are of speculative nature and further analysis is necessary to validate or disprove the claims made, since the correspondence with the experimental results may occur for the wrong reasons as happens from time to time in the field of turbulence.
Heterogeneous anomalous diffusion in view of superstatistics
Itto, Yuichi
2014-01-01
It is experimentally known that virus exhibits stochastic motion in cytoplasm of a living cell in the free form as well as the form being contained in the endosome and the exponent of anomalous diffusion of the virus fluctuates depending on localized areas of the cytoplasm. Here, a theory is developed for establishing a generalized fractional kinetics for the infection pathway of the virus in the cytoplasm in view of superstatistics, which offers a general framework for describing nonequilibrium complex systems with two largely separated time scales. In the present theory, the existence of a large time-scale separation in the infection pathway is explicitly taken into account. A comment is also made on scaling nature of the motion of the virus that is suggested by the theory.
Anomalous diffusion on the Hanoi networks
Boettcher, S.; Gonçalves, B.
2008-11-01
Diffusion is modeled on the recently proposed Hanoi networks by studying the mean-square displacement of random walks with time, langr2rang~t2/dw. It is found that diffusion —the quintessential mode of transport throughout Nature— proceeds faster than ordinary, in one case with an exact, anomalous exponent dw=2- log2(phi)=1.30576... . It is an instance of a physical exponent containing the "golden ratio"\\phi=(1+\\sqrt{5})/2 that is intimately related to Fibonacci sequences and since Euclid's time has been found to be fundamental throughout geometry, architecture, art, and Nature itself. It originates from a singular renormalization group fixed point with a subtle boundary layer, for whose resolution phi is the main protagonist. The origin of this rare singularity is easily understood in terms of the physics of the process. Yet, the connection between network geometry and the emergence of phi in this context remains elusive. These results provide an accurate test of recently proposed universal scaling forms for first passage times.
Generalized Langevin equation formulation for anomalous polymer dynamics
Panja, D.
2010-01-01
For reproducing the anomalous—i.e., sub-diffusive or super-diffusive—behavior in some stochastic dynamical systems, the generalized Langevin equation (GLE) has gained considerable popularity in recent years. Motivated by the question of whether or not a system with anomalous dynamics can have the GL
Skaug, Michael; Longo, Marjorie; Faller, Roland
2011-03-01
Anomalous diffusion has been observed abundantly in the plasma membrane, but the underlying mechanisms are still unclear. In general, it has not been possible to directly image the obstacles to diffusion in membranes, so the dynamics of diffusing particles are used to deduce the obstacle characteristics. We present a supported lipid bilayer system in which we characterized the anomalous diffusion of lipid molecules using single molecule tracking, while at the same time imaging the obstacles to diffusion with atomic force microscopy. To explain our experimental results, we performed lattice Monte Carlo simulations of tracer diffusion in the presence of the experimentally determined obstacle configurations. We correlate the observed anomalous diffusion with obstacle area fraction, fractal dimension and correlation length. We further discuss our results in the context of confinement models and the generating stochastic process. Supported by NSF grant CBET 0506602.
Skaug, Michael J.; Faller, Roland; Longo, Marjorie L.
2011-06-01
Anomalous diffusion has been observed abundantly in the plasma membrane of biological cells, but the underlying mechanisms are still unclear. In general, it has not been possible to directly image the obstacles to diffusion in membranes, which are thought to be skeleton bound proteins, protein aggregates, and lipid domains, so the dynamics of diffusing particles is used to deduce the obstacle characteristics. We present a supported lipid bilayer system in which we characterized the anomalous diffusion of lipid molecules using single molecule tracking, while at the same time imaging the obstacles to diffusion with atomic force microscopy. To explain our experimental results, we performed lattice Monte Carlo simulations of tracer diffusion in the presence of the experimentally determined obstacle configurations. We correlate the observed anomalous diffusion with obstacle area fraction, fractal dimension, and correlation length. To accurately measure an anomalous diffusion exponent, we derived an expression to account for the time-averaging inherent to all single molecule tracking experiments. We show that the length of the single molecule trajectories is critical to the determination of the anomalous diffusion exponent. We further discuss our results in the context of confinement models and the generating stochastic process.
Viscoelastic hydrodynamic interactions and anomalous CM diffusion in polymer melts
Meyer, Hendrik
We have recently discovered that anomalous center-of-mass (CM) diffusion occurring on intermediate time scales in polymer melts can be explained by the interplay of viscoelastic and hydrodynamic interactions (VHI). The theory has been solved for unentangled melts in 3D and 2D and excellent agreement between theory and simulation is found, also for alkanes with a force field optimized from neutron scattering. The physical mechanism considers that hydrodynamic interactions are not screened: they are time dependent because of increasing viscosity before the terminal relaxation time. The VHI are generally active in melts of any topology. They are most important at early times well before the terminal relaxation time and thus affect the nanosecond time range typically observable in dynamic neutron scattering experiments. We illustrate the effects with recent molecular dynamics simulations of linear, ring and star polymers. Work performed with A.N. Semenov and J. Farago.
From Sturm-Liouville problems to fractional and anomalous diffusions
D'Ovidio, Mirko
2010-01-01
Some fractional and anomalous diffusions are driven by equations involving fractional derivatives in both time and space. Such diffusions are processes with randomly varying times. In representing the solutions to those diffusions, the explicit laws of certain stable processes turn out to be fundamental. This paper directs one's efforts towards the explicit representation of solutions to fractional and anomalous diffusions related to Sturm-Liouville problems of fractional order associated to fractional power function spaces. Furthermore, we study a new version of the Bochner's subordination rule and we establish some connections between subordination and space-fractional operator
A variable-order fractal derivative model for anomalous diffusion
Directory of Open Access Journals (Sweden)
Liu Xiaoting
2017-01-01
Full Text Available This paper pays attention to develop a variable-order fractal derivative model for anomalous diffusion. Previous investigations have indicated that the medium structure, fractal dimension or porosity may change with time or space during solute transport processes, results in time or spatial dependent anomalous diffusion phenomena. Hereby, this study makes an attempt to introduce a variable-order fractal derivative diffusion model, in which the index of fractal derivative depends on temporal moment or spatial position, to characterize the above mentioned anomalous diffusion (or transport processes. Compared with other models, the main advantages in description and the physical explanation of new model are explored by numerical simulation. Further discussions on the dissimilitude such as computational efficiency, diffusion behavior and heavy tail phenomena of the new model and variable-order fractional derivative model are also offered.
Anomalous transports in a time-delayed system subjected to anomalous diffusion
Chen, Ru-Yin; Tong, Lu-Mei; Nie, Lin-Ru; Wang, Chaojie; Pan, Wanli
2017-02-01
We investigate anomalous transports of an inertial Brownian particle in a time-delayed periodic potential subjected to an external time-periodic force, a constant bias force, and the Lévy noise. By means of numerical calculations, effect of the time delay and the Lévy noise on its mean velocity are discussed. The results indicate that: (i) The time delay can induce both multiple current reversals (CRs) and absolute negative mobility (ANM) phenomena in the system; (ii) The CRs and ANM phenomena only take place in the region of superdiffusion, while disappear in the regions of normal diffusion; (iii) The time delay can cause state transition of the system from anomalous →normal →anomalous →normal →anomalous →normal transport in the case of superdiffusion.
Underdamped scaled Brownian motion: (non-)existence of the overdamped limit in anomalous diffusion
Bodrova, Anna S.; Chechkin, Aleksei V.; Cherstvy, Andrey G.; Safdari, Hadiseh; Sokolov, Igor M.; Metzler, Ralf
2016-07-01
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.
Crossover from normal to anomalous diffusion in systems of field-aligned dipolar particles.
Jordanovic, Jelena; Jäger, Sebastian; Klapp, Sabine H L
2011-01-21
Using molecular dynamics simulations we investigate the translational dynamics of particles with dipolar interactions in homogenous external fields. For a broad range of concentrations, we find that the anisotropic, yet normal diffusive behavior characterizing weakly coupled systems becomes anomalous both parallel and perpendicular to the field at sufficiently high dipolar coupling and field strength. After the ballistic regime, chain formation first yields cagelike motion in all directions, followed by transient, mixed diffusive-superdiffusive behavior resulting from cooperative motion of the chains. The enhanced dynamics disappears only at higher densities close to crystallization.
Tortuosity and anomalous diffusion in the neuromuscular junction
Lacks, Daniel J.
2008-04-01
The signal transfer from nerve to muscle occurs by diffusion across the neuromuscular junction. The continuum level analysis of diffusion processes is based on the diffusion equation, which in one dimension is ∂c/∂t=D(∂2c/∂x2) , where c is the molecular concentration and D is the diffusivity. However, in confined systems such as the neuromuscular junction, the diffusion equation may not be valid, and even if valid the value of D may be altered by the confinement. In this paper, Monte Carlo simulations are used to probe diffusion at the molecular level in a realistic model of a neuromuscular junction. The results show that diffusion is anomalous (i.e., not described by the diffusion equation) for time scales less than ˜0.01s , which is the time scale relevant for signaling processes in the synapse. At longer time scales, the diffusion is normal (i.e., described by the diffusion equation), but with a value of D that is reduced by a factor of ˜5 times compared to the value for diffusion in open space. As the width of the synaptic cleft decreases, these effects become even more pronounced. The physical basis of these results is described in terms of the structure of the neuromuscular junction.
Oscillatory variation of anomalous diffusion in pendulum systems
Indian Academy of Sciences (India)
G Sakthivel; S Rajasekar
2011-03-01
Numerical studies of anomalous diffusion in undamped but periodically-driven and parametrically-driven pendulum systems are presented. When the frequency of the periodic driving force is varied, the exponent , which is the rate of divergence of the mean square displacement with time, is found to vary in an oscillatory manner. We show the presence of such a variation in other statistical measures such as variance of position, kurtosis, and exponents in the power-exponential law of probability distribution of position.
Anomalous diffusion for inertial particles under gravity in parallel flows
Afonso, Marco Martins
2014-01-01
We investigate the bounds between normal or anomalous effective diffusion for inertial particles transported by parallel flows. The infrared behavior of the fluid kinetic-energy spectrum, i.e. the possible presence of long-range spatio-temporal correlations, is modeled as a power law by means of two parameters, and the problem is studied as a function of these latter. Our results, obtained in the limit of weak relative inertia, extend well-known results for tracers and apply to particles of any mass density, subject to gravity and Brownian diffusion. We consider both steady and time-dependent flows, and cases of both vanishing and finite particle sedimentation.
A Fractional Fokker-Planck Model for Anomalous Diffusion
anderson, Johan; Moradi, Sara
2014-01-01
In this paper we present a study of anomalous diffusion using a Fokker-Planck description with fractional velocity derivatives. The distribution functions are found using numerical means for varying degree of fractionality observing the transition from a Gaussian distribution to a L\\'evy distribution. The statistical properties of the distribution functions are assessed by a generalized expectation measure and entropy in terms of Tsallis statistical mechanics. We find that the ratio of the generalized entropy and expectation is increasing with decreasing fractionality towards the well known so-called sub-diffusive domain, indicating a self-organising behavior.
Front propagation in anomalous diffusive media governed by time-fractional diffusion
Mentrelli, Andrea; Pagnini, Gianni
2015-07-01
In this paper, a multi-dimensional model is proposed to study the propagation of random fronts in media in which anomalous diffusion takes place. The front position is obtained as the weighted mean of fronts calculated by means of the level set method, using as weight-function the probability density function which characterizes the anomalous diffusion process. Since anomalous diffusion is assumed to be governed by a time-fractional diffusion equation, its fundamental solution is the required probability density function. It is shown that this fundamental solution can be expressed in the multi-dimensional case in terms of the well-known M-Wright/Mainardi function, as in the one-dimensional case. Making use of this representation for the practical purpose of numerical evaluation, the propagation of random fronts in two-dimensional subdiffusive media is discussed and investigated.
Anomalous Diffusion and Long-range Correlations in the Score Evolution of the Game of Cricket
Ribeiro, H V; Zeng, Xiao Han T
2012-01-01
We investigate the time evolution of the scores of the second most popular sport in world: the game of cricket. By analyzing the scores event-by-event of more than two thousand matches, we point out that the score dynamics is an anomalous diffusive process. Our analysis reveals that the variance of the process is described by a power-law dependence with a super-diffusive exponent, that the scores are statistically self-similar following a universal Gaussian distribution, and that there are long-range correlations in the score evolution. We employ a generalized Langevin equation with a power-law correlated noise that describe all the empirical findings very well. These observations suggest that competition among agents may be a mechanism leading to anomalous diffusion and long-range correlation.
Liang, Yingjie; Ye, Allen Q.; Chen, Wen; Gatto, Rodolfo G.; Colon-Perez, Luis; Mareci, Thomas H.; Magin, Richard L.
2016-10-01
Non-Gaussian (anomalous) diffusion is wide spread in biological tissues where its effects modulate chemical reactions and membrane transport. When viewed using magnetic resonance imaging (MRI), anomalous diffusion is characterized by a persistent or 'long tail' behavior in the decay of the diffusion signal. Recent MRI studies have used the fractional derivative to describe diffusion dynamics in normal and post-mortem tissue by connecting the order of the derivative with changes in tissue composition, structure and complexity. In this study we consider an alternative approach by introducing fractal time and space derivatives into Fick's second law of diffusion. This provides a more natural way to link sub-voxel tissue composition with the observed MRI diffusion signal decay following the application of a diffusion-sensitive pulse sequence. Unlike previous studies using fractional order derivatives, here the fractal derivative order is directly connected to the Hausdorff fractal dimension of the diffusion trajectory. The result is a simpler, computationally faster, and more direct way to incorporate tissue complexity and microstructure into the diffusional dynamics. Furthermore, the results are readily expressed in terms of spectral entropy, which provides a quantitative measure of the overall complexity of the heterogeneous and multi-scale structure of biological tissues. As an example, we apply this new model for the characterization of diffusion in fixed samples of the mouse brain. These results are compared with those obtained using the mono-exponential, the stretched exponential, the fractional derivative, and the diffusion kurtosis models. Overall, we find that the order of the fractal time derivative, the diffusion coefficient, and the spectral entropy are potential biomarkers to differentiate between the microstructure of white and gray matter. In addition, we note that the fractal derivative model has practical advantages over the existing models from the
Anomalous diffusion in correlated continuous time random walks
Energy Technology Data Exchange (ETDEWEB)
Tejedor, Vincent; Metzler, Ralf, E-mail: metz@ph.tum.d [Physics Department T30 g, Technical University of Munich, 85747 Garching (Germany)
2010-02-26
We demonstrate that continuous time random walks in which successive waiting times are correlated by Gaussian statistics lead to anomalous diffusion with the mean squared displacement (r{sup 2}(t)) {approx_equal} t{sup 2/3}. Long-ranged correlations of the waiting times with a power-law exponent alpha (0 < alpha <= 2) give rise to subdiffusion of the form (r{sup 2}(t)) {approx_equal} t{sup {alpha}/(1+{alpha})}. In contrast, correlations in the jump lengths are shown to produce superdiffusion. We show that in both cases weak ergodicity breaking occurs. Our results are in excellent agreement with simulations. (fast track communication)
Anomalous diffusion and long-range correlations in the score evolution of the game of cricket
Ribeiro, Haroldo V.; Mukherjee, Satyam; Zeng, Xiao Han T.
2012-08-01
We investigate the time evolution of the scores of the second most popular sport in the world: the game of cricket. By analyzing, event by event, the scores of more than 2000 matches, we point out that the score dynamics is an anomalous diffusive process. Our analysis reveals that the variance of the process is described by a power-law dependence with a superdiffusive exponent, that the scores are statistically self-similar following a universal Gaussian distribution, and that there are long-range correlations in the score evolution. We employ a generalized Langevin equation with a power-law correlated noise that describes all the empirical findings very well. These observations suggest that competition among agents may be a mechanism leading to anomalous diffusion and long-range correlation.
Strong plasma turbulence and anomalous diffusion in a magnetic field
Energy Technology Data Exchange (ETDEWEB)
Okuda, H.
1979-04-01
Plasma diffusion in the presence of strong turbulence has been studied by means of analytic theory and numerical simulations. First, diffusion and turbulent fluctuation spectrum in the presence of convective cells are studied using a two-dimensional guiding center model and a two-fluid model keeping the ion inertia. Second, particle diffusion associated with drift wave turbulence using full dynamic ions and Debye shielding electrons is considered.
Deviation of the statistical fluctuation in heterogeneous anomalous diffusion
Itto, Yuichi
2016-01-01
The exponent of anomalous diffusion of virus in cytoplasm of a living cell is experimentally known to fluctuate depending on localized areas of the cytoplasm, indicating heterogeneity of diffusion. In a recent paper (Itto, 2012), a maximum-entropy-principle approach has been developed in order to propose an Ansatz for the statistical distribution of such exponent fluctuations. Based on this approach, here the deviation of the statistical distribution of the fluctuations from the proposed one is studied from the viewpoint of Einstein's theory of fluctuations (of the thermodynamic quantities). This may present a step toward understanding the statistical property of the deviation. It is shown in a certain class of small deviations that the deviation obeys the multivariate Gaussian distribution.
Lattice Monte Carlo simulation of Galilei variant anomalous diffusion
Energy Technology Data Exchange (ETDEWEB)
Guo, Gang, E-mail: hndzgg@aliyun.com [School of Information System and Management, National University of Defense Technology, Changsha, 410073 (China); Institute of Computer Science, University of Rostock, Albert Einstein Str. 22, Rostock, 18059 (Germany); Bittig, Arne, E-mail: arne.bittig@uni-rostock.de [Institute of Computer Science, University of Rostock, Albert Einstein Str. 22, Rostock, 18059 (Germany); Uhrmacher, Adelinde, E-mail: lin@informatik.uni-rostock.de [Institute of Computer Science, University of Rostock, Albert Einstein Str. 22, Rostock, 18059 (Germany)
2015-05-01
The observation of an increasing number of anomalous diffusion phenomena motivates the study to reveal the actual reason for such stochastic processes. When it is difficult to get analytical solutions or necessary to track the trajectory of particles, lattice Monte Carlo (LMC) simulation has been shown to be particularly useful. To develop such an LMC simulation algorithm for the Galilei variant anomalous diffusion, we derive explicit solutions for the conditional and unconditional first passage time (FPT) distributions with double absorbing barriers. According to the theory of random walks on lattices and the FPT distributions, we propose an LMC simulation algorithm and prove that such LMC simulation can reproduce both the mean and the mean square displacement exactly in the long-time limit. However, the error introduced in the second moment of the displacement diverges according to a power law as the simulation time progresses. We give an explicit criterion for choosing a small enough lattice step to limit the error within the specified tolerance. We further validate the LMC simulation algorithm and confirm the theoretical error analysis through numerical simulations. The numerical results agree with our theoretical predictions very well.
Anomalous/Fractional Diffusion in Particle Acceleration Processes.
Bian, Nicolas
2016-07-01
This talk is aimed at reviewing a certain number of theoretical aspects concerning the relation between stochastic acceleration and anomalous/fractional transport of particles. As a matter of fact, anomalous velocity-space diffusion is required within any stochastic acceleration scenario to explain the formation of the ubiquitous power-law tail of non-thermal particles, as observed e.g. in the accelerated distribution of electrons during solar flares. I will establish a classification scheme for stochastic acceleration models involving turbulence in magnetized plasmas. This classification takes into account both the properties of the accelerating electromagnetic field, and the nature of the spatial transport (possibly fractional) of charged particles in the acceleration region. I will also discuss recent attempts to obtain spatially non-local and fractional diffusion equations directly from first principles, starting either from the Fokker-Planck equation in the large mean free-path regime or the Boltzmann equation involving velocity-space relaxation toward the kappa distribution instead of the standard Maxwellian distribution.
Anomalous diffusion in stochastic systems with nonhomogeneously distributed traps.
Srokowski, Tomasz
2015-05-01
The stochastic motion in a nonhomogeneous medium with traps is studied and diffusion properties of that system are discussed. The particle is subjected to a stochastic stimulation obeying a general Lévy stable statistics and experiences long rests due to nonhomogeneously distributed traps. The memory is taken into account by subordination of that process to a random time; then the subordination equation is position dependent. The problem is approximated by a decoupling of the medium structure and memory and exactly solved for a power-law position dependence of the memory. In the case of the Gaussian statistics, the density distribution and moments are derived: depending on geometry and memory parameters, the system may reveal both the subdiffusion and enhanced diffusion. The similar analysis is performed for the Lévy flights where the finiteness of the variance follows from a variable noise intensity near a boundary. Two diffusion regimes are found: in the bulk and near the surface. The anomalous diffusion exponent as a function of the system parameters is derived.
Anomalous diffusion of a polymer chain in an unentangled melt
Farago, Jean; Meyer, Hendrik; Semenov, Alexander
2012-02-01
Contrary to common belief, the hydrodynamic interactions (HI) in polymer melts are not screened beyond the monomer length and are important in transient regimes. We show that the viscoelastic HI effects (VHI) lead to anomalous dynamics of a tagged chain in an unentangled melt at t VHI-controlled chain dynamics yielding negative CM velocity autocorrelation function which quantitatively agrees with our MD simulations without any fitting parameter. It is also shown that the Langevin friction force, when added in the model, strongly affects the short-t CM dynamics which, however, can remain strongly enhanced. The transient VHI effects thus provide the dominant contribution to the subdiffusive CM motion universally observed in simulations and experiments on polymer melts.
Weak ergodicity breaking, irreproducibility, and ageing in anomalous diffusion processes
Energy Technology Data Exchange (ETDEWEB)
Metzler, Ralf [Institute for Physics and Astronomy, University of Potsdam, D-14476 Potsdam-Golm, Germany and Department of Physics, Tampere University of Technology, FI-33101 Tampere (Finland)
2014-01-14
Single particle traces are standardly evaluated in terms of time averages of the second moment of the position time series r(t). For ergodic processes, one can interpret such results in terms of the known theories for the corresponding ensemble averaged quantities. In anomalous diffusion processes, that are widely observed in nature over many orders of magnitude, the equivalence between (long) time and ensemble averages may be broken (weak ergodicity breaking), and these time averages may no longer be interpreted in terms of ensemble theories. Here we detail some recent results on weakly non-ergodic systems with respect to the time averaged mean squared displacement, the inherent irreproducibility of individual measurements, and methods to determine the exact underlying stochastic process. We also address the phenomenon of ageing, the dependence of physical observables on the time span between initial preparation of the system and the start of the measurement.
Anomalous chain diffusion in unentangled model polymer nanocomposites
Schneider, G.; Nusser, K.; Neueder, S.; Brodeck, M.; Willner, L.; Farago, B.; Holderer, O.; Briels, W.J.; Richter, D.
2013-01-01
We studied unentangled poly(ethylene-alt-propylene) (PEP) in a composite with hydrophobic silica particles as a function of the filler concentration. Our neutron spin echo (NSE) experiments cover both the internal dynamics as well as the center of mass diffusion beyond the Rouse time. The key experi
Onset of anomalous diffusion from local motion rules
de Nigris, Sarah; Lambiotte, Renaud
2016-01-01
Anomalous diffusion processes, in particular superdiffusive ones, are known to be efficient strategies for searching and navigation by animals and also in human mobility. One way to create such regimes are L\\'evy flights, where the walkers are allowed to perform jumps, the "flights", that can eventually be very long as their length distribution is asymptotically power-law distributed. In our work, we present a model in which walkers are allowed to perform, on a 1D lattice, "cascades" of $n$ unitary steps instead of one jump of a randomly generated length, as in the L\\'evy case. Instead of imposing a length distribution, we thus define our process by its cascade distribution $p_n$. We first derive the connections between the two distributions and show that this local mechanism may give rise to superdiffusion or normal diffusion when $p_n$ is distributed as a power law. We also investigate the interplay of this process with the possibility to be stuck on a node, introducing waiting times that are power-law dist...
Modeling of 1D Anomalous Diffusion in Fractured Nanoporous Media
Directory of Open Access Journals (Sweden)
Albinali Ali
2016-07-01
Full Text Available Fractured nanoporous reservoirs include multi-scale and discontinuous fractures coupled with a complex nanoporous matrix. Such systems cannot be described by the conventional dual-porosity (or multi-porosity idealizations due to the presence of different flow mechanisms at multiple scales. More detailed modeling approaches, such as Discrete Fracture Network (DFN models, similarly suffer from the extensive data requirements dictated by the intricacy of the flow scales, which eventually deter the utility of these models. This paper discusses the utility and construction of 1D analytical and numerical anomalous diffusion models for heterogeneous, nanoporous media, which is commonly encountered in oil and gas production from tight, unconventional reservoirs with fractured horizontal wells. A fractional form of Darcy’s law, which incorporates the non-local and hereditary nature of flow, is coupled with the classical mass conservation equation to derive a fractional diffusion equation in space and time. Results show excellent agreement with established solutions under asymptotic conditions and are consistent with the physical intuitions.
Anomalous diffusion in strong cellular flows: Averaging and homogenization
Pajor-Gyulai, Zsolt
This thesis considers the possible limit behaviors of a strong Hamiltonian cellular flow that is subjected to a Brownian stochastic perturbation. Three possible limits are identified. When long timescales are considered, the limit behavior is described by classical homogenization theory. In the intermediate (finite) time case, it is shown that the limit behavior is anomalously diffusive. This means that the limit is given by a Brownian motion that is time changed by the local time of a process on the graph which is associated with the structure of the unperturbed flow lines (Reeb graph) that one obtains by Freidlin-Wentzell type averaging. Finally, we consider the case when the motion starts close to, or on, the cell boundary and derive a limit for the displacement on timescales of order proportional to some power of a small parameter with exponent between zero and one. (modulo a logarithmic correction to compensate for the slowdown of the flow near the saddle points of the Hamiltonian). The latter two cases are novel results obtained by the author and his collaborators. We also consider two applications of the above results to associated partial differential equation (PDE) problems. Namely, we study a two-parameter averaging-homogenization type elliptic boundary value problem and obtain a precise description of the limit behavior of the solution as a function of the parameters using the well-known stochastic representation. Additionally, we study a similar parabolic Cauchy problem.
Méndez, Vicenç; Bartumeus, Frederic
2014-01-01
This book presents the fundamental theory for non-standard diffusion problems in movement ecology. Lévy processes and anomalous diffusion have shown to be both powerful and useful tools for qualitatively and quantitatively describing a wide variety of spatial population ecological phenomena and dynamics, such as invasion fronts and search strategies. Adopting a self-contained, textbook-style approach, the authors provide the elements of statistical physics and stochastic processes on which the modeling of movement ecology is based and systematically introduce the physical characterization of ecological processes at the microscopic, mesoscopic and macroscopic levels. The explicit definition of these levels and their interrelations is particularly suitable to coping with the broad spectrum of space and time scales involved in bio-ecological problems. Including numerous exercises (with solutions), this text is aimed at graduate students and newcomers in this field at the interface of theoretical ecology, mat...
Jeon, Jae-Hyung; Javanainen, Matti; Martinez-Seara, Hector; Metzler, Ralf; Vattulainen, Ilpo
2016-04-01
Biomembranes are exceptionally crowded with proteins with typical protein-to-lipid ratios being around 1 ∶50 -1 ∶100 . Protein crowding has a decisive role in lateral membrane dynamics as shown by recent experimental and computational studies that have reported anomalous lateral diffusion of phospholipids and membrane proteins in crowded lipid membranes. Based on extensive simulations and stochastic modeling of the simulated trajectories, we here investigate in detail how increasing crowding by membrane proteins reshapes the stochastic characteristics of the anomalous lateral diffusion in lipid membranes. We observe that correlated Gaussian processes of the fractional Langevin equation type, identified as the stochastic mechanism behind lipid motion in noncrowded bilayer, no longer adequately describe the lipid and protein motion in crowded but otherwise identical membranes. It turns out that protein crowding gives rise to a multifractal, non-Gaussian, and spatiotemporally heterogeneous anomalous lateral diffusion on time scales from nanoseconds to, at least, tens of microseconds. Our investigation strongly suggests that the macromolecular complexity and spatiotemporal membrane heterogeneity in cellular membranes play critical roles in determining the stochastic nature of the lateral diffusion and, consequently, the associated dynamic phenomena within membranes. Clarifying the exact stochastic mechanism for various kinds of biological membranes is an important step towards a quantitative understanding of numerous intramembrane dynamic phenomena.
Anomalous diffusion of proteins in sheared lipid membranes
Khoshnood, Atefeh
2013-01-01
We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow conditions. Protein embedded membranes behave quite differently: by imposing a simple shear flow and sliding the monolayers of the membrane over each other, the motion of protein clusters becomes strongly superdiffusive in the shear direction. In such a circumstance, subdiffusion regime is predominant perpendicular to the flow. We show that superdiffusion is a result of accelerated chaotic motions of protein--lipid complexes within the membrane voids, which are generated by hydrophobic mismatch or the transport of lipids by proteins.
Anomalous diffusion and dielectric relaxation in an N-fold cosine potential.
Coffey, W T; Kalmykov, Yu P; Titov, S V
2003-06-01
The fractional Klein-Kramers (Fokker-Planck) equation describing the fractal time dynamics of an assembly of fixed axis dipoles rotating in an N-fold cosine potential representing the internal field due to neighboring molecules is solved using matrix continued fractions. The result can be considered as a generalization of the solution for the normal Brownian motion in a cosine periodic potential to fractional dynamics (giving rise to anomalous diffusion) and also represents a generalization of Fröhlich's model of relaxation over a potential barrier. The solution includes both inertial and strong internal field effects, which in combination produce a strong resonance peak (Poley absorption) at high frequencies due to librations of the dipoles in the potential, an anomalous relaxation band at low frequencies mainly arising from overbarrier relaxation, and a weaker relaxation band at midfrequencies due to the fast intrawell modes. The high-frequency behavior is controlled by the inertia of the dipole, so that the Gordon sum rule for dipolar absorption is satisfied, ensuring a return to optical transparency at very high frequencies. Application of the model to the broadband (0-THz) dielectric loss spectrum of a dilute solution of the probe dipolar molecule CH2Cl2 in glassy decalin is demonstrated.
Directory of Open Access Journals (Sweden)
Lund Frederik W
2012-10-01
Full Text Available Abstract Background Cholesterol is an important membrane component, but our knowledge about its transport in cells is sparse. Previous imaging studies using dehydroergosterol (DHE, an intrinsically fluorescent sterol from yeast, have established that vesicular and non-vesicular transport modes contribute to sterol trafficking from the plasma membrane. Significant photobleaching, however, limits the possibilities for in-depth analysis of sterol dynamics using DHE. Co-trafficking studies with DHE and the recently introduced fluorescent cholesterol analog BODIPY-cholesterol (BChol suggested that the latter probe has utility for prolonged live-cell imaging of sterol transport. Results We found that BChol is very photostable under two-photon (2P-excitation allowing the acquisition of several hundred frames without significant photobleaching. Therefore, long-term tracking and diffusion measurements are possible. Two-photon temporal image correlation spectroscopy (2P-TICS provided evidence for spatially heterogeneous diffusion constants of BChol varying over two orders of magnitude from the cell interior towards the plasma membrane, where D ~ 1.3 μm2/s. Number and brightness (N&B analysis together with stochastic simulations suggest that transient partitioning of BChol into convoluted membranes slows local sterol diffusion. We observed sterol endocytosis as well as fusion and fission of sterol-containing endocytic vesicles. The mobility of endocytic vesicles, as studied by particle tracking, is well described by a model for anomalous subdiffusion on short time scales with an anomalous exponent α ~ 0.63 and an anomalous diffusion constant of Dα = 1.95 x 10-3 μm2/sα. On a longer time scale (t > ~5 s, a transition to superdiffusion consistent with slow directed transport with an average velocity of v ~ 6 x 10-3 μm/s was observed. We present an analytical model that bridges the two regimes and fit this model to vesicle
Anisotropic Anomalous Diffusion assessed in the human brain by scalar invariant indices
De Santis, S; Bozzali, M; Maraviglia, B; Macaluso, E; Capuani, S
2010-01-01
A new method to investigate anomalous diffusion in human brain is proposed. The method has been inspired by both the stretched-exponential model proposed by Hall and Barrick (HB) and DTI. Quantities extracted using HB method were able to discriminate different cerebral tissues on the basis of their complexity, expressed by the stretching exponent gamma and of the anisotropy of gamma across different directions. Nevertheless, these quantities were not defined as scalar invariants like mean diffusivity and fractional anisotropy, which are eigenvalues of the diffusion tensor. We hypotesize instead that the signal may be espressed as a simple stretched-exponential only along the principal axes of diffusion, while in a generic direction the signal is modeled as a combination of three different stretched-exponentials. In this way, we derived indices to quantify both the tissue anomalous diffusion and its anisotropy, independently of the reference frame of the experiment. We tested and compare our new method with DT...
Kosevich, Yuriy A.; Savin, Alexander V.
2016-10-01
We provide molecular dynamics simulation of heat transport and energy diffusion in one-dimensional molecular chains with different interparticle pair potentials at zero and non-zero temperature. We model the thermal conductivity (TC) and energy diffusion (ED) in the chain of coupled rotators and in the Lennard-Jones chain either without or with the confining parabolic interparticle potential. The considered chains without the confining potential have normal TC and ED at non-zero temperature, while the corresponding chains with the confining potential are characterized by anomalous (diverging with the system length) TC and superdiffusion of energy. Similar effect is produced by the anharmonic quartic confining pair potential. We confirm in such a way that, surprisingly, the confining pair potential makes both heat transport and energy diffusion anomalous in one-dimensional phononic systems. We show that the normal TC is always accompanied by the normal ED in the thermalized anharmonic chains, while the superdiffusion of energy occurs in the thermalized chains with only anomalous heat transport.
Molecular dynamics simulation of diffusivity
Institute of Scientific and Technical Information of China (English)
Juanfang LIU; Danling ZENG; Qin LI; Hong GAO
2008-01-01
Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addition, the diffusivities obtained by the SPCE model conform well to the experimental values.
Anomalous flow behavior in nanochannels: A molecular dynamics study
Murad, Sohail; Luo, Lin; Chu, Liang-Yin
2010-06-01
We report molecular dynamics simulations of flow of water in nanochannels with a range of surface wettability characteristics (hydrophobic to strongly hydrophilic) and driving forces (pressures). Our results show apparently anomalous behavior. At low pressures, the rate is higher in nanochannels with hydrophilic surfaces than that with hydrophobic surfaces; however, with high pressure driven flow we observe opposite trends. This apparently anomalous behavior can be explained on the basis of molecular thermodynamics and fluid mechanics considerations. Understanding such behavior is important in many nanofluidic devices such as nanoreactors, nanosensors, and nanochips that are increasingly being designed and used.
Akimoto, Takuma; Yamamoto, Eiji
2016-06-01
We consider the Langevin equation with dichotomously fluctuating diffusivity, where the diffusion coefficient changes dichotomously over time, in order to study fluctuations of time-averaged observables in temporally heterogeneous diffusion processes. We find that the time-averaged mean-square displacement (TMSD) can be represented by the occupation time of a state in the asymptotic limit of the measurement time and hence occupation time statistics is a powerful tool for calculating the TMSD in the model. We show that the TMSD increases linearly with time (normal diffusion) but the time-averaged diffusion coefficients are intrinsically random when the mean sojourn time for one of the states diverges, i.e., intrinsic nonequilibrium processes. Thus, we find that temporally heterogeneous environments provide anomalous fluctuations of time-averaged diffusivity, which have relevance to large fluctuations of the diffusion coefficients obtained by single-particle-tracking trajectories in experiments.
Malacarne, L C; Mendes, R S; Pedron, I T; Lenzi, E K
2001-03-01
The nonlinear diffusion equation partial delta rho/delta t=D Delta rho(nu) is analyzed here, where Delta[triple bond](1/r(d-1))(delta/delta r)r(d-1-theta) delta/delta r, and d, theta, and nu are real parameters. This equation unifies the anomalous diffusion equation on fractals (nu=1) and the spherical anomalous diffusion for porous media (theta=0). An exact point-source solution is obtained, enabling us to describe a large class of subdiffusion [ theta>(1-nu)d], "normal" diffusion [theta=(1-nu)d] and superdiffusion [theta<(1-nu)d]. Furthermore, a thermostatistical basis for this solution is given from the maximum entropic principle applied to the Tsallis entropy.
In vivo Anomalous Diffusion and Weak Ergodicity Breaking of Lipid Granules
DEFF Research Database (Denmark)
Jeon, J.-H.; Tejedor, V.; Burov, S.;
2011-01-01
Combining extensive single particle tracking microscopy data of endogenous lipid granules in living fission yeast cells with analytical results we show evidence for anomalous diffusion and weak ergodicity breaking. Namely we demonstrate that at short times the granules perform subdiffusion accord...
Lin, Guoxing
2016-01-01
Pulsed field gradient (PFG) has been increasingly employed to study anomalous diffusions in Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI). However, the analysis of PFG anomalous diffusion is complicated. In this paper, a fractal derivative model based modified Gaussian phase distribution method is proposed to describe PFG anomalous diffusion. By using the phase distribution obtained from the effective phase shift diffusion method based on fractal derivatives, and employing some of the traditional Gaussian phase distribution approximation techniques, a general signal attenuation expression for free fractional diffusion is derived. This expression describes a stretched exponential function based attenuation, which is distinct from both the exponential attenuation for normal diffusion obtained from conventional Gaussian phase distribution approximation, and the Mittag-Leffler function based attenuation for anomalous diffusion obtained from fractional derivative. The obtained signal attenu...
Marshall, Wallace F.; Fung, Jennifer C.
2016-04-01
The recognition and pairing of homologous chromosomes during meiosis is a complex physical and molecular process involving a combination of polymer dynamics and molecular recognition events. Two highly conserved features of meiotic chromosome behavior are the attachment of telomeres to the nuclear envelope and the active random motion of telomeres driven by their interaction with cytoskeletal motor proteins. Both of these features have been proposed to facilitate the process of homolog pairing, but exactly what role these features play in meiosis remains poorly understood. Here we investigate the roles of active motion and nuclear envelope tethering using a Brownian dynamics simulation in which meiotic chromosomes are represented by a Rouse polymer model subjected to tethering and active forces at the telomeres. We find that tethering telomeres to the nuclear envelope slows down pairing relative to the rates achieved by unattached chromosomes, but that randomly directed active forces applied to the telomeres speed up pairing dramatically in a manner that depends on the statistical properties of the telomere force fluctuations. The increased rate of initial pairing cannot be explained by stretching out of the chromosome conformation but instead seems to correlate with anomalous diffusion of sub-telomeric regions.
Lin, Guoxing
2017-02-01
Pulsed field gradient (PFG) technique is a noninvasive tool, and has been increasingly employed to study anomalous diffusions in Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI). However, the analysis of PFG anomalous diffusion is much more complicated than normal diffusion. In this paper, a fractal derivative model based modified Gaussian phase distribution method is proposed to describe PFG anomalous diffusion. By using the phase distribution obtained from the effective phase shift diffusion method based on fractal derivatives, and employing some of the traditional Gaussian phase distribution approximation techniques, a general signal attenuation expression for free fractional diffusion is derived. This expression describes a stretched exponential function based attenuation, which is distinct from both the exponential attenuation for normal diffusion obtained from conventional Gaussian phase distribution approximation, and the Mittag-Leffler function based attenuation for anomalous diffusion obtained from fractional derivative. The obtained signal attenuation expression can analyze the finite gradient pulse width (FGPW) effect. Additionally, it can generally be applied to all three types of PFG fractional diffusions classified based on time derivative order α and space derivative order β. These three types of fractional diffusions include time-fractional diffusion with { 0 reported results based on effective phase shift diffusion equation method and instantaneous signal attenuation method. This method provides a new, convenient approximation formalism for analyzing PFG anomalous diffusion experiments. The expression that can simultaneously interpret general fractional diffusion and FGPW effect could be especially important in PFG MRI, where the narrow gradient pulse limit cannot be satisfied.
Metzler, Ralf; Jeon, Jae-Hyung; Cherstvy, Andrey G; Barkai, Eli
2014-11-28
Modern microscopic techniques following the stochastic motion of labelled tracer particles have uncovered significant deviations from the laws of Brownian motion in a variety of animate and inanimate systems. Such anomalous diffusion can have different physical origins, which can be identified from careful data analysis. In particular, single particle tracking provides the entire trajectory of the traced particle, which allows one to evaluate different observables to quantify the dynamics of the system under observation. We here provide an extensive overview over different popular anomalous diffusion models and their properties. We pay special attention to their ergodic properties, highlighting the fact that in several of these models the long time averaged mean squared displacement shows a distinct disparity to the regular, ensemble averaged mean squared displacement. In these cases, data obtained from time averages cannot be interpreted by the standard theoretical results for the ensemble averages. Here we therefore provide a comparison of the main properties of the time averaged mean squared displacement and its statistical behaviour in terms of the scatter of the amplitudes between the time averages obtained from different trajectories. We especially demonstrate how anomalous dynamics may be identified for systems, which, on first sight, appear to be Brownian. Moreover, we discuss the ergodicity breaking parameters for the different anomalous stochastic processes and showcase the physical origins for the various behaviours. This Perspective is intended as a guidebook for both experimentalists and theorists working on systems, which exhibit anomalous diffusion.
Quantifying Chiral Magnetic Effect from Anomalous-Viscous Fluid Dynamics
Jiang, Yin; Yin, Yi; Liao, Jinfeng
2016-01-01
Chiral Magnetic Effect (CME) is the macroscopic manifestation of the fundamental chiral anomaly in a many-body system of chiral fermions, and emerges as anomalous transport current in the fluid dynamics framework. Experimental observation of CME is of great interest and has been reported in Dirac and Weyl semimetals. Significant efforts have also been made to search for CME in heavy ion collisions. Encouraging evidence of CME-induced charge separation in those collisions has been reported, albeit with ambiguity due to background contamination. Crucial for addressing such issue, is the need of quantitative predictions for CME signal with sophisticated modelings. In this paper we develop such a tool, the Anomalous Viscous Fluid Dynamics (AVFD) framework, which simulates the evolution of fermion currents in QGP on top of the data-validated VISHNU bulk hydrodynamic flow. With realistic initial conditions and magnetic field lifetime, the AVFD-predicted CME signal could be quantitatively consistent with measured ch...
Control of DNA replication by anomalous reaction-diffusion kinetics
Bechhoefer, John; Gauthier, Michel
2010-03-01
DNA replication requires two distinct processes: the initiation of pre-licensed replication origins and the propagation of replication forks away from the fired origins. Experiments indicate that these origins are triggered over the whole genome at a rate I(t) (the number of initiations per unreplicated length per time) that increases throughout most of the synthesis (S) phase, before rapidly decreasing to zero at the end of the replication process. We propose a simple model for the control of DNA replication in which the rate of initiation of replication origins is controlled by protein-DNA interactions. Analyzing recent data from Xenopus frog embryos, we find that the initiation rate is reaction limited until nearly the end of replication, when it becomes diffusion limited. Initiation of origins is suppressed when the diffusion-limited search time dominates. To fit the experimental data, we find that the interaction between DNA and the rate-limiting protein must be subdiffusive.
Lin, Guoxing
2016-01-01
Anomalous diffusion exists widely in polymer and biological systems. Pulsed field gradient (PFG) techniques have been increasingly used to study anomalous diffusion in NMR and MRI. However, the interpretation of PFG anomalous diffusion is complicated. Moreover, there is not an exact signal attenuation expression based on fractional derivatives for PFG anomalous diffusion, which includes the finite gradient pulse width effect. In this paper, a new method, a Mainardi-Luchko-Pagnini (MLP) phase distribution approximation, is proposed to describe PFG fractional diffusion. MLP phase distribution is a non-Gaussian phase distribution. From the fractional diffusion equation based on fractional derivatives in both real space and phase space, the obtained probability distribution function is a MLP distribution. The MLP distribution leads to a Mittag-Leffler function based PFG signal attenuation rather than the exponential or stretched exponential attenuation that is obtained from a Gaussian phase distribution (GPD) und...
Energy Technology Data Exchange (ETDEWEB)
Zimbardo, G.; Veltri, P. [Arcavacata di Rende, Cosenza, Univ. della Calabria (Italy). Dipt. di Fisica
1997-11-01
The magnetic fluctuations due to, e.g., magnetohydrodynamic turbulence cause a magnetic-field line random walk that influences many cosmic plasma phenomena. The results of a three-dimensional numerical simulation of a turbulent magnetic field in plane geometry are presented here. Magnetic percolation, Levy flights, and non-Gaussian random walk of the magnetic-field lines are found for moderate perturbation levels. In such a case plasma transport can be anomalous, i.e., either super diffusive or sub diffusive. Increasing the perturbation level a Gaussian diffusion regime is attained. The implications on the structure of the electron fore shock and of planetary magneto pauses are discussed.
Anomalous enhancement in interfacial perpendicular magnetic anisotropy through uphill diffusion.
Das, Tanmay; Kulkarni, Prabhanjan D; Purandare, S C; Barshilia, Harish C; Bhattacharyya, Somnath; Chowdhury, Prasanta
2014-06-17
We observed interfacial chemical sharpening due to uphill diffusion in post annealed ultrathin multilayer stack of Co and Pt, which leads to enhanced interfacial perpendicular magnetic anisotropy (PMA). This is surprising as these elements are considered as perfectly miscible. This chemical sharpening was confirmed through quantitative energy dispersive x-ray (EDX) spectroscopy and intensity distribution of images taken on high angle annular dark field (HAADF) detector in Scanning Transmission Electron Microscopic (STEM) mode. This observation demonstrates an evidence of miscibility gap in ultrathin coherent Co/Pt multilayer stacks.
Origin of anomalous anharmonic lattice dynamics of lead telluride
Shiga, Takuma; Hori, Takuma; Delaire, Olivier; Shiomi, Junichiro
2015-01-01
The origin of the anomalous anharmonic lattice dynamics of lead telluride is investigated using molecular dynamics simulations with interatomic force constants (IFCs) up to quartic terms obtained from first principles. The calculations reproduce the peak asymmetry of the radial distribution functions and the double peaks of transverse optical phonon previously observed with neutron diffraction and scattering experiments. They are identified to be due to the extremely large nearest-neighbor cubic IFCs in the [100] direction. The outstanding strength of the nearest-neighbor cubic IFCs relative to the longer-range ones explains the reason why the distortion in the radial distribution function is local.
The precise time-dependent solution of the Fokker–Planck equation with anomalous diffusion
Energy Technology Data Exchange (ETDEWEB)
Guo, Ran; Du, Jiulin, E-mail: jiulindu@aliyun.com
2015-08-15
We study the time behavior of the Fokker–Planck equation in Zwanzig’s rule (the backward-Ito’s rule) based on the Langevin equation of Brownian motion with an anomalous diffusion in a complex medium. The diffusion coefficient is a function in momentum space and follows a generalized fluctuation–dissipation relation. We obtain the precise time-dependent analytical solution of the Fokker–Planck equation and at long time the solution approaches to a stationary power-law distribution in nonextensive statistics. As a test, numerically we have demonstrated the accuracy and validity of the time-dependent solution. - Highlights: • The precise time-dependent solution of the Fokker–Planck equation with anomalous diffusion is found. • The anomalous diffusion satisfies a generalized fluctuation–dissipation relation. • At long time the time-dependent solution approaches to a power-law distribution in nonextensive statistics. • Numerically we have demonstrated the accuracy and validity of the time-dependent solution.
Nonlinear Theory of Anomalous Diffusion and Application to Fluorescence Correlation Spectroscopy
Boon, Jean Pierre; Lutsko, James F.
2015-12-01
The nonlinear theory of anomalous diffusion is based on particle interactions giving an explicit microscopic description of diffusive processes leading to sub-, normal, or super-diffusion as a result of competitive effects between attractive and repulsive interactions. We present the explicit analytical solution to the nonlinear diffusion equation which we then use to compute the correlation function which is experimentally measured by correlation spectroscopy. The theoretical results are applicable in particular to the analysis of fluorescence correlation spectroscopy of marked molecules in biological systems. More specifically we consider the cases of fluorescently labeled lipids in the plasma membrane and of fluorescent apoferritin (a spherically shaped oligomer) in a crowded dextran solution and we find that the nonlinear correlation spectra reproduce very well the experimental data indicating sub-diffusive molecular motion.
Analysis of aggregated tick returns: evidence for anomalous diffusion
Weber, P
2006-01-01
In order to investigate the origin of large price fluctuations, we analyze stock price changes of ten frequently traded NASDAQ stocks in the year 2002. Though the influence of the trading frequency on the aggregate return in a certain time interval is important, it cannot alone explain the heavy tailed distribution of stock price changes. For this reason, we analyze intervals with a fixed number of trades in order to eliminate the influence of the trading frequency and investigate the relevance of other factors for the aggregate return. We show that in tick time the price follows a discrete diffusion process with a variable step width while the difference between the number of steps in positive and negative direction in an interval is Gaussian distributed. The step width is given by the return due to a single trade and is long-term correlated in tick time. Hence, its mean value can well characterize an interval of many trades and turns out to be an important determinant for large aggregate returns. We also pr...
Analysis of aggregated tick returns: Evidence for anomalous diffusion
Weber, Philipp
2007-01-01
In order to investigate the origin of large price fluctuations, we analyze stock price changes of ten frequently traded NASDAQ stocks in the year 2002. Though the influence of the trading frequency on the aggregate return in a certain time interval is important, it cannot alone explain the heavy-tailed distribution of stock price changes. For this reason, we analyze intervals with a fixed number of trades in order to eliminate the influence of the trading frequency and investigate the relevance of other factors for the aggregate return. We show that in tick time the price follows a discrete diffusion process with a variable step width while the difference between the number of steps in positive and negative direction in an interval is Gaussian distributed. The step width is given by the return due to a single trade and is long-term correlated in tick time. Hence, its mean value can well characterize an interval of many trades and turns out to be an important determinant for large aggregate returns. We also present a statistical model reproducing the cumulative distribution of aggregate returns. For an accurate agreement with the empirical distribution, we also take into account asymmetries of the step widths in different directions together with cross correlations between these asymmetries and the mean step width as well as the signs of the steps.
Improved estimation of anomalous diffusion exponents in single particle tracking experiments
Bronshtein, Eldad Kepten Irena
2013-01-01
The Mean Square Displacement is a central tool in the analysis of Single Particle Tracking experiments, shedding light on various biophysical phenomena. Frequently, parameters are extracted by performing time-averages on single particle trajectories followed by ensemble averaging. This procedure however, suffers from two systematic errors when applied to particles that perform anomalous diffusion. The first is significant at short time lags and is induced by measurement errors. The second arises from the natural heterogeneity in biophysical systems. We show how to estimate and correct these two errors and improve the estimation of the anomalous parameters for the whole particle distribution. As a consequence we manage to characterize ensembles of heterogeneous particles even for rather short and noisy measurements where regular time averaged mean square displacement analysis fails. We apply this method to both simulations and in vivo measurements of telomere diffusion in 3T3 mouse embryonic fibroblast cells. ...
An extended anomalous fine structure of X-ray quasi-Bragg diffuse scattering from multilayers
Chernov, V A; Mytnichenko, S V
2001-01-01
An X-ray quasi-Bragg diffuse scattering anomalous fine structure technique was probed near the absorption Ni K-edge to study the interfacial structure of the Ni/C multilayer deposited by the laser ablation. Like other combinations of the EXAFS and diffraction techniques, this method has a spatial selectivity and was shown qualitatively to provide atomic structural information from the mixed interfacial layers. The possibilities and advantages of this technique are discussed.
Avena, L
2012-01-01
We perform simulations for one dimensional continuous-time random walks in two dynamic random environments with fast (independent spin-flips) and slow (simple symmetric exclusion) decay of space-time correlations, respectively. We focus on the asymptotic speeds and the scaling limits of such random walks. We observe different behaviors depending on the dynamics of the underlying random environment and the ratio between the jump rate of the random walk and the one of the environment. We compare our data with well known results for static random environment. We observe that the non-diffusive regime known so far only for the static case can occur in the dynamic setup too. Such anomalous fluctuations emerge in a new phase diagram. Further we discuss possible consequences for general static and dynamic random environments.
Elastic cell membranes induce long-lived anomalous thermal diffusion on nearby particles
Daddi-Moussa-Ider, Abdallah; Gekle, Stephan
2016-01-01
The physical approach of a small particle (virus, medical drug) to the cell membrane represents the crucial first step before active internalization and is governed by thermal diffusion. Using a fully analytical theory we show that the stretching and bending of the elastic membrane by the approaching particle induces a memory in the system which leads to anomalous diffusion, even though the particle is immersed in a purely Newtonian liquid. For typical cell membranes the transient subdiffusive regime extends beyond 10ms and can enhance residence times and binding rates up to 50\\%. Our analytical predictions are validated by numerical simulations.
Directory of Open Access Journals (Sweden)
Gianni Pagnini
2012-01-01
inhomogeneity and nonstationarity properties of the medium. For instance, when this superposition is applied to the time-fractional diffusion process, the resulting Master Equation emerges to be the governing equation of the Erdélyi-Kober fractional diffusion, that describes the evolution of the marginal distribution of the so-called generalized grey Brownian motion. This motion is a parametric class of stochastic processes that provides models for both fast and slow anomalous diffusion: it is made up of self-similar processes with stationary increments and depends on two real parameters. The class includes the fractional Brownian motion, the time-fractional diffusion stochastic processes, and the standard Brownian motion. In this framework, the M-Wright function (known also as Mainardi function emerges as a natural generalization of the Gaussian distribution, recovering the same key role of the Gaussian density for the standard and the fractional Brownian motion.
Qomi, Mohammad Javad Abdolhosseini; Bauchy, Mathieu; Ulm, Franz-Josef; Pellenq, Roland J-M
2014-02-07
With shear interest in nanoporous materials, the ultraconfining interlayer spacing of calcium-silicate-hydrate (C-S-H) provides an excellent medium to study reactivity, structure, and dynamic properties of water. In this paper, we present how substrate composition affects chemo-physical properties of water in ultraconfined hydrophilic media. This is achieved by performing molecular dynamics simulation on a set of 150 realistic models with different compositions of calcium and silicon contents. It is demonstrated that the substrate chemistry directly affects the structural properties of water molecules. The motion of confined water shows a multi-stage dynamics which is characteristic of supercooled liquids and glassy phases. Inhomogeneity in that dynamics is used to differentiate between mobile and immobile water molecules. Furthermore, it is shown that the mobility of water molecules is composition-dependent. Similar to the pressure-driven self-diffusivity anomaly observed in bulk water, we report the first study on composition-driven diffusion anomaly, the self diffusivity increases with increasing confined water density in C-S-H. Such anomalous behavior is explained by the decrease in the typical activation energy required for a water molecule to escape its dynamical cage.
Diffusive dynamics on paper matrix
Chaudhury, Kaustav; Kar, Shantimoy; Chakraborty, Suman
2016-11-01
Writing with ink on a paper and the rapid diagnostics of diseases using paper cartridge, despite their remarkable diversities from application perspective, both involve the motion of a liquid from a source on a porous hydrophilic substrate. Here we bring out a generalization in the pertinent dynamics by appealing to the concerned ensemble-averaged transport with reference to the underlying molecular picture. Our results reveal that notwithstanding the associated complexities and diversities, the resultant liquid transport characteristics on a paper matrix, in a wide variety of applications, resemble universal diffusive dynamics. Agreement with experimental results from diversified applications is generic and validates our unified theory.
Anomalous dynamics of capillary rise in porous media
Shikhmurzaev, Yulii D.
2012-07-09
The anomalous dynamics of capillary rise in a porous medium discovered experimentally more than a decade ago is described. The developed theory is based on considering the principal modes of motion of the menisci that collectively form the wetting front on the Darcy scale. These modes, which include (i) dynamic wetting mode, (ii) threshold mode, and (iii) interface depinning process, are incorporated into the boundary conditions for the bulk equations formulated in the regular framework of continuum mechanics of porous media, thus allowing one to consider a general case of three-dimensional flows. The developed theory makes it possible to describe all regimes observed in the experiment, with the time spanning more than four orders of magnitude, and highlights the dominant physical mechanisms at different stages of the process. © 2012 American Physical Society.
Directory of Open Access Journals (Sweden)
Eldad Kepten
Full Text Available Single particle tracking is an essential tool in the study of complex systems and biophysics and it is commonly analyzed by the time-averaged mean square displacement (MSD of the diffusive trajectories. However, past work has shown that MSDs are susceptible to significant errors and biases, preventing the comparison and assessment of experimental studies. Here, we attempt to extract practical guidelines for the estimation of anomalous time averaged MSDs through the simulation of multiple scenarios with fractional Brownian motion as a representative of a large class of fractional ergodic processes. We extract the precision and accuracy of the fitted MSD for various anomalous exponents and measurement errors with respect to measurement length and maximum time lags. Based on the calculated precision maps, we present guidelines to improve accuracy in single particle studies. Importantly, we find that in some experimental conditions, the time averaged MSD should not be used as an estimator.
Anomalous diffusion of Ibuprofen in cyclodextrin nanosponge hydrogels: an HRMAS NMR study
Directory of Open Access Journals (Sweden)
Monica Ferro
2014-11-01
Full Text Available Ibuprofen sodium salt (IP was encapsulated in cyclodextrin nanosponges (CDNS obtained by cross-linking of β-cyclodextrin with ethylenediaminetetraacetic acid dianhydride (EDTAn in two different preparations: CDNSEDTA 1:4 and 1:8, where the 1:n notation indicates the CD to EDTAn molar ratio. The entrapment of IP was achieved by swelling the two polymers with a 0.27 M solution of IP in D2O, leading to colourless, homogeneous hydrogels loaded with IP. The molecular environment and the transport properties of IP in the hydrogels were studied by high resolution magic angle spinning (HRMAS NMR spectroscopy. The mean square displacement (MSD of IP in the gels was obtained by a pulsed field gradient spin echo (PGSE NMR pulse sequence at different observation times td. The MSD is proportional to the observation time elevated to a scaling factor α. The α values define the normal Gaussian random motion (α = 1, or the anomalous diffusion (α 1 superdiffusion. The experimental data here reported point out that IP undergoes subdiffusive regime in CDNSEDTA 1:4, while a slightly superdiffusive behaviour is observed in CDNSEDTA 1:8. The transition between the two dynamic regimes is triggered by the polymer structure. CDNSEDTA 1:4 is characterized by a nanoporous structure able to induce confinement effects on IP, thus causing subdiffusive random motion. CDNSEDTA 1:8 is characterized not only by nanopores, but also by dangling EDTA groups ending with ionized COO− groups. The negative potential provided by such groups to the polymer backbone is responsible for the acceleration effects on the IP anion thus leading to the superdiffusive behaviour observed. These results point out that HRMAS NMR spectroscopy is a powerful direct method for the assessment of the transport properties of a drug encapsulated in polymeric scaffolds. The diffusion properties of IP in CDNS can be modulated by suitable polymer synthesis; this finding opens the possibility to design
On The Anomalous Fast Ion Energy Diffusion in Toroidal Plasmas Due to Cavity Modes
Energy Technology Data Exchange (ETDEWEB)
N.N. Gorelenkov, N.J. Fisch and E. Fredrickson
2010-03-09
An enormous wave-particle diffusion coefficient along paths suitable for alpha channeling had been deduced in mode converted ion Bernstein wave experiments on Tokamak Fusion Test Reactor (TFTR) the only plausible explanation advanced for such a large diffusion coefficient was the excitation of internal cavity modes which induce particle diffusion along identical diffusion paths, but at much higher rates. Although such a mode was conjectured, it was never observed. However, recent detailed observations of high frequency compressional Alfven eigenmodes (CAEs) on the National Spherical torus Experiment (NSTX) indirectly support the existence of the related conjectured modes on TFTR. The eigenmodes responsible for the high frequency magnetic activity can be identified as CAEs through the polarization of the observed magnetic field oscillations in NSTX and through a comparison with the theoretically derived freuency dispersion relation. Here, we show how these recent observations of high frequency CAEs lend support to this explanation of the long-standing puzzle of anomalous fast ion energy diffusion on TFTR. The support of the conjecure that these internal modes could have caused the remarkable ion energy diffusion on TFTR carries significant and favorable implications for the possibilities in achieving the alpha channeling effect with small injected power in a tokamak reactor.
The nuclear pore complex mystery and anomalous diffusion in reversible gels.
Bickel, Thomas; Bruinsma, Robijn
2002-01-01
The exchange of macromolecules between the cytoplasm and the nucleus of eukaryotic cells takes place through the nuclear pore complex (NPC), which contains a selective permeability barrier. Experiments on the physical properties of this barrier appear to be in conflict with current physical understanding of the rheology of reversible gels. This paper proposes that the NPC gel is anomalous and characterized by connectivity fluctuations. It develops a simplified model to demonstrate the possibility of enhanced diffusion constants of macromolecules trapped in such a gel. PMID:12496079
Zhao, Jiong; Deng, Qingming; Avdoshenko, Stanislav M; Fu, Lei; Eckert, Jürgen; Rümmeli, Mark H
2014-11-01
Single-atom catalysts are of great interest because of their high efficiency. In the case of chemically deposited sp(2) carbon, the implementation of a single transition metal atom for growth can provide crucial insight into the formation mechanisms of graphene and carbon nanotubes. This knowledge is particularly important if we are to overcome fabrication difficulties in these materials and fully take advantage of their distinct band structures and physical properties. In this work, we present atomically resolved transmission EM in situ investigations of single Fe atoms at graphene edges. Our in situ observations show individual iron atoms diffusing along an edge either removing or adding carbon atoms (viz., catalytic action). The experimental observations of the catalytic behavior of a single Fe atom are in excellent agreement with supporting theoretical studies. In addition, the kinetics of Fe atoms at graphene edges are shown to exhibit anomalous diffusion, which again, is in agreement with our theoretical investigations.
Real-time approach to tunnelling in open quantum systems: decoherence and anomalous diffusion
Energy Technology Data Exchange (ETDEWEB)
Calzetta, Esteban [Departmento de Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellon I, 1428 Buenos Aires (Argentina); Verdaguer, Enric [Departament de Fisica Fonamental and CER en AstrofIsica, Fisica de PartIcules i Cosmologia, Universitat de Barcelona, Av. Diagonal 647, 08028 Barcelona (Spain)
2006-07-28
Macroscopic quantum tunnelling is described using the master equation for the reduced Wigner function of an open quantum system at zero temperature. Our model consists of a particle trapped in a cubic potential interacting with an environment characterized by dissipative and normal and anomalous diffusion coefficients. A representation based on the energy eigenfunctions of the isolated system, i.e. the system uncoupled to the environment, is used to write the reduced Wigner function, and the master equation becomes simpler in that representation. The energy eigenfunctions computed in a WKB approximation incorporate the tunnelling effect of the isolated system and the effect of the environment is described by an equation that is in many ways similar to a Fokker-Planck equation. Decoherence is easily identified from the master equation and we find that when the decoherence time is much shorter than the tunnelling time the master equation can be approximated by a Kramers-like equation describing thermal activation due to the zero point fluctuations of the quantum environment. The effect of anomalous diffusion can be dealt with perturbatively and its overall effect is to inhibit tunnelling.
Improved estimation of anomalous diffusion exponents in single-particle tracking experiments.
Kepten, Eldad; Bronshtein, Irena; Garini, Yuval
2013-05-01
The mean square displacement is a central tool in the analysis of single-particle tracking experiments, shedding light on various biophysical phenomena. Frequently, parameters are extracted by performing time averages on single-particle trajectories followed by ensemble averaging. This procedure, however, suffers from two systematic errors when applied to particles that perform anomalous diffusion. The first is significant at short-time lags and is induced by measurement errors. The second arises from the natural heterogeneity in biophysical systems. We show how to estimate and correct these two errors and improve the estimation of the anomalous parameters for the whole particle distribution. As a consequence, we manage to characterize ensembles of heterogeneous particles even for rather short and noisy measurements where regular time-averaged mean square displacement analysis fails. We apply this method to both simulations and in vivo measurements of telomere diffusion in 3T3 mouse embryonic fibroblast cells. The motion of telomeres is found to be subdiffusive with an average exponent constant in time. Individual telomere exponents are normally distributed around the average exponent. The proposed methodology has the potential to improve experimental accuracy while maintaining lower experimental costs and complexity.
Lin, Guoxing
2016-11-01
Anomalous diffusion exists widely in polymer and biological systems. Pulsed-field gradient (PFG) techniques have been increasingly used to study anomalous diffusion in nuclear magnetic resonance and magnetic resonance imaging. However, the interpretation of PFG anomalous diffusion is complicated. Moreover, the exact signal attenuation expression including the finite gradient pulse width effect has not been obtained based on fractional derivatives for PFG anomalous diffusion. In this paper, a new method, a Mainardi-Luchko-Pagnini (MLP) phase distribution approximation, is proposed to describe PFG fractional diffusion. MLP phase distribution is a non-Gaussian phase distribution. From the fractional derivative model, both the probability density function (PDF) of a spin in real space and the PDF of the spin's accumulating phase shift in virtual phase space are MLP distributions. The MLP phase distribution leads to a Mittag-Leffler function based PFG signal attenuation, which differs significantly from the exponential attenuation for normal diffusion and from the stretched exponential attenuation for fractional diffusion based on the fractal derivative model. A complete signal attenuation expression Eα(-Dfbα,β * ) including the finite gradient pulse width effect was obtained and it can handle all three types of PFG fractional diffusions. The result was also extended in a straightforward way to give a signal attenuation expression of fractional diffusion in PFG intramolecular multiple quantum coherence experiments, which has an nβ dependence upon the order of coherence which is different from the familiar n2 dependence in normal diffusion. The results obtained in this study are in agreement with the results from the literature. The results in this paper provide a set of new, convenient approximation formalisms to interpret complex PFG fractional diffusion experiments.
Turbulence-induced anomalous electron diffusion in the plume of the VASIMR VX-200
Olsen, Christopher; Ballenger, Maxwell; Squire, Jared; Longmier, Benjamin; Carter, Mark; Glover, Tim
2012-10-01
The separation of electrons from magnetic nozzles is critical to the function of the VASIMR engine and is of general importance to the field of electric propulsion. Separation of electrons by means of anomalous cross field diffusion is considered. Plume measurements using spectral analysis of custom high frequency probes characterizes the nature of oscillating electric fields in the expanding magnetic nozzle. The oscillating electric field results in frequency dependent density variations that can lead to anomalously high transport in the absence of collisions mimicking collisional transport. The spatial structure of the fluctuating fields is consistent with turbulence caused by separation of energetic (> 100 eV) non-magnetized ions and low energy magnetized electrons via the modified two-stream instability (MTSI) and generalized lower hybrid drift instability (GLHDI). Electric fields as high as 300 V/m are observed at frequencies up to an order of magnitude above the lower hybrid frequency. The electric field fluctuations dissipate with increasing axial distance consistent with changes in ion flux streamlines as plasma detachment occurs.
Consistent gauge interaction involving dynamical coupling and anomalous current
Guendelman, Eduardo I
2015-01-01
We show a possible way to construct a consistent formalism where the effective electric charge can change with space and time without destroying the invariance. In the previous work [1][2] we took the gauge coupling to be of the form $g(\\phi)j_\\mu (A^{\\mu} +\\partial^{\\mu}B)$ where $B$ is an auxiliary field, $ \\phi $ is a scalar field and the current $j_\\mu$ is the Dirac current. This term produces a constraint $ (\\partial_{\\mu}\\phi) j^{\\mu}=0 $ which can be related to M.I.T bag model by boundary condition. In this paper we show that when we use the term $ g(\\phi)j_{\\mu}(A^{\\mu} - \\partial^{\\mu}(\\frac{1}{\\square}\\partial_{\\rho}A^{\\rho})) $, instead of the auxiliary field $ B $, there is a possibility to produce a theory with dynamical coupling constant, which does not produce any constraint or confinement. The coupling $ j_{\\mu}^{A}(A^{\\mu} - \\partial^{\\mu}(\\frac{1}{\\square}\\partial_{\\rho}A^{\\rho})) $ where $ j_{\\mu}^{A} $ is an anomalous current also discussed.
Pagnini, Gianni; Mura, Antonio; Mainardi, Francesco
2013-05-13
Two-particle dispersion is investigated in the context of anomalous diffusion. Two different modelling approaches related to time subordination are considered and unified in the framework of self-similar stochastic processes. By assuming a single-particle fractional Brownian motion and that the two-particle correlation function decreases in time with a power law, the particle relative separation density is computed for the cases with time sub-ordination directed by a unilateral M-Wright density and by an extremal Lévy stable density. Looking for advisable mathematical properties (for instance, the stationarity of the increments), the corresponding self-similar stochastic processes are represented in terms of fractional Brownian motions with stochastic variance, whose profile is modelled by using the M-Wright density or the Lévy stable density.
Filipovitch, N.; Hill, K. M.; Longjas, A.; Voller, V. R.
2016-07-01
Transport in systems containing heterogeneity distributed over multiple length scales can exhibit anomalous diffusion behaviors, where the time exponent, determining the spreading length scale of the transported scalar, differs from the expected value of n=1/2. Here we present experimental measurements of the infiltration of glycerin, under a fixed pressure head, into a Hele-Shaw cell containing a 3-D printed distribution of flow obstacles; a system that is an analog for infiltration into a porous medium. In support of previously presented direct simulation results, we experimentally demonstrate that, when the obstacles are distributed as a fractal carpet with fractal dimension H < 2, the averaged progress of infiltration exhibits a subdiffusive behavior n<1/2. We further show that observed values of the subdiffusion time exponent appear to be quadratically related to the fractal dimension of the carpet.
A simple mathematical model for anomalous diffusion via Fisher's information theory
Energy Technology Data Exchange (ETDEWEB)
Ubriaco, Marcelo R., E-mail: ubriaco@ltp.upr.clu.ed [Laboratory of Theoretical Physics, Department of Physics, University of Puerto Rico, Rio Piedras Campus, San Juan, PR 00931 (Puerto Rico)
2009-10-26
Starting with the relative entropy based on a previously proposed entropy function S{sub q}[p]=integraldxp(x)x(-lnp(x)){sup q}, we find the corresponding Fisher's information measure. After function redefinition we then maximize the Fisher information measure with respect to the new function and obtain a differential operator that reduces to a space coordinate second derivative in the q->1 limit. We then propose a simple differential equation for anomalous diffusion and show that its solutions are a generalization of the functions in the Barenblatt-Pattle solution. We find that the mean squared displacement, up to a q-dependent constant, has a time dependence according to
Anomalous diffusion approach to non-exponential relaxation in complex physical systems
Stanislavsky, Aleksander; Weron, Karina; Weron, Aleksander
2015-07-01
We derive the relaxation function from the simple model of two-state systems under memory effects caused by the subordination. The non-exponential relaxation is shown to result from subordination by inverse infinity divisible random processes. The wide class of such random processes includes ordinary α-stable, tempered α-stable, exponential, gamma processes and many others as particular cases. This approach generalizes the Cole-Cole, Cole-Davidson and Havriliak-Negami laws well known in experimental physics of relaxation. The presented considerations discover a direct (one-to-one) relationship between the method of random relaxation rates and the anomalous diffusion approach based on subordination of random processes that are applied for the theory of relaxation phenomena. Moreover, it is found that the space and time clusterizations are responsible on equal foots for power-law memory effects in relaxation of complex physical systems.
Mardoukhi, Yousof; Jeon, Jae-Hyung; Metzler, Ralf
2015-11-28
We investigate the ergodic properties of a random walker performing (anomalous) diffusion on a random fractal geometry. Extensive Monte Carlo simulations of the motion of tracer particles on an ensemble of realisations of percolation clusters are performed for a wide range of percolation densities. Single trajectories of the tracer motion are analysed to quantify the time averaged mean squared displacement (MSD) and to compare this with the ensemble averaged MSD of the particle motion. Other complementary physical observables associated with ergodicity are studied, as well. It turns out that the time averaged MSD of individual realisations exhibits non-vanishing fluctuations even in the limit of very long observation times as the percolation density approaches the critical value. This apparent non-ergodic behaviour concurs with the ergodic behaviour on the ensemble averaged level. We demonstrate how the non-vanishing fluctuations in single particle trajectories are analytically expressed in terms of the fractal dimension and the cluster size distribution of the random geometry, thus being of purely geometrical origin. Moreover, we reveal that the convergence scaling law to ergodicity, which is known to be inversely proportional to the observation time T for ergodic diffusion processes, follows a power-law ∼T(-h) with h fractal structure of the accessible space. These results provide useful measures for differentiating the subdiffusion on random fractals from an otherwise closely related process, namely, fractional Brownian motion. Implications of our results on the analysis of single particle tracking experiments are provided.
Anomalous diffusion and Levy random walk of magnetic field lines in three dimensional turbulence
Energy Technology Data Exchange (ETDEWEB)
Zimbardo, G.; Veltri, P.; Basile, G.; Principato, S. [Dipartimento di Fisica, Universita della Calabria, I-87030 Arcavacata di Rende (Italy)
1995-07-01
The transport of magnetic field lines is studied numerically where three dimensional (3-D) magnetic fluctuations, with a power law spectrum, and periodic over the simulation box are superimposed on an average uniform magnetic field. The weak and the strong turbulence regime, {delta}{ital B}{similar_to}{ital B}{sub 0}, are investigated. In the weak turbulence case, magnetic flux tubes are separated from each other by percolating layers in which field lines undergo a chaotic motion. In this regime the field lines may exhibit Levy, rather than Gaussian, random walk, changing from Levy flights to trapped motion. The anomalous diffusion laws {l_angle}{Delta}{ital x}{sup 2}{sub {ital i}}{r_angle}{proportional_to}{ital s}{sup {alpha}} with {alpha}{gt}1 and {alpha}{lt}1, are obtained for a number of cases, and the non-Gaussian character of the field line random walk is pointed out by computing the kurtosis. Increasing the fluctuation level, and, therefore stochasticity, normal diffusion ({alpha}{congruent}1) is recovered and the kurtoses reach their Gaussian value. However, the numerical results show that neither the quasi-linear theory nor the two dimensional percolation theory can be safely extrapolated to the considered 3-D strong turbulence regime. {copyright} {ital 1995} {ital American} {ital Institute} {ital of} {ital Physics}.
Survival times of anomalous melt inclusions from element diffusion in olivine and chromite.
Spandler, C; O'Neill, H St C; Kamenetsky, V S
2007-05-17
The chemical composition of basaltic magma erupted at the Earth's surface is the end product of a complex series of processes, beginning with partial melting and melt extraction from a mantle source and ending with fractional crystallization and crustal assimilation at lower pressures. It has been proposed that studying inclusions of melt trapped in early crystallizing phenocrysts such as Mg-rich olivine and chromite may help petrologists to see beyond the later-stage processes and back to the origin of the partial melts in the mantle. Melt inclusion suites often span a much greater compositional range than associated erupted lavas, and a significant minority of inclusions carry distinct compositions that have been claimed to sample melts from earlier stages of melt production, preserving separate contributions from mantle heterogeneities. This hypothesis is underpinned by the assumption that melt inclusions, once trapped, remain chemically isolated from the external magma for all elements except those that are compatible in the host minerals. Here we show that the fluxes of rare-earth elements through olivine and chromite by lattice diffusion are sufficiently rapid at magmatic temperatures to re-equilibrate completely the rare-earth-element patterns of trapped melt inclusions in times that are short compared to those estimated for the production and ascent of mantle-derived magma or for magma residence in the crust. Phenocryst-hosted melt inclusions with anomalous trace-element signatures must therefore form shortly before magma eruption and cooling. We conclude that the assumption of chemical isolation of incompatible elements in olivine- and chromite-hosted melt inclusions is not valid, and we call for re-evaluation of the popular interpretation that anomalous melt inclusions represent preserved samples of unmodified mantle melts.
Anomalous diffusion in nonhomogeneous media: time-subordinated Langevin equation approach.
Srokowski, Tomasz
2014-03-01
Diffusion in nonhomogeneous media is described by a dynamical process driven by a general Lévy noise and subordinated to a random time; the subordinator depends on the position. This problem is approximated by a multiplicative process subordinated to a random time: it separately takes into account effects related to the medium structure and the memory. Density distributions and moments are derived from the solutions of the corresponding Langevin equation and compared with the numerical calculations for the exact problem. Both subdiffusion and enhanced diffusion are predicted. Distribution of the process satisfies the fractional Fokker-Planck equation.
Zhang, Yong; Green, Christopher T.; Tick, Geoffrey R.
2015-01-01
This study evaluates the role of the Peclet number as affected by molecular diffusion in transient anomalous transport, which is one of the major knowledge gaps in anomalous transport, by combining Monte Carlo simulations and stochastic model analysis. Two alluvial settings containing either short- or long-connected hydrofacies are generated and used as media for flow and transport modeling. Numerical experiments show that 1) the Peclet number affects both the duration of the power-law segment of tracer breakthrough curves (BTCs) and the transition rate from anomalous to Fickian transport by determining the solute residence time for a given low-permeability layer, 2) mechanical dispersion has a limited contribution to the anomalous characteristics of late-time transport as compared to molecular diffusion due to an almost negligible velocity in floodplain deposits, and 3) the initial source dimensions only enhance the power-law tail of the BTCs at short travel distances. A tempered stable stochastic (TSS) model is then applied to analyze the modeled transport. Applications show that the time-nonlocal parameters in the TSS model relate to the Peclet number, Pe. In particular, the truncation parameter in the TSS model increases nonlinearly with a decrease in Pe due to the decrease of the mean residence time, and the capacity coefficient increases with an increase in molecular diffusion which is probably due to the increase in the number of immobile particles. The above numerical experiments and stochastic analysis therefore reveal that the Peclet number as affected by molecular diffusion controls transient anomalous transport in alluvial aquifer–aquitard complexes.
Diffuse radio foregrounds: all-sky polarisation and anomalous microwave emission
Vidal Navarro, M. A.
2014-07-01
In this Thesis, we present work on the diffuse Galactic emission in the 23-43 GHz frequency range. We studied the polarised emission, which is dominated by synchrotron radiation at these frequencies. We also present work on the anomalous microwave emission (AME), both in total intensity and polarisation. These observations are useful to quantify the CMB foreground contribution and give us information about the ISM of our Galaxy. Polarisation observations are affected by a positive bias, particularly important in regions with low signal-to-noise ratio. We present a method to correct the bias in the case where the uncertainties in the Q, U Stokes parameters are not symmetric. We show that this method successfully corrects the polarisation maps, with a residual bias smaller than the random uncertainties on the maps, outperforming the methods that are previously described in the literature. We use the de-biasing method to set upper limits for the polarisation of AME in the ρ Ophiuchi and Perseus molecular clouds. In both clouds the AME polarisation fraction is found to be less than 2% at 23 GHz and33 GHz.We use data from the WMAP satellite at 23, 33 and 41 GHz to study the diffuse polarised emission over the entire sky. This emission is due to synchrotron radiation and it originates mostly from filamentary structures with well-ordered magnetic fields.We identify new filaments and studied their observational properties, such as polarisation spectral indices, polarisation fraction and Faraday rotation. We explore the link between the large scale filaments and the local ISM, using the model of an expanding shell in the vicinity of the Sun. We also quantify the level of contamination added by the diffuse filaments to the CMB E- and B-mode power spectra.The Q/U Imaging ExperimenT (QUIET) observed the polarised sky at 43 and 95 GHz, in order to measure the CMB spectra. We describe the instrument, the observations and data processing, focusing on two regions of the Galactic
THE DIFFUSE INTERSTELLAR BANDS AND ANOMALOUS MICROWAVE EMISSION MAY ORIGINATE FROM THE SAME CARRIERS
Energy Technology Data Exchange (ETDEWEB)
Bernstein, L. S.; Cline, J. A. [Spectral Sciences, Inc., 4 Fourth Avenue, Burlington, MA 01803 (United States); Clark, F. O. [Wopeco Research 125 South Great Road, Lincoln, MA 01773 (United States); Lynch, D. K., E-mail: larry@spectral.com, E-mail: jcline@spectral.com, E-mail: frank.clark@gmail.com, E-mail: dave@thulescientific.com [Thule Scientific, P.O. Box 953, Topanga, CA 90290 (United States)
2015-11-10
We argue that the observed spectroscopic and statistical properties of the diffuse interstellar band (DIB) carriers are those that are needed to produce the anomalous microwave emission (AME). We explore this idea using a carrier-impartial model for AME based on the observed DIB statistical properties. We show that an observed distribution of profile widths for narrow DIBs can be mapped into an AME spectrum. The mapping model is applied to width distributions observed for HD 204827 and HD 183143, selected because their spectroscopic and statistical properties bracket those for most other sight lines. The predicted AME spectra for these sight lines agree well with the range of spectral shapes, and peak frequencies, ∼23–31 GHz, typically observed for AME. We use the AME spectral profiles to derive a strong constraint between the average carrier size and its rotational temperature. The constraint is applied to a variety of postulated molecular carrier classes, including polycyclic aromatic hydrocarbons, fulleranes, hydrocarbon chains, and amorphous hydrocarbon clusters. The constraint favors small, cold carriers with average sizes of ∼8–15 carbon atoms, and average rotational temperatures of ∼3–10 K, depending on carrier type. We suggest new observations, analyses, and modeling efforts to help resolve the ambiguities with regard to carrier size and class, and to further clarify the DIB–AME relationship.
Universality in edge-source diffusion dynamics
DEFF Research Database (Denmark)
Mortensen, Asger; Okkels, Fridolin; Bruus, Henrik
2006-01-01
We show that in edge-source diffusion dynamics the integrated concentration N(t) has a universal dependence with a characteristic time scale tau=(A/P)(2)pi/(4D), where D is the diffusion constant while A and P are the cross-sectional area and perimeter of the domain, respectively. For the short......-time dynamics we find a universal square-root asymptotic dependence N(t)=N(0)root t/tau while in the long-time dynamics N(t) saturates exponentially at N-0. The exponential saturation is a general feature while the associated coefficients are weakly geometry dependent....
da Silva, Roberto; Vainstein, Mendeli H.; Gonçalves, Sebastián; Paula, Felipe S. F.
2013-08-01
Statistics of soccer tournament scores based on the double round robin system of several countries are studied. Exploring the dynamics of team scoring during tournament seasons from recent years we find evidences of superdiffusion. A mean-field analysis results in a drift velocity equal to that of real data but in a different diffusion coefficient. Along with the analysis of real data we present the results of simulations of soccer tournaments obtained by an agent-based model which successfully describes the final scoring distribution [da Silva , Comput. Phys. Commun.CPHCBZ0010-465510.1016/j.cpc.2012.10.030 184, 661 (2013)]. Such model yields random walks of scores over time with the same anomalous diffusion as observed in real data.
Diffusion in randomly perturbed dissipative dynamics
Rodrigues, Christian S; de Moura, Alessandro P S; Grebogi, Celso; Klages, Rainer
2014-01-01
Dynamical systems having many coexisting attractors present interesting properties from both fundamental theoretical and modelling points of view. When such dynamics is under bounded random perturbations, the basins of attraction are no longer invariant and there is the possibility of transport among them. Here we introduce a basic theoretical setting which enables us to study this hopping process from the perspective of anomalous transport using the concept of a random dynamical system with holes. We apply it to a simple model by investigating the role of hyperbolicity for the transport among basins. We show numerically that our system exhibits non-Gaussian position distributions, power-law escape times, and subdiffusion. Our simulation results are reproduced consistently from stochastic Continuous Time Random Walk theory.
Anomalous diffusion in heterogeneous glass-forming liquids: temperature-dependent behavior.
Langer, J S
2008-11-01
In a preceding paper, Langer and Mukhopadhyay [Phys. Rev. E 77, 061505 (2008)] studied the diffusive motion of a tagged molecule in an heterogeneous glass-forming liquid at temperatures just above a glass transition. Among other features of this system, we postulated a relation between heterogeneity and stretched-exponential decay of correlations, and we also confirmed that systems of this kind generally exhibit non-Gaussian diffusion on intermediate length and time scales. Here I extend this analysis to higher temperatures approaching the point where the heterogeneities disappear and thermal activation barriers become small. I start by modifying the continuous-time random-walk theory proposed in Langer and Mukhopadhyay and supplement this analysis with an extension of the excitation-chain theory of glass dynamics. I also use a key result from the shear-transformation-zone theory of viscous deformation of amorphous materials. Elements of each of these theories are then used to interpret experimental data for orthoterphenyl, specifially, the diffusion and viscosity coefficients and neutron-scattering measurements of the self-intermediate scattering function. Reconciling the theory with these data sets provides insights into the crossover between super-Arrhenius and Arrhenius dynamics, length scales of spatial heterogeneities, violation of the Stokes-Einstein relation in glass-forming liquids, and the origin of stretched-exponential decay of correlations.
Diffusion Dynamics with Changing Network Composition
Baños, Raquel A; Wang, Ning; Moreno, Yamir; González-Bailón, Sandra
2013-01-01
We analyze information diffusion using empirical data that tracks online communication around two instances of mass political mobilization, including the year that lapsed in-between the protests. We compare the global properties of the topological and dynamic networks through which communication took place as well as local changes in network composition. We show that changes in network structure underlie aggregated differences on how information diffused: an increase in network hierarchy is accompanied by a reduction in the average size of cascades. The increasing hierarchy affects not only the underlying communication topology but also the more dynamic structure of information exchange; the increase is especially noticeable amongst certain categories of nodes (or users). This suggests that the relationship between the structure of networks and their function in diffusing information is not as straightforward as some theoretical models of diffusion in networks imply.
Rao, E. V. K.; Krauz, Ph.; Thibierge, H.; Azoulay, R.; Vieu, C.
1994-03-01
We present here evidence on the deep diffusion of isoelectronic Sb implant induced defects in thick GaAs-AlGaAs multiquantum well structures (MQW) to depths as far as ˜30 times the implant projected range (Rp). This observation has been confirmed by performing low temperature photoluminescence depth scanning measurements and cross-sectional transmission electron microscopy (XTEM) analysis on room temperature Sb implanted thick MQW samples. An explanation based on the isoelectronic nature of Sb and its substitution on As site (SbAs) has been proposed to understand the anomalous diffusion of defects during implant and their contribution to Al/Ga disordering during post-implant annealing.
Dynamical corrections to the anomalous holographic soft-wall model: the pomeron and the odderon
Energy Technology Data Exchange (ETDEWEB)
Capossoli, Eduardo Folco [Instituto de Fisica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ (Brazil); Colegio Pedro II, Departamento de Fisica, Rio de Janeiro, RJ (Brazil); Li, Danning [Institute of Theoretical Physics, Chinese Academy of Science (ITP, CAS), Beijing (China); Boschi-Filho, Henrique [Instituto de Fisica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ (Brazil)
2016-06-15
In this work we use the holographic soft-wall AdS/QCD model with anomalous dimension contributions coming from two different QCD beta functions to calculate the masses of higher spin glueball states for both even and odd spins and their Regge trajectories, related to the pomeron and the odderon, respectively. We further investigate this model taking into account dynamical corrections due to a dilaton potential consistent with the Einstein equations in five dimensions. The results found in this work for the Regge trajectories within the anomalous soft-wall model with dynamical corrections are consistent with those present in the literature. (orig.)
Bickel, David R.; Verklan, M. Terese; Moon, Jon
1998-11-01
The scaling exponent of the root mean square (rms) displacement quantifies the roughness of fractal or multifractal time series; it is equivalent to other second-order measures of scaling, such as the power-law exponents of the spectral density and autocorrelation function. For self-similar time series, the rms scaling exponent equals the Hurst parameter, which is related to the fractal dimension. A scaling exponent of 0.5 implies that the process is normal diffusion, which is equivalent to an uncorrelated random walk; otherwise, the process can be modeled as anomalous diffusion. Higher exponents indicate that the increments of the signal have positive correlations, while exponents below 0.5 imply that they have negative correlations. Scaling exponent estimates of successive segments of the increments of a signal are used to test the null hypothesis that the signal is normal diffusion, with the alternate hypothesis that the diffusion is anomalous. Dispersional analysis, a simple technique which does not require long signals, is used to estimate the scaling exponent from the slope of the linear regression of the logarithm of the standard deviation of binned data points on the logarithm of the number of points per bin. Computing the standard error of the scaling exponent using successive segments of the signal is superior to previous methods of obtaining the standard error, such as that based on the sum of squared errors used in the regression; the regression error is more of a measure of the deviation from power-law scaling than of the uncertainty of the scaling exponent estimate. Applying this test to preterm neonate heart rate data, it is found that time intervals between heart beats can be modeled as anomalous diffusion with negatively correlated increments. This corresponds to power spectra between 1/f2 and 1/f, whereas healthy adults are usually reported to have 1/f spectra, suggesting that the immaturity of the neonatal nervous system affects the scaling
Rashid, Rafi; Chee, Stella Min Ling; Raghunath, Michael; Wohland, Thorsten
2015-05-01
Macromolecular crowding (MMC) has been used in various in vitro experimental systems to mimic in vivo physiology. This is because the crowded cytoplasm of cells contains many different types of solutes dissolved in an aqueous medium. MMC in the extracellular microenvironment is involved in maintaining stem cells in their undifferentiated state (niche) as well as in aiding their differentiation after they have travelled to new locations outside the niche. MMC at physiologically relevant fractional volume occupancies (FVOs) significantly enhances the adipogenic differentiation of human bone marrow-derived mesenchymal stem cells during chemically induced adipogenesis. The mechanism by which MMC produces this enhancement is not entirely known. In the context of extracellular collagen deposition, we have recently reported the importance of optimizing the FVO while minimizing the bulk viscosity. Two opposing properties will determine the net rate of a biochemical reaction: the negative effect of bulk viscosity and the positive effect of the excluded volume, the latter being expressed by the FVO. In this study we have looked more closely at the effect of viscosity on reaction rates. We have used fluorimetry to measure the rate of actin polymerization and fluorescence correlation spectroscopy (FCS) to measure diffusion of various probes in solutions containing the crowder Ficoll at physiological concentrations. Similar to its effect on collagen, Ficoll enhanced the actin polymerization rate despite increasing the bulk viscosity. Our FCS measurements reveal a relatively minor component of anomalous diffusion. In addition, our measurements do suggest that microviscosity becomes relevant in a crowded environment. We ruled out bulk viscosity as a cause of the rate enhancement by performing the actin polymerization assay in glycerol. These opposite effects of Ficoll and glycerol led us to conclude that microviscosity becomes relevant at the length scale of the reacting
Michas, Georgios; Vallianatos, Filippos; Karakostas, Vassilios; Papadimitriou, Eleftheria; Sammonds, Peter
2014-05-01
result that is in accordance to earthquake triggering in global scale (Huc and Main, 2003) and aftershocks diffusion in California (Helmstetter et al., 2003). While other mechanisms may be plausible, the results indicate that anomalous stress transfer due to the occurrence of the two major events control the migration of the aftershock activity, activating different fault segments and having strong implications for the seismic hazard of the area. Acknowledgments. G. Michas wishes to acknowledge the partial financial support from the Greek State Scholarships Foundation (IKY). This work has been accomplished in the framework of the postgraduate program and co-funded through the action "Program for scholarships provision I.K.Y. through the procedure of personal evaluation for the 2011-2012 academic year" from resources of the educational program "Education and Life Learning" of the European Social Register and NSRF 2007- 2013. References Ganas, A., Chousianitis, K., Batsi, E., Kolligri, M., Agalos, A., Chouliaras, G., Makropoulos, K. (2013). The January 2010 Efpalion earthquakes (Gulf of Corinth, central Greece): Earthquake interactions and blind normal faulting. J. of Seism., 17(2), 465-484. Helmstetter, A., Ouillon, G., Sornette, D. (2003). Are aftershocks of large California earthquakes diffusing? J. of Geophys. Res. B, 108(10), 2483. Huc, M., Main, I. G. (2003). Anomalous stress diffusion in earthquake triggering: Correlation length, time dependence, and directionality. J. of Geophys. Res. B, 108(7), 2324. Karakostas, V., Karagianni, E., Paradisopoulou, P. (2012). Space-time analysis, faulting and triggering of the 2010 earthquake doublet in western Corinth gulf. Nat.Haz., 63(2), 1181-1202. Metzler, R., Klafter, J. (2000). The random walk's guide to anomalous diffusion: a fractional dynamics approach. Physics Reports, 339, 1-77. Michas, G., Vallianatos, F., Sammonds, P. (2013). Non-extensivity and long-range correlations in the earthquake activity at the West Corinth
Institute of Scientific and Technical Information of China (English)
徐明瑜; 谭文长
2001-01-01
The velocity field of generalized second order fluid with fractional anomalous diffusion caused by a plate moving impulsively in its own plane is investigated and the anomalous diffusion problems of the stress field and vortex sheet caused by this process are studied. Many previous and classical results can be considered as particular cases of this paper, such as the solutions of the fractional diffusion equations obtained by Wyss; the classical Rayleigh' s time-space similarity solution; the relationship between stress field and velocity field obtained by Bagley and co-worker and Podlubny' s results on the fractional motion equation of a plate. In addition, a lot of significant results also are obtained. For example, the necessary condition for causing the vortex sheet is that the time fractional diffusion index β must be greater than that of generalized second order fluid α; the establishment of the vorticity distribution function depends on the time history of the velocity profile at a given point, and the time history can be described by the fractional calculus.
Diffusion-damped domain wall dynamics
Energy Technology Data Exchange (ETDEWEB)
Varga, R; Infante, G [Inst. Phys., Fac. Sci., UPJS, Park Angelinum 9, 04154 Kosice (Slovakia); Badini-Confalonieri, G A; Vazquez, M, E-mail: rvarga@upjs.s [Instituto de Ciencia de Materiales de Madrid, CSIC, Cantoblanco, 28049, Madrid (Spain)
2010-01-01
In the given work, the influence of diffusional damping on the domain wall dynamics of heat treated FeSiBP microwires is presented. Two regions of the domain wall dynamics have been found. At low applied fields diffusion damping prevails, keeping the domain wall velocity and mobility low. At higher fields, the diffusional effects are overcomed and domain wall velocity increases steeply and so does the domain wall mobility.
Directory of Open Access Journals (Sweden)
Giane Gonçalves
2005-07-01
Full Text Available Neste trabalho investigaremos as equações de difusão, usualmente aplicadas na descrição da difusão anômala, que empregam derivadas fracionárias tanto na variável temporal quanto na variável espacial. Em particular, para essas equações obteremos soluções exatas levando em conta uma condição inicial genérica e formularemos uma teoria deperturbação para o estudo de situações mais complexas. Também verificaremos que as derivadas fracionárias, quando aplicadas na parte temporal, possibilitam-nos o estudo de um processo de difusão anômala com o segundo momento finito, i.e., x 2 µ t a ( 0 1 , correspondendo aos casos, sub e superdifusivo, respectivamente. Em contraste, com a derivada fracionária aplicada na variável espacial que resulta em uma difusão anômala cujo segundo momento não é finito. Complementando o cenário acima, empregaremos o formalismo de caminhantes aleatórios para explorar as implicações obtidas por usar derivadas fracionárias na equação de difusão.In this work we investigate the anomalous diffusion equations, usually applied to describe the anomalous diffusion, which employ fractional derivatives for the time or the spatial variables. Inparticular, we obtain exact solutions by taking a generic initial condition into account and developing a perturbation theory to investigate complex situations. We also verify that the fractional derivatives, when applied to the time variable, lead us to a anomalous diffusion with second moment finite, i.e., x 2 µ t a ( 0 1 , corresponding to sub and superdifusive behavior, respectively. By way of contrast, the fractional derivative applied to the spatial variable results in a anomalous diffusion where the second moment is not finite. These equations generalize the usual diffusion equation in order to incorporate several situations. We also employ the continuous time random walking formalism to investigate the implications obtained by using fractional
Panja, D.
2010-01-01
Any first course on polymer physics teaches that the dynamics of a tagged monomer of a polymer is anomalously subdiffusive, i.e., the mean-square displacement of a tagged monomer increases as tα for some α < 1 until the terminal relaxation time τ of the polymer. Beyond time τ the motion of the tagge
Wei, Song; Chen, Wen; Hon, Y. C.
2016-11-01
This paper investigates the temporal effects in the modeling of flows through porous media and particles transport. Studies will be made among the time fractional diffusion model and two classical nonlinear diffusion models. The effects of the parameters upon the mentioned models have been studied. By simulating the sub-diffusion processes and comparing the numerical results of these models under different boundary conditions, we can conclude that the time fractional diffusion model is more suitable for simulating the sub-diffusion with steady diffusion rate; whereas the nonlinear models are more appropriate for depicting the sub-diffusion under changing diffusion rate.
Diffusive dynamics of nanoparticles in aqueous dispersions
He, Kai
2012-01-01
The diffusive dynamics of 100 nm to 400 nm diameter polystyrene nanoparticles dispersed in water were studied using brightfield and fluorescence based differential dynamic microscopy (DDM) and compared to those obtained from dynamic light scattering. The relaxation times measured with brightfield and fluorescence DDM over a broad range of concentration of nanoparticles (10 -6 ≤ φ ≤ 10-3) and scattering vectors (0.5 μm-1 < q < 10 μm-1) are in excellent agreement with each other and extrapolate quantitatively to those obtained from DLS measurements. The diffusion coefficients extracted from the q-dependent relaxation times using all three methods are independent of the nanoparticle concentration. © 2012 The Royal Society of Chemistry.
Sub 100-ps dynamics of the anomalous Hall effect at THz frequencies
Huisman, T J; Tsukamoto, A; Ma, L; Fan, W J; Zhou, S M; Rasing, Th; Kimel, A V
2016-01-01
We report about the anomalous Hall effect in 4f 3d metallic alloys measured using terahertz time-domain spectroscopy. The strength of the observed terahertz spin-dependent transport phenomenon is in good agreement with expectations based on electronic transport measurements. Employing this effect, we succeeded to reveal ultrafast dynamics of the anomalous Hall effect which accompanies the sub-100 picosecond optically induced magnetization reversal in a GdFeCo alloy. The experiments demonstrate the ability to control currents at terahertz frequencies in spintronic devices magnetically and ultrafast.
Diffusion dynamics in microfluidic dye lasers
DEFF Research Database (Denmark)
Gersborg-Hansen, Morten; Balslev, Søren; Mortensen, Niels Asger
2007-01-01
We have investigated the bleaching dynamics that occur in opto-fluidic dye lasers, where the liquid laser dye in a channel is locally bleached due to optical pumping. Our studies suggest that for micro-fluidic devices, the dye bleaching may be compensated through diffusion of dye molecules alone....... By relying on diffusion rather than convection to generate the necessary dye replenishment, our observation potentially allows for a significant simplification of opto-fluidic dye laser device layouts, omitting the need for cumbersome and costly external fluidic handling or on-chip micro-fluidic pumping...
Energy Technology Data Exchange (ETDEWEB)
Berard, A.; Grandati, Y.; Mohrbach, H. [Universite Paul Verlaine, Institut de Physique, Laboratoire de Physique Moleculaire et des Collisions, ICPMB, IF CNRS 2843, Metz, Cedex 3 (France); Ghosh, Subir [Indian Statistical Institute, Physics and Applied Mathematics Unit, Kolkata (India); Pal, Probir [S.N. Bose National Centre for Basic Sciences, Kolkata (India)
2011-11-15
In this paper we have considered the dynamics of an anomalous (g{ne}2) charged relativistic spinning particle in the presence of an external electromagnetic field. A constraint analysis is done and the complete set of Dirac brackets are provided that generate the canonical Lorentz algebra and dynamics through Hamiltonian equations of motion. The spin-induced effective curvature of spacetime and its possible connection with Analogue Gravity models are commented upon. (orig.)
Bouchet, Freddy; Dauxois, Thierry
2005-10-01
We explain the ubiquity and extremely slow evolution of non-Gaussian out-of-equilibrium distributions for the Hamiltonian mean-field model, by means of traditional kinetic theory. Deriving the Fokker-Planck equation for a test particle, one also unambiguously explains and predicts striking slow algebraic relaxation of the momenta autocorrelation, previously found in numerical simulations. Finally, angular anomalous diffusion are predicted for a large class of initial distributions. Non-extensive statistical mechanics is shown to be unnecessary for the interpretation of these phenomena.
Anomalous dynamics of intruders in a crowded environment of mobile obstacles
Sentjabrskaja, Tatjana; Zaccarelli, Emanuela; de Michele, Cristiano; Sciortino, Francesco; Tartaglia, Piero; Voigtmann, Thomas; Egelhaaf, Stefan U.; Laurati, Marco
2016-04-01
Many natural and industrial processes rely on constrained transport, such as proteins moving through cells, particles confined in nanocomposite materials or gels, individuals in highly dense collectives and vehicular traffic conditions. These are examples of motion through crowded environments, in which the host matrix may retain some glass-like dynamics. Here we investigate constrained transport in a colloidal model system, in which dilute small spheres move in a slowly rearranging, glassy matrix of large spheres. Using confocal differential dynamic microscopy and simulations, here we discover a critical size asymmetry, at which anomalous collective transport of the small particles appears, manifested as a logarithmic decay of the density autocorrelation functions. We demonstrate that the matrix mobility is central for the observed anomalous behaviour. These results, crucially depending on size-induced dynamic asymmetry, are of relevance for a wide range of phenomena ranging from glassy systems to cell biology.
Anomalous dynamics of interstitial dopants in soft crystals
Tauber, Justin; Higler, Ruben; Sprakel, Joris
2016-11-01
The dynamics of interstitial dopants govern the properties of a wide variety of doped crystalline materials. To describe the hopping dynamics of such interstitial impurities, classical approaches often assume that dopant particles do not interact and travel through a static potential energy landscape. Here we show, using computer simulations, how these assumptions and the resulting predictions from classical Eyring-type theories break down in entropically stabilized body-centered cubic (BCC) crystals due to the thermal excitations of the crystalline matrix. Deviations are particularly severe close to melting where the lattice becomes weak and dopant dynamics exhibit strongly localized and heterogeneous dynamics. We attribute these anomalies to the failure of both assumptions underlying the classical description: (i) The instantaneous potential field experienced by dopants becomes largely disordered due to thermal fluctuations and (ii) elastic interactions cause strong dopant-dopant interactions even at low doping fractions. These results illustrate how describing nonclassical dopant dynamics requires taking the effective disordered potential energy landscape of strongly excited crystals and dopant-dopant interactions into account.
Diffusion processes through social groups' dynamics
Apolloni, Andrea
2011-01-01
Axelrod's model describes the dissemination of a set of cultural traits in a society constituted by individual agents. In a social context, nevertheless, individual choices toward a specific attitude are also at the basis of the formation of communities, groups and parties. The membership in a group changes completely the behavior of single agents who start acting according to a social identity. Groups act and interact among them as single entities, but still conserve an internal dynamics. We show that, under certain conditions of social dynamics, the introduction of group dynamics in a cultural dissemination process avoids the flattening of the culture into a single entity and preserves the multiplicity of cultural attitudes. We also considered diffusion processes on this dynamical background, showing the conditions under which information as well as innovation can spread through the population in a scenario where the groups' choices determine the social structure.
Anomalous Contagion and Renormalization in Dynamical Networks with Nodal Mobility
Manrique, Pedro D; Zheng, Minzhang; Xu, Chen; Hui, Pak Ming; Johnson, Neil F
2015-01-01
The common real-world feature of individuals migrating through a network -- either in real space or online -- significantly complicates understanding of network processes. Here we show that even though a network may appear static on average, underlying nodal mobility can dramatically distort outbreak profiles. Highly nonlinear dynamical regimes emerge in which increasing mobility either amplifies or suppresses outbreak severity. Predicted profiles mimic recent outbreaks of real-space contagion (social unrest) and online contagion (pro-ISIS support). We show that this nodal mobility can be renormalized in a precise way for a particular class of dynamical networks.
Dynamics of three anomalous SST events in the Coral Sea
Schiller, A.; Ridgway, K. R.; Steinberg, C. R.; Oke, P. R.
2009-03-01
Variability of the circulation in the Coral Sea, accompanied by large heat transport anomalies, has the potential to have detrimental impacts on underlying ecosystems, including the Great Barrier Reef. In this study we analyze the dynamics of three events, characterized by extremes in sea-surface temperature, as simulated in an eddy-resolving ocean reanalysis. We show that a cooling in April 1997 results from strong wind anomalies and is supported by vertical and horizontal advective heat losses. A warm event in October 1998 is attributable to a heat gain by horizontal advection. A heat budget of the mixed-layer within a closed box shows that warm anomalies in January 2002 involve a quasi-balance between horizontal advection and vertical entrainment with a large local heat gain through the ocean surface near-shore that apparently caused a coral bleaching event. The dynamics of these extreme events are all quite different, with both local and remote influences.
Lattice dynamical investigations on Zn diffusion in zinc oxide
Indian Academy of Sciences (India)
P Vinotha Boorana Lakshmi; K Ramachandran
2011-04-01
Zinc self diffusion in bulk zinc oxide is studied by lattice dynamical approach here to get more insight into the diffusion in nano ZnO. The results reveal that only cationic self diffusion is dominant over anionic self diffusion and that too by single vacancy mechanism. The results are compared with the available experiments and discussed.
Galactic civilizations - Population dynamics and interstellar diffusion
Newman, W. I.; Sagan, C.
1981-01-01
A model is developed of the interstellar diffusion of galactic civilizations which takes into account the population dynamics of such civilizations. The problem is formulated in terms of potential theory, with a family of nonlinear partial differential and difference equations specifying population growth and diffusion for an organism with advantageous genes that undergoes random dispersal while increasing in population locally, and a population at zero population growth. In the case of nonlinear diffusion with growth and saturation, it is found that the colonization wavefront from the nearest independently arisen galactic civilization can have reached the earth only if its lifetime exceeds 2.6 million years, or 20 million years if discretization can be neglected. For zero population growth, the corresponding lifetime is 13 billion years. It is concluded that the earth is uncolonized not because interstellar spacefaring civilizations are rare, but because there are too many worlds to be colonized in the plausible colonization lifetime of nearby civilizations, and that there exist no very old galactic civilizations with a consistent policy of the conquest of inhabited worlds.
Shin, Hyun Kyung; Choi, Bongsik; Talkner, Peter; Lee, Eok Kyun
2014-12-07
Based on the generalized Langevin equation for the momentum of a Brownian particle a generalized asymptotic Einstein relation is derived. It agrees with the well-known Einstein relation in the case of normal diffusion but continues to hold for sub- and super-diffusive spreading of the Brownian particle's mean square displacement. The generalized asymptotic Einstein relation is used to analyze data obtained from molecular dynamics simulations of a two-dimensional soft disk fluid. We mainly concentrated on medium densities for which we found super-diffusive behavior of a tagged fluid particle. At higher densities a range of normal diffusion can be identified. The motion presumably changes to sub-diffusion for even higher densities.
Anomalous Thermal Diffusivity in Underdoped YBa$_2$Cu$_3$O$_{6+x}$
Zhang, J -C; Ramshaw, B J; Bonn, D A; Liang, R; Hardy, W N; Hartnoll, S A; Kapitulnik, A
2016-01-01
We present local optical measurements of thermal diffusivity in the $ab$ plane of underdoped YBCO crystals. We find that the diffusivity anisotropy is comparable to reported values of the electrical resistivity anisotropy, suggesting that the anisotropies have the same origin. The anisotropy drops sharply below the charge order transition. We interpret our results through a strong electron-phonon scattering picture and find that both electronic and phononic contributions to the diffusivity saturate a proposed bound. Our results suggest that neither well-defined electron nor phonon quasiparticles are present in this material.
Ribeiro, H V; Alves, L G A; Zola, R S; Lenzi, E L
2014-01-01
The comb model is a simplified description for anomalous diffusion under geometric constraints. It represents particles spreading out in a two-dimensional space where the motions in the x-direction are allowed only when the y coordinate of the particle is zero. Here, we propose an extension for the comb model via Langevin-like equations driven by fractional Gaussian noises (long-range correlated). By carrying out computer simulations, we show that the correlations in the y-direction affect the diffusive behavior in the x-direction in a non-trivial fashion, resulting in a quite rich diffusive scenario characterized by usual, superdiffusive or subdiffusive scaling of second moment in the x-direction. We further show that the long-range correlations affect the probability distribution of the particle positions in the x-direction, making their tails longer when noise in the y-direction is persistent and shorter for anti-persistent noise. Our model thus combines and allows the study/analysis of the interplay betwe...
Liu, Lin; Zheng, Liancun; Liu, Fawang; Zhang, Xinxin
2016-09-01
An improved Cattaneo-Christov flux model is proposed which can be used to capture the effects of the time and spatial relaxations, the time and spatial inhomogeneous diffusion and the spatial transition probability of cell transport in a highly non-homogeneous medium. Solutions are obtained by numerical discretization method where the time and spatial fractional derivative are discretized by the L1-approximation and shifted Grünwald definition, respectively. The solvability, stability and convergence of the numerical method for the special case of the Cattaneo-Christov equation are proved. Results indicate that the fractional convection diffusion-wave equation is an evolution equation which displays the coexisting characteristics of parabolicity and hyperbolicity. In other words, for α in (0, 1), the cells transport occupies the characteristics of coupling convection diffusion and wave spreading. Moreover, the effects of pertinent time parameter, time and spatial fractional derivative parameters, relaxation parameter, weight coefficient and the convection velocity on the anomalous transport of cells are shown graphically and analyzed in detail.
A new numerical method for solving two-dimensional variable-order anomalous sub-diffusion equation
Directory of Open Access Journals (Sweden)
Jiang Wei
2016-01-01
Full Text Available The novelty and innovativeness of this paper are the combination of reproducing kernel theory and spline, this leads to a new simple but effective numerical method for solving variable-order anomalous sub-diffusion equation successfully. This combination overcomes the weaknesses of piecewise polynomials that can not be used to solve differential equations directly because of lack of the smoothness. Moreover, new bases of reproducing kernel spaces are constructed. On the other hand, the existence of any ε-approximate solution is proved and an effective method for obtaining the ε-approximate solution is established. A numerical example is given to show the accuracy and effectiveness of theoretical results.
Anomalous diffusion of water in [BMIM][TFSI] room-temperature ionic liquid.
Rollet, Anne-Laure; Porion, Patrice; Vaultier, Michel; Billard, Isabelle; Deschamps, Michael; Bessada, Catherine; Jouvensal, Laurence
2007-10-18
We have studied the self-diffusion properties of butyl-methyl-imidazolium bis(trifluoromethylsulfonyl)-imide ([BMIM][TFSI]) + water system. The self-diffusion coefficients of cations, anions, and water molecules were determined by pulsed field gradient NMR. These measures were performed with increased water quantity up to saturation (from 0.3 to 30 mol %). Unexpected variations have been observed. The self-diffusion coefficient of every species increases with the quantity of water but not in the same order of magnitude. Whereas very similar evolutions are observed for the anion and cation, the increase is 25 times greater for water molecules. We interpret our data by the existence of phase separation at microscopic scale.
Energy Technology Data Exchange (ETDEWEB)
Zimbardo, G.
2005-07-01
Plasma transport in the presence of turbulence depends on a variety of parameters like the fluctuation level ? B/B0, the ratio between the particle Larmor radius and the turbulence correlation lengths, and the turbulence anisotropy. In this presentation, we review the results of numerical simulations of plasma and magnetic field line transport in the case of anisotropic magnetic turbulence, for parameter values close to those of the solar wind. We assume a uniform background magnetic field B0 = B0ez and a Fourier representation for magnetic fluctuations, with wavectors forming any angle with respect to B0. The energy density spectrum is a power law, and in k space the constant amplitude surfaces are ellipsoids, described by the correlation lengths lx, ly, lz, which quantify the anisotropy of turbulence. For magnetic field lines, we find that transport perpendicular to the background field depends on the Kubo number R = ? B B0 lz lx . For small Kubo numbers, R ? 1, we find anomalous, non Gaussian transport regimes (both sub and superdiffusive) which can be described as a Levy random walk. Increasing the Kubo number, i.e., the fluctuation level ? B/B0 and/or the ratio lz/lx, we find first a quasilinear and then a percolative regime, both corresponding to Gaussian diffusion. For particles, we find that transport parallel and perpendicular to the background magnetic field heavily depends on the turbulence anisotropy and on the particle Larmor radius. For turbulence levels typical of the solar wind, ? B/B0 ? 0.5 ?1, when the ratio between the particle Larmor radius and the turbulence correlation lengths is small, anomalous regimes are found in the case lz/lx ? 1, with Levy random walk (superdiffusion) along the magnetic field and subdiffusion in the perpendicular directions. Conversely, for lz/lx > 1 normal, Gaussian diffusion is found. Increasing the ratio between the particle Larmor radius and the turbulence correlation lengths, the parallel superdiffusion is
Energy Technology Data Exchange (ETDEWEB)
Zimbardo, Gaetano [Dipartimento di Fisica, Universita della Calabria, Ponte P. Bucci, Cubo 31C, I-87036 Arcavacata di Rende (Italy)
2005-12-15
Plasma transport in the presence of turbulence depends on a variety of parameters such as the fluctuation level, {delta}B/B{sub 0}, the ratio between the particle Larmor radius and the turbulence correlation length, and the turbulence anisotropy. In this paper, we present the results of numerical simulations of plasma and magnetic field line transport in the case of anisotropic magnetic turbulence, for parameter values close to those of the solar wind. We assume a uniform background magnetic field B{sub 0} = B{sub 0} e{sub z} and a Fourier representation for magnetic fluctuations, which includes wavectors oblique with respect to B{sub 0}. The energy density spectrum is a power law, and in k space it is described by the correlation lengths l{sub x}, l{sub y}, l{sub z}, which quantify the anisotropy of turbulence. For magnetic field lines, transport perpendicular to the background field depends on the Kubo number R ({delta}B/B{sub 0}) (l{sub z}/l{sub x}). For small Kubo numbers, R << 1, anomalous, non-Gaussian transport regimes (both sub- and superdiffusive) are found, which can be described as a Levy random walk. Increasing the Kubo number, i.e. the fluctuation level, {delta}B/B{sub 0}, or the ratio l{sub z}/l{sub x}, we find first a quasilinear regime and then a percolative regime, both corresponding to Gaussian diffusion. For particles, we find that transport parallel and perpendicular to the background magnetic field depends heavily on the turbulence anisotropy and on the particle Larmor radius. For turbulence levels typical of the solar wind, {delta}B/B{sub 0}{approx_equal} 0.5-1, when the ratio between the particle Larmor radius and the turbulence correlation lengths is small, anomalous regimes are found in the case l{sub z}/l{sub x} {<=} 1, with a Levy random walk (superdiffusion) along the magnetic field and subdiffusion in the perpendicular directions. Conversely, for l{sub z}/l{sub x} > 1 normal Gaussian diffusion is found. A possible expression for
Dynamic analysis of a diffusing particle in a trapping potential
Lindner, M.; Nir, G.; Vivante, A.; Young, I.T.; Garini, Y.
2013-01-01
The dynamics of a diffusing particle in a potential field is ubiquitous in physics, and it plays a pivotal role in single-molecule studies. We present a formalism for analyzing the dynamics of diffusing particles in harmonic potentials at low Reynolds numbers using the time evolution of the particle
Anomalous dynamical scaling in anharmonic chains and plasma models with multi-particle collisions
Di Cintio, Pierfrancesco; Bufferand, Hugo; Ciraolo, Guido; Lepri, Stefano; Straka, Mika J
2015-01-01
We study the anomalous dynamical scaling of equilibrium correlations in one dimensional systems. Two different models are compared: the Fermi-Pasta-Ulam chain with cubic and quartic nonlinearity and a gas of point particles interacting stochastically through the Multi-Particle Collision dynamics. For both models -that admit three conservation laws- by means of detailed numerical simulations we verify the predictions of Nonlinear Fluctuating Hydrodynamics for the structure factors of density and energy fluctuations at equilibrium. Despite of this, violations of the expected scaling in the currents correlation are found in some regimes, hindering the observation of the asymptotic scaling predicted by the theory. In the case of the gas model this crossover is clearly demonstrated upon changing the coupling constant.
Watkins, N. W.; Credgington, D.; Sanchez, R.; Chapman, S. C.
2007-12-01
Since the 1960s Mandelbrot has advocated the use of fractals for the description of the non-Euclidean geometry of many aspects of nature. In particular he proposed two kinds of model to capture persistence in time (his Joseph effect, common in hydrology and with fractional Brownian motion as the prototpe) and/or prone to heavy tailed jumps (the Noah effect, typical of economic indices, for which he proposed Lévy flights as an exemplar). Both effects are now well demonstrated in space plasmas, notably in indices quantifying Earth's auroral currents and in the turbulent solar wind. Models have, however, typically emphasised one of the Noah and Joseph parameters (the Lévy exponent μ and the temporal exponent β) at the other's expense. I will describe recent work [1] in which we studied a simple self-affine stable model-linear fractional stable motion, LFSM, which unifies both effects. I will discuss how this resolves some contradictions seen in earlier work. Such Noah-Joseph hybrid ("ambivalent" [2]) behaviour is highly topical in physics but is typically studied in the paradigm of the continuous time random walk (CTRW) [2,3] rather than LFSM. I will clarify the physical differences between these two pictures and present a recently-derived diffusion equation for LFSM. This replaces the second order spatial derivative in the equation of fBm [4] with a fractional derivative of order μ, but retains a diffusion coefficient with a power law time dependence rather than a fractional derivative in time (c.f. [2,3]). Intriguingly the self-similarity exponent extracted from the CTRW differs from that seen in LFSM. In the CTRW it is the ratio of μ to a temporal exponent, in LFSM it is an additive function of them. I will also show work in progress using an LFSM model and simple analytic scaling arguments to study the problem of the area between an LFSM curve and a threshold-related to the burst size measure introduced by Takalo and Consolini into solar- terrestrial physics
Crossover of two power laws in the anomalous diffusion of a two lipid membrane
Energy Technology Data Exchange (ETDEWEB)
Bakalis, Evangelos, E-mail: ebakalis@gmail.com, E-mail: francesco.zerbetto@unibo.it; Höfinger, Siegfried; Zerbetto, Francesco, E-mail: ebakalis@gmail.com, E-mail: francesco.zerbetto@unibo.it [Dipartimento di Chimica “G. Ciamician”, Universita’ di Bologna, Via F. Selmi 2, 40126 Bologna (Italy); Venturini, Alessandro [Institute for the Organic Synthesis and Photoreactivity, National Research Council of Italy, Via Gobetti 101, 40129 Bologna (Italy)
2015-06-07
Molecular dynamics simulations of a bi-layer membrane made by the same number of 1-palmitoyl-2-oleoyl-glycero-3-phospho-ethanolamine and palmitoyl-oleoyl phosphatidylserine lipids reveal sub-diffusional motion, which presents a crossover between two different power laws. Fractional Brownian motion is the stochastic mechanism that governs the motion in both regimes. The location of the crossover point is justified with simple geometrical arguments and is due to the activation of the mechanism of circumrotation of lipids about each other.
A dynamic Monte Carlo study of anomalous current voltage behaviour in organic solar cells
Energy Technology Data Exchange (ETDEWEB)
Feron, K., E-mail: Krishna.Feron@csiro.au; Fell, C. J. [Centre for Organic Electronics, University of Newcastle, Callaghan, NSW 2308 (Australia); CSIRO Energy Flagship, Newcastle, NSW 2300 (Australia); Zhou, X.; Belcher, W. J.; Dastoor, P. C. [Centre for Organic Electronics, University of Newcastle, Callaghan, NSW 2308 (Australia)
2014-12-07
We present a dynamic Monte Carlo (DMC) study of s-shaped current-voltage (I-V) behaviour in organic solar cells. This anomalous behaviour causes a substantial decrease in fill factor and thus power conversion efficiency. We show that this s-shaped behaviour is induced by charge traps that are located at the electrode interface rather than in the bulk of the active layer, and that the anomaly becomes more pronounced with increasing trap depth or density. Furthermore, the s-shape anomaly is correlated with interface recombination, but not bulk recombination, thus highlighting the importance of controlling the electrode interface. While thermal annealing is known to remove the s-shape anomaly, the reason has been not clear, since these treatments induce multiple simultaneous changes to the organic solar cell structure. The DMC modelling indicates that it is the removal of aluminium clusters at the electrode, which act as charge traps, that removes the anomalous I-V behaviour. Finally, this work shows that the s-shape becomes less pronounced with increasing electron-hole recombination rate; suggesting that efficient organic photovoltaic material systems are more susceptible to these electrode interface effects.
Understanding Dynamic Competitive Technology Diffusion in Electronic Markets
Zhang, Cheng; Song, Peijian; Xu, Yunjie; Xue, Ling
The extant literature on information technology (IT) diffusion has largely treated technology diffusion as a generic and independent process. This study, in contrast, examines the diffusion of different IT products with brand differentiation and competition. Drawing upon existing theories of product diffusion, we propose a research model to capture the dynamics of the competitive diffusion of web-based IT products and validate it with longitudinal field data of e-business platforms. Our findings suggest that IT product diffusion can be better predicted by a competitive model than by an independent-diffusion-process model. This research extends IT research to the context of competitive diffusion and provides practitioners an effective model to predict the dissemination of their products. The research also suggests the existence of asymmetric interactions among competing products, prompting scholars and practitioners to pay attention to the influence of competing products when making forecast of their product market.
El-Ganainy, Ramy; Christodoulides, Demetrios N
2013-01-01
We investigate the dynamics of nonclassical states of light in coupled optical structures and we demonstrate a number of intriguing features associated with such arrangements. By diagonalizing the system's Hamiltonian, we show that these geometries can support eigenstates having anomalous optical intensity distribution with no classical counterpart. These features may provide new avenues towards manipulating light flow at the quantum level. By projecting the Hamiltonian operator on Hilbert subspaces spanning different numbers of photon excitations, we demonstrate that processes such as coherent transport, state localization and surface Bloch oscillations can take place in Fock space. Furthermore, we show that Hamiltonian representations of Fock space manifolds differing by one photon obey a discrete supersymmetry relation
Diffusive Dynamics of Nanoparticles in Arrays of Nanoposts
He, Kai
2013-06-25
The diffusive dynamics of dilute dispersions of nanoparticles of diameter 200-400 nm were studied in microfabricated arrays of nanoposts using differential dynamic microscopy and single particle tracking. Posts of diameter 500 nm and height 10 μm were spaced by 1.2-10 μm on a square lattice. As the spacing between posts was decreased, the dynamics of the nanoparticles slowed. Moreover, the dynamics at all length scales were best represented by a stretched exponential rather than a simple exponential. Both the relative diffusivity and the stretching exponent decreased linearly with increased confinement and, equivalently, with decreased void volume. The slowing of the overall diffusive dynamics and the broadening distribution of nanoparticle displacements with increased confinement are consistent with the onset of dynamic heterogeneity and the approach to vitrification. © 2013 American Chemical Society.
Diffusive dynamics of nanoparticles in arrays of nanoposts.
He, Kai; Babaye Khorasani, Firoozeh; Retterer, Scott T; Thomas, Darrell K; Conrad, Jacinta C; Krishnamoorti, Ramanan
2013-06-25
The diffusive dynamics of dilute dispersions of nanoparticles of diameter 200-400 nm were studied in microfabricated arrays of nanoposts using differential dynamic microscopy and single particle tracking. Posts of diameter 500 nm and height 10 μm were spaced by 1.2-10 μm on a square lattice. As the spacing between posts was decreased, the dynamics of the nanoparticles slowed. Moreover, the dynamics at all length scales were best represented by a stretched exponential rather than a simple exponential. Both the relative diffusivity and the stretching exponent decreased linearly with increased confinement and, equivalently, with decreased void volume. The slowing of the overall diffusive dynamics and the broadening distribution of nanoparticle displacements with increased confinement are consistent with the onset of dynamic heterogeneity and the approach to vitrification.
Anomalous Thermalization in Ergodic Systems
Luitz, David J.; Bar Lev, Yevgeny
2016-10-01
It is commonly believed that quantum isolated systems satisfying the eigenstate thermalization hypothesis (ETH) are diffusive. We show that this assumption is too restrictive since there are systems that are asymptotically in a thermal state yet exhibit anomalous, subdiffusive thermalization. We show that such systems satisfy a modified version of the ETH ansatz and derive a general connection between the scaling of the variance of the off-diagonal matrix elements of local operators, written in the eigenbasis of the Hamiltonian, and the dynamical exponent. We find that for subdiffusively thermalizing systems the variance scales more slowly with system size than expected for diffusive systems. We corroborate our findings by numerically studying the distribution of the coefficients of the eigenfunctions and the off-diagonal matrix elements of local operators of the random field Heisenberg chain, which has anomalous transport in its thermal phase. Surprisingly, this system also has non-Gaussian distributions of the eigenfunctions, thus, directly violating Berry's conjecture.
Interestingness-Driven Diffusion Process Summarization in Dynamic Networks
DEFF Research Database (Denmark)
Qu, Qiang; Liu, Siyuan; Jensen, Christian S.
2014-01-01
tool in this regard is data summarization. However, few existing studies aim to summarize graphs/networks for dynamics. Dynamic networks raise new challenges not found in static settings, including time sensitivity and the needs for online interestingness evaluation and summary traceability, which......The widespread use of social networks enables the rapid diffusion of information, e.g., news, among users in very large communities. It is a substantial challenge to be able to observe and understand such diffusion processes, which may be modeled as networks that are both large and dynamic. A key...... render existing techniques inapplicable. We study the topic of dynamic network summarization: how to summarize dynamic networks with millions of nodes by only capturing the few most interesting nodes or edges over time, and we address the problem by finding interestingness-driven diffusion processes...
Diffusion Dynamics of Cux Cluster on Cu(111) Surface
Institute of Scientific and Technical Information of China (English)
Jian-feng Tang; Mai-chang Xu; Xue-song Li; Wo-yun Long
2008-01-01
The diffusion dynamics of small two-dimensional atomic clusters Cux(1≤x≤8) on Cu(111) surface were studied using the molecular dynamics simulations and a modified analytic embedded-atom method in the temperature range from 200 K to 800 K.The cluster size and temperature dependence of the diffusion coefficients and migration energies are presented.Our simulations show that the diffusion migration energy of the Cu7 cluster is the highest and the prefactor for the CuT cluster is almost three orders of magnitude larger than that for single atom diffusion.This conclusion is consistent with the experimental results for similar metals.In addition,the dependence of cluster diffusion on film growth is also discussed.
Anomalous carrier dynamics in bilayer graphene in presence of mechanical strain: A theoretical study
Enamullah
2016-05-01
One of the optical response of charge carriers in bilayer graphene, anomalous Rabi oscillation is investigated theoretically in presence of mechanical strain. Rabi oscillation in extreme non-resonance regime is known as anomalous Rabi oscillation, has been predicted theoretically in single layer graphene by new technique known as asymptotic rotating wave approximation. In this article, we have shown a strong dependence of anomalous Rabi oscillations of charge carriers on the mechanical strain near the vanishing point of conduction and valance band.
Dynamics Studies on Molecular Diffusion in Zeolites
Institute of Scientific and Technical Information of China (English)
王秋霞; 樊建芬; 肖鹤鸣
2003-01-01
A review about the applications of molecular dynamics（MD）simulation in zeolites is presented. MD simulation has been proved to be a useful tool due to its applications in this field for the recent two decades. The fundamental theory of MD is introduced and the hydrocarbon diffusion in zeolites is mainly focused on in this paper.
Diffusion-Oscillatory Dynamics in Liquid Water on Data of Dielectric Spectroscopy
Volkov, A A; Volkov, A A; Sysoev, N N
2016-01-01
When analyzing the broadband absorption spectrum of liquid water (10^10 - 10^13 Hz), we find its relaxation-resonance features to be an indication of Frenkel's translation-oscillation motion of particles, which is fundamentally inherent to liquids. We have developed a model of water structure, of which the dynamics is due to diffusion of particles, neutral H2O molecules and H3O+ and OH- ions - with their periodic localizations and mutual transformations. This model establishes for the first time a link between the dc conductivity, the Debye and the high frequency sub-Debye relaxations and the infrared absorption peak at 180 cm-1. The model reveals the characteristic times of the relaxations, 50 ps and 3 ps, as the lifetimes of water molecules and water ions, respectively. The model sheds light on the anomalous mobility of a proton and casts doubt on the long lifetime of a water molecule, 10 hours, commonly associated with autoionization.
Anomalous dynamic back-action in interferometers: beyond the scaling law
Tarabrin, Sergey P; Kaufer, Henning; Schnabel, Roman; Hammerer, Klemens
2013-01-01
We analyze dynamic optomechanical back-action effects in signal-recycled Michelson and Michelson-Sagnac interferometers that are operated off dark port. Up to now, their optomechanics has been studied under dark port condition only. For the dark port case and in the context of gravitational wave detectors, the `scaling law' assured that all back-action effects can be understood on the basis of the much simpler topology of a Fabry-Perot interferometer. Off dark port, our theoretical and experimental analysis reveals certain `anomalous' features as compared to the ones of `canonical' back-action, obtained within the scope of scaling law. In particular, optical damping as a function of detuning acquires a non-zero value on cavity resonance, and several stability/instability regions on either side of the cavity resonance appear. We report on the experimental observation of these instabilities on both sides of the cavity resonance in a Michelson-Sagnac interferometer with a micromechanical membrane. For a certain ...
Energy Technology Data Exchange (ETDEWEB)
Liu, Siyang; Zhang, Chunwei; Sun, Weifeng, E-mail: swffrog@seu.edu.cn [National ASIC System Engineering Research Center, Southeast University, Nanjing 210096 (China); Su, Wei; Wang, Shaorong; Ma, Shulang; Huang, Yu [CSMC Technologies Corporation, Wuxi 214061 (China)
2014-04-14
Anomalous output characteristic shift of the n-type lateral diffused metal-oxide-semiconductor transistor with floating P-top layer is investigated. It shows that the linear drain current has obvious decrease when the output characteristic of fresh device is measured for two consecutive times. The charge pumping experiments demonstrate that the decrease is not from hot-carrier degradation. The reduction of cross section area for the current flowing, which results from the squeezing of the depletion region surrounding the P-top layer, is responsible for the shift. Consequently, the current capability of this special device should be evaluated by the second measured output characteristic.
Institute of Scientific and Technical Information of China (English)
XU; Mingyu(
2001-01-01
［1］Nonnemacher, T. F., Metzler, R., On the Riemann-Liouville fractional calculus and some recent applications, Fractals,1995, 3(3): 557－566.［2］Mainardi, F., Fractional calculus: some basic problems in continuum and statistical mechanics, in Fractals and Fractional Calculus in Continuum Mechanics (eds. Cappinteri, A., Mainardi, F.), New York: Springer Wien, 1997, 291－348.［3］Rossikhin, Y. A., Shitikova, M. V. , Applications of fractional calculus to dynamic problems of linear and nonlinear hereditary mechanics of solids, Appl. Mech. Rev., 1997, 50(1): 15－67.［4］Podlubny, I., Fractional Differential Equations, San Diego: Academic Press, 1999, 86－231.［5］Henry, B. I. , Wearne, S. L. , Fractional reaction-diffusion, Physica A, 2000, 276(3): 448－455.［6］Wyss, W., The fractional diffusion equation, J. Math. Phys., 1986, 27(11): 2782－2785.［7］Bagley, R. L. , Torvik, P. J., On the appearance of the fractional derivative in the behavior of real materials, J. Appl.Mech., 1984, 51(2): 294－298.［8］Mathai, A. M., Saxena, R. K., The H-function with Applications in Statistics and Other Disciplines, New Delhi-BangaloreBombay: Wiley Eastern Limited, 1978, 1－12.［9］Gorentlo, R. , Luchko, Y., Mainardi, F., Wright function as scale-invariant solutions of the diffusion-wave equation, J.Comput. Appl. Math., 2000, 118(1): 175－191.［10］Yih, C. S. , Fluid Mechanics: A Concise Introduction to the Theory, New York: MeGraw-Hill, Inc. , 1969, 321－324.［11］Wu Wangyi, Fluid Mechanics (in Chinese), Beijing: Peking Univ. Press, 1983, 226－230.［12］Mainardi, F., Gorenflo, R., On Mittag-Leffler-Type function in fractional evolution processes, J. Comput. Appl. Math.2000, 118(2): 283－299.［13］Anhand, V. V., Leonenko, N. N., Scaling law for fractional diffusion-wave equations with singular data, Statistics and Probability Letters, 2000, 48(3): 239－252.［14］Kivyakova, V., Multiple (multiindex) Mittag-Leffler functions and relations to
Diffusive dynamics of nanoparticles in ultra-confined media.
Jacob, Jack Deodato C; He, Kai; Retterer, Scott T; Krishnamoorti, Ramanan; Conrad, Jacinta C
2015-10-14
Differential dynamic microscopy (DDM) was used to investigate the diffusive dynamics of nanoparticles of diameter 200-400 nm that were strongly confined in a periodic square array of cylindrical nanoposts. The minimum distance between posts was 1.3-5 times the diameter of the nanoparticles. The image structure functions obtained from the DDM analysis were isotropic and could be fit by a stretched exponential function. The relaxation time scaled diffusively across the range of wave vectors studied, and the corresponding scalar diffusivities decreased monotonically with increased confinement. The decrease in diffusivity could be described by models for hindered diffusion that accounted for steric restrictions and hydrodynamic interactions. The stretching exponent decreased linearly as the nanoparticles were increasingly confined by the posts. Together, these results are consistent with a picture in which strongly confined nanoparticles experience a heterogeneous spatial environment arising from hydrodynamics and volume exclusion on time scales comparable to cage escape, leading to multiple relaxation processes and Fickian but non-Gaussian diffusive dynamics.
The interstitialcy diffusion in FCC copper: A molecular dynamics study
Energy Technology Data Exchange (ETDEWEB)
Bukkuru, S., E-mail: srinivasaraobukkuru@gmail.com; Rao, A. D. P. [Nucl. Phys Dept., Andhra University, Visakhapatnam– 530003 (India); Warrier, M. [Computational Analysis Division, Bhabha Atomic Research Centre, Visakhapatnam – 530012 (India)
2015-06-24
Damage of materials due to neutron irradiation occurs via energetic cascades caused by energetic primary knock-on atoms (PKA) created by the energetic neutron as it passes through the material. These cascades result in creation of Frenkel Pairs (interstitials and vacancies). The interstitials and vacancies diffuse and recombine to (I) nullify the damage when an interstitial recombines with a vacancy, (II) form interstitial clusters when two or more interstitials recombine, and (III) form vacancy clusters when several vacancies come together. The latter two processes result in change of material properties. Interstitial diffusion has reported time-scales of microseconds and vacancy diffusion has diffusion time-scales of the order of seconds. We have carried out molecular dynamics (MD) simulations of interstitial diffusion in crystal Cu to study the mechanism of diffusion. It is found that interstitialcy diffusion – wherein an interstitial displaces a lattice atom thereby making the lattice atom an interstitial – has time-scales of a few tens of pico-seconds. Therefore we propose that the “interstitialcy diffusion” mechanism could play a major part in the diffusive-recombinations of the Frenkel Pairs created during the cascade.
Measurement of the phase diffusion dynamics in the micromaser
Casagrande, Federico; Lulli, A; Bonifacio, R; Solano, E; Walther, H
2003-01-01
We propose a realistic scheme for measuring the micromaser linewidth by monitoring the phase diffusion dynamics of the cavity field. Our strategy consists in exciting an initial coherent state with the same photon number distribution as the micromaser steady-state field, singling out a purely diffusive process in the system dynamics. After the injection of a counter-field, measurements of the population statistics of a probe atom allow us to derive the micromaser linewidth. Our proposal aims at solving a classic and relevant decoherence problem in cavity quantum electrodynamics, allowing to establish experimentally the distinctive features appearing in the micromaser spectrum due to the discreteness of the electromagnetic field.
Rumor Diffusion in an Interests-Based Dynamic Social Network
Directory of Open Access Journals (Sweden)
Mingsheng Tang
2013-01-01
Full Text Available To research rumor diffusion in social friend network, based on interests, a dynamic friend network is proposed, which has the characteristics of clustering and community, and a diffusion model is also proposed. With this friend network and rumor diffusion model, based on the zombie-city model, some simulation experiments to analyze the characteristics of rumor diffusion in social friend networks have been conducted. The results show some interesting observations: (1 positive information may evolve to become a rumor through the diffusion process that people may modify the information by word of mouth; (2 with the same average degree, a random social network has a smaller clustering coefficient and is more beneficial for rumor diffusion than the dynamic friend network; (3 a rumor is spread more widely in a social network with a smaller global clustering coefficient than in a social network with a larger global clustering coefficient; and (4 a network with a smaller clustering coefficient has a larger efficiency.
Weak diffusion limits of dynamic conditional correlation models
DEFF Research Database (Denmark)
Hafner, Christian M.; Laurent, Sebastien; Violante, Francesco
The properties of dynamic conditional correlation (DCC) models are still not entirely understood. This paper fills one of the gaps by deriving weak diffusion limits of a modified version of the classical DCC model. The limiting system of stochastic differential equations is characterized by a dif......The properties of dynamic conditional correlation (DCC) models are still not entirely understood. This paper fills one of the gaps by deriving weak diffusion limits of a modified version of the classical DCC model. The limiting system of stochastic differential equations is characterized...... by a diffusion matrix of reduced rank. The degeneracy is due to perfect collinearity between the innovations of the volatility and correlation dynamics. For the special case of constant conditional correlations, a non-degenerate diffusion limit can be obtained. Alternative sets of conditions are considered...... for the rate of convergence of the parameters, obtaining time-varying but deterministic variances and/or correlations. A Monte Carlo experiment confirms that the quasi approximate maximum likelihood (QAML) method to estimate the diffusion parameters is inconsistent for any fixed frequency, but that it may...
Knowledge epidemics and population dynamics models for describing idea diffusion
Vitanov, Nikolay K
2012-01-01
The diffusion of ideas is often closely connected to the creation and diffusion of knowledge and to the technological evolution of society. Because of this, knowledge creation, exchange and its subsequent transformation into innovations for improved welfare and economic growth is briefly described from a historical point of view. Next, three approaches are discussed for modeling the diffusion of ideas in the areas of science and technology, through (i) deterministic, (ii) stochastic, and (iii) statistical approaches. These are illustrated through their corresponding population dynamics and epidemic models relative to the spreading of ideas, knowledge and innovations. The deterministic dynamical models are considered to be appropriate for analyzing the evolution of large and small societal, scientific and technological systems when the influence of fluctuations is insignificant. Stochastic models are appropriate when the system of interest is small but when the fluctuations become significant for its evolution...
Bleaching and diffusion dynamics in optofluidic dye lasers
DEFF Research Database (Denmark)
Gersborg-Hansen, Morten; Balslev, Søren; Mortensen, Asger
2007-01-01
The authors have investigated the bleaching dynamics that occur in optofluidic dye lasers where the liquid laser dye in a microfluidic channel is locally bleached due to optical pumping. They find that for microfluidic devices, the dye bleaching may be compensated through diffusion of dye molecules...... pumping devices. ©2007 American Institute of Physics....
On the origin of the anomalous ultraslow solvation dynamics in heterogeneous environments
Indian Academy of Sciences (India)
Kankan Bhattacharyya; Biman Bagchi
2007-03-01
Many recent experimental studies have reported a surprising ultraslow component (even >10 ns) in the solvation dynamics of a polar probe in an organized assembly, the origin of which is not understood at present. Here we propose two molecular mechanisms in explanation. The first one involves the motion of the `buried water’ molecules (both translation and rotation), accompanied by cooperative relaxation (‘local melting’) of several surfactant chains. An estimate of the time is obtained by using an effective Rouse chain model of chain dynamics, coupled with a mean first passage time calculation. The second explanation invokes self-diffusion of the (di)polar probe itself from a less polar to a more polar region. This may also involve cooperative motion of the surfactant chains in the hydrophobic core, if the probe has a sizeable distribution inside the core prior to excitation, or escape of the probe to the bulk from the surface of the self-assembly. The second mechanism should result in the narrowing of the full width of the emission spectrum with time, which has indeed been observed in recent experiments. It is argued that both the mechanisms may give rise to an ultraslow time constant and may be applicable to different experimental situations. The effectiveness of solvation as a dynamical probe in such complex systems has been discussed.
Gurunathan, Kaushik; Levitus, Marcia
2009-01-01
The use of Fluorescence Correlation Spectroscopy (FCS) to study conformational dynamics in diffusing biopolymers requires that the contributions to the signal due to translational diffusion are separated from those due to conformational dynamics. A simple approach that has been proposed to achieve this goal involves the analysis of fluctuations in Fluorescence Resonance Energy Transfer (FRET) efficiency. In this work, we investigate the applicability of this methodology by combining Monte Carlo simulations and experiments. Results show that diffusion does not contribute to the measured fluctuations in FRET efficiency in conditions where the relaxation time of the kinetic process is much shorter than the mean transit time of the molecules in the optical observation volume. However, in contrast to what has been suggested in previous work, the contributions of diffusion are otherwise significant. Neglecting the contributions of diffusion can potentially lead to an erroneous interpretation of the kinetic mechanisms. As an example, we demonstrate that the analysis of FRET fluctuations in terms of a purely kinetic model would generally lead to the conclusion that the system presents complex kinetic behavior even for an idealized two-state system PMID:20030305
Global dynamics and diffusion in triaxial galactic models
Papaphilippou, Y.
We apply the Frequency Map Analysis method to the 3--dimensional logarithmic galactic potential in order to clarify the dynamical behaviour of triaxial power--law galactic models. All the fine dynamical details are displayed in the complete frequency map, a direct representation of the system's Arnol'd web. The influence of resonant lines and the extent of the chaotic zones are directly associated with the physical space of the system. Some new results related with the diffusion of galactic orbits are also discussed. This approach reveals many unknown dynamical features of triaxial galactic potentials and provides strong indications that chaos should be an innate characteristic of triaxial configurations.
Memristors with diffusive dynamics as synaptic emulators for neuromorphic computing
Wang, Zhongrui; Joshi, Saumil; Savel'Ev, Sergey E.; Jiang, Hao; Midya, Rivu; Lin, Peng; Hu, Miao; Ge, Ning; Strachan, John Paul; Li, Zhiyong; Wu, Qing; Barnell, Mark; Li, Geng-Lin; Xin, Huolin L.; Williams, R. Stanley; Xia, Qiangfei; Yang, J. Joshua
2017-01-01
The accumulation and extrusion of Ca2+ in the pre- and postsynaptic compartments play a critical role in initiating plastic changes in biological synapses. To emulate this fundamental process in electronic devices, we developed diffusive Ag-in-oxide memristors with a temporal response during and after stimulation similar to that of the synaptic Ca2+ dynamics. In situ high-resolution transmission electron microscopy and nanoparticle dynamics simulations both demonstrate that Ag atoms disperse under electrical bias and regroup spontaneously under zero bias because of interfacial energy minimization, closely resembling synaptic influx and extrusion of Ca2+, respectively. The diffusive memristor and its dynamics enable a direct emulation of both short- and long-term plasticity of biological synapses, representing an advance in hardware implementation of neuromorphic functionalities.
Post-processing interstitialcy diffusion from molecular dynamics simulations
Energy Technology Data Exchange (ETDEWEB)
Bhardwaj, U., E-mail: haptork@gmail.com [Computational Analysis Division, BARC, Visakhapatnam, Andhra Pradesh, 530012 (India); Bukkuru, S. [Nuclear Physics Dept., Andhra University, Visakhapatnam, 530003 (India); Warrier, M. [Computational Analysis Division, BARC, Visakhapatnam, Andhra Pradesh, 530012 (India)
2016-01-15
An algorithm to rigorously trace the interstitialcy diffusion trajectory in crystals is developed. The algorithm incorporates unsupervised learning and graph optimization which obviate the need to input extra domain specific information depending on crystal or temperature of the simulation. The algorithm is implemented in a flexible framework as a post-processor to molecular dynamics (MD) simulations. We describe in detail the reduction of interstitialcy diffusion into known computational problems of unsupervised clustering and graph optimization. We also discuss the steps, computational efficiency and key components of the algorithm. Using the algorithm, thermal interstitialcy diffusion from low to near-melting point temperatures is studied. We encapsulate the algorithms in a modular framework with functionality to calculate diffusion coefficients, migration energies and other trajectory properties. The study validates the algorithm by establishing the conformity of output parameters with experimental values and provides detailed insights for the interstitialcy diffusion mechanism. The algorithm along with the help of supporting visualizations and analysis gives convincing details and a new approach to quantifying diffusion jumps, jump-lengths, time between jumps and to identify interstitials from lattice atoms. -- Graphical abstract:.
Molecular dynamics simulations of diffusion mechanisms in NiAl
Energy Technology Data Exchange (ETDEWEB)
Soule De Bas, B.; Farkas, D
2003-03-14
Molecular dynamics simulations of the diffusion process in ordered B2 NiAl at high temperature were performed using an embedded atom interatomic potential. Diffusion occurs through a variety of cyclic mechanisms that accomplish the motion of the vacancy through nearest neighbor jumps restoring order to the alloy at the end of the cycle. The traditionally postulated six-jump cycle is only one of the various cycles observed and some of these are quite complex. A detailed sequential analysis of the observed six-jump cycles was performed and the results are analyzed in terms of the activation energies for individual jumps calculated using molecular statics simulations.
Diffusive limit for a quantum linear Boltzmann dynamics
Clark, Jeremy
2010-01-01
We study the diffusive behavior for a quantum test particle interacting with a dilute background gas. The model we begin with is a reduced picture for the test particle dynamics given by a quantum linear Boltzmann equation in which the scattering with the gas particles is assumed to occur through a hard-sphere interaction. The state of the particle is represented by a density matrix evolving according to a translation-covariant Lindblad equation. Our main result is a proof that the particle diffuses for large times.
Dynamics Of Innovation Diffusion With Two Step Decision Process
Directory of Open Access Journals (Sweden)
Szymczyk Michał
2014-02-01
Full Text Available The paper discusses the dynamics of innovation diffusion among heterogeneous consumers. We assume that customers’ decision making process is divided into two steps: testing the innovation and later potential adopting. Such a model setup is designed to imitate the mobile applications market. An innovation provider, to some extent, can control the innovation diffusion by two parameters: product quality and marketing activity. Using the multi-agent approach we identify factors influencing the saturation level and the speed of innovation adaptation in the artificial population. The results show that the expected level of innovation adoption among customer’s friends and relative product quality and marketing campaign intensity are crucial factors explaining them. It has to be stressed that the product quality is more important for innovation saturation level and marketing campaign has bigger influence on the speed of diffusion. The topology of social network between customers is found important, but within investigated parameter range it has lover impact on innovation diffusion dynamics than the above mentioned factors
Untangling knots via reaction-diffusion dynamics of vortex strings
Maucher, Fabian
2016-01-01
We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.
Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings
Maucher, Fabian; Sutcliffe, Paul
2016-04-01
We introduce and illustrate a new approach to the unknotting problem via the dynamics of vortex strings in a nonlinear partial differential equation of reaction-diffusion type. To untangle a given knot, a Biot-Savart construction is used to initialize the knot as a vortex string in the FitzHugh-Nagumo equation. Remarkably, we find that the subsequent evolution preserves the topology of the knot and can untangle an unknot into a circle. Illustrative test case examples are presented, including the untangling of a hard unknot known as the culprit. Our approach to the unknotting problem has two novel features, in that it applies field theory rather than particle mechanics and uses reaction-diffusion dynamics in place of energy minimization.
Spatiotemporal mapping of diffusion dynamics and organization in plasma membranes
Bag, Nirmalya; Ng, Xue Wen; Sankaran, Jagadish; Wohland, Thorsten
2016-09-01
Imaging fluorescence correlation spectroscopy (FCS) and the related FCS diffusion law have been applied in recent years to investigate the diffusion modes of lipids and proteins in membranes. These efforts have provided new insights into the membrane structure below the optical diffraction limit, new information on the existence of lipid domains, and on the influence of the cytoskeleton on membrane dynamics. However, there has been no systematic study to evaluate how domain size, domain density, and the probe partition coefficient affect the resulting imaging FCS diffusion law parameters. Here, we characterize the effects of these factors on the FCS diffusion law through simulations and experiments on lipid bilayers and live cells. By segmenting images into smaller 7 × 7 pixel areas, we can evaluate the FCS diffusion law on areas smaller than 2 µm and thus provide detailed maps of information on the membrane structure and heterogeneity at this length scale. We support and extend this analysis by deriving a mathematical expression to calculate the mean squared displacement (MSDACF) from the autocorrelation function of imaging FCS, and demonstrate that the MSDACF plots depend on the existence of nanoscopic domains. Based on the results, we derive limits for the detection of domains depending on their size, density, and relative viscosity in comparison to the surroundings. Finally, we apply these measurements to bilayers and live cells using imaging total internal reflection FCS and single plane illumination microscopy FCS.
Dynamics of Robertson–Walker spacetimes with diffusion
Energy Technology Data Exchange (ETDEWEB)
Alho, A., E-mail: aalho@math.ist.utl.pt [Centro de Análise Matemática, Geometria e Sistemas Dinâmicos, Instituto Superior Técnico, Lisboa (Portugal); Calogero, S., E-mail: calogero@chalmers.se [Department of Mathematical Sciences, Chalmers University of Technology, University of Gothenburg, Gothenburg (Sweden); Machado Ramos, M.P., E-mail: mpr@mct.uminho.pt [Departamento de Matemática e Aplicações, Universidade do Minho, Guimarães (Portugal); Soares, A.J., E-mail: ajsoares@math.uminho.pt [Centro de Matemática, Universidade do Minho, Braga (Portugal)
2015-03-15
We study the dynamics of spatially homogeneous and isotropic spacetimes containing a fluid undergoing microscopic velocity diffusion in a cosmological scalar field. After deriving a few exact solutions of the equations, we continue by analyzing the qualitative behavior of general solutions. To this purpose we recast the equations in the form of a two dimensional dynamical system and perform a global analysis of the flow. Among the admissible behaviors, we find solutions that are asymptotically de-Sitter both in the past and future time directions and which undergo accelerated expansion at all times.
Basu, Tania; Tarafdar, Sujata
2016-08-01
Solid polymer electrolytes with gelatin as host polymer are subjected to gamma irradiation with dose varying from 0 to 100 kGy. Two sets of samples are studied, one with and one without addition of lithium perchlorate as ionic salt. The effect of varying plasticizer content, salt fraction and radiation dose on the impedance is measured. The dc (direct current) ion-conductivity is determined from impedance spectroscopy results. It is shown that relative to the unirradiated sample, the room temperature dc ion-conductivity decreases in general on irradiation, by an order of magnitude. However on comparing results for the irradiated samples, a dose of 60 kGy is seen to produce the highest ion-conductivity. Considering the variation of all parameters, the highest dc-conductivity of 6.06x10-2 S/m is obtained for the un-irradiated sample at room temperature, with 12.5 wt% LiClO4 and 35.71 wt% of glycerol as plasticizer. The samples are characterized in addition by XRD, SEM and FTIR respectively. Cyclic voltametry is performed for the confirmation of the electrolytic performance for pristine and gamma irradiated samples. To understand the experimental results, a model incorporating normal, as well as anomalous diffusion has been applied. Generalized calculus is used to model the anomalous diffusion. It is shown that this model successfully reproduces the experimental frequency dependence of the complex impedance for samples subjected to varying gamma dose. The physical interpretation of the model parameters and their variation with sample composition and irradiation dose is discussed.
Implantation damage and anomalous diffusion of implanted boron in silicon through SiO[sub 2] films
Energy Technology Data Exchange (ETDEWEB)
Kaabi, L. (Lab. de Physique de la Matiere, Inst. National des Sciences Appliquees de Lyon, 69 - Villeurbanne (France)); Gontrand, C. (Lab. de Physique de la Matiere, Inst. National des Sciences Appliquees de Lyon, 69 - Villeurbanne (France)); Lemiti, M. (Lab. de Physique de la Matiere, Inst. National des Sciences Appliquees de Lyon, 69 - Villeurbanne (France)); Balland, B. (Lab. de Physique de la Matiere, Inst. National des Sciences Appliquees de Lyon, 69 - Villeurbanne (France))
1993-07-16
Boron is implanted in crystalline silicon through oxide layers with different thicknesses. The implantation is carried out at various doses and energies of interest in ultra large scale integration (ULSI) application. Rapid thermal annealings (RTA) are used to obtain shallow junctions and electrical activation of the B atoms. However, transient enhanced diffusion induced by implantation damage can be observed. The boron concentration profiles before and after annealing are obtained with secondary ion mass spectrometry (SIMS). It is found that the diffusion transient in the tail region of the boron profile increases with decreasing oxide thickness. Even more, if the implantation damage concerns mostly the oxide, i.e. when the concentration peak is located in this oxide, the oxygen knocked into the silicon substrate could play this way an important role in restricting the boron diffusion, which is good to obtain very shallow junctions. On the other hand, for thinner oxide, boron enhanced diffusion is attributed to the implantation induced damage into silicon at high doses. The diffusion process of boron in oxide and moncrystalline silicon during rapid thermal annealing is investigated. The boron diffusion profiles obtained by computer simulation are compared with the measured results. It is shown by this comparison that the intrinsic coefficient cannot be considered as constant along all the silicon depth. (orig.)
Origins of Anomalous Transport in Disordered Media: Structural and Dynamic Controls
Edery, Yaniv; Guadagnini, Alberto; Berkowitz, Brian
2013-01-01
We quantitatively identify the origin of anomalous transport in a representative model of a heterogeneous system---tracer migration in the complex flow patterns of a lognormally distributed hydraulic conductivity ($K$) field. The transport, determined by a particle tracking technique, is characterized by breakthrough curves; the ensemble averaged curves document anomalous transport in this system, which is entirely accounted for by a truncated power-law distribution of local transition times $\\psi(t)$ within the framework of a continuous time random walk. Unique to this study is the linking of $\\psi(t)$ directly to the system heterogeneity. We assess the statistics of the dominant preferred pathways by forming a particle-visitation weighted histogram $\\{wK\\}$. Converting the ln($K$) dependence of $\\{wK\\}$ into time yields the equivalence of $\\{wK\\}$ and $\\psi(t)$, and shows the part of $\\{wK\\}$ that forms the power-law of $\\psi(t)$, which is the origin of anomalous transport. We also derive an expression defi...
Dynamics of the diffusive DM-DE interaction--dynamical system approach
Haba, Zbigniew; Szydlowski, Marek
2016-01-01
We discuss dynamics of a model of an energy transfer between dark energy (DE) and dark matter (DM). The energy transfer is determined by a non-conservation law resulting from a diffusion of dark matter in an environment of dark energy. The relativistic invariance defines the diffusion in a unique way. The system can contain baryonic matter and radiation which do not interact with the dark sector. We treat the Friedman equation and the conservation laws as a closed dynamical system. The dynamics of the model is examined using the dynamical systems methods for demonstration how solutions depend on initial conditions. We also fit the model parameters using astronomical observation: SNIa, $H(z)$, BAO and Alcock-Paczynski test. We show that the model with diffuse DM-DE is consistent with the data.
Diffusion dynamics in liquid and undercooled Al-Ni alloys
Energy Technology Data Exchange (ETDEWEB)
Stueber, Sebastian
2009-10-05
This work presents data on Ni self-diffusion in binary Al-Ni alloys with high precision. For this, we combined two techniques: containerless electromagnetic levitation to position the samples, and neutron time-of-flight spectroscopy to measure the decay of the self-correlation. This combination offers new measurement ranges, especially at low temperatures, several hundreds of Kelvin below the liquidus temperature. Because without container, the primary cristallization seeds for the metallic melt are avoided. But it is also possible to measure reactive samples, and at very high temperatures at and above 2000K, as problematic reactions with the containing cask won't occur. Furthermore this technique also enables measurements at higher momentum transfer q, as one does not have to limit the q-range of the measurement to avoid Bragg peaks of the solid container material. By this time-of-flight spectroscopy on levitated metallic melts, it is possible to determine the Ni self-diffusion in these alloys directly and on an absolute scale. The dependence of the Ni self-diffusion coefficient on temperature and concentration was studied in pure Ni and binary Al-Ni alloys. In a temperature range of several hundred degrees, we always found Arrhenius-like temperature dependence of the diffusion, irrespective of possible undercooling. In the context of these measurements, we also studied the interdependence between diffusivity in the metallic melt and its quasielastic structure factor. Time-of-flight spectroscopy made it also possible to derive the dynamic partial structure factors of the binary alloy Al{sub 80}Ni{sub 20}. All this to enable a better understanding of the atomic processes in the metallic melt, especially of the undercooled melt, as an alloy is always formed out of the (undercooled) melt of its stoichiometric compounds. For this, material transport and diffusion are immensely important. The final goal would be materials design from the melt, i.e. the prediction
Diffusive and Arrestedlike Dynamics in Currency Exchange Markets
Clara-Rahola, J.; Puertas, A. M.; Sánchez-Granero, M. A.; Trinidad-Segovia, J. E.; de las Nieves, F. J.
2017-02-01
This work studies the symmetry between colloidal dynamics and the dynamics of the Euro-U.S. dollar currency exchange market (EURUSD). We consider the EURUSD price in the time range between 2001 and 2015, where we find significant qualitative symmetry between fluctuation distributions from this market and the ones belonging to colloidal particles in supercooled or arrested states. In particular, we find that models used for arrested physical systems are suitable for describing the EURUSD fluctuation distributions. Whereas the corresponding mean-squared price displacement (MSPD) to the EURUSD is diffusive for all years, when focusing in selected time frames within a day, we find a two-step MSPD when the New York Stock Exchange market closes, comparable to the dynamics in supercooled systems. This is corroborated by looking at the price correlation functions and non-Gaussian parameters and can be described by the theoretical model. We discuss the origin and implications of this analogy.
MO-G-BRF-07: Anomalously Fast Diffusion of Carbon Nanotubes Carriers in 3D Tissue Model
Energy Technology Data Exchange (ETDEWEB)
Wang, Y; Bahng, J; Kotov, N [University of Michigan, Ann Arbor, MI (United States)
2014-06-15
Purpose: We aim to investigate and understand diffusion process of carbon nanotubes (CNTs) and other nanoscale particles in tissue and organs. Methods: In this research, we utilized a 3D model tissue of hepatocellular carcinoma (HCC)cultured in inverted colloidal crystal (ICC) scaffolds to compare the diffusivity of CNTs with small molecules such as Rhodamine and FITC in vitro, and further investigated the transportation of CNTs with and without targeting ligand, TGFβ1. The real-time permeation profiles of CNTs in HCC tissue model with high temporal and spatial resolution was demonstrated by using standard confocal microscopy. Quantitative analysis of the diffusion process in 3D was carried out using luminescence intensity in a series of Z-stack images obtained for different time points of the diffusion process after initial addition of CNTs or small molecules to the cell culture and the image data was analyzed by software ImageJ and Mathematica. Results: CNTs display diffusion rate in model tissues substantially faster than small molecules of the similar charge such as FITC, and the diffusion rate of CNTs are significantly enhanced with targeting ligand, TGFβ1. Conclusion: In terms of the advantages of in-vitro model, we were able to have access to measuring the rate of CNT penetration at designed conditions with variable parameters. And the findings by using this model, changed our understanding about advantages of CNTs as nanoscale drug carriers and provides design principles for making new drug carriers for both treatment and diagnostics. Additionally the fast diffusion opens the discussion of the best possible drug carriers to reach deep parts of cancerous tissues, which is often a prerequisite for successful cancer treatment. This work was supported by the Center for Photonic and Multiscale Nanomaterials funded by National Science Foundation Materials Research Science and Engineering Center program DMR 1120923. The work was also partially supported by NSF
Mechanical reaction-diffusion model for bacterial population dynamics
Ngamsaad, Waipot
2015-01-01
The effect of mechanical interaction between cells on the spreading of bacterial population was investigated in one-dimensional space. A nonlinear reaction-diffusion equation has been formulated as a model for this dynamics. In this model, the bacterial cells are treated as the rod-like particles that interact, when contacting each other, through the hard-core repulsion. The repulsion introduces the exclusion process that causes the fast diffusion in bacterial population at high density. The propagation of the bacterial density as the traveling wave front in long time behavior has been analyzed. The analytical result reveals that the front speed is enhanced by the exclusion process---and its value depends on the packing fraction of cell. The numerical solutions of the model have been solved to confirm this prediction.
Diffusion in crowded biological environments: applications of Brownian dynamics
Directory of Open Access Journals (Sweden)
Długosz Maciej
2011-03-01
Full Text Available Abstract Biochemical reactions in living systems occur in complex, heterogeneous media with total concentrations of macromolecules in the range of 50 - 400 mgml. Molecular species occupy a significant fraction of the immersing medium, up to 40% of volume. Such complex and volume-occupied environments are generally termed 'crowded' and/or 'confined'. In crowded conditions non-specific interactions between macromolecules may hinder diffusion - a major process determining metabolism, transport, and signaling. Also, the crowded media can alter, both qualitatively and quantitatively, the reactions in vivo in comparison with their in vitro counterparts. This review focuses on recent developments in particle-based Brownian dynamics algorithms, their applications to model diffusive transport in crowded systems, and their abilities to reproduce and predict the behavior of macromolecules under in vivo conditions.
Molecular simulation of protein dynamics in nanopores. II. Diffusion.
Javidpour, Leili; Tabar, M Reza Rahimi; Sahimi, Muhammad
2009-02-28
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model of proteins, is used to carry out long (several microsecond) simulations in order to study transport of proteins in nanopores. We simulated single-domain proteins with the alpha-helical native structure. Both attractive and repulsive interaction potentials between the proteins and the pores' walls are considered. The diffusivity D of the proteins is computed not only under the bulk conditions but also as a function of their "length" (the number of the amino-acid groups), temperature T, pore size, and interaction potentials with the walls. Compared with the experimental data, the computed diffusivities under the bulk conditions are of the correct order of magnitude. The diffusivities both in the bulk and in the pores follow a power law in the length [script-l] of the proteins and are larger in pores with repulsive walls. D(+)/D(-), the ratio of the diffusivities in pores with attractive and repulsive walls, exhibits two local maxima in its dependence on the pore size h, which are attributed to the pore sizes and protein configurations that induce long-lasting simultaneous interactions with both walls of the pores. Far from the folding temperature T(f), D increases about linearly with T, but due to the thermal fluctuations and their effect on the proteins' structure near T(f), the dependence of D on T in this region is nonlinear. We propose a novel and general "phase diagram," consisting of four regions, that describes qualitatively the effect of h, T, and interaction potentials with the walls on the diffusivity D of a protein.
Spatio-temporal diffusion of dynamic PET images
Energy Technology Data Exchange (ETDEWEB)
Tauber, C; Chalon, S; Guilloteau, D [Inserm U930, CNRS ERL3106, Universite Francois Rabelais, Tours (France); Stute, S; Buvat, I [IMNC, IN2P3, UMR 8165 CNRS-Paris 7 and Paris 11 Universities, Orsay (France); Chau, M [ASA-Advanced Solutions Accelerator, Montpellier (France); Spiteri, P, E-mail: clovis.tauber@univ-tours.fr [IRIT-ENSEEIHT, UMR CNRS 5505, Toulouse (France)
2011-10-21
Positron emission tomography (PET) images are corrupted by noise. This is especially true in dynamic PET imaging where short frames are required to capture the peak of activity concentration after the radiotracer injection. High noise results in a possible bias in quantification, as the compartmental models used to estimate the kinetic parameters are sensitive to noise. This paper describes a new post-reconstruction filter to increase the signal-to-noise ratio in dynamic PET imaging. It consists in a spatio-temporal robust diffusion of the 4D image based on the time activity curve (TAC) in each voxel. It reduces the noise in homogeneous areas while preserving the distinct kinetics in regions of interest corresponding to different underlying physiological processes. Neither anatomical priors nor the kinetic model are required. We propose an automatic selection of the scale parameter involved in the diffusion process based on a robust statistical analysis of the distances between TACs. The method is evaluated using Monte Carlo simulations of brain activity distributions. We demonstrate the usefulness of the method and its superior performance over two other post-reconstruction spatial and temporal filters. Our simulations suggest that the proposed method can be used to significantly increase the signal-to-noise ratio in dynamic PET imaging.
Saadatfar, M; Sahimi, Muhammad
2002-03-01
We present the results of extensive Monte Carlo simulation of diffusion in disordered media with long-range correlations, a problem which is relevant to transport of contaminants in field-scale porous media, such as aquifers, gas transport in soils, and transport in composite materials. The correlations are generated by a fractional Brownian motion characterized by a Hurst exponent H. For H>1/2 the correlations appear to have no effect, and the transport process is diffusive. However, for Hpower-law growth of the mean square displacements with the time in which the effective exponents characterizing the power-law oscillates log periodically with the time. This result cannot be predicted by any of the currently available continuum theories of transport in disordered media.
Al-Shakran, Mohammad; Kibler, Ludwig A.; Jacob, Timo; Ibach, Harald; Beltramo, Guillermo L.; Giesen, Margret
2016-09-01
This is Part I of two closely related papers, where we show that the specific adsorption of anions leads to a failure of the nearest-neighbor Ising model to describe island perimeter curvatures on Au(100) electrodes in dilute KBr, HCl and H2SO4 electrolytes and the therewith derived step diffusivity vs. step orientation. This result has major consequences for theoretical studies aiming at the understanding of growth, diffusion and degradation phenomena. Part I focuses on the experimental data. As shown theoretically in detail in Part II (doi:10.1016/j.susc.2016.03.022), a set of nearest-neighbor and next-nearest-neighbor interaction energies (ɛNN, ɛNNN) can uniquely be derived from the diffusivity of steps along and . We find strong repulsive next-nearest neighbor (NNN) interaction in KBr and HCl, whereas NNN interaction is negligibly for H2SO4. The NNN repulsive interaction energy ɛNNN therefore correlates positively with the Gibbs adsorption energy of the anions. We find furthermore that ɛNNN increases with increasing Br- and Cl- coverage. The results for ɛNN and ɛNNN are quantitatively consistent with the coverage dependence of the step line tension. We thereby establish a sound experimental base for theoretical studies on the energetics of steps in the presence of specific adsorption.
Dynamic hysteresis modeling including skin effect using diffusion equation model
Hamada, Souad; Louai, Fatima Zohra; Nait-Said, Nasreddine; Benabou, Abdelkader
2016-07-01
An improved dynamic hysteresis model is proposed for the prediction of hysteresis loop of electrical steel up to mean frequencies, taking into account the skin effect. In previous works, the analytical solution of the diffusion equation for low frequency (DELF) was coupled with the inverse static Jiles-Atherton (JA) model in order to represent the hysteresis behavior for a lamination. In the present paper, this approach is improved to ensure the reproducibility of measured hysteresis loops at mean frequency. The results of simulation are compared with the experimental ones. The selected results for frequencies 50 Hz, 100 Hz, 200 Hz and 400 Hz are presented and discussed.
Directory of Open Access Journals (Sweden)
Francesc Alías
2017-02-01
Full Text Available Traffic noise is one of the main pollutants in urban and suburban areas. European authorities have driven several initiatives to study, prevent and reduce the effects of exposure of population to traffic. Recent technological advances have allowed the dynamic computation of noise levels by means of Wireless Acoustic Sensor Networks (WASN such as that developed within the European LIFE DYNAMAP project. Those WASN should be capable of detecting and discarding non-desired sound sources from road traffic noise, denoted as anomalous noise events (ANE, in order to generate reliable noise level maps. Due to the local, occasional and diverse nature of ANE, some works have opted to artificially build ANE databases at the cost of misrepresentation. This work presents the production and analysis of a real-life environmental audio database in two urban and suburban areas specifically conceived for anomalous noise events’ collection. A total of 9 h 8 min of labelled audio data is obtained differentiating among road traffic noise, background city noise and ANE. After delimiting their boundaries manually, the acoustic salience of the ANE samples is automatically computed as a contextual signal-to-noise ratio (SNR. The analysis of the real-life environmental database shows high diversity of ANEs in terms of occurrences, durations and SNRs, as well as confirming both the expected differences between the urban and suburban soundscapes in terms of occurrences and SNRs, and the rare nature of ANE.
Dynamics of stochastic nonclassical diffusion equations on unbounded domains
Directory of Open Access Journals (Sweden)
Wenqiang Zhao
2015-11-01
Full Text Available This article concerns the dynamics of stochastic nonclassical diffusion equation on $\\mathbb{R}^N$ perturbed by a $\\epsilon$-random term, where $\\epsilon\\in(0,1]$ is the intension of noise. By using an energy approach, we prove the asymptotic compactness of the associated random dynamical system, and then the existence of random attractors in $H^1(\\mathbb{R}^N$. Finally, we show the upper semi-continuity of random attractors at $\\epsilon=0$ in the sense of Hausdorff semi-metric in $H^1(\\mathbb{R}^N$, which implies that the obtained family of random attractors indexed by $\\epsilon$ converge to a deterministic attractor as $\\epsilon$ vanishes.
Multiscale reaction-diffusion algorithms: PDE-assisted Brownian dynamics
Franz, Benjamin; Chapman, S Jonathan; Erban, Radek
2012-01-01
Two algorithms that combine Brownian dynamics (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the domain, whilst making use of a mean-field reaction-diffusion PDE description elsewhere. The first PBD algorithm couples BD simulations with PDEs by randomly creating new particles close to the interface which partitions the domain and by reincorporating particles into the continuum PDE-description when they cross the interface. The second PBD algorithm introduces an overlap region, where both descriptions exist in parallel. It is shown that to accurately compute variances using the PBD simulation requires the overlap region. Advantages of both PBD approaches are discussed and illustrative numerical examples are presented.
Diffusive and dynamical radiating stars with realistic equations of state
Brassel, Byron P.; Maharaj, Sunil D.; Goswami, Rituparno
2017-03-01
We model the dynamics of a spherically symmetric radiating dynamical star with three spacetime regions. The local internal atmosphere is a two-component system consisting of standard pressure-free, null radiation and an additional string fluid with energy density and nonzero pressure obeying all physically realistic energy conditions. The middle region is purely radiative which matches to a third region which is the Schwarzschild exterior. A large family of solutions to the field equations are presented for various realistic equations of state. We demonstrate that it is possible to obtain solutions via a direct integration of the second order equations resulting from the assumption of an equation of state. A comparison of our solutions with earlier well known results is undertaken and we show that all these solutions, including those of Husain, are contained in our family. We then generalise our class of solutions to higher dimensions. Finally we consider the effects of diffusive transport and transparently derive the specific equations of state for which this diffusive behaviour is possible.
Dynamics of Diffusion Flames in von Karman Swirling Flows Studied
Nayagam, Vedha; Williams, Forman A.
2002-01-01
Von Karman swirling flow is generated by the viscous pumping action of a solid disk spinning in a quiescent fluid media. When this spinning disk is ignited in an oxidizing environment, a flat diffusion flame is established adjacent to the disk, embedded in the boundary layer (see the preceding illustration). For this geometry, the conservation equations reduce to a system of ordinary differential equations, enabling researchers to carry out detailed theoretical models to study the effects of varying strain on the dynamics of diffusion flames. Experimentally, the spinning disk burner provides an ideal configuration to precisely control the strain rates over a wide range. Our original motivation at the NASA Glenn Research Center to study these flames arose from a need to understand the flammability characteristics of solid fuels in microgravity where slow, subbuoyant flows can exist, producing very small strain rates. In a recent work (ref. 1), we showed that the flammability boundaries are wider and the minimum oxygen index (below which flames cannot be sustained) is lower for the von Karman flow configuration in comparison to a stagnation-point flow. Adding a small forced convection to the swirling flow pushes the flame into regions of higher strain and, thereby, decreases the range of flammable strain rates. Experiments using downward facing, polymethylmethacrylate (PMMA) disks spinning in air revealed that, close to the extinction boundaries, the flat diffusion flame breaks up into rotating spiral flames (refs. 2 and 3). Remarkably, the dynamics of these spiral flame edges exhibit a number of similarities to spirals observed in biological systems, such as the electric pulses in cardiac muscles and the aggregation of slime-mold amoeba. The tail of the spiral rotates rigidly while the tip executes a compound, meandering motion sometimes observed in Belousov-Zhabotinskii reactions.
Chaotic dynamics and diffusion in a piecewise linear equation
Energy Technology Data Exchange (ETDEWEB)
Shahrear, Pabel, E-mail: pabelshahrear@yahoo.com [Department of Mathematics, Shah Jalal University of Science and Technology, Sylhet–3114 (Bangladesh); Glass, Leon, E-mail: glass@cnd.mcgill.ca [Department of Physiology, 3655 Promenade Sir William Osler, McGill University, Montreal, Quebec H3G 1Y6 (Canada); Edwards, Rod, E-mail: edwards@uvic.ca [Department of Mathematics and Statistics, University of Victoria, P.O. Box 1700 STN CSC, Victoria, British Columbia V8W 2Y2 (Canada)
2015-03-15
Genetic interactions are often modeled by logical networks in which time is discrete and all gene activity states update simultaneously. However, there is no synchronizing clock in organisms. An alternative model assumes that the logical network is preserved and plays a key role in driving the dynamics in piecewise nonlinear differential equations. We examine dynamics in a particular 4-dimensional equation of this class. In the equation, two of the variables form a negative feedback loop that drives a second negative feedback loop. By modifying the original equations by eliminating exponential decay, we generate a modified system that is amenable to detailed analysis. In the modified system, we can determine in detail the Poincaré (return) map on a cross section to the flow. By analyzing the eigenvalues of the map for the different trajectories, we are able to show that except for a set of measure 0, the flow must necessarily have an eigenvalue greater than 1 and hence there is sensitive dependence on initial conditions. Further, there is an irregular oscillation whose amplitude is described by a diffusive process that is well-modeled by the Irwin-Hall distribution. There is a large class of other piecewise-linear networks that might be analyzed using similar methods. The analysis gives insight into possible origins of chaotic dynamics in periodically forced dynamical systems.
Dahlstrom, Julie; Welty, Daniel E; Oka, Takeshi; Hobbs, L M; Johnson, Sean; Friedman, Scott D; Jiang, Zihao; Rachford, Brian L; Sherman, Reid; Snow, Theodore P; Sonnentrucker, Paule
2013-01-01
Anomalously broad diffuse interstellar bands (DIBs) at 5780.5, 5797.1, 6196.0, and 6613.6 A are found in absorption along the line of sight to Herschel 36, the star illuminating the bright Hourglass region of the H II region Messier 8. Interstellar absorption from excited CH+ in the J=1 level and from excited CH in the J=3/2 level is also seen. To our knowledge, neither those excited molecular lines nor such strongly extended DIBs have previously been seen in absorption from interstellar gas. These unusual features appear to arise in a small region near Herschel 36 which contains most of the neutral interstellar material in the sight line. The CH+ and CH in that region are radiatively excited by strong far-IR radiation from the adjacent infrared source Her 36 SE. Similarly, the broadening of the DIBs toward Herschel 36 may be due to radiative pumping of closely spaced high-J rotational levels of relatively small, polar carrier molecules. If this picture of excited rotational states for the DIB carriers is cor...
Lapas, Luciano C.; Ferreira, Rogelma M. S.; Rubí, J. Miguel; Oliveira, Fernando A.
2015-03-01
We analyze the temperature relaxation phenomena of systems in contact with a thermal reservoir that undergoes a non-Markovian diffusion process. From a generalized Langevin equation, we show that the temperature is governed by a law of cooling of the Newton's law type in which the relaxation time depends on the velocity autocorrelation and is then characterized by the memory function. The analysis of the temperature decay reveals the existence of an anomalous cooling in which the temperature may oscillate. Despite this anomalous behavior, we show that the variation of entropy remains always positive in accordance with the second law of thermodynamics.
Lapas, Luciano C; Ferreira, Rogelma M S; Rubí, J Miguel; Oliveira, Fernando A
2015-03-14
We analyze the temperature relaxation phenomena of systems in contact with a thermal reservoir that undergoes a non-Markovian diffusion process. From a generalized Langevin equation, we show that the temperature is governed by a law of cooling of the Newton's law type in which the relaxation time depends on the velocity autocorrelation and is then characterized by the memory function. The analysis of the temperature decay reveals the existence of an anomalous cooling in which the temperature may oscillate. Despite this anomalous behavior, we show that the variation of entropy remains always positive in accordance with the second law of thermodynamics.
Ageing dynamics of translational and rotational diffusion in a colloidal glass
Energy Technology Data Exchange (ETDEWEB)
Jabbari-Farouji, Sara [Van der Waals-Zeeman Institute, University of Amsterdam, Valckenierstraat 65, 1018XE Amsterdam (Netherlands); Eiser, Erika [van' t Hoff Institute for Molecular Sciences, University of Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam (Netherlands); Wegdam, Gerard H [Van der Waals-Zeeman Institute, University of Amsterdam, Valckenierstraat 65, 1018XE Amsterdam (Netherlands); Bonn, Daniel [Van der Waals-Zeeman Institute, University of Amsterdam, Valckenierstraat 65, 1018XE Amsterdam (Netherlands)
2004-10-20
We study the dynamics of translational and rotational diffusion during the ageing of a colloidal glass of Laponite using polarized and depolarized dynamic light scattering. The dynamics are qualitatively similar between the two degrees of freedom. The short-time diffusion is independent of the time elapsed since the sample preparation. The intermediate- and long-time diffusion, on the other hand, slows down by several orders of magnitude during the ageing. The slowing down of the rotational diffusion is found to be much faster than that of the translational diffusion. (letter to the editor)
DEFF Research Database (Denmark)
Lund, F. W.; Lomholt, M. A.; Solanko, L. M.;
2012-01-01
Background: Cholesterol is an important membrane component, but our knowledge about its transport in cells is sparse. Previous imaging studies using dehydroergosterol (DHE), an intrinsically fluorescent sterol from yeast, have established that vesicular and non-vesicular transport modes contribute...... to sterol trafficking from the plasma membrane. Significant photobleaching, however, limits the possibilities for in-depth analysis of sterol dynamics using DHE. Co-trafficking studies with DHE and the recently introduced fluorescent cholesterol analog BODIPY-cholesterol (BChol) suggested that the latter...
Panda, Manas K; Centore, Roberto; Causà, Mauro; Tuzi, Angela; Borbone, Fabio; Naumov, Panče
2016-07-12
The ability of thermosalient solids, organic analogues of inorganic martensites, to move by rapid mechanical reconfiguration or ballistic event remains visually appealing and potentially useful, yet mechanistically elusive phenomenon. Here, with a material that undergoes both thermosalient and non-thermosalient phase transitions, we demonstrate that the thermosalient effect is preceded by anomalous thermal expansion of the unit cell. The crystal explosion occurs as sudden release of the latent strain accumulated during the anisotropic, exceedingly strong expansion of the unit cell with αa = 225.9 × 10(-6) K(-1), αb = 238.8 × 10(-6) K(-1) and αc = -290.0 × 10(-6) K(-1), the latter being the largest negative thermal expansivity observed for an organic compound thus far. The results point out to the occurence of the thermosalient effect in phase transitions as means to identify new molecular materials with strong positive and/or negative thermal expansion which prior to this work could only be discovered serendipitously.
Multiscale Reaction-Diffusion Algorithms: PDE-Assisted Brownian Dynamics
Franz, Benjamin
2013-06-19
Two algorithms that combine Brownian dynami cs (BD) simulations with mean-field partial differential equations (PDEs) are presented. This PDE-assisted Brownian dynamics (PBD) methodology provides exact particle tracking data in parts of the domain, whilst making use of a mean-field reaction-diffusion PDE description elsewhere. The first PBD algorithm couples BD simulations with PDEs by randomly creating new particles close to the interface, which partitions the domain, and by reincorporating particles into the continuum PDE-description when they cross the interface. The second PBD algorithm introduces an overlap region, where both descriptions exist in parallel. It is shown that the overlap region is required to accurately compute variances using PBD simulations. Advantages of both PBD approaches are discussed and illustrative numerical examples are presented. © 2013 Society for Industrial and Applied Mathematics.
Physiologically structured populations with diffusion and dynamic boundary conditions.
Farkas, József Z; Hinow, Peter
2011-04-01
We consider a linear size-structured population model with diffusion in the size-space. Individuals are recruited into the population at arbitrary sizes. We equip the model with generalized Wentzell-Robin (or dynamic) boundary conditions. This approach allows the modelling of populations in which individuals may have distinguished physiological states. We establish existence and positivity of solutions by showing that solutions are governed by a positive quasicontractive semigroup of linear operators on the biologically relevant state space. These results are obtained by establishing dissipativity of a suitably perturbed semigroup generator. We also show that solutions of the model exhibit balanced exponential growth, that is, our model admits a finite-dimensional global attractor. In case of strictly positive fertility we are able to establish that solutions in fact exhibit asynchronous exponential growth.
Dense and diffuse gas in dynamically active clouds
Garrod, R T; Rawlings, J M C
2006-01-01
We investigate the chemical and observational implications of repetitive transient dense core formation in molecular clouds. We allow a transient density fluctuation to form and disperse over a period of 1 Myr, tracing its chemical evolution. We then allow the same gas immediately to undergo further such formation and dispersion cycles. The chemistry of the dense gas in subsequent cycles is similar to that of the first, and a limit cycle is reached quickly (2 - 3 cycles). Enhancement of hydrocarbon abundances during a specific period of evolution is the strongest indicator of previous dynamical history. The molecular content of the diffuse background gas in the molecular cloud is expected to be strongly enhanced by the core formation and dispersion process. Such enhancement may remain for as long as 0.5 Myr. The frequency of repetitive core formation should strongly determine the level of background molecular enhancement. We also convolve the emission from a synthesised dark cloud, comprised of ensembles of t...
Diffusion of innovations dynamics, biological growth and catenary function
Guseo, Renato
2016-12-01
The catenary function has a well-known role in determining the shape of chains and cables supported at their ends under the force of gravity. This enables design using a specific static equilibrium over space. Its reflected version, the catenary arch, allows the construction of bridges and arches exploiting the dual equilibrium property under uniform compression. In this paper, we emphasize a further connection with well-known aggregate biological growth models over time and the related diffusion of innovation key paradigms (e.g., logistic and Bass distributions over time) that determine self-sustaining evolutionary growth dynamics in naturalistic and socio-economic contexts. Moreover, we prove that the 'local entropy function', related to a logistic distribution, is a catenary and vice versa. This special invariance may be explained, at a deeper level, through the Verlinde's conjecture on the origin of gravity as an effect of the entropic force.
Multi-Loop Calculations of Anomalous Exponents in the Models of Critical Dynamics
Directory of Open Access Journals (Sweden)
Adzhemyan L. Ts.
2016-01-01
Full Text Available The Renormalization group method (RG is applied to the investigation of the E model of critical dynamics, which describes the transition from the normal to the superfluid phase in He4. The technique “Sector decomposition” with R’ operation is used for the calculation of the Feynman diagrams. The RG functions, critical exponents and critical dynamical exponent z, which determines the growth of the relaxation time near the critical point, have been calculated in the two-loop approximation in the framework of ε-expansion. The relevance of a fixed point for helium, where the dynamic scaling is weakly violated, is briefly discussed.
Test of the diffusing-diffusivity mechanism using near-wall colloidal dynamics
Matse, Mpumelelo
2016-01-01
The diffusing-diffusivity mechanism proposed by Chubynsky and Slater [PRL 113, 098302, 2014] predicts that, in environments where the diffusivity changes gradually, the displacement distribution becomes non-Gaussian, even though the mean-squared displacement (MSD) grows linearly with time. Here, we report single-particle tracking measurements of the diffusion of colloidal spheres near a planar wall. Because the local effective diffusivity is known, we have been able to carry out the first direct test of this mechanism for diffusion in inhomogeneous media.
Energy Technology Data Exchange (ETDEWEB)
Oka, Takeshi; Welty, Daniel E.; Johnson, Sean; York, Donald G.; Hobbs, L. M. [Department of Astronomy and Astrophysics, University of Chicago, 5640 South Ellis Avenue, Chicago, IL 60637 (United States); Dahlstrom, Julie, E-mail: t-oka@uchicago.edu [Department of Physics and Astronomy, Carthage College, 2001 Alford Park Drive, Kenosha, WI 53140 (United States)
2013-08-10
Absorption spectra toward Herschel 36 (Her 36) for the A-bar{sup 1}{Pi} Leftwards-Open-Headed-Arrow X-tilde{sup 1}{Sigma} transitions of CH{sup +} in the J = 1 excited rotational level and for the A-bar{sup 2}{Delta} Leftwards-Open-Headed-Arrow X-tilde{sup 2}{Pi} transitions of CH in the J = 3/2 excited fine structure level have been analyzed. These excited levels are above their ground levels by 40.1 K and {approx}25.7 K and indicate high radiative temperatures of the environment of 14.6 K and 6.7 K, respectively. The effect of the high radiative temperature is more spectacular in some diffuse interstellar bands (DIBs) observed toward Her 36; remarkable extended tails toward red (ETRs) were observed. We interpret these ETRs as being due to a small decrease of the rotational constants upon excitation of the excited electronic states. Along with radiative pumping of a great many high-J rotational levels, this causes the ETRs. In order to study this effect quantitatively, we have developed a model calculation in which the effects of collisions and radiation are treated simultaneously. The simplest case of linear molecules is considered. It has been found that the ETR is reproduced if the fraction of the variation of the rotational constant, {beta} {identical_to} (B' - B)/B, is sufficiently high (3%-5%) and the radiative temperature is high (T{sub r} > 50 K). Although modeling for general molecules is beyond the scope of this paper, the results indicate that the prototypical DIBs {lambda}5780.5, {lambda}5797.1, and {lambda}6613.6 which show the pronounced ETRs are due to polar molecules that are sensitive to the radiative excitation. The requirement of high {beta} favors relatively small molecules with three to six heavy atoms. DIBs {lambda}5849.8, {lambda}6196.0, and {lambda}6379.3 that do not show the pronounced ETRs are likely due to non-polar molecules or large polar molecules with small {beta}.
Oka, Takeshi; Welty, Daniel E.; Johnson, Sean; York, Donald G.; Dahlstrom, Julie; Hobbs, L. M.
2013-08-01
Absorption spectra toward Herschel 36 (Her 36) for the \\tilde{A}^1\\Pi \\leftarrow \\tilde{X}^1\\Sigma transitions of CH+ in the J = 1 excited rotational level and for the \\tilde{A}^2\\Delta \\leftarrow \\tilde{X}^2\\Pi transitions of CH in the J = 3/2 excited fine structure level have been analyzed. These excited levels are above their ground levels by 40.1 K and ~25.7 K and indicate high radiative temperatures of the environment of 14.6 K and 6.7 K, respectively. The effect of the high radiative temperature is more spectacular in some diffuse interstellar bands (DIBs) observed toward Her 36; remarkable extended tails toward red (ETRs) were observed. We interpret these ETRs as being due to a small decrease of the rotational constants upon excitation of the excited electronic states. Along with radiative pumping of a great many high-J rotational levels, this causes the ETRs. In order to study this effect quantitatively, we have developed a model calculation in which the effects of collisions and radiation are treated simultaneously. The simplest case of linear molecules is considered. It has been found that the ETR is reproduced if the fraction of the variation of the rotational constant, β ≡ (B' - B)/B, is sufficiently high (3%-5%) and the radiative temperature is high (T r > 50 K). Although modeling for general molecules is beyond the scope of this paper, the results indicate that the prototypical DIBs λ5780.5, λ5797.1, and λ6613.6 which show the pronounced ETRs are due to polar molecules that are sensitive to the radiative excitation. The requirement of high β favors relatively small molecules with three to six heavy atoms. DIBs λ5849.8, λ6196.0, and λ6379.3 that do not show the pronounced ETRs are likely due to non-polar molecules or large polar molecules with small β.
Navigation by anomalous random walks on complex networks
Weng, Tongfeng; Zhang, Jie; Khajehnejad, Moein; Small, Michael; Zheng, Rui; Hui, Pan
2016-11-01
Anomalous random walks having long-range jumps are a critical branch of dynamical processes on networks, which can model a number of search and transport processes. However, traditional measurements based on mean first passage time are not useful as they fail to characterize the cost associated with each jump. Here we introduce a new concept of mean first traverse distance (MFTD) to characterize anomalous random walks that represents the expected traverse distance taken by walkers searching from source node to target node, and we provide a procedure for calculating the MFTD between two nodes. We use Lévy walks on networks as an example, and demonstrate that the proposed approach can unravel the interplay between diffusion dynamics of Lévy walks and the underlying network structure. Moreover, applying our framework to the famous PageRank search, we show how to inform the optimality of the PageRank search. The framework for analyzing anomalous random walks on complex networks offers a useful new paradigm to understand the dynamics of anomalous diffusion processes, and provides a unified scheme to characterize search and transport processes on networks.
Energy Technology Data Exchange (ETDEWEB)
Bhatia, S.K.; Liu, F.; Arvind, G.
2000-04-18
Isotherm hysteresis and pore-clocking effects of trapped molecules on adsorption dynamics is studied here, using the iodine-carbon system in the 300--343 K temperature range. It is found that a portion of the iodine is strongly adsorbed, and does not desorb, even over very long time scales, while the remainder adsorbs reversibly as a homogeneous monolayer with a Langmuirian isotherm in mesopores. The strongly adsorbed iodine appears to adsorb in micropores and at the mesopore mouths, hindering uptake of the reversible iodine. The uptake data for the adsorption and desorption dynamics of the reversible part is found to be best explained by means of a pore mouth resistance control mechanism. it is concluded that the dynamics of the adsorption and desorption at the pore mouth is important at early stages of the process.
Swenson, Jan; Elamin, Khalid; Chen, Guo; Lohstroh, Wiebke; Sakai, Victoria Garcia
2014-12-01
The molecular dynamics of solutions of di-propylene glycol methylether (2PGME) and H2O (or D2O) confined in 28 Å pores of MCM-41 have been studied by quasielastic neutron scattering and differential scanning calorimetry over the concentration range 0-90 wt.% water. This system is of particular interest due to its pronounced non-monotonic concentration dependent dynamics of 2PGME in the corresponding bulk system, showing the important role of hydrogen bonding for the dynamics. In this study we have elucidated how this non-monotonic concentration dependence is affected by the confined geometry. The results show that this behaviour is maintained in the confinement, but the slowest diffusive dynamics of 2PGME is now observed at a considerably higher water concentration; at 75 wt.% water in MCM-41 compared to 30 wt.% water in the corresponding bulk system. This difference can be explained by an improper mixing of the two confined liquids. The results suggest that water up to a concentration of about 20 wt.% is used to hydrate the hydrophilic hydroxyl surface groups of the silica pores, and that it is only at higher water contents the water becomes partly mixed with 2PGME. Hence, due to this partial micro-phase separation of the two liquids larger, and thereby slower relaxing, structural entities of hydrogen bonded water and 2PGME molecules can only be formed at higher water contents than in the bulk system. However, the Q-dependence is unchanged with confinement, showing that the nature of the molecular motions is preserved. Thus, there is no indication of localization of the dynamics at length scales of less than 20 Å. The dynamics of both water and 2PGME is strongly dominated by translational diffusion at a temperature of 280 K.
Energy Technology Data Exchange (ETDEWEB)
Swenson, Jan, E-mail: jan.swenson@chalmers.se; Elamin, Khalid; Chen, Guo [Department of Applied Physics, Chalmers University of Technology, SE-412 96 Göteborg (Sweden); Lohstroh, Wiebke [Heinz Maier-Leibnitz Zentrum (MLZ), Technische Universität München, Lichtenbergstr. 1, 85748 Garching (Germany); Sakai, Victoria Garcia [ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX Oxfordshire (United Kingdom)
2014-12-07
The molecular dynamics of solutions of di-propylene glycol methylether (2PGME) and H{sub 2}O (or D{sub 2}O) confined in 28 Å pores of MCM-41 have been studied by quasielastic neutron scattering and differential scanning calorimetry over the concentration range 0–90 wt.% water. This system is of particular interest due to its pronounced non-monotonic concentration dependent dynamics of 2PGME in the corresponding bulk system, showing the important role of hydrogen bonding for the dynamics. In this study we have elucidated how this non-monotonic concentration dependence is affected by the confined geometry. The results show that this behaviour is maintained in the confinement, but the slowest diffusive dynamics of 2PGME is now observed at a considerably higher water concentration; at 75 wt.% water in MCM-41 compared to 30 wt.% water in the corresponding bulk system. This difference can be explained by an improper mixing of the two confined liquids. The results suggest that water up to a concentration of about 20 wt.% is used to hydrate the hydrophilic hydroxyl surface groups of the silica pores, and that it is only at higher water contents the water becomes partly mixed with 2PGME. Hence, due to this partial micro-phase separation of the two liquids larger, and thereby slower relaxing, structural entities of hydrogen bonded water and 2PGME molecules can only be formed at higher water contents than in the bulk system. However, the Q-dependence is unchanged with confinement, showing that the nature of the molecular motions is preserved. Thus, there is no indication of localization of the dynamics at length scales of less than 20 Å. The dynamics of both water and 2PGME is strongly dominated by translational diffusion at a temperature of 280 K.
Anomalous magnetic structure and spin dynamics in magnetoelectric LiFePO_{4}
DEFF Research Database (Denmark)
Toft-Petersen, Rasmus; Reehuis, Manfred; Jensen, Thomas Bagger Stibius
2015-01-01
We report significant details of the magnetic structure and spin dynamics of LiFePO4 obtained by single-crystal neutron scattering. Our results confirm a previously reported collinear rotation of the spins away from the principal b axis, and they determine that the rotation is toward the a axis...
Institute of Scientific and Technical Information of China (English)
肖吉; 陆九芳; 陈健; 李以圭
2001-01-01
Molecular dynamics simulation has been performed to determine the infinite-dilution diffusion coefficients of oxygen and nitrogen, and the diffusion coefficients of NaCl in supercritical water from 703.2- 763.2 K and 30-45 MPa.The results obtained show that the diffusion coefficients in supercritical water increase with temperature, while decreasing with pressure. Nevertheless, the diffusion coefficients in supercritical water are much larger than those in normal water.
Lapas, Luciano C.; Ferreira, Rogelma M. S.; Oliveira, Fernando A.; Rubí, J. Miguel
2014-01-01
We analyze the temperature relaxation phenomena of systems in contact with a thermal reservoir that undergo a non-Markovian diffusion process. From a generalized Langevin equation, we show that the temperature is governed by a law of cooling of the Newton's law type in which the relaxation time depends on the velocity autocorrelation and is then characterized by the memory function. The analysis of the temperature decay reveals the existence of an anomalous cooling in which the temperature ma...
Contributions of microtubule dynamic instability and rotational diffusion to kinetochore capture
Blackwell, Robert; Edelmaier, Christopher; Gergely, Zachary R; Flynn, Patrick J; Montes, Salvador; Crapo, Ammon; Doostan, Alireza; McIntosh, J Richard; Glaser, Matthew A; Betterton, Meredith D
2016-01-01
Microtubule dynamic instability allows search and capture of kinetochores during spindle formation, an important process for accurate chromosome segregation during cell division. Recent work has found that microtubule rotational diffusion about minus-end attachment points contributes to kinetochore capture in fission yeast, but the relative contributions of dynamic instability and rotational diffusion are not well understood. We have developed a biophysical model of kinetochore capture in small fission-yeast nuclei using hybrid Brownian dynamics/kinetic Monte Carlo simulation techniques. With this model, we have studied the importance of dynamic instability and microtubule rotational diffusion for kinetochore capture, both to the lateral surface of a microtubule and at or near its end. Over a range of biologically relevant parameters, microtubule rotational diffusion decreased capture time, but made a relatively small contribution compared to dynamic instability. At most, rotational diffusion reduced capture ...
The dynamics of multimodal integration: The averaging diffusion model.
Turner, Brandon M; Gao, Juan; Koenig, Scott; Palfy, Dylan; L McClelland, James
2017-03-08
We combine extant theories of evidence accumulation and multi-modal integration to develop an integrated framework for modeling multimodal integration as a process that unfolds in real time. Many studies have formulated sensory processing as a dynamic process where noisy samples of evidence are accumulated until a decision is made. However, these studies are often limited to a single sensory modality. Studies of multimodal stimulus integration have focused on how best to combine different sources of information to elicit a judgment. These studies are often limited to a single time point, typically after the integration process has occurred. We address these limitations by combining the two approaches. Experimentally, we present data that allow us to study the time course of evidence accumulation within each of the visual and auditory domains as well as in a bimodal condition. Theoretically, we develop a new Averaging Diffusion Model in which the decision variable is the mean rather than the sum of evidence samples and use it as a base for comparing three alternative models of multimodal integration, allowing us to assess the optimality of this integration. The outcome reveals rich individual differences in multimodal integration: while some subjects' data are consistent with adaptive optimal integration, reweighting sources of evidence as their relative reliability changes during evidence integration, others exhibit patterns inconsistent with optimality.
Anomalous diffusion of volcanic earthquakes
Abe, Sumiyoshi
2015-01-01
Volcanic seismicity at Mt. Etna is studied. It is found that the associated stochastic process exhibits a subdiffusive phenomenon. The jump probability distribution well obeys an exponential law, whereas the waiting-time distribution follows a power law in a wide range. Although these results would seem to suggest that the phenomenon could be described by temporally-fractional kinetic theory based on the viewpoint of continuous-time random walks, the exponent of the power-law waiting-time distribution actually lies outside of the range allowed in the theory. In addition, there exists the aging phenomenon in the event-time averaged mean squared displacement, in contrast to the picture of fractional Brownian motion. Comments are also made on possible relevances of random walks on fractals as well as nonlinear kinetics. Thus, problems of volcanic seismicity are highly challenging for science of complex systems.
Disentangling sources of anomalous diffusion
Thiel, Felix; Sokolov, Igor M
2013-01-01
We show that some important properties of subbdiffusion of unknown origin (including those of mixed origin) can be easily assessed when findeng the "fundamental moment" of the corresponding process, i.e., the one which is additive in time. In subordinated processes, the index of the fundamental moment is inherited from the parent process and its time-dependence from the leading one. In models of particle's motion in disordered potentials, the index is governed by the structural part of the disorder while the time dependence is given by its energetic part.
Anomalous effect of turning off long-range mobility interactions in Stokesian Dynamics
Wilson, Adam K Townsend Helen J
2016-01-01
In Stokesian Dynamics, particles are assumed to interact in two ways: through long-range mobility interactions and through short-range lubrication interactions. To speed up computations, in concentrated suspensions it is common to consider only lubrication. We show that, although this approximation provides acceptable results in monodisperse suspensions, in bidisperse suspensions it produces physically unreasonable results - "bunching" - whenever external forces are applied. We suggest that this problem could be mitigated by a careful choice of pairs of particles on which lubrication interactions should be included.
Schiffer, Christian; Nielsen, Søren Bom
2016-08-01
With convergent plate boundaries at some distance, the sources of the lithospheric stress field of the North Atlantic Realm are mainly mantle tractions at the base of the lithosphere, lithospheric density structure and topography. Given this, we estimate horizontal deviatoric stresses using a well-established thin sheet model in a global finite element representation. We adjust the lithospheric thickness and the sub-lithospheric pressure iteratively, comparing modelled in plane stress with the observations of the World Stress Map. We find that an anomalous mantle pressure associated with the Iceland and Azores melt anomalies, as well as topography are able to explain the general pattern of the principle horizontal stress directions. The Iceland melt anomaly overprints the classic ridge push perpendicular to the Mid Atlantic ridge and affects the conjugate passive margins in East Greenland more than in western Scandinavia. The dynamic support of topography shows a distinct maximum of c. 1000 m in Iceland and amounts Greenland. Considering that large areas of the North Atlantic Realm have been estimated to be sub-aerial during the time of break-up, two components of dynamic topography seem to have affected the area: a short-lived, which affected a wider area along the rift system and quickly dissipated after break-up, and a more durable in the close vicinity of Iceland. This is consistent with the appearance of a buoyancy anomaly at the base of the North Atlantic lithosphere at or slightly before continental breakup, relatively fast dissipation of the fringes of this, and continued melt generation below Iceland.
Anomalous dynamics of the extremely compressed magnetosphere during 21 January 2005 magnetic storm
Dmitriev, A V; Chao, J -K; Wang, C B; Rastaetter, L; Panasyuk, M I; Lazutin, L L; Kovtyukh, A S; Veselovsky, I S; Myagkova, I N
2014-01-01
Dynamics of the dayside magnetosphere and proton radiation belt was analyzed during unusual magnetic storm on 21 January 2005. We have found that during the storm from 1712 to 2400 UT, the subsolar magnetopause was continuously located inside geosynchronous orbit due to strong compression. The compression was found to be extremely strong from 1846 to 2035 UT when the dense plasma of fast erupting filament produced the solar wind dynamic pressure Pd peaked up to >100 nPa and, in the first time, the upstream solar wind was observed at geosynchronous orbit during almost 2 hours. Under the extreme compression, the outer magnetosphere at L > 5 was pushed inward and the outer radiation belt particles with energies of several tens of keV moved earthward, became adiabatically accelerated and accumulated in the inner magnetosphere at L 20%, which is well appropriate for erupting filaments and which is in agreement with the upper 27% threshold for the He/H ratio obtained from Cluster measurements.
Diffusive Boltzmann equation, its fluid dynamics, Couette flow and Knudsen layers
Abramov, Rafail V
2016-01-01
In the current work we propose a diffusive modification of the Boltzmann equation. This naturally leads to the corresponding diffusive fluid dynamics equations, which we numerically investigate in a simple Couette flow setting. This diffusive modification is based on the assumption of the "imperfect" model collision term, which is unable to track all collisions in the corresponding real gas particle system. The effect of missed collisions is then modeled by an appropriately scaled long-term homogenization process of the particle dynamics. The corresponding diffusive fluid dynamics equations are produced in a standard way by closing the hierarchy of the moment equations using either the Euler or the Grad closure. In the numerical experiments with the Couette flow, we discover that the diffusive Euler equations behave similarly to the conventional Navier-Stokes equations, while the diffusive Grad equations additionally exhibit Knudsen-like velocity boundary layers. We compare the simulations with the correspond...
Crystal structural and diffusion property in titanium carbides: A molecular dynamics study
Lv, Yanan; Gao, Weimin
2016-09-01
Titanium carbides were studied via molecular dynamics simulation to characterize TiCx structures with respect to the carbon diffusion properties in this study. The effect of carbon concentration on atomic structures of titanium carbides was investigated through discussing the structure variation and the radial distribution functions of carbon atoms in titanium carbides. The carbon diffusion in titanium carbides was also analyzed, focusing on the dependence on carbon concentration and carbide structure. Carbon diffusivity with different carbon concentrations was determined by molecular dynamics (MD) calculations and compared with the available experimental data. The simulation results showed an atomic exchange mechanism for carbon diffusion in titanium carbide.
Diffusion dynamics of vacancy on Re(0 0 0 1), compared with adatom
Energy Technology Data Exchange (ETDEWEB)
Yang Jianyu, E-mail: wuliyangjianyu@yahoo.com.c [Department of Maths and Physics, Hunan Institute of Engineering, Xiangtan 411104 (China); Hu Wangyu, E-mail: wangyuhu2001@yahoo.com.c [Department of Applied Physics, Hunan University, Changsha 410082 (China); Liu Yanhui [Department of Maths and Physics, Hunan Institute of Engineering, Xiangtan 411104 (China)
2009-05-01
Using molecular dynamics (MD) simulations along with our recently constructed modified analytic embedded-atom method, the diffusion dynamics of single vacancy and adatom on Re(0 0 0 1) surface are studied. The diffusion coefficients of Re adatom and vacancy are calculated, and are found to present Arrhenius diagram. The diffusion migration energies (E{sub m}) and prefactors (D{sub 0}) are obtained from the Arrhenius relation. The calculated E{sub m} for adatom is in agreement with the recent low-temperature field ion microscope experimental data. The E{sub m} and D{sub 0} show that the vacancy has very low diffusive rate.
Dynamic polarization of the LiH molecule in strong light field in anomalous-dispersion domain
Shtoff, A V; Gusarov, S I; Dmitriev, Yu
1995-01-01
A new method is proposed to calculate the polarization vector of a molecule in a monochromatic external field in the anomalous-despersion domain. The method takes into account the instantaneous switching of the field. A simple modification of the method allows one to consider a more general switching procedure. As an illustration of the method Fourier components of the polarization vector of the LiH molecule in the anomalous -dispersion domain is calculated.
The spring 2011 final stratospheric warming above Eureka: anomalous dynamics and chemistry
Directory of Open Access Journals (Sweden)
C. Adams
2012-08-01
Full Text Available In spring 2011, the Arctic polar vortex was stronger than in any other year on record. As the polar vortex started to break up in April, ozone and NO_{2} columns were measured with UV-visible spectrometers above the Polar Environment Atmospheric Research Laboratory (PEARL in Eureka, Canada (80.05° N, 86.42° W using the differential optical absorption spectroscopy (DOAS technique. These ground-based column measurements were complemented by Ozone Monitoring Instrument (OMI and Optical Spectrograph and Infra-Red Imager System (OSIRIS satellite measurements, Global Modeling Initiative (GMI simulations, and dynamical parameters. On 8 April 2011, NO_{2} columns above PEARL from the DOAS, OMI, and GMI datasets were approximately twice as large as in previous years. On this day, temperatures and ozone volume mixing ratios above Eureka were high, suggesting enhanced chemical production of NO_{2} from NO. Additionally, GMI NO_{x} and N_{2}O fields suggest that downward transport along the vortex edge and horizontal transport from lower latitudes also contributed to the enhanced NO_{2}. The anticyclone that transported lower-latitude NO_{x} above PEARL became frozen-in and persisted in dynamical and GMI N_{2}O fields until the end of the measurement period on 31 May 2011. Ozone isolated within this frozen-in anticyclone (FrIAC in the middle stratosphere was depleted due to reactions with the enhanced NO_{x}. Ozone loss was calculated using the passive tracer technique, with passive ozone profiles from the Lagrangian Chemistry and Transport Model, ATLAS. At 600 K, ozone losses between 1 December 2010 and 20 May 2011 reached 4.2 parts per million by volume (ppmv (58% and 4.4 ppmv (61%, when calculated using GMI and OSIRIS ozone profiles, respectively. This middle-stratosphere gas-phase ozone loss led to a more rapid decrease in ozone column amounts in April/May 2011 compared with
Friction and diffusion dynamics of adsorbates at surfaces
Fusco, C.
2005-01-01
A theoretical study of the motion of adsorbates (e. g. atoms, molecules or clusters) on solid surfaces is presented, with a focus on surface diffusion and atomic-scale friction. These two phenomena are inextricably linked, because when an atomic or molecular adsorbate diffuses, or is pulled, it unav
Hsu, Po Jen; Lai, S K; Rapallo, Arnaldo
2014-03-14
Improved basis sets for the study of polymer dynamics by means of the diffusion theory, and tests on a melt of cis-1,4-polyisoprene decamers, and a toluene solution of a 71-mer syndiotactic trans-1,2-polypentadiene were presented recently [R. Gaspari and A. Rapallo, J. Chem. Phys. 128, 244109 (2008)]. The proposed hybrid basis approach (HBA) combined two techniques, the long time sorting procedure and the maximum correlation approximation. The HBA takes advantage of the strength of these two techniques, and its basis sets proved to be very effective and computationally convenient in describing both local and global dynamics in cases of flexible synthetic polymers where the repeating unit is a unique type of monomer. The question then arises if the same efficacy continues when the HBA is applied to polymers of different monomers, variable local stiffness along the chain and with longer persistence length, which have different local and global dynamical properties against the above-mentioned systems. Important examples of this kind of molecular chains are the proteins, so that a fragment of the protein transthyretin is chosen as the system of the present study. This peptide corresponds to a sequence that is structured in β-sheets of the protein and is located on the surface of the channel with thyroxin. The protein transthyretin forms amyloid fibrils in vivo, whereas the peptide fragment has been shown [C. P. Jaroniec, C. E. MacPhee, N. S. Astrof, C. M. Dobson, and R. G. Griffin, Proc. Natl. Acad. Sci. U.S.A. 99, 16748 (2002)] to form amyloid fibrils in vitro in extended β-sheet conformations. For these reasons the latter is given considerable attention in the literature and studied also as an isolated fragment in water solution where both experimental and theoretical efforts have indicated the propensity of the system to form β turns or α helices, but is otherwise predominantly unstructured. Differing from previous computational studies that employed implicit
The spring 2011 final stratospheric warming above Eureka: anomalous dynamics and chemistry
Directory of Open Access Journals (Sweden)
C. Adams
2013-01-01
Full Text Available In spring 2011, the Arctic polar vortex was stronger than in any other year on record. As the polar vortex started to break up in April, ozone and NO_{2} columns were measured with UV-visible spectrometers above the Polar Environment Atmospheric Research Laboratory (PEARL in Eureka, Canada (80.05° N, 86.42° W using the differential optical absorption spectroscopy (DOAS technique. These ground-based column measurements were complemented by Ozone Monitoring Instrument (OMI and Optical Spectrograph and Infra-Red Imager System (OSIRIS satellite measurements, Global Modeling Initiative (GMI simulations, and meteorological quantities. On 8 April 2011, NO_{2} columns above PEARL from the DOAS, OMI, and GMI datasets were approximately twice as large as in previous years. On this day, temperatures and ozone volume mixing ratios above Eureka were high, suggesting enhanced chemical production of NO_{2} from NO. Additionally, GMI NO_{x} (NO + NO_{2} and N_{2}O fields suggest that downward transport along the vortex edge and horizontal transport from lower latitudes also contributed to the enhanced NO_{2}. The anticyclone that transported lower-latitude NO_{x} above PEARL became frozen-in and persisted in dynamical and GMI N_{2}O fields until the end of the measurement period on 31 May 2011. Ozone isolated within this frozen-in anticyclone (FrIAC in the middle stratosphere was lost due to reactions with the enhanced NO_{x}. Below the FrIAC (from the tropopause to 700 K, NO_{x} driven ozone loss above Eureka was larger than in previous years, according to GMI monthly average ozone loss rates. Using the passive tracer technique, with passive ozone profiles from the Lagrangian Chemistry and Transport Model, ATLAS, ozone losses since 1 December 2010 were calculated at 600 K. In the air mass that was above Eureka on 20 May 2011, ozone losses reached 4.2 parts per million by
Simulation of dimer diffusion on metal fcc (001)surfaces by molecular dynamics
Institute of Scientific and Technical Information of China (English)
LIU; Qingwei; ZHUANG; Jun
2004-01-01
We study systematically the dimer diffusion on metal fcc (001) surfaces through molecular dynamics calculations based on embedded atom method. Besides the conventional hopping and exchange mechanisms, some other interesting diffusion mechanisms are observed, such as the exchange rotation mechanism, the cooperative hopping mechanism, and the cooperative exchange mechanism. On the different kinds of metal surfaces, we find that not only the dominant diffusion mechanism but also the physical model for the exchange mechanism is different.
Simple deterministic dynamical systems with fractal diffusion coefficients
Klages, R
1999-01-01
We analyze a simple model of deterministic diffusion. The model consists of a one-dimensional periodic array of scatterers in which point particles move from cell to cell as defined by a piecewise linear map. The microscopic chaotic scattering process of the map can be changed by a control parameter. This induces a parameter dependence for the macroscopic diffusion coefficient. We calculate the diffusion coefficent and the largest eigenmodes of the system by using Markov partitions and by solving the eigenvalue problems of respective topological transition matrices. For different boundary conditions we find that the largest eigenmodes of the map match to the ones of the simple phenomenological diffusion equation. Our main result is that the difffusion coefficient exhibits a fractal structure by varying the system parameter. To understand the origin of this fractal structure, we give qualitative and quantitative arguments. These arguments relate the sequence of oscillations in the strength of the parameter-dep...
Inter-diffusion and its correlation with dynamical cross correlation in liquid Ce80Ni20
Hu, J. L.; Zhong, L. X.; Zhu, C. A.; Zhang, B.
2017-03-01
We reported the inter-diffusion coefficients in liquid Ce_{80}Ni_{20} measured by the sliding cell technique. Combined with the self-diffusion data of Ni measured by quasi-elastic neutron scattering in the literature, it was found that the relationship between inter-diffusion and self-diffusion in liquid Ce_{80}Ni_{20} was strongly deviated from the standard Darken equation with an abnormally small dynamical cross correlation factor S (the so called Manning factor) in a range of 0.6-0.8, less than unity in standard systems. Through the calculated distinct diffusion coefficient and its deviation from the standard one, it was discovered that the small S value was directly originated from enhanced distinct diffusion between Ce and Ni atoms and reduced distinct diffusion between Ni and Ni atoms. Because the inter-atomic interaction was not considered in the standard liquids, the present small S factor and intrinsic distinct diffusion coefficients were believed to be resulted from the chemical interaction between Ce and Ni in the liquid. The results provide new evidence of the dynamic cross correlation in liquid diffusion, and thus shed light on the understanding of the correlation between dynamics and structure in liquid alloys.
Anomalous transport in the crowded world of biological cells.
Höfling, Felix; Franosch, Thomas
2013-04-01
A ubiquitous observation in cell biology is that the diffusive motion of macromolecules and organelles is anomalous, and a description simply based on the conventional diffusion equation with diffusion constants measured in dilute solution fails. This is commonly attributed to macromolecular crowding in the interior of cells and in cellular membranes, summarizing their densely packed and heterogeneous structures. The most familiar phenomenon is a sublinear, power-law increase of the mean-square displacement (MSD) as a function of the lag time, but there are other manifestations like strongly reduced and time-dependent diffusion coefficients, persistent correlations in time, non-Gaussian distributions of spatial displacements, heterogeneous diffusion and a fraction of immobile particles. After a general introduction to the statistical description of slow, anomalous transport, we summarize some widely used theoretical models: Gaussian models like fractional Brownian motion and Langevin equations for visco-elastic media, the continuous-time random walk model, and the Lorentz model describing obstructed transport in a heterogeneous environment. Particular emphasis is put on the spatio-temporal properties of the transport in terms of two-point correlation functions, dynamic scaling behaviour, and how the models are distinguished by their propagators even if the MSDs are identical. Then, we review the theory underlying commonly applied experimental techniques in the presence of anomalous transport like single-particle tracking, fluorescence correlation spectroscopy (FCS) and fluorescence recovery after photobleaching (FRAP). We report on the large body of recent experimental evidence for anomalous transport in crowded biological media: in cyto- and nucleoplasm as well as in cellular membranes, complemented by in vitro experiments where a variety of model systems mimic physiological crowding conditions. Finally, computer simulations are discussed which play an important
Institute of Scientific and Technical Information of China (English)
曾建平; 王爱民; 贡雪东; 陈景文; 陈松; 薛锋
2012-01-01
Under different temperatures and concentrations, the diffusion of Vitamin C （VC） in water solution was exam- ined by molecular dynamics simulation. The diffusion coefficients were calculated based on the Einstein equation. The influences of temperature, concentration, and simulation time on the diffusion coefficient were discussed. The results showed that at higher temperature and lower concentration the normal diffusions appear relatively late, but the linear range of mean square displacement curves continues longer than that at lower temperature and higher concentration. At the same temperature, the normal diffusion time increases and the diffusion coefficient decreases as the simulation concentration increases. These simulation results are in good agreement with experiments. Analyses of the pair correlation functions of the simulation systems showed that hydrogen bonds are mainly formed be- tween the hydrogen atoms of VC molecules and oxygen atoms of H20 molecules, rather than between the O atoms of VC molecules and H atoms of H20 molecules. The diffusion coefficient is higher as the interaction between water molecules and VC molecules is stronger when VC concentration is lower. The water in the model systems affects the diffusion of VC molecules by the short-range repulsion of O（H20）-O（H20） pairs and the non-bond interaction of H（H20）-H（H20） pairs. The short-range repulsion of O（H20）-O（H20） pairs is greater when VC concentration is higher, the diffusion of VC is weaker. The greater the non-bond interaction of H（H20）-H（H20） pairs is, the higher the VC diffusion is. It is expected that this study can provide a theoretical direction for the experiments on the mass transfer of VC in water solution.
Coexistence and efficiency of normal and anomalous transport by molecular motors in living cells
Goychuk, Igor; Metzler, R
2013-01-01
Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included.
Dynamics of information diffusion and its applications on complex networks
Zhang, Zi-Ke; Liu, Chuang; Zhan, Xiu-Xiu; Lu, Xin; Zhang, Chu-Xu; Zhang, Yi-Cheng
2016-09-01
The ongoing rapid expansion of the Word Wide Web (WWW) greatly increases the information of effective transmission from heterogeneous individuals to various systems. Extensive research for information diffusion is introduced by a broad range of communities including social and computer scientists, physicists, and interdisciplinary researchers. Despite substantial theoretical and empirical studies, unification and comparison of different theories and approaches are lacking, which impedes further advances. In this article, we review recent developments in information diffusion and discuss the major challenges. We compare and evaluate available models and algorithms to respectively investigate their physical roles and optimization designs. Potential impacts and future directions are discussed. We emphasize that information diffusion has great scientific depth and combines diverse research fields which makes it interesting for physicists as well as interdisciplinary researchers.
Energy Technology Data Exchange (ETDEWEB)
Bordin, José Rafael, E-mail: josebordin@unipampa.edu.br [Campus Caçapava do Sul, Universidade Federal do Pampa, Caixa Postal 15051, CEP 96570-000, Caçapava do Sul, RS (Brazil); Krott, Leandro B., E-mail: leandro.krott@ufrgs.br; Barbosa, Marcia C., E-mail: marcia.barbosa@ufrgs.br [Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, CEP 91501-970, Porto Alegre, RS (Brazil)
2014-10-14
The behavior of a confined spherical symmetric anomalous fluid under high external pressure was studied with Molecular Dynamics simulations. The fluid is modeled by a core-softened potential with two characteristic length scales, which in bulk reproduces the dynamical, thermodynamical, and structural anomalous behavior observed for water and other anomalous fluids. Our findings show that this system has a superdiffusion regime for sufficient high pressure and low temperature. As well, our results indicate that this superdiffusive regime is strongly related with the fluid structural properties and the superdiffusion to diffusion transition is a first order phase transition. We show how the simulation time and statistics are important to obtain the correct dynamical behavior of the confined fluid. Our results are discussed on the basis of the two length scales.
Calculation of the coefficient and dynamics of water diffusion in graphite joints
Institute of Scientific and Technical Information of China (English)
WANG Jun; LIU Wen-bin
2006-01-01
The coefficient and dynamics of water diffusion in adhesive-graphite joints were calculated insitu with energy dispersive X-ray (EDX) analysis, a method that is significantly simpler than elemental analysis. Water diffusion coefficient and dynamics of adhesive-graphite joints treated by different surface treatment methods were also investigated. Calculation results indicated that the water diffusion rate in adhesive-graphite joints treated by sandpaper was higher than that treated by chemical oxidation or by silane couple agent. Also the durability of graphite joints treated by coupling agent is superior to that treated by chemical oxidation or sandpaper burnishing.
Directory of Open Access Journals (Sweden)
Kiyotaka Ide
2014-09-01
Full Text Available Modular structure is a typical structure that is observed in most of real networks. Diffusion dynamics in network is getting much attention because of dramatic increasing of the data flows via the www. The diffusion dynamics in network have been well analysed as probabilistic process, but the proposed frameworks still shows the difference from the real observations. In this paper, we analysed spectral properties of the networks and diffusion dynamics. Especially, we focus on studying the relationship between modularity and diffusion dynamics. Our analysis as well as simulation results show that the relative influences from the non-largest eigenvalues and the corresponding eigenvectors increase when modularity of network increases. These results have the implication that, although network dynamics have been often analysed with the approximation manner utilizing only the largest eigenvalue, the consideration of the other eigenvalues is necessary for the analysis of the network dynamics on real networks. We also investigated Node-level Eigenvalue Influence Index (NEII which can quantify the relative influence from each eigenvalues on each node. This investigation indicates that the influence from each eigenvalue is confined within the modular structures in the network. These findings should be made consideration by researchers interested in diffusion dynamics analysis on real networks for deeper analysis.
Molecular dynamics simulation on diffusion properties of Pb-Mg alloy
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
A new method to calculate mutual-diffusion coefficients of the binary alloy has been proposed in this report.At first self-diffusion coefficient of the constituent element was calculated using molecular dynamics method,thermodynamic factor of the alloy was got with the NRTL (non-random-two-liquid) equation,then mutual-diffusion coefficient was obtained with Darken formula.Using this method the mutual-diffusion coefficient of Pb-Mg alloy with different Pb content was calculated.The calculated values were compared with the available experimental ones and the reason of the maximal mutual-diffusion coefficient appearing at 33.3 at.%Pb was discussed.Partial pair correlation function and partial coordination number were calculated to analyze the effect of the melt structure on mutual-diffusion coefficient.
Dynamic analysis of house price diffusion across Asian financial centres
Nanda, Anupam; Yeh, Jia-Huey
2012-01-01
The aim of this paper is to explore effects of macroeconomic variables on house prices and also, the lead-lag relationships of real estate markets to examine house price diffusion across Asian financial centres. The analysis is based on the Global Vector Auto-Regression (GVAR) model estimated using quarterly data for six Asian financial centres (Hong Kong, Tokyo, Seoul, Singapore, Taipei and Bangkok) from 1991Q1 to 2011Q2. The empirical results indicate that the global economic conditions pla...
First Numerical Simulations of Anomalous Hydrodynamics
Hongo, Masaru; Hirano, Tetsufumi
2013-01-01
Anomalous hydrodynamics is a low-energy effective theory that captures effects of quantum anomalies. We develop a numerical code of anomalous hydrodynamics and apply it to dynamics of heavy-ion collisions, where anomalous transports are expected to occur. This is the first attempt to perform fully non-linear numerical simulations of anomalous hydrodynamics. We discuss implications of the simulations for possible experimental observations of anomalous transport effects. From analyses of the charge-dependent elliptic flow parameters ($v_2^\\pm$) as a function of the net charge asymmetry $A_\\pm$, we quantitatively verify that the linear dependence of $\\Delta v_2 \\equiv v_2^- - v_2^+$ on the net charge asymmetry $A_\\pm$ cannot be regarded as a sensitive signal of anomalous transports, contrary to previous studies. We, however, find that the intercept $\\Delta v_2(A_\\pm=0)$ is sensitive to anomalous transport effects.
Michael, Fredrick; Johnson, M. D.
2003-03-01
A necessary precondition for modeling financial markets is a complete understanding of their statistics, including dynamics. Distributions derived from nonextensive Tsallis statistics are closely connected with dynamics described by a nonlinear Fokker-Planck equation. The combination shows promise in describing stochastic processes with power-law distributions and superdiffusive dynamics. We investigate intra-day price changes in the S& P500 stock index within this framework. We find that the power-law tails of the distributions, and the index's anomalously diffusing dynamics, are very accurately described by this approach. Our results show good agreement between market data and Fokker-Planck dynamics. This approach may be applicable in any anomalously diffusing system in which the correlations in time can be accounted for by an Ito-Langevin process with a simple time-dependent diffusion coefficient.
Global dynamics of a reaction-diffusion system
Directory of Open Access Journals (Sweden)
Yuncheng You
2011-02-01
Full Text Available In this work the existence of a global attractor for the semiflow of weak solutions of a two-cell Brusselator system is proved. The method of grouping estimation is exploited to deal with the challenge in proving the absorbing property and the asymptotic compactness of this type of coupled reaction-diffusion systems with cubic autocatalytic nonlinearity and linear coupling. It is proved that the Hausdorff dimension and the fractal dimension of the global attractor are finite. Moreover, the existence of an exponential attractor for this solution semiflow is shown.
Blogviz: mapping the dynamics of information diffusion in blogspace
Lima, Manuel S.
2006-01-01
Blogviz is a visualization model for mapping the transmission and internal structure of top links across the blogosphere. It explores the idea of meme propagation by assuming a parallel with the spreading of most cited URLs in daily weblog entries. The main goal of Blogviz is to unravel hidden patterns in the topics diffusion process. What's the life cycle of a topic? How does it start and how does it evolve through time? Are topics constrained to a specific community of users? Who are the most influential and innovative blogs in any topic? Are there any relationships amongst topic proliferators?
Chaudhury, Srabanti; Cherayil, Binny J
2007-09-14
Single-molecule equations for the Michaelis-Menten [Biochem. Z. 49, 333 (1913)] mechanism of enzyme action are analyzed within the Wilemski-Fixman [J. Chem. Phys. 58, 4009 (1973); 60, 866 (1974)] approximation after the effects of dynamic disorder--modeled by the anomalous diffusion of a particle in a harmonic well--are incorporated into the catalytic step of the reaction. The solution of the Michaelis-Menten equations is used to calculate the distribution of waiting times between successive catalytic turnovers in the enzyme beta-galactosidase. The calculated distribution is found to agree qualitatively with experimental results on this enzyme obtained at four different substrate concentrations. The calculations are also consistent with measurements of correlations in the fluctuations of the fluorescent light emitted during the course of catalysis, and with measurements of the concentration dependence of the randomness parameter.
Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study.
Yang, Jianjun; Tse, John S
2011-11-17
The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.
Wall, Michael E; Van Benschoten, Andrew H; Sauter, Nicholas K; Adams, Paul D; Fraser, James S; Terwilliger, Thomas C
2014-12-16
X-ray diffraction from protein crystals includes both sharply peaked Bragg reflections and diffuse intensity between the peaks. The information in Bragg scattering is limited to what is available in the mean electron density. The diffuse scattering arises from correlations in the electron density variations and therefore contains information about collective motions in proteins. Previous studies using molecular-dynamics (MD) simulations to model diffuse scattering have been hindered by insufficient sampling of the conformational ensemble. To overcome this issue, we have performed a 1.1-μs MD simulation of crystalline staphylococcal nuclease, providing 100-fold more sampling than previous studies. This simulation enables reproducible calculations of the diffuse intensity and predicts functionally important motions, including transitions among at least eight metastable states with different active-site geometries. The total diffuse intensity calculated using the MD model is highly correlated with the experimental data. In particular, there is excellent agreement for the isotropic component of the diffuse intensity, and substantial but weaker agreement for the anisotropic component. Decomposition of the MD model into protein and solvent components indicates that protein-solvent interactions contribute substantially to the overall diffuse intensity. We conclude that diffuse scattering can be used to validate predictions from MD simulations and can provide information to improve MD models of protein motions.
Turing pattern dynamics and adaptive discretization for a super-diffusive Lotka-Volterra model.
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.
Dissipative particle dynamics of diffusion-NMR requires high Schmidt-numbers
Azhar, Mueed; Greiner, Andreas; Korvink, Jan G.; Kauzlarić, David
2016-06-01
We present an efficient mesoscale model to simulate the diffusion measurement with nuclear magnetic resonance (NMR). On the level of mesoscopic thermal motion of fluid particles, we couple the Bloch equations with dissipative particle dynamics (DPD). Thereby we establish a physically consistent scaling relation between the diffusion constant measured for DPD-particles and the diffusion constant of a real fluid. The latter is based on a splitting into a centre-of-mass contribution represented by DPD, and an internal contribution which is not resolved in the DPD-level of description. As a consequence, simulating the centre-of-mass contribution with DPD requires high Schmidt numbers. After a verification for fundamental pulse sequences, we apply the NMR-DPD method to NMR diffusion measurements of anisotropic fluids, and of fluids restricted by walls of microfluidic channels. For the latter, the free diffusion and the localisation regime are considered.
Application of the Clustering Method in Molecular Dynamics Simulation of the Diffusion Coefficient
Institute of Scientific and Technical Information of China (English)
无
2008-01-01
Using molecular dynamics (MD) simulation, the diffusion of oxygen, methane, ammonia and carbon dioxide in water was simulated in the canonical NVT ensemble, and the diffusion coefficient was analyzed by the clustering method. By comparing to the conventional method (using the Einstein model) and the differentiation-interval variation method, we found that the results obtained by the clustering method used in this study are more close to the experimental values. This method proved to be more reasonable than the other two methods.
Fractional Chemotaxis Diffusion Equations
Langlands, T A M
2010-01-01
We introduce mesoscopic and macroscopic model equations of chemotaxis with anomalous subdiffusion for modelling chemically directed transport of biological organisms in changing chemical environments with diffusion hindered by traps or macro-molecular crowding. The mesoscopic models are formulated using Continuous Time Random Walk master equations and the macroscopic models are formulated with fractional order differential equations. Different models are proposed depending on the timing of the chemotactic forcing. Generalizations of the models to include linear reaction dynamics are also derived. Finally a Monte Carlo method for simulating anomalous subdiffusion with chemotaxis is introduced and simulation results are compared with numerical solutions of the model equations. The model equations developed here could be used to replace Keller-Segel type equations in biological systems with transport hindered by traps, macro-molecular crowding or other obstacles.
The study of Cu/Nb interface diffusion using molecular dynamics simulation
Directory of Open Access Journals (Sweden)
Ivan V. Nelasov
2016-06-01
Full Text Available The peculiarities of interfacial boundary diffusion where the boundary goes between nonmiscible metals with body-centered cubic (BCC and face-centered cubic (FCC lattices have been studied taking, as a case in point, the Cu/Nb system, and using the molecular dynamics method. The diffusion atomic displacements were shown to occur mainly near the mismatch dislocations and their intersections. The diffusion of the high-melting component was found to be characterized by high anisotropy with the predominant atomic displacement along the dense-packed direction in the interfacial boundary plane being common to FCC and BCC lattices with the Kurdyumov–Sachs mutual orientation.
Copper diffusivity in boron-doped silicon wafer measured by dynamic secondary ion mass spectrometry
Energy Technology Data Exchange (ETDEWEB)
Koh, Songfoo [S.E.H (M) Sdn. Bhd., Lot 2, Lorong Enggang 35, Ulu Klang FTZ, 54200 Selangor (Malaysia); You, Ahheng [Faculty of Engineering and Technology, Multimedia University, Jalan Ayer Keroh Lama, Bukit Beruang, 75450 Melaka (Malaysia); Tou, Teckyong, E-mail: tytou@mmu.edu.my [Faculty of Engineering, Multimedia Univesity, Jalan Multimedia, 63100 Cyberjaya (Malaysia)
2013-03-20
Highlights: ► Effective copper diffusivity in boron-doped silicon wafer was measured. ► Dynamic secondary ion mass spectrometry was used. ► Interstitial copper ions were first drifted to surface region and allowed to back-diffuse. ► Boron concentration largely influenced the effect copper diffusivity. -- Abstract: The effective copper diffusivity (D{sub eff}) in boron-doped silicon wafer was measured using a Dynamic Secondary Ion Mass Spectrometry (D-SIMS) that was incorporated with an out-drift technique. By this technique, positive interstitial copper ions (Cu{sub I}{sup +}) migrated to the surface region when a continuous charge of electrons showered on the oxidized silicon wafer, which was also bombarded by primary O{sub 2}{sup +} ions. The Cu{sub I}{sup +} ions at the surface region diffused back to the bulk when the electron showering stopped. The D-SIMS recorded the real-time distribution of Cu{sub I}{sup +} ions, generating depth profiles for in-diffusion of copper for silicon-wafer samples with different boron concentrations. These were curve-fitted using the standard diffusion expressions to obtain different D{sub eff} values, and compared with other measurement techniques.
Feynman–Kac equation for anomalous processes with space- and time-dependent forces
Cairoli, Andrea; Baule, Adrian
2017-04-01
Functionals of a stochastic process Y(t) model many physical time-extensive observables, for instance particle positions, local and occupation times or accumulated mechanical work. When Y(t) is a normal diffusive process, their statistics are obtained as the solution of the celebrated Feynman–Kac equation. This equation provides the crucial link between the expected values of diffusion processes and the solutions of deterministic second-order partial differential equations. When Y(t) is non-Brownian, e.g. an anomalous diffusive process, generalizations of the Feynman–Kac equation that incorporate power-law or more general waiting time distributions of the underlying random walk have recently been derived. A general representation of such waiting times is provided in terms of a Lévy process whose Laplace exponent is directly related to the memory kernel appearing in the generalized Feynman–Kac equation. The corresponding anomalous processes have been shown to capture nonlinear mean square displacements exhibiting crossovers between different scaling regimes, which have been observed in numerous experiments on biological systems like migrating cells or diffusing macromolecules in intracellular environments. However, the case where both space- and time-dependent forces drive the dynamics of the generalized anomalous process has not been solved yet. Here, we present the missing derivation of the Feynman–Kac equation in such general case by using the subordination technique. Furthermore, we discuss its extension to functionals explicitly depending on time, which are of particular relevance for the stochastic thermodynamics of anomalous diffusive systems. Exact results on the work fluctuations of a simple non-equilibrium model are obtained. An additional aim of this paper is to provide a pedagogical introduction to Lévy processes, semimartingales and their associated stochastic calculus, which underlie the mathematical formulation of anomalous diffusion as a
Dynamical tunneling versus fast diffusion for a non-convex Hamiltonian.
Pittman, S M; Tannenbaum, E; Heller, E J
2016-08-07
This paper attempts to resolve the issue of the nature of the 0.01-0.1 cm(-1) peak splittings observed in high-resolution IR spectra of polyatomic molecules. One hypothesis is that these splittings are caused by dynamical tunneling, a quantum-mechanical phenomenon whereby energy flows between two disconnected regions of phase-space across dynamical barriers. However, a competing classical mechanism for energy flow is Arnol'd diffusion, which connects different regions of phase-space by a resonance network known as the Arnol'd web. The speed of diffusion is bounded by the Nekhoroshev theorem, which guarantees stability on exponentially long time scales if the Hamiltonian is steep. Here we consider a non-convex Hamiltonian that contains the characteristics of a molecular Hamiltonian, but does not satisfy the Nekhoroshev theorem. The diffusion along the Arnol'd web is expected to be fast for a non-convex Hamiltonian. While fast diffusion is an unlikely competitor for longtime energy flow in molecules, we show how dynamical tunneling dominates compared to fast diffusion in the nearly integrable regime for a non-convex Hamiltonian, as well as present a new kind of dynamical tunneling.
Dynamical tunneling versus fast diffusion for a non-convex Hamiltonian
Pittman, S. M.; Tannenbaum, E.; Heller, E. J.
2016-08-01
This paper attempts to resolve the issue of the nature of the 0.01-0.1 cm-1 peak splittings observed in high-resolution IR spectra of polyatomic molecules. One hypothesis is that these splittings are caused by dynamical tunneling, a quantum-mechanical phenomenon whereby energy flows between two disconnected regions of phase-space across dynamical barriers. However, a competing classical mechanism for energy flow is Arnol'd diffusion, which connects different regions of phase-space by a resonance network known as the Arnol'd web. The speed of diffusion is bounded by the Nekhoroshev theorem, which guarantees stability on exponentially long time scales if the Hamiltonian is steep. Here we consider a non-convex Hamiltonian that contains the characteristics of a molecular Hamiltonian, but does not satisfy the Nekhoroshev theorem. The diffusion along the Arnol'd web is expected to be fast for a non-convex Hamiltonian. While fast diffusion is an unlikely competitor for longtime energy flow in molecules, we show how dynamical tunneling dominates compared to fast diffusion in the nearly integrable regime for a non-convex Hamiltonian, as well as present a new kind of dynamical tunneling.
Indian Academy of Sciences (India)
Bhabani S Mallik; Amalendu Chandra
2012-01-01
We present an ab initio molecular dynamics study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous solution of acetone at room temperature. It is found that the frequencies of OD bonds in the acetone hydration shell have a higher stretch frequency than those in the bulk water. Also, on average, the frequencies of hydration shell OD modes are found to increase with increase in the acetone-water hydrogen bond distance. The vibrational spectral diffusion of the hydration shell water molecules reveals three time scales: A short-time relaxation (∼80 fs) corresponding to the dynamics of intact acetone-water hydrogen bonds, a slower relaxation (∼1.3 ps) corresponding to the lifetime of acetone-water hydrogen bonds and another longer time constant (∼12 ps) corresponding to the escape dynamics of water from the solute hydration shell. The present first principles results are compared with those of available experiments and classical simulations.
Diffusion in a soft confining environment: Dynamic effects of thermal fluctuations
Palmieri, Benoit; Safran, Samuel
2013-03-01
A dynamical model of a soft, thermally fluctuating two-dimensional tube is used to study the effect of thermal fluctuations of a confining environment on diffusive transport. The tube fluctuations in both space and time are driven by Brownian motion and suppressed by surface tension and the rigidity of the surrounding environment. The dynamical fluctuations modify the concentration profile boundary condition at the tube surface. They decrease the diffusive transport rate through the tube for two important cases: uniform tube fluctuations (wave vector, q = 0 mode) for finite tube lengths and fluctuations of any wave vector for infinitely long tubes.
Diffusive dynamics and stochastic models of turbulent axisymmetric wakes
Rigas, G; Brackston, R D; Morrison, J F
2015-01-01
A modelling methodology to reproduce the experimental measurements of a turbulent flow under the presence of symmetry is presented. The flow is a three-dimensional wake generated by an axisymmetric body. We show that the dynamics of the turbulent wake- flow can be assimilated by a nonlinear two-dimensional Langevin equation, the deterministic part of which accounts for the broken symmetries which occur at the laminar and transitional regimes at low Reynolds numbers and the stochastic part of which accounts for the turbulent fluctuations. Comparison between theoretical and experimental results allows the extraction of the model parameters.
The Dynamics of Controlled Flow Separation within a Diverter Duct Diffuser
Peterson, C. J.; Vukasinovic, B.; Glezer, A.
2016-11-01
The evolution and receptivity to fluidic actuation of the flow separation within a rectangular, constant-width, diffuser that is branched off of a primary channel is investigated experimentally at speeds up to M = 0.4. The coupling between the diffuser's adverse pressure gradient and the internal separation that constricts nearly half of the flow passage through the duct is controlled using a spanwise array of fluidic actuators on the surface upstream of the diffuser's inlet plane. The dynamics of the separating surface vorticity layer in the absence and presence of actuation are investigated using high-speed particle image velocimetry combined with surface pressure measurements and total pressure distributions at the primary channel's exit plane. It is shown that the actuation significantly alters the incipient dynamics of the separating vorticity layer as the characteristic cross stream scales of the boundary layer upstream of separation and of the ensuing vorticity concentrations within the separated flow increase progressively with actuation level. It is argued that the dissipative (high frequency) actuation alters the balance between large- and small-scale motions near separation by intensifying the large-scale motions and limiting the small-scale dynamics. Controlling separation within the diffuser duct also has a profound effect on the global flow. In the presence of actuation, the mass flow rate in the primary duct increases 10% while the fraction of the diverted mass flow rate in the diffuser increases by more than 45% at 0.7% actuation mass fraction. Supported by the Boeing Company.
Goychuk, Igor; Kharchenko, Vasyl O; Metzler, Ralf
2014-01-01
Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included.
Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems
Li, Zhen; 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 a...
Institute of Scientific and Technical Information of China (English)
Wang Chun-Yang
2013-01-01
The diffusion process in an extemal noise-activated non-equilibrium open system-reservoir coupling environment is studied by analytically solving the generalized Langevin equation.The dynamical property of the system near the barrier top is investigated in detail by numerically calculating the quantities such as mean diffusion path,invariance,barrier passing probability,and so on.It is found that,comparing with the unfavorable effect of internal fluctuations,the external noise activation is sometimes beneficial to the diffusion process.An optimal strength of external activation or correlation time of the internal fluctuation is expected for the diffusing particle to have a maximal probability to escape from the potential well.
Molecular dynamics simulation of tensile behavior of diffusion bonded Ni/Al nanowires
Energy Technology Data Exchange (ETDEWEB)
Hu, Zhenjiang; Yan, Yongda; Yan, Jiuchun; Zhang, Junjie; Sun, Tao [Harbin Institute of Technology, Harbin (China)
2013-01-15
Interfaces play key roles in determining mechanical properties of materials. In current work we perform molecular dynamics simulations of diffusion bonding to evaluate the effect of temperature on the morphology of the Ni/Al interface and the strength of the diffusion bonded Ni/Al nanowires. The centro-symmetry parameter is adopted to identify defect atoms generated. Simulation results show that the thickness of the Ni/Al interface has strong dependence on the temperature of diffusion bonding. Following uniaxial tension tests indicate that the yield strength of Ni/Al nanowires is smaller than both the single crystalline Ni and Al nanowires, because of the Ni/Al interface acting as dislocation source and the mobilization of pre-existing dislocations at high temperature. It is shown that the mechanical properties of diffusion bonded Ni/Al nanowires strongly depend on the temperature.
DSOM: a novel self-organizing model based on NO dynamic diffusing mechanism
Institute of Scientific and Technical Information of China (English)
YIN Junsong; HU Dewen; CHEN Shuang; ZHOU Zongtan
2005-01-01
In this paper the four-dimensional dynamic diffusing mechanism and the enhancement in Long-Term Potentiation (LTP) of intrinsic nitric oxide (NO) in nervous system are studied computationally. A novel unsupervised Diffusing Self-Organizing Maps (DSOM) model is presented on the union of SOM with NO diffusing mechanism. Based on the spatial prototype mapping, temporal enhancement is introduced in DSOM and the fine-tuning manner is improved by the simplified NO diffusing mechanism. Furthermore, the quantization error of optimal weights is valuated and the detailed noise analysis of DSOM is presented. Finally some typical stimulation experiments are presented to illustrate how DSOM gracefully handles time warping and multiple patterns with overlapping reference vectors.
Dense fluid self-diffusion coefficient calculations using perturbation theory and molecular dynamics
Directory of Open Access Journals (Sweden)
COELHO L. A. F.
1999-01-01
Full Text Available A procedure to correlate self-diffusion coefficients in dense fluids by using the perturbation theory (WCA coupled with the smooth-hard-sphere theory is presented and tested against molecular simulations and experimental data. This simple algebraic expression correlates well the self-diffusion coefficients of carbon dioxide, ethane, propane, ethylene, and sulfur hexafluoride. We have also performed canonical ensemble molecular dynamics simulations by using the Hoover-Nosé thermostat and the mean-square displacement formula to compute self-diffusion coefficients for the reference WCA intermolecular potential. The good agreement obtained from both methods, when compared with experimental data, suggests that the smooth-effective-sphere theory is a useful procedure to correlate diffusivity of pure substances.
Directory of Open Access Journals (Sweden)
Amninder S Virk
2015-02-01
Full Text Available Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction. Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.
Dynamical Behavior of Core 3 He Nuclear Reaction-Diffusion Systems and Sun's Gravitational Field
Institute of Scientific and Technical Information of China (English)
DU Jiulin; SHEN Hong
2005-01-01
The coupling of the sun's gravitational field with processes of diffusion and convection exerts a significant influence on the dynamical behavior of the core 3He nuclear reaction-diffusion system. Stability analyses of the system are made in this paper by using the theory of nonequilibrium dynamics. It is showed that, in the nuclear reaction regions extending from the center to about 0.38 times of the radius of the sun, the gravitational field enables the core 3He nuclear reaction-diffusion system to become unstable and, after the instability, new states to appear in the system have characteristic of time oscillation. This may change the production rates of both 7Be and 8B neutrinos.
Accelerated molecular dynamics and equation-free methods for simulating diffusion in solids.
Energy Technology Data Exchange (ETDEWEB)
Deng, Jie; Zimmerman, Jonathan A.; Thompson, Aidan Patrick; Brown, William Michael (Oak Ridge National Laboratories, Oak Ridge, TN); Plimpton, Steven James; Zhou, Xiao Wang; Wagner, Gregory John; Erickson, Lindsay Crowl
2011-09-01
Many of the most important and hardest-to-solve problems related to the synthesis, performance, and aging of materials involve diffusion through the material or along surfaces and interfaces. These diffusion processes are driven by motions at the atomic scale, but traditional atomistic simulation methods such as molecular dynamics are limited to very short timescales on the order of the atomic vibration period (less than a picosecond), while macroscale diffusion takes place over timescales many orders of magnitude larger. We have completed an LDRD project with the goal of developing and implementing new simulation tools to overcome this timescale problem. In particular, we have focused on two main classes of methods: accelerated molecular dynamics methods that seek to extend the timescale attainable in atomistic simulations, and so-called 'equation-free' methods that combine a fine scale atomistic description of a system with a slower, coarse scale description in order to project the system forward over long times.
Institute of Scientific and Technical Information of China (English)
XIAO Fu-Liang; HE Zhao-Guo; ZHANG Sai; SU Zhen-Peng; CHEN Liang-Xu
2011-01-01
Temporal evolution of outer radiation belt electron dynamics resulting from superluminous L-O mode waves is simulated at L＝6.5. Diffusion rates are evaluated and then used as inputs to solve a 2D momentum-pitch-angle diffusion equation, particularly with and without cross diffusion terms. Simulated results demonstrate that phase space density(PSD) of energetic electrons due to L-O mode waves can enhance significantly within 24 h, covering a broader pitch-angle range in the absence of cross terms than that in the presence of cross terms. PSD evolution is also determined by the peak wave frequency, particularly at high kinetic energies. This result indicates that superluminous waves can be a potential candidate responsible for outer radiation belt electron dynamics.
Molecular dynamics simulation of hydrogen dissolution and diffusion in a tungsten grain boundary
Energy Technology Data Exchange (ETDEWEB)
Yu, Yi; Shu, Xiaolin; Liu, Yi-Nan; Lu, Guang-Hong, E-mail: lgh@buaa.edu.cn
2014-12-15
We employ a classic molecular dynamics method to investigate the dissolution and diffusion properties of hydrogen (H) in a Σ5(3 1 0) tilt grain boundary (GB). A maximum binding energy of 2.5 eV and a diffusion barrier of 1.65 eV indicate that GB plays an important role in H trapping. Dynamic simulations with temperature ranging from 600 K to 1200 K verify the diffusion and the aggregation of H in the GB are closely associated with the temperature. Pair radius distribution function analysis suggests a high local GB concentration of H such as 30% at 900 K can lead to a disordered GB structure.
Eastwood, C.; Klerkx, L.; Nettle, R.
2017-01-01
Precision farming technologies represent an innovation challenge in terms of their diffusion into farming practice, and create a new dynamic for research and extension roles. The purpose of this paper is to examine the interaction and distribution of research and extension roles of public, private,
Energy Technology Data Exchange (ETDEWEB)
Barbante, Paolo [Dipartimento di Matematica, Politecnico di Milano - Piazza Leonardo da Vinci 32 - 20133 Milano (Italy); Frezzotti, Aldo; Gibelli, Livio [Dipartimento di Scienze e Tecnologie Aerospaziali, Politecnico di Milano - Via La Masa 34 - 20156 Milano (Italy)
2014-12-09
The unsteady evaporation of a thin planar liquid film is studied by molecular dynamics simulations of Lennard-Jones fluid. The obtained results are compared with the predictions of a diffuse interface model in which capillary Korteweg contributions are added to hydrodynamic equations, in order to obtain a unified description of the liquid bulk, liquid-vapor interface and vapor region. Particular care has been taken in constructing a diffuse interface model matching the thermodynamic and transport properties of the Lennard-Jones fluid. The comparison of diffuse interface model and molecular dynamics results shows that, although good agreement is obtained in equilibrium conditions, remarkable deviations of diffuse interface model predictions from the reference molecular dynamics results are observed in the simulation of liquid film evaporation. It is also observed that molecular dynamics results are in good agreement with preliminary results obtained from a composite model which describes the liquid film by a standard hydrodynamic model and the vapor by the Boltzmann equation. The two mathematical model models are connected by kinetic boundary conditions assuming unit evaporation coefficient.
Kogut, A J
1999-01-01
Improved knowledge of diffuse Galactic emission is important to maximize the scientific return from scheduled CMB anisotropy missions. Cross-correlation of microwave maps with maps of the far-IR dust continuum show a ubiquitous microwave emission component whose spatial distribution is traced by far-IR dust emission. The spectral index of this emission, beta_{radio} = -2.2 (+0.5 -0.7) is suggestive of free-free emission but does not preclude other candidates. Comparison of H-alpha and microwave results show that both data sets have positive correlations with the far-IR dust emission. Microwave data, however, are consistently brighter than can be explained solely from free-free emission traced by H-alpha. This ``anomalous'' microwave emission can be explained as electric dipole radiation from small spinning dust grains. The anomalous component at 53 GHz is 2.5 times as bright as the free-free emission traced by H-alpha, providing an approximate normalization for models with significant spinning dust emission.
Panda, Debashis; Mishra, Padmaja P; Khatua, Saumyakanti; Koner, Apurba L; Sunoj, Raghavan B; Datta, Anindya
2006-05-04
The photophysics of the fluorescent probe Lucifer yellow CH has been investigated using fluorescence spectroscopic and computational techniques. The nonradiative rate is found to pass through a minimum in solvents of intermediate empirical polarity. This apparently anomalous behavior is rationalized by considering the possibility of predominance of different kinds of nonradiative processes, viz. intersystem crossing (ISC) and excited-state proton transfer (ESPT), in solvents of low and high empirical polarity, respectively. The feasibility of the proton transfer is examined by the structure determined by the density functional theory (DFT) calculations. The predicted energy levels based on the time-dependent density functional theory (TD-DFT) method in the gas phase identifies the energy gap between the S(1) and nearest triplet state to be close enough to facilitate ISC. Photophysical investigation in solvent mixtures and in deuterated solvents clearly indicates the predominance of the solvent-mediated intramolecular proton transfer in the excited state of the fluorophore in protic solvents.
Fixation, transient landscape, and diffusion dilemma in stochastic evolutionary game dynamics.
Zhou, Da; Qian, Hong
2011-09-01
Agent-based stochastic models for finite populations have recently received much attention in the game theory of evolutionary dynamics. Both the ultimate fixation and the pre-fixation transient behavior are important to a full understanding of the dynamics. In this paper, we study the transient dynamics of the well-mixed Moran process through constructing a landscape function. It is shown that the landscape playing a central theoretical "device" that integrates several lines of inquiries: the stable behavior of the replicator dynamics, the long-time fixation, and continuous diffusion approximation associated with asymptotically large population. Several issues relating to the transient dynamics are discussed: (i) multiple time scales phenomenon associated with intra- and inter-attractoral dynamics; (ii) discontinuous transition in stochastically stationary process akin to Maxwell construction in equilibrium statistical physics; and (iii) the dilemma diffusion approximation facing as a continuous approximation of the discrete evolutionary dynamics. It is found that rare events with exponentially small probabilities, corresponding to the uphill movements and barrier crossing in the landscape with multiple wells that are made possible by strong nonlinear dynamics, plays an important role in understanding the origin of the complexity in evolutionary, nonlinear biological systems.
Role of depletion on the dynamics of a diffusing forager
Bénichou, O.; Chupeau, M.; Redner, S.
2016-09-01
We study the dynamics of a starving random walk in general spatial dimension d. This model represents an idealized description for the fate of an unaware forager whose motion is not affected by the presence or absence of resources. The forager depletes its environment by consuming resources and dies if it wanders too long without finding food. In the exactly solvable case of one dimension, we explicitly derive the average lifetime of the walk and the distribution for the number of distinct sites visited by the walk at the instant of starvation. We also give a heuristic derivation for the averages of these two quantities. We tackle the complex but ecologically relevant case of two dimensions by an approximation in which the depleted zone is assumed to always be circular and which grows incrementally each time the walk reaches the edge of this zone. Within this framework, we derive a lower bound for the scaling of the average lifetime and number of distinct sites visited at starvation. We also determine the asymptotic distribution of the number of distinct sites visited at starvation. Finally, we solve the case of high spatial dimensions within a mean-field approach.
Room temperature compressibility and the diffusivity anomaly of liquid water from first principles
Corsetti, Fabiano; Soler, José M; Alexandre, S S; Fernández-Serra, M -V
2013-01-01
The isothermal compressibility of water is essential to understand its anomalous properties. We compute it by ab initio molecular dynamics simulations of 200 molecules at five densities, using two different van der Waals density functionals. While both functionals predict compressibilities within ~30% of experiment, only one of them reproduces the density dependence of the self-diffusion constant and its anomalous behavior. Their discrepancies are explained in terms of the low- and high-density structures of the liquid.
Order book dynamics in liquid markets: limit theorems and diffusion approximations
Cont, Rama; De Larrard, Adrien
2011-01-01
Revision 2012; We propose a model for the dynamics of a limit order book in a liquid market where buy and sell orders are submitted at high frequency. We derive a functional central limit theorem for the joint dynamics of the bid and ask queues and show that, when the frequency of order arrivals is large, the intraday dynamics of the limit order book may be approximated by a Markovian jump-diffusion process in the positive orthant, whose characteristics are explicitly described in terms of th...
Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters
Muhammad, Imran; Fayyaz, Hussain; Muhammad, Rashid; Muhammad, Ismail; Hafeez, Ullah; Yongqing, Cai; M Arshad, Javid; Ejaz, Ahmad; S, A. Ahmad
2016-07-01
Molecular dynamics simulation employing the embedded atom method potential is utilized to investigate nanoscale surface diffusion mechanisms of binary heterogeneous adatoms clusters at 300 K, 500 K, and 700 K. Surface diffusion of heterogeneous adatoms clusters can be vital for the binary island growth on the surface and can be useful for the formation of alloy-based thin film surface through atomic exchange process. The results of the diffusion process show that at 300 K, the diffusion of small adatoms clusters shows hopping, sliding, and shear motion; whereas for large adatoms clusters (hexamer and above), the diffusion is negligible. At 500 K, small adatoms clusters, i.e., dimer, show almost all possible diffusion mechanisms including the atomic exchange process; however no such exchange is observed for adatoms clusters greater than dimer. At 700 K, the exchange mechanism dominates for all types of clusters, where Zr adatoms show maximum tendency and Ag adatoms show minimum or no tendency toward the exchange process. Separation and recombination of one or more adatoms are also observed at 500 K and 700 K. The Ag adatoms also occupy pop-up positions over the adatoms clusters for short intervals. At 700 K, the vacancies are also generated in the vicinity of the adatoms cluster, vacancy formation, filling, and shifting can be observed from the results.
Molecular dynamics simulation of nanoscale surface diffusion of heterogeneous adatoms clusters
Institute of Scientific and Technical Information of China (English)
Muhammad Imran; Fayyaz Hussain; Muhammad Rashid; Muhammad Ismail; Hafeez Ullah; Yongqing Cai; M Arshad Javid; Ejaz Ahmad; S A Ahmad
2016-01-01
Molecular dynamics simulation employing the embedded atom method potential is utilized to investigate nanoscale surface diffusion mechanisms of binary heterogeneous adatoms clusters at 300 K, 500 K, and 700 K. Surface diffusion of heterogeneous adatoms clusters can be vital for the binary island growth on the surface and can be useful for the formation of alloy-based thin film surface through atomic exchange process. The results of the diffusion process show that at 300 K, the diffusion of small adatoms clusters shows hopping, sliding, and shear motion;whereas for large adatoms clusters (hexamer and above), the diffusion is negligible. At 500 K, small adatoms clusters, i.e., dimer, show almost all possible diffusion mechanisms including the atomic exchange process;however no such exchange is observed for adatoms clusters greater than dimer. At 700 K, the exchange mechanism dominates for all types of clusters, where Zr adatoms show maximum tendency and Ag adatoms show minimum or no tendency toward the exchange process. Separation and recombination of one or more adatoms are also observed at 500 K and 700 K. The Ag adatoms also occupy pop-up positions over the adatoms clusters for short intervals. At 700 K, the vacancies are also generated in the vicinity of the adatoms cluster, vacancy formation, filling, and shifting can be observed from the results.
molecular dynamics study of the gallium vacancy diffusion in GaAs
Bockstedte, Michel; Scheffler, Matthias
1996-03-01
Experimentally(T. Y. Tan et al.), Rev. Solid State Mater. Sci. 17, 47 (1991). it is well established that cation self-diffusion in GaAs proceeds by gallium vacancies. An analysis(J-L. Rouviere et al.), Phys. Rev. Lett. 68, 2798 (1992). of diffusion experiments yielded an exceptionally high value for the formation entropy of 32.9 kB and a migration energy barrier of 1.7 eV. The physics underlying this result is quite puzzling. Even the question whether the diffusion involves only the gallium sublattice or whether it proceeds by nearest neighbor hops is unanswered. Employing ab initio molecular dynamics simulations we analyze the motion of atoms and evaluate the free energy of vacancy formation and the diffusion constant. For the Ga vacancy we obtain a value for the formation entropy of 8 kB - comparable to that of the vacancy in silicon - but significantly lower than that extracted from experimentfootnotemark[2]. Based on our studies we therefore dare to question the experimental analysis. The calculated motion of a gallium vacancy close to the melting temperature of GaAs and the analysis of the different diffusion events exclude a diffusion mechanism by nearest neighbor hops. We discuss the microscopic picture of the second nearest neighbor hop, and determine its rate constant.
Heavy-Quark Diffusion Dynamics in Quark-Gluon Plasma under Strong Magnetic Fields
Hattori, Koichi; Yee, Ho-Ung; Yin, Yi
2016-01-01
We discuss heavy-quark dynamics in the quark-gluon plasma under a strong magnetic field induced by colliding nuclei. By the use of the diagrammatic resummation techniques for Hard Thermal Loop and the external magnetic field, we show analytic results of heavy-quark diffusion coefficient and drag force which become anisotropic due to the preferred spatial orientation in the magnetic field. We argue that the anisotropic diffusion coefficient gives rise to an enhancement/suppression of the heavy-quark elliptic flow depending on the transverse momentum.
Self-diffusion in FCC metals: Static and dynamic simulations in aluminium and nickel
Energy Technology Data Exchange (ETDEWEB)
Garcia Ortega, M.; Ramos de Debiaggi, S.B. [Departamento de Fisica, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquen (Argentina); Monti, A.M. [Departamento de Materiales, Comision Nacional de Energia Atomica, Avda. del Libertador 8250, 1429 Buenos Aires (Argentina)
2002-11-08
Self-diffusion in model Al and Ni has been studied by molecular static and molecular dynamic techniques. The structure of defect-lattice configurations has been obtained with the former technique. With the latter, the vacancy diffusion mechanism has been analysed over a wide temperature range, and particular attention has been paid to multiple jumps in the high temperature region. The possible contribution of divacancies, within the limits imposed by the interatomic potentials used, has also been considered. (Abstract Copyright [2002], Wiley Periodicals, Inc.)
Zhou, Sainan; Lu, Xiaoqing; Wu, Zhonghua; Jin, Dongliang; Guo, Chen; Wang, Maohuai; Wei, Shuxian
2016-09-01
Diffusion and separation of CH4/N2 in pillared graphene were investigated by molecular dynamics. The pillared graphene with (6, 6) carbon nanotube (CNT) exhibited the higher diffusion and selectivity of CH4 over N2 than that with (7, 7) CNT due to the cooperative effect of pore topological characteristics and interaction energy. The stronger interaction facilitated CH4 to enter CNT prior to N2, and higher pressure promoted CH4 to pass CNT more easily. The relative concentrations profiles showed that CH4 reached equilibrium state faster than N2 at low pressure. Our results highlight potential use of pillared graphene in gas purification and separation.
Navigation by anomalous random walks on complex networks
Weng, Tongfeng; Khajehnejad, Moein; Small, Michael; Zheng, Rui; Hui, Pan
2016-01-01
Anomalous random walks having long-range jumps are a critical branch of dynamical processes on networks, which can model a number of search and transport processes. However, traditional measurements based on mean first passage time are not useful as they fail to characterize the cost associated with each jump. Here we introduce a new concept of mean first traverse distance (MFTD) to characterize anomalous random walks that represents the expected traverse distance taken by walkers searching from source node to target node, and we provide a procedure for calculating the MFTD between two nodes. We use Levy walks on networks as an example, and demonstrate that the proposed approach can unravel the interplay between diffusion dynamics of Levy walks and the underlying network structure. Interestingly, applying our framework to the famous PageRank search, we can explain why its damping factor empirically chosen to be around 0.85. The framework for analyzing anomalous random walks on complex networks offers a new us...
Directory of Open Access Journals (Sweden)
Pranab Biswas
2014-05-01
Full Text Available The diffusion behavior of arsenic (As and gallium (Ga atoms from semi-insulating GaAs (SI-GaAs into ZnO films upon post-growth annealing vis-à-vis the resulting charge compensation was investigated with the help of x-ray photoelectron spectroscopy (XPS and secondary ion mass spectroscopy. The films, annealed at 600 ºC and 700 ºC showed p-type conductivity with a hole concentration of 1.1 × 1018 cm−3 and 2.8 × 1019 cm−3 respectively, whereas those annealed at 800 ºC showed n-type conductivity with a carrier concentration of 6.5 × 1016 cm−3. It is observed that at lower temperatures, large fraction of As atoms diffused from the SI-GaAs substrates into ZnO and formed acceptor related complex, (AsZn–2VZn, by substituting Zn atoms (AsZn and thereby creating two zinc vacancies (VZn. Thus as-grown ZnO which was supposed to be n-type due to nonstoichiometric nature showed p-type behavior. On further increasing the annealing temperature to 800 ºC, Ga atoms diffused more than As atoms and substitute Zn atoms thereby forming shallow donor complex, GaZn. Electrons from donor levels then compensate the p-type carriers and the material reverts back to n-type. Thus the conversion of carrier type took place due to charge compensation between the donors and acceptors in ZnO and this compensation is the possible origin of anomalous conduction in wide band gap materials.
Cheverry, Christophe
2017-02-01
This article is concerned with the relativistic Vlasov equation, for collisionless axisymmetric plasmas immersed in a strong magnetic field, like in tokamaks. It provides a consistent kinetic treatment of the microscopic particle phase-space dynamics. It shows that the turbulent transport can be completely described through WKB expansions.
Yousefnezhad, Mohsen; Fotouhi, Morteza; Vejdani, Kaveh; Kamali-Zare, Padideh
2016-09-01
We present a universal model of brain tissue microstructure that dynamically links osmosis and diffusion with geometrical parameters of brain extracellular space (ECS). Our model robustly describes and predicts the nonlinear time dependency of tortuosity (λ =√{D /D* } ) changes with very high precision in various media with uniform and nonuniform osmolarity distribution, as demonstrated by previously published experimental data (D = free diffusion coefficient, D* = effective diffusion coefficient). To construct this model, we first developed a multiscale technique for computationally effective modeling of osmolarity in the brain tissue. Osmolarity differences across cell membranes lead to changes in the ECS dynamics. The evolution of the underlying dynamics is then captured by a level set method. Subsequently, using a homogenization technique, we derived a coarse-grained model with parameters that are explicitly related to the geometry of cells and their associated ECS. Our modeling results in very accurate analytical approximation of tortuosity based on time, space, osmolarity differences across cell membranes, and water permeability of cell membranes. Our model provides a unique platform for studying ECS dynamics not only in physiologic conditions such as sleep-wake cycles and aging but also in pathologic conditions such as stroke, seizure, and neoplasia, as well as in predictive pharmacokinetic modeling such as predicting medication biodistribution and efficacy and novel biomolecule development and testing.
INTRODUCTION: Surface Dynamics, Phonons, Adsorbate Vibrations and Diffusion
Bruch, L. W.
2004-07-01
well infrared photodetectors (QWIPs) and resonant cavity-enhanced photodiodes (RCEPDs) based on dilute nitrides need to be investigated extensively. To date, most theoretical attention has been focused on understanding the band structure of the GaInAsN/GaAs system and on evaluating gain spectra and threshold conditions for 1.3 µm lasers. However, as our understanding of band structure and the effects of strain, defects, etc in dilute nitrides improves we can calculate the electrical and optical properties, including radiative and non-radiative recombination for the materials and structures of interest. The spontaneous and stimulated emission rates have already been calculated for GaInNAs at 1.3 µm by many authors, but extension to other dilute nitrides and other wavelength ranges still represents a major challenge. Many-body effects, including exchange-correlation effects, are essential for accurate models of gain spectra in lasers and optical amplifiers. The differential gain is a key parameter for laser modulation and remains an important subject of study as new materials and structures are explored. Similarly the differential refractive index and linewidth enhancement factor have strong influences on laser spectrum (chirp, linewidth), dynamics and noise, and these must also be studied theoretically. As regards to non-radiative recombination, in addition to recombination through defects, the Auger effect is of especial significance for wavelengths beyond 1 µm and is a worthy subject for theoretical study. The converse effect, impact ionization, is of key importance for avalanche photodiodes (APDs) and has yet to be evaluated for the dilute nitride materials. Inter-valence band absorption (IVBA) is of significance, as a possible cause of temperature sensitivity in lasers and this must be investigated theoretically in the dilute nitrides. Third-order non-linear optical coefficients should be calculated in order to assess the scope for all-optical signal processing
Nonlinear Diffusion Filtering of the GOCE-Based Satellite-Only Mean Dynamic Topography
Cunderlik, Robert; Mikula, Karol
2015-03-01
The paper presents nonlinear diffusion filtering of the GOCE-based satellite-only mean dynamic topography (MDT). Our approach is based on a numerical solution to the nonlinear diffusion equation defined on the discretized Earth’s surface using the regularized surface Perona-Malik Model. For its numerical discretization we use a surface finite volume method. A key idea is that the diffusivity coefficient depends on the edge detector. It allows effectively reduce the stripping noise while preserve important gradients in filtered data. Numerical experiments present nonlinear filtering of the geopotential evaluated from the GO_CONS_GCF_2_ DIR_R5 model on the DTU13 mean sea surface. After filtering the geopotential is transformed into the MDT.
Coherent dynamical recoupling of diffusion-driven decoherence in magnetic resonance
Alvarez, Gonzalo A; Frydman, Lucio
2013-01-01
During recent years, dynamical decoupling (DD) has gained relevance as a tool for manipulating quantum systems and extracting information from them. This is particularly relevant for spins involved in nuclear magnetic resonance (NMR), where DD sequences can be used to prolong quantum coherences, or for selectively couple/decouple the effects imposed by random environmental fluctuations. In this Letter, we show that one can exploit these concepts in order to selectively recouple diffusion processes in restricted spaces. The ensuing method provides a novel tool to measure restriction lengths in confined systems such as capillaries, pores or cells. The principles of this method for selectively recoupling diffusion-driven decoherence, its standing within the context of diffusion NMR, and corroborating experiments, are presented.
Álvarez, Gonzalo A.; Shemesh, Noam; Frydman, Lucio
2014-02-01
Dynamical decoupling, a generalization of the original NMR spin-echo sequence, is becoming increasingly relevant as a tool for reducing decoherence in quantum systems. Such sequences apply non-equidistant refocusing pulses for optimizing the coupling between systems, and environmental fluctuations characterized by a given noise spectrum. One such sequence, dubbed Selective Dynamical Recoupling (SDR) [P. E. S. Smith, G. Bensky, G. A. Álvarez, G. Kurizki, and L. Frydman, Proc. Natl. Acad. Sci. 109, 5958 (2012)], allows one to coherently reintroduce diffusion decoherence effects driven by fluctuations arising from restricted molecular diffusion [G. A. Álvarez, N. Shemesh, and L. Frydman, Phys. Rev. Lett. 111, 080404 (2013)]. The fully-refocused, constant-time, and constant-number-of-pulses nature of SDR also allows one to filter out "intrinsic" T1 and T2 weightings, as well as pulse errors acting as additional sources of decoherence. This article explores such features when the fluctuations are now driven by unrestricted molecular diffusion. In particular, we show that diffusion-driven SDR can be exploited to investigate the decoherence arising from the frequency fluctuations imposed by internal gradients. As a result, SDR presents a unique way of probing and characterizing these internal magnetic fields, given an a priori known free diffusion coefficient. This has important implications in studies of structured systems, including porous media and live tissues, where the internal gradients may serve as fingerprints for the system's composition or structure. The principles of this method, along with full analytical solutions for the unrestricted diffusion-driven modulation of the SDR signal, are presented. The potential of this approach is demonstrated with the generation of a novel source of MRI contrast, based on the background gradients active in an ex vivo mouse brain. Additional features and limitations of this new method are discussed.
Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates
Directory of Open Access Journals (Sweden)
Najmul Arfin
2013-11-01
Full Text Available The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement ⟨R2⟩ exhibits a scaling with time as ⟨R2⟩ ∼ tα, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t, which follows the scaling, S(t ∼ tβ/ln (t. Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.
Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates
Arfin, Najmul; Yadav, Avinash Chand; Bohidar, H. B.
2013-11-01
The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement ⟨R2⟩ exhibits a scaling with time as ⟨R2⟩ ˜ tα, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ˜ tβ/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.
Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates
Energy Technology Data Exchange (ETDEWEB)
Arfin, Najmul [Polymer and Biophysics Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067 (India); Yadav, Avinash Chand [Nonlinear Dynamics Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067 (India); Bohidar, H. B., E-mail: bohi0700@mail.jnu.ac.in [Polymer and Biophysics Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi-110067 (India); Special Centre for Nanosciences, Jawaharlal Nehru University, New Delhi-110067 (India)
2013-11-15
The physical mechanism leading to the formation of large intermolecular DNA-protein complexes has been studied. Our study aims to explain the occurrence of fast coacervation dynamics at the charge neutralization point, followed by the appearance of smaller complexes and slower coacervation dynamics as the complex experiences overcharging. Furthermore, the electrostatic potential and probe mobility was investigated to mimic the transport of DNA / DNA-protein complex in a DNA-protein complex coacervate medium [N. Arfin and H. B. Bohidar, J. Phys. Chem. B 116, 13192 (2012)] by assigning neutral, negative, or positive charge to the probe particle. The mobility of the neutral probe was maximal at low matrix concentrations and showed random walk behavior, while its mobility ceased at the jamming concentration of c = 0.6, showing sub-diffusion and trapped dynamics. The positively charged probe showed sub-diffusive random walk followed by trapped dynamics, while the negatively charged probe showed trapping with occasional hopping dynamics at much lower concentrations. Sub-diffusion of the probe was observed in all cases under consideration, where the electrostatic interaction was used exclusively as the dominant force involved in the dynamics. For neutral and positive probes, the mean square displacement 〈R{sup 2}〉 exhibits a scaling with time as 〈R{sup 2}〉 ∼ t{sup α}, distinguishing random walk and trapped dynamics at α = 0.64 ± 0.04 at c = 0.12 and c = 0.6, respectively. In addition, the same scaling factors with the exponent β = 0.64 ± 0.04 can be used to distinguish random walk and trapped dynamics for the neutral and positive probes using the relation between the number of distinct sites visited by the probe, S(t), which follows the scaling, S(t) ∼ t{sup β}/ln (t). Our results established the occurrence of a hierarchy of diffusion dynamics experienced by a probe in a dense medium that is either charged or neutral.
Self-diffusion dynamic behavior of atomic clusters on Re(0 0 0 1) surface
Energy Technology Data Exchange (ETDEWEB)
Liu Fusheng [Department of Applied Physics, Hunan University, Changsha 410082 (China); Hu Wangyu, E-mail: wangyuhu2001cn@yahoo.com.cn [Department of Applied Physics, Hunan University, Changsha 410082 (China); Deng Huiqiu; Luo Wenhua; Xiao Shifang [Department of Applied Physics, Hunan University, Changsha 410082 (China); Yang Jianyu [Department of Maths and Physics, Hunan Institute of Engineering, Xiangtan 411104 (China)
2009-08-15
Using molecular dynamics simulations and a modified analytic embedded atom potential, the self-diffusion dynamics of rhenium atomic clusters up to seven atoms on Re(0 0 0 1) surface have been studied in the temperature ranges from 600 K to 1900 K. The simulation time varies from 20 ns to 200 ns according to the cluster sizes and the temperature. The heptamer and trimer are more stable comparing to other neighboring non-compact clusters. The diffusion coefficients of clusters are derived from the mean square displacement of cluster's mass-center, and diffusion prefactors D{sub 0} and activation energies E{sub a} are derived from the Arrhenius relation. It is found that the Arrhenius relation of the adatom can be divided into two parts at different temperature range. The activation energy of clusters increases with the increasing of the atom number in clusters. The prefactor of the heptamer is 2-3 orders of magnitude higher than a usual prefactor because of a large number of nonequivalent diffusion processes. The trimer and heptamer are the nuclei at different temperature range according to the nucleation theory.
Zhang, Wei; Ye, Chao; Hong, Linbi; Yang, Zaixing; Zhou, Ruhong
2016-12-01
Phosphorene, a newly fabricated two-dimensional (2D) nanomaterial, has emerged as a promising material for biomedical applications with great potential. Nonetheless, understanding the wetting and diffusive properties of bio-fluids on phosphorene which are of fundamental importance to these applications remains elusive. In this work, using molecular dynamics (MD) simulations, we investigated the structural and dynamic properties of water on both pristine and strained phosphorene. Our simulations indicate that the diffusion of water molecules on the phosphorene surface is anisotropic, with strain-enhanced diffusion clearly present, which arises from strain-induced smoothing of the energy landscape. The contact angle of water droplet on phosphorene exhibits a non-monotonic variation with the transverse strain. The structure of water on transverse stretched phosphorene is demonstrated to be different from that on longitudinal stretched phosphorene. Moreover, the contact angle of water on strained phosphorene is proportional to the quotient of the longitudinal and transverse diffusion coefficients of the interfacial water. These findings thereby offer helpful insights into the mechanism of the wetting and transport of water at nanoscale, and provide a better foundation for future biomedical applications of phosphorene.
Mathematical model of diffusion-limited gas bubble dynamics in unstirred tissue with finite volume.
Srinivasan, R Srini; Gerth, Wayne A; Powell, Michael R
2002-02-01
Models of gas bubble dynamics for studying decompression sickness have been developed by considering the bubble to be immersed in an extravascular tissue with diffusion-limited gas exchange between the bubble and the surrounding unstirred tissue. In previous versions of this two-region model, the tissue volume must be theoretically infinite, which renders the model inapplicable to analysis of bubble growth in a finite-sized tissue. We herein present a new two-region model that is applicable to problems involving finite tissue volumes. By introducing radial deviations to gas tension in the diffusion region surrounding the bubble, the concentration gradient can be zero at a finite distance from the bubble, thus limiting the tissue volume that participates in bubble-tissue gas exchange. It is shown that these deviations account for the effects of heterogeneous perfusion on gas bubble dynamics, and are required for the tissue volume to be finite. The bubble growth results from a difference between the bubble gas pressure and an average gas tension in the surrounding diffusion region that explicitly depends on gas uptake and release by the bubble. For any given decompression, the diffusion region volume must stay above a certain minimum in order to sustain bubble growth.
A comparative molecular dynamics study of diffusion of -decane and 3-methyl pentane in Y zeolite
Indian Academy of Sciences (India)
F G Pazzona; B J Borah; P Demontis; G B Suffritti; S Yashonath
2009-09-01
Molecular dynamics simulations are reported on the structure and dynamics of -decane and 3-methylpentane in zeolite NaY. We have calculated several properties such as the center of mass-center of mass rdf, the end-end distance distribution, bond angle distribution and dihedral angle distribution. We have also analysed trajectory to obtain diffusivity and velocity autocorrelation function (VACF). Surprisingly, the diffusivity of 3-methylpentane which is having larger cross-section perpendicular to the long molecular axis is higher than -decane at 300 K. Activation energies have been obtained from simulations performed at 200 K, 300 K, 350 K, 400 K and 450 K in the NVE ensemble. These results can be understood in terms of the previously known levitation effect. Arrhenious plot has higher value of slope for -decane (5.9 kJ/mol) than 3-methylpentane (3.7 kJ/mol) in agreement with the prediction of levitation effect.
Water self-diffusivity confined in graphene nanogap using molecular dynamics simulations
Moulod, M.; Hwang, G.
2016-11-01
Fundamental understanding of water confined in graphene is crucial to optimally design and operate sustainable energy, water desalination, and bio-medical systems. However, the current understanding predominantly remains in the static properties near the graphene surfaces. In this paper, a key water transport property, i.e., self-diffusivity, is examined under confinement by various graphene nanogap sizes (Lz = 0.7-4.17 nm), using molecular dynamics simulations with various graphene-water interatomic potentials (Simple Point Charge (SPC/E) and TIP3P water models). It is found that the water self-diffusivity nearly linearly decreases as the graphene-water interatomic potential energy increases at a given nanogap size. It also decreases as the graphene nanogap size decreases down to Lz = 1.34 nm; however, it shows the peak water self-diffusivity at Lz = 0.8 nm and then continues to decrease. The peak water self-diffusivity is related to the significant change of the overlapping surface force, and associated, nonlinear local water density distribution. The in-plane water self-diffusivity is higher up to nearly an order of magnitude than that of the out-of-plane due to the geometrical confinement effect by the graphene nanogap. The obtained results provide a roadmap to fundamentally understand the water transport properties in the graphene geometries and surface interactions.
Diffusion Models for Information Dissemination Dynamics in Wireless Complex Communication Networks
Shin-Ming Cheng; Vasileios Karyotis; Pin-Yu Chen; Kwang-Cheng Chen; Symeon Papavassiliou
2013-01-01
Information dissemination has become one of the most important services of communication networks. Modeling the diffusion of information through such networks is crucial for our modern information societies. In this work, novel models, segregating between useful and malicious types of information, are introduced, in order to better study Information Dissemination Dynamics (IDD) in wireless complex communication networks, and eventually allow taking into account special network features in IDD...
Insights into diffusion of gases in zeolites gained from molecular dynamics simulations
Krishna, R.; van Baten, J.M.
2008-01-01
The Maxwell-Stefan (M-S) diffusivities Đi of a variety of gases (He, Ne, Ar, Kr, H2, N2, CO2, CH4) in six different all-silica zeolite structures (MFI, AFI, FAU, CHA, DDR, and LTA) have been determined using molecular dynamics (MD) simulations for a range of molar loadings, qi. In all cases the Đi a
Spatio-temporal patterns with hyperchaotic dynamics in diffusively coupled biochemical oscillators
Directory of Open Access Journals (Sweden)
Gerold Baier
1997-01-01
Full Text Available We present three examples how complex spatio-temporal patterns can be linked to hyperchaotic attractors in dynamical systems consisting of nonlinear biochemical oscillators coupled linearly with diffusion terms. The systems involved are: (a a two-variable oscillator with two consecutive autocatalytic reactions derived from the Lotka–Volterra scheme; (b a minimal two-variable oscillator with one first-order autocatalytic reaction; (c a three-variable oscillator with first-order feedback lacking autocatalysis. The dynamics of a finite number of coupled biochemical oscillators may account for complex patterns in compartmentalized living systems like cells or tissue, and may be tested experimentally in coupled microreactors.
Exploring the dynamics of balance data — movement variability in terms of drift and diffusion
Gottschall, Julia; Peinke, Joachim; Lippens, Volker; Nagel, Volker
2009-02-01
We introduce a method to analyze postural control on a balance board by reconstructing the underlying dynamics in terms of a Langevin model. Drift and diffusion coefficients are directly estimated from the data and fitted by a suitable parametrization. The governing parameters are utilized to evaluate balance performance and the impact of supra-postural tasks on it. We show that the proposed method of analysis gives not only self-consistent results but also provides a plausible model for the reconstruction of balance dynamics.
Exploring the dynamics of balance data - movement variability in terms of drift and diffusion
Energy Technology Data Exchange (ETDEWEB)
Gottschall, Julia [Institute of Physics, University of Oldenburg, D-26111 Oldenburg (Germany)], E-mail: julia.gottschall@uni-oldenburg.de; Peinke, Joachim [Institute of Physics, University of Oldenburg, D-26111 Oldenburg (Germany)], E-mail: peinke@uni-oldenburg.de; Lippens, Volker [Department of Human Movement, University of Hamburg, Moller Street 10, D-20148 Hamburg (Germany)], E-mail: vlippens@uni-hamburg.de; Nagel, Volker [Department of Human Movement, University of Hamburg, Moller Street 10, D-20148 Hamburg (Germany)
2009-02-23
We introduce a method to analyze postural control on a balance board by reconstructing the underlying dynamics in terms of a Langevin model. Drift and diffusion coefficients are directly estimated from the data and fitted by a suitable parametrization. The governing parameters are utilized to evaluate balance performance and the impact of supra-postural tasks on it. We show that the proposed method of analysis gives not only self-consistent results but also provides a plausible model for the reconstruction of balance dynamics.
Transport dissipative particle dynamics model for mesoscopic advection- diffusion-reaction problems
Energy Technology Data Exchange (ETDEWEB)
Zhen, Li; Yazdani, Alireza; Tartakovsky, Alexandre M.; Karniadakis, George E.
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 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 DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.
Institute of Scientific and Technical Information of China (English)
WANG Chao; WANG Zhi; WANG Jing; SU Tao
2007-01-01
To determinate the water diffusion coefficients and dynamics in adhesive/carbon fiber reinforced epoxy resin composite joints, energy dispersive X-ray spectroscopy analysis(EDX) is used to establish the content change of oxygen in the adhesive in adhesive/carbon fiber reinforced epoxy resin composite joints. As water is made up of oxygen and hydrogen, the water diffusion coefficients and dynamics in adhesive/carbon fiber reinforced epoxy resin composite joints can be obtained from the change in the content of oxygen in the adhesive during humidity aging, via EDX analysis. The authors have calculated the water diffusion coefficients and dynamics in the adhesive/carbon fiber reinforced epoxy resin composite joints with the aid of both energy dispersive X-ray spectroscopy and elemental analysis. The determined results with EDX analysis are almost the same as those determined with elemental analysis and the results also show that the durability of the adhesive/carbon fiber reinforced epoxy resin composite joints subjected to silane coupling agent treatment is better than those subjected to sand paper burnishing treatment and chemical oxidation treatment.
Image processing analysis of vortex dynamics of lobed jets from three-dimensional diffusers
Energy Technology Data Exchange (ETDEWEB)
Nastase, Ilinca [Technical University of Civil Engineering in Bucharest, Building Services Department, 66 Avenue Pache Protopopescu, 020396, Bucharest (Romania); Meslem, Amina; El Hassan, Mouhammad, E-mail: inastase@instal.utcb.ro, E-mail: ameslem@univ-lr.fr [LEPTIAB, University of La Rochelle, Pole Sciences et Technologie, avenue Michel Crepeau, 17042 La Rochelle (France)
2011-12-01
The passive control of jet flows with the aim to enhance mixing and entrainment is of wide practical interest. Our purpose here is to develop new air diffusers for heating ventilating air conditioning systems by using lobed geometry nozzles, in order to ameliorate the users' thermal comfort. Two turbulent six-lobed air jets, issued from a lobed tubular nozzle and an innovative hemispherical lobed nozzle, were studied experimentally. It was shown that the proposed innovative concept of a lobed jet, which can be easily integrated in air diffusion devices, is very efficient regarding induction capability. A vortical dynamics analysis for the two jets is performed using a new method of image processing, namely dynamic mode decomposition. A validation of this method is also proposed suggesting that the dynamical mode decomposition (DMD) image processing method succeeds in capturing the most dominant frequencies of the flow dynamics, which in our case are related to the quite special dynamics of the Kelvin-Helmholtz vortices.
Relaxation and diffusion models with non-singular kernels
Sun, HongGuang; Hao, Xiaoxiao; Zhang, Yong; Baleanu, Dumitru
2017-02-01
Anomalous relaxation and diffusion processes have been widely quantified by fractional derivative models, where the definition of the fractional-order derivative remains a historical debate due to its limitation in describing different kinds of non-exponential decays (e.g. stretched exponential decay). Meanwhile, many efforts by mathematicians and engineers have been made to overcome the singularity of power function kernel in its definition. This study first explores physical properties of relaxation and diffusion models where the temporal derivative was defined recently using an exponential kernel. Analytical analysis shows that the Caputo type derivative model with an exponential kernel cannot characterize non-exponential dynamics well-documented in anomalous relaxation and diffusion. A legitimate extension of the previous derivative is then proposed by replacing the exponential kernel with a stretched exponential kernel. Numerical tests show that the Caputo type derivative model with the stretched exponential kernel can describe a much wider range of anomalous diffusion than the exponential kernel, implying the potential applicability of the new derivative in quantifying real-world, anomalous relaxation and diffusion processes.
Proton-driven spin diffusion in rotating solids via reversible and irreversible quantum dynamics.
Veshtort, Mikhail; Griffin, Robert G
2011-10-07
Proton-driven spin diffusion (PDSD) experiments in rotating solids have received a great deal of attention as a potential source of distance constraints in large biomolecules. However, the quantitative relationship between the molecular structure and observed spin diffusion has remained obscure due to the lack of an accurate theoretical description of the spin dynamics in these experiments. We start with presenting a detailed relaxation theory of PDSD in rotating solids that provides such a description. The theory applies to both conventional and radio-frequency-assisted PDSD experiments and extends to the non-Markovian regime to include such phenomena as rotational resonance (R(2)). The basic kinetic equation of the theory in the non-Markovian regime has the form of a memory function equation, with the role of the memory function played by the correlation function. The key assumption used in the derivation of this equation expresses the intuitive notion of the irreversible dissipation of coherences in macroscopic systems. Accurate expressions for the correlation functions and for the spin diffusion constants are given. The theory predicts that the spin diffusion constants governing the multi-site PDSD can be approximated by the constants observed in the two-site diffusion. Direct numerical simulations of PDSD dynamics via reversible Liouville-von Neumann equation are presented to support and compliment the theory. Remarkably, an exponential decay of the difference magnetization can be observed in such simulations in systems consisting of only 12 spins. This is a unique example of a real physical system whose typically macroscopic and apparently irreversible behavior can be traced via reversible microscopic dynamics. An accurate value for the spin diffusion constant can be usually obtained through direct simulations of PDSD in systems consisting of two (13)C nuclei and about ten (1)H nuclei from their nearest environment. Spin diffusion constants computed by this
Nikolaev, V P
2000-07-01
To gain insight into the special nature of gas bubbles that may form in astronauts, aviators and divers, we developed a mathematical model which describes the following: 1) the dynamics of extravascular bubbles formed in intercellular cavities of a hypothetical tissue undergoing decompression; and 2) the dynamics of nitrogen tension in a thin layer of intercellular fluid and in a thick layer of cells surrounding the bubbles. This model is based on the assumption that, due to limited cellular membrane permeability for gas, a value of effective nitrogen diffusivity in the massive layer of cells in the radial direction is essentially lower compared to conventionally accepted values of nitrogen diffusivity in water and body tissues. Due to rather high nitrogen diffusivity in intercellular fluid, a bubble formed just at completion of fast one-stage reduction of ambient pressure almost instantly grows to the size determined by the initial volume of the intercellular cavity, surface tension of the fluid, the initial nitrogen tension in the tissue, and the level of final pressure. The rate of further bubble growth and maximum bubble size depend on comparatively low effective nitrogen diffusivity in the cell layer, the tissue perfusion rate, the initial nitrogen tension in the tissue, and the final ambient pressure. The tissue deformation pressure performs its conservative action on bubble dynamics only in a limited volume of tissue (at a high density of formed bubbles). Our model is completely consistent with the available data concerning the random latency times to the onset of decompression sickness (DCS) symptoms associated with hypobaric decompressions simulating extravehicular activity. We believe that this model could be used as a theoretical basis for development of more adequate methods for the DCS risk prediction.
Yang, Hua; Lu, Zhong-Yuan; Li, Ze-Sheng; Sun, Chia-Chung
2006-03-01
Molecular-dynamics simulations have been used to study the diffusion of a short single model carbonic chain on the graphite (001) surface. The calculated diffusion coefficient (D) first increases, then decreases with increasing chain length (N). This abnormal behavior is similar to polymer lateral diffusion at the solid-liquid interface. Furthermore, we have studied the relation between the mean-square gyration radius and N. [Figure: see text].
Wagner, Johannes; Adjaoud, Omar; Marquardt, Katharina; Jahn, Sandro
2016-12-01
Diffusion rates and associated deformation behaviour in olivine have been subjected to many studies, due to the major abundance of this mineral group in the Earth's upper mantle. However, grain boundary (GB) transport studies yield controversial results. The relation between transport rate, energy, and geometry of individual GBs is the key to understand transport in aggregates with lattice preferred orientation that favours the presence and/or alignment of specific GBs over random ones in an undeformed rock. In this contribution, we perform classical molecular dynamics simulations of a series of symmetric and one asymmetric tilt GBs of Mg_2 SiO_4 forsterite, ranging from 9.58° to 90° in misorientation and varying surface termination. Our emphasis lies on unravelling structural characteristics of high- and low-angle grain boundaries and how the atomic structure influences grain boundary excess volume and self-diffusion processes. To obtain diffusion rates for different GB geometries, we equilibrate the respective systems at ambient pressure and temperatures from 1900 to 2200 K and trace their evolution for run durations of at least 1000 ps. We then calculate the mean square displacement of the different atomic species within the GB interface to estimate self-diffusion coefficients in the individual systems. Grain boundary diffusion coefficients for Mg, Si and O range from 10^{-18} to 10^{-21} m^3/s, falling in line with extrapolations from lower temperature experimental data. Our data indicate that higher GB excess volumes enable faster diffusion within the GB. Finally, we discuss two types of transport mechanisms that may be distinguished in low- and high-angle GBs.
Molecular dynamics study of strain-induced diffusivity of nitrogen in pure iron nanocrystalline
Mohammadzadeh, Roghayeh; Razmara, Naiyer; Razmara, Fereshteh
2016-12-01
In the present study, the self-diffusion process of nitrogen in pure iron nanocrystalline under strain conditions has been investigated by Molecular Dynamics (MD). The interactions between particles are modeled using Modified Embedded Atom Method (MEAM). Mean Square Displacement (MSD) of nitrogen in iron structure under strain is calculated. Strain is applied along [ 11 2 ¯ 0 ] and [ 0001 ] directions in both tensile and compression conditions. The activation energy and pre-exponential diffusion factor for nitrogen diffusion is comparatively high along [ 0001 ] direction of compressed structure of iron. The strain-induced diffusion coefficient at 973 K under the compression rate of 0.001 Å/ps along [ 0001 ] direction is about 6.72E-14 m2/s. The estimated activation energy of nitrogen under compression along [ 0001 ] direction is equal to 12.39 kcal/mol. The higher activation energy might be due to the fact that the system transforms into a more dense state when compressive stress is applied.
Molecular dynamics simulations of NMR relaxation and diffusion of bulk hydrocarbons and water
Singer, Philip M.; Asthagiri, Dilip; Chapman, Walter G.; Hirasaki, George J.
2017-04-01
Molecular dynamics (MD) simulations are used to investigate 1H nuclear magnetic resonance (NMR) relaxation and diffusion of bulk n-C5H12 to n-C17H36 hydrocarbons and bulk water. The MD simulations of the 1H NMR relaxation times T1,2 in the fast motion regime where T1 =T2 agree with measured (de-oxygenated) T2 data at ambient conditions, without any adjustable parameters in the interpretation of the simulation data. Likewise, the translational diffusion DT coefficients calculated using simulation configurations agree with measured diffusion data at ambient conditions. The agreement between the predicted and experimentally measured NMR relaxation times and diffusion coefficient also validate the forcefields used in the simulation. The molecular simulations naturally separate intramolecular from intermolecular dipole-dipole interactions helping bring new insight into the two NMR relaxation mechanisms as a function of molecular chain-length (i.e. carbon number). Comparison of the MD simulation results of the two relaxation mechanisms with traditional hard-sphere models used in interpreting NMR data reveals important limitations in the latter. With increasing chain length, there is substantial deviation in the molecular size inferred on the basis of the radius of gyration from simulation and the fitted hard-sphere radii required to rationalize the relaxation times. This deviation is characteristic of the local nature of the NMR measurement, one that is well-captured by molecular simulations.
Effects of Structured Ionomer Interfaces on Water Diffusion: Molecular Dynamics Simulation Insight
Aryal, Dipak; Perahia, Dvora; Grest, Gary
The dynamics of solvent molecules across structured ionomers interfaces is crucial to innovative technologies with selective controlled transport. These polymers consist of ionizable blocks facilitating transport tethered to mechanical stability enhancing ones, where their incompatibility drives compounded interfaces. Here water penetration through the interface of an A-B-C-B-A co-polymer is probed by atomistic molecular dynamics simulations where C is a randomly sulfonated polystyrene with sulfonation fractions f = 0 to 0.55, B is poly (ethylene-r-propylene) and A is poly (t-butyl styrene). For f>0, a two-step process with slow diffusion at the early stages is observed where water molecules transverse the hydrophobic rich surface before reaching the hydrophilic regime. Water molecules then diffuse along the percolating network of the ionic center block. Increasing the temperature and sulfonation fraction enhances both the rate of diffusion and the overall water uptake. This work is partially supported by DOE: DE-SC007908.
Population dynamics and wave propagation in a Lotka-Volterra system with spatial diffusion.
Wang, Mao-Xiang; Lai, Pik-Yin
2012-11-01
We consider the competitive population dynamics of two species described by the Lotka-Volterra model in the presence of spatial diffusion. The model is described by the diffusion coefficient (d(α)) and proliferation rate (r(α)) of the species α (α = 1,2 is the species label). Propagating wave front solutions in one dimension are investigated analytically and by numerical solutions. It is found that the wave profiles and wave speeds are determined by the speed parameters, v(α) ≡ 2 sqrt [d(α)r(α)], of the two species, and the phase diagrams for various inter- and intracompetitive scenarios are determined. The steady wave front speeds are obtained analytically via nonlinear dynamics analysis and verified by numerical solutions. The effect of the intermediate stationary state is investigated and propagating wave profiles beyond the simple Fisher wave fronts are revealed. The wave front speed of a species can display abrupt increase as its speed parameter is increased. In particular for the case in which both species are aggressive, our results show that the speed parameter is the deciding factor that determines the ultimate surviving species, in contrast to the case without diffusion in which the final surviving species is decided by its initial population advantage. Possible relations to the biological relevance of modeling cancer development and wound healing are also discussed.
Wang, Wei; Ma, Wanbiao; Lai, Xiulan
2017-01-01
From a biological perspective, a diffusive virus infection dynamic model with nonlinear functional response, absorption effect and chemotaxis is proposed. In the model, the diffusion of virus consists of two parts, the random diffusion and the chemotactic movement. The chemotaxis flux of virus depends not only on their own density, but also on the density of infected cells, and the density gradient of infected cells. The well posedness of the proposed model is deeply investigated. For the proposed model, the linear stabilities of the infection-free steady state E0 and the infection steady state E* are extensively performed. We show that the threshold dynamics can be expressed by the basic reproduction number R0 of the model without chemotaxis. That is, the infection-free steady state E0 is globally asymptotically stable if R0 virus is uniformly persistent if R0 > 1. In addition, we use the cross iteration method and the Schauder's fixed point theorem to prove the existence of travelling wave solutions connecting the infection-free steady state E0 and the infection steady state E* by constructing a pair of upper-lower solutions. At last, numerical simulations are presented to confirm theoretical findings.
Ni, Wenjie; Wang, Mingxin
2016-10-01
This paper is devoted to study the dynamical properties and stationary patterns of a diffusive Leslie-Gower prey-predator model with strong Allee effect in the prey population. We first analyze the nonnegative constant equilibrium solutions and their stabilities, and then study the dynamical properties of time-dependent solutions. Moreover, we investigate the stationary patterns induced by diffusions (Turing pattern). Our results show that the impact of the strong Allee effect essentially increases the system spatiotemporal complexity.
Indian Academy of Sciences (India)
Srinivasa R Varanasi; S Yashonath
2012-01-01
A molecular dynamics study of the dependence of diffusivity of the cation on ionic radii in molten AgI is reported.We have employed modified Parinello-Rahman-Vashistha interionic pair potential proposed by Shimojo and Kobayashi. Our results suggest that the diffusivity of the cation exhibits an increase followed by a decrease as the ionic radius is increased. Several structural and dynamical properties are reported.
Anomalous magnetohydrodynamics in the extreme relativistic domain
Giovannini, Massimo
2016-01-01
The evolution equations of anomalous magnetohydrodynamics are derived in the extreme relativistic regime and contrasted with the treatment of hydromagnetic nonlinearities pioneered by Lichnerowicz in the absence of anomalous currents. In particular we explore the situation where the conventional vector currents are complemented by the axial-vector currents arising either from the pseudo Nambu-Goldstone bosons of a spontaneously broken symmetry or because of finite fermionic density effects. After expanding the generally covariant equations in inverse powers of the conductivity, the relativistic analog of the magnetic diffusivity equation is derived in the presence of vortical and magnetic currents. While the anomalous contributions are generally suppressed by the diffusivity, they are shown to disappear in the perfectly conducting limit. When the flow is irrotational, boost-invariant and with vanishing four-acceleration the corresponding evolution equations are explicitly integrated so that the various physic...
Institute of Scientific and Technical Information of China (English)
Pin Lv; Zhenan Tang; Jun Yu; Yanbing Xue
2006-01-01
For gas sensor application, adsorption and diffusion of formaldehyde gas in single-wall carbon nanotube were investigated by using molecular dynamics simulation. The conformations of formaldehyde molecule adsorbed in carbon nanotube were optimized according to principle of minimum energy. The axis of conformatiot is parallel to the axis of carbon nanotube and about 0.3 nm～0.4 nm away from carbon nanotube wall. The conformation, which is different from that of the formaldehyde molecule in the gas-phase, rotates around carbon nanotube axis. The adsorption energy and diffusivity of formaldehyde molecule in single-wall carbon nanotube is of-56.2 kJ/mol and of 0.2× 10-4 cm2/s, respectively.
DEFF Research Database (Denmark)
Galliero, Guillaume; Medvedev, Oleg; Shapiro, Alexander
2005-01-01
Mutual diffusion in condensed phases is a theoretically and practically important subject of active research. One of the most rigorous and theoretically advanced approaches to the problem is a recently developed approach based on the concept of penetration lengths (Physica A 320 (2003) 211; Physi...... fluctuation theory and molecular dynamics scheme exhibit consistent trends and average deviations from experimental data around 10-20%. (c) 2004 Elsevier B.V. All rights reserved....... binary liquid mixtures of non-polar components that computed penetration lengths, for various temperatures and compositions, are consistent with those deduced from experiments in the framework of the formalism of the fluctuation theory. Moreover, the mutual diffusion coefficients obtained from a coupled...
Molecular dynamics study on ion diffusion in LiFePO4 olivine materials.
Zhang, Peixin; Wu, Yanpeng; Zhang, Dongyun; Xu, Qiming; Liu, Jianhong; Ren, Xiangzhong; Luo, Zhongkuan; Wang, Mingliang; Hong, Weiliang
2008-06-19
Molecular dynamics (MD) simulations have been employed to investigate the ionic diffusion and the structure of LiFePO 4 cathode material. The results correspond well with the published experimental observations. The simulation results indicated that the diffusion of lithium ions was thermally activated and more significant than those of other ions. Compared with other cathode materials, the shifts of ions were less significant in LiFePO 4. This suggested that LiFePO 4 was more thermally stable. The snapshots of the positions of lithium atoms over a range of the steps provided a microscopic picture and the picture showed the lithium ions migrated through one-dimension channels.
Goyal, Gaurav; Freedman, Kevin J; Kim, Min Jun
2013-09-01
This paper describes the use of gold nanoparticles to study particle translocation dynamics through silicon nitride solid-state nanopores. Gold nanoparticles were dispersed in 20 mM KCl solution containing nonionic surfactant Triton X-100 and their translocation was studied at different applied voltages. The use of low electrolyte concentration resulted in current enhancement upon particle translocation. The counterion cloud around the nanoparticles is proposed to be the reason for current enhancement phenomena because associated counterion cloud is believed to increase the ion density inside the pore during particle translocation. Further, single particle diffusion events were also recorded at 0 mV voltage bias and 0 pA background ionic current with high signal-to-noise ratio as the particles moved down their concentration gradient. The ability of nanopore sensors to detect single particle diffusion can be extended to field-free analysis of biomolecules in their native state and at or near physiological salt concentrations.
Zhao, Tongyang; Wang, Xiaogong
2013-09-01
In this study, dissipative particle dynamics (DPD) method was employed to investigate the translational diffusion of rodlike polymer in its nematic phase. The polymer chain was modeled by a rigid rod composed of consecutive DPD particles and solvent was represented by independent DPD particles. To fully understand the translational motion of the rods in the anisotropic phase, four diffusion coefficients, D_{||}u, D_ bot u, D_{||}n, D_ bot n were obtained from the DPD simulation. By definition, D_{||}n and D_ bot n denote the diffusion coefficients parallel and perpendicular to the nematic director, while D_{||}u and D_ bot u denote the diffusion coefficients parallel and perpendicular to the long axis of a rigid rod u. In the simulation, the velocity auto-correlation functions were used to calculate the corresponding diffusion coefficients from the simulated velocity of the rods. Simulation results show that the variation of orientational order caused by concentration and temperature changes has substantial influences on D_{||}u and D_ bot u. In the nematic phase, the changes of concentration and temperature will result in a change of local environment of rods, which directly influence D_{||}u and D_ bot u. Both D_{||}n and D_ bot n can be represented as averages of D_{||}u and D_ bot u, and the weighted factors are functions of the orientational order parameter S2. The effect of concentration and temperature on D_{||}n and D_ bot n demonstrated by the DPD simulation can be rationally interpreted by considering their influences on D_{||}u, D_ bot u and the order parameter S2.
Energy Technology Data Exchange (ETDEWEB)
Tringe, J.W., E-mail: tringe2@llnl.gov [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Ileri, N. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Levie, H.W. [Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, CA (United States); Stroeve, P.; Ustach, V.; Faller, R. [Department of Chemical Engineering & Materials Science, University of California, Davis, CA (United States); Renaud, P. [Swiss Federal Institute of Technology, Lausanne, (EPFL) (Switzerland)
2015-08-18
Highlights: • WGA proteins in nanochannels modeled by Molecular Dynamics and Monte Carlo. • Protein surface coverage characterized by atomic force microscopy. • Models indicate transport characteristics depend strongly on surface coverage. • Results resolve of a four orders of magnitude difference in diffusion coefficient values. - Abstract: We use Molecular Dynamics and Monte Carlo simulations to examine molecular transport phenomena in nanochannels, explaining four orders of magnitude difference in wheat germ agglutinin (WGA) protein diffusion rates observed by fluorescence correlation spectroscopy (FCS) and by direct imaging of fluorescently-labeled proteins. We first use the ESPResSo Molecular Dynamics code to estimate the surface transport distance for neutral and charged proteins. We then employ a Monte Carlo model to calculate the paths of protein molecules on surfaces and in the bulk liquid transport medium. Our results show that the transport characteristics depend strongly on the degree of molecular surface coverage. Atomic force microscope characterization of surfaces exposed to WGA proteins for 1000 s show large protein aggregates consistent with the predicted coverage. These calculations and experiments provide useful insight into the details of molecular motion in confined geometries.
Computing the blood brain barrier (BBB) diffusion coefficient: A molecular dynamics approach
Energy Technology Data Exchange (ETDEWEB)
Shamloo, Amir, E-mail: shamloo@sharif.edu; Pedram, Maysam Z.; Heidari, Hossein; Alasty, Aria, E-mail: aalasti@sharif.edu
2016-07-15
Various physical and biological aspects of the Blood Brain Barrier (BBB) structure still remain unfolded. Therefore, among the several mechanisms of drug delivery, only a few have succeeded in breaching this barrier, one of which is the use of Magnetic Nanoparticles (MNPs). However, a quantitative characterization of the BBB permeability is desirable to find an optimal magnetic force-field. In the present study, a molecular model of the BBB is introduced that precisely represents the interactions between MNPs and the membranes of Endothelial Cells (ECs) that form the BBB. Steered Molecular Dynamics (SMD) simulations of the BBB crossing phenomenon have been carried out. Mathematical modeling of the BBB as an input-output system has been considered from a system dynamics modeling viewpoint, enabling us to analyze the BBB behavior based on a robust model. From this model, the force profile required to overcome the barrier has been extracted for a single NP from the SMD simulations at a range of velocities. Using this data a transfer function model has been obtained and the diffusion coefficient is evaluated. This study is a novel approach to bridge the gap between nanoscale models and microscale models of the BBB. The characteristic diffusion coefficient has the nano-scale molecular effects inherent, furthermore reducing the computational costs of a nano-scale simulation model and enabling much more complex studies to be conducted. - Highlights: • Molecular dynamics simulation of crossing nano-particles through the BBB membrane at different velocities. • Recording the position of nano-particle and the membrane-NP interaction force profile. • Identification of a frequency domain model for the membrane. • Calculating the diffusion coefficient based on MD simulation and identified model. • Obtaining a relation between continuum medium and discrete medium.
Dynamical Analysis of a Delayed Reaction-Diffusion Predator-Prey System
Directory of Open Access Journals (Sweden)
Yanuo Zhu
2012-01-01
Full Text Available This work deals with the analysis of a delayed diffusive predator-prey system under Neumann boundary conditions. The dynamics are investigated in terms of the stability of the nonnegative equilibria and the existence of Hopf bifurcation by analyzing the characteristic equations. The direction of Hopf bifurcation and the stability of bifurcating periodic solution are also discussed by employing the normal form theory and the center manifold reduction. Furthermore, we prove that the positive equilibrium is asymptotically stable when the delay is less than a certain critical value and unstable when the delay is greater than the critical value.
Carrier diffusion and higher order transversal modes in spectral dynamics of the semiconductor laser
DEFF Research Database (Denmark)
Buus, Jens; Danielsen, Magnus
1977-01-01
The dynamic and spectral behavior of the semiconductor stripe laser has been investigated. For this purpose the rate equations have been generalized to include several longitudinal and transversal modes, spontaneous emission into the active modes, and position dependence of the electron density...... through a term describing the charge-carrier diffusion in the plane of the active layer. The parameters used for solving these equations are found by theoretical and experimental considerations. The results show a broadening of the spectrum together with a significant content of higher order transversal...
Atlan, Michael; Gross, Michel; Coppey-Moisan, Maite; 10.1364/OL.35.000787
2010-01-01
We developed a microscope intended to probe, using a parallel heterodyne receiver, the fluctuation spectrum of light quasi-elastically scattered by gold nanoparticles diffusing in viscous fluids. The cutoff frequencies of the recorded spectra scale up linearly with those expected from single scattering formalism in a wide range of dynamic viscosities (1 to 15 times water viscosity at room temperature). Our scheme enables ensemble-averaged optical fluctuations measurements over multispeckle recordings in low light, at temporal frequencies up to 10 kHz, with a 12 Hz framerate array detector.
Wang, Shaojie
2016-07-01
Anomalous current pinch, in addition to the anomalous diffusion due to stochastic magnetic perturbations, is theoretically found, which may qualitatively explain the recent DIII-D experiment on resonant magnetic field perturbation. The anomalous current pinch, which may resolve the long-standing issue of seed current in a fully bootstrapped tokamak, is also discussed for the electrostatic turbulence.
Kamerlin, Natasha; Elvingson, Christer
2016-11-01
We have investigated an alternative to the standard periodic boundary conditions for simulating the diffusion of tracer particles in a polymer gel by performing Brownian dynamics simulations using spherical boundary conditions. The gel network is constructed by randomly distributing tetravalent cross-linking nodes and connecting nearest pairs. The final gel structure is characterised by the radial distribution functions, chain lengths and end-to-end distances, and the pore size distribution. We have looked at the diffusion of tracer particles with a wide range of sizes, diffusing in both static and dynamic networks of two different volume fractions. It is quantitatively shown that the dynamical effect of the network becomes more important in facilitating the diffusional transport for larger particle sizes, and that one obtains a finite diffusion also for particle sizes well above the maximum in the pore size distribution.
The role of Frenkel defect diffusion in dynamic annealing in ion-irradiated Si
Wallace, J. B.; Aji, L. B. Bayu; Martin, A. A.; Shin, S. J.; Shao, L.; Kucheyev, S. O.
2017-01-01
The formation of stable radiation damage in crystalline solids often proceeds via complex dynamic annealing processes, involving migration and interaction of ballistically-generated point defects. The dominant dynamic annealing processes, however, remain unknown even for crystalline Si. Here, we use a pulsed ion beam method to study defect dynamics in Si bombarded in the temperature range from −20 to 140 °C with 500 keV Ar ions. Results reveal a defect relaxation time constant of ~10–0.2 ms, which decreases monotonically with increasing temperature. The dynamic annealing rate shows an Arrhenius dependence with two well-defined activation energies of 73 ± 5 meV and 420 ± 10 meV, below and above 60 °C, respectively. Rate theory modeling, bench-marked against this data, suggests a crucial role of both vacancy and interstitial diffusion, with the dynamic annealing rate limited by the migration and interaction of vacancies. PMID:28059109
Interface dynamics of a metastable mass-conserving spatially extended diffusion
Berglund, Nils
2015-01-01
We study the metastable dynamics of a discretised version of the mass-conserving stochastic Allen-Cahn equation. Consider a periodic one-dimensional lattice with $N$ sites, and attach to each site a real-valued variable, which can be interpreted as a spin, as the concentration of one type of metal in an alloy, or as a particle density. Each of these variables is subjected to a local force deriving from a symmetric double-well potential, to a weak ferromagnetic coupling with its nearest neighbours, and to independent white noise. In addition, the dynamics is constrained to have constant total magnetisation or mass. Using tools from the theory of metastable diffusion processes, we show that the long-term dynamics of this system is similar to a Kawasaki-type exchange dynamics, and determine explicit expressions for its transition probabilities. This allows us to describe the system in terms of the dynamics of its interfaces, and to compute an Eyring-Kramers formula for its spectral gap. In particular, we obtain ...
Energy Technology Data Exchange (ETDEWEB)
Dahlstrom, Julie [Carthage College, 2001 Alford Park Dr., Kenosha, WI 53140 (United States); York, Donald G.; Welty, Daniel E.; Oka, Takeshi; Johnson, Sean; Jiang Zihao; Sherman, Reid [University of Chicago, Astronomy and Astrophysics Center, 5640 S. Ellis Avenue, Chicago, IL 60637 (United States); Hobbs, L. M. [University of Chicago, Yerkes Observatory, Williams Bay, WI 53191 (United States); Friedman, Scott D.; Sonnentrucker, Paule [Space Telescope Science Institute, 3700 San Martin Dr., Baltimore, MD 21218 (United States); Rachford, Brian L. [Department of Physics, Embry-Riddle Aeronautical University, 3700 Willow Creek Road, Prescott, AZ 86301 (United States); Snow, Theodore P., E-mail: jdahlstrom1@carthage.edu [University of Colorado, CASA-Campus Box 389, Boulder, CO 80309 (United States)
2013-08-10
Anomalously broad diffuse interstellar bands (DIBs) at 5780.5, 5797.1, 6196.0, and 6613.6 A are found in absorption along the line of sight to Herschel 36, the star illuminating the bright Hourglass region of the H II region Messier 8. Interstellar absorption from excited CH{sup +} in the J = 1 level and from excited CH in the J = 3/2 level is also seen. To our knowledge, neither those excited molecular lines nor such strongly extended DIBs have previously been seen in absorption from interstellar gas. These unusual features appear to arise in a small region near Herschel 36 which contains most of the neutral interstellar material in the sight line. The CH{sup +} and CH in that region are radiatively excited by strong far-IR radiation from the adjacent infrared source Her 36 SE. Similarly, the broadening of the DIBs toward Herschel 36 may be due to radiative pumping of closely spaced high-J rotational levels of relatively small, polar carrier molecules. If this picture of excited rotational states for the DIB carriers is correct and applicable to most DIBs, the 2.7 K cosmic microwave background may set the minimum widths (about 0.35 A) of known DIBs, with molecular processes and/or local radiation fields producing the larger widths found for the broader DIBs. Despite the intense local UV radiation field within the cluster NGC 6530, no previously undetected DIBs stronger than 10 mA in equivalent width are found in the optical spectrum of Herschel 36, suggesting that neither dissociation nor ionization of the carriers of the known DIBs by this intense field creates new carriers with easily detectable DIB-like features. Possibly related profile anomalies for several other DIBs are noted.
Modeling dual-scale epidemic dynamics on complex networks with reaction diffusion processes
Institute of Scientific and Technical Information of China (English)
Xiao-gang JIN; Yong MIN
2014-01-01
The frequent outbreak of severe foodborne diseases (e.g., haemolytic uraemic syndrome and Listeriosis) in 2011 warns of a potential threat that world trade could spread fatal pathogens (e.g., enterohemorrhagic Escherichia coli). The epidemic potential from trade involves both intra-proliferation and inter-diffusion. Here, we present a worldwide vegetable trade network and a stochastic computational model to simulate global trade-mediated epidemics by considering the weighted nodes and edges of the network and the dual-scale dynamics of epidemics. We address two basic issues of network structural impact in global epi-demic patterns:(1) in contrast to the prediction of heterogeneous network models, the broad variability of node degree and edge weights of the vegetable trade network do not determine the threshold of global epidemics;(2) a‘penetration effect’, by which community structures do not restrict propagation at the global scale, quickly facilitates bridging the edges between communities, and leads to synchronized diffusion throughout the entire network. We have also defined an appropriate metric that combines dual-scale behavior and enables quantification of the critical role of bridging edges in disease diffusion from widespread trading. The unusual structure mechanisms of the trade network model may be useful in producing strategies for adaptive immunity and reducing international trade frictions.
Diffusive Heat Transport in Budyko's Energy Balance Climate Model with a Dynamic Ice Line
Walsh, James
2016-01-01
M. Budyko and W. Sellers independently introduced seminal energy balance climate models in 1969, each with a goal of investigating the role played by positive ice albedo feedback in climate dynamics. In this paper we replace the relaxation to the mean horizontal heat transport mechanism used in the models of Budyko and Sellers with diffusive heat transport. We couple the resulting surface temperature equation with an equation for movement of the edge of the ice sheet (called the ice line), recently introduced by E. Widiasih. We apply the spectral method to the temperature-ice line system and consider finite approximations. We prove there exists a stable equilibrium solution with a small ice cap, and an unstable equilibrium solution with a large ice cap, for a range of parameter values. If the diffusive transport is too efficient, however, the small ice cap disappears and an ice free Earth becomes a limiting state. In addition, we analyze a variant of the coupled diffusion equations appropriate as a model for ...
Cluster dynamics modeling of accumulation and diffusion of helium in neutron irradiated tungsten
Energy Technology Data Exchange (ETDEWEB)
Li, Y.G.; Zhou, W.H.; Huang, L.F. [Key Laboratory for Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China); Zeng, Z., E-mail: zzeng@theory.issp.ac.cn [Key Laboratory for Materials Physics, Institute of Solid State Physics, Chinese Academy of Sciences, Hefei 230031 (China); Ju, X. [Department of Physics, University of Science and Technology Beijing, Beijing 100083 (China)
2012-12-15
A cluster dynamics model based on rate theory has been developed to study the accumulation and diffusion processes of helium in tungsten under synergistic effects of helium implantation and neutron irradiation. By including self-interstitial atoms, vacancies and helium atoms as well as their clusters and further using more reliable parameters, the evolution of different types of defects with time and depth is investigated. The calculated results are comparable with experiments. The cases of helium plasma corresponding to the first wall and to the divertor are taken into account. The accumulation and diffusion behaviors of helium in tungsten are illustrated by the time and depth dependence of helium concentration in tungsten with or without the neutron irradiation, the contribution of different types of helium clusters/complexes to helium concentration and the depth profiles of different mobile defects and helium-vacancy complexes. It is concluded that the competition of trapping and diffusion effects dominates the behavior of helium atoms in tungsten for these two typical cases. Understanding these mechanisms is important for estimating damages to the plasma-facing materials.
Multicomponent Diffusion of Penetrant Mixtures in Rubbery Polymers: A Molecular Dynamics Study
Bringuier, Stefan; Varady, Mark; Knox, Craig; Cabalo, Jerry; Pearl, Thomas; Mantooth, Brent
The importance of understanding transport of chemical species across liquid-solid boundaries is of particular interest in the decontamination of harmful chemicals absorbed within polymeric materials. To characterize processes associated with liquid-phase extraction of absorbed species from polymers, it is necessary to determine an appropriate physical description of species transport in multicomponent systems. The Maxwell-Stefan (M-S) formulation is a rigorous description of mass transport in multicomponent solutions, in which, mutual diffusivities determine the degree of relative motion between interacting molecules in response to a chemical potential gradient. The work presented focuses on the determination of M-S diffusivities from molecular dynamics (MD) simulations of nerve agent O-ethyl S-[2(diisopropylamino)ethyl] methylphosphonothioate (VX), water, and methanol mixtures within a poly(dimethylsiloxane) matrix. We investigate the composition dependence of M-S diffusivities and compare the results to values predicted using empirical relations for binary and ternary mixtures. Finally, we highlight the pertinent differences in molecular mechanisms associated with species transport and employ non-equilibrium MD to probe transport across the mixture-polymer interface.
Correlation networks from flows. The case of forced and time-dependent advection-diffusion dynamics
Tupikina, Liubov; López, Cristóbal; Hernández-García, Emilio; Marwan, Norbert; Kurths, Jürgen
2016-01-01
Complex network theory provides an elegant and powerful framework to statistically investigate different types of systems such as society, brain or the structure of local and long-range dynamical interrelationships in the climate system. Network links in climate networks typically imply information, mass or energy exchange. However, the specific connection between oceanic or atmospheric flows and the climate network's structure is still unclear. We propose a theoretical approach for verifying relations between the correlation matrix and the climate network measures, generalizing previous studies and overcoming the restriction to stationary flows. Our methods are developed for correlations of a scalar quantity (temperature, for example) which satisfies an advection-diffusion dynamics in the presence of forcing and dissipation. Our approach reveals that correlation networks are not sensitive to steady sources and sinks and the profound impact of the signal decay rate on the network topology. We illustrate our r...
Zhao, Xinyu; Corn, Brittany; Yu, Ting; 10.1103/PhysRevA.84.032101
2011-01-01
Non-Markovian dynamics is studied for two interacting quibts strongly coupled to a dissipative bosonic environment. For the first time, we have derived the non-Markovian quantum state diffusion (QSD) equation for the coupled two-qubit system without any approximations, and in particular, without the Markov approximation. As an application and illustration of our derived time-local QSD equation, we investigate the temporal behavior of quantum coherence dynamics. In particular, we find a strongly non-Markovian regime where entanglement generation is significantly modulated by the environmental memory. Additionally, we studied the residual entanglement in the steady state by analyzing the steady state solution of the QSD equation. Finally, we have discussed an approximate QSD equation.
The dynamics of nonlinear reaction-diffusion equations with small Lévy noise
Debussche, Arnaud; Imkeller, Peter
2013-01-01
This work considers a small random perturbation of alpha-stable jump type nonlinear reaction-diffusion equations with Dirichlet boundary conditions over an interval. It has two stable points whose domains of attraction meet in a separating manifold with several saddle points. Extending a method developed by Imkeller and Pavlyukevich it proves that in contrast to a Gaussian perturbation, the expected exit and transition times between the domains of attraction depend polynomially on the noise intensity in the small intensity limit. Moreover the solution exhibits metastable behavior: there is a polynomial time scale along which the solution dynamics correspond asymptotically to the dynamic behavior of a finite-state Markov chain switching between the stable states.
Effective reduced diffusion-models: a data driven approach to the analysis of neuronal dynamics.
Directory of Open Access Journals (Sweden)
Gustavo Deco
2009-12-01
Full Text Available We introduce in this paper a new method for reducing neurodynamical data to an effective diffusion equation, either experimentally or using simulations of biophysically detailed models. The dimensionality of the data is first reduced to the first principal component, and then fitted by the stationary solution of a mean-field-like one-dimensional Langevin equation, which describes the motion of a Brownian particle in a potential. The advantage of such description is that the stationary probability density of the dynamical variable can be easily derived. We applied this method to the analysis of cortical network dynamics during up and down states in an anesthetized animal. During deep anesthesia, intracellularly recorded up and down states transitions occurred with high regularity and could not be adequately described by a one-dimensional diffusion equation. Under lighter anesthesia, however, the distributions of the times spent in the up and down states were better fitted by such a model, suggesting a role for noise in determining the time spent in a particular state.
Directory of Open Access Journals (Sweden)
A. Bennia
2016-01-01
Full Text Available In the present work, we are interested to the experimental and numerical study of the free turbulent lobed jet, used in residential heating and air conditioning. The objective of our study is the improvement of the diffusion performance of the ventilation driving air flow, in the occupancy zone. The experiments have been conducted in a room where the dimensions enables a better execution in the conditions of free and hot vertical jet at unfavorable pushing forces. The installation contains a hot air blowing diffuser oriented from top to bottom. The velocities of the flow were measured by a multi-functional thermo-anemometer. The probe is supported by a stem guided vertically and horizontally in order to sweep a maximum space. Experimentally, we measured the axial and radial velocity field. The dynamics field analysis, show that in the potential core region, the dynamic profiles are more spread at the principal plane and this is due to the widening of the lobes’ opening. While, in the transition zone and in the region where the flow is fully developed, these profiles are not influenced by the type of plane and then the jet will be similar to the circular one. Numerically, we used the commercial software Fluent. The obtained numerical results with turbulence method, (RNG k-ε, were in good accordance with the experimental one.
Computing the blood brain barrier (BBB) diffusion coefficient: A molecular dynamics approach
Shamloo, Amir; Pedram, Maysam Z.; Heidari, Hossein; Alasty, Aria
2016-07-01
Various physical and biological aspects of the Blood Brain Barrier (BBB) structure still remain unfolded. Therefore, among the several mechanisms of drug delivery, only a few have succeeded in breaching this barrier, one of which is the use of Magnetic Nanoparticles (MNPs). However, a quantitative characterization of the BBB permeability is desirable to find an optimal magnetic force-field. In the present study, a molecular model of the BBB is introduced that precisely represents the interactions between MNPs and the membranes of Endothelial Cells (ECs) that form the BBB. Steered Molecular Dynamics (SMD) simulations of the BBB crossing phenomenon have been carried out. Mathematical modeling of the BBB as an input-output system has been considered from a system dynamics modeling viewpoint, enabling us to analyze the BBB behavior based on a robust model. From this model, the force profile required to overcome the barrier has been extracted for a single NP from the SMD simulations at a range of velocities. Using this data a transfer function model has been obtained and the diffusion coefficient is evaluated. This study is a novel approach to bridge the gap between nanoscale models and microscale models of the BBB. The characteristic diffusion coefficient has the nano-scale molecular effects inherent, furthermore reducing the computational costs of a nano-scale simulation model and enabling much more complex studies to be conducted.
Molecular dynamics simulation of diffusion of gases in a carbon-nanotube-polymer composite
Lim, Seong Y.; Sahimi, Muhammad; Tsotsis, Theodore T.; Kim, Nayong
2007-07-01
Extensive molecular dynamics (MD) simulations were carried out to compute the solubilities and self-diffusivities of CO2 and CH4 in amorphous polyetherimide (PEI) and mixed-matrix PEI generated by inserting single-walled carbon nanotubes into the polymer. Atomistic models of PEI and its composites were generated using energy minimizations, MD simulations, and the polymer-consistent force field. Two types of polymer composite were generated by inserting (7,0) and (12,0) zigzag carbon nanotubes into the PEI structure. The morphologies of PEI and its composites were characterized by their densities, radial distribution functions, and the accessible free volumes, which were computed with probe molecules of different sizes. The distributions of the cavity volumes were computed using the Voronoi tessellation method. The computed self-diffusivities of the gases in the polymer composites are much larger than those in pure PEI. We find, however, that the increase is not due to diffusion of the gases through the nanotubes which have smooth energy surfaces and, therefore, provide fast transport paths. Instead, the MD simulations indicate a squeezing effect of the nanotubes on the polymer matrix that changes the composite polymers’ free-volume distributions and makes them more sharply peaked. The presence of nanotubes also creates several cavities with large volumes that give rise to larger diffusivities in the polymer composites. This effect is due to the repulsive interactions between the polymer and the nanotubes. The solubilities of the gases in the polymer composites are also larger than those in pure PEI, hence indicating larger gas permeabilities for mixed-matrix PEI than PEI itself.
Ma, Xiao-guang; Lai, Pik-Yin; Ackerson, Bruce J; Tong, Penger
2015-02-14
A tilted two-layer colloidal system is constructed for the study of force-assisted barrier-crossing dynamics over a periodic potential. The periodic potential is provided by the bottom layer colloidal spheres forming a fixed crystalline pattern on a glass substrate. The corrugated surface of the bottom colloidal crystal provides a gravitational potential field for the top layer diffusing particles. By tilting the sample at an angle θ with respect to the vertical (gravity) direction, a tangential component of the gravitational force F is applied to the diffusing particles. The measured mean drift velocity v(F, Eb) and diffusion coefficient D(F, Eb) of the particles as a function of F and energy barrier height Eb agree well with the exact results of the one-dimensional drift velocity (R. L. Stratonovich, Radiotekh. Elektron, 1958, 3, 497) and diffusion coefficient (P. Reimann, et al., Phys. Rev. Lett., 2001, 87, 010602 and P. Reimann, et al., Phys. Rev. E, 2002, 65, 031104). Based on these exact results, we show analytically and verify experimentally that there exists a scaling region, in which v(F, Eb) and D(F, Eb) both scale as ν'(F)exp[-E(F)/kBT], where the Arrhenius pre-factor ν'(F) and effective barrier height E(F) are both modified by F. The experiment demonstrates the applications of this model system in evaluating different scaling forms of ν'(F) and E(F) and their accuracy, in order to extract useful information about the external potential, such as the intrinsic barrier height Eb.
Yemloul, Mehdi; Steiner, Emilie; Robert, Anthony; Bouguet-Bonnet, Sabine; Allix, Florent; Jamart-Grégoire, Brigitte; Canet, Daniel
2011-03-24
An organogelation process depends on the gelator-solvent pair. This study deals with the solvent dynamics once the gelation process is completed. The first approach used is relaxometry, i.e., the measurement of toluene proton longitudinal relaxation time T(1) as a function of the proton NMR resonance frequency (here in the 5 kHz to 400 MHz range). Pure toluene exhibits an unexpected T(1) variation, which has been identified as paramagnetic relaxation resulting from an interaction of toluene with dissolved oxygen. In the gel phase, this contribution is retrieved with, in addition, a strong decay at low frequencies assigned to toluene molecules within the gel fibers. Comparison of dispersion curves of pure toluene and toluene in the gel phase leads to an estimate of the proportion of toluene embedded within the organogel (found around 40%). The second approach is based on carbon-13 T(1) and nuclear Overhauser effect measurements, the combination of these two parameters providing direct information about the reorientation of C-H bonds. It appears clearly that reorientation of toluene is the same in pure liquid and in the gel phase. The only noticeable changes in carbon-13 longitudinal relaxation times are due to the so-called chemical shift anisotropy (csa) mechanism and reflect slight modifications of the toluene electronic distribution in the gel phase. NMR diffusion measurements by the pulse gradient spin-echo (PGSE) method allow us to determine the diffusion coefficient of toluene inside the organogel. It is roughly two-thirds of the one in pure toluene, thus indicating that self-diffusion is the only dynamical parameter to be slightly affected when the solvent is inside the gel structure. The whole set of experimental observations leads to the conclusion that, once the gel is formed, the solvent becomes essentially passive, although an important fraction is located within the gel structure.
Diffusion within α-CuI studied using ab initio molecular dynamics simulations
Mohn, Chris E.; Stølen, Svein; Hull, Stephen
2009-08-01
The structure and dynamics of superionic α-CuI are studied in detail by means of ab initio Born-Oppenheimer molecular dynamics simulations. The extreme cation disorder and a soft immobile face centred cubic sublattice are evident from the highly diffuse atomic density profiles. The Cu-Cu pair distribution function and distribution of Cu-I-Cu bond angles possess distinct peaks at 2.6 Å and 60° respectively, which are markedly lower than the values expected from the average cationic density, pointing to the presence of pronounced short-range copper-copper correlations. Comparison with lattice static calculations shows that these correlations and the marked shift in the cationic density profile in the lang111rang directions are associated with a locally distorted cation sublattice, and that the movements within the tetrahedral cavities involve rapid jumps into and out of shallow basins on the system potential energy surface. On average, the iodines are surrounded by three coppers within their first coordination shell, with the fourth copper being located in a transition zone between two neighbouring iodine cavities. However, time-resolved analysis reveals that the local structure actually involves a mixture of threefold-, fourfold- and fivefold-coordinated iodines. Examination of the ionic trajectories shows that the copper ions jump rapidly to nearest neighbouring tetrahedral cavities (aligned in the lang100rang directions) following a markedly curved trajectory and often involving short-lived (~1 ps) interstitial positions. The nature of the correlated diffusion underlying the unusually high fraction of coppers with short residence time can be attributed to the presence of a large number of 'unsuccessful' jumps and the likelihood of cooperative motion of pairs of coppers. The calculated diffusion coefficient at 750 K, DCu = 2.8 × 10-5 cm2 s-1, is in excellent agreement with that found experimentally.
Dynamics of a thin film flowing down a heated wall with finite thermal diffusivity
Dallaston, Michael C.; Tseluiko, Dmitri; Kalliadasis, Serafim
2016-11-01
Consider the dynamics of a thin film flowing down a heated substrate. The substrate heating generates a temperature distribution on the free surface, which in turn induces surface-tension gradients and corresponding thermocapillary stresses that affect the free surface and therefore the fluid flow. We study here the effect of finite substrate thermal diffusivity on the film dynamics. Linear stability analysis of the full Navier-Stokes and heat transport equations indicates if the substrate diffusivity is sufficiently small, the film becomes unstable at a finite wavelength and at a Reynolds number smaller than that predicted in the long-wavelength limit. This property is captured in a reduced-order system of equations derived using a weighted-residual integral-boundary-layer method. This reduced-order model is also used to compute the bifurcation diagrams of solution branches connecting the trivial flat film to traveling waves including solitary pulses. The effect of finite diffusivity is to separate a simultaneous Hopf-transcritical bifurcation into its individual component bifurcations. The appropriate Hopf bifurcation then connects only to the solution branch of negative-hump pulses, with wave speed less than the linear wave speed, while the branch of positive-single-hump pulses merges with the branch of positive-two-hump pulses at a supercritical Reynolds number. In the regime where finite-wavelength instability occurs, there exists a Hopf-bifurcation pair connected by a branch of periodic solutions, whose period cannot be increased indefinitely. Numerical simulation of the reduced-order system shows the development of a train of coherent structures, each of which resembles a stationary positive-hump pulse, and, in the regime of finite-wavelength instability, wavelength selection and saturation to periodic traveling waves.
Data mining of molecular dynamics data reveals Li diffusion characteristics in garnet Li7La3Zr2O12
Chen, Chi; Lu, Ziheng; Ciucci, Francesco
2017-01-01
Understanding Li diffusion in solid conductors is essential for the next generation Li batteries. Here we show that density-based clustering of the trajectories computed using molecular dynamics simulations helps elucidate the Li diffusion mechanism within the Li7La3Zr2O12 (LLZO) crystal lattice. This unsupervised learning method recognizes lattice sites, is able to give the site type, and can identify Li hopping events. Results show that, while the cubic LLZO has a much higher hopping rate compared to its tetragonal counterpart, most of the Li hops in the cubic LLZO do not contribute to the diffusivity due to the dominance of back-and-forth type jumps. The hopping analysis and local Li configuration statistics give evidence that Li diffusivity in cubic LLZO is limited by the low vacancy concentration. The hopping statistics also shows uncorrelated Poisson-like diffusion for Li in the cubic LLZO, and correlated diffusion for Li in the tetragonal LLZO in the temporal scale. Further analysis of the spatio-temporal correlation using site-to-site mutual information confirms the weak site dependence of Li diffusion in the cubic LLZO as the origin for the uncorrelated diffusion. This work puts forward a perspective on combining machine learning and information theory to interpret results of molecular dynamics simulations.
Data mining of molecular dynamics data reveals Li diffusion characteristics in garnet Li7La3Zr2O12
Chen, Chi; Lu, Ziheng; Ciucci, Francesco
2017-01-01
Understanding Li diffusion in solid conductors is essential for the next generation Li batteries. Here we show that density-based clustering of the trajectories computed using molecular dynamics simulations helps elucidate the Li diffusion mechanism within the Li7La3Zr2O12 (LLZO) crystal lattice. This unsupervised learning method recognizes lattice sites, is able to give the site type, and can identify Li hopping events. Results show that, while the cubic LLZO has a much higher hopping rate compared to its tetragonal counterpart, most of the Li hops in the cubic LLZO do not contribute to the diffusivity due to the dominance of back-and-forth type jumps. The hopping analysis and local Li configuration statistics give evidence that Li diffusivity in cubic LLZO is limited by the low vacancy concentration. The hopping statistics also shows uncorrelated Poisson-like diffusion for Li in the cubic LLZO, and correlated diffusion for Li in the tetragonal LLZO in the temporal scale. Further analysis of the spatio-temporal correlation using site-to-site mutual information confirms the weak site dependence of Li diffusion in the cubic LLZO as the origin for the uncorrelated diffusion. This work puts forward a perspective on combining machine learning and information theory to interpret results of molecular dynamics simulations. PMID:28094317
Non-Brownian diffusion in lipid membranes: Experiments and simulations.
Metzler, R; Jeon, J-H; Cherstvy, A G
2016-10-01
The dynamics of constituents and the surface response of cellular membranes-also in connection to the binding of various particles and macromolecules to the membrane-are still a matter of controversy in the membrane biophysics community, particularly with respect to crowded membranes of living biological cells. We here put into perspective recent single particle tracking experiments in the plasma membranes of living cells and supercomputing studies of lipid bilayer model membranes with and without protein crowding. Special emphasis is put on the observation of anomalous, non-Brownian diffusion of both lipid molecules and proteins embedded in the lipid bilayer. While single component, pure lipid bilayers in simulations exhibit only transient anomalous diffusion of lipid molecules on nanosecond time scales, the persistence of anomalous diffusion becomes significantly longer ranged on the addition of disorder-through the addition of cholesterol or proteins-and on passing of the membrane lipids to the gel phase. Concurrently, experiments demonstrate the anomalous diffusion of membrane embedded proteins up to macroscopic time scales in the minute time range. Particular emphasis will be put on the physical character of the anomalous diffusion, in particular, the occurrence of ageing observed in the experiments-the effective diffusivity of the measured particles is a decreasing function of time. Moreover, we present results for the time dependent local scaling exponent of the mean squared displacement of the monitored particles. Recent results finding deviations from the commonly assumed Gaussian diffusion patterns in protein crowded membranes are reported. The properties of the displacement autocorrelation function of the lipid molecules are discussed in the light of their appropriate physical anomalous diffusion models, both for non-crowded and crowded membranes. In the last part of this review we address the upcoming field of membrane distortion by elongated membrane
Distributed-order diffusion equations and multifractality: Models and solutions
Sandev, Trifce; Chechkin, Aleksei V.; Korabel, Nickolay; Kantz, Holger; Sokolov, Igor M.; Metzler, Ralf
2015-10-01
We study distributed-order time fractional diffusion equations characterized by multifractal memory kernels, in contrast to the simple power-law kernel of common time fractional diffusion equations. Based on the physical approach to anomalous diffusion provided by the seminal Scher-Montroll-Weiss continuous time random walk, we analyze both natural and modified-form distributed-order time fractional diffusion equations and compare the two approaches. The mean squared displacement is obtained and its limiting behavior analyzed. We derive the connection between the Wiener process, described by the conventional Langevin equation and the dynamics encoded by the distributed-order time fractional diffusion equation in terms of a generalized subordination of time. A detailed analysis of the multifractal properties of distributed-order diffusion equations is provided.
Gaspari, Roberto; Rapallo, Arnaldo
2008-06-28
In this work a new method is proposed for the choice of basis functions in diffusion theory (DT) calculations. This method, named hybrid basis approach (HBA), combines the two previously adopted long time sorting procedure (LTSP) and maximum correlation approximation (MCA) techniques; the first emphasizing contributions from the long time dynamics, the latter being based on the local correlations along the chain. In order to fulfill this task, the HBA procedure employs a first order basis set corresponding to a high order MCA one and generates upper order approximations according to LTSP. A test of the method is made first on a melt of cis-1,4-polyisoprene decamers where HBA and LTSP are compared in terms of efficiency. Both convergence properties and numerical stability are improved by the use of the HBA basis set whose performance is evaluated on local dynamics, by computing the correlation times of selected bond vectors along the chain, and on global ones, through the eigenvalues of the diffusion operator L. Further use of the DT with a HBA basis set has been made on a 71-mer of syndiotactic trans-1,2-polypentadiene in toluene solution, whose dynamical properties have been computed with a high order calculation and compared to the "numerical experiment" provided by the molecular dynamics (MD) simulation in explicit solvent. The necessary equilibrium averages have been obtained by a vacuum trajectory of the chain where solvent effects on conformational properties have been reproduced with a proper screening of the nonbonded interactions, corresponding to a definite value of the mean radius of gyration of the polymer in vacuum. Results show a very good agreement between DT calculations and the MD numerical experiment. This suggests a further use of DT methods with the necessary input quantities obtained by the only knowledge of some experimental values, i.e., the mean radius of gyration of the chain and the viscosity of the solution, and by a suitable vacuum
DEFF Research Database (Denmark)
Tian, Yihui; Govindan, Kannan; Zhu, Qinghua
2014-01-01
In this study, a system dynamics (SD) model is developed to guide the subsidy policies to promote the diffusion of green supply chain management (GSCM) in China. The relationships of stakeholders such as government, enterprises and consumers are analyzed through evolutionary game theory. Finally......, the GSCM diffusion process is simulated by the model with a case study on Chinese automotive manufacturing industry. The results show that the subsidies for manufacturers are better than that for consumers to promote GSCM diffusion, and the environmental awareness is another influential key factor. © 2014...
Energy Technology Data Exchange (ETDEWEB)
Gaspersic, Natasa [University Medical Centre, Department of Rheumatology, Ljubljana (Slovenia); Sersa, Igor [Jozef Stefan Institute, Ljubljana (Slovenia); Jevtic, Vladimir [Medical Faculty, Department of Radiology, Ljubljana (Slovenia); Tomsic, Matija; Praprotnik, Sonja [University Medical Centre, Department of Rheumatology, Ljubljana (Slovenia)
2008-02-15
The effects of different therapies on enthesitis/osteitis in active ankylosing spondylitis (AS) were evaluated by magnetic resonance imaging (MRI). The aim was to assess the role of quantitative MRI in the evaluation of AS treatment efficacy. Thirty patients with active spondylitis or bilateral sacroilitis were selected and followed up for 1 year. Ten of the patients were treated only with non-steroidal anti-inflammatory drugs, 10 patients additionally received at baseline an intravenous pulse of glucocorticoids and 10 patients were treated with regular infusions of infliximab. Disease activity was measured according to clinical instruments and laboratory tests. For each patient, one selected inflamed lesion was followed from baseline through control visits quantitatively by diffusion-weighted imaging (DWI) measuring the apparent diffusion coefficient (ADC) and by dynamic contrast-enhanced imaging (DCEI) with evaluation of the enhancement factor (f{sub enh}) and enhancement gradient (g{sub enh}). Clinical and quantitative MRI parameters diminished significantly with regression of the inflammatory activity. The improvement in AS was most pronounced in patients treated with infliximab; after 12 months the ADC diminished from an average of 1.31 to 0.88 x 10{sup -3} mm{sup 2}/s, f{sub enh} from 1.85 to 0.60, and g{sub enh} from 3.09 to 1.40 %/s. Diffusion-weighted imaging and DCEI were shown to be effective in quantifying changes in inflammation in skeletal lesions during the treatment of AS, and could therefore be convenient for assessing treatment efficacy. To the best of our knowledge this is the first time DWI was used to evaluate the activity of skeletal inflammation in rheumatic diseases such as AS. (orig.)
Structure, hydrolysis, and diffusion of aqueous vanadium ions from Car-Parrinello molecular dynamics
Jiang, Zhen; Klyukin, Konstantin; Alexandrov, Vitaly
2016-09-01
A molecular level understanding of the properties of electroactive vanadium species in aqueous solution is crucial for enhancing the performance of vanadium redox flow batteries. Here, we employ Car-Parrinello molecular dynamics simulations based on density functional theory to investigate the hydration structures, first hydrolysis reaction, and diffusion of aqueous V2+, V3+, VO2+, and VO 2+ ions at 300 K. The results indicate that the first hydration shell of both V2+ and V3+ contains six water molecules, while VO2+ is coordinated to five and VO 2+ to three water ligands. The first acidity constants (pKa) estimated using metadynamics simulations are 2.47, 3.06, and 5.38 for aqueous V3+, VO 2+ , and VO2+, respectively, while V2+ is predicted to be a fairly weak acid in aqueous solution with a pKa value of 6.22. We also show that the presence of chloride ions in the first coordination sphere of the aqueous VO 2+ ion has a significant impact on water hydrolysis leading to a much higher pKa value of 4.8. This should result in a lower propensity of aqueous VO 2+ for oxide precipitation reaction in agreement with experimental observations for chloride-based electrolyte solutions. The computed diffusion coefficients of vanadium species in water at room temperature are found to increase as V 3 + < VO 2 + < V O 2 + < V 2 + and thus correlate with the simulated hydrolysis constants, namely, the higher the pKa value, the greater the diffusion coefficient.
Anomalous transport from holography: Part II
Bu, Yanyan; Sharon, Amir
2016-01-01
This is a second study of chiral anomaly induced transport within a holographic model consisting of anomalous $U(1)_V\\times U(1)_A$ Maxwell theory in Schwarzschild-$AdS_5$ spacetime. In the first part, chiral magnetic/separation effects (CME/CSE) are considered in presence of a static spatially-inhomogeneous external magnetic field. Gradient corrections to CME/CSE are analytically evaluated up to third order in the derivative expansion. Some of the third order gradient corrections lead to an anomaly-induced negative $B^2$-correction to the diffusion constant. We also find non-linear modifications to the chiral magnetic wave (CMW). In the second part, we focus on the experimentally interesting case of the axial chemical potential being induced dynamically by a constant magnetic and time-dependent electric fields. Constitutive relations for the vector/axial currents are computed employing two different approximations: (a) derivative expansion (up to third order) but fully nonlinear in the external fields, and (...
Energy Technology Data Exchange (ETDEWEB)
Bhatia, Harsh [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gyulassy, Attila [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ong, Mitchell [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Lordi, Vincenzo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Draeger, Erik [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pask, John [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Pascucci, Valerio [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Bremer, Peer -Timo [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2016-09-27
The performance of lithium-ion batteries is strongly influenced by the ionic conductivity of the electrolyte, which depends on the speed at which Li ions migrate across the cell and relates to their solvation structure. The choice of solvent can greatly impact, both, the solvation and diffusivity of Li ions. In this work, we present our application of the topological techniques to extract and predict such behavior in the data generated by the first-principles molecular dynamics simulation of Li ions in an important organic solvent -ethylene carbonate. More specifically, we use the scalar topology of the electron charge density field to analyze the evolution of the solvation structures. This allows us to derive a parameter-free bond definition for lithium-oxygen bonds, to provide a quantitative measure for bond strength, and to understand the regions of influence of each atom in the simulation. This has provided new insights into how and under what conditions certain bonds may form and break. As a result, we can identify and, more importantly, predict, unstable configurations in solvation structures. This can be very useful in understanding when small changes to the atoms' movements can cause significantly different bond structures to evolve. Ultimately, this promises to allow scientists to explore lithium ion solvation and diffusion more systematically, with the aim of new insights and potentially accelerating the calculations themselves.
Molecular Dynamics Simulations Reveal that Water Diffusion between Graphene Oxide Layers is Slow
Devanathan, Ram; Chase-Woods, Dylan; Shin, Yongsoon; Gotthold, David W.
2016-07-01
Membranes made of stacked layers of graphene oxide (GO) hold the tantalizing promise of revolutionizing desalination and water filtration if selective transport of molecules can be controlled. We present the findings of an integrated study that combines experiment and molecular dynamics simulation of water intercalated between GO layers. We simulated a range of hydration levels from 1 wt.% to 23.3 wt.% water. The interlayer spacing increased upon hydration from 0.8 nm to 1.1 nm. We also synthesized GO membranes that showed an increase in layer spacing from about 0.7 nm to 0.8 nm and an increase in mass of about 15% on hydration. Water diffusion through GO layers is an order of magnitude slower than that in bulk water, because of strong hydrogen bonded interactions. Most of the water molecules are bound to OH groups even at the highest hydration level. We observed large water clusters that could span graphitic regions, oxidized regions and holes that have been experimentally observed in GO. Slow interlayer diffusion can be consistent with experimentally observed water transport in GO if holes lead to a shorter path length than previously assumed and sorption serves as a key rate-limiting step.
Indirect Prediction of Welding Fume Diffusion inside a Room Using Computational Fluid Dynamics
Directory of Open Access Journals (Sweden)
Sujit Dahal
2016-05-01
Full Text Available Welding is an important and widely used process in the manufacturing and maintenance of various works involving metals and alloys. While welding has broad applications, the welding fume generated during the process has impacts on workers’ health, which needs to be addressed. One of the major steps that can be undertaken to take care of this issue is the use of ventilation, which requires knowledge of characteristics and dispersion of the welding fume in the workers’ breathing zone. It is difficult to assess welding fume dispersion from manual measurement due to numerous welding processes and sufficient data requirement. Numerical prediction of welding fume is dubious due to several errors. This paper considers the use of numerically predicted CO2 concentrations to indirectly predict welding fume distribution in workshops. This is based on the assumption that if the particles are sufficiently small size, they follow the diffusion pattern of gases. Experiments are carried out in a room with an opening and a welding fume generation system for measurement of CO2 and fume diffusion. The results show high possibility of predicting welding fume concentration based on Computational Fluid Dynamics (CFD simulated CO2 concentration with a correlation coefficient of 0.74.
Rapid exploration of configuration space with diffusion-map-directed molecular dynamics.
Zheng, Wenwei; Rohrdanz, Mary A; Clementi, Cecilia
2013-10-24
The gap between the time scale of interesting behavior in macromolecular systems and that which our computational resources can afford often limits molecular dynamics (MD) from understanding experimental results and predicting what is inaccessible in experiments. In this paper, we introduce a new sampling scheme, named diffusion-map-directed MD (DM-d-MD), to rapidly explore molecular configuration space. The method uses a diffusion map to guide MD on the fly. DM-d-MD can be combined with other methods to reconstruct the equilibrium free energy, and here, we used umbrella sampling as an example. We present results from two systems: alanine dipeptide and alanine-12. In both systems, we gain tremendous speedup with respect to standard MD both in exploring the configuration space and reconstructing the equilibrium distribution. In particular, we obtain 3 orders of magnitude of speedup over standard MD in the exploration of the configurational space of alanine-12 at 300 K with DM-d-MD. The method is reaction coordinate free and minimally dependent on a priori knowledge of the system. We expect wide applications of DM-d-MD to other macromolecular systems in which equilibrium sampling is not affordable by standard MD.
Testing a Dynamical Equilibrium Model of the Extraplanar Diffuse Ionized Gas in NGC 891
Boettcher, Erin; Gallagher, J S; Benjamin, Robert A
2016-01-01
The observed scale heights of extraplanar diffuse ionized gas (eDIG) layers exceed their thermal scale heights by a factor of a few in the Milky Way and other nearby edge-on disk galaxies. Here, we test a dynamical equilibrium model of the extraplanar diffuse ionized gas layer in NGC 891, where we ask whether the thermal, turbulent, magnetic field, and cosmic ray pressure gradients are sufficient to support the layer. In optical emission line spectroscopy from the SparsePak integral field unit on the WIYN 3.5-meter telescope, the H-alpha emission in position-velocity space suggests that the eDIG is found in a ring between galactocentric radii of R_min = 2 kpc. We find that the thermal (sigma_th = 11 km/s) and turbulent (sigma_turb = 25 km/s) velocity dispersions are insufficient to satisfy the hydrostatic equilibrium equation given an exponential electron scale height of h_z = 1.0 kpc. Using a literature analysis of radio continuum observations from the CHANG-ES survey, we demonstrate that the magnetic field ...
On the dynamics of flame edges in diffusion-flame/vortex interactions
Energy Technology Data Exchange (ETDEWEB)
Hermanns, Miguel; Linan, Amable [Departamento de Motopropulsion y Termofluidodinamica, Universidad Politecnica de Madrid, Pza. Cardenal Cisneros 3, 28040 Madrid (Spain); Vera, Marcos [Area de Mecanica de Fluidos, Universidad Carlos III de Madrid, 28911 Leganes (Spain)
2007-04-15
We analyze the local flame extinction and reignition of a counterflow diffusion flame perturbed by a laminar vortex ring. Local flame extinction leads to the appearance of flame edges separating the burning and extinguished regions of the distorted mixing layer. The dynamics of these edges is modeled based on previous numerical results, with heat release effects fully taken into account, which provide the propagation velocity of triple and edge flames in terms of the upstream unperturbed value of the scalar dissipation. The temporal evolution of the mixing layer is determined using the classical mixture fraction approach, with both unsteady and curvature effects taken into account. Although variable density effects play an important role in exothermic reacting mixing layers, in this paper the description of the mixing layer is carried out using the constant density approximation, leading to a simplified analytical description of the flow field. The mathematical model reveals the relevant nondimensional parameters governing diffusion-flame/vortex interactions and provides the parameter range for the more relevant regime of local flame extinction followed by reignition via flame edges. Despite the simplicity of the model, the results show very good agreement with previously published experimental results. (author)
Chalub, Fabio A C C
2008-01-01
We study the large population limit of the Moran process, assuming weak-selection, and for different scalings. Depending on the particular choice of scalings, we obtain a continuous model that may highlight the genetic-drift (neutral evolution) or natural selection; for one precise scaling, both effects are present. For the scalings that take the genetic-drift into account, the continuous model is given by a singular diffusion equation, together with two conservation laws that are already present at the discrete level. For scalings that take into account only natural selection, we obtain a hyperbolic singular equation that embeds the Replicator Dynamics and satisfies only one conservation law. The derivation is made in two steps: a formal one, where the candidate limit model is obtained, and a rigorous one, where convergence of the probability density is proved. Additional results on the fixation probabilities are also presented.
A strong diffusive ion mode in dense ionized matter predicted by Langevin dynamics.
Mabey, P; Richardson, S; White, T G; Fletcher, L B; Glenzer, S H; Hartley, N J; Vorberger, J; Gericke, D O; Gregori, G
2017-01-30
The state and evolution of planets, brown dwarfs and neutron star crusts is determined by the properties of dense and compressed matter. Due to the inherent difficulties in modelling strongly coupled plasmas, however, current predictions of transport coefficients differ by orders of magnitude. Collective modes are a prominent feature, whose spectra may serve as an important tool to validate theoretical predictions for dense matter. With recent advances in free electron laser technology, X-rays with small enough bandwidth have become available, allowing the investigation of the low-frequency ion modes in dense matter. Here, we present numerical predictions for these ion modes and demonstrate significant changes to their strength and dispersion if dissipative processes are included by Langevin dynamics. Notably, a strong diffusive mode around zero frequency arises, which is not present, or much weaker, in standard simulations. Our results have profound consequences in the interpretation of transport coefficients in dense plasmas.
Faster is More Different: Mean-Field Dynamics of Innovation Diffusion
Baek, Seung Ki; Kim, Mina
2013-01-01
Based on a recent model of paradigm shifts by Bornholdt et al., we studied mean-field opinion dynamics in an infinite population where an infinite number of ideas compete simultaneously with their values publicly known. We found that a highly innovative society is not characterized by heavy concentration in highly valued ideas: Rather, ideas are more broadly distributed in a more innovative society with faster progress, provided that the rate of adoption is constant, which suggests a positive correlation between innovation and technological disparity. Furthermore, the distribution is generally skewed in such a way that the fraction of innovators is substantially smaller than has been believed in conventional innovation-diffusion theory based on normality. Thus, the typical adoption pattern is predicted to be asymmetric with slow saturation in the ideal situation, which is compared with empirical data sets.
Experimental measurement of non-Markovian dynamics and self-diffusion in a strongly coupled plasma
Strickler, T S; McQuillen, P; Daligault, J; Killian, T C
2015-01-01
We present a study of the collisional relaxation of ion velocities in a strongly coupled, ultracold neutral plasma on short timescales compared to the inverse collision rate. Non-exponential decay towards equilibrium for the average velocity of a tagged population of ions heralds non-Markovian dynamics and a breakdown of assumptions underlying standard kinetic theory. We prove the equivalence of the average-velocity curve to the velocity autocorrelation function, a fundamental statistical quantity that provides access to equilibrium transport coefficients and aspects of individual particle trajectories in a regime where experimental measurements have been lacking. From our data, we calculate the ion self-diffusion constant. This demonstrates the utility of ultracold neutral plasmas for isolating the effects of strong coupling on collisional processes, which is of interest for dense laboratory and astrophysical plasmas.
Faster is more different: mean-field dynamics of innovation diffusion.
Directory of Open Access Journals (Sweden)
Seung Ki Baek
Full Text Available Based on a recent model of paradigm shifts by Bornholdt et al., we studied mean-field opinion dynamics in an infinite population where an infinite number of ideas compete simultaneously with their values publicly known. We found that a highly innovative society is not characterized by heavy concentration in highly valued ideas: Rather, ideas are more broadly distributed in a more innovative society with faster progress, provided that the rate of adoption is constant, which suggests a positive correlation between innovation and technological disparity. Furthermore, the distribution is generally skewed in such a way that the fraction of innovators is substantially smaller than has been believed in conventional innovation-diffusion theory based on normality. Thus, the typical adoption pattern is predicted to be asymmetric with slow saturation in the ideal situation, which is compared with empirical data sets.
Institute of Scientific and Technical Information of China (English)
Chuanming; Wang; Bowei; Li; Yangdong; Wang; Zaiku; Xie
2013-01-01
Selectivity control is a difficult scientific and industrial challenge in methanol-to-olefins(MTO)conversion.It has been experimentally established that the topology of zeolite catalysts influenced the distribution of products.Besides the topology effect on reaction kinetics,the topology influences the diffusion of reactants and products in catalysts as well.In this work,by using COMPASS force-field molecular dynamics method,we investigated the intracrystalline diffusion of ethene and propene in four different zeolites,CHA,MFI,BEA and FAU,at different temperatures.The self-diffusion coefficients and diffusion activation barriers were calculated.A strong restriction on the diffusion of propene in CHA was observed because the self-diffusion coefficient ratio of ethene to propene is larger than 18 and the diffusion activation barrier of propene is more than 20 kJ/mol in CHA.This ratio decreases with the increase of temperature in the four investigated zeolites.The shape selectivity on products from diffusion perspective can provide some implications on the understanding of the selectivity difference between HSAPO-34 and HZSM-5 catalysts for the MTO conversion.
Anomalous Transport Foundations and Applications
Klages, Rainer; Sokolov, Igor M
2008-01-01
This multi-author reference work provides a unique introduction to the currently emerging, highly interdisciplinary field of those transport processes that cannot be described by using standard methods of statistical mechanics. It comprehensively summarizes topics ranging from mathematical foundations of anomalous dynamics to the most recent experiments in this field. In so doing, this monograph extracts and emphasizes common principles and methods from many different disciplines while providing up-to-date coverage of this new field of research, considering such diverse applications as plasma
Three types of anomalous nickel-iron magnetic films characterized by hysteresigraph and torque-magnetometer measurements; bitter-pattern observations; reprint from ’ Journal of Applied Physics .’
Social Dynamics Shaping the Diffusion of Sustainable Aquaculture Innovations in the Solomon Islands
Directory of Open Access Journals (Sweden)
Jessica Blythe
2017-01-01
Full Text Available Sustainably feeding the world’s growing population represents one of our most significant challenges. Aquaculture is well positioned to make contributions towards this challenge. Yet, the translation of aquaculture production innovations into benefits for rural communities is constrained by a limited understanding of the social dynamics that influence the adoption of new agricultural practices. In this paper, we investigate the factors that shape the spread of small-scale tilapia aquaculture through rural Solomon Islands. Based on diffusion of innovation theory, we focus on three potentially influential factors: (i socio-economic characteristics of adopters; (ii the role of opinion leaders; and (iii characteristics of the innovation. We find that farmers who were wealthier, older, and had more diverse livelihoods were most likely to be adopters. Opinion leaders facilitated the adoption of tilapia aquaculture, but lacked the capacity to provide fundamental knowledge necessary to realize its potential benefits to food security. The paper argues for more explicit attention to the poorest households and makes the case for a deeper engagement with the broader social and institutional contexts that shape the adoption process. Aquaculture interventions that account for these social dynamics are critical for translating production innovations into sustainable benefits to rural communities.
Turbulent structure and dynamics of swirled, strongly pulsed jet diffusion flames
Liao, Ying-Hao
2013-11-02
The structure and dynamics of swirled, strongly pulsed, turbulent jet diffusion flames were examined experimentally in a co-flow swirl combustor. The dynamics of the large-scale flame structures, including variations in flame dimensions, the degree of turbulent flame puff interaction, and the turbulent flame puff celerity were determined from high-speed imaging of the luminous flame. All of the tests presented here were conducted with a fixed fuel injection velocity at a Reynolds number of 5000. The flame dimensions were generally found to be more impacted by swirl for the cases of longer injection time and faster co-flow flow rate. Flames with swirl exhibited a flame length up to 34% shorter compared to nonswirled flames. Both the turbulent flame puff separation and the flame puff celerity generally decreased when swirl was imposed. The decreased flame length, flame puff separation, and flame puff celerity are consistent with a greater momentum exchange between the flame and the surrounding co-flow, resulting from an increased rate of air entrainment due to swirl. Three scaling relations were developed to account for the impact of the injection time, the volumetric fuel-to-air flow rate ratio, and the jet-on fraction on the visible flame length. © 2013 Copyright Taylor and Francis Group, LLC.
Institute of Scientific and Technical Information of China (English)
WANGChunhong; XUMingcheng; 等
2000-01-01
The adsorption dynamics for phenol in aqueous solution of the adsorbent based on polystyrene was studied.In order to distinguish with the Boyd quasi-homogeneous model of the inner structure of ion-exchanger,the particle diffusion model including surface diffustion model and porediffusion model was suggested which is suitable to the macroporous adsorbent.The diffusiondetermination step of the adsorption pocess was established and the effective diffusion coefficient was also determined.The influence of surface diffusion and pore difusion on the particle diffusion rate was investigated qualitatively.All of these were very important to improve the structure of the macroporous adsorbent in order to improve the mass-transfer rate.
Martelloni, Gianluca; Guarino, Alessio
2016-01-01
We present a three-dimensional model, based on cohesive spherical particles, of rain-induced landslides. The rainwater infiltration into the soil follow the either the fractional or the fractal diffusion equations. We solve analytically the fractal diffusion partial differential equation (PDE) with particular boundary conditions to simulate a rainfall event. Then, for the PDE, we developed a numerical integration scheme that we integrate with MD (Molecular Dynamics) algorithm for the triggering and propagation of the simulated landslide. Therefore we test the numerical integration scheme of fractal diffusion equation with the analytical solution. We adopt the fractal diffusion equation in term of gravimetric water content that we use as input of triggering scheme based on Mohr-Coulomb limit-equilibrium criterion, adapted to particle level. Moreover, taking into account an interacting force Lennard-Jones inspired, we use a standard MD algorithm to update particle positions and velocities. Then we present resul...
Institute of Scientific and Technical Information of China (English)
LI Junbai; YIN Rui; MA Rongjiu; Shen Jiacong
1992-01-01
The technique of dynamic light scattering has been used to investigate the translation diffusion behavior of 8-arm star polystyrene (SPS)in a good solvent, tetrahydrofuran (THF) or benzene (BZ)and a theta solvent, cyclohexane (CH), by homodyne photon correlation spectroscopy .The intensityintensity autocorrelation function was analyzed by the method of cumulant. The translation diffusion coefficients have been obtained as a function of temperature and concentration. Under theta condition ,the non-concentration dependence of diffusion coefficient showed the unperturbed Gaussian state of the SPS molecular chain. The different hydrodynamic radii estimated from Stokes-Einstein equation reflected the stretch extent of the arm chain for regular star polymer. The data of diffusion activation energy of SPS in THF, BZ and CH were also obtained respectively.
Zhao, Qian; Burns, Susan E
2013-03-19
Organoclays are highly sorptive engineered materials that can be used as amendments in barrier systems or geosynthetic liners. The performance of confining and isolating the nonpolar organic contaminants by those barrier/lining systems is essentially controlled by the process of organic contaminant mass transport in nanopores of organoclays. In this article, we use molecular dynamics (MD) simulations to study the sorption and diffusion of organic sorbates in interlayers of sodium montmorillonite and hexadecyltrimethylammonium (HDTMA(+))-modified montmorillonite clays. Simulated system consisted of the clay framework, interlayer organic cation, water, and organic sorbate. Their interactions were addressed by the combined force field of ClayFF, constant-valence force field, and SPC water model. Simulation results indicated that in HDTMA coated clay nanopores, diffusion of nonpolar species benzene was slowed because they were subjected to influence of both the pore wall and the HDTMA surfactant. This suggested the nonpolar organic compound diffusion in organophilic clays can be affected by molecular size of diffusive species, clay pore size, and organic surfactant loading. Additionally, a model that connected the diffusion rate of organic compounds in the bulk organoclay matrix with macropores and nanopores was established. The impact of intercalated organic cations on the diffusion dominated mass transport of organic compounds yielded insight into the prediction of the apparent diffusion behavior of organic compounds in organic-modified clays.
Direct observation of the spatial and temporal dynamics of polaron diffusion in SrTiO3
Kohmoto, T.; Ikeda, D.; Liang, X.; Moriyasu, T.
2013-06-01
The generation, relaxation, and diffusion dynamics of optically induced lattice distortion in the relaxed excited state of SrTiO3 are studied by using polarization spectroscopy with the pump-probe technique. The relaxed excited state is generated with a rise time on the order of 100 ps. Three kinds of thermal activation processes of the localized lattice distortion are found, and these processes are considered to be caused by photogenerated carriers in trapped states, which play important roles in photoluminescence or photoconductivity. We observed the lattice distortion induced by a separated pump beam from the probe beam to investigate its itineracy. The lattice-distortion signal appears later as the separation along the [100] axis becomes larger. The temperature dependence of the mobility suggests that the observed diffusive lattice distortion is caused by photogenerated electrons accompanied by lattice distortion, or electron polarons. Thus, the spatial and temporal dynamics of polaron diffusion were observed directly in our experiment.
Mercure, J -F; Foley, A M; Chewpreecha, U; Pollitt, H
2013-01-01
This paper presents an analysis of possible uses of climate policy instruments for the decarbonisation of the global electricity sector in a non-equilibrium economic and technology innovation-diffusion perspective. Emissions reductions occur through changes in technology and energy consumption; in this context, investment decision-making opportunities occur periodically, which energy policy can incentivise in order to transform energy systems and meet reductions targets. Energy markets are driven by innovation, dynamic costs and technology diffusion; yet, the incumbent systems optimisation methodology in energy modelling does not address these aspects nor the effectiveness of policy onto decision-making since the dynamics modelled take their source from the top-down `social-planner' assumption. This leads to an underestimation of strong technology lock-ins in cost-optimal scenarios of technology. Our approach explores the global diffusion of low carbon technology in connection to a highly disaggregated sector...
DEFF Research Database (Denmark)
Hansen, Flemming Yssing; Criswell, L.; Fuhrmann, D;
2004-01-01
Molecular dynamics simulations of a tetracosane (n-C24H50) monolayer adsorbed on a graphite basal-plane surface show that there are diffusive motions associated with the creation and annihilation of gauche defects occurring on a time scale of similar to0.1-4 ns. We present evidence that these rel...
Qin, C.
2015-01-01
The pore-scale modeling is a powerful tool for increasing our understanding of water transport in the fibrous gas diffusion layer (GDL) of a polymer electrolyte fuel cell (PEFC). In this work, a new dynamic pore-network model for air-water flow in the GDL is developed. It incorporates water vapor tr
Anomalous drift of spiral waves in heterogeneous excitable media
Sridhar, S; Panfilov, Alexander V
2009-01-01
We study the drift of spiral waves in a simple model of heterogeneous excitable medium, having gradients in local excitability or cellular coupling. For the first time, we report the anomalous drift of spiral waves towards regions having higher excitability, in contrast to all earlier observations in reaction-diffusion models of excitable media. Such anomalous drift can promote the onset of complex spatio-temporal patterns, e.g., those responsible for life-threatening arrhythmias in the heart.
Gui-Jun, Cheng; Bao-Qin, Fu; Qing, Hou; Xiao-Song, Zhou; Jun, Wang
2016-07-01
The microstructures of titanium (Ti), an attractive tritium (T) storage material, will affect the evolution process of the retained helium (He). Understanding the diffusion behavior of He at the atomic scale is crucial for the mechanism of material degradation. The novel diffusion behavior of He has been reported by molecular dynamics (MD) simulation for the bulk hcp-Ti system and the system with grain boundary (GB). It is observed that the diffusion of He in the bulk hcp-Ti is significantly anisotropic (the diffusion coefficient of the [0001] direction is higher than that of the basal plane), as represented by the different migration energies. Different from convention, the GB accelerates the diffusion of He in one direction but not in the other. It is observed that a twin boundary (TB) can serve as an effective trapped region for He. The TB accelerates diffusion of He in the direction perpendicular to the twinning direction (TD), while it decelerates the diffusion in the TD. This finding is attributable to the change of diffusion path caused by the distortion of the local favorable site for He and the change of its number in the TB region. Project supported by the National Natural Science Foundation of China (Grant No. 51501119), the Scientific Research Starting Foundation for Younger Teachers of Sichuan University, China (Grant No. 2015SCU11058), the National Magnetic Confinement Fusion Science Program of China (Grant No. 2013GB109002), and the Cooperative Research Project “Research of Diffusion Behaviour of He in Grain Boundary of HCP-Titanium”, China.
Coarse-grained molecular dynamics simulation of water diffusion in the presence of carbon nanotubes.
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.
ReaDDy--a software for particle-based reaction-diffusion dynamics in crowded cellular environments.
Directory of Open Access Journals (Sweden)
Johannes Schöneberg
Full Text Available We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics.
Energy Technology Data Exchange (ETDEWEB)
Tsili, Athina C., E-mail: a_tsili@yahoo.gr [Department of Radiology, Medical School, University of Ioannina, 45110 Ioannina (Greece); Sylakos, Anastasios, E-mail: anasylakos@yahoo.gr [Department of Urology, Medical School, University of Ioannina, 45110 Ioannina (Greece); Ntorkou, Alexandra, E-mail: alexdorkou@yahoo.com [Department of Radiology, Medical School, University of Ioannina, 45110 Ioannina (Greece); Stavrou, Sotirios, E-mail: s.sotiris@yahoo.gr [Department of Urology, Medical School, University of Ioannina, 45110 Ioannina (Greece); Astrakas, Loukas G., E-mail: astrakas@uoi.gr [Department of Medical Physics, Medical School, University of Ioannina, 45110 Ioannina (Greece); Sofikitis, Nikolaos, E-mail: akrosnin@hotmail.com [Department of Urology, Medical School, University of Ioannina, 45110 Ioannina (Greece); Argyropoulou, Maria I., E-mail: margyrop@cc.uoi.gr [Department of Radiology, Medical School, University of Ioannina, 45110 Ioannina (Greece)
2015-07-15
Highlights: • Functional MRI in the characterization of testicular germ cell tumors was assessed. • ADC values proved useful in the characterization of testicular germ cell tumors. • Testicular germ cell tumors had similar enhancement patterns of dynamic MRI. - Abstract: Introduction: The aim of this study is to investigate the role of apparent diffusion coefficient (ADC) values and dynamic contrast enhancement (DCE) patterns in differentiating seminomas from nonseminomatous germ cell tumors (NSGCTs). Materials and methods: The MRI examinations of the scrotum of 26 men with histologically proven testicular GCTs were reviewed. DWI was performed in all patients, using a single shot, multi-slice spin-echo planar diffusion pulse sequence and b-values of 0 and 900 s/mm{sup 2}. Subtraction DCE-MRI was performed in 20 cases using a 3D fast-field echo sequence after gadolinium administration. Time-signal intensity curves were created and semi-quantitative parameters (peak enhancement, time to peak, wash-in and wash-out rate) were calculated. The Student's t-test was used to compare the mean values of ADC, peak enhancement, time to peak, wash-in and wash-out rate between seminomas and NSGCTs. ROC analysis was also performed. Results: Histopathology disclosed the presence of 15 seminomas and 11 NSGCTs. The mean ± s.d. of ADC values (× 10{sup −3} mm{sup 2}/s) of seminomas (0.59 ± 0.009) were significantly lower than those of NSGCTs (0.90 ± 0.33) (P = 0.01). The optimal ADC cut-off value was 0.68 × 10{sup −3} mm{sup 2}/s. No differences between the two groups were observed for peak enhancement (P = 0.18), time to peak (P = 0.63) wash-in rate (P = 0.32) and wash-out rate (P = 0.18). Conclusions: ADC values may be used to preoperatively differentiate seminomas from NSGCTs.
Collective dynamics and self-diffusion in a diblock copolymer melt in the body-centered cubic phase.
Papadakis, C M; Rittig, F; Almdal, K; Mortensen, K; Stĕpánek, P
2004-12-01
The structure and dynamics of a strongly asymmetric poly(ethylene propylene)-poly(dimethylsiloxane) (PEP-PDMS) diblock copolymer in the melt have been studied over a wide temperature range. Small-angle neutron scattering reveals that the sample exhibits two stable phases in this temperature range: Above the order-to-disorder transition temperature, it is disordered, whereas the domain structure is body-centered cubic (bcc) below, being stable down to the lowest temperatures measured. In the disordered state, dynamic light scattering (DLS) in the polarized geometry reveals the heterogeneity mode and the cluster mode. In the bcc phase, the PEP and the PDMS blocks form the micellar cores and the matrix, respectively. Here, two modes are observed in DLS, and the diffusion coefficients measured using pulsed field gradient (PFG) NMR are broadly distributed with the most probable diffusion coefficient coinciding with the slow DLS mode. We attribute the fast process in the bcc state to concentration fluctuations of the micellar cores (PEP), relaxing by mutual diffusion of the micelles with copolymers dissolved in the PDMS matrix. The slower process in the bcc state is ascribed to activated long-range self-diffusion of single copolymers from micelle to micelle through the PDMS matrix. This assignment is corroborated by the good coincidence of the reduced diffusivities with the ones from the literature. However, this mode may also be assigned to the rearrangement of entire micelles.
Anomalous mass dimension in multiflavor QCD
Doff, A.; Natale, A. A.
2016-10-01
Models of strongly interacting theories with a large mass anomalous dimension (γm) provide an interesting possibility for the dynamical origin of the electroweak symmetry breaking. A laboratory for these models is QCD with many flavors, which may present a nontrivial fixed point associated to a conformal region. Studies based on conformal field theories and on Schwinger-Dyson equations have suggested the existence of bounds on the mass anomalous dimension at the fixed points of these models. In this note we discuss γm values of multiflavor QCD exhibiting a nontrivial fixed point and affected by relevant four-fermion interactions.
Diffusion of Biomass Pyrolysis Products in H-ZSM-5 by Molecular Dynamics Simulations
Energy Technology Data Exchange (ETDEWEB)
Bu, Lintao; Nimlos, Mark R.; Robichaud, David J.; Kim, Seonah
2017-01-12
Diffusion of biomass pyrolysis vapors and their upgraded products is an essential catalytic property of zeolites during catalytic fast pyrolysis and likely plays a critical role in the selectivity of these catalysts. Characterizing the diffusivities of representative biofuel molecules is critical to understand shape selectivity and interpret product distribution. Yet, experimental measurements on the diffusivities of oxygenated biofuel molecules at pyrolysis temperatures are very limited in the literature. As an alternative approach, we conducted MD simulations to measure the diffusion coefficients of several selected molecules that are representative of biomass pyrolysis vapors, namely water, methanol, glycolaldehyde, and toluene in H-ZSM-5 zeolite. The results show the diffusion coefficients calculated via MD simulations are consistent with available NMR measurements at room temperature. The effect of molecular weight and molecular critical diameter on the diffusivity among the chosen model compounds is also examined. Furthermore, we have characterized the diffusivities of representative biofuel molecules, namely xylene isomers, in H-ZSM-5. Our calculations determined that the ratio of the diffusion coefficients for xylene isomers is p-xylene:o-xylene:m-xylene almost equal to 83:3:1 at 700 K. Additionally, our results also demonstrate the different diffusivity between p-xylene and toluene is due to the molecular orientations when the molecules diffuse along the channels in H-ZSM-5 and provide deep insight into the effect of molecular orientation on its diffusivity.
Fast recovery of free energy landscapes via diffusion-map-directed molecular dynamics.
Preto, Jordane; Clementi, Cecilia
2014-09-28
The reaction pathways characterizing macromolecular systems of biological interest are associated with high free energy barriers. Resorting to the standard all-atom molecular dynamics (MD) to explore such critical regions may be inappropriate as the time needed to observe the relevant transitions can be remarkably long. In this paper, we present a new method called Extended Diffusion-Map-directed Molecular Dynamics (extended DM-d-MD) used to enhance the sampling of MD trajectories in such a way as to rapidly cover all important regions of the free energy landscape including deep metastable states and critical transition paths. Moreover, extended DM-d-MD was combined with a reweighting scheme enabling to save on-the-fly information about the Boltzmann distribution. Our algorithm was successfully applied to two systems, alanine dipeptide and alanine-12. Due to the enhanced sampling, the Boltzmann distribution is recovered much faster than in plain MD simulations. For alanine dipeptide, we report a speedup of one order of magnitude with respect to plain MD simulations. For alanine-12, our algorithm allows us to highlight all important unfolded basins in several days of computation when one single misfolded event is barely observable within the same amount of computational time by plain MD simulations. Our method is reaction coordinate free, shows little dependence on the a priori knowledge of the system, and can be implemented in such a way that the biased steps are not computationally expensive with respect to MD simulations thus making our approach well adapted for larger complex systems from which little information is known.
Energy Technology Data Exchange (ETDEWEB)
Bourg, I.C.; Sposito, G.
2007-05-25
Despite their great importance in low-temperaturegeochemistry, self-diffusion coefficients of noble gas isotopes in liquidwater (D) have been measured only for the major isotopes of helium, neon,krypton and xenon. Data on the self-diffusion coefficients of minor noblegas isotopes are essentially non-existent and so typically are estimatedby a kinetic theory model in which D varies as the inverse square root ofthe isotopic mass (m): D proportional to m-0.5. To examine the validityof the kinetic theory model, we performed molecular dynamics (MD)simulations of the diffusion of noble gases in ambient liquid water withan accurate set of noble gas-water interaction potentials. Our simulationresults agree with available experimental data on the solvation structureand self-diffusion coefficients of the major noble gas isotopes in liquidwater and reveal for the first time that the isotopic mass-dependence ofall noble gas self-diffusion coefficients has the power-law form Dproportional to m-beta with 0
Muller, Christian; Zienicke, Egbert; Adams, Stefan; Habasaki, Junko; Maass, Philipp
2006-01-01
Based on molecular dynamics simulations of a lithium metasilicate glass we study the potential of bond valence sum calculations to identify sites and diffusion pathways of mobile Li ions in a glassy silicate network. We find that the bond valence method is not well suitable to locate the sites, but allows one to estimate the number of sites. Spatial regions of the glass determined as accessible for the Li ions by the bond valence method can capture up to 90% of the diffusion path. These regio...
Structure, hydrolysis and diffusion of aqueous vanadium ions from Car-Parrinello molecular dynamics
Jiang, Zhen; Alexandrov, Vitaly
2016-01-01
A molecular level understanding of the properties of electroactive vanadium species in aqueous solution is crucial for enhancing the performance of vanadium redox flow batteries (RFB). Here, we employ Car-Parrinello molecular dynamics (CPMD) simulations based on density functional theory to investigate the hydration structures, first hydrolysis reaction and diffusion of aqueous V$^{2+}$, V$^{3+}$, VO$^{2+}$, and VO$_2^+$ ions at 300 K. The results indicate that the first hydration shell of both V$^{2+}$ and V$^{3+}$ contains six water molecules, while VO$^{2+}$ is coordinated to five and VO$_2^+$ to three water ligands. The first acidity constants (p$K_\\mathrm{a}$) estimated using metadynamics simulations are 2.47, 3.06 and 5.38 for aqueous V$^{3+}$, VO$_2^+$ and VO$^{2+}$, respectively, while V$^{2+}$ is predicted to be a fairly weak acid in aqueous solution with a p$K_\\mathrm{a}$ value of 6.22. We also show that the presence of chloride ions in the first coordination sphere of the aqueous VO$_2^+$ ion has a...
Optimal Analysis Method for Dynamic Contrast-Enhanced Diffuse Optical Tomography
Directory of Open Access Journals (Sweden)
Michael Ghijsen
2011-01-01
Full Text Available Diffuse Optical Tomography (DOT is an optical imaging modality that has various clinical applications. However, the spatial resolution and quantitative accuracy of DOT is poor due to strong photon scatting in biological tissue. Structural a priori information from another high spatial resolution imaging modality such as Magnetic Resonance Imaging (MRI has been demonstrated to significantly improve DOT accuracy. In addition, a contrast agent can be used to obtain differential absorption images of the lesion by using dynamic contrast enhanced DOT (DCE-DOT. This produces a relative absorption map that consists of subtracting a reconstructed baseline image from reconstructed images in which optical contrast is included. In this study, we investigated and compared different reconstruction methods and analysis approaches for regular endogenous DOT and DCE-DOT with and without MR anatomical a priori information for arbitrarily-shaped objects. Our phantom and animal studies have shown that superior image quality and higher accuracy can be achieved using DCE-DOT together with MR structural a priori information. Hence, implementation of a combined MRI-DOT system to image ICG enhancement can potentially be a promising tool for breast cancer imaging.
Po, Giacomo; Ghoniem, Nasr
2014-05-01
We present a formulation of the discrete Dislocation Dynamics (DD) method based on Onsager's variational principle. The motion of discrete dislocations is treated as a generalized irreversible flux associated with conjugate thermodynamic forces causing internal production of entropy. Intrinsic in the variational principle is the role of physical constraints that limit the choice of generalized fluxes. We leverage the concept of constrained maximization to introduce the requirement that dislocation climb must be sustained by the flux of vacancies into the dislocation core. The constrained variational approach results naturally in the coupling between plastic deformation induced by discrete dislocations, vacancy diffusion, and heat propagation in solid crystals. In particular, this coupling requires that dislocation velocity and chemical potential of vacancies at the dislocation core be found simultaneously. A new numerical formulation of DD that accounts for generalized constraints imposed on dislocations is presented, based on a network discretization of the dislocation configuration. Applications illustrate the significance of constrained motion of dislocations confined in channels and pillars, and the attainment of heterogeneous dislocation structures.
ON THE SOURCE OF ASTROMETRIC ANOMALOUS REFRACTION
Energy Technology Data Exchange (ETDEWEB)
Taylor, M. Suzanne [Department of Natural and Environmental Sciences, Western State Colorado University, 128 Hurst Hall, Gunnison, CO 81230 (United States); McGraw, John T.; Zimmer, Peter C. [Department of Physics and Astronomy, University of New Mexico, MSC07 4220, Albuquerque, NM 87131 (United States); Pier, Jeffrey R., E-mail: mstaylor@western.edu [Division of Astronomical Sciences, NSF 4201 Wilson Blvd, Arlington, VA 22230 (United States)
2013-03-15
More than a century ago, astronomers using transit telescopes to determine precise stellar positions were hampered by an unexplained periodic shifting of the stars they were observing. With the advent of CCD transit telescopes in the past three decades, this unexplained motion, termed 'anomalous refraction' by these early astronomers, is again being observed. Anomalous refraction is described as a low-frequency, large angular scale ({approx}2 Degree-Sign ) motion of the entire image plane with respect to the celestial coordinate system as observed and defined by astrometric catalogs. These motions, of typically several tenths of an arcsecond amplitude with timescales on the order of 10 minutes, are ubiquitous to ground-based drift-scan astrometric measurements regardless of location or telescopes used and have been attributed to the effect of tilting of equal-density layers of the atmosphere. The cause of this tilting has often been attributed to atmospheric gravity waves, but this cause has never been confirmed. Although theoretical models of atmospheric refraction show that atmospheric gravity waves are a plausible cause of anomalous refraction, an observational campaign specifically directed at defining this relationship provides clear evidence that anomalous refraction is not consistent with the passage of atmospheric gravity waves. The source of anomalous refraction is found to be meter-scale, slowly evolving quasi-coherent dynamical structures in the boundary layer below 60 m above ground level.
On the Source of Astrometric Anomalous Refraction
Taylor, M. Suzanne; McGraw, John T.; Zimmer, Peter C.; Pier, Jeffrey R.
2013-03-01
More than a century ago, astronomers using transit telescopes to determine precise stellar positions were hampered by an unexplained periodic shifting of the stars they were observing. With the advent of CCD transit telescopes in the past three decades, this unexplained motion, termed "anomalous refraction" by these early astronomers, is again being observed. Anomalous refraction is described as a low-frequency, large angular scale (~2°) motion of the entire image plane with respect to the celestial coordinate system as observed and defined by astrometric catalogs. These motions, of typically several tenths of an arcsecond amplitude with timescales on the order of 10 minutes, are ubiquitous to ground-based drift-scan astrometric measurements regardless of location or telescopes used and have been attributed to the effect of tilting of equal-density layers of the atmosphere. The cause of this tilting has often been attributed to atmospheric gravity waves, but this cause has never been confirmed. Although theoretical models of atmospheric refraction show that atmospheric gravity waves are a plausible cause of anomalous refraction, an observational campaign specifically directed at defining this relationship provides clear evidence that anomalous refraction is not consistent with the passage of atmospheric gravity waves. The source of anomalous refraction is found to be meter-scale, slowly evolving quasi-coherent dynamical structures in the boundary layer below 60 m above ground level.
Anomalous chiral superfluidity
Energy Technology Data Exchange (ETDEWEB)
Lublinsky, Michael, E-mail: lublinsky@phys.uconn.ed [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794 (United States); Physics Department, Ben-Gurion University, Beer Sheva 84105 (Israel); Zahed, Ismail [Department of Physics and Astronomy, Stony Brook University, Stony Brook, NY 11794 (United States)
2010-02-08
We discuss both the anomalous Cartan currents and the energy-momentum tensor in a left chiral theory with flavor anomalies as an effective theory for flavored chiral phonons in a chiral superfluid with the gauged Wess-Zumino-Witten term. In the mean-field (leading tadpole) approximation the anomalous Cartan currents and the energy-momentum tensor take the form of constitutive currents in the chiral superfluid state. The pertinence of higher order corrections and the Adler-Bardeen theorem is briefly noted.
Oberthuer, Dominik; Melero-García, Emilio; Dierks, Karsten; Meyer, Arne; Betzel, Christian; Garcia-Caballero, Alfonso; Gavira, Jose A
2012-01-01
In this paper, we demonstrate the feasibility of using in situ Dynamic Light Scattering (DLS) to monitor counter-diffusion crystallization experiments in capillaries. Firstly, we have validated the quality of the DLS signal in thin capillaries, which is comparable to that obtained in standard quartz cuvettes. Then, we have carried out DLS measurements of a counter-diffusion crystallization experiment of glucose isomerase in capillaries of different diameters (0.1, 0.2 and 0.3 mm) in order to follow the temporal evolution of protein supersaturation. Finally, we have compared DLS data with optical recordings of the progression of the crystallization front and with a simulation model of counter-diffusion in 1D.
Anomalous pion decay revisited
Battistel, O A; Nemes, M C; Hiller, B
1999-01-01
An implicit four dimensional regularization is applied to calculate the axial-vector-vector anomalous amplitude. The present technique always complies with results of Dimensional Regularization and can be easily applied to processes involving odd numbers of $\\gamma_5$ matrices. This is illustrated explicitely in the example of this letter.
Dolag, K; Borgani, S
2009-01-01
Member galaxies within galaxy clusters nowadays can be routinely identified in cosmological, hydrodynamical simulations using methods based on identifying self bound, locally over dense substructures. However, distinguishing the central galaxy from the stellar diffuse component within clusters is notoriously difficult, and in the center it is not even clear if two distinct stellar populations exist. Here, after subtracting all member galaxies, we use the velocity distribution of the remaining stars and detect two dynamically, well-distinct stellar components within simulated galaxy clusters. These differences in the dynamics can be used to apply an un-binding procedure which leads to a spatial separation of the two components into a cD and a diffuse stellar component (DSC). Applying our new algorithm to a cosmological, hydrodynamical simulation we find that -- in line with previous studies -- these two components have clearly distinguished spatial and velocity distributions as well as different star formation...
Mezzasalma, Stefano A
2007-03-15
The theoretical basis of a recent theory of Brownian relativity for polymer solutions is deepened and reexamined. After the problem of relative diffusion in polymer solutions is addressed, its two postulates are formulated in all generality. The former builds a statistical equivalence between (uncorrelated) timelike and shapelike reference frames, that is, among dynamical trajectories of liquid molecules and static configurations of polymer chains. The latter defines the "diffusive horizon" as the invariant quantity to work with in the special version of the theory. Particularly, the concept of universality in polymer physics corresponds in Brownian relativity to that of covariance in the Einstein formulation. Here, a "universal" law consists of a privileged observation, performed from the laboratory rest frame and agreeing with any diffusive reference system. From the joint lack of covariance and simultaneity implied by the Brownian Lorentz-Poincaré transforms, a relative uncertainty arises, in a certain analogy with quantum mechanics. It is driven by the difference between local diffusion coefficients in the liquid solution. The same transformation class can be used to infer Fick's second law of diffusion, playing here the role of a gauge invariance preserving covariance of the spacetime increments. An overall, noteworthy conclusion emerging from this view concerns the statistics of (i) static macromolecular configurations and (ii) the motion of liquid molecules, which would be much more related than expected.
Anomalous properties and the liquid-liquid phase transition in gallium
Li, Renzhong; Sun, Gang; Xu, Limei
2016-08-01
A group of materials including water and silicon exhibit many anomalous behaviors, e.g., density anomaly and diffusivity anomaly (increase upon compression). These materials are hypothesized to have a liquid-liquid phase transition (LLPT) and the critical fluctuation in the vicinity of the liquid-liquid critical point is considered as the origin of different anomalies. Liquid gallium was also reported to have a LLPT, yet whether it shows similar water-like anomalies is not yet studied. Using molecular dynamics simulations on a modified embedded-atom model, we study the thermodynamic, dynamic, and structural properties of liquid gallium as well as its LLPT. We find that, similar to water-like materials predicted to have the LLPT, gallium also shows different anomalous behaviors (e.g., density anomaly, diffusivity anomaly, and structural anomaly). We also find that its thermodynamic and structural response functions are continuous and show maxima in the supercritical region, the loci of which asymptotically approach to the other and merge to the Widom line. These phenomena are consistent with the supercritical phenomenon in a category of materials with a liquid-liquid critical point, which could be common features in most materials with a LLPT.
Bayoumi, Maged Fouad
2014-10-06
Single-molecule localization and tracking has been used to translate spatiotemporal information of individual molecules to map their diffusion behaviours. However, accurate analysis of diffusion behaviours and including other parameters, such as the conformation and size of molecules, remain as limitations to the method. Here, we report a method that addresses the limitations of existing single-molecular localization methods. The method is based on temporal tracking of the cumulative area occupied by molecules. These temporal fluctuations are tied to molecular size, rates of diffusion and conformational changes. By analysing fluorescent nanospheres and double-stranded DNA molecules of different lengths and topological forms, we demonstrate that our cumulative-area method surpasses the conventional single-molecule localization method in terms of the accuracy of determined diffusion coefficients. Furthermore, the cumulative-area method provides conformational relaxation times of structurally flexible chains along with diffusion coefficients, which together are relevant to work in a wide spectrum of scientific fields.
Sanghi, T; Aluru, N R
2013-03-28
In this work, we combine our earlier proposed empirical potential based quasi-continuum theory, (EQT) [A. V. Raghunathan, J. H. Park, and N. R. Aluru, J. Chem. Phys. 127, 174701 (2007)], which is a coarse-grained multiscale framework to predict the static structure of confined fluids, with a phenomenological Langevin equation to simulate the dynamics of confined fluids in thermal equilibrium. An attractive feature of this approach is that all the input parameters to the Langevin equation (mean force profile of the confined fluid and the static friction coefficient) can be determined using the outputs of the EQT and the self-diffusivity data of the corresponding bulk fluid. The potential of mean force profile, which is a direct output from EQT is used to compute the mean force profile of the confined fluid. The density profile, which is also a direct output from EQT, along with the self-diffusivity data of the bulk fluid is used to determine the static friction coefficient of the confined fluid. We use this approach to compute the mean square displacement and survival probabilities of some important fluids such as carbon-dioxide, water, and Lennard-Jones argon confined inside slit pores. The predictions from the model are compared with those obtained using molecular dynamics simulations. This approach of combining EQT with a phenomenological Langevin equation provides a mathematically simple and computationally efficient means to study the impact of structural inhomogeneity on the self-diffusion dynamics of confined fluids.
Anomalous diffraction in hyperbolic materials
Alberucci, Alessandro; Boardman, Allan D; Assanto, Gaetano
2016-01-01
We demonstrate that light is subject to anomalous (i.e., negative) diffraction when propagating in the presence of hyperbolic dispersion. We show that light propagation in hyperbolic media resembles the dynamics of a quantum particle of negative mass moving in a two-dimensional potential. The negative effective mass implies time reversal if the medium is homogeneous. Such property paves the way to diffraction compensation, spatial analogue of dispersion compensating fibers in the temporal domain. At variance with materials exhibiting standard elliptic dispersion, in inhomogeneous hyperbolic materials light waves are pulled towards regions with a lower refractive index. In the presence of a Kerr-like optical response, bright (dark) solitons are supported by a negative (positive) nonlinearity.
Anomalous diffraction in hyperbolic materials
Alberucci, Alessandro; Jisha, Chandroth P.; Boardman, Allan D.; Assanto, Gaetano
2016-09-01
We demonstrate that light is subject to anomalous (i.e., negative) diffraction when propagating in the presence of hyperbolic dispersion. We show that light propagation in hyperbolic media resembles the dynamics of a quantum particle of negative mass moving in a two-dimensional potential. The negative effective mass implies time reversal if the medium is homogeneous. Such property paves the way to diffraction compensation, i.e., spatial analog of dispersion compensating fibers in the temporal domain. At variance with materials exhibiting standard elliptic dispersion, in inhomogeneous hyperbolic materials light waves are pulled towards regions with a lower refractive index. In the presence of a Kerr-like optical response, bright (dark) solitons are supported by a negative (positive) nonlinearity.
Reithmann, Emanuel; Frey, Erwin
2016-01-01
Diffusive motion of regulatory enzymes on biopolymers with eventual capture at a reaction site is a common feature in cell biology. Using a lattice gas model we study the impact of diffusion and capture for a microtubule polymerase and a depolymerase. Our results show that the capture mechanism localizes the proteins and creates large-scale spatial correlations. We develop an analytic approximation that globally accounts for relevant correlations and yields results that are in excellent agreement with experimental data. Our results show that diffusion and capture operates most efficiently at cellular enzyme concentrations which points to in vivo relevance.
Ryabov, Yaroslav; Clore, G Marius; Schwieters, Charles D
2012-01-21
We present a general formalism for the computation of orientation correlation functions involving a molecular system undergoing rotational diffusion in the presence of transitions between discrete conformational states. In this formalism, there are no proscriptions on the time scales of conformational rearrangement relative to that for rotational diffusion, and the rotational diffusion tensors of the different states can be completely arbitrary. Although closed-form results are limited to the frequency domain, this is generally useful for many spectroscopic observables as the result allows the computation of the spectral density function. We specialize the results for the computation of the frequency-domain correlation function associated with the NMR relaxation.
Ansari, Rafat R.; Suh, Kwang I.; Sebag, J.
2006-02-01
PURPOSE: Pharmacologic vitreolysis is a new approach to improve vitreo-retinal surgery. Ultimately, the development of drugs to liquefy and detach vitreous from retina should prevent disease by mitigating the contribution of vitreous to retinopathy and eliminate the need for surgery. However, the mechanism of action of pharmacologic vitreolysis remains unclear. The technique of Dynamic light scattering (DLS) was used to evaluate the effects of microplasmin by following the diffusion coefficients of spherical polystyrene nano-particles injected with microplasmin into the vitreous. METHODS: Diffusion coefficients in dissected (n=9) porcine eyes were measured in vitro. DLS was performed on all specimens at 37°C as often as every 10 minutes for up to 6 hours following injections of human recombinant microplasmin at doses ranging from 0.125 mg to 0.8 mg, with 20 nm diameter tracer nanospheres. RESULTS: DLS findings in untreated porcine vitreous were similar to the previously described findings in bovine and human vitreous, demonstrating a fast (early) component, resulting from the flexible hyaluronan molecules, and a slow (late) component, resulting form the stiff collagen molecules. Microplasmin increased porcine vitreous diffusion coefficients. A new approach was developed to use DLS measurements of vitreous diffusion coefficients to evaluate the effects of microplasmin in intact eyes. CONCLUSIONS: Pharmacologic vitreolysis with human recombinant microplasmin increases vitreous diffusion coefficients in vitro. The results of these studies indicate that this new approach using DLS to measure vitreous diffusion coefficients can be used to study the effects of pharmacologic vitreolysis using microplasmin and other agents in intact eyes and ultimately in vivo.
Dynamics of the connectome in Huntington's disease : A longitudinal diffusion MRI study
Odish, Omar F F; Caeyenberghs, Karen; Hosseini, Hadi; Van Den Bogaard, Simon J A; Roos, Raymund A C; Leemans, A
2015-01-01
Abstract Objectives To longitudinally investigate the connectome in different stages of Huntington's disease (HD) by applying graph theoretical analysis to diffusion MRI data. Experimental design We constructed weighted structural networks and calculated their topological properties. Twenty-two prem
Gallium surface diffusion on GaAs (001) surfaces measured by crystallization dynamics of Ga droplets
Energy Technology Data Exchange (ETDEWEB)
Bietti, Sergio, E-mail: sergio.bietti@mater.unimib.it; Somaschini, Claudio; Esposito, Luca; Sanguinetti, Stefano [L–NESS and Dipartimento di Scienza dei Materiali, Università di Milano Bicocca, Via Cozzi 55, I–20125 Milano (Italy); Fedorov, Alexey [L–NESS and CNR–IFN, via Anzani 42, I-22100 Como (Italy)
2014-09-21
We present accurate measurements of Ga cation surface diffusion on GaAs surfaces. The measurement method relies on atomic force microscopy measurement of the morphology of nano–disks that evolve, under group V supply, from nanoscale group III droplets, earlier deposited on the substrate surface. The dependence of the radius of such nano-droplets on crystallization conditions gives direct access to Ga diffusion length. We found an activation energy for Ga on GaAs(001) diffusion E{sub A}=1.31±0.15 eV, a diffusivity prefactor of D₀=0.53(×2.1±1) cm² s⁻¹ that we compare with the values present in literature. The obtained results permit to better understand the fundamental physics governing the motion of group III ad–atoms on III–V crystal surfaces and the fabrication of designable nanostructures.
Self-consistent molecular dynamics calculation of diffusion in higher n-alkanes
Kondratyuk, Nikolay D.; Norman, Genri E.; Stegailov, Vladimir V.
2016-11-01
Diffusion is one of the key subjects of molecular modeling and simulation studies. However, there is an unresolved lack of consistency between Einstein-Smoluchowski (E-S) and Green-Kubo (G-K) methods for diffusion coefficient calculations in systems of complex molecules. In this paper, we analyze this problem for the case of liquid n-triacontane. The non-conventional long-time tails of the velocity autocorrelation function (VACF) are found for this system. Temperature dependence of the VACF tail decay exponent is defined. The proper inclusion of the long-time tail contributions to the diffusion coefficient calculation results in the consistency between G-K and E-S methods. Having considered the major factors influencing the precision of the diffusion rate calculations in comparison with experimental data (system size effects and force field parameters), we point to hydrogen nuclear quantum effects as, presumably, the last obstacle to fully consistent n-alkane description.
Diffusion dynamics of energy-efficient renovations causalities and policy recommendations
Müller, Matthias Otto
2013-01-01
Focusing on ways that energy-efficient building renovation can be accelerated, this book reviews current literature, offers policy recommendations and proposed regulations and sketches a business model supporting the diffusion of energy-efficient renovations.
Diffusion inside living human cells
DEFF Research Database (Denmark)
Leijnse, N.; Jeon, J. -H.; Loft, Steffen;
2012-01-01
Naturally occurring lipid granules diffuse in the cytoplasm and can be used as tracers to map out the viscoelastic landscape inside living cells. Using optical trapping and single particle tracking we found that lipid granules exhibit anomalous diffusion inside human umbilical vein endothelial ce...
Thermal Diffusion in Liquid Mixtures and Polymer Solutions by Molecular Dynamics Simulations
2007-01-01
This thesis is focused on simulating the transport processes of heat and matter under a sufficiently weak temperature gradient where the system linearly responds. The systems we are interested in are binary isotropic liquids with no convection and no viscous flows. Four related transport coefficients of the systems, the thermal conductivity of heat conduction, the diffusion coefficient of matter transfer, the Soret coefficient and the thermal diffusion coefficient of the cross effect between ...
Energy Technology Data Exchange (ETDEWEB)
Upadhyay, Ranjit Kumar [Department of Applied Mathematics, Indian School of Mines University, Dhanbad, Jharkhand 826 004 (India)], E-mail: ranjit_ism@yahoo.com; Kumari, Nitu [Department of Applied Mathematics, Indian School of Mines University, Dhanbad, Jharkhand 826 004 (India)], E-mail: nituism@gmail.com; Rai, Vikas [Department of Applied Mathematics, HMR Institute of Technology and Management, GT Karnal Road, Hamidpur, Delhi 110 036 (India)
2009-10-15
In this paper, dynamical complexities in two reaction-diffusion (RD) model systems are explored. A spatial heterogeneity in the form of linear spatial gradient in the reproductive growth rate of the phytoplankton is incorporated in both the model systems. Extra mortality of the zooplankton due to toxin production by the phytoplankton is included in the second reaction diffusion model system. Effect of toxin production and spatial heterogeneity in the model systems are studied. Toxin production does not seem to have an appreciable effect on the asymptotic dynamics of the model systems. On the other hand, spatial heterogeneity does influence the dynamics. In particular, it increases the frequency of occurrence of chaos as evident from two dimensional parameter scans. Both these model systems display short term recurrent chaos [Rai V. Chaos in natural populations: edge or wedge? Ecol Complex 2004;1: 127-38] as they reside on 'edges of chaos' (EOC) [Rai V, Upadhyay RK. Evolving to the edge of chaos: chance or necessity? Chaos, Solitons and Fractals 2006;30:1074-87]. This suggests that the ecological systems have a tendency to evolve to EOC. The study corroborates the inferences drawn from an earlier study by Rai and Upadhyay [Rai V, Upadhyay RK. Evolving to the edge of chaos: chance or necessity? Chaos, Solitons and Fractals 2006;30:1074-87]. The system's dynamics is largely unpredictable and admits bursts of short-term predictability.
Lotka systems with directed dispersal dynamics: Competition and influence of diffusion strategies.
Braverman, E; Kamrujjaman, Md
2016-09-01
We study a Lotka system describing two competing populations, and each of them chooses its diffusion strategy as the tendency to have a distribution proportional to a certain positive prescribed function. For instance, the standard diffusion corresponds to the choice of a uniform distribution. The paper is focused on the interplay of species competition and diffusion strategies. In the case when one of the diffusion strategies is proportional to the carrying capacity, while the other is not, and the competition does not discriminate the former species, we prove the competitive exclusion of the latter one. If the competition favors the latter species, there is still a range of parameters for which there is a coexistence, thanks to the better dispersal strategy chosen by the former species. The dependency on the interaction type, diffusion coefficients and intrinsic growth rates is explored. We prove that in the limit case, higher diffusion coefficients are detrimental while higher growth rates, as well as lower resources sharing, are beneficial for population survival.
Cerbino, Roberto; Sun, Yifei; Donev, Aleksandar; Vailati, Alberto
2015-09-01
Diffusion processes are widespread in biological and chemical systems, where they play a fundamental role in the exchange of substances at the cellular level and in determining the rate of chemical reactions. Recently, the classical picture that portrays diffusion as random uncorrelated motion of molecules has been revised, when it was shown that giant non-equilibrium fluctuations develop during diffusion processes. Under microgravity conditions and at steady-state, non-equilibrium fluctuations exhibit scale invariance and their size is only limited by the boundaries of the system. In this work, we investigate the onset of non-equilibrium concentration fluctuations induced by thermophoretic diffusion in microgravity, a regime not accessible to analytical calculations but of great relevance for the understanding of several natural and technological processes. A combination of state of the art simulations and experiments allows us to attain a fully quantitative description of the development of fluctuations during transient diffusion in microgravity. Both experiments and simulations show that during the onset the fluctuations exhibit scale invariance at large wave vectors. In a broader range of wave vectors simulations predict a spinodal-like growth of fluctuations, where the amplitude and length-scale of the dominant mode are determined by the thickness of the diffuse layer.
Diffusion dynamics of the Keap1–Cullin3 interaction in single live cells
Energy Technology Data Exchange (ETDEWEB)
Baird, Liam [Jacqui Wood Cancer Centre, Division of Cancer Research, Medical Research Institute, University of Dundee, Dundee, Scotland (United Kingdom); Dinkova-Kostova, Albena T., E-mail: a.dinkovakostova@dundee.ac.uk [Jacqui Wood Cancer Centre, Division of Cancer Research, Medical Research Institute, University of Dundee, Dundee, Scotland (United Kingdom); Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD (United States)
2013-03-29
Highlights: ► We developed a quantitative FRAP-based system to study the Keap1–Cul3 interaction. ► We show that Keap1–EGFP and mCherry–Cul3 interact in single live cells. ► We used inducers which target distinct cysteine sensors of Keap1 and differ 4000-fold in potency. ► Inducers cause Nrf2 stabilization, nuclear translocation, and target gene expression. ► Inducers of four different types do not dissociate the Keap1–EGFP:mCherry–Cul3 complex. -- Abstract: Transcription factor NF-E2 p45-related factor 2 (Nrf2) regulates the expression of a network of genes encoding drug-detoxification, anti-inflammatory, and metabolic enzymes, as well as proteins involved in the regulation of cellular redox homeostasis. Under basal conditions, Kelch-like ECH associated protein 1 (Keap1) targets Nrf2 for ubiquitination and proteasomal degradation via association with Cullin3 (Cul3)-based Rbx1 E3 ubiquitin ligase. Various small molecules (inducers) activate Nrf2 leading to upregulation of cytoprotective gene expression. Inducers chemically modify specific cysteine residues of Keap1 which ultimately loses its ability to target Nrf2 for degradation. Dissociation of the Keap1–Cul3 complex by inducers is one possible mechanism, but evidence in single live cells is lacking. To investigate the diffusion dynamics of the Keap1–Cul3 interaction and the effect of inducers, we developed a quantitative fluorescence recovery after photobleaching (FRAP)-based system using Keap1–EGFP and mCherry–Cul3 fusion proteins. We show that Keap1–EGFP and mCherry–Cul3 interact in single live cells. Exposure for 1 h to small-molecule inducers of 4 different types, the oleanane triterpenoid CDDO, the isothiocyanate sulforaphane, the sulfoxythiocarbamate STCA, and the oxidant hydrogen peroxide which target distinct cysteine sensors within Keap1 with potencies which differ by nearly 4000-fold, does not dissociate the Keap1–Cul3 complex. As inducers cause conformational changes
Nonlocal Anomalous Hall Effect.
Zhang, Steven S-L; Vignale, Giovanni
2016-04-01
The anomalous Hall (AH) effect is deemed to be a unique transport property of ferromagnetic metals, caused by the concerted action of spin polarization and spin-orbit coupling. Nevertheless, recent experiments have shown that the effect also occurs in a nonmagnetic metal (Pt) in contact with a magnetic insulator [yttrium iron garnet (YIG)], even when precautions are taken to ensure that there is no induced magnetization in the metal. We propose a theory of this effect based on the combined action of spin-dependent scattering from the magnetic interface and the spin-Hall effect in the bulk of the metal. At variance with previous theories, we predict the effect to be of first order in the spin-orbit coupling, just as the conventional anomalous Hall effect-the only difference being the spatial separation of the spin-orbit interaction and the magnetization. For this reason we name this effect the nonlocal anomalous Hall effect and predict that its sign will be determined by the sign of the spin-Hall angle in the metal. The AH conductivity that we calculate from our theory is in order of magnitude agreement with the measured values in Pt/YIG structures.
Nonlocal Anomalous Hall Effect
Zhang, Steven S.-L.; Vignale, Giovanni
2016-04-01
The anomalous Hall (AH) effect is deemed to be a unique transport property of ferromagnetic metals, caused by the concerted action of spin polarization and spin-orbit coupling. Nevertheless, recent experiments have shown that the effect also occurs in a nonmagnetic metal (Pt) in contact with a magnetic insulator [yttrium iron garnet (YIG)], even when precautions are taken to ensure that there is no induced magnetization in the metal. We propose a theory of this effect based on the combined action of spin-dependent scattering from the magnetic interface and the spin-Hall effect in the bulk of the metal. At variance with previous theories, we predict the effect to be of first order in the spin-orbit coupling, just as the conventional anomalous Hall effect—the only difference being the spatial separation of the spin-orbit interaction and the magnetization. For this reason we name this effect the nonlocal anomalous Hall effect and predict that its sign will be determined by the sign of the spin-Hall angle in the metal. The AH conductivity that we calculate from our theory is in order of magnitude agreement with the measured values in Pt /YIG structures.
Siebert, Julien; Alonso, Sergio; Bär, Markus; Schöll, Eckehard
2014-05-01
A one-component bistable reaction-diffusion system with asymmetric nonlocal coupling is derived as a limiting case of a two-component activator-inhibitor reaction-diffusion model with differential advection. The effects of asymmetric nonlocal couplings in such a bistable reaction-diffusion system are then compared to the previously studied case of a system with symmetric nonlocal coupling. We carry out a linear stability analysis of the spatially homogeneous steady states of the model and numerical simulations of the model to show how the asymmetric nonlocal coupling controls and alters the steady states and the front dynamics in the system. In a second step, a third fast reaction-diffusion equation is included which induces the formation of more complex patterns. A linear stability analysis predicts traveling waves for asymmetric nonlocal coupling, in contrast to a stationary Turing patterns for a system with symmetric nonlocal coupling. These findings are verified by direct numerical integration of the full equations with nonlocal coupling.
Govers, K.; Verwerft, M.
2013-07-01
The High Burnup Structure (HBS) observed at pellet periphery in conventional Light Water Reactor nuclear fuels and around spots presenting high plutonium content in mixed (U, Pu) oxide fuel - MOX fuel - consists of a restructuration of the original grains into smaller ones. The process is often postulated to occur because of the accumulation of irradiation damage and the retention of fission products in the matrix. The computing power nowadays available enables for simulating larger systems at the atomic scale up to the point that nano-polycrystalline material can now be investigated by empirical potential molecular dynamics. Simulations of nano-polycrystalline UO2 structures have been carried out at various temperatures to investigate atom mobility close to grain boundaries. The variation of Arrhénius parameters for the diffusion coefficient of oxygen, uranium and xenon as a function of the distance from a grain boundary was studied, leading to the distinction of three zones: the grain boundary layers (up to 1 nm depth) presenting enhanced diffusion, an intermediate zone (1 to roughly 2 nm depth) with intermediate diffusion values and the bulk of the grains. The following Arrhénius relations for grain boundary diffusion were derived:
Colmenares, Pedro J; López, Floralba; Olivares-Rivas, Wilmer
2009-12-01
We carried out a molecular-dynamics (MD) study of the self-diffusion tensor of a Lennard-Jones-type fluid, confined in a slit pore with attractive walls. We developed Bayesian equations, which modify the virtual layer sampling method proposed by Liu, Harder, and Berne (LHB) [P. Liu, E. Harder, and B. J. Berne, J. Phys. Chem. B 108, 6595 (2004)]. Additionally, we obtained an analytical solution for the corresponding nonhomogeneous Langevin equation. The expressions found for the mean-squared displacement in the layers contain naturally a modification due to the mean force in the transverse component in terms of the anisotropic diffusion constants and mean exit time. Instead of running a time consuming dual MD-Langevin simulation dynamics, as proposed by LHB, our expression was used to fit the MD data in the entire survival time interval not only for the parallel but also for the perpendicular direction. The only fitting parameter was the diffusion constant in each layer.
Linear optical studies of metal surfaces: Diffusion, growth, and surface dynamics
Nabighian, Edward Ara
Through the use of laser-induced thermal desorption, a monolayer density grating is produced on a Ni(111) substrate. Using linear optical diffraction from this grating we monitor surface diffusion. By varying the angular direction of the grating we also monitor the azimuthal dependence of diffusion over 360° rotation. For hydrogen on Ni(111) we measured the diffusion rates from 65 K to 240 K, yielding diffusion rates which vary from 2 × 10 -15 cm2/sec to 2 × 10-7 cm2/sec. The results reveal energies of diffusion in both the classical overbarrier hopping and phonon-assisted quantum regimes. For xenon on Ni(111) we measured the diffusion rates from 30 K to 60 K, yielding diffusion rates which vary from 1.3 × 10-10 cm2/sec to 1 × 10-9 cm2/sec. In the case of xenon diffusion, the results also reveal an unusually low diffusivity. In addition, growth measurements of xenon on Ni(111) were studied from 35 K to 60 K using an optical reflectance difference technique. The growth of xenon was found to change mechanisms as temperature varied. At 35 K xenon grows in 3-dimensional islands (Volmer-Weber growth), at 40 K xenon grows as 2-dimensional islands (Frank van der Merwe growth), and above 60 K xenon grows to a thickness of only one monolayer. We can not only monitor the growth mechanism, but the growth rate as well. Finally we use optical reflectance difference to monitor sputtering and annealing on the Ni(111) substrate. The competing surface roughening of sputtering and surface reordering of annealing was found to follow an Arrhenius form with an activation energy of Ea = 1.1 eV/atom given by direct atom evaporation from step edges. By monitoring the formation of islands and pits on the surface during sputtering at various temperatures we are able to determine that above 823 K the annealing process reorders the surface faster than sputtering can create surface roughness. As temperature decreases we see an increase in island and pit formation due to the lessened
Directory of Open Access Journals (Sweden)
Zhi-Jun Shuai
2015-08-01
Full Text Available The complex three-dimensional turbulent flow field in a centrifugal water pump with three asymmetrical diffusers was numerically simulated. The characteristics of pressure and force fluctuations inside the model pump were investigated. Fast Fourier transformation was performed to obtain the spectra of pressure and force fluctuations. It indicates that the dominant frequency of pressure fluctuations is the blade passing frequency in all the sub-domains inside the pump and the first blade passing frequency energy (first order of blade passing frequency is the most significant. The dominant frequency of pressure fluctuations at the location of diffuser outlet is featured by low frequency (less than 1 Hz, which may be due to the locally generated eddy structures. Besides, the dominant frequency force fluctuations on the impeller blades are also the blade passing frequency. The existence of the three asymmetrical diffusers has damping effect on the pressure fluctuation amplitude and energy amplitude of pressure fluctuations in the diffuser domain dramatically, which indicates that the diffusers can effectively control the hydraulically excited vibration in the pump. Besides, the prediction of the dominant frequency of pressure fluctuations inside the pump can help to utilize the pump effectively and to extend the pump life. The main findings of this work can provide prediction of the pump performance and information for further optimal design of centrifugal pumps as well.
Wang, Wenting; Li, Wenlong; Li, Zizhen; Zhang, Hui
2011-04-01
Spatiotemporal dynamics of a predator-prey system is considered under the assumption that the predator is sensitive to colored noise. Mathematically, the model consists of two coupled diffusion-reactions. By means of extensive numerical simulations, the complex invasion pattern formations of the system are identified. The results show that a geographical invasion emerges without regional persistence when the intensity of colored noise is small. Remarkably, as the noise intensity increases, the species spreads via a patchy invasion only when the system is affected by red noise. Meanwhile, the relationship between local stability and global invasion is also considered. The predator, which becomes extinct in the system without diffusion, could invade locally when the system is affected by white noise. However, the local invasion is not followed by geographical spread.
Anomalous cross-B field transport and spokes in HiPIMS plasma
Hecimovic, A.
2016-05-01
Localized light emission patterns observed during on time of a high power impulse magnetron sputtering (HiPIMS) discharge on a planar magnetron, known as spokes or ionization zones, have been identified as a potential source of anomalous cross-B field diffusion. In this paper experimental evidence is presented that anomalous diffusion is triggered by the appearance of spokes. The Hall parameter {ω\\text{ce}}{τ\\text{c}} , product of the electron cyclotron frequency and the classical collision time, reduces from Bohm diffusion values (∼ 16 and higher) down to the value of 3 as spokes appear, indicating anomalous cross-B field transport. A combination of intensified charge coupled device imaging and electric probe measurements reveals that the ions from the spokes are instantaneously diffusing away from the target. The ion diffusion coefficients calculated from a sideways image of the spoke are six times higher than Bohm diffusion coefficients, which is consistent with the reduction of the Hall parameter.
Dynamics of comb-of-comb-network polymers in random layered flows
Katyal, Divya; Kant, Rama
2016-12-01
We analyze the dynamics of comb-of-comb-network polymers in the presence of external random flows. The dynamics of such structures is evaluated through relevant physical quantities, viz., average square displacement (ASD) and the velocity autocorrelation function (VACF). We focus on comparing the dynamics of the comb-of-comb network with the linear polymer. The present work displays an anomalous diffusive behavior of this flexible network in the random layered flows. The effect of the polymer topology on the dynamics is analyzed by varying the number of generations and branch lengths in these networks. In addition, we investigate the influence of external flow on the dynamics by varying flow parameters, like the flow exponent α and flow strength Wα. Our analysis highlights two anomalous power-law regimes, viz., subdiffusive (intermediate-time polymer stretching and flow-induced diffusion) and superdiffusive (long-time flow-induced diffusion). The anomalous long-time dynamics is governed by the temporal exponent ν of ASD, viz., ν =2 -α /2 . Compared to a linear polymer, the comb-of-comb network shows a shorter crossover time (from the subdiffusive to superdiffusive regime) but a reduced magnitude of ASD. Our theory displays an anomalous VACF in the random layered flows that scales as t-α /2. We show that the network with greater total mass moves faster.
Braverman, E; Kamrujjaman, Md; Korobenko, L
2015-06-01
We study the interaction between different types of dispersal, intrinsic growth rates and carrying capacities of two competing species in a heterogeneous environment: one of them is subject to a regular diffusion while the other moves in the direction of most per capita available resources. If spatially heterogeneous carrying capacities coincide, and intrinsic growth rates are proportional then competitive exclusion of a regularly diffusing population is inevitable. However, the situation may change if intrinsic growth rates for the two populations have different spatial forms. We also consider the case when carrying capacities are different. If the carrying capacity of a regularly diffusing population is higher than for the other species, the two populations may coexist; as the difference between the two carrying capacities grows, competitive exclusion of the species with a lower carrying capacity occurs.
Directory of Open Access Journals (Sweden)
François Rebaudo
2011-10-01
Full Text Available Worldwide, the theory and practice of agricultural extension system have been dominated for almost half a century by Rogers' "diffusion of innovation theory". In particular, the success of integrated pest management (IPM extension programs depends on the effectiveness of IPM information diffusion from trained farmers to other farmers, an important assumption which underpins funding from development organizations. Here we developed an innovative approach through an agent-based model (ABM combining social (diffusion theory and biological (pest population dynamics models to study the role of cooperation among small-scale farmers to share IPM information for controlling an invasive pest. The model was implemented with field data, including learning processes and control efficiency, from large scale surveys in the Ecuadorian Andes. Our results predict that although cooperation had short-term costs for individual farmers, it paid in the long run as it decreased pest infestation at the community scale. However, the slow learning process placed restrictions on the knowledge that could be generated within farmer communities over time, giving rise to natural lags in IPM diffusion and applications. We further showed that if individuals learn from others about the benefits of early prevention of new pests, then educational effort may have a sustainable long-run impact. Consistent with models of information diffusion theory, our results demonstrate how an integrated approach combining ecological and social systems would help better predict the success of IPM programs. This approach has potential beyond pest management as it could be applied to any resource management program seeking to spread innovations across populations.
Rebaudo, François; Dangles, Olivier
2011-10-01
Worldwide, the theory and practice of agricultural extension system have been dominated for almost half a century by Rogers' "diffusion of innovation theory". In particular, the success of integrated pest management (IPM) extension programs depends on the effectiveness of IPM information diffusion from trained farmers to other farmers, an important assumption which underpins funding from development organizations. Here we developed an innovative approach through an agent-based model (ABM) combining social (diffusion theory) and biological (pest population dynamics) models to study the role of cooperation among small-scale farmers to share IPM information for controlling an invasive pest. The model was implemented with field data, including learning processes and control efficiency, from large scale surveys in the Ecuadorian Andes. Our results predict that although cooperation had short-term costs for individual farmers, it paid in the long run as it decreased pest infestation at the community scale. However, the slow learning process placed restrictions on the knowledge that could be generated within farmer communities over time, giving rise to natural lags in IPM diffusion and applications. We further showed that if individuals learn from others about the benefits of early prevention of new pests, then educational effort may have a sustainable long-run impact. Consistent with models of information diffusion theory, our results demonstrate how an integrated approach combining ecological and social systems would help better predict the success of IPM programs. This approach has potential beyond pest management as it could be applied to any resource management program seeking to spread innovations across populations.
New sensitive micro-measurements of dynamic surface tension and diffusion coefficients
DEFF Research Database (Denmark)
Kinoshita, Koji; Ortiz, Elisa Parra; Needham, David
2017-01-01
. These limitations create inconsistencies for the kinetic analysis of surfactant adsorption/desorption, especially significant for ionic surfactants. Here, the “micropipette interfacial area-expansion method” was introduced and validated as a new DST measurement having a high enough sensitivity to detect diffusion...... controlled molecular adsorption at the air-water interfaces. To validate the new technique, the diffusion coefficient of 1-Octanol in water was investigated with existing models: the Ward Tordai model for the long time adsorption regime (1–100 s), and the Langmuir and Frumkin adsorption isotherm models...
Diffusion of active chiral particles
Sevilla, Francisco J.
2016-12-01
The diffusion of chiral active Brownian particles in three-dimensional space is studied analytically, by consideration of the corresponding Fokker-Planck equation for the probability density of finding a particle at position x and moving along the direction v ̂ at time t , and numerically, by the use of Langevin dynamics simulations. The analysis is focused on the marginal probability density of finding a particle at a given location and at a given time (independently of its direction of motion), which is found from an infinite hierarchy of differential-recurrence relations for the coefficients that appear in the multipole expansion of the probability distribution, which contains the whole kinematic information. This approach allows the explicit calculation of the time dependence of the mean-squared displacement and the time dependence of the kurtosis of the marginal probability distribution, quantities from which the effective diffusion coefficient and the "shape" of the positions distribution are examined. Oscillations between two characteristic values were found in the time evolution of the kurtosis, namely, between the value that corresponds to a Gaussian and the one that corresponds to a distribution of spherical shell shape. In the case of an ensemble of particles, each one rotating around a uniformly distributed random axis, evidence is found of the so-called effect "anomalous, yet Brownian, diffusion," for which particles follow a non-Gaussian distribution for the positions yet the mean-squared displacement is a linear function of time.
Rudin, Sven P.; Bock, Nicolas; Wallace, Duane C.
2014-11-01
Density functional theory (DFT) calculations reliably aid in understanding the relative stability of different crystal phases as functions of pressure and temperature. Our purpose here is to employ DFT to analyze the character of the melting process, with an emphasis on comparing normal and anomalous melting. The normal-anomalous distinction is the absence or presence, respectively, of a significant electronic structure change between crystal and liquid. We study the normal melters Na and Cu, which are metallic in both phases, and the anomalous melter Ga, which has a partially covalent crystal and a nearly free-electron liquid. We calculate free energies from lattice dynamics for the crystal and from vibration-transit (V-T) theory for the liquid, where the liquid formulation is similar to that of the crystal but has an additional term representing the diffusive transits. Internal energies U and entropies S calculated for both phases of Na and Cu were previously shown to be in good agreement with experiment; here we find the same agreement for Ga. The dominant theoretical terms in the melting Δ U and Δ S are the structural potential energy, the vibrational entropy, and the purely liquid transit terms in both U and S . The melting changes in structural energy and vibrational entropy are much larger in Ga than in Na and Cu. This behavior arises from the change in electronic structure in Ga, and is the identifying characteristic of anomalous melting. We interpret our DFT results in terms of the physical effects of the relatively few covalent bonds in the otherwise metallic Ga crystal.
Beta Function and Anomalous Dimensions
Pica, Claudio
2010-01-01
We demonstrate that it is possible to determine the coefficients of an all-order beta function linear in the anomalous dimensions using as data the two-loop coefficients together with the first one of the anomalous dimensions which are universal. The beta function allows to determine the anomalous dimension of the fermion masses at the infrared fixed point, and the resulting values compare well with the lattice determinations.
Anomalous Dimensions of Conformal Baryons
Pica, Claudio
2016-01-01
We determine the anomalous dimensions of baryon operators for the three color theory as function of the number of massless flavours within the conformal window to the maximum known order in perturbation theory. We show that the anomalous dimension of the baryon is controllably small for a wide range of number of flavours. We also find that this is always smaller than the anomalous dimension of the fermion mass operator. These findings challenge the partial compositeness paradigm.
Directory of Open Access Journals (Sweden)
Felicia Shirly Peace
2014-01-01
Full Text Available A mathematical model of the dynamics of the self-ignition of a reaction-diffusion system is studied in this paper. An approximate analytical method (modified Adomian decomposition method is used to solve nonlinear differential equations under steady-state condition. Analytical expressions for concentrations of the gas reactant and the temperature have been derived for Lewis number (Le and parameters β, γ, and ϕ2. Furthermore, in this work, the numerical simulation of the problem is also reported using MATLAB program. An agreement between analytical and numerical results is noted.
Singh, Jagdev; Rashidi, M. M.; Kumar, Devendra; Swroop, Ram
2016-12-01
In this paper, we study a dynamical Brusselator reaction-diffusion system arising in triple collision and enzymatic reactions with time fractional Caputo derivative. The present article involves a more generalized effective approach, proposed for the Brusselator system say q-homotopy analysis transform method (q-HATM), providing the family of series solutions with nonlocal generalized effects. The convergence of the q-HATM series solution is adjusted and controlled by auxiliary parameter ℏ and asymptotic parameter n. The numerical results are demonstrated graphically. The outcomes of the study show that the q-HATM is computationally very effective and accurate to analyze nonlinear fractional differential equations.
Energy Technology Data Exchange (ETDEWEB)
Jiao Jianjun, E-mail: jiaojianjun05@126.co [Guizhou Key Laboratory of Economic System Simulation, Guizhou College of Finance and Economics, Guiyang 550004 (China); Ye Kaili [School of Economics and Management, Xinyang Normal University, Xinyang 464000, Henan (China); Chen Lansun [Institute of Mathematics, Academy of Mathematics and System Sciences, Beijing 100080 (China)
2011-01-15
Research Highlights: This work improves on existing chemostat models. The proposed model accounts for natural phenomena. This work improves on the existing mathematical methods. - Abstract: In this paper, we consider a five-dimensioned chemostat model with impulsive diffusion and pulse input environmental toxicant. Using the discrete dynamical system determined by the stroboscopic map, we obtain a microorganism-extinction periodic solution. Further, it is globally asymptotically stable. The permanent condition of the investigated system is also analyzed by the theory on impulsive differential equation. Our results reveal that the chemostat environmental changes play an important role on the outcome of the chemostat.
Anomalous radiative transitions
Ishikawa, Kenzo; Tobita, Yutaka
2014-01-01
Anomalous transitions involving photons derived by many-body interaction of the form, $\\partial_{\\mu} G^{\\mu}$, in the standard model are studied. This does not affect the equation of motion in the bulk, but makes wave functions modified, and causes the unusual transition characterized by the time-independent probability. In the transition probability at a time-interval T expressed generally in the form $P=T \\Gamma_0 +P^{(d)}$, now with $\\Gamma_0=0, P^{(d)} \
Visualizing MR diffusion tensor fields by dynamic fiber tracking and uncertainty mapping
Ehricke, HH; Klose, U; Grodd, W
2006-01-01
Recent advances in magnetic resonance imaging have provided methods for the acquisition of high-resolution diffusion tensor fields. Their 3D-visualization with streamline-based techniques-called fiber tracking-allow analysis of cerebral white matter tracts for diagnostic, therapeutic as well as neur
Weakly nonlinear dynamics in reaction-diffusion systems with Levy flights
Energy Technology Data Exchange (ETDEWEB)
Nec, Y; Nepomnyashchy, A A [Department of Mathematics, Technion-Israel Institute of Technology, Haifa 32000 (Israel); Golovin, A A [Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208 (United States)], E-mail: flyby@techunix.technion.ac.il
2008-12-15
Reaction-diffusion equations with a fractional Laplacian are reduced near a long wave Hopf bifurcation. The obtained amplitude equation is shown to be the complex Ginzburg-Landau equation with a fractional Laplacian. Some of the properties of the normal complex Ginzburg-Landau equation are generalized for the fractional analogue. In particular, an analogue of the Kuramoto-Sivashinsky equation is derived.
Weiss, M.; Dittmar, L.; Junginger, H.M.; Patel, M.K.; Blok, K.
2009-01-01
High costs often prevent the market diffusion of novel and efficient energy technologies. Monitoring cost and price decline for these technologies is thus important in order to establish effective energy policy. Here, we present experience curves and cost-benefit analyses for condensing gas boilers
A MATHEMATICAL ANALYSIS FOR A DIFFUSIVE EPIDEMIC MODEL WITH CRISS-CROSS DYNAMICS
Institute of Scientific and Technical Information of China (English)
LiZhenayuan; Taoliyuan; YeQixiao
1999-01-01
Abstract. In this paper, an initial boundary value problem with homogeneous Neumann bound-ary condition is studied for a reaction diffusion system which models the spread of infectious dis-eases within two population groups by means of serf and criss-cross infection mechanism, Exis-tence, uniqueness and houndedness of the nonnegative global solution
Time-resolved diffusing wave spectroscopy applied to dynamic heterogeneity imaging
Cheikh, M; Ettori, D; Tinet, E; Avrillier, S; Tualle, J M; Cheikh, Monia; Nghiem, Ha Lien; Ettori, Dominique; Tinet, Eric; Avrillier, Sigrid; Tualle, Jean-Michel
2006-01-01
We report in this paper what is to our knowledge the first observation of a time-resolved diffusing wave spectroscopy signal recorded by transillumination through a thick turbid medium: the DWS signal is measured for a fixed photon transit time, which opens the possibility of improving the spatial resolution. This technique could find biomedical applications, especially in mammography.
Directory of Open Access Journals (Sweden)
Yuan Hung Lo
2013-01-01
Full Text Available Little is known about how small variations in ionic currents and Ca2+ and Na+ diffusion coefficients impact action potential and Ca2+ dynamics in rabbit ventricular myocytes. We applied sensitivity analysis to quantify the sensitivity of Shannon et al. model (Biophys. J., 2004 to 5%–10% changes in currents conductance, channels distribution, and ion diffusion in rabbit ventricular cells. We found that action potential duration and Ca2+ peaks are highly sensitive to 10% increase in L-type Ca2+ current; moderately influenced by 10% increase in Na+-Ca2+ exchanger, Na+-K+ pump, rapid delayed and slow transient outward K+ currents, and Cl− background current; insensitive to 10% increases in all other ionic currents and sarcoplasmic reticulum Ca2+ fluxes. Cell electrical activity is strongly affected by 5% shift of L-type Ca2+ channels and Na+-Ca2+ exchanger in between junctional and submembrane spaces while Ca2+-activated Cl−-channel redistribution has the modest effect. Small changes in submembrane and cytosolic diffusion coefficients for Ca2+, but not in Na+ transfer, may alter notably myocyte contraction. Our studies highlight the need for more precise measurements and further extending and testing of the Shannon et al. model. Our results demonstrate usefulness of sensitivity analysis to identify specific knowledge gaps and controversies related to ventricular cell electrophysiology and Ca2+ signaling.
Chushnyakova, M. V.; Gontchar, I. I.
2013-01-01
We attempt to make some progress in the problem of the apparently large diffuseness of the Woods-Saxon strong nucleus-nucleus interaction potential (SnnP) needed to fit a large number of precision fusion excitation functions. This problem has been formulated in Newton [Phys. Lett. B10.1016/j.physletb.2004.02.052 586, 219 (2004);Phys. Rev. C10.1103/PhysRevC.70.024605 70, 024605 (2004)]. We applied the classical dissipative trajectory model to describe the data on fusion (capture) of 16O with 92Zr, 144Sm, and 208Pb. No fluctuations or dynamical deformations of the interacting nuclei are accounted for. The friction force is supposed to be proportional to the squared derivative of the SnnP (the surface friction model). The SnnP is calculated within the framework of the double-folding model with the density-dependent M3Y NN forces. This potential is known to possess rather small diffuseness in contradistinction to what is required by the data analysis in Newton [Phys. Lett. B10.1016/j.physletb.2004.02.052 586, 219 (2004);Phys. Rev. C10.1103/PhysRevC.70.024605 70, 024605 (2004)]. Varying slightly the strength of radial friction (universally for all three reactions) and the diffuseness of the charge density of 208Pb we have obtained satisfactory agreement of the calculated excitation functions with the data.
Energy Technology Data Exchange (ETDEWEB)
Jost, Sarah C. [Swedish Neuroscience Institute, Department of Neurosurgery, Seattle, WA (United States); Ackerman, Joseph W. [Washington University School of Medicine, Department of Radiology, 660 South Euclid Ave., Box 8131, St. Louis, MO (United States); Garbow, Joel R. [Washington University School of Medicine, Department of Radiology, 660 South Euclid Ave., Box 8131, St. Louis, MO (United States); Alvin J. Siteman Cancer Center, St. Louis, MO (United States); Manwaring, Linda P. [Washington University School of Medicine, Department of Pediatrics, St. Louis, MO (United States); Washington University School of Medicine, Department of Genetics and Genomic Medicine, St. Louis, MO (United States); Gutmann, David H. [Washington University School of Medicine, Department of Neurology, St. Louis, MO (United States); Alvin J. Siteman Cancer Center, St. Louis, MO (United States); McKinstry, Robert C. [Washington University School of Medicine, Department of Radiology, 660 South Euclid Ave., Box 8131, St. Louis, MO (United States); Washington University School of Medicine, Department of Pediatrics, St. Louis, MO (United States)
2008-12-15
Optic pathway gliomas (OPGs) are common pediatric brain tumors that pose significant clinical challenges with regard to predicting which tumors are likely to become symptomatic and require treatment. These tumors can arise sporadically or in the context of the inherited cancer predisposition syndrome neurofibromatosis type 1 (NF1). Few studies have suggested biological or imaging markers that predict the clinical course of this disease. In this cross-sectional study, we hypothesized that the clinical behavior of OPGs in children can be differentiated by diffusion-weighted (DW) and dynamic contrast-enhanced (DCE) MRI. A total of 27 children with OPG were studied using DW and DCE MRI protocols. Diffusivity and permeability were calculated and correlated with the clinical behavior the OPG. Mean diffusivity values of 1.39 {mu}m{sup 2}/ms and mean permeability values of 2.10 ml/min per 100 cm{sup 3} of tissue were measured. Clinically aggressive OPGs had significantly higher mean permeability values (P = 0.05) than clinically stable tumors. In addition, there was a strong correlation between clinical aggressiveness and the absence of NF1 (P < 0.01). These results suggest that DCE MRI might be a useful biomarker for clinically aggressive OPG, which should be confirmed in larger prospective longitudinal studies. (orig.)
Indian Academy of Sciences (India)
K S Mali; G B Dutt
2007-03-01
This article describes our ongoing efforts to understand dynamical processes such as rotational diffusion and photoisomerization in polymorphic environments of a block copolymer. The objective is to explore how the typical properties of a block copolymer solution such as critical micelle temperature (CMT) and temperature-induced sol-gel transition influence the rotational diffusion of hydrophobic solute molecules. Rotational diffusion of solute molecules differs significantly below and above the CMT of a block copolymer solution, while there is no influence of sol-gel transition on solute rotation. This is rationalized on the basis of the site of solubilization of the solute molecules which is the palisade layer of the micelles in both phases and unaffected by gelation. A similar result has been obtained in case of photoisomerization studies carried out with a carbocyanine derivative in the sol and gel phases of the block copolymer. The isomerization studies have been extended to the reverse phases (sol and gel phases) of the block copolymer to explore the nature of the water present in the cores of the reverse micelles. Our results provide evidence for the existence of water droplets with properties resembling bulk water. In essence, we show that despite having vastly differing bulk properties, both the solution and gel phases (normal as well as reverse) offer identical microscopic environment.
Berezkin, Anatoly V; Kudryavtsev, Yaroslav V
2013-10-21
A novel hybrid approach combining dissipative particle dynamics (DPD) and finite difference (FD) solution of partial differential equations is proposed to simulate complex reaction-diffusion phenomena in heterogeneous systems. DPD is used for the detailed molecular modeling of mass transfer, chemical reactions, and phase separation near the liquid∕liquid interface, while FD approach is applied to describe the large-scale diffusion of reactants outside the reaction zone. A smooth, self-consistent procedure of matching the solute concentration is performed in the buffer region between the DPD and FD domains. The new model is tested on a simple model system admitting an analytical solution for the diffusion controlled regime and then applied to simulate practically important heterogeneous processes of (i) reactive coupling between immiscible end-functionalized polymers and (ii) interfacial polymerization of two monomers dissolved in immiscible solvents. The results obtained due to extending the space and time scales accessible to modeling provide new insights into the kinetics and mechanism of those processes and demonstrate high robustness and accuracy of the novel technique.
Fickian dispersion is anomalous
Cushman, John H.; O'Malley, Dan
2015-12-01
The thesis put forward here is that the occurrence of Fickian dispersion in geophysical settings is a rare event and consequently should be labeled as anomalous. What people classically call anomalous is really the norm. In a Lagrangian setting, a process with mean square displacement which is proportional to time is generally labeled as Fickian dispersion. With a number of counter examples we show why this definition is fraught with difficulty. In a related discussion, we show an infinite second moment does not necessarily imply the process is super dispersive. By employing a rigorous mathematical definition of Fickian dispersion we illustrate why it is so hard to find a Fickian process. We go on to employ a number of renormalization group approaches to classify non-Fickian dispersive behavior. Scaling laws for the probability density function for a dispersive process, the distribution for the first passage times, the mean first passage time, and the finite-size Lyapunov exponent are presented for fixed points of both deterministic and stochastic renormalization group operators. The fixed points of the renormalization group operators are p-self-similar processes. A generalized renormalization group operator is introduced whose fixed points form a set of generalized self-similar processes. Power-law clocks are introduced to examine multi-scaling behavior. Several examples of these ideas are presented and discussed.
González, Ramón E. R.; de Figueirêdo, Pedro Hugo; Coutinho, Sérgio
2013-10-01
We study a cellular automata model to test the timing of antiretroviral therapy strategies for the dynamics of infection with human immunodeficiency virus (HIV). We focus on the role of virus diffusion when its population is included in previous cellular automata model that describes the dynamics of the lymphocytes cells population during infection. This inclusion allows us to consider the spread of infection by the virus-cell interaction, beyond that which occurs by cell-cell contagion. The results show an acceleration of the infectious process in the absence of treatment, but show better efficiency in reducing the risk of the onset of AIDS when combined antiretroviral therapies are used even with drugs of low effectiveness. Comparison of results with clinical data supports the conclusions of this study.
Yadav, Vivek Kumar; Chandra, Amalendu
2013-06-14
A first principles study of the dynamics of supercritical methanol is carried out by means of ab initio molecular dynamics simulations. In particular, the fluctuation dynamics of hydroxyl stretch frequencies, hydrogen bonds, dangling hydroxyl groups, and orientation of methanol molecules are investigated for three different densities at 523 K. Apart from the dynamical properties, various equilibrium properties of supercritical methanol such as the local density distributions and structural correlations, hydrogen bonding aspects, frequency-structure correlations, and dipole distributions of methanol molecules are also investigated. In addition to the density dependence of various equilibrium and dynamical properties, their dependencies on dispersion interactions are also studied by carrying out additional simulations using a dispersion corrected density functional for all the systems. It is found that the hydrogen bonding between methanol molecules decreases significantly as we move to the supercritical state from the ambient one. The inclusion of dispersion interactions is found to increase the number of hydrogen bonds to some extent. Calculations of the frequency-structure correlation coefficient reveal that a statistical correlation between the hydroxyl stretch frequency and the nearest hydrogen-oxygen distance continues to exist even at supercritical states of methanol, although it is weakened with increase of temperature and decrease of density. In the supercritical state, the frequency time correlation function is found to decay with two time scales: One around or less than 100 fs and the other in the region of 250-700 fs. It is found that, for supercritical methanol, the times scales of vibrational spectral diffusion are determined by an interplay between the dynamics of hydrogen bonds, dangling OD groups, and inertial rotation of methanol molecules and the roles of these various components are found to vary with density of the supercritical solvent. Effects
Liang, Xiao; Wang, Linshan; Wang, Yangfan; Wang, Ruili
2016-09-01
In this paper, we focus on the long time behavior of the mild solution to delayed reaction-diffusion Hopfield neural networks (DRDHNNs) driven by infinite dimensional Wiener processes. We analyze the existence, uniqueness, and stability of this system under the local Lipschitz function by constructing an appropriate Lyapunov-Krasovskii function and utilizing the semigroup theory. Some easy-to-test criteria affecting the well-posedness and stability of the networks, such as infinite dimensional noise and diffusion effect, are obtained. The criteria can be used as theoretic guidance to stabilize DRDHNNs in practical applications when infinite dimensional noise is taken into consideration. Meanwhile, considering the fact that the standard Brownian motion is a special case of infinite dimensional Wiener process, we undertake an analysis of the local Lipschitz condition, which has a wider range than the global Lipschitz condition. Two samples are given to examine the availability of the results in this paper. Simulations are also given using the MATLAB.
Dynamical Analysis of a Plateau Pika with Cross-Diffusion under Contraception Control
Directory of Open Access Journals (Sweden)
Xiaoyan Wang
2014-01-01
Full Text Available A plateau pika model with spatial cross-diffusion is investigated. By analyzing the corresponding characteristic equations, the local stability of an coexistence steady state is discussed when d21 is small enough. However, when d21 is large enough, the model shows Turing bifurcation if B2 -4AC > 0. Furthermore, it is proved that if, R > R0, βK > d and cross-diffusion rates are zero, the positive coexistence steady state is globally asymptotically stable. A nonconstant positive solution bifurcates from the coexistent steady state by the Leray-Schauder degree theory. Numerical simulations are carried out to illustrate the main results.
Hybrid stochastic simulation of reaction-diffusion systems with slow and fast dynamics
Energy Technology Data Exchange (ETDEWEB)
Strehl, Robert; Ilie, Silvana, E-mail: silvana@ryerson.ca [Department of Mathematics, Ryerson University, Toronto, Ontario M5B 2K3 (Canada)
2015-12-21
In this paper, we present a novel hybrid method to simulate discrete stochastic reaction-diffusion models arising in biochemical signaling pathways. We study moderately stiff systems, for which we can partition each reaction or diffusion channel into either a slow or fast subset, based on its propensity. Numerical approaches missing this distinction are often limited with respect to computational run time or approximation quality. We design an approximate scheme that remedies these pitfalls by using a new blending strategy of the well-established inhomogeneous stochastic simulation algorithm and the tau-leaping simulation method. The advantages of our hybrid simulation algorithm are demonstrated on three benchmarking systems, with special focus on approximation accuracy and efficiency.
Diffusive Spin Dynamics in Ferromagnetic Thin Films with a Rashba Interaction
Wang, Xuhui
2012-03-13
In a ferromagnetic metal layer, the coupled charge and spin diffusion equations are obtained in the presence of both Rashba spin-orbit interaction and magnetism. The misalignment between the magnetization and the nonequilibrium spin density induced by the Rashba field gives rise to Rashba spin torque acting on the ferromagnetic order parameter. In a general form, we find that the Rashba torque consists of both in-plane and out-of-plane components, i.e., T=T Sy×m+T Sm×(y×m). Numerical simulations on a two-dimensional nanowire consider the impact of diffusion on the Rashba torque and reveal a large enhancement to the ratio T/T S for thin wires. Our theory provides an explanation for the mechanism driving the magnetization switching in a single ferromagnet as observed in the recent experiments. © 2012 American Physical Society.
Dynamics of a molecular glass former: Energy landscapes for diffusion in ortho-terphenyl
Niblett, S. P.; de Souza, V. K.; Stevenson, J. D.; Wales, D. J.
2016-07-01
Relaxation times and transport processes of many glass-forming supercooled liquids exhibit a super-Arrhenius temperature dependence. We examine this phenomenon by computer simulation of the Lewis-Wahnström model for ortho-terphenyl. We propose a microscopic definition for a single-molecule cage-breaking transition and show that, when correlation behaviour is taken into account, these rearrangements are sufficient to reproduce the correct translational diffusion constants over an intermediate temperature range in the supercooled regime. We show that super-Arrhenius behaviour can be attributed to increasing negative correlation in particle movement at lower temperatures and relate this to the cage-breaking description. Finally, we sample the potential energy landscape of the model and show that it displays hierarchical ordering. Substructures in the landscape, which may correspond to metabasins, have boundaries defined by cage-breaking transitions. The cage-breaking formulation provides a direct link between the potential energy landscape and macroscopic diffusion behaviour.
Dynamics of the connectome in Huntington's disease: A longitudinal diffusion MRI study
Odish, Omar F F; Karen Caeyenberghs; Hadi Hosseini; van den Bogaard, Simon J. A.; Roos, Raymund A.C.; Alexander Leemans
2015-01-01
Abstract Objectives To longitudinally investigate the connectome in different stages of Huntington's disease (HD) by applying graph theoretical analysis to diffusion MRI data. Experimental design We constructed weighted structural networks and calculated their topological properties. Twenty-two premanifest (preHD), 10 early manifest HD and 24 healthy controls completed baseline and 2 year follow-up scans. We stratified the preHD group based on their predicted years to disease onset into a far...
Proteinaceous Light Diffusers and Dynamic 3D Skin Texture in Cephalopods
2014-02-24
characterize leucophore reflectance properties (spectral reflectance UV-IR, polarization, diffusing properties) in cephalopod and fish species. Aim 2...contrast pattern. B. Close up of the bold zebra -stripe pattern and the white fin spots located at the bottom of the image. C. Micrograph of a single...in the activation of other skin structures in cephalopods and fish (chromatophores and/or iridophores): serotonin (5-HT; relaxes cephalopod
Anomalous feedback and negative domain wall resistance
Cheng, Ran; Zhu, Jian-Gang; Xiao, Di
2016-11-01
Magnetic induction can be regarded as a negative feedback effect, where the motive-force opposes the change of magnetic flux that generates the motive-force. In artificial electromagnetics emerging from spintronics, however, this is not necessarily the case. By studying the current-induced domain wall dynamics in a cylindrical nanowire, we show that the spin motive-force exerting on electrons can either oppose or support the applied current that drives the domain wall. The switching into the anomalous feedback regime occurs when the strength of the dissipative torque β is about twice the value of the Gilbert damping constant α. The anomalous feedback manifests as a negative domain wall resistance, which has an analogy with the water turbine.
Anomalous Transport of High Energy Cosmic Rays in Galactic Superbubbles
Barghouty, Nasser F.
2014-01-01
High-energy cosmic rays may exhibit anomalous transport as they traverse and are accelerated by a collection of supernovae explosions in a galactic superbubble. Signatures of this anomalous transport can show up in the particles' evolution and their spectra. In a continuous-time-random- walk (CTRW) model assuming standard diffusive shock acceleration theory (DSA) for each shock encounter, and where the superbubble (an OB stars association) is idealized as a heterogeneous region of particle sources and sinks, acceleration and transport in the superbubble can be shown to be sub-diffusive. While the sub-diffusive transport can be attributed to the stochastic nature of the acceleration time according to DSA theory, the spectral break appears to be an artifact of transport in a finite medium. These CTRW simulations point to a new and intriguing phenomenon associated with the statistical nature of collective acceleration of high energy cosmic rays in galactic superbubbles.
Stopper, Daniel; Roth, Roland; Hansen-Goos, Hendrik
2016-11-01
Within the Asakura-Oosawa model, we study structural relaxation in mixtures of colloids and polymers subject to Brownian motion in the overdamped limit. We obtain the time evolution of the self and distinct parts of the van Hove distribution function G(r,t) by means of dynamical density functional theory (DDFT) using an accurate free-energy functional based on Rosenfeld’s fundamental measure theory. In order to remove unphysical interactions within the self part, we extend the recently proposed quenched functional framework (Stopper et al 2015 J. Chem. Phys. 143 181105) toward mixtures. In addition, we obtain results for the long-time self diffusion coefficients of colloids and polymers from dynamic Monte Carlo simulations, which we incorporate into the DDFT. From the resulting DDFT equations we calculate G(r, t), which we find to agree very well with our simulations. In particular, we examine the influence of polymers which are slow relative to the colloids—a scenario for which both DDFT and simulation show a significant peak forming at r = 0 in the colloid-colloid distribution function, akin to experimental findings involving gelation of colloidal suspensions. Moreover, we observe that, in the presence of slow polymers, the long-time self diffusivity of the colloids displays a maximum at an intermediate colloid packing fraction. This behavior is captured by a simple semi-empirical formula, which provides an excellent description of the data.
Energy Technology Data Exchange (ETDEWEB)
Agusdinata, Datu Buyung, E-mail: bagusdinata@niu.edu; Amouie, Mahbod [Northern Illinois University, Department of Industrial & Systems Engineering and Environment, Sustainability, & Energy Institute (United States); Xu, Tao [Northern Illinois University, Department of Chemistry and Biochemistry (United States)
2015-01-15
Due to their favorable electrical and optical properties, quantum dots (QDs) nanostructures have found numerous applications including nanomedicine and photovoltaic cells. However, increased future production, use, and disposal of engineered QD products also raise concerns about their potential environmental impacts. The objective of this work is to establish a modeling framework for predicting the diffusion dynamics and concentration of toxic materials released from Trioctylphosphine oxide-capped CdSe. To this end, an agent-based model simulation with reaction kinetics and Brownian motion dynamics was developed. Reaction kinetics is used to model the stability of surface capping agent particularly due to oxidation process. The diffusion of toxic Cd{sup 2+} ions in aquatic environment was simulated using an adapted Brownian motion algorithm. A calibrated parameter to reflect sensitivity to reaction rate is proposed. The model output demonstrates the stochastic spatial distribution of toxic Cd{sup 2+} ions under different values of proxy environmental factor parameters. With the only chemistry considered was oxidation, the simulation was able to replicate Cd{sup 2+} ion release from Thiol-capped QDs in aerated water. The agent-based method is the first to be developed in the QDs application domain. It adds both simplicity of the solubility and rate of release of Cd{sup 2+} ions and complexity of tracking of individual atoms of Cd at the same time.
Carrier Decay and Diffusion Dynamics in Single-Crystalline CdTe as seen via Microphotoluminescence
Mascarenhas, Angelo; Fluegel, Brian; Alberi, Kirstin; Zhang, Yong-Hang
2015-03-01
The ability to spatially resolve the degree to which extended defects impact carrier diffusion lengths and lifetimes is important for determining upper limits for defect densities in semiconductor devices. We show that a new spatially and temporally resolved photoluminescence (PL) imaging technique can be used to accurately extract carrier lifetimes in the immediate vicinity of dark-line defects in CdTe/MgCdTe double heterostructures. A series of PL images captured during the decay process show that extended defects with a density of 1.4x10-5 cm-2 deplete photogenerated charge carriers from the surrounding semiconductor material on a nanosecond time scale. The technique makes it possible to elucidate the interplay between nonradiative carrier recombination and carrier diffusion and reveals that they both combine to degrade the PL intensity over a fractional area that is much larger than the physical size of the defects. Carrier lifetimes are correctly determined from numerical simulations of the decay behavior by taking these two effects into account. Our study demonstrates that it is crucial to measure and account for the influence of local defects in the measurement of carrier lifetime and diffusion, which are key transport parameters for the design and modeling of advanced solar-cell and light-emitting devices. We acknowledge the financial support of the Department of Energy Office of Science under Grant No. DE-AC36-08GO28308.
Hemphill, Ashton S.; Tay, Jian Wei; Wang, Lihong V.
2016-12-01
One of the prime limiting factors of optical imaging in biological applications is the diffusion of light by tissue, which prevents focusing at depths greater than the optical diffusion limit (typically ˜1 mm). To overcome this challenge, wavefront shaping techniques that use a spatial light modulator (SLM) to correct the phase of the incident wavefront have recently been developed. These techniques are able to focus light through scattering media beyond the optical diffusion limit. However, the low speeds of typically used liquid crystal SLMs limit the focusing speed. Here, we present a method using a digital micromirror device (DMD) and an electro-optic modulator (EOM) to measure the scattering-induced aberrations, and using a liquid crystal SLM to apply the correction to the illuminating wavefront. By combining phase modulation from an EOM with the DMD's ability to provide selective illumination, we exploit the DMD's higher refresh rate for phase measurement. We achieved focusing through scattering media in less than 8 ms, which is sufficiently short for certain in vivo applications, as it is comparable to the speckle correlation time of living tissue.
Bhattarai, Ajaya; Wilczura-Wachnik, Hanna
2015-01-30
Presented paper is a continuation of our studies on morin interaction with AOT (sodium bis(2-ethylhexyl) sulfosuccinate) reversed micelles solutions in two solvents: ethanol and n-decanol. Now we focused on morin influence on size and diffusion phenomena in the system morin/solvent/AOT/water. In this paper precise measurements of dynamic light scattering (DLS) of the effects of temperature, solvents (alcohols), water on the size and diffusion of AOT reversed micelles in the morin/AOT/alcohol/water system are reported. The concentrations of AOT were varied from 0.51 to 0.78mol/L. Morin concentration in during auto-correlation function registration was not the same in each solvent because of its different solubility depending on the solvent. Water concentration in the studied systems was defined by R parameter according to relation: R=(H2O)/(AOT) and was equal 0 and 30 in ethanol, and 0 in n-decanol. DLS measurements were done at 298.15 and 308.15K. DLS experiment involved on detection two relaxation modes (fast and slow) in the systems containing AOT reversed micelles, water, morin and solvents (ethanol and n-decanol). The DLS data clearly show the solvent influence as well as morin presence on AOT reversed micelles size and consequently their diffusion coefficients. Contrary to n-decanol strong competition between morin and ethanol molecules in AOT reversed micelles palisade layer has been found. It suggests that morin molecules replaced ethanol in AOT reversed micelles and locate in their palisade layer strongly increasing AOT reversed micelles size. Furthermore, it was found a sharp increase in correlation radii of slow modes of AOT reversed micelles containing morin molecules and their diffusion coefficients diminishing.
Epidemic Diffusion on Complex Networks
Institute of Scientific and Technical Information of China (English)
WU Xiao-Yan; LIU Zong-Hua
2007-01-01
Boyh diffusion and epidemic are well studied in the stochastic systems and complex networks,respetively.Here we combine these two fields and study epidemic diffusion in complex networks.Instead of studying the threshold of infection,which was focused on in previous works,we focus on the diffusion.behaviour.We find that the epidemic diffusion in a complex network is an anomalous superdiffusion with varyingg diffusion exponext γand that γ is influenced seriously by the network structure,such as the clustering coefficient and the degree distribution.Numerical simulations have confirmed the theoretical predictions.
Chakraborty, Brahmananda
2015-08-20
Applying Green-Kubo formalism and equilibrium molecular dynamics (MD) simulations, we have studied for the first time the dynamic correlation, Onsager coefficients, and Maxwell-Stefan (MS) diffusivities of molten salt LiF-BeF2, which is a potential candidate for a coolant in a high temperature reactor. We observe an unusual composition dependence and strikingly a crossover in sign for all the MS diffusivities at a composition of around 7% of LiF where the MS diffusivity between cation-anion pair (Đ(BeF) and Đ(LiF)) jumps from positive to negative value while the MS diffusivity between cation-cation pair (Đ(LiBe)) becomes positive from a negative value. Even though the negative MS diffusivities have been observed for electrolyte solutions between cation-cation pair, here we report negative MS diffusivity between cation-anion pair where Đ(BeF) shows a sharp rise around 66% of BeF2, reaches maximum value at 70% of BeF2, and then decreases almost exponentially with a sign change for BeF2 around 93%. For low mole fraction of LiF, Đ(BeF) follows the Debye-Huckel theory and rises with the square root of LiF mole fraction similar to the MS diffusivity between cation-anion pair in aqueous solution of electrolyte salt. Negative MS diffusivities while unusual are, however, shown to satisfy the non-negative entropy constraints at all thermodynamic states as required by the second law of thermodynamics. We have established a strong correlation between the structure and dynamics and predict that the formation of flouride polyanion network between Be and F ions and coulomb interaction is responsible for sharp variation of the MS diffusivities which controls the multicomponent diffusion phenomenon in LiF-BeF2 which has a strong impact on the performance of the reactor.
Anomalous Dimensions of Conformal Baryons
DEFF Research Database (Denmark)
Pica, Claudio; Sannino, Francesco
2016-01-01
We determine the anomalous dimensions of baryon operators for the three color theory as function of the number of massless flavours within the conformal window to the maximum known order in perturbation theory. We show that the anomalous dimension of the baryon is controllably small, within...
Anomalous Dimensions of Conformal Baryons
DEFF Research Database (Denmark)
Pica, Claudio; Sannino, Francesco
2016-01-01
We determine the anomalous dimensions of baryon operators for the three color theory as function of the number of massless flavours within the conformal window to the maximum known order in perturbation theory. We show that the anomalous dimension of the baryon is controllably small, within the $...
Beta Function and Anomalous Dimensions
DEFF Research Database (Denmark)
Pica, Claudio; Sannino, Francesco
2011-01-01
We demonstrate that it is possible to determine the coefficients of an all-order beta function linear in the anomalous dimensions using as data the two-loop coefficients together with the first one of the anomalous dimensions which are universal. The beta function allows to determine the anomalou...
Energy Technology Data Exchange (ETDEWEB)
Kubota, M.; Oohara, Y.; Yoshizawa, H. [Neutron Scattering Laboratory, I.S.S.P., University of Tokyo, Tokai, Ibaraki 319-1106 (Japan); Hirota, K. [CREST, Department of Physics, Tohoku University, Aoba-ku, Sendai 980-8578 (Japan); Moritomo, Y. [PRESTO and CIRSE, Nagoya University, Nagoya 464-8601 (Japan); Endoh, Y. [CREST, Institute for Materials Research, Tohoku University, Aoba-ku, Sendai 980-8577 (Japan)
2002-07-01
We performed neutron-diffraction measurements on single crystals of La{sub 2-2x}Sr{sub 1+2x}Mn{sub 2}O{sub 7}. For x=0.45, in an intermediate phase (T{sub C}
A Model of Charge Transfer Excitons: Diffusion, Spin Dynamics, and Magnetic Field Effects
Lee, Chee Kong; Willard, Adam P
2016-01-01
In this letter we explore how the microscopic dynamics of charge transfer (CT) excitons are influenced by the presence of an external magnetic field in disordered molecular semiconductors. This influence is driven by the dynamic interplay between the spin and spatial degrees of freedom of the electron-hole pair. To account for this interplay we have developed a numerical framework that combines a traditional model of quantum spin dynamics with a coarse-grained model of stochastic charge transport. This combination provides a general and efficient methodology for simulating the effects of magnetic field on CT state dynamics, therefore providing a basis for revealing the microscopic origin of experimentally observed magnetic field effects. We demonstrate that simulations carried out on our model are capable of reproducing experimental results as well as generating theoretical predictions related to the efficiency of organic electronic materials.
Energy Technology Data Exchange (ETDEWEB)
Ferragut, Erik M.; Laska, Jason A.; Bridges, Robert A.
2016-06-07
A system is described for receiving a stream of events and scoring the events based on anomalousness and maliciousness (or other classification). The system can include a plurality of anomaly detectors that together implement an algorithm to identify low-probability events and detect atypical traffic patterns. The anomaly detector provides for comparability of disparate sources of data (e.g., network flow data and firewall logs.) Additionally, the anomaly detector allows for regulatability, meaning that the algorithm can be user configurable to adjust a number of false alerts. The anomaly detector can be used for a variety of probability density functions, including normal Gaussian distributions, irregular distributions, as well as functions associated with continuous or discrete variables.
Shtukenberg, Alexander; Kahr, Bart
2007-01-01
Optical anomalies in crystals are puzzles that collectively constituted the greatest unsolved problems in crystallography in the 19th Century. The most common anomaly is a discrepancy between a crystal’s symmetry as determined by its shape or by X-ray analysis, and that determined by monitoring the polarization state of traversing light. These discrepancies were perceived as a great impediment to the development of the sciences of crystals on the basis of Curie’s Symmetry Principle, the grand organizing idea in the physical sciences to emerge in the latter half of the 19th Century. Optically Anomalous Crystals begins with an historical introduction covering the contributions of Brewster, Biot, Mallard, Brauns, Tamman, and many other distinguished crystallographers. From this follows a tutorial in crystal optics. Further chapters discuss the two main mechanisms of optical dissymmetry: 1. the piezo-optic effect, and 2. the kinetic ordering of atoms. The text then tackles complex, inhomogeneous crystals, and...
A Dynamic Density Functional Theory Approach to Diffusion in White Dwarfs and Neutron Star Envelopes
Diaw, A.; Murillo, M. S.
2016-09-01
We develop a multicomponent hydrodynamic model based on moments of the Born-Bogolyubov-Green-Kirkwood-Yvon hierarchy equations for physical conditions relevant to astrophysical plasmas. These equations incorporate strong correlations through a density functional theory closure, while transport enters through a relaxation approximation. This approach enables the introduction of Coulomb coupling correction terms into the standard Burgers equations. The diffusive currents for these strongly coupled plasmas is self-consistently derived. The settling of impurities and its impact on cooling can be greatly affected by strong Coulomb coupling, which we show can be quantified using the direct correlation function.
X-ray diffuse scattering measurements of nucleation dynamics at femtosecond resolution.
Lindenberg, A M; Engemann, S; Gaffney, K J; Sokolowski-Tinten, K; Larsson, J; Hillyard, P B; Reis, D A; Fritz, D M; Arthur, J; Akre, R A; George, M J; Deb, A; Bucksbaum, P H; Hajdu, J; Meyer, D A; Nicoul, M; Blome, C; Tschentscher, Th; Cavalieri, A L; Falcone, R W; Lee, S H; Pahl, R; Rudati, J; Fuoss, P H; Nelson, A J; Krejcik, P; Siddons, D P; Lorazo, P; Hastings, J B
2008-04-01
Femtosecond time-resolved small and wide angle x-ray diffuse scattering techniques are applied to investigate the ultrafast nucleation processes that occur during the ablation process in semiconducting materials. Following intense optical excitation, a transient liquid state of high compressibility characterized by large-amplitude density fluctuations is observed and the buildup of these fluctuations is measured in real time. Small-angle scattering measurements reveal snapshots of the spontaneous nucleation of nanoscale voids within a metastable liquid and support theoretical predictions of the ablation process.
From gas dynamics with large friction to gradient flows describing diffusion theories
Lattanzio, Corrado
2016-12-09
We study the emergence of gradient flows in Wasserstein distance as high friction limits of an abstract Euler flow generated by an energy functional. We develop a relative energy calculation that connects the Euler flow to the gradient flow in the diffusive limit regime. We apply this approach to prove convergence from the Euler-Poisson system with friction to the Keller-Segel system in the regime that the latter has smooth solutions. The same methodology is used to establish convergence from the Euler-Korteweg theory with monotone pressure laws to the Cahn-Hilliard equation.
X-ray diffuse scattering measurements of nucleation dynamics at femtosecond resolution.
Energy Technology Data Exchange (ETDEWEB)
Lindenberg, A. M.; Engemann, S.; Gaffney, K. J.; Sokolowski-Tinten, K.; Larsson, J.; Rudati, J.; Fuoss, P. H. (Advanced Photon Source); ( MSD); (Stanford Linear Acelerator Center); (Stanford Univ.); (Stanford Synchrotron Radiation Lab.); (Univ. Duisberg-Essen); (Lund Inst. of Tech.); (Univ. of Michigan); (Deutsches Elektronen-Synchrotron DESY); (Max-Planck Inst. Quantum Optics); (Univ. of California at Berkeley); (Korea Research Inst. Standards and Science); (Univ. of Chicago); (LLNL); (BNL); (Ecole Polytechnique de Montreal)
2008-03-01
Femtosecond time-resolved small and wide angle x-ray diffuse scattering techniques are applied to investigate the ultrafast nucleation processes that occur during the ablation process in semiconducting materials. Following intense optical excitation, a transient liquid state of high compressibility characterized by large-amplitude density fluctuations is observed and the buildup of these fluctuations is measured in real time. Small-angle scattering measurements reveal snapshots of the spontaneous nucleation of nanoscale voids within a metastable liquid and support theoretical predictions of the ablation process.
Energy Technology Data Exchange (ETDEWEB)
Zha, Yunfei; Li, Maojin [Renmin Hospital of Wuhan University, Wuhan (China); Yang, Jianyong [the First Affiliated Hospital, Sun Yat-Sen University, Guangzhou (China)
2010-04-15
To investigate the significance of the dynamic contrast enhanced magnetic resonance imaging (DCE-MRI) parameters of diffuse spinal bone marrow infiltration in patients with hematological malignancies. Dynamic gadolinium-enhanced MR imaging of the lumbar spine was performed in 26 patients with histologically proven diffuse bone marrow infiltration, including multiple myeloma (n = 6), acute lymphoblastic leukemia (n = 6), acute myeloid leukemia (n = 5), chronic myeloid leukemia (n = 7), and non-Hodgkin lymphoma (n = 2). Twenty subjects whose spinal MRI was normal, made up the control group. Peak enhancement percentage (E{sub max}), enhancement slope (ES), and time to peak (TTP) were determined from a time intensity curve (TIC) of lumbar vertebral bone marrow. A comparison between baseline and follow-up MR images and its histological correlation were evaluated in 10 patients. The infiltration grade of hematopoietic marrow with plasma cells was evaluated by a histological assessment of bone marrow. Differences in E{sub max}, ES, and TTP values between the control group and the patients with diffuse bone marrow infiltration were significant (t = -11.51, -9.81 and 3.91, respectively, p < 0.01). E{sub max}, ES, and TTP values were significantly different between bone marrow infiltration groups Grade 1 and Grade 2 (Z = -2.72, -2.24 and -2.89 respectively, p < 0.05). E{sub max}, ES and TTP values were not significantly different between bone marrow infiltration groups Grade 2 and Grade 3 (Z = -1.57, -1.82 and -1.58 respectively, p > 0.05). A positive correlation was found between E{sub max}, ES values and the histological grade of bone marrow infiltration (r = 0.86 and 0.84 respectively, p < 0.01). A negative correlation was found between the TTP values and bone marrow infiltration histological grade (r = -0.54, p < 0.01). A decrease in the E{sub max} and ES values was observed with increased TTP values after treatment in all of the 10 patients who responded to treatment (t
Directory of Open Access Journals (Sweden)
Marco Fronzi
2016-08-01
Full Text Available Abstract First-principles molecular dynamics simulations have been employed to analyse the proton diffusion in cubic BaZrO $$_3$$ 3 perovskite at 1300 K. A non-linear effect on the proton diffusion coefficient arising from an applied isometric strain up to 2 $$\\%$$ % of the lattice parameter, and an evident enhancement of proton diffusion under compressive conditions have been observed. The structural and electronic properties of BaZrO $$_3$$ 3 are analysed from Density Functional Theory calculations, and after an analysis of the electronic structure, we provide a possible explanation for an enhanced ionic conductivity of this bulk structure that can be caused by the formation of a preferential path for proton diffusion under compressive strain conditions. By means of Nudged Elastic Band calculations, diffusion barriers were also computed with results supporting our conclusions.
Gas dynamic analysis of the performance of diffuser augmented wind turbine
Indian Academy of Sciences (India)
M T S Badawy; M E Aly
2000-10-01
A diffuser augmented wind turbine (DAWT) is considered an important application of the advanced concepts to improve the attractiveness of wind energy. The present paper aims to find a theoretical demonstration of DAWT by using theoretical analysis, mathematical models, assumptions, estimations and maximization of power coefficients and augmentation ratios, in addition to computer programs for calculations and drawings. The final results show that the maximum power coefficient $(Cpd_0)$ and augmentation ratio $(R_b)-$ relative to Betz — are directly proportional to pressure recovery factor (Cr), turbine factor (Ct), and maximum velocity ratio (No), but inversely proportional to overall recovery factor $(C_0)$ of diffuser. The power coefficient $(Cpd_0)$ of DAWT reaches 1.5 at $C_0 \\cong -0.5$, $No \\cong 1.0$ and $Cr \\cong 0.5$, but the augmentation ratio $(R_b)$ reaches 6.0 at $C_0 \\cong -0.5, Cr \\cong 0.9$, and reaches 7.0 at $N0 \\cong 1.0$ and $Ct \\cong 1.0$, which gives a good application for DAWT systems.
Modeling and finite difference numerical analysis of reaction-diffusion dynamics in a microreactor.
Plazl, Igor; Lakner, Mitja
2010-03-01
A theoretical description with numerical experiments and analysis of the reaction-diffusion processes of homogeneous and non-homogeneous reactions in a microreactor is presented considering the velocity profile for laminar flows of miscible and immiscible fluids in a microchannel at steady-state conditions. A Mathematical model in dimensionless form, containing convection, diffusion, and reaction terms are developed to analyze and to forecast the reactor performance. To examine the performance of different types of reactors, the outlet concentrations for the plug-flow reactor (PFR), and the continuous stirred-tank reactor (CSTR) are also calculated for the case of an irreversible homogeneous reaction of two components. The comparison of efficiency between ideal conventional macroscale reactors and the microreactor is presented for a wide range of operating conditions, expressed as different Pe numbers (0.01 < Pe < 10). The numerical procedure of complex non-linear systems based on an implicit finite-difference method improved by non-equidistant differences is proposed.
On the role of mass diffusion and fluid dynamics in the dissipation of chunk mix
Energy Technology Data Exchange (ETDEWEB)
Cloutman, L D
1999-03-01
When numerically simulating multicomponent turbulent flows, subgrid-scale diffusion of chemical species requires closure. This mixing of chemical species at the molecular level dissipates concentration uctuations, which limits possible demixing and affects other pro- cesses such as energy transport and reaction rates at the subgrid level. We discuss some of the physical processes that reduce small chunks of a heavy material in a light gas or plasma to a mixture at the atomic level. Preliminary direct numerical simulations of these processes are presented using the dissipation of small spheres of heavy gas in a light gas as an archetypal process in turbulent micromixing in multicomponent ows, including classical uid instabilities and shock ejecta. We use a detailed approach for the diffusion process, directly solving the Stefan-Maxwell equations for the mass fluxes. We discuss the dissipa- tion of a 24µm sphere of xenon in helium in three different flow regimes, and we present suggestions for future work intended as input to improved subgrid-scale turbulence models.
Dynamics of an optically confined nanoparticle diffusing normal to a surface
Schein, Perry; O'Dell, Dakota; Erickson, David
2016-06-01
Here we measure the hindered diffusion of an optically confined nanoparticle in the direction normal to a surface, and we use this to determine the particle-surface interaction profile in terms of the absolute height. These studies are performed using the evanescent field of an optically excited single-mode silicon nitride waveguide, where the particle is confined in a height-dependent potential energy well generated from the balance of optical gradient and surface forces. Using a high-speed cmos camera, we demonstrate the ability to capture the short time-scale diffusion dominated motion for 800-nm-diam polystyrene particles, with measurement times of only a few seconds per particle. Using established theory, we show how this information can be used to estimate the equilibrium separation of the particle from the surface. As this measurement can be made simultaneously with equilibrium statistical mechanical measurements of the particle-surface interaction energy landscape, we demonstrate the ability to determine these in terms of the absolute rather than relative separation height. This enables the comparison of potential energy landscapes of particle-surface interactions measured under different experimental conditions, enhancing the utility of this technique.
Anomalous specific heat in ultradegenerate QED and QCD
Gerhold, A; Rebhan, Anton K
2004-01-01
We discuss the origin of the anomalous $T\\ln T^{-1}$ behavior of the low-temperature entropy and specific heat in ultradegenerate QED and QCD and report on a recent calculation which is complete to leading order in the coupling and which contains an infinite series of anomalous terms involving also fractional powers in $T$. This result involves dynamical hard-dense-loop resummation and interpolates between Debye screening effects at larger temperatures and non-Fermi-liquid behavior from only dynamically screened magnetic fields at low temperature.
Le Floch, Francois; Harris, Wesley L.
2009-11-01
A novel methodology has been developed to address sickle cell disease, based on highly descriptive mathematical models for blood flow in the capillaries. Our investigations focus on the coupling between oxygen delivery and red blood cell dynamics, which is crucial to understanding sickle cell crises and is unique to this blood disease. The main part of our work is an extensive study of blood dynamics through simulations of red cells deforming within the capillary vessels, and relies on the use of a large mathematical system of equations describing oxygen transfer, blood plasma dynamics and red cell membrane mechanics. This model is expected to lead to the development of new research strategies for sickle cell disease. Our simulation model could be used not only to assess current researched remedies, but also to spur innovative research initiatives, based on our study of the physical properties coupled in sickle cell disease.
Tripathy, Mukta; Schweizer, Kenneth S
2011-04-01
In paper II of this series we apply the center-of-mass version of Nonlinear Langevin Equation theory to study how short-range attractive interactions influence the elastic shear modulus, transient localization length, activated dynamics, and kinetic arrest of a variety of nonspherical particle dense fluids (and the spherical analog) as a function of volume fraction and attraction strength. The activation barrier (roughly the natural logarithm of the dimensionless relaxation time) is predicted to be a rich function of particle shape, volume fraction, and attraction strength, and the dynamic fragility varies significantly with particle shape. At fixed volume fraction, the barrier grows in a parabolic manner with inverse temperature nondimensionalized by an onset value, analogous to what has been established for thermal glass-forming liquids. Kinetic arrest boundaries lie at significantly higher volume fractions and attraction strengths relative to their dynamic crossover analogs, but their particle shape dependence remains the same. A limited universality of barrier heights is found based on the concept of an effective mean-square confining force. The mean hopping time and self-diffusion constant in the attractive glass region of the nonequilibrium phase diagram is predicted to vary nonmonotonically with attraction strength or inverse temperature, qualitatively consistent with recent computer simulations and colloid experiments.
Nagazi, Med-Yassine; Brambilla, Giovanni; Meunier, Gérard; Marguerès, Philippe; Périé, Jean-Noël; Cipelletti, Luca
2017-01-01
We couple a laser-based, space-resolved dynamic light scattering apparatus to a universal traction machine for mechanical extensional tests. We perform simultaneous optical and mechanical measurements on polyether ether ketone, a semi-crystalline polymer widely used in the industry. Due to the high turbidity of the sample, light is multiply scattered by the sample and the diffusing wave spectroscopy (DWS) formalism is used to interpret the data. Space-resolved DWS yields spatial maps of the sample strain and of the microscopic dynamics. An excellent agreement is found between the strain maps thus obtained and those measured by a conventional stereo-digital image correlation technique. The microscopic dynamics reveals both affine motion and plastic rearrangements. Thanks to the extreme sensitivity of DWS to displacements as small as 1 nm, plastic activity and its spatial localization can be detected at an early stage of the sample strain, making the technique presented here a valuable complement to existing material characterization methods.
Energy Technology Data Exchange (ETDEWEB)
Goyault, G.; Beregi, J.P. [University Hospital, Department of Cardiovascular imaging, Cardiologic Hospital, Lille (France); Bierry, G.; Holl, N.; Dietemann, J.L.; Kremer, S. [University Hospital, Department of Neuroradiology, Strasbourg (France); Lhermitte, B. [University Hospital, Department of Pathology, Strasbourg (France)
2012-01-15
The purpose of this study was to assess denervated muscle perfusion using dynamic susceptibility contrast MRI (DSCMRI) and contrast-enhanced ultrasound (CEUS), and to measure denervated muscle apparent diffusion coefficient (ADC) on b1000 diffusion-weighted MRI (DWMRI) at 3 T in order to clarify whether muscle denervation leads to an increase in the extracellular extravascular space, or an increase in blood flow - or both. Axotomy of the right sciatic nerve of six white rabbits was performed at day 0. At day 9, hind limb muscles MRI and CEUS were performed to assess the consequences of denervation and both semimembranosus muscles of each rabbit were explanted for histological studies. Signal intensity on T2- and T1-weighted MRI, ADC on DWMRI, maximum signal drop (MSD) on DSCMRI and the area under the curve (AUC) on CEUS were measured over circular regions of interest (ROI), in both semimembranosus muscles. Non-parametric Wilcoxon matched-pairs tests were used to assess the mean differences between denervated and normal muscles. T2 fat-saturated (FS) MRI studies showed a strong signal in the right semimembranosus muscles compared with the left side, and gadolinium enhancement was observed on T1 FS MRI. Denervated muscles show a significant increase in ADC on DWMRI (p < 0.01) and a significant signal enhancement on DSCMR imaging (p < 0.05) and on first-pass CEUS (p < 0.05). The results of this study - based on perfusion- and diffusion-weighted images - suggest that, after denervation, both increased blood flow through muscle tissue and expansion of the extracellular water volume are present. (orig.)
Wang, Jinyang; Zhong, Haimin; Feng, Huajie; Qiu, Wenda; Chen, Liuping
2014-03-14
The binary infinite dilute diffusion coefficients, D₁₂(∞), of some alkylbenzenes (Ph-C(n), from Ph-H to Ph-C12) from 313 K to 333 K at 15 MPa in supercritical carbon dioxide (scCO2) have been studied by molecular dynamics (MD) simulation. The MD values agree well with the experimental ones, which indicate MD simulation technique is a powerful way to predict and obtain diffusion coefficients of solutes in supercritical fluids. Besides, the local structures of Ph-C(n)/CO2 fluids are further investigated by calculating radial distribution functions and coordination numbers. It qualitatively convinces that the first solvation shell of Ph-C(n) in scCO2 is significantly influenced by the structure of Ph-C(n) solute. Meanwhile, the mean end-to-end distance, the mean radius of gyration and dihedral angle distribution are calculated to gain an insight into the structural properties of Ph-C(n) in scCO2. The abnormal trends of radial distribution functions and coordination numbers can be reasonably explained in term of molecular flexibility. Moreover, the computed results of dihedral angle clarify that flexibility of long-chain Ph-C(n) is the result of internal rotation of C-C single bond (σ(c-c)) in alkyl chain. It is interesting that compared with n-alkane, because of the existence of benzene ring, the flexibility of alkyl chain in Ph-C(n) with same carbon atom number is significantly reduced, as a result, the carbon chain dependence of diffusion behaviors for long-chain n-alkane (n ≥ 5) and long-chain Ph-C(n) (n ≥ 4) in scCO2 are different.
Cluster geometry and survival probability in systems driven by reaction-diffusion dynamics
Energy Technology Data Exchange (ETDEWEB)
Windus, Alastair; Jensen, Henrik J [The Institute for Mathematical Sciences, 53 Prince' s Gate, South Kensington, London SW7 2PG (United Kingdom)], E-mail: h.jensen@imperial.ac.uk
2008-11-15
We consider a reaction-diffusion model incorporating the reactions A{yields}{phi}, A{yields}2A and 2A{yields}3A. Depending on the relative rates for sexual and asexual reproduction of the quantity A, the model exhibits either a continuous or first-order absorbing phase transition to an extinct state. A tricritical point separates the two phase lines. While we comment on this critical behaviour, the main focus of the paper is on the geometry of the population clusters that form. We observe the different cluster structures that arise at criticality for the three different types of critical behaviour and show that there exists a linear relationship for the survival probability against initial cluster size at the tricritical point only.
The diffusion dynamics of choice: From durable goods markets to fashion first names
Coulmont, Baptiste; Breban, Romulus
2014-01-01
Goods, styles, ideologies are adopted by society through various mechanisms. In particular, adoption driven by innovation is extensively studied by marketing economics. Mathematical models are currently used to forecast the sales of innovative goods. Inspired by the theory of diffusion processes developed for marketing economics, we propose, for the first time, a predictive framework for the mechanism of fashion, which we apply to first names. Analyses of French, Dutch and US national databases validate our modelling approach for thousands of first names, covering, on average, more than 50% of the yearly incidence in each database. In these cases, it is thus possible to forecast how popular the first names will become and when they will run out of fashion. Furthermore, we uncover a clear distinction between popularity and fashion: less popular names, typically not included in studies of fashion, may be driven by fashion, as well.
Robustness of avalanche dynamics in sheared amorphous solids as probed by transverse diffusion.
Chattoraj, Joyjit; Caroli, Christiane; Lemaître, Anaël
2011-07-01
Using numerical simulations, we perform an extensive finite-size analysis of the transverse diffusion coefficient in a sheared 2D amorphous solid over a broad range of strain rates at temperatures up to the supercooled liquid regime. We thus obtain direct qualitative evidence for the persistence of correlations between elementary plastic events up to the vicinity of the glass transition temperature T(g). A quantitative analysis of the data, combined with a previous study of the T and γ dependence of the macroscopic stress [Phys. Rev. Lett. 105, 266001 (2010)], leads us to conclude that the average avalanche size remains essentially unaffected by temperature up to T ~ 0.75T(g).
Transnational networks, diffusion dynamics, and electoral revolutions in the postcommunist world
Bunce, Valerie; Wolchik, Sharon L.
2007-05-01
Since 1996, eight elections have taken place in postcommunist Europe and Eurasia that have replaced illiberal with liberal governments. There is ample evidence that these “electoral revolutions” reflected the cross-national diffusion of a distinctive model of regime change that was developed elsewhere and that was designed to promote democratization in authoritarian political contexts featuring semi-competitive elections. This electoral model spread throughout the postcommunist region because of both shared perceptions by opposition groups of similar local conditions and the existence of transnational democracy promotion networks that included local, regional and American participants. As these revolutions spread, however, they were less successful in carrying through democratic change-in part because local conditions were less supportive and in part because authoritarian leaders and their international allies were both forewarned and forearmed.