Transient fluctuation relations for time-dependent particle transport

Science.gov (United States)

Altland, Alexander; de Martino, Alessandro; Egger, Reinhold; Narozhny, Boris

2010-09-01

We consider particle transport under the influence of time-varying driving forces, where fluctuation relations connect the statistics of pairs of time-reversed evolutions of physical observables. In many “mesoscopic” transport processes, the effective many-particle dynamics is dominantly classical while the microscopic rates governing particle motion are of quantum-mechanical origin. We here employ the stochastic path-integral approach as an optimal tool to probe the fluctuation statistics in such applications. Describing the classical limit of the Keldysh quantum nonequilibrium field theory, the stochastic path integral encapsulates the quantum origin of microscopic particle exchange rates. Dynamically, it is equivalent to a transport master equation which is a formalism general enough to describe many applications of practical interest. We apply the stochastic path integral to derive general functional fluctuation relations for current flow induced by time-varying forces. We show that the successive measurement processes implied by this setup do not put the derivation of quantum fluctuation relations in jeopardy. While in many cases the fluctuation relation for a full time-dependent current profile may contain excessive information, we formulate a number of reduced relations, and demonstrate their application to mesoscopic transport. Examples include the distribution of transmitted charge, where we show that the derivation of a fluctuation relation requires the combined monitoring of the statistics of charge and work.

Fluctuating hydrodynamics for multiscale modeling and simulation: energy and heat transfer in molecular fluids.

Science.gov (United States)

Shang, Barry Z; Voulgarakis, Nikolaos K; Chu, Jhih-Wei

2012-07-28

This work illustrates that fluctuating hydrodynamics (FHD) simulations can be used to capture the thermodynamic and hydrodynamic responses of molecular fluids at the nanoscale, including those associated with energy and heat transfer. Using all-atom molecular dynamics (MD) trajectories as the reference data, the atomistic coordinates of each snapshot are mapped onto mass, momentum, and energy density fields on Eulerian grids to generate a corresponding field trajectory. The molecular length-scale associated with finite molecule size is explicitly imposed during this coarse-graining by requiring that the variances of density fields scale inversely with the grid volume. From the fluctuations of field variables, the response functions and transport coefficients encoded in the all-atom MD trajectory are computed. By using the extracted fluid properties in FHD simulations, we show that the fluctuations and relaxation of hydrodynamic fields quantitatively match with those observed in the reference all-atom MD trajectory, hence establishing compatibility between the atomistic and field representations. We also show that inclusion of energy transfer in the FHD equations can more accurately capture the thermodynamic and hydrodynamic responses of molecular fluids. The results indicate that the proposed MD-to-FHD mapping with explicit consideration of finite molecule size provides a robust framework for coarse-graining the solution phase of complex molecular systems.

Molecular dynamics for irradiation driven chemistry

DEFF Research Database (Denmark)

Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

2016-01-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes...... that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package...... involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields...

Stochastic thermodynamics, fluctuation theorems and molecular machines

International Nuclear Information System (INIS)

Seifert, Udo

2012-01-01

Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics such as work, heat and entropy production to the level of individual trajectories of well-defined non-equilibrium ensembles. It applies whenever a non-equilibrium process is still coupled to one (or several) heat bath(s) of constant temperature. Paradigmatic systems are single colloidal particles in time-dependent laser traps, polymers in external flow, enzymes and molecular motors in single molecule assays, small biochemical networks and thermoelectric devices involving single electron transport. For such systems, a first-law like energy balance can be identified along fluctuating trajectories. For a basic Markovian dynamics implemented either on the continuum level with Langevin equations or on a discrete set of states as a master equation, thermodynamic consistency imposes a local-detailed balance constraint on noise and rates, respectively. Various integral and detailed fluctuation theorems, which are derived here in a unifying approach from one master theorem, constrain the probability distributions for work, heat and entropy production depending on the nature of the system and the choice of non-equilibrium conditions. For non-equilibrium steady states, particularly strong results hold like a generalized fluctuation–dissipation theorem involving entropy production. Ramifications and applications of these concepts include optimal driving between specified states in finite time, the role of measurement-based feedback processes and the relation between dissipation and irreversibility. Efficiency and, in particular, efficiency at maximum power can be discussed systematically beyond the linear response regime for two classes of molecular machines, isothermal ones such as molecular motors, and heat engines such as thermoelectric devices, using a common framework based on a cycle decomposition of entropy production. (review article)

Molecular-dynamics study of propane-hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis.

Science.gov (United States)

Ghaani, Mohammad Reza; English, Niall J

2018-03-21

Equilibrium and non-equilibrium molecular-dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar propane-hydrate interfaces in contact with liquid water over the 260-320 K range. Two types of hydrate-surface water-lattice molecular termination were adopted, at the hydrate edge with water, for comparison: a 001-direct surface cleavage and one with completed cages. Statistically significant differences in melting temperatures and initial break-up rates were observed between both interface types. Dissociation rates were observed to be strongly dependent on temperature, with higher rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model, developed previously, was applied to fit the observed dissociation profiles, and this helps us to identify clearly two distinct hydrate-decomposition régimes; following a highly temperature-dependent break-up phase, a second well-defined stage is essentially independent of temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. Further equilibrium MD-analysis of the two-phase systems at their melting point, with consideration of the relaxation times gleaned from the auto-correlation functions of fluctuations in a number of enclathrated guest molecules, led to statistically significant differences between the two surface-termination cases; a consistent correlation emerged in both cases between the underlying, non-equilibrium, thermal-driven dissociation rates sampled directly from melting with that from an equilibrium-MD fluctuation-dissipation approach.

Temperature driven transport of gold nanoparticles physisorbed inside carbon nanotubes

DEFF Research Database (Denmark)

Schoen, P.A.E.; Poulikakos, D.; Walther, Jens Honore

2006-01-01

We use molecular dynamics simulations to demonstrate the temperature driven mass transport of solid gold nanoparticles, physisorbed inside carbon nanotubes (CNTs). Our results indicate that the nanoparticle experiences a guided motion, in the direction opposite to the direction of the temperature...... affects the nanoparticle motion along the carbon lattice....

Fluctuation Solution Theory Properties from Molecular Simulation

DEFF Research Database (Denmark)

Abildskov, Jens; Wedberg, R.; O’Connell, John P.

2013-01-01

The thermodynamic properties obtained in the Fluctuation Solution Theory are based on spatial integrals of molecular TCFs between component pairs in the mixture. Molecular simulation, via either MD or MC calculations, can yield these correlation functions for model inter- and intramolecular...

Dynamic Structure Factor and Transport Coefficients of a Homogeneously Driven Granular Fluid in Steady State

Science.gov (United States)

Vollmayr-Lee, Katharina; Zippelius, Annette; Aspelmeier, Timo

2011-03-01

We study the dynamic structure factor of a granular fluid of hard spheres, driven into a stationary nonequilibrium state by balancing the energy loss due to inelastic collisions with the energy input due to driving. The driving is chosen to conserve momentum, so that fluctuating hydrodynamics predicts the existence of sound modes. We present results of computer simulations which are based on an event driven algorithm. The dynamic structure factor F (q , ω) is determined for volume fractions 0.05, 0.1 and 0.2 and coefficients of normal restitution 0.8 and 0.9. We observe sound waves, and compare our results for F (q , ω) with the predictions of generalized fluctuating hydrodynamics which takes into account that temperature fluctuations decay either diffusively or with a finite relaxation rate, depending on wave number and inelasticity. We determine the speed of sound and the transport coefficients and compare them to the results of kinetic theory. K.V.L. thanks the Institute of Theoretical Physics, University of Goettingen, for financial support and hospitality.

Redistribution of phase fluctuations in a periodically driven cuprate superconductor

Energy Technology Data Exchange (ETDEWEB)

Hoeppner, Robert; Zhu, Beilei; Rexin, Tobias [Zentrum fuer Optische Quantentechnologien und Institut fuer Laserphysik, Hamburg (Germany); Mathey, Ludwig [Zentrum fuer Optische Quantentechnologien und Institut fuer Laserphysik, Hamburg (Germany); The Hamburg Centre for Ultrafast Imaging, Hamburg (Germany); Cavalleri, Andrea [Max Planck Institute for the Structure and Dynamics of Matter, Hamburg (Germany); Department of Physics, Oxford University, Clarendon Laboratory, Parks Road, Oxford (United Kingdom)

2015-07-01

We study the thermally fluctuating state of a bi-layer cuprate superconductor under the periodic action of a staggered field oscillating at optical frequencies. This analysis distills essential elements of the recently discovered phenomenon of light enhanced coherence in YBCO, which was achieved by periodically driving infrared active apical oxygen distortions. The effect of a staggered periodic perturbation is studied using a Langevin description of driven, coupled Josephson junctions, which represent two neighboring pairs of layers and their two plasmons. We demonstrate that the external driving leads to a suppression of phase fluctuations of the low-energy plasmon, an effect which is amplified via the resonance of the high energy plasmon, with a striking suppression of the low-energy fluctuations, as visible in the power spectrum. We also find that this effect acts onto the in-plane fluctuations, which are reduced on long length scales and we discuss the behavior of vortices in the ab-planes and across the weakly coupled junctions.

Remarks on transport theories of interplanetary fluctuations

International Nuclear Information System (INIS)

Ye Zhou; Matthaeus, W.H.

1990-01-01

The structure of approximate transport theories for the radial behavior of interplanetary fluctuations is reconsidered. The emphasis is on theories derived under the assumption of scale separation; i.e., the correlation length of the fluctuations is much less than the scale of large inhomogeneities. In these cases the zero-wavelength limit provides a first approximation to the spectral evolution equations for the radial dependence of interplanetary fluctuation spectra. The goal here is to investigate the structure of a recently presented (Zhou and Matthaeus, 1989) transport theory, in which coupling of inward- and outward-type fluctuations appears in the leading order, an effect the authors call mixing. In linear theory, mixing-type couplings of inward-type and outward-type waves are formally a nonresonant effect. However, leading order mixing terms do not vanish at zero wavelength for fluctuations that vary nearly perpendicular to the local magnetic field, or when the mean magnetic field is weak. Leading order mixing terms also survive when the dispersion relation fails and there is a nonunique relationship between frequency and wave number. The former case corresponds to nearly two-dimensional structures; these are included, for example, in isotropic models of turbulence. The latter instance occurs when wave-wave couplings are sufficiently strong. Thus there are a variety of situations in which leading order mixing effects are expected to be present

Photon counting and fluctuation of molecular movement

International Nuclear Information System (INIS)

Inohara, Koichi

1978-01-01

The direct measurement of the fluctuation of molecular motions, which provides with useful information on the molecular movement, was conducted by introducing photon counting method. The utilization of photon counting makes it possible to treat the molecular system consisting of a small number of molecules like a radioisotope in the detection of a small number of atoms, which are significant in biological systems. This method is based on counting the number of photons of the definite polarization emitted in a definite time interval from the fluorescent molecules excited by pulsed light, which are bound to the marked large molecules found in a definite spatial region. Using the probability of finding a number of molecules oriented in a definite direction in the definite spatial region, the probability of counting a number of photons in a definite time interval can be calculated. Thus the measurable count rate of photons can be related with the fluctuation of molecular movement. The measurement was carried out under the condition, in which the probability of the simultaneous arrival of more than two photons at a detector is less than 1/100. As the experimental results, the resolving power of photon-counting apparatus, the frequency distribution of the number of photons of some definite polarization counted for 1 nanosecond are shown. In the solution, the variance of the number of molecules of 500 on the average is 1200, which was estimated from the experimental data by assuming normal distribution. This departure from the Poisson distribution means that a certain correlation does exist in molecular movement. In solid solution, no significant deviation was observed. The correlation existing in molecular movement can be expressed in terms of the fluctuation of the number of molecules. (Nakai, Y.)

Fluctuations and transport in an inhomogeneous plasma

International Nuclear Information System (INIS)

Nevins, W.M.; Chen, L.

1979-11-01

A formalism is developed for calculating the equilibrium fluctuation level in an inhomogeneous plasma. This formalism is applied to the collisionless drift wave in a sheared magnetic field. The fluctuation level is found to be anomalously large due to both the presence of weakly damped normal modes and convective amplification. As the magnetic shear is reduced, the steady-state fluctuation spectrum is found to increase both in coherence and in amplitude. The transport associated with this mode is evaluated. The diffusion coefficient is found to scale as D is proportional to B 2 /nT/sup 1/2/

Investigation of Fluctuation-Induced Electron Transport in Hall Thrusters with a 2D Hybrid Code in the Azimuthal and Axial Coordinates

Science.gov (United States)

Fernandez, Eduardo; Borelli, Noah; Cappelli, Mark; Gascon, Nicolas

2003-10-01

Most current Hall thruster simulation efforts employ either 1D (axial), or 2D (axial and radial) codes. These descriptions crucially depend on the use of an ad-hoc perpendicular electron mobility. Several models for the mobility are typically invoked: classical, Bohm, empirically based, wall-induced, as well as combinations of the above. Experimentally, it is observed that fluctuations and electron transport depend on axial distance and operating parameters. Theoretically, linear stability analyses have predicted a number of unstable modes; yet the nonlinear character of the fluctuations and/or their contribution to electron transport remains poorly understood. Motivated by these observations, a 2D code in the azimuthal and axial coordinates has been written. In particular, the simulation self-consistently calculates the azimuthal disturbances resulting in fluctuating drifts, which in turn (if properly correlated with plasma density disturbances) result in fluctuation-driven electron transport. The characterization of the turbulence at various operating parameters and across the channel length is also the object of this study. A description of the hybrid code used in the simulation as well as the initial results will be presented.

Particle transport due to magnetic fluctuations

International Nuclear Information System (INIS)

Stoneking, M.R.; Hokin, S.A.; Prager, S.C.; Fiksel, G.; Ji, H.; Den Hartog, D.J.

1994-01-01

Electron current fluctuations are measured with an electrostatic energy analyzer at the edge of the MST reversed-field pinch plasma. The radial flux of fast electrons (E>T e ) due to parallel streaming along a fluctuating magnetic field is determined locally by measuring the correlated product e B r >. Particle transport is small just inside the last closed flux surface (Γ e,mag e,total ), but can account for all observed particle losses inside r/a=0.8. Electron diffusion is found to increase with parallel velocity, as expected for diffusion in a region of field stochasticity

Molecular dynamics study of CO2 hydrate dissociation: Fluctuation-dissipation and non-equilibrium analysis.

Science.gov (United States)

English, Niall J; Clarke, Elaine T

2013-09-07

Equilibrium and non-equilibrium molecular dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar CO2 hydrate interfaces in liquid water at 300-320 K. Different guest compositions, at 85%, 95%, and 100% of maximum theoretical occupation, led to statistically-significant differences in the observed initial dissociation rates. The melting temperatures of each interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model developed previously was applied to fit the observed dissociation profiles, and this helps to identify clearly two distinct régimes of break-up; a second well-defined region is essentially independent of composition and temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. From equilibrium MD of the two-phase systems at their melting point, the relaxation times of the auto-correlation functions of fluctuations in number of enclathrated guest molecules were used as a basis for comparison of the variation in the underlying, non-equilibrium, thermal-driven dissociation rates via Onsager's hypothesis, and statistically significant differences were found, confirming the value of a fluctuation-dissipation approach in this case.

Anomalous transport in tokamaks

International Nuclear Information System (INIS)

Wootton, A.J.

1989-01-01

A review is presented of what is known about anomalous transport in tokamaks. It is generally thought that this anomalous transport is the result of fluctuations in various plasma parameters. In the plasma edge detailed measurements of the quantities required to directly determine the fluctuation driven fluxes are available. The total flux of particles is well explained by the measured electrostatic fluctuation driven flux. However, a satisfactory model to explain the origin of the fluctuations has not been identified. The processes responsible for determining the edge energy flux are less clear, but electrostatic convection plays an important part. In the confinement region experimental observations are presently restricted to measurements of density and potential fluctuations and their correlations. The characteristics of the measured fluctuations are discussed and compared with the predictions of various models. Comparisons between measured particle, electron heat and ion heat fluxes, and those fluxes predicted to result from the measured fluctuations, are made. Magnetic fluctuations is discussed

Edge transport and fluctuation induced turbulence characteristics in early SST-1 plasma

Energy Technology Data Exchange (ETDEWEB)

Kakati, B., E-mail: bharat.kakati@ipr.res.in; Pradhan, S., E-mail: pradhan@ipr.res.in; Dhongde, J.; Semwal, P.; Yohan, K.; Banaudha, M.

2017-02-15

Highlights: • Anomalous particle transport during the high MHD activity at SST-1. • Electrostatic turbulence is modulated by MHD activity at SST-1 tokamak. • Edge floating potential fluctuations shows poloidal long-range cross correlation. - Abstract: Plasma edge transport characteristics are known to be heavily influenced by the edge fluctuation induced turbulences. These characteristics play a critical role towards the confinement of plasma column in a Tokamak. The edge magnetic fluctuations and its subsequent effect on electrostatic fluctuations have been experimentally investigated for the first time at the edge of the SST-1 plasma column. This paper reports the correlations that exist and is experimentally been observed between the edge densities and floating potential fluctuations with the magnetic fluctuations. The edge density and floating potential fluctuations have been measured with the help of poloidally separated Langmuir probes, whereas the magnetic fluctuations have been measured with poloidally spaced Mirnov coils. Increase in magnetic fluctuations associated with enhanced MHD activities has been found to increase the floating potential and ion saturation current. These observations indicate electrostatic turbulence getting influenced with the MHD activities and reveal the edge anomalous particle transport during SST-1 tokamak discharge. Large-scale coherent structures have been observed in the floating potential fluctuations, indicating long-distance cross correlation in the poloidal directions. From bispectral analysis, a strong nonlinear coupling among the floating potential fluctuations is observed in the low-frequency range about 0–15 kHz.

Fluctuation theorem for channel-facilitated membrane transport of interacting and noninteracting solutes.

Science.gov (United States)

Berezhkovskii, Alexander M; Bezrukov, Sergey M

2008-05-15

In this paper, we discuss the fluctuation theorem for channel-facilitated transport of solutes through a membrane separating two reservoirs. The transport is characterized by the probability, P(n)(t), that n solute particles have been transported from one reservoir to the other in time t. The fluctuation theorem establishes a relation between P(n)(t) and P-(n)(t): The ratio P(n)(t)/P-(n)(t) is independent of time and equal to exp(nbetaA), where betaA is the affinity measured in the thermal energy units. We show that the same fluctuation theorem is true for both single- and multichannel transport of noninteracting particles and particles which strongly repel each other.

Fluctuation-driven mechanotransduction regulates mitochondrial-network structure and function

Science.gov (United States)

Bartolák-Suki, Erzsébet; Imsirovic, Jasmin; Parameswaran, Harikrishnan; Wellman, Tyler J.; Martinez, Nuria; Allen, Philip G.; Frey, Urs; Suki, Béla

2015-10-01

Cells can be exposed to irregular mechanical fluctuations, such as those arising from changes in blood pressure. Here, we report that ATP production, assessed through changes in mitochondrial membrane potential, is downregulated in vascular smooth muscle cells in culture exposed to monotonous stretch cycles when compared with cells exposed to a variable cyclic stretch that incorporates physiological levels of cycle-by-cycle variability in stretch amplitude. Variable stretch enhances ATP production by increasing the expression of ATP synthase’s catalytic domain, cytochrome c oxidase and its tyrosine phosphorylation, mitofusins and PGC-1α. Such a fluctuation-driven mechanotransduction mechanism is mediated by motor proteins and by the enhancement of microtubule-, actin- and mitochondrial-network complexity. We also show that, in aorta rings isolated from rats, monotonous stretch downregulates--whereas variable stretch maintains--physiological vessel-wall contractility through mitochondrial ATP production. Our results have implications for ATP-dependent and mechanosensitive intracellular processes.

RF current drive and plasma fluctuations

International Nuclear Information System (INIS)

Peysson, Yves; Decker, Joan; Morini, L; Coda, S

2011-01-01

The role played by electron density fluctuations near the plasma edge on rf current drive in tokamaks is assessed quantitatively. For this purpose, a general framework for incorporating density fluctuations in existing modelling tools has been developed. It is valid when rf power absorption takes place far from the fluctuating region of the plasma. The ray-tracing formalism is modified in order to take into account time-dependent perturbations of the density, while the Fokker–Planck solver remains unchanged. The evolution of the electron distribution function in time and space under the competing effects of collisions and quasilinear diffusion by rf waves is determined consistently with the time scale of fluctuations described as a statistical process. Using the ray-tracing code C3PO and the 3D linearized relativistic bounce-averaged Fokker–Planck solver LUKE, the effect of electron density fluctuations on the current driven by the lower hybrid (LH) and the electron cyclotron (EC) waves is estimated quantitatively. A thin fluctuating layer characterized by electron drift wave turbulence at the plasma edge is considered. The effect of fluctuations on the LH wave propagation is equivalent to a random scattering process with a broadening of the poloidal mode spectrum proportional to the level of the perturbation. However, in the multipass regime, the LH current density profile remains sensitive to the ray chaotic behaviour, which is not averaged by fluctuations. The effect of large amplitude fluctuations on the EC driven current is found to be similar to an anomalous radial transport of the fast electrons. The resulting lower current drive efficiency and broader current profile are in better agreement with experimental observations. Finally, applied to the ITER ELMy H-mode regime, the model predicts a significant broadening of the EC driven current density profile with the fluctuation level, which can make the stabilization of neoclassical tearing mode potentially

Electrostatic fluctuation and fluctuation-induced particle flux during formation of the edge transport barrier in the JFT-2M tokamak

International Nuclear Information System (INIS)

Ido, T.; Hamada, Y.; Nagashima, Y.; Nishizawa, A.; Kawasumi, Y.; Miura, Y.; Hoshino, K.; Ogawa, H.; Shinohara, K.; Kamiya, K.; Kusama, Y.

2005-01-01

The electrostatic fluctuation with Geodesic-Acoustic-Mode (GAM) frequency is observed in L-mode plasmas. The fluctuation has the poloidal wave number (k θ ) of (-2 ± 24) x 10 -3 (cm -1 ), that corresponds to the poloidal mode number of 1.5 or less, and the radial wave number (k r ) of 0.94 ± 0.05 (cm -1 ), that is corresponds to k r ρ i = 0.26 < 1. The amplitude of the fluctuation changes in the radial direction; it is small near the separatrix and it has maximum at 3 cm inside the separatrix. The relation between the amplitude of potential fluctuation and that of density fluctuation is the same as that of the predicted GAM. The fluctuation is probably GAM. The envelope of ambient density fluctuation and the potential fluctuation have a significant coherence at the GAM frequency. Thus, it is clearly verified that the fluctuation with the GAM frequency correlates with the ambient density fluctuation. The fluctuation with the GAM frequency affects the particle transport through the modulation of the ambient fluctuation. But the effect is not large, and it is not a sufficient condition to form the edge transport barrier and to drive the intermittent particle flux. (author)

Electrostatic fluctuation and fluctuation-induced particle flux during formation of the edge transport barrier in the JFT-2M tokamak

International Nuclear Information System (INIS)

Ido, T.; Miura, K.; Hoshino, K.

2005-01-01

The electrostatic fluctuation with Geodesic-Acoustic-Mode (GAM) frequency is observed in L-mode plasmas. The fluctuation has the poloidal wave number (k θ ) of (-2 ± 24) x 10 -3 (cm -1 ), that corresponds to the poloidal mode number of 1.5 or less, and the radial wave number (k γ ) of 0.94±0.05 (cm -1 ), that is corresponds to k γ ρ i =0.26 < 1. The amplitude of the fluctuation changes in the radial direction; it is small near the separatrix and it has maximum at 3 cm inside the separatrix. The relation between the amplitude of potential fluctuation and that of density fluctuation is the same as that of the predicted GAM. The fluctuation is probably GAM. The envelope of ambient density fluctuation and the potential fluctuation have a significant coherence at the GAM frequency. Thus, it is clearly verified that the fluctuation with the GAM frequency correlates with the ambient density fluctuation. The fluctuation with the GAM frequency affects the particle transport through the modulation of the ambient fluctuation. But the effect is not large, and it is not a sufficient condition to form the edge transport barrier and to drive the intermittent particle flux. (author)

Molecular thermodynamics using fluctuation solution theory

DEFF Research Database (Denmark)

Ellegaard, Martin Dela

. The framework relates thermodynamic variables to molecular pair correlation functions of liquid mixtures. In this thesis, application of the framework is illustrated using two approaches: 1. Solubilities of solid solutes in mixed solvent systems are determined from fluctuation solution theory application......Properties of chemicals and their mutual phase equilibria are critical variables in process design. Reliable estimates of relevant equilibrium properties, from thermodynamic models, can form the basis of good decision making in the development phase of a process design, especially when access...... to relevant experimental data is limited. This thesis addresses the issue of generating and using simple thermodynamic models within a rigorous statistical mechanical framework, the so-called fluctuation solution theory, from which relations connecting properties and phase equilibria can be obtained...

The physicist's companion to current fluctuations: one-dimensional bulk-driven lattice gases

Science.gov (United States)

Lazarescu, Alexandre

2015-12-01

One of the main features of statistical systems out of equilibrium is the currents they exhibit in their stationary state: microscopic currents of probability between configurations, which translate into macroscopic currents of mass, charge, etc. Understanding the general behaviour of these currents is an important step towards building a universal framework for non-equilibrium steady states akin to the Gibbs-Boltzmann distribution for equilibrium systems. In this review, we consider one-dimensional bulk-driven particle gases, and in particular the asymmetric simple exclusion process (ASEP) with open boundaries, which is one of the most popular models of one-dimensional transport. We focus, in particular, on the current of particles flowing through the system in its steady state, and on its fluctuations. We show how one can obtain the complete statistics of that current, through its large deviation function, by combining results from various methods: exact calculation of the cumulants of the current, using the integrability of the model; direct diagonalization of a biased process in the limits of very high or low current; hydrodynamic description of the model in the continuous limit using the macroscopic fluctuation theory. We give a pedagogical account of these techniques, starting with a quick introduction to the necessary mathematical tools, as well as a short overview of the existing works relating to the ASEP. We conclude by drawing the complete dynamical phase diagram of the current. We also remark on a few possible generalizations of these results.

Extreme concentration fluctuations due to local reversibility of mixing in turbulent flows

Science.gov (United States)

Xia, Hua; Francois, Nicolas; Punzmann, Horst; Szewc, Kamil; Shats, Michael

2018-05-01

Mixing of a passive scalar in a fluid (e.g. a radioactive spill in the ocean) is the irreversible process towards homogeneous distribution of a substance. In a moving fluid, due to the chaotic advection [H. Aref, J. Fluid Mech. 143 (1984) 1; J. M. Ottino, The Kinematics of Mixing: Stretching,Chaos and Transport (Cambridge University Press, Cambridge, 1989)] mixing is much faster than if driven by molecular diffusion only. Turbulence is known as the most efficient mixing flow [B. I. Shraiman and E. D. Siggia, Nature 405 (2000) 639]. We show that in contrast to spatially periodic flows, two-dimensional turbulence exhibits local reversibility in mixing, which leads to the generation of unpredictable strong fluctuations in the scalar concentration. These fluctuations can also be detected from the analysis of the fluid particle trajectories of the underlying flow.

The effect of plasma fluctuations on parallel transport parameters in the SOL

DEFF Research Database (Denmark)

Havlíčková, E.; Fundamenski, W.; Naulin, Volker

2011-01-01

The effect of plasma fluctuations due to turbulence at the outboard midplane on parallel transport properties is investigated. Time-dependent fluctuating signals at different radial locations are used to study the effect of signal statistics. Further, a computational analysis of parallel transport...... to a comparison of steady-state and time-dependent modelling....

Diagnostic needs for fluctuations and transport studies

International Nuclear Information System (INIS)

Carreras, B.A.

1992-01-01

The identification of fundamental transport mechanisms in magnetically confined plasmas is a critical issue for the magnetic fusion program. Recent progress in understanding fluctuations and transport is well correlated with the development and use of new diagnostics, but there a great deal of information is still missing. Some of the required measurements are well beyond our present diagnostic capabilities, but some are within reach and could answer critical questions in this area of research. Some of these critical issues are discussed

Effect of thermal fluctuations in spin-torque driven magnetization dynamics

International Nuclear Information System (INIS)

Bonin, R.; Bertotti, G.; Serpico, C.; Mayergoyz, I.D.; D'Aquino, M.

2007-01-01

Nanomagnets with uniaxial symmetry driven by an external field and spin-polarized currents are considered. Anisotropy, applied field, and spin polarization are all aligned along the symmetry axis. Thermal fluctuations are described by adding a Gaussian white noise stochastic term to the Landau-Lifshitz-Gilbert equation for the deterministic dynamics. The corresponding Fokker-Planck equation is derived. It is shown that deterministic dynamics, thermal relaxation, and transition rate between stable states are governed by an effective potential including the effect of current injection

Effect of thermal fluctuations in spin-torque driven magnetization dynamics

Energy Technology Data Exchange (ETDEWEB)

Bonin, R. [INRiM, I-10135 Turin (Italy)]. E-mail: bonin@inrim.it; Bertotti, G. [INRiM, I-10135 Turin (Italy); Serpico, C. [Dipartimento di Ingegneria Elettrica, Universita di Napoli ' Federico II' I-80125 Naples (Italy); Mayergoyz, I.D. [Department of Electrical and Computer Engineering, University of Maryland, College Park, MD 20742 (United States); D' Aquino, M. [Dipartimento per le Tecnologie, Universita di Napoli ' Parthenope' , I-80133 Naples (Italy)

2007-09-15

Nanomagnets with uniaxial symmetry driven by an external field and spin-polarized currents are considered. Anisotropy, applied field, and spin polarization are all aligned along the symmetry axis. Thermal fluctuations are described by adding a Gaussian white noise stochastic term to the Landau-Lifshitz-Gilbert equation for the deterministic dynamics. The corresponding Fokker-Planck equation is derived. It is shown that deterministic dynamics, thermal relaxation, and transition rate between stable states are governed by an effective potential including the effect of current injection.

Transport barrier fluctuations governed by SOL turbulence spreading

International Nuclear Information System (INIS)

Ghendrih, Ph.; Sarazin, Y.; Ciraolo, G.; Darmet, G.; Garbet, X.; Grangirard, V.; Tamain, P.; Benkadda, S.; Beyer, P.

2007-01-01

Turbulence spreading, namely turbulent transport extending into a stable region is reported both for the flat density profiles in the far SOL and into a modeled H-mode barrier. It is shown that due to turbulence penetration, the pedestal width fluctuates and that its effective width is a factor 2 smaller than the linear predicted width. Turbulence overshooting throughout the pedestal leads to a non-vanishing turbulent transport within the barrier and provides a coupling of core and SOL turbulence despite the transport barrier

Kac limit and thermodynamic characterization of stochastic dynamics driven by Poisson-Kac fluctuations

Science.gov (United States)

Giona, Massimiliano; Brasiello, Antonio; Crescitelli, Silvestro

2017-07-01

We analyze the thermodynamic properties of stochastic differential equations driven by smooth Poisson-Kac fluctuations, and their convergence, in the Kac limit, towards Wiener-driven Langevin equations. Using a Markovian embedding of the stochastic work variable, it is proved that the Kac-limit convergence implies a Stratonovich formulation of the limit Langevin equations, in accordance with the Wong-Zakai theorem. Exact moment analysis applied to the case of a purely frictional system shows the occurrence of different regimes and crossover phenomena in the parameter space.

Fluctuations and transport in fusion plasmas. Annual progress report, October 1, 1983-September 30, 1984

International Nuclear Information System (INIS)

Gould, R.W.

1984-01-01

This grant supports an integrated program of experiment and theory in tokamak plasma physics. Emphasis is placed on microscopic fluctuations and anomalous transport. The primary objective is to characterize the properties of the microscopic fluctuations observed in tokamaks and to try to develop an understanding of the fluctuation-induced transport of particles and heat. Anomalous transport, which causes energy losses one to two orders of magnitude larger than predicted by neoclassical transport theory, occurs in all tokamaks and underlies empirical scaling laws

Molecular Dynamics Simulations of a Linear Nanomotor Driven by Thermophoretic Forces

DEFF Research Database (Denmark)

Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard L.

Molecular Dynamics of a Linear Nanomotor Driven by Thermophoresis Harvey A. Zambrano1, Jens H. Walther1,2 and Richard L. Jaffe3 1Department of Mechanical Engineering, Fluid Mechanics, Technical University of Denmark, DK-2800 Lyngby, Denmark; 2Computational Science and Engineering Laboratory, ETH...... future molecular machines a complete understanding of the friction forces involved on the transport process at the molecular level have to be addressed.18 In this work we perform Molecular Dynamics (MD) simulations using the MD package FASTTUBE19 to study a molecular linear motor consisting of coaxial...... the valence forces within the CNT using Morse, harmonic angle and torsion potentials.19We include a nonbonded carbon-carbon Lennard-Jones potential to describe the vdW interaction between the carbon atoms within the double wall portion of the system. We equilibrate the system at 300K for 0.1 ns, by coupling...

Fluctuation in Interface and Electronic Structure of Single-Molecule Junctions Investigated by Current versus Bias Voltage Characteristics.

Science.gov (United States)

Isshiki, Yuji; Fujii, Shintaro; Nishino, Tomoaki; Kiguchi, Manabu

2018-03-14

Structural and electronic detail at the metal-molecule interface has a significant impact on the charge transport across the molecular junctions, but its precise understanding and control still remain elusive. On the single-molecule scale, the metal-molecule interface structures and relevant charge transport properties are subject to fluctuation, which contain the fundamental science of single-molecule transport and implication for manipulability of the transport properties in electronic devices. Here, we present a comprehensive approach to investigate the fluctuation in the metal-molecule interface in single-molecule junctions, based on current-voltage ( I- V) measurements in combination with first-principles simulation. Contrary to conventional molecular conductance studies, this I- V approach provides a correlated statistical description of both the degree of electronic coupling across the metal-molecule interface and the molecular orbital energy level. This statistical approach was employed to study fluctuation in single-molecule junctions of 1,4-butanediamine (DAB), pyrazine (PY), 4,4'-bipyridine (BPY), and fullerene (C 60 ). We demonstrate that molecular-dependent fluctuation of σ-, π-, and π-plane-type interfaces can be captured by analyzing the molecular orbital (MO) energy level under mechanical perturbation. While the MO level of DAB with the σ-type interface shows weak distance dependence and fluctuation, the MO level of PY, BPY, and C 60 features unique distance dependence and molecular-dependent fluctuation against the mechanical perturbation. The MO level of PY and BPY with the σ+π-type interface increases with the increase in the stretch distance. In contrast, the MO level of C 60 with the π-plane-type interface decreases with the increase in the stretching perturbation. This study provides an approach to resolve the structural and electronic fluctuation in the single-molecule junctions and insight into the molecular-dependent fluctuation in

Dynamical interplay between fluctuations, electric fields and transport in fusion plasmas

International Nuclear Information System (INIS)

Hidalgo, C.; Pedrosa, M.A.; Goncalves, B.

2003-01-01

A view of recent experimental results and progress in the characterization of the statistical properties of electrostatic turbulence in magnetically confined devices is given. An empirical similarity in the scaling properties of the probability distribution function (PDF) of turbulent transport has been observed in the plasma edge region in fusion plasmas. The investigation of the dynamical interplay between fluctuation in gradients, turbulent transport and radial electric fields has shows that these parameters are strongly coupled both in tokamak and stellarator plasmas. The bursty behaviour of turbulent transport is linked with a departure from the most probable radial gradient. The dynamical relation between fluctuations in gradients and transport is strongly affected by the presence of sheared poloidal flows which organized themselves near marginal stability. These results emphasize the importance of the statistical description of transport processes in fusion plasmas as an alternative approach to the traditional way to characterize transport based on the computation of effective transport coefficients. (author)

Transport barriers in bootstrap-driven tokamaks

Science.gov (United States)

Staebler, G. M.; Garofalo, A. M.; Pan, C.; McClenaghan, J.; Van Zeeland, M. A.; Lao, L. L.

2018-05-01

Experiments have demonstrated improved energy confinement due to the spontaneous formation of an internal transport barrier in high bootstrap fraction discharges. Gyrokinetic analysis, and quasilinear predictive modeling, demonstrates that the observed transport barrier is caused by the suppression of turbulence primarily from the large Shafranov shift. It is shown that the Shafranov shift can produce a bifurcation to improved confinement in regions of positive magnetic shear or a continuous reduction in transport for weak or negative magnetic shear. Operation at high safety factor lowers the pressure gradient threshold for the Shafranov shift-driven barrier formation. Two self-organized states of the internal and edge transport barrier are observed. It is shown that these two states are controlled by the interaction of the bootstrap current with magnetic shear, and the kinetic ballooning mode instability boundary. Election scale energy transport is predicted to be dominant in the inner 60% of the profile. Evidence is presented that energetic particle-driven instabilities could be playing a role in the thermal energy transport in this region.

Colloid mobilization and transport during capillary fringe fluctuations.

Science.gov (United States)

Aramrak, Surachet; Flury, Markus; Harsh, James B; Zollars, Richard L

2014-07-01

Capillary fringe fluctuations due to changing water tables lead to displacement of air-water interfaces in soils and sediments. These moving air-water interfaces can mobilize colloids. We visualized colloids interacting with moving air-water interfaces during capillary fringe fluctuations by confocal microscopy. We simulated capillary fringe fluctuations in a glass-bead-filled column. We studied four specific conditions: (1) colloids suspended in the aqueous phase, (2) colloids attached to the glass beads in an initially wet porous medium, (3) colloids attached to the glass beads in an initially dry porous medium, and (4) colloids suspended in the aqueous phase with the presence of a static air bubble. Confocal images confirmed that the capillary fringe fluctuations affect colloid transport behavior. Hydrophilic negatively charged colloids initially suspended in the aqueous phase were deposited at the solid-water interface after a drainage passage, but then were removed by subsequent capillary fringe fluctuations. The colloids that were initially attached to the wet or dry glass bead surface were detached by moving air-water interfaces in the capillary fringe. Hydrophilic negatively charged colloids did not attach to static air-bubbles, but hydrophobic negatively charged and hydrophilic positively charged colloids did. Our results demonstrate that capillary fringe fluctuations are an effective means for colloid mobilization.

The effect on stellarator neoclassical transport of a fluctuating electrostatic spectrum

International Nuclear Information System (INIS)

Mynick, H.E.; Boozer, A.H.

2005-01-01

A study is presented of the effect on neoclassical transport of a fluctuating electrostatic spectrum, such as produced either by plasma turbulence, or imposed externally. For tokamaks, it is usually assumed that the neoclassical and 'anomalous' contributions to the transport roughly superpose, D=D nc +D an , an intuition also used in modeling stellarators. An alternate intuition, however, is one where it is the collisional and anomalous scattering frequencies which superpose, ν ef =ν+ν an . For nonaxisymmetric systems, in regimes where ∂D/∂ν ef picture' implies that turning on the fluctuations can decrease the total radial transport. Using numerical and analytic means, it is found that the total transport has contributions conforming to each of these intuitions, either of which can dominate. In particular, for stellarators, the ν ef picture is often valid, producing transport behavior differing from tokamaks

Controlling fluctuations in an ITB and comparison with gyrokinetic simulations

Science.gov (United States)

Ernst, D. R.; Fiore, C. L.; Dominguez, A.; Podpaly, Y.; Reinke, M. L.; Terry, J. L.; Tsujii, N.; Bespamyatnov, I.; Churchill, M.; Greenwald, M.; Hubbard, A.; Hughes, J. W.; Lee, J.; Ma, Y.; Wolfe, S.; Wukitch, S.

2011-10-01

We have modulated on-axis ICRF minority heating to trigger fluctuations and core electron transport in Alcator C-Mod Internal Transport Barriers (ITB's). Temperature swings of 50% produced strong bursts of density fluctuations, measured by phase contrast imaging (PCI), while edge fluctuations from reflectometry, Mirnov coils, and gas puff imaging (GPI) simultaneously diminished. The PCI fluctuations are in phase with sawteeth, further evidence that they originate within the ITB foot. Linear gyrokinetic analysis with GS2 shows TEMs are driven unstable in the ITB by the on-axis heating, as in Refs.,. Nonlinear gyrokinetic simulations of turbulence in the ITB are compared with fluctuation data using a synthetic diagnostic. Strong ITB's were produced with high quality ion and electron profile data. Supported by U.S. DoE awards DE-FC02-99ER54512, DE-FG02-91ER54109, DE-FC02-08ER54966.

Intracellular transport driven by cytoskeletal motors: General mechanisms and defects

Science.gov (United States)

Appert-Rolland, C.; Ebbinghaus, M.; Santen, L.

2015-09-01

Cells are the elementary units of living organisms, which are able to carry out many vital functions. These functions rely on active processes on a microscopic scale. Therefore, they are strongly out-of-equilibrium systems, which are driven by continuous energy supply. The tasks that have to be performed in order to maintain the cell alive require transportation of various ingredients, some being small, others being large. Intracellular transport processes are able to induce concentration gradients and to carry objects to specific targets. These processes cannot be carried out only by diffusion, as cells may be crowded, and quite elongated on molecular scales. Therefore active transport has to be organized. The cytoskeleton, which is composed of three types of filaments (microtubules, actin and intermediate filaments), determines the shape of the cell, and plays a role in cell motion. It also serves as a road network for a special kind of vehicles, namely the cytoskeletal motors. These molecules can attach to a cytoskeletal filament, perform directed motion, possibly carrying along some cargo, and then detach. It is a central issue to understand how intracellular transport driven by molecular motors is regulated. The interest for this type of question was enhanced when it was discovered that intracellular transport breakdown is one of the signatures of some neuronal diseases like the Alzheimer. We give a survey of the current knowledge on microtubule based intracellular transport. Our review includes on the one hand an overview of biological facts, obtained from experiments, and on the other hand a presentation of some modeling attempts based on cellular automata. We present some background knowledge on the original and variants of the TASEP (Totally Asymmetric Simple Exclusion Process), before turning to more application oriented models. After addressing microtubule based transport in general, with a focus on in vitro experiments, and on cooperative effects in the

Phase transitions and transport in anisotropic superconductors with large thermal fluctuations

International Nuclear Information System (INIS)

Fisher, D.S.

1991-01-01

Fluctuation effects in conventional superconductors such as broadening of phase transitions and flux creep tend to be very small primarily because of the large coherence lengths. Thus mean field theory, with only small fluctuation corrections, usually provides an adequate description of these systems. Regimes in which fluctuation effects cause qualitatively different physics are very difficult to study as they typically occur in very small regions of the phase diagram or, in transport, require measuring extremely small voltages. In striking contrast, in the high temperature cuprate superconductors a combination of factors - short coherence lengths, anisotropy and higher temperatures - make fluctuation effects many orders of magnitude larger. The current understanding of transport and phase transitions in the cuprate superconductors-particularly YBCO and BSCCO-is reviewed. New results are presented on the two-dimensional regimes and 2D-3D crossover in the strongly anisotropic case of BSCCO. The emphasis is on pinning and vortex glass behavior

Transport Barriers in Bootstrap Driven Tokamaks

Science.gov (United States)

Staebler, Gary

2017-10-01

Maximizing the bootstrap current in a tokamak, so that it drives a high fraction of the total current, reduces the external power required to drive current by other means. Improved energy confinement, relative to empirical scaling laws, enables a reactor to more fully take advantage of the bootstrap driven tokamak. Experiments have demonstrated improved energy confinement due to the spontaneous formation of an internal transport barrier in high bootstrap fraction discharges. Gyrokinetic analysis, and quasilinear predictive modeling, demonstrates that the observed transport barrier is due to the suppression of turbulence primarily due to the large Shafranov shift. ExB velocity shear does not play a significant role in the transport barrier due to the high safety factor. It will be shown, that the Shafranov shift can produce a bifurcation to improved confinement in regions of positive magnetic shear or a continuous reduction in transport for weak or negative magnetic shear. Operation at high safety factor lowers the pressure gradient threshold for the Shafranov shift driven barrier formation. The ion energy transport is reduced to neoclassical and electron energy and particle transport is reduced, but still turbulent, within the barrier. Deeper into the plasma, very large levels of electron transport are observed. The observed electron temperature profile is shown to be close to the threshold for the electron temperature gradient (ETG) mode. A large ETG driven energy transport is qualitatively consistent with recent multi-scale gyrokinetic simulations showing that reducing the ion scale turbulence can lead to large increase in the electron scale transport. A new saturation model for the quasilinear TGLF transport code, that fits these multi-scale gyrokinetic simulations, can match the data if the impact of zonal flow mixing on the ETG modes is reduced at high safety factor. This work was supported by the U.S. Department of Energy under DE-FG02-95ER54309 and DE-FC02

Lognormal firing rate distribution reveals prominent fluctuation-driven regime in spinal motor networks

DEFF Research Database (Denmark)

Petersen, Peter C.; Berg, Rune W.

2016-01-01

fraction that operates within either a ‘mean-driven’ or a ‘fluctuation–driven’ regime. Fluctuation-driven neurons have a ‘supralinear’ input-output curve, which enhances sensitivity, whereas the mean-driven regime reduces sensitivity. We find a rich diversity of firing rates across the neuronal population...... as reflected in a lognormal distribution and demonstrate that half of the neurons spend at least 50 %% of the time in the ‘fluctuation–driven’ regime regardless of behavior. Because of the disparity in input–output properties for these two regimes, this fraction may reflect a fine trade–off between stability...

Effect of static porosity fluctuations on reactive transport in a porous medium

Science.gov (United States)

L'Heureux, Ivan

2018-02-01

Reaction-diffusive transport phenomena in porous media are ubiquitous in engineering applications, biological and geochemical systems. The porosity field is usually random in space, but most models consider the porosity field as a well-defined deterministic function of space and time and ignore the porosity fluctuations. They use a reaction-diffusion equation written in terms of an average porosity and average concentration fields. In this contribution, we treat explicitly the effect of spatial porosity fluctuations on the dynamics of a concentration field for the case of a one-dimensional reaction-transport system with nonlinear kinetics. Three basic assumptions are considered. (i) The porosity fluctuations are assumed to have Gaussian properties and an arbitrary variance; (ii) we assume that the noise correlation length is small compared to the relevant macroscopic length scale; (iii) and we assume that the kinetics of the reactive term in the equations for the fluctuations is a self-consistently determined constant. Elimination of the fluctuating part of the concentration field from the dynamics leads to a renormalized equation involving the average concentration field. It is shown that the noise leads to a renormalized (generally smaller) diffusion coefficient and renormalized kinetics. Within the framework of the approximations used, numerical simulations are in agreement with our theory. We show that the porosity fluctuations may have a significant effect on the transport of a reactive species, even in the case of a homogeneous average porosity.

The origin of fluctuations and cross-field transport in idealized magnetic confinement systems

International Nuclear Information System (INIS)

Riviere, A.C.; Ashby, D.E.T.F.; Cordey, J.G.; Edlington, T.; Rusbridge, M.G.

1981-01-01

The study of plasma fluctuations and confinement in idealized systems such as octupoles and levitrons has contributed to the understanding of cross-field transport processes. The linear theory of plasma instabilities that cause fluctuations can predict growth rates and wavelengths around lines of force. However, the theoretical prediction of cross-field transport coefficient is restricted to quasilinear estimates which usually far exceed the measured values. A general view of the results from octupole and levitron experiments shows that under collisional conditions the diffusion coefficient scales in the same way as classical collisional diffusion. Agreement is closely approached in many cases, sometimes even in the presence of fluctuations. Under collisionless conditions, Bohm diffusion scaling is found in the few cases where the scaling law has been determined. There is also experimental and theoretical evidence that long-wavelength low-frequency electric fields (convection cells) can be generated nonlinearly from high-frequency fluctuations and can contribute to cross-field transport. (author)

Light-driven solute transport in Halobacterium halobium

Science.gov (United States)

Lanyi, J. K.

1979-01-01

The cell membrane of Halobacterium halobium exhibits differential regions which contain crystalline arrays of a single kind of protein, termed bacteriorhodopsin. This bacterial retinal-protein complex resembles the visual pigment and, after the absorption of protons, translocates H(+) across the cell membrane, leading to an electrochemical gradient for protons between the inside and the outside of the cell. Thus, light is an alternate source of energy in these bacteria, in addition to terminal oxidation. The paper deals with work on light-driven transport in H. halobium with cell envelope vesicles. The discussion covers light-driven movements of H(+), Na(+), and K(+); light-driven amino acid transport; and apparent allosteric control of amino acid transport. The scheme of energy coupling in H. halobium vesicles appears simple, its quantitative details are quite complex and reveal regulatory phenomena. More knowledge is required of the way the coupling components are regulated by the ion gradients present.

A Langevin model for fluctuating contact angle behaviour parametrised using molecular dynamics.

Science.gov (United States)

Smith, E R; Müller, E A; Craster, R V; Matar, O K

2016-12-06

Molecular dynamics simulations are employed to develop a theoretical model to predict the fluid-solid contact angle as a function of wall-sliding speed incorporating thermal fluctuations. A liquid bridge between counter-sliding walls is studied, with liquid-vapour interface-tracking, to explore the impact of wall-sliding speed on contact angle. The behaviour of the macroscopic contact angle varies linearly over a range of capillary numbers beyond which the liquid bridge pinches off, a behaviour supported by experimental results. Nonetheless, the liquid bridge provides an ideal test case to study molecular scale thermal fluctuations, which are shown to be well described by Gaussian distributions. A Langevin model for contact angle is parametrised to incorporate the mean, fluctuation and auto-correlations over a range of sliding speeds and temperatures. The resulting equations can be used as a proxy for the fully-detailed molecular dynamics simulation allowing them to be integrated within a continuum-scale solver.

The physicist's companion to current fluctuations: one-dimensional bulk-driven lattice gases

International Nuclear Information System (INIS)

Lazarescu, Alexandre

2015-01-01

One of the main features of statistical systems out of equilibrium is the currents they exhibit in their stationary state: microscopic currents of probability between configurations, which translate into macroscopic currents of mass, charge, etc. Understanding the general behaviour of these currents is an important step towards building a universal framework for non-equilibrium steady states akin to the Gibbs–Boltzmann distribution for equilibrium systems. In this review, we consider one-dimensional bulk-driven particle gases, and in particular the asymmetric simple exclusion process (ASEP) with open boundaries, which is one of the most popular models of one-dimensional transport. We focus, in particular, on the current of particles flowing through the system in its steady state, and on its fluctuations. We show how one can obtain the complete statistics of that current, through its large deviation function, by combining results from various methods: exact calculation of the cumulants of the current, using the integrability of the model; direct diagonalization of a biased process in the limits of very high or low current; hydrodynamic description of the model in the continuous limit using the macroscopic fluctuation theory. We give a pedagogical account of these techniques, starting with a quick introduction to the necessary mathematical tools, as well as a short overview of the existing works relating to the ASEP. We conclude by drawing the complete dynamical phase diagram of the current. We also remark on a few possible generalizations of these results. (topical review)

Transmembrane molecular transport during versus after extremely large, nanosecond electric pulses.

Science.gov (United States)

Smith, Kyle C; Weaver, James C

2011-08-19

Recently there has been intense and growing interest in the non-thermal biological effects of nanosecond electric pulses, particularly apoptosis induction. These effects have been hypothesized to result from the widespread creation of small, lipidic pores in the plasma and organelle membranes of cells (supra-electroporation) and, more specifically, ionic and molecular transport through these pores. Here we show that transport occurs overwhelmingly after pulsing. First, we show that the electrical drift distance for typical charged solutes during nanosecond pulses (up to 100 ns), even those with very large magnitudes (up to 10 MV/m), ranges from only a fraction of the membrane thickness (5 nm) to several membrane thicknesses. This is much smaller than the diameter of a typical cell (∼16 μm), which implies that molecular drift transport during nanosecond pulses is necessarily minimal. This implication is not dependent on assumptions about pore density or the molecular flux through pores. Second, we show that molecular transport resulting from post-pulse diffusion through minimum-size pores is orders of magnitude larger than electrical drift-driven transport during nanosecond pulses. While field-assisted charge entry and the magnitude of flux favor transport during nanosecond pulses, these effects are too small to overcome the orders of magnitude more time available for post-pulse transport. Therefore, the basic conclusion that essentially all transmembrane molecular transport occurs post-pulse holds across the plausible range of relevant parameters. Our analysis shows that a primary direct consequence of nanosecond electric pulses is the creation (or maintenance) of large populations of small pores in cell membranes that govern post-pulse transmembrane transport of small ions and molecules. Copyright © 2011 Elsevier Inc. All rights reserved.

Statistical properties of turbulent transport and fluctuations in tokamak and stellarator devices

Energy Technology Data Exchange (ETDEWEB)

Hidalgo, C; Pedrosa, M A; Milligen, B Van; Sanchez, E; Balbin, R; Garcia-Cortes, I [Euratom-CIEMAT Association, Madrid (Spain); Bleuel, J; Giannone, L.; Niedermeyer, H [Euratom-IPP Association, Garching (Germany)

1997-05-01

The statistical properties of fluctuations and turbulent transport have been studied in the plasma boundary region of stellarator (TJ-IU, W7-AS) and tokamak (TJ-I) devices. The local flux probability distribution function shows the bursty character of the flux and presents a systematic change as a function of the radial location. There exist large amplitude transport bursts that account for a significant part of the total flux. There is a strong similarity between the statistical properties of the turbulent fluxes in different devices. The value of the radial coherence associated with fluctuations and turbulent transport is strongly intermittent. This result emphasizes the importance of measurements with time resolution in understanding the interplay between the edge and the core regions in the plasma. For measurements in the plasma edge region of the TJ-IU torsatron, the turbulent flux does not, in general, show a larger radial coherence than the one associated with the fluctuations. (author). 14 refs, 6 figs.

Effect of magnetic configuration on density fluctuation and particle transport in LHD

International Nuclear Information System (INIS)

Tanaka, K.; Michael, C.; Yamagishi, O.; Ida, K.; Yamada, H.; Yoshinuma, M.; Yokoyama, M.; Miyazawa, J.; Morita, S.; Kawahata, K.; Tokzawa, T.; Shoji, M.; Vyacheslavov, L.N.; Sanin, A.L.

2005-01-01

The study of fluctuations and particle transport is important issue in heliotron and stellarator devices as well as in tokamaks. A two dimensional phase contrast interferometer (2D PCI) was developed to investigate fluctuation characteristics, which play role in confinement. The current 2D PCI can detect fluctuations for which -1 0.3 -1 and 5< f<500kHz. With the use of magnetic shear and the 2D detector, the spatial resolution around 20% of averaged minor radius is possible presently. The strongest fluctuations are localized in the plasma edge, where density gradients are negative, but fluctuations also exist in the positive density gradient region of the hollow density profile. The phase velocity of fluctuations in the positive gradient region is close to plasma ErxBt rotation. On the other hand, fluctuations in the negative density gradient region propagate in the ion diamagnetic direction in the plasma frame and do not follow ErxBt rotation. This suggests there is a different nature of the fluctuations in the positive and negative density gradient regions. A particle transport was studied by means of density modulation experiments. The systematic study was done at Rax=3.6m, which is so-called standard configuration. The density profiles vary from peaked to hollow with increasing heating power. It was also found that particle diffusion and convection are functions of electron temperature and its gradient respectively. The magnetic configuration is another parameter, which characterizes particle confinement. At more outward shifted configurations, helical ripple becomes larger and the ergodic region becomes thicker, then neoclassical transport becomes larger. However estimated diffusion coefficients are still around one order of magnitude larger than neoclassical values in edge region, where ρ = 0.7 ∼ 1.0 and they are larger at more outward configurations. At the same time the convection velocity is found to be comparable with neoclassical prediction at Rax=3

Mesoscopic fluctuations in biharmonically driven flux qubits

Science.gov (United States)

Ferrón, Alejandro; Domínguez, Daniel; Sánchez, María José

2017-01-01

We investigate flux qubits driven by a biharmonic magnetic signal, with a phase lag that acts as an effective time reversal broken parameter. The driving induced transition rate between the ground and the excited state of the flux qubit can be thought of as an effective transmittance, profiting from a direct analogy between interference effects at avoided level crossings and scattering events in disordered electronic systems. For time scales prior to full relaxation, but large compared to the decoherence time, this characteristic rate has been accessed experimentally by Gustavsson et al. [Phys. Rev. Lett. 110, 016603 (2013)], 10.1103/PhysRevLett.110.016603 and its sensitivity with both the phase lag and the dc flux detuning explored. In this way, signatures of universal conductance fluctuationslike effects have been analyzed and compared with predictions from a phenomenological model that only accounts for decoherence, as a classical noise. Here we go beyond the classical noise model and solve the full dynamics of the driven flux qubit in contact with a quantum bath employing the Floquet-Born-Markov master equation. Within this formalism, the computed relaxation and decoherence rates turn out to be strongly dependent on both the phase lag and the dc flux detuning. Consequently, the associated pattern of fluctuations in the characteristic rates display important differences with those obtained within the mentioned phenomenological model. In particular, we demonstrate the weak localizationlike effect in the average values of the relaxation rate. Our predictions can be tested for accessible but longer time scales than the current experimental times.

Transport and fluctuation studies on RFX

International Nuclear Information System (INIS)

Martini, S.; Martines, E.; Carraro, L.

2003-01-01

The paper highlights the progress made in the modelling and understanding of the mechanisms underlying particle and energy transport in the RFP. A transport analysis has been performed on the perturbed transport coefficients for pellets of different characteristics launched both in standard RFP plasmas and in combination with pulsed poloidal current drive, this latter scenario potentially allowing an efficient fuelling and a good energy confinement. The study has confirmed the importance of large-scale MHD modes in determining the transport properties in the RFP core. As far as confinement in the edge is concerned, the analysis has been focussed on the role played by burst events on the electrostatic particle flux and to the 'intermittent events'. The intermittent events cluster during relaxation processes and such behaviour is more evident close to the magnetic reversal surface. This result confirms an interplay between the small scale edge turbulence and the large scale relaxation events driven by core-resonant tearing modes. (author)

Molecular dynamics for irradiation driven chemistry: application to the FEBID process*

Science.gov (United States)

Sushko, Gennady B.; Solov'yov, Ilia A.; Solov'yov, Andrey V.

2016-10-01

A new molecular dynamics (MD) approach for computer simulations of irradiation driven chemical transformations of complex molecular systems is suggested. The approach is based on the fact that irradiation induced quantum transformations can often be treated as random, fast and local processes involving small molecules or molecular fragments. We advocate that the quantum transformations, such as molecular bond breaks, creation and annihilation of dangling bonds, electronic charge redistributions, changes in molecular topologies, etc., could be incorporated locally into the molecular force fields that describe the classical MD of complex molecular systems under irradiation. The proposed irradiation driven molecular dynamics (IDMD) methodology is designed for the molecular level description of the irradiation driven chemistry. The IDMD approach is implemented into the MBN Explorer software package capable to operate with a large library of classical potentials, many-body force fields and their combinations. IDMD opens a broad range of possibilities for modelling of irradiation driven modifications and chemistry of complex molecular systems ranging from radiotherapy cancer treatments to the modern technologies such as focused electron beam deposition (FEBID). As an example, the new methodology is applied for studying the irradiation driven chemistry caused by FEBID of tungsten hexacarbonyl W(CO)6 precursor molecules on a hydroxylated SiO2 surface. It is demonstrated that knowing the interaction parameters for the fragments of the molecular system arising in the course of irradiation one can reproduce reasonably well experimental observations and make predictions about the morphology and molecular composition of nanostructures that emerge on the surface during the FEBID process.

Cytoskeleton dynamics: Fluctuations within the network

International Nuclear Information System (INIS)

Bursac, Predrag; Fabry, Ben; Trepat, Xavier; Lenormand, Guillaume; Butler, James P.; Wang, Ning; Fredberg, Jeffrey J.; An, Steven S.

2007-01-01

Out-of-equilibrium systems, such as the dynamics of a living cytoskeleton (CSK), are inherently noisy with fluctuations arising from the stochastic nature of the underlying biochemical and molecular events. Recently, such fluctuations within the cell were characterized by observing spontaneous nano-scale motions of an RGD-coated microbead bound to the cell surface [Bursac et al., Nat. Mater. 4 (2005) 557-561]. While these reported anomalous bead motions represent a molecular level reorganization (remodeling) of microstructures in contact with the bead, a precise nature of these cytoskeletal constituents and forces that drive their remodeling dynamics are largely unclear. Here, we focused upon spontaneous motions of an RGD-coated bead and, in particular, assessed to what extent these motions are attributable to (i) bulk cell movement (cell crawling), (ii) dynamics of focal adhesions, (iii) dynamics of lipid membrane, and/or (iv) dynamics of the underlying actin CSK driven by myosin motors

Fluctuations and correlations in nucleus-nucleus collisions within transport approaches

International Nuclear Information System (INIS)

Konchakovski, Volodymyr P.

2009-01-01

The current thesis is devoted to a systematic study of fluctuations and correlations in heavy-ion collisions, which might be considered as probes for the phase transition and the critical point in the phase diagram, within the Hadron-String- Dynamics (HSD) microscopic transport approach. This is a powerful tool to study nucleus-nucleus collisions and allows to completely simulate experimental collisions on an event-by-event basis. Thus, the transport model has been used to study fluctuations and correlations including the influence of experimental acceptance as well as centrality, system size and collision energy. The comparison to experimental data can separate the effects induced by a phase transition since there is no phase transition in the HSD version used here. Firstly the centrality dependence of multiplicity fluctuations has been studied. Different centrality selections have been performed in the analysis in correspondence to the experimental situation. For the fixed target experiment NA49 events with fixed numbers of the projectile participants have been studied while in the collider experiment PHENIX centrality classes of events have been defined by the multiplicity in certain phase space region. A decrease of participant number fluctuations (and thus volume fluctuations) in more central collisions for both experiments has been obtained. Another area of this work addresses to transport model calculations of multiplicity fluctuations in nucleus-nucleus collisions as a function of colliding energy and system size. This study is in full correspondence to the experimental program of the NA61 Collaboration at the SPS. Central C+C, S+S, In+In, and Pb+Pb nuclear collisions at Elab = 10, 20, 30, 40, 80, 158 AGeV have been investigated. The expected enhanced fluctuations - attributed to the critical point and phase transition - can be observed experimentally on top of a monotonic and smooth 'hadronic background'. These findings should be helpful for the optimal

Fluctuations and correlations in nucleus-nucleus collisions within transport approaches

Energy Technology Data Exchange (ETDEWEB)

Konchakovski, Volodymyr P.

2009-10-01

The current thesis is devoted to a systematic study of fluctuations and correlations in heavy-ion collisions, which might be considered as probes for the phase transition and the critical point in the phase diagram, within the Hadron-String- Dynamics (HSD) microscopic transport approach. This is a powerful tool to study nucleus-nucleus collisions and allows to completely simulate experimental collisions on an event-by-event basis. Thus, the transport model has been used to study fluctuations and correlations including the influence of experimental acceptance as well as centrality, system size and collision energy. The comparison to experimental data can separate the effects induced by a phase transition since there is no phase transition in the HSD version used here. Firstly the centrality dependence of multiplicity fluctuations has been studied. Different centrality selections have been performed in the analysis in correspondence to the experimental situation. For the fixed target experiment NA49 events with fixed numbers of the projectile participants have been studied while in the collider experiment PHENIX centrality classes of events have been defined by the multiplicity in certain phase space region. A decrease of participant number fluctuations (and thus volume fluctuations) in more central collisions for both experiments has been obtained. Another area of this work addresses to transport model calculations of multiplicity fluctuations in nucleus-nucleus collisions as a function of colliding energy and system size. This study is in full correspondence to the experimental program of the NA61 Collaboration at the SPS. Central C+C, S+S, In+In, and Pb+Pb nuclear collisions at Elab = 10, 20, 30, 40, 80, 158 AGeV have been investigated. The expected enhanced fluctuations - attributed to the critical point and phase transition - can be observed experimentally on top of a monotonic and smooth 'hadronic background'. These findings should be helpful for the

Computing molecular fluctuations in biochemical reaction systems based on a mechanistic, statistical theory of irreversible processes.

Science.gov (United States)

Kulasiri, Don

2011-01-01

We discuss the quantification of molecular fluctuations in the biochemical reaction systems within the context of intracellular processes associated with gene expression. We take the molecular reactions pertaining to circadian rhythms to develop models of molecular fluctuations in this chapter. There are a significant number of studies on stochastic fluctuations in intracellular genetic regulatory networks based on single cell-level experiments. In order to understand the fluctuations associated with the gene expression in circadian rhythm networks, it is important to model the interactions of transcriptional factors with the E-boxes in the promoter regions of some of the genes. The pertinent aspects of a near-equilibrium theory that would integrate the thermodynamical and particle dynamic characteristics of intracellular molecular fluctuations would be discussed, and the theory is extended by using the theory of stochastic differential equations. We then model the fluctuations associated with the promoter regions using general mathematical settings. We implemented ubiquitous Gillespie's algorithms, which are used to simulate stochasticity in biochemical networks, for each of the motifs. Both the theory and the Gillespie's algorithms gave the same results in terms of the time evolution of means and variances of molecular numbers. As biochemical reactions occur far away from equilibrium-hence the use of the Gillespie algorithm-these results suggest that the near-equilibrium theory should be a good approximation for some of the biochemical reactions. © 2011 Elsevier Inc. All rights reserved.

Transport properties of molecular junctions

CERN Document Server

Zimbovskaya, Natalya A

2013-01-01

A comprehensive overview of the physical mechanisms that control electron transport and the characteristics of metal-molecule-metal (MMM) junctions is presented. As far as possible, methods and formalisms presented elsewhere to analyze electron transport through molecules are avoided. This title introduces basic concepts—a description of the electron transport through molecular junctions—and briefly describes relevant experimental methods. Theoretical methods commonly used to analyze the electron transport through molecules are presented. Various effects that manifest in the electron transport through MMMs, as well as the basics of density-functional theory and its applications to electronic structure calculations in molecules are presented. Nanoelectronic applications of molecular junctions and similar systems are discussed as well. Molecular electronics is a diverse and rapidly growing field. Transport Properties of Molecular Junctions presents an up-to-date survey of the field suitable for researchers ...

A perspective on the structural studies of inner membrane electrochemical potential-driven transporters.

Science.gov (United States)

Lemieux, M Joanne

2008-09-01

Electrochemical potential-driven transporters represent a vast array of proteins with varied substrate specificities. While diverse in size and substrate specificity, they are all driven by electrochemical potentials. Over the past five years there have been increasing numbers of X-ray structures reported for this family of transporters. Structural information is available for five subfamilies of electrochemical potential-driven transporters. No structural information exists for the remaining 91 subfamilies. In this review, the various subfamilies of electrochemical potential-driven transporters are discussed. The seven reported structures for the electrochemical potential-driven transporters and the methods for their crystallization are also presented. With a few exceptions, overall crystallization trends have been very similar for the transporters despite their differences in substrate specificity and topology. Also discussed is why the structural studies on these transporters were successful while others are not as fruitful. With the plethora of transporters with unknown structures, this review provides incentive for crystallization of transporters in the remaining subfamilies for which no structural information exists.

Thermodynamic Models from Fluctuation Solution Theory Analysis of Molecular Simulations

DEFF Research Database (Denmark)

Christensen, Steen; Peters, Günther H.j.; Hansen, Flemming Yssing

2007-01-01

Fluctuation solution theory (FST) is employed to analyze results of molecular dynamics (MD) simulations of liquid mixtures. The objective is to generate parameters for macroscopic GE-models, here the modified Margules model. We present a strategy for choosing the number of parameters included...

Density fluctuation measurement at edge and internal transport barriers in JT-60U

International Nuclear Information System (INIS)

Oyama, N; Bruskin, L G; Takenaga, H; Shinohara, K; Isayama, A; Ide, S; Sakamoto, Y; Suzuki, T; Fujita, T; Kamada, Y; Miura, Y

2004-01-01

A new analytical method using a combination of the O-mode reflectometer and a time-dependent two-dimensional full-wave simulation code has been developed for the quantitative evaluation of density fluctuations in JT-60U. Two statistical parameters of the reflectometer signals, fluctuation index (F) and elongation factor (χ), are introduced as measures of the fluctuation amplitude (γ) and the width of the poloidal wave number spectrum (k θ0 ). This method is applied to the edge transport barrier (ETB) and internal transport barrier (ITB). At the transition to the ELM free H-mode phase, analysis suggests that the density fluctuation level reduced from 1.9-3.2% to 0.29-0.44%, while the value of k θ0 changed from 1.6-2.0 to 0.77-0.81 cm -1 in the ETB region. On the other hand, the amplitude of the density fluctuation was evaluated as 1.0-2.0% at the ITB region, even after the formation of the box type ITB. Instead, when a pellet was injected into the plasma with a box type ITB as an external perturbation, a remarkable change in the frequency spectrum was observed. Analysis suggests a reduction in the density fluctuation level to 0.4-0.6% after the pellet injection

Anomalous transport phenomena in Fermi liquids with strong magnetic fluctuations

International Nuclear Information System (INIS)

Kontani, Hiroshi

2008-01-01

In this paper, we present recent developments in the theory of transport phenomena based on the Fermi liquid theory. In conventional metals, various transport coefficients are scaled according to the quasiparticles relaxation time, τ, which implies that the relaxation time approximation (RTA) holds well. However, such a simple scaling does not hold in many strongly correlated electron systems. The most famous example would be high-T c superconductors (HTSCs), where almost all the transport coefficients exhibit a significant deviation from the RTA results. This issue has been one of the most significant unresolved problems in HTSCs for a long time. Similar anomalous transport phenomena have been observed in metals near their antiferromagnetic (AF) quantum critical point (QCP). The main goal of this study is to demonstrate whether the anomalous transport phenomena in HTSC is evidence of a non-Fermi liquid ground state, or just RTA violation in strongly correlated Fermi liquids. Another goal is to establish a unified theory of anomalous transport phenomena in metals with strong magnetic fluctuations. For these purposes, we develop a method for calculating various transport coefficients beyond the RTA by employing field theoretical techniques. In a Fermi liquid, an excited quasiparticle induces other excited quasiparticles by collision, and current due to these excitations is called a current vertex correction (CVC). Landau noticed the existence of CVC first, which is indispensable for calculating transport coefficients in accord with the conservation laws. Here, we develop a transport theory involving resistivity and the Hall coefficient on the basis of the microscopic Fermi liquid theory, by considering the CVC. In nearly AF Fermi liquids, we find that the strong backward scattering due to AF fluctuations induces the CVC with prominent momentum dependence. This feature of the CVC can account for the significant enhancement in the Hall coefficient, magnetoresistance

Charge Transport Processes in Molecular Junctions

Science.gov (United States)

Smith, Christopher Eugene

Molecular electronics (ME) has evolved into a rich area of exploration that combines the fields of chemistry, materials, electronic engineering and computational modeling to explore the physics behind electronic conduction at the molecular level. Through studying charge transport properties of single molecules and nanoscale molecular materials the field has gained the potential to bring about new avenues for the miniaturization of electrical components where quantum phenomena are utilized to achieve solid state molecular device functionality. Molecular junctions are platforms that enable these studies and consist of a single molecule or a small group of molecules directly connected to electrodes. The work presented in this thesis has built upon the current understanding of the mechanisms of charge transport in ordered junctions using self-assembled monolayer (SAM) molecular thin films. Donor and acceptor compounds were synthesized and incorporated into SAMs grown on metal substrates then the transport properties were measured with conducting probe atomic force microscopy (CP-AFM). In addition to experimentally measured current-voltage (I-V) curves, the transport properties were addressed computationally and modeled theoretically. The key objectives of this project were to 1) investigate the impact of molecular structure on hole and electron charge transport, 2) understand the nature of the charge carriers and their structure-transport properties through long (chemically gated to modulate the transport. These results help advance our understanding of transport behavior in semiconducting molecular thin films, and open opportunities to engineer improved electronic functionality into molecular devices.

Photoinduced diffusion molecular transport

Energy Technology Data Exchange (ETDEWEB)

Rozenbaum, Viktor M., E-mail: vik-roz@mail.ru, E-mail: litrakh@gmail.com [Chuiko Institute of Surface Chemistry, National Academy of Sciences of Ukraine, Generala Naumova St. 17, Kiev 03164 (Ukraine); Dekhtyar, Marina L. [Institute of Organic Chemistry, National Academy of Sciences of Ukraine, Murmanskaya St. 5, Kiev 02094 (Ukraine); Lin, Sheng Hsien [Department of Applied Chemistry, National Chiao Tung University, 1001 Ta Hsuen Road, Hsinchu 300, Taiwan (China); Trakhtenberg, Leonid I., E-mail: vik-roz@mail.ru, E-mail: litrakh@gmail.com [Semenov Institute of Chemical Physics, Russian Academy of Sciences, Kosygin Street 4, Moscow 119991, Russia and Moscow Institute of Physics and Technology (State University), Institutskii Per. 9, Dolgoprudnyi, Moscow Region 141700 (Russian Federation)

2016-08-14

We consider a Brownian photomotor, namely, the directed motion of a nanoparticle in an asymmetric periodic potential under the action of periodic rectangular resonant laser pulses which cause charge redistribution in the particle. Based on the kinetics for the photoinduced electron redistribution between two or three energy levels of the particle, the time dependence of its potential energy is derived and the average directed velocity is calculated in the high-temperature approximation (when the spatial amplitude of potential energy fluctuations is small relative to the thermal energy). The thus developed theory of photoinduced molecular transport appears applicable not only to conventional dichotomous Brownian motors (with only two possible potential profiles) but also to a much wider variety of molecular nanomachines. The distinction between the realistic time dependence of the potential energy and that for a dichotomous process (a step function) is represented in terms of relaxation times (they can differ on the time intervals of the dichotomous process). As shown, a Brownian photomotor has the maximum average directed velocity at (i) large laser pulse intensities (resulting in short relaxation times on laser-on intervals) and (ii) excited state lifetimes long enough to permit efficient photoexcitation but still much shorter than laser-off intervals. A Brownian photomotor with optimized parameters is exemplified by a cylindrically shaped semiconductor nanocluster which moves directly along a polar substrate due to periodically photoinduced dipole moment (caused by the repetitive excited electron transitions to a non-resonant level of the nanocylinder surface impurity).

Fluctuating Navier-Stokes equations for inelastic hard spheres or disks.

Science.gov (United States)

Brey, J Javier; Maynar, P; de Soria, M I García

2011-04-01

Starting from the fluctuating Boltzmann equation for smooth inelastic hard spheres or disks, closed equations for the fluctuating hydrodynamic fields to Navier-Stokes order are derived. This requires deriving constitutive relations for both the fluctuating fluxes and the correlations of the random forces. The former are identified as having the same form as the macroscopic average fluxes and involving the same transport coefficients. On the other hand, the random force terms exhibit two peculiarities as compared with their elastic limit for molecular systems. First, they are not white but have some finite relaxation time. Second, their amplitude is not determined by the macroscopic transport coefficients but involves new coefficients. ©2011 American Physical Society

Charge Fluctuations in Nanoscale Capacitors

Science.gov (United States)

Limmer, David T.; Merlet, Céline; Salanne, Mathieu; Chandler, David; Madden, Paul A.; van Roij, René; Rotenberg, Benjamin

2013-09-01

The fluctuations of the charge on an electrode contain information on the microscopic correlations within the adjacent fluid and their effect on the electronic properties of the interface. We investigate these fluctuations using molecular dynamics simulations in a constant-potential ensemble with histogram reweighting techniques. This approach offers, in particular, an efficient, accurate, and physically insightful route to the differential capacitance that is broadly applicable. We demonstrate these methods with three different capacitors: pure water between platinum electrodes and a pure as well as a solvent-based organic electrolyte each between graphite electrodes. The total charge distributions with the pure solvent and solvent-based electrolytes are remarkably Gaussian, while in the pure ionic liquid the total charge distribution displays distinct non-Gaussian features, suggesting significant potential-driven changes in the organization of the interfacial fluid.

Charge fluctuations in nanoscale capacitors.

Science.gov (United States)

Limmer, David T; Merlet, Céline; Salanne, Mathieu; Chandler, David; Madden, Paul A; van Roij, René; Rotenberg, Benjamin

2013-09-06

The fluctuations of the charge on an electrode contain information on the microscopic correlations within the adjacent fluid and their effect on the electronic properties of the interface. We investigate these fluctuations using molecular dynamics simulations in a constant-potential ensemble with histogram reweighting techniques. This approach offers, in particular, an efficient, accurate, and physically insightful route to the differential capacitance that is broadly applicable. We demonstrate these methods with three different capacitors: pure water between platinum electrodes and a pure as well as a solvent-based organic electrolyte each between graphite electrodes. The total charge distributions with the pure solvent and solvent-based electrolytes are remarkably Gaussian, while in the pure ionic liquid the total charge distribution displays distinct non-Gaussian features, suggesting significant potential-driven changes in the organization of the interfacial fluid.

Measurement of the internal magnetic fluctuation by the transport of runaways on J-TEXT

Energy Technology Data Exchange (ETDEWEB)

Chen, Z. Y., E-mail: zychen@hust.edu.cn; Huang, D. W.; Tong, R. H.; Yan, W.; Wei, Y. N.; Ma, T. K.; Jiang, Z. H.; Zhang, X. Q.; Chen, Z. P.; Yang, Z. J.; Zhuang, G. [State Key Laboratory of Advanced Electromagnetic Engineering and Technology, School of Electrical and Electronic Engineering, Huazhong University of Science and Technology, Wuhan 430074 (China)

2016-11-15

The measurement of internal magnetic fluctuation is important for the study of transport in tokamak plasmas. The runaway electron transport induced by the sawtooth crash can be used to obtain the internal magnetic fluctuation. Inversed sawtooth-like activities on hard x-ray (HXR) fluxes following sawtooth activities were observed after the application of electrode biasing on J-TEXT tokamak. The runaway diffusion coefficient D{sub r} is deduced to be about 30 m{sup 2}/s according to the time delay of HXR flux peaks to the sawtooth crashes. The averaged value of normalized magnetic fluctuation in the discharges with electrode biasing was increased to the order of 1 × 10{sup −4}.

Non-classical radiation transport in random media with fluctuating densities

International Nuclear Information System (INIS)

Dyuldya, S.V.; Bratchenko, M.I.

2012-01-01

The ensemble averaged propagation kernels of the non-classical radiation transport are studied by means of the proposed application of the stochastic differential equation random medium generators. It is shown that the non-classical transport is favored in long-correlated weakly fluctuating media. The developed kernel models have been implemented in GEANT4 and validated against the d ouble Monte Carlo m odeling of absorptions curves of disperse neutron absorbers and γ-albedos from a scatterer/absorber random mix

Thermally driven convective cells and tokamak edge turbulence

International Nuclear Information System (INIS)

Thayer, D.R.; Diamond, P.H.

1987-07-01

A unified theory for the dynamics of thermally driven convective cell turbulence is presented. The cells are excited by the combined effects of radiative cooling and resistivity gradient drive. The model also includes impurity dynamics. Parallel thermal and impurity flows enhanced by turbulent radial duffusion regulate and saturate overlapping cells, even in regimes dominated by thermal instability. Transport coefficients and fluctuation levels characteristic of the saturated turbulence are calculated. It is found that the impurity radiation increases transport coefficients for high density plasmas, while the parallel conduction damping, elevated by radial diffusion, in turn quenches the thermal instability. The enhancement due to radiative cooling provides a resolution to the dilemma of explaining the experimental observation that potential fluctuations exceed density fluctuations in the edge plasma (e PHI/T/sub e/ > n/n 0 )

Role of molecular charge in nucleocytoplasmic transport.

Directory of Open Access Journals (Sweden)

Alexander Goryaynov

Full Text Available Transport of genetic materials and proteins between the nucleus and cytoplasm of eukaryotic cells is mediated by nuclear pore complexes (NPCs. A selective barrier formed by phenylalanine-glycine (FG nucleoporins (Nups with net positive charges in the NPC allows for passive diffusion of signal-independent small molecules and transport-receptor facilitated translocation of signal-dependent cargo molecules. Recently, negative surface charge was postulated to be another essential criterion for selective passage through the NPC. However, the charge-driven mechanism in determining the transport kinetics and spatial transport route for either passive diffusion or facilitated translocation remains obscure. Here we employed high-speed single-molecule fluorescence microscopy with an unprecedented spatiotemporal resolution of 9 nm and 400 µs to uncover these mechanistic fundamentals for nuclear transport of charged substrates through native NPCs. We found that electrostatic interaction between negative surface charges on transiting molecules and the positively charged FG Nups, although enhancing their probability of binding to the NPC, never plays a dominant role in determining their nuclear transport mode or spatial transport route. A 3D reconstruction of transport routes revealed that small signal-dependent endogenous cargo protein constructs with high positive surface charges that are destined to the nucleus, rather than repelled from the NPC as suggested in previous models, passively diffused through an axial central channel of the NPC in the absence of transport receptors. Finally, we postulated a comprehensive map of interactions between transiting molecules and FG Nups during nucleocytoplasmic transport by combining the effects of molecular size, signal and surface charge.

Effects of fueling profiles on plasma transport

International Nuclear Information System (INIS)

Houlberg, W.A.; Mense, A.T.; Attenberger, S.E.; Milora, S.L.

1977-01-01

The effects of cold particle fueling profiles on particle and energy transport in an ignition sized tokamak plasma are investigated in this study with a one-dimensional, multifluid transport model. A density gradient driven trapped particle microinstability model for plasma transport is used to demonstrate potential effects of fueling profiles on ignition requirements. Important criteria for the development of improved transport models under the conditions of shallow particle fueling profiles are outlined. A discrete pellet fueling model indicates that large fluctuations in density and temperature may occur in the outer regions of the plasma with large, shallowly penetrating pellets, but fluctuations in the pressure profile are small. The hot central core of the plasma remains unaffected by the large fluctuations near the plasma edge

Light-driven molecular current switch

Czech Academy of Sciences Publication Activity Database

Nešpůrek, Stanislav; Toman, Petr; Sworakowski, J.; Lipinski, J.

2002-01-01

Roč. 2, č. 4 (2002), s. 299-304 ISSN 1567-1739. [Multilateral Symposium between the Korean Academy of Science and Technology and the Foreign Academies. Seoul, 08.05.2002-10.05.2002] R&D Projects: GA AV ČR IAA1050901 Grant - others:GA-(PL) 4T09A 13222 Institutional research plan: CEZ:AV0Z4050913 Keywords : molecular switch * molecular electronics * charge transport Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 1.117, year: 2002

Molecular Dynamics of Equilibrium and Pressure-Driven Transport Properties of Water through LTA-Type Zeolites

KAUST Repository

Turgman-Cohen, Salomon; Araque, Juan C.; Hoek, Eric M. V.; Escobedo, Fernando A.

2013-01-01

We consider an atomistic model to investigate the flux of water through thin Linde type A (LTA) zeolite membranes with differing surface chemistries. Using molecular dynamics, we have studied the flow of water under hydrostatic pressure through a fully hydrated LTA zeolite film (∼2.5 nm thick) capped with hydrophilic and hydrophobic moieties. Pressure drops in the 50-400 MPa range were applied across the membrane, and the flux of water was monitored for at least 15 ns of simulation time. For hydrophilic membranes, water molecules adsorb at the zeolite surface, creating a highly structured fluid layer. For hydrophobic membranes, a depletion of water molecules occurs near the water/zeolite interface. For both types of membranes, the water structure is independent of the pressure drop established in the system and the flux through the membranes is lower than that observed for the bulk zeolitic material; the latter allows an estimation of surface barrier effects to pressure-driven water transport. Mechanistically, it is observed that (i) bottlenecks form at the windows of the zeolite structure, preventing the free flow of water through the porous membrane, (ii) water molecules do not move through a cage in a single-file fashion but rather exhibit a broad range of residence times and pronounced mixing, and (iii) a periodic buildup of a pressure difference between inlet and outlet cages takes place which leads to the preferential flow of water molecules toward the low-pressure cages. © 2013 American Chemical Society.

Molecular Dynamics of Equilibrium and Pressure-Driven Transport Properties of Water through LTA-Type Zeolites

KAUST Repository

Turgman-Cohen, Salomon

2013-10-08

We consider an atomistic model to investigate the flux of water through thin Linde type A (LTA) zeolite membranes with differing surface chemistries. Using molecular dynamics, we have studied the flow of water under hydrostatic pressure through a fully hydrated LTA zeolite film (∼2.5 nm thick) capped with hydrophilic and hydrophobic moieties. Pressure drops in the 50-400 MPa range were applied across the membrane, and the flux of water was monitored for at least 15 ns of simulation time. For hydrophilic membranes, water molecules adsorb at the zeolite surface, creating a highly structured fluid layer. For hydrophobic membranes, a depletion of water molecules occurs near the water/zeolite interface. For both types of membranes, the water structure is independent of the pressure drop established in the system and the flux through the membranes is lower than that observed for the bulk zeolitic material; the latter allows an estimation of surface barrier effects to pressure-driven water transport. Mechanistically, it is observed that (i) bottlenecks form at the windows of the zeolite structure, preventing the free flow of water through the porous membrane, (ii) water molecules do not move through a cage in a single-file fashion but rather exhibit a broad range of residence times and pronounced mixing, and (iii) a periodic buildup of a pressure difference between inlet and outlet cages takes place which leads to the preferential flow of water molecules toward the low-pressure cages. © 2013 American Chemical Society.

Limiter effects on scrape-off layer fluctuations and transport

International Nuclear Information System (INIS)

Thayer, D.R.; Diamond, P.H.; Wootton, A.J.

1987-01-01

Edge turbulence experiments indicate that radial particle flux increases as a function of radius up to the scrape-off layer (SOL), and that the Boltzman relation is violated. Resistivity gradient driven turbulence (RGDT) theory has been shown to track the radial dependence of the particle flux in the plasma edge closer than dissipative density gradient driven turbulence (DDGDT) theory. Also, the Boltzman relation is not invoked for RGDT while it is usually assumed for DDGDT. Consequently, RGDT is a more likely candidate for an edge turbulence model. However, Langmuir probe experiments indicate that the particle flux is reduced by as much as 50% in the SOL. Thus, since basic turbulence theories do not account for limiter effects, the primary focus of this study is to include such effects in a RGDT theory of the SOL. We present an analysis of SOL fluctuations using a rippling mode or RGDT calculation which incorporates the essential limiter boundary condition.(orig./GG)

Spectral decomposition of regulatory thresholds for climate-driven fluctuations in hydro- and wind power availability

Science.gov (United States)

Wörman, A.; Bottacin-Busolin, A.; Zmijewski, N.; Riml, J.

2017-08-01

Climate-driven fluctuations in the runoff and potential energy of surface water are generally large in comparison to the capacity of hydropower regulation, particularly when hydropower is used to balance the electricity production from covarying renewable energy sources such as wind power. To define the bounds of reservoir storage capacity, we introduce a dedicated reservoir volume that aggregates the storage capacity of several reservoirs to handle runoff from specific watersheds. We show how the storage bounds can be related to a spectrum of the climate-driven modes of variability in water availability and to the covariation between water and wind availability. A regional case study of the entire hydropower system in Sweden indicates that the longest regulation period possible to consider spans from a few days of individual subwatersheds up to several years, with an average limit of a couple of months. Watershed damping of the runoff substantially increases the longest considered regulation period and capacity. The high covariance found between the potential energy of the surface water and wind energy significantly reduces the longest considered regulation period when hydropower is used to balance the fluctuating wind power.

Molecular dynamics simulations of Na+/Cl--dependent neurotransmitter transporters in a membrane-aqueous system

DEFF Research Database (Denmark)

Jørgensen, Anne Marie; Tagmose, L.; Jørgensen, A.M.M.

2007-01-01

We have performed molecular dynamics simulations of a homology model of the human serotonin transporter (hSERT) in a membrane environment and in complex with either the natural substrate S-HT or the selective serotonin reuptake inhibitor escitaloprom. We have also included a transporter homologue......, the Aquifex aeolicus leucine transporter (LeuT), in our study to evaluate the applicability of a simple and computationally attractive membrane system. Fluctuations in LeuT extracted from simulations are in good agreement with crystal logrophic B factors. Furthermore, key interactions identified in the X....... Specific interactions responsible for ligand recognition, are identified in the hSERT-5HT and hSERT-escitaloprom complexes. Our finding5 are in good agreement with predictions from mutagenesis studies....

Solvent fluctuations and nuclear quantum effects modulate the molecular hyperpolarizability of water

Science.gov (United States)

Liang, Chungwen; Tocci, Gabriele; Wilkins, David M.; Grisafi, Andrea; Roke, Sylvie; Ceriotti, Michele

2017-07-01

Second-harmonic scattering (SHS) experiments provide a unique approach to probe noncentrosymmetric environments in aqueous media, from bulk solutions to interfaces, living cells, and tissue. A central assumption made in analyzing SHS experiments is that each molecule scatters light according to a constant molecular hyperpolarizability tensor β(2 ). Here, we investigate the dependence of the molecular hyperpolarizability of water on its environment and internal geometric distortions, in order to test the hypothesis of constant β(2 ). We use quantum chemistry calculations of the hyperpolarizability of a molecule embedded in point-charge environments obtained from simulations of bulk water. We demonstrate that both the heterogeneity of the solvent configurations and the quantum mechanical fluctuations of the molecular geometry introduce large variations in the nonlinear optical response of water. This finding has the potential to change the way SHS experiments are interpreted: In particular, isotopic differences between H2O and D2O could explain recent SHS observations. Finally, we show that a machine-learning framework can predict accurately the fluctuations of the molecular hyperpolarizability. This model accounts for the microscopic inhomogeneity of the solvent and represents a step towards quantitative modeling of SHS experiments.

Development of an electrically driven molecular motor.

Science.gov (United States)

Murphy, Colin J; Sykes, E Charles H

2014-10-01

For molecules to be used as components in molecular machinery, methods are required that couple individual molecules to external energy sources in order to selectively excite motion in a given direction. While significant progress has been made in the construction of synthetic molecular motors powered by light and by chemical reactions, there are few experimental examples of electrically driven molecular motors. To this end, we pioneered the use of a new, stable and tunable molecular rotor system based on surface-bound thioethers to comprehensively study many aspects of molecular rotation. As biological molecular motors often operate at interfaces, our synthetic system is especially amenable to microscopic interrogation as compared to solution-based systems. Using scanning tunneling microscopy (STM) and density functional theory, we studied the rotation of surface-bound thioethers, which can be induced either thermally or by electrons from the STM tip in a two-terminal setup. Moreover, the temperature and electron flux can be adjusted to allow each rotational event to be monitored at the molecular scale in real time. This work culminated in the first experimental demonstration of a single-molecule electric motor, where the electrically driven rotation of a butyl methyl sulfide molecule adsorbed on a copper surface could be directionally biased. The direction and rate of the rotation are related to the chirality of both the molecule and the STM tip (which serves as the electrode), illustrating the importance of the symmetry of the metal contacts in atomic-scale electrical devices. Copyright © 2014 The Chemical Society of Japan and Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fluctuating chemohydrodynamics and the stochastic motion of self-diffusiophoretic particles

Science.gov (United States)

Gaspard, Pierre; Kapral, Raymond

2018-04-01

The propulsion of active particles by self-diffusiophoresis is driven by asymmetric catalytic reactions on the particle surface that generate a mechanochemical coupling between the fluid velocity and the concentration fields of fuel and product in the surrounding solution. Because of thermal and molecular fluctuations in the solution, the motion of micrometric or submicrometric active particles is stochastic. Coupled Langevin equations describing the translation, rotation, and reaction of such active particles are deduced from fluctuating chemohydrodynamics and fluctuating boundary conditions at the interface between the fluid and the particle. These equations are consistent with microreversibility and the Onsager-Casimir reciprocal relations between affinities and currents and provide a thermodynamically consistent basis for the investigation of the dynamics of active particles propelled by diffusiophoretic mechanisms.

Patterns and singular features of extreme fluctuational paths of a periodically driven system

International Nuclear Information System (INIS)

Chen, Zhen; Liu, Xianbin

2016-01-01

Large fluctuations of an overdamped periodically driven oscillating system are investigated theoretically and numerically in the limit of weak noise. Optimal paths fluctuating to certain point are given by statistical analysis using the concept of prehistory probability distribution. The validity of statistical results is verified by solutions of boundary value problem. Optimal paths are found to change topologically when terminating points lie at opposite side of a switching line. Patterns of extreme paths are plotted through a proper parameterization of Lagrangian manifold having complicated structures. Several extreme paths to the same point are obtained by multiple solutions of boundary value solutions. Actions along various extreme paths are calculated and associated analysis is performed in relation to the singular features of the patterns. - Highlights: • Both extreme and optimal paths are obtained by various methods. • Boundary value problems are solved to ensure the validity of statistical results. • Topological structure of Lagrangian manifold is considered. • Singularities of the pattern of extreme paths are studied.

Molecular motor transport through hollow nanowires

DEFF Research Database (Denmark)

Lard, Mercy; Ten Siethoff, Lasse; Generosi, Johanna

2014-01-01

-driven motion of fluorescent probes (actin filaments) through 80 nm wide, Al2O 3 hollow nanowires of micrometer length. The motor-driven transport is orders of magnitude faster than would be possible by passive diffusion. The system represents a necessary element for advanced devices based on gliding assays...

ELECTRON TEMPERATURE FLUCTUATIONS AND CROSS-FIELD HEAT TRANSPORT IN THE EDGE OF DIII-D

International Nuclear Information System (INIS)

RUDAKOV, DL; BOEDO, JA; MOYER, RA; KRASENINNIKOV, S; MAHDAVI, MA; McKEE, GR; PORTER, GD; STANGEBY, PC; WATKINS, JG; WEST, WP; WHYTE, DG.

2003-01-01

OAK-B135 The fluctuating E x B velocity due to electrostatic turbulence is widely accepted as a major contributor to the anomalous cross-field transport of particles and heat in the tokamak edge and scrape-off layer (SOL) plasmas. This has been confirmed by direct measurements of the turbulent E x B transport in a number of experiments. Correlated fluctuations of the plasma radial velocity v r , density n, and temperature T e result in time-average fluxes of particles and heat given by (for electrons): Equation 1--Λ r ES = r > = 1/B varφ θ ; Equation 2--Q r ES = e (tilde v) r > ∼ 3/2 kT e Λ r ES + 3 n e /2 B varφ e (tilde E) θ > Q conv + Q cond . The first term in Equation 2 is referred to as convective and the second term as conductive heat flux. Experimental determination of fluxes given by Equations 1 and 2 requires simultaneous measurements of the density, temperature and poloidal electric field fluctuations with high spatial and temporal resolution. Langmuir probes provide most readily available (if not the only) tool for such measurements. However, fast measurements of electron temperature using probes are non-trivial and are not always performed. Thus, the contribution of the T e fluctuations to the turbulent fluxes is usually neglected. Here they report results of the studies of T e fluctuations and their effect on the cross-field transport in the SOL of DIII-D

Core density fluctuations in reverse magnetic shear plasmas with internal transport barrier on JT-60U

International Nuclear Information System (INIS)

Nazikian, R.; Shinohara, K.; Yoshino, R.; Fujita, T.; Shirai, H.; Kramer, G.T.

1999-01-01

First measurements of the radial correlation length of density fluctuations in JT-60U plasmas with internal transport barrier (ITB) is reported. The measurements are obtained using a newly installed correlation reflectometer operating in the upper X-mode. Before transport barrier formation in the low beam power current ramp-up phase of the discharge, reflectometer measurements indicate density fluctuation levels n-tilde/n∼0.1-0.2% and radial correlation lengths 2-3 cm (k r p i ≤0.5) in the central plasma region (r/a r p i ∼3. However, fluctuation levels are considerably higher than measured near the magnetic axis. Reflectometer measurements obtained at the foot of the ITB also indicate high fluctuation levels compared to measurements in the central region of the discharge. (author)

Measurements of fluctuations in the flux of runaway electrons to the PLT limiter

International Nuclear Information System (INIS)

Barnes, C.W.; Strachan, J.D.

1982-07-01

Fluctuations in the flux of runaway electrons to the limiter have been measured during many PLT discharges. Oscillations at 60, 120, and 720 Hz are driven by variations in the vertical magnetic field which moves the plasma major radius. Fluctuations are seen in the range of 2 → 20 kHz due to MHD magnetic islands which extend to the plasma surface. A continuous spectrum of fluctuations is observed up to 200 kHz which correlates with drift-wave turbulence. The magnitude of the driven fluctuations can be used to measure transport properties of the runaway electrons. The amplitude of electron motion due to the MHD and drift-wave oscillations, and hence a measure of the radial size of the instability, can be determined as a function of frequency. The slope of the frequency power spectrum of the drift-wave-induced fluctuations steepens with increasing runaway electron drift orbit displacement during the current drop at the end of the discharge, and as the power in the MHD oscillations increases. A magnetic probe was used to confirm the presence of oscillating magnetic fields capable of perturbing the electron orbits

Turbulent fluctuations and radial transport in the scrape-off layer of the ASDEX tokamak

Energy Technology Data Exchange (ETDEWEB)

Endler, M [Max-Planck-Institut fuer Plasmaphysik, EURATOM Association, 85740 Garching (Germany); Giannone, L. [Max-Planck-Institut fuer Plasmaphysik, EURATOM Association, 85740 Garching (Germany); McCormick, K [Max-Planck-Institut fuer Plasmaphysik, EURATOM Association, 85740 Garching (Germany); Niedermeyer, H [Max-Planck-Institut fuer Plasmaphysik, EURATOM Association, 85740 Garching (Germany); Rudyj, A [Max-Planck-Institut fuer Plasmaphysik, EURATOM Association, 85740 Garching (Germany); Theimer, G [Max-Planck-Institut fuer Plasmaphysik, EURATOM Association, 85740 Garching (Germany); Tsois, N [NCSR ` Demokritos` , Athens (Greece); ASDEX Team

1995-04-01

Electrostatic fluctuations have been measured in the scrape-off layer of ASDEX by Langmuir probes and by observation of H{sub {alpha}} light with high poloidal and temporal resolution. It was demonstrated that these fluctuations contribute a significant, if not dominant, fraction of the ``anomalous`` radial particle transport. A model for an instability mechanism specific to the SOL is presented including density, temperature and electric potential fluctuations. From this model mixing length estimates for the radial transport and resulting density and pressure gradients in the SOL are derived and compared to measurements in the mid-plane and in the divertor of ASDEX. In spite of several simplifications in the model a quantitative agreement up to factors of 1-3 and a qualitative agreement for variations of discharge parameters is achieved between the model predictions and the measurements. ((orig.)).

Turbulent fluctuations and radial transport in the scrape-off layer of the ASDEX tokamak

International Nuclear Information System (INIS)

Endler, M.; Giannone, L.; McCormick, K.; Niedermeyer, H.; Rudyj, A.; Theimer, G.; Tsois, N.

1995-01-01

Electrostatic fluctuations have been measured in the scrape-off layer of ASDEX by Langmuir probes and by observation of H α light with high poloidal and temporal resolution. It was demonstrated that these fluctuations contribute a significant, if not dominant, fraction of the ''anomalous'' radial particle transport. A model for an instability mechanism specific to the SOL is presented including density, temperature and electric potential fluctuations. From this model mixing length estimates for the radial transport and resulting density and pressure gradients in the SOL are derived and compared to measurements in the mid-plane and in the divertor of ASDEX. In spite of several simplifications in the model a quantitative agreement up to factors of 1-3 and a qualitative agreement for variations of discharge parameters is achieved between the model predictions and the measurements. ((orig.))

Energetic-particle-driven instabilities and induced fast-ion transport in a reversed field pinch

International Nuclear Information System (INIS)

Lin, L.; Brower, D. L.; Ding, W. X.; Anderson, J. K.; Capecchi, W.; Eilerman, S.; Forest, C. B.; Koliner, J. J.; Nornberg, M. D.; Reusch, J.; Sarff, J. S.; Liu, D.

2014-01-01

Multiple bursty energetic-particle (EP) driven modes with fishbone-like structure are observed during 1 MW tangential neutral-beam injection in a reversed field pinch (RFP) device. The distinguishing features of the RFP, including large magnetic shear (tending to add stability) and weak toroidal magnetic field (leading to stronger drive), provide a complementary environment to tokamak and stellarator configurations for exploring basic understanding of EP instabilities. Detailed measurements of the EP mode characteristics and temporal-spatial dynamics reveal their influence on fast ion transport. Density fluctuations exhibit a dynamically evolving, inboard-outboard asymmetric spatial structure that peaks in the core where fast ions reside. The measured mode frequencies are close to the computed shear Alfvén frequency, a feature consistent with continuum modes destabilized by strong drive. The frequency pattern of the dominant mode depends on the fast-ion species. Multiple frequencies occur with deuterium fast ions compared to single frequency for hydrogen fast ions. Furthermore, as the safety factor (q) decreases, the toroidal mode number of the dominant EP mode transits from n=5 to n=6 while retaining the same poloidal mode number m=1. The transition occurs when the m=1, n=5 wave-particle resonance condition cannot be satisfied as the fast-ion safety factor (q fi ) decreases. The fast-ion temporal dynamics, measured by a neutral particle analyzer, resemble a classical predator-prey relaxation oscillation. It contains a slow-growth phase arising from the beam fueling followed by a rapid drop when the EP modes peak, indicating that the fluctuation-induced transport maintains a stiff fast-ion density profile. The inferred transport rate is strongly enhanced with the onset of multiple EP modes

Theoretical investigations of molecular wires: Electronic spectra and electron transport

Science.gov (United States)

Palma, Julio Leopoldo

The results of theoretical and computational research are presented for two promising molecular wires, the Nanostar dendrimer, and a series of substituted azobenzene derivatives connected to aluminum electrodes. The electronic absorption spectra of the Nanostar (a phenylene-ethynylene dendrimer attached to an ethynylperylene chromophore) were calculated using a sequential Molecular Dynamics/Quantum Mechanics (MD/QM) method to perform an analysis of the temperature dependence of the electronic absorption process. We modeled the Nanostar as a series of connected units, and performed MD simulations for each chromophore at 10 K and 300 K to study how the temperature affected the structures and, consequently, the spectra. The absorption spectra of the Nanostar were computed using an ensemble of 8000 structures for each chromophore. Quantum Mechanical (QM) ZINDO/S calculations were performed for each conformation in the ensemble, including 16 excited states, for a total of 128,000 excitation energies. The spectral intensity was then scaled linearly with the number of conjugated units. Our calculations for both the individual chromophores and the Nanostar, are in good agreement with experiments. We explain in detail the effects of temperature and the consequences for the absorption process. The second part of this thesis presents a study of the effects of chemical substituents on the electron transport properties of the azobenzene molecule, which has been proposed recently as a component of a light-driven molecular switch. This molecule has two stable conformations (cis and trans) in its electronic ground state, with considerable differences in their conductance. The electron transport properties were calculated using first-principles methods combining non-equilibrium Green's function (NEGF) techniques with density functional theory (DFT). For the azobenzene studies, we included electron-donating groups and electron-withdrawing groups in meta- and ortho-positions with

Quantum Transport Through Tunable Molecular Diodes

KAUST Repository

Obodo, Tobechukwu Joshua

2017-07-31

Employing self-interaction corrected density functional theory combined with the non-equilibrium Green\\'s function method, we study the quantum transport through molecules with different numbers of phenyl (donor) and pyrimidinyl (acceptor) rings in order to evaluate the effects of the molecular composition on the transport properties. Excellent agreement with the results of recent experiments addressing the rectification behavior of molecular junctions is obtained, which demonstrates the potential of quantum transport simulations for designing high performance junctions by tuning the molecular specifications.

Fluid simulations of ∇Te-driven turbulence and transport in boundary plasmas

International Nuclear Information System (INIS)

Xu, X.Q.

1992-01-01

It is clear that the edge plasma plays a crucial role in global tokamak confinement. This paper is a report on simulations of a new drift wave type instability driven by the electron temperature gradient in tokamak scrapeoff-layers (SOL). A 2d fluid code has been developed in order to explore the anomalous transport in the boundary plasmas. The simulation consists of a set of fluid equations for the vorticity ∇ perpendicular 2 φ, the electron density n c and the temperature T c in a shearless plasma slab confined by a uniform, straight magnetic field B z with two divertor (or limiter) plates intercepting the magnetic field. The model has two regions separated by a magnetic separatrix: in the edge region inside the separatrix, the model is periodic along the magnetic field while in the SOL region outside the separatrix, the magnetic field is taken to be of finite length with model boundary conditions at diverter plates. The simulation results show that the observed linear instability agrees well with theory, and that a saturated state of turbulence is reached. In saturated turbulence, clear evidence of the expected long-wavelength mode penetration into the edge is seen, an inverse cascade of wave energy is observed. The simulation results also show that amplitudes of potential and the electron temperature fluctuations are somewhat above and the heat flux are somewhat below those of the simplest mixing-length estimates, and furthermore the large-scale radial structures of fluctuation quantities indicate that the cross-field transport is not diffusive. After saturation, the electron density and temperature profiles are flattened. A self-consistent simulation to determine the microturbulent SOL electron temperature profile has been done, the results of which reasonably agree with the experimental measurements

Diffusive smoothing of surfzone bathymetry by gravity-driven sediment transport

Science.gov (United States)

Moulton, M. R.; Elgar, S.; Raubenheimer, B.

2012-12-01

Gravity-driven sediment transport often is assumed to have a small effect on the evolution of nearshore morphology. Here, it is shown that down-slope gravity-driven sediment transport is an important process acting to smooth steep bathymetric features in the surfzone. Gravity-driven transport can be modeled as a diffusive term in the sediment continuity equation governing temporal (t) changes in bed level (h): ∂h/∂t ≈ κ ▽2h, where κ is a sediment diffusion coefficient that is a function of the bed shear stress (τb) and sediment properties, such as the grain size and the angle of repose. Field observations of waves, currents, and the evolution of large excavated holes (initially 10-m wide and 2-m deep, with sides as steep as 35°) in an energetic surfzone are consistent with diffusive smoothing by gravity. Specifically, comparisons of κ estimated from the measured bed evolution with those estimated with numerical model results for several transport theories suggest that gravity-driven sediment transport dominates the bed evolution, with κ proportional to a power of τb. The models are initiated with observed bathymetry and forced with observed waves and currents. The diffusion coefficients from the measurements and from the model simulations were on average of order 10-5 m2/s, implying evolution time scales of days for features with length scales of 10 m. The dependence of κ on τb varies for different transport theories and for high and low shear stress regimes. The US Army Corps of Engineers Field Research Facility, Duck, NC provided excellent logistical support. Funded by a National Security Science and Engineering Faculty Fellowship, a National Defense Science and Engineering Graduate Fellowship, and the Office of Naval Research.

Changes in transport and confinement in the EXTRAP-T2 reversed field pinch

Science.gov (United States)

Sallander, E.; Sallander, J.; Hedqvist, A.

1999-09-01

At the EXTRAP-T2 reversed field pinch a non-intrusive approach has been undertaken to monitor transport driven by magnetic fluctuations. Correlations are presented between fluctuations observed in the core and at the edge of the plasma. The fluctuations are characterized and their effect on the confinement of core electron energy is estimated.

Changes in transport and confinement in the EXTRAP-T2 reversed field pinch

International Nuclear Information System (INIS)

Sallander, E.; Sallander, J.; Hedqvist, A.

1999-01-01

At the EXTRAP-T2 reversed field pinch a non-intrusive approach has been undertaken to monitor transport driven by magnetic fluctuations. Correlations are presented between fluctuations observed in the core and at the edge of the plasma. The fluctuations are characterized and their effect on the confinement of core electron energy is estimated. (author)

Entropy transport in high-Tc superconductors in the fluctuation regime

International Nuclear Information System (INIS)

Maki, K.

1991-01-01

Making use of the expression for the heat current associated with the space-time-dependent order parameter for the s-wave superconductor, we calculate, in the clean limit, the heat current induced by an electric field. In the absence of a magnetic field we find an extra Peltier coefficient associated with the fluctuations, which diverges logarithmically as the temperature T approaches the transition temperature T c . In the presence of a magnetic field perpendicular to the ab plane, the fluctuation gives rise to the Ettingshausen effect. In a small magnetic field, the corresponding entropy transported by magnetic flux is calculated: left-angle S φ right-angle f =[2π 3 τT/21ζ(3)d](h/var-epsilon)(1 +2α) -1/2 where τ and d are the transport lifetime and the interlayer spacing, ζ(3)=1.202. . ., h=2eξ a 2 B, var-epsilon=ln(T/T c ), and α=2(ξ c /d) 2 var-epsilon -1 . The result is compared with a recent observation of the Ettinghausen effect in a single crystal of YBa 2 Cu 3 O 7

En route to surface-bound electric field-driven molecular motors.

Science.gov (United States)

Jian, Huahua; Tour, James M

2003-06-27

Four caltrop-shaped molecules that might be useful as surface-bound electric field-driven molecular motors have been synthesized. The caltrops are comprised of a pair of electron donor-acceptor arms and a tripod base. The molecular arms are based on a carbazole or oligo(phenylene ethynylene) core with a strong net dipole. The tripod base uses a silicon atom as its core. The legs of the tripod bear sulfur-tipped bonding units, as acetyl-protected benzylic thiols, for bonding to a gold surface. The geometry of the tripod base allows the caltrop to project upward from a metallic surface after self-assembly. Ellipsometric studies show that self-assembled monolayers of the caltrops are formed on Au surfaces with molecular thicknesses consistent with the desired upright-shaft arrangement. As a result, the zwitterionic molecular arms might be controllable when electric fields are applied around the caltrops, thereby constituting field-driven motors.

Report of planning workshop on fluctuations and anomalous transport in tokamaks

Energy Technology Data Exchange (ETDEWEB)

1982-10-01

The workshop was divided into three sections: review of experiments on fluctuations in tokamaks, review of theories of anomalous transport, and discussion of directions for future research and experimental/theoretical collaboration. Each session was assigned a recording secretary to take notes which were used in preparing this report. The report includes the activities, conclusions, and recommendations of the workshop.

Report of planning workshop on fluctuations and anomalous transport in tokamaks

International Nuclear Information System (INIS)

1982-10-01

The workshop was divided into three sections: review of experiments on fluctuations in tokamaks, review of theories of anomalous transport, and discussion of directions for future research and experimental/theoretical collaboration. Each session was assigned a recording secretary to take notes which were used in preparing this report. The report includes the activities, conclusions, and recommendations of the workshop

Predictability and environmental drivers of chlorophyll fluctuations vary across different time scales and regions of the North Sea

Science.gov (United States)

Blauw, Anouk N.; Benincà, Elisa; Laane, Remi W. P. M.; Greenwood, Naomi; Huisman, Jef

2018-02-01

Phytoplankton concentrations display strong temporal variability at different time scales. Recent advances in automated moorings enable detailed investigation of this variability. In this study, we analyzed phytoplankton fluctuations at four automated mooring stations in the North Sea, which measured phytoplankton abundance (chlorophyll) and several environmental variables at a temporal resolution of 12-30 min for two to nine years. The stations differed in tidal range, water depth and freshwater influence. This allowed comparison of the predictability and environmental drivers of phytoplankton variability across different time scales and geographical regions. We analyzed the time series using wavelet analysis, cross correlations and generalized additive models to quantify the response of chlorophyll fluorescence to various environmental variables (tidal and meteorological variables, salinity, suspended particulate matter, nitrate and sea surface temperature). Hour-to-hour and day-to-day fluctuations in chlorophyll fluorescence were substantial, and mainly driven by sinking and vertical mixing of phytoplankton cells, horizontal transport of different water masses, and non-photochemical quenching of the fluorescence signal. At the macro-tidal stations, these short-term phytoplankton fluctuations were strongly driven by the tides. Along the Dutch coast, variation in salinity associated with the freshwater influence of the river Rhine played an important role, while in the central North Sea variation in weather conditions was a major determinant of phytoplankton variability. At time scales of weeks to months, solar irradiance, nutrient conditions and thermal stratification were the dominant drivers of changes in chlorophyll concentrations. These results show that the dominant drivers of phytoplankton fluctuations differ across marine environments and time scales. Moreover, our findings show that phytoplankton variability on hourly to daily time scales should not be

Investigations of transport properties of molten sodium fluoride using molecular dynamics simulations

International Nuclear Information System (INIS)

Chattaraj, D.; Dash, Smruti

2013-01-01

The thermal conductivity and coefficient of shear viscosity of molten sodium fluoride were calculated using Green-Kubo equilibrium molecular dynamics (EMD) simulation. The Green-Kubo method is an equilibrium technique based on the fluctuation-dissipation theorem of statistical thermodynamics. The canonical ensemble (N, V, T) was used in the MD simulation to obtain the transport properties of molten NaF. In this simulation, several state points were investigated using the Born-Meyer-Huggins-Tosi-Fumi interionic potential model. The electrostatic interactions present in this ionic fluid were calculated through the Ewald method. The results obtained in this study were found to be in good agreement with the reported experimental data. (author)

Energy fluctuations in a biharmonically driven nonlinear system

Indian Academy of Sciences (India)

analyse the nature of work and heat fluctuations and show that the steady state fluctuation .... The above equation is the statement of the first law of thermodynamics and ..... One of the authors (AMJ) thanks DST, India for financial support.

ARE THE VARIATIONS IN QUASAR OPTICAL FLUX DRIVEN BY THERMAL FLUCTUATIONS?

International Nuclear Information System (INIS)

Kelly, Brandon C.; Siemiginowska, Aneta; Bechtold, Jill

2009-01-01

We analyze a sample of optical light curves for 100 quasars, 70 of which have black hole mass estimates. Our sample is the largest and broadest used yet for modeling quasar variability. The sources in our sample have z 42 ∼ λ (5100 A) ∼ 46 , and 10 6 ∼ BH /M sun ∼ 10 . We model the light curves as a continuous time stochastic process, providing a natural means of estimating the characteristic timescale and amplitude of quasar variations. We employ a Bayesian approach to estimate the characteristic timescale and amplitude of flux variations; our approach is not affected by biases introduced from discrete sampling effects. We find that the characteristic timescales strongly correlate with black hole mass and luminosity, and are consistent with disk orbital or thermal timescales. In addition, the amplitude of short-timescale variations is significantly anticorrelated with black hole mass and luminosity. We interpret the optical flux fluctuations as resulting from thermal fluctuations that are driven by an underlying stochastic process, such as a turbulent magnetic field. In addition, the intranight variations in optical flux implied by our empirical model are ∼<0.02 mag, consistent with current microvariability observations of radio-quiet quasars. Our stochastic model is therefore able to unify both long- and short-timescale optical variations in radio-quiet quasars as resulting from the same underlying process, while radio-loud quasars have an additional variability component that operates on timescales ∼<1 day.

Electronic and magnetic phase separation in EuB6. Fluctuation spectroscopy and nonlinear transport

International Nuclear Information System (INIS)

Amyan, Adham

2013-01-01

The main topics of this thesis are electrical, stationary, and time-resolved transport measurements on EuB 6 as well as the further development of measuring methods and analysis procedures of the fluctuation spectroscopy. The first part of this thesis was dedicated to the further development of the already known measuring methods under application of a fast data-acquisition card. The second part deals with the electrical transport properties of EuB 6 and the understanding of the coupling between charge and magnetic degrees of freedom. By means of resistance and nonlinear-transport measurements as well as fluctuation spectroscopy hypotheses of other scientists were systematically verified as well as new knowledge obtained. The magnetoresistance was studied as function of the temperature in small external magnetic fields between 1 mT and 700 mT. Measurements of the third harmonic resistance as function of the temperature show maxima at T MI and T C . Electrical-resistance fluctuations were measured without external magnetic field between 5 and 100 K as well in presence of a magnetic field between 18 K and 32 K. At constant temperature measurements of the spectral power density in external magnetic fields were performed in the temperature range from 18 K to 32 K. Highly resolving measurements of the thermal expansion coefficient showed a very strong coupling of the magnetic (polaronic) degrees of freedom to the crystal lattice.

Experimental study of particle transport and density fluctuation in LHD

International Nuclear Information System (INIS)

Tanaka, K.; Morita, S.; Sanin, A.; Michael, C.; Kawahata, K.; Yamada, H.; Miyazawa, J.; Tokuzawa, T.; Akiyama, T.; Goto, M.; Ida, K.; Yoshinuma, M.; Narihara, K.; Yamada, I.; Yokoyama, M.; Masuzaki, S.; Morisaki, T.; Sakamoto, R.; Funaba, H.; Komori, A.; Vyacheslavov, L.N.; Murakami, S.; Wakasa, A.

2005-01-01

A variety of electron density (n e ) profiles have been observed in Large Helical Device (LHD). The density profiles change dramatically with heating power and toroidal magnetic field (B t ) under the same line averaged density. The particle transport coefficients, i.e., diffusion coefficient (D) and convection velocity (V) are experimentally obtained from density modulation experiments in the standard configuration. The values of D and V are estimated separately at the core and edge. The diffusion coefficients are strong function of electron temperature (T e ) and are proportional to T e 1.7±0.9 in core and T e 1.1±0.14 in edge. And edge diffusion coefficients are proportional to B t -2.08 . It is found that the scaling of D in edge is close to gyro-Bohm-like in nature. The existence of non-zero V is observed. It is observed that the electron temperature (T e ) gradient can drive particle convection. This is particularly clear in the core region. The convection velocity in the core region reverses direction from inward to outward as the T e gradient increases. In the edge, the convection is inward directed in the most of the case of the present data set. And it shows modest tendency, whose value is proportional to T e gradient keeping inward direction. However, the toroidal magnetic field also significantly affects value and direction of V. The spectrum of density fluctuation changes at different heating power suggesting that it has an influence on particle transport. The peak wavenumber is around 0.1 times the inversed ion Larmor radius, as is expected from gyro-Bohm diffusion. The peaks of fluctuation intensity are localized at the plasma edge, where density gradient becomes negative and diffusion contributes most to the particle flux. These results suggest a qualitative correlation of fluctuations with particle diffusion. (author)

Experimental study of particle transport and density fluctuation in LHD

International Nuclear Information System (INIS)

Tanaka, K.; Michael, C.; Sanin, A.

2005-01-01

A variety of electron density (n e ) profiles have been observed in Large Helical Device (LHD). The density profiles change dramatically with heating power and toroidal magnetic field (B t ) under the same line averaged density. The particle transport coefficients, i.e., diffusion coefficient (D) and convection velocity (V) are experimentally obtained in the standard configuration from density modulation experiments. The values of D and V are estimated separately in the core and edge. The diffusion coefficients are found to be a strong function of electron temperature (T e ) and are proportional to T e 1.7±0.9 in the core and T e 1.1±0.14 in the edge. Edge diffusion coefficients are proportional to B t -2.08 . It is found that the scaling of D in the edge is close to gyro-Bohm-like in nature. Non-zero V is observed and it is found that the electron temperature gradient can drive particle convection, particularly in the core region. The convection velocity in the core reverses direction from inward to outward as the T e gradient increases. In the edge, convection is inward directed in most cases of the present data set. It shows a modest tendency, being proportional to T e gradient and remaining inward directed. However, the toroidal magnetic field also significantly affects the value and direction of V. The density fluctuation spectrum varies with heating power suggesting that it has an influence on particle transport. The value of K sub(perpendicular) ρ i is around 0.1, as expected for gyro-Bohm diffusion. Fluctuations are localized in both positive and negative density gradient regions of the hollow density profiles. The fluctuation power in each region is clearly distinguished having different phase velocity profiles. (author)

Edge turbulence and transport: Text and ATF modeling

International Nuclear Information System (INIS)

Ritz, C.P.; Rhodes, T.L.; Lin, H.; Rowan, W.L.; Bengtson, R.; Wootton, A.J.; Diamond, P.H.; Ware, A.S.; Thayer, D.R.

1990-01-01

We present experimental results on edge turbulence and transport from the tokamak TEXT and the torsatron ATF. The measured electrostatic fluctuations can explain the edge transport of particles and energy. Certain drive (radiation) and stabilizing (velocity shear) terms are suggested by the results. The experimental fluctuation levels and spectral widths can be reproduced by considering the nonlinear evolution of the reduced MHD equations, incorporating a thermal drive from line radiation. In the tokamak limit (with toroidal electric field) the model corresponds to the resistivity gradient mode, while in the currentless torsatron or stellarator limit it corresponds to a thermally driven drift wave

Electron and Phonon Transport in Molecular Junctions

DEFF Research Database (Denmark)

Li, Qian

Molecular electronics provide the possibility to investigate electron and phonon transport at the smallest imaginable scale, where quantum effects can be investigated and exploited directly in the design. In this thesis, we study both electron transport and phonon transport in molecular junctions....... The system we are interested in here are π-stacked molecules connected with two semi-infinite leads. π-stacked aromatic rings, connected via π-π electronic coupling, provides a rather soft mechanical bridge while maintaining high electronic conductivity. We investigate electron transport...... transmission at the Fermi energy. We propose and analyze a way of using π   stacking to design molecular junctions to control heat transport. We develop a simple model system to identify optimal parameter regimes and then use density functional theory (DFT) to extract model parameters for a number of specific...

Measurement of magnetic fluctuation induced energy transport

International Nuclear Information System (INIS)

Fiksel, G.; Prager, S.C.; Shen, W.; Stoneking, M.

1993-11-01

The local electron energy flux produced by magnetic fluctuations has been measured directly in the MST reversed field pinch (over the radial range r/a > 0.75). The flux, produced by electrons traveling parallel to a fluctuating magnetic field, is obtained from correlation between the fluctuations in the parallel heat flux and the radial magnetic field. The fluctuation induced flux is large (100 kW/cm 2 ) in the ''core'' (r/a 2 ) in the edge

Currents and fluctuations of quantum heat transport in harmonic chains

International Nuclear Information System (INIS)

Motz, T; Ankerhold, J; Stockburger, J T

2017-01-01

Heat transport in open quantum systems is particularly susceptible to the modeling of system–reservoir interactions. It thus requires us to consistently treat the coupling between a quantum system and its environment. While perturbative approaches are successfully used in fields like quantum optics and quantum information, they reveal deficiencies—typically in the context of thermodynamics, when it is essential to respect additional criteria such as fluctuation-dissipation theorems. We use a non-perturbative approach for quantum dissipative dynamics based on a stochastic Liouville–von Neumann equation to provide a very general and extremely efficient formalism for heat currents and their correlations in open harmonic chains. Specific results are derived not only for first- but also for second-order moments, which requires us to account for both real and imaginary parts of bath–bath correlation functions. Spatiotemporal patterns are compared with weak coupling calculations. The regime of stronger system–reservoir couplings gives rise to an intimate interplay between reservoir fluctuations and heat transfer far from equilibrium. (paper)

Asymmetric Synthesis of Second-Generation Light-Driven Molecular Motors

NARCIS (Netherlands)

van Leeuwen, Thomas; Danowski, Wojciech; Otten, Edwin; Wezenberg, Sander J; Feringa, Ben L

2017-01-01

The enantiomeric homogeneity of light-driven molecular motors based on overcrowded alkenes is crucial in their application as either unidirectional rotors or as chiral multistate switches. It was challenging to obtain these compounds as single enantiomers via the established synthetic procedures due

Escape routes, weak links, and desynchronization in fluctuation-driven networks

DEFF Research Database (Denmark)

Schäfer, Benjamin; Matthiae, Moritz; Zhang, Xiaozhu

2017-01-01

Shifting our electricity generation from fossil fuel to renewable energy sources introduces large fluctuations to the power system. Here, we demonstrate how increased fluctuations, reduced damping, and reduced intertia may undermine the dynamical robustness of power grid networks. Focusing...... on fundamental noise models, we derive analytic insights into which factors limit the dynamic robustness and how fluctuations may induce a system escape from an operating state. Moreover, we identify weak links in the grid that make it particularly vulnerable to fluctuations. These results thereby not only...

Molecular electronic junction transport

DEFF Research Database (Denmark)

Solomon, Gemma C.; Herrmann, Carmen; Ratner, Mark

2012-01-01

Whenasinglemolecule,oracollectionofmolecules,isplacedbetween two electrodes and voltage is applied, one has a molecular transport junction. We discuss such junctions, their properties, their description, and some of their applications. The discussion is qualitative rather than quantitative, and f...

Fluctuation-driven directional flow of energy in biochemical cycle: Electric activation of Na,K ATPase

Science.gov (United States)

Yow Tsong, Tian

1998-03-01

Na,K ATPase is an ion pump which uses chemical bond energy of ATP to pump Na ion out of, and K ion into living cell thus maintaining ionic and osmotic balances of the cell. Both are uphill transport reactions. Surprisingly we have found that electric energy can also substitute chemical energy to fuel the pump activity. However, in this case only electric fields of certain waveforms, amplitudes, and frequencies are effective. Waveform, amplitude and frequency are three elements of signal. In other words, Na,K ATPase can recognize, process, and harvest energy from an oscillating or a fluctuating electric field to drive an endergonic reaction. The enzyme is a molecular transducer of electric signal. This report will describe electric activation experiment to define electric signal. Electric signal will then mixed with electric noise of broad power spectrum for experiment. Effect of white noise (WN) on the efficiency of Na,K ATPase will be investigated. It will be shown that WN of appropriate power level can improve the pump efficiency when a sub-optimal electric field is used. WN can also carry a sub-threshold signal to cross over the threshold. Stochastic resonance will be discussed in reference to these observations.

Transport reduction via shear flow modification of the cross phase

International Nuclear Information System (INIS)

Ware, A.S.; Terry, P.W.; Diamond, P.H.; Carreras, B.A.

1996-01-01

As a model example of the effect of E x B shear flow on the cross phase between electrostatic potential and pressure fluctuations, a nonlinear theory of resistive pressure gradient driven turbulence (RPGDT) in a shear flow is presented. This work builds on numerical studies of RPGDT, which have shown that both flow shear and curvature can affect the cross phase as well as the fluctuation levels. In this work, we show that the effect of shear flow on transport can be expressed through the temporal response of pressure to potential. It is shown heuristically that even in the case where the fluctuation levels are not modified, the flow shear still acts to reduce the phase angle between potential and pressure fluctuations, thereby suppressing transport. The scaling of the cross phase with flow shear and flow curvature is presented. (author)

Local synaptic signaling enhances the stochastic transport of motor-driven cargo in neurons

KAUST Repository

Newby, Jay; Bressloff, Paul C

2010-01-01

The tug-of-war model of motor-driven cargo transport is formulated as an intermittent trapping process. An immobile trap, representing the cellular machinery that sequesters a motor-driven cargo for eventual use, is located somewhere within a

Particle transport and fluctuation characteristics around neoclassically optimized configurations in LHD

International Nuclear Information System (INIS)

Tanaka, K.; Michael, C.; Vyacheslavov, L.N.

2008-01-01

Density profiles in LHD were measured and particle transport coefficients were estimated from density modulation experiments in LHD. The data set contains the wide region of discharge condition. The dataset of different magnetic axis, toroidal magnetic field and heating power provided data set of widely scanned neoclassical transport. At minimized neoclassical transport configuration in the dataset (Rax=3.5m, Bt=2.8T) showed peaked density profile. Its peaking factor increased gradually with decrease of collisional frequency. This is a similar result observed in tokamak data base. At other configuration, peaking factor reduced with decrease of collisional frequency. Data set showed that larger contribution of neoclassical transport produced hollowed density profile. Comparison between neoclassical and experimental estimated particle diffusivity showed different minimum condition. This suggests neoclassical optimization is not same as anomalous optimization. Clear difference of spatial profile of turbulence was observed between hollowed and peaked density profiles. Major part of fluctuation existed in the unstable region of linear growth rate of ion temperature gradient mode. (author)

Interwell Connectivity Evaluation Using Injection and Production Fluctuation Data

Science.gov (United States)

Shang, Barry Zhongqi

-off between processivity and jamming. Highly processive enzymes cleave a large fraction of a glucan chain during each processive run but are prone to jamming at obstacles. Less processive enzymes avoid jamming but cleave only a small fraction of a chain. Optimizing this trade-off maximizes the cellulose conversion rate. We also elucidate the molecular-scale kinetic origins for synergy among cellulases in enzyme mixtures. In contrast to the currently accepted theory, we show that the ability of an endoglucanase to increase the concentration of chain ends for exoglucanases is insufficient for synergy to occur. Rather, endoglucanases must enhance the rate of complexation between exoglucanases and the newly created chain ends. This enhancement occurs when the endoglucanase is able to partially decrystallize the cellulose surface. We show generally that the driving forces for complexation and jamming, which govern the kinetics of pure exoglucanases, also control the degree of synergy in endo-exo mixtures. In Part II, we focus our attention on a different multiscale problem. This challenge is the development of coarse-grained models from atomistic models to access larger length- and time-scales in a simulation. This problem is difficult because it requires a delicate balance between maintaining (1) physical simplicity in the coarse-grained model and (2) physical consistency with the atomistic model. To achieve these goals, we develop a scheme to coarse-grain an atomistic fluid model into a fluctuating hydrodynamics (FHD) model. The FHD model describes the solvent as a field of fluctuating mass, momentum, and energy densities. The dynamics of the fluid are governed by continuum balance equations and fluctuation-dissipation relations based on the constitutive transport laws. The incorporation of both macroscopic transport and microscopic fluctuation phenomena could provide richer physical insight into the behaviors of biophysical systems driven by hydrodynamic fluctuations, such as

The role of fluctuation-induced transport in a toroidal plasma with strong radial electric fields

Science.gov (United States)

Roth, J. R.; Krawczonek, W. M.; Powers, E. J.; Hong, J. Y.; Kim, Y. C.

1981-01-01

Previous work employing digitally implemented spectral analysis techniques is extended to demonstrate that radial fluctuation-induced transport is the dominant ion transport mechanism in an electric field dominated toroidal plasma. Such transport can be made to occur against a density gradient, and hence may have a very beneficial effect on confinement in toroidal plasmas of fusion interest. It is shown that Bohm or classical diffusion down a density gradient, the collisional Pedersen-current mechanism, and the collisionless electric field gradient mechanism described by Cole (1976) all played a minor role, if any, in the radial transport of this plasma.

Models of charge transport and transfer in molecular switch tunnel junctions of bistable catenanes and rotaxanes

International Nuclear Information System (INIS)

Flood, Amar H.; Wong, Eric W.; Stoddart, J. Fraser

2006-01-01

The processes by which charge transfer can occur play a foundational role in molecular electronics. Here we consider simplified models of the transfer processes that could be present in bistable molecular switch tunnel junction (MSTJ) devices during one complete cycle of the device from its low- to high- and back to low-conductance state. The bistable molecular switches, which are composed of a monolayer of either switchable catenanes or rotaxanes, exist in either a ground-state co-conformation or a metastable one in which the conduction properties of the two co-conformations, when measured at small biases (+0.1 V), are significantly different irrespective of whether transport is dominated by tunneling or hopping. The voltage-driven generation (±2 V) of molecule-based redox states, which are sufficiently long-lived to allow the relative mechanical movements necessary to switch between the two co-conformations, rely upon unequal charge transfer rates on to and/or off of the molecules. Surface-enhanced Raman spectroscopy has been used to image the ground state of the bistable rotaxane in MSTJ-like devices. Consideration of these models provide new ways of looking at molecular electronic devices that rely, not only on nanoscale charge-transport, but also upon the bustling world of molecular motion in mechanically interlocked bistable molecules

Neutron fluctuations in accelerator driven and power reactors via backward master equations

International Nuclear Information System (INIS)

Zhifeng Kuang

2000-05-01

The transport of neutrons in a reactor is a random process, and thus the number of neutrons in a reactor is a random variable. Fluctuations in the number of neutrons in a reactor can be divided into two categories, namely zero noise and power reactor noise. As the name indicates, they dominate (i.e. are observable) at different power levels. The reasons for their occurrences and utilization are also different. In addition, they are described via different mathematical tools, namely master equations and the Langevin equation, respectively. Zero noise carries information about some nuclear properties such as reactor reactivity. Hence methods such as Feynman- and Rossi-alpha methods have been established to determine the subcritical reactivity of a subcritical system. Such methods received a renewed interest recently with the advent of the so-called accelerator driven systems (ADS). Such systems, intended to be used either for energy production or transuranium transmutation, will use a subcritical core with a strong spallation source. A spallation source has statistical properties that are different from those of the traditionally used radioactive sources which were also assumed in the derivation of the Feynman- and Rossi-alpha formulae. Therefore it is necessary to re-derive the Feynman- and Rossi-alpha formulae. Such formulae for ADS have been derived recently but in simpler neutronic models. One subject of this thesis is the extension of such formulae to a more general case in which six groups of delayed neutron precursors are taken into account, and the full joint statistics of the prompt and all delayed groups is included. The involved complexity problems are solved with a combination of effective analytical techniques and symbolic algebra codes. Power reactor noise carries information about parametric perturbation of the system. Langevin technique has been used to extract such information. In such a treatment, zero noise has been neglected. This is a pragmatic

Non-diffusive transport in 3-D pressure driven plasma turbulence

International Nuclear Information System (INIS)

Del-Castillo-Negrete, D.; Carreras, B.A.; Lynch, V.

2005-01-01

Numerical evidence of non-diffusive transport in 3-dimensional, resistive, pressure-gradient-driven plasma turbulence is presented. It is shown that the probability density function (pdf) of tracers is strongly non-Gaussian and exhibits algebraic decaying tails. To describe these results, a transport model using fractional derivative operators in proposed. The model incorporates in a unified way non-locality (i.e., non-Fickian transport), memory effects (i.e., non-Markovian transport), and non-diffusive scaling features known to be present in fusion plasmas. There is quantitative agreement between the model and the turbulent transport numerical calculations. In particular, the model reproduces the shape and space-time scaling of the pdf, and the super-diffusive scaling of the moments. (author)

Understanding charge transport in molecular electronics.

Science.gov (United States)

Kushmerick, J J; Pollack, S K; Yang, J C; Naciri, J; Holt, D B; Ratner, M A; Shashidhar, R

2003-12-01

For molecular electronics to become a viable technology the factors that control charge transport across a metal-molecule-metal junction need to be elucidated. We use an experimentally simple crossed-wire tunnel junction to interrogate how factors such as metal-molecule coupling, molecular structure, and the choice of metal electrode influence the current-voltage characteristics of a molecular junction.

Transport Coefficients from Large Deviation Functions

OpenAIRE

Gao, Chloe Ya; Limmer, David T.

2017-01-01

We describe a method for computing transport coefficients from the direct evaluation of large deviation functions. This method is general, relying on only equilibrium fluctuations, and is statistically efficient, employing trajectory based importance sampling. Equilibrium fluctuations of molecular currents are characterized by their large deviation functions, which are scaled cumulant generating functions analogous to the free energies. A diffusion Monte Carlo algorithm is used to evaluate th...

Particle transport patterns of short-distance soil erosion by wind-driven rain, rain and wind

Science.gov (United States)

Marzen, Miriam; Iserloh, Thomas; de Lima, João L. M. P.; Ries, Johannes B.

2015-04-01

Short distance erosion of soil surface material is one of the big question marks in soil erosion studies. The exact measurement of short-distance transported soil particles, prior to the occurrence of overland flow, is a challenge to soil erosion science due to the particular requirements of the experimental setup and test procedure. To approach a quantification of amount and distance of each type of transport, we applied an especially developed multiple-gutter system installed inside the Trier Portable Wind and Rainfall Simulator (PWRS). We measured the amount and travel distance of soil particles detached and transported by raindrops (splash), wind-driven rain (splash-saltation and splash-drift) and wind (saltation). The test setup included three different erosion agents (rain/ wind-driven rain/ wind), two substrates (sandy/ loamy), three surface structures (grain roughness/ rills lengthwise/ rills transversal) and three slope angles (0°/+7°/-7°). The results present detailed transport patterns of the three erosion agents under the varying soil and surface conditions up to a distance of 1.6 m. Under the applied rain intensity and wind velocity, wind-driven rain splash generates the highest erosion. The erodibility and travel distance of the two substrates depend on the erosion agent. The total erosion is slightly higher for the slope angle -7° (downslope), but for wind-driven rain splash, the inclination is not a relevant factor. The effect of surface structures (rills) changes with traveling distance. The wind driven rain splash generates a much higher amount of erosion and a further travel distance of the particles due to the combined action of wind and rain. The wind-driven rain factor appears to be much more significant than the other factors. The study highlights the effects of different erosion agents and surface parameters on short-distance particle transport and the powerful impact of wind-driven rain on soil erosion.

Physics of Intrinsic Rotation in Flux-Driven ITG Turbulence

International Nuclear Information System (INIS)

Ku, S.; Abiteboul, J.; Dimond, P.H.; Dif-Pradalier, G.; Kwon, J.M.; Sarazin, Y.; Hahm, T.S.; Garbet, X.; Chang, C.S.; Latu, G.; Yoon, E.S.; Ghendrih, Ph.; Yi, S.; Strugarek, A.; Solomon, W.; Grandgirard, V.

2012-01-01

Global, heat flux-driven ITG gyrokinetic simulations which manifest the formation of macroscopic, mean toroidal flow profiles with peak thermal Mach number 0.05, are reported. Both a particle-in-cell (XGC1p) and a semi-Lagrangian (GYSELA) approach are utilized without a priori assumptions of scale-separation between turbulence and mean fields. Flux-driven ITG simulations with different edge flow boundary conditions show in both approaches the development of net unidirectional intrinsic rotation in the co-current direction. Intrinsic torque is shown to scale approximately linearly with the inverse scale length of the ion temperature gradient. External momentum input is shown to effectively cancel the intrinsic rotation profile, thus confirming the existence of a local residual stress and intrinsic torque. Fluctuation intensity, intrinsic torque and mean flow are demonstrated to develop inwards from the boundary. The measured correlations between residual stress and two fluctuation spectrum symmetry breakers, namely E x B shear and intensity gradient, are similar. Avalanches of (positive) heat flux, which propagate either outwards or inwards, are correlated with avalanches of (negative) parallel momentum flux, so that outward transport of heat and inward transport of parallel momentum are correlated and mediated by avalanches. The probability distribution functions of the outward heat flux and the inward momentum flux show strong structural similarity

Interaction of bootstrap-current-driven magnetic islands

International Nuclear Information System (INIS)

Hegna, C.C.; Callen, J.D.

1991-10-01

The formation and interaction of fluctuating neoclassical pressure gradient driven magnetic islands is examined. The interaction of magnetic islands produces a stochastic region around the separatrices of the islands. This interaction causes the island pressure profile to be broadened, reducing the island bootstrap current and drive for the magnetic island. A model is presented that describes the magnetic topology as a bath of interacting magnetic islands with low to medium poloidal mode number (m congruent 3-30). The islands grow by the bootstrap current effect and damp due to the flattening of the pressure profile near the island separatrix caused by the interaction of the magnetic islands. The effect of this sporadic growth and decay of the islands (''magnetic bubbling'') is not normally addressed in theories of plasma transport due to magnetic fluctuations. The nature of the transport differs from statistical approaches to magnetic turbulence since the radial step size of the plasma transport is now given by the characteristic island width. This model suggests that tokamak experiments have relatively short-lived, coherent, long wavelength magnetic oscillations present in the steep pressure-gradient regions of the plasma. 42 refs

Molecular dynamics simulations of the penetration lengths: application within the fluctuation theory for diffusion coefficients

DEFF Research Database (Denmark)

Galliero, Guillaume; Medvedev, Oleg; Shapiro, Alexander

2005-01-01

A 322 (2004) 151). In the current study, a fast molecular dynamics scheme has been developed to determine the values of the penetration lengths in Lennard-Jones binary systems. Results deduced from computations provide a new insight into the concept of penetration lengths. It is shown for four different...... 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....

Transport Coefficients from Large Deviation Functions

Directory of Open Access Journals (Sweden)

Chloe Ya Gao

2017-10-01

Full Text Available We describe a method for computing transport coefficients from the direct evaluation of large deviation functions. This method is general, relying on only equilibrium fluctuations, and is statistically efficient, employing trajectory based importance sampling. Equilibrium fluctuations of molecular currents are characterized by their large deviation functions, which are scaled cumulant generating functions analogous to the free energies. A diffusion Monte Carlo algorithm is used to evaluate the large deviation functions, from which arbitrary transport coefficients are derivable. We find significant statistical improvement over traditional Green–Kubo based calculations. The systematic and statistical errors of this method are analyzed in the context of specific transport coefficient calculations, including the shear viscosity, interfacial friction coefficient, and thermal conductivity.

Transport Coefficients from Large Deviation Functions

Science.gov (United States)

Gao, Chloe; Limmer, David

2017-10-01

We describe a method for computing transport coefficients from the direct evaluation of large deviation function. This method is general, relying on only equilibrium fluctuations, and is statistically efficient, employing trajectory based importance sampling. Equilibrium fluctuations of molecular currents are characterized by their large deviation functions, which is a scaled cumulant generating function analogous to the free energy. A diffusion Monte Carlo algorithm is used to evaluate the large deviation functions, from which arbitrary transport coefficients are derivable. We find significant statistical improvement over traditional Green-Kubo based calculations. The systematic and statistical errors of this method are analyzed in the context of specific transport coefficient calculations, including the shear viscosity, interfacial friction coefficient, and thermal conductivity.

Periodic thermodynamics of laser-driven molecular motor

International Nuclear Information System (INIS)

Li Dan; Zheng Wenwei; Wang Zhisong

2008-01-01

Operation of a laser-driven nano-motor inevitably generates a non-trivial amount of heat, which can possibly lead to instability or even hinder the motor's continual running. This work quantitatively examines the overheating problem for a recently proposed laser-operated molecular locomotive. We present a single-molecule cooling theory, in which molecular details of the locomotive system are explicitly treated. This theory is able to quantitatively predict cooling efficiency for various candidates of molecular systems for the locomotive, and also suggests concrete strategies for improving the locomotive's cooling. It is found that water environment is able to cool the hot locomotive down to room temperature within 100 picoseconds after photon absorption. This cooling time is a few orders of magnitude shorter than the typical time for laser operation, effectively preventing any overheating for the nano-locomotive. However, when the cooling is less effective in non-aqueous environment, residual heat may build up. A continuous running of the motor will then lead to a periodic thermodynamics, which is a common character of many laser-operated nano-devices

Mesoscopic conductance fluctuations in high-T{sub c} grain boundary Josephson junctions: Coherent quasiparticle transport

Energy Technology Data Exchange (ETDEWEB)

Tafuri, F. [Dip. Ingegneria dell' Informazione, Seconda Universita di Napoli, 81031 Aversa (Italy); CNR-INFM Coherentia, Dip. Scienze Fisiche, Universita di Napoli Federico II, 80125 Naples (Italy)], E-mail: tafuri@na.infn.it; Tagliacozzo, A.; Born, D.; Stornaiuolo, D. [CNR-INFM Coherentia, Dip. Scienze Fisiche, Universita di Napoli Federico II, 80125 Naples (Italy); Gambale, E.; Dalena, D. [Dip. Ingegneria dell' Informazione, Seconda Universita di Napoli, 81031 Aversa (Italy); Lombardi, F. [Department of Microelectronics and Nanoscience, MINA, Chalmers University of Technology, 41296 Goeteborg (Sweden)

2007-09-01

Magneto-fluctuations of the normal resistance R{sub N} have been reproducibly observed in YBa{sub 2}Cu{sub 3}O{sub 7-{delta}} (HTS) biepitaxial grain boundary junctions at low temperatures. We attribute them to mesoscopic transport in narrow channels across the grain boundary line. The Thouless energy appears to be the relevant energy scale. Possible implications on the understanding of coherent transport of quasiparticles in HTS and of the dissipation mechanisms are discussed.

Core fluctuations and current profile dynamics in the MST reversed-field pinch

International Nuclear Information System (INIS)

Brower, D.L.; Ding, W.X.; Lei, J.

2003-01-01

First measurements of the current density profile, magnetic field fluctuations and electrostatic (e.s.) particle flux in the core of a high-temperature reversed-field pinch (RFP) are presented. We report three new results: (1) The current density peaks during the slow ramp phase of the sawtooth cycle and flattens promptly at the crash. Profile flattening can be linked to magnetic relaxation and the dynamo which is predicted to drive anti-parallel current in the core. Measured core magnetic fluctuations are observed to increases four-fold at the crash. Between sawtooth crashes, measurements indicate the particle flux driven by e.s. fluctuations is too small to account for the total radial particle flux. (2) Core magnetic fluctuations are observed to decrease at least twofold in plasmas where energy confinement time improves ten-fold. In this case, the radial particle flux is also reduced, suggesting core e.s. fluctuation-induced transport may play role in confinement. (3) The parallel current density increases in the outer region of the plasma during high confinement, as expected, due to the applied edge parallel electric field. However, the core current density also increases due to dynamo reduction and the emergence of runaway electrons. (author)

The dynamics of marginality and self-organized criticality as a paradigm for turbulent transport

International Nuclear Information System (INIS)

Newman, D.E.; Carreras, B.A.; Diamond, P.H.; Hahm, T.S.

1995-01-01

A general paradigm, based on the concept of self-organized criticality (SOC), for turbulent transport in magnetically confined plasmas has been recently suggested as an explanation for some of the apparent discrepancies between most theoretical models of turbulent transport and experimental observations of the transport in magnetically confined plasmas. This model describes the dynamics of the transport without relying on the underlying local fluctuation mechanisms. Computations based on a cellular automata realization of such a model have found that noise driven SOC systems can maintain average profiles that are linearly stable (submarginal) and yet are able to sustain active transport dynamics. It is also found that the dominant scales in the transport dynamics in the absence of sheared flow are system scales rather than the underlying local fluctuation scales. The addition of sheared flow into the dynamics leads to a large reduction of the system-scale transport events and a commensurate increase in the fluctuation-scale transport events needed to maintain the constant flux. The dynamics of these models and the potential ramifications for transport studies are discussed

Note: Local thermal conductivities from boundary driven non-equilibrium molecular dynamics simulations

International Nuclear Information System (INIS)

Bresme, F.; Armstrong, J.

2014-01-01

We report non-equilibrium molecular dynamics simulations of heat transport in models of molecular fluids. We show that the “local” thermal conductivities obtained from non-equilibrium molecular dynamics simulations agree within numerical accuracy with equilibrium Green-Kubo computations. Our results support the local equilibrium hypothesis for transport properties. We show how to use the local dependence of the thermal gradients to quantify the thermal conductivity of molecular fluids for a wide range of thermodynamic states using a single simulation

Nonadiabaticity and single-electron transport driven by surface acoustic waves

DEFF Research Database (Denmark)

Flensberg, Karsten; Niu, Q.; Pustilnik, M.

1999-01-01

Single-electron transport driven by surface acoustic waves (SAW) through a narrow constriction, formed in a two-dimensional electron gas, is studied theoretically. Due to long-range Coulomb interaction, the tunneling coupling between the electron gas and the moving minimum of the SAW...

Nonequilibrium fluctuations in a resistor.

Science.gov (United States)

Garnier, N; Ciliberto, S

2005-06-01

In small systems where relevant energies are comparable to thermal agitation, fluctuations are of the order of average values. In systems in thermodynamical equilibrium, the variance of these fluctuations can be related to the dissipation constant in the system, exploiting the fluctuation-dissipation theorem. In nonequilibrium steady systems, fluctuations theorems (FT) additionally describe symmetry properties of the probability density functions (PDFs) of the fluctuations of injected and dissipated energies. We experimentally probe a model system: an electrical dipole driven out of equilibrium by a small constant current I, and show that FT are experimentally accessible and valid. Furthermore, we stress that FT can be used to measure the dissipated power P = R I2 in the system by just studying the PDFs' symmetries.

Density Fluctuation in Aqueous Solutions and Molecular Origin of Salting-Out Effect for CO2

International Nuclear Information System (INIS)

Ho, Tuan Anh; Ilgen, Anastasia

2017-01-01

Using molecular dynamics simulation, we studied the density fluctuations and cavity formation probabilities in aqueous solutions and their effect on the hydration of CO 2 . With increasing salt concentration, we report an increased probability of observing a larger than the average number of species in the probe volume. Our energetic analyses indicate that the van der Waals and electrostatic interactions between CO 2 and aqueous solutions become more favorable with increasing salt concentration, favoring the solubility of CO 2 (salting in). However, due to the decreasing number of cavities forming when salt concentration is increased, the solubility of CO 2 decreases. The formation of cavities was found to be the primary control on the dissolution of gas, and is responsible for the observed CO 2 salting-out effect. Finally, our results provide the fundamental understanding of the density fluctuation in aqueous solutions and the molecular origin of the salting-out effect for real gas.

TEM heat transport and fluctuations in the HSX stellarator: experiments and comparison with gyrokinetic simulation

Science.gov (United States)

Smoniewski, J.; Faber, B. J.; Sánchez, E.; Calvo, I.; Pueschel, M. J.; Likin, K. M.; Deng, C. B.; Talmadge, J. N.

2017-10-01

The Helically Symmetric eXperiment (HSX) has demonstrated reduced neoclassical transport in the plasma core with quasi-symmetry [Lore Thesis 2010], while outside this region the electron thermal diffusivity is well above the neoclassical level, likely due to the Trapped Electron Mode (TEM) [Weir PoP 2015, Faber PoP 2015]. We compare gyrokinetic simulations of the TEM to experimental heat flux and density fluctuation measurements for two configurations: Quasi-Helical Symmetry (QHS) and broken symmetry (Mirror). Both experiment and simulation show that the heat flux for Mirror is larger than for QHS by about a factor of two. Initial interferometer measurements provide evidence that density-gradient-driven TEMs are driving turbulence. Calculations of the collisionless damping of zonal flows provide another perspective into the difference between geometries. Similar to other stellarators [Monreal PPCF 2016], the zonal flow residual goes to zero at long wavelengths in both configurations. Additionally, the very short time decay of the zonal flow due to neoclassical polarization is constant between configurations. However, the collisionless damping time is longer and the zonal flow oscillation frequency is smaller in QHS than Mirror, consistent with reduced radial particle drifts. Work supported by the US DOE under Grant DE-FG02-93ER54222.

Diffusion and transport in locally disordered driven lattices

International Nuclear Information System (INIS)

Wulf, Thomas; Okupnik, Alexander; Schmelcher, Peter

2016-01-01

We study the effect of disorder on the particle density evolution in a classical Hamiltonian driven lattice setup. If the disorder is localized within a finite sub-domain of the lattice, the emergence of strong tails in the density distribution which even increases towards larger positions is shown, thus yielding a highly non-Gaussian particle density evolution. As the key underlying mechanism, we identify the conversion between different components of the unperturbed systems mixed phase space which is induced by the disorder. Based on the introduction of individual conversion rates between chaotic and regular components, a theoretical model is developed which correctly predicts the scaling of the particle density. The effect of disorder on the transport properties is studied where a significant enhancement of the transport for cases of localized disorder is shown, thereby contrasting strongly the merely weak modification of the transport for global disorder.

Diffusion and transport in locally disordered driven lattices

Energy Technology Data Exchange (ETDEWEB)

Wulf, Thomas, E-mail: Thomas.Wulf@physnet.uni-hamburg.de; Okupnik, Alexander [Zentrum für Optische Quantentechnologien, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); Schmelcher, Peter, E-mail: Peter.Schmelcher@physnet.uni-hamburg.de [Zentrum für Optische Quantentechnologien, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany); The Hamburg Centre for Ultrafast Imaging, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg (Germany)

2016-09-15

We study the effect of disorder on the particle density evolution in a classical Hamiltonian driven lattice setup. If the disorder is localized within a finite sub-domain of the lattice, the emergence of strong tails in the density distribution which even increases towards larger positions is shown, thus yielding a highly non-Gaussian particle density evolution. As the key underlying mechanism, we identify the conversion between different components of the unperturbed systems mixed phase space which is induced by the disorder. Based on the introduction of individual conversion rates between chaotic and regular components, a theoretical model is developed which correctly predicts the scaling of the particle density. The effect of disorder on the transport properties is studied where a significant enhancement of the transport for cases of localized disorder is shown, thereby contrasting strongly the merely weak modification of the transport for global disorder.

Generation of sheared poloidal flows via Reynolds stress and transport barrier physics

International Nuclear Information System (INIS)

Hidalgo, C.; Pedrosa, M.A.; Sanchez, E.; Balbin, R.; Lopez-Fraguas, A.; Milligen, B. van; Silva, C.; Fernandes, H.; Varandas, C.A.F.; Riccardi, C.; Carrozza, R.; Fontanesi, M.; Carreras, B.A.; Garcia, L.

2000-01-01

A view of the latest experimental results and progress in the understanding of the role of poloidal flows driven by fluctuations via Reynolds stress is given. Reynolds stress shows a radial gradient close to the velocity shear layer location in tokamaks and stellarators, indicating that this mechanism may drive significant poloidal flows in the plasma boundary. Observation of the generation of ExB sheared flows via Reynolds stress at the ion Bernstein resonance layer has been noticed in toroidal magnetized plasmas. The experimental evidence of sheared ExB flows linked to the location of rational surfaces in stellarator plasmas might be interpreted in terms of Reynolds stress sheared driven flows. These results show that ExB sheared flows driven by fluctuations can play an important role in the generation of transport barriers. (author)

Electron Transport through Porphyrin Molecular Junctions

Science.gov (United States)

Zhou, Qi

The goal of this work is to study the properties that would affect the electron transport through a porphyrin molecular junction. This work contributes to the field of electron transport in molecular junctions in the following 3 aspects. First of all, by carrying out experiments comparing the conductance of the iron (III) porphyrin (protected) and the free base porphyrin (protected), it is confirmed that the molecular energy level broadening and shifting occurs for porphyrin molecules when coupled with the metal electrodes, and this level broadening and shifting plays an important role in the electron transport through molecular junctions. Secondly, by carrying out an in-situ deprotection of the acetyl-protected free base porphyrin molecules, it is found out that the presence of acetyl groups reduces the conductance. Thirdly, by incorporating the Matrix-assisted laser desorption/ionization (MALDI) spectrum and the in-situ deprotection prior to formation of molecular junctions, it allows a more precise understanding of the molecules involved in the formation of molecular junctions, and therefore allows an accurate analysis of the conductance histogram. The molecules are prepared by self-assembly and the junctions are formed using a Scanning Tunneling Microscopy (STM) molecular break junction technique. The porphyrin molecules are characterized by MALDI in solution before self-assembly to a gold/mica substrate. The self-assembled monolayers (SAMs) of porphyrins on gold are characterized by Ultraviolet-visible (UV-Vis) reflection spectroscopy to confirm that the molecules are attached to the substrate. The SAMs are then characterized by Angle-Resolved X-ray photoelectron spectroscopy (ARXPS) to determine the thickness and the average molecular orientation of the molecular layer. The electron transport is measured by conductance-displacement (G-S) experiments under a given bias (-0.4V). The conductance value of a single molecule is identified by a statistical analysis

Fluid simulations of ∇Te-driven turbulence and transport in boundary plasmas

International Nuclear Information System (INIS)

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

1993-01-01

This paper is a report on simulations of a new drift wave type instability driven by the electron temperature gradient in tokamak scrapeoff-layers (SOL). A 2D(x,y) fluid code has been developed in order to explore the anomalous transport in the boundary plasmas. The simulation consists of a set of fluid equations (in the electrostatic limit) for the vorticity ∇ perpendicular 2 φ, the electron density n e and the temperature T e in a shearless plasma slab confined by a uniform, straight magnetic field B z with two diverter (or limiter) plates intercepting the magnetic field. The model has two regions separated by a magnetic separatrix: in the edge region inside the separatrix, the model is periodic along the magnetic field while in the SOL region outside the separatrix, the magnetic field is taken to be of finite length with model (logical sheath) boundary conditions at diverter (or limiter) plates. The simulation results show that the observed linear instability agrees well with theory, and that a saturated state of turbulence is reached. In saturated turbulence, clear evidence of the expected long-wavelength mode penetration into the edge is seen, an inverse cascade of wave energy (toward both long wavelengths and low frequencies) is observed. The simulation results also show that amplitudes of potential and the electron temperature fluctuations are somewhat above and the heat flux are somewhat below those of the simplest mixing-length estimates. The results from the self-consistent simulations to determine the microturbulent SOL electron temperature profile agree reasonably with the experimental measurements. The effects on the mode of neutral gas collisions at the divertor sheath and comparisons with the ionization driven turbulence are discussed

Critical current fluctuation in a microwave-driven Josephson junction

International Nuclear Information System (INIS)

Dong Ning; Sun Guozhu; Wang Yiwen; Cao Junyu; Yu Yang; Chen Jian; Kang Lin; Xu Weiwei; Han Siyuan; Wu Peiheng

2007-01-01

Josephson junction devices are good candidates for quantum computation. A large energy splitting was observed in the spectroscopy of a superconducting Josephson junction. The presence of the critical current fluctuation near the energy splitting indicated coupling between the junction and a two-level system. Furthermore, we find that this fluctuation is microwave dependent. It only appears at certain microwave frequency. This relation suggested that the decoherence of qubits is influenced by the necessary computing operations

Adhesion of Photon-Driven Molecular Motors to Surfaces via 1,3-Dipolar Cycloadditions : Effect of Interfacial Interactions on Molecular Motion

NARCIS (Netherlands)

Carroll, Gregory T.; London, Gabor; Fernández Landaluce, Tatiana; Rudolf, Petra; Feringa, Ben L.

We report the attachment of altitudinal light-driven molecular motors to surfaces using 1,3-dipolar cycloaddition reactions. Molecular motors were designed containing azide or alkyne groups for attachment to alkyne- or azide-modified surfaces. Surface attachment was characterized by UV-vis, IR, XPS,

On the origin of shape fluctuations of the cell nucleus.

Science.gov (United States)

Chu, Fang-Yi; Haley, Shannon C; Zidovska, Alexandra

2017-09-26

The nuclear envelope (NE) presents a physical boundary between the cytoplasm and the nucleoplasm, sandwiched in between two highly active systems inside the cell: cytoskeleton and chromatin. NE defines the shape and size of the cell nucleus, which increases during the cell cycle, accommodating for chromosome decondensation followed by genome duplication. In this work, we study nuclear shape fluctuations at short time scales of seconds in human cells. Using spinning disk confocal microscopy, we observe fast fluctuations of the NE, visualized by fluorescently labeled lamin A, and of the chromatin globule surface (CGS) underneath the NE, visualized by fluorescently labeled histone H2B. Our findings reveal that fluctuation amplitudes of both CGS and NE monotonously decrease during the cell cycle, serving as a reliable cell cycle stage indicator. Remarkably, we find that, while CGS and NE typically fluctuate in phase, they do exhibit localized regions of out-of-phase motion, which lead to separation of NE and CGS. To explore the mechanism behind these shape fluctuations, we use biochemical perturbations. We find the shape fluctuations of CGS and NE to be both thermally and actively driven, the latter caused by forces from chromatin and cytoskeleton. Such undulations might affect gene regulation as well as contribute to the anomalously high rates of nuclear transport by, e.g., stirring of molecules next to NE, or increasing flux of molecules through the nuclear pores.

On turbulent motion caused by temperature fluctuations - a critical review on the Boussinesq approximation

International Nuclear Information System (INIS)

Ruediger, R.

1977-01-01

Fluctuating motions which are caused by a given stochastical temperature field acting in a gas with gravitation and T = constant are dealt with. It results that the often used Boussinesq approximation much underestimates the horizontal motions in case wide-spread temperature fluctuations occur. For sufficiently large scales the horizontal motion exceeds the vertical ones even in the case of the temperature field fluctuating completely isotropically. Scales of 1,000 km and 1 day in the Earth atmosphere lead to the observed value u'(horizontal)/u'(vertical) approximately 10. Finally besides the relation between density correlation and pressure correlation the expression for the turbulent mass transport vanishing with the molecular viscosity is determined. (author)

Quantum Fluctuations of Low Dimensional Bose-Einstein ...

African Journals Online (AJOL)

A system of low dimensional condensed ultracold atomic gases inside a field of a laser-driven optical cavity exhibits dispersive optical bistability. During such a process the system also shows quantum fluctuations. Condensate fluctuations are highly manifested particularly in low dimensional systems. In this paper we have ...

Molecular electronics: some views on transport junctions and beyond.

Science.gov (United States)

Joachim, Christian; Ratner, Mark A

2005-06-21

The field of molecular electronics comprises a fundamental set of issues concerning the electronic response of molecules as parts of a mesoscopic structure and a technology-facing area of science. We will overview some important aspects of these subfields. The most advanced ideas in the field involve the use of molecules as individual logic or memory units and are broadly based on using the quantum state space of the molecule. Current work in molecular electronics usually addresses molecular junction transport, where the molecule acts as a barrier for incoming electrons: This is the fundamental Landauer idea of "conduction as scattering" generalized to molecular junction structures. Another point of view in terms of superexchange as a guiding mechanism for coherent electron transfer through the molecular bridge is discussed. Molecules generally exhibit relatively strong vibronic coupling. The last section of this overview focuses on vibronic effects, including inelastic electron tunneling spectroscopy, hysteresis in junction charge transport, and negative differential resistance in molecular transport junctions.

Analysis of fluctuations in semiconductor devices

Science.gov (United States)

Andrei, Petru

The random nature of ion implantation and diffusion processes as well as inevitable tolerances in fabrication result in random fluctuations of doping concentrations and oxide thickness in semiconductor devices. These fluctuations are especially pronounced in ultrasmall (nanoscale) semiconductor devices when the spatial scale of doping and oxide thickness variations become comparable with the geometric dimensions of devices. In the dissertation, the effects of these fluctuations on device characteristics are analyzed by using a new technique for the analysis of random doping and oxide thickness induced fluctuations. This technique is universal in nature in the sense that it is applicable to any transport model (drift-diffusion, semiclassical transport, quantum transport etc.) and it can be naturally extended to take into account random fluctuations of the oxide (trapped) charges and channel length. The technique is based on linearization of the transport equations with respect to the fluctuating quantities. It is computationally much (a few orders of magnitude) more efficient than the traditional Monte-Carlo approach and it yields information on the sensitivity of fluctuations of parameters of interest (e.g. threshold voltage, small-signal parameters, cut-off frequencies, etc.) to the locations of doping and oxide thickness fluctuations. For this reason, it can be very instrumental in the design of fluctuation-resistant structures of semiconductor devices. Quantum mechanical effects are taken into account by using the density-gradient model as well as through self-consistent Poisson-Schrodinger computations. Special attention is paid to the presenting of the technique in a form that is suitable for implementation on commercial device simulators. The numerical implementation of the technique is discussed in detail and numerous computational results are presented and compared with those previously published in literature.

Storm-driven sediment transport in Massachusetts Bay

Science.gov (United States)

Warner, J.C.; Butman, B.; Dalyander, P.S.

2008-01-01

Massachusetts Bay is a semi-enclosed embayment in the western Gulf of Maine about 50 km wide and 100 km long. Bottom sediment resuspension is controlled predominately by storm-induced surface waves and transport by the tidal- and wind-driven circulation. Because the Bay is open to the northeast, winds from the northeast ('Northeasters') generate the largest surface waves and are thus the most effective in resuspending sediments. The three-dimensional oceanographic circulation model Regional Ocean Modeling System (ROMS) is used to explore the resuspension, transport, and deposition of sediment caused by Northeasters. The model transports multiple sediment classes and tracks the evolution of a multilevel sediment bed. The surficial sediment characteristics of the bed are coupled to one of several bottom-boundary layer modules that calculate enhanced bottom roughness due to wave-current interaction. The wave field is calculated from the model Simulating WAves Nearshore (SWAN). Two idealized simulations were carried out to explore the effects of Northeasters on the transport and fate of sediments. In one simulation, an initially spatially uniform bed of mixed sediments exposed to a series of Northeasters evolved to a pattern similar to the existing surficial sediment distribution. A second set of simulations explored sediment-transport pathways caused by storms with winds from the northeast quadrant by simulating release of sediment at selected locations. Storms with winds from the north cause transport southward along the western shore of Massachusetts Bay, while storms with winds from the east and southeast drive northerly nearshore flow. The simulations show that Northeasters can effectively transport sediments from Boston Harbor and the area offshore of the harbor to the southeast into Cape Cod Bay and offshore into Stellwagen Basin. This transport pattern is consistent with Boston Harbor as the source of silver found in the surficial sediments of Cape Cod Bay and

Propulsion of a Molecular Machine by Asymmetric Distribution of Reaction Products

Science.gov (United States)

Golestanian, Ramin; Liverpool, Tanniemola B.; Ajdari, Armand

2005-06-01

A simple model for the reaction-driven propulsion of a small device is proposed as a model for (part of) a molecular machine in aqueous media. The motion of the device is driven by an asymmetric distribution of reaction products. The propulsive velocity of the device is calculated as well as the scale of the velocity fluctuations. The effects of hydrodynamic flow as well as a number of different scenarios for the kinetics of the reaction are addressed.

Stochastic approach and fluctuation theorem for charge transport in diodes

Science.gov (United States)

Gu, Jiayin; Gaspard, Pierre

2018-05-01

A stochastic approach for charge transport in diodes is developed in consistency with the laws of electricity, thermodynamics, and microreversibility. In this approach, the electron and hole densities are ruled by diffusion-reaction stochastic partial differential equations and the electric field generated by the charges is determined with the Poisson equation. These equations are discretized in space for the numerical simulations of the mean density profiles, the mean electric potential, and the current-voltage characteristics. Moreover, the full counting statistics of the carrier current and the measured total current including the contribution of the displacement current are investigated. On the basis of local detailed balance, the fluctuation theorem is shown to hold for both currents.

Charge carrier transport on molecular wire controlled by dipolar species: towards light-driven molecular switch

Czech Academy of Sciences Publication Activity Database

Nešpůrek, Stanislav; Toman, Petr; Sworakowski, J.

438-439, - (2003), s. 268-278 ISSN 0040-6090. [International Conference on Nano- Molecular Electronics /5./. Kobe, 10.12.2002-12.12.2002] R&D Projects: GA AV ČR KSK4050111 Keywords : molecular electronics * polymers * quantum effects Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 1.598, year: 2003

Current Driven Instabilities and Anomalous Mobility in Hall-effect Thrusters

Science.gov (United States)

Tran, Jonathan; Eckhardt, Daniel; Martin, Robert

2017-10-01

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

A consistent transported PDF model for treating differential molecular diffusion

Science.gov (United States)

Wang, Haifeng; Zhang, Pei

2016-11-01

Differential molecular diffusion is a fundamentally significant phenomenon in all multi-component turbulent reacting or non-reacting flows caused by the different rates of molecular diffusion of energy and species concentrations. In the transported probability density function (PDF) method, the differential molecular diffusion can be treated by using a mean drift model developed by McDermott and Pope. This model correctly accounts for the differential molecular diffusion in the scalar mean transport and yields a correct DNS limit of the scalar variance production. The model, however, misses the molecular diffusion term in the scalar variance transport equation, which yields an inconsistent prediction of the scalar variance in the transported PDF method. In this work, a new model is introduced to remedy this problem that can yield a consistent scalar variance prediction. The model formulation along with its numerical implementation is discussed, and the model validation is conducted in a turbulent mixing layer problem.

Hydrogel Walkers with Electro-Driven Motility for Cargo Transport.

Science.gov (United States)

Yang, Chao; Wang, Wei; Yao, Chen; Xie, Rui; Ju, Xiao-Jie; Liu, Zhuang; Chu, Liang-Yin

2015-08-28

In this study, soft hydrogel walkers with electro-driven motility for cargo transport have been developed via a facile mould-assisted strategy. The hydrogel walkers consisting of polyanionic poly(2-acrylamido-2-methylpropanesulfonic acid-co-acrylamide) exhibit an arc looper-like shape with two "legs" for walking. The hydrogel walkers can reversibly bend and stretch via repeated "on/off" electro-triggers in electrolyte solution. Based on such bending/stretching behaviors, the hydrogel walkers can move their two "legs" to achieve one-directional walking motion on a rough surface via repeated "on/off" electro-triggering cycles. Moreover, the hydrogel walkers loaded with very heavy cargo also exhibit excellent walking motion for cargo transport. Such hydrogel systems create new opportunities for developing electro-controlled soft systems with simple design/fabrication strategies in the soft robotic field for remote manipulation and transportation.

Electrostatic and magnetic measurements of turbulence and transport in Extrap T2

International Nuclear Information System (INIS)

Moeller, A.; Sallander, E.

1999-01-01

Langmuir probe and magnetic pick-up coil measurements are used to study edge turbulence in the Extrap T2 reversed field pinch. Magnetic fluctuations resonant outside the toroidal field reversal surface are observed where previously only fluctuations in the spectra of potential and electron density and temperature have been measured. Results are presented which imply that these fluctuations are coupled to and also correlated to the internally resonant tearing mode fluctuations. Evidence of coupling between low-frequency (<100 kHz) and high-frequency fluctuations is also presented. The normalized floating potential fluctuations are seen to increase with the edge electron temperature. This causes an increase of the potential and density fluctuation driven transport with the temperature which is faster than linear. These results, in combination, are consistent with a picture where internally resonant fluctuations couple to edge fluctuations through radial heat conduction from the stochastic core to the edge. (author)

Electrostatic and magnetic measurements of turbulence and transport in Extrap T2

Science.gov (United States)

Möller, Anders; Sallander, Eva

1999-10-01

Langmuir probe and magnetic pick-up coil measurements are used to study edge turbulence in the Extrap T2 reversed field pinch. Magnetic fluctuations resonant outside the toroidal field reversal surface are observed where previously only fluctuations in the spectra of potential and electron density and temperature have been measured. Results are presented which imply that these fluctuations are coupled to and also correlated to the internally resonant tearing mode fluctuations. Evidence of coupling between low-frequency (<100 kHz) and high-frequency fluctuations is also presented. The normalized floating potential fluctuations are seen to increase with the edge electron temperature. This causes an increase of the potential and density fluctuation driven transport with the temperature which is faster than linear. These results, in combination, are consistent with a picture where internally resonant fluctuations couple to edge fluctuations through radial heat conduction from the stochastic core to the edge.

Molecular electronics--resonant transport through single molecules.

Science.gov (United States)

Lörtscher, Emanuel; Riel, Heike

2010-01-01

The mechanically controllable break-junction technique (MCBJ) enables us to investigate charge transport through an individually contacted and addressed molecule in ultra-high vacuum (UHV) environment at variable temperature ranging from room temperature down to 4 K. Using a statistical measurement and analysis approach, we acquire current-voltage (I-V) characteristics during the repeated formation, manipulation, and breaking of a molecular junction. At low temperatures, voltages accessing the first molecular orbitals in resonance can be applied, providing spectroscopic information about the junction's energy landscape, in particular about the molecular level alignment in respect to the Fermi energy of the electrodes. Thereby, we can investigate the non-linear transport properties of various types of functional molecules and explore their potential use as functional building blocks for future nano-electronics. An example will be given by the reversible and controllable switching between two distinct conductive states of a single molecule. As a proof-of-principle for functional molecular devices, a single-molecule memory element will be demonstrated.

Solitons in proteins at non-zero temperatures with allowance for the fluctuations of polarization

International Nuclear Information System (INIS)

Simo, E.; Caputo, J.G.

2007-06-01

A model for the nonlinear transfer of vibrational energy in molecular chains is derived at temperatures of realistic interest for transport in proteins. The study includes the influence of the fluctuations of polarization in the chain. This theory exhibits a new form of temperature-dependence in intrinsic parameters of alpha-helix, and consequently in the coefficients of the nonlinear Schroedinger equation governing the system and in the solitons' parameters. Thermal fluctuations are analysed in the basis of the non-Gaussian approximation and the total free-energy of the alpha-helix is determined to elucidate the denaturation process of the protein. (author)

Charge Transport Phenomena in Peptide Molecular Junctions

International Nuclear Information System (INIS)

Luchini, A.; Petricoin, E.F.; Geho, D.H.; Liotta, L.A.; Long, D.P.; Vaisman, I.I.

2008-01-01

Inelastic electron tunneling spectroscopy (IETS) is a valuable in situ spectroscopic analysis technique that provides a direct portrait of the electron transport properties of a molecular species. In the past, IETS has been applied to small molecules. Using self-assembled nano electronic junctions, IETS was performed for the first time on a large polypeptide protein peptide in the phosphorylated and native form, yielding interpretable spectra. A reproducible 10-fold shift of the I/V characteristics of the peptide was observed upon phosphorylation. Phosphorylation can be utilized as a site-specific modification to alter peptide structure and thereby influence electron transport in peptide molecular junctions. It is envisioned that kinases and phosphatases may be used to create tunable systems for molecular electronics applications, such as biosensors and memory devices.

A self-organized criticality model for plasma transport

International Nuclear Information System (INIS)

Carreras, B.A.; Newman, D.; Lynch, V.E.

1996-01-01

Many models of natural phenomena manifest the basic hypothesis of self-organized criticality (SOC). The SOC concept brings together the self-similarity on space and time scales that is common to many of these phenomena. The application of the SOC modelling concept to the plasma dynamics near marginal stability opens new possibilities of understanding issues such as Bohm scaling, profile consistency, broad band fluctuation spectra with universal characteristics and fast time scales. A model realization of self-organized criticality for plasma transport in a magnetic confinement device is presented. The model is based on subcritical resistive pressure-gradient-driven turbulence. Three-dimensional nonlinear calculations based on this model show the existence of transport under subcritical conditions. This model that includes fluctuation dynamics leads to results very similar to the running sandpile paradigm

Fully Quantum Fluctuation Theorems

Science.gov (United States)

Åberg, Johan

2018-02-01

Systems that are driven out of thermal equilibrium typically dissipate random quantities of energy on microscopic scales. Crooks fluctuation theorem relates the distribution of these random work costs to the corresponding distribution for the reverse process. By an analysis that explicitly incorporates the energy reservoir that donates the energy and the control system that implements the dynamic, we obtain a quantum generalization of Crooks theorem that not only includes the energy changes in the reservoir but also the full description of its evolution, including coherences. Moreover, this approach opens up the possibility for generalizations of the concept of fluctuation relations. Here, we introduce "conditional" fluctuation relations that are applicable to nonequilibrium systems, as well as approximate fluctuation relations that allow for the analysis of autonomous evolution generated by global time-independent Hamiltonians. We furthermore extend these notions to Markovian master equations, implicitly modeling the influence of the heat bath.

Magnetic fluctuations can contribute to plasma transport, ''self-consistency constraints'' notwithstanding

International Nuclear Information System (INIS)

Krommes, J.A.; Kim, Chang-Bae.

1987-09-01

The recent conclusion that in a turbulent, collisionless plasma ''magnetic transport including quasilinear magnetic flutter transport ... does not contribute to the relaxation of (f), and thus is not responsible for electron energy or momentum transport'' is shown to be incorrect for a variety of situations of physical interest, including saturation by quasilinear plateau formation, induced scattering, and, most importantly, conventional mode coupling. The well-established theory of the mean infinitesimal response function and the spectral balance equation provides a unifying framework for understanding the above conclusion. In particular, the cancellations which lead to their conclusion are special cases of well-known relationships between the response function, particle propagator, and dielectric function. A more general, concise, and manifestly gauge-invariant algebraic derivation of the cancellations is given. Though the cancellations occur in a certain limit, these conclusions do not follow in general: The picture of steady-state turbulence as consisting of small-scale ''incoherent'' ballistic ''clumps'' shielded by long-wavelength ''coherent'' dielectric response is physically misleading and mathematically incomplete, as it ignores or mistreates the often dominant process of renormalized n-wave coupling. Thus, when ion nonlinearities are considered, formulas for the magnetic contribution to transport emerge which are quite similar to the quasilinear one. Furthermore, limits are possible in which all or part of the noise can be negligible, yet in which the total fluctuation spectrum remains finite. 56 refs

Charge Fluctuations in Nanoscale Capacitors

NARCIS (Netherlands)

Limmer, D.T.; Merlet, C.; Salanne, M.; Chandler, D.; Madden, P.A.; van Roij, R.H.H.G.; Rotenberg, B.

2013-01-01

The fluctuations of the charge on an electrode contain information on the microscopic correlations within the adjacent fluid and their effect on the electronic properties of the interface. We investigate these fluctuations using molecular dynamics simulations in a constant-potential ensemble with

Fluctuation-enhanced electric conductivity in electrolyte solutions.

Science.gov (United States)

Péraud, Jean-Philippe; Nonaka, Andrew J; Bell, John B; Donev, Aleksandar; Garcia, Alejandro L

2017-10-10

We analyze the effects of an externally applied electric field on thermal fluctuations for a binary electrolyte fluid. We show that the fluctuating Poisson-Nernst-Planck (PNP) equations for charged multispecies diffusion coupled with the fluctuating fluid momentum equation result in enhanced charge transport via a mechanism distinct from the well-known enhancement of mass transport that accompanies giant fluctuations. Although the mass and charge transport occurs by advection by thermal velocity fluctuations, it can macroscopically be represented as electrodiffusion with renormalized electric conductivity and a nonzero cation-anion diffusion coefficient. Specifically, we predict a nonzero cation-anion Maxwell-Stefan coefficient proportional to the square root of the salt concentration, a prediction that agrees quantitatively with experimental measurements. The renormalized or effective macroscopic equations are different from the starting PNP equations, which contain no cross-diffusion terms, even for rather dilute binary electrolytes. At the same time, for infinitely dilute solutions the renormalized electric conductivity and renormalized diffusion coefficients are consistent and the classical PNP equations with renormalized coefficients are recovered, demonstrating the self-consistency of the fluctuating hydrodynamics equations. Our calculations show that the fluctuating hydrodynamics approach recovers the electrophoretic and relaxation corrections obtained by Debye-Huckel-Onsager theory, while elucidating the physical origins of these corrections and generalizing straightforwardly to more complex multispecies electrolytes. Finally, we show that strong applied electric fields result in anisotropically enhanced "giant" velocity fluctuations and reduced fluctuations of salt concentration.

Current-driven dynamics in molecular-scale devices

International Nuclear Information System (INIS)

Seideman, Tamar

2003-01-01

We review recent theoretical work on current-triggered processes in molecular-scale devices - a field at the interface between solid state physics and chemical dynamics with potential applications in diverse areas, including artificial molecular machines, unimolecular transport, surface nanochemistry and nanolithography. The qualitative physics underlying current-triggered dynamics is first discussed and placed in context with several well-studied phenomena with which it shares aspects. A theory for modelling these dynamics is next formulated within a time-dependent scattering approach. Our end result provides useful insight into the system properties that determine the reaction outcome as well as a computationally convenient framework for numerical realization. The theory is applied to study single-molecule surface reactions induced by a scanning tunnelling microscope and current-triggered dynamics in single-molecule transistors. We close with a discussion of several potential applications of current-induced dynamics in molecular devices and several opportunities for future research. (topical review)

Shear flow effects on ion thermal transport in tokamaks

International Nuclear Information System (INIS)

Tajima, T.; Horton, W.; Dong, J.Q.; Kishimoto, Y.

1995-03-01

From various laboratory and numerical experiments, there is clear evidence that under certain conditions the presence of sheared flows in a tokamak plasma can significantly reduce the ion thermal transport. In the presence of plasma fluctuations driven by the ion temperature gradient, the flows of energy and momentum parallel and perpendicular to the magnetic field are coupled with each other. This coupling manifests itself as significant off-diagonal coupling coefficients that give rise to new terms for anomalous transport. The authors derive from the gyrokinetic equation a set of velocity moment equations that describe the interaction among plasma turbulent fluctuations, the temperature gradient, the toroidal velocity shear, and the poloidal flow in a tokamak plasma. Four coupled equations for the amplitudes of the state variables radially extended over the transport region by toroidicity induced coupling are derived. The equations show bifurcations from the low confinement mode without sheared flows to high confinement mode with substantially reduced transport due to strong shear flows. Also discussed is the reduced version with three state variables. In the presence of sheared flows, the radially extended coupled toroidal modes driven by the ion temperature gradient disintegrate into smaller, less elongated vortices. Such a transition to smaller spatial correlation lengths changes the transport from Bohm-like to gyrobohm-like. The properties of these equations are analyzed. The conditions for the improved confined regime are obtained as a function of the momentum-energy deposition rates and profiles. The appearance of a transport barrier is a consequence of the present theory

Event-by-Event Elliptic Flow Fluctuations from PHOBOS

Science.gov (United States)

Wosiek, B.; Alver, B.; Back, B. B.; Baker, M. D.; Ballintijn, M.; Barton, D. S.; Betts, R. R.; Bickley, A. A.; Bindel, R.; Busza, W.; Carroll, A.; Chai, Z.; Chetluru, V.; Decowski, M. P.; García, E.; Gburek, T.; George, N.; Gulbrandsen, K.; Halliwell, C.; Hamblen, J.; Harnarine, I.; Hauer, M.; Henderson, C.; Hofman, D. J.; Hollis, R. S.; Hołyński, R.; Holzman, B.; Iordanova, A.; Johnson, E.; Kane, J. L.; Khan, N.; Kulinich, P.; Kuo, C. M.; Li, W.; Lin, W. T.; Loizides, C.; Manly, S.; Mignerey, A. C.; Nouicer, R.; Olszewski, A.; Pak, R.; Reed, C.; Richardson, E.; Roland, C.; Roland, G.; Sagerer, J.; Seals, H.; Sedykh, I.; Smith, C. E.; Stankiewicz, M. A.; Steinberg, P.; Stephans, G. S. F.; Sukhanov, A.; Szostak, A.; Tonjes, M. B.; Trzupek, A.; Vale, C.; van Nieuwenhuizen, G. J.; Vaurynovich, S. S.; Verdier, R.; Veres, G. I.; Walters, P.; Wenger, E.; Willhelm, D.; Wolfs, F. L. H.; Woźniak, K.; Wyngaardt, S.; Wysłouch, B.

2009-04-01

Recently PHOBOS has focused on the study of fluctuations and correlations in particle production in heavy-ion collisions at the highest energies delivered by the Relativistic Heavy Ion Collider (RHIC). In this report, we present results on event-by-event elliptic flow fluctuations in (Au+Au) collisions at sqrt {sNN}=200 GeV. A data-driven method was used to estimate the dominant contribution from non-flow correlations. Over the broad range of collision centralities, the observed large elliptic flow fluctuations are in agreement with the fluctuations in the initial source eccentricity.

High-frequency fluctuation measurements by far-infrared laser Faraday-effect polarimetry-interferometry and forward scattering system on MST.

Science.gov (United States)

Ding, W X; Lin, L; Duff, J R; Brower, D L

2014-11-01

Magnetic fluctuation-induced transport driven by global tearing modes has been measured by Faraday-effect polarimetry and interferometry (phase measurements) in the MST reversed field pinch. However, the role of small-scale broadband magnetic and density turbulence in transport remains unknown. In order to investigate broadband magnetic turbulence, we plan to upgrade the existing detector system by using planar-diode fundamental waveguide mixers optimized for high sensitivity. Initial tests indicate these mixers have ×10 sensitivity improvement compared to currently employed corner-cube Schottky-diode mixers and ×5 lower noise. Compact mixer design will allow us to resolve the wavenumbers up to k ∼ 1-2 cm(-1) for beam width w = 1.5 cm and 15 cm(-1) for beam width w = 2 mm. The system can also be used to measure the scattered signal (amplitude measurement) induced by both plasma density and magnetic fluctuations.

Transition from direct to inverted charge transport Marcus regions in molecular junctions via molecular orbital gating

Science.gov (United States)

Yuan, Li; Wang, Lejia; Garrigues, Alvar R.; Jiang, Li; Annadata, Harshini Venkata; Anguera Antonana, Marta; Barco, Enrique; Nijhuis, Christian A.

2018-04-01

Solid-state molecular tunnel junctions are often assumed to operate in the Landauer regime, which describes essentially activationless coherent tunnelling processes. In solution, on the other hand, charge transfer is described by Marcus theory, which accounts for thermally activated processes. In practice, however, thermally activated transport phenomena are frequently observed also in solid-state molecular junctions but remain poorly understood. Here, we show experimentally the transition from the Marcus to the inverted Marcus region in a solid-state molecular tunnel junction by means of intra-molecular orbital gating that can be tuned via the chemical structure of the molecule and applied bias. In the inverted Marcus region, charge transport is incoherent, yet virtually independent of temperature. Our experimental results fit well to a theoretical model that combines Landauer and Marcus theories and may have implications for the interpretation of temperature-dependent charge transport measurements in molecular junctions.

Nonequilibrium quantum fluctuations of work.

Science.gov (United States)

Allahverdyan, A E

2014-09-01

The concept of work is basic for statistical thermodynamics. To gain a fuller understanding of work and its (quantum) features, it needs to be represented as an average of a fluctuating quantity. Here I focus on the work done between two moments of time for a thermally isolated quantum system driven by a time-dependent Hamiltonian. I formulate two natural conditions needed for the fluctuating work to be physically meaningful for a system that starts its evolution from a nonequilibrium state. The existing definitions do not satisfy these conditions due to issues that are traced back to noncommutativity. I propose a definition of fluctuating work that is free of previous drawbacks and that applies for a wide class of nonequilibrium initial states. It allows the deduction of a generalized work-fluctuation theorem that applies for an arbitrary (out-of-equilibrium) initial state.

Phenotype-driven molecular autopsy for sudden cardiac death.

Science.gov (United States)

Cann, F; Corbett, M; O'Sullivan, D; Tennant, S; Hailey, H; Grieve, J H K; Broadhurst, P; Rankin, R; Dean, J C S

2017-01-01

A phenotype-driven approach to molecular autopsy based in a multidisciplinary team comprising clinical and laboratory genetics, forensic medicine and cardiology is described. Over a 13 year period, molecular autopsy was undertaken in 96 sudden cardiac death cases. A total of 46 cases aged 1-40 years had normal hearts and suspected arrhythmic death. Seven (15%) had likely pathogenic variants in ion channelopathy genes [KCNQ1 (1), KCNH2 (4), SCN5A (1), RyR2(1)]. Fifty cases aged between 2 and 67 had a cardiomyopathy. Twenty-five had arrhythmogenic right ventricular cardiomyopathy (ARVC), 10 dilated cardiomyopathy (DCM) and 15 hypertrophic cardiomyopathy (HCM). Likely pathogenic variants were found in three ARVC cases (12%) in PKP2, DSC2 or DSP, two DCM cases (20%) in MYH7, and four HCM cases (27%) in MYBPC3 (3) or MYH7 (1). Uptake of cascade screening in relatives was higher when a molecular diagnosis was made at autopsy. In three families, variants previously published as pathogenic were detected, but clinical investigation revealed no abnormalities in carrier relatives. With a conservative approach to defining pathogenicity of sequence variants incorporating family phenotype information and population genomic data, a molecular diagnosis was made in 15% of sudden arrhythmic deaths and 18% of cardiomyopathy deaths. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Molecular Dynamics Investigation of Cl− and Water Transport through a Eukaryotic CLC Transporter

OpenAIRE

Cheng, Mary Hongying; Coalson, Rob D.

2012-01-01

Early crystal structures of prokaryotic CLC proteins identified three Cl– binding sites: internal (Sint), central (Scen), and external (Sext). A conserved external GLU (GLUex) residue acts as a gate competing for Sext. Recently, the first crystal structure of a eukaryotic transporter, CmCLC, revealed that in this transporter GLUex competes instead for Scen. Here, we use molecular dynamics simulations to investigate Cl– transport through CmCLC. The gating and Cl–/H+ transport cycle are inferre...

Fluctuation theory for radiative transfer in random media

International Nuclear Information System (INIS)

Bal, Guillaume; Jing Wenjia

2011-01-01

We consider the effect of small scale random fluctuations of the constitutive coefficients on boundary measurements of solutions to radiative transfer equations. As the correlation length of the random oscillations tends to zero, the transport solution is well approximated by a deterministic, averaged, solution. In this paper, we analyze the random fluctuations to the averaged solution, which may be interpreted as a central limit correction to homogenization. With the inverse transport problem in mind, we characterize the random structure of the singular components of the transport measurement operator. In regimes of moderate scattering, such components provide stable reconstructions of the constitutive parameters in the transport equation. We show that the random fluctuations strongly depend on the decorrelation properties of the random medium.

A n-vector model for charge transport in molecular semiconductors.

Science.gov (United States)

Jackson, Nicholas E; Kohlstedt, Kevin L; Chen, Lin X; Ratner, Mark A

2016-11-28

We develop a lattice model utilizing coarse-grained molecular sites to study charge transport in molecular semiconducting materials. The model bridges atomistic descriptions and structureless lattice models by mapping molecular structure onto sets of spatial vectors isomorphic with spin vectors in a classical n-vector Heisenberg model. Specifically, this model incorporates molecular topology-dependent orientational and intermolecular coupling preferences, including the direct inclusion of spatially correlated transfer integrals and site energy disorder. This model contains the essential physics required to explicitly simulate the interplay of molecular topology and correlated structural disorder, and their effect on charge transport. As a demonstration of its utility, we apply this model to analyze the effects of long-range orientational correlations, molecular topology, and intermolecular interaction strength on charge motion in bulk molecular semiconductors.

First Observation of the High Field Side Sawtooth Crash and Heat Transfer during Driven Reconnection Processes in Magnetically Confined Plasmas

International Nuclear Information System (INIS)

Park, HK; Luhmann, NC; Donne, AJH; Classen, IGJ; Domier, CW; Mazzucato, E; Munsat, T; van de Pol, MJ; Xia, Z

2005-01-01

High resolution (temporal and spatial), two-dimensional images of electron temperature fluctuations during sawtooth oscillations were employed to study driven reconnection processes in magnetically confined toroidal plasmas. The combination of kink and local pressure driven instabilities leads to an 'X-point' reconnection process that is localized in the toroidal and poloidal planes. The reconnection is not always confined to the magnetic surfaces with minimum energy. The heat transport process from the core is demonstrated to be highly collective rather than stochastic

A nanojet: propulsion of a molecular machine by an asymmetric distribution of reaction--products

Science.gov (United States)

Liverpool, Tanniemola; Golestanian, Ramin; Ajdari, Armand

2006-03-01

A simple model for the reaction-driven propulsion of a small device is proposed as a model for (part of) a molecular machine in aqueous media. Motion of the device is driven by an asymmetric distribution of reaction products. We calculate the propulsive velocity of the device as well as the scale of the velocity fluctuations. We also consider the effects of hydrodynamic flow as well as a number of different scenarios for the kinetics of the reaction.

Molecular and ionic mimicry and the transport of toxic metals

Science.gov (United States)

Bridges, Christy C.; Zalups, Rudolfs K.

2008-01-01

Despite many scientific advances, human exposure to, and intoxication by, toxic metal species continues to occur. Surprisingly, little is understood about the mechanisms by which certain metals and metal-containing species gain entry into target cells. Since there do not appear to be transporters designed specifically for the entry of most toxic metal species into mammalian cells, it has been postulated that some of these metals gain entry into target cells, through the mechanisms of ionic and/or molecular mimicry, at the site of transporters of essential elements and/or molecules. The primary purpose of this review is to discuss the transport of selective toxic metals in target organs and provide evidence supporting a role of ionic and/or molecular mimicry. In the context of this review, molecular mimicry refers to the ability of a metal ion to bond to an endogenous organic molecule to form an organic metal species that acts as a functional or structural mimic of essential molecules at the sites of transporters of those molecules. Ionic mimicry refers to the ability of a cationic form of a toxic metal to mimic an essential element or cationic species of an element at the site of a transporter of that element. Molecular and ionic mimics can also be sub-classified as structural or functional mimics. This review will present the established and putative roles of molecular and ionic mimicry in the transport of mercury, cadmium, lead, arsenic, selenium, and selected oxyanions in target organs and tissues. PMID:15845419

Molecular and ionic mimicry and the transport of toxic metals

International Nuclear Information System (INIS)

Bridges, Christy C.; Zalups, Rudolfs K.

2005-01-01

Despite many scientific advances, human exposure to, and intoxication by, toxic metal species continues to occur. Surprisingly, little is understood about the mechanisms by which certain metals and metal-containing species gain entry into target cells. Since there do not appear to be transporters designed specifically for the entry of most toxic metal species into mammalian cells, it has been postulated that some of these metals gain entry into target cells, through the mechanisms of ionic and/or molecular mimicry, at the site of transporters of essential elements and/or molecules. The primary purpose of this review is to discuss the transport of selective toxic metals in target organs and provide evidence supporting a role of ionic and/or molecular mimicry. In the context of this review, molecular mimicry refers to the ability of a metal ion to bond to an endogenous organic molecule to form an organic metal species that acts as a functional or structural mimic of essential molecules at the sites of transporters of those molecules. Ionic mimicry refers to the ability of a cationic form of a toxic metal to mimic an essential element or cationic species of an element at the site of a transporter of that element. Molecular and ionic mimics can also be sub-classified as structural or functional mimics. This review will present the established and putative roles of molecular and ionic mimicry in the transport of mercury, cadmium, lead, arsenic, selenium, and selected oxyanions in target organs and tissues

Noise induced chaos in optically driven colloidal rings.

Science.gov (United States)

Roichman, Yael; Zaslavsky, George; Grier, David G.

2007-03-01

Given a constant flux of energy, many driven dissipative systems rapidly organize themselves into configurations that support steady state motion. Examples include swarming of bacterial colonies, convection in shaken sandpiles, and synchronization in flowing traffic. How simple objects interacting in simple ways self-organize generally is not understood, mainly because so few of the available experimental systems afford the necessary access to their microscopic degrees of freedom. This talk introduces a new class of model driven dissipative systems typified by three colloidal spheres circulating around a ring-like optical trap known as an optical vortex. By controlling the interplay between hydrodynamic interactions and fixed disorder we are able to drive a transition from a previously predicted periodic steady state to fully developed chaos. In addition, by tracking both microscopic trajectories and macroscopic collective fluctuations the relation between the onset of microscopic weak chaos and the evolution of space-time self-similarity in macroscopic transport properties is revealed. In a broader scope, several optical vortices can be coupled to create a large dissipative system where each building block has internal degrees of freedom. In such systems the little understood dynamics of processes like frustration and jamming, fluctuation-dissipation relations and the propagation of collective motion can be tracked microscopically.

The ELIMED transport and dosimetry beamline for laser-driven ion beams

Energy Technology Data Exchange (ETDEWEB)

Romano, F., E-mail: francesco.romano@lns.infn.it [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); Schillaci, F.; Cirrone, G.A.P.; Cuttone, G. [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); Scuderi, V. [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); ELI-Beamlines Project, Institute of Physics ASCR, v.v.i. (FZU), 182 21 Prague (Czech Republic); Allegra, L.; Amato, A.; Amico, A.; Candiano, G.; De Luca, G.; Gallo, G. [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); Giordanengo, S.; Guarachi, L. Fanola [Istituto Nazionale di Fisica Nucleare, Sezione di Torino, Via P. Giuria 1, Torino (Italy); Universita' di Torino, Dipartimento di Fisica, Via P. Giuria 1, Torino (Italy); Korn, G. [ELI-Beamlines Project, Institute of Physics ASCR, v.v.i. (FZU), 182 21 Prague (Czech Republic); Larosa, G. [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); Leanza, R. [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); Universita' di Catania, Dipartimento di Fisica e Astronomia, Via S. Sofia 64, Catania (Italy); Manna, R.; Marchese, V. [Istituto Nazionale di Fisica Nucleare, Laboratori Nazionali del Sud, Via Santa Sofia 62, Catania (Italy); Marchetto, F. [Istituto Nazionale di Fisica Nucleare, Sezione di Torino, Via P. Giuria 1, Torino (Italy); Margarone, D. [ELI-Beamlines Project, Institute of Physics ASCR, v.v.i. (FZU), 182 21 Prague (Czech Republic); and others

2016-09-01

A growing interest of the scientific community towards multidisciplinary applications of laser-driven beams has led to the development of several projects aiming to demonstrate the possible use of these beams for therapeutic purposes. Nevertheless, laser-accelerated particles differ from the conventional beams typically used for multiscipilinary and medical applications, due to the wide energy spread, the angular divergence and the extremely intense pulses. The peculiarities of optically accelerated beams led to develop new strategies and advanced techniques for transport, diagnostics and dosimetry of the accelerated particles. In this framework, the realization of the ELIMED (ELI-Beamlines MEDical and multidisciplinary applications) beamline, developed by INFN-LNS (Catania, Italy) and that will be installed in 2017 as a part of the ELIMAIA beamline at the ELI-Beamlines (Extreme Light Infrastructure Beamlines) facility in Prague, has the aim to investigate the feasibility of using laser-driven ion beams for multidisciplinary applications. In this contribution, an overview of the beamline along with a detailed description of the main transport elements as well as the detectors composing the final section of the beamline will be presented.

Observation of quantum interference in molecular charge transport

DEFF Research Database (Denmark)

Guedon, Constant M.; Valkenier, Hennie; Markussen, Troels

2012-01-01

for such behaviour has been indirect. Here, we report the observation of destructive quantum interference in charge transport through two-terminal molecular junctions at room temperature. We studied five different rigid p-conjugated molecular wires, all of which form self-assembled monolayers on a gold surface......, and find that the degree of interference can be controlled by simple chemical modifications of the molecular wire....

Strain fluctuations and elastic constants

Energy Technology Data Exchange (ETDEWEB)

Parrinello, M.; Rahman, A.

1982-03-01

It is shown that the elastic strain fluctuations are a direct measure of elastic compliances in a general anisotropic medium; depending on the ensemble in which the fluctuation is measured either the isothermal or the adiabatic compliances are obtained. These fluctuations can now be calculated in a constant enthalpy and pressure, and hence, constant entropy, ensemble due to recent develpments in the molecular dynamics techniques. A calculation for a Ni single crystal under uniform uniaxial 100 tensile or compressive load is presented as an illustration of the relationships derived between various strain fluctuations and the elastic modulii. The Born stability criteria and the behavior of strain fluctuations are shown to be related.

How molecular motors are arranged on a cargo is important for vesicular transport.

Directory of Open Access Journals (Sweden)

Robert P Erickson

2011-05-01

Full Text Available The spatial organization of the cell depends upon intracellular trafficking of cargos hauled along microtubules and actin filaments by the molecular motor proteins kinesin, dynein, and myosin. Although much is known about how single motors function, there is significant evidence that cargos in vivo are carried by multiple motors. While some aspects of multiple motor function have received attention, how the cargo itself--and motor organization on the cargo--affects transport has not been considered. To address this, we have developed a three-dimensional Monte Carlo simulation of motors transporting a spherical cargo, subject to thermal fluctuations that produce both rotational and translational diffusion. We found that these fluctuations could exert a load on the motor(s, significantly decreasing the mean travel distance and velocity of large cargos, especially at large viscosities. In addition, the presence of the cargo could dramatically help the motor to bind productively to the microtubule: the relatively slow translational and rotational diffusion of moderately sized cargos gave the motors ample opportunity to bind to a microtubule before the motor/cargo ensemble diffuses out of range of that microtubule. For rapidly diffusing cargos, the probability of their binding to a microtubule was high if there were nearby microtubules that they could easily reach by translational diffusion. Our simulations found that one reason why motors may be approximately 100 nm long is to improve their 'on' rates when attached to comparably sized cargos. Finally, our results suggested that to efficiently regulate the number of active motors, motors should be clustered together rather than spread randomly over the surface of the cargo. While our simulation uses the specific parameters for kinesin, these effects result from generic properties of the motors, cargos, and filaments, so they should apply to other motors as well.

Fluctuations When Driving Between Nonequilibrium Steady States

Science.gov (United States)

Riechers, Paul M.; Crutchfield, James P.

2017-08-01

Maintained by environmental fluxes, biological systems are thermodynamic processes that operate far from equilibrium without detailed-balanced dynamics. Yet, they often exhibit well defined nonequilibrium steady states (NESSs). More importantly, critical thermodynamic functionality arises directly from transitions among their NESSs, driven by environmental switching. Here, we identify the constraints on excess heat and dissipated work necessary to control a system that is kept far from equilibrium by background, uncontrolled "housekeeping" forces. We do this by extending the Crooks fluctuation theorem to transitions among NESSs, without invoking an unphysical dual dynamics. This and corresponding integral fluctuation theorems determine how much work must be expended when controlling systems maintained far from equilibrium. This generalizes thermodynamic feedback control theory, showing that Maxwellian Demons can leverage mesoscopic-state information to take advantage of the excess energetics in NESS transitions. We also generalize an approach recently used to determine the work dissipated when driving between functionally relevant configurations of an active energy-consuming complex system. Altogether, these results highlight universal thermodynamic laws that apply to the accessible degrees of freedom within the effective dynamic at any emergent level of hierarchical organization. By way of illustration, we analyze a voltage-gated sodium ion channel whose molecular conformational dynamics play a critical functional role in propagating action potentials in mammalian neuronal membranes.

Detecting Urban Transport Modes Using a Hybrid Knowledge Driven Framework from GPS Trajectory

Directory of Open Access Journals (Sweden)

Rahul Deb Das

2016-11-01

Full Text Available Transport mode information is essential for understanding people’s movement behavior and travel demand estimation. Current approaches extract travel information once the travel is complete. Such approaches are limited in terms of generating just-in-time information for a number of mobility based applications, e.g., real time mode specific patronage estimation. In order to detect the transport modalities from GPS trajectories, various machine learning approaches have already been explored. However, the majority of them produce only a single conclusion from a given set of evidences, ignoring the uncertainty of any mode classification. Also, the existing machine learning approaches fall short in explaining their reasoning scheme. In contrast, a fuzzy expert system can explain its reasoning scheme in a human readable format along with a provision of inferring different outcome possibilities, but lacks the adaptivity and learning ability of machine learning. In this paper, a novel hybrid knowledge driven framework is developed by integrating a fuzzy logic and a neural network to complement each other’s limitations. Thus the aim of this paper is to automate the tuning process in order to generate an intelligent hybrid model that can perform effectively in near-real time mode detection using GPS trajectory. Tests demonstrate that a hybrid knowledge driven model works better than a purely knowledge driven model and at per the machine learning models in the context of transport mode detection.

A new interferometry-based electron density fluctuation diagnostic on Alcator C-Moda)

Science.gov (United States)

Kasten, C. P.; Irby, J. H.; Murray, R.; White, A. E.; Pace, D. C.

2012-10-01

The two-color interferometry diagnostic on the Alcator C-Mod tokamak has been upgraded to measure fluctuations in the electron density and density gradient for turbulence and transport studies. Diagnostic features and capabilities are described. In differential mode, fast phase demodulation electronics detect the relative phase change between ten adjacent, radially-separated (ΔR = 1.2 cm, adjustable), vertical-viewing chords, which allows for measurement of the line-integrated electron density gradient. The system can be configured to detect the absolute phase shift of each chord by comparison to a local oscillator, measuring the line-integrated density. Each chord is sensitive to density fluctuations with kR < 20.3 cm-1 and is digitized at up to 10 MS/s, resolving aspects of ion temperature gradient-driven modes and other long-wavelength turbulence. Data from C-Mod discharges is presented, including observations of the quasi-coherent mode in enhanced D-alpha H-mode plasmas and the weakly coherent mode in I-mode.

Electric discharge microplasmas generated in highly fluctuating fluids: Characteristics and application to the synthesis of molecular diamond

Science.gov (United States)

Stauss, Sven

2014-10-01

Plasma-based fabrication of novel nanomaterials and nanostructures is paramount for the development of next-generation electronic devices and for green energy applications. In particular, controlling the interactions between plasmas and materials interfaces, and the plasma fluctuations are crucial for further development of plasma-based processes and bottom-up growth of nanomaterials. Discharge microplasmas generated in supercritical fluids represent a special class of high-pressure plasmas, where fluctuations on the molecular scale influence the discharge properties and the possible bottom-up growth of nanomaterials. In the first part of the talk, we will discuss an anomaly observed for microplasmas generated near the critical point, a local decrease in the breakdown voltage, which has been observed for both molecular and monoatomic gases. This anomalous behavior is suggested to be caused by the concomitant decrease of the ionization potential due to the formation of clusters near the critical point, and the formation of extended electron mean free paths induced by the high-density fluctuation near the critical point. We will also show that when generating microplasma discharges close to the critical point, that the high-density fluctuation of the supercritical fluid persists. In the second part of the presentation, we will first introduce the basic properties of diamondoids and their potential for application in many different fields - biotechnology, medicine, opto- and nanoelectronics - before discussing their synthesis by microplasmas generated inside both conventional batch-type and continuous flow reactors, using the smallest diamondoid, adamantane, as a precursor and seed. Finally we show that one possible growth mechanism of larger diamondoids from smaller ones consists in the repeated abstraction of hydrogen terminations and the addition of methyl radicals. Supported financially in part by Grant No. 23760688 and Grant No. 21110002 from the Ministry of

Elucidation of the glucose transport pathway in glucose transporter 4 via steered molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Aswathy Sheena

Full Text Available BACKGROUND: GLUT4 is a predominant insulin regulated glucose transporter expressed in major glucose disposal tissues such as adipocytes and muscles. Under the unstimulated state, GLUT4 resides within intracellular vesicles. Various stimuli such as insulin translocate this protein to the plasma membrane for glucose transport. In the absence of a crystal structure for GLUT4, very little is known about the mechanism of glucose transport by this protein. Earlier we proposed a homology model for GLUT4 and performed a conventional molecular dynamics study revealing the conformational rearrangements during glucose and ATP binding. However, this study could not explain the transport of glucose through the permeation tunnel. METHODOLOGY/PRINCIPAL FINDINGS: To elucidate the molecular mechanism of glucose transport and its energetic, a steered molecular dynamics study (SMD was used. Glucose was pulled from the extracellular end of GLUT4 to the cytoplasm along the pathway using constant velocity pulling method. We identified several key residues within the tunnel that interact directly with either the backbone ring or the hydroxyl groups of glucose. A rotation of glucose molecule was seen near the sugar binding site facilitating the sugar recognition process at the QLS binding site. CONCLUSIONS/SIGNIFICANCE: This study proposes a possible glucose transport pathway and aids the identification of several residues that make direct interactions with glucose during glucose transport. Mutational studies are required to further validate the observation made in this study.

Effects of high frequency fluctuations on DNS of turbulent open-channel flow with high Pr passive scalar transport

International Nuclear Information System (INIS)

Yamamoto, Yoshinobu; Kunugi, Tomoaki; Serizawa, Akimi

2002-01-01

In this study, investigation on effects of high frequency fluctuations on DNS of turbulent open-channel flows with high Pr passive scalar transport was conducted. As the results, although significant differences of energy spectra behaviors in temperature fields, are caused at high wave number region where insignificant area for velocity components, large difference dose not caused in mean and statistic behaviors in temperature component. But, if the buoyancy were considered, this temperature high-frequency fluctuations would be greatly changed mean and statistics behaviors from the difference of the accuracy and resolution at high wave number region. (author)

Communication: Finding destructive interference features in molecular transport junctions

Energy Technology Data Exchange (ETDEWEB)

Reuter, Matthew G., E-mail: mgreuter@u.northwestern.edu [Department of Chemistry, Northwestern University, Evanston, Illinois 60208 (United States); Hansen, Thorsten [Department of Chemistry, H. C. Ørsted Institute, University of Copenhagen, DK 2100 Copenhagen (Denmark)

2014-11-14

Associating molecular structure with quantum interference features in electrode-molecule-electrode transport junctions has been difficult because existing guidelines for understanding interferences only apply to conjugated hydrocarbons. Herein we use linear algebra and the Landauer-Büttiker theory for electron transport to derive a general rule for predicting the existence and locations of interference features. Our analysis illustrates that interferences can be directly determined from the molecular Hamiltonian and the molecule–electrode couplings, and we demonstrate its utility with several examples.

Fluctuations and stability in the Advanced Toroidal Facility (ATF) torsatron

International Nuclear Information System (INIS)

Harris, J.H.; Charlton, L.A.; Bell, J.D.; Bigelow, T.S.; Carreras, B.A.; Colchin, R.J.; Crume, E.C.; Dominguez, N.; Dunlap, J.L.; Dyer, G.R.; England, A.C.; Glowienka, J.C.; Hillis, D.L.; Hiroe, S.; Horton, L.D.; Howe, H.C.; Isler, R.C.; Jernigan, T.C.; Leboeuf, J.N.; Lee, D.K.; Lynch, V.E.; Lyon, J.F.; Menon, M.M.; Murakami, M.; Rasmussen, D.A.; Uckan, T.; Wilgen, J.B.; Wing, W.R.; Bell, G.L.; Crocker, N.A.; Hanson, G.R.; Thomas, C.E.; Wade, M.R.; Ritz, C.P.

1990-01-01

We present the results of experimental and theoretical studies of fluctuations and instabilities in the ATF torsatron, a type of stellarator. Measurements of globally coherent magnetic fluctuations in high-β plasmas with narrow pressure profiles produced by a field error show evidence of self-stabilization ('second stability'); the trends are compatible with theoretical analysis of self-stabilization of resistive curvature-driven instabilities, but there are discrepancies between the absolute experimental and theoretical fluctuation amplitudes. Fluctuation measurements in plasma with broad pressure profiles reveal new phenomena--specifically, toroidally localized magnetic fluctuations, whose amplitudes increase with plasma pressure, and coherent density fluctuations with significant radial width

Characterisation of temperature gradient driven turbulence and transport

International Nuclear Information System (INIS)

Ottaviani, M.A.

2002-01-01

We report on extensive numerical studies aimed at characterising various aspects of temperature gradient driven turbulence. We specifically discuss results from 3D fluid models of ETG and of ITG turbulence, and results from a 2D+2D gyrokinetic model of trapped ion turbulence. Global transport exhibits gyro-Bohm scaling in both the ETG and the ITG model. The conductivity of the ETG model decreases weakly with beta. The heat transport is due to the EXB advection, the effect of the magnetic flutter is negligible. However the transport level is much lower than experimentally observed. In both 3D models the correlation lengths scale with the gyroradius, but they are typically a factor 10 larger. Vortices are elongated but their aspect ratio is independent of the gyroradius. Their radial size is limited by LD. The trapped ion model gives larger vortices due to the absence of LD from passing ions. Avalanches are observed in all the models, the weakest occurring in the ITG system. Their range increases with gyroradius, but more weakly than linearly. Finally, ZFs can limit the range of the avalanches, which explains why avalanches are weaker in the ITG model which is more sensitive to ZFs. (author)

Soc dynamics in a 2D model of turbulent particle transport in the sol

International Nuclear Information System (INIS)

Ghendrih, Ph.; Sarazin, Y.

1998-01-01

Interchange turbulence in two-dimensions is investigated in the Scrape-Off Layer of fusion devices, when driven by a constant core particle influx. Contrary to the standard gradient driven approach, density is allowed to fluctuate around its average profile. Transverse transport exhibits some of the features of Self-organised Critical systems, namely, inward and outward avalanches, together with a frequency spectrum decrease in 1 / f and f -2 at intermediate and high frequencies respectively. An avalanches occurs when follows the large radial structures of the electric potential. As experimentally, the radial profile of density relative fluctuations decreases from the wall into the core plasma, while that of density relative fluctuations peaks inside the SOL. Equilibrium density exhibits the experimental exponential decrease. An analytical expression of the SOL width Δ SOL is obtained, which maximizes the linear growth rate, when the poloidal modulation of electric potential equilibrium is taken into account. The parametric dependence of Δ SOL well agrees with experimental data. (authors)

Charge transport through molecular rods with reduced pi-conjugation.

Science.gov (United States)

Lörtscher, Emanuel; Elbing, Mark; Tschudy, Meinrad; von Hänisch, Carsten; Weber, Heiko B; Mayor, Marcel; Riel, Heike

2008-10-24

A series of oligophenylene rods of increasing lengths is synthesized to investigate the charge-transport mechanisms. Methyl groups are attached to the phenyl rings to weaken the electronic overlap of the pi-subsystems along the molecular backbones. Out-of-plane rotation of the phenyl rings is confirmed in the solid state by means of X-ray analysis and in solution by using UV/Vis spectroscopy. The influence of the reduced pi-conjugation on the resonant charge transport is studied at the single-molecule level by using the mechanically controllable break-junction technique. Experiments are performed under ultra-high-vacuum conditions at low temperature (50 K). A linear increase of the conductance gap with increasing number of phenyl rings (from 260 meV for one ring to 580 meV for four rings) is revealed. In addition, the absolute conductance of the first resonant peaks does not depend on the length of the molecular wire. Resonant transport through the first molecular orbital is found to be dominated by charge-carrier injection into the molecule, rather than by the intrinsic resistance of the molecular wire length.

Phase space fluctuations and dynamics of fluctuations of collective variables

Energy Technology Data Exchange (ETDEWEB)

Benhassine, B.; Farine, M.; Idier, D.; Remaud, B.; Sebille, F. (Lab. de Physique Nucleaire, IN2P3/CNRS, 44 - Nantes (France) Nantes Univ., 44 (France)); Hernandez, E.S. (Dept. de Fisica, Ciudad Universitaria, Buenos Aires (Argentina))

1992-08-03

Within the framework of theoretical approaches based on stochastic transport equation of one-body distribution function, a numerical treatment of the fluctuations of collective observables is studied and checked in comparison with analytical results either at equilibrium or close to it. (orig.).

Phase space fluctuations and dynamics of fluctuations of collective variables

International Nuclear Information System (INIS)

Benhassine, B.; Farine, M.; Idier, D.; Remaud, B.; Sebille, F.; Hernandez, E.S.

1992-01-01

Within the framework of theoretical approaches based on stochastic transport equation of one-body distribution function, a numerical treatment of the fluctuations of collective observables is studied and checked in comparison with analytical results either at equilibrium or close to it. (orig.)

Modulating Hole Transport in Multilayered Photocathodes with Derivatized p-Type Nickel Oxide and Molecular Assemblies for Solar-Driven Water Splitting

Energy Technology Data Exchange (ETDEWEB)

Shan, Bing [Department; Sherman, Benjamin D. [Department; Klug, Christina M. [Center; Nayak, Animesh [Department; Marquard, Seth L. [Department; Liu, Qing [Department; Bullock, R. Morris [Center; Meyer, Thomas J. [Department

2017-08-31

We report here a new photocathode composed of a bi-layered doped NiO film topped by a macro-mesoporous ITO (ioITO) layer with molecular assemblies attached to the ioITO surface. The NiO film containing a 2% K+ doped NiO inner layer and a 2% Cu2+ doped NiO outer layer provides sufficient driving force for hole transport after injection to NiO by the molecular assembly. The tri-layered oxide, NiK0.02O | NiCu0.02O | ioITO, sensitized by a ruthenium polypyridyl dye and functionalized with a nickel-based hydrogen evolution catalyst, outperforms its counterpart, NiO | NiO | ioITO, in photocatalytic hydrogen evolution from water over a period of several hours with a Faradaic yield of ~90%.

Leggett-Garg Inequalities for Quantum Fluctuating Work

Directory of Open Access Journals (Sweden)

Harry J. D. Miller

2018-03-01

Full Text Available The Leggett-Garg inequalities serve to test whether or not quantum correlations in time can be explained within a classical macrorealistic framework. We apply this test to thermodynamics and derive a set of Leggett-Garg inequalities for the statistics of fluctuating work done on a quantum system unitarily driven in time. It is shown that these inequalities can be violated in a driven two-level system, thereby demonstrating that there exists no general macrorealistic description of quantum work. These violations are shown to emerge within the standard Two-Projective-Measurement scheme as well as for alternative definitions of fluctuating work that are based on weak measurement. Our results elucidate the influences of temporal correlations on work extraction in the quantum regime and highlight a key difference between quantum and classical thermodynamics.

Transportation dose analysis using an interactive menu-driven computer program

International Nuclear Information System (INIS)

Strenge, D.L.; Peloquin, R.A.

1984-10-01

An easy-to-use software package is described for performing radiological consequence analyses for transportation scenarios involving truck or rail transport of spent fuel, HLW and other radioactive waste forms. The consequence analysis is based on the unit radiological factors (person-rem/km) developed by the Transportation Technology Center (Sandia National Laboratories). These generic unit radiological factors are combined with user-supplied information describing transporation distances, routes and waste types to estimate total exposure of the population. The software was developed for use in preparing the Environmental Assessment for the Monitored Retrievable Storage Program and is suitable for such analyses as siting waste repositories. The key feature of the software is the user-oriented, menu-driven interactive input mode available as an alternative to formatted input. The interactive input option allows the user to supply all input data, edit the data and run the program. Output reports can be diverted to a high-speed printer

Electronic and magnetic phase separation in EuB{sub 6}. Fluctuation spectroscopy and nonlinear transport; Elektronische und magnetische Phasenseparation in EuB{sub 6}. Fluktuationsspektroskopie und nichtlinearer Transport

Energy Technology Data Exchange (ETDEWEB)

Amyan, Adham

2013-07-09

The main topics of this thesis are electrical, stationary, and time-resolved transport measurements on EuB{sub 6} as well as the further development of measuring methods and analysis procedures of the fluctuation spectroscopy. The first part of this thesis was dedicated to the further development of the already known measuring methods under application of a fast data-acquisition card. The second part deals with the electrical transport properties of EuB{sub 6} and the understanding of the coupling between charge and magnetic degrees of freedom. By means of resistance and nonlinear-transport measurements as well as fluctuation spectroscopy hypotheses of other scientists were systematically verified as well as new knowledge obtained. The magnetoresistance was studied as function of the temperature in small external magnetic fields between 1 mT and 700 mT. Measurements of the third harmonic resistance as function of the temperature show maxima at T{sub MI} and T{sub C}. Electrical-resistance fluctuations were measured without external magnetic field between 5 and 100 K as well in presence of a magnetic field between 18 K and 32 K. At constant temperature measurements of the spectral power density in external magnetic fields were performed in the temperature range from 18 K to 32 K. Highly resolving measurements of the thermal expansion coefficient showed a very strong coupling of the magnetic (polaronic) degrees of freedom to the crystal lattice.

Time-dependent perpendicular fluctuations in the driven lattice Lorentz gas

Science.gov (United States)

Leitmann, Sebastian; Schwab, Thomas; Franosch, Thomas

2018-02-01

We present results for the fluctuations of the displacement of a tracer particle on a planar lattice pulled by a step force in the presence of impenetrable, immobile obstacles. The fluctuations perpendicular to the applied force are evaluated exactly in first order of the obstacle density for arbitrarily strong pulling and all times. The complex time-dependent behavior is analyzed in terms of the diffusion coefficient, local exponent, and the non-Skellam parameter, which quantifies deviations from the dynamics on the lattice in the absence of obstacles. The non-Skellam parameter along the force is analyzed in terms of an asymptotic model and reveals a power-law growth for intermediate times.

Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis.

Directory of Open Access Journals (Sweden)

Leandro Martínez

Full Text Available The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD and Root Mean Square Fluctuations (RMSF of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit.

Molecular Dynamics Investigation of Cl− and Water Transport through a Eukaryotic CLC Transporter

Science.gov (United States)

Cheng, Mary Hongying; Coalson, Rob D.

2012-01-01

Early crystal structures of prokaryotic CLC proteins identified three Cl– binding sites: internal (Sint), central (Scen), and external (Sext). A conserved external GLU (GLUex) residue acts as a gate competing for Sext. Recently, the first crystal structure of a eukaryotic transporter, CmCLC, revealed that in this transporter GLUex competes instead for Scen. Here, we use molecular dynamics simulations to investigate Cl– transport through CmCLC. The gating and Cl–/H+ transport cycle are inferred through comparative molecular dynamics simulations with protonated and deprotonated GLUex in the presence/absence of external potentials. Adaptive biasing force calculations are employed to estimate the potential of mean force profiles associated with transport of a Cl– ion from Sext to Sint, depending on the Cl– occupancy of other sites. Our simulations demonstrate that protonation of GLUex is essential for Cl– transport from Sext to Scen. The Scen site may be occupied by two Cl– ions simultaneously due to a high energy barrier (∼8 Kcal/mol) for a single Cl– ion to translocate from Scen to Sint. Binding two Cl– ions to Scen induces a continuous water wire from Scen to the extracellular solution through the side chain of the GLUex gate. This may initiate deprotonation of GLUex, which then drives the two Cl– ions out of Scen toward the intracellular side via two putative Cl– transport paths. Finally, a conformational cycle is proposed that would account for the exchange stoichiometry. PMID:22455919

Studies of Fluctuation Processes in Nuclear Collisions

Energy Technology Data Exchange (ETDEWEB)

Ayik, Sakir [Tennessee Technological Univ., Cookeville, TN (United States). Dept. of Physics

2016-04-14

The standard one-body transport approaches have been extensively applied to investigate heavy-ion collision dynamics at low and intermediate energies. At low energies the approach is the mean-field description of the time-dependent Hartree-Fock (TDHF) theory. At intermediate energies the approach is extended by including a collision term, and its application has been carried out mostly in the semi-classical framework of the Boltzmann-Uhling-Uhlenbeck (BUU) model. The standard transport models provide a good understanding of the average properties of the collision dynamics in terms of the effective interactions in both low and intermediate energies. However, the standard models are inadequate for describing the fluctuation dynamics of collective motion at low energies and disassembling of the nuclear system into fragments at intermediate energies resulting from the growth of density fluctuations in the spinodal region. Our tasks have been to improve the standard transport approaches by incorporating fluctuation mechanisms into the description. There are mainly two different mechanisms for fluctuations: (i) Collisional fluctuations generated by binary nucleon collisions, which provide the dominant mechanism at intermediate energies, and (ii) One-body mechanism or mean-field fluctuations, which is the dominant mechanism at low energies. In the first part of our project, the PI extended the standard transport model at intermediate energies by incorporating collisional mechanism according to the “Generalized Langevin Description” of Mori formalism. The PI and his collaborators carried out a number of applications for describing dynamical mechanism of nuclear multi fragmentations, and nuclear collective response in the semi-classical framework of the approach, which is known as the Boltzmann-Langevin model. In the second part of the project, we considered dynamical description at low energies. Because of the effective Pauli blocking, the collisional dissipation and

Evaluate transport processes in MERRA driven chemical transport models using updated 222Rn emission inventories and global observations

Science.gov (United States)

Zhang, B.; Liu, H.; Crawford, J. H.; Fairlie, T. D.; Chen, G.; Chambers, S. D.; Kang, C. H.; Williams, A. G.; Zhang, K.; Considine, D. B.; Payer Sulprizio, M.; Yantosca, R.

2015-12-01

Convective and synoptic processes play a major role in determining the transport and distribution of trace gases and aerosols in the troposphere. The representation of these processes in global models (at ~100-1000 km horizontal resolution) is challenging, because convection is a sub-grid process and needs to be parameterized, while synoptic processes are close to the grid scale. Depending on the parameterization schemes used in climate models, the role of convection in transporting trace gases and aerosols may vary from model to model. 222Rn is a chemically inert and radioactive gas constantly emitted from soil and has a half-life (3.8 days) comparable to synoptic timescale, which makes it an effective tracer for convective and synoptic transport. In this study, we evaluate the convective and synoptic transport in two chemical transport models (GMI and GEOS-Chem), both driven by the NASA's MERRA reanalysis. Considering the uncertainties in 222Rn emissions, we incorporate two more recent scenarios with regionally varying 222Rn emissions into GEOS-Chem/MERRA and compare the simulation results with those using the relatively uniform 222Rn emissions in the standard model. We evaluate the global distribution and seasonality of 222Rn concentrations simulated by the two models against an extended collection of 222Rn observations from 1970s to 2010s. The intercomparison will improve our understanding of the spatial variability in global 222Rn emissions, including the suspected excessive 222Rn emissions in East Asia, and provide useful feedbacks on 222Rn emission models. We will assess 222Rn vertical distributions at different latitudes in the models using observations at surface sites and in the upper troposphere and lower stratosphere. Results will be compared with previous models driven by other meteorological fields (e.g., fvGCM and GEOS4). Since the decay of 222Rn is the source of 210Pb, a useful radionuclide tracer attached to submicron aerosols, improved

Reducing and measuring fluctuations in the MST RFP: Enhancement of energy confinement and measurement of the MHD dynamo

International Nuclear Information System (INIS)

Den Hartog, D.J.; Almagri, A.F.

1996-09-01

A three- to five-fold enhancement of the energy confinement time in a reversed-field pinch (RFP) has been achieved in the Madison Symmetric Torus (MST) by reducing the amplitude of tearing mode fluctuations responsible for anomalous transport in the core of the RFP. By applying a transient poloidal inductive electric field to flatten the current density profile, the fluctuation amplitude b/B decreases from 1.5% to 0.8%, the electron temperature T e0 increases from 250 eV to 370 eV, the ohmic input power decreases from 4.5 MW to approximately 1.5 MW, the poloidal beta β 0 increases from 6% to 9%, and the energy confinement time τ E increases from 1 ms to ∼5 ms in I φ = 340 kA plasmas with density n = 1 x 10 19 m -3 . Current profile control methods are being developed for the RFP in a program to eliminate transport associated with these current-gradient-driven fluctuations. In addition to controlling the amplitude of the tearing modes, we are vigorously pursuing an understanding of the physics of these fluctuations. In particular, plasma flow, both equilibrium and fluctuating, plays a critical role in a diversity of physical phenomena in MST. The key results: 1) Edge probe measurements show that the MHD dynamo is active in low collisionality plasmas, while at high collisionality a new mechanism, the 'electron diamagnetic dynamo,' is observed. 2) Core spectroscopic measurements show that the toroidal velocity fluctuations of the plasma are coherent with the large-scale magnetic tearing modes; the scalar product of these two fluctuating quantities is similar to that expected for the MHD dynamo electromotive force. 3) Toroidal plasma flow in MST exhibits large radial shear and can be actively controlled, including unlocking locked discharges, by modifying E r with a robust biased probe. 24 refs

Fluctuations and structure of amphiphilic films; Fluctuations et structure de films d`amphiphiles

Energy Technology Data Exchange (ETDEWEB)

Gourier, CH

1996-07-01

This thesis is divided in three parts.The first part exposes in a theoretical point of view, how the fluctuations spectrum of an amphiphilic film is governed by its properties and its bidimensional characteristics.The measurements of fluctuations spectra of an interface are accessible with the measurement of intensity that interface diffuses out of the specular angle, we present in the second chapter the principles of the X rays diffusion by a real interface and see how the diffuse diffusion experiments allow to determine the fluctuations spectrum of an amphiphilic film. The second part is devoted to the different experimental techniques that have allowed to realize the study of fluctuation as well as the structural study.The third part is devoted to experimental results concerning the measurements of fluctuations spectra and to the study of the structure of amphiphilic films. We show that it is possible by using an intense source of X rays (ESRF: European Synchrotron Radiation Facility) to measure the water and amphiphilic films fluctuations spectra until molecular scales. The last chapter is devoted to the structural study and film fluctuations made of di-acetylenic molecules. (N.C.)

Stochastic models of intracellular transport

KAUST Repository

Bressloff, Paul C.

2013-01-09

The interior of a living cell is a crowded, heterogenuous, fluctuating environment. Hence, a major challenge in modeling intracellular transport is to analyze stochastic processes within complex environments. Broadly speaking, there are two basic mechanisms for intracellular transport: passive diffusion and motor-driven active transport. Diffusive transport can be formulated in terms of the motion of an overdamped Brownian particle. On the other hand, active transport requires chemical energy, usually in the form of adenosine triphosphate hydrolysis, and can be direction specific, allowing biomolecules to be transported long distances; this is particularly important in neurons due to their complex geometry. In this review a wide range of analytical methods and models of intracellular transport is presented. In the case of diffusive transport, narrow escape problems, diffusion to a small target, confined and single-file diffusion, homogenization theory, and fractional diffusion are considered. In the case of active transport, Brownian ratchets, random walk models, exclusion processes, random intermittent search processes, quasi-steady-state reduction methods, and mean-field approximations are considered. Applications include receptor trafficking, axonal transport, membrane diffusion, nuclear transport, protein-DNA interactions, virus trafficking, and the self-organization of subcellular structures. © 2013 American Physical Society.

Size Effect on Transport Properties of Gaseous Argon: A Molecular Dynamics Simulation Study

International Nuclear Information System (INIS)

Lee, Songhi

2014-01-01

We have carried out a series of equilibrium molecular dynamics (EMD) simulations of gaseous argon at 273.15 K and 1.00 atm for the calculation of transport properties as a function of the number of argon molecules (N). While the diffusion coefficients (D) of gaseous argon approach to the experimental measure with increasing N, the viscosities (η) and thermal conductivities (λ) obtained for N = 432 are unreliable due to the high fluctuation of the time correlation functions and those for N = 1728 are rather acceptable. Increasing further to N = 6912 has improved the MD results a little closer to the experimental measures for η and λ. Both the EMD results for η and λ for N = 6912 underestimate the experimental measures and it is not expected that the more increasing N makes the closer results to the experimental measures. One possible explanation for the large disagreement between MD results and the experimental measures for η and λ may be due to the use of LJ parameters which were used for liquid argon. In a recent study, we have examined the Green-Kubo formula for the calculation of transport properties (diffusion coefficient, viscosity, and thermal conductivity) of noble gases (He, Ne, Ar, Kr, and Xe) by carrying out a series of equilibrium molecular dynamics (EMD) simulations for the system of N=1728 at 273.15 K and 1.00 atm.1 While the diffusion coefficients (D) of noble gases were obtained through the original Green-Kubo formula, the viscosities (η) and thermal conductivities (λ) were obtained by utilizing the revised Green-Kubo formulas. The structural and dynamic properties of gaseous argon are completely different from those of liquid argon at 94.4 K and 1.374 g/cm 3 . The results for transport properties (D, η, and λ) at 273.15 K and 1.00 atm obtained from our EMD simulations are in general agreement with the experimental data and superior to the rigorous results of the kinetic theory

Variation in polydispersity in pump- and pressure-driven micro-droplet generators

Science.gov (United States)

Zeng, Wen; Jacobi, Ian; Li, Songjing; Stone, Howard A.

2015-11-01

The polydispersity of droplets produced in a typical T-junction microfluidic channel under both syringe-pump-driven and pressure-driven flow configurations is measured quantitatively. Both flow systems exhibit high-frequency flow fluctuations that result in an intrinsic polydispersity due to the mechanism of droplet generation. In addition to this intrinsic polydispersity, the syringe-pump-driven device also exhibits low-frequency fluctuations due to mechanical oscillations of the pump, which overwhelm the high-frequency flow fluctuations and produce a signficantly heightened level of polydispersity. The quantitative difference in polydispersity between the two configurations and time-resolved measurements of individual droplet sizes are presented in order to enable the design of better flow control systems for droplet production.

Photosynthetic antennae systems: energy transport and optical absorption

International Nuclear Information System (INIS)

Reineker, P.; Supritz, Ch.; Warns, Ch.; Barvik, I.

2004-01-01

The energy transport and the optical line shape of molecular aggregates, modeling bacteria photosynthetic light-harvesting systems (chlorosomes in the case of Chlorobium tepidum or Chloroflexus aurantiacus and LH2 in the case of Rhodopseudomonas acidophila) is investigated theoretically. The molecular units are described by two-level systems with an average excitation energy ε and interacting with each other through nearest-neighbor interactions. For LH2 an elliptical deformation of the ring is also allowed. Furthermore, dynamic and in the case of LH2 also quasi-static fluctuations of the local excitation energies are taken into account, simulating fast molecular vibrations and slow motions of the protein backbone, respectively. The fluctuations are described by Gaussian Markov processes in the case of the chlorosomes and by colored dichotomic Markov processes, with exponentially decaying correlation functions, with small (λ s ) and large (λ) decay constants, in the case of LH2

Electron transport in unipolar InGaN/GaN multiple quantum well structures grown by NH3 molecular beam epitaxy

KAUST Repository

Browne, David A.

2015-05-14

© 2015 AIP Publishing LLC. Unipolar-light emitting diode like structures were grown by NH3 molecular beam epitaxy on c plane (0001) GaN on sapphire templates. Studies were performed to experimentally examine the effect of random alloy fluctuations on electron transport through quantum well active regions. These unipolar structures served as a test vehicle to test our 2D model of the effect of compositional fluctuations on polarization-induced barriers. Variables that were systematically studied included varying quantum well number from 0 to 5, well thickness of 1.5 nm, 3 nm, and 4.5 nm, and well compositions of In0.14Ga0.86N and In0.19Ga0.81N. Diode-like current voltage behavior was clearly observed due to the polarization-induced conduction band barrier in the quantum well region. Increasing quantum well width and number were shown to have a significant impact on increasing the turn-on voltage of each device. Temperature dependent IV measurements clearly revealed the dominant effect of thermionic behavior for temperatures from room temperature and above. Atom probe tomography was used to directly analyze parameters of the alloy fluctuations in the quantum wells including amplitude and length scale of compositional variation. A drift diffusion Schrödinger Poisson method accounting for two dimensional indium fluctuations (both in the growth direction and within the wells) was used to correctly model the turn-on voltages of the devices as compared to traditional 1D simulation models.

Molecular fundamentals of nitrogen uptake and transport in trees.

Science.gov (United States)

Castro-Rodríguez, Vanessa; Cañas, Rafael A; de la Torre, Fernando N; Pascual, Ma Belén; Avila, Concepción; Cánovas, Francisco M

2017-05-01

Nitrogen (N) is frequently a limiting factor for tree growth and development. Because N availability is extremely low in forest soils, trees have evolved mechanisms to acquire and transport this essential nutrient along with biotic interactions to guarantee its strict economy. Here we review recent advances in the molecular basis of tree N nutrition. The molecular characteristics, regulation, and biological significance of membrane proteins involved in the uptake and transport of N are addressed. The regulation of N uptake and transport in mycorrhized roots and transcriptome-wide studies of N nutrition are also outlined. Finally, several areas of future research are suggested. © The Author 2017. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Transport and fluctuations in granular fluids from Boltzmann equation to hydrodynamics, diffusion and motor effects

CERN Document Server

Puglisi, Andrea

2015-01-01

This brief offers a concise presentation of granular fluids from the  point of view of non-equilibrium statistical physics. The emphasis is on fluctuations, which can be large in granular fluids due to the small system size (the number of grains is many orders of magnitude smaller than in molecular fluids). Firstly, readers will be introduced to the most intriguing experiments on fluidized granular fluids. Then granular fluid theory, which goes through increasing levels of coarse-graining and emerging collective phenomena, is described. Problems and questions are initially posed at the level of kinetic theory, which describes particle densities in full or reduced phase-space. Some answers become clear through hydrodynamics, which describes the evolution of slowly evolving fields. Granular fluctuating hydrodynamics, which builds a bridge to the most recent results in non-equilibrium statistical mechanics, is also introduced. Further and more interesting answers come when the dynamics of a massive intruder are...

NanoShuttles: Harnessing Motor Proteins to Transport Cargo in Synthetic Environments

Science.gov (United States)

Vogel, V.; Hess, H.

Motors have become a crucial commodity in our daily lives, from transportation to driving conveyor belts that enable the sequential assembly of cars and other industrial machines. For the sequential assembly of building blocks at the nanoscale that would not assemble spontaneously into larger functional systems, however, active transport systems are not yet available. In contrast, cells have evolved sophisticated molecular machinery that drives movement and active transport. Driven by the conversion of chemical into mechanical energy, namely through hydrolysis of the biological fuel ATP, molecular motors enable cells to operate far away from equilibrium by transporting organelles and molecules to designated locations within the cell, often against concentration gradients. Inspired by the biological concept of active transport, major efforts are underway to learn how to build nanoscale transport systems that are driven by molecular motors. Emerging engineering principles are discussed of how to build tracks and junctions to guide such nanoshuttles, how to load them with cargo and control their speed, how to use active transport to assemble mesoscopic structures that would otherwise not assemble spontaneously and what polymeric materials to choose to integrate motors into MEMS and other biohybrid devices. Finally, two applications that exploit the physical properties of microtubules are discussed, surface imaging by a swarm of microtubules and a self-assembled picoNewton force meter to probe receptor-ligand interactions.

Models for microtubule cargo transport coupling the Langevin equation to stochastic stepping motor dynamics: Caring about fluctuations.

Science.gov (United States)

Bouzat, Sebastián

2016-01-01

One-dimensional models coupling a Langevin equation for the cargo position to stochastic stepping dynamics for the motors constitute a relevant framework for analyzing multiple-motor microtubule transport. In this work we explore the consistence of these models focusing on the effects of the thermal noise. We study how to define consistent stepping and detachment rates for the motors as functions of the local forces acting on them in such a way that the cargo velocity and run-time match previously specified functions of the external load, which are set on the base of experimental results. We show that due to the influence of the thermal fluctuations this is not a trivial problem, even for the single-motor case. As a solution, we propose a motor stepping dynamics which considers memory on the motor force. This model leads to better results for single-motor transport than the approaches previously considered in the literature. Moreover, it gives a much better prediction for the stall force of the two-motor case, highly compatible with the experimental findings. We also analyze the fast fluctuations of the cargo position and the influence of the viscosity, comparing the proposed model to the standard one, and we show how the differences on the single-motor dynamics propagate to the multiple motor situations. Finally, we find that the one-dimensional character of the models impede an appropriate description of the fast fluctuations of the cargo position at small loads. We show how this problem can be solved by considering two-dimensional models.

Optimal control of quantum systems: Origins of inherent robustness to control field fluctuations

International Nuclear Information System (INIS)

Rabitz, Herschel

2002-01-01

The impact of control field fluctuations on the optimal manipulation of quantum dynamics phenomena is investigated. The quantum system is driven by an optimal control field, with the physical focus on the evolving expectation value of an observable operator. A relationship is shown to exist between the system dynamics and the control field fluctuations, wherein the process of seeking optimal performance assures an inherent degree of system robustness to such fluctuations. The presence of significant field fluctuations breaks down the evolution of the observable expectation value into a sequence of partially coherent robust steps. Robustness occurs because the optimization process reduces sensitivity to noise-driven quantum system fluctuations by taking advantage of the observable expectation value being bilinear in the evolution operator and its adjoint. The consequences of this inherent robustness are discussed in the light of recent experiments and numerical simulations on the optimal control of quantum phenomena. The analysis in this paper bodes well for the future success of closed-loop quantum optimal control experiments, even in the presence of reasonable levels of field fluctuations

Theoretical studies on rapid fluctuations in solar flares

International Nuclear Information System (INIS)

Vlahos, L.

1986-01-01

Rapid fluctuations in the emission of solar bursts may have many different origins, e.g., the acceleration process can have a pulsating structure, the propagation of energetic electrons and ions can be interrupted from plasma instabilities and finally the electromagnetic radiation produced by the interaction of electrostatic and electromagnetic waves may have a pulsating behavior in time. In two separate studies the conditions for rapid fluctuations in solar flare driven emission were analyzed

Theoretical studies on rapid fluctuations in solar flares

Science.gov (United States)

Vlahos, Loukas

1986-01-01

Rapid fluctuations in the emission of solar bursts may have many different origins e.g., the acceleration process can have a pulsating structure, the propagation of energetic electrons and ions can be interrupted from plasma instabilities and finally the electromagnetic radiation produced by the interaction of electrostatic and electromagnetic waves may have a pulsating behavior in time. In two separate studies the conditions for rapid fluctuations in solar flare driven emission were analyzed.

Ultrafast Dynamics in Light-Driven Molecular Rotary Motors Probed by Femtosecond Stimulated Raman Spectroscopy

NARCIS (Netherlands)

Hall, Christopher R.; Conyard, Jamie; Heisler, Ismael A.; Jones, Garth; Frost, James; Browne, Wesley R.; Feringa, Ben L.; Meech, Stephen R.

2017-01-01

Photochemical isomerization in sterically crowded chiral alkenes is the driving force for molecular rotary motors in nanoscale machines. Here the excited-state dynamics and structural evolution of the prototypical light-driven rotary motor are followed on the ultrafast time scale by femtosecond

Pressure-driven sound turbulence in a high-β plasma

International Nuclear Information System (INIS)

Stenzel, R.L.

1990-01-01

In a large laboratory plasma [1 m diamx2 m, n e ≤10 12 cm -3 , β 0 ≅15 G, β e =nkT e /(β 0 2 /2μ 0 )≅0.5], strong density fluctuations (δn/n≅50%) near the lower hybrid frequency (ω ce ω ci ) 1/2 are identified as cross-field sound waves (k perpendicular much-gt k parallel , ω/k perpendicular ≅c s ) driven unstable by the electron diamagnetic drift v d =∇pxB/neβ 2 , v d >c s . Wave steepening and refraction saturate the instability. Wave-enhanced transport but insignificant particle acceleration are observed

Effect of molecular topology on the transport properties of dendrimers in dilute solution at Θ temperature: A Brownian dynamics study

Science.gov (United States)

Bosko, Jaroslaw T.; Ravi Prakash, J.

2008-01-01

Structure and transport properties of dendrimers in dilute solution are studied with the aid of Brownian dynamics simulations. To investigate the effect of molecular topology on the properties, linear chain, star, and dendrimer molecules of comparable molecular weights are studied. A bead-spring chain model with finitely extensible springs and fluctuating hydrodynamic interactions is used to represent polymer molecules under Θ conditions. Structural properties as well as the diffusivity and zero-shear-rate intrinsic viscosity of polymers with varied degrees of branching are analyzed. Results for the free-draining case are compared to and found in very good agreement with the Rouse model predictions. Translational diffusivity is evaluated and the difference between the short-time and long-time behavior due to dynamic correlations is observed. Incorporation of hydrodynamic interactions is found to be sufficient to reproduce the maximum in the intrinsic viscosity versus molecular weight observed experimentally for dendrimers. Results of the nonequilibrium Brownian dynamics simulations of dendrimers and linear chain polymers subjected to a planar shear flow in a wide range of strain rates are also reported. The flow-induced molecular deformation of molecules is found to decrease hydrodynamic interactions and lead to the appearance of shear thickening. Further, branching is found to suppress flow-induced molecular alignment and deformation.

Transport barriers with and without shear flows in a magnetized plasma

International Nuclear Information System (INIS)

Martinell, Julio J.

2014-01-01

Different ways of producing a transport barrier in a toroidal magnetized plasma are discussed and the properties of the barriers are analyzed. The first mechanism is associated with the presence of a sheared plasma flow that is present in a limited region of the plasma, which creates a zonal flow. In contrast to the usual paradigm stating that the sheared flow reduces the turbulence correlation length and leads to suppression of the fluctuation driven transport in the region of highest shear, it is shown that from the perspective of chaotic transport of plasma particles in the fluctuation fields, the transport barrier is formed in the region of zero shear and it can be destroyed when the fluctuation level is high enough. It is also shown that finite gyroradius effects modify the dynamics and introduces new conditions for barrier formation. The second mechanism considers a method in which radio-frequency waves injected into the plasma can stabilize the drift waves and therefore the anomalous transport is reduced, creating a barrier. This process does not involve the presence of sheared flows and depends only on the effect of the RF wave field on the drift waves. The stabilizing effect in this case is due to the nonlinear ponderomotive force which acts in a way that offsets the pressure gradient destabilization. Finally, a mechanism based on the ponderomotive force of RF waves is described which produces poloidal plasma rotation around the resonant surface due to the asymmetry of induced transport; it creates a transport barrier by shear flow stabilization of turbulence

Molecular mechanisms of water transport in the eye

DEFF Research Database (Denmark)

Hamann, Steffen

2002-01-01

The four major sites for ocular water transport, the corneal epithelium and endothelium, the ciliary epithelium, and the retinal pigment epithelium, are reviewed. The cornea has an inherent tendency to swell, which is counteracted by its two surface cell layers, the corneal epithelium...... and endothelium. The bilayered ciliary epithelium secretes the aqueous humor into the posterior chamber, and the retinal pigment epithelium transports water from the retinal to the choroidal site. For each epithelium, ion transport mechanisms are associated with fluid transport, but the exact molecular coupling...... sites between ion and water transport remain undefined. In the retinal pigment epithelium, a H+-lactate cotransporter transports water. This protein could be the site of coupling between salt and water in this epithelium. The distribution of aquaporins does not suggest a role for these proteins...

Local Polar Fluctuations in Lead Halide Perovskite Crystals

Science.gov (United States)

Yaffe, Omer; Guo, Yinsheng; Tan, Liang Z.; Egger, David A.; Hull, Trevor; Stoumpos, Constantinos C.; Zheng, Fan; Heinz, Tony F.; Kronik, Leeor; Kanatzidis, Mercouri G.; Owen, Jonathan S.; Rappe, Andrew M.; Pimenta, Marcos A.; Brus, Louis E.

2017-03-01

Hybrid lead-halide perovskites have emerged as an excellent class of photovoltaic materials. Recent reports suggest that the organic molecular cation is responsible for local polar fluctuations that inhibit carrier recombination. We combine low-frequency Raman scattering with first-principles molecular dynamics (MD) to study the fundamental nature of these local polar fluctuations. Our observations of a strong central peak in the cubic phase of both hybrid (CH3 NH3 PbBr3 ) and all-inorganic (CsPbBr3 ) lead-halide perovskites show that anharmonic, local polar fluctuations are intrinsic to the general lead-halide perovskite structure, and not unique to the dipolar organic cation. MD simulations indicate that head-to-head Cs motion coupled to Br face expansion, occurring on a few hundred femtosecond time scale, drives the local polar fluctuations in CsPbBr3 .

Local Polar Fluctuations in Lead Halide Perovskite Crystals

Energy Technology Data Exchange (ETDEWEB)

Yaffe, Omer; Guo, Yinsheng; Tan, Liang Z.; Egger, David A.; Hull, Trevor; Stoumpos, Constantinos C.; Zheng, Fan; Heinz, Tony F.; Kronik, Leeor; Kanatzidis, Mercouri G.; Owen, Jonathan S.; Rappe, Andrew M.; Pimenta, Marcos A.; Brus, Louis E.

2017-03-01

Hybrid lead-halide perovskites have emerged as an excellent class of photovoltaic materials. Recent reports suggest that the organic molecular cation is responsible for local polar fluctuations that inhibit carrier recombination. We combine low-frequency Raman scattering with first-principles molecular dynamics (MD) to study the fundamental nature of these local polar fluctuations. Our observations of a strong central peak in the cubic phase of both hybrid (CH3NH3PbBr3) and all-inorganic (CsPbBr3) leadhalide perovskites show that anharmonic, local polar fluctuations are intrinsic to the general lead-halide perovskite structure, and not unique to the dipolar organic cation. MD simulations indicate that head-tohead Cs motion coupled to Br face expansion, occurring on a few hundred femtosecond time scale, drives the local polar fluctuations in CsPbBr3.

Transport coefficients for dense hard-disk systems

NARCIS (Netherlands)

García-Rojo, R.; Luding, S.; Brey, J.J.

2006-01-01

A study of the transport coefficients of a system of elastic hard disks based on the use of Helfand-Einstein expressions is reported. The self-diffusion, the viscosity, and the heat conductivity are examined with averaging techniques especially appropriate for event-driven molecular dynamics

Current and noise in driven heterostructures

Energy Technology Data Exchange (ETDEWEB)

Kaiser, Franz

2009-02-18

In this thesis we consider the electron transport in nanoscale systems driven by an external energy source. We introduce a tight-binding Hamiltonian containing an interaction term that describes a very strong Coulomb repulsion between electrons in the system. Since we deal with time-dependent situations, we employ a Floquet theory to take into account the time periodicity induced by different external oscillating fields. For the two-level system, we even provide an analytical solution for the eigenenergies with arbitrary phase shift between the levels for a cosine-shaped driving. To describe time-dependent driven transport, we derive a master equation by tracing out the influence of the surrounding leads in order to obtain the reduced density operator of the system. We generalise the common master equation for the reduced density operator to perform an analysis of the noise characteristics. The concept of Full Counting Statistics in electron transport gained much attention in recent years proven its value as a powerful theoretical technique. Combining its advantages with the master equation approach, we find a hierarchy in the moments of the electron number in one lead that allows us to calculate the first two cumulants. The first cumulant can be identified as the current passing through the system, while the noise of this transmission process is reflected by the second cumulant. Moreover, in combination with our Floquet approach, the formalism is not limited to static situations, which we prove by calculating the current and noise characteristics for the non-adiabatic electron pump. We study the influence of a static energy disorder on the maximal possible current for different realisations. Further, we explore the possibility of non-adiabatically pumping electrons in an initially symmetric system if random fluctuations break this symmetry. Motivated by recent and upcoming experiments, we use our extended Floquet model to properly describe systems driven by

Mass transport thermodynamics in nonisothermal molecular liquid mixtures

Energy Technology Data Exchange (ETDEWEB)

Semenov, Semen N [Institute for Biochemical Physics, Russian Academy of Sciences, Moscow (Russian Federation); Schimpf, M E [Department of Chemistry and Biochemistry, Boise State University, Boise, ID (United States)

2009-10-31

Mass transport in a nonisothermal binary molecular mixture is systematically discussed in terms of nonequilibrium thermodynamics, which for the first time allows a consistent and unambiguous description of the process. The thermodynamic and hydrodynamic approaches are compared, revealing that nonequilibrium thermodynamics and physicochemical hydrodynamics yield essentially the same results for molecular systems. The applicability limits for the proposed version of the thermodynamic approach are determined for large particles. (methodological notes)

Quantum work fluctuation theorem: Nonergodic Brownian motion case

International Nuclear Information System (INIS)

Bai, Zhan-Wu

2014-01-01

The work fluctuations of a quantum Brownian particle driven by an external force in a general nonergodic heat bath are studied under a general initial state. The exact analytical expression of the work probability distribution function is derived. Results show the existence of a quantum asymptotic fluctuation theorem, which is in general not a direct generalization of its classical counterpart. The form of this theorem is dependent on the structure of the heat bath and the specified initial condition.

Molecular Rayleigh Scattering Diagnostic for Measurement of High Frequency Temperature Fluctuations

Science.gov (United States)

Mielke, Amy F.; Elam, Kristie A.

2005-01-01

A novel technique for measurement of high frequency temperature fluctuations in unseeded gas flows using molecular Rayleigh scattering is investigated. The spectrum of laser light scattered from molecules in a gas flow is resolved using a Fabry-Perot interferometer. The width of the spectral peak is broadened by thermal motion of the molecules and hence is related to gas temperature. The interference fringe pattern containing spectral information is divided into four concentric regions using a series of mirrors angled with respect to one another. Light from each of these regions is directed towards photomultiplier tubes and sampled at 10 kHz using photon counting electronics. Monitoring the relative change in intensity within each region allows measurement of gas temperature. Independently monitoring the total scattered intensity provides a measure of gas density. This technique also has the potential to simultaneously measure a single component of flow velocity by monitoring the spectral peak location. Measurements of gas temperature and density are demonstrated using a low speed heated air jet surrounded by an unheated air co-flow. Mean values of temperature and density are shown for radial scans across the jet flow at a fixed axial distance from the jet exit plane. Power spectra of temperature and density fluctuations at several locations in the jet are also shown. The instantaneous measurements have fairly high uncertainty; however, long data records provide highly accurate statistically quantities, which include power spectra. Mean temperatures are compared with thermocouple measurements as well as the temperatures derived from independent density measurements. The accuracy for mean temperature measurements was +/- 7 K.

Hydration effect on the electronic transport properties of oligomeric phenylene ethynylene molecular junctions

International Nuclear Information System (INIS)

Zong-Liang, Li; Huai-Zhi, Li; Yong, Ma; Guang-Ping, Zhang; Chuan-Kui, Wang

2010-01-01

A first-principles computational method based on the hybrid density functional theory is developed to simulate the electronic transport properties of oligomeric phenylene ethynylene molecular junctions with H 2 O molecules accumulated in the vicinity as recently reported by Na et al. [Nanotechnology 18 424001 (2007)]. The numerical results show that the hydrogen bonds between the oxygen atoms of the oligomeric phenylene ethynylene molecule and H 2 O molecules result in the localisation of the molecular orbitals and lead to the lower transition peaks. The H 2 O molecular chains accumulated in the vicinity of the molecular junction can not only change the electronic structure of the molecular junctions, but also open additional electronic transport pathways. The obvious influence of H 2 O molecules on the electronic structure of the molecular junction and its electronic transport properties is thus demonstrated. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

Fluctuation of heat current in Josephson junctions

Directory of Open Access Journals (Sweden)

P. Virtanen

2015-02-01

Full Text Available We discuss the statistics of heat current between two superconductors at different temperatures connected by a generic weak link. As the electronic heat in superconductors is carried by Bogoliubov quasiparticles, the heat transport fluctuations follow the Levitov–Lesovik relation. We identify the energy-dependent quasiparticle transmission probabilities and discuss the resulting probability density and fluctuation relations of the heat current. We consider multichannel junctions, and find that heat transport in diffusive junctions is unique in that its statistics is independent of the phase difference between the superconductors.

Role of Reynolds stress and toroidal momentum transport in the dynamics of internal transport barriers

International Nuclear Information System (INIS)

Kim, S. S.; Jhang, Hogun; Diamond, P. H.

2012-01-01

We study the interplay between intrinsic rotation and internal transport barrier (ITB) dynamics through the dynamic change of the parallel Reynolds stress. Global flux-driven gyrofluid simulations are used for this study. In particular, we investigate the role of parallel velocity gradient instability (PVGI) in the ITB formation and the back transition. It is found that the excitation of PVGI is followed by a change in the Reynolds stress which drives a momentum redistribution. This significantly influences E×B shear evolution and subsequent ITB dynamics. Nonlocal interactions among fluctuations are also observed during the PVGI excitation, resulting in turbulence suppression at the ITB.

Fluctuation and thermal energy balance for drift-wave turbulence

International Nuclear Information System (INIS)

Kim, Chang-Bae; Horton, W.

1990-05-01

Energy conservation for the drift-wave system is shown to be separated into the wave-energy power balance equation and an ambient thermal-energy transport equation containing the anomalous transport fluxes produced by the fluctuations. The wave energy equation relates the wave energy density and wave energy flux to the anomalous transport flux and the dissipation of the fluctuations. The thermal balance equation determines the evolution of the temperature profiles from the divergence of the anomalous heat flux, the collisional heating and cooling mechanisms and the toroidal pumping effect. 16 refs., 1 tab

Fluctuation and thermal energy balance for drift-wave turbulence

International Nuclear Information System (INIS)

Changbae Kim; Horton, W.

1991-01-01

Energy conservation for the drift-wave system is shown to be separated into the wave-energy power balance equation and an ambient thermal-energy transport equation containing the anomalous transport fluxes produced by the fluctuations. The wave energy equation relates the wave energy density and wave energy flux to the anomalous transport flux and the dissipation of the fluctuations. The thermal balance equation determines the evolution of the temperature profiles from the divergence of the anomalous heat flux, the collisional heating and cooling mechanisms and the toroidal pumping effect. (author)

Theoretical studies of turbulence and anomalous transport in toroidal confinement devices

International Nuclear Information System (INIS)

Terry, P.W.

1990-01-01

The research performed under this grant during the current year has focused on key issues with respect to turbulence and transport in toroidal confinement devices. This work includes theoretical and computational studies of electron thermal confinement which have concentrated on the role of sheared poloidal flow in suppressing turbulence and transport, trapped ion convective cell turbulence and microtearing turbulence; analytical studies of anomalous particle transport and pinch mechanisms, and comparison with experimental measurement; development of the theory of self-consistent radial transport of field-aligned momentum in the tokamak and RFP; and work on other topics (ion temperature gradient driven turbulence, RFP fluctuation theory, coherent structures). Progress and publications in these areas are briefly summarized in this report. 20 refs

Computer simulation of transport driven current in tokamaks

International Nuclear Information System (INIS)

Nunan, W.J.; Dawson, J.M.

1993-01-01

Plasma transport phenomena can drive large currents parallel to an externally applied magnetic field. The Bootstrap Current Theory accounts for the effect of Banana diffusion on toroidal current, but the effect is not confined to that transport regime. The authors' 2 1/2-D, electromagnetic, particle simulations have demonstrated that Maxwellian plasmas in static toroidal and vertical fields spontaneously develop significant toroidal current, even in the absence of the open-quotes seed currentclose quotes which the Bootstrap Theory requires. Other simulations, in both toroidal and straight cylindrical geometries, and without any externally imposed electric field, show that if the plasma column is centrally fueled, and if the particle diffusion coefficient exceeds the magnetic diffusion coefficient (as is true in most tokamaks) then the toroidal current grows steadily. The simulations indicate that such fueling, coupled with central heating due to fusion reactions may drive all of the tokamak's toroidal current. The Bootstrap and dynamo mechanisms do not drive toroidal current where the poloidal magnetic field is zero. The simulations, as well as initial theoretical work, indicate that in tokamak plasmas, various processes naturally transport current from the outer regions of the plasma to the magnetic axis. The mechanisms which cause this effective electron viscosity include conventional binary collisions, wave emission and reabsorption, and also convection associated with rvec E x rvec B vortex motion. The simulations also exhibit preferential loss of particles carrying current opposing the bulk plasma current. This preferential loss generates current even at the magnetic axis. If these self-seeding mechanisms function in experiments as they do in the simulations, then transport driven current would eliminate the need for any external current drive in tokamaks, except simple ohmic heating for initial generation of the plasma

Transport phenomena

International Nuclear Information System (INIS)

Kirczenow, G.; Marro, J.

1974-01-01

Some simple remarks on the basis of transport theory. - Entropy, dynamics and scattering theory. - Response, relaxation and fluctuation. - Fluctuating hydrodynamics and renormalization of susceptibilities and transport coefficients. - Irreversibility of the transport equations. - Ergodic theory and statistical mechanics. - Correlation functions in Heisenberg magnets. - On the Enskog hard-sphere kinetic eqquation and the transport phenomena of dense simple gases. - What can one learn from Lorentz models. - Conductivity in a magnetic field. - Transport properties in gases in presence of external fields. - Transport properties of dilute gases with internal structure. (orig.) [de

Theory of transport through molecular magnets

Science.gov (United States)

Schoeller, Herbert

2007-03-01

Quantum transport through single molecular magnets (SMM) is starting to become a new exciting field in molecular spin electronics. Recent experiments [1,2] have shown that magnetic excitations can be identified in transport measurements and that NDC effects and complete current suppression can be explained by charge dependent anisotropies. Recent theoretical investigations [3,4,5] are presented which demonstrate fingerprints of quantum tunneling of magnetization (QTM). For weak tunneling, the violation of spin-selection rules leads to the occurence of fake resonances with temperature-dependent position [3]. For strongtunneling, it is show that a pseudo spin-1/2 Kondo effect is induced by QTM. If the Kondo temperature TK is smaller than the distance to excited magnetic states, selection rules depending on spin and symmetry of the SMM are derived for the Kondo effect to occur [4]. If TK exceeds the anisotropy barrier, it is shown that a reentrant Kondo effect can be induced by application of a longitudinal magnetic field for SMM with half-integer or integer spin [5]. This effect can be used for transport spectroscopy of the various anisotropies characterizing a SMM. [1] H.B. Heersche et al., Phys. Rev. Lett. 96, 206801 (2006). [2] Moon-Ho Jo et al., Nano Lett. 6, 2014 (2006). [3] C. Romeike, M.R. Wegewijs, H. Schoeller, Phys. Rev. Lett. 96, 196805 (2006). [4] C. Romeike, M.R. Wegewijs, W. Hofstetter, H. Schoeller, Phys. Rev. Lett. 96, 196601 (2006). [5] C. Romeike, M.R. Wegewijs, W. Hofstetter, H. Schoeller, to be published in Phys. Rev. Lett., cond-mat/0605514.

Role of Molecular Weight Distribution on Charge Transport in Semiconducting Polymers

KAUST Repository

Himmelberger, Scott

2014-10-28

© 2014 American Chemical Society. Model semiconducting polymer blends of well-controlled molecular weight distributions are fabricated and demonstrated to be a simple method to control intermolecular disorder without affecting intramolecular order or degree of aggregation. Mobility measurements exhibit that even small amounts of low molecular weight material are detrimental to charge transport. Trends in charge carrier mobility can be reproduced by a simple analytical model which indicates that carriers have no preference for high or low molecular weight chains and that charge transport is limited by interchain hopping. These results quantify the role of long polymer tie-chains and demonstrate the need for controlled polydispersity for achieving high carrier mobilities.

Capillary-Driven Solute Transport and Precipitation in Porous Media during Dry-Out

Science.gov (United States)

Ott, Holger; Andrew, Matthew; Blunt, Martin; Snippe, Jeroen

2014-05-01

The injection of dry or under-saturated gases or supercritical (SC) fluids into water bearing formations might lead to a formation dry-out in the vicinity of the injection well. The dry-out is caused by the evaporation/dissolution of formation water into the injected fluid and the subsequent transport of dissolved water in the injected fluid away from the injection well. Dry-out results in precipitation from solutes of the formation brine and consequently leads to a reduction of the rock's pore space (porosity) and eventually to a reduction of permeability near the injection well, or even to the loss of injectivity. Recently evidence has been found that the complexity of the pore space and the respective capillary driven solute transport plays a key role. While no effective-permeability (Keff) reduction was observed in a single-porosity sandstone, multi porosity carbonate rocks responded to precipitation with a strong reduction of Keff. The reason for the different response of Keff to salt precipitation is suspected to be in the exact location of the precipitate (solid salt) in the pore space. In this study, we investigate dry-out and salt precipitation due to supercritical CO2 injection in single and multi-porosity systems under near well-bore conditions. We image fluid saturation changes by means of μCT scanning during desaturation. We are able to observe capillary driven transport of the brine phase and the respective transport of solutes on the rock's pore scale. Finally we have access to the precipitated solid-salt phase and their distribution. The results can proof the thought models behind permeability porosity relationships K(φ) for injectivity modeling. The topic and the mechanisms we show are of general interest for drying processes in porous material such as soils and paper.

Temporal fluctuations after a quantum quench: Many-particle dephasing

Science.gov (United States)

Marquardt, Florian; Kiendl, Thomas

After a quantum quench, the expectation values of observables continue to fluctuate in time. In the thermodynamic limit, one expects such fluctuations to decrease to zero, in order for standard statistical physics to hold. However, it is a challenge to determine analytically how the fluctuations decay as a function of system size. So far, there have been analytical predictions for integrable models (which are, naturally, somewhat special), analytical bounds for arbitrary systems, and numerical results for moderate-size systems. We have discovered a dynamical regime where the decrease of fluctuations is driven by many-particle dephasing, instead of a redistribution of occupation numbers. On the basis of this insight, we are able to provide exact analytical expressions for a model with weak integrability breaking (transverse Ising chain with additional terms). These predictions explicitly show how fluctuations are exponentially suppressed with system size.

Directed transport of confined Brownian particles with torque

Science.gov (United States)

Radtke, Paul K.; Schimansky-Geier, Lutz

2012-05-01

We investigate the influence of an additional torque on the motion of Brownian particles confined in a channel geometry with varying width. The particles are driven by random fluctuations modeled by an Ornstein-Uhlenbeck process with given correlation time τc. The latter causes persistent motion and is implemented as (i) thermal noise in equilibrium and (ii) noisy propulsion in nonequilibrium. In the nonthermal process a directed transport emerges; its properties are studied in detail with respect to the correlation time, the torque, and the channel geometry. Eventually, the transport mechanism is traced back to a persistent sliding of particles along the even boundaries in contrast to scattered motion at uneven or rough ones.

Structure of density fluctuations in the edge plasma of ASDEX

International Nuclear Information System (INIS)

Rudyj, A.; Carlson, A.; Endler, M.; Giannone, L.; Niedermeyer, H.; Theimer, G.

1990-01-01

It is now generally believed that the anomalous particle and energy transport in tokamaks is caused by turbulent fluctuations. The physical nature of these fluctuations (mode type, the driving mechanism) have still to be identified experimentally before a self consistent transport theory can be developed. In contrast to the confinement region the plasma edge can be well diagnosed. H α -light, which is emitted at the edge, reacts to density and to some extend to temperature fluctuations. It delivers information about radially integrated spectra and correlations. Langmuir probes measure density and potential fluctuations with good spatial resolution. The edge transport governs the physics in the scrape-off layer and in the divertor which is extremely important for a reactor and therefore deserves a major experimental effort. In this paper we report on an attempt to gain detailed information about the spatial and temporal structure of the edge turbulence hoping to reduce the degrees of freedom for theoretical models to a manageable number. (author) 3 refs., 3 figs

Magnetic fluctuation measurements in the Tokapole II tokamak

International Nuclear Information System (INIS)

LaPointe, M.A.

1990-09-01

Magnetic fluctuation measurements have been made in the Tokapole II tokamak in the frequency range 10 kHz ≤ f ≤ 5 MHz. The fluctuations above 500 kHz varied greatly as the effective edge safety factor, q a , was varied over the range 0.8 ≤ q a ≤ 3.8. As q a was varied from 3.8 to 0.8 the high frequency magnetic fluctuation amplitude increased by over three orders of magnitude. The fluctuation amplitude for 0.5 to 2.0 MHz was a factor of 10 lower than the fluctuation amplitude in the range 100 to 400 kHz for q a of 0.8. When q a was increased to 3.8 the difference between the differing frequency ranges increased to a factor of 10 3 . Comparison of the measured broadband fluctuation amplitudes with those predicted from thermally driven Alfven and magnetosonic waves shows that the amplitudes are at least 1000 times larger than the theoretical predictions. This indicates that there is some other mechanism driving the higher frequency magnetic fluctuations. Estimates show that the contribution by the magnetic fluctuations above 500 kHz to the estimated electron energy loss from stochastic fields is negligible. The profiles of the various components of the magnetic fluctuations indicate the possibility that the shear in the magnetic field may stabilize whatever instabilities drive the magnetic fluctuations

Density Fluctuations in the Solar Wind Driven by Alfvén Wave Parametric Decay

Science.gov (United States)

Bowen, Trevor A.; Badman, Samuel; Hellinger, Petr; Bale, Stuart D.

2018-02-01

Measurements and simulations of inertial compressive turbulence in the solar wind are characterized by anti-correlated magnetic fluctuations parallel to the mean field and density structures. This signature has been interpreted as observational evidence for non-propagating pressure balanced structures, kinetic ion-acoustic waves, as well as the MHD slow-mode. Given the high damping rates of parallel propagating compressive fluctuations, their ubiquity in satellite observations is surprising and suggestive of a local driving process. One possible candidate for the generation of compressive fluctuations in the solar wind is the Alfvén wave parametric instability. Here, we test the parametric decay process as a source of compressive waves in the solar wind by comparing the collisionless damping rates of compressive fluctuations with growth rates of the parametric decay instability daughter waves. Our results suggest that generation of compressive waves through parametric decay is overdamped at 1 au, but that the presence of slow-mode-like density fluctuations is correlated with the parametric decay of Alfvén waves.

Propagation characteristics and relation between electrostatic and magnetic fluctuations in DITE

International Nuclear Information System (INIS)

Vayakis, G.

1993-01-01

An account is given of experiments on the DITE tokamak, using a fast reciprocating set of combined Langmuir and magnetic probes in the same discharge to compare the propagation characteristics of the turbulent electrostatic and magnetic perturbations with those expected from the measured local electric field and pressure gradient, and to investigate the effect of shear on cross-field transport. In addition, the relation between the electrostatic and magnetic aspects of the turbulence is investigated using direct cross-spectral measurements. The results are consistent with a picture in which magnetic fluctuations in the edge are due to currents driven by the basically electrostatic turbulence, whose own propagation behaviour is dominated by the effects of the sheared E X B/B 2 velocity. (author). 35 refs, 18 figs, 1 tab

A review on nanomechanical resonators and their applications in sensors and molecular transportation

International Nuclear Information System (INIS)

Arash, Behrouz; Rabczuk, Timon; Jiang, Jin-Wu

2015-01-01

Nanotechnology has opened a new area in science and engineering, leading to the development of novel nano-electromechanical systems such as nanoresonators with ultra-high resonant frequencies. The ultra-high-frequency resonators facilitate wide-ranging applications such as ultra-high sensitive sensing, molecular transportation, molecular separation, high-frequency signal processing, and biological imaging. This paper reviews recent studies on dynamic characteristics of nanoresonators. A variety of theoretical approaches, i.e., continuum modeling, molecular simulations, and multiscale methods, in modeling of nanoresonators are reviewed. The potential application of nanoresonators in design of sensor devices and molecular transportation systems is introduced. The essence of nanoresonator sensors for detection of atoms and molecules with vibration and wave propagation analyses is outlined. The sensitivity of the resonator sensors and their feasibility in detecting different atoms and molecules are particularly discussed. Furthermore, the applicability of molecular transportation using the propagation of mechanical waves in nanoresonators is presented. An extended application of the transportation methods for building nanofiltering systems with ultra-high selectivity is surveyed. The article aims to provide an up-to-date review on the mechanical properties and applications of nanoresonators, and inspire additional potential of the resonators

A review on nanomechanical resonators and their applications in sensors and molecular transportation

Energy Technology Data Exchange (ETDEWEB)

Arash, Behrouz; Rabczuk, Timon, E-mail: timon.rabczuk@uni-weimar.de [Institute of Structural Mechanics, Bauhaus Universität Weimar, Marienstr 15, D-99423 Weimar (Germany); Jiang, Jin-Wu [Shanghai Institute of Applied Mathematics and Mechanics, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200072 (China)

2015-06-15

Nanotechnology has opened a new area in science and engineering, leading to the development of novel nano-electromechanical systems such as nanoresonators with ultra-high resonant frequencies. The ultra-high-frequency resonators facilitate wide-ranging applications such as ultra-high sensitive sensing, molecular transportation, molecular separation, high-frequency signal processing, and biological imaging. This paper reviews recent studies on dynamic characteristics of nanoresonators. A variety of theoretical approaches, i.e., continuum modeling, molecular simulations, and multiscale methods, in modeling of nanoresonators are reviewed. The potential application of nanoresonators in design of sensor devices and molecular transportation systems is introduced. The essence of nanoresonator sensors for detection of atoms and molecules with vibration and wave propagation analyses is outlined. The sensitivity of the resonator sensors and their feasibility in detecting different atoms and molecules are particularly discussed. Furthermore, the applicability of molecular transportation using the propagation of mechanical waves in nanoresonators is presented. An extended application of the transportation methods for building nanofiltering systems with ultra-high selectivity is surveyed. The article aims to provide an up-to-date review on the mechanical properties and applications of nanoresonators, and inspire additional potential of the resonators.

Fluctuations in the multiparticle dynamics

International Nuclear Information System (INIS)

Bozek, P.; Ploszajczak, M.

1993-01-01

The appearance and properties of intermittent fluctuations in physical systems, in particular the formation of rare structures in transport phenomena are discussed. The distribution of fluctuations approaches a limiting log-normal statistical distribution. The log-normal distribution is introduced as a simple parametrization of the energy fluctuations leading to the subthreshold production of particles in nuclear collisions, and it is shown that it fits all available data both for total π 0 production cross section as well as the π 0 kinetic energy spectra for E/A < 90 MeV. It is suggested that the same universal distribution should also describe the subthreshold production of other hadrons like η and K. (author) 36 refs., 11 figs

Experimental evidence for anisotropic double exchange interaction driven anisotropic transport in manganite heterostructures

NARCIS (Netherlands)

Liao, Zhaoliang; Koster, Gertjan; Huijben, Mark; Rijnders, A.J.H.M.

2017-01-01

An anisotropic double exchange interaction driven giant transport anisotropy is demonstrated in a canonic double exchange system of La2/3Sr1/3MnO3 ultrathin films epitaxially grown on NdGaO3 (110) substrates. The oxygen octahedral coupling at the La2/3Sr1/3MnO3/NdGaO3 interface induces a planar

Charge transport through molecular switches

International Nuclear Information System (INIS)

Jan van der Molen, Sense; Liljeroth, Peter

2010-01-01

We review the fascinating research on charge transport through switchable molecules. In the past decade, detailed investigations have been performed on a great variety of molecular switches, including mechanically interlocked switches (rotaxanes and catenanes), redox-active molecules and photochromic switches (e.g. azobenzenes and diarylethenes). To probe these molecules, both individually and in self-assembled monolayers (SAMs), a broad set of methods have been developed. These range from low temperature scanning tunneling microscopy (STM) via two-terminal break junctions to larger scale SAM-based devices. It is generally found that the electronic coupling between molecules and electrodes has a profound influence on the properties of such molecular junctions. For example, an intrinsically switchable molecule may lose its functionality after it is contacted. Vice versa, switchable two-terminal devices may be created using passive molecules ('extrinsic switching'). Developing a detailed understanding of the relation between coupling and switchability will be of key importance for both future research and technology. (topical review)

Charge transport through molecular switches

Energy Technology Data Exchange (ETDEWEB)

Jan van der Molen, Sense [Kamerlingh Onnes Laboratorium, Leiden University, Niels Bohrweg 2, 2333 CA Leiden (Netherlands); Liljeroth, Peter, E-mail: molen@physics.leidenuniv.n [Condensed Matter and Interfaces, Debye Institute for Nanomaterials Science, University of Utrecht, PO Box 80000, 3508 TA Utrecht (Netherlands)

2010-04-07

We review the fascinating research on charge transport through switchable molecules. In the past decade, detailed investigations have been performed on a great variety of molecular switches, including mechanically interlocked switches (rotaxanes and catenanes), redox-active molecules and photochromic switches (e.g. azobenzenes and diarylethenes). To probe these molecules, both individually and in self-assembled monolayers (SAMs), a broad set of methods have been developed. These range from low temperature scanning tunneling microscopy (STM) via two-terminal break junctions to larger scale SAM-based devices. It is generally found that the electronic coupling between molecules and electrodes has a profound influence on the properties of such molecular junctions. For example, an intrinsically switchable molecule may lose its functionality after it is contacted. Vice versa, switchable two-terminal devices may be created using passive molecules ('extrinsic switching'). Developing a detailed understanding of the relation between coupling and switchability will be of key importance for both future research and technology. (topical review)

Density fluctuations in ohmic Asdex discharges

International Nuclear Information System (INIS)

Dodel, G.; Holzhauer, E.

1989-01-01

The investigations on the wave-number and frequency spectra of the density fluctuations, occurring in the different operational modes of ASDEX, are summarized. The aim of the experiments is to study the physical nature of fluctuations and their influence on anomalous transport. The scattering system is described. The results reported were obtained using a 100 mW, λ = 119 μm CW CH-30H laser and homodyne detection

Molecular mechanism of ligand recognition by membrane transport protein, Mhp1

Science.gov (United States)

Simmons, Katie J; Jackson, Scott M; Brueckner, Florian; Patching, Simon G; Beckstein, Oliver; Ivanova, Ekaterina; Geng, Tian; Weyand, Simone; Drew, David; Lanigan, Joseph; Sharples, David J; Sansom, Mark SP; Iwata, So; Fishwick, Colin WG; Johnson, A Peter; Cameron, Alexander D; Henderson, Peter JF

2014-01-01

The hydantoin transporter Mhp1 is a sodium-coupled secondary active transport protein of the nucleobase-cation-symport family and a member of the widespread 5-helix inverted repeat superfamily of transporters. The structure of Mhp1 was previously solved in three different conformations providing insight into the molecular basis of the alternating access mechanism. Here, we elucidate detailed events of substrate binding, through a combination of crystallography, molecular dynamics, site-directed mutagenesis, biochemical/biophysical assays, and the design and synthesis of novel ligands. We show precisely where 5-substituted hydantoin substrates bind in an extended configuration at the interface of the bundle and hash domains. They are recognised through hydrogen bonds to the hydantoin moiety and the complementarity of the 5-substituent for a hydrophobic pocket in the protein. Furthermore, we describe a novel structure of an intermediate state of the protein with the external thin gate locked open by an inhibitor, 5-(2-naphthylmethyl)-L-hydantoin, which becomes a substrate when leucine 363 is changed to an alanine. We deduce the molecular events that underlie acquisition and transport of a ligand by Mhp1. PMID:24952894

Spectrum of resistivity gradient driven turbulence

International Nuclear Information System (INIS)

Terry, P.W.; Diamond, P.H.; Shaing, K.C.; Garcia, L.; Carreras, B.A.

1986-01-01

The resistivity fluctuation correlation function and electrostatic potential spectrum of resistivity gradient driven turbulence are calculated analytically and compared to the results of three dimensional numerical calculations. Resistivity gradient driven turbulence is characterized by effective Reynolds' numbers of order unity. Steady-state solution of the renormalized spectrum equations yields an electrostatic potential spectrum (circumflex phi 2 )/sub ktheta/ approx. k/sub theta//sup -3.25/. Agreement of the analytically calculated potential spectrum and mean-square radial velocity with the results of multiple helicity numerical calculations is excellent. This comparison constitutes a quantitative test of the analytical turbulence theory used. The spectrum of magnetic fluctuations is also calculated, and agrees well with that obtained from the numerical computations. 13 refs., 8 figs

Power plant by deuteron beams using indirect-driven target

International Nuclear Information System (INIS)

Niu, Keishiro

1989-01-01

An indirect-driven target is proposed to be used for 6-beam nonuniform irradiation of deuteron particles. The target consists of 5 layers; tamper, radiator, smoother (radiation gap), absorber (pusher) and solid DT fuel. The fluctuation comes from nonuniform energy deposition in the radiator layer. Through the smoother layer, radiative energy transport from the radiator layer to the absorber layer is expected to smooth out the temperature fluctuation in the absorber layer. The total beam energy of 12 MJ is launched to the target by 6 beams. In order to delete the charge of the front edge of the propagating deuteron beam, the electron beam is proposed to be launched to the target with the same velocity and with the same number density at the same time of the deuteron extraction form the diode. To stabilize the beam propagation, the electron beam has a rotation velocity which induces the magnetic field in the propagation direction. The construction of the power supply system whose total stored energy is 12 MJ seems to be not difficult and to be economical. (author)

Efficiency evaluation of gas fuelled and electric driven buses in the public transport sector

Energy Technology Data Exchange (ETDEWEB)

Aigner, Tobias Alexander

2013-07-01

The following report evaluates the efficiency of gas fuelled and electric driven buses in the public transport sector on a theoretical basis. The results indicate that the combination of CHP power plants and electric driven buses reach an overall efficiency of about 51% throughout the production chain (Well-to-Wheel), including heat distribution losses. The overall Well-to-Wheel efficiency for conventional gas turbines without heat recovery decreases to around 28%. For gas fuelled buses the Well-to-Wheel efficiency is about 30%. The Co2-emissions are evaluated based on the example of a #Left Double Quotation Mark#Volvo B10L CNG#Right Double Quotation Mark# gas bus and the electric driven #Left Double Quotation Mark#Eurabus 600#Right Double Quotation Mark#. The low energy consumption of the electric driven bus results in Co2-emissions of only 181.4 g Co2/km (Grid-to-Wheel). Depending on the utilised power plant technology the overall Co2-emissions (Well-to-Wheel) amount to 307.5 g Co2/km for a CHP power plant and 553.5 g Co2/km for a conventional gas turbine. On the other hand, gas fuelled buses emit about 1.25 kg Co2/km (Tank-to-Wheel), which is eightfold the emissions of an electrical bus. The Well-to-Tank emissions further increase to about 1.32 kg Co2/km. The emission calculation is based on real gas consumption data from a Norwegian public transport utility. The results indicate that the combination of CHP plants and electrical buses provide a much higher efficiency while reducing Co2-emissions. (author)

The physics of transport barrier formation in the PBX-M H-mode

International Nuclear Information System (INIS)

Tynan, G.R.; Schmitz, L.; Blush, L.

1994-01-01

Measurements of edge profiles, turbulence, and turbulent-driven transport were made inside the last-closed flux surface (LCFS) and in the scrape-off layer (SOL) of PBX-M L-mode and H-mode plasmas using a fast reciprocating Langmuir probe diagnostic. Direct measurements of the potential profile confirm the generation of a strong inward radial electric field (E r ∼ -100 V/cm) just inside the LCFS in H-mode. Density and potential fluctuations levels are reduced at the L-H transition, resulting in significantly lower turbulent transport. The reduction in turbulent transport occurs across the LCFS and SOL regions and is not localized to the region of strong radial electric field. (author)

Weak antilocalization and conductance fluctuation in a single crystalline Bi nanowire

International Nuclear Information System (INIS)

Kim, Jeongmin; Lee, Seunghyun; Kim, MinGin; Lee, Wooyoung; Brovman, Yuri M.; Kim, Philip

2014-01-01

We present the low temperature transport properties of an individual single-crystalline Bi nanowire grown by the on-film formation of nanowire method. The temperature dependent resistance and magnetoresistance of Bi nanowires were investigated. The phase coherence length was obtained from the fluctuation pattern of the magnetoresistance below 40 K using universal conductance fluctuation theory. The obtained temperature dependence of phase coherence length and the fluctuation amplitude indicates that the transport of electrons shows 2-dimensional characteristics originating from the surface states. The temperature dependence of the coherence length derived from the weak antilocalization effect using the Hikami–Larkin–Nagaoka model is consistent with that from the universal conductance fluctuations theory

Exploring coherent transport through π-stacked systems for molecular electronic devices

DEFF Research Database (Denmark)

Li, Qian; Solomon, Gemma

2014-01-01

Understanding electron transport across π-stacked systems can help to elucidate the role of intermolecular tunneling in molecular junctions and potentially with the design of high-efficiency molecular devices. Here we show how conjugation length and substituent groups influence the electron trans...

Giant current fluctuations in an overheated single-electron transistor

Science.gov (United States)

Laakso, M. A.; Heikkilä, T. T.; Nazarov, Yuli V.

2010-11-01

Interplay of cotunneling and single-electron tunneling in a thermally isolated single-electron transistor leads to peculiar overheating effects. In particular, there is an interesting crossover interval where the competition between cotunneling and single-electron tunneling changes to the dominance of the latter. In this interval, the current exhibits anomalous sensitivity to the effective electron temperature of the transistor island and its fluctuations. We present a detailed study of the current and temperature fluctuations at this interesting point. The methods implemented allow for a complete characterization of the distribution of the fluctuating quantities, well beyond the Gaussian approximation. We reveal and explore the parameter range where, for sufficiently small transistor islands, the current fluctuations become gigantic. In this regime, the optimal value of the current, its expectation value, and its standard deviation differ from each other by parametrically large factors. This situation is unique for transport in nanostructures and for electron transport in general. The origin of this spectacular effect is the exponential sensitivity of the current to the fluctuating effective temperature.

Spin-polarized transport properties of a pyridinium-based molecular spintronics device

Science.gov (United States)

Zhang, J.; Xu, B.; Qin, Z.

2018-05-01

By applying a first-principles approach based on non-equilibrium Green's functions combined with density functional theory, the transport properties of a pyridinium-based "radical-π-radical" molecular spintronics device are investigated. The obvious negative differential resistance (NDR) and spin current polarization (SCP) effect, and abnormal magnetoresistance (MR) are obtained. Orbital reconstruction is responsible for novel transport properties such as that the MR increases with bias and then decreases and that the NDR being present for both parallel and antiparallel magnetization configurations, which may have future applications in the field of molecular spintronics.

Measurement of magnetic fluctuations on ZT-40(M)

International Nuclear Information System (INIS)

Miller, G.

1990-01-01

The mathematical basis for experimental measurement of magnetic fluctuations in a Reversed Field Pinch is reviewed. A quasi-static drift model is introduced as the frame-work for analysis of the five-fixed-probe technique. The extrapolation of edge-measured rvec B r fluctuations into the plasma is discussed. Correlations between magnetic and other fluctuations expected from a quasi-static model are derived and transport-relevant correlations are discussed. Data from ZT-40(M) are presented

Instability and transport driven by an electron temperature gradient close to critical

International Nuclear Information System (INIS)

Dong, J.Q.; Jian, G.D.; Wang, A.K.; Sanuki, H.; Itoh, K.

2003-01-01

Electron temperature gradient (ETG) driven instability in toroidal plasmas is studied with gyrokinetic theory. The full electron kinetics is considered. The upgraded numerical scheme for solving the integral eigenvalue equations allows the study of both growing and damping modes, and thus direct calculation of critical gradient. Algebraic formulas for the critical gradient with respect to ratio of electron temperature over ion temperature and to toroidicity are given. An estimation for turbulence induced transport is presented. (author)

Structure of density fluctuations in the edge plasma of ASDEX

Energy Technology Data Exchange (ETDEWEB)

Rudyj, A; Carlson, A; Endler, M; Giannone, L.; Niedermeyer, H; Theimer, G [Max-Planck-Institut fuer Plasmaphysik, Garching (Germany)

1990-01-01

It is now generally believed that the anomalous particle and energy transport in tokamaks is caused by turbulent fluctuations. The physical nature of these fluctuations (mode type, the driving mechanism) have still to be identified experimentally before a self consistent transport theory can be developed. In contrast to the confinement region the plasma edge can be well diagnosed. H{sub {alpha}}-light, which is emitted at the edge, reacts to density and to some extend to temperature fluctuations. It delivers information about radially integrated spectra and correlations. Langmuir probes measure density and potential fluctuations with good spatial resolution. The edge transport governs the physics in the scrape-off layer and in the divertor which is extremely important for a reactor and therefore deserves a major experimental effort. In this paper we report on an attempt to gain detailed information about the spatial and temporal structure of the edge turbulence hoping to reduce the degrees of freedom for theoretical models to a manageable number. (author) 3 refs., 3 figs.

Quantum control of a chiral molecular motor driven by femtosecond laser pulses: Mechanisms of regular and reverse rotations

International Nuclear Information System (INIS)

Yamaki, M.; Hoki, K.; Kono, H.; Fujimura, Y.

2008-01-01

Rotational mechanisms of a chiral molecular motor driven by femtosecond laser pulses were investigated on the basis of results of a quantum control simulation. A chiral molecule, (R)-2-methyl-cyclopenta-2,4-dienecarboaldehyde, was treated as a molecular motor within a one-dimensional model. It was assumed that the motor is fixed on a surface and driven in the low temperature limit. Electric fields of femtosecond laser pulses driving both regular rotation of the molecular motor with a plus angular momentum and reverse rotation with a minus one were designed by using a global control method. The mechanism of the regular rotation is similar to that obtained by a conventional pump-dump pulse method: the direction of rotation is the same as that of the initial wave packet propagation on the potential surface of the first singlet (nπ*) excited state S 1 . A new control mechanism has been proposed for the reverse rotation that cannot be driven by a simple pump-dump pulse method. In this mechanism, a coherent Stokes pulse creates a wave packet localized on the ground state potential surface in the right hand side. The wave packet has a negative angular momentum to drive reverse rotation at an early time

Fluctuations and structure of amphiphilic films

International Nuclear Information System (INIS)

Gourier, CH.

1996-01-01

This thesis is divided in three parts.The first part exposes in a theoretical point of view, how the fluctuations spectrum of an amphiphilic film is governed by its properties and its bidimensional characteristics.The measurements of fluctuations spectra of an interface are accessible with the measurement of intensity that interface diffuses out of the specular angle, we present in the second chapter the principles of the X rays diffusion by a real interface and see how the diffuse diffusion experiments allow to determine the fluctuations spectrum of an amphiphilic film. The second part is devoted to the different experimental techniques that have allowed to realize the study of fluctuation as well as the structural study.The third part is devoted to experimental results concerning the measurements of fluctuations spectra and to the study of the structure of amphiphilic films. We show that it is possible by using an intense source of X rays (ESRF: European Synchrotron Radiation Facility) to measure the water and amphiphilic films fluctuations spectra until molecular scales. The last chapter is devoted to the structural study and film fluctuations made of di-acetylenic molecules. (N.C.)

Modification of boundary fluctuations by LHCD in the HT-7 tokamak

International Nuclear Information System (INIS)

Song Mei; Wan Baonian; Xu Guosheng; Ling Bili

2003-01-01

Measurements of boundary fluctuations and fluctuation driven electron fluxes have been performed in ohmic and lower hybrid current drive enhanced confinement plasma using a graphite Langmuir probe array on HT-7 tokamak. The fluctuations are significantly suppressed and the turbulent fluxes are remarkably depressed in the enhanced plasma. We characterized the statistical properties of fluctuations and the particle flux and found a non-Gaussian character in the whole scrape-off layer with minimum deviations from Gaussian in the proximity of the velocity shear layer in ohmic plasma. In the enhanced plasma the deviations in the boundary region are all reduces obviously. The fluctuations and induced electron fluxes show sporadic bursts asymmetric in time and the asymmetry is remarkably weakened in the lower hybrid current driving (LHCD) phase. The results suggest a coupling between the statistical behaviour of fluctuations and the turbulent flow

New Development on Modelling Fluctuations and Fragmentation in Heavy-Ion Collisions

Science.gov (United States)

Lin, Hao; Danielewicz, Pawel

2017-09-01

During heavy-ion collisions (HIC), colliding nuclei form an excited composite system. Instabilities present in the system may deform the shape of the system exotically, leading to a break-up into fragments. Many experimental efforts have been devoted to the nuclear multifragmentation phenomenon, while traditional HIC models, lacking in proper treatment of fluctuations, fall short in explaining it. In view of this, we are developing a new model to implement realistic fluctuations into transport simulation. The new model is motivated by the Brownian motion description of colliding particles. The effects of two-body collisions are recast in one-body diffusion processes. Vastly different dynamical paths are sampled by solving Langevin equations in momentum space. It is the stochastic sampling of dynamical paths that leads to a wide spread of exit channels. In addition, the nucleon degree of freedom is used to enhance the fluctuations. The model has been tested in reactions such as 112Sn + 112Sn and 58Ni + 58Ni, where reasonable results are yielded. An exploratory comparison on the 112Sn + 112Sn reaction at 50 MeV/nucleon with two other models, the stochastic mean-field (SMF) and the antisymmetrized molecular dynamics (AMD) models, has also been conducted. Work supported by the NSF Grant No. PHY-1403906.

Nonlinear entropy transfer in ETG-TEM turbulence via TEM driven zonal flows

International Nuclear Information System (INIS)

Asahi, Yuuichi; Tsutsui, Hiroaki; Tsuji-Iio, Shunji; Ishizawa, Akihiro; Sugama, Hideo; Watanabe, Tomohiko

2015-01-01

Nonlinear interplay of the electron temperature gradient (ETG) modes and the trapped electron modes (TEMs) was investigated by means of gyrokinetic simulation. Focusing on the situation where both TEMs and ETG modes are linearly unstable, the effects of TEM-driven zonal flows on ETG turbulence were examined by means of entropy transfer analysis. In a statistically steady turbulence where the TEM driven zonal flows are dominant, it turned out that the zonal flows meditate the entropy transfer of the ETG modes from the low to high radial wavenumber regions. The successive entropy transfer broadens the potential fluctuation spectrum in the radial wavenumber direction. In contrast, in the situation where ETG modes are unstable but TEMs are stable, the pure ETG turbulence does not produce strong zonal flows, leading to a rather narrow spectrum in the radial wavenumber space and a higher transport level. (author)

Multifractal fluctuations in joint angles during infant spontaneous kicking reveal multiplicativity-driven coordination

International Nuclear Information System (INIS)

Stephen, Damian G.; Hsu, Wen-Hao; Young, Diana; Saltzman, Elliot L.; Holt, Kenneth G.; Newman, Dava J.; Weinberg, Marc; Wood, Robert J.; Nagpal, Radhika; Goldfield, Eugene C.

2012-01-01

Previous research has considered infant spontaneous kicking as a form of exploration. According to this view, spontaneous kicking provides information about motor degrees of freedom and may shape multijoint coordinations for more complex movement patterns such as gait. Recent work has demonstrated that multifractal, multiplicative fluctuations in exploratory movements index energy flows underlying perceptual-motor information. If infant spontaneous kicking is exploratory and occasions an upstream flow of information from the motor periphery, we expected not only that multiplicativity of fluctuations at the hip should promote multiplicativity of fluctuations at more distal joints (i.e., reflecting downstream effects of neural control) but also that multiplicativity at more distal joints should promote multiplicativity at the hip. Multifractal analysis demonstrated that infant spontaneous kicking in four typically developing infants for evidence of multiplicative fluctuations in multiple joint angles along the leg (i.e., hip, knee, and ankle) exhibited multiplicativity. Vector autoregressive modeling demonstrated that only one leg exhibited downstream effects but that both legs exhibited upstream effects. These results confirm the exploratory aspect of infant spontaneous kicking and suggest chaotic dynamics in motor coordination. They also resonate with existing models of chaos-controlled robotics and noise-based interventions for rehabilitating motor coordination in atypically developing patients.

Transport-level description of the 252Cf-source method using the Langevin technique

International Nuclear Information System (INIS)

Stolle, A.M.; Akcasu, A.Z.

1991-01-01

The fluctuations in the neutron number density and detector outputs in a nuclear reactor can be analyzed conveniently by using the Langevin equation approach. This approach can be implemented at any level of approximation to describe the time evolution of the neutron population, from the most complete transport-level description to the very basic point reactor analysis of neutron number density fluctuations. In this summary, the complete space- and velocity-dependent transport-level formulation of the Langevin equation approach is applied to the analysis of the 252 Cf-source-driven noise analysis (CSDNA) method, an experimental technique developed by J.T. Mihalczo at Oak Ridge National Laboratory, which makes use of noise analysis to determine the reactivity of subcritical media. From this analysis, a theoretical expression for the subcritical multiplication factor is obtained that can then be used to interpret the experimental data. Results at the transport level are in complete agreement with an independent derivation performed by Sutton and Doub, who used the probability density method to interpret the CSDNA experiment, but differed from other expressions that have appeared in the literature

Electron and phonon drag in thermoelectric transport through coherent molecular conductors

DEFF Research Database (Denmark)

Lü, Jing-Tao; Wang, Jian-Sheng; Hedegård, Per

2016-01-01

We study thermoelectric transport through a coherent molecular conductor connected to two electron and two phonon baths using the nonequilibrium Green's function method. We focus on the mutual drag between electron and phonon transport as a result of ‘momentum’ transfer, which happens only when...

Fluctuations and Anharmonicity in Lead Iodide Perovskites from Molecular Dynamics Supercell Simulationss

KAUST Repository

Carignano, Marcelo Andrés

2017-09-05

We present a systematic study based on first principles molecular dynamics simulations of lead iodide perovskites with three different cations, including methylammonium (MA), formamidinium (FA) and cesium. Using the high temperature perovskite structure as a reference, we investigate the instabilities that develop as the material is cooled down to 370 K. All three perovskites display anharmonicity in the motion of the iodine atoms, with the stronger effect observed for the MAPbI$_3$ and CsPbI$_3$. At high temperature, this behavior can be traced back to the reduced effective size of the Cs$^+$ and MA$^+$ cations. MAPbI$_3$ undergoes a spontaneous phase transition within our simulation model driven by the dipolar interaction between neighboring MA cations as the temperature is decreased from 450 K. The reverse transformation from tetragonal to cubic is also monitored through the large distribution of the octahedral tilting angles accompanied by an increase in the anharmonicity of the iodine atoms motion. Both MA and FA hybrid perovskites show a strong coupling between the molecular orientations and the local lattice deformations, suggesting mixed order-disorder/displacive characters of the high temperature phase transitions.

Edge fluctuations in the MST [Madison Symmetric Torus] reversed field pinch

International Nuclear Information System (INIS)

Almagri, A.; Assadi, S.; Beckstead, J.; Chartas, G.; Crocker, N.; Den Hartog, D.; Dexter, R.; Hokin, S.; Holly, D.; Nilles, E.; Prager, S.; Rempel, T.; Sarff, J.; Scime, E.; Shen, W.; Spragins, C.; Sprott, J.; Starr, G.; Stoneking, M.; Watts, C.

1990-10-01

Edge magnetic and electrostatic fluctuations are measured in the Madison Symmetric Torus (MST) reversed field pinch. At low frequency ( e > p e /p e where φ and p e are the fluctuating potential and pressure, respectively). From measurements of the fluctuating density, temperature, and potential we infer that the electrostatic fluctuation induced transport of particles and energy can be substantial. 13 refs., 11 figs

Effect of torsion angle on electronic transport through different anchoring groups in molecular junction

International Nuclear Information System (INIS)

Xia Caijuan; Fang Changfeng; Zhao Peng; Xie Shijie; Liu Desheng

2009-01-01

By applying nonequilibrium Green's function formalism combined with first-principles density functional theory, we investigate effect of torsion angle on electronic transport properties of 4,4 ' -biphenyl molecule connected with different anchoring groups (dithiocarboxylate and thiol group) to Au(111) electrodes. The influence of the HOMO-LUMO gaps and the spatial distributions of molecular orbitals on the quantum transport through the molecular device are discussed. Theoretical results show that the torsion angle plays important role in conducting behavior of molecular devices. By changing the torsion angle between two phenyl rings, namely changing the magnitude of the intermolecular coupling effect, a different transport behavior can be observed in these two systems.

Nonequilibrium statistical physics of small systems: fluctuation relations and beyond (annual reviews of nonlinear dynamics and complexity (vch))

CERN Document Server

2013-01-01

This book offers a comprehensive picture of nonequilibrium phenomena in nanoscale systems. Written by internationally recognized experts in the field, this book strikes a balance between theory and experiment, and includes in-depth introductions to nonequilibrium fluctuation relations, nonlinear dynamics and transport, single molecule experiments, and molecular diffusion in nanopores. The authors explore the application of these concepts to nano- and biosystems by cross-linking key methods and ideas from nonequilibrium statistical physics, thermodynamics, stochastic theory, and dynamical s

Photoinduced Coherent Spin Fluctuation in Primary Dynamics of Insulator to Metal Transition in Perovskite Cobalt Oxide

Directory of Open Access Journals (Sweden)

Arima T.

2013-03-01

Full Text Available Coherent spin fluctuation was detected in the photoinduced Mott insulator-metal transition in perovskite cobalt oxide by using 3 optical-cycle infrared pulse. Such coherent spin fluctuation is driven by the perovskite distortion changing orbital gap.

Shiga Toxin—A Model for Glycolipid-Dependent and Lectin-Driven Endocytosis

Directory of Open Access Journals (Sweden)

Ludger Johannes

2017-10-01

Full Text Available The cellular entry of the bacterial Shiga toxin and the related verotoxins has been scrutinized in quite some detail. This is due to their importance as a threat to human health. At the same time, the study of Shiga toxin has allowed the discovery of novel molecular mechanisms that also apply to the intracellular trafficking of endogenous proteins at the plasma membrane and in the endosomal system. In this review, the individual steps that lead to Shiga toxin uptake into cells will first be presented from a purely mechanistic perspective. Membrane-biological concepts will be highlighted that are often still poorly explored, such as fluctuation force-driven clustering, clathrin-independent membrane curvature generation, friction-driven scission, and retrograde sorting on early endosomes. It will then be explored whether and how these also apply to other pathogens, pathogenic factors, and cellular proteins. The molecular nature of Shiga toxin as a carbohydrate-binding protein and that of its cellular receptor as a glycosylated raft lipid will be an underlying theme in this discussion. It will thereby be illustrated how the study of Shiga toxin has led to the proposal of the GlycoLipid-Lectin (GL-Lect hypothesis on the generation of endocytic pits in processes of clathrin-independent endocytosis.

Plasma Turbulence Suppression and Transport Barrier Formation by Externally Driven RF Waves in Spherical Tokamaks

International Nuclear Information System (INIS)

Bruma, C.; Cuperman, S.C.; Komoshvili, K.

2002-01-01

Turbulent transport of heat and particles is the principle obstacle confronting controlled fusion today. Thus, we investigate quantitatively the suppression of turbulence and formation of transport barriers in spherical tokamaks by sheared electric fields generated by externally driven radio-frequency (RF) waves, in the frequency range o)A n o] < o)ci (e)A and o)ci are the Alfven and ion cyclotron frequencies). This investigation consists of the solution of the full-wave equation for a spherical tokamak in the presence of externally driven fast waves and the evaluation of the power dissipation by the mode-converted Alfven waves. This in turn, provides a radial flow shear responsible for the suppression of plasma turbulence. Thus, a strongly non-linear equation for the radial sheared electric field is solved, the turbulent transport suppression rate is evaluated and compared with the ion temperature gradient (ITG) instability increment. For illustration, the case of START-like device (Sykes 2000) is treated. Thus, (i) the exact D-shape cross-section is considered; (ii) additional kinetic (including Landau damping) and particle trapping effects are added to the resistive two-fluid dielectric tensor operator; (iii) a finite extension antenna located on the low-field-side of the plasma is considered; (iv) a rigorous 2.5 finite elements numerical code (Sewell 1993) is used; and (v) the turbulence and transport barrier generated as a result of wave-plasma interaction is evaluated

Droplet spreading driven by van der Waals force: a molecular dynamics study

KAUST Repository

Wu, Congmin

2010-07-07

The dynamics of droplet spreading is investigated by molecular dynamics simulations for two immiscible fluids of equal density and viscosity. All the molecular interactions are modeled by truncated Lennard-Jones potentials and a long-range van der Waals force is introduced to act on the wetting fluid. By gradually increasing the coupling constant in the attractive van der Waals interaction between the wetting fluid and the substrate, we observe a transition in the initial stage of spreading. There exists a critical value of the coupling constant, above which the spreading is pioneered by a precursor film. In particular, the dynamically determined critical value quantitatively agrees with that determined by the energy criterion that the spreading coefficient equals zero. The latter separates partial wetting from complete wetting. In the regime of complete wetting, the radius of the spreading droplet varies with time as R(t) ∼ √t, a behavior also found in molecular dynamics simulations where the wetting dynamics is driven by the short-range Lennard-Jones interaction between liquid and solid. © 2010 IOP Publishing Ltd.

Near resonant absorption by atoms in intense, fluctuating fields: [Progress report

International Nuclear Information System (INIS)

1989-01-01

During the present grant period preparations for photon echo studies of the role of phase fluctuations of an optical driving field resonant with the 1 S 0 - 3 P 1 transition in 174 Yb are moving forward. This experimental study emphasizes the role of fluctuations as a decorrelating mechanism on a phased array of excited atoms. Improvements in laser stabilization and in the quality of the fluctuation spectrum have been carried out and the first spectroscopic measurements will be carried out during this grant year. In response to an important recent theoretical study we have also applied the phase fluctuation synthesizing capability to the study of the atomic sodium resonance fluorescence line profile, driven by a phase fluctuating laser. The measured fluctuations in the fluorescence, characterized in terms of the standard deviation of the fluorescence intensity, have an unexpected and strong dependence on detuning of the driving laser

Electric Field Fluctuations in Water

Science.gov (United States)

Thorpe, Dayton; Limmer, David; Chandler, David

2013-03-01

Charge transfer in solution, such as autoionization and ion pair dissociation in water, is governed by rare electric field fluctuations of the solvent. Knowing the statistics of such fluctuations can help explain the dynamics of these rare events. Trajectories short enough to be tractable by computer simulation are virtually certain not to sample the large fluctuations that promote rare events. Here, we employ importance sampling techniques with classical molecular dynamics simulations of liquid water to study statistics of electric field fluctuations far from their means. We find that the distributions of electric fields located on individual water molecules are not in general gaussian. Near the mean this non-gaussianity is due to the internal charge distribution of the water molecule. Further from the mean, however, there is a previously unreported Bjerrum-like defect that stabilizes certain large fluctuations out of equilibrium. As expected, differences in electric fields acting between molecules are gaussian to a remarkable degree. By studying these differences, though, we are able to determine what configurations result not only in large electric fields, but also in electric fields with long spatial correlations that may be needed to promote charge separation.

Energy and Heat Fluctuations in a Temperature Quench

Energy Technology Data Exchange (ETDEWEB)

Zannetti, M.; Corberi, F. [Dipartimento di Fisica “E. Caianiello”, and CNISM, Unità di Salerno, Università di Salerno, via Giovanni Paolo II 132, 84084 Fisciano (Italy); Gonnella, G. [Dipartimento di Fisica, Università di Bari and INFN, Sezione di Bari, via Amendola 173, 70126 Bari (Italy); Piscitelli, A., E-mail: mrc.zannetti@gmail.com, E-mail: corberi@sa.infn.it, E-mail: gonnella@ba.infn.it, E-mail: antps@hotmial.it [Division of Physical Sciences, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, 637371 (Singapore)

2014-10-15

Fluctuations of energy and heat are investigated during the relaxation following the instantaneous temperature quench of an extended system. Results are obtained analytically for the Gaussian model and for the large N model quenched below the critical temperature T{sub c}. The main finding is that fluctuations exceeding a critical threshold do condense. Though driven by a mechanism similar to that of Bose—Einstein condensation, this phenomenon is an out-of-equilibrium feature produced by the breaking of energy equipartition occurring in the transient regime. The dynamical nature of the transition is illustrated by phase diagrams extending in the time direction. (general)

Stochastic transport models for mixing in variable-density turbulence

Science.gov (United States)

Bakosi, J.; Ristorcelli, J. R.

2011-11-01

In variable-density (VD) turbulent mixing, where very-different- density materials coexist, the density fluctuations can be an order of magnitude larger than their mean. Density fluctuations are non-negligible in the inertia terms of the Navier-Stokes equation which has both quadratic and cubic nonlinearities. Very different mixing rates of different materials give rise to large differential accelerations and some fundamentally new physics that is not seen in constant-density turbulence. In VD flows material mixing is active in a sense far stronger than that applied in the Boussinesq approximation of buoyantly-driven flows: the mass fraction fluctuations are coupled to each other and to the fluid momentum. Statistical modeling of VD mixing requires accounting for basic constraints that are not important in the small-density-fluctuation passive-scalar-mixing approximation: the unit-sum of mass fractions, bounded sample space, and the highly skewed nature of the probability densities become essential. We derive a transport equation for the joint probability of mass fractions, equivalent to a system of stochastic differential equations, that is consistent with VD mixing in multi-component turbulence and consistently reduces to passive scalar mixing in constant-density flows.

Quantifying fluctuations in reversible enzymatic cycles and clocks

Science.gov (United States)

Wierenga, Harmen; ten Wolde, Pieter Rein; Becker, Nils B.

2018-04-01

Biochemical reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but it also allows fluctuation measurements that may reveal the structure and dynamics of the underlying biochemical network. Here, we study nonequilibrium reaction cycles, such as the mechanochemical cycle of molecular motors, the phosphorylation cycle of circadian clock proteins, or the transition state cycle of enzymes. Fluctuations in such cycles may be measured using either of two classical definitions of the randomness parameter, which we show to be equivalent in general microscopically reversible cycles. We define a stochastic period for reversible cycles and present analytical solutions for its moments. Furthermore, we associate the two forms of the randomness parameter with the thermodynamic uncertainty relation, which sets limits on the timing precision of the cycle in terms of thermodynamic quantities. Our results should prove useful also for the study of temporal fluctuations in more general networks.

Identifying the molecular functions of electron transport proteins using radial basis function networks and biochemical properties.

Science.gov (United States)

Le, Nguyen-Quoc-Khanh; Nguyen, Trinh-Trung-Duong; Ou, Yu-Yen

2017-05-01

The electron transport proteins have an important role in storing and transferring electrons in cellular respiration, which is the most proficient process through which cells gather energy from consumed food. According to the molecular functions, the electron transport chain components could be formed with five complexes with several different electron carriers and functions. Therefore, identifying the molecular functions in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. This work includes two phases for discriminating electron transport proteins from transport proteins and classifying categories of five complexes in electron transport proteins. In the first phase, the performances from PSSM with AAIndex feature set were successful in identifying electron transport proteins in transport proteins with achieved sensitivity of 73.2%, specificity of 94.1%, and accuracy of 91.3%, with MCC of 0.64 for independent data set. With the second phase, our method can approach a precise model for identifying of five complexes with different molecular functions in electron transport proteins. The PSSM with AAIndex properties in five complexes achieved MCC of 0.51, 0.47, 0.42, 0.74, and 1.00 for independent data set, respectively. We suggest that our study could be a power model for determining new proteins that belongs into which molecular function of electron transport proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

Transport, shot noise, and topology in AC-driven dimer arrays

Science.gov (United States)

Niklas, Michael; Benito, Mónica; Kohler, Sigmund; Platero, Gloria

2016-11-01

We analyze an AC-driven dimer chain connected to a strongly biased electron source and drain. It turns out that the resulting transport exhibits fingerprints of topology. They are particularly visible in the driving-induced current suppression and the Fano factor. Thus, shot noise measurements provide a topological phase diagram as a function of the driving parameters. The observed phenomena can be explained physically by a mapping to an effective time-independent Hamiltonian and the emergence of edge states. Moreover, by considering quantum dissipation, we determine the requirements for the coherence properties in a possible experimental realization. For the computation of the zero-frequency noise, we develop an efficient method based on matrix-continued fractions.

Surface area changes of Himalayan ponds as a proxy of hydrological climate-driven fluctuations

Science.gov (United States)

Salerno, Franco; Thakuri, Sudeep; Guyennon, Nicolas; Viviano, Gaetano; Tartari, Gianni

2016-04-01

The meteorological measurements at high-elevations of the Himalayan range are scarce due to the harsh conditions of these environments which limit the suitable maintenance of weather stations. As a consequence, the meager knowledge on how the climate is changed in the last decades at Himalayan high-elevations sets a serious limit upon the interpretation of relationships between causes and recent observed effects on the cryosphere. Although the glaciers masses reduction in Himalaya is currently sufficiently well described, how changes in climate drivers (precipitation and temperature) have influenced the melting and shrinkage processes are less clear. Consequently, the uncertainty related to the recent past amplifies when future forecasts are done, both for climate and impacts. In this context, a substantial body of research has already demonstrated the high sensitivity of lakes and ponds to climate. Some climate-related signals are highly visible and easily measurable in lakes. For example, climate-driven fluctuations in lake surface area have been observed in many remote sites. On interior Tibetan Plateau the lake growth since the late 1990s is mainly attributed to increased regional precipitation and weakened evaporation. Differently, other authors attribute at the observed increases of lake surfaces at the enhanced glacier melting. In our opinion these divergences found in literature are due to the type of glacial lakes considered in the study and in particular their relationship with glaciers. In general, in Himalaya three types of glacial lakes can be distinguished: (i) lakes that are not directly connected with glaciers, but that may have a glacier located in their basin (unconnected glacial lakes); (ii) supraglacial lakes, which develop on the surface of the glacier downstream; or (iii) proglacial lakes, which are moraine-dammed lakes that are in contact with the glacier front. Some of these lakes store large quantities of water and are susceptible to GLOFs

On-wire lithography-generated molecule-based transport junctions: a new testbed for molecular electronics.

Science.gov (United States)

Chen, Xiaodong; Jeon, You-Moon; Jang, Jae-Won; Qin, Lidong; Huo, Fengwei; Wei, Wei; Mirkin, Chad A

2008-07-02

On-wire lithography (OWL) fabricated nanogaps are used as a new testbed to construct molecular transport junctions (MTJs) through the assembly of thiolated molecular wires across a nanogap formed between two Au electrodes. In addition, we show that one can use OWL to rapidly characterize a MTJ and optimize gap size for two molecular wires of different dimensions. Finally, we have used this new testbed to identify unusual temperature-dependent transport mechanisms for alpha,omega-dithiol terminated oligo(phenylene ethynylene).

Molecular modeling of auxin transport inhibitors

International Nuclear Information System (INIS)

Gardner, G.; Black-Schaefer, C.; Bures, M.G.

1990-01-01

Molecular modeling techniques have been used to study the chemical and steric properties of auxin transport inhibitors. These bind to a specific site on the plant plasma membrane characterized by its affinity for N-1-naphthylphthalamic acid (NPA). A three-dimensional model was derived from critical features of ligands for the NPA receptor, and a suggested binding conformation is proposed. This model, along with three-dimensional structural searching techniques, was then used to search the Abbott corporate database of chemical structures. Of the 467 compounds that satisfied the search criteria, 77 representative molecules were evaluated for their ability to compete for [ 3 H]NPA binding to corn microsomal membranes. Nineteen showed activity that ranged from 16 to 85% of the maximum NPA binding. Four of the most active of these, from chemical classes not included in the original compound set, also inhibited polar auxin transport through corn coleoptile sections

Molecular electronics: insight from first-principles transport simulations.

Science.gov (United States)

Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

2010-01-01

Conduction properties of nanoscale contacts can be studied using first-principles simulations. Such calculations give insight into details behind the conductance that is not readily available in experiments. For example, we may learn how the bonding conditions of a molecule to the electrodes affect the electronic transport. Here we describe key computational ingredients and discuss these in relation to simulations for scanning tunneling microscopy (STM) experiments with C60 molecules where the experimental geometry is well characterized. We then show how molecular dynamics simulations may be combined with transport calculations to study more irregular situations, such as the evolution of a nanoscale contact with the mechanically controllable break-junction technique. Finally we discuss calculations of inelastic electron tunnelling spectroscopy as a characterization technique that reveals information about the atomic arrangement and transport channels.

Electron transport in doped fullerene molecular junctions

Science.gov (United States)

Kaur, Milanpreet; Sawhney, Ravinder Singh; Engles, Derick

The effect of doping on the electron transport of molecular junctions is analyzed in this paper. The doped fullerene molecules are stringed to two semi-infinite gold electrodes and analyzed at equilibrium and nonequilibrium conditions of these device configurations. The contemplation is done using nonequilibrium Green’s function (NEGF)-density functional theory (DFT) to evaluate its density of states (DOS), transmission coefficient, molecular orbitals, electron density, charge transfer, current, and conductance. We conclude from the elucidated results that Au-C16Li4-Au and Au-C16Ne4-Au devices behave as an ordinary p-n junction diode and a Zener diode, respectively. Moreover, these doped fullerene molecules do not lose their metallic nature when sandwiched between the pair of gold electrodes.

Anomalous cross-field current and fluctuating equilibrium of magnetized plasmas

DEFF Research Database (Denmark)

Rypdal, K.; Garcia, O.E.; Paulsen, J.V.

1997-01-01

It is shown by simple physical arguments and fluid simulations that electrostatic flute-mode fluctuations can sustain a substantial cross-field current in addition to mass and energy transport. The simulations show that this current determines essential features of the fluctuating plasma...

Transport of negative hydrogen and deuterium ions in RF-driven ion sources

International Nuclear Information System (INIS)

Gutser, R; Wuenderlich, D; Fantz, U

2010-01-01

Negative hydrogen ion sources are major components of neutral beam injection systems for plasma heating in future large-scale fusion experiments such as ITER. In order to fulfill the requirements of the ITER neutral beam injection, a high-performance, large-area RF-driven ion source for negative ions is being developed at the MPI fuer Plasmaphysik. Negative hydrogen ions are mainly generated on a converter surface by impinging neutral particles and positive ions under the influence of magnetic fields and the plasma sheath potential. The 3D transport code TrajAn has been applied in order to obtain the total and spatially resolved extraction probabilities for H - and D - ions under identical plasma parameters and the realistic magnetic field topology of the ion source. A comparison of the isotopes shows a lower total extraction probability in the case of deuterium ions, caused by a different transport effect. The transport calculation shows that distortions of the spatial distributions of ion birth and extraction by the magnetic electron suppression field are present for both negative hydrogen and deuterium ions.

Analysis of Intelligent Transportation Systems Using Model-Driven Simulations

Directory of Open Access Journals (Sweden)

Alberto Fernández-Isabel

2015-06-01

Full Text Available Intelligent Transportation Systems (ITSs integrate information, sensor, control, and communication technologies to provide transport related services. Their users range from everyday commuters to policy makers and urban planners. Given the complexity of these systems and their environment, their study in real settings is frequently unfeasible. Simulations help to address this problem, but present their own issues: there can be unintended mistakes in the transition from models to code; their platforms frequently bias modeling; and it is difficult to compare works that use different models and tools. In order to overcome these problems, this paper proposes a framework for a model-driven development of these simulations. It is based on a specific modeling language that supports the integrated specification of the multiple facets of an ITS: people, their vehicles, and the external environment; and a network of sensors and actuators conveniently arranged and distributed that operates over them. The framework works with a model editor to generate specifications compliant with that language, and a code generator to produce code from them using platform specifications. There are also guidelines to help researchers in the application of this infrastructure. A case study on advanced management of traffic lights with cameras illustrates its use.

Fluctuation theorems and orbital magnetism in nonequilibrium state

Indian Academy of Sciences (India)

We study Langevin dynamics of a driven charged particle in the presence as well as in the absence of magnetic field. We discuss the validity of various work fluctuation theorems using different model potentials and external drives. We also show that one can generate an orbital magnetic moment in a nonequilibrium state ...

Rational surfaces, ExB sheared flows and transport interplay in fusion plasmas

International Nuclear Information System (INIS)

Hidalgo, C.; Pedrosa, M.A.; Erents, K.

2002-01-01

Experimental evidence of a strong interplay between magnetic topology (rational surfaces) and the generation of ExB sheared flows has been observed in the plasma edge region of stellarator (TJ-II) and tokamak (JET) devices. Both constant and varying in time ExB sheared flows are close to the critical value to trigger the transition to improved confinement regimes, but below the power threshold to trigger the formation of transport barriers. Flows driven by fluctuations are candidates to explain these experimental results. (author)

Nucleon matter equation of state, particle number fluctuations, and shear viscosity within UrQMD box calculations

Science.gov (United States)

Motornenko, A.; Bravina, L.; Gorenstein, M. I.; Magner, A. G.; Zabrodin, E.

2018-03-01

Properties of equilibrated nucleon system are studied within the ultra-relativistic quantum molecular dynamics (UrQMD) transport model. The UrQMD calculations are done within a finite box with periodic boundary conditions. The system achieves thermal equilibrium due to nucleon-nucleon elastic scattering. For the UrQMD-equilibrium state, nucleon energy spectra, equation of state, particle number fluctuations, and shear viscosity η are calculated. The UrQMD results are compared with both, statistical mechanics and Chapman-Enskog kinetic theory, for a classical system of nucleons with hard-core repulsion.

Spectra of turbulent static pressure fluctuations in jet mixing layers

Science.gov (United States)

Jones, B. G.; Adrian, R. J.; Nithianandan, C. K.; Planchon, H. P., Jr.

1977-01-01

Spectral similarity laws are derived for the power spectra of turbulent static pressure fluctuations by application of dimensional analysis in the limit of large turbulent Reynolds number. The theory predicts that pressure spectra are generated by three distinct types of interaction in the velocity fields: a fourth order interaction between fluctuating velocities, an interaction between the first order mean shear and the third order velocity fluctuations, and an interaction between the second order mean shear rate and the second order fluctuating velocity. Measurements of one-dimensional power spectra of the turbulent static pressure fluctuations in the driven mixing layer of a subsonic, circular jet are presented, and the spectra are examined for evidence of spectral similarity. Spectral similarity is found for the low wavenumber range when the large scale flow on the centerline of the mixing layer is self-preserving. The data are also consistent with the existence of universal inertial subranges for the spectra of each interaction mode.

Fluctuation characteristics in detached recombining plasmas

International Nuclear Information System (INIS)

Ohno, Noriyasu; Tanaka, Naoyuki; Takamura, Shuichi; Budaev, Viatcheslav

2002-01-01

Fluctuation in detached recombining plasmas has been investigated experimentally in the linear divertor plasma simulator, NAGDIS-II. As increasing neutral gas pressure, floating potential fluctuation of the target plate installed at the end of the NADIS-II device becomes larger and bursty negative spikes are observed in the signal associated with a transition from attached to detached a plasmas. The fluctuation property has been analyzed by using Fast Fourier Transform (FFT), probability distribution function (PDF) and wavelet transform. The PDF of the floating potential fluctuation in the attached plasma condition obeys the Gaussian distribution function, on the other hand, the PDF in detached plasma shows a strong deviation from the Gaussian distribution function, which can be characterized by flatness and skewness. Comparison of the fluctuation properties between the floating potential and the optical emission from the detached plasma has been done based on the wavelet transform to show that a strong correlation between them, which could indicate bursty transport of energetic electrons from upstream to downstream region along the magnetic field. (author)

Measurement of current density fluctuations and ambipolar particle flux due to magnetic fluctuations in MST

International Nuclear Information System (INIS)

Shen, Weimin.

1992-08-01

Studies of magnetic fluctuation induced particle transport on Reversed Field Pinch plasmas were done on the Madison Symmetric Torus. Plasma current density and current density fluctuations were measured using a multi-coil magnetic probes. The low frequency (f parallel B r >. The result of zero net charged particle loss was obtained, meaning the flux is ambipolar. The ambipolarity of low frequency global tearing modes is satisfied through the phase relations determined by tearing instabilities. The ambipolarity of high frequency localized modes could be partially explained by the simple model of Waltz based on the radial average of small scale turbulence

Weak antilocalization and universal conductance fluctuations in bismuth telluro-sulfide topological insulators

Energy Technology Data Exchange (ETDEWEB)

Trivedi, Tanuj, E-mail: tanuj@utexas.edu; Sonde, Sushant; Movva, Hema C. P.; Banerjee, Sanjay K., E-mail: banerjee@ece.utexas.edu [Microelectronics Research Center, The University of Texas at Austin, Austin, Texas 78758 (United States)

2016-02-07

We report on van der Waals epitaxial growth, materials characterization, and magnetotransport experiments in crystalline nanosheets of Bismuth Telluro-Sulfide (BTS). Highly layered, good-quality crystalline nanosheets of BTS are obtained on SiO{sub 2} and muscovite mica. Weak-antilocalization (WAL), electron-electron interaction-driven insulating ground state and universal conductance fluctuations are observed in magnetotransport experiments on BTS devices. Temperature, thickness, and magnetic field dependence of the transport data indicate the presence of two-dimensional surface states along with bulk conduction, in agreement with theoretical models. An extended-WAL model is proposed and utilized in conjunction with a two-channel conduction model to analyze the data, revealing a surface component and evidence of multiple conducting channels. A facile growth method and detailed magnetotransport results indicating BTS as an alternative topological insulator material system are presented.

Manifestly non-Gaussian fluctuations in superconductor-normal metal tunnel nanostructures

Energy Technology Data Exchange (ETDEWEB)

Laakso, Matti [Institut fuer Theorie der Statistischen Physik, RWTH Aachen University, Aachen (Germany); Low Temperature Laboratory, Aalto University, Espoo (Finland); Heikkilae, Tero [Low Temperature Laboratory, Aalto University, Espoo (Finland); Nazarov, Yuli [Kavli Institute of Nanoscience, Delft University of Technology, Delft (Netherlands)

2013-07-01

Recently, temperature fluctuation statistics has been studied in non-interacting islands and overheated single-electron transistors. We propose a mesoscopic setup which exhibits strong and manifestly non-Gaussian fluctuations of energy and temperature when suitably driven out of equilibrium. The setup consists of a normal metal island (N) coupled by tunnel junctions (I) to two superconducting leads (S), forming a SINIS structure, and is biased near the threshold voltage for quasiparticle tunneling, eV ∼ 2Δ. The fluctuations can be measured by monitoring the time-dependent electric current through the system, which makes the setup suitable for the realization of feedback schemes which allow to stabilize the temperature to the desired value.

Biomarkers: Delivering on the expectation of molecularly driven, quantitative health.

Science.gov (United States)

Wilson, Jennifer L; Altman, Russ B

2018-02-01

Biomarkers are the pillars of precision medicine and are delivering on expectations of molecular, quantitative health. These features have made clinical decisions more precise and personalized, but require a high bar for validation. Biomarkers have improved health outcomes in a few areas such as cancer, pharmacogenetics, and safety. Burgeoning big data research infrastructure, the internet of things, and increased patient participation will accelerate discovery in the many areas that have not yet realized the full potential of biomarkers for precision health. Here we review themes of biomarker discovery, current implementations of biomarkers for precision health, and future opportunities and challenges for biomarker discovery. Impact statement Precision medicine evolved because of the understanding that human disease is molecularly driven and is highly variable across patients. This understanding has made biomarkers, a diverse class of biological measurements, more relevant for disease diagnosis, monitoring, and selection of treatment strategy. Biomarkers' impact on precision medicine can be seen in cancer, pharmacogenomics, and safety. The successes in these cases suggest many more applications for biomarkers and a greater impact for precision medicine across the spectrum of human disease. The authors assess the status of biomarker-guided medical practice by analyzing themes for biomarker discovery, reviewing the impact of these markers in the clinic, and highlight future and ongoing challenges for biomarker discovery. This work is timely and relevant, as the molecular, quantitative approach of precision medicine is spreading to many disease indications.

Bursty fluctuation characteristics in SOL/divertor plasmas of large helical device

International Nuclear Information System (INIS)

Ohno, N.

2006-01-01

Full text: Fluctuation properties in the SOL plasmas were intensively studied to understand the crossfield plasma transport, which determines the SOL structure and heat/particle deposition onto the first wall. Recent studies in tokamaks showed that the SOL density fluctuation is highly intermittent. Convective cross-field transport associated with the intermittent events would have strong influence on recycling processes and impurity generation from the first wall. On the other hand, in helical devices, there are few systematic studies on the SOL fluctuation property focusing on the intermittent bursty fluctuations related to plasma blob transport. Recent theory predicts that the blobs propagate toward a low field side in tokamaks. On the other hand, in the Large Helical Device (LHD), the direction of the gradient in B is not uniform because the high-field and the low-field sides rotates poloidally along the torus in the helical system. Comparison between the intermittent bursty fluctuations in the edge plasma of tokamaks and helical devices makes it possible to understand the essential physics of the blob transport. Recently, fast camera observation showed the radial motion of filaments in the edge of the LHD, suggesting the convective cross-field transport. In this paper, bursty fluctuation properties in the edge of the LHD have been investigated by analyzing the ion saturation currents measured with a probe array embedded in an outboard divertor plate. Statistical analysis based on probability distribution function was employed to determine the intermittent evens in the density fluctuation. Large positive bursty events were often observed in the ion saturation current measured with a divertor probe near a divertor leg at which the magnetic line of force connected to the area of a low-field side with a short connection length. Condition averaging result of the positive bursty events indicates the intermittent feature with a rapid increase and a slow decay is

Addendum to ''Density fluctuations in liquid rubidium''

International Nuclear Information System (INIS)

Haan, S.W.; Mountain, R.D.; Hsu, C.S.; Rahman, A.

1980-01-01

We performed molecular-dynamics simulations of liquid rubidium and the Lennard-Jones fluid at several densities and temperatures, and of a system whose pair potential is the repulsive core of the rubidium potential. In all cases, propagating density fluctuations occurred in the rubidiumlike systems at much shorter wavelengths than in the Lennard-Jones system. This indicates that the repulsive part of the pair potential is the dominant factor in determining the relaxation of short-wavelength density fluctuations

Spherical harmonics analysis of surface density fluctuations of spherical ionic SDS and nonionic C12E8 micelles: A molecular dynamics study.

Science.gov (United States)

Yoshii, Noriyuki; Nimura, Yuki; Fujimoto, Kazushi; Okazaki, Susumu

2017-07-21

The surface structure and its fluctuation of spherical micelles were investigated using a series of density correlation functions newly defined by spherical harmonics and Legendre polynomials based on the molecular dynamics calculations. To investigate the influence of head-group charges on the micelle surface structure, ionic sodium dodecyl sulfate and nonionic octaethyleneglycol monododecylether (C 12 E 8 ) micelles were investigated as model systems. Large-scale density fluctuations were observed for both micelles in the calculated surface static structure factor. The area compressibility of the micelle surface evaluated by the surface static structure factor was tens-of-times larger than a typical value of a lipid membrane surface. The structural relaxation time, which was evaluated from the surface intermediate scattering function, indicates that the relaxation mechanism of the long-range surface structure can be well described by the hydrostatic approximation. The density fluctuation on the two-dimensional micelle surface has similar characteristics to that of three-dimensional fluids near the critical point.

Neutron fluctuations a treatise on the physics of branching processes

CERN Document Server

Pazsit, Imre; Pzsit, Imre

2007-01-01

The transport of neutrons in a multiplying system is an area of branching processes with a clear formalism. This book presents an account of the mathematical tools used in describing branching processes, which are then used to derive a large number of properties of the neutron distribution in multiplying systems with or without an external source. In the second part of the book, the theory is applied to the description of the neutron fluctuations in nuclear reactor cores as well as in small samples of fissile material. The question of how to extract information about the system under study is discussed. In particular the measurement of the reactivity of subcritical cores, driven with various Poisson and non-Poisson (pulsed) sources, and the identification of fissile material samples, is illustrated. The book gives pragmatic information for those planning and executing and evaluating experiments on such systems. - Gives a complete treatise of the mathematics of branching particle processes, and in particular n...

Light-Driven Alignment

CERN Document Server

Antonyuk, Boris P

2009-01-01

This book deals with influencing the properties of solids by light-driven electron transport. The theoretical basis of these effects, light-driven ordering and self-organisation, as well as optical motors are presented. With light as a tool, new ways to produce materials are opened.

Transport and dosimetric solutions for the ELIMED laser-driven beam line

Czech Academy of Sciences Publication Activity Database

Cirrone, G.A.P.; Romano, F.; Scuderi, Valentina; Amato, A.; Candiano, G.; Cuttone, G.; Giove, D.; Korn, Georg; Krása, Josef; Leanza, R.; Manna, R.; Maggiore, M.; Marchese, V.; Margarone, Daniele; Milluzzo, G.; Petringa, G.; Sabini, M.G.; Schillaci, F.; Tramontana, A.; Valastro, L.; Velyhan, Andriy

2015-01-01

Roč. 796, Oct (2015), s. 99-103 ISSN 0168-9002 R&D Projects: GA MŠk ED1.1.00/02.0061; GA MŠk EE2.3.20.0279; GA MŠk EE2.3.30.0057 Grant - others:ELI Beamlines(XE) CZ.1.05/1.1.00/02.0061; LaserZdroj (OP VK 3)(XE) CZ.1.07/2.3.00/20.0279; OP VK 4 POSTDOK(XE) CZ.1.07/2.3.00/30.0057 Institutional support: RVO:68378271 Keywords : laser-driven ion * beam-transport * Faraday cup dosimetry * absolute dosimetry Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 1.200, year: 2015

Queues and Lévy fluctuation theory

CERN Document Server

Dębicki, Krzysztof

2015-01-01

The book provides an extensive introduction to queueing models driven by Lévy-processes as well as a systematic account of the literature on Lévy-driven queues. The objective is to make the reader familiar with the wide set of probabilistic techniques that have been developed over the past decades, including transform-based techniques, martingales, rate-conservation arguments, change-of-measure, importance sampling, and large deviations. On the application side, it demonstrates how Lévy traffic models arise when modelling current queueing-type systems (as communication networks) and includes applications to finance. Queues and Lévy Fluctuation Theory will appeal to graduate/postgraduate students and researchers in mathematics, computer science, and electrical engineering. Basic prerequisites are probability theory and stochastic processes.

Fluctuation theorems and atypical trajectories

International Nuclear Information System (INIS)

Sahoo, M; Lahiri, S; Jayannavar, A M

2011-01-01

In this work, we have studied simple models that can be solved analytically to illustrate various fluctuation theorems. These fluctuation theorems provide symmetries individually to the distributions of physical quantities such as the classical work (W c ), thermodynamic work (W), total entropy (Δs tot ) and dissipated heat (Q), when the system is driven arbitrarily out of equilibrium. All these quantities can be defined for individual trajectories. We have studied the number of trajectories which exhibit behaviour unexpected at the macroscopic level. As the time of observation increases, the fraction of such atypical trajectories decreases, as expected at the macroscale. The distributions for the thermodynamic work and entropy production in nonlinear models may exhibit a peak (most probable value) in the atypical regime without violating the expected average behaviour. However, dissipated heat and classical work exhibit a peak in the regime of typical behaviour only.

Channel-facilitated molecular transport: The role of strength and spatial distribution of interactions

Energy Technology Data Exchange (ETDEWEB)

Uppulury, Karthik, E-mail: karthik.uppulury@gmail.com [Department of Chemistry, Texas Tech University, Lubbock, TX 79409 (United States); Kolomeisky, Anatoly B. [Department of Chemistry, Department of Chemical and Biomolecular Engineering, Center for Theoretical Biological Physics, Rice University, Houston, TX 77005 (United States)

2016-12-20

Highlights: • Molecular flux strongly depends on the strength of the molecule-pore interactions. • There exists an optimal molecule-pore interaction potential for maximal flux. • Volume of interactions depends inversely on the strength for maximal flux. • Stronger interactions need more number of attractive sites for maximal flux. • Channels with few special sites need more attractive sites for higher flux. - Abstract: Molecular transport across channels and pores is critically important for multiple natural and industrial processes. Recent advances in single-molecule techniques have allowed researchers to probe translocation through nanopores with unprecedented spatial and temporal resolution. However, our understanding of the mechanisms of channel-facilitated molecular transport is still not complete. We present a theoretical approach that investigates the role of molecular interactions in the transport through channels. It is based on the discrete-state stochastic analysis that provides a fully analytical description of this complex process. It is found that a spatial distribution of the interactions strongly influences the translocation dynamics. We predict that there is the optimal distribution that leads to the maximal flux through the channel. It is also argued that the channel transport depends on the strength of the molecule-pore interactions, on the shape of interaction potentials and on the relative contributions of entrance and diffusion processes in the system. These observations are discussed using simple physical-chemical arguments.

Channel-facilitated molecular transport: The role of strength and spatial distribution of interactions

International Nuclear Information System (INIS)

Uppulury, Karthik; Kolomeisky, Anatoly B.

2016-01-01

Highlights: • Molecular flux strongly depends on the strength of the molecule-pore interactions. • There exists an optimal molecule-pore interaction potential for maximal flux. • Volume of interactions depends inversely on the strength for maximal flux. • Stronger interactions need more number of attractive sites for maximal flux. • Channels with few special sites need more attractive sites for higher flux. - Abstract: Molecular transport across channels and pores is critically important for multiple natural and industrial processes. Recent advances in single-molecule techniques have allowed researchers to probe translocation through nanopores with unprecedented spatial and temporal resolution. However, our understanding of the mechanisms of channel-facilitated molecular transport is still not complete. We present a theoretical approach that investigates the role of molecular interactions in the transport through channels. It is based on the discrete-state stochastic analysis that provides a fully analytical description of this complex process. It is found that a spatial distribution of the interactions strongly influences the translocation dynamics. We predict that there is the optimal distribution that leads to the maximal flux through the channel. It is also argued that the channel transport depends on the strength of the molecule-pore interactions, on the shape of interaction potentials and on the relative contributions of entrance and diffusion processes in the system. These observations are discussed using simple physical-chemical arguments.

Electron transport in dipyridazine and dipyridimine molecular junctions: a first-principles investigation

Science.gov (United States)

Parashar, Sweta

2018-05-01

We present density functional theory-nonequilibrium Green’s function method for electron transport of dipyridazine and dipyridimine molecular junctions with gold, copper and nickel electrodes. Our investigation reveals that the junctions formed with gold and copper electrodes bridging dipyridazine molecule through thiol anchoring group enhance current as compared to the junctions in which the molecule and electrode were coupled directly. Further, nickel electrode displays weak decrease of current with increase of voltage at about 1.2 V. The result is fully rationalized by means of the distribution of molecular orbitals as well as shift in molecular energy levels and HOMO-LUMO gap with applied bias voltage. Our findings are compared with theoretical and experimental results available for other molecular junctions. Present results predict potential avenues for changing the transport behavior by not only changing the electrodes, but also the position of nitrogen atom and type of anchoring-atom that connect molecule and electrodes, thus extending applications of dipyridazine and dipyridimine molecule in future integrated circuits.

Transport and Stability in C-Mod ITBs in Diverse Regimes

Science.gov (United States)

Fiore, C. L.; Ernst, D. R.; Howard, N. T.; Kasten, C. P.; Mikkelsen, D.; Reinke, M. L.; Rice, J. E.; White, A. E.; Rowan, W. L.; Bespamyatnov, I.

2012-10-01

Internal Transport Barriers (ITBs) in C-Mod feature highly peaked density and pressure profiles and are typically induced by the introduction of radio frequency power in the ion cyclotron range of frequencies (ICRF) with the second harmonic of the resonance for minority hydrogen ions positioned off-axis at the plasma half radius on either the low or high field side of the plasma. These ITBs are formed in the absence of particle or momentum injection, and with monotonic q profiles with qminITB dynamics in a reactor relevant regime. Recently, linear and non-linear gyrokinetic simulations have demonstrated that changes in the ion temperature and plasma rotation profiles, coincident with the application of off-axis ICRF heating, contribute to greater stability to ion temperature gradient driven fluctuation in the plasma. This results in reduced turbulent driven outgoing heat flux. To date, ITB formation in C-Mod has only been observed in EDA H-mode plasmas with moderate (2-3 MW) ICRF power. Experiments to explore the formation of ITBs in other operating regimes such as I-mode and also with high ICRF power are being undertaken to understand further the process of ITB formation and sustainment, especially with regard to turbulent driven transport.

Final Technical Report: Numerical and Experimental Investigation of Turbulent Transport Control via Shaping of Radial Plasma Flow Profiles

Energy Technology Data Exchange (ETDEWEB)

Schuster, Eugenio

2014-05-02

The strong coupling between the different physical variables involved in the plasma transport phenomenon and the high complexity of its dynamics call for a model-based, multivariable approach to profile control where those predictive models could be exploited. The overall objective of this project has been to extend the existing body of work by investigating numerically and experimentally active control of unstable fluctuations, including fully developed turbulence and the associated cross-field particle transport, via manipulation of flow profiles in a magnetized laboratory plasma device. Fluctuations and particle transport can be monitored by an array of electrostatic probes, and Ex B flow profiles can be controlled via a set of biased concentric ring electrodes that terminate the plasma column. The goals of the proposed research have been threefold: i- to develop a predictive code to simulate plasma transport in the linear HELCAT (HELicon-CAThode) plasma device at the University of New Mexico (UNM), where the experimental component of the proposed research has been carried out; ii- to establish the feasibility of using advanced model-based control algorithms to control cross-field turbulence-driven particle transport through appropriate manipulation of radial plasma flow profiles, iii- to investigate the fundamental nonlinear dynamics of turbulence and transport physics. Lehigh University (LU), including Prof. Eugenio Schuster and one full-time graduate student, has been primarily responsible for control-oriented modeling and model-based control design. Undergraduate students have also participated in this project through the National Science Foundation Research Experience for Undergraduate (REU) program. The main goal of the LU Plasma Control Group has been to study the feasibility of controlling turbulence-driven transport by shaping the radial poloidal flow profile (i.e., by controlling flow shear) via biased concentric ring electrodes.

Current-driven turbulence in plasmas

International Nuclear Information System (INIS)

Kluiver, H. de.

1977-10-01

Research on plasma heating in linear and toroidal systems using current-driven turbulence is reviewed. The motivation for this research is presented. Relations between parameters describing the turbulent plasma state and macroscopic observables are given. Several linear and toroidal devices used in current-driven turbulence studies are described, followed by a discussion of special diagnostic methods used. Experimental results on the measurement of electron and ion heating, anomalous plasma conductivity and associated turbulent fluctuation spectra are reviewed. Theories on current-driven turbulence are discussed and compared with experiments. It is demonstrated from the experimental results that current-driven turbulence occurs not only for extreme values of the electric field but also for an experimentally much more accessible and wide range of parameters. This forms a basis for a discussion on possible future applications in fusion-oriented plasma research

Gravity wave-driven fluctuations in OH nightglow from an extended, dissipative emission region

International Nuclear Information System (INIS)

Schubert, G.; Walterscheid, R.L.; Hickey, M.P.

1991-01-01

The theory of gravity wave-driven fluctuations in the OH nightglow from an extended source region is generalized to account for effects of eddy kinematic viscosity v and eddy thermal diffusivity κ. In the nondiffusive case, the amplitudes and phases of vertically integrated normalized intensity (δI)/(bar I) and temperature (δT 1 )/(bar T 1 ) perturbations and vertically integrated Krassovsky's ratio (η) as functions of period are influenced by the upper limit of vertical integration of the extended source, especially at long periods when vertical wavelengths γ v are small. The effects, which include oscillations in (δT)/(bar I), (δT 1 )/(bar T 1 ), and (η), particularly at long periods, are due to constructive and destructive interference of nightglow signals from vertically separated levels of the OH emitting region that occur when γ v is comparable to or smaller than the thickness of the main emission region. The sensitivity of these ratios to the upper limit of vertical integration occurs because of the relatively small rate of decay of the intensity of OH emission with height above the peak emission level and the exponential growth with altitude of nondissipative gravity waves. Because eddy diffusion increases γ v , especially at long periods, and reduces wave growth with height compared with the case v = κ = 0, inclusion of eddy diffusion removes the sensitivity of (η) and the other ratios ot the maximum height of vertical integration. It is essential to account for both eddy diffusion and emission from the entire vertically extended emission region to correctly predict (η), (δI)/(bar I), and (δT 1 )/(bar T 1 ) at long gravity wave periods

Three dimensional numerical simulation of a full scale CANDU reactor moderator to study temperature fluctuations

International Nuclear Information System (INIS)

Sarchami, Araz; Ashgriz, Nasser; Kwee, Marc

2014-01-01

Highlights: • 3D model of a Candu reactor is modeled to investigate flow distribution. • The results show the temperature distribution is not symmetrical. • Temperature contours show the hot regions at the top left-hand side of the tank. • Interactions of momentum flows and buoyancy flows create circulation zones. • The results indicate that the moderator tank operates in the buoyancy driven mode. -- Abstract: Three dimensional numerical simulations are conducted on a full scale CANDU Moderator and transient variations of the temperature and velocity distributions inside the tank are determined. The results show that the flow and temperature distributions inside the moderator tank are three dimensional and no symmetry plane can be identified. Competition between the upward moving buoyancy driven flows and the downward moving momentum driven flows in the center region of the tank, results in the formation of circulation zones. The moderator tank operates in the buoyancy driven mode and any small disturbances in the flow or temperature makes the system unstable and asymmetric. Different types of temperature fluctuations are noted inside the tank: (i) large amplitude are at the boundaries between the hot and cold; (ii) low amplitude are in the core of the tank; (iii) high frequency fluctuations are in the regions with high velocities and (iv) low frequency fluctuations are in the regions with lower velocities

Mechanism of molecular transport in novel reverse-selective nanocomposite membranes

International Nuclear Information System (INIS)

Merkel, T.C.; Freeman, B.D.; Spontak, R.J.; Meakin, P.; Hill, A.J.; Monash University, VIC

2002-01-01

Full text: Polymer nanocomposites continue to receive tremendous attention as organic-inorganic hybrid materials exhibiting a wide range of interesting, as well as technologically relevant, properties. This work reports a novel use of polymer nanocomposites as reverse-selective membranes. We have found that physical dispersion of nonporous fumed silica [FS] into glassy poly(4-methyl-2-pentyne) [PMP] simultaneously enhances membrane permeability (by as much as 240%) and selectivity for large organic molecules over small permanent gases. This surprising observation, in stark contrast to conventional filled polymer systems, reflects silica-induced disruption of local polymer chain packing and, as discerned by positron annihilation lifetime spectroscopy [PALS], a resulting subtle increase in the size of free volume elements through which molecular transport occurs. Such nanoscale hybridization represents an innovative means of tuning the transport properties of glassy polymeric media through control of molecular ordering

Anomalous transport in the tokamak edge

International Nuclear Information System (INIS)

Vayakis, G.

1991-04-01

The tokamak edge has been studied with arrays of Langmuir and magnetic probes on the DITE and COMPASS-C devices. Measurements of plasma parameters such as density, temperature and radial magnetic field were taken in order to elucidate the character, effect on transport and origin of edge fluctuations. The tokamak edge is a strongly-turbulent environment, with large electrostatic fluctuation levels and broad spectra. The observations, including direct correlation measurements, are consistent with a picture in which the observed magnetic field fluctuations are driven by the perturbations in electrostatic parameters. The propagation characteristics of the turbulence, investigated using digital spectral techniques, appear to be dominated by the variation of the radial electric field, both in limiter and divertor plasmas. A shear layer is formed, associated in each case with the last closed flux surface. In the shear layer, the electrostatic wavenumber spectra are significantly broader. The predictions of a drift wave model (DDGDT) and of a family of models evolving from the rippling mode (RGDT group), are compared with experimental results. RGDT, augmented by impurity radiation effects, is shown to be the most reasonable candidate to explain the nature of the edge turbulence, only failing in its estimate of the wavenumber range. (Author)

Electrolyte transport in neutral polymer gels embedded with charged inclusions

Science.gov (United States)

Hill, Reghan

2005-11-01

Ion permeable membranes are the basis of a variety of molecular separation technologies, including ion exchange, gel electrophoresis and dialysis. This work presents a theoretical model of electrolyte transport in membranes comprised of a continuous polymer gel embedded with charged spherical inclusions, e.g., biological cells and synthetic colloids. The microstructure mimics immobilized cell cultures, where electric fields have been used to promote nutrient transport. Because several important characteristics can, in principle, be carefully controlled, the theory provides a quantitative framework to help tailor the bulk properties for enhanced molecular transport, microfluidic pumping, and physicochemical sensing applications. This talk focuses on the electroosmotic flow driven by weak electric fields and electrolyte concentration gradients. Also of importance is the influence of charge on the effective ion diffusion coefficients, bulk electrical conductivity, and membrane diffusion potential.

Electronic transport properties of phenylacetylene molecular junctions

International Nuclear Information System (INIS)

Liu Wen; Cheng Jie; Yan Cui-Xia; Li Hai-Hong; Wang Yong-Juan; Liu De-Sheng

2011-01-01

Electronic transport properties of a kind of phenylacetylene compound— (4-mercaptophenyl)-phenylacetylene are calculated by the first-principles method in the framework of density functional theory and the nonequilibrium Green's function formalism. The molecular junction shows an obvious rectifying behaviour at a bias voltage larger than 1.0 V. The rectification effect is attributed to the asymmetry of the interface contacts. Moreover, at a bias voltage larger than 2.0 V, which is not referred to in a relevant experiment [Fang L, Park J Y, Ma H, Jen A K Y and Salmeron M 2007 Langmuir 23 11522], we find a negative differential resistance phenomenon. The negative differential resistance effect may originate from the change of the delocalization degree of the molecular orbitals induced by the bias. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

Eddy-driven sediment transport in the Argentine Basin: Is the height of the Zapiola Rise hydrodynamically controlled?

NARCIS (Netherlands)

Weijer, Wilbert; Maltrud, Mathew E.; Homoky, William B.; Polzin, Kurt L.; Maas, Leo R. M.

In this study, we address the question whether eddy-driven transports in the Argentine Basin can be held responsible for enhanced sediment accumulation over the Zapiola Rise, hence accounting for the existence and growth of this sediment drift. To address this question, we perform a 6 year

SIGNATURES OF MRI-DRIVEN TURBULENCE IN PROTOPLANETARY DISKS: PREDICTIONS FOR ALMA OBSERVATIONS

Energy Technology Data Exchange (ETDEWEB)

Simon, Jacob B. [Department of Space Studies, Southwest Research Institute, Boulder, CO 80302 (United States); Hughes, A. Meredith; Flaherty, Kevin M. [Astronomy Department, Van Vleck Observatory, Wesleyan University, 96 Foss Hill Dr., Middletown, CT 06459 (United States); Bai, Xue-Ning [Harvard-Smithsonian Center for Astrophysics, 60 Garden St., MS-51, Cambridge, MA 02138 (United States); Armitage, Philip J., E-mail: jbsimon.astro@gmail.com [JILA, University of Colorado and NIST, 440 UCB, Boulder, CO 80309-0440 (United States)

2015-08-01

Spatially resolved observations of molecular line emission have the potential to yield unique constraints on the nature of turbulence within protoplanetary disks. Using a combination of local non-ideal magnetohydrodynamics (MHD) simulations and radiative transfer calculations, tailored to properties of the disk around HD 163296, we assess the ability of ALMA to detect turbulence driven by the magnetorotational instability (MRI). Our local simulations show that the MRI produces small-scale turbulent velocity fluctuations that increase in strength with height above the mid-plane. For a set of simulations at different disk radii, we fit a Maxwell–Boltzmann distribution to the turbulent velocity and construct a turbulent broadening parameter as a function of radius and height. We input this broadening into radiative transfer calculations to quantify observational signatures of MRI-driven disk turbulence. We find that the ratio of the peak line flux to the flux at line center is a robust diagnostic of turbulence that is only mildly degenerate with systematic uncertainties in disk temperature. For the CO(3–2) line, which we expect to probe the most magnetically active slice of the disk column, variations in the predicted peak-to-trough ratio between our most and least turbulent models span a range of approximately 15%. Additional independent constraints can be derived from the morphology of spatially resolved line profiles, and we estimate the resolution required to detect turbulence on different spatial scales. We discuss the role of lower optical depth molecular tracers, which trace regions closer to the disk mid-plane where velocities in MRI-driven models are systematically lower.

Geophysical monitoring and reactive transport modeling of ureolytically-driven calcium carbonate precipitation

Energy Technology Data Exchange (ETDEWEB)

Wu, Y.; Ajo-Franklin, J.B.; Spycher, N.; Hubbard, S.S.; Zhang, G.; Williams, K.H.; Taylor, J.; Fujita, Y.; Smith, R.

2011-07-15

Ureolytically-driven calcium carbonate precipitation is the basis for a promising in-situ remediation method for sequestration of divalent radionuclide and trace metal ions. It has also been proposed for use in geotechnical engineering for soil strengthening applications. Monitoring the occurrence, spatial distribution, and temporal evolution of calcium carbonate precipitation in the subsurface is critical for evaluating the performance of this technology and for developing the predictive models needed for engineering application. In this study, we conducted laboratory column experiments using natural sediment and groundwater to evaluate the utility of geophysical (complex resistivity and seismic) sensing methods, dynamic synchrotron x-ray computed tomography (micro-CT), and reactive transport modeling for tracking ureolytically-driven calcium carbonate precipitation processes under site relevant conditions. Reactive transport modeling with TOUGHREACT successfully simulated the changes of the major chemical components during urea hydrolysis. Even at the relatively low level of urea hydrolysis observed in the experiments, the simulations predicted an enhanced calcium carbonate precipitation rate that was 3-4 times greater than the baseline level. Reactive transport modeling results, geophysical monitoring data and micro-CT imaging correlated well with reaction processes validated by geochemical data. In particular, increases in ionic strength of the pore fluid during urea hydrolysis predicted by geochemical modeling were successfully captured by electrical conductivity measurements and confirmed by geochemical data. The low level of urea hydrolysis and calcium carbonate precipitation suggested by the model and geochemical data was corroborated by minor changes in seismic P-wave velocity measurements and micro-CT imaging; the latter provided direct evidence of sparsely distributed calcium carbonate precipitation. Ion exchange processes promoted through NH{sub 4}{sup

Coupled electron-phonon transport from molecular dynamics with quantum baths

DEFF Research Database (Denmark)

Lu, Jing Tao; Wang, J. S.

2009-01-01

Based on generalized quantum Langevin equations for the tight-binding wavefunction amplitudes and lattice displacements, electron and phonon quantum transport are obtained exactly using molecular dynamics (MD) in the ballistic regime. The electron-phonon interactions can be handled with a quasi...

Thermal and electron transport studies on the valence fluctuating compound YbNiAl4

Science.gov (United States)

Falkowski, M.; Kowalczyk, A.

2018-05-01

We report the thermoelectric power S and thermal conductivity κ measurements on the valence fluctuating compound YbNiAl4, furthermore taking into account the impact of the applied magnetic field. We discuss our new results with revisiting the magnetic [χ(T)], transport [ρ(T)], and thermodynamic [Cp(T)] properties in order to better understand the phenomenon of thermal and electron transport in this compound. The field dependence of the magnetoresistivity data is also given. The temperature dependence of thermoelectric power S(T) was found to exhibit a similar behaviour as expected for Yb-based compounds with divalent or nearly divalent Yb ions. In addition, the values of total thermal conductivity as a function of temperature κ(T) of YbNiAl4 are fairly low compared to those of pure metals which may be linked to the fact that the conduction band is perturbed by strong hybridization. A deeper analysis of the specific heat revealed the low-T anomaly of the ratio Cp(T)/T3, most likely associated with the localized low-frequency oscillators in this alloy. In addition, the Kadowaki-Woods ratio and the Wilson ratio are discussed with respect to the electronic correlations in YbNiAl4.

Coherent transport of matter waves in disordered optical potentials

Energy Technology Data Exchange (ETDEWEB)

Kuhn, Robert

2007-07-01

The development of modern techniques for the cooling and the manipulation of atoms in recent years, and the possibility to create Bose-Einstein condensates and degenerate Fermi gases and to load them into regular optical lattices or disordered optical potentials, has evoked new interest for the disorder-induced localization of ultra-cold atoms. This work studies the transport properties of matter waves in disordered optical potentials, which are also known as speckle potentials. The effect of correlated disorder on localization is first studied numerically in the framework of the Anderson model. The relevant transport parameters in the configuration average over many different realizations of the speckle potential are then determined analytically, using self-consistent diagrammatic perturbation techniques. This allows to make predictions for a possible experimental observation of coherent transport phenomena for cold atoms in speckle potentials. Of particular importance are the spatial correlations of the speckle fluctuations, which are responsible for the anisotropic character of the single scattering processes in the effective medium. Coherent multiple scattering leads to quantum interference effects, which entail a renormalization of the diffusion constant as compared to the classical description. This so-called weak localization of matter waves is studied as the underlying mechanism for the disorder-driven transition to the Anderson-localization regime, explicitly taking into account the correlations of the speckle fluctuations. (orig.)

Coherent transport of matter waves in disordered optical potentials

International Nuclear Information System (INIS)

Kuhn, Robert

2007-01-01

The development of modern techniques for the cooling and the manipulation of atoms in recent years, and the possibility to create Bose-Einstein condensates and degenerate Fermi gases and to load them into regular optical lattices or disordered optical potentials, has evoked new interest for the disorder-induced localization of ultra-cold atoms. This work studies the transport properties of matter waves in disordered optical potentials, which are also known as speckle potentials. The effect of correlated disorder on localization is first studied numerically in the framework of the Anderson model. The relevant transport parameters in the configuration average over many different realizations of the speckle potential are then determined analytically, using self-consistent diagrammatic perturbation techniques. This allows to make predictions for a possible experimental observation of coherent transport phenomena for cold atoms in speckle potentials. Of particular importance are the spatial correlations of the speckle fluctuations, which are responsible for the anisotropic character of the single scattering processes in the effective medium. Coherent multiple scattering leads to quantum interference effects, which entail a renormalization of the diffusion constant as compared to the classical description. This so-called weak localization of matter waves is studied as the underlying mechanism for the disorder-driven transition to the Anderson-localization regime, explicitly taking into account the correlations of the speckle fluctuations. (orig.)

Molecular transport network security using multi-wavelength optical spins.

Science.gov (United States)

Tunsiri, Surachai; Thammawongsa, Nopparat; Mitatha, Somsak; Yupapin, Preecha P

2016-01-01

Multi-wavelength generation system using an optical spin within the modified add-drop optical filter known as a PANDA ring resonator for molecular transport network security is proposed. By using the dark-bright soliton pair control, the optical capsules can be constructed and applied to securely transport the trapped molecules within the network. The advantage is that the dark and bright soliton pair (components) can securely propagate for long distance without electromagnetic interference. In operation, the optical intensity from PANDA ring resonator is fed into gold nano-antenna, where the surface plasmon oscillation between soliton pair and metallic waveguide is established.

Fluctuating hydrodynamics for ionic liquids

Energy Technology Data Exchange (ETDEWEB)

Lazaridis, Konstantinos [Department of Mathematics and Statistics, Washington State University, Pullman, 99163 (United States); Wickham, Logan [Department of Computer Science, Washington State University, Richland, 99354 (United States); Voulgarakis, Nikolaos, E-mail: n.voulgarakis@wsu.edu [Department of Mathematics and Statistics, Washington State University, Pullman, 99163 (United States)

2017-04-25

We present a mean-field fluctuating hydrodynamics (FHD) method for studying the structural and transport properties of ionic liquids in bulk and near electrified surfaces. The free energy of the system consists of two competing terms: (1) a Landau–Lifshitz functional that models the spontaneous separation of the ionic groups, and (2) the standard mean-field electrostatic interaction between the ions in the liquid. The numerical approach used to solve the resulting FHD-Poisson equations is very efficient and models thermal fluctuations with remarkable accuracy. Such density fluctuations are sufficiently strong to excite the experimentally observed spontaneous formation of liquid nano-domains. Statistical analysis of our simulations provides quantitative information about the properties of ionic liquids, such as the mixing quality, stability, and the size of the nano-domains. Our model, thus, can be adequately parameterized by directly comparing our prediction with experimental measurements and all-atom simulations. Conclusively, this work can serve as a practical mathematical tool for testing various theories and designing more efficient mixtures of ionic liquids. - Highlights: • A new fluctuating hydrodynamics method for ionic liquids. • Description of ionic liquid morphology in bulk and near electrified surfaces. • Direct comparison with experimental measurements.

A portable and independent edge fluctuation diagnostic

International Nuclear Information System (INIS)

Tsui, H.Y.W.; Ritz, C.P.; Wootton, A.J.

1991-01-01

The measurements of fluctuations and its associated transport with Langmuir probes have provided essential experimental information for some understanding of the turbulent transport. While such measurements have been conducted in the edge region of several tokamaks, only limited effort has been devoted to link and to consolidate these results: such effort can provide information for a more global understanding of the transport process. The purpose of this project is to provide a portable diagnostic facility to measure the edge turbulence on different devices, a signal processing package to analyze the data in a systematic manner and a database to consolidate the experimental results. The end product which provides a collection of information for the comparisons with the theoretical models may lead to a more global understanding of the transport process. A compact self contained portable system has been designed and developed to diagnose the edge plasma of devices with a wide range of sizes and configurations. The system is capable of measuring both the mean and the fluctuation quantities of density, temperature and potential from a standardized Langmuir probe array using a fast reciprocating probe drive. The system can also be used for other fluctuation diagnostics, such as magnetic probes, if necessary. The data acquisition and analysis is performed on a Macintosh 2fx which provides a user-friendly environment. The results obtained by the signal processing routines are stored in a tabloid format to allow comparative studies. The database is a core part of the portable signal analysis system. It allows a fast display of shot data versus each other, as well as comparison between different devices

Tuning electron transport through a single molecular junction by bridge modification

International Nuclear Information System (INIS)

Li, Xiao-Fei; Qiu, Qi; Luo, Yi

2014-01-01

The possibility of controlling electron transport in a single molecular junction represents the ultimate goal of molecular electronics. Here, we report that the modification of bridging group makes it possible to improve the performance and obtain new functions in a single cross-conjugated molecular junction, designed from a recently synthesized bipolar molecule bithiophene naphthalene diimide. Our first principles results show that the bipolar characteristic remains after the molecule was modified and sandwiched between two metal electrodes. Rectifying is the intrinsic characteristic of the molecular junction and its performance can be enhanced by replacing the saturated bridging group with an unsaturated group. A further improvement of the rectifying and a robust negative differential resistance (NDR) behavior can be achieved by the modification of unsaturated bridge. It is revealed that the modification can induce a deviation angle about 4° between the donor and the acceptor π-conjugations, making it possible to enhance the communication between the two π systems. Meanwhile, the low energy frontier orbitals of the junction can move close to the Fermi level and encounter in energy at certain biases, thus a transport channel with a considerable transmission can be formed near the Fermi level only at a narrow bias regime, resulting in the improvement of rectifying and the robust NDR behavior. This finding could be useful for the design of single molecular devices.

Inward open characterization of EmrD transporter with molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Tan, Xianwei [School of Life Sciences, Tsinghua University, Beijing 100084 (China); Wang, Boxiong, E-mail: boxiong_wang@yahoo.com [Department of Precision Instrument, Tsinghua University, Beijing 100084 (China)

2016-06-10

EmrD is a member of the multidrug resistance exporter family. Up to now, little is known about the structural dynamics that underline the function of the EmrD protein in inward-facing open state and how the EmrD transits from an occluded state to an inward open state. For the first time the article applied the AT simulation to investigate the membrane transporter protein EmrD, and described the dynamic features of the whole protein, the domain, the helices, and the amino acid residues during an inward-open process from its occluded state. The gradual inward-open process is different from the current model of rigid-body domain motion in alternating-access mechanism. Simulation results show that the EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. In addition, it is observed that the helices exposed to the surrounding membrane show a higher level of flexibility than the other regions, and the protonated E227 plays a key role in the transition from the occluded to the open state. -- Highlights: •This study described the dynamic features of the whole EmrD protein, during an inward-open process from its occluded state. •The EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. •The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. •The protonated E227 plays a key role in the transition from the occluded to the open state.

Inward open characterization of EmrD transporter with molecular dynamics simulation

International Nuclear Information System (INIS)

Tan, Xianwei; Wang, Boxiong

2016-01-01

EmrD is a member of the multidrug resistance exporter family. Up to now, little is known about the structural dynamics that underline the function of the EmrD protein in inward-facing open state and how the EmrD transits from an occluded state to an inward open state. For the first time the article applied the AT simulation to investigate the membrane transporter protein EmrD, and described the dynamic features of the whole protein, the domain, the helices, and the amino acid residues during an inward-open process from its occluded state. The gradual inward-open process is different from the current model of rigid-body domain motion in alternating-access mechanism. Simulation results show that the EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. In addition, it is observed that the helices exposed to the surrounding membrane show a higher level of flexibility than the other regions, and the protonated E227 plays a key role in the transition from the occluded to the open state. -- Highlights: •This study described the dynamic features of the whole EmrD protein, during an inward-open process from its occluded state. •The EmrD inward-open conformational fluctuation propagates from a C-terminal domain to an N-terminal domain via the linker region during the transition from its occluded state. •The conformational fluctuation of the C-terminal domain is larger than that of the N-terminal domain. •The protonated E227 plays a key role in the transition from the occluded to the open state.

Extracellular matrix fluctuations during early embryogenesis

International Nuclear Information System (INIS)

Szabó, A; Rupp, P A; Rongish, B J; Little, C D; Czirók, A

2011-01-01

Extracellular matrix (ECM) movements and rearrangements were studied in avian embryos during early stages of development. We show that the ECM moves as a composite material, whereby distinct molecular components as well as spatially separated layers exhibit similar displacements. Using scanning wide field and confocal microscopy we show that the velocity field of ECM displacement is smooth in space and that ECM movements are correlated even at locations separated by several hundred micrometers. Velocity vectors, however, strongly fluctuate in time. The autocorrelation time of the velocity fluctuations is less than a minute. Suppression of the fluctuations yields a persistent movement pattern that is shared among embryos at equivalent stages of development. The high resolution of the velocity fields allows a detailed spatio-temporal characterization of important morphogenetic processes, especially tissue dynamics surrounding the embryonic organizer (Hensen's node)

Self-consistent Kinetic Simulation of RMP-driven Transport: Collisionality and Rotation Effects on RMP Penetration and Transport

Energy Technology Data Exchange (ETDEWEB)

Park, G.; Jeon, Y.; Kim, J., E-mail: gypark@nfri.re.kr [NFRI, Daejeon (Korea, Republic of); Chang, C. [Princeton Plasma Physics Laboratory, Princeton (United States)

2012-09-15

Full text: Control of the edge localized modes (ELMs) is one of the most critical issues for a more successful operation of ITER and the future tokamak fusion reactors. This paper reports ITER relevant simulation results from the XGC0 drift-kinetic code, with respect to the collisionality, plasma density, and rotation dependence of the RMP penetration and the RMP-driven transport in diverted DIII-D geometry with neutral recycling. The simulation results are consistent with the experimental results, and contribute to the physics understanding needed for more confident extrapolation of the present RMP experiments to ITER. It is found that plasma-responded stochasticity becomes weaker as the collisionality gets higher and RMP-driven transport (i.e., density pump-out) is much weaker in the high collisionality case compared with that in the low collisionality one, which is consistent with the recent experimental results on DIII-D and ASDEX-U tokamaks. As for rotation effect, low rotation is found not to affect the stochasticity much in the edge region, while high rotation significantly suppresses the RMPs in the core. The clear difference in RMP behavior between the low and high collisionality regimes can be understood by examining the perturbed current Fourier amplitude profiles within the range of resonant poloidal mode numbers (m = 8 - 15, n = 3). It can be seen that primary shielding currents are strongly concentrated around the steep pedestal region just inside the separatrix, which naturally produces very strong suppression of RMPs there, in low collisionality case. However, in high collisionality case, primary shielding currents are very weak and accumulating toward inner radii leading to the shielding of RMPs further into the plasma. Our kinetic simulation method is also applied to the modeling of RMP ELM control experiments on KSTAR tokamak and the results will be presented together. (author)

Association of manual or engine-driven glide path preparation with canal centring and apical transportation: a systematic review.

Science.gov (United States)

Hartmann, R C; Peters, O A; de Figueiredo, J A P; Rossi-Fedele, G

2018-04-28

The role and effect of glide path preparation in root canal treatment remain controversial. This systematic review aims to compare apical transportation and canal centring of different glide path preparation techniques, with or without subsequent engine-driven root canal preparation. A database search in PubMed, PubMed Central, Embase, Scopus, EBSCO Dentistry & Oral Sciences Source and Virtual Health Library was conducted, using appropriate key words to identify the effect of glide path preparation (or its absence) on apical transportation and canal centring. An assessment for the risk of bias in included studies was carried out. Amongst 2146 studies, 18 satisfied the inclusion criteria. Nine studies assessed glide path preparation per se, comparing apical transportation and canal centring of rotary systems and/or manual files; eleven further investigations examined the efficacy of the glide path prior to final canal preparation with different engine-driven systems. Risk of bias and other study design features with potential influence on study outcomes and clinical implications were assessed. Based on the available evidence, and within the limitation of the studies included, preparation of a glide path using rotary sequences performs similarly (in most of the component studies) or significantly better than manual preparation when assessing apical transportation or canal centring. When compared to the absence of a glide path, canal shaping following glide path preparation was of similar, or significantly better quality, in regard to apical transportation or canal centring. © 2018 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Nucleocytoplasmic Transport: A Paradigm for Molecular Logistics in Artificial Systems.

Science.gov (United States)

Vujica, Suncica; Zelmer, Christina; Panatala, Radhakrishnan; Lim, Roderick Y H

2016-01-01

Artificial organelles, molecular factories and nanoreactors are membrane-bound systems envisaged to exhibit cell-like functionality. These constitute liposomes, polymersomes or hybrid lipo-polymersomes that display different membrane-spanning channels and/or enclose molecular modules. To achieve more complex functionality, an artificial organelle should ideally sustain a continuous influx of essential macromolecular modules (i.e. cargoes) and metabolites against an outflow of reaction products. This would benefit from the incorporation of selective nanopores as well as specific trafficking factors that facilitate cargo selectivity, translocation efficiency, and directionality. Towards this goal, we describe how proteinaceous cargoes are transported between the nucleus and cytoplasm by nuclear pore complexes and the biological trafficking machinery in living cells (i.e. nucleocytoplasmic transport). On this basis, we discuss how biomimetic control may be implemented to selectively import, compartmentalize and accumulate diverse macromolecular modules against concentration gradients in artificial organelles.

Turbulent transport in the MST reversed-field pinch

International Nuclear Information System (INIS)

Rempel, T.D.; Almagri, A.F.; Assadi, S.; Den Hartog, D.J.; Hokin, S.A.; Prager, S.C.; Sarff, J.S.; Shen, W.; Sidikman, K.L.; Spragins, C.W.; Sprott, J.C.; Stoneking, M.R.; Zita, E.J.

1991-11-01

Measurements of edge turbulence and the associated transport are ongoing in the Madison Symmetric Torus (R = 1.5 m, a = 0.52 m) reversed-field pinch using magnetic and electrostatic probes. Magnetic fluctuations are dominated by m = 1 and n ∼ 2R/a tearing modes. Particle losses induced by magnetic field fluctuations have been found to be ambipolar ( parallel B r > = O). Electrostatic fluctuations are broadband and turbulent, with mode widths δm ∼ 3--7 and δn ∼70--150. Particle, parallel current, and energy transport arising from coherent motion with the fluctuating ExB drift has been measured. Particle transport via this channel is comparable to the total particle loss from MST. Energy transport (from phi >/B o ) due to electrostatic fluctuations is relatively small, and parallel current transport (from parallel E chi >/B o ) may be small as well

Rational surfaces, ExB sheared flows and transport interplay in fusion plasmas

International Nuclear Information System (INIS)

Hidalgo, Carlos; Pedrosa, Maria A.; Erents, Kevin

2001-01-01

Experimental evidence of a strong interplay between magnetic topology (rational surfaces) and the generation of ExB sheared flows has been observed in the plasma edge region of stellarator (TJ-II) and tokamak (JET) devices. Constant and varying in time ExB sheared flows are close to the critical value to trigger the transition to improved confinement regimes. The plasma conditions where this has been observed are clearly below the power threshold to trigger the formation of transport barriers. Flows driven by fluctuations are candidates to explain these experimental results. (author)

Uniaxial stress-driven coupled grain boundary motion in hexagonal close-packed metals: A molecular dynamics study

International Nuclear Information System (INIS)

Zong, Hongxiang; Ding, Xiangdong; Lookman, Turab; Li, Ju; Sun, Jun

2015-01-01

Stress-driven grain boundary (GB) migration has been evident as a dominant mechanism accounting for plastic deformation in crystalline solids. Using molecular dynamics (MD) simulations on a Ti bicrystal model, we show that a uniaxial stress-driven coupling is associated with the recently observed 90° GB reorientation in shock simulations and nanopillar compression measurements. This is not consistent with the theory of shear-induced coupled GB migration. In situ atomic configuration analysis reveals that this GB motion is accompanied by the glide of two sets of parallel dislocation arrays, and the uniaxial stress-driven coupling is explained through a composite action of symmetrically distributed dislocations and deformation twins. In addition, the coupling factor is calculated from MD simulations over a wide range of temperatures. We find that the coupled motion can be thermally damped (i.e., not thermally activated), probably due to the absence of the collective action of interface dislocations. This uniaxial coupled mechanism is believed to apply to other hexagonal close-packed metals

Nonlinear correlations in phase-space resolved fluctuations at drift wave frequencies

Energy Technology Data Exchange (ETDEWEB)

Skiff, F [Department of Physics and Astronomy, University of Iowa, Iowa City, Iowa 52242 (United States); Uzun, I [Institute for Plasma Research, University of Maryland, College Park, Maryland 20742 (United States); Diallo, A [Centre de Recherches en Physique des Plasams EPF, Lausanne (Switzerland)

2007-12-15

In an effort to better understand plasma transport, we measure fluctuations associated with drift instabilities resolved in the ion phase-space. Primary attention is given to fluctuations near the electron drift frequency where there are two general components to the observed fluctuations. From two (spatial) point measurements of the ion distribution function with a variable separation along the magnetic field, a number of statistical measures of the fluctuations are calculated including cross-correlation and cross-bicoherence. Both fluid ({omega}/k >> v{sub ti}) and kinetic ({omega}/k {approx} v{sub ti}) components are observed in the fluctuations. The nonlinear interactions are found to depend strongly on the ion particle velocity.

Thermophoretically driven water droplets on graphene and boron nitride surfaces

Science.gov (United States)

Rajegowda, Rakesh; Kannam, Sridhar Kumar; Hartkamp, Remco; Sathian, Sarith P.

2018-05-01

We investigate thermally driven water droplet transport on graphene and hexagonal boron nitride (h-BN) surfaces using molecular dynamics simulations. The two surfaces considered here have different wettabilities with a significant difference in the mode of droplet transport. The water droplet travels along a straighter path on the h-BN sheet than on graphene. The h-BN surface produced a higher driving force on the droplet than the graphene surface. The water droplet is found to move faster on h-BN surface compared to graphene surface. The instantaneous contact angle was monitored as a measure of droplet deformation during thermal transport. The characteristics of the droplet motion on both surfaces is determined through the moment scaling spectrum. The water droplet on h-BN surface showed the attributes of the super-diffusive process, whereas it was sub-diffusive on the graphene surface.

Fractional Stochastic Differential Equations Satisfying Fluctuation-Dissipation Theorem

Science.gov (United States)

Li, Lei; Liu, Jian-Guo; Lu, Jianfeng

2017-10-01

We propose in this work a fractional stochastic differential equation (FSDE) model consistent with the over-damped limit of the generalized Langevin equation model. As a result of the `fluctuation-dissipation theorem', the differential equations driven by fractional Brownian noise to model memory effects should be paired with Caputo derivatives, and this FSDE model should be understood in an integral form. We establish the existence of strong solutions for such equations and discuss the ergodicity and convergence to Gibbs measure. In the linear forcing regime, we show rigorously the algebraic convergence to Gibbs measure when the `fluctuation-dissipation theorem' is satisfied, and this verifies that satisfying `fluctuation-dissipation theorem' indeed leads to the correct physical behavior. We further discuss possible approaches to analyze the ergodicity and convergence to Gibbs measure in the nonlinear forcing regime, while leave the rigorous analysis for future works. The FSDE model proposed is suitable for systems in contact with heat bath with power-law kernel and subdiffusion behaviors.

Mechanistic logic underlying the axonal transport of cytosolic proteins

Science.gov (United States)

Scott, David A.; Das, Utpal; Tang, Yong; Roy, Subhojit

2011-01-01

Proteins vital to presynaptic function are synthesized in the neuronal perikarya and delivered into synapses via two modes of axonal transport. While membrane-anchoring proteins are conveyed in fast axonal transport via motor-driven vesicles, cytosolic proteins travel in slow axonal transport; via mechanisms that are poorly understood. We found that in cultured axons, populations of cytosolic proteins tagged to photoactivable-GFP (PA-GFP) move with a slow motor-dependent anterograde bias; distinct from vesicular-trafficking or diffusion of untagged PA-GFP. The overall bias is likely generated by an intricate particle-kinetics involving transient assembly and short-range vectorial spurts. In-vivo biochemical studies reveal that cytosolic proteins are organized into higher-order structures within axon-enriched fractions that are largely segregated from vesicles. Data-driven biophysical modeling best predicts a scenario where soluble molecules dynamically assemble into mobile supra-molecular structures. We propose a model where cytosolic proteins are transported by dynamically assembling into multi-protein complexes that are directly/indirectly conveyed by motors. PMID:21555071

Effect of altering local protein fluctuations using artificial intelligence

Directory of Open Access Journals (Sweden)

Katsuhiko Nishiyama

2017-03-01

Full Text Available The fluctuations in Arg111, a significantly fluctuating residue in cathepsin K, were locally regulated by modifying Arg111 to Gly111. The binding properties of 15 dipeptides in the modified protein were analyzed by molecular simulations, and modeled as decision trees using artificial intelligence. The decision tree of the modified protein significantly differed from that of unmodified cathepsin K, and the Arg-to-Gly modification exerted a remarkable effect on the peptide binding properties. By locally regulating the fluctuations of a protein, we may greatly alter the original functions of the protein, enabling novel applications in several fields.

Effect of altering local protein fluctuations using artificial intelligence

Science.gov (United States)

Nishiyama, Katsuhiko

2017-03-01

The fluctuations in Arg111, a significantly fluctuating residue in cathepsin K, were locally regulated by modifying Arg111 to Gly111. The binding properties of 15 dipeptides in the modified protein were analyzed by molecular simulations, and modeled as decision trees using artificial intelligence. The decision tree of the modified protein significantly differed from that of unmodified cathepsin K, and the Arg-to-Gly modification exerted a remarkable effect on the peptide binding properties. By locally regulating the fluctuations of a protein, we may greatly alter the original functions of the protein, enabling novel applications in several fields.

Paleoclassical transport explains electron transport barriers in RTP and TEXTOR

NARCIS (Netherlands)

Hogeweij, G. M. D.; Callen, J.D.

2008-01-01

The recently developed paleoclassical transport model sets the minimum level of electron thermal transport in a tokamak. This transport level has proven to be in good agreement with experimental observations in many cases when fluctuation-induced anomalous transport is small, i.e. in (near-) ohmic

Measurements and modelling of electrostatic fluctuations in the scrape-off layer of ASDEX

Energy Technology Data Exchange (ETDEWEB)

Endler, M; Niedermeyer, H; Giannone, L.; Holzhauer, E; Rudyj, A; Theimer, G; Tsois, N [Association Euratom-Max-Planck-Institut fuer Plasmaphysik, Garching (Germany); ASDEX Team

1995-11-01

In the edge plasma of the ASDEX tokamak, electrostatic fluctuations were observed with Langmuir probes and in H{sub {alpha}} light with high poloidal and temporal resolution. These fluctuations contribute a significant fraction to the `anomalous` radial particle transport in the scrape-off layer (SOL). The basic properties and the dependence of the fluctuations parameters on the discharge conditions are documented. A model for an instability mechanism specific to the SOL is introduced and the experimentally observed fluctuation parameters are compared with the predictions of the linearized version of this model. For plasma temperatures above {approx} 10eV in the SOL the observed parameter dependences of the fluctuations are well reproduced by the model. By mixing length arguments the radial transport and the resulting density and pressure gradients in the SOL are estimated from the model. Their dependence on plasma temperature and density qualitatively agrees with the behaviour observed in ohmic discharges on ASDEX. (author). 54 refs, 25 figs.

Measurements and modelling of electrostatic fluctuations in the scrape-off layer of ASDEX

International Nuclear Information System (INIS)

Endler, M.; Niedermeyer, H.; Giannone, L.; Holzhauer, E.; Rudyj, A.; Theimer, G.; Tsois, N.

1995-01-01

In the edge plasma of the ASDEX tokamak, electrostatic fluctuations were observed with Langmuir probes and in H α light with high poloidal and temporal resolution. These fluctuations contribute a significant fraction to the 'anomalous' radial particle transport in the scrape-off layer (SOL). The basic properties and the dependence of the fluctuations parameters on the discharge conditions are documented. A model for an instability mechanism specific to the SOL is introduced and the experimentally observed fluctuation parameters are compared with the predictions of the linearized version of this model. For plasma temperatures above ∼ 10eV in the SOL the observed parameter dependences of the fluctuations are well reproduced by the model. By mixing length arguments the radial transport and the resulting density and pressure gradients in the SOL are estimated from the model. Their dependence on plasma temperature and density qualitatively agrees with the behaviour observed in ohmic discharges on ASDEX. (author). 54 refs, 25 figs

Effects of premixed flames on turbulence and turbulent scalar transport

Energy Technology Data Exchange (ETDEWEB)

Lipatnikov, A.N.; Chomiak, J. [Department of Applied Mechanics, Chalmers University of Technology, 412 75 Goeteborg (Sweden)

2010-02-15

Experimental data and results of direct numerical simulations are reviewed in order to show that premixed combustion can change the basic characteristics of a fluctuating velocity field (the so-called flame-generated turbulence) and the direction of scalar fluxes (the so-called countergradient or pressure-driven transport) in a turbulent flow. Various approaches to modeling these phenomena are discussed and the lack of a well-elaborated and widely validated predictive approach is emphasized. Relevant basic issues (the transition from gradient to countergradient scalar transport, the role played by flame-generated turbulence in the combustion rate, the characterization of turbulence in premixed flames, etc.) are critically considered and certain widely accepted concepts are disputed. Despite the substantial progress made in understanding the discussed effects over the past decades, these basic issues strongly need further research. (author)

Theoretical modeling of electronic transport in molecular devices

Science.gov (United States)

Piccinin, Simone

In this thesis a novel approach for simulating electronic transport in nanoscale structures is introduced. We consider an open quantum system (the electrons of structure) accelerated by an external electromotive force and dissipating energy through inelastic scattering with a heat bath (phonons) acting on the electrons. This method can be regarded as a quantum-mechanical extension of the semi-classical Boltzmann transport equation. We use periodic boundary conditions and employ Density Functional Theory to recast the many-particle problem in an effective single-particle mean-field problem. By explicitly treating the dissipation in the electrodes, the behavior of the potential is an outcome of our method, at variance with the scattering approaches based on the Landauer formalism. We study the self-consistent steady-state solution, analyzing the out-of-equilibrium electron distribution, the electrical characteristics, the behavior of the self-consistent potential and the density of states of the system. We apply the method to the study of electronic transport in several molecular devices, consisting of small organic molecules or atomic wires sandwiched between gold surfaces. For gold wires we recover the experimental evidence that transport in short wires is ballistic, independent of the length of the wire and with conductance of one quantum. In benzene-1,4-dithiol we find that the delocalization of the frontier orbitals of the molecule is responsible for the high value of conductance and that, by inserting methylene groups to decouple the sulfur atoms from the carbon ring, the current is reduced, in agreement with the experimental measurements. We study the effect a geometrical distortion in a molecular device, namely the relative rotation of the carbon rings in a biphenyl-4,4'-dithiol molecule. We find that the reduced coupling between pi orbitals of the rings induced by the rotation leads to a reduction of the conductance and that this behavior is captured by a

Theory of neoclassical ion temperature-gradient-driven turbulence

Science.gov (United States)

Kim, Y. B.; Diamond, P. H.; Biglari, H.; Callen, J. D.

1991-02-01

The theory of collisionless fluid ion temperature-gradient-driven turbulence is extended to the collisional banana-plateau regime. Neoclassical ion fluid evolution equations are developed and utilized to investigate linear and nonlinear dynamics of negative compressibility ηi modes (ηi≡d ln Ti/d ln ni). In the low-frequency limit (ωB2p. As a result of these modifications, growth rates are dissipative, rather than sonic, and radial mode widths are broadened [i.e., γ˜k2∥c2s(ηi -(2)/(3) )/μi, Δx˜ρs(Bt/Bp) (1+ηi)1/2, where k∥, cs, and ρs are the parallel wave number, sound velocity, and ion gyroradius, respectively]. In the limit of weak viscous damping, enhanced neoclassical polarization persists and broadens radial mode widths. Linear mixing length estimates and renormalized turbulence theory are used to determine the ion thermal diffusivity in both cases. In both cases, a strong favorable dependence of ion thermal diffusivity on Bp (and hence plasma current) is exhibited. Furthermore, the ion thermal diffusivity for long wavelength modes exhibits favorable density scaling. The possible role of neoclassical ion temperature-gradient-driven modes in edge fluctuations and transport in L-phase discharges and the L to H transition is discussed.

An Event-Driven Hybrid Molecular Dynamics and Direct Simulation Monte Carlo Algorithm

Energy Technology Data Exchange (ETDEWEB)

Donev, A; Garcia, A L; Alder, B J

2007-07-30

A novel algorithm is developed for the simulation of polymer chains suspended in a solvent. The polymers are represented as chains of hard spheres tethered by square wells and interact with the solvent particles with hard core potentials. The algorithm uses event-driven molecular dynamics (MD) for the simulation of the polymer chain and the interactions between the chain beads and the surrounding solvent particles. The interactions between the solvent particles themselves are not treated deterministically as in event-driven algorithms, rather, the momentum and energy exchange in the solvent is determined stochastically using the Direct Simulation Monte Carlo (DSMC) method. The coupling between the solvent and the solute is consistently represented at the particle level, however, unlike full MD simulations of both the solvent and the solute, the spatial structure of the solvent is ignored. The algorithm is described in detail and applied to the study of the dynamics of a polymer chain tethered to a hard wall subjected to uniform shear. The algorithm closely reproduces full MD simulations with two orders of magnitude greater efficiency. Results do not confirm the existence of periodic (cycling) motion of the polymer chain.

Effects of fueling profiles on plasma transport

International Nuclear Information System (INIS)

Mense, A.T.; Houlberg, W.A.; Attenberger, S.E.; Milora, S.L.

1978-04-01

A one-dimensional (1-D), multifluid transport model is used to investigate the effects of particle fueling profiles on plasma transport in an ignition-sized tokamak (TNS). Normal diffusive properties of plasmas will likely maintain the density at the center of the discharge even if no active fueling is provided there. This significantly relaxes the requirements for fuel penetration. Not only is lower fuel penetration easier to achieve, but it may have the advantage of reducing or eliminating density gradient-driven trapped particle microinstabilities. Simulation of discrete pellet fueling indicates that relatively low velocity (approximately 10 3 m/sec) pellets may be sufficient to fuel a TNS-sized device (approximately 1.25-m minor radius), to produce a relatively broad, cool edge region of plasma which should reduce the potential for sputtering, and also to reduce the likelihood of trapped particle mode dominated transport. Low penetrating pellets containing up to 10 to 20 percent of the total plasma ions can produce fluctuations in density and temperature at the plasma edge, but the pressure profile and fusion alpha production remain almost constant

The role of statistical fluctuations on the stability of shockwaves through gases with activated inelastic collisions

Science.gov (United States)

Sirmas, Nick; Radulescu, Matei

2016-11-01

The present study addresses the stability of piston driven shock waves through a system of hard particles subject to activated inelastic collisions. Molecular Dynamics (MD) simulations have previously revealed an unstable structure for such a system in the form of high density non-uniformities and convective rolls within the shock structure. The work has now been extended to the continuum level by considering the Euler and Navier-Stokes equations for granular gases with a modified cooling rate to include an impact threshold necessary for inelastic collisions. We find that the pattern formations produced in MD can be reproduced at the continuum level by continually perturbing the incoming density field. By varying the perturbation amplitude and wavelength, we find that fluctuations consistent with the statistical fluctuations seen in MD yield similar instabilities to those previously observed. While the inviscid model predicts a highly chaotic structure from these perturbations, the inclusion of viscosity and heat conductivity yields equivalent wavelengths of pattern formations to those seen in MD, which is equal to the relaxation length scale of the dissipative shock structure. The authors acknowledged funding through the Alexander Graham Bell Canada Graduate Scholarship (NSERC) and Ontario Graduate Scholarship.

Electron-phonon interaction in quantum transport through quantum dots and molecular systems

Science.gov (United States)

Ojeda, J. H.; Duque, C. A.; Laroze, D.

2016-12-01

The quantum transport and effects of decoherence properties are studied in quantum dots systems and finite homogeneous chains of aromatic molecules connected to two semi-infinite leads. We study these systems based on the tight-binding approach through Green's function technique within a real space renormalization and polaron transformation schemes. In particular, we calculate the transmission probability following the Landauer-Büttiker formalism, the I - V characteristics and the noise power of current fluctuations taken into account the decoherence. Our results may explain the inelastic effects through nanoscopic systems.

Longitudinal fluctuations and decorrelation of anisotropic flow

Energy Technology Data Exchange (ETDEWEB)

Pang, Long-Gang [Frankfurt Institute for Advanced Studies, Ruth-Moufang-Strasse 1, 60438 Frankfurt am Main (Germany); Petersen, Hannah [Frankfurt Institute for Advanced Studies, Ruth-Moufang-Strasse 1, 60438 Frankfurt am Main (Germany); Institute for Theoretical Physics, Goethe University, Max-von-Laue-Strasse 1, 60438 Frankfurt am Main (Germany); GSI Helmholtzzentrum für Schwerionenforschung, Planckstr. 1, 64291 Darmstadt (Germany); Qin, Guang-You [Key Laboratory of Quark & Lepton Physics (MOE) and Institute of Particle Physics, Central China Normal University, Wuhan 430079 (China); Roy, Victor [Institute for Theoretical Physics, Goethe University, Max-von-Laue-Strasse 1, 60438 Frankfurt am Main (Germany); Wang, Xin-Nian [Key Laboratory of Quark & Lepton Physics (MOE) and Institute of Particle Physics, Central China Normal University, Wuhan 430079 (China); Nuclear Science Division MS70R0319, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (United States)

2016-12-15

We investigate the decorrelation of 2nd and 3rd order anisotropic flow for charged particles in two different pseudo rapidity (η) windows by varying the pseudo rapidity gap, in an event-by-event (3+1)D ideal hydrodynamic model, with fluctuating initial conditions from A Multi-Phase Transport (AMPT) model. We visualize the parton distribution at initial state for Pb+Pb collisions at LHC and Au+Au collisions at RHIC, and demonstrate the longitudinal fluctuations originating from the asymmetry between forward and backward going participants, the fluctuations of the string length and the fluctuations due to finite number of partons at different beam energies. The decorrelation of anisotropic flow of final hadrons with large η gaps is found to originate from the spatial decorrelation along the longitudinal direction in the AMPT initial conditions through hydrodynamic evolution. The agreement between our results and recent CMS data in most centralities suggests that the string-like mechanism of initial parton production in AMPT model captures the initial longitudinal fluctuation that is responsible for the measured decorrelation of anisotropic flow in Pb+Pb collisions at LHC. Our predictions for Au+Au collisions at the highest RHIC energy show stronger longitudinal decorrelation than at LHC, indicating larger longitudinal fluctuations at lower beam energies.

Energy flux due to electromagnetic fluctuations during guide field magnetic reconnection

International Nuclear Information System (INIS)

Kuwahata, Akihiro; Inomoto, Michiaki; Ono, Yasushi; Yanai, Ryoma

2016-01-01

Large electromagnetic fluctuations inside the current sheet and large reconnection electric fields are observed during fast magnetic reconnection in the presence of a guide field. The fluctuations transport 2.5% of the dissipated magnetic energy from the reconnection region. Although the energy gains of the ions and electrons are approximately 60% and 12%, respectively, of the dissipated magnetic energy after the fast reconnection, the energy of fluctuations is not comparable to their energy gains. The fluctuations do not directly contribute to the energy conversion but might cause the fast reconnection leading to the rapid release of magnetic energy. (author)

Development of simulation approach for two-dimensional chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface

Science.gov (United States)

Qin, Yuan; Yao, Man; Hao, Ce; Wan, Lijun; Wang, Yunhe; Chen, Ting; Wang, Dong; Wang, Xudong; Chen, Yonggang

2017-09-01

Two-dimensional (2D) chiral self-assembly system of 5-(benzyloxy)-isophthalic acid derivative/(S)-(+)-2-octanol/highly oriented pyrolytic graphite was studied. A combined density functional theory/molecular mechanics/molecular dynamics (DFT/MM/MD) approach for system of 2D chiral molecular self-assembly driven by hydrogen bond at the liquid/solid interface was thus proposed. Structural models of the chiral assembly were built on the basis of scanning tunneling microscopy (STM) images and simplified for DFT geometry optimization. Merck Molecular Force Field (MMFF) was singled out as the suitable force field by comparing the optimized configurations of MM and DFT. MM and MD simulations for hexagonal unit model which better represented the 2D assemble network were then preformed with MMFF. The adhesion energy, evolution of self-assembly process and characteristic parameters of hydrogen bond were obtained and analyzed. According to the above simulation, the stabilities of the clockwise and counterclockwise enantiomorphous networks were evaluated. The calculational results were supported by STM observations and the feasibility of the simulation method was confirmed by two other systems in the presence of chiral co-absorbers (R)-(-)-2-octanol and achiral co-absorbers 1-octanol. This theoretical simulation method assesses the stability trend of 2D enantiomorphous assemblies with atomic scale and can be applied to the similar hydrogen bond driven 2D chirality of molecular self-assembly system.

Fluctuations in ammonia oxidizing communities across agricultural soils are driven by soil structure and pH

Directory of Open Access Journals (Sweden)

Michele C ePereira e Silva

2012-03-01

Full Text Available The milieu in soil in which microorganisms dwell is never constant. Conditions such as temperature, water availability, pH and nutrients frequently change, impacting the overall functioning of the soil system. To understand the effects of such factors on soil functioning, proxies (indicators of soil function are needed that, in a sensitive manner, reveal normal amplitude of variation. Thus, the so-called normal operating range (NOR of soil can be defined. In this study we determined different components of nitrification by analyzing, in eight agricultural soils, how the community structures and sizes of ammonia oxidizing bacteria and archaea (AOB and AOA, respectively, and their activity, fluctuate over spatial and temporal scales. The results indicated that soil pH and soil type are the main factors that influence the size and structure of the AOA and AOB, as well as their function. The nitrification rates varied between 0.11 ± 0.03 µgN.h-1.gdw-1 and 1.68 ± 0.11 µgN.h-1.gdw-1, being higher in soils with higher clay content (1.09 ± 0.12 µgN.h-1.gdw-1 and lower in soils with lower clay percentages (0.27 ± 0.04 µgN.h-1.gdw-1. Nitrifying activity was driven by soil pH, mostly related to its effect on AOA but not on AOB abundance. Regarding the influence of soil parameters, clay content was the main soil factor shaping the structure of both the AOA and AOB communities. Overall, the potential nitrifying activities were higher and more variable over time in the clayey than in the sandy soils. Whereas the structure of AOB fluctuated more (62.7 ± 2.10% the structure of AOA communities showed lower amplitude of variation (53.65 ± 3.37%. Similar trends were observed for the sizes of these communities. The present work represents a first step towards defining a NOR for soil nitrification. Moreover, the clear effect of soil texture established here suggests that the NOR should be defined in a soil-type-specific manner.

Time evolution of temperature fluctuation in a non-equilibrated system

International Nuclear Information System (INIS)

Bhattacharyya, Trambak; Garg, Prakhar; Sahoo, Raghunath; Samantray, Prasant

2016-01-01

The evolution equation for inhomogeneous and anisotropic temperature fluctuation inside a medium is derived within the ambit of Boltzmann Transport Equation (BTE) for a hot gas of massless particles. Also, specializing to a situation created after a heavy-ion collision (HIC), we analyze the Fourier space variation of temperature fluctuation of the medium using its temperature profile. The effect of viscosity on the variation of fluctuations in the latter case is investigated and possible implications for early universe cosmology, and its connection with HICs are also explored. (orig.)

Time evolution of temperature fluctuation in a non-equilibrated system

Energy Technology Data Exchange (ETDEWEB)

Bhattacharyya, Trambak; Garg, Prakhar; Sahoo, Raghunath [Indian Institute of Technology Indore, Discipline of Physics, School of Basic Sciences, Simrol (India); Samantray, Prasant [Indian Institute of Technology Indore, Centre of Astronomy, School of Basic Sciences, Simrol (India)

2016-09-15

The evolution equation for inhomogeneous and anisotropic temperature fluctuation inside a medium is derived within the ambit of Boltzmann Transport Equation (BTE) for a hot gas of massless particles. Also, specializing to a situation created after a heavy-ion collision (HIC), we analyze the Fourier space variation of temperature fluctuation of the medium using its temperature profile. The effect of viscosity on the variation of fluctuations in the latter case is investigated and possible implications for early universe cosmology, and its connection with HICs are also explored. (orig.)

Molecular Dynamics Simulations of the Human Glucose Transporter GLUT1.

Directory of Open Access Journals (Sweden)

Min-Sun Park

Full Text Available Glucose transporters (GLUTs provide a pathway for glucose transport across membranes. Human GLUTs are implicated in devastating diseases such as heart disease, hyper- and hypo-glycemia, type 2 diabetes and cancer. The human GLUT1 has been recently crystalized in the inward-facing open conformation. However, there is no other structural information for other conformations. The X-ray structures of E. coli Xylose permease (XylE, a glucose transporter homolog, are available in multiple conformations with and without the substrates D-xylose and D-glucose. XylE has high sequence homology to human GLUT1 and key residues in the sugar-binding pocket are conserved. Here we construct a homology model for human GLUT1 based on the available XylE crystal structure in the partially occluded outward-facing conformation. A long unbiased all atom molecular dynamics simulation starting from the model can capture a new fully opened outward-facing conformation. Our investigation of molecular interactions at the interface between the transmembrane (TM domains and the intracellular helices (ICH domain in the outward- and inward-facing conformation supports that the ICH domain likely stabilizes the outward-facing conformation in GLUT1. Furthermore, inducing a conformational transition, our simulations manifest a global asymmetric rocker switch motion and detailed molecular interactions between the substrate and residues through the water-filled selective pore along a pathway from the extracellular to the intracellular side. The results presented here are consistent with previously published biochemical, mutagenesis and functional studies. Together, this study shed light on the structure and functional relationships of GLUT1 in multiple conformational states.

Peclet number as affected by molecular diffusion controls transient anomalous transport in alluvial aquifer-aquitard complexes

Science.gov (United States)

Zhang, Yong; Green, Christopher T.; Tick, Geoffrey R.

2015-01-01

This study evaluates the role of the Peclet number as affected by molecular diffusion in transient anomalous transport, which is one of the major knowledge gaps in anomalous transport, by combining Monte Carlo simulations and stochastic model analysis. Two alluvial settings containing either short- or long-connected hydrofacies are generated and used as media for flow and transport modeling. Numerical experiments show that 1) the Peclet number affects both the duration of the power-law segment of tracer breakthrough curves (BTCs) and the transition rate from anomalous to Fickian transport by determining the solute residence time for a given low-permeability layer, 2) mechanical dispersion has a limited contribution to the anomalous characteristics of late-time transport as compared to molecular diffusion due to an almost negligible velocity in floodplain deposits, and 3) the initial source dimensions only enhance the power-law tail of the BTCs at short travel distances. A tempered stable stochastic (TSS) model is then applied to analyze the modeled transport. Applications show that the time-nonlocal parameters in the TSS model relate to the Peclet number, Pe. In particular, the truncation parameter in the TSS model increases nonlinearly with a decrease in Pe due to the decrease of the mean residence time, and the capacity coefficient increases with an increase in molecular diffusion which is probably due to the increase in the number of immobile particles. The above numerical experiments and stochastic analysis therefore reveal that the Peclet number as affected by molecular diffusion controls transient anomalous transport in alluvial aquifer–aquitard complexes.

Soliton Coupling Driven by Phase Fluctuations in Auto-Parametric Resonance

CERN Document Server

Binder, B

2002-01-01

In this paper the interaction of sine-Gordon solitons and mediating linear waves is modelled by a special case of auto-parametric resonance, the Rayleigh-type self-excited non-linear autonomous system driven by a statistical phase gradient related to the soliton energy. Spherical symmetry can stimulate "whispering gallery modes" (WGM) with integral coupling number M=137.

NON-EQUILIBRIUM MOLECULAR DYNAMICS USED TO OBTAIN SORET COEFFICIENTS OF BINARY HYDROCARBON MIXTURES

Directory of Open Access Journals (Sweden)

F. A. Furtado

2015-09-01

Full Text Available AbstractThe Boundary Driven Non-Equilibrium Molecular Dynamics (BD-NEMD method is employed to evaluate Soret coefficients of binary mixtures. Using a n-decane/n-pentane mixture at 298 K, we study several parameters and conditions of the simulation procedure such as system size, time step size, frequency of perturbation, and the undesired warming up of the system during the simulation. The Soret coefficients obtained here deviated around 20% when comparing with experimental data and with simulated results from the literature. We showed that fluctuations in composition gradients and the consequent deviations of the Soret coefficient may be due to characteristic fluctuations of the composition gradient. Best results were obtained with the smallest time steps and without using a thermostat, which shows that there is room for improvement and/or development of new BD-NEMD algorithms.

The molecular mechanism for overcoming the rate-limiting step in monoamine neurotransmitter transport

DEFF Research Database (Denmark)

Sinning, Steffen; Said, Saida; Malinauskaite, Lina

The monoamine transporter family consists of dopamine (DAT), norepinephrine (NET) and serotonin transporters (SERT) that mediate the reuptake of the monoamine neurotransmitters after their release during neurotransmission. These transporters play prominent roles in psychiatric disorders and are t......The monoamine transporter family consists of dopamine (DAT), norepinephrine (NET) and serotonin transporters (SERT) that mediate the reuptake of the monoamine neurotransmitters after their release during neurotransmission. These transporters play prominent roles in psychiatric disorders...... membrane. The rate-limiting step in monoamine reuptake is the return of the empty transporter from an inward-facing to an outward-facing conformation without neurotransmitter and sodium bound. The molecular mechanism underlying this important conformational transition has not been described. Crystal...

Frontiers in Fluctuation Spectroscopy: Measuring protein dynamics and protein spatio-temporal connectivity

Science.gov (United States)

Digman, Michelle

Fluorescence fluctuation spectroscopy has evolved from single point detection of molecular diffusion to a family of microscopy imaging correlation tools (i.e. ICS, RICS, STICS, and kICS) useful in deriving spatial-temporal dynamics of proteins in living cells The advantage of the imaging techniques is the simultaneous measurement of all points in an image with a frame rate that is increasingly becoming faster with better sensitivity cameras and new microscopy modalities such as the sheet illumination technique. A new frontier in this area is now emerging towards a high level of mapping diffusion rates and protein dynamics in the 2 and 3 dimensions. In this talk, I will discuss the evolution of fluctuation analysis from the single point source to mapping diffusion in whole cells and the technology behind this technique. In particular, new methods of analysis exploit correlation of molecular fluctuations originating from measurement of fluctuation correlations at distant points (pair correlation analysis) and methods that exploit spatial averaging of fluctuations in small regions (iMSD). For example the pair correlation fluctuation (pCF) analyses done between adjacent pixels in all possible radial directions provide a window into anisotropic molecular diffusion. Similar to the connectivity atlas of neuronal connections from the MRI diffusion tensor imaging these new tools will be used to map the connectome of protein diffusion in living cells. For biological reaction-diffusion systems, live single cell spatial-temporal analysis of protein dynamics provides a mean to observe stochastic biochemical signaling in the context of the intracellular environment which may lead to better understanding of cancer cell invasion, stem cell differentiation and other fundamental biological processes. National Institutes of Health Grant P41-RRO3155.

Influence of Signal and Noise on Statistical Fluctuation of Single-Mode Laser System

International Nuclear Information System (INIS)

Xu Dahai; Cheng Qinghua; Cao Li; Wu Dajin

2006-01-01

On the basis of calculating the steady-state mean normalized intensity fluctuation of a signal-mode laser system driven by both colored pump noise with signal modulation and the quantum noise with cross-correlation between its real and imaginary parts, we analyze the influence of modulation signal, noise, and its correlation form on the statistical fluctuation of the laser system. We have found that when the amplitude of modulation signal weakens and its frequency quickens, the statistical fluctuation will reduce rapidly. The statistical fluctuation of the laser system can be restrained by reducing the intensity of pump noise and quantum noise. Moreover, with prolonging of colored cross-correlation time, the statistical fluctuation of laser system experiences a repeated changing process, that is, from decreasing to augmenting, then to decreasing, and finally to augmenting again. With the decreasing of the value of cross-correlation coefficient, the statistical fluctuation will decrease too. When the cross-correlation form between the real part and imaginary part of quantum noise is zero correlation, the statistical fluctuation of laser system has a minimum. Compared with the influence of intensity of pump noise, the influence of intensity of quantum noise on the statistical fluctuation is smaller.

Visualizing functional motions of membrane transporters with molecular dynamics simulations.

Science.gov (United States)

Shaikh, Saher A; Li, Jing; Enkavi, Giray; Wen, Po-Chao; Huang, Zhijian; Tajkhorshid, Emad

2013-01-29

Computational modeling and molecular simulation techniques have become an integral part of modern molecular research. Various areas of molecular sciences continue to benefit from, indeed rely on, the unparalleled spatial and temporal resolutions offered by these technologies, to provide a more complete picture of the molecular problems at hand. Because of the continuous development of more efficient algorithms harvesting ever-expanding computational resources, and the emergence of more advanced and novel theories and methodologies, the scope of computational studies has expanded significantly over the past decade, now including much larger molecular systems and far more complex molecular phenomena. Among the various computer modeling techniques, the application of molecular dynamics (MD) simulation and related techniques has particularly drawn attention in biomolecular research, because of the ability of the method to describe the dynamical nature of the molecular systems and thereby to provide a more realistic representation, which is often needed for understanding fundamental molecular properties. The method has proven to be remarkably successful in capturing molecular events and structural transitions highly relevant to the function and/or physicochemical properties of biomolecular systems. Herein, after a brief introduction to the method of MD, we use a number of membrane transport proteins studied in our laboratory as examples to showcase the scope and applicability of the method and its power in characterizing molecular motions of various magnitudes and time scales that are involved in the function of this important class of membrane proteins.

An Efficient Null Model for Conformational Fluctuations in Proteins

DEFF Research Database (Denmark)

Harder, Tim Philipp; Borg, Mikael; Bottaro, Sandro

2012-01-01

Protein dynamics play a crucial role in function, catalytic activity, and pathogenesis. Consequently, there is great interest in computational methods that probe the conformational fluctuations of a protein. However, molecular dynamics simulations are computationally costly and therefore are often...... limited to comparatively short timescales. TYPHON is a probabilistic method to explore the conformational space of proteins under the guidance of a sophisticated probabilistic model of local structure and a given set of restraints that represent nonlocal interactions, such as hydrogen bonds or disulfide...... on conformational fluctuations that is in correspondence with experimental measurements. TYPHON provides a flexible, yet computationally efficient, method to explore possible conformational fluctuations in proteins....

Supersonic Ionization Wave Driven by Radiation Transport in a Short-Pulse Laser-Produced Plasma

International Nuclear Information System (INIS)

Ditmire, T.; Gumbrell, E.T.; Smith, R.A.; Mountford, L.; Hutchinson, M.H.

1996-01-01

Through the use of an ultrashort (2ps) optical probe, we have time resolved the propagation of an ionization wave into solid fused silica. This ionization wave results when a plasma is created by the intense irradiation of a solid target with a 2ps laser pulse. We find that the velocity of the ionization wave is consistent with radiation driven thermal transport, exceeding the velocity expected from simple electron thermal conduction by nearly an order of magnitude. copyright 1996 The American Physical Society

Beam transient analyses of Accelerator Driven Subcritical Reactors based on neutron transport method

Energy Technology Data Exchange (ETDEWEB)

He, Mingtao; Wu, Hongchun [School of Nuclear Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi (China); Zheng, Youqi, E-mail: yqzheng@mail.xjtu.edu.cn [School of Nuclear Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi (China); Wang, Kunpeng [Nuclear and Radiation Safety Center, PO Box 8088, Beijing 100082 (China); Li, Xunzhao; Zhou, Shengcheng [School of Nuclear Science and Technology, Xi’an Jiaotong University, Xi’an 710049, Shaanxi (China)

2015-12-15

Highlights: • A transport-based kinetics code for Accelerator Driven Subcritical Reactors is developed. • The performance of different kinetics methods adapted to the ADSR is investigated. • The impacts of neutronic parameters deteriorating with fuel depletion are investigated. - Abstract: The Accelerator Driven Subcritical Reactor (ADSR) is almost external source dominated since there is no additional reactivity control mechanism in most designs. This paper focuses on beam-induced transients with an in-house developed dynamic analysis code. The performance of different kinetics methods adapted to the ADSR is investigated, including the point kinetics approximation and space–time kinetics methods. Then, the transient responds of beam trip and beam overpower are calculated and analyzed for an ADSR design dedicated for minor actinides transmutation. The impacts of some safety-related neutronics parameters deteriorating with fuel depletion are also investigated. The results show that the power distribution varying with burnup leads to large differences in temperature responds during transients, while the impacts of kinetic parameters and feedback coefficients are not very obvious. Classification: Core physic.

Theory of neoclassical resistivity-gradient-driven turbulence

International Nuclear Information System (INIS)

Kwon, O.J.; Diamond, P.H.; Hahm, T.S.

1988-12-01

It is shown that rippling instabilities can tap the density gradient expansion free energy source through the density dependence of the neoclassical resistivity. Linear analyses show that the region where neoclassical rippling modes are significantly excited extends from the edge of the plasma to the region where ν/sub *e/ ≤ 1. Since these modes are non-dispersive, diamagnetic effects are negligible in comparison to the nonlinear decorrelation rate at saturation. Thus, the relevant regime is the 'strong turbulence' regime. The turbulent radial diffusivities of the temperature and the density are obtained as eigenvalues of the renormalized eigenmode equations at steady state. The density gradient acts to enhance the level of turbulence, compared to that driven by the temperature gradient alone. The saturated turbulent state is characterized by: current decoupling, the breakdown of Boltzmann relation, a radial mode scale of density fluctuations exceeding that of temperature fluctuations, implying that density diffusivity exceeds temperature diffusivity, and that density fluctuation levels exceed temperature fluctuation levels. Magnetic fluctuation levels are negligible. 29 refs., 1 fig

Experimental Studies of Phase Change and Microencapsulated Phase Change Materials in a Cold Storage/Transportation System with Solar Driven Cooling Cycle

Directory of Open Access Journals (Sweden)

Lin Zheng

2017-11-01

Full Text Available The paper presents the different properties of phase change material (PCM and Microencapsulated phase change material (MEPCM employed to cold storage/transportation system with a solar-driven cooling cycle. Differential Scanning Calorimeter (DSC tests have been performed to analyze the materials enthalpy, melting temperature range, and temperature range of solidification. KD2 Pro is used to test the thermal conductivities of phase change materials slurry and the results were used to compare the materials heat transfer performance. The slurry flow characteristics of MEPCM slurry also have been tested. Furthermore, in order to analyze the improvement effect on stability, the stability of MEPCM slurry with different surfactants have been tested. The researches of the PCM and MEPCM thermal properties revealed a more prospective application for phase change materials in energy storage/transportation systems. The study aims to find the most suitable chilling medium to further optimize the design of the cold storage/transportation systems with solar driven cooling cycles.

Method for delivery of small molecules and proteins across the cell wall of algae using molecular transporters

Science.gov (United States)

Geihe, Erika; Trantow, Brian; Wender, Paul; Hyman, Joel M.; Parvin, Bahram

2017-11-14

The introduction of tools to study, control or expand the inner-workings of algae has been slow to develop. Provided are embodiments of a molecular method based on guanidinium-rich molecular transporters (GR-MoTrs) for bringing molecular cargos into algal cells. The methods of the disclosure have been shown to work in wild-type algae that have an intact cell wall. Developed using Chlamydomonas reinhardtii, this method is also successful with less studied algae, including Neochloris oleoabundans and Scenedesmus dimorphus, thus providing a new and versatile tool for algal research and modification. The method of delivering a cargo compound to an algal cell comprises contacting an algal cell with a guanidinium-rich delivery vehicle comprising a guanidinium-rich molecular transporter (GR-MoTr) linked to a cargo compound desired to be delivered to the algal cell, whereby the guanidinium-rich molecular transporter can traverse the algal cell wall, thereby delivering the cargo compound to the algal cell.

Concentration fluctuations in non-isothermal reaction-diffusion systems. II. The nonlinear case

NARCIS (Netherlands)

Bedeaux, D.; Ortiz de Zárate, J.M.; Pagonabarraga, I.; Sengers, J.V.; Kjelstrup, S.

2011-01-01

In this paper, we consider a simple reaction-diffusion system, namely, a binary fluid mixture with an association-dissociation reaction between two species. We study fluctuations at hydrodynamic spatiotemporal scales when this mixture is driven out of equilibrium by the presence of a temperature

Functional reconstitution of an ATP-driven Ca2+-transport system from the plasma membrane of Commelina communis L

International Nuclear Information System (INIS)

Graef, P.; Weiler, E.W.

1990-01-01

The protein(s) that constitute(s) the ATP-driven Ca 2+ -translocator of plasma membrane enriched vesicles obtained by aqueous two-phase partitioning from leaves of Commelina communis L. has/have been solubilized and reincorporated into tightly sealed liposomes. The reconstituted Ca 2+ -transport system was studied using ATP-driven 45 Ca 2+ import into the proteoliposomes as a measure of activity. The detergent, 3-[(3-cholamidopropyl)dimethylammonio]-1-propane-sulfonate proved to be the most suitable and was used at 10 millimolar concentration, i.e. just above its critical micellar concentration. The presence of additional phospholipid and ATP improved the solubilization and/or reconstitution. The characteristics of the reconstituted system were similar to those of the plasma membrane-bound activity, including the apparent K m for Ca 2+ inhibition by relatively high levels of vanadate and lacking response to added calmodulin. The reconstituted transport system was very strongly inhibited by erythrosine B and had a low apparent K m for ATP levels of the Ca 2+ -ionophore A 23187 instantaneously discharged 90% of the Ca 2+ associated with the vesicles, proving that it had been accumulated in the intravesicular volume in soluble, freely exchangeable form. Ca 2+ -transport in the reconstituted system was thus primary active, through a Ca 2+ -translocating ATPase

Nonequilibrium fluctuation-dissipation relations for one- and two-particle correlation functions in steady-state quantum transport

International Nuclear Information System (INIS)

Ness, H.; Dash, L. K.

2014-01-01

We study the non-equilibrium (NE) fluctuation-dissipation (FD) relations in the context of quantum thermoelectric transport through a two-terminal nanodevice in the steady-state. The FD relations for the one- and two-particle correlation functions are derived for a model of the central region consisting of a single electron level. Explicit expressions for the FD relations of the Green's functions (one-particle correlations) are provided. The FD relations for the current-current and charge-charge (two-particle) correlations are calculated numerically. We use self-consistent NE Green's functions calculations to treat the system in the absence and in the presence of interaction (electron-phonon) in the central region. We show that, for this model, there is no single universal FD theorem for the NE steady state. There are different FD relations for each different class of problems. We find that the FD relations for the one-particle correlation function are strongly dependent on both the NE conditions and the interactions, while the FD relations of the current-current correlation function are much less dependent on the interaction. The latter property suggests interesting applications for single-molecule and other nanoscale transport experiments

Single molecule detection, thermal fluctuation and life

Science.gov (United States)

YANAGIDA, Toshio; ISHII, Yoshiharu

2017-01-01

Single molecule detection has contributed to our understanding of the unique mechanisms of life. Unlike artificial man-made machines, biological molecular machines integrate thermal noises rather than avoid them. For example, single molecule detection has demonstrated that myosin motors undergo biased Brownian motion for stepwise movement and that single protein molecules spontaneously change their conformation, for switching to interactions with other proteins, in response to thermal fluctuation. Thus, molecular machines have flexibility and efficiency not seen in artificial machines. PMID:28190869

Fluctuations and thermodynamic response functions in a Lennard-Jones solid

International Nuclear Information System (INIS)

Li, M.; Johnson, W.L.

1992-01-01

Thermodynamic response functions of a nearest-neighbor Lennard-Jones solid--heat capacity, thermal-expansion coefficient, compressibility, and elastic constants--are calculated directly from fluctuations using molecular-dynamics simulations. The algorithm used is the earlier Parrinello-Rahman molecular dynamics modified to take into account symmetry and rotation invariance of the system under investigation. The convergence is very fast and results are in good agreement with existing Monte Carlo and molecular-dynamics results

Higher-Order Extended Lagrangian Born-Oppenheimer Molecular Dynamics for Classical Polarizable Models.

Science.gov (United States)

Albaugh, Alex; Head-Gordon, Teresa; Niklasson, Anders M N

2018-02-13

Generalized extended Lagrangian Born-Oppenheimer molecular dynamics (XLBOMD) methods provide a framework for fast iteration-free simulations of models that normally require expensive electronic ground state optimizations prior to the force evaluations at every time step. XLBOMD uses dynamically driven auxiliary degrees of freedom that fluctuate about a variationally optimized ground state of an approximate "shadow" potential which approximates the true reference potential. While the requirements for such shadow potentials are well understood, constructing such potentials in practice has previously been ad hoc, and in this work, we present a systematic development of XLBOMD shadow potentials that match the reference potential to any order. We also introduce a framework for combining friction-like dissipation for the auxiliary degrees of freedom with general-order integration, a combination that was not previously possible. These developments are demonstrated with a simple fluctuating charge model and point induced dipole polarization models.

Carrier-Mediated Transport of Nicotine Across the Inner Blood-Retinal Barrier: Involvement of a Novel Organic Cation Transporter Driven by an Outward H(+) Gradient.

Science.gov (United States)

Tega, Yuma; Kubo, Yoshiyuki; Yuzurihara, Chihiro; Akanuma, Shin-Ichi; Hosoya, Ken-Ichi

2015-09-01

The present study was carried out to investigate the blood-to-retina transport of nicotine across the inner blood-retinal barrier (BRB). Using the in vivo vascular injection method, the blood-to-retina influx clearance of nicotine across the BRB was determined as 131 μL/(min?g retina), which is much higher than that of a nonpermeable paracellular marker, and blood-to-retina transport of nicotine was inhibited by organic cations such as pyrilamine and verapamil. The nicotine uptake by a conditionally immortalized rat retinal capillary endothelial cell line (TR-iBRB2 cells), an in vitro model of the inner BRB, exhibited time, temperature, and concentration dependence with a Km of 492 μM. These results suggest the involvement of a carrier-mediated transport process in nicotine transport in the inner BRB. The nicotine uptake by TR-iBRB2 cells was stimulated by an outwardly directed H(+) gradient, and the uptake was significantly inhibited by bulky and hydrophobic cationic drugs, whereas inhibitors of organic cation transporters did not show inhibitory effect. These results suggest that the novel organic cation transport system driven by an outwardly directed H(+) gradient is involved in the blood-to-retina transport of nicotine across the inner BRB. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Binding induced conformational changes of proteins correlate with their intrinsic fluctuations: a case study of antibodies

Directory of Open Access Journals (Sweden)

Keskin Ozlem

2007-05-01

Full Text Available Abstract Background How antibodies recognize and bind to antigens can not be totally explained by rigid shape and electrostatic complimentarity models. Alternatively, pre-existing equilibrium hypothesis states that the native state of an antibody is not defined by a single rigid conformation but instead with an ensemble of similar conformations that co-exist at equilibrium. Antigens bind to one of the preferred conformations making this conformation more abundant shifting the equilibrium. Results Here, two antibodies, a germline antibody of 36–65 Fab and a monoclonal antibody, SPE7 are studied in detail to elucidate the mechanism of antibody-antigen recognition and to understand how a single antibody recognizes different antigens. An elastic network model, Anisotropic Network Model (ANM is used in the calculations. Pre-existing equilibrium is not restricted to apply to antibodies. Intrinsic fluctuations of eight proteins, from different classes of proteins, such as enzymes, binding and transport proteins are investigated to test the suitability of the method. The intrinsic fluctuations are compared with the experimentally observed ligand induced conformational changes of these proteins. The results show that the intrinsic fluctuations obtained by theoretical methods correlate with structural changes observed when a ligand is bound to the protein. The decomposition of the total fluctuations serves to identify the different individual modes of motion, ranging from the most cooperative ones involving the overall structure, to the most localized ones. Conclusion Results suggest that the pre-equilibrium concept holds for antibodies and the promiscuity of antibodies can also be explained this hypothesis: a limited number of conformational states driven by intrinsic motions of an antibody might be adequate to bind to different antigens.

Local synaptic signaling enhances the stochastic transport of motor-driven cargo in neurons

KAUST Repository

Newby, Jay

2010-08-23

The tug-of-war model of motor-driven cargo transport is formulated as an intermittent trapping process. An immobile trap, representing the cellular machinery that sequesters a motor-driven cargo for eventual use, is located somewhere within a microtubule track. A particle representing a motor-driven cargo that moves randomly with a forward bias is introduced at the beginning of the track. The particle switches randomly between a fast moving phase and a slow moving phase. When in the slow moving phase, the particle can be captured by the trap. To account for the possibility that the particle avoids the trap, an absorbing boundary is placed at the end of the track. Two local signaling mechanisms-intended to improve the chances of capturing the target-are considered by allowing the trap to affect the tug-of-war parameters within a small region around itself. The first is based on a localized adenosine triphosphate (ATP) concentration gradient surrounding a synapse, and the second is based on a concentration of tau-a microtubule-associated protein involved in Alzheimer\\'s disease-coating the microtubule near the synapse. It is shown that both mechanisms can lead to dramatic improvements in the capture probability, with a minimal increase in the mean capture time. The analysis also shows that tau can cause a cargo to undergo random oscillations, which could explain some experimental observations. © 2010 IOP Publishing Ltd.

A simplified tether model for molecular motor transporting cargo

International Nuclear Information System (INIS)

Fang-Zhen, Li; Li-Chun, Jiang

2010-01-01

Molecular motors are proteins or protein complexes which function as transporting engines in biological cells. This paper models the tether between motor and its cargo as a symmetric linear potential. Different from Elston and Peskin's work for which performance of the system was discussed only in some limiting cases, this study produces analytic solutions of the problem for general cases by simplifying the transport system into two physical states, which makes it possible to discuss the dynamics of the motor–cargo system in detail. It turns out that the tether strength between motor and cargo should be greater than a threshold or the motor will fail to transport the cargo, which was not discussed by former researchers yet. Value of the threshold depends on the diffusion coefficients of cargo and motor and also on the strength of the Brownian ratchets dragging the system. The threshold approaches a finite constant when the strength of the ratchet tends to infinity. (general)

Critical current enhancement driven by suppression of superconducting fluctuation in ion-gated ultrathin FeSe

Science.gov (United States)

Harada, T.; Shiogai, J.; Miyakawa, T.; Nojima, T.; Tsukazaki, A.

2018-05-01

The framework of phase transition, such as superconducting transition, occasionally depends on the dimensionality of materials. Superconductivity is often weakened in the experimental conditions of two-dimensional thin films due to the fragile superconducting state against defects and interfacial effects. In contrast to this general trend, superconductivity in the thin limit of FeSe exhibits an opposite trend, such as an increase in critical temperature (T c) and the superconducting gap exceeding the bulk values; however, the dominant mechanism is still under debate. Here, we measured thickness-dependent electrical transport properties of the ion-gated FeSe thin films to evaluate the superconducting critical current (I c) in the ultrathin FeSe. Upon systematically decreasing the FeSe thickness by the electrochemical etching technique in the Hall bar-shaped electric double-layer transistors, we observed a dramatic enhancement of I c reaching about 10 mA and corresponding to about 107 A cm‑2 in the thinnest condition. By analyzing the transition behavior, we clarify that the suppressed superconducting fluctuation is one of the origins of the large I c in the ion-gated ultrathin FeSe films. These results indicate the existence of a robust superconducting state possibly with dense Cooper pairs at the thin limit of FeSe.

The influence of non-equilibrium fluctuations on radiation damage and recovery of metals under irradiation

International Nuclear Information System (INIS)

Dubinko, V.I.; Klepikov, V.F.

2007-01-01

In the conventional theory of radiation damage, it is assumed that the main effect of irradiation is due to formation of Frenkel pairs of vacancies and self-interstitial atoms (SIAs) and their clusters. The difference in absorption of vacancies and SIAs by primary or radiation-induced extended defects (EDs) is thought to be the main reason of microstructural evolution under irradiation. On the other hand, the recovery of radiation damage is thought to be driven exclusively by thermal fluctuations resulting in the vacancy evaporation from voids (void annealing) or dislocations (thermal creep) and in the fluctuation-driven overcoming of obstacles by gliding dislocations (plastic strain). However, these recovery mechanisms can be efficient only at sufficiently high temperatures. At lower irradiation temperatures, the main driving force of the recovery processes may be due to nonequilibrium fluctuations of energy states of the atoms surrounding EDs arising as a result of scattering of radiation-induced excitations of atomic and electronic structure at EDs. In the present paper, the mechanisms of nonequilibrium fluctuations that result in such phenomena as the void shrinkage under irradiation at low temperatures (or high dose rates), irradiation creep and irradiation-induced increase of plasticity under sub-threshold irradiation was considered

Electron temperature fluctuation in the HT-7 tokamak plasma observed by electron cyclotron emission imaging

International Nuclear Information System (INIS)

Xiao-Yuan, Xu; Jun, Wang; Yi, Yu; Yi-Zhi, Wen; Chang-Xuan, Yu; Wan-Dong, Liu; Bao-Nian, Wan; Xiang, Gao; Luhmann, N. C.; Domier, C. W.; Wang, Jian; Xia, Z. G.; Shen, Zuowei

2009-01-01

The fluctuation of the electron temperature has been measured by using the electron cyclotron emission imaging in the Hefei Tokamak-7 (HT-7) plasma. The electron temperature fluctuation with a broadband spectrum shows that it propagates in the electron diamagnetic drift direction, and the mean poloidal wave-number k-bar θ is calculated to be about 1.58 cm −1 , or k-bar θρ s thickapprox 0.34. It indicates that the fluctuation should come from the electron drift wave turbulence. The linear global scaling of the electron temperature fluctuation with the gradient of electron temperature is consistent with the mixing length scale qualitatively. Evolution of spectrum of the fluctuation during the sawtooth oscillation phases is investigated, and the fluctuation is found to increase with the gradient of electron temperature increasing during most phases of the sawtooth oscillation. The results indicate that the electron temperature gradient is probably the driver of the fluctuation enhancement. The steady heat flux driven by electron temperature fluctuation is estimated and compared with the results from power balance estimation. (fluids, plasmas and electric discharges)

Magnetic fluctuations in heavy fermion systems

International Nuclear Information System (INIS)

Broholm, C.L.

1989-06-01

Magnetic order and fluctuations in the heavy Fermion systems UPt 3 , U 2 Zn 17 and URu 2 Si 2 have been studied by neutron scattering. Single crystalline samples and triple-axis neutron-scattering techniques with energy transfers between 0 and 40 meV and energy resolutions between 0.1 meV and 4 meV have been employed. UPt 3 develops an antiferromagnetically ordered moment of (0.02±0.005) μ B below T N = 5 K which doubles the unit cell in the basal plane and coexists with superconductivity below T c = 0.5 K. The magnetic fluctuations are relaxational, and enhanced at the antiferromagnetic zone center in a low-energy regime. The characteristic zone-center relaxation energy is 0.3 meV. The temperature- and field-dependence of the antiferromagnetic order in the superconducting phase suggest a close relation between these two properties in UPt 3 . U 2 Zn 17 has a broad spectrum of magnetic fluctuations, even below T N = 9.7 K, of which the transverse part below 10 meV is strongly enhanced at the antiferromagnetic zone center. The system has an anomalously extended critical region and the antiferromagnetic phase transition seems to be driven by the temperature-dependence of an effective RKKY interaction, as anticipated theoretically. URu 2 Si 2 , a strongly anisotropic heavy Fermion system, has a high-energy regime of antiferromagnetically-correlated overdamped magnetic fluctuations. Below T N = 17.5 K weak antiferromagnetic order, μ = (0.04±0.01)μ B , with finite correlations along the tetragonal c axis, develops along with a low-energy regime of strongly dispersive singlet-singlet excitations. Below T c = 1 K antiferromagnetism coexists with superconductivity. A phenomenological model describing the exchange-enhanced overdamped magnetic fluctuations of heavy Fermion systems is proposed. Our experimental results are compared to the anomalous bulk properties of heavy Fermion systems, and to magnetic fluctuations in other metallic magnets. (orig.)

Stress-induced electric current fluctuations in rocks: a superstatistical model

Science.gov (United States)

Cartwright-Taylor, Alexis; Vallianatos, Filippos; Sammonds, Peter

2017-04-01

equilibrium processes whose variance fluctuates over time. The appearance of q-Gaussian statistics are caused by the fluctuating β parameter, which effectively models the fluctuating energy dissipation rate in the system. This concept is known as superstatistics and is physically relevant for modelling driven non-equilibrium systems where the environmental conditions fluctuate on a large scale. The idea is that the environmental variable, such as temperature or pressure, changes so slowly that a rapidly fluctuating variable within that environment has time to relax back to equilibrium between each change in the environment. The application of superstatistical techniques to our experimental electric current fluctuations show that they can indeed be described, to good approximation, by the superposition of local Gaussian processes with fluctuating variance. We conclude, then, that the measured electric current fluctuates in response to intermittent energy dissipation and is driven to varying temporary local equilibria during deformation by the variations in stress intensity. The advantage of this technique is that, once the model has been established to be a good description of the system in question, the average β parameter (a measure of the average energy dissipation rate) for the system can be obtained simply from the macroscopic q-Gaussian distribution parameters.

Towards uncovering the structure of power fluctuations of wind farms.

Science.gov (United States)

Liu, Huiwen; Jin, Yaqing; Tobin, Nicolas; Chamorro, Leonardo P

2017-12-01

The structure of the turbulence-driven power fluctuations in a wind farm is fundamentally described from basic concepts. A derived tuning-free model, supported with experiments, reveals the underlying spectral content of the power fluctuations of a wind farm. It contains two power-law trends and oscillations in the relatively low- and high-frequency ranges. The former is mostly due to the turbulent interaction between the flow and the turbine properties, whereas the latter is due to the advection between turbine pairs. The spectral wind-farm scale power fluctuations Φ_{P} exhibit a power-law decay proportional to f^{-5/3-2} in the region corresponding to the turbulence inertial subrange and at relatively large scales, Φ_{P}∼f^{-2}. Due to the advection and turbulent diffusion of large-scale structures, a spectral oscillation exists with the product of a sinusoidal behavior and an exponential decay in the frequency domain.

Thermally driven molecular linear motors - A molecular dynamics study

DEFF Research Database (Denmark)

Zambrano, Harvey A; Walther, Jens Honore; Jaffe, Richard Lawrence

2009-01-01

We conduct molecular dynamics simulations of a molecular linear motor consisting of coaxial carbon nanotubes with a long outer carbon nanotube confining and guiding the motion of an inner short, capsule-like nanotube. The simulations indicate that the motion of the capsule can be controlled by th...

Pick-up, transport and release of a molecular cargo using a small-molecule robotic arm

Science.gov (United States)

Kassem, Salma; Lee, Alan T. L.; Leigh, David A.; Markevicius, Augustinas; Solà, Jordi

2016-02-01

Modern-day factory assembly lines often feature robots that pick up, reposition and connect components in a programmed manner. The idea of manipulating molecular fragments in a similar way has to date only been explored using biological building blocks (specifically DNA). Here, we report on a wholly artificial small-molecule robotic arm capable of selectively transporting a molecular cargo in either direction between two spatially distinct, chemically similar, sites on a molecular platform. The arm picks up/releases a 3-mercaptopropanehydrazide cargo by formation/breakage of a disulfide bond, while dynamic hydrazone chemistry controls the cargo binding to the platform. Transport is controlled by selectively inducing conformational and configurational changes within an embedded hydrazone rotary switch that steers the robotic arm. In a three-stage operation, 79-85% of 3-mercaptopropanehydrazide molecules are transported in either (chosen) direction between the two platform sites, without the cargo at any time fully dissociating from the machine nor exchanging with other molecules in the bulk.

Hollow Nanospheres with Fluorous Interiors for Transport of Molecular Oxygen in Water

KAUST Repository

Vu, Khanh B.; Chen, Tianyou; Almahdali, Sarah; Bukhriakov, Konstantin; Rodionov, Valentin

2016-01-01

are gas-permeable and feature reactive functional groups for easy modification of the exterior. These features make the SFC-filled nanospheres promising vehicles for respiratory oxygen storage and transport. Uptake of molecular oxygen into nanosphere

Ligand-Receptor Interaction-Mediated Transmembrane Transport of Dendrimer-like Soft Nanoparticles: Mechanisms and Complicated Diffusive Dynamics.

Science.gov (United States)

Liang, Junshi; Chen, Pengyu; Dong, Bojun; Huang, Zihan; Zhao, Kongyin; Yan, Li-Tang

2016-05-09

Nearly all nanomedical applications of dendrimer-like soft nanoparticles rely on the functionality of attached ligands. Understanding how the ligands interact with the receptors in cell membrane and its further effect on the cellular uptake of dendrimer-like soft nanoparticles is thereby a key issue for their better application in nanomedicine. However, the essential mechanism and detailed kinetics for the ligand-receptor interaction-mediated transmembrane transport of such unconventional nanoparticles remain poorly elucidated. Here, using coarse-grained simulations, we present the very first study of molecular mechanism and kinetics behaviors for the transmembrane transport of dendrimer-like soft nanoparticles conjugated with ligands. A phase diagram of interaction states is constructed through examining ligand densities and membrane tensions that allows us to identify novel endocytosis mechanisms featured by the direct wrapping and the penetration-extraction vesiculation. The results provide an in-depth insight into the diffusivity of receptors and dendrimer in the membrane plane and demonstrate how the ligand density influences receptor diffusion and uptake kinetics. It is interesting to find that the ligand-conjugated dendrimers present superdiffusive behaviors on a membrane, which is revealed to be driven by the random fluctuation dynamics of the membrane. The findings facilitate our understanding of some recent experimental observations and could establish fundamental principles for the future development of such important nanomaterials for widespread nanomedical applications.

Electron transport in unipolar InGaN/GaN multiple quantum well structures grown by NH3 molecular beam epitaxy

KAUST Repository

Browne, David A.; Mazumder, Baishakhi; Wu, Yuh-Renn; Speck, James S.

2015-01-01

on electron transport through quantum well active regions. These unipolar structures served as a test vehicle to test our 2D model of the effect of compositional fluctuations on polarization-induced barriers. Variables that were systematically studied included

Phase Transition in Protocols Minimizing Work Fluctuations

Science.gov (United States)

Solon, Alexandre P.; Horowitz, Jordan M.

2018-05-01

For two canonical examples of driven mesoscopic systems—a harmonically trapped Brownian particle and a quantum dot—we numerically determine the finite-time protocols that optimize the compromise between the standard deviation and the mean of the dissipated work. In the case of the oscillator, we observe a collection of protocols that smoothly trade off between average work and its fluctuations. However, for the quantum dot, we find that as we shift the weight of our optimization objective from average work to work standard deviation, there is an analog of a first-order phase transition in protocol space: two distinct protocols exchange global optimality with mixed protocols akin to phase coexistence. As a result, the two types of protocols possess qualitatively different properties and remain distinct even in the infinite duration limit: optimal-work-fluctuation protocols never coalesce with the minimal-work protocols, which therefore never become quasistatic.

TITAN'S TRANSPORT-DRIVEN METHANE CYCLE

International Nuclear Information System (INIS)

Mitchell, Jonathan L.

2012-01-01

The mechanisms behind the occurrence of large cloud outbursts and precipitation on Titan have been disputed. A global- and annual-mean estimate of surface fluxes indicated only 1% of the insolation, or ∼0.04 W m –2 , is exchanged as sensible and/or latent fluxes. Since these fluxes are responsible for driving atmospheric convection, it has been argued that moist convection should be quite rare and precipitation even rarer, even if evaporation globally dominates the surface-atmosphere energy exchange. In contrast, climate simulations indicate substantial cloud formation and/or precipitation. We argue that the top-of-atmosphere (TOA) radiative imbalance is diagnostic of horizontal heat transport by Titan's atmosphere, and thus constrains the strength of the methane cycle. Simple calculations show the TOA radiative imbalance is ∼0.5-1 W m –2 in Titan's equatorial region, which implies 2-3 MW of latitudinal heat transport by the atmosphere. Our simulation of Titan's climate suggests this transport may occur primarily as latent heat, with net evaporation at the equator and net accumulation at higher latitudes. Thus, the methane cycle could be 10-20 times previous estimates. Opposing seasonal transport at solstices, compensation by sensible heat transport, and focusing of precipitation by large-scale dynamics could further enhance the local, instantaneous strength of Titan's methane cycle by a factor of several. A limited supply of surface liquids in regions of large surface radiative imbalance may throttle the methane cycle, and if so, we predict more frequent large storms over the lakes district during Titan's northern summer.

Thermal transport in semicrystalline polyethylene by molecular dynamics simulation

Science.gov (United States)

Lu, Tingyu; Kim, Kyunghoon; Li, Xiaobo; Zhou, Jun; Chen, Gang; Liu, Jun

2018-01-01

Recent research has highlighted the potential to achieve high-thermal-conductivity polymers by aligning their molecular chains. Combined with other merits, such as low-cost, corrosion resistance, and light weight, such polymers are attractive for heat transfer applications. Due to their quasi-one-dimensional structural nature, the understanding on the thermal transport in those ultra-drawn semicrystalline polymer fibers or films is still lacking. In this paper, we built the ideal repeating units of semicrystalline polyethylene and studied their dependence of thermal conductivity on different crystallinity and interlamellar topology using the molecular dynamics simulations. We found that the conventional models, such as the Choy-Young's model, the series model, and Takayanagi's model, cannot accurately predict the thermal conductivity of the quasi-one-dimensional semicrystalline polyethylene. A modified Takayanagi's model was proposed to explain the dependence of thermal conductivity on the bridge number at intermediate and high crystallinity. We also analyzed the heat transfer pathways and demonstrated the substantial role of interlamellar bridges in the thermal transport in the semicrystalline polyethylene. Our work could contribute to the understanding of the structure-property relationship in semicrystalline polymers and shed some light on the development of plastic heat sinks and thermal management in flexible electronics.

Characterization of intermittency of impurity turbulent transport in tokamak edge plasmas

International Nuclear Information System (INIS)

Futatani, S.; Benkadda, S.; Nakamura, Y.; Kondo, K.

2008-01-01

The statistical properties of impurity transport of a tokamak edge plasma embedded in a dissipative drift-wave turbulence are investigated using structure function analysis. The impurities are considered as a passive scalar advected by the plasma flow. Two cases of impurity advection are studied and compared: A decaying impurities case (given by a diffusion-advection equation) and a driven case (forced by a mean scalar gradient). The use of extended self-similarity enables us to show that the relative scaling exponent of structure functions of impurity density and vorticity exhibit similar multifractal scaling in the decaying case and follows the She-Leveque model. However, this property is invalidated for the impurity driven advection case. For both cases, potential fluctuations are self-similar and exhibit a monofractal scaling in agreement with Kolmogorov-Kraichnan theory for two-dimensional turbulence. These results obtained with a passive scalar model agree also with test-particle simulations.

Finding evidence for density fluctuation effects on electron cyclotron heating deposition profiles on DIII-D

International Nuclear Information System (INIS)

Brookman, M. W.; Austin, M. E.; Petty, C. C.

2015-01-01

Theoretical work, computation, and results from TCV [J. Decker “Effect of density fluctuations on ECCD in ITER and TCV,” EPJ Web of Conf. 32, 01016 (2012)] suggest that density fluctuations in the edge region of a tokamak plasma can cause broadening of the ECH deposition profile. In this paper, a GUI tool is presented which is used for analysis of ECH deposition as a first step towards looking for this broadening, which could explain effects seen in previous DIII-D ECH transport studies [K.W. Gentle “Electron energy transport inferences from modulated electron cyclotron heating in DIII-D,” Phys. Plasmas 13, 012311 (2006)]. By applying an FFT to the T e measurements from the University of Texas’s 40-channel ECE Radiometer, and using a simplified thermal transport equation, the flux surface extent of ECH deposition is determined. The Fourier method analysis is compared with a Break-In-Slope (BIS) analysis and predictions from the ray-tracing code TORAY. Examination of multiple Fourier harmonics and BIS fitting methods allow an estimation of modulated transport coefficients and thereby the true ECH deposition profile. Correlations between edge fluctuations and ECH deposition in legacy data are also explored as a step towards establishing a link between fluctuations and deposition broadening in DIII-D

Finding evidence for density fluctuation effects on electron cyclotron heating deposition profiles on DIII-D

Energy Technology Data Exchange (ETDEWEB)

Brookman, M. W., E-mail: brookmanmw@fusion.gat.com; Austin, M. E. [Institute for Fusion Studies, University of Texas at Austin, MS 13-505, 3483 Dunhill St, San Diego, CA 92121-1200 (United States); Petty, C. C. [General Atomics, PO Box 85608, San Diego, CA 92186-5608 (United States)

2015-12-10

Theoretical work, computation, and results from TCV [J. Decker “Effect of density fluctuations on ECCD in ITER and TCV,” EPJ Web of Conf. 32, 01016 (2012)] suggest that density fluctuations in the edge region of a tokamak plasma can cause broadening of the ECH deposition profile. In this paper, a GUI tool is presented which is used for analysis of ECH deposition as a first step towards looking for this broadening, which could explain effects seen in previous DIII-D ECH transport studies [K.W. Gentle “Electron energy transport inferences from modulated electron cyclotron heating in DIII-D,” Phys. Plasmas 13, 012311 (2006)]. By applying an FFT to the T{sub e} measurements from the University of Texas’s 40-channel ECE Radiometer, and using a simplified thermal transport equation, the flux surface extent of ECH deposition is determined. The Fourier method analysis is compared with a Break-In-Slope (BIS) analysis and predictions from the ray-tracing code TORAY. Examination of multiple Fourier harmonics and BIS fitting methods allow an estimation of modulated transport coefficients and thereby the true ECH deposition profile. Correlations between edge fluctuations and ECH deposition in legacy data are also explored as a step towards establishing a link between fluctuations and deposition broadening in DIII-D.

Characterization and isolation of a light driven sodium pump from membranes of Halobacterium halobium. Final technical progress report

International Nuclear Information System (INIS)

MacDonald, R.E.

1982-01-01

We investigated three aspects of the light driven sodium pump (halorhodopsin, which appear to be crucial to our understanding of the mechanisms employed by Halobacterium halobium and to further investigate this unique system of energy conservation. We characterized the molecular mechanisms of transmembrane sodium transport in vesicles from H. halobium with particular reference to the mechanism of couplins of light energy to net sodium translocation. We develop procedures and techniques for extracting the components of the light driven sodium pump from membranes and incorporating them into artificial membrane systems. We examine the mechanism of conversion of bacteriorhodopsin from an active to an inactive form in membrane vesicles and to relate this alternative state of this pigment to the presence of the light driven sodium pump

Role of rational surfaces on fluctuations and transport in the plasma edge of the TJ-II stellarator

International Nuclear Information System (INIS)

Pedrosa, M.A.; Hidalgo, C.; Lopez-Fraguas, A.

2000-01-01

It has been shown that transport barriers in toroidal magnetically confined plasmas tend to be linked to regions of unique magnetic topology such as the location of a minimum in the safety factor, rational surfaces or the boundary between closed and open flux surfaces. In the absence of E x B sheared flows, fluctuations are expected to show maximum amplitude near rational surfaces, and plasma confinement might tend to deteriorate. On the other hand, if the generation of E x B sheared flows were linked to low order rational surfaces, these would be beneficial to confinement. Experimental evidence of E x B sheared flows linked to rational surfaces has been obtained in the plasma edge region of the TJ-II stellarator. (author)

Cross-separatrix Coupling in Nonlinear Global Electrostatic Turbulent Transport in C-2U

Science.gov (United States)

Lau, Calvin; Fulton, Daniel; Bao, Jian; Lin, Zhihong; Binderbauer, Michl; Tajima, Toshiki; Schmitz, Lothar; TAE Team

2017-10-01

In recent years, the progress of the C-2/C-2U advanced beam-driven field-reversed configuration (FRC) experiments at Tri Alpha Energy, Inc. has pushed FRCs to transport limited regimes. Understanding particle and energy transport is a vital step towards an FRC reactor, and two particle-in-cell microturbulence codes, the Gyrokinetic Toroidal Code (GTC) and A New Code (ANC), are being developed and applied toward this goal. Previous local electrostatic GTC simulations find the core to be robustly stable with drift-wave instability only in the scrape-off layer (SOL) region. However, experimental measurements showed fluctuations in both regions; one possibility is that fluctuations in the core originate from the SOL, suggesting the need for non-local simulations with cross-separatrix coupling. Current global ANC simulations with gyrokinetic ions and adiabatic electrons find that non-local effects (1) modify linear growth-rates and frequencies of instabilities and (2) allow instability to move from the unstable SOL to the linearly stable core. Nonlinear spreading is also seen prior to mode saturation. We also report on the progress of the first turbulence simulations in the SOL. This work is supported by the Norman Rostoker Fellowship.

Cellular automaton model of coupled mass transport and chemical reactions

International Nuclear Information System (INIS)