Computational analysis of the roles of biochemical reactions in anomalous diffusion dynamics
Naruemon, Rueangkham; Charin, Modchang
2016-04-01
Most biochemical processes in cells are usually modeled by reaction–diffusion (RD) equations. In these RD models, the diffusive process is assumed to be Gaussian. However, a growing number of studies have noted that intracellular diffusion is anomalous at some or all times, which may result from a crowded environment and chemical kinetics. This work aims to computationally study the effects of chemical reactions on the diffusive dynamics of RD systems by using both stochastic and deterministic algorithms. Numerical method to estimate the mean-square displacement (MSD) from a deterministic algorithm is also investigated. Our computational results show that anomalous diffusion can be solely due to chemical reactions. The chemical reactions alone can cause anomalous sub-diffusion in the RD system at some or all times. The time-dependent anomalous diffusion exponent is found to depend on many parameters, including chemical reaction rates, reaction orders, and chemical concentrations. Project supported by the Thailand Research Fund and Mahidol University (Grant No. TRG5880157), the Thailand Center of Excellence in Physics (ThEP), CHE, Thailand, and the Development Promotion of Science and Technology.
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
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
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
Yuste, S B; Abad, E; Baumgaertner, A
2016-07-01
We address the problem of diffusion on a comb whose teeth display varying lengths. Specifically, the length ℓ of each tooth is drawn from a probability distribution displaying power law behavior at large ℓ,P(ℓ)∼ℓ^{-(1+α)} (α>0). To start with, we focus on the computation of the anomalous diffusion coefficient for the subdiffusive motion along the backbone. This quantity is subsequently used as an input to compute concentration recovery curves mimicking fluorescence recovery after photobleaching experiments in comblike geometries such as spiny dendrites. Our method is based on the mean-field description provided by the well-tested continuous time random-walk approach for the random-comb model, and the obtained analytical result for the diffusion coefficient is confirmed by numerical simulations of a random walk with finite steps in time and space along the backbone and the teeth. We subsequently incorporate retardation effects arising from binding-unbinding kinetics into our model and obtain a scaling law characterizing the corresponding change in the diffusion coefficient. Finally, we show that recovery curves obtained with the help of the analytical expression for the anomalous diffusion coefficient cannot be fitted perfectly by a model based on scaled Brownian motion, i.e., a standard diffusion equation with a time-dependent diffusion coefficient. However, differences between the exact curves and such fits are small, thereby providing justification for the practical use of models relying on scaled Brownian motion as a fitting procedure for recovery curves arising from particle diffusion in comblike systems. PMID:27575088
Dynamics of pulses and spiral waves in excitable media with an anomalous diffusion
Yuan, Guoyong; Bao, Xueping; Yang, Shiping; Wang, Guangrui; Chen, Shaoying
2016-06-01
Spiral waves and pulses in the excitable medium with an anomalous diffusion are studied. In the medium with an one-sided fractional diffusion in the x-direction and a normal diffusion in the y-direction, a pulse, traveling along the positive x-direction, has a smaller velocity, which is different from the diffusion of a source in the other media. Its propagating velocity is a linear and increasing function of the square root of diffusion parameter, whose increasing rate depends on the fractional order. A minimal value of the diffusion parameter is needed for successfully propagating pulses, and the threshold becomes large with a decrease of the fractional order. For pulse trains, the frequency-locked bands are shifted along the increasing direction of the perturbation period when the fractional order is decreased. In the propagating process of a spiral wave, the tip drift is induced by the one-sided fractional diffusion, which may be explained by analyzing the SV area in front of the tip.
Anomalous Diffusion in Velocity Space
Trigger, S. A.
2009-01-01
The problem of anomalous diffusion in the momentum space is considered on the basis of the appropriate probability transition function (PTF). New general equation for description of the diffusion of heavy particles in the gas of the light particles is formulated on basis of the new approach similar to one in coordinate space (S. Trigger et al.). The obtained results permit to describe the various situations when the probability transition function (PTF) has a long tail in the momentum space. ...
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
International Nuclear Information System (INIS)
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) ∼ 2Dαtα, where Dα is the fractional diffusion constant and 0 < α < 2. In this article we show that both Dα 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
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 extracellular diffusion in rat cerebellum.
Xiao, Fanrong; Hrabe, Jan; Hrabetova, Sabina
2015-05-01
Extracellular space (ECS) is a major channel transporting biologically active molecules and drugs in the brain. Diffusion-mediated transport of these substances is hindered by the ECS structure but the microscopic basis of this hindrance is not fully understood. One hypothesis proposes that the hindrance originates in large part from the presence of dead-space (DS) microdomains that can transiently retain diffusing molecules. Because previous theoretical and modeling work reported an initial period of anomalous diffusion in similar environments, we expected that brain regions densely populated by DS microdomains would exhibit anomalous extracellular diffusion. Specifically, we targeted granular layers (GL) of rat and turtle cerebella that are populated with large and geometrically complex glomeruli. The integrative optical imaging (IOI) method was employed to evaluate diffusion of fluorophore-labeled dextran (MW 3000) in GL, and the IOI data analysis was adapted to quantify the anomalous diffusion exponent dw from the IOI records. Diffusion was significantly anomalous in rat GL, where dw reached 4.8. In the geometrically simpler turtle GL, dw was elevated but not robustly anomalous (dw = 2.6). The experimental work was complemented by numerical Monte Carlo simulations of anomalous ECS diffusion in several three-dimensional tissue models containing glomeruli-like structures. It demonstrated that both the duration of transiently anomalous diffusion and the anomalous exponent depend on the size of model glomeruli and the degree of their wrapping. In conclusion, we have found anomalous extracellular diffusion in the GL of rat cerebellum. This finding lends support to the DS microdomain hypothesis. Transiently anomalous diffusion also has a profound effect on the spatiotemporal distribution of molecules released into the ECS, especially at diffusion distances on the order of a few cell diameters, speeding up short-range diffusion-mediated signals in less permeable
Anomalous Diffusion on the Percolating Networks
Institute of Scientific and Technical Information of China (English)
DeLIU; HouqiangLI; 等
1997-01-01
According to the standard diffusion equation,by introducing reasonably into a anomalous diffusion coefficient,the generalized diffusion equation,which describes anomalous diffusion on the percolating networks with a power-law distribution of waiting times,is derived in this paper.The solution of the generalized diffusion equation is obtained by using the method,which is used by Barta,The problems of anomaloous diffusion on percolating networks with a power-law distribution of waiting times,which aren't solved by Barta,are resolved.
Anomalous Diffusion with Absorbing Boundary
Kantor, Yacov; Kardar, Mehran
2007-01-01
In a very long Gaussian polymer on time scales shorter that the maximal relaxation time, the mean squared distance travelled by a tagged monomer grows as ~t^{1/2}. We analyze such sub-diffusive behavior in the presence of one or two absorbing boundaries and demonstrate the differences between this process and the sub-diffusion described by the fractional Fokker-Planck equation. In particular, we show that the mean absorption time of diffuser between two absorbing boundaries is finite. Our res...
Anomalous diffusion spreads its wings
Energy Technology Data Exchange (ETDEWEB)
Klafter, J. [School of Chemistry, Tel Aviv University, Tel-Aviv (Israel)]. E-mail: klafter@post.tau.ac.il; Sokolov, I.M. [Institute of Physics, Humboldt University, Berlin (Germany)]. E-mail: igor.sokolov@physik.hu-berlin.de
2005-08-01
An increasing number of natural phenomena do not fit into the relatively simple description of diffusion developed by Einstein a century ago. As all of us are no doubt aware, this year has been declared 'world year of physics' to celebrate the three remarkable breakthroughs made by Albert Einstein in 1905. However, it is not so well known that Einstein's work on Brownian motion - the random motion of tiny particles first observed and investigated by the botanist Robert Brown in 1827 - has been cited more times in the scientific literature than his more famous papers on special relativity and the quantum nature of light. In a series of publications that included his doctoral thesis, Einstein derived an equation for Brownian motion from microscopic principles - a feat that ultimately enabled Jean Perrin and others to prove the existence of atoms (see 'Einstein's random walk' Physics World January pp19-22). Einstein was not the only person thinking about this type of problem. The 27 July 1905 issue of Nature contained a letter with the title 'The problem of the random walk' by the British statistician Karl Pearson, who was interested in the way that mosquitoes spread malaria, which he showed was described by the well-known diffusion equation. As such, the displacement of a mosquito from its initial position is proportional to the square root of time, and the distribution of the positions of many such 'random walkers' starting from the same origin is Gaussian in form. The random walk has since turned out to be intimately linked to Einstein's work on Brownian motion, and has become a major tool for understanding diffusive processes in nature. (U.K.)
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 ⟨X2(t )⟩˜tαF 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.
Anomalous diffusions induced by enhancement of memory
Kim, Hyun-Joo
2014-01-01
We introduced simple microscopic non-Markovian walk models which describe underlying mechanism of anomalous diffusions. In the models, we considered the competitions between randomness and memory effects of previous history by introducing the probability parameters. The memory effects were considered in two aspects, one is the perfect memory of whole history and the other is the latest memory improved with time. In the perfect memory model superdiffusion was induced with the relation the Hurs...
Anomalous diffusion induced by enhancement of memory
Kim, Hyun-Joo
2014-07-01
We introduced simple microscopic non-Markovian walk models which describe the underlying mechanism of anomalous diffusions. In the models, we considered the competitions between randomness and memory effects of previous history by introducing the probability parameters. The memory effects were considered in two aspects: one is the perfect memory of whole history and the other is the latest memory enhanced with time. In the perfect memory model superdiffusion was induced with the relation of the Hurst exponent H to the controlling parameter p as H =p for p >1/2, while in the latest memory enhancement models, anomalous diffusions involving both superdiffusion and subdiffusion were induced with the relations H =(1+α)/2 and H =(1-α)/2 for 0≤α≤1, where α is the parameter controlling the degree of the latest memory enhancement. Also we found that, although the latest memory was only considered, the memory improved with time results in the long-range correlations between steps and the correlations increase as time goes on. Thus we suggest the memory enhancement as a key origin describing anomalous diffusions.
Anomalous Diffusion on the Hanoi Networks
Boettcher, S.; B. Goncalves
2008-01-01
Diffusion is modeled on the recently proposed Hanoi networks by studying the mean- square displacement of random walks with time, ~t^{2/d_w}. 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-log_2(\\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 Eucli...
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.
Anomalous Diffusion of Mo Implanted into Aluminium
Institute of Scientific and Technical Information of China (English)
张通和; 吴瑜光; 邓志威; 钱卫东
2001-01-01
Mo ions are implanted into aluminium with a high ion flux and high dose at elevated temperatures of 300℃, 400℃ and 500℃ . X-ray diffraction spectra show that the Al12Mo phases are formed. Rutherford backscattering spectroscopy indicates that a profile of Mo appears in Al around the depth of 550nm and with an atomic concentration of ～7%, when Mo is implanted to the dose of 3 × 1017/cm2 with an ion flux of 45μA/cm2 (400℃).If the dose increases to 1 × 1018/cm2 at the same ion flux, the penetration of Mo ions in Al can reach a depth of 2μm, which is greater than the ion project range Rp (52.5nm). The results show that anomalous diffusion takes place. Owing to the intense atom collision cascades, the diffusion coefficient increases greatly with the increase of the ion flux and dose. The Mo diffusion coefficients in Al are calculated. The Mo retained dose in A1 increases obviously with the increase of the ion flux.
Heterogeneous anomalous diffusion in view of superstatistics
Energy Technology Data Exchange (ETDEWEB)
Itto, Yuichi
2014-08-22
Highlights: • A theory is developed for a generalized fractional kinetics in view of superstatistics. • The present theory explicitly takes into account the existence of a large time-scale separation in the infection pathway. • The present theory implies a scaling nature of the motion of the virus. - Abstract: 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.
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
Normal and anomalous diffusion of Brownian particles on disordered potentials
Salgado-García, R.
2016-07-01
In this work we study the transition from normal to anomalous diffusion of Brownian particles on disordered potentials. The potential model consists of a series of "potential hills" (defined on a unit cell of constant length) whose heights are chosen randomly from a given distribution. We calculate the exact expression for the diffusion coefficient in the case of uncorrelated potentials for arbitrary distributions. We show that when the potential heights have a Gaussian distribution (with zero mean and a finite variance) the diffusion of the particles is always normal. In contrast, when the distribution of the potential heights is exponentially distributed the diffusion coefficient vanishes when the system is placed below a critical temperature. We calculate analytically the diffusion exponent for the anomalous (subdiffusive) phase by using the so-called "random trap model". Our predictions are tested by means of Langevin simulations obtaining good agreement within the accuracy of our numerical calculations.
On anomalous diffusion in a plasma in velocity space
Trigger, SA; Ebeling, W.; Heijst, van, A.F.; Schram, PPJM Piet; Sokolov, M
2010-01-01
The problem of anomalous diffusion in momentum space is considered for plasma-like systems on the basis of a new collision integral, which is appropriate for consideration of the probability transition function (PTF) with long tails in momentum space. The generalized Fokker-Planck equation for description of diffusion (in momentum space) of particles (ions, grains etc.) in a stochastic system of light particles (electrons, or electrons and ions, respectively) is applied to the evolution of th...
Continuous time anomalous diffusion in a composite medium.
Stickler, B A; Schachinger, E
2011-08-01
The one-dimensional continuous time anomalous diffusion in composite media consisting of a finite number of layers in immediate contact is investigated. The diffusion process itself is described with the help of two probability density functions (PDFs), one of which is an arbitrary jump-length PDF, and the other is a long-tailed waiting-time PDF characterized by the waiting-time index β∈(0,1). The former is assumed to be a function of the space coordinate x and the time coordinate t while the latter is a function of x and the time interval. For such an environment a very general form of the diffusion equation is derived which describes the continuous time anomalous diffusion in a composite medium. This result is then specialized to two particular forms of the jump-length PDF, namely the continuous time Lévy flight PDF and the continuous time truncated Lévy flight PDF. In both cases the PDFs are characterized by the Lévy index α∈(0,2) which is regarded to be a function of x and t. It is possible to demonstrate that for particular choices of the indices α and β other equations for anomalous diffusion, well known from the literature, follow immediately. This demonstrates the very general applicability of the derivation and of the resulting fractional differential equation discussed here. PMID:21928958
Advances in the studies of anomalous diffusion in velocity space
Dubinova, A. A.; Trigger, S. A.
2011-01-01
A generalized Fokker-Planck equation is derived to describe particle kinetics in specific situations when the probability transition function (PTF) has a long tail in momentum space. The equation is valid for an arbitrary value of the transferred in a collision act momentum and for the arbitrary mass ratio of the interacting particles. On the basis of the generalized Fokker-Planck equation anomalous diffusion in velocity space is considered for hard sphere model of particle interactions, Coul...
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.
A Fractional Fokker-Planck Model for Anomalous Diffusion
Anderson, Johan; Kim, Eun-Jin; 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 ge...
Area and perimeter covered by anomalous diffusion processes
Luković, Mirko; Geisel, Theo; Eule, Stephan
2013-06-01
We investigate the geometric properties of two-dimensional continuous time random walks that are used extensively to model stochastic processes exhibiting anomalous diffusion in a variety of different fields. Using the concept of subordination, we determine exact analytical expressions for the average perimeter and area of the convex hulls for this class of non-Markovian processes. As the convex hull is a simple measure to estimate the home range of animals, our results give analytical estimates for the home range of foraging animals that perform sub-diffusive search strategies such as some Mediterranean seabirds and animals that ambush their prey. We also apply our results to Levy flights where possible.
A fractional Fokker-Planck model for anomalous diffusion
Energy Technology Data Exchange (ETDEWEB)
Anderson, Johan, E-mail: anderson.johan@gmail.com [Department of Earth and Space Sciences, Chalmers University of Technology, SE-412 96 Göteborg (Sweden); Kim, Eun-jin [Department of Mathematics and Statistics, University of Sheffield, Hicks Building, Hounsfield Road, Sheffield S3 7RH (United Kingdom); Moradi, Sara [Ecole Polytechnique, CNRS UMR7648, LPP, F-91128 Palaiseau (France)
2014-12-15
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 of the stable Lévy distribution. The statistical properties of the distribution functions are assessed by a generalized normalized 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.
Asymptotic neutron scattering laws for anomalously diffusing quantum particles.
Kneller, Gerald R
2016-07-28
The paper deals with a model-free approach to the analysis of quasielastic neutron scattering intensities from anomalously diffusing quantum particles. All quantities are inferred from the asymptotic form of their time-dependent mean square displacements which grow ∝t(α), with 0 ≤ α diffusion (α = 0) is here explicitly included. We discuss in particular the intermediate scattering function for long times and the Fourier spectrum of the velocity autocorrelation function for small frequencies. Quantum effects enter in both cases through the general symmetry properties of quantum time correlation functions. It is shown that the fractional diffusion constant can be expressed by a Green-Kubo type relation involving the real part of the velocity autocorrelation function. The theory is exact in the diffusive regime and at moderate momentum transfers. PMID:27475344
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.
Magin, Richard L.; Akpa, Belinda S.; Neuberger, Thomas; Webb, Andrew G.
2011-12-01
We report the appearance of anomalous water diffusion in hydrophilic Sephadex gels observed using pulse field gradient (PFG) nuclear magnetic resonance (NMR). The NMR diffusion data was collected using a Varian 14.1 Tesla imaging system with a home-built RF saddle coil. A fractional order analysis of the data was used to characterize heterogeneity in the gels for the dynamics of water diffusion in this restricted environment. Several recent studies of anomalous diffusion have used the stretched exponential function to model the decay of the NMR signal, i.e., exp[-( bD) α], where D is the apparent diffusion constant, b is determined the experimental conditions (gradient pulse separation, durations and strength), and α is a measure of structural complexity. In this work, we consider a different case where the spatial Laplacian in the Bloch-Torrey equation is generalized to a fractional order model of diffusivity via a complexity parameter, β, a space constant, μ, and a diffusion coefficient, D. This treatment reverts to the classical result for the integer order case. The fractional order decay model was fit to the diffusion-weighted signal attenuation for a range of b-values (0 < b < 4000 s mm -2). Throughout this range of b values, the parameters β, μ and D, were found to correlate with the porosity and tortuosity of the gel structure.
Anomalous and anisotropic nanoscale diffusion of hydration water molecules in fluid lipid membranes.
Toppozini, Laura; Roosen-Runge, Felix; Bewley, Robert I; Dalgliesh, Robert M; Perring, Toby; Seydel, Tilo; Glyde, Henry R; García Sakai, Victoria; Rheinstädter, Maikel C
2015-11-14
We have studied nanoscale diffusion of membrane hydration water in fluid-phase lipid bilayers made of 1,2-dimyristoyl-3-phosphocholine (DMPC) using incoherent quasi-elastic neutron scattering. Dynamics were fit directly in the energy domain using the Fourier transform of a stretched exponential. By using large, 2-dimensional detectors, lateral motions of water molecules and motions perpendicular to the membranes could be studied simultaneously, resulting in 2-dimensional maps of relaxation time, τ, and stretching exponent, β. We present experimental evidence for anomalous (sub-diffusive) and anisotropic diffusion of membrane hydration water molecules over nanometer distances. By combining molecular dynamics and Brownian dynamics simulations, the potential microscopic origins for the anomaly and anisotropy of hydration water were investigated. Bulk water was found to show intrinsic sub-diffusive motion at time scales of several picoseconds, likely related to caging effects. In membrane hydration water, however, the anisotropy of confinement and local dynamical environments leads to an anisotropy of relaxation times and stretched exponents, indicative of anomalous dynamics. PMID:26338138
Asymptotic neutron scattering laws for anomalously diffusing quantum particles
Kneller, Gerald R.
2016-07-01
The paper deals with a model-free approach to the analysis of quasielastic neutron scattering intensities from anomalously diffusing quantum particles. All quantities are inferred from the asymptotic form of their time-dependent mean square displacements which grow ∝tα, with 0 ≤ α scattering function for long times and the Fourier spectrum of the velocity autocorrelation function for small frequencies. Quantum effects enter in both cases through the general symmetry properties of quantum time correlation functions. It is shown that the fractional diffusion constant can be expressed by a Green-Kubo type relation involving the real part of the velocity autocorrelation function. The theory is exact in the diffusive regime and at moderate momentum transfers.
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
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
International Nuclear Information System (INIS)
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
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.
Anomalously Weak Dynamical Friction in Halos
Sellwood, J A
2005-01-01
A bar rotating in a pressure-supported halo generally loses angular momentum and slows down due to dynamical friction. Valenzuela & Klypin report a counter-example of a bar that rotates in a dense halo with little friction for several Gyr, and argue that their result invalidates the claim by Debattista & Sellwood that fast bars in real galaxies require a low halo density. We show that it is possible for friction to cease for a while should the pattern speed of the bar fluctuate upward. The reduced friction is due to an anomalous gradient in the phase-space density of particles at the principal resonance created by the earlier evolution. The result obtained by Valenzuela & Klypin is probably an artifact of their adaptive mesh refinement method, but anyway could not persist in a real galaxy. The conclusion by Debattista & Sellwood still stands.
Anomalous Diffusion of Water in Lamellar Membranes Formed by Pluronic Polymers
Zhang, Zhe; Ohl, Michael; Han, Youngkyu; Smith, Gregory; Do, Changwoo; Biology; Soft-Matter Division, Oak Ridge National Laboratory Team; Julich Center for Neutron Science Team
Water diffusion is playing an important role in polymer systems. We calculated the water diffusion coefficient at different layers along z-direction which is perpendicular to the lamellar membrane formed by Pluronic block copolymers (L62: (EO6-PO34-EO6)) with the molecular dynamics simulation trajectories. Water molecules at bulk layers are following the normal diffusion, while that at hydration layers formed by polyethylene oxide (PEO) and hydrophobic layers formed by polypropylene oxide (PPO) are following anomalous diffusion. We find that although the subdiffusive regimes at PEO layers and PPO layers are the same, which is the fractional Brownian motion, however, the dynamics are different, i.e. diffusion at the PEO layers is much faster than that at the PPO layers, and meanwhile it exhibits a normal diffusive approximation within a short time period which is governed by the localized free self-diffusion, but becomes subdiffusive after t >8 ps, which is governed by the viscoelastic medium. The Scientific User Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy; and Zhe Zhang gratefully acknowledges financial support from Julich Center for Neutron Science.
Cisternas, Jaime; Descalzi, Orazio; Albers, Tony; Radons, Günter
2016-05-20
We demonstrate the occurrence of anomalous diffusion of dissipative solitons in a "simple" and deterministic prototype model: the cubic-quintic complex Ginzburg-Landau equation in two spatial dimensions. The main features of their dynamics, induced by symmetric-asymmetric explosions, can be modeled by a subdiffusive continuous-time random walk, while in the case dominated by only asymmetric explosions, it becomes characterized by normal diffusion. PMID:27258868
Lagrangian stochastic modeling of anomalous diffusion in two-dimensional turbulence
Reynolds, A. M.
2002-04-01
It is shown that at intermediate times, the Langevin equation corresponding to the nonlinear Fokker-Planck equation with exponents μ=1 and ν>1 produces trajectories with multifractal scaling and anomalous power-law dispersion, in common with observations of drifters in the ocean and numerical simulations of tracer particles in two-dimensional turbulence. The extent of this regime and the occurrence of anomalously large normal diffusion at much later times are shown to be in close agreement with dispersion data from numerical simulations of two-dimensional turbulence. In analogy with the dynamics of point vortices in two-dimensional turbulence, the modeled dynamics are nonergodic and effectively comprise of a background Ornstein-Uhlenbeck process punctuated by occasional fast long flights. It is shown that these dynamics optimize the nonextensive (Tsallis) entropy. It is tentatively suggested that the anomalous dispersion in two-dimensional turbulence is a consequence of smaller than average Lagrangian accelerations in regions of the flow with faster than average velocities.
Anomalous diffusion in the nematic phase of thin disks
Alavi, A.; Frenkel, D.
1992-01-01
We report molecular-dynamics simulations of the anisotropic diffusion of infinitely thin platelets in the nematic phase. Our simulations are used to distinguish between the predictions of two different theories. The first theory, based on a mapping of the nematic phase of ellipsoidal particles on th
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...
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...
Cages and anomalous diffusion in vibrated dense granular media.
Scalliet, Camille; Gnoli, Andrea; Puglisi, Andrea; Vulpiani, Angelo
2015-05-15
A vertically shaken granular medium hosts a blade rotating around a fixed vertical axis, which acts as a mesorheological probe. At high densities, independently of the shaking intensity, the blade's dynamics shows strong caging effects, marked by transient subdiffusion and a maximum in the velocity power density spectrum, at a resonant frequency ~10 Hz. Interpreting the data through a diffusing harmonic cage model allows us to retrieve the elastic constant of the granular medium and its collective diffusion coefficient. For high frequencies f, a tail ~1/f in the velocity power density spectrum reveals nontrivial correlations in the intracage microdynamics. At very long times (larger than 10 s), a superdiffusive behavior emerges, ballistic in the most extreme cases. Consistently, the distribution of slow velocity inversion times τ displays a power-law decay, likely due to persistent collective fluctuations of the host medium. PMID:26024199
Anomalous chain diffusion in polymer nanocomposites for varying polymer-filler interaction strengths
Goswami, Monojoy; Sumpter, Bobby G.
2010-04-01
Anomalous diffusion of polymer chains in a polymer nanocomposite melt is investigated for different polymer-nanoparticle interaction strengths using stochastic molecular dynamics simulations. For spherical nanoparticles dispersed in a polymer matrix the results indicate that the chain motion exhibits three distinct regions of diffusion, the Rouse-like motion, an intermediate subdiffusive regime followed by a normal Fickian diffusion. The motion of the chain end monomers shows a scaling that can be attributed to the formation of strong “networklike” structures, which have been seen in a variety of polymer nanocomposite systems. Irrespective of the polymer-particle interaction strengths, these three regimes seem to be present with small deviations. Further investigation on dynamic structure factor shows that the deviations simply exist due to the presence of strong enthalpic interactions between the monomers with the nanoparticles, albeit preserving the anomaly in the chain diffusion. The time-temperature superposition principle is also tested for this system and shows a striking resemblance with systems near glass transition and biological systems with molecular crowding. The universality class of the problem can be enormously important in understanding materials with strong affinity to form either a glass, a gel or networklike structures.
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.
Anomalous structure and dynamics of the Gaussian-core fluid
Krekelberg, William P.; Kumar, Tanuj; Mittal, Jeetain; Errington, Jeffrey R.; Truskett, Thomas M.
2009-01-01
It is known that there are thermodynamic states for which the Gaussian-core (GC) fluid displays anomalous properties such as expansion upon isobaric cooling (density anomaly) and increased single-particle mobility upon isothermal compression (self-diffusivity anomaly). We investigate how temperature and density affect its short-range translational structural order, as characterized by the two-body excess entropy. We find that there is a wide range of conditions for which the short-range trans...
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
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.
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...
Analysis of Reaction-Diffusion Systems with Anomalous Subdiffusion
Haugh, Jason M
2009-01-01
Reaction-diffusion equations are the cornerstone of modeling biochemical systems with spatial gradients, which are relevant to biological processes such as signal transduction. Implicit in the formulation of these equations is the assumption of Fick's law, which states that the local diffusive flux of species i is proportional to its concentration gradient; however, in the context of complex fluids such as cytoplasm and cell membranes, the use of Fick's law is based on empiricism, whereas evi...
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.
Crouseilles, Nicolas; Hivert, Hélène; Lemou, Mohammed
2015-01-01
In this work, we propose some numerical schemes for linear kinetic equations in the diffusion and anomalous diffusion limit. When the equilibrium distribution function is a Maxwellian distribution, it is well known that for an appropriate time scale, the small mean free path limit gives rise to a diffusion type equation. However, when a heavy-tailed distribution is considered, another time scale is required and the small mean free path limit leads to a fractional anomalous diffusion equation....
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.
Anomalously Weak Dynamical Friction in Halos
Sellwood, J. A.; Debattista, Victor P.
2005-01-01
A bar rotating in a pressure-supported halo generally loses angular momentum and slows down due to dynamical friction. Valenzuela & Klypin report a counter-example of a bar that rotates in a dense halo with little friction for several Gyr, and argue that their result invalidates the claim by Debattista & Sellwood that fast bars in real galaxies require a low halo density. We show that it is possible for friction to cease for a while should the pattern speed of the bar fluctuate upward. The re...
Dynamic Bayesian diffusion estimation
Dedecius, K
2012-01-01
The rapidly increasing complexity of (mainly wireless) ad-hoc networks stresses the need of reliable distributed estimation of several variables of interest. The widely used centralized approach, in which the network nodes communicate their data with a single specialized point, suffers from high communication overheads and represents a potentially dangerous concept with a single point of failure needing special treatment. This paper's aim is to contribute to another quite recent method called diffusion estimation. By decentralizing the operating environment, the network nodes communicate just within a close neighbourhood. We adopt the Bayesian framework to modelling and estimation, which, unlike the traditional approaches, abstracts from a particular model case. This leads to a very scalable and universal method, applicable to a wide class of different models. A particularly interesting case - the Gaussian regressive model - is derived as an example.
Subdiffusion, Anomalous Diffusion and Propagation of a Particle Moving in Random and Periodic Media
Mishra, Shradha; Bhattacharya, Sanchari; Webb, Benjamin; Cohen, E. G. D.
2016-02-01
We investigate the motion of a single particle moving on a two-dimensional square lattice whose sites are occupied by right and left rotators. These left and right rotators deterministically rotate the particle's velocity to the right or left, respectively and flip orientation from right to left or from left to right after scattering the particle. We study three types of configurations of left and right rotators, which we think of as types of media, through with the particle moves. These are completely random (CR), random periodic (RP), and completely periodic (CP) configurations. For CR configurations the particle's dynamics depends on the ratio r of right to left scatterers in the following way. For small r˜eq 0, when the configuration is nearly homogeneous, the particle subdiffuses with an exponent of 2/3, similar to the diffusion of a macromolecule in a crowded environment. Also, the particle's trajectory has a fractal dimension of d_f˜eq 4/3, comparable to that of a self-avoiding walk. As the ratio increases to r˜eq 1, the particle's dynamics transitions from subdiffusion to anomalous diffusion with a fractal dimension of d_f˜eq 7/4, similar to that of a percolating cluster in 2-d. In RP configurations, which are more structured than CR configurations but also randomly generated, we find that the particle has the same statistic as in the CR case. In contrast, CP configurations, which are highly structured, typically will cause the particle to go through a transient stage of subdiffusion, which then abruptly changes to propagation. Interestingly, the subdiffusive stage has an exponent of approximately 2/3 and a fractal dimension of d_f˜eq 4/3, similar to the case of CR and RP configurations for small r.
Zonal flow dynamics and anomalous transport
International Nuclear Information System (INIS)
Nonlinear equations for the slow space-time evolution of the radial drift wave-ion-temperature gradient (DW-ITG) envelope and zonal flow (ZF) amplitude have been derived within a coherent four-wave drift wave-zonal flow model. In the local limit this model demonstrates spontaneous generation of zonal flow and nonlinear drift wave-zonal flow dynamics in toroidal plasmas. The model allows slow temporal and spatial variations of the DW-ITG radial envelope, incorporating the effects of equilibrium variations, i.e., turbulence spreading and size dependence of the saturated wave intensities and transport coefficients. The competition between linear drive/damping and drift wave spreading due to linear and nonlinear group velocities and nonlinear energy transfer between DW and ZF determines the saturation levels of the fluctuating fields. The turbulence intensity level exhibits a transition from Bohm scaling at small system size (Lp/ρi) to gyro-Bohm for large system size. This system exhibits chaotic behavior and intermittency, depending on system size and proximity to marginal stability
Density approach to ballistic anomalous diffusion: An exact analytical treatment
Bologna, Mauro; Ascolani, Gianluca; Grigolini, Paolo
2010-04-01
This paper addresses the problem of deriving the probability distribution density of a diffusion process generated by a nonergodic dichotomous fluctuation using the Liouville equation (density method). The velocity of the diffusing particles fluctuates from the value of 1 to the value of -1, and back, with the distribution density of time durations τ of the two states proportional to 1/τμ in the asymptotic time limit. The adopted density method allows us to establish an exact analytical expression for the probability distribution density of the diffusion process generated by these fluctuations. Contrary to intuitive expectations, the central part of the diffusion distribution density is not left empty when moving from μ >2 (ergodic condition) to μ μcr, the monomodal distribution density with a minimum at the origin is turned into a bimodal one, with a central bump whose intensity increases for μ →2. The exact theoretical treatment applies to the asymptotic time limit, which establishes for the diffusion process the ballistic scaling value δ =1. To assess the time evolution toward this asymptotic time condition, we use a numerical approach which relates the emergence of the central bump at μ =μcr with the generation of the ordinary scaling δ =0.5, which lasts for larger and larger times for μ coming closer and closer to the critical value μ =2. We assign to the waiting time distribution density two different analytical forms: one derived from the Manneville intermittence (MI) theory and one from the Mittag-Leffler (ML) survival probability. The adoption of the ML waiting time distribution density generates an exact analytical prediction, whereas the MI method allows us to get the same asymptotic time limit as the ML one for μ adoption of these two waiting time distribution densities sheds light into the critical nature of the condition μ =2 and into why this is the critical point for the MI process, representing the phase transition from the
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...
Serva, Maurizio; Vergni, Davide; Vulpiani, Angelo
2016-07-01
We investigate front propagation in systems with diffusive and subdiffusive behavior. The scaling behavior of moments of the diffusive problem, both in the standard and in the anomalous cases, is not enough to determine the features of the reactive front. In fact, the shape of the bulk of the probability distribution of the transport process, which determines the diffusive properties, is important just for preasymptotic behavior of front propagation, while the precise shape of the tails of the probability distribution determines asymptotic behavior of front propagation. PMID:27575110
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.
Anomalous structure and dynamics of the Gaussian-core fluid.
Krekelberg, William P; Kumar, Tanuj; Mittal, Jeetain; Errington, Jeffrey R; Truskett, Thomas M
2009-03-01
It is known that there are thermodynamic states for which the Gaussian-core fluid displays anomalous properties such as expansion upon isobaric cooling (density anomaly) and increased single-particle mobility upon isothermal compression (self-diffusivity anomaly). Here, we investigate how temperature and density affect its short-range translational structural order, as characterized by the two-body excess entropy. We find that there is a wide range of conditions for which the short-range translational order of the Gaussian-core fluid decreases upon isothermal compression (structural order anomaly). As we show, the origin of the structural anomaly is qualitatively similar to that of other anomalous fluids (e.g., water or colloids with short-range attractions) and is connected to how compression affects static correlations at different length scales. Interestingly, we find that the self-diffusivity of the Gaussian-core fluid obeys a scaling relationship with the two-body excess entropy that is very similar to the one observed for a variety of simple liquids. One consequence of this relationship is that the state points for which structural, self-diffusivity, and density anomalies of the Gaussian-core fluid occur appear as cascading regions on the temperature-density plane; a phenomenon observed earlier for models of waterlike fluids. There are, however, key differences between the anomalies of Gaussian-core and waterlike fluids, and we discuss how those can be qualitatively understood by considering the respective interparticle potentials of these models. Finally, we note that the self-diffusivity of the Gaussian-core fluid obeys different scaling laws depending on whether the two-body or total excess entropy is considered. This finding, which deserves more comprehensive future study, appears to underscore the significance of higher-body correlations for the behavior of fluids with bounded interactions. PMID:19391927
Nonlinear dynamics induced anomalous Hall effect in topological insulators
Wang, Guanglei; Xu, Hongya; Lai, Ying-Cheng
2016-01-01
We uncover an alternative mechanism for anomalous Hall effect. In particular, we investigate the magnetisation dynamics of an insulating ferromagnet (FM) deposited on the surface of a three-dimensional topological insulator (TI), subject to an external voltage. The spin-polarised current on the TI surface induces a spin-transfer torque on the magnetisation of the top FM while its dynamics can change the transmission probability of the surface electrons through the exchange coupling and hence the current. We find a host of nonlinear dynamical behaviors including multistability, chaos, and phase synchronisation. Strikingly, a dynamics mediated Hall-like current can arise, which exhibits a nontrivial dependence on the channel conductance. We develop a physical understanding of the mechanism that leads to the anomalous Hall effect. The nonlinear dynamical origin of the effect stipulates that a rich variety of final states exist, implying that the associated Hall current can be controlled to yield desirable behaviors. The phenomenon can find applications in Dirac-material based spintronics.
Anomalous shift of magnetic diffuse scattering studied by neutron diffraction
Energy Technology Data Exchange (ETDEWEB)
Prokes, K [Helmholtz Centre Berlin for Materials and Energy, SF-2, Glienicker Strasse 100, 14109 Berlin (Germany); Lander, G H [European Commission, JRC, Institute for Transuranium Elements, Postfach 2340, 76125 Karlsruhe (Germany); Bernhoeft, N [CEA Grenoble, DRFMC/SPSMS, F-38054 Grenoble (France)], E-mail: prokes@helmholtz-berlin.de
2009-07-15
Neutron diffraction results, in the vicinity of the magnetic phase transition of USb and MnF{sub 2}, are reported. The thermal evolution of the magnetic diffuse signal and nuclear Bragg reflections demonstrate that the centre of gravity of the magnetic signals does not lie at the predicted position as calculated from nuclear reflections. This phenomenon, called the q-shift, was first found using resonance x-ray scattering (RXS). The present results show that, (i) the effect is not an artefact of RXS and is also found with neutrons (ii) that the effect arises from the bulk of the sample and is not restricted to the near surface layer ({approx}2000 A) associated with the RXS probe in actinide systems, (iii) the effect is not restricted to actinide compounds.
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.
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.
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. ...
Improved estimation of anomalous diffusion exponents in single particle tracking experiments
Bronshtein, Eldad Kepten Irena; Garini, Yuval
2012-01-01
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 ari...
Convective cell formation and anomalous diffusion due to electromagnetic drift wave turbulence
International Nuclear Information System (INIS)
Convective cell formation and spectral cascade processes due to gravitational drift Alfven waves are studied using a new type of model equation. Conservation relations are derived and explosive instability is found for systems near marginal finite β stability. This instability also remains when the effects of poor as well as favorable curvature regions are included, i.e., for ballooning modes. The anomalous diffusion due to convective cells and quasi-linear effects are compared
CONCENTRATION DISTRIBUTION OF FRACTIONAL ANOMALOUS DIFFUSION CAUSED BY AN INSTANTANEOUS POINT SOURCE
Institute of Scientific and Technical Information of China (English)
段俊生; 徐明瑜
2003-01-01
The Fox function expression and the analytic expression for the concentration distribution of fractional anomalous diffusion caused by an instantaneous point source in ndimensional space ( n = 1, 2 or 3 ) are derived by means of the condition of mass conservation, the time-space similarity of the solution, Mellin transform and the properties of the Fox function. And the asymptotic behaviors for the solutions are also given.
Self-similar motion for modeling anomalous diffusion and nonextensive statistical distributions
Huang, Zhifu; Su, Guozhen; Wang, Qiuping A.; Chen, Jincan
2010-01-01
We introduce a new universality class of one-dimensional iteration model giving rise to self-similar motion, in which the Feigenbaum constants are generalized as self-similar rates and can be predetermined. The curves of the mean-square displacement versus time generated here show that the motion is a kind of anomalous diffusion with the diffusion coefficient depending on the self-similar rates. In addition, it is found that the distribution of displacement agrees to a reliable precision with...
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.
Long-lived anomalous thermal diffusion induced by elastic cell membranes on nearby particles
Daddi-Moussa-Ider, Abdallah; Guckenberger, Achim; 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 10 ms and can enhance residence times and possibly 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.
Water ingress in Y-type zeolite: anomalous moisture-dependent transport diffusivity.
de Azevedo, Eduardo N; da Silva, D Vitoreti; de Souza, R E; Engelsberg, M
2006-10-01
Nuclear magnetic resonance imaging measurements of liquid water ingress in a large number of nonactivated Y-type (Na) zeolite samples prepared under different conditions are reported on. Using an experimental arrangement that permits the application of Boltzmann's transformation of the 1D (one-dimensional) diffusion equation, the spatiotemporal scaling variables required for a collapse of the measured profiles into universal curves revealed subdiffusive behavior in all cases. It is shown that the one-dimensional fractal time diffusion equation constitutes a powerful tool to analyze the data and provides a connection between the moisture dependence of the effective transport diffusivities and the shapes of the universal curves. Thus, even for anomalous diffusion, the relationship between the universal curves and structural characteristics of the system; such as porosity, tortuosity of the pore space and, in some cases, the interplay between mesopores and nanopores can be addressed. PMID:17155023
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.
York, D. G.; Dahlstrom, J.; Welty, D. E.; Oka, T.; Hobbs, L. M.; Johnson, S.; Friedman, S. D.; Jiang, Z.; Rachford, B. L.; Snow, T. P.; Sherman, R.; Sonnentrucker, P.
2014-02-01
Anomalously broad diffuse interstellar bands (DIBs) at 5780.5, 5797.1, 6196.0, and 6613.6 Å are found in absorption along the line of sight to Herschel 36, an O star system next to the bright Hourglass nebula of the Hii region Messier 8. Excited lines of CH and CH+ are seen as well. We show that the region is very compact and itemize other anomalies of the gas. An infrared-bright star within 400 AU is noted. The combination of these effects produces anomalous DIBs, interpreted by Oka et al. (2013, see also this volume) as being caused predominantly by infrared pumping of rotational levels of relatively small molecules.
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.
On The Anomalous Fast Ion Energy Diffusion in Toroidal Plasmas Due to Cavity Modes
International Nuclear Information System (INIS)
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, Yi; Cao, Xiangyu; Gao, Jun; Liu, Xiao; Li, Sijia
2016-05-16
We demonstrate a simple reconfigurable metasurface with multiple functions. Anisotropic tiles are investigated and manufactured as fundamental elements. Then, the tiles are combined in a certain sequence to construct a metasurface. Each of the tiles can be adjusted independently which is like a jigsaw puzzle and the whole metasurface can achieve diverse functions by different layouts. For demonstration purposes, we realize polarization conversion, anomalous reflection and diffusion by a jigsaw puzzle metasurface with 6 × 6 pieces of anisotropic tile. Simulated and measured results prove that our method offers a simple and effective strategy for metasurface design. PMID:27409942
From moving averages to anomalous diffusion: a Rényi-entropy approach
International Nuclear Information System (INIS)
Moving averages, also termed convolution filters, are widely applied in science and engineering at large. As moving averages transform inputs to outputs by convolution, they induce correlation. In effect, moving averages are perhaps the most fundamental and ubiquitous mechanism of transforming uncorrelated inputs to correlated outputs. In this paper we study the correlation structure of general moving averages, unveil the Rényi-entropy meaning of a moving-average's overall correlation, address the maximization of this overall correlation, and apply this overall correlation to the dispersion-measurement and to the classification of regular and anomalous diffusion transport processes. (fast track communication)
Volpe, Giorgio; Volpe, Giovanni; Gigan, Sylvain
2014-01-01
The motion of particles in random potentials occurs in several natural phenomena ranging from the mobility of organelles within a biological cell to the diffusion of stars within a galaxy. A Brownian particle moving in the random optical potential associated to a speckle pattern, i.e., a complex interference pattern generated by the scattering of coherent light by a random medium, provides an ideal model system to study such phenomena. Here, we derive a theory for the motion of a Brownian particle in a speckle field and, in particular, we identify its universal characteristic timescale. Based on this theoretical insight, we show how speckle light fields can be used to control the anomalous diffusion of a Brownian particle and to perform some basic optical manipulation tasks such as guiding and sorting. Our results might broaden the perspectives of optical manipulation for real-life applications. PMID:24496461
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.
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.
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.
Replicator dynamics with diffusion on multiplex networks
Requejo, R. J.; Díaz-Guilera, A.
2016-08-01
In this study we present an extension of the dynamics of diffusion in multiplex graphs, which makes the equations compatible with the replicator equation with mutations. We derive an exact formula for the diffusion term, which shows that, while diffusion is linear for numbers of agents, it is necessary to account for nonlinear terms when working with fractions of individuals. We also derive the transition probabilities that give rise to such macroscopic behavior, completing the bottom-up description. Finally, it is shown that the usual assumption of constant population sizes induces a hidden selective pressure due to the diffusive dynamics, which favors the increase of fast diffusing strategies.
International Nuclear Information System (INIS)
We present a classical molecular dynamics simulation of uranium dioxide in the temperature range of 300-3000 K. Temperature dependences of thermal conductivity, heat capacity and ionic conductivity are investigated. Our study shows the rise of thermal conductivity of uranium dioxide at very high temperatures (above 2500 K), which is not predicted by the former anharmonic theories. Several pair potentials are used in the simulation, and they depict similar effects. Long range forces are accounted by Ewald sums. Static thermal properties are evaluated in NPT ensemble. It is shown that a high-temperature peak on heat capacity is present and is more legible in large systems. To ensure the best reliability, transport properties are evaluated using the theory of autocorrelation functions in NVE ensemble. In order to properly define thermal conductivity in ionic systems with charge fluxes, an expression which accounts the thermoelectric effect is derived from Onsager reciprocal relations. The rise on temperature dependence of thermal conductivity is accompanied by the peak on heat capacity and an anomalous rise of ionic conductivity. However, it is shown that there is no partial melting of the oxygen sublattice, which suggests that the system does not necessarily exhibit a superionic transition. Instead, kick-out diffusion in oxygen sublattice is proposed to be the origin of such anomalous behavior of thermophysical properties. (author)
Quantum diffusion dynamics in nonlinear systems: A modified kicked-rotor model
International Nuclear Information System (INIS)
Using a simple method analogous to a quantum rephasing technique, a simple modification to a paradigm of classical and quantum chaos is proposed. The interesting quantum maps thus obtained display remarkably rich quantum dynamics. Emphasis is placed on the destruction of dynamical localization without breaking periodicity, unbounded quantum anomalous diffusion in integrable systems, and transient dynamical localization. Experimental realizations of this work are also discussed
International Nuclear Information System (INIS)
The understanding of the thermodynamic properties of solids has important applications in diverse areas like condensed matter physics, materials science, mineralogy, geophysics, etc. We have been extensively investigating anomalous thermodynamic properties of compounds using the techniques of lattice dynamics, inelastic neutron scattering, inelastic x-ray scattering and synchrotron x-ray diffraction. Here we present some of the results from our recent studies. Studies of materials exhibiting anomalous thermal expansion are of interest due to their fundamental scientific importance and potential applications in ceramic, optical and electronic industry etc. We have studied the thermodynamic properties of negative thermal expansion (NTE) compounds ZrWO8, HfW2O8, ZrMO2O8, Zn(CN)2, Cu2O, Ag2O; Ag3Co(CN)6 and Ag3Fe(CN)6. Our calculations predicted that large softening of the phonon spectrum involving librational and translational modes below 10 MeV would be responsible for anomalous thermal expansion behaviour. High pressure inelastic neutron scattering experiments carried by us on cubic ZrW2O8, ZrMo2O8 and Zn(CN)2 confirmed the phonon softening. The thermal expansion as derived from the phonon measurements is in good agreement with that obtained from diffraction data. This indicates that unusual phonon softening of low energy modes is able to account for the thermal expansion behaviour in these compounds. Superionic conduction in fluorite-structured (anti-fluorite, Li2O) oxides and LiMPO4 (M=Fe, Mn) have applications in energy storage, conversion and nuclear industry. Fast ion conductors exhibit high ionic conductivity, which allow macroscopic movement of ions through their structure. The possible role of phonon in initiation of diffusion has been studied in Li2O and LiMPO4 (M=Fe, Mn). The simulations play a pivotal role in understanding the conduction processes at high temperatures in these compounds. (author)
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.
O'Brien, T. P.
2015-01-01
in the magnetospheric magnetic field produce drift shell splitting, which causes the radial (drift shell) invariant to sometimes depend on pitch angle. Where drift shell splitting is significant, pitch angle scattering leads to diffusion in all three invariants of the particle's motion, including cross diffusion. We examine the magnitude of drift shell splitting-related anomalous diffusion for outer zone electrons compared to conventional diffusion in the absence of drift shell splitting. We assume that the primary local scattering process is wave-particle interactions with chorus. We find that anomalous radial diffusion can exceed that of conventional drift-resonant radial diffusion for particles with energies near 0.1 MeV at all radial distances outside the plasmasphere during quiet to moderate geomagnetic activity, and it is significant at 0.5 MeV. Cross diffusion involving the radial invariant can exceed the geometric mean of the corresponding pure diffusion coefficients at 0.1 MeV, and that such cross diffusion is significant even at 0.5-1 MeV. At 1 MeV, cross diffusion is often significant. The highest radial distances and magnetic activity levels in our study do not always exhibit as much significant anomalous diffusion as moderate radial distances and activity levels. This can be explained by (a) stronger dependence of conventional diffusion on magnetic activity and radius, and (b) strongest drift shell splitting at moderate magnetic activity. Simulation codes that neglect the possibility for cross terms will likely systematically underperform, especially for 0.1-0.5 MeV electrons, for much of the outer zone for quiet to moderate levels of magnetic activity.
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.
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...
Diffusion dynamics on multiplex networks
Gomez, S; Gomez-Gardeñes, J; Perez-Vicente, C J; Moreno, Y; Arenas, A
2012-01-01
We study the time scales associated to diffusion processes that take place on multiplex networks (a set of networks structured in interconnected layers). To this end we propose the construction of a supra-Laplacian matrix, which consists of a dimensional lifting of the Laplacian matrix of each layer of the multiplex network. We use perturbative analysis to reveal analytically the structure of eigenvectors and eigenvalues of the complete network in terms of the spectral properties of the individual layers. The spectrum of the supra-Laplacian allows us to understand the physics of diffusion-like processes on top of multiplex networks.
Protein Dynamical Transition: Role of Methyl Dynamics and Local Diffusion
Krishnan, M.; Schulz, R.; Smith, Jeremy C.
2009-03-01
The temperature-dependent protein dynamical transition is investigated using the Instanteous Normal mode analysis (INM) and molecular dynamics (MD) simulation of crystalline myoglobin and Toxin II. The onset of anharmonic dynamics in myoglobin is observed at 150 K, far below the much-studied solvent-activated dynamical transition at 220 K. A significant fraction of methyl groups exhibit nanosecond anharmonic rotational jump diffusion at 150 K indicating the essential role of methyl dynamics in the low-temperature onset of anharmonic protein dynamics. The methyl groups that exhibit many rotational excitations are located near xenon cavities, suggesting that cavities in proteins act as activation centers of anharmonic dynamics. INM analysis of Toxin II indicates the presence of non-zero barrier-crossing, diffusive degrees of freedom accessible to the protein below the dynamical transition. The number of these diffusive degrees of freedom increases abruptly at the dynamical transition. In summary, the present investigation suggests that local diffusive processes (for example, methyl dynamics) are activated at low temperatures (much below 220 K) leading to global diffusive protein dynamics (this involves excitation of many protein atoms) at the dynamical transition.
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
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.
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.
Dynamical corrections to the anomalous holographic softwall model: the pomeron and the odderon
Capossoli, Eduardo Folco; Boschi-Filho, Henrique
2016-01-01
In this work we use the holographic softwall 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 its respective 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 Einstein equations in 5 dimensions. The results found in this work for the Regge trajectories within the anomalous softwall model with dynamical corrections are consistent with those presented in the literature.
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.)
Anomalous scaling of Cu-island dynamics on Ag(100)
Energy Technology Data Exchange (ETDEWEB)
Zaum, Christopher; Morgenstern, Karina [Institut fuer Festkoerperphysik, Gottfried Wilhelm Leibniz Universitaet, Appelstr. 2, D-30167 Hannover (Germany)
2008-07-01
We deposited Cu-islands containing 10 to 500 atoms on a clean Ag(100) surface at room temperature and investigated diffusion and decay of these islands with a fast scanning tunneling microscope. Islands at sizes above 80 atoms per island are adsorbed in hollow-sites. Islands at sizes below 80 atoms per island are adsorbed in bridge-sites. Diffusion and decay behavior of the hollow-site islands is similar to the behavior of both Ag-islands on Ag(100) and Cu-islands on Cu(100). In contrast, the diffusivity and the decay time of the bridge-site islands are significantly higher than any previously measured values. This indicates a novel mechanism of diffusion.
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.
D. Panja
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
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.
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...
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.
Diffuse-dynamic multiparameter diffractometry: A review
Molodkin, V. B.; Shpak, A. P.; Kovalchuk, M. V.; Nosik, V. L.; Machulin, V. F.
2010-12-01
The results reported at the Conference on Application of X-Rays, Synchrotron Radiation, Neutrons, and Electrons in Nano-, Bio-, Information-, and Cognitive Technologies (RSNE-NBIC 2009) are briefly reviewed. This review is based on a cycle of studies [1-6] where a new method for studying the structure of real crystals—diffuse-dynamic multiparameter diffractometry (DDMD)—was proposed and substantiated.
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.
Anomalous behavior of the coherent light diffusion by a tilted translucent rough surface: part I
Rebollo, M. A.; Perez Quintian, F.; Hogert, Elsa N.; Landau, Monica R.; Gaggioli, Nestor G.
1996-02-01
When a translucent rough surface is illuminated, light is diffused in different directions. The envelope the intensity distribution is called diffusion curve. As the diffuser is rotated with respect to the incident beam, the diffuser curve changes its appearance: the maximum suffers a displacement and changes its shape. Some authors have studied this phenomenon, but none of them explained it properly. In this work we make an additional contribution to address the problem, showing experimentally that the maximum displacement depends on the incident angle and the diffuser ratio T/(sigma) . We compare our experimental results with those that can be calculated with the reformulated Beckmann's theory. We could observe important agreements and differences. For example, Beckmann's theory predicts that the diffusion results are asymmetric, while our measured results are indefectibly symmetric.
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
2014-12-01
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.
Energy Technology Data Exchange (ETDEWEB)
Migliori, A.; Maxton, P.M.; Clogston, A.M.; Zirngiebl, E.; Lowe, M.
1988-12-15
We measured the temperature dependence of the intensity of the two lowest Raman modes in single crystals of l-alanine. The sum of the intensities obeys Maxwell-Boltzman statistics accurately from 20 to 340 K but the intensities of the individual lines are anomalous. This behavior is explained by assuming that both lines share the same degrees of freedom but that a mode instability is triggered abruptly at an occupation of seven quanta. This instability, which has an activation energy of 500 K, is observed at temperatures as low as 20 K, possibly indicating the existence of dynamic localization of vibrational energy.
Raudino, Antonio; Raciti, Domenica; Grassi, Antonio; Pannuzzo, Martina; Corti, Mario
2016-08-30
We investigate, both theoretically and experimentally, the role played by the oscillations of the cell membrane on the capture rate of substances freely diffusing around the cell. To obtain quantitative results, we propose and build up a reproducible and tunable biomimetic experimental model system to simulate the phenomenon of an oscillation-enhanced (or depressed) capture rate (chemoreception) of a diffusant. The main advantage compared to real biological systems is that the different oscillation parameters (type of deformation, frequencies, and amplitudes) can be finely tuned. The model system that we use is an anchored gas drop submitted to a diffusive flow of charged surfactants. When the surfactant meets the surface of the bubble, it is reversibly adsorbed. Bubble oscillations of the order of a few nanometers are selectively excited, and surfactant transport is accurately measured. The surfactant concentration past the oscillating bubbles was detected by conductivity measurements. The results highlight the role of surface oscillations on the diffusant capture rate. Particularly unexpected is the onset of intense overshoots during the adsorption process. The phenomenon is particularly relevant when the bubbles are exposed to intense forced oscillations near resonance. PMID:27509197
Balankin, Alexander S.; Valdivia, Juan-Carlos; Marquez, Jesús; Susarrey, Orlando; Solorio-Avila, Marco A.
2016-08-01
In this Letter, we report experimental and theoretical studies of Newtonian fluid flow through permeable media with fractal porosity. Darcy flow experiments were performed on samples with a deterministic pre-fractal pore network. We found that the seepage velocity is linearly proportional to the pressure drop, but the apparent absolute permeability increases with the increase of sample length in the flow direction L. We claim that a violation of the Hagen-Poiseuille law is due to an anomalous diffusion of the fluid momentum. In this regard we argue that the momentum diffusion is governed by the flow metric induced by the fractal topology of the pore network. The Darcy-like equation for laminar flow in a fractal pore network is derived. This equation reveals that the apparent absolute permeability is independent of L, only if the number of effective spatial degrees of freedom in the pore-network ν is equal to the network fractal (self-similarity) dimension D, e.g. it is in the case of fractal tree-like networks. Otherwise, the apparent absolute permeability either decreases with L, if ν fractal channels, or increases with L, if ν > D, as this is in the case of the inverse Menger sponge.
Diffusion of Particle in Hyaluronan Solution, a Brownian Dynamics Simulation
Takasu, Masako; Tomita, Jungo
2004-04-01
Diffusion of a particle in hyaluronan solution is investigated using Brownian dynamics simulation. The slowing down of diffusion is observed, in accordance with the experimental results. The temperature dependence of the diffusion is calculated, and a turnover is obtained when the temperature is increased.
Volpe, Giorgio; Volpe, Giovanni; Gigan, Sylvain
2014-01-01
The motion of particles in random potentials occurs in several natural phenomena ranging from the mobility of organelles within a biological cell to the diffusion of stars within a galaxy. A Brownian particle moving in the random optical potential associated to a speckle, i.e., a complex interference pattern generated by the scattering of coherent light by a random medium, provides an ideal mesoscopic model system to study such phenomena. Here, we derive a theory for the motion of a Brownian ...
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.
Dynamic Nuclear Polarization as Kinetically Constrained Diffusion
Karabanov, A.; Wiśniewski, D.; Lesanovsky, I.; Köckenberger, W.
2015-07-01
Dynamic nuclear polarization (DNP) is a promising strategy for generating a significantly increased nonthermal spin polarization in nuclear magnetic resonance (NMR) and its applications that range from medicine diagnostics to material science. Being a genuine nonequilibrium effect, DNP circumvents the need for strong magnetic fields. However, despite intense research, a detailed theoretical understanding of the precise mechanism behind DNP is currently lacking. We address this issue by focusing on a simple instance of DNP—so-called solid effect DNP—which is formulated in terms of a quantum central spin model where a single electron is coupled to an ensemble of interacting nuclei. We show analytically that the nonequilibrium buildup of polarization heavily relies on a mechanism which can be interpreted as kinetically constrained diffusion. Beyond revealing this insight, our approach furthermore permits numerical studies of ensembles containing thousands of spins that are typically intractable when formulated in terms of a quantum master equation. We believe that this represents an important step forward in the quest of harnessing nonequilibrium many-body quantum physics for technological applications.
Dynamic Nuclear Polarization as Kinetically Constrained Diffusion.
Karabanov, A; Wiśniewski, D; Lesanovsky, I; Köckenberger, W
2015-07-10
Dynamic nuclear polarization (DNP) is a promising strategy for generating a significantly increased nonthermal spin polarization in nuclear magnetic resonance (NMR) and its applications that range from medicine diagnostics to material science. Being a genuine nonequilibrium effect, DNP circumvents the need for strong magnetic fields. However, despite intense research, a detailed theoretical understanding of the precise mechanism behind DNP is currently lacking. We address this issue by focusing on a simple instance of DNP-so-called solid effect DNP-which is formulated in terms of a quantum central spin model where a single electron is coupled to an ensemble of interacting nuclei. We show analytically that the nonequilibrium buildup of polarization heavily relies on a mechanism which can be interpreted as kinetically constrained diffusion. Beyond revealing this insight, our approach furthermore permits numerical studies of ensembles containing thousands of spins that are typically intractable when formulated in terms of a quantum master equation. We believe that this represents an important step forward in the quest of harnessing nonequilibrium many-body quantum physics for technological applications. PMID:26207453
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.
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.
Thermodynamic and dynamic controls on changes in the zonally anomalous hydrological cycle
Wills, Robert C.; Byrne, Michael P.; Schneider, Tapio
2016-05-01
The wet gets wetter, dry gets drier paradigm explains the expected moistening of the extratropics and drying of the subtropics as the atmospheric moisture content increases with global warming. Here we show, using precipitation minus evaporation (P - E) data from climate models, that it cannot be extended to apply regionally to deviations from the zonal mean. Wet and dry zones shift substantially in response to shifts in the stationary-eddy circulations that cause them. Additionally, atmospheric circulation changes lead to a smaller increase in the zonal variance of P - E than would be expected from atmospheric moistening alone. The P - E variance change can be split into dynamic and thermodynamic components through an analysis of the atmospheric moisture budget. This reveals that a weakening of stationary-eddy circulations and changes in the zonal variation of transient-eddy moisture fluxes moderate the strengthening of the zonally anomalous hydrological cycle with global warming.
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
Restoration of rhythmicity in diffusively coupled dynamical networks
Zou, W.; Senthilkumar, D. V.; Nagao, R.; Kiss, I Z; Tang, Y; KOSESKA, A.; Duan, J.; Kurths, J.
2015-01-01
Oscillatory behaviour is essential for proper functioning of various physical and biological processes. However, diffusive coupling is capable of suppressing intrinsic oscillations due to the manifestation of the phenomena of amplitude and oscillation deaths. Here we present a scheme to revoke these quenching states in diffusively coupled dynamical networks, and demonstrate the approach in experiments with an oscillatory chemical reaction. By introducing a simple feedback factor in the diffus...
Suppression and Enhancement of Diffusion in Disordered Dynamical Systems
Klages, R.
2001-01-01
The impact of quenched disorder on deterministic diffusion in chaotic dynamical systems is studied. As a simple example, we consider piecewise linear maps on the line. In computer simulations we find a complicated scenario of multiple suppression and enhancement of normal diffusion under variation of the perturbation strength. These results are explained by a theoretical argument showing that the oscillations emerge as a direct consequence of the unperturbed diffusion coefficient, which is kn...
Fluid dynamics of double diffusive systems
Energy Technology Data Exchange (ETDEWEB)
Koseff, J.R.
1988-05-01
A study of mixing processes in doubly diffusive systems is being conducted. Continuous gradients of two diffusing components (heat and salinity) are being used as initial conditions, and forcing is introduced by lateral heating, surface shear and sloping boundaries. The goals of the proposed work include: quantification of the effects of finite amplitude disturbances on stable, double diffusive systems, particularly with respect to lateral heating, development of an improved understanding of the physical phenomena present in wind-driven shear flows in double diffusive stratified environments, increasing our knowledge-base on turbulent flow in stratified environments and how to represent it, and formulation of numerical code for such flows. The work is being carried out in a new experimental facility at Stanford and on laboratory minicomputers and CRAY computers. In particular we are focusing on the following key issues. The formation and propagation of double diffusive intrusions away from a heated wall and the effects of lateral heating on the double diffusive system; The interaction between the double diffusively influenced fluxes and the turbulence induced fluxes; The formation of gravitational intrusions; and The influence of double diffusive gradients on mixed layer deepening. The goals of the project were as follows. Physical experiments: Construct experimental facility; Modify and fabricate instrument rakes; Develop sampling and calibration software; Develop stratification techniques; Conduct flow visualization studies; Qualify wind tunnel over a range of wind speeds. Numerical experiments: Adapt REMIXCS to handle turbulent flows; Investigate approaches for specifying wind field; Perform calculations for low wind speeds. With the exception of the wind tunnel qualification, all the tasks have already been completed and we are now conducting quantitative experiments. 2 figs.
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.
Kuentz, M
2003-01-01
A two-dimensional lattice gas automaton (LGA) is used for simulating concentration-dependent diffusion in a microscopically random heterogeneous structure. The heterogeneous medium is initialized at a low density rho sub 0 and then submitted to a steep concentration gradient by continuous injection of particles at a concentration rho sub 1 >rho sub 0 from a one-dimensional source to model spreading of a density front. Whereas the nonlinear diffusion equation generally used to describe concentration-dependent diffusion processes predicts a scaling law of the type phi = xt sup - sup 1 sup / sup 2 in one dimension, the spreading process is shown to deviate from the expected t sup 1 sup / sup 2 scaling. The time exponent is found to be larger than 1/2, i.e. diffusion of the density front is enhanced with respect to standard Fickian diffusion. It is also established that the anomalous time exponent decreases as time elapses: anomalous spreading is thus not a timescaling process. We demonstrate that occurrence of a...
Dynamic structure factor study of diffusion in strongly sheared suspensions
Leshansky, Alexander M.; Brady, John F.
2005-01-01
Diffusion of neutrally buoyant spherical particles in concentrated monodisperse suspensions under simple shear flow is investigated. We consider the case of non-Brownian particles in Stokes flow, which corresponds to the limits of infinite Péclet number and zero Reynolds number. Using an approach based upon ideas of dynamic light scattering we compute self- and gradient diffusion coefficients in the principal directions normal to the flow numerically from Accelerated Stokesian Dynamics simula...
Galactic civilizations: Population dynamics and interstellar diffusion
Newman, W. I.; Sagan, C.
1978-01-01
The interstellar diffusion of galactic civilizations is reexamined by potential theory; both numerical and analytical solutions are derived for the nonlinear partial differential equations which specify a range of relevant models, drawn from blast wave physics, soil science, and, especially, population biology. An essential feature of these models is that, for all civilizations, population growth must be limited by the carrying capacity of the environment. Dispersal is fundamentally a diffusion process; a density-dependent diffusivity describes interstellar emigration. Two models are considered: the first describing zero population growth (ZPG), and the second which also includes local growth and saturation of a planetary population, and for which an asymptotic traveling wave solution is found.
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 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...
Interestingness-Driven Diffusion Process Summarization in Dynamic Networks
DEFF Research Database (Denmark)
Qu, Qiang; Liu, Siyuan; Jensen, Christian Søndergaard;
2014-01-01
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...... 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...... 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...
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.
Dynamics and pattern formation in a cancer network with diffusion
Zheng, Qianqian; Shen, Jianwei
2015-10-01
Diffusion is ubiquitous inside cells, and it is capable of inducing spontaneous pattern formation in reaction-diffusion systems on a spatially homogeneous domain. In this paper, we investigate the dynamics of a diffusive cancer network regulated by microRNA and obtain the condition that the network undergoes a Hopf bifurcation and a Turing pattern bifurcation. In addition, we also develop the amplitude equation of the network model by using Taylor series expansion, multi-scaling and further expansion in powers of a small parameter. As a result of these analyses, we obtain the explicit condition on how the dynamics of the diffusive cancer network evolve. These results reveal that this system has rich dynamics, such as spotted stripe and hexagon patterns. The bifurcation diagram helps us understand the biological mechanism in the cancer network. Finally, numerical simulations confirm our analytical results.
Hydrodynamic theory of convective transport across a dynamically stabilized diffuse boundary layer
International Nuclear Information System (INIS)
The diffuse boundary layer between miscible liquids is subject to Rayleigh-Taylor instabilities if the heavy fluid is supported by the light one. The resulting rapid interchange of the liquids can be suppressed by enforcing vertical oscillations on the whole system. This dynamic stabilization is incomplete and produces some peculiar novel transport phenomena such as decay off the density profile into several steps, periodic peeling of density sheets of the boundary layer and the appearance of steady vortex flow. The theory presented in this paper identifies the basic mechanism as formation of convective cells leading to enhanced diffusion, and explains previous experimental results with water and ZnJ2-solutions. A nonlinear treatment of the stationary convective flow problem gives the saturation amplitude of the ground mode and provides an upper bound for the maximum convective transport. The hydrodynamic model can be used for visualizing similar transport processes in the plasma of toroidal confinement devices such as sawtooth oscillations in soft disruptions of tokamak discharges and anomalous diffusion by excitation of convective cells. The latter process is investigated here in some detail, leading to the result that the maximum possible transport is of the order of Bohm diffusion. (orig.)
Arrese-Igor, Silvia; Alegría, Ángel; Moreno Segurado, Ángel J.; Colmenero de León, Juan
2011-01-01
We address the general question of how the molecular weight dependence of chain dynamics in unentangled polymers is modified by blending. By dielectric spectroscopy we measure the normal mode relaxation of polyisoprene in blends with a slower component of poly(ter-butylstyrene). Unentangled polyisoprene in the blend exhibits strong deviations from Rouse scaling, approaching 'entangled-like' behavior at low temperatures in concomitance with the increase of the dynamic asymmetry in the blend. T...
Anomalous Raman scattering and lattice dynamics in mono- and few-layer WTe2
Kim, Younghee; Jhon, Young In; Park, June; Kim, Jae Hun; Lee, Seok; Jhon, Young Min
2016-01-01
Tungsten ditelluride (WTe2) is a layered material that exhibits excellent magnetoresistance and thermoelectric behaviors, which are deeply related with its distorted orthorhombic phase that may critically affect the lattice dynamics of this material. Here, we report comprehensive characterization of Raman spectra of WTe2 from bulk to monolayer using experimental and computational methods. We find that mono and bi-layer WTe2 are easily identified by Raman spectroscopy since two or one Raman modes that are observed in higher-layer WTe2 are greatly suppressed below the noise level in the mono- and bi-layer WTe2, respectively. In addition, the frequency of in-plane A17 mode of WTe2 remains almost constant as the layer number decreases, while all the other Raman modes consistently blueshift, which is completely different from the vibrational behavior of hexagonal metal dichalcogenides. First-principles calculation validates experimental results and reveals that anomalous lattice vibrations in WTe2 are attributed to the formation of tungsten chains that make WTe2 structurally one-dimensional.Tungsten ditelluride (WTe2) is a layered material that exhibits excellent magnetoresistance and thermoelectric behaviors, which are deeply related with its distorted orthorhombic phase that may critically affect the lattice dynamics of this material. Here, we report comprehensive characterization of Raman spectra of WTe2 from bulk to monolayer using experimental and computational methods. We find that mono and bi-layer WTe2 are easily identified by Raman spectroscopy since two or one Raman modes that are observed in higher-layer WTe2 are greatly suppressed below the noise level in the mono- and bi-layer WTe2, respectively. In addition, the frequency of in-plane A17 mode of WTe2 remains almost constant as the layer number decreases, while all the other Raman modes consistently blueshift, which is completely different from the vibrational behavior of hexagonal metal dichalcogenides
Jourdan, Fred; Benedix, Gretchen; Eroglu, Ela.; Bland, Phil. A.; Bouvier, Audrey.
2014-09-01
The Bunburra Rockhole meteorite is a brecciated anomalous basaltic achondrite containing coarse-, medium- and fine-grained lithologies. Petrographic observations constrain the limited shock pressure to between ca. 10 GPa and 20 GPa. In this study, we carried out nine 40Ar/39Ar step-heating experiments on distinct single-grain fragments extracted from the coarse and fine lithologies. We obtained six plateau ages and three mini-plateau ages. These ages fall into two internally concordant populations with mean ages of 3640 ± 21 Ma (n = 7; P = 0.53) and 3544 ± 26 Ma (n = 2; P = 0.54), respectively. Based on these results, additional 40Ar/39Ar data of fusion crust fragments, argon diffusion modelling, and petrographic observations, we conclude that the principal components of the Bunburra Rockhole basaltic achondrite are from a melt rock formed at ∼3.64 Ga by a medium to large impact event. The data imply that this impact generated high enough energy to completely melt the basaltic target rock and reset the Ar systematics, but only partially reset the Pb-Pb age. We also conclude that a complete 40Ar∗ resetting of pyroxene and plagioclase at this time could not have been achieved at solid-state conditions. Comparison with a terrestrial analog (Lonar crater) shows that the time-temperature conditions required to melt basaltic target rocks upon impact are relatively easy to achieve. Ar data also suggest that a second medium-size impact event occurred on a neighbouring part of the same target rock at ∼3.54 Ga. Concordant low-temperature step ages of the nine aliquots suggest that, at ∼3.42 Ga, a third smaller impact excavated parts of the ∼3.64 Ga and ∼3.54 Ga melt rocks and brought the fragments together. The lack of significant impact activity after 3.5 Ga, as recorded by the Bunburra Rockhole suggests that (1) either the meteorite was ejected in a small secondary parent body where it resided untouched by large impacts, or (2) it was covered by a porous heat
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.
Effects of Lateral Diffusion on the Dynamics of Desorption
Juwono, Tjipto; Hamad, Ibrahim Abou; Rikvold, Per Arne
2012-01-01
The adsorbate dynamics during simultaneous action of desorption and lateral adsorbate diffusion is studied in a simple lattice-gas model by kinetic Monte Carlo simulations. It is found that the action of the coverage-conserving diffusion process during the course of the desorption has two distinct, competing effects: a general acceleration of the desorption process, and a coarsening of the adsorbate configuration through Ostwald ripening. The balance between these two effects is governed by t...
Dynamics Of Innovation Diffusion With Two Step Decision Process
Szymczyk Michał; Kamiński Bogumił
2014-01-01
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 sa...
Energy Technology Data Exchange (ETDEWEB)
Vermeersch, B; Mey, G de [Department of Electronics and Information Systems, Ghent University, Sint Pietersnieuwstraat 41, Gent 9000 (Belgium)
2007-04-21
This paper presents a theoretical investigation of the temperature distributions generated by a small heat source mounted on or embedded in semiconductor material. The dynamic thermal behaviour of the structures is studied in the frequency domain using phasor notation for the temperature and heat flux fields. Both classical and hyperbolic thermal conductions are considered. The latter accounts for the finite heat propagation speed, which is necessary for accurately describing very fast transitions. Although a uniform power density is applied, the temperature distribution inside the source is spatially non-uniform. As is already well known, this even holds for steady state conditions. For high frequencies, however, the maximum magnitude (i.e. largest oscillations) of the temperature occurs near the edges and corners of the heat source, rather than in the centre where it could intuitively be expected. This anomalous behaviour is observed for a wide variety of configurations, ranging from a simple 1D analytical slab model to numerical results for a 3D multi-layered electronic package. The classical theory clearly underestimates the edge effect, particularly for submicrometre structures. The substantial deviation from the distributions obtained by non-Fourier theory illustrates that special care should be taken when analysing fast heat transfer in small electronic devices.
Crossover from superdiffusive to diffusive dynamics in fluctuating light fields
Marqués, Manuel I.
2016-06-01
The expressions for the optical drag force, the equilibrium kinetic energy, and the diffusion constant of an electric dipole in a light field consisting of electromagnetic plane waves with polarizations randomly distributed and fluctuating phases are obtained. The drag force is proportional to the extinction cross section of the dipole and to the intensity. The diffusion constant does not depend on the amplitude of the electromagnetic field and is proportional to the time interval between fluctuations. Numerical simulations for the dynamics of a resonant dipole, initially at rest, show the crossover between the superdiffusive and the diffusive regimes theoretically predicted.
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.
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...... 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 similar to 1.3 mu m(2)/s. Number and brightness (N&B) analysis...
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
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.
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.
Classical diffusive dynamics for the quasiperiodic kicked rotor
Lemarié, Gabriel; Delande, Dominique; Garreau, Jean Claude; Szriftgiser, Pascal
2010-01-01
We study the classical dynamics of a quasiperiodic kicked rotor, whose quantum counterpart is known to be an equivalent of the 3D Anderson model. Using this correspondence allowed for a recent experimental observation of the Anderson transition with atomic matter waves. In such a context, it is particularly important to assert the chaotic character of the classical dynamics of this system. We show here that it is a 3D anisotropic diffusion. Our simple analytical predictions for the associated...
Extracting the diffusion tensor from molecular dynamics simulation with Milestoning.
Mugnai, Mauro L; Elber, Ron
2015-01-01
We propose an algorithm to extract the diffusion tensor from Molecular Dynamics simulations with Milestoning. A Kramers-Moyal expansion of a discrete master equation, which is the Markovian limit of the Milestoning theory, determines the diffusion tensor. To test the algorithm, we analyze overdamped Langevin trajectories and recover a multidimensional Fokker-Planck equation. The recovery process determines the flux through a mesh and estimates local kinetic parameters. Rate coefficients are converted to the derivatives of the potential of mean force and to coordinate dependent diffusion tensor. We illustrate the computation on simple models and on an atomically detailed system-the diffusion along the backbone torsions of a solvated alanine dipeptide. PMID:25573551
Measurement of the dynamic characteristics of atmospheric diffusion
International Nuclear Information System (INIS)
A new method is proposed for studying the diffusion of atmospheric pollutants above real sites which considers the actual magnitudes encountered. The dynamic application of this method yields original information. In view of justifying the method, fundamental theories concerning diffusion are presented together with different models for the atmosphere. The atmosphere is then considered as a linear filter to which the process identification method is applied. The pulse response of the filter is examined in the pollutant - time plane. The limits of the method and its field of application are discussed. The concept of ergodism and stationariness are introduced. Various diffusion experiments carried out under different conditions are reviewed. Information on the effect of obstacles, and the roughness of the ground is given together with calculations of the longitudinal diffusion and the transport velocity. A brief description is then given of the apparatus used to measure the concentrations and the meteorological conditions. The correlation calculation is also briefly presented. (author)
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
Catastrophe in diffusion-controlled annihilation dynamics: general scaling properties
Shipilevsky, Boris M.
2015-11-01
We present a systematic analytical and numerical study of the annihilation catastrophe phenomenon which develops in an open system, where species A and B diffuse from the bulk of restricted medium and die on its surface (desorb) by the reaction A + B → 0. This phenomenon arises in the diffusion-controlled limit as a result of self-organizing explosive growth (drop) of the surface concentrations of, respectively, slow and fast particles (concentration explosion) and manifests itself in the form of an abrupt singular jump of the desorption flux relaxation rate. In the recent work [B.M. Shipilevsky, Phys. Rev. E 76, 031126 (2007)] a closed scaling theory of catastrophe development has been given for the asymptotic limit when the characteristic time scale of explosion becomes much less than the characteristic time scales of diffusion of slow and fast particles at an arbitrary ratio of their diffusivities 0 < p < 1. In this paper we consider the behavior of the system at strong difference of species diffusivities p ≪ 1 and reveal a rich general pattern of catastrophe development for an arbitrary ratio of the characteristic time scales of explosion and fast particle diffusion. As striking results we find remarkable scaling properties of catastrophe evolution at the crossover between two limiting regimes with radically different dynamics.
Effects of Lateral Diffusion on the Dynamics of Desorption
Juwono, Tjipto; Rikvold, Per Arne
2012-01-01
The adsorbate dynamics during simultaneous action of desorption and lateral adsorbate diffusion is studied in a simple lattice-gas model by kinetic Monte Carlo simulations. It is found that the action of the coverage-conserving diffusion process during the course of the desorption has two distinct, competing effects: a general acceleration of the desorption process, and a coarsening of the adsorbate configuration through Ostwald ripening. The balance between these two effects is governed by the structure of the adsorbate layer at the beginning of the desorption process.
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.
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; Sutcliffe, Paul
2016-04-29
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. PMID:27176541
Untangling Knots Via Reaction-Diffusion Dynamics of Vortex Strings.
Maucher, Fabian; Sutcliffe, Paul
2016-04-29
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.
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.
Anomalous bootstrap current due to drift waves
International Nuclear Information System (INIS)
An anomalous parallel current driven by radial flux in tokamak is discussed. Drift waves, which cause an anomalous cross field diffusion, can generate a parallel current in a sheared magnetic field, if the fluctuation level has radial dependence. (author)
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.
Zhigao Liao; Jiuping Xu; Liming Yao
2013-01-01
This paper studies the innovation diffusion problem with the affection of urbanization, proposing a dynamical innovation diffusion model with fuzzy coefficient, and uses the shifting rate of people from rural areas stepping into urban areas to show the process of urbanization. The numerical simulation shows the diffusion process for telephones in China with Genetic Algorithms and this model is effective to show the process of innovation diffusion with the condition of urbanization process.
Diffusion measurements in fluids by dynamic light scattering
Fröba, Andreas P.; Leipertz, Alfred
2016-01-01
In the course of the last thirty years, light scattering techniques have been used with increasing effort and attention for the measurement of the thermophysical properties of pure fluids and fluid mixtures. Here, an introduction is given to dynamic light scattering (DLS) as a valuable tool for the measurement of diffusion processes. First, the basic principles of the method and its experimental realization are presented in some detail. A survey on various applications is given, which espe...
Dynamic diffuse optical tomography imaging of peripheral arterial disease
Khalil, Michael A.; Kim, Hyun K.; Kim, In-Kyong; Flexman, Molly; Dayal, Rajeev; Shrikhande, Gautam; Hielscher, Andreas H.
2012-01-01
Peripheral arterial disease (PAD) is the narrowing of arteries due to plaque accumulation in the vascular walls. This leads to insufficient blood supply to the extremities and can ultimately cause cell death. Currently available methods are ineffective in diagnosing PAD in patients with calcified arteries, such as those with diabetes. In this paper we investigate the potential of dynamic diffuse optical tomography (DDOT) as an alternative way to assess PAD in the lower extremities. DDOT is a ...
Dynamics of diffusive bubble growth in magmas: Isothermal case
Prousevitch, A. A.; Sahagian, D. L.; Anderson, A. T.
1993-12-01
We have conducted a parametric study and developed a new cell model describing diffusion-induced growth of closely spaced bubbles in magmatic sytems. The model accounts for (1) the effects of advection of melt resulting from bubble growth, and its affect on the local concentration profile; (2) dynamic resistence of the viscous melt during diffusive growth; (3) diffusion of volatiles in response to evolving concentration gradients; (4) mass balance between dissolved volatiles and gas inside the bubble; (5) changes in the equilibrium saturation concentration at the bubble-melt interface; (6) total pressure within the bubble consisting of ambient, surface tension, and dynamic pressures. The results of this study reveal that bubble growth depends strongly on ambient pressure, volatile oversaturation in the melt, and diffusivity coefficients, but only weakly on bubble separation and inital bubble radius. Increased volatile oversaturation increases growth rate to the point at which it actually reduces time for complete bubble growth. This counterintuitive result is due to significant advective volatile flux toward the bubble interface during growth. Viscosity controls growth dynamics only for cases of high viscosity (greater than 10(exp 4) Pa s). The documentation of the evolution of gas fraction in the melt and bubble wall thickness as a function of time makes it possible to estimate bubble disruption thresholds which bear on volcanic eruption mechanisms. Model results can be applied to the larger-scale problem of magmatic degassing in terms of bubble coalescence, flotation and the development of foams in magma chambers and vent systems, and ultimately to the dynamics of eruption mechanisms.
Estimation of water diffusivity parameters on grape dynamic drying
Ramos, Inês N.; Miranda, João M.R.; Brandão, Teresa R. S.; Cristina L.M. Silva
2010-01-01
A computer program was developed, aiming at estimating water diffusivity parameters in a dynamic drying process with grapes, assessing the predictability of corresponding non-isothermal drying curves. It numerically solves Fick’s second law for a sphere, by explicit finite differences, in a shrinking system, with anisotropic properties and changing boundary conditions. Experiments were performed in a pilot convective dryer, with simulated air conditions observed in a solar dryer, for modellin...
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.
Convection-diffusion effects in marathon race dynamics
Rodriguez, E.; Espinosa-Paredes, G.; Alvarez-Ramirez, J.
2014-01-01
In the face of the recent terrorist attack event on the 2013 Boston Marathon, the increasing participation of recreational runners in large marathon races has imposed important logistical and safety issues for organizers and city authorities. An accurate understanding of the dynamics of the marathon pack along the race course can provide important insights for improving safety and performance of these events. On the other hand, marathon races can be seen as a model of pedestrian movement under confined conditions. This work used data of the 2011 Chicago Marathon event for modeling the dynamics of the marathon pack from the corral zone to the finish line. By considering the marathon pack as a set of particles moving along the race course, the dynamics are modeled as a convection-diffusion partial differential equation with position-dependent mean velocity and diffusion coefficient. A least-squares problem is posed and solved with optimization techniques for fitting field data from the 2011 Chicago Marathon. It was obtained that the mean pack velocity decreases while the diffusion coefficient increases with distance. This means that the dispersion rate of the initially compact marathon pack increases as the marathon race evolves along the race course.
Modeling Dynamics of Diffusion Across Heterogeneous Social Networks: News Diffusion in Social Media
Directory of Open Access Journals (Sweden)
Peter Christen
2013-10-01
Full Text Available Diverse online social networks are becoming increasingly interconnected by sharing information. Accordingly, emergent macro-level phenomena have been observed, such as the synchronous spread of information across different types of social media. Attempting to analyze the emergent global behavior is impossible from the examination of a single social platform, and dynamic influences between different social networks are not negligible. Furthermore, the underlying structural property of networks is important, as it drives the diffusion process in a stochastic way. In this paper, we propose a macro-level diffusion model with a probabilistic approach by combining both the heterogeneity and structural connectivity of social networks. As real-world phenomena, we explore instances of news diffusion across different social media platforms from a dataset that contains over 386 million web documents covering a one-month period in early 2011. We find that influence between different media types is varied by the context of information. News media are the most influential in the arts and economy categories, while social networking sites (SNS and blog media are in the politics and culture categories, respectively. Furthermore, controversial topics, such as political protests and multiculturalism failure, tend to spread concurrently across social media, while entertainment topics, such as film releases and celebrities, are more likely driven by interactions within single social platforms. We expect that the proposed model applies to a wider class of diffusion phenomena in diverse fields and that it provides a way of interpreting the dynamics of diffusion in terms of the strength and directionality of influences among populations.
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.
Dynamics of the diffusive DM-DE interaction – Dynamical system approach
Haba, Zbigniew; Stachowski, Aleksander; Szydłowski, Marek
2016-07-01
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.
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.
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...
Diffusion dynamics in liquid and undercooled Al-Ni alloys
International Nuclear Information System (INIS)
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 Al80Ni20. 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 of alloy
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
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.
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.
Reaction-Diffusion Modeling ERK- and STAT-Interaction Dynamics
Directory of Open Access Journals (Sweden)
Georgiev Nikola
2006-01-01
Full Text Available The modeling of the dynamics of interaction between ERK and STAT signaling pathways in the cell needs to establish the biochemical diagram of the corresponding proteins interactions as well as the corresponding reaction-diffusion scheme. Starting from the verbal description available in the literature of the cross talk between the two pathways, a simple diagram of interaction between ERK and STAT5a proteins is chosen to write corresponding kinetic equations. The dynamics of interaction is modeled in a form of two-dimensional nonlinear dynamical system for ERK—and STAT5a —protein concentrations. Then the spatial modeling of the interaction is accomplished by introducing an appropriate diffusion-reaction scheme. The obtained system of partial differential equations is analyzed and it is argued that the possibility of Turing bifurcation is presented by loss of stability of the homogeneous steady state and forms dissipative structures in the ERK and STAT interaction process. In these terms, a possible scaffolding effect in the protein interaction is related to the process of stabilization and destabilization of the dissipative structures (pattern formation inherent to the model of ERK and STAT cross talk.
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.
Diffusion dynamics of an electron gas confined between two plates
Degond, Pierre; Latocha, Vladimir; Mancini, Simona; Mellet, Antoine
2002-01-01
We consider electrons constrained to move in the gap between two plane parallel plates, confined by a magnetic field perpendicular to the plates and accelerated by an electric field parallel to them. The electrons are subject to elastic collisions against the solid plates on the one hand and against atoms or ions in the gap between the plates on the other hand. Under the assumption that the dynamics is dominated by the collisions, we derive a diffusion type model for the energy distribution f...
Dynamics of the diffusive DM-DE interaction--dynamical system approach
Haba, Zbigniew; Stachowski, Aleksander; 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 dynami...
Colmenero, J.
2013-05-01
In a recent paper by Ngai and Capaccioli ["Unified explanation of the anomalous dynamic properties of highly asymmetric polymer blends," J. Chem. Phys. 138, 054903 (2013), 10.1063/1.4789585] the authors claimed that the so-called coupling model (CM) provides a unified explanation of all dynamical anomalies that have been reported for dynamically asymmetric blends over last ten years. Approximately half of the paper is devoted to chain-dynamic properties involving un-entangled polymers. According to the authors, the application of the CM to these results is based on the existence of a crossover at a time tc ≈ 1-2 ns of the magnitudes describing chain-dynamics. Ngai and Capaccioli claimed that the existence of such a crossover is supported by the neutron scattering and MD-simulation results, corresponding to the blend poly(methyl methacrylate)/poly(ethylene oxide), by Niedzwiedz et al. [Phys. Rev. Lett. 98, 168301 (2007), 10.1103/PhysRevLett.98.168301] and Brodeck et al. [Macromolecules 43, 3036 (2010), 10.1021/ma902820a], respectively. Being one of the authors of these two papers, I will demonstrate here that there is no evidence supporting such a crossover in the data reported in these papers.
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.
Parallel Algorithm and Dynamic Exponent for Diffusion-limited Aggregation
Moriarty, K J M; Greenlaw, R
1997-01-01
A parallel algorithm for ``diffusion-limited aggregation'' (DLA) is described and analyzed from the perspective of computational complexity. The dynamic exponent z of the algorithm is defined with respect to the probabilistic parallel random-access machine (PRAM) model of parallel computation according to $T \\sim L^{z}$, where L is the cluster size, T is the running time, and the algorithm uses a number of processors polynomial in D_2 is the second generalized dimension. Simulations of DLA are carried out to measure D_2 and to test scaling assumptions employed in the complexity analysis of the parallel algorithm. It is plausible that the parallel algorithm attains the minimum possible value of the dynamic exponent in which case z characterizes the intrinsic history dependence of DLA.
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.
Diffusion dynamics in the disordered Bose Hubbard model
Wadleigh, Laura; Russ, Philip; Demarco, Brian
2016-05-01
We explore the dynamics of diffusion for out-of-equilibrium superfluid, Mott insulator, and Bose glass states using an atomic realization of the disordered Bose Hubbard (DBH) model. Dynamics in strongly correlated systems, especially far from equilibrium, are not well understood. The introduction of disorder further complicates these systems. We realize the DBH model--which has been central to our understanding of quantum phase transitions in disordered systems--using ultracold Rubidium-87 atoms trapped in a cubic disordered optical lattice. By tightly focusing a beam into the center of the gas, we create a hole in the atomic density profile. We achieve Mott insulator, superfluid, or Bose glass states by varying the interaction and disorder strength, and measure the time evolution of the density profile after removing the central barrier. This allows us to infer diffusion rates from the velocities at the edge of the hole and to look for signatures of superfluid puddles in the Bose glass state. We acknowledge funding from NSF Grant PHY 15-05468, NSF Grant DGE-1144245, and ARO Grant W911NF-12-1-0462.
Chaotic dynamics and diffusion in a piecewise linear equation
Shahrear, Pabel; Glass, Leon; Edwards, Rod
2015-03-01
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.
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.
Dynamic Simulation of Backward Diffusion Based on Random Walk Theory
Dung, Vu Ba; Nguyen, Bui Huu
2016-06-01
Results of diffusion study in silicon showed that diffusion of the selfinterstitial and vacancy could be backward diffusion and their diffusivity could be negative [1]. The backward diffusion process and negative diffusivity is contrary to the fundamental laws of diffusion such as the law of Fick law, namely the diffusive flux of backward diffusion goes from regions of low concentration to regions of high concentration. The backward diffusion process have been explained [2]. In this paper, the backward diffusion process is simulated. Results is corresponding to theory and show that when thermal velocity of the low concentration area is greater than thermal velocity of the high concentration area, the backward diffusion can be occurred.
Dynamical Properties of Diffusion Process on Complex Networks with Arbitrary Degree Distribution
International Nuclear Information System (INIS)
Dynamical properties of diffusion process on complex networks with arbitrary degree distribution are investigated. The rule of the diffusion process encompasses both the structural characteristics and the information processing dynamics. Considering the influence of a node on the global dynamical behavior, the dynamical generating function of the process, which is deeply reflecting the basic characteristic of the process and mutually decided with the dynamical process, is proposed. Based on the analysis of the dynamical generating function we introduce dynamical centrality for each node, which determines the relative importance of nodes and the capability of the given node to collect and communicate information with its neighbouring environment in the network via the diffusion process. Furthermore, a new parameter, dynamical entropy, is proposed to measure the interplay between dynamical centrality and diffusion dynamics. The experimental results on large-scale complex networks with Poisson distribution confirm our analytical prediction. (authors)
Scherer, Christoph
2015-01-01
Molecular dynamics simulations of silicate and borate glasses and melts: Structure, diffusion dynamics and vibrational properties. In this work computer simulations of the model glass formers SiO2 and B2O3 are presented, using the techniques of classical molecular dynamics (MD) simulations and quantum mechanical calculations, based on density functional theory (DFT). The latter limits the system size to about 100−200 atoms. SiO2 and B2O3 are the two most important network formers for industri...
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.
International Nuclear Information System (INIS)
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
Energy Technology Data Exchange (ETDEWEB)
Lapas, Luciano C., E-mail: luciano.lapas@unila.edu.br [Universidade Federal da Integração Latino-Americana, Caixa Postal 2067, 85867-970 Foz do Iguaçu, Paraná (Brazil); Ferreira, Rogelma M. S., E-mail: rogelma.maria@gmail.com [Centro de Ciências Exatas e Tecnológicas, Universidade Federal do Recôncavo da Bahia, 44380-000 Cruz das Almas, Bahia (Brazil); Rubí, J. Miguel, E-mail: mrubi@ub.edu [Departament de Física Fonamental, Facultat de Física, Universitat de Barcelona, Av. Diagonal 647, 08028 Barcelona (Spain); Oliveira, Fernando A., E-mail: fernando.oliveira@pq.cnpq.br [Instituto de Física and Centro Internacional de Física da Matéria Condensada, Universidade de Brasília, Caixa Postal 04513, 70919-970 Brasília, Distrito Federal (Brazil)
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.
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...
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.
Panda, Manas K.; Centore, Roberto; Causà, Mauro; Tuzi, Angela; Borbone, Fabio; Naumov, Panče
2016-01-01
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. PMID:27403616
Panda, Manas K; Centore, Roberto; Causà, Mauro; Tuzi, Angela; Borbone, Fabio; Naumov, Panče
2016-01-01
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. PMID:27403616
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.
Anomalous thermal dynamics of Bragg gratings inscribed in germanosilicate optical fiber
Rahman, A.; Madhav, Venu K; B. Srinivasan; S. Asokan
2009-01-01
An interesting, periodic appearance of a new peak has been observed in the reflected spectrum of a Fiber Bragg Grating (FBG) inscribed in a germanosilicate fiber during thermal treatment. The new peak occurs on the longer wavelength side of the spectrum during heating and on the shorter wavelength side during cooling, following an identical reverse dynamics. Comparison with a commercial grating with 99.9% reflectivity shows a similar decay dynamics. It is proposed that the distortion due to s...
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.
Network Structure and Innovation Ambiguity Effects on Diffusion in Dynamic Organizational Fields
Gibbons, Deborah E.
2004-01-01
Computational modeling simulated innovation diffusion through six prototypical interregional network structures and two distributions of partnering tendencies in dynamic organizational fields. Compared to regional constraints, connections among all geographic regions decreased clearly beneficial innovation diffusion (a low-threshold adoption model) but increased ambiguous innovation diffusion (a social influence model). Compared with uniform partnering tendencies, normally dist...
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.
International Nuclear Information System (INIS)
Absorption spectra toward Herschel 36 (Her 36) for the A-bar1Π ⇽ X-tilde1Σ transitions of CH+ in the J = 1 excited rotational level and for the A-bar2Δ ⇽ X-tilde2Π 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 (Tr > 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
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.
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.
Diffusion of dynamic innovations : A case study of residential solar PV systems
Karakaya, Emrah
2015-01-01
In the literature on diffusion of innovations, it is widely known that the characteristics and socio-environmental settings of adopters do evolve in space and time. What about innovations themselves? During the diffusion process, don’t some innovations continuously alter in space and time? If so, how does the dynamic character of an innovation influence the diffusion process? In previous research, it has been often assumed that innovations do not continuously alter or get modified when diffus...
Lithium diffusion in silicon and induced structure disorder: A molecular dynamics study
Huanyu Wang; Xiao Ji; Chi Chen; Kui Xu; Ling Miao
2013-01-01
Using molecular dynamics method, we investigate the diffusion property of lithium in different silicon structures and silicon structure's disorder extent during lithium's diffusion process. We find that the pathway and the incident angle between the direction of barrier and diffusion of lithium are also the essential factors to the lithium's diffusion property in silicon anode besides the barrier. Smaller incident angle could decrease the scattering of lithium in silicon structure effectively...
Anomalous Magnetohydrodynamics
Giovannini, Massimo
2013-01-01
Anomalous symmetries induce currents which can be parallel rather than orthogonal to the hypermagnetic field. Building on the analogy with charged liquids at high magnetic Reynolds numbers, the persistence of anomalous currents is scrutinized for parametrically large conductivities when the plasma approximation is accurate. Different examples in globally neutral systems suggest that the magnetic configurations minimizing the energy density with the constraint that the helicity be conserved co...
Dahlstrom, Julie; York, Donald G.; 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
2013-08-01
Anomalously broad diffuse interstellar bands (DIBs) at 5780.5, 5797.1, 6196.0, and 6613.6 Å 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 correct and applicable to most DIBs, the 2.7 K cosmic microwave background may set the minimum widths (about 0.35 Å) 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 mÅ 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. Based in part on data obtained from the ESO Science Archive Facility by user DWELTY.
International Nuclear Information System (INIS)
Anomalously broad diffuse interstellar bands (DIBs) at 5780.5, 5797.1, 6196.0, and 6613.6 Å 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 correct and applicable to most DIBs, the 2.7 K cosmic microwave background may set the minimum widths (about 0.35 Å) 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 mÅ 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
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 ...
Anomalous Lattice Dynamics of Mono-, Bi-, and Tri-layer WTe2
Kim, YoungHee; Jhon, Young In; Park, June; Kim, Jae Hun; Lee, Seok; Jhon, Young Min
2015-01-01
Tungsten ditelluride (WTe2) is a layered material that exhibits excellent magnetoresistance and thermoelectric behaviors, which are deeply related with its distorted orthorhombic phase that may critically affect the lattice dynamics. Here, for the first time, we present comprehensive characterization of the Raman spectroscopic behavior of WTe2 from bulk to monolayer using experimental and computational methods. We discover that mono and bi-layer WTe2 can be easily identified by Raman spectros...
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...
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.
Bhattacharya, Sukanya; Sharma, Dharmendar Kumar; Saurabh, Saumya; De, Suman; Sain, Anirban; Nandi, Amitabha; Chowdhury, Arindam
2013-06-27
Studies on diffusion dynamics of single molecules (SMs) have been useful in revealing inhomogeneity of polymer thin films near and above the glass-transition temperature (T(g)). However, despite several applications of polymer thin films where exposure to solvent (or vapor) is common, the effect of absorbed solvent molecules on local morphology and rigidity of polymer matrices is yet to be explored in detail. High-T(g) hydrophilic polymers such as poly(vinylpyrrolidone) (PVP) are used as pharmaceutical coatings for drug release in aqueous medium, as they readily absorb moisture, which results in effective lowering of the T(g) and thereby leads to plasticization. The effect of moisture absorption on swelling and softening of PVP thin films was investigated by visualizing the diffusion dynamics of rhodamine 6G (Rh6G) tracer molecules at various ambient relative humidities (RH). Wide-field epifluorescence microscopy, in conjunction with high-resolution SM tracking, was used to monitor the spatiotemporal evolution of individual tracers under varied moisture contents of the matrix. In the absence of atmospheric moisture, Rh6G molecules in dry PVP films are translationally inactive, suggestive of rigid local environments. Under low moisture contents (RH 30-50%), translational mobility remains arrested but rotational motion is augmented, indicating slight swelling of the polymer network which marks the onset of plasticization. The translational mobility of Rh6G was found to be triggered only at a threshold ambient RH, beyond which a large proportion of tracers exhibit extensive diffusion dynamics. Interestingly, SM tracking data at higher moisture contents of the film (RH ≥ 60%) reveal that the distributions of dynamic parameters (such as diffusivity) are remarkably broad, spanning several orders of magnitude. Furthermore, Rh6G molecules display a wide variety of translational motion even at a fixed ambient RH, clearly pointing out the extremely inhomogeneous
Adsorption and diffusion of argon confined in ordered and disordered microporous carbons
International Nuclear Information System (INIS)
We use a combination of grand canonical Monte Carlo and microcanonical molecular dynamics simulations to study the adsorption and diffusion of argon at 77 K and 120 K confined in previously generated models of a disordered bituminous coal-based carbon, BPL, and an ordered carbon replica of Faujasite zeolite (C-FAU). Both materials exhibit a maximum in the diffusion coefficient as well as anomalous (sub-diffusive) behavior in the mean-squared displacements at short times at some relative pressures. In BPL, the anomalous diffusion occurs at low relative pressures, due to the trapping of argon atoms in small pores. In C-FAU, the anomalous diffusion occurs at high relative pressures, due to competitive diffusion of atoms traveling through windows and constrictions which interconnect the pores. All diffusion eventually tends to Fickian diffusion at longer times.
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.
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...
Investigating Diffusion Coefficient Using Dynamic Light Scattering Technique
Sun, Yong
2006-01-01
In this work, the Z-average, effective, apparent diffusion coefficients and their poly-dispersity indexes were investigated for dilute poly-disperse homogeneous spherical particles in dispersion where the Rayleigh-Gans-Debye approximation is valid. The results reveal that the values of the apparent and effective diffusion coefficients at a scattering angle investigated are consistent and the difference between the effective and Z-average diffusion coefficients is a function of the mean partic...
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.
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.
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
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.
Role of ice dynamics in anomalous ice conditions in the Beaufort Sea during 2006 and 2007
Hutchings, J. K.; Rigor, I. G.
2012-05-01
A new record minimum in summer sea ice extent was set in 2007 and an unusual polynya formed in the Beaufort Sea ice cover during the summer of 2006. Using a combination of visual observations from cruises, ice drift, and satellite passive microwave sea ice concentration, we show that ice dynamics during preceding years included events that preconditioned the Beaufort ice pack for the unusual patterns of opening observed in both summers. Intrusions of first year ice from the Chukchi Sea to the Northern Beaufort, and increased pole-ward ice transport from the western Arctic during summer has led to reduced replenishment of multiyear ice, older than five years, in the western Beaufort, resulting in a younger, thinner ice pack in most of the Beaufort. We find ice younger than five years melts out completely by the end of summer, south of 76N. The 2006 unusual polynya was bounded to the south by an ice tongue composed of sea ice older than 5 years, and formed when first year and second year ice melted between 76N and the older ice to the south. In this paper we demonstrate that a recent shift in ice circulation patterns in the western Arctic preconditions the Beaufort ice pack for increased seasonal ice zone extent.
TRAWA, LWR Dynamic by Coupled Neutron Diffusion and Thermohydraulics Calculation
International Nuclear Information System (INIS)
1 - Description of problem or function: The purpose of the program is to study reactor dynamics in thermal water-cooled reactors. It treats the core as one or a few axially one-dimensional subregions. The two group neutron diffusion equations are solved simultaneously with the heat conduction equations and the two-phase hydraulic equations for one or more channels. Neither thermal nor hydraulic mixing appear between channels. Doppler, coolant density, coolant temperature, and soluble poison density feedbacks due to the thermo- hydraulics of the channels are described by using polynomial expansions for the group constants. The hydraulic circuit outside the reactor core consists of by-pass channels and risers with two- phase flow and of pump lines with incompressible flow. Various transients can be calculated by applying external disturbances. They can affect e.g. on movements of control rods, core inlet hydraulic conditions, system pressure or coefficients of neutronic shape function expansion between subregions. 2 - Method of solution: Nontrivial implicit methods are employed in the discretization of the equations to allow for sparse spatial mesh and flexible choice of time steps. The same spatial and temporal discretization is used for neutronics and thermohydraulics. 3 - Restrictions on the complexity of the problem: The dimensions of the program variable tables can easily be extended. Now the main dimensions are: 52 axial mesh points in core; 3 subregions; 10 axial regions with different fuel compositions; 7 radial mesh points in fuel rod; 6 delayed neutron groups; 6 coupled legs in pressure balance calculation; No flow reversals are allowed
The spring 2011 final stratospheric warming above Eureka: anomalous dynamics and chemistry
Adams, C.; Strong, K.; Zhao, X.; Bourassa, A. E.; Daffer, W. H.; Degenstein, D.; Drummond, J. R.; Farahani, E. E.; Fraser, A.; Lloyd, N. D.; Manney, G. L.; McLinden, C. A.; Rex, M.; Roth, C.; Strahan, S. E.; Walker, K. A.; Wohltmann, I.
2013-01-01
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 NO2 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, NO2 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 NO2 from NO. Additionally, GMI NOx (NO + NO2) and N2O fields suggest that downward transport along the vortex edge and horizontal transport from lower latitudes also contributed to the enhanced NO2. The anticyclone that transported lower-latitude NOx above PEARL became frozen-in and persisted in dynamical and GMI N2O 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 NOx. Below the FrIAC (from the tropopause to 700 K), NOx 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 volume (ppmv) (58%) and 4.4 ppmv (61%), when calculated using GMI and OSIRIS ozone profiles, respectively. This gas-phase ozone loss
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
RELATION BETWEEN DYNAMIC LOSS MODULUS AND DIFFUSION COEFFICIENT IN A MODIFIED PET FIBER
Institute of Scientific and Technical Information of China (English)
YU Jianming
1994-01-01
The mobility of polymer chain segments is shown to play a major role in the diffusion of disperse dyes in a copolymerization modified PET system, monoepoxy compound CH3(CH2)3OCH2CH-CH2/O modified PET.The rate of dye diffusion (diffusion coefficient D) has been related to the time-dependent mechanical property, dynamic loss modulus E", which is controlled by the mobility of chain segments. In this modified copolyester system, the variance of amount of modifier in the copolyester fibers causes the change in disperse dye diffusion coefficient to fiber, and in the dynamic loss modulus of the fibers ,but the relationship between the diffusion and the dynamic loss modulus is in agreement with the theoretical relation derived by Bell and Dumbleton. The relation obtained in this paper is:Ln D =- 2.28Ln E"+26.81
Diffusing-wave spectroscopy: dynamic light scattering in the multiple scattering limit
Pine, D. J.; Weitz, D. A.; Zhu, J.X.; Herbolzheimer, E.
1990-01-01
Dynamic light scattering is extended to optically thick (opaque) media which exhibit a very high degree of multiple scattering. This new technique, called diffusing-wave spectroscopy (DWS), exploits the diffusive nature of the transport of light in strongly scattering media to relate the temporal fluctuations of the multiply scattered light to the motion of the scatterers. A simple theory of DWS, based on the diffusion approximation for the transport of light, is developed to calculate the te...
Molecular Dynamics Simulation of Solvent-Polymer Interdiffusion. I. Fickian diffusion
Tsige, Mesfin; Grest, Gary S.
2003-01-01
The interdiffusion of a solvent into a polymer melt has been studied using large scale molecular dynamics and Monte Carlo simulation techniques. The solvent concentration profile and weight gain by the polymer have been measured as a function of time. The weight gain is found to scale as t^{1/2}, which is expected for Fickian type of diffusion. The concentration profiles are fit very well assuming Fick's second law with a constant diffusivity. The diffusivity found from fitting Fick's second ...
Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions
Bauler, Patricia; Huber, Gary A.; McCammon, J. Andrew
2012-01-01
Diffusion is often the rate determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. This paper proposes a new hybrid diffusion method that couples the strengths of each of these two methods. The method is derived for a general multidimensional system, and is presented using a basic test case for 1D linear and radially symmetri...
Lithium diffusion in silicon and induced structure disorder: A molecular dynamics study
Directory of Open Access Journals (Sweden)
Huanyu Wang
2013-11-01
Full Text Available Using molecular dynamics method, we investigate the diffusion property of lithium in different silicon structures and silicon structure's disorder extent during lithium's diffusion process. We find that the pathway and the incident angle between the direction of barrier and diffusion of lithium are also the essential factors to the lithium's diffusion property in silicon anode besides the barrier. Smaller incident angle could decrease the scattering of lithium in silicon structure effectively. Moreover, lithium diffuses easier in the Li-Si alloy structure of higher lithium concentration with deeper injection depth. The silicon's structure will be damaged gradually during the charge and discharge process. However, it will also recover to initial state to a great extent after relaxation. Therefore, the damage of lithium diffusion to silicon anode in the structure of low lithium concentration is reversible to a great degree. In addition, the silicon structure of crystal orientation perform better properties in both lithium's diffusivity and structural stability.
Molecular Dynamics Simulation of Gas Diffusion in B2O3 and SiC
Institute of Scientific and Technical Information of China (English)
Yajing YE; Litong ZHANG; Laifei CHENG; Yongdong XU
2003-01-01
Molecular dynamics simulation using a universal force field has been employed to determine the diffusion coefficients of O2 and Na2SO4 vapor into B2O3 and SiC from 700 K to 1273 K, respectively. Einstein diffusion was observed in a 250～300 ps simulation.
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.
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
Numerical Diffusion Effect in Dynamic Simulation of Thermohydraulic Systems
International Nuclear Information System (INIS)
In this work, the behavior of the explicit - up-wind method is studied in two phase natural convection circuit, near the instabilities boundaries.The effect of the numerical diffusion of the scheme upon the system stability is evaluated by means of linearization by small perturbations.The results are compared with a non-diffusive method, in the frequency domain, that solves analytically the linearized equations around a steady state condition.Moreover, a conservation equation transport model using the method of characteristics is implemented and studied.This method is compared with the explicit - up-wind scheme and it is found that it significantly reduces numerical diffusion in the equations solution. Several advantages are visualized for particular cases
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.
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.
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.
New dynamic model for non-Fickian diffusion of calcium spark in cardiac myocytes
Institute of Scientific and Technical Information of China (English)
TAN Wenchang; LIU Shiqiang; GUO Jingjing; WANG Shiqiang; CHENG Heping; T. Masuoka
2003-01-01
A new dynamic model for non-Fickian diffusion of calcium spark in cardiac myocytes was developed by introducing time lags on the basis of the microscale mass transport theory. Numerical simulation showed that the size of the calcium spark produced by the new dynamic model was larger than that of Fick diffusion and was in more agreement with experimental results. In addition, the time lags of the calcium spark in cardiac myocytes were about 0.1-0.8 ms. These results can be used to understand the mechanism of calcium spark diffusion in cardiac myocytes.
Molecular Simulation Study of Hexane Diffusion in Dynamic Metal-0rganic Frameworks
Institute of Scientific and Technical Information of China (English)
XUE,Chunyu; ZHONG,Chongli
2009-01-01
The modified MM3 force field for describing flexible IRMOF-1 was extended to include other IRMOFs,and a molecular dynamics simulation study was performed on hexane diffusion in IRMOF-1 and IRMOF-16.The self-diffusion coefficients and diffusion pathways of hexane,as well as the mobility of the frameworks were inves-tigated,as a function of both temperature and loading.The results revealed that the diffusion pathway of hexane Was largely influenced by loading,and the flexibility of IRMOF-16 was much larger than that of IRMOF-1.The microscopic information obtained is useful for understanding the diffusion mechanism of chain molecules in dy-namic MOF.
Anomalous transport effects in magnetically-confined plasma columns
International Nuclear Information System (INIS)
The evolution of density structure in a magnetized plasma column is analyzed accounting for anomalous diffusion due to the lower hybrid drift instability. The plasma column is found to be divided into regions of classical, anomalous, and intermediate diffusivity. The bulk behavior, described in terms of radial confinement time, depends most sensitively upon the particle line density (ion/cm). For broad plasmas (large line density), the transport is characteristic of classical diffusion, and for slender plasmas (small line density) the transport is characteristic of anomalous diffusion. For intermediate line densities, the transport undertakes a rapid transition from classical to anomalous. Correlations between the theoretical results and past experiments are described
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.
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.
Experimental investigation of the starting process of short diffusers for gas dynamic lasers
Energy Technology Data Exchange (ETDEWEB)
Oudekerk, M.M.
1975-06-01
The diffuser section of a Gas Dynamic Laser (GDL) is one of the largest components in the system. The purpose of this investigation was to examine the problem of starting supersonic flow in short diffusers with fixed walls, incorporating various bleed arrangements for boundary layer control (BLC). A Mach number of 4, ramp angle of 19 degrees diffuser length of 4.5 in. and a diffuser width of 1.0 in. were used throughout this investigation. Intrusion by the atmosphere into the diffuser causes a separation region or bubble to form. The presence of this 'bubble' could be made to improve the diffuser performance by making a variable area diffuser out of a fixed wall diffuser without the use of any external apparatus. BLC was helpful in increasing the over all pressure recovery of the diffuser. BLC also affects the unsteady flow, which was present in the diffuser, but only when it is applied at a point prior to the converging section of the GDL.
Metzler, Ralf; Klafter, Joseph
2004-08-01
Fractional dynamics has experienced a firm upswing during the past few years, having been forged into a mature framework in the theory of stochastic processes. A large number of research papers developing fractional dynamics further, or applying it to various systems have appeared since our first review article on the fractional Fokker-Planck equation (Metzler R and Klafter J 2000a, Phys. Rep. 339 1-77). It therefore appears timely to put these new works in a cohesive perspective. In this review we cover both the theoretical modelling of sub- and superdiffusive processes, placing emphasis on superdiffusion, and the discussion of applications such as the correct formulation of boundary value problems to obtain the first passage time density function. We also discuss extensively the occurrence of anomalous dynamics in various fields ranging from nanoscale over biological to geophysical and environmental systems.
Dipole diffusion in a random electrical potential
Energy Technology Data Exchange (ETDEWEB)
Touya, Clement; Dean, David S; Sire, Clement [Laboratoire de Physique Theorique, IRSAMC, Universite de Toulouse, CNRS, 31062 Toulouse (France)
2009-09-18
We study the Langevin dynamics of a dipole diffusing in a random electrical field E derived from a quenched Gaussian potential. We show that in a suitable adiabatic limit (where the dynamics of the dipole moment is much faster than the dynamics of its position), one can reduce the coupled stochastic equations to an effective Langevin equation for a particle diffusing in an effective potential with a spatially varying and anisotropic local diffusivity {kappa}{sub ij}. Analytic results, close to the adiabatic limit, for the diffusion constant {kappa}{sub e} are found in one dimension and a finite temperature dynamical transition is found. The system is also studied numerically. In particular, we study the anomalous diffusion exponent in the low-temperature regime. Our findings strongly support the conclusion that the location of the dynamical transition and the anomalous diffusion exponents are determined by purely static considerations, i.e. they are independent of the relative values of the diffusion constants of the particle position and its dipole moment.
Diffusion dynamics of socially learned foraging techniques in squirrel monkeys.
Claidière, Nicolas; Messer, Emily J E; Hoppitt, William; Whiten, Andrew
2013-07-01
Social network analyses and experimental studies of social learning have each become important domains of animal behavior research in recent years yet have remained largely separate. Here we bring them together, providing the first demonstration of how social networks may shape the diffusion of socially learned foraging techniques. One technique for opening an artificial fruit was seeded in the dominant male of a group of squirrel monkeys and an alternative technique in the dominant male of a second group. We show that the two techniques spread preferentially in the groups in which they were initially seeded and that this process was influenced by monkeys' association patterns. Eigenvector centrality predicted both the speed with which an individual would first succeed in opening the artificial fruit and the probability that they would acquire the cultural variant seeded in their group. These findings demonstrate a positive role of social networks in determining how a new foraging technique diffuses through a population. PMID:23810529
International Nuclear Information System (INIS)
In order to quantify effect of temperature on diffusivity of deuterated water (HDO) in compacted sodium-bentonite, through-diffusion experiments were conducted at elevated temperature from 298 to 333 K. Kunipia F (Na-montmorillonite content > 98 wt. %; Kunimine Industry Co.) was compacted to a dry density of 0.9 and 1.35 Mg/m3. Since smectite flakes were perpendicularly oriented to a direction of compaction, anisotropy of diffusivity was investigated parallel and normal to the preferred orientation of smectite. Effective diffusion coefficient De of HDO was larger for a diffusional direction parallel to the preferred orientation than normal to that for both dry densities. These results well agreed to the previously reported ones for tritiated water. Activation energies of De in compacted bentonite increased with increasing dry density in the range of 19-25 kJ/mol which was slightly larger than that in bulk water (18 kJ/mol). This relationship can be considered to be due to both the pore structure development and high activation energy of water (18-23 kJ/mol) in the vicinity of smectite surface (within 2 nm) on the basis of molecular dynamics simulations. (author)
Global Dynamics Analysis of Homogeneous New Products Diffusion Model
Shuping Li; Zhen Jin
2013-01-01
A mathematical model with stage structures is presented that incorporates the awareness stage and the decision-making stage; individuals exchange product information by two channels: mass media and interpersonal communication. When the persuasive advertisement is neglected in the decision-making stage, we find a threshold value about whether new products diffusion is successful or not. When the persuasive advertisement is considered, there must exist a positive equilibrium unde...
Space-dependent self-diffusion processes in molten copper halides: a molecular dynamics study
Alcaraz Sendra, Olga; Trullàs Simó, Joaquim
2001-01-01
This work is concerned with single ion dynamics in molten copper halides (CuI and CuCl) which exhibit fast ionic conduction before melting. The self-dynamic structure factor of the two ionic species in each melt have been calculated by molecular dynamics simulations and the corresponding effective wavelength-dependent self-diffusion coefficients have been studied. The results have been compared with those obtained for molten alkali halides (KCl and RbCl).
Two competing species in super-diffusive dynamical regimes
La Cognata, A.; Valenti, D.; Spagnolo, B.; Dubkov, A. A.
2010-09-01
The dynamics of two competing species within the framework of the generalized Lotka-Volterra equations, in the presence of multiplicative α-stable Lévy noise sources and a random time dependent interaction parameter, is studied. The species dynamics is characterized by two different dynamical regimes, exclusion of one species and coexistence of both, depending on the values of the interaction parameter, which obeys a Langevin equation with a periodically fluctuating bistable potential and an additive α-stable Lévy noise. The stochastic resonance phenomenon is analyzed for noise sources asymmetrically distributed. Finally, the effects of statistical dependence between multiplicative noise and additive noise on the dynamics of the two species are studied.
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?
Comparison of kinetic and dynamical models of DNA-protein interaction and facilitated diffusion
Florescu, Ana-Maria; 10.1021/jp101151a
2010-01-01
It has long been asserted that proteins like transcription factors may locate their target in DNA sequences at rates that surpass by several orders of magnitude the three-dimensional diffusion limit thank to facilitated diffusion, that is the combination of one-dimensional (sliding along the DNA) and three-dimensional diffusion. This claim has been supported along the years by several mass action kinetic models, while the dynamical model we proposed recently (J. Chem. Phys. 130, 015103 (2009)) suggests that acceleration of targeting due to facilitated diffusion cannot be large. In order to solve this apparent contradiction, we performed additional simulations to compare the results obtained with our model to those obtained with the kinetic model of Klenin et al (Phys. Rev. Letters 96, 018104 (2006)). We show in this paper that the two models actually support each other and agree in predicting a low efficiency for facilitated diffusion. Extrapolation of these results to real systems even indicates that facilit...
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. PMID:26219250
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.
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.
Self-diffusion and structural properties of confined fluids in dynamic coexistence
International Nuclear Information System (INIS)
Self-diffusion and radial distribution functions are studied in a strongly confined Lennard-Jones fluid. Surprisingly, in the solid–liquid phase transition region, where the system exhibits dynamic coexistence, the self-diffusion constants are shown to present up to three-fold variations from solid to liquid phases at fixed temperature, while the radial distribution function corresponding to both the liquid and the solid phases are essentially indistinguishable. (paper)
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.
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.
Wu, Xiaobin; Qiu, Jian; Luo, Kaiqing; Han, Peng
2015-08-01
Dynamic Light Scattering is used for measuring particle size distribution of nano-particle under Brownian motion. Signal is detected through a photomultiplier and processed by correlation analysis, and results are inverted at last. Method by using CCD camera can record the procedure of motion. However, there are several weaknesses such as low refresh speed and noise from CCD camera, and this method depends on particle size and detecting angle. A simulation of nano-particle under Brownian motion is proposed to record dynamic images, studies contrast of dynamic images which can represent speed of diffusion, and its characteristic under different conditions. The results show that through contrast of dynamic images diffusion coefficient can be obtained, which is independent on density of scattering volume.
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.
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.
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.
Emerging dynamics in neuronal networks of diffusively coupled hard oscillators.
Ponta, L; Lanza, V; Bonnin, M; Corinto, F
2011-06-01
Oscillatory networks are a special class of neural networks where each neuron exhibits time periodic behavior. They represent bio-inspired architectures which can be exploited to model biological processes such as the binding problem and selective attention. In this paper we investigate the dynamics of networks whose neurons are hard oscillators, namely they exhibit the coexistence of different stable attractors. We consider a constant external stimulus applied to each neuron, which influences the neuron's own natural frequency. We show that, due to the interaction between different kinds of attractors, as well as between attractors and repellors, new interesting dynamics arises, in the form of synchronous oscillations of various amplitudes. We also show that neurons subject to different stimuli are able to synchronize if their couplings are strong enough.
Large-scale dynamics of sandy coastlines: diffusivity and instability
Falqués Serra, Albert; Calvete Manrique, Daniel
2005-01-01
The dynamics of small-amplitude perturbations of an otherwise rectilinear coastline due to the wave-driven alongshore sediment transport is examined at large time and length scales (years and kilometers). A linear stability analysis is performed by using an extended one-line shoreline model with two main improvements: (1) the curvature of the coastline features is accounted for and (2) the coastline features are assumed to extend offshore as a bathymetric perturbation up to a finite distance....
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.
Chen, Wei; Huang, Dayu; Kulkarni, Ankur A.; Unnikrishnan, Jayakrishnan; Zhu, Quanyan; Mehta, Prashant; Meyn, Sean; Wierman, Adam
2013-01-01
Neuro-dynamic programming is a class of powerful techniques for approximating the solution to dynamic programming equations. In their most computationally attractive formulations, these techniques provide the approximate solution only within a prescribed finite-dimensional function class. Thus, the question that always arises is how should the function class be chosen? The goal of this paper is to propose an approach using the solutions to associated fluid and diffusion approximations. In ord...
How Local and Average Particle Diffusivities of Inhomogeneous Fluids Depend on Microscopic Dynamics.
Bollinger, Jonathan A; Jain, Avni; Truskett, Thomas M
2015-07-23
Computer simulations and a stochastic Fokker-Planck equation based approach are used to compare the single-particle diffusion coefficients of equilibrium hard-sphere fluids exhibiting identical inhomogeneous static structure and governed by either Brownian (i.e., overdamped Langevin) or Newtonian microscopic dynamics. The physics of inhomogeneity is explored via the imposition of one-dimensional sinusoidal density profiles of different wavelengths and amplitudes. When imposed density variations are small in magnitude for distances on the scale of a particle diameter, bulk-like average correlations between local structure and mobility are observed. In contrast, when density variations are significant on that length scale, qualitatively different structure-mobility correlations emerge that are sensitive to the governing microscopic dynamics. Correspondingly, a previously proposed scaling between long-time diffusivities for bulk isotropic fluids of particles exhibiting Brownian versus Newtonian dynamics [Pond et al. Soft Matter 2011, 7, 9859-9862] cannot be generalized to describe the position-dependent behaviors of strongly inhomogeneous fluids. While average diffusivities in the inhomogeneous and homogeneous directions are coupled, their qualitative dependencies on inhomogeneity wavelength are sensitive to the details of the microscopic dynamics. Nonetheless, average diffusivities of the inhomogeneous fluids can be approximately predicted for either type of dynamics based on knowledge of bulk isotropic fluid behavior and how inhomogeneity modifies the distribution of available volume. Analogous predictions for average diffusivities of experimental, inhomogeneous colloidal dispersions (based on known bulk behavior) suggest that they will exhibit qualitatively different trends than those predicted by models governed by overdamped Langevin dynamics that do not account for hydrodynamic interactions. PMID:25350488
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.
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.
Shape optimization of the diffuser blade of an axial blood pump by computational fluid dynamics.
Zhu, Lailai; Zhang, Xiwen; Yao, Zhaohui
2010-03-01
Computational fluid dynamics (CFD) has been a viable and effective way to predict hydraulic performance, flow field, and shear stress distribution within a blood pump. We developed an axial blood pump with CFD and carried out a CFD-based shape optimization of the diffuser blade to enhance pressure output and diminish backflow in the impeller-diffuser connecting region at a fixed design point. Our optimization combined a computer-aided design package, a mesh generator, and a CFD solver in an automation environment with process integration and optimization software. A genetic optimization algorithm was employed to find the pareto-optimal designs from which we could make trade-off decisions. Finally, a set of representative designs was analyzed and compared on the basis of the energy equation. The role of the inlet angle of the diffuser blade was analyzed, accompanied by its relationship with pressure output and backflow in the impeller-diffuser connecting region. PMID:20447042
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.
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.
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.
A model of riots dynamics: shocks, diffusion and thresholds
Berestycki, Henri; Rodriguez, Nancy
2015-01-01
We introduce and analyze several variants of a system of differential equations which model the dynamics of social outbursts, such as riots. The systems involve the coupling of an explicit variable representing the intensity of rioting activity and an underlying (implicit) field of social tension. Our models include the effects of exogenous and endogenous factors as well as various propagation mechanisms. From numerical and mathematical analysis of these models we show that the assumptions made on how different locations influence one another and how the tension in the system disperses play a major role on the qualitative behavior of bursts of social unrest. Furthermore, we analyze here various properties of these systems, such as the existence of traveling wave solutions, and formulate some new open mathematical problems which arise from our work.
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.
Effects of Heterogeneous Diffuse Fibrosis on Arrhythmia Dynamics and Mechanism.
Kazbanov, Ivan V; ten Tusscher, Kirsten H W J; Panfilov, Alexander V
2016-01-01
Myocardial fibrosis is an important risk factor for cardiac arrhythmias. Previous experimental and numerical studies have shown that the texture and spatial distribution of fibrosis may play an important role in arrhythmia onset. Here, we investigate how spatial heterogeneity of fibrosis affects arrhythmia onset using numerical methods. We generate various tissue textures that differ by the mean amount of fibrosis, the degree of heterogeneity and the characteristic size of heterogeneity. We study the onset of arrhythmias using a burst pacing protocol. We confirm that spatial heterogeneity of fibrosis increases the probability of arrhythmia induction. This effect is more pronounced with the increase of both the spatial size and the degree of heterogeneity. The induced arrhythmias have a regular structure with the period being mostly determined by the maximal local fibrosis level. We perform ablations of the induced fibrillatory patterns to classify their type. We show that in fibrotic tissue fibrillation is usually of the mother rotor type but becomes of the multiple wavelet type with increase in tissue size. Overall, we conclude that the most important factor determining the formation and dynamics of arrhythmia in heterogeneous fibrotic tissue is the value of maximal local fibrosis. PMID:26861111
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.
Energy Technology Data Exchange (ETDEWEB)
Shirdel-Havar, A. H., E-mail: Amir.hushang.shirdel@gmail.com; Masoudian Saadabad, R. [Department of Physics, University of Sistan and Baluchestan, Zahedan 98135-674 (Iran, Islamic Republic of)
2015-03-21
Based on ballistic-diffusive approximation, a method is presented to model heat transfer in nanocomposites containing metal nanoparticles. This method provides analytical expression for the temperature dynamics of metallic nanoparticles embedded in a dielectric medium. In this study, nanoparticles are considered as spherical shells, so that Boltzmann equation is solved using ballistic-diffusive approximation to calculate the electron and lattice thermal dynamics in gold nanoparticles, while thermal exchange between the particles is taken into account. The model was used to investigate the influence of particle size and metal concentration of the medium on the electron and lattice thermal dynamics. It is shown that these two parameters are crucial in determining the nanocomposite thermal behavior. Our results showed that the heat transfer rate from nanoparticles to the matrix decreases as the nanoparticle size increases. On the other hand, increasing the metal concentration of the medium can also decrease the heat transfer rate.
International Nuclear Information System (INIS)
Based on ballistic-diffusive approximation, a method is presented to model heat transfer in nanocomposites containing metal nanoparticles. This method provides analytical expression for the temperature dynamics of metallic nanoparticles embedded in a dielectric medium. In this study, nanoparticles are considered as spherical shells, so that Boltzmann equation is solved using ballistic-diffusive approximation to calculate the electron and lattice thermal dynamics in gold nanoparticles, while thermal exchange between the particles is taken into account. The model was used to investigate the influence of particle size and metal concentration of the medium on the electron and lattice thermal dynamics. It is shown that these two parameters are crucial in determining the nanocomposite thermal behavior. Our results showed that the heat transfer rate from nanoparticles to the matrix decreases as the nanoparticle size increases. On the other hand, increasing the metal concentration of the medium can also decrease the heat transfer rate
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.
Kim, Changho; Borodin, Oleg; Karniadakis, George Em
2015-12-01
We analyze two standard methods to compute the diffusion coefficient of a tracer particle in a medium from molecular dynamics (MD) simulation, the velocity autocorrelation function (VACF) method, and the mean-squared displacement (MSD) method. We show that they are equivalent in the sense that they provide the same mean values with the same level of statistical errors. We obtain analytic expressions for the level of the statistical errors present in the time-dependent diffusion coefficient as well as the VACF and the MSD. Under the assumption that the velocity of the tracer particle is a Gaussian process, all results are expressed in terms of the VACF. Hence, the standard errors of all relevant quantities are computable once the VACF is obtained from MD simulation. By using analytic models described by the Langevin equations driven by Gaussian white noise and Poissonian white shot noise, we verify our theoretical error estimates and discuss the non-Gaussianity effect in the error estimates when the Gaussian process approximation does not hold exactly. For validation, we perform MD simulations for the self-diffusion of a Lennard-Jones fluid and the diffusion of a large and massive colloid particle suspended in the fluid. Our theoretical framework is also applicable to mesoscopic simulations, e.g., Langevin dynamics and dissipative particle dynamics.
On an explicit finite difference method for fractional diffusion equations
S. B. Yuste; Acedo, L.
2003-01-01
A numerical method to solve the fractional diffusion equation, which could also be easily extended to many other fractional dynamics equations, is considered. These fractional equations have been proposed in order to describe anomalous transport characterized by non-Markovian kinetics and the breakdown of Fick's law. In this paper we combine the forward time centered space (FTCS) method, well known for the numerical integration of ordinary diffusion equations, with the Grunwald-Letnikov defin...
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.
Chen, J. -Y.; Echekki, T.
1999-01-01
Triple flames arise in a number of practical configurations where fuel and oxidizer are partially premixed, such as in the base of a lifted jet flame. Past experimental studies, theoretical analyses, and numerical modeling of triple flames suggested the potential role of triple flames in stabilizing turbulent flames and in promoting flame propagation. From recent numerical simulations of laminar triple flames, a strong influence of differential diffusion among species and heat on the triple flame structure has been gradually appreciated. This paper reports preliminary numerical results on the influence of gravity and differential diffusion effects on the structure and dynamics of triple flames with a one-step global irreversible chemistry model.
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.
International Nuclear Information System (INIS)
We have developed an N-body interatomic potential, based on the second moment approximation of the tight-binding scheme, by fitting its four adjustable parameters to the cohesive energy, atomic volume, and elastic constants of hcp-Zr. We then showed that various properties of this potential compare favorably with those of zirconium in both the low temperatures hcp phase and the high temperature bcc phase. Such is the case in particular for the elastic constants, the phonon dispersion curves, the thermal expansion, and the melting temperature. We reproduced by molecular dynamics (MD) simulations on this potential the hcp/bcc phase transformation in both ways. It indeed occurs following the mechanism predicted by Burgers. We find a vibrational entropy of transformation equal to 0.13 kB. Our calculations suggest that in real zirconium the electronic contribution to the transformation entropy is important. We show that some interatomic potential lead to a higher value of the vibrational entropy in the hcp phase than in the bcc phase. We specified the dynamics of the vacancy migration in the bcc phase. The atomic jumps are almost exclusively nearest neighbour ones. The walk of the vacancy becomes strongly correlated at high temperatures. The vacancy jump frequency is very large and has a perfectly arrhenian behaviour. There is no evicence of a dynamical lowering of the vacancy migration barrier: the static and dynamic values of the vacancy migration energy are almost equal, both being unusually small (0.3 eV). The self diffusion coefficent of our model for the vacancy mechanism reproduces an anomalous fast diffusion close to that measured experimentally in bcc-Zr. In our model at high temperatures the time interval between successive jumps is almost equal to the time of flight. The migration events will therefore influence the formation of the vacancies
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...
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.
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.
Sub-diffusion and trapped dynamics of neutral and charged probes in DNA-protein coacervates
International Nuclear Information System (INIS)
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
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.
Ionization dynamics in ionic liquids probed via self-diffusion coefficient measurements
International Nuclear Information System (INIS)
Graphical abstract: - Highlights: • Exploiting non-Arrhenius nature of physiochemical properties of ionic liquids to understand ion dynamics. • Estimation of ion concentration in ionic liquids via self-diffusion coefficient measurements. • Thermodynamics of the ionization process in ionic liquids. • Thermodynamics of the self-diffusion of cations and anions through Arrhenius and Eyring equations. - Abstract: Ionic liquids contain ions and ion pairs with fast exchange between them. We propose a novel process to deduce the fraction of ions present in an ionic liquid and the equilibrium constants of ionization processes from measured ion self-diffusion coefficients using Pulsed Field Gradient (PFG) NMR. The enthalpy and entropy changes of ionization and ion self-diffusion processes are obtained for a series of ionic liquids using this method. These data were used to explain the interactions between cations and anions of ionic liquids. The interactions are also interpreted by the delocalization of the ion’s charge densities. The self-diffusion coefficients of cations and anions for measured ionic liquids are discussed
Ionization dynamics in ionic liquids probed via self-diffusion coefficient measurements
Energy Technology Data Exchange (ETDEWEB)
Mao, Yougang; Damodaran, Krishnan, E-mail: damodak@pitt.edu
2014-08-31
Graphical abstract: - Highlights: • Exploiting non-Arrhenius nature of physiochemical properties of ionic liquids to understand ion dynamics. • Estimation of ion concentration in ionic liquids via self-diffusion coefficient measurements. • Thermodynamics of the ionization process in ionic liquids. • Thermodynamics of the self-diffusion of cations and anions through Arrhenius and Eyring equations. - Abstract: Ionic liquids contain ions and ion pairs with fast exchange between them. We propose a novel process to deduce the fraction of ions present in an ionic liquid and the equilibrium constants of ionization processes from measured ion self-diffusion coefficients using Pulsed Field Gradient (PFG) NMR. The enthalpy and entropy changes of ionization and ion self-diffusion processes are obtained for a series of ionic liquids using this method. These data were used to explain the interactions between cations and anions of ionic liquids. The interactions are also interpreted by the delocalization of the ion’s charge densities. The self-diffusion coefficients of cations and anions for measured ionic liquids are discussed.
A molecular dynamics simulation of self-diffusion on Fe surfaces
Energy Technology Data Exchange (ETDEWEB)
Wang Changqing, E-mail: cqw@lit.edu.cn [School of Physics and Engineering, Center for Clean Energy and Quantum Structures, Zhengzhou University, Zhengzhou 450052 (China); Department of Mathematics and Physics, Luoyang Institute of Science and Technology, Luoyang 471023 (China); Qin Zhen [School of Mathematics and Information Science, North China University of Water Resources and Electric Power, Zhengzhou 450011 (China); Zhang Yongsheng [Department of Mathematics and Physics, Luoyang Institute of Science and Technology, Luoyang 471023 (China); Sun Qiang; Jia Yu [School of Physics and Engineering, Center for Clean Energy and Quantum Structures, Zhengzhou University, Zhengzhou 450052 (China)
2012-03-01
Using embedded-atom-method (EAM) potential, an adatom and a vacancy diffusion processes have been simulated in detail by molecular dynamics on three Fe surfaces, Fe (1 1 0), Fe (1 0 0), and Fe (1 1 1). Our results reveal that adatom adsorption energies and diffusion migration energies on these surfaces have similar monotonic trend to the relative layer spacing relaxation, R{sub (110)} < R{sub (100)} < R{sub (111)}, adsorption energy, E{sub a(110)}{sup a}
Investigation of the performance of a variable area diffuser for gas dynamic lasers
Energy Technology Data Exchange (ETDEWEB)
Nuttbrock, D.L.
1974-06-01
An experimental study was performed to determine the performance of a variable area diffuser downstrem of an array of supersonic nozzles, and to determine the Mach number profile between the nozzle exit and the diffuser entrance. The study was conducted on a blowdown wind tunnel and the test section was designed to model a gas dynamic laser with an array of five nozzle blades, a constant area section, and a converging-diverging diffuser. Air at a temperature of 70/sup 0/F and at total pressures ranging from 100 to 210 psig was expanded through an area ratio of approximately 66. Using various pressure measurements the Mach number was found to decrease from M = 6.4 at the nozzle exit to approximately M = 4.0 at the diffuser entrance. The rapid decrease was attributed to the irreversible effects of friction, the nozzle blade wakes, and the nozzle throat shocks. The minimum starting area ratio of the diffuser was 0.59, which agrees well with one dimensional theory.
Dynamics for a diffusive prey-predator model with different free boundaries
Wang, Mingxin
2015-01-01
To understand the spreading and interaction of prey and predator, in this paper we study the dynamics of the diffusive Lotka-Volterra type prey-predator model with different free boundaries. These two free boundaries, which may intersect each other as time evolves, are used to describe the spreading of prey and predator. We investigate the existence and uniqueness, regularity and uniform estimates, and long time behaviors of global solution. Some sufficient conditions for spreading and vanish...
On the dynamic programming principle for controlled diffusion processes in a cylindrical region
Dmitry B. Rokhlin
2012-01-01
We prove the dynamic programming principle for a class of diffusion processes controlled up to the time of exit from a cylindrical region $[0,T)\\times G$. It is assumed that the functional to be maximized is in the Lagrange form with nonnegative integrand. Besides this we only adopt the standard assumptions, ensuring the existence of a unique strong solution of a stochastic differential equation for the state process.
Relaxation time in a non-conserving driven-diffusive system with parallel dynamics
International Nuclear Information System (INIS)
We introduce a two-state non-conserving driven-diffusive system in one dimension under a discrete-time updating scheme. We show that the steady state of the system can be obtained using a matrix product approach. On the other hand, the steady state of the system can be expressed in terms of a linear superposition of Bernoulli shock measures with random walk dynamics. The dynamics of a shock position is studied in detail. The spectrum of the transfer matrix and the relaxation times to the steady state have also been studied in the limit of large system size. (paper)
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
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.
The Dynamics of a Diffusive Nutrient-Algae Model Based upon the Sanyang Wetland
Directory of Open Access Journals (Sweden)
Yi Wang
2015-01-01
Full Text Available The stability and spatiotemporal dynamics of a diffusive nutrient-algae model are investigated mathematically and numerically. Mathematical theoretical studies have considered the positivity and boundedness of the solution and the existence, local stability, and global stability of equilibria. Turing instability has also been studied. Furthermore, a series of numerical simulations was performed and a complex Turing pattern found. These results indicate that the nutrient input rate has an important influence on the density and spatial distribution of algae populations. This may help us to obtain a better understanding of the interactions of nutrient and algae and to investigate plankton dynamics in aquatic ecosystems.
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.
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.
Active-Site Hydration and Water Diffusion in Cytochrome P450cam: A Highly Dynamic Process
Energy Technology Data Exchange (ETDEWEB)
Miao, Yinglong [ORNL; Baudry, Jerome Y [ORNL
2011-01-01
Long-timescale molecular dynamics simulations (300 ns) are performed on both the apo- (i.e., camphor-free) and camphor-bound cytochrome P450cam (CYP101). Water diffusion into and out of the protein active site is observed without biased sampling methods. During the course of the molecular dynamics simulation, an average of 6.4 water molecules is observed in the camphor-binding site of the apo form, compared to zero water molecules in the binding site of the substrate-bound form, in agreement with the number of water molecules observed in crystal structures of the same species. However, as many as 12 water molecules can be present at a given time in the camphor-binding region of the active site in the case of apo-P450cam, revealing a highly dynamic process for hydration of the protein active site, with water molecules exchanging rapidly with the bulk solvent. Water molecules are also found to exchange locations frequently inside the active site, preferentially clustering in regions surrounding the water molecules observed in the crystal structure. Potential-of-mean-force calculations identify thermodynamically favored trans-protein pathways for the diffusion of water molecules between the protein active site and the bulk solvent. Binding of camphor in the active site modifies the free-energy landscape of P450cam channels toward favoring the diffusion of water molecules out of the protein active site.
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].
Rotational diffusion affects the dynamical self-assembly pathways of patchy particles.
Newton, Arthur C; Groenewold, Jan; Kegel, Willem K; Bolhuis, Peter G
2015-12-15
Predicting the self-assembly kinetics of particles with anisotropic interactions, such as colloidal patchy particles or proteins with multiple binding sites, is important for the design of novel high-tech materials, as well as for understanding biological systems, e.g., viruses or regulatory networks. Often stochastic in nature, such self-assembly processes are fundamentally governed by rotational and translational diffusion. Whereas the rotational diffusion constant of particles is usually considered to be coupled to the translational diffusion via the Stokes-Einstein relation, in the past decade it has become clear that they can be independently altered by molecular crowding agents or via external fields. Because virus capsids naturally assemble in crowded environments such as the cell cytoplasm but also in aqueous solution in vitro, it is important to investigate how varying the rotational diffusion with respect to transitional diffusion alters the kinetic pathways of self-assembly. Kinetic trapping in malformed or intermediate structures often impedes a direct simulation approach of a kinetic network by dramatically slowing down the relaxation to the designed ground state. However, using recently developed path-sampling techniques, we can sample and analyze the entire self-assembly kinetic network of simple patchy particle systems. For assembly of a designed cluster of patchy particles we find that changing the rotational diffusion does not change the equilibrium constants, but significantly affects the dynamical pathways, and enhances (suppresses) the overall relaxation process and the yield of the target structure, by avoiding (encountering) frustrated states. Besides insight, this finding provides a design principle for improved control of nanoparticle self-assembly. PMID:26621742
An Asymptotic Analysis of a 2-D Model of Dynamically Active Compartments Coupled by Bulk Diffusion
Gou, J.; Ward, M. J.
2016-08-01
A class of coupled cell-bulk ODE-PDE models is formulated and analyzed in a two-dimensional domain, which is relevant to studying quorum-sensing behavior on thin substrates. In this model, spatially segregated dynamically active signaling cells of a common small radius ɛ ≪ 1 are coupled through a passive bulk diffusion field. For this coupled system, the method of matched asymptotic expansions is used to construct steady-state solutions and to formulate a spectral problem that characterizes the linear stability properties of the steady-state solutions, with the aim of predicting whether temporal oscillations can be triggered by the cell-bulk coupling. Phase diagrams in parameter space where such collective oscillations can occur, as obtained from our linear stability analysis, are illustrated for two specific choices of the intracellular kinetics. In the limit of very large bulk diffusion, it is shown that solutions to the ODE-PDE cell-bulk system can be approximated by a finite-dimensional dynamical system. This limiting system is studied both analytically, using a linear stability analysis and, globally, using numerical bifurcation software. For one illustrative example of the theory, it is shown that when the number of cells exceeds some critical number, i.e., when a quorum is attained, the passive bulk diffusion field can trigger oscillations through a Hopf bifurcation that would otherwise not occur without the coupling. Moreover, for two specific models for the intracellular dynamics, we show that there are rather wide regions in parameter space where these triggered oscillations are synchronous in nature. Unless the bulk diffusivity is asymptotically large, it is shown that a diffusion-sensing behavior is possible whereby more clustered spatial configurations of cells inside the domain lead to larger regions in parameter space where synchronous collective oscillations between the small cells can occur. Finally, the linear stability analysis for these cell
Spectrum of anomalous magnetohydrodynamics
Giovannini, Massimo
2016-05-01
The equations of anomalous magnetohydrodynamics describe an Abelian plasma where conduction and chiral currents are simultaneously present and constrained by the second law of thermodynamics. At high frequencies the magnetic currents play the leading role, and the spectrum is dominated by two-fluid effects. The system behaves instead as a single fluid in the low-frequency regime where the vortical currents induce potentially large hypermagnetic fields. After deriving the physical solutions of the generalized Appleton-Hartree equation, the corresponding dispersion relations are scrutinized and compared with the results valid for cold plasmas. Hypermagnetic knots and fluid vortices can be concurrently present at very low frequencies and suggest a qualitatively different dynamics of the hydromagnetic nonlinearities.
International Nuclear Information System (INIS)
The measurement of volatile organic compound (VOC) concentration changes, in the range of 10 ppt–1ppb, is essential in several applications. The World Meteorological Organization has identified a set of VOCs that are critical because of their long-term instability. The measurement of such changes demands generation of reference mixtures at a high accuracy and stability level. The dynamic preparation of gas mixtures based on diffusion is a suitable way of generating accurate reference mixtures, particularly of unstable VOCs. Diffusion rate and dilution gas flow rate uncertainties are the main contributors to the overall VOC concentration uncertainty. This paper presents a comprehensive overview of the uncertainty of the diffusion rate. Stress is laid on the advantages offered by a modified measurand equation. The validity of this analysis and the modified equation has been confirmed experimentally. Temperature variability and mass difference uncertainty make the main contributions to the uncertainty: a 0.01 °C variability results in a 0.2% uncertainty. The new measurand equation provides both a better indication of the systematic effects at a narrow temperature variability and a more realistic calculation of the uncertainty. The modified equation enhances calculation of uncertainty at the low diffusion rates needed to generate very low VOC concentration mixtures
Molecular-Dynamics Simulation of Self-Diffusion of Molecular Hydrogen in X-Type Zeolite
Directory of Open Access Journals (Sweden)
Xiaoming Du
2013-01-01
Full Text Available The self-diffusion of hydrogen in NaX zeolite has been studied by molecular-dynamics simulations for various temperatures and pressures. The results indicate that in the temperature range of 77–293 K and the pressure range of 10–2700 kPa, the self-diffusion coefficients are found to range from 1.61 × 10−9 m2·s−1 to 3.66 × 10−8 m2·s−1 which are in good agreement with the experimental values from the quasielastic neutron scattering (QENS and pulse field gradients nuclear magnetic resonance (PFG NMR measurements. The self-diffusion coefficients decrease with increasing pressure due to packing of sorbate-sorbate molecules which causes frequent collusion among hydrogen molecules in pores and increase with increasing temperature because increasing the kinetic energy of the gas molecules enlarges the mean free path of gas molecule. The activated energy for hydrogen diffusion determined from the simulation is pressure-dependent.
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.
Transport dissipative particle dynamics model for mesoscopic advection-diffusion-reaction problems
Li, Zhen; Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em
2015-07-01
We present a transport dissipative particle dynamics (tDPD) model for simulating mesoscopic problems involving advection-diffusion-reaction (ADR) processes, along with a methodology for implementation of the correct Dirichlet and Neumann boundary conditions in tDPD simulations. tDPD is an extension of the classic dissipative particle dynamics (DPD) framework with extra variables for describing the evolution of concentration fields. The transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of these Lagrangian particles. An analytical formula is proposed to relate the tDPD parameters to the effective diffusion coefficient. To validate the present tDPD model and the boundary conditions, we perform three tDPD simulations of one-dimensional diffusion with different boundary conditions, and the results show excellent agreement with the theoretical solutions. We also performed two-dimensional simulations of ADR systems and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, we present an application of the tDPD model to the dynamic process of blood coagulation involving 25 reacting species in order to demonstrate the potential of tDPD in simulating biological dynamics at the mesoscale. We find that the tDPD solution of this comprehensive 25-species coagulation model is only twice as computationally expensive as the conventional DPD simulation of the hydrodynamics only, which is a significant advantage over available continuum solvers.
Zha, Yunfei; Li, Maojin; YANG, JIANYONG
2010-01-01
Objective 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. Materials and Methods 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 m...
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.
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
different 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......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; Physica...... coupled 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....
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.
Critical Role of Dynamic Flexibility in Ge-Containing Zeolites: Impact on Diffusion.
Gutiérrez-Sevillano, Juan José; Calero, Sofía; Hamad, Said; Grau-Crespo, Ricardo; Rey, Fernando; Valencia, Susana; Palomino, Miguel; Balestra, Salvador R G; Ruiz-Salvador, A Rabdel
2016-07-11
Incorporation of germanium in zeolites is well known to confer static flexibility to their framework, by stabilizing the formation of small rings. In this work, we show that the flexibility associated to Ge atoms in zeolites goes beyond this static effect, manifesting also a clear dynamic nature, in the sense that it leads to enhanced molecular diffusion. Our study combines experimental and theoretical methods providing evidence for this effect, which has not been described previously, as well as a rationalization for it, based on atomistic grounds. We have used both pure-silica and silico-germanate ITQ-29 (LTA topology) zeolites as a case study. Based on our simulations, we identify the flexibility associated to the pore breathing-like behavior induced by the Ge atoms, as the key factor leading to the enhanced diffusion observed experimentally in Ge-containing zeolites. PMID:27305363
Lateral diffusivity coefficients from the dynamics of a SF6 patch in a coastal environment
Kersalé, M.; Petrenko, A. A.; Doglioli, A. M.; Nencioli, F.; Bouffard, J.; Blain, S.; Diaz, F.; Labasque, T.; Quéguiner, B.; Dekeyser, I.
2016-01-01
The dispersion of a patch of the tracer sulfur hexafluoride (SF6) is used to assess the lateral diffusivity in the coastal waters of the western part of the Gulf of Lion (GoL), northwestern Mediterranean Sea, during the Latex10 experiment (September 2010). Immediately after the release, the spreading of the patch is associated with a strong decrease of the SF6 concentrations due to the gas exchange from the ocean to the atmosphere. This has been accurately quantified, evidencing the impact of the strong wind conditions during the first days of this campaign. Few days after the release, as the atmospheric loss of SF6 decreased, lateral diffusivity coefficient at spatial scales of 10 km has been computed using two approaches. First, the evolution of the patch with time was combined with a diffusion-strain model to obtain estimates of the strain rate (γ = 2.5 10- 6 s- 1) and of the lateral diffusivity coefficient (Kh = 23.2 m2 s- 1). Second, a steady state model was applied, showing Kh values similar to the previous method after a period of adjustment between 2 and 4.5 days. This implies that after such period, our computation of Kh becomes insensitive to the inclusion of further straining of the patch. Analysis of sea surface temperature satellite imagery shows the presence of a strong front in the study area. The front clearly affected the dynamics within the region and thus the temporal evolution of the patch. Our results are consistent with previous studies in open ocean and demonstrate the success and feasibility of those methods also under small-scale, rapidly-evolving dynamics typical of coastal environments.
Directory of Open Access Journals (Sweden)
Stamatakis Michail
2010-04-01
Full Text Available Abstract Background An adaptive coarse-grained (kinetic Monte Carlo (ACGMC simulation framework is applied to reaction and diffusion dynamics in inhomogeneous domains. The presented model is relevant to the diffusion and dimerization dynamics of epidermal growth factor receptor (EGFR in the presence of plasma membrane heterogeneity and specifically receptor clustering. We perform simulations representing EGFR cluster dissipation in heterogeneous plasma membranes consisting of higher density clusters of receptors surrounded by low population areas using the ACGMC method. We further investigate the effect of key parameters on the cluster lifetime. Results Coarse-graining of dimerization, rather than of diffusion, may lead to computational error. It is shown that the ACGMC method is an effective technique to minimize error in diffusion-reaction processes and is superior to the microscopic kinetic Monte Carlo simulation in terms of computational cost while retaining accuracy. The low computational cost enables sensitivity analysis calculations. Sensitivity analysis indicates that it may be possible to retain clusters of receptors over the time scale of minutes under suitable conditions and the cluster lifetime may depend on both receptor density and cluster size. Conclusions The ACGMC method is an ideal platform to resolve large length and time scales in heterogeneous biological systems well beyond the plasma membrane and the EGFR system studied here. Our results demonstrate that cluster size must be considered in conjunction with receptor density, as they synergistically affect EGFR cluster lifetime. Further, the cluster lifetime being of the order of several seconds suggests that any mechanisms responsible for EGFR aggregation must operate on shorter timescales (at most a fraction of a second, to overcome dissipation and produce stable clusters observed experimentally.
Michailidou, V. N.; Swan, J. W.; Brady, J. F.; Petekidis, G.
2013-01-01
Evanescent wave dynamic light scattering and Stokesian dynamics simulations were employed to study the dynamics of hard-sphere colloidal particles near a hard wall in concentrated suspensions. The evanescent wave averaged short-time diffusion coefficients were determined from experimental correlation functions over a range of scattering wave vectors and penetration depths. Stokesian dynamics simulations performed for similar conditions allow a direct comparison of both the short-time self- an...
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...
Aldrin-Denny, R
1998-01-01
The methodology of formulating spatio-temporal diffusion-migration equations in an applied electric field for two competing diffusion processes is outlined using kinetic Ising model versions with the help of spin-exchange dynamics due to Kawasaki. The two transport processes considered here correspond to bounded displacement of species attached to supramolecular structures and electron hopping between spatially separated electron transfer active centres. The dependence of the diffusion coefficient on number density as well as the microscopic basis underlying phenomenological diffusion-migration equations are pointed out. (author)
Investigation of cation self-diffusion mechanisms in UO2±x using molecular dynamics
International Nuclear Information System (INIS)
This article is devoted to investigation of cation self-diffusion mechanisms, taking place in UO2, UO2+x, and UO2−x crystals simulated under periodic (PBC) and isolated (IBC) boundary conditions using the method of molecular dynamics in the approximation of rigid ions and pair interactions. It is shown that under PBC the cations diffuse via an exchange mechanism (with the formation of Frenkel defects) with activation energy of 15–22 eV, while under IBC there is competition between the exchange and vacancy (via Schottky defects) diffusion mechanisms, which give the effective activation energy of 11–13 eV near the melting temperature of the simulated UO2.00 nanocrystals. Vacancy diffusion with lower activation energy of 6–7 eV was dominant in the non-stoichiometric crystals UO2.10, UO2.15 and UO1.85. Observations showed that a cation vacancy is accompanied by different number of anion vacancies depending on the deviation from stoichiometry: no vacancies in UO2.15, single vacancy in UO2.00 and four vacancies in UO1.85. The corresponding law of mass action formulas derived within the Lidiard–Matzke model allowed explaining the obtained activation energies and predicting a change in the activation energy within the temperature range of the superionic phase transition. The diffusion of cations on the surface of nanocrystals had activation energy of 3.1–3.6 eV
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.
DEFF Research Database (Denmark)
Boned, C.; Allal, A.; Baylaucq, A.;
2004-01-01
In this work, a simultaneous modeling of the self-diffusion coefficient and the dynamic viscosity is presented. In the microstructural theory these two quantities are governed by the same friction coefficient related to the mobility of the molecule. A recent free-volume model, already successfully......, chlorotrifluoromethane, cyclohexane, methylcyclohexane, and tetramethylsilane. For these pure compounds we have found in the literature several data for both the self-diffusion and the dynamic viscosity in large viscosity, diffusion, temperature, and pressure intervals (up to around 500 MPa for methylcyclohexane...
Nemoto, Yuya; Ohno, Fumitaka; Maeshima, Nobuya; Hino, Ken-ichi
2016-09-01
We examine a resonance structure of Floquet state in dynamic fractional Stark ladder (DFSL) realized in biased semiconductor superlattices driven by a terahertz cw laser on the basis of the R-matrix Floquet theory. To do this, we calculate an excess density of state ρ (ex)(E) corresponding to lifetime of the Floquet state with a fractional matching ratio η, where η is the ratio of a Bloch frequency ΩB to a laser frequency ω, namely, η =ΩB / ω. The results for η = 3 / 2 demonstrate the appearance of discernibly large peaks associated with Floquet states with longevity in a region of relatively high laser-intensity. The underlying physics is discussed in terms of an analytical expression of ρ (ex)(E) and the associated Green function in which ponderomotive couplings are included in a non-perturbative way.
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.
Gunther, Jacqueline E.; Lim, Emerson; Kim, Hyun Keol; Brown, Mindy; Refice, Susan; Kalinsky, Kevin; Hershman, Dawn; Hielscher, Andreas H.
2015-03-01
We have developed a dynamic diffuse optical tomography imaging system that is capable of 3D imaging of both breasts simultaneously. In an ongoing study subjects receiving neoadjuvant chemotherapy are imaged at 6 time points throughout their 5-month treatment. At each time point the subjects preform a breath hold to observe the hemodynamic effects in the breasts. For each session the percent change of various hemodynamic parameters during the breath hold is determined. Preliminary results from show statistically significant differences in washout rates and deoxyhemoglobin changes at the 2-week imaging point between subjects that respond and do not respond to treatment.
Energy Technology Data Exchange (ETDEWEB)
Hebden, Jeremy C; Brunker, Joanna; Correia, Teresa; Price, Ben D; Gibson, Adam P; Everdell, N L [Department of Medical Physics and Bioengineering, University College London, Gower Street, London WC1E 6BT (United Kingdom)
2008-01-21
A novel design of solid dynamic phantom with tissue-like optical properties is presented, which contains variable regions of contrast which are activated electrically. Reversible changes in absorption are produced by localized heating of targets impregnated with thermochromic pigment. A portable, battery-operated prototype has been constructed, and its optical and temporal characteristics have been investigated. The phantom has been developed as a means of assessing the performance of diffuse optical imaging systems, such as those used to monitor haemodynamic changes in the brain and other tissues. Images of the phantom have been reconstructed using data acquired with a continuous wave optical topography system.
Hebden, Jeremy C.; Brunker, Joanna; Correia, Teresa; Price, Ben D.; Gibson, Adam P.; Everdell, N. L.
2008-01-01
A novel design of solid dynamic phantom with tissue-like optical properties is presented, which contains variable regions of contrast which are activated electrically. Reversible changes in absorption are produced by localized heating of targets impregnated with thermochromic pigment. A portable, battery-operated prototype has been constructed, and its optical and temporal characteristics have been investigated. The phantom has been developed as a means of assessing the performance of diffuse optical imaging systems, such as those used to monitor haemodynamic changes in the brain and other tissues. Images of the phantom have been reconstructed using data acquired with a continuous wave optical topography system.
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.
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.
Kamerlin, Natasha; Elvingson, Christer
2016-11-30
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. PMID:27662260
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 ...
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.
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.
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...
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 ...
Christien, F.; Barbu, A.
2005-11-01
A model based on the cluster dynamics approach was proposed in [A. Hardouin Duparc, C. Moingeon, N. Smetniansky-de-Grande, A. Barbu, J. Nucl. Mater. 302 (2002) 143] to describe point defect agglomeration in metals under irradiation. This model is restricted to materials where point defect diffusion is isotropic and is thus not applicable to anisotropic metals such as zirconium. Following the approach proposed by Woo [C.H. Woo, J. Nucl. Mater. 159 (1988) 237], we extended in this work the model to the case where self-interstitial atoms (SIA) diffusion is anisotropic. The model was then applied to the loop microstructure evolution of a zirconium thin foil irradiated with electrons in a high-voltage microscope. First, the inputs were validated by comparing the numerical results with Hellio et al. experimental results [C. Hellio, C.H. de Novion, L. Boulanger, J. Nucl. Mater. 159 (1988) 368]. Further calculations were made to evidence the effect of the thin foil orientation on the dislocation loop microstructure under irradiation. The result is that it is possible to reproduce for certain orientations the 'unexpected' vacancy loop growth experimentally observed in electron-irradiated zirconium [M. Griffiths, M.H. Loretto, R.E. Sallmann, J. Nucl. Mater. 115 (1983) 313; J. Nucl. Mater. 115 (1983) 323; Philos. Mag. A 49 (1984) 613]. This effect is directly linked to SIA diffusion anisotropy.
Energy Technology Data Exchange (ETDEWEB)
Christien, F. [Service de Recherches de Metallurgie Physique, CEA Saclay, 91191 Gif-sur-Yvette cedex (France)]. E-mail: frederic.christien@polytech.univ-nantes.fr; Barbu, A. [Service de Recherches de Metallurgie Physique, CEA Saclay, 91191 Gif-sur-Yvette cedex (France)
2005-11-15
A model based on the cluster dynamics approach was proposed in [A. Hardouin Duparc, C. Moingeon, N. Smetniansky-de-Grande, A. Barbu, J. Nucl. Mater. 302 (2002) 143] to describe point defect agglomeration in metals under irradiation. This model is restricted to materials where point defect diffusion is isotropic and is thus not applicable to anisotropic metals such as zirconium. Following the approach proposed by Woo [C.H. Woo, J. Nucl. Mater. 159 (1988) 237], we extended in this work the model to the case where self-interstitial atoms (SIA) diffusion is anisotropic. The model was then applied to the loop microstructure evolution of a zirconium thin foil irradiated with electrons in a high-voltage microscope. First, the inputs were validated by comparing the numerical results with Hellio et al. experimental results [C. Hellio, C.H. de Novion, L. Boulanger, J. Nucl. Mater. 159 (1988) 368]. Further calculations were made to evidence the effect of the thin foil orientation on the dislocation loop microstructure under irradiation. The result is that it is possible to reproduce for certain orientations the 'unexpected' vacancy loop growth experimentally observed in electron-irradiated zirconium [M. Griffiths, M.H. Loretto, R.E. Sallmann, J. Nucl. Mater. 115 (1983) 313; J. Nucl. Mater. 115 (1983) 323; Philos. Mag. A 49 (1984) 613]. This effect is directly linked to SIA diffusion anisotropy.
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.
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.
Duality of diffusion dynamics in particle motion in soft-mode turbulence
Suzuki, Masaru; Sueto, Hiroshi; Hosokawa, Yusaku; Muramoto, Naoyuki; Narumi, Takayuki; Hidaka, Yoshiki; Kai, Shoichi
2013-10-01
Nonthermal Brownian motion is investigated experimentally by injecting a particle into soft-mode turbulence (SMT), in the electroconvection of a nematic liquid crystal. It is clarified that the particle motion can be classified into two phases: fast motion, where particles move with the local convective flow, and slow motion, where they are carried by global slow pattern dynamics. We propose a simplified model to clarify the mechanism of the short-time and asymptotic behavior of diffusion. In our model, the correlation time is estimated as a function of a control parameter ɛ. The scaling of the SMT pattern correlation time, τd˜ɛ-1, is estimated from the particle dynamics, which is consistent with a previous report observed from the Eulerian viewpoint. The origin of the non-Gaussian distribution of the displacement in the short-time regime is also discussed and an analytical curve is introduced that quantitatively agrees with the experimental data. Our results clearly illustrate the characteristics of diffusive motion in SMT, which are considerably different from the conventional Brownian motion.
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.
Modeling of advection-diffusion-reaction processes using transport dissipative particle dynamics
Li, Zhen; Yazdani, Alireza; Tartakovsky, Alexandre; Karniadakis, George Em
2015-11-01
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. In particular, the transport of concentration is modeled by a Fickian flux and a random flux between tDPD particles, and the advection is implicitly considered by the movements of Lagrangian particles. To validate the proposed tDPD model and the boundary conditions, three benchmark simulations of one-dimensional diffusion with different boundary conditions are performed, and the results show excellent agreement with the theoretical solutions. Also, two-dimensional simulations of ADR systems are performed and the tDPD simulations agree well with the results obtained by the spectral element method. Finally, an application of tDPD to the spatio-temporal dynamics of blood coagulation involving twenty-five reacting species is performed to demonstrate the promising biological applications of the tDPD model. Supported by the DOE Center on Mathematics for Mesoscopic Modeling of Materials (CM4) and an INCITE grant.
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.
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.
Diffusion within α-CuI studied using ab initio molecular dynamics simulations
International Nuclear Information System (INIS)
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 A and 60 deg. 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 (111) 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 (100) 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 x 10-5 cm2 s-1, is in excellent agreement with that found experimentally.
Huang, J.; Meyer, M.; Pontikis, V.
1991-06-01
The atomic core structure of two Schockley partial dislocations in copper has been investigated as a function of temperature using molecular dynamics. We employed a resonant model pseudopotential adapted to copper. Our results show that at increasing temperature, the core of the partials becomes increasingly extended and invades entirely the fault ribbon, yet, the separation distance between the partials remains unchanged. At high temperatures vibrational amplitudes of atoms are much larger in the core of the partials than in the bulk of the perfect crystal and the local atomic structure becomes highly disordered. Although disordered, the core structure remains solid-like up to temperatures close to the melting point. Pipe diffusion along this dissociated dislocation has also been investigated. The formation energies of a vacancy and an interstitial are obtained by quasi-dynamics relaxation at T = 0 K while the migration energies for pipe diffusion are calculated at high temperature. Contrary to current assumptions in favour of a vacancy mechanism, we found that in our model the two types of defects may contribute comparably to pipe diffusion since their activation energies are very close. The trajectories of the migrating defects involve not only the partials' cores but also the stacking fault ribbon extending between them, thus explaining why pipe diffusion is slower when the dislocations are dissociated. La structure de coeur de deux dislocations partielles de Schockley a été étudiée, par dynamique moléculaire, en fonction de la température. Nous avons utilisé un pseudopotentiel calculé pour le cuivre à l'aide d'un modèle de résonance. Nos résultats montrent que le coeur des partielles s'étend de plus en plus à mesure que la température augmente et qu'il recouvre complètement le ruban de faute. Cependant la distance de dissociation entre les partielles ne change pas. A haute température, les amplitudes de vibration atomique sont nettement plus
Anomalous transport equations in toroidal plasmas
International Nuclear Information System (INIS)
Reduced transport equations for a toroidal plasma with fluctuations are derived. These equations include the effects of both anomalous and standard neoclassical transport, and allow clarification of the structure of convective fluxes caused by electrostatic and magnetic fluctuations. Special attention is paid to the combined effects of fluctuations and toroidicity on the transport. The formulation retains the effects of a magnetic field inhomogeneity on the anomalous transport. It is shown that phase space diffusion caused by the gradient in the equilibrium magnetic field appears as a pinch flux in the real space
Sanjay Bhushan
2013-01-01
This paper shows the utility of systems approach by extending the traditional innovation models and incorporating and integrating into them selective critical structural variables to map their interaction and explain the inherent dynamism. Conventionally, the approaches in explaining the innovation diffusion process assume that the process takes place in a stable and homogeneous system in which the innovation diffuses or spreads without being affected by the systemâ€™s structural variables ev...
Farid Chighoub; Brahim Mezerdi
2014-01-01
The main objective of this paper is to explore the relationship between the stochastic maximum principle (SMP in short) and dynamic programming principle (DPP in short), for singular control problems of jump diffusions. First, we establish necessary as well as sufficient conditions for optimality by using the stochastic calculus of jump diffusions and some properties of singular controls. Then, we give, under smoothness conditions, a useful verification theorem and we show that the solution o...
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
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.
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.
Dynamic free energy surfaces for sodium diffusion in type II silicon clathrates.
Slingsby, J G; Rorrer, N A; Krishna, L; Toberer, E S; Koh, C A; Maupin, C M
2016-02-21
Earth abundant semiconducting type II Si clathrates have attracted attention as photovoltaic materials due to their wide band gaps. To realize the semiconducting properties of these materials, guest species that arise during the synthesis process must be completely evacuated from the host cage structure post synthesis. A common guest species utilized in the synthesis of Si clathrates is Na (metal), which templates the clathrate cage formation. Previous experimental investigations have identified that it is possible to evacuate Na from type II clathrates to an occupancy of less than 1 Na per unit cell. This work investigates the energetics, kinetics, and resulting mechanism of Na diffusion through type II Si clathrates by means of biased molecular dynamics and kinetic Monte Carlo simulations. Well-tempered metadynamics has been used to determine the potential of mean force for Na moving between clathrate cages, from which the thermodynamic preferences and transition barrier heights have been obtained. Kinetic Monte Carlo simulations based on the metadynamics results have identified the mechanism of Na diffusion in type II Si clathrates. The overall mechanism consists of a coupled diffusive process linked via electrostatic guest-guest interactions. The large occupied hexakaidechedral cages initially empty their Na guests to adjacent empty large cages, thereby changing the local electrostatic environment around the occupied small pentagonal dodecahedral cages and increasing the probability of Na guests to leave the small cages. This coupled process continues through the cross-over point that is identified as the point where large and small cages are equally occupied by Na guests. Further Na removal results in the majority of guests residing in the large cages as opposed to the small cages, in agreement with experiments, and ultimately a Na free structure. PMID:26658349
International Nuclear Information System (INIS)
The variation of the core structure of an easy glide dislocation with temperature and its influence on the stacking fault energy (γ) have been investigated for the first time by molecular-dynamics simulation in copper. The calculations have been performed at various temperatures, using an ab-initio pseudo-potential. Our results show that the core of the Shockley partials, into which the perfect edge dislocation dissociates, becomes increasingly extended as temperature increases. However their separation remains constant. The calculated energy values of the infinite extension stacking fault and the ribbon fault between the partials are quite different, but the evolution of the core structure does not affect the temperature dependence of the latter. We have found that a high disorder appears in the core region when temperature increases due to important anharmonicity effects of the atomic vibrations. The core structure remains solid-like for T m (Tm: melting point of bulk) in spite of the high disorder. Above Tm, the liquid nucleus germinates in the core region, and then propagates into the bulk. In addition we studied the mobility of vacancies and interstitials trapped on the partials. Although fast diffusion is thought to occur exclusively in a pipe surrounding the dislocation core, in the present study a quasi two-dimensional diffusion is observed for both defects not only in the cores but also in the stacking fault ribbon. On the opposite of current assumptions, the activation energy for diffusion is found to be identical for both defects, which may therefore comparably contribute to mass transport along the dislocations. (author)
Non-Markovian Dynamics and Self-Diffusion in Strongly Coupled Plasmas
Strickler, Trevor; Langin, Thomas; McQuillen, Patrick; Daligault, Jerome; Maksimovich, Nikola; Killian, Thomas
2015-11-01
In weakly coupled plasmas, collisions are dominated by long range, small angle scattering, and each collision is an uncorrelated binary event. In contrast, collisions in strongly coupled plasmas (coupling parameter Γ > 1) are dominated by short range, large angle scattering in which the collisions may be correlated and non-independent in time, i.e., non-Markovian. In this work, we present experimental results indicative of non-Markovian processes in a strongly coupled ultracold neutral plasma (UCNP) created by photoionizing strontium atoms in a magneto-optical trap. We use optical pumping to create spin ``tagged'' subpopulations of ions having non-zero average velocity , and use laser induced fluorescence (LIF) imaging to measure the relaxation of back to equilibrium. We observe clear non-exponential decay in , which indicates non-Markovian dynamics. We further demonstrate there is a theoretical basis to consider as an approximation to the ion velocity autocorrelation function (VAF). We then calculate diffusion coefficients from our data, demonstrating experimental measurement of self-diffusion coefficients for 0 . 3 Air Force Office of Scientific Research (FA9550- 12-1-0267).
McDonnell, Marshall T; Greeley, Duncan A; Kit, Kevin M; Keffer, David J
2016-09-01
The effects of hydration on the solvation, diffusivity, solubility, and permeability of oxygen molecules in sustainable, biodegradable chitosan/chitin food packaging films were studied via molecular dynamics and confined random walk simulations. With increasing hydration, the membrane has a more homogeneous water distribution with the polymer chains being fully solvated. The diffusivity increased by a factor of 4 for oxygen molecules and by an order of magnitude for water with increasing the humidity. To calculate the Henry's constant and solubility of oxygen in the membranes with changing hydration, the excess chemical potential was calculated via free energy perturbation, thermodynamic integration and direct particle deletion methods. The simulations predicted a higher solubility and permeability for the lower humidity, in contradiction to experimental results. All three methods for calculating the solubility were in good agreement. It was found that the Coulombic interactions in the potential caused the oxygen to bind too strongly to the protonated amine group. Insight from this work will help guide molecular modeling of chitosan/chitin membranes, specifically permeability measurements for small solute molecules. Efforts to chemically tailor chitosan/chitin membranes to favor discrete as opposed to continuous aqueous domains could reduce oxygen permeability. PMID:27487964
Molecular Dynamics Simulations Reveal that Water Diffusion between Graphene Oxide Layers is Slow
Devanathan, Ram; Chase-Woods, Dylan; Shin, Yongsoon; Gotthold, David W.
2016-01-01
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. PMID:27388562
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)
Diffusive and rotational dynamics of condensed n-H2 confined in MCM-41
Energy Technology Data Exchange (ETDEWEB)
Prisk, Timothy R [ORNL; Bryan, Matthew [Indiana University; Sokol, Paul E [ORNL
2014-01-01
In this paper, we report an inelastic neutron scattering study of liquid and solid n-H2 confined within MCM-41. This is a high surface area, mesoporous silica glass with a narrow pore size distribution centered at 3.5 nm. The scattering data provides information about the diffusive and rotational dynamics of the adsorbed n-H2 at low temperatures. In the liquid state, the neutron scattering data demonstrates that only a fraction of the adsorbed o-H2 is mobile on the picosecond time scale. This mobile fraction undergoes liquid-like jump diffusion, and values for the residence time t and effective mean-squared displacement hu2i are reported as a function of pore filling. In the solid state, the rotational energy levels of adsorbed H2 are strongly perturbed from their free quantum rotor behavior in the bulk solid. The underlying orientational potential of the hindered rotors is due to the surface roughness and heterogeneity of the MCM-41 pore walls. This potential is compared to the hindering potential of other porous silicas, such as Vycor. Strong selective adsorption makes the interfacial layer rich in o-H2, leaving the inner core volume consisting of a depleted mixture of o-H2 and p-H2.
The dynamics of localized spot patterns for reaction-diffusion systems on the sphere
Trinh, Philippe H.; Ward, Michael J.
2016-03-01
In the singularly perturbed limit corresponding to a large diffusivity ratio between two components in a reaction-diffusion (RD) system, quasi-equilibrium spot patterns are often admitted, producing a solution that concentrates at a discrete set of points in the domain. In this paper, we derive and study the differential algebraic equation (DAE) that characterizes the slow dynamics for such spot patterns for the Brusselator RD model on the surface of a sphere. Asymptotic and numerical solutions are presented for the system governing the spot strengths, and we describe the complex bifurcation structure and demonstrate the occurrence of imperfection sensitivity due to higher order effects. Localized spot patterns can undergo a fast time instability and we derive the conditions for this phenomena, which depend on the spatial configuration of the spots and the parameters in the system. In the absence of these instabilities, our numerical solutions of the DAE system for N = 2 to N = 8 spots suggest a large basin of attraction to a small set of possible steady-state configurations. We discuss the connections between our results and the study of point vortices on the sphere, as well as the problem of determining a set of elliptic Fekete points, which correspond to globally minimizing the discrete logarithmic energy for N points on the sphere.
Diffusive and rotational dynamics of condensed n-H₂ confined in MCM-41.
Prisk, T R; Bryan, M S; Sokol, P E
2014-09-01
In this paper, we report an inelastic neutron scattering study of liquid and solid n-H2 confined within MCM-41. This is a high surface area, mesoporous silica glass with a narrow pore size distribution centered at 3.5 nm. The scattering data provides information about the diffusive and rotational dynamics of the adsorbed n-H2 at low temperatures. In the liquid state, the neutron scattering data demonstrates that only a fraction of the adsorbed o-H2 is mobile on the picosecond time scale. This mobile fraction undergoes liquid-like jump diffusion, and values for the residence time τ and effective mean-squared displacement 〈u(2)〉 are reported as a function of pore filling. In the solid state, the rotational energy levels of adsorbed H2 are strongly perturbed from their free quantum rotor behavior in the bulk solid. The underlying orientational potential of the hindered rotors is due to the surface roughness and heterogeneity of the MCM-41 pore walls. This potential is compared to the hindering potential of other porous silicas, such as Vycor. Strong selective adsorption makes the interfacial layer rich in o-H2, leaving the inner core volume consisting of a depleted mixture of o-H2 and p-H2. PMID:25047147
Molecular Dynamics Study of Stability and Diffusion of Graphene-Based Drug Delivery Systems
Directory of Open Access Journals (Sweden)
Xiunan Wang
2015-01-01
Full Text Available Graphene, a two-dimensional nanomaterial with unique biomedical properties, has attracted great attention due to its potential applications in graphene-based drug delivery systems (DDS. In this work graphene sheets with various sizes and graphene oxide functionalized with polyethylene glycol (GO-PEG are utilized as nanocarriers to load anticancer drug molecules including CE6, DOX, MTX, and SN38. We carried out molecular dynamics calculations to explore the energetic stabilities and diffusion behaviors of the complex systems with focuses on the effects of the sizes and functionalization of graphene sheets as well as the number and types of drug molecules. Our study shows that the binding of graphene-drug complex is favorable when the drug molecules and finite graphene sheets become comparable in sizes. The boundaries of finite sized graphene sheets restrict the movement of drug molecules. The double-side loading often slows down the diffusion of drug molecules compared with the single-side loading. The drug molecules bind more strongly with GO-PEG than with pristine graphene sheets, demonstrating the advantages of functionalization in improving the stability and biocompatibility of graphene-based DDS.
Wang, Sibo; Xu, Junbo; Wen, Hao
2014-12-01
The heavy crude oil consists of thousands of compounds and much of them have large molecular weights and complex structures. Studying the aggregation and diffusion behavior of asphaltenes can facilitate the understanding of the heavy crude oil. In previous studies, the fused aromatic rings were treated as rigid bodies so that dissipative particle dynamics (DPD) integrated with the quaternion method can be used to study asphaltene systems. In this work, DPD integrated with the quaternion method is implemented on graphics processing units (GPUs). Compared with the serial program, tens of times speedup can be achieved when simulations performed on a single GPU. Using multiple GPUs can provide faster computation speed and more storage space for simulations of significant large systems. By using large systems, simulations of the asphaltene-toluene system at extremely dilute concentrations can be performed. The determined diffusion coefficients of asphaltenes are similar to that in experimental studies. At last, the aggregation behavior of asphaltenes in heptane was investigated, and the simulation results agreed with the modified Yen model. Monomers, nanoaggregates and clusters were observed from the simulations at different concentrations.
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.
Molecular Dynamics Simulations Reveal that Water Diffusion between Graphene Oxide Layers is Slow
Energy Technology Data Exchange (ETDEWEB)
Devanathan, Ram; Chase-Woods, Dylan G.; Shin, Yongsoon; Gotthold, David W.
2016-07-08
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 a molecular dynamics simulation study of water intercalated between GO layers that have a C/O ratio of 4. 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 spacing from about 0.7 nm to 0.8 nm and an increase in mass of about 14% 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.
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.
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.
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.
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.
Institute of Scientific and Technical Information of China (English)
程贵钧; 付宝勤; 侯氢; 周晓松; 汪俊
2016-01-01
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.
International Nuclear Information System (INIS)
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/mm2. 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 (× 10−3 mm2/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 × 10−3 mm2/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
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 (...
Reduced Lorenz models for anomalous transport and profile resilience
DEFF Research Database (Denmark)
Rypdal, K.; Garcia, Odd Erik
2007-01-01
to resilience of the profile. Particular emphasis is put on the diffusionless limit, where these equations reduce to a simple dynamical system depending only on one single forcing parameter. This model is studied numerically, stressing experimentally observable signatures, and some of the perils of dimension......The physical basis for the Lorenz equations for convective cells in stratified fluids, and for magnetized plasmas imbedded in curved magnetic fields, are reexamined with emphasis on anomalous transport. It is shown that the Galerkin truncation leading to the Lorenz equations for the closed boundary...... problem is incompatible with finite fluxes through the system in the limit of vanishing diffusion. An alternative formulation leading to the Lorenz equations is proposed, invoking open boundaries and the notion of convective streamers and their back-reaction on the profile gradient, giving rise...
Correlation Networks from Flows. The Case of Forced and Time-Dependent Advection-Diffusion Dynamics.
Directory of Open Access Journals (Sweden)
Liubov Tupikina
Full Text Available 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 results with calculations of degree and clustering for a meandering flow resembling a geophysical ocean jet.
Correlation Networks from Flows. The Case of Forced and Time-Dependent Advection-Diffusion Dynamics.
Tupikina, Liubov; Molkenthin, Nora; 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 results with calculations of degree and clustering for a meandering flow resembling a geophysical ocean jet. PMID:27128846
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.
Forecasting Latin America’s Country Risk Scores by Means of a Dynamic Diffusion Model
Directory of Open Access Journals (Sweden)
R. Cervelló-Royo
2013-01-01
Full Text Available Over the last years, worldwide financial market instability has shaken confidence in global economies. Global financial crisis and changes in sovereign debts ratings have affected the Latin American financial markets and their economies. However, Latin American’s relative resilience to the more acute rise in risk seen in other regions like Europe during last years is offering investors new options for improving risk-return trade-offs. Therefore, forecasting the future of economic situation involves high levels of uncertainty. The Country Risk Score (CRS represents a broadly used indicator to measure the current situation of a country regarding measures of economic, political, and financial risk in order to determine country risk ratings. In this contribution, we present a diffusion model to study the dynamics of the CRS in 18 Latin American countries which considers both the endogenous effect of each country policies and the contagion effect among them. The model predicts quite well the evolution of the CRS in the short term despite the economic and political instability. Furthermore, the model reproduces and forecasts a slight increasing trend, on average, in the CRS dynamics for almost all Latin American countries over the next months.
Chun, Myung-Suk; Kim, Chongyoup; Lee, Duck E.
2009-05-01
In our recent Brownian dynamics (BD) simulation study, the structure and dynamics of anionic polyelectrolyte xanthan in bulk solution as well as confined spaces of slitlike channel were examined by applying a coarse-grained model with nonlinear bead-spring discretization of a whole chain [J. Jeon and M.-S. Chun, J. Chem. Phys. 126, 154904 (2007)]. This model goes beyond other simulations as they did not consider both long-range electrostatic and hydrodynamic interactions between pairs of beads. Simulation parameters are obtained from the viscometric method of rheology data on the native and sonicated xanthan polysaccharides, which have a contour length less than 1μm . The size of the semiflexible polyelectrolyte can be well described by the wormlike chain model once the electrostatic effects are taken into account by the persistence length measured at a long length scale. For experimental verifications, single molecule visualization was performed on fluorescein-labeled xanthan using an inverted fluorescence microscope, and the motion of an individual molecule was quantified. Experimental results on the conformational changes in xanthan chain in the electrolyte solution have a reasonable trend to agree with the prediction by BD simulations. In the translational diffusion induced by the Debye screening effect, the simulation prediction reveals slightly higher values compared to those of our measurements, although it agrees with the literature data. Considering the experimental restrictions, our BD simulations are verified to model the single polyelectrolyte well.
Anomalous transport in high-temperature plasmas with applications to solenoidal fusion systems
International Nuclear Information System (INIS)
The linear, non-linear, and anomalous transport properties associated with various micro-instabilities driven by cross-field currents in high-temperature plasmas are reviewed. Particular emphasis is placed on instabilities pertinent to the implosion and post-implosion phases of theta-pinch plasmas, e.g. Buneman (electron-ion two-stream), ion acoustic, lower-hybrid-drift, electromagnetic ion cyclotron, and ion-ion cross-field instabilities. Analytic studies of the non-linear and quasi-linear evolution of these instabilities are presented, together with a detailed comparison with computer simulation experiments to test the validity of the various theoretical models and non-linear saturation mechanisms. A general theoretical formalism is presented which describes, in a self-consistent manner, the macroscopic transport produced by the (short-wave-length) turbulence associated with the microinstabilities enumerated above. The experimental evidence that such a self-consistent anomalous transport model is required for describing the implosion behaviour (characterized by diffuse current sheaths) in rapidly pulsed theta pinches is reviewed, together with the early attempts at modelling these implosions numerically with a one-fluid (MHD) model including artificial viscosity. It is shown that fluid-numerical simulations that include (at each space and time step) the effects of anomalous transport in a fully self-consistent manner, explain several features of the experimental observations. The relevance of reflected ions to sheath structure and implosion dynamics is also discussed, and state-of-the-art hybrid-numerical studies (Vlasov ions and fluid electrons) of pinch implosions are presented, which include reflected ion dynamics as well as the anomalous transport associated with cross-field instabilities. Finally, instability mechanisms for producing long-time interpenetration of plasma and magnetic field in post-implosion theta pinches are discussed, together with estimates
DEFF Research Database (Denmark)
Yu, Tao; Heiselberg, Per Kvols; Lei, Bo;
2016-01-01
Highlights • Dynamic experiments are performed to study energy performance of a new HVAC system. • Designed control strategies show good utilization of natural ventilation cooling. • TABS work well with the diffuse ceiling in the dynamic measurements. • No local thermal comfort problem is found...... even in the extreme winter case. • Designed control strategies can be used in the future application of this system....
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.
Mondelo-Martell, Manel; Huarte-Larrañaga, Fermín
2016-08-25
We present quantum dynamics calculations of the diffusion constant of H2 and D2 along a single-walled carbon nanotube at temperatures between 50 and 150 K. We calculate the respective diffusion rates in the low-pressure limit by adapting well-known approaches and methods from the chemical dynamics field using two different potential energy surfaces to model the C-H interaction. Our results predict a usual kinetic isotope effect, with H2 diffusing faster than D2 in the higher temperature range but a reverse trend at temperatures below 50-70 K. These findings are consistent with experimental observation in similar systems and can be explained by the different effective size of both isotopes resulting from their different zero-point energy. PMID:27459476
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...
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.
Michailidou, V. N.; Swan, J. W.; Brady, J. F.; Petekidis, G.
2013-10-01
Evanescent wave dynamic light scattering and Stokesian dynamics simulations were employed to study the dynamics of hard-sphere colloidal particles near a hard wall in concentrated suspensions. The evanescent wave averaged short-time diffusion coefficients were determined from experimental correlation functions over a range of scattering wave vectors and penetration depths. Stokesian dynamics simulations performed for similar conditions allow a direct comparison of both the short-time self- and collective diffusivity. As seen earlier [V. N. Michailidou, G. Petekidis, J. W. Swan, and J. F. Brady, Phys. Rev. Lett. 102, 068302 (2009)] while the near wall dynamics in the dilute regime slow down compared to the free bulk diffusion, the reduction is negligible at higher volume fractions due to an interplay between the particle-wall and particle-particle hydrodynamic interactions. Here, we provide a comprehensive comparison between experiments and simulations and discuss the interplay of particle-wall and particle-particle hydrodynamics in the self- and cooperative dynamics determined at different scattering wave vectors and penetration depths.
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...
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...
Anomalous Chiral Superfluidity
Lublinsky, Michael(Physics Department, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel); Zahed, Ismail
2009-01-01
We discuss both the anomalous Cartan currents and the energy-momentum tensor in a left chiral theory with flavour 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 ...
Inverse Spin Hall Effect and Anomalous Hall Effect in a Two-Dimensional Electron Gas
Schwab, Peter; Raimondi, Roberto; Gorini, Cosimo
2010-01-01
We study the coupled dynamics of spin and charge currents in a two-dimensional electron gas in the transport diffusive regime. For systems with inversion symmetry there are established relations between the spin Hall effect, the anomalous Hall effect and the inverse spin Hall effect. However, in two-dimensional electron gases of semiconductors like GaAs, inversion symmetry is broken so that the standard arguments do not apply. We demonstrate that in the presence of a Rashba type of spin-orbit...
Hui, Zi; Tang, Xiaoyue; Li, Wei; Greneche, Jean-Marc; Wang, Qiuping A.
2015-04-01
In this work, we study the problem of diffusing a product (idea, opinion, disease etc.) among agents on spatial network. The network is constructed by random addition of nodes on the planar. The probability for a previous node to be connected to the new one is inversely proportional to their spatial distance to the power of α. The diffusion rate between two connected nodes is inversely proportional to their spatial distance to the power of β as well. Inspired from the Fick's first law, we introduce the diffusion coefficient to measure the diffusion ability of the spatial network. Using both theoretical analysis and Monte Carlo simulation, we get the fact that the diffusion coefficient always decreases with the increasing of parameter α and β, and the diffusion sub-coefficient follows the power-law of the spatial distance with exponent equals to -α-β+2. Since both short-range diffusion and long-range diffusion exist, we use anomalous diffusion method in diffusion process. We get the fact that the slope index δ in anomalous diffusion is always smaller that 1. The diffusion process in our model is sub-diffusion.
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.
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.
Anomalous energy transport in hot plasmas: solar corona and Tokamak
International Nuclear Information System (INIS)
Anomalous energy transport is studied in two hot plasmas and appears to be associated with a heating of the solar corona and with a plasma deconfining process in tokamaks. The magnetic structure is shown to play a fundamental role in this phenomenon through small scale instabilities which are modelized by means of a nonlinear dynamical system: the Beasts' Model. Four behavior classes are found for this system, which are automatically classified in the parameter space thanks to a neural network. We use a compilation of experimental results relative to the solar corona to discuss current-based heating processes. We find that a simple Joule effect cannot provide the required heating rates, and therefore propose a dimensional model involving a resistive reconnective instability which leads to an efficient and discontinuous heating mechanism. Results are in good agreement with the observations. We give an analytical expression for a diffusion coefficient in tokamaks when magnetic turbulence is perturbing the topology, which we validate thanks to the standard mapping. A realistic version of the Beasts' Model allows to test a candidate to anomalous transport: the thermal filamentation instability
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.
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.
A classical picture of anomalous effects in a Tokamak
Hirano, K.
1984-01-01
Atomic collisions between plasma ions and a very small amount of neutral particles remaining in a hot plasma plays a very important role for plasma transports and may be an origin of anomalous effects observed in a Tokamak such as the diffusion coefficient independent of the field strength, a rapid plasma density increase during gas puffing and current penetration with anomalously high speed in the start-up phase. The Ohm's law derived by Cowling is used for the analysis.
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
Shi, Hong-Bo; Ruan, Shigui; Su, Ying; Zhang, Jia-Fang
This paper is devoted to the study of spatiotemporal dynamics of a diffusive Leslie-Gower predator-prey system with ratio-dependent Holling type III functional response under homogeneous Neumann boundary conditions. It is shown that the model exhibits spatial patterns via Turing (diffusion-driven) instability and temporal patterns via Hopf bifurcation. Moreover, the existence of spatiotemporal patterns is established via Turing-Hopf bifurcation at the degenerate points where the Turing instability curve and the Hopf bifurcation curve intersect. Various numerical simulations are also presented to illustrate the theoretical results.
Dynamics of salt diffusion and yield of three types of goat's milk cheese
Directory of Open Access Journals (Sweden)
Sonja Srbinovska
2001-01-01
Full Text Available This paper studies the dynamics of salt diffusion during the ageing ofthree types of cheese from goat's milk: Mozzarella, White Brined andPecorino. The salt concentration was consistently analyzed at the 72nd hour and on the 5th, 10th, 20th, 40th, 50th, 60th and 90th day of the cheese ageing period. The distribution of salt in the three layers of cheese – inner (I, middle (II and outer (III was also studied. The salt equilibration in the cheese mass of Mozzarella occurred on the 15th day, in the White Brined - on the 60th day,whereas in Pecorino the content of salt even on the 90th day was by 1% lower, in the inner layer than in the two other layers of this cheese. The utilization rate of dry matter was 52.17% in Mozzarella, 50.64% in the White Brined and 48.32% in Pecorino. Accordingly, the yield of Mozzarella is 18.13 ±0.43%, of White Brined - 12.50 ±0.37% and the yield of Pecorino is 9.18 ±0.13%.
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.
Anomalous water absorption in porous materials
Lockington, D A
2003-01-01
The absorption of fluid by unsaturated, rigid porous materials may be characterized by the sorptivity. This is a simple parameter to determine and is increasingly being used as a measure of a material's resistance to exposure to fluids (especially moisture and reactive solutes) in aggressive environments. The complete isothermal absorption process is described by a nonlinear diffusion equation, with the hydraulic diffusivity being a strongly nonlinear function of the degree of saturation of the material. This diffusivity can be estimated from the sorptivity test. In a typical test the cumulative absorption is proportional to the square root of time. However, a number of researchers have observed deviation from this behaviour when the infiltrating fluid is water and there is some potential for chemo-mechanical interaction with the material. In that case the current interpretation of the test and estimation of the hydraulic diffusivity is no longer appropriate. Kuentz and Lavallee (2001) discuss the anomalous b...
González-Garciá, M Concepción
1999-01-01
We review the effects of new effective interactions on Higgs-boson phenomenology. New physics in the electroweak bosonic sector is expected to induce additional interactions between the Higgs doublet field and the electroweak gauge bosons, leading to anomalous Higgs couplings as well as anomalous gauge-boson self-interactions. Using a linearly realized SU(2)/sub L/*U(1)/sub Y/ invariant effective Lagrangian to describe the bosonic sector of the Standard Model, we review the effects of the new effective interactions on the Higgs- boson production rates and decay modes. We summarize the results from searches for the new Higgs signatures induced by the anomalous interactions in order to constrain the scale of new physics, in particular at CERN LEP and Fermilab Tevatron colliders. (43 refs).
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.
Fractional Fokker-Planck Equation and Black-Scholes Formula in Composite-Diffusive Regime
Liang, Jin-Rong; Wang, Jun; Lǔ, Long-Jin; Gu, Hui; Qiu, Wei-Yuan; Ren, Fu-Yao
2012-01-01
In statistical physics, anomalous diffusion plays an important role, whose applications have been found in many areas. In this paper, we introduce a composite-diffusive fractional Brownian motion X α, H ( t)= X H ( S α ( t)), 0Black-Scholes formula. We obtain the fractional Fokker-Planck equation governing the dynamics of the probability density function of the composite-diffusive fractional Brownian motion and find the Black-Scholes differential equation driven by the stock asset X α, H ( t) and the corresponding Black-Scholes formula for the fair prices of European option.
Directory of Open Access Journals (Sweden)
N. Santatriniaina
2015-01-01
Full Text Available This work investigates the mass transfer of the Airborne Molecular cross Contamination (AMCs between the Front Opening Unified Pod (FOUP and wafer (silicon substrates during the microelectronics devices manufacturing using dynamic boundary conditions. Such cross-contamination phenomena lead to detrimental impact on production yield in microelectronic industry and a predictive approach using modelling and computational methods is a very strong way to understand and qualify the AMCs cross contamination processes. The FOUP is made of polymeric materials and it is considered as a heterogeneous porous media, it can adsorb and desorb the contaminant, thus the modelled processes are the contamination of two-component in transient flow. Coupled diffusion and convection-diffusion model with heat effects are used to define the phenomena. The present methodology is, first using the optimization methods with the numerical solution in order to define the physical constants of various materials which have been studied experimentally and separately, and the second using the finite element methods including these physical constants and relevant interface condition in order to take into account the adsorption kinetics law. Numerical methods to solve the problem are proposed. The dynamics behaviour of the AMCs analysis was determined thanks to the switch of Dirichlet to Neumann condition. The mathematical model preserves the classical forms of the diffusion and convection diffusion equations and yields to consistent form of the Fick's law. The computed results are in correlation with the experimental measurements. Some numerical results are presented in this work.
Shin, Seunghwan; Dorfman, Kevin; Cheng, Xiang
2015-03-01
Double-stranded DNA (dsDNA) labeled with cyanine dyes such as YOYO-1 has been extensively used as a model to study equilibrium and dynamic properties of semiflexible polyelectrolytes. The ability to directly visualize the polymer dynamics is an attractive feature of these experiments, but positively charged cyanine dyes affect the physical properties of dsDNA, distorting the double helix and counterbalancing the intrinsic negative charge of the backbone. A variety of studies have been conducted to reveal the effect of the dye on the contour length and the persistence length of dsDNA. However, fewer efforts have been made to directly quantify the effect of dye on the diffusion behavior of dsDNA. In order to resolve this issue, we measured the in-plane diffusion coefficient of unconfined dsDNA using confocal microscopy. Although there is widespread consensus that intercalation increases the contour length of dsDNA, we find that increasing the dye:base pair ratio for YOYO-1 actually enhances the diffusion of dsDNA. This enhancement is more significant at lower ionic strengths, which implies that the increase in the diffusion coefficient by dye-DNA intercalation is mainly due to a reduction of excluded volume effect resulting from charge neutralization on the backbone.
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...
International Nuclear Information System (INIS)
A new approach to calculating diffusivities, both transport as well as equilibrium, is presented. The dual control volume grand canonical molecular dynamics (or DCV-GCMD) method employs two local control volumes for chemical potential control via particle creation/destruction as in grand canonical Monte Carlo (GCMC) simulations. The control volumes are inserted in a standard NVT molecular dynamics simulation yielding a simulation with stochastic chemical potential control that may be thought of as a hybrid GCMC-MD approach. The geometrical control of the chemical potential enables a steady state chemical potential gradient to be established in the system. By measuring the density profile and flux, Fick's law is used to determine the diffusivity. An example calculation is presented for a simple Lennard-Jones system
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. PMID:17223124
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.
Molecular Dynamics Simulations of Self-diffusion Coefficients ofExponential-six Fluids
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
Self-diffusion coefficients of exponential-six fluids are studied using equilibrium moleculardynamics simulation technique. Mean-square displacements and velocity autocorrelationfunctions are used to calculate self-diffusion coefficients through Einstein equation and Green-Kuboformula. It has been found that simulation results are in good agreement with experimental data for liquidargon which is taken as exponential-six fluid. The effects of density, temperature and steepness factor forrepulsive part of exponential-six potential on self-diffusion coefficients are also investigated. Thesimulation results indicate that the self-diffusion coefficient of exponential-six fluid increases astemperature increases and density decreases. In addition, the larger self-diffusion coefficients are obtainedas the steepness factor increases at the same temperature and density condition.
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.
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.
International Nuclear Information System (INIS)
The idea that the dynamics of a spin is determined by the size of its neighbouring domains was recently introduced (Biswas and Sen 2009 Phys. Rev. E 80 027101) in a Ising spin model (henceforth, referred to as model I). A parameter p is now defined to modify the dynamics such that a spin can sense domain sizes up to R = pL/2 in a one-dimensional system of size L. For the cutoff factor p → 0, the dynamics is Ising like and the domains grow with time t diffusively as t1/z with z = 2, while for p = 1, the original model I showed ballistic dynamics with z ≅ 1. For intermediate values of p, the domain growth, magnetization and persistence show a model-I-like behaviour up to a macroscopic crossover time t1 ∼ pL/2. Beyond t1, characteristic power-law variations of the dynamic quantities are no longer observed. The total time to reach equilibrium is found to be t = apL + b(1 - p)3L2, from which we conclude that the later time behaviour is diffusive. We also consider the case when a random but quenched value of p is used for each spin for which ballistic behaviour is once again obtained.
Directory of Open Access Journals (Sweden)
T. Turiv
2015-06-01
Full Text Available As recently reported [Turiv T. et al., Science, 2013, Vol. 342, 1351], fluctuations in the orientation of the liquid crystal (LC director can transfer momentum from the LC to a colloid, such that the diffusion of the colloid becomes anomalous on a short time scale. Using video microscopy and single particle tracking, we investigate random thermal motion of colloidal particles in a nematic liquid crystal for the time scales shorter than the expected time of director fluctuations. At long times, compared to the characteristic time of the nematic director relaxation we observe typical anisotropic Brownian motion with the mean square displacement (MSD linear in time τ and inversly proportional to the effective viscosity of the nematic medium. At shorter times, however, the dynamics is markedly nonlinear with MSD growing more slowly (subdiffusion or faster (superdiffusion than τ. These results are discussed in the context of coupling of colloidal particle's dynamics to the director fluctuation dynamics.
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 anomalous...
Reithmann, Emanuel; Reese, Louis; Frey, Erwin
2016-08-01
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.
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.
Anomalous Growth of Aging Populations
Grebenkov, Denis S.
2016-04-01
We consider a discrete-time population dynamics with age-dependent structure. At every time step, one of the alive individuals from the population is chosen randomly and removed with probability q_k depending on its age, whereas a new individual of age 1 is born with probability r. The model can also describe a single queue in which the service order is random while the service efficiency depends on a customer's "age" in the queue. We propose a mean field approximation to investigate the long-time asymptotic behavior of the mean population size. The age dependence is shown to lead to anomalous power-law growth of the population at the critical regime. The scaling exponent is determined by the asymptotic behavior of the probabilities q_k at large k. The mean field approximation is validated by Monte Carlo simulations.
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.
Jameson, Antony
1994-01-01
The effect of artificial diffusion on discrete shock structures is examined for a family of schemes which includes scalar diffusion, convective upwind and split pressure (CUSP) schemes, and upwind schemes with characteristics splitting. The analysis leads to conditions on the diffusive flux such that stationary discrete shocks can contain a single interior point. The simplest formulation which meets these conditions is a CUSP scheme in which the coefficients of the pressure differences is fully determined by the coefficient of convective diffusion. It is also shown how both the characteristic and CUSP schemes can be modified to preserve constant stagnation enthalpy in steady flow, leading to four variants, the E and H-characteristic schemes, and the E and H-CUSP schemes. Numerical results are presented which confirm the properties of these schemes.
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.
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.
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.
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. PMID:27353014
Nonlocal electrical diffusion equation
Gómez-Aguilar, J. F.; Escobar-Jiménez, R. F.; Olivares-Peregrino, V. H.; Benavides-Cruz, M.; Calderón-Ramón, C.
2016-07-01
In this paper, we present an analysis and modeling of the electrical diffusion equation using the fractional calculus approach. This alternative representation for the current density is expressed in terms of the Caputo derivatives, the order for the space domain is 0solar panels, electrochemical phenomena and the description of anomalous complex processes.
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
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:
Roques, Lionel; Bonnefon, Olivier
2016-01-01
We propose and develop a general approach based on reaction-diffusion equations for modelling a species dynamics in a realistic two-dimensional (2D) landscape crossed by linear one-dimensional (1D) corridors, such as roads, hedgerows or rivers. Our approach is based on a hybrid "2D/1D model", i.e, a system of 2D and 1D reaction-diffusion equations with homogeneous coefficients, in which each equation describes the population dynamics in a given 2D or 1D element of the landscape. Using the example of the range expansion of the tiger mosquito Aedes albopictus in France and its main highways as 1D corridors, we show that the model can be fitted to realistic observation data. We develop a mechanistic-statistical approach, based on the coupling between a model of population dynamics and a probabilistic model of the observation process. This allows us to bridge the gap between the data (3 levels of infestation, at the scale of a French department) and the output of the model (population densities at each point of the landscape), and to estimate the model parameter values using a maximum-likelihood approach. Using classical model comparison criteria, we obtain a better fit and a better predictive power with the 2D/1D model than with a standard homogeneous reaction-diffusion model. This shows the potential importance of taking into account the effect of the corridors (highways in the present case) on species dynamics. With regard to the particular case of A. albopictus, the conclusion that highways played an important role in species range expansion in mainland France is consistent with recent findings from the literature. PMID:26986201
Burda, Zdzislaw; Nowak, Maciej A; Tarnowski, Wojciech; Warchoł, Piotr
2015-01-01
Following our recent letter, we study in detail an entry-wise diffusion of non-hermitian complex matrices. We obtain an exact partial differential equation (valid for any matrix size $N$ and arbitrary initial conditions) for evolution of the averaged extended characteristic polynomial. The logarithm of this polynomial has an interpretation of a potential which generates a Burgers dynamics in quaternionic space. The dynamics of the ensemble in the large $N$ is completely determined by the coevolution of the spectral density and a certain eigenvector correlation function. This coevolution is best visible in an electrostatic potential of a quaternionic argument built of two complex variables, the first of which governs standard spectral properties while the second unravels the hidden dynamics of eigenvector correlation function. We obtain general large $N$ formulas for both spectral density and 1-point eigenvector correlation function valid for any initial conditions. We exemplify our studies by solving three ex...
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.
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
Rao, Zhong-Hao; Liu, Xin-Jian; Zhang, Rui-Kai; Li, Xiang; Wei, Chang-Xing; Wang, Hao-Dong; Li, Yi-Min
2014-01-01
The straight chain n-alkanes and their mixture, which can be used as phase change materials (PCM) for thermal energy storage, have attracted much attention in recent years. We employ the molecular dynamics (MD) simulation to investigate their thermophysical properties, including self diffusion and melting of n-octadecane with crystal and amorphous structures. Our results show that, although the initial and melted structures of n-octadecane with crystal and amorphous are different, the melting behaviors of n-octadecane judged by the self diffusion behavior are consistent. The MD simulation indicates that both the crystal and amorphous structures are effective for the property investigation of n-octadecane and the simulated conclusion can be used as reference for modeling the alkanes-based PCM system.
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.
Dependence of O{sub 2} diffusion dynamics on pressure and temperature in silica nanoparticles
Energy Technology Data Exchange (ETDEWEB)
Iovino, G., E-mail: giuseppe.iovino@unipa.it; Agnello, S., E-mail: simonpietro.agnello@unipa.it; Gelardi, F. M., E-mail: franco.gelardi@unipa.it [University of Palermo, Department of Physics and Chemistry (Italy)
2013-10-15
An experimental study of the molecular O{sub 2} diffusion process in high purity non-porous silica nanoparticles having 50 m{sup 2}/g BET specific surface and 20 nm average radius was carried out in the temperature range from 127 to 177 Degree-Sign C at O{sub 2} pressure in the range from 0.2 to 66 bar. The study was performed by measuring the volume average interstitial O{sub 2} concentration by a Raman and photoluminescence technique using a 1,064 nm excitation laser to detect the singlet to triplet emission at 1,272 nm of the molecular oxygen in silica. A dependence of the diffusion kinetics on the O{sub 2} absolute pressure, in addition to temperature dependence, was found. The kinetics can be fit by the solution of Fick's diffusion equation using an effective diffusion coefficient related to temperature and O{sub 2} external pressure. The fit results have evidenced that the temperature and pressure dependencies can be disentangled and that the pressure effects are more pronounced at lower temperatures. An Arrhenius temperature law is determined for the effective diffusion coefficient and the activation energy and pre-exponential factor are found in the explored experimental range. The reported findings have not been evidenced previously in the studies in bulk silica and could probably be originated by the reduced spatial extension of the considered system.
The Anomalous Response of Elastoplatic Circular Plates Under Impulsive Loading
Institute of Scientific and Technical Information of China (English)
Wu guiying; Liu wei; Yang guitong
2004-01-01
The anomalous nonlinear elastic, perfectly plastic response behaviors of circular plate subjected to short transverse pulse load is studied. The plate is assumed fixed-pin along the boundary. 'Anomalous' here means that the final deflection may be in the direction opposite that of the load. It has been found by detailed numerical analyses that there exists anomalous response in some narrow loading ranges, so called slots. By further calculations it is shown that this special dynamic behavior is related to coupling affects of internal forces and large plastic deformation after removal loading. Further plastic dissipation will be lead to anomalous dynamic response. This phenomena could be considered as the coupling of the geometry nonlinearity, material nonlinearity,elastic effects and the irrecoverable of the plastic deformation.
Glasslike Membrane Protein Diffusion in a Crowded Membrane.
Munguira, Ignacio; Casuso, Ignacio; Takahashi, Hirohide; Rico, Felix; Miyagi, Atsushi; Chami, Mohamed; Scheuring, Simon
2016-02-23
Many functions of the plasma membrane depend critically on its structure and dynamics. Observation of anomalous diffusion in vivo and in vitro using fluorescence microscopy and single particle tracking has advanced our concept of the membrane from a homogeneous fluid bilayer with freely diffusing proteins to a highly organized crowded and clustered mosaic of lipids and proteins. Unfortunately, anomalous diffusion could not be related to local molecular details given the lack of direct and unlabeled molecular observation capabilities. Here, we use high-speed atomic force microscopy and a novel analysis methodology to analyze the pore forming protein lysenin in a highly crowded environment and document coexistence of several diffusion regimes within one membrane. We show the formation of local glassy phases, where proteins are trapped in neighbor-formed cages for time scales up to 10 s, which had not been previously experimentally reported for biological membranes. Furthermore, around solid-like patches and immobile molecules a slower glass phase is detected leading to protein trapping and creating a perimeter of decreased membrane diffusion. PMID:26859708
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.
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.
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.
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.
Interplay between microscopic diffusion and local structure of liquid water.
Cunsolo, Alessandro; Orecchini, Andrea; Petrillo, Caterina; Sacchetti, Francesco
2010-12-23
We present a quasielastic neutron scattering (QENS) study of single-particle dynamics in pure water, measured at temperatures between 256 and 293 K along an isobaric path at 200 MPa. A thorough analysis of the spectral line shapes reveals a departure from simple models of continuous or jump diffusion, with such an effect becoming stronger at lower temperatures. We show that such a diverging trend of dynamical quantities upon cooling closely resembles the divergent (anomalous) compressibility observed in water by small-angle diffraction. Such an analogy suggests an interesting interplay between single-particle diffusion and structural arrangements in liquid water, both bearing witness of the well-known water anomalies. In particular, a fit of dynamical parameters by a Vogel-Tammann-Fulcher law provides a critical temperature of about 220 K, interestingly close to the hypothesized position of the second critical point of water and to the so-called Widom line. PMID:21114328
A Diffusion Equation on Fractals in Random Media
Institute of Scientific and Technical Information of China (English)
DeLIU; HouqiangLI; 等
1997-01-01
The proper transformation method is used in this paper to extend the diffusion equation on Euclidean space to the standard diffusion equation on fractals,By this standard diffusion equation,it is proved that the fractal Brownian particle moving belongs to the anomalous diffusion.At the same time,the generalized diffusion equation and its asymptotic solution is discussed.