CO oxidation reaction on Pt(111) studied by the dynamic Monte Carlo method including lateral interactions of adsorbates.

PubMed

Nagasaka, Masanari; Kondoh, Hiroshi; Nakai, Ikuyo; Ohta, Toshiaki

2007-01-28

The dynamics of adsorbate structures during CO oxidation on Pt(111) surfaces and its effects on the reaction were studied by the dynamic Monte Carlo method including lateral interactions of adsorbates. The lateral interaction energies between adsorbed species were calculated by the density functional theory method. Dynamic Monte Carlo simulations were performed for the oxidation reaction over a mesoscopic scale, where the experimentally determined activation energies of elementary paths were altered by the calculated lateral interaction energies. The simulated results reproduced the characteristics of the microscopic and mesoscopic scale adsorbate structures formed during the reaction, and revealed that the complicated reaction kinetics is comprehensively explained by a single reaction path affected by the surrounding adsorbates. We also propose from the simulations that weakly adsorbed CO molecules at domain boundaries promote the island-periphery specific reaction.

Numerical Simulation of the Perrin-Like Experiments

ERIC Educational Resources Information Center

Mazur, Zygmunt; Grech, Dariusz

2008-01-01

A simple model of the random Brownian walk of a spherical mesoscopic particle in viscous liquids is proposed. The model can be solved analytically and simulated numerically. The analytic solution gives the known Einstein-Smoluchowski diffusion law r[superscript 2] = 2Dt, where the diffusion constant D is expressed by the mass and geometry of a…

Convergence of methods for coupling of microscopic and mesoscopic reaction-diffusion simulations

NASA Astrophysics Data System (ADS)

Flegg, Mark B.; Hellander, Stefan; Erban, Radek

2015-05-01

In this paper, three multiscale methods for coupling of mesoscopic (compartment-based) and microscopic (molecular-based) stochastic reaction-diffusion simulations are investigated. Two of the three methods that will be discussed in detail have been previously reported in the literature; the two-regime method (TRM) and the compartment-placement method (CPM). The third method that is introduced and analysed in this paper is called the ghost cell method (GCM), since it works by constructing a "ghost cell" in which molecules can disappear and jump into the compartment-based simulation. Presented is a comparison of sources of error. The convergent properties of this error are studied as the time step Δt (for updating the molecular-based part of the model) approaches zero. It is found that the error behaviour depends on another fundamental computational parameter h, the compartment size in the mesoscopic part of the model. Two important limiting cases, which appear in applications, are considered: Δt → 0 and h is fixed; Δt → 0 and h → 0 such that √{ Δt } / h is fixed. The error for previously developed approaches (the TRM and CPM) converges to zero only in the limiting case (ii), but not in case (i). It is shown that the error of the GCM converges in the limiting case (i). Thus the GCM is superior to previous coupling techniques if the mesoscopic description is much coarser than the microscopic part of the model.

Multi-Dimensional, Mesoscopic Monte Carlo Simulations of Inhomogeneous Reaction-Drift-Diffusion Systems on Graphics-Processing Units

PubMed Central

Vigelius, Matthias; Meyer, Bernd

2012-01-01

For many biological applications, a macroscopic (deterministic) treatment of reaction-drift-diffusion systems is insufficient. Instead, one has to properly handle the stochastic nature of the problem and generate true sample paths of the underlying probability distribution. Unfortunately, stochastic algorithms are computationally expensive and, in most cases, the large number of participating particles renders the relevant parameter regimes inaccessible. In an attempt to address this problem we present a genuine stochastic, multi-dimensional algorithm that solves the inhomogeneous, non-linear, drift-diffusion problem on a mesoscopic level. Our method improves on existing implementations in being multi-dimensional and handling inhomogeneous drift and diffusion. The algorithm is well suited for an implementation on data-parallel hardware architectures such as general-purpose graphics processing units (GPUs). We integrate the method into an operator-splitting approach that decouples chemical reactions from the spatial evolution. We demonstrate the validity and applicability of our algorithm with a comprehensive suite of standard test problems that also serve to quantify the numerical accuracy of the method. We provide a freely available, fully functional GPU implementation. Integration into Inchman, a user-friendly web service, that allows researchers to perform parallel simulations of reaction-drift-diffusion systems on GPU clusters is underway. PMID:22506001

Nanoscale patterning of electronic devices at the amorphous LaAlO3/SrTiO3 oxide interface using an electron sensitive polymer mask

NASA Astrophysics Data System (ADS)

Bjørlig, Anders V.; von Soosten, Merlin; Erlandsen, Ricci; Dahm, Rasmus Tindal; Zhang, Yu; Gan, Yulin; Chen, Yunzhong; Pryds, Nini; Jespersen, Thomas S.

2018-04-01

A simple approach is presented for designing complex oxide mesoscopic electronic devices based on the conducting interfaces of room temperature grown LaAlO3/SrTiO3 heterostructures. The technique is based entirely on methods known from conventional semiconductor processing technology, and we demonstrate a lateral resolution of ˜100 nm. We study the low temperature transport properties of nanoscale wires and demonstrate the feasibility of the technique for defining in-plane gates allowing local control of the electrostatic environment in mesoscopic devices.

Modeling snow-crystal growth: a three-dimensional mesoscopic approach.

PubMed

Gravner, Janko; Griffeath, David

2009-01-01

We introduce a three-dimensional, computationally feasible, mesoscopic model for snow-crystal growth, based on diffusion of vapor, anisotropic attachment, and a boundary layer. Several case studies are presented that faithfully replicate most observed snow-crystal morphology, an unusual achievement for a mathematical model. In particular, many of the most striking physical specimens feature both facets and branches, and our model provides an explanation for this phenomenon. We also duplicate many other observed traits, including ridges, ribs, sandwich plates, and hollow columns, as well as various dynamic instabilities. The concordance of observed phenomena suggests that the ingredients in our model are the most important ones in the development of physical snow crystals.

Neuroanatomy from Mesoscopic to Nanoscopic Scales: An Improved Method for the Observation of Semithin Sections by High-Resolution Scanning Electron Microscopy

PubMed Central

Rodríguez, José-Rodrigo; Turégano-López, Marta; DeFelipe, Javier; Merchán-Pérez, Angel

2018-01-01

Semithin sections are commonly used to examine large areas of tissue with an optical microscope, in order to locate and trim the regions that will later be studied with the electron microscope. Ideally, the observation of semithin sections would be from mesoscopic to nanoscopic scales directly, instead of using light microscopy and then electron microscopy (EM). Here we propose a method that makes it possible to obtain high-resolution scanning EM images of large areas of the brain in the millimeter to nanometer range. Since our method is compatible with light microscopy, it is also feasible to generate hybrid light and electron microscopic maps. Additionally, the same tissue blocks that have been used to obtain semithin sections can later be used, if necessary, for transmission EM, or for focused ion beam milling and scanning electron microscopy (FIB-SEM). PMID:29568263

Neuroanatomy from Mesoscopic to Nanoscopic Scales: An Improved Method for the Observation of Semithin Sections by High-Resolution Scanning Electron Microscopy.

PubMed

Rodríguez, José-Rodrigo; Turégano-López, Marta; DeFelipe, Javier; Merchán-Pérez, Angel

2018-01-01

Semithin sections are commonly used to examine large areas of tissue with an optical microscope, in order to locate and trim the regions that will later be studied with the electron microscope. Ideally, the observation of semithin sections would be from mesoscopic to nanoscopic scales directly, instead of using light microscopy and then electron microscopy (EM). Here we propose a method that makes it possible to obtain high-resolution scanning EM images of large areas of the brain in the millimeter to nanometer range. Since our method is compatible with light microscopy, it is also feasible to generate hybrid light and electron microscopic maps. Additionally, the same tissue blocks that have been used to obtain semithin sections can later be used, if necessary, for transmission EM, or for focused ion beam milling and scanning electron microscopy (FIB-SEM).

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

PubMed

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

2015-09-21

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

Mesoscopic description of random walks on combs

NASA Astrophysics Data System (ADS)

Méndez, Vicenç; Iomin, Alexander; Campos, Daniel; Horsthemke, Werner

2015-12-01

Combs are a simple caricature of various types of natural branched structures, which belong to the category of loopless graphs and consist of a backbone and branches. We study continuous time random walks on combs and present a generic method to obtain their transport properties. The random walk along the branches may be biased, and we account for the effect of the branches by renormalizing the waiting time probability distribution function for the motion along the backbone. We analyze the overall diffusion properties along the backbone and find normal diffusion, anomalous diffusion, and stochastic localization (diffusion failure), respectively, depending on the characteristics of the continuous time random walk along the branches, and compare our analytical results with stochastic simulations.

Nonlocal electrical detection of spin accumulation generated by anomalous Hall effect in mesoscopic N i81F e19 films

NASA Astrophysics Data System (ADS)

Qin, Chuan; Chen, Shuhan; Cai, Yunjiao; Kandaz, Fatih; Ji, Yi

2017-10-01

Spin accumulation generated by the anomalous Hall effect (AHE) in mesoscopic ferromagnetic N i81F e19 (permalloy, Py) films is detected electrically by a nonlocal method. The reciprocal phenomenon, the inverse spin Hall effect (ISHE), can also be generated and detected all electrically in the same structure. For accurate quantitative analysis, a series of nonlocal AHE/ISHE structures and supplementary structures are fabricated on each sample substrate to account for statistical variations and to accurately determine all essential physical parameters in situ. By exploring Py thicknesses of 4, 8, and 12 nm, the Py spin diffusion length λPy is found to be much shorter than the film thicknesses. The product of λPy and the Py spin Hall angle αSH is determined to be independent of thickness and resistivity: αSHλPy=(0.066 ±0.009 ) nm at 5 K and (0.041 ±0.010 )nm at 295 K. These values are comparable to those obtained from mesoscopic Pt films.

Imaging of mesoscopic-scale organisms using selective-plane optoacoustic tomography.

PubMed

Razansky, Daniel; Vinegoni, Claudio; Ntziachristos, Vasilis

2009-05-07

Mesoscopic-scale living organisms (i.e. 1 mm to 1 cm sized) remain largely inaccessible by current optical imaging methods due to intensive light scattering in tissues. Therefore, imaging of many important model organisms, such as insects, fishes, worms and similarly sized biological specimens, is currently limited to embryonic or other transparent stages of development. This makes it difficult to relate embryonic cellular and molecular mechanisms to consequences in organ function and animal behavior in more advanced stages and adults. Herein, we have developed a selective-plane illumination optoacoustic tomography technique for in vivo imaging of optically diffusive organisms and tissues. The method is capable of whole-body imaging at depths from the sub-millimeter up to centimeter range with a scalable spatial resolution in the order of magnitude of a few tenths of microns. In contrast to pure optical methods, the spatial resolution here is not determined nor limited by light diffusion; therefore, such performance cannot be achieved by any other optical imaging technology developed so far. The utility of the method is demonstrated on several whole-body models and small-animal extremities.

Mesoscopic modeling and parameter estimation of a lithium-ion battery based on LiFePO4/graphite

NASA Astrophysics Data System (ADS)

Jokar, Ali; Désilets, Martin; Lacroix, Marcel; Zaghib, Karim

2018-03-01

A novel numerical model for simulating the behavior of lithium-ion batteries based on LiFePO4(LFP)/graphite is presented. The model is based on the modified Single Particle Model (SPM) coupled to a mesoscopic approach for the LFP electrode. The model comprises one representative spherical particle as the graphite electrode, and N LFP units as the positive electrode. All the SPM equations are retained to model the negative electrode performance. The mesoscopic model rests on non-equilibrium thermodynamic conditions and uses a non-monotonic open circuit potential for each unit. A parameter estimation study is also carried out to identify all the parameters needed for the model. The unknown parameters are the solid diffusion coefficient of the negative electrode (Ds,n), reaction-rate constant of the negative electrode (Kn), negative and positive electrode porosity (εn&εn), initial State-Of-Charge of the negative electrode (SOCn,0), initial partial composition of the LFP units (yk,0), minimum and maximum resistance of the LFP units (Rmin&Rmax), and solution resistance (Rcell). The results show that the mesoscopic model can simulate successfully the electrochemical behavior of lithium-ion batteries at low and high charge/discharge rates. The model also describes adequately the lithiation/delithiation of the LFP particles, however, it is computationally expensive compared to macro-based models.

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

PubMed Central

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

2015-01-01

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

NMR relaxometric probing of ionic liquid dynamics and diffusion under mesoscopic confinement within bacterial cellulose ionogels

NASA Astrophysics Data System (ADS)

Smith, Chip J.; Gehrke, Sascha; Hollóczki, Oldamur; Wagle, Durgesh V.; Heitz, Mark P.; Baker, Gary A.

2018-05-01

Bacterial cellulose ionogels (BCIGs) represent a new class of material comprising a significant content of entrapped ionic liquid (IL) within a porous network formed from crystalline cellulose microfibrils. BCIGs suggest unique opportunities in separations, optically active materials, solid electrolytes, and drug delivery due to the fact that they can contain as much as 99% of an IL phase by weight, coupled with an inherent flexibility, high optical transparency, and the ability to control ionogel cross-sectional shape and size. To allow for the tailoring of BCIGs for a multitude of applications, it is necessary to better understand the underlying principles of the mesoscopic confinement within these ionogels. Toward this, we present a study of the structural, relaxation, and diffusional properties of the ILs, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([emim][Tf2N]) and 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide ([bmpy][Tf2N]), using 1H and 19F NMR T1 relaxation times, rotational correlation times, and diffusion ordered spectroscopy (DOSY) diffusion coefficients, accompanied by molecular dynamics (MD) simulations. We observed that the cation methyl groups in both ILs were primary points of interaction with the cellulose chains and, while the pore size in cellulose is rather large, [emim]+ diffusion was slowed by ˜2-fold, whereas [Tf2N]- diffusion was unencumbered by incorporation in the ionogel. While MD simulations of [bmpy][Tf2N] confinement at the interface showed a diffusion coefficient decrease roughly 3-fold compared to the bulk liquid, DOSY measurements did not reveal any significant changes in diffusion. This suggests that the [bmpy][Tf2N] alkyl chains dominate diffusion through formation of apolar domains. This is in contrast to [emim][Tf2N] where delocalized charge appears to preclude apolar domain formation, allowing interfacial effects to be manifested at a longer range in [emim][Tf2N].

Signature of phase singularities in diffusive regimes in disordered waveguide lattices: interplay and qualitative analysis

NASA Astrophysics Data System (ADS)

Ghosh, Somnath

2018-05-01

Co-existence and interplay between mesoscopic light dynamics with singular optics in spatially random but temporally coherent disordered waveguide lattices is reported. Two CW light beams of 1.55 micron operating wavelength are launched as inputs to 1D waveguide lattices with controllable weak disorder in refractive index profile. Direct observation of phase singularities in the speckle pattern along the length is numerically demonstrated. Quantitative analysis of onset of such singular behavior and diffusive wave propagation is analyzed for the first time.

Dissipative particle dynamics of diffusion-NMR requires high Schmidt-numbers

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

Azhar, Mueed; Greiner, Andreas; Korvink, Jan G., E-mail: jan.korvink@kit.edu, E-mail: david.kauzlaric@imtek.uni-freiburg.de

We present an efficient mesoscale model to simulate the diffusion measurement with nuclear magnetic resonance (NMR). On the level of mesoscopic thermal motion of fluid particles, we couple the Bloch equations with dissipative particle dynamics (DPD). Thereby we establish a physically consistent scaling relation between the diffusion constant measured for DPD-particles and the diffusion constant of a real fluid. The latter is based on a splitting into a centre-of-mass contribution represented by DPD, and an internal contribution which is not resolved in the DPD-level of description. As a consequence, simulating the centre-of-mass contribution with DPD requires high Schmidt numbers. Aftermore » a verification for fundamental pulse sequences, we apply the NMR-DPD method to NMR diffusion measurements of anisotropic fluids, and of fluids restricted by walls of microfluidic channels. For the latter, the free diffusion and the localisation regime are considered.« less

Coarse-grained hydrodynamics from correlation functions

NASA Astrophysics Data System (ADS)

Palmer, Bruce

2018-02-01

This paper will describe a formalism for using correlation functions between different grid cells as the basis for determining coarse-grained hydrodynamic equations for modeling the behavior of mesoscopic fluid systems. Configurations from a molecular dynamics simulation or other atomistic simulation are projected onto basis functions representing grid cells in a continuum hydrodynamic simulation. Equilibrium correlation functions between different grid cells are evaluated from the molecular simulation and used to determine the evolution operator for the coarse-grained hydrodynamic system. The formalism is demonstrated on a discrete particle simulation of diffusion with a spatially dependent diffusion coefficient. Correlation functions are calculated from the particle simulation and the spatially varying diffusion coefficient is recovered using a fitting procedure.

Are morphological changes necessary to mediate the therapeutic effects of electroconvulsive therapy?

PubMed

Nickl-Jockschat, Thomas; Palomero Gallagher, Nicola; Kumar, Vinod; Hoffstaedter, Felix; Brügmann, Elisabeth; Habel, Ute; Eickhoff, Simon B; Grözinger, Michael

2016-04-01

The neurotrophic hypothesis has become the favorite model to explain the antidepressant properties of electroconvulsive therapy (ECT). It is based on the assumption that a restoration of previously defective neural networks drives therapeutic effects. Recent data in rather young patients suggest that neurotrophic effects of ECT might be detectable by diffusion tensor imaging. We here aimed to investigate whether the therapeutic response to ECT necessarily goes along with mesoscopic effects in gray matter (GM) or white matter (WM) in our patients in advanced age. Patients (n = 21, 15 males and 7 females) suffering from major depressive disorder were treated with ECT. Before the start of treatment and after the completion of the index series, they underwent magnetic resonance imaging, including a diffusion-weighed sequence. We used voxel-based morphometry to assess GM changes and tract-based spatial statistics and an SPM-based whole-brain analysis to detect WM changes in the course of treatment. Patients significantly improved clinically during the course of ECT. This was, however, not accompanied by GM or WM changes. This result challenges the notion that mesoscopic brain structure changes are an obligatory prerequisite for the antidepressant effects of ECT.

Mesoscopic Effects in an Agent-Based Bargaining Model in Regular Lattices

PubMed Central

Poza, David J.; Santos, José I.; Galán, José M.; López-Paredes, Adolfo

2011-01-01

The effect of spatial structure has been proved very relevant in repeated games. In this work we propose an agent based model where a fixed finite population of tagged agents play iteratively the Nash demand game in a regular lattice. The model extends the multiagent bargaining model by Axtell, Epstein and Young [1] modifying the assumption of global interaction. Each agent is endowed with a memory and plays the best reply against the opponent's most frequent demand. We focus our analysis on the transient dynamics of the system, studying by computer simulation the set of states in which the system spends a considerable fraction of the time. The results show that all the possible persistent regimes in the global interaction model can also be observed in this spatial version. We also find that the mesoscopic properties of the interaction networks that the spatial distribution induces in the model have a significant impact on the diffusion of strategies, and can lead to new persistent regimes different from those found in previous research. In particular, community structure in the intratype interaction networks may cause that communities reach different persistent regimes as a consequence of the hindering diffusion effect of fluctuating agents at their borders. PMID:21408019

Mesoscopic effects in an agent-based bargaining model in regular lattices.

PubMed

Poza, David J; Santos, José I; Galán, José M; López-Paredes, Adolfo

2011-03-09

The effect of spatial structure has been proved very relevant in repeated games. In this work we propose an agent based model where a fixed finite population of tagged agents play iteratively the Nash demand game in a regular lattice. The model extends the multiagent bargaining model by Axtell, Epstein and Young modifying the assumption of global interaction. Each agent is endowed with a memory and plays the best reply against the opponent's most frequent demand. We focus our analysis on the transient dynamics of the system, studying by computer simulation the set of states in which the system spends a considerable fraction of the time. The results show that all the possible persistent regimes in the global interaction model can also be observed in this spatial version. We also find that the mesoscopic properties of the interaction networks that the spatial distribution induces in the model have a significant impact on the diffusion of strategies, and can lead to new persistent regimes different from those found in previous research. In particular, community structure in the intratype interaction networks may cause that communities reach different persistent regimes as a consequence of the hindering diffusion effect of fluctuating agents at their borders.

Signature of phase singularities in diffusive regimes in disordered waveguide lattices: interplay and qualitative analysis.

PubMed

Ghosh, Somnath

2018-05-10

Coexistence and interplay between mesoscopic light dynamics with singular optics in spatially disordered waveguide lattices are reported. Two CW light beams of a 1.55 μm operating wavelength are launched as inputs to 1D waveguide lattices with controllable weak disorder in a complex refractive index profile. Direct observation of phase singularities in the speckle pattern along the length is numerically demonstrated. Quantitative analysis of the onset of such singular behavior and diffusive wave propagation is analyzed for the first time, to the best of our knowledge.

Anomalous diffusion with linear reaction dynamics: from continuous time random walks to fractional reaction-diffusion equations.

PubMed

Henry, B I; Langlands, T A M; Wearne, S L

2006-09-01

We have revisited the problem of anomalously diffusing species, modeled at the mesoscopic level using continuous time random walks, to include linear reaction dynamics. If a constant proportion of walkers are added or removed instantaneously at the start of each step then the long time asymptotic limit yields a fractional reaction-diffusion equation with a fractional order temporal derivative operating on both the standard diffusion term and a linear reaction kinetics term. If the walkers are added or removed at a constant per capita rate during the waiting time between steps then the long time asymptotic limit has a standard linear reaction kinetics term but a fractional order temporal derivative operating on a nonstandard diffusion term. Results from the above two models are compared with a phenomenological model with standard linear reaction kinetics and a fractional order temporal derivative operating on a standard diffusion term. We have also developed further extensions of the CTRW model to include more general reaction dynamics.

Multiscale Modeling of Diffusion in a Crowded Environment.

PubMed

Meinecke, Lina

2017-11-01

We present a multiscale approach to model diffusion in a crowded environment and its effect on the reaction rates. Diffusion in biological systems is often modeled by a discrete space jump process in order to capture the inherent noise of biological systems, which becomes important in the low copy number regime. To model diffusion in the crowded cell environment efficiently, we compute the jump rates in this mesoscopic model from local first exit times, which account for the microscopic positions of the crowding molecules, while the diffusing molecules jump on a coarser Cartesian grid. We then extract a macroscopic description from the resulting jump rates, where the excluded volume effect is modeled by a diffusion equation with space-dependent diffusion coefficient. The crowding molecules can be of arbitrary shape and size, and numerical experiments demonstrate that those factors together with the size of the diffusing molecule play a crucial role on the magnitude of the decrease in diffusive motion. When correcting the reaction rates for the altered diffusion we can show that molecular crowding either enhances or inhibits chemical reactions depending on local fluctuations of the obstacle density.

Isotropic stochastic rotation dynamics

NASA Astrophysics Data System (ADS)

Mühlbauer, Sebastian; Strobl, Severin; Pöschel, Thorsten

2017-12-01

Stochastic rotation dynamics (SRD) is a widely used method for the mesoscopic modeling of complex fluids, such as colloidal suspensions or multiphase flows. In this method, however, the underlying Cartesian grid defining the coarse-grained interaction volumes induces anisotropy. We propose an isotropic, lattice-free variant of stochastic rotation dynamics, termed iSRD. Instead of Cartesian grid cells, we employ randomly distributed spherical interaction volumes. This eliminates the requirement of a grid shift, which is essential in standard SRD to maintain Galilean invariance. We derive analytical expressions for the viscosity and the diffusion coefficient in relation to the model parameters, which show excellent agreement with the results obtained in iSRD simulations. The proposed algorithm is particularly suitable to model systems bound by walls of complex shape, where the domain cannot be meshed uniformly. The presented approach is not limited to SRD but is applicable to any other mesoscopic method, where particles interact within certain coarse-grained volumes.

Self-assembled titanium phosphonate nanomaterial having a mesoscopic void space and its optoelectronic application.

PubMed

Pramanik, Malay; Patra, Astam K; Bhaumik, Asim

2013-04-14

Here we report the synthesis of a new crystalline titanium phosphonate material (HTiP-7) having a self-assembled nanostructure and a mesoscopic void space without the aid of any surfactant or templating agent. The material has been synthesized hydrothermally through the reaction between benzene-1,3,5-triphosphonic acid (BTPA) and titanium(iv) isopropoxide at neutral pH at 453 K for 24 h. This hybrid phosphonate material has been thoroughly characterized by powder X-ray diffraction, N2 sorption, HR TEM, FE SEM, TG-DTA, FT IR and UV-Vis diffuse reflectance spectroscopic studies. Two very well-known software packages, REFLEX and CELSIZ unit cell refinement programs, are employed to establish the triclinic crystal phase of this hybrid material (HTiP-7). Very tiny nanocrystals of HTiP-7 self-aggregated to form spherical nanoparticles of dimension ca. 25 nm together with a mesoscopic void space and good BET surface area (255 m(2) g(-1)). The framework is thermally stable up to 650 K. The material showed excellent carrier mobility for photocurrent generation in the presence of a photosensitizer molecule (Rose Bengal). To the best of our knowledge this is the first report of a photon-to-electron energy transfer process over a dye doped titanium phosphonate nanomaterial.

Viscoelastic representation of surface waves in patchy saturated poroelastic media

NASA Astrophysics Data System (ADS)

Zhang, Yu; Xu, Yixian; Xia, Jianghai; Ping, Ping; Zhang, Shuangxi

2014-08-01

Wave-induced flow is observed as the dominated factor for P wave propagation at seismic frequencies. This mechanism has a mesoscopic scale nature. The inhomogeneous unsaturated patches are regarded larger than the pore size, but smaller than the wavelength. Surface wave, e.g., Rayleigh wave, which propagates along the free surface, generated by the interfering of body waves is also affected by the mesoscopic loss mechanisms. Recent studies have reported that the effect of the wave-induced flow in wave propagation shows a relaxation behavior. Viscoelastic equivalent relaxation function associated with the wave mode can describe the kinetic nature of the attenuation. In this paper, the equivalent viscoelastic relaxation functions are extended to take into account the free surface for the Rayleigh surface wave propagation in patchy saturated poroelastic media. Numerical results for the frequency-dependent velocity and attenuation and the time-dependent dynamical responses for the equivalent Rayleigh surface wave propagation along an interface between vacuum and patchy saturated porous media are reported in the low-frequency range (0.1-1,000 Hz). The results show that the dispersion and attenuation and kinetic characteristics of the mesoscopic loss effect for the surface wave can be effectively represented in the equivalent viscoelastic media. The simulation of surface wave propagation within mesoscopic patches requires solving Biot's differential equations in very small grid spaces, involving the conversion of the fast P wave energy diffusion into the Biot slow wave. This procedure requires a very large amount of computer consumption. An efficient equivalent approach for this patchy saturated poroelastic media shows a more convenient way to solve the single phase viscoelastic differential equations.

Simulation of stochastic diffusion via first exit times

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

Lötstedt, Per, E-mail: perl@it.uu.se; Meinecke, Lina, E-mail: lina.meinecke@it.uu.se

2015-11-01

In molecular biology it is of interest to simulate diffusion stochastically. In the mesoscopic model we partition a biological cell into unstructured subvolumes. In each subvolume the number of molecules is recorded at each time step and molecules can jump between neighboring subvolumes to model diffusion. The jump rates can be computed by discretizing the diffusion equation on that unstructured mesh. If the mesh is of poor quality, due to a complicated cell geometry, standard discretization methods can generate negative jump coefficients, which no longer allows the interpretation as the probability to jump between the subvolumes. We propose a methodmore » based on the mean first exit time of a molecule from a subvolume, which guarantees positive jump coefficients. Two approaches to exit times, a global and a local one, are presented and tested in simulations on meshes of different quality in two and three dimensions.« less

Simulation of stochastic diffusion via first exit times

PubMed Central

Lötstedt, Per; Meinecke, Lina

2015-01-01

In molecular biology it is of interest to simulate diffusion stochastically. In the mesoscopic model we partition a biological cell into unstructured subvolumes. In each subvolume the number of molecules is recorded at each time step and molecules can jump between neighboring subvolumes to model diffusion. The jump rates can be computed by discretizing the diffusion equation on that unstructured mesh. If the mesh is of poor quality, due to a complicated cell geometry, standard discretization methods can generate negative jump coefficients, which no longer allows the interpretation as the probability to jump between the subvolumes. We propose a method based on the mean first exit time of a molecule from a subvolume, which guarantees positive jump coefficients. Two approaches to exit times, a global and a local one, are presented and tested in simulations on meshes of different quality in two and three dimensions. PMID:26600600

Size, Shape, and Lateral Correlation of Highly Uniform, Mesoscopic, Self-Assembled Domains of Fluorocarbon-Hydrocarbon Diblocks at the Air/Water Interface: A GISAXS Study.

PubMed

Veschgini, Mariam; Abuillan, Wasim; Inoue, Shigeto; Yamamoto, Akihisa; Mielke, Salomé; Liu, Xianhe; Konovalov, Oleg; Krafft, Marie Pierre; Tanaka, Motomu

2017-10-06

The shape and size of self-assembled mesoscopic surface domains of fluorocarbon-hydrocarbon (FnHm) diblocks and the lateral correlation between these domains were quantitatively determined from grazing incidence small-angle X-ray scattering (GISAXS). The full calculation of structure and form factors unravels the influence of fluorocarbon and hydrocarbon block lengths on the diameter and height of the domains, and provides the inter-domain correlation length. The diameter of the domains, as determined from the form factor analysis, exhibits a monotonic increase in response to the systematic lengthening of each block, which can be attributed to the increase in van der Waals attraction between molecules. The pair correlation function in real space calculated from the structure factor implies that the inter-domain correlation can reach a distance that is over 25 times larger than the domain's size. The full calculation of the GISAXS signals introduced here opens a potential towards the hierarchical design of mesoscale domains of self-assembled small organic molecules, covering several orders of magnitude in space. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mesoscopic structural phase progression in photo-excited VO 2 revealed by time-resolved x-ray diffraction microscopy

DOE PAGES

Zhu, Yi; Cai, Zhonghou; Chen, Pice; ...

2016-02-26

Dynamical phase separation during a solid-solid phase transition poses a challenge for understanding the fundamental processes in correlated materials. Critical information underlying a phase transition, such as localized phase competition, is difficult to reveal by measurements that are spatially averaged over many phase seperated regions. The ability to simultanousely track the spatial and temporal evolution of such systems is essential to understanding mesoscopic processes during a phase transition. Using state-of- the-art time-resolved hard x-ray diffraction microscopy, we directly visualize the structural phase progression in a VO 2 film upon photoexcitation. Following a homogenous in-plane optical excitation, the phase transformation ismore » initiated at discrete sites and completed by the growth of one lattice structure into the other, instead of a simultaneous isotropic lattice symmetry change. The time-dependent x-ray diffraction spatial maps show that the in-plane phase progression in laser-superheated VO 2 is via a displacive lattice transformation as a result of relaxation from an excited monoclinic phase into a rutile phase. The speed of the phase front progression is quantitatively measured, which is faster than the process driven by in-plane thermal diffusion but slower than the sound speed in VO 2. Lastly, the direct visualization of localized structural changes in the time domain opens a new avenue to study mesoscopic processes in driven systems.« less

Mesoscopic structural phase progression in photo-excited VO2 revealed by time-resolved x-ray diffraction microscopy

NASA Astrophysics Data System (ADS)

Zhu, Yi; Cai, Zhonghou; Chen, Pice; Zhang, Qingteng; Highland, Matthew J.; Jung, Il Woong; Walko, Donald A.; Dufresne, Eric M.; Jeong, Jaewoo; Samant, Mahesh G.; Parkin, Stuart S. P.; Freeland, John W.; Evans, Paul G.; Wen, Haidan

2016-02-01

Dynamical phase separation during a solid-solid phase transition poses a challenge for understanding the fundamental processes in correlated materials. Critical information underlying a phase transition, such as localized phase competition, is difficult to reveal by measurements that are spatially averaged over many phase separated regions. The ability to simultaneously track the spatial and temporal evolution of such systems is essential to understanding mesoscopic processes during a phase transition. Using state-of-the-art time-resolved hard x-ray diffraction microscopy, we directly visualize the structural phase progression in a VO2 film upon photoexcitation. Following a homogenous in-plane optical excitation, the phase transformation is initiated at discrete sites and completed by the growth of one lattice structure into the other, instead of a simultaneous isotropic lattice symmetry change. The time-dependent x-ray diffraction spatial maps show that the in-plane phase progression in laser-superheated VO2 is via a displacive lattice transformation as a result of relaxation from an excited monoclinic phase into a rutile phase. The speed of the phase front progression is quantitatively measured, and is faster than the process driven by in-plane thermal diffusion but slower than the sound speed in VO2. The direct visualization of localized structural changes in the time domain opens a new avenue to study mesoscopic processes in driven systems.

Mesoscopic structural phase progression in photo-excited VO2 revealed by time-resolved x-ray diffraction microscopy.

PubMed

Zhu, Yi; Cai, Zhonghou; Chen, Pice; Zhang, Qingteng; Highland, Matthew J; Jung, Il Woong; Walko, Donald A; Dufresne, Eric M; Jeong, Jaewoo; Samant, Mahesh G; Parkin, Stuart S P; Freeland, John W; Evans, Paul G; Wen, Haidan

2016-02-26

Dynamical phase separation during a solid-solid phase transition poses a challenge for understanding the fundamental processes in correlated materials. Critical information underlying a phase transition, such as localized phase competition, is difficult to reveal by measurements that are spatially averaged over many phase separated regions. The ability to simultaneously track the spatial and temporal evolution of such systems is essential to understanding mesoscopic processes during a phase transition. Using state-of-the-art time-resolved hard x-ray diffraction microscopy, we directly visualize the structural phase progression in a VO2 film upon photoexcitation. Following a homogenous in-plane optical excitation, the phase transformation is initiated at discrete sites and completed by the growth of one lattice structure into the other, instead of a simultaneous isotropic lattice symmetry change. The time-dependent x-ray diffraction spatial maps show that the in-plane phase progression in laser-superheated VO2 is via a displacive lattice transformation as a result of relaxation from an excited monoclinic phase into a rutile phase. The speed of the phase front progression is quantitatively measured, and is faster than the process driven by in-plane thermal diffusion but slower than the sound speed in VO2. The direct visualization of localized structural changes in the time domain opens a new avenue to study mesoscopic processes in driven systems.

Thermal force approach to molecular evolution.

PubMed

Braun, Dieter; Libchaber, Albert

2004-06-01

Recent experiments are discussed where temperature gradients across mesoscopic pores are shown to provide essential mechanisms for autonomous molecular evolution. On the one hand, laminar thermal convection can drive DNA replication as the molecules are continuously cycled between hot and cold regions of a chamber. On the other hand, thermophoresis can accumulate charged biopolymers in similar convection settings. The experiments show that temperature differences analogous to those across porous rocks present a robust nonequilibrium boundary condition to feed the replication and accumulation of evolving molecules. It is speculated that similar nonequilibrium conditions near porous submarine hydrothermal mounds could have triggered the origin of life. In such a scenario, the encapsulation of cells with membranes would be a later development. It is expected that detailed studies of mesoscopic boundary conditions under nonequilibrium conditions will reveal new connecting pieces in the fascinating puzzle of the origins of life.

Charactrisation of particle assemblies by 3D cross correlation light scattering and diffusing wave spectroscopy

NASA Astrophysics Data System (ADS)

Scheffold, Frank

2014-08-01

To characterize the structural and dynamic properties of soft materials and small particles, information on the relevant mesoscopic length scales is required. Such information is often obtained from traditional static and dynamic light scattering (SLS/DLS) experiments in the single scattering regime. In many dense systems, however, these powerful techniques frequently fail due to strong multiple scattering of light. Here I will discuss some experimental innovations that have emerged over the last decade. New methods such as 3D static and dynamic light scattering (3D LS) as well as diffusing wave spectroscopy (DWS) can cover a much extended range of experimental parameters ranging from dilute polymer solutions, colloidal suspensions to extremely opaque viscoelastic emulsions.

Systematic parameter inference in stochastic mesoscopic modeling

NASA Astrophysics Data System (ADS)

Lei, Huan; Yang, Xiu; Li, Zhen; Karniadakis, George Em

2017-02-01

We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the prior knowledge that the coefficients are "sparse". The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.

Visible light-induced water oxidation on mesoscopic alpha-Fe2O3 films made by ultrasonic spray pyrolysis.

PubMed

Duret, Alexis; Grätzel, Michael

2005-09-15

Alpha-Fe(2)O(3) films having a mesoscopic leaflet type structure were produced for the first time by ultrasonic spray pyrolysis (USP) to explore their potential as oxygen-evolving photoanodes. The target of these studies is to use translucent hematite films deposited on conducting fluorine doped tin oxide (FTO) glass as top electrodes in a tandem cell that accomplishes the cleavage of water into hydrogen and oxygen by sunlight. The properties of layers made by USP were compared to those deposited by conventional spray pyrolysis (SP). Although both types of films show similar XRD and UV-visible and Raman spectra, they differ greatly in their morphology. The mesoscopic alpha-Fe(2)O(3) layers produced by USP consist mainly of 100 nm-sized platelets with a thickness of 5-10 nm. These nanosheets are oriented mainly perpendicularly to the FTO support, their flat surface exposing (001) facets. The mesoscopic leaflet structure has the advantage that it allows for efficient harvesting of visible light, while offering at the same time the very short distance required for the photogenerated holes to reach the electrolyte interface before recombining with conduction band electrons. This allows for water oxidation by the valence band holes even though their diffusion length is only a few nanometers. Distances are longer in the particles produced by SP favoring recombination of photoinduced charge carriers. Open-circuit photovoltage measurements indicate a lower surface state density for the nanoplatelets as compared to the round particles. These factors explain the much higher photoactivity of the USP compared to the SP deposited alpha-Fe(2)O(3) layers. Addition of hydrogen peroxide to the alkaline electrolyte further improves the photocurrent-voltage characteristics of films generated by USP indicating the hole transfer from the valence band of the semiconductor oxide to the adsorbed water to be the rate-limiting kinetic step in the oxygen generation reaction.

Molecular, mesoscopic and microscopic structure evolution during amylase digestion of extruded maize and high amylose maize starches.

PubMed

Shrestha, Ashok K; Blazek, Jaroslav; Flanagan, Bernadine M; Dhital, Sushil; Larroque, Oscar; Morell, Matthew K; Gilbert, Elliot P; Gidley, Michael J

2015-03-15

Extrusion processing of cereal starch granules with high (>50%) amylose content is a promising approach to create nutritionally desirable resistant starch, i.e. starch that escapes digestion in the small intestine. Whilst high amylose content seems to be required, the structural features responsible for the slow digestion of extrudates are not fully understood. We report the effects of partial enzyme digestion of extruded maize starches on amylopectin branch length profiles, double and single helix contents, crystallinity and lamellar periodicity. Comparing results for three extruded maize starches (27, 57, and 84% apparent amylose) that differ in amylase-sensitivity allows conclusions to be drawn concerning the rate-determining features operating under the digestion conditions used. Enzyme resistance is shown to originate from a combination of molecular and mesoscopic factors, including both recrystallization and an increase in very short branches during the digestion process. This is in contrast to the behaviour of the same starches in the granular form (Shrestha et al., 2012) where molecular and mesoscopic factors are secondary to microscopic structures in determining enzyme susceptibility. Based on the structure of residual material after long-time digestion (>8h), a model for resistant starch from processed high amylose maize starches is proposed based on a fringed micelle structure with lateral aggregation and enzyme susceptibility both limited by attached clusters of branch points. Copyright © 2014 Elsevier Ltd. All rights reserved.

Coarse-grained stochastic processes and kinetic Monte Carlo simulators for the diffusion of interacting particles

NASA Astrophysics Data System (ADS)

Katsoulakis, Markos A.; Vlachos, Dionisios G.

2003-11-01

We derive a hierarchy of successively coarse-grained stochastic processes and associated coarse-grained Monte Carlo (CGMC) algorithms directly from the microscopic processes as approximations in larger length scales for the case of diffusion of interacting particles on a lattice. This hierarchy of models spans length scales between microscopic and mesoscopic, satisfies a detailed balance, and gives self-consistent fluctuation mechanisms whose noise is asymptotically identical to the microscopic MC. Rigorous, detailed asymptotics justify and clarify these connections. Gradient continuous time microscopic MC and CGMC simulations are compared under far from equilibrium conditions to illustrate the validity of our theory and delineate the errors obtained by rigorous asymptotics. Information theory estimates are employed for the first time to provide rigorous error estimates between the solutions of microscopic MC and CGMC, describing the loss of information during the coarse-graining process. Simulations under periodic boundary conditions are used to verify the information theory error estimates. It is shown that coarse-graining in space leads also to coarse-graining in time by q2, where q is the level of coarse-graining, and overcomes in part the hydrodynamic slowdown. Operation counting and CGMC simulations demonstrate significant CPU savings in continuous time MC simulations that vary from q3 for short potentials to q4 for long potentials. Finally, connections of the new coarse-grained stochastic processes to stochastic mesoscopic and Cahn-Hilliard-Cook models are made.

Deformation associated with the Ste. Genevieve fault zone and mid-continent tectonics

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

Schultz, A.; Baker, G.S.; Harrison, R.W.

1992-01-01

The Ste. Genevieve fault is a northwest-trending deformation zone on the northeast edge of the Ozark Dome in Missouri. The fault has been described as a high-angle block fault resulting from vertical uplift of Proterozoic basement rocks, and also as a left-lateral, strike-slip or transpressive wrench fault associated with the Reelfoot rift. Recent mapping across the fault zone documents significant changes in the style of deformation along strike, including variations in the number and the spacing of fault strands, changes in the orientation of rocks within and adjacent to the fault zone, and changes in the direction of stratigraphic offsetmore » between different fault slices. These data are inconsistent with existing Ste. Genevieve models of monoclinal folding over basement upthrusts. Mesoscopic structural analysis of rocks in and near the fault zone indicates highly deformed noncylindrical folds, faults with normal, reverse, oblique, and strike-slip components of movement, and complex joint systems. Fabric orientation, calcite shear fibers, and slickensides indicate that the majority of these mesoscopic structures are kinematically related to left-lateral oblique slip with the southwest side up. Within the fault zone are highly fractured rocks, microscopic to coarse-grained carbonate breccia, and siliciclastic cataclasite. Microscopic deformation includes twinning in carbonate rocks, deformation banding, undulose extinction, and strain-induced polygonization in quartz, tectonic stylolites, extension veining, microfractures, and grain-scale cataclasis. Data are consistent with models relating the Ste. Genevieve fault zone to left-lateral oblique slip possibly associated with New Madrid tectonism.« less

GPU-accelerated Red Blood Cells Simulations with Transport Dissipative Particle Dynamics.

PubMed

Blumers, Ansel L; Tang, Yu-Hang; Li, Zhen; Li, Xuejin; Karniadakis, George E

2017-08-01

Mesoscopic numerical simulations provide a unique approach for the quantification of the chemical influences on red blood cell functionalities. The transport Dissipative Particles Dynamics (tDPD) method can lead to such effective multiscale simulations due to its ability to simultaneously capture mesoscopic advection, diffusion, and reaction. In this paper, we present a GPU-accelerated red blood cell simulation package based on a tDPD adaptation of our red blood cell model, which can correctly recover the cell membrane viscosity, elasticity, bending stiffness, and cross-membrane chemical transport. The package essentially processes all computational workloads in parallel by GPU, and it incorporates multi-stream scheduling and non-blocking MPI communications to improve inter-node scalability. Our code is validated for accuracy and compared against the CPU counterpart for speed. Strong scaling and weak scaling are also presented to characterizes scalability. We observe a speedup of 10.1 on one GPU over all 16 cores within a single node, and a weak scaling efficiency of 91% across 256 nodes. The program enables quick-turnaround and high-throughput numerical simulations for investigating chemical-driven red blood cell phenomena and disorders.

The persistent current and energy spectrum on a driven mesoscopic LC-circuit with Josephson junction

NASA Astrophysics Data System (ADS)

Pahlavanias, Hassan

2018-03-01

The quantum theory for a mesoscopic electric circuit including a Josephson junction with charge discreteness is studied. By considering coupling energy of the mesoscopic capacitor in Josephson junction device, a Hamiltonian describing the dynamics of a quantum mesoscopic electric LC-circuit with charge discreteness is introduced. We first calculate the persistent current on a quantum driven ring including Josephson junction. Then we obtain the persistent current and energy spectrum of a quantum mesoscopic electrical circuit which includes capacitor, inductor, time-dependent external source and Josephson junction.

Epidemic spreading on complex networks with community structures

PubMed Central

Stegehuis, Clara; van der Hofstad, Remco; van Leeuwaarden, Johan S. H.

2016-01-01

Many real-world networks display a community structure. We study two random graph models that create a network with similar community structure as a given network. One model preserves the exact community structure of the original network, while the other model only preserves the set of communities and the vertex degrees. These models show that community structure is an important determinant of the behavior of percolation processes on networks, such as information diffusion or virus spreading: the community structure can both enforce as well as inhibit diffusion processes. Our models further show that it is the mesoscopic set of communities that matters. The exact internal structures of communities barely influence the behavior of percolation processes across networks. This insensitivity is likely due to the relative denseness of the communities. PMID:27440176

Differential conductance fluctuation of curved nanographite sheets in the mesoscopic regime

NASA Astrophysics Data System (ADS)

Wang, Haomin; Choong, Catherine; Zhang, Jun; Teo, Kie Leong; Wu, Yihong

2008-02-01

Excess conductance fluctuations with peculiar temperature dependence from 1.4 to 250 K were observed in curved nanographite sheets with electrode gap lengths of 300 and 450 nm, whereas the conductance fluctuation is greatly suppressed above 4.2 K when the electrode gap lengths increase to 800 and 1000 nm. The former is discussed in the context of the presence of a small energy bandgap in the nanographite sheets, while the latter is attributed to the crossover from the coherent transport to diffusive transport regime.

Taylor dispersion of colloidal particles in narrow channels

NASA Astrophysics Data System (ADS)

Sané, Jimaan; Padding, Johan T.; Louis, Ard A.

2015-09-01

We use a mesoscopic particle-based simulation technique to study the classic convection-diffusion problem of Taylor dispersion for colloidal discs in confined flow. When the disc diameter becomes non-negligible compared to the diameter of the pipe, there are important corrections to the original Taylor picture. For example, the colloids can flow more rapidly than the underlying fluid, and their Taylor dispersion coefficient is decreased. For narrow pipes, there are also further hydrodynamic wall effects. The long-time tails in the velocity autocorrelation functions are altered by the Poiseuille flow.

Systematic parameter inference in stochastic mesoscopic modeling

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

Lei, Huan; Yang, Xiu; Li, Zhen

2017-02-01

We propose a method to efficiently determine the optimal coarse-grained force field in mesoscopic stochastic simulations of Newtonian fluid and polymer melt systems modeled by dissipative particle dynamics (DPD) and energy conserving dissipative particle dynamics (eDPD). The response surfaces of various target properties (viscosity, diffusivity, pressure, etc.) with respect to model parameters are constructed based on the generalized polynomial chaos (gPC) expansion using simulation results on sampling points (e.g., individual parameter sets). To alleviate the computational cost to evaluate the target properties, we employ the compressive sensing method to compute the coefficients of the dominant gPC terms given the priormore » knowledge that the coefficients are “sparse”. The proposed method shows comparable accuracy with the standard probabilistic collocation method (PCM) while it imposes a much weaker restriction on the number of the simulation samples especially for systems with high dimensional parametric space. Fully access to the response surfaces within the confidence range enables us to infer the optimal force parameters given the desirable values of target properties at the macroscopic scale. Moreover, it enables us to investigate the intrinsic relationship between the model parameters, identify possible degeneracies in the parameter space, and optimize the model by eliminating model redundancies. The proposed method provides an efficient alternative approach for constructing mesoscopic models by inferring model parameters to recover target properties of the physics systems (e.g., from experimental measurements), where those force field parameters and formulation cannot be derived from the microscopic level in a straight forward way.« less

Variable-order fractional MSD function to describe the evolution of protein lateral diffusion ability in cell membranes

NASA Astrophysics Data System (ADS)

Yin, Deshun; Qu, Pengfei

2018-02-01

Protein lateral diffusion is considered anomalous in the plasma membrane. And this diffusion is related to membrane microstructure. In order to better describe the property of protein lateral diffusion and find out the inner relationship between protein lateral diffusion and membrane microstructure, this article applies variable-order fractional mean square displacement (f-MSD) function for characterizing the anomalous diffusion. It is found that the variable order can reflect the evolution of diffusion ability. The results of numerical simulation demonstrate variable-order f-MSD function can predict the tendency of anomalous diffusion during the process of confined diffusion. It is also noted that protein lateral diffusion ability during the processes of confined and hop diffusion can be split into three parts. In addition, the comparative analyses reveal that the variable order is related to the confinement-domain size and microstructure of compartment boundary too.

Numerical Evaluation of Lateral Diffusion Inside Diffusive Gradients in Thin Films Samplers

PubMed Central

2015-01-01

Using numerical simulation of diffusion inside diffusive gradients in thin films (DGT) samplers, we show that the effect of lateral diffusion inside the sampler on the solute flux into the sampler is a nonlinear function of the diffusion layer thickness and the physical sampling window size. In contrast, earlier work concluded that this effect was constant irrespective of parameters of the sampler geometry. The flux increase caused by lateral diffusion inside the sampler was determined to be ∼8.8% for standard samplers, which is considerably lower than the previous estimate of ∼20%. Lateral diffusion is also propagated to the diffusive boundary layer (DBL), where it leads to a slightly stronger decrease in the mass uptake than suggested by the common 1D diffusion model that is applied for evaluating DGT results. We introduce a simple correction procedure for lateral diffusion and demonstrate how the effect of lateral diffusion on diffusion in the DBL can be accounted for. These corrections often result in better estimates of the DBL thickness (δ) and the DGT-measured concentration than earlier approaches and will contribute to more accurate concentration measurements in solute monitoring in waters. PMID:25877251

Computational methods for diffusion-influenced biochemical reactions.

PubMed

Dobrzynski, Maciej; Rodríguez, Jordi Vidal; Kaandorp, Jaap A; Blom, Joke G

2007-08-01

We compare stochastic computational methods accounting for space and discrete nature of reactants in biochemical systems. Implementations based on Brownian dynamics (BD) and the reaction-diffusion master equation are applied to a simplified gene expression model and to a signal transduction pathway in Escherichia coli. In the regime where the number of molecules is small and reactions are diffusion-limited predicted fluctuations in the product number vary between the methods, while the average is the same. Computational approaches at the level of the reaction-diffusion master equation compute the same fluctuations as the reference result obtained from the particle-based method if the size of the sub-volumes is comparable to the diameter of reactants. Using numerical simulations of reversible binding of a pair of molecules we argue that the disagreement in predicted fluctuations is due to different modeling of inter-arrival times between reaction events. Simulations for a more complex biological study show that the different approaches lead to different results due to modeling issues. Finally, we present the physical assumptions behind the mesoscopic models for the reaction-diffusion systems. Input files for the simulations and the source code of GMP can be found under the following address: http://www.cwi.nl/projects/sic/bioinformatics2007/

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

NASA Astrophysics Data System (ADS)

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

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

Molecular version of the resistive pulse technique: counting ATP by a single ion channel

NASA Astrophysics Data System (ADS)

Rostovtseva, T. K.; Bezrukov, S. M.

1998-03-01

The ``molecular Coulter counter'' concept has been used to study transport of ATP molecules through the nanometer-scale aqueous pore of the voltage-dependent mitochondrial ion channel, VDAC. We examine the ATP-induced current fluctuations and the change in average current through a single fully open channel reconstituted into a planar lipid bilayer. At high salt concentration (1M NaCl), the addition of ATP reduces both solution specific conductivity and channel conductance, but the effect on the channel is several times stronger and shows saturation behavior at 50 mM ATP concentration. ATP addition also generates an excess noise in the ionic current through the channel. By relating the low-frequency spectral density of the noise to the equilibrium diffusion of ATP molecules in the aqueous pore, we calculate a diffusion coefficient D = (1.6-3.3)x10-11 m^2 /s. We show that the mesoscopic VDAC pore is a Coulter counter with the added features of attraction and diffusion.

Mesoscopic Modeling of Blood Clotting: Coagulation Cascade and Platelets Adhesion

NASA Astrophysics Data System (ADS)

Yazdani, Alireza; Li, Zhen; Karniadakis, George

2015-11-01

The process of clot formation and growth at a site on a blood vessel wall involve a number of multi-scale simultaneous processes including: multiple chemical reactions in the coagulation cascade, species transport and flow. To model these processes we have incorporated advection-diffusion-reaction (ADR) of multiple species into an extended version of Dissipative Particle Dynamics (DPD) method which is considered as a coarse-grained Molecular Dynamics method. At the continuum level this is equivalent to the Navier-Stokes equation plus one advection-diffusion equation for each specie. The chemistry of clot formation is now understood to be determined by mechanisms involving reactions among many species in dilute solution, where reaction rate constants and species diffusion coefficients in plasma are known. The role of blood particulates, i.e. red cells and platelets, in the clotting process is studied by including them separately and together in the simulations. An agonist-induced platelet activation mechanism is presented, while platelets adhesive dynamics based on a stochastic bond formation/dissociation process is included in the model.

An adaptive tau-leaping method for stochastic simulations of reaction-diffusion systems

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

Padgett, Jill M. A.; Ilie, Silvana, E-mail: silvana@ryerson.ca

2016-03-15

Stochastic modelling is critical for studying many biochemical processes in a cell, in particular when some reacting species have low population numbers. For many such cellular processes the spatial distribution of the molecular species plays a key role. The evolution of spatially heterogeneous biochemical systems with some species in low amounts is accurately described by the mesoscopic model of the Reaction-Diffusion Master Equation. The Inhomogeneous Stochastic Simulation Algorithm provides an exact strategy to numerically solve this model, but it is computationally very expensive on realistic applications. We propose a novel adaptive time-stepping scheme for the tau-leaping method for approximating themore » solution of the Reaction-Diffusion Master Equation. This technique combines effective strategies for variable time-stepping with path preservation to reduce the computational cost, while maintaining the desired accuracy. The numerical tests on various examples arising in applications show the improved efficiency achieved by the new adaptive method.« less

Fundamental and functional aspects of mesoscopic architectures with examples in physics, cell biology, and chemistry.

PubMed

Kalay, Ziya

2011-08-01

How small can a macroscopic object be made without losing its intended function? Obviously, the smallest possible size is determined by the size of an atom, but it is not so obvious how many atoms are required to assemble an object so small, and yet that performs the same function as its macroscopic counterpart. In this review, we are concerned with objects of intermediate nature, lying between the microscopic and the macroscopic world. In physics and chemistry literature, this regime in-between is often called mesoscopic, and is known to bear interesting and counterintuitive features. After a brief introduction to the concept of mesoscopic systems from the perspective of physics, we discuss the functional aspects of mesoscopic architectures in cell biology, and supramolecular chemistry through many examples from the literature. We argue that the biochemistry of the cell is largely regulated by mesoscopic functional architectures; however, the significance of mesoscopic phenomena seems to be quite underappreciated in biological sciences. With this motivation, one of our main purposes here is to emphasize the critical role that mesoscopic structures play in cell biology and biochemistry.

Mesoscopic Ni particles and nanowires by pulsed electrodeposition into porous Si

NASA Astrophysics Data System (ADS)

Michelakaki, E.; Valalaki, K.; G. Nassiopoulou, A.

2013-04-01

We report in this article on the formation of mesoscopic Ni particles and filling of continuous Ni nanowires into porous Si layers of thickness in the range of 0.5-4 μm with anisotropic vertical pores of average diameter in the range of 30-45 nm using pulsed electrodeposition from a Ni salt solution. The effect of pulse duration, number of pulses, and total process time on pore filling was investigated for porous Si with different porosities and porous Si layer thicknesses in the above thickness range. Scanning and transmission electron microscopy were used to characterize the samples. It was found that pore filling starts with Ni nucleation and nanoparticle formation at different points of the pore walls along the whole pore length and continues with nanoparticle coalescence to form continuous Ni nanowires that completely fill the pores. The mechanism involved in pore filling is particle nucleation and diffusion-controlled growth of Ni nanoparticles that coalesce to nanowires. From the beginning of the process, a metal film starts to form on the porous Si surface, and its thickness increases with increasing the process time. However, the presence of this film does not impede further pore filling and nanowire formation into the pores. This supports further the diffusion-controlled growth mechanism. Finally, it was demonstrated that full pore filling and continuous Ni nanowire formation were also achieved under direct current electrodeposition, and the results are quite similar to those obtained with pulsed electrodeposition when the same total deposition time is used in both cases.

Efficient Tuning of Optical Properties and Morphology of Mesoscopic CdS via a Facile Route

NASA Astrophysics Data System (ADS)

Aslam, Samia; Mustafa, Faiza; Jamil, Ayesha; Abbas, Ghazanfar; Raza, Rizwan; Ahmad, Muhammad Ashfaq

2018-03-01

A facile and simple synthetic route has been employed to synthesize rod-shaped optically efficient cadmium sulfide (CdS) mesoscopic structures using high concentrations of cetyl trimethyl ammonium bromide (CTAB) as the stabilizing agent. The mesoscopic structures were characterized using x-ray diffaractometer (XRD), scanning electron microscopy, UV-visible, photoluminescence (PL), and Fourier transform and infrared (FTIR) spectroscopy. It was found that, if the concentration of CTAB is significantly higher than its critical micelle concentration, the nucleation of CdS mesoscopic structures resulted in rod-like structures. The size of the mesoscopic structures initially increased and then decreased with band gaps 2.5-2.7 eV. XRD analysis showed that the samples had a pure cubic phase confirming the particle size. The values of Urbach energy for the absorption tail states were determined and found to be in agreement with the single crystal. PL spectra showed sharp green emission peaks in the 530-nm to 560-nm wavelength range. FTIR spectra showed the adsorption mode of CTAB onto the CdS mesoscopic structures. A possible mechanism of formation of rod-shaped CdS mesoscopic structures is also elucidated.

Electronic transport in low dimensions: Carbon nanotubes and mesoscopic silver wires

NASA Astrophysics Data System (ADS)

Ghanem, Tarek Khairy

This thesis explores the physics of low-dimensional electronic conductors using two materials systems, carbon nanotubes (CNTs) and lithographically-defined silver nanowires. In order to understand the intrinsic electronic properties of CNTs, it is important to eliminate the contact effects from the measurements. Here, this is accomplished by using a conductive-tip atomic force microscope cantilever as a local electrode in order to obtain length dependent transport properties. The CNT-movable electrode contact is fully characterized, and is largely independent of voltage bias conditions, and independent of the contact force beyond a certain threshold. The contact is affected by the fine positioning of the cantilever relative to the CNT due to parasitic lateral motion of the cantilever during the loading cycle, which, if not controlled, can lead to non-monotonic behavior of contact resistance vs. force. Length dependent transport measurements are reported for several metallic and semiconducting CNTs. The resistance versus length R(L) of semiconducting CNTs is linear in the on state. For the depleted state R(L) is linear for long channel lengths, but non-linear for short channel lengths due to the long depletion lengths in one-dimensional semiconductors. Transport remains diffusive under all depletion conditions, due to both low disorder and high temperature. The study of quantum corrections to classical conductivity in mesoscopic conductors is an essential tool for understanding phase coherence in these systems. A long standing discrepancy between theory and experiment regards the phase coherence time, which is expected theoretically to grow as a power law at low temperatures, but is experimentally found to saturate. The origins of this saturation have been debated for the last decade, with the main contenders being intrinsic decoherence by zero-point fluctuations of the electrons, and decoherence by dilute magnetic impurities. Here, the phase coherence time in quasi-one-dimensional silver wires is measured. The phase coherence times obtained from the weak localization correction to the conductivity at low magnetic field show saturation, while those obtained from universal conductance fluctuations at high field do not. This indicates that, for these samples, the origin of phase coherence time saturation obtained from weak localization is extrinsic, due to the presence of dilute magnetic impurities.

Simultaneous characterization of lateral lipid and prothrombin diffusion coefficients by z-scan fluorescence correlation spectroscopy.

PubMed

Stefl, Martin; Kułakowska, Anna; Hof, Martin

2009-08-05

A new (to our knowledge) robust approach for the determination of lateral diffusion coefficients of weakly bound proteins is applied for the phosphatidylserine specific membrane interaction of bovine prothrombin. It is shown that z-scan fluorescence correlation spectroscopy in combination with pulsed interleaved dual excitation allows simultaneous monitoring of the lateral diffusion of labeled protein and phospholipids. Moreover, from the dependencies of the particle numbers on the axial sample positions at different protein concentrations phosphatidylserine-dependent equilibrium dissociation constants are derived confirming literature values. Increasing the amount of membrane-bound prothrombin retards the lateral protein and lipid diffusion, indicating coupling of both processes. The lateral diffusion coefficients of labeled lipids are considerably larger than the simultaneously determined lateral diffusion coefficients of prothrombin, which contradicts findings reported for the isolated N-terminus of prothrombin.

Nonmonotonic spatial structure of interneuronal correlations in prefrontal microcircuits

PubMed Central

Safavi, Shervin; Dwarakanath, Abhilash; Kapoor, Vishal; Werner, Joachim; Hatsopoulos, Nicholas G.; Logothetis, Nikos K.; Panagiotaropoulos, Theofanis I.

2018-01-01

Correlated fluctuations of single neuron discharges, on a mesoscopic scale, decrease as a function of lateral distance in early sensory cortices, reflecting a rapid spatial decay of lateral connection probability and excitation. However, spatial periodicities in horizontal connectivity and associational input as well as an enhanced probability of lateral excitatory connections in the association cortex could theoretically result in nonmonotonic correlation structures. Here, we show such a spatially nonmonotonic correlation structure, characterized by significantly positive long-range correlations, in the inferior convexity of the macaque prefrontal cortex. This functional connectivity kernel was more pronounced during wakefulness than anesthesia and could be largely attributed to the spatial pattern of correlated variability between functionally similar neurons during structured visual stimulation. These results suggest that the spatial decay of lateral functional connectivity is not a common organizational principle of neocortical microcircuits. A nonmonotonic correlation structure could reflect a critical topological feature of prefrontal microcircuits, facilitating their role in integrative processes. PMID:29588415

Suppression of Lateral Diffusion and Surface Leakage Currents in nBn Photodetectors Using an Inverted Design

NASA Astrophysics Data System (ADS)

Du, X.; Savich, G. R.; Marozas, B. T.; Wicks, G. W.

2018-02-01

Surface leakage and lateral diffusion currents in InAs-based nBn photodetectors have been investigated. Devices fabricated using a shallow etch processing scheme that etches through the top contact and stops at the barrier exhibited large lateral diffusion current but undetectably low surface leakage. Such large lateral diffusion current significantly increased the dark current, especially in small devices, and causes pixel-to-pixel crosstalk in detector arrays. To eliminate the lateral diffusion current, two different approaches were examined. The conventional solution utilized a deep etch process, which etches through the top contact, barrier, and absorber. This deep etch processing scheme eliminated lateral diffusion, but introduced high surface current along the device mesa sidewalls, increasing the dark current. High device failure rate was also observed in deep-etched nBn structures. An alternative approach to limit lateral diffusion used an inverted nBn structure that has its absorber grown above the barrier. Like the shallow etch process on conventional nBn structures, the inverted nBn devices were fabricated with a processing scheme that only etches the top layer (the absorber, in this case) but avoids etching through the barrier. The results show that inverted nBn devices have the advantage of eliminating the lateral diffusion current without introducing elevated surface current.

Mesoscopic pairing without superconductivity

NASA Astrophysics Data System (ADS)

Hofmann, Johannes

2017-12-01

We discuss pairing signatures in mesoscopic nanowires with a variable attractive pairing interaction. Depending on the wire length, density, and interaction strength, these systems realize a simultaneous bulk-to-mesoscopic and BCS-BEC crossover, which we describe in terms of the parity parameter that quantifies the odd-even energy difference and generalizes the bulk Cooper pair binding energy to mesoscopic systems. We show that the parity parameter can be extracted from recent measurements of conductance oscillations in SrTiO3 nanowires by Cheng et al. [Nature (London) 521, 196 (2015), 10.1038/nature14398], where it marks the critical magnetic field that separates pair and single-particle currents. Our results place the experiment in the fluctuation-dominated mesoscopic regime on the BCS side of the crossover.

Phase Competition and Magnetotransport Phenomena in Manganite Films and Mesoscopic Structures

NASA Astrophysics Data System (ADS)

Wu, Tom

2006-03-01

The importance of competition between ferromagnetic metallic (FMM) and charge-ordered insulating (COI) phases in the physics of bulk manganites has been established through a wide variety of techniques. One exotic consequence of this phase competition is step-like features in magnetotransport observed in bulk and single-crystals of Pr0.65(CaySr1-y)0.35MnO3 (PCSMO) with 0.7<=y<=0.8. The length-scale of the phase coexistence is ˜1 micron, motivating a study of structures with dimensions similar to this natural length scale where phenomenology distinct from that of bulk counterparts is expected. Toward that end, we have synthesized films and laterally confined mesoscopic bridges of PCSMO and studied their magnetotransport properties. In particular, we observed: (1) Intrinsic ultrasharp magnetization steps below 5 K in both bulk and film samples and their dependence on the extrinsic measurement protocols; (2) Spontaneous jumps of resistance during both the ramping of magnetic field and the relaxation after the field cycle; (3) I-V curves exhibiting negative differential resistance (NDR) in certain ranges of temperature and magnetic field. All of these phenomena can be explained in the context of interconversion between the COI phase and the FMM phase. As expected, this interconversion can be triggered by external magnetic field, as found in the case of the magnetization and resistance steps. Alternatively, in the mesoscopic structures with dimensions similar to the size of the competing FMM and COI domains, a local Joule heating-induced annihilation of conducting filaments causes the anomalous NDR.

Information transfer in community structured multiplex networks

NASA Astrophysics Data System (ADS)

Solé Ribalta, Albert; Granell, Clara; Gómez, Sergio; Arenas, Alex

2015-08-01

The study of complex networks that account for different types of interactions has become a subject of interest in the last few years, specially because its representational power in the description of users interactions in diverse online social platforms (Facebook, Twitter, Instagram, etc.). The mathematical description of these interacting networks has been coined under the name of multilayer networks, where each layer accounts for a type of interaction. It has been shown that diffusive processes on top of these networks present a phenomenology that cannot be explained by the naive superposition of single layer diffusive phenomena but require the whole structure of interconnected layers. Nevertheless, the description of diffusive phenomena on multilayer networks has obviated the fact that social networks have strong mesoscopic structure represented by different communities of individuals driven by common interests, or any other social aspect. In this work, we study the transfer of information in multilayer networks with community structure. The final goal is to understand and quantify, if the existence of well-defined community structure at the level of individual layers, together with the multilayer structure of the whole network, enhances or deteriorates the diffusion of packets of information.

Lateral diffusion in model membranes is independent of the size of the hydrophobic region of molecules.

PubMed Central

Balcom, B J; Petersen, N O

1993-01-01

We have systematically investigated the probe size and shape dependence of lateral diffusion in model dimyristoyl phosphatidylcholine membranes. Linear hydrophobic polymers, which differ in length by an order of magnitude, were used to explore the effect on the lateral diffusion coefficient of hydrodynamic restrictions in the bilayer interior. The polymers employed are isoprenoid alcohols--citronellol, solanesol, and dolichol. Tracer lateral diffusion coefficients were measured by fluorescence photobleaching recovery. Despite the large difference in lengths, the nitrobenzoxadiazole labelled alcohols all diffuse at the rate of lipid self-diffusion (5.0 x 10(-12) m2 s-1, 29 degrees C) in the liquid crystal phase. Companion measurements in isotropic polymer solution, in gel phase lipid membranes and with nonpolar fluorescent polyaromatic hydrocarbons, show a marked dependence of the lateral diffusion coefficient on the probe molecule size. Our results in the liquid crystal phase are in accord with free area theory which asserts that lateral diffusion in the membrane is restricted by the surface-free area. Probe molecules which are significantly longer than the host phospholipid, seven times longer in the case of dolichol, are still restricted in their lateral motion by the surface properties of the bilayer in the liquid crystal phase. Fluorescence quenching experiments indicate that the nitrobenzoxadiazole label does not reside at the aqueous interface, although it must reside in close proximity according to the diffusion measurements. PMID:8218892

Manipulating surface diffusion and elastic interactions to obtain quantum dot multilayer arrangements over different length scales

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

Placidi, E., E-mail: ernesto.placidi@ism.cnr.it; Arciprete, F.; Università di Roma “Tor Vergata”, Dipartimento di Fisica, via della Ricerca Scientifica 1, 00133 Rome

2014-09-15

An innovative multilayer growth of InAs quantum dots on GaAs(100) is demonstrated to lead to self-aggregation of correlated quantum dot chains over mesoscopic distances. The fundamental idea is that at critical growth conditions is possible to drive the dot nucleation only at precise locations corresponding to the local minima of the Indium chemical potential. Differently from the known dot multilayers, where nucleation of new dots on top of the buried ones is driven by the surface strain originating from the dots below, here the spatial correlations and nucleation of additional dots are mostly dictated by a self-engineering of the surfacemore » occurring during the growth, close to the critical conditions for dot formation under the fixed oblique direction of the incoming As flux, that drives the In surface diffusion.« less

Hydrodynamic effects on phase transition in active matter

NASA Astrophysics Data System (ADS)

Gidituri, Harinadha; Akella, V. S.; Panchagnula, Mahesh; Vedantam, Srikanth; Multiphase flow physics lab Team

2017-11-01

Organized motion of active (self-propelled) objects are ubiquitous in nature. The objective of this study to investigate the effect of hydrodynamics on the coherent structures in active and passive particle mixtures. We use a mesoscopic method Dissipative Particle Dynamics (DPD). The system shows three different states viz. meso-turbulent (disordered state), polar flock and vortical (ordered state) for different values of activity and volume fraction of active particles. From our numerical simulations we construct a phase diagram between activity co-efficient, volume fraction and viscosity of the passive fluid. Transition from vortical to polar is triggered by increasing the viscosity of passive fluid which causes strong short-range hydrodynamic interactions. However, as the viscosity of the fluid decreases, both vortical and meso-turbulent states transition to polar flock phase. We also calculated the diffusion co-efficients via mean square displacement (MSD) for passive and active particles. We observe ballistic and diffusive regimes in the present system.

Multiscale simulations of patchy particle systems combining Molecular Dynamics, Path Sampling and Green's Function Reaction Dynamics

NASA Astrophysics Data System (ADS)

Bolhuis, Peter

Important reaction-diffusion processes, such as biochemical networks in living cells, or self-assembling soft matter, span many orders in length and time scales. In these systems, the reactants' spatial dynamics at mesoscopic length and time scales of microns and seconds is coupled to the reactions between the molecules at microscopic length and time scales of nanometers and milliseconds. This wide range of length and time scales makes these systems notoriously difficult to simulate. While mean-field rate equations cannot describe such processes, the mesoscopic Green's Function Reaction Dynamics (GFRD) method enables efficient simulation at the particle level provided the microscopic dynamics can be integrated out. Yet, many processes exhibit non-trivial microscopic dynamics that can qualitatively change the macroscopic behavior, calling for an atomistic, microscopic description. The recently developed multiscale Molecular Dynamics Green's Function Reaction Dynamics (MD-GFRD) approach combines GFRD for simulating the system at the mesocopic scale where particles are far apart, with microscopic Molecular (or Brownian) Dynamics, for simulating the system at the microscopic scale where reactants are in close proximity. The association and dissociation of particles are treated with rare event path sampling techniques. I will illustrate the efficiency of this method for patchy particle systems. Replacing the microscopic regime with a Markov State Model avoids the microscopic regime completely. The MSM is then pre-computed using advanced path-sampling techniques such as multistate transition interface sampling. I illustrate this approach on patchy particle systems that show multiple modes of binding. MD-GFRD is generic, and can be used to efficiently simulate reaction-diffusion systems at the particle level, including the orientational dynamics, opening up the possibility for large-scale simulations of e.g. protein signaling networks.

Mesoscopic homogenization of semi-insulating GaAs by two-step post growth annealing

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

Hoffmann, B.; Jurisch, M.; Koehler, A.

1996-12-31

Mesoscopic homogenization of the electrical properties of s.i. LEC-GaAs is commonly realized by thermal treatment of the crystals including the steps of dissolution of arsenic precipitates, homogenization of excess As and re-precipitation by creating a controlled supersaturation. Caused by the inhomogeneous distribution of dislocations and the corresponding cellular structure along and across LEC-grown crystals a proper choice of the time-temperature program is necessary to minimize fluctuations of mesoscopic homogeneity. A modified two-step ingot annealing process is demonstrated to ensure the homogeneous distribution of mesoscopic homogeneity.

Exploratory laboratory study of lateral turbulent diffusion at the surface of an alluvial channel

USGS Publications Warehouse

Sayre, William W.; Chamberlain, A.R.

1964-01-01

In natural streams turbulent diffusion is one of the principal mechanisms by which liquid and suspended-particulate contaminants are dispersed in the flow. A knowledge of turbulence characteristics is therefore essential in predicting the dispersal rates of contaminants in streams. In this study the theory of diffusion by continuous movements for homogeneous turbulence is applied to lateral diffusion at the surface of an open channel in which there is uniform flow. An exploratory-laboratory investigation was conducted in which the lateral dispersion at the water surface of a sand-Led flume was studied by measuring the lateral spread from a point source of small floating polyethylene articles. The experiment was restricted to a single set of low and channel geometry conditions. The results of the study indicate that with certain restrictions lateral dispersion in alluvial channels may be successfully described by the theory of diffusion by continuous movements. The experiment demonstrates a means for evaluating the lateral diffusion coefficient and also methods for quantitatively estimating fundamental turbulence properties, such as the intensity and the Lagrangian integral scale of turbulence in an alluvial channel. The experimental results show that with increasing distance from the source the coefficient of lateral turbulent diffusion increases initially but tends toward a constant limiting value. This result is in accordance with turbulent diffusion theory. Indications are that the distance downstream from the source required for the diffusion coefficient to reach its limiting value is actually very small when compared to the length scale of most diffusion phenomena in natural streams which are of practical interest.

Fully printable transparent monolithic solid-state dye-sensitized solar cell with mesoscopic indium tin oxide counter electrode.

PubMed

Yang, Ying; Ri, Kwangho; Rong, Yaoguang; Liu, Linfeng; Liu, Tongfa; Hu, Min; Li, Xiong; Han, Hongwei

2014-09-07

We present a new transparent monolithic mesoscopic solid-state dye-sensitized solar cell based on trilamellar films of mesoscopic TiO2 nanocrystalline photoanode, a ZrO2 insulating layer and an indium tin oxide counter electrode (ITO-CE), which were screen-printed layer by layer on a single substrate. When the thickness of the ITO-CE was optimized to 2.1 μm, this very simple and fully printable solid-state DSSC with D102 dye and spiro-OMeTAD hole transport materials presents efficiencies of 1.73% when irradiated from the front side and 1.06% when irradiated from the rear side under a standard simulated sunlight condition (AM 1.5 Global, 100 mW cm(-2)). Higher parameters could be expected with a better transparent mesoscopic counter electrode and hole conductor for the printable monolithic mesoscopic solid-state DSSC.

Local Chain Segregation and Entanglements in a Confined Polymer Melt

NASA Astrophysics Data System (ADS)

Lee, Nam-Kyung; Diddens, Diddo; Meyer, Hendrik; Johner, Albert

2017-02-01

The reptation mechanism, introduced by de Gennes and Edwards, where a polymer diffuses along a fluffy tube, defined by the constraints imposed by its surroundings, convincingly describes the relaxation of long polymers in concentrated solutions and melts. We propose that the scale for the tube diameter is set by local chain segregation, which we study analytically. We show that the concept of local segregation is especially operational for confined geometries, where segregation extends over mesoscopic domains, drastically reducing binary contacts, and provide an estimate of the entanglement length. Our predictions are quantitatively supported by extensive molecular dynamics simulations on systems consisting of long, entangled chains.

Hydrodynamics of confined colloidal fluids in two dimensions

NASA Astrophysics Data System (ADS)

Sané, Jimaan; Padding, Johan T.; Louis, Ard A.

2009-05-01

We apply a hybrid molecular dynamics and mesoscopic simulation technique to study the dynamics of two-dimensional colloidal disks in confined geometries. We calculate the velocity autocorrelation functions and observe the predicted t-1 long-time hydrodynamic tail that characterizes unconfined fluids, as well as more complex oscillating behavior and negative tails for strongly confined geometries. Because the t-1 tail of the velocity autocorrelation function is cut off for longer times in finite systems, the related diffusion coefficient does not diverge but instead depends logarithmically on the overall size of the system. The Langevin equation gives a poor approximation to the velocity autocorrelation function at both short and long times.

Nonlinear Acoustic Landmine Detection: Profiling Soil Surface Vibrations and Modeling Mesoscopic Elastic Behavior

DTIC Science & Technology

2007-05-04

TITLE AND SUBTITLE Nonlinear Acoustic Landmine Detection: Profiling Soil Surface Vibrations and Modeling Mesoscopic Elastic Behavior 6. AUTHOR(S...project report; no. 352 (2007) NONLINEAR ACOUSTIC LANDMINE DETECTION: PROFILING SOIL SURFACE VIBRATIONS AND MODELING MESOSCOPIC ELASTIC... model (Caughey 1966). Nonlinear acoustic landmine detection experiments are performed in the anechoic chamber facility using both a buried acrylic

Direct construction of mesoscopic models from microscopic simulations

NASA Astrophysics Data System (ADS)

Lei, Huan; Caswell, Bruce; Karniadakis, George Em

2010-02-01

Starting from microscopic molecular-dynamics (MD) simulations of constrained Lennard-Jones (LJ) clusters (with constant radius of gyration Rg ), we construct two mesoscopic models [Langevin dynamics and dissipative particle dynamics (DPD)] by coarse graining the LJ clusters into single particles. Both static and dynamic properties of the coarse-grained models are investigated and compared with the MD results. The effective mean force field is computed as a function of the intercluster distance, and the corresponding potential scales linearly with the number of particles per cluster and the temperature. We verify that the mean force field can reproduce the equation of state of the atomistic systems within a wide density range but the radial distribution function only within the dilute and the semidilute regime. The friction force coefficients for both models are computed directly from the time-correlation function of the random force field of the microscopic system. For high density or a large cluster size the friction force is overestimated and the diffusivity underestimated due to the omission of many-body effects as a result of the assumed pairwise form of the coarse-grained force field. When the many-body effect is not as pronounced (e.g., smaller Rg or semidilute system), the DPD model can reproduce the dynamic properties of the MD system.

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

Zhu, Yi; Cai, Zhonghou; Chen, Pice

Dynamical phase separation during a solid-solid phase transition poses a challenge for understanding the fundamental processes in correlated materials. Critical information underlying a phase transition, such as localized phase competition, is difficult to reveal by measurements that are spatially averaged over many phase seperated regions. The ability to simultanousely track the spatial and temporal evolution of such systems is essential to understanding mesoscopic processes during a phase transition. Using state-of- the-art time-resolved hard x-ray diffraction microscopy, we directly visualize the structural phase progression in a VO 2 film upon photoexcitation. Following a homogenous in-plane optical excitation, the phase transformation ismore » initiated at discrete sites and completed by the growth of one lattice structure into the other, instead of a simultaneous isotropic lattice symmetry change. The time-dependent x-ray diffraction spatial maps show that the in-plane phase progression in laser-superheated VO 2 is via a displacive lattice transformation as a result of relaxation from an excited monoclinic phase into a rutile phase. The speed of the phase front progression is quantitatively measured, which is faster than the process driven by in-plane thermal diffusion but slower than the sound speed in VO 2. Lastly, the direct visualization of localized structural changes in the time domain opens a new avenue to study mesoscopic processes in driven systems.« less

Biological Applications of Extraordinary Electroconductance and Photovoltaic Effects in Inverse Extraordinary Optoconductance

NASA Astrophysics Data System (ADS)

Tran, Lauren Christine

The Extraordinary Electroconductance (EEC) sensor has been previously demonstrated to have an electric field sensitivity of 3.05V/cm in a mesoscopic-scale structure fabricated at the center of a parallel plate capacitor. In this thesis, we demonstrate the first successful application of EEC sensors as electrochemical detectors of protein binding and biological molecule concentration. Using the avidin derivative, captavidin, in complex with the vitamin biotin, the change in four-point measured resistance with fluid protein concentration of bare EEC sensors was shown to increase by a factor of four in the presence of biomolecular binding as compared to baseline. Calculations for approximate field strengths introduced by a bound captavidin molecule are also presented. The development of Inverse-Extraordinary Optoconductance (I-EOC), an effect which occurs in nanoscale sensors, is also discussed. In the I-EOC effect, electron transport transitions from ballistic to diffusive with increasing light intensity. In these novel, room temperature optical detectors, the resistance is low at low light intensity and resistance increases by 9462% in a 250nm device mesa upon full illumination with a 5 mW HeNe laser. This is the inverse of bulk and mesoscopic device behavior, in which resistance decreases with increasing photon density.

Viscous electron flow in mesoscopic two-dimensional electron gas

NASA Astrophysics Data System (ADS)

Gusev, G. M.; Levin, A. D.; Levinson, E. V.; Bakarov, A. K.

2018-02-01

We report electrical and magneto transport measurements in mesoscopic size, two-dimensional (2D) electron gas in a GaAs quantum well. Remarkably, we find that the probe configuration and sample geometry strongly affects the temperature evolution of local resistance. We attribute all transport properties to the presence of hydrodynamic effects. Experimental results confirm the theoretically predicted significance of viscous flow in mesoscopic devices.

Definitions of state variables and state space for brain-computer interface : Part 2. Extraction and classification of feature vectors.

PubMed

Freeman, Walter J

2007-06-01

The hypothesis is proposed that the central dynamics of the action-perception cycle has five steps: emergence from an existing macroscopic brain state of a pattern that predicts a future goal state; selection of a mesoscopic frame for action control; execution of a limb trajectory by microscopic spike activity; modification of microscopic cortical spike activity by sensory inputs; construction of mesoscopic perceptual patterns; and integration of a new macroscopic brain state. The basis is the circular causality between microscopic entities (neurons) and the mesoscopic and macroscopic entities (populations) self-organized by axosynaptic interactions. Self-organization of neural activity is bidirectional in all cortices. Upwardly the organization of mesoscopic percepts from microscopic spike input predominates in primary sensory areas. Downwardly the organization of spike outputs that direct specific limb movements is by mesoscopic fields constituting plans to achieve predicted goals. The mesoscopic fields in sensory and motor cortices emerge as frames within macroscopic activity. Part 1 describes the action-perception cycle and its derivative reflex arc qualitatively. Part 2 describes the perceptual limb of the arc from microscopic MSA to mesoscopic wave packets, and from these to macroscopic EEG and global ECoG fields that express experience-dependent knowledge in successive states. These macroscopic states are conceived to embed and control mesoscopic frames in premotor and motor cortices that are observed in local ECoG and LFP of frontoparietal areas. The fields sampled by ECoG and LFP are conceived as local patterns of neural activity in which trajectories of multiple spike activities (MSA) emerge that control limb movements. Mesoscopic frames are located by use of the analytic signal from the Hilbert transform after band pass filtering. The state variables in frames are measured to construct feature vectors by which to describe and classify frame patterns. Evidence is cited to justify use of linear analysis. The aim of the review is to enable researchers to conceive and identify goal-oriented states in brain activity for use as commands, in order to relegate the details of execution to adaptive control devices outside the brain.

Magnetization reversal and confinement effects across the metamagnetic phase transition in mesoscale FeRh structures

NASA Astrophysics Data System (ADS)

Ander Arregi, Jon; Horký, Michal; Fabianová, Kateřina; Tolley, Robert; Fullerton, Eric E.; Uhlíř, Vojtěch

2018-03-01

The effects of mesoscale confinement on the metamagnetic behavior of lithographically patterned FeRh structures are investigated via Kerr microscopy. Combining the temperature- and field-dependent magnetization reversal of individual sub-micron FeRh structures provides specific phase-transition characteristics of single mesoscale objects. Relaxation of the epitaxial strain caused by patterning lowers the metamagnetic phase transition temperature by more than 15 K upon confining FeRh films below 500 nm in one lateral dimension. We also observe that the phase transition becomes highly asymmetric when comparing the cooling and heating cycles for 300 nm-wide FeRh structures. The investigation of FeRh under lateral confinement provides an interesting platform to explore emergent metamagnetic phenomena arising from the interplay of the structural, magnetic and electronic degrees of freedom at the mesoscopic length scale.

Coupling of light into the fundamental diffusion mode of a scattering medium (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ojambati, Oluwafemi S.; Yılmaz, Hasan; Lagendijk, Ad; Mosk, Allard P.; Vos, Willem L.

2016-03-01

Diffusion equation describes the energy density inside a scattering medium such as biological tissues and paint [1]. The solution of the diffusion equation is a sum over a complete set of eigensolutions that shows a characteristic linear decrease with depth in the medium. It is of particular interest if one could launch energy in the fundamental eigensolution, as this opens the opportunity to achieve a much greater internal energy density. For applications in optics, an enhanced energy density is vital for solid-state lighting, light harvesting in solar cells, low-threshold random lasers, and biomedical optics. Here we demonstrate the first ever selective coupling of optical energy into a diffusion eigensolution of a scattering medium of zinc oxide (ZnO) paint. To this end, we exploit wavefront shaping to selectively couple energy into the fundamental diffusion mode, employing fluorescence of nanoparticles randomly positioned inside the medium as a probe of the energy density. We observe an enhanced fluorescence in case of optimized incident wavefronts, and the enhancement increases with sample thickness, a typical mesoscopic control parameter. We interpret successfully our result by invoking the fundamental eigensolution of the diffusion equation, and we obtain excellent agreement with our observations, even in absence of adjustable parameters [2]. References [1] R. Pierrat, P. Ambichl, S. Gigan, A. Haber, R. Carminati, and R. Rotter, Proc. Natl. Acad. Sci. U.S.A. 111, 17765 (2014). [2] O. S. Ojambati, H. Yilmaz, A. Lagendijk, A. P. Mosk, and W. L. Vos, arXiv:1505.08103.

On a common critical state in localized and diffuse failure modes

NASA Astrophysics Data System (ADS)

Zhu, Huaxiang; Nguyen, Hien N. G.; Nicot, François; Darve, Félix

2016-10-01

Accurately modeling the critical state mechanical behavior of granular material largely relies on a better understanding and characterizing the critical state fabric in different failure modes, i.e. localized and diffuse failure modes. In this paper, a mesoscopic scale is introduced, in which the organization of force-transmission paths (force-chains) and cells encompassed by contacts (meso-loops) can be taken into account. Numerical drained biaxial tests using a discrete element method are performed with different initial void ratios, in order to investigate the critical state fabric on the meso-scale in both localized and diffuse failure modes. According to the displacement and strain fields extracted from tests, the failure mode and failure area of each specimen are determined. Then convergent critical state void ratios are observed in failure area of specimens. Different mechanical features of two kinds of meso-structures (force-chains and meso-loops) are investigated, to clarify whether there exists a convergent meso-structure inside the failure area of granular material, as the signature of critical state. Numerical results support a positive answer. Failure area of both localized and diffuse failure modes therefore exhibits the same fabric in critical state. Hence, these two failure modes prove to be homological with respect to the concept of the critical state.

[Lateral diffusion of saturated phosphatidylcholines in cholesterol-containing bilayers].

PubMed

Filippov, A V; Rudakova, M A; Oradd, G; Lindblom, J

2007-01-01

Lateral diffusion in oriented bilayers of saturated cholesterol-containing phosphatidylcholines, dipalmitoylphosphatidylcholine and dimyrilstoylphosphatidylcholine upon their limiting hydration has been studied by NMR with impulse gradient of magnetic field. For both systems, similar dependences of the coefficient of lateral diffusion on temperature and cholesterol concentration were observed, which agree with the phase diagram showing the presence of regions of ordered and unordered liquid-crystalline phases and a two-phase region. Under similar conditions, the coefficient of lateral diffusion for dipalmytoylphosphatidylcholine has lower values, which is in qualitative agreement with its greater molecular mass. A comparison of data for dipalmytoylphosphatidylcholine with the results obtained earlier for dipalmytoylsphyngomyelin/cholesterol under the same conditions shows, despite a similarity in phase diagrams, greater (two- to threefold) differences in the values of the coefficient of lateral diffusion and a different mode of dependence of the coefficient on cholesterol concentration. A comparison of data for dimyrilstoylphosphatidylcholine with the results obtained previously shows that the values of the coefficient of lateral diffusion and the mode of its dependence on cholesterol concentration coincide in the region of higher concentrations (more than 15 mole %) and differ in the region of lower concentrations (below 15 mole %). The discrepancies may be explained by different contents of water in the systems during the measurements. At a limiting hydration (more than 35%) of water, the coefficient of lateral diffusion decreases with increasing cholesterol concentration. If the content of water is about 25% (as a result of equilibrium hydration from vapors), the coefficient of lateral diffusion of phosphatidylcholine is probably independent of cholesterol concentration. This results from a denser packing of molecules in the bilayer at a lower water concentration, an effect that competes with the ordering effect of cholesterol.

A molecular fragment cheminformatics roadmap for mesoscopic simulation.

PubMed

Truszkowski, Andreas; Daniel, Mirco; Kuhn, Hubert; Neumann, Stefan; Steinbeck, Christoph; Zielesny, Achim; Epple, Matthias

2014-12-01

Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix (array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility. This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted f SMILES) with connected molecular fragments to represent a molecular structure. The f SMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and conceptual usage hurdles. Molecular Fragment Cheminformatics may be regarded as a crucial accelerator to propagate MFD and similar mesoscopic simulation techniques in the molecular sciences. Graphical abstractA molecular fragment cheminformatics roadmap for mesoscopic simulation.

Calculation method for steady-state pollutant concentration in mixing zones considering variable lateral diffusion coefficient.

PubMed

Wu, Wen; Wu, Zhouhu; Song, Zhiwen

2017-07-01

Prediction of the pollutant mixing zone (PMZ) near the discharge outfall in Huangshaxi shows large error when using the methods based on the constant lateral diffusion assumption. The discrepancy is due to the lack of consideration of the diffusion coefficient variation. The variable lateral diffusion coefficient is proposed to be a function of the longitudinal distance from the outfall. Analytical solution of the two-dimensional advection-diffusion equation of a pollutant is derived and discussed. Formulas to characterize the geometry of the PMZ are derived based on this solution, and a standard curve describing the boundary of the PMZ is obtained by proper choices of the normalization scales. The change of PMZ topology due to the variable diffusion coefficient is then discussed using these formulas. The criterion of assuming the lateral diffusion coefficient to be constant without large error in PMZ geometry is found. It is also demonstrated how to use these analytical formulas in the inverse problems including estimating the lateral diffusion coefficient in rivers by convenient measurements, and determining the maximum allowable discharge load based on the limitations of the geometrical scales of the PMZ. Finally, applications of the obtained formulas to onsite PMZ measurements in Huangshaxi present excellent agreement.

Josephson junction in the quantum mesoscopic electric circuits with charge discreteness

NASA Astrophysics Data System (ADS)

Pahlavani, H.

2018-04-01

A quantum mesoscopic electrical LC-circuit with charge discreteness including a Josephson junction is considered and a nonlinear Hamiltonian that describing the dynamic of such circuit is introduced. The quantum dynamical behavior (persistent current probability) is studied in the charge and phase regimes by numerical solution approaches. The time evolution of charge and current, number-difference and the bosonic phase and also the energy spectrum of a quantum mesoscopic electric LC-circuit with charge discreteness that coupled with a Josephson junction device are investigated. We show the role of the coupling energy and the electrostatic Coulomb energy of the Josephson junction in description of the quantum behavior and the spectral properties of a quantum mesoscopic electrical LC-circuits with charge discreteness.

Determination of axial and lateral exciton diffusion length in GaN by electron energy dependent cathodoluminescence

NASA Astrophysics Data System (ADS)

Hocker, Matthias; Maier, Pascal; Jerg, Lisa; Tischer, Ingo; Neusser, Gregor; Kranz, Christine; Pristovsek, Markus; Humphreys, Colin J.; Leute, Robert A. R.; Heinz, Dominik; Rettig, Oliver; Scholz, Ferdinand; Thonke, Klaus

2016-08-01

We demonstrate the application of low-temperature cathodoluminescence (CL) with high lateral, depth, and spectral resolution to determine both the lateral (i.e., perpendicular to the incident primary electron beam) and axial (i.e., parallel to the electron beam) diffusion length of excitons in semiconductor materials. The lateral diffusion length in GaN is investigated by the decrease of the GaN-related luminescence signal when approaching an interface to Ga(In)N based quantum well stripes. The axial diffusion length in GaN is evaluated from a comparison of the results of depth-resolved CL spectroscopy (DRCLS) measurements with predictions from Monte Carlo simulations on the size and shape of the excitation volume. The lateral diffusion length was found to be (95 ± 40) nm for nominally undoped GaN, and the axial exciton diffusion length was determined to be (150 ± 25) nm. The application of the DRCLS method is also presented on a semipolar (11 2 ¯ 2 ) sample, resulting in a value of (70 ± 10) nm in p-type GaN.

Dewetting of thin polymer films: an X-ray scattering study

NASA Astrophysics Data System (ADS)

Müller-Buschbaum, P.; Stamm, M.

1998-06-01

The surface morphology of different dewetting states of thin polymer films (polystyrene) on top of silicon substrates was investigated. With diffuse X-ray scattering in the region of total external reflection a high in-plane resolution was achieved. We observe a new nano-dewetting structure which coexists with the well known mesoscopic dewetting structures of holes, cellular pattern and drops. This nano-dewetting structure consists of small dimples with a diameter in the nanometer range. It results from the dewetting of a remaining ultra-thin polymer layer and can be explained with theoretical predictions of spinodal decomposition. The experimental results of the scattering study are confirmed with scanning-force microscopy measurements.

Recursion equations in predicting band width under gradient elution.

PubMed

Liang, Heng; Liu, Ying

2004-06-18

The evolution of solute zone under gradient elution is a typical problem of non-linear continuity equation since the local diffusion coefficient and local migration velocity of the mass cells of solute zones are the functions of position and time due to space- and time-variable mobile phase composition. In this paper, based on the mesoscopic approaches (Lagrangian description, the continuity theory and the local equilibrium assumption), the evolution of solute zones in space- and time-dependent fields is described by the iterative addition of local probability density of the mass cells of solute zones. Furthermore, on macroscopic levels, the recursion equations have been proposed to simulate zone migration and spreading in reversed-phase high-performance liquid chromatography (RP-HPLC) through directly relating local retention factor and local diffusion coefficient to local mobile phase concentration. This new approach differs entirely from the traditional theories on plate concept with Eulerian description, since band width recursion equation is actually the accumulation of local diffusion coefficients of solute zones to discrete-time slices. Recursion equations and literature equations were used in dealing with same experimental data in RP-HPLC, and the comparison results show that the recursion equations can accurately predict band width under gradient elution.

Intermediate scattering function of an anisotropic active Brownian particle

PubMed Central

Kurzthaler, Christina; Leitmann, Sebastian; Franosch, Thomas

2016-01-01

Various challenges are faced when animalcules such as bacteria, protozoa, algae, or sperms move autonomously in aqueous media at low Reynolds number. These active agents are subject to strong stochastic fluctuations, that compete with the directed motion. So far most studies consider the lowest order moments of the displacements only, while more general spatio-temporal information on the stochastic motion is provided in scattering experiments. Here we derive analytically exact expressions for the directly measurable intermediate scattering function for a mesoscopic model of a single, anisotropic active Brownian particle in three dimensions. The mean-square displacement and the non-Gaussian parameter of the stochastic process are obtained as derivatives of the intermediate scattering function. These display different temporal regimes dominated by effective diffusion and directed motion due to the interplay of translational and rotational diffusion which is rationalized within the theory. The most prominent feature of the intermediate scattering function is an oscillatory behavior at intermediate wavenumbers reflecting the persistent swimming motion, whereas at small length scales bare translational and at large length scales an enhanced effective diffusion emerges. We anticipate that our characterization of the motion of active agents will serve as a reference for more realistic models and experimental observations. PMID:27830719

Intermediate scattering function of an anisotropic active Brownian particle.

PubMed

Kurzthaler, Christina; Leitmann, Sebastian; Franosch, Thomas

2016-10-10

Various challenges are faced when animalcules such as bacteria, protozoa, algae, or sperms move autonomously in aqueous media at low Reynolds number. These active agents are subject to strong stochastic fluctuations, that compete with the directed motion. So far most studies consider the lowest order moments of the displacements only, while more general spatio-temporal information on the stochastic motion is provided in scattering experiments. Here we derive analytically exact expressions for the directly measurable intermediate scattering function for a mesoscopic model of a single, anisotropic active Brownian particle in three dimensions. The mean-square displacement and the non-Gaussian parameter of the stochastic process are obtained as derivatives of the intermediate scattering function. These display different temporal regimes dominated by effective diffusion and directed motion due to the interplay of translational and rotational diffusion which is rationalized within the theory. The most prominent feature of the intermediate scattering function is an oscillatory behavior at intermediate wavenumbers reflecting the persistent swimming motion, whereas at small length scales bare translational and at large length scales an enhanced effective diffusion emerges. We anticipate that our characterization of the motion of active agents will serve as a reference for more realistic models and experimental observations.

Intermediate scattering function of an anisotropic active Brownian particle

NASA Astrophysics Data System (ADS)

Kurzthaler, Christina; Leitmann, Sebastian; Franosch, Thomas

2016-10-01

Various challenges are faced when animalcules such as bacteria, protozoa, algae, or sperms move autonomously in aqueous media at low Reynolds number. These active agents are subject to strong stochastic fluctuations, that compete with the directed motion. So far most studies consider the lowest order moments of the displacements only, while more general spatio-temporal information on the stochastic motion is provided in scattering experiments. Here we derive analytically exact expressions for the directly measurable intermediate scattering function for a mesoscopic model of a single, anisotropic active Brownian particle in three dimensions. The mean-square displacement and the non-Gaussian parameter of the stochastic process are obtained as derivatives of the intermediate scattering function. These display different temporal regimes dominated by effective diffusion and directed motion due to the interplay of translational and rotational diffusion which is rationalized within the theory. The most prominent feature of the intermediate scattering function is an oscillatory behavior at intermediate wavenumbers reflecting the persistent swimming motion, whereas at small length scales bare translational and at large length scales an enhanced effective diffusion emerges. We anticipate that our characterization of the motion of active agents will serve as a reference for more realistic models and experimental observations.

A Multimodality Ultramicrospectroscope (MUMS): Nanoscale Imaging with Integrated Spectroscopies for Chemical and Biomolecular Identification

DTIC Science & Technology

2010-11-10

nanoparticles, and nanoshells by making sub 100 nm diameter nanoshells to mesoscopic sized nanoparticles (gold meatballs ) and micron sized nanoshells. In...mesoscopic gold ‘ meatballs ’, gold bipyrimids etc. In addition nanoparticles such as the nanostar demonstrate some of the highest LSPR sensitivity but...20, 535-538 (2008). 64. H. Wang and N. J. Halas, “Mesoscopic Au ‘ Meatball ’ Particles”, Advanced Materials 20, 820-825 (2008). 65. S. Priya

Lateral diffusion study of the Pt-Al system using the NAC nuclear microprobe.

NASA Astrophysics Data System (ADS)

de Waal, H.; Pretorius, R.

1999-10-01

In this study a nuclear microprobe (NMP) was used to analyse phase formation during reaction in Pt-Al lateral diffusion couples. Phase identification was done by Rutherford backscattering spectroscopy. These results were compared with phase formation during conventional thin film Pt-Al interactions. The co-existence of multiple phases in lateral diffusion couples is discussed with reference to the effective heat of formation (EHF) model.

Ligand binding affinity and changes in the lateral diffusion of receptor for advanced glycation endproducts (RAGE).

PubMed

Syed, Aleem; Zhu, Qiaochu; Smith, Emily A

2016-12-01

The effect of ligand on the lateral diffusion of receptor for advanced glycation endproducts (RAGE), a receptor involved in numerous pathological conditions, remains unknown. Single particle tracking experiments that use quantum dots specifically bound to hemagglutinin (HA)-tagged RAGE (HA-RAGE) are reported to elucidate the effect of ligand binding on HA-RAGE diffusion in GM07373 cell membranes. The ligand used in these studies is methylglyoxal modified-bovine serum albumin (MGO-BSA) containing advanced glycation end products modifications. The binding affinity between soluble RAGE and MGO-BSA increases by 1.8 to 9.7-fold as the percent primary amine modification increases from 24 to 74% and with increasing negative charge on the MGO-BSA. Ligand incubation affects the HA-RAGE diffusion coefficient, the radius of confinement, and duration of confinement. There is, however, no correlation between MGO-BSA ligand binding affinity with soluble RAGE and the extent of the changes in HA-RAGE lateral diffusion. The ligand induced changes to HA-RAGE lateral diffusion do not occur when cholesterol is depleted from the cell membrane, indicating the mechanism for ligand-induced changes to HA-RAGE diffusion is cholesterol dependent. The results presented here serve as a first step in unraveling how ligand influences RAGE lateral diffusion. Copyright © 2016. Published by Elsevier B.V.

High Resolution Higher Energy X-ray Microscope for Mesoscopic Materials

NASA Astrophysics Data System (ADS)

Snigireva, I.; Snigirev, A.

2013-10-01

We developed a novel X-ray microscopy technique to study mesoscopically structured materials, employing compound refractive lenses. The easily seen advantage of lens-based methodology is the possibility to retrieve high resolution diffraction pattern and real-space images in the same experimental setup. Methodologically the proposed approach is similar to the studies of crystals by high resolution transmission electron microscopy. The proposed microscope was applied for studying of mesoscopic materials such as natural and synthetic opals, inverted photonic crystals.

Lifetime of Major Histocompatibility Complex Class-I Membrane Clusters Is Controlled by the Actin Cytoskeleton

PubMed Central

Lavi, Yael; Gov, Nir; Edidin, Michael; Gheber, Levi A.

2012-01-01

Lateral heterogeneity of cell membranes has been demonstrated in numerous studies showing anomalous diffusion of membrane proteins; it has been explained by models and experiments suggesting dynamic barriers to free diffusion, that temporarily confine membrane proteins into microscopic patches. This picture, however, comes short of explaining a steady-state patchy distribution of proteins, in face of the transient opening of the barriers. In our previous work we directly imaged persistent clusters of MHC-I, a type I transmembrane protein, and proposed a model of a dynamic equilibrium between proteins newly delivered to the cell surface by vesicle traffic, temporary confinement by dynamic barriers to lateral diffusion, and dispersion of the clusters by diffusion over the dynamic barriers. Our model predicted that the clusters are dynamic, appearing when an exocytic vesicle fuses with the plasma membrane and dispersing with a typical lifetime that depends on lateral diffusion and the dynamics of barriers. In a subsequent work, we showed this to be the case. Here we test another prediction of the model, and show that changing the stability of actin barriers to lateral diffusion changes cluster lifetimes. We also develop a model for the distribution of cluster lifetimes, consistent with the function of barriers to lateral diffusion in maintaining MHC-I clusters. PMID:22500754

Insight into the CH3NH3PbI3/C interface in hole-conductor-free mesoscopic perovskite solar cells.

PubMed

Li, Jiangwei; Niu, Guangda; Li, Wenzhe; Cao, Kun; Wang, Mingkui; Wang, Liduo

2016-08-07

Perovskite solar cells (PSCs) with hole-conductor-free mesoscopic architecture have shown superb stability and great potential in practical application. The printable carbon counter electrodes take full responsibility of extracting holes from the active CH3NH3PbI3 absorbers. However, an in depth study of the CH3NH3PbI3/C interface properties, such as the structural formation process and the effect of interfacial conditions on hole extraction, is still lacking. Herein, we present, for the first time, an insight into the spatial confinement induced CH3NH3PbI3/C interface formation by in situ photoluminescence observations during the crystallization process of CH3NH3PbI3. The derived reaction kinetics allows a quantitative description of the perovskite formation process. In addition, we found that the interfacial contact between carbon and perovskite was dominant for hole extraction efficiency and associated with the photovoltaic parameter of short circuit current density (JSC). Consequently, we conducted a solvent vapor assisted process of PbI2 diffusion to carefully control the CH3NH3PbI3/C interface with less unreacted PbI2 barrier. The improvement of interface conditions thereby contributes to a high hole extraction proved by the charge extraction resistance and PL lifetime change, resulting in the increased JSC valve.

Evolution of colloidal dispersions in novel time-varying optical potentials

NASA Astrophysics Data System (ADS)

Koss, Brian Alan

Optical traps use forces exerted by a tightly focused light beam to trap objects from tens of nanometers to tens of micrometers in size. Since their introduction in 1986, optical tweezers have become very useful to biology, chemistry, and soft condensed-matter physics. Work presented here, promises to advance optical tweezers not only in fundamental scientific research, but also in applications outside of the laboratory and into the mainstream of miniaturized manufacturing and diagnostics. By providing unprecedented access to the mesoscopic world, a new generation of optical traps, called Dynamic Holographic Optical Tweezers (HOTs) offers revolutionary new opportunities for fundamental and applied research. To demonstrate this technique, HOTs will be used to pump particles via a new method of transport called Optical Peristalsis (OP). OP is efficient method for transporting mesoscopic objects in three dimensions using short repetitive sequences of holographic optical trapping patterns. Transport in this process is analogous to peristaltic pumping, with the configurations of optical traps mimicking states of a peristaltic pump. While not limited to the deterministic particle transport, OP, can also be a platform to investigate the stochastic limit of particle transport. Advances in recent years have demonstrated that a variety of time-varying perturbations can induce drift in a diffusive system without exerting an overall force. Among these, are thermal ratchet models in which the system is subjected to time-varying energy landscapes that break spatiotemporal symmetry and thereby induce drift. Typically, the potential energy landscape is chosen to be the sawtooth potential. This work describes an alternate class of symmetric thermal ratchet models, that are not sawtooth, and demonstrates their efficacy in biasing the diffusion of colloidal spheres in both the stochastic and deterministic limits. Unlike previous models, each state in this thermal ratchet consists of discrete spatially-symmetric potential wells, which are implemented with an array of HOTs.

Hyperlens-array-implemented optical microscopy

NASA Astrophysics Data System (ADS)

Iwanaga, Masanobu

2014-08-01

Limit of resolution of conventional optical microscopes has never reached below 100 nm under visible light illumination. We show that numerically designed high-transmittance hyperlens array (HLA) is implemented in an optical microscope and works in practice for achieving one-shot-recording optical images of in-situ placed objects with sub 50 nm resolution in lateral direction. Direct resolution test employing well-defined nanopatterns proves that the HLA-implemented imaging is super-resolution optical microscopy, which works even under nW/mm2 visible illumination for objects. The HLA implementation makes the resolution of conventional microscopes one-scale higher, leading to the 1/10 illumination wavelength range, that is, mesoscopic range.

Graphene Foam: Uniaxial Tension Behavior and Fracture Mode Based on a Mesoscopic Model.

PubMed

Pan, Douxing; Wang, Chao; Wang, Tzu-Chiang; Yao, Yugui

2017-09-26

Because of the combined advantages of both porous materials and two-dimensional (2D) graphene sheets, superior mechanical properties of three-dimensional (3D) graphene foams have received much attention from material scientists and energy engineers. Here, a 2D mesoscopic graphene model (Modell. Simul. Mater. Sci. Eng. 2011, 19, 054003), was expanded into a 3D bonded graphene foam system by utilizing physical cross-links and van der Waals forces acting among different mesoscopic graphene flakes by considering the debonding behavior, to evaluate the uniaxial tension behavior and fracture mode based on in situ SEM tensile testing (Carbon 2015, 85, 299). We reasonably reproduced a multipeak stress-strain relationship including its obvious yielding plateau and a ductile fracture mode near 45° plane from the tensile direction including the corresponding fracture morphology. Then, a power scaling law of tensile elastic modulus with mass density and an anisotropic strain-dependent Poisson's ratio were both deduced. The mesoscopic physical mechanism of tensile deformation was clearly revealed through the local stress state and evolution of mesostructure. The fracture feature of bonded graphene foam and its thermodynamic state were directly navigated to the tearing pattern of mesoscopic graphene flakes. This study provides an effective way to understand the mesoscopic physical nature of 3D graphene foams, and hence it may contribute to the multiscale computations of micro/meso/macromechanical performances and optimal design of advanced graphene-foam-based materials.

Tailoring of quantum dot emission efficiency by localized surface plasmon polaritons in self-organized mesoscopic rings.

PubMed

Margapoti, Emanuela; Gentili, Denis; Amelia, Matteo; Credi, Alberto; Morandi, Vittorio; Cavallini, Massimiliano

2014-01-21

We report on the tailoring of quantum dot (QD) emission efficiency by localized surface plasmon polaritons in self-organized mesoscopic rings. Ag nanoparticles (NPs) with CdSe QDs embedded in a polymeric matrix are spatially organised in mesoscopic rings and coupled in a tuneable fashion by breath figure formation. The mean distance between NPs and QDs and consequently the intensity of QD photoluminescence, which is enhanced by the coupling of surface plasmons and excitons, are tuned by acting on the NP concentration.

A new transport phenomenon in nanostructures: a mesoscopic analog of the Braess paradox encountered in road networks

PubMed Central

2012-01-01

The Braess paradox, known for traffic and other classical networks, lies in the fact that adding a new route to a congested network in an attempt to relieve congestion can degrade counterintuitively the overall network performance. Recently, we have extended the concept of the Braess paradox to semiconductor mesoscopic networks, whose transport properties are governed by quantum physics. In this paper, we demonstrate theoretically that, alike in classical systems, congestion plays a key role in the occurrence of a Braess paradox in mesoscopic networks. PMID:22913510

Diffusional correlations among multiple active sites in a single enzyme.

PubMed

Echeverria, Carlos; Kapral, Raymond

2014-04-07

Simulations of the enzymatic dynamics of a model enzyme containing multiple substrate binding sites indicate the existence of diffusional correlations in the chemical reactivity of the active sites. A coarse-grain, particle-based, mesoscopic description of the system, comprising the enzyme, the substrate, the product and solvent, is constructed to study these effects. The reactive and non-reactive dynamics is followed using a hybrid scheme that combines molecular dynamics for the enzyme, substrate and product molecules with multiparticle collision dynamics for the solvent. It is found that the reactivity of an individual active site in the multiple-active-site enzyme is reduced substantially, and this effect is analyzed and attributed to diffusive competition for the substrate among the different active sites in the enzyme.

Nonclassical “Explosive” nucleation in Pb/Si(111) at low temperatures

DOE PAGES

Hershberger, M. T.; Hupalo, M.; Thiel, P. A.; ...

2014-12-03

In this study, the onset of nucleation is defined in terms of a critical cluster of the condensed phase, which forms from the gradual aggregation of randomly diffusing adatoms. Experiments in Pb/Si(111) at low temperature have discovered a dramatically different type of nucleation, with perfect crystalline islands emerging “explosively” out of the compressed wetting layer after a critical coverage Θ c=1.22 ML is reached. The unexpectedly high island growth rates, the directional correlations in the growth of neighboring islands and the persistence in time of where mass is added in individual islands, suggest that nucleation is a result of themore » highly coherent motion of the wetting layer, over mesoscopic distances.« less

Frenetic Bounds on the Entropy Production

NASA Astrophysics Data System (ADS)

Maes, Christian

2017-10-01

We give a systematic derivation of positive lower bounds for the expected entropy production (EP) rate in classical statistical mechanical systems obeying a dynamical large deviation principle. The logic is the same for the return to thermodynamic equilibrium as it is for steady nonequilibria working under the condition of local detailed balance. We recover there recently studied "uncertainty" relations for the EP, appearing in studies about the effectiveness of mesoscopic machines. In general our refinement of the positivity of the expected EP rate is obtained in terms of a positive and even function of the expected current(s) which measures the dynamical activity in the system, a time-symmetric estimate of the changes in the system's configuration. Also underdamped diffusions can be included in the analysis.

Many-Body Effects in the Mesoscopic x-Ray Edge Problem

NASA Astrophysics Data System (ADS)

Hentschel, M.; R"Oder, G.; Ullmo, D.

Many-body phenomena, a key interest in the investigation ofbulk solid state systems, are studied here in the context of the x-ray edge problem for mesoscopic systems. We investigate the many-body effects associated with the sudden perturbation following the x-ray excition of a core electron into the conduction band. For small systems with dimensions at the nanoscale we find considerable deviations from the well-understood metallic case where Anderson orthogonality catastrophe and the Mahan-Nozières-DeDominicis response cause characteristic deviations of the photoabsorption cross section from the naive expectation. Whereas the K-edge is typically rounded in metallic systems, we find a slightly peaked K-edge in generic mesoscopic systems with chaotic-coherent electron dynamics. Thus the behavior of the photoabsorption cross section at threshold depends on the system size and is different for the metallic and the mesoscopic case.

What can we learn from noise? — Mesoscopic nonequilibrium statistical physics —

PubMed Central

KOBAYASHI, Kensuke

2016-01-01

Mesoscopic systems — small electric circuits working in quantum regime — offer us a unique experimental stage to explorer quantum transport in a tunable and precise way. The purpose of this Review is to show how they can contribute to statistical physics. We introduce the significance of fluctuation, or equivalently noise, as noise measurement enables us to address the fundamental aspects of a physical system. The significance of the fluctuation theorem (FT) in statistical physics is noted. We explain what information can be deduced from the current noise measurement in mesoscopic systems. As an important application of the noise measurement to statistical physics, we describe our experimental work on the current and current noise in an electron interferometer, which is the first experimental test of FT in quantum regime. Our attempt will shed new light in the research field of mesoscopic quantum statistical physics. PMID:27477456

What can we learn from noise? - Mesoscopic nonequilibrium statistical physics.

PubMed

Kobayashi, Kensuke

2016-01-01

Mesoscopic systems - small electric circuits working in quantum regime - offer us a unique experimental stage to explorer quantum transport in a tunable and precise way. The purpose of this Review is to show how they can contribute to statistical physics. We introduce the significance of fluctuation, or equivalently noise, as noise measurement enables us to address the fundamental aspects of a physical system. The significance of the fluctuation theorem (FT) in statistical physics is noted. We explain what information can be deduced from the current noise measurement in mesoscopic systems. As an important application of the noise measurement to statistical physics, we describe our experimental work on the current and current noise in an electron interferometer, which is the first experimental test of FT in quantum regime. Our attempt will shed new light in the research field of mesoscopic quantum statistical physics.

Tunable quasiparticle trapping in Meissner and vortex states of mesoscopic superconductors.

PubMed

Taupin, M; Khaymovich, I M; Meschke, M; Mel'nikov, A S; Pekola, J P

2016-03-16

Nowadays, superconductors serve in numerous applications, from high-field magnets to ultrasensitive detectors of radiation. Mesoscopic superconducting devices, referring to those with nanoscale dimensions, are in a special position as they are easily driven out of equilibrium under typical operating conditions. The out-of-equilibrium superconductors are characterized by non-equilibrium quasiparticles. These extra excitations can compromise the performance of mesoscopic devices by introducing, for example, leakage currents or decreased coherence time in quantum devices. By applying an external magnetic field, one can conveniently suppress or redistribute the population of excess quasiparticles. In this article, we present an experimental demonstration and a theoretical analysis of such effective control of quasiparticles, resulting in electron cooling both in the Meissner and vortex states of a mesoscopic superconductor. We introduce a theoretical model of quasiparticle dynamics, which is in quantitative agreement with the experimental data.

Tunable quasiparticle trapping in Meissner and vortex states of mesoscopic superconductors

PubMed Central

Taupin, M.; Khaymovich, I. M.; Meschke, M.; Mel'nikov, A. S.; Pekola, J. P.

2016-01-01

Nowadays, superconductors serve in numerous applications, from high-field magnets to ultrasensitive detectors of radiation. Mesoscopic superconducting devices, referring to those with nanoscale dimensions, are in a special position as they are easily driven out of equilibrium under typical operating conditions. The out-of-equilibrium superconductors are characterized by non-equilibrium quasiparticles. These extra excitations can compromise the performance of mesoscopic devices by introducing, for example, leakage currents or decreased coherence time in quantum devices. By applying an external magnetic field, one can conveniently suppress or redistribute the population of excess quasiparticles. In this article, we present an experimental demonstration and a theoretical analysis of such effective control of quasiparticles, resulting in electron cooling both in the Meissner and vortex states of a mesoscopic superconductor. We introduce a theoretical model of quasiparticle dynamics, which is in quantitative agreement with the experimental data. PMID:26980225

Electron Waiting Times in Mesoscopic Conductors

NASA Astrophysics Data System (ADS)

Albert, Mathias; Haack, Géraldine; Flindt, Christian; Büttiker, Markus

2012-05-01

Electron transport in mesoscopic conductors has traditionally involved investigations of the mean current and the fluctuations of the current. A complementary view on charge transport is provided by the distribution of waiting times between charge carriers, but a proper theoretical framework for coherent electronic systems has so far been lacking. Here we develop a quantum theory of electron waiting times in mesoscopic conductors expressed by a compact determinant formula. We illustrate our methodology by calculating the waiting time distribution for a quantum point contact and find a crossover from Wigner-Dyson statistics at full transmission to Poisson statistics close to pinch-off. Even when the low-frequency transport is noiseless, the electrons are not equally spaced in time due to their inherent wave nature. We discuss the implications for renewal theory in mesoscopic systems and point out several analogies with level spacing statistics and random matrix theory.

Innovation Becoming Trajectories: Leveraging Lateral and Vertical Moves for Collaborative Diffusion of Twenty-First Century Learning Practices

ERIC Educational Resources Information Center

Hung, David; Toh, Yancy; Jamaludin, Azilawati; So, Hyo-Jeong

2017-01-01

This paper argues for innovation diffusion as a "becoming" process in the context of lateral and vertical moves. The context of these innovations involves technology-mediated innovations and their diffusion trajectories in the Singapore education system. Embedded in a centralized-decentralized dialectics, this paper traces particular…

A material combination principle for highly efficient polymer solar cells investigated by mesoscopic phase heterogeneity

NASA Astrophysics Data System (ADS)

Yan, Han; Li, Denghua; He, Chang; Wei, Zhixiang; Yang, Yanlian; Li, Yongfang

2013-11-01

Organic solar cells have become a promising energy conversion candidate because of their unique advantages. Novel fullerene derivatives, as a common acceptor, can increase power conversion efficiency (PCE) by increasing the open-circuit voltage. As a representative acceptor, Indene-C60 bisadduct (ICBA) can reach high efficiency with poly(3-hexylthiophene) (P3HT). On the other hand, the novel synthesized polymers mainly aimed to broaden the optical absorption range have steadily promoted efficiency to higher than 9%. However, it is challenging to obtain the desired result by simply combining ICBA with other high-efficiency donors. Thus, P3HT or a high-efficiency polymer PBDTTT-C-T (copolymer of thienyl-substituted BDT with substituted TT) is used as donor and PCBM or ICBA as acceptor in this article to clarify the mechanism behind these materials. The optical and photovoltaic properties of the materials are studied for pair-wise combination. Among these four material groups, the highest PCE of 6.2% is obtained for the PBDTTT-C-T/PCBM combination while the lowest PCE of 3.5% is obtained for the PBDTTT-C-T/ICBA combination. The impact of the mesoscopic heterogeneity on the local mesoscopic photoelectric properties is identified by photo-conductive AFM (pc-AFM), and the consistence between the mesoscopic properties and the macroscopic device performances is also observed. Based on these results, an interface combined model is proposed based on the mesoscopic phase heterogeneity. This study provides a new view on the rational selection of photovoltaic materials, where, aside from the traditional energy level and absorption spectrum matching, the matching of mesoscopic heterogeneity must also be considered.Organic solar cells have become a promising energy conversion candidate because of their unique advantages. Novel fullerene derivatives, as a common acceptor, can increase power conversion efficiency (PCE) by increasing the open-circuit voltage. As a representative acceptor, Indene-C60 bisadduct (ICBA) can reach high efficiency with poly(3-hexylthiophene) (P3HT). On the other hand, the novel synthesized polymers mainly aimed to broaden the optical absorption range have steadily promoted efficiency to higher than 9%. However, it is challenging to obtain the desired result by simply combining ICBA with other high-efficiency donors. Thus, P3HT or a high-efficiency polymer PBDTTT-C-T (copolymer of thienyl-substituted BDT with substituted TT) is used as donor and PCBM or ICBA as acceptor in this article to clarify the mechanism behind these materials. The optical and photovoltaic properties of the materials are studied for pair-wise combination. Among these four material groups, the highest PCE of 6.2% is obtained for the PBDTTT-C-T/PCBM combination while the lowest PCE of 3.5% is obtained for the PBDTTT-C-T/ICBA combination. The impact of the mesoscopic heterogeneity on the local mesoscopic photoelectric properties is identified by photo-conductive AFM (pc-AFM), and the consistence between the mesoscopic properties and the macroscopic device performances is also observed. Based on these results, an interface combined model is proposed based on the mesoscopic phase heterogeneity. This study provides a new view on the rational selection of photovoltaic materials, where, aside from the traditional energy level and absorption spectrum matching, the matching of mesoscopic heterogeneity must also be considered. Electronic Supplementary Information (ESI) available. See DOI: 10.1039/c3nr03165a

Statewide mesoscopic simulation for Wyoming.

DOT National Transportation Integrated Search

2013-10-01

This study developed a mesoscopic simulator which is capable of representing both city-level and statewide roadway : networks. The key feature of such models are the integration of (i) a traffic flow model which is efficient enough to : scale to larg...

An effective rate equation approach to reaction kinetics in small volumes: theory and application to biochemical reactions in nonequilibrium steady-state conditions.

PubMed

Grima, R

2010-07-21

Chemical master equations provide a mathematical description of stochastic reaction kinetics in well-mixed conditions. They are a valid description over length scales that are larger than the reactive mean free path and thus describe kinetics in compartments of mesoscopic and macroscopic dimensions. The trajectories of the stochastic chemical processes described by the master equation can be ensemble-averaged to obtain the average number density of chemical species, i.e., the true concentration, at any spatial scale of interest. For macroscopic volumes, the true concentration is very well approximated by the solution of the corresponding deterministic and macroscopic rate equations, i.e., the macroscopic concentration. However, this equivalence breaks down for mesoscopic volumes. These deviations are particularly significant for open systems and cannot be calculated via the Fokker-Planck or linear-noise approximations of the master equation. We utilize the system-size expansion including terms of the order of Omega(-1/2) to derive a set of differential equations whose solution approximates the true concentration as given by the master equation. These equations are valid in any open or closed chemical reaction network and at both the mesoscopic and macroscopic scales. In the limit of large volumes, the effective mesoscopic rate equations become precisely equal to the conventional macroscopic rate equations. We compare the three formalisms of effective mesoscopic rate equations, conventional rate equations, and chemical master equations by applying them to several biochemical reaction systems (homodimeric and heterodimeric protein-protein interactions, series of sequential enzyme reactions, and positive feedback loops) in nonequilibrium steady-state conditions. In all cases, we find that the effective mesoscopic rate equations can predict very well the true concentration of a chemical species. This provides a useful method by which one can quickly determine the regions of parameter space in which there are maximum differences between the solutions of the master equation and the corresponding rate equations. We show that these differences depend sensitively on the Fano factors and on the inherent structure and topology of the chemical network. The theory of effective mesoscopic rate equations generalizes the conventional rate equations of physical chemistry to describe kinetics in systems of mesoscopic size such as biological cells.

Lateral eddy diffusivity estimates from simulated and observed drifter trajectories: a case study for the Agulhas Current system

NASA Astrophysics Data System (ADS)

Rühs, Siren; Zhurbas, Victor; Durgadoo, Jonathan V.; Biastoch, Arne

2017-04-01

The Lagrangian description of fluid motion by sets of individual particle trajectories is extensively used to characterize connectivity between distinct oceanic locations. One important factor influencing the connectivity is the average rate of particle dispersal, generally quantified as Lagrangian diffusivity. In addition to Lagrangian observing programs, Lagrangian analyses are performed by advecting particles with the simulated flow field of ocean general circulation models (OGCMs). However, depending on the spatio-temporal model resolution, not all scale-dependent processes are explicitly resolved in the simulated velocity fields. Consequently, the dispersal of advective Lagrangian trajectories has been assumed not to be sufficiently diffusive compared to observed particle spreading. In this study we present a detailed analysis of the spatially variable lateral eddy diffusivity characteristics of advective drifter trajectories simulated with realistically forced OGCMs and compare them with estimates based on observed drifter trajectories. The extended Agulhas Current system around South Africa, known for its intricate mesoscale dynamics, serves as a test case. We show that a state-of-the-art eddy-resolving OGCM indeed features theoretically derived dispersion characteristics for diffusive regimes and realistically represents Lagrangian eddy diffusivity characteristics obtained from observed surface drifter trajectories. The estimates for the maximum and asymptotic lateral single-particle eddy diffusivities obtained from the observed and simulated drifter trajectories show a good agreement in their spatial pattern and magnitude. We further assess the sensitivity of the simulated lateral eddy diffusivity estimates to the temporal and lateral OGCM output resolution and examine the impact of the different eddy diffusivity characteristics on the Lagrangian connectivity between the Indian Ocean and the South Atlantic.

Lateral diffusion of proteins in the periplasm of Escherichia coli.

PubMed Central

Brass, J M; Higgins, C F; Foley, M; Rugman, P A; Birmingham, J; Garland, P B

1986-01-01

We have introduced biologically active, fluorescently labeled maltose-binding protein into the periplasmic space of Escherichia coli and measured its lateral diffusion coefficient by the fluorescence photobleaching recovery method. Diffusion of this protein in the periplasm was found to be surprisingly low (lateral diffusion coefficient, 0.9 X 10(-10) cm2 s-1), about 1,000-fold lower than would be expected for diffusion in aqueous medium and almost 100-fold lower than for an equivalent-size protein in the cytoplasm. Galactose-binding protein, myoglobin, and cytochrome c were also introduced into the periplasm and had diffusion coefficients identical to that determined for the maltose-binding protein. For all proteins nearly 100% recovery of fluorescence was obtained after photobleaching, indicating that the periplasm is a single contiguous compartment surrounding the cell. These data have considerable implications for periplasmic structure and for the role of periplasmic proteins in transport and chemotaxis. Images PMID:3005237

Spatial and temporal dynamics of receptor for advanced glycation endproducts, integrins, and actin cytoskeleton as probed with fluorescence-based imaging techniques

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

Syed, Aleem

Systematic spatial and temporal fluctuations are a fundamental part of any biological process. For example, lateral diffusion of membrane proteins is one of the key mechanisms in their cellular function. Lateral diffusion governs how membrane proteins interact with intracellular, transmembrane, and extracellular components to achieve their function. Herein, fluorescence-based techniques are used to elucidate the dynamics of receptor for advanced glycation end-products (RAGE) and integrin membrane proteins. RAGE is a transmembrane protein that is being used as a biomarker for various diseases. RAGE dependent signaling in numerous pathological conditions is well studied. However, RAGE lateral diffusion in the cell membranemore » is poorly understood. For this purpose, effect of cholesterol, cytoskeleton dynamics, and presence of ligand on RAGE lateral diffusion is investigated.« less

The adiabatic piston: a perpetuum mobile in the mesoscopic realm

NASA Astrophysics Data System (ADS)

Crosignani, Bruno; Porto, Paolo; Conti, Claudio

2004-03-01

A detailed analysis of the adiabatic-piston problem reveals, for a finely-tuned choice of the spatial dimensions of the system, peculiar dynamical features that challenge the statement that an isolated system necessarily reaches a time-independent equilibrium state. In particular, the piston behaves like a perpetuum mobile, i.e., it never comes to a stop but keeps wandering, undergoing sizeable oscillations around the position corresponding to maximum entropy; this has remarkable implications on the entropy changes of a mesoscopic isolated system and on the limits of validity of the second law of thermodynamics in the mesoscopic realm.

Mesoscopic Length Scale Controls the Rheology of Dense Suspensions

NASA Astrophysics Data System (ADS)

Bonnoit, Claire; Lanuza, Jose; Lindner, Anke; Clement, Eric

2010-09-01

From the flow properties of dense granular suspensions on an inclined plane, we identify a mesoscopic length scale strongly increasing with volume fraction. When the flowing layer height is larger than this length scale, a diverging Newtonian viscosity is determined. However, when the flowing layer height drops below this scale, we evidence a nonlocal effective viscosity, decreasing as a power law of the flow height. We establish a scaling relation between this mesoscopic length scale and the suspension viscosity. These results support recent theoretical and numerical results implying collective and clustered granular motion when the jamming point is approached from below.

Mesoscopic length scale controls the rheology of dense suspensions.

PubMed

Bonnoit, Claire; Lanuza, Jose; Lindner, Anke; Clement, Eric

2010-09-03

From the flow properties of dense granular suspensions on an inclined plane, we identify a mesoscopic length scale strongly increasing with volume fraction. When the flowing layer height is larger than this length scale, a diverging Newtonian viscosity is determined. However, when the flowing layer height drops below this scale, we evidence a nonlocal effective viscosity, decreasing as a power law of the flow height. We establish a scaling relation between this mesoscopic length scale and the suspension viscosity. These results support recent theoretical and numerical results implying collective and clustered granular motion when the jamming point is approached from below.

Static and dynamic light scattering by red blood cells: A numerical study.

PubMed

Mauer, Johannes; Peltomäki, Matti; Poblete, Simón; Gompper, Gerhard; Fedosov, Dmitry A

2017-01-01

Light scattering is a well-established experimental technique, which gains more and more popularity in the biological field because it offers the means for non-invasive imaging and detection. However, the interpretation of light-scattering signals remains challenging due to the complexity of most biological systems. Here, we investigate static and dynamic scattering properties of red blood cells (RBCs) using two mesoscopic hydrodynamics simulation methods-multi-particle collision dynamics and dissipative particle dynamics. Light scattering is studied for various membrane shear elasticities, bending rigidities, and RBC shapes (e.g., biconcave and stomatocyte). Simulation results from the two simulation methods show good agreement, and demonstrate that the static light scattering of a diffusing RBC is not very sensitive to the changes in membrane properties and moderate alterations in cell shapes. We also compute dynamic light scattering of a diffusing RBC, from which dynamic properties of RBCs such as diffusion coefficients can be accessed. In contrast to static light scattering, the dynamic measurements can be employed to differentiate between the biconcave and stomatocytic RBC shapes and generally allow the differentiation based on the membrane properties. Our simulation results can be used for better understanding of light scattering by RBCs and the development of new non-invasive methods for blood-flow monitoring.

Static and dynamic light scattering by red blood cells: A numerical study

PubMed Central

Mauer, Johannes; Peltomäki, Matti; Poblete, Simón; Gompper, Gerhard

2017-01-01

Light scattering is a well-established experimental technique, which gains more and more popularity in the biological field because it offers the means for non-invasive imaging and detection. However, the interpretation of light-scattering signals remains challenging due to the complexity of most biological systems. Here, we investigate static and dynamic scattering properties of red blood cells (RBCs) using two mesoscopic hydrodynamics simulation methods—multi-particle collision dynamics and dissipative particle dynamics. Light scattering is studied for various membrane shear elasticities, bending rigidities, and RBC shapes (e.g., biconcave and stomatocyte). Simulation results from the two simulation methods show good agreement, and demonstrate that the static light scattering of a diffusing RBC is not very sensitive to the changes in membrane properties and moderate alterations in cell shapes. We also compute dynamic light scattering of a diffusing RBC, from which dynamic properties of RBCs such as diffusion coefficients can be accessed. In contrast to static light scattering, the dynamic measurements can be employed to differentiate between the biconcave and stomatocytic RBC shapes and generally allow the differentiation based on the membrane properties. Our simulation results can be used for better understanding of light scattering by RBCs and the development of new non-invasive methods for blood-flow monitoring. PMID:28472125

Diffusion in an expanding medium: Fokker-Planck equation, Green's function, and first-passage properties

NASA Astrophysics Data System (ADS)

Yuste, S. B.; Abad, E.; Escudero, C.

2016-09-01

We present a classical, mesoscopic derivation of the Fokker-Planck equation for diffusion in an expanding medium. To this end, we take a conveniently generalized Chapman-Kolmogorov equation as the starting point. We obtain an analytical expression for the Green's function (propagator) and investigate both analytically and numerically how this function and the associated moments behave. We also study first-passage properties in expanding hyperspherical geometries. We show that in all cases the behavior is determined to a great extent by the so-called Brownian conformal time τ (t ) , which we define via the relation τ ˙=1 /a2 , where a (t ) is the expansion scale factor. If the medium expansion is driven by a power law [a (t ) ∝tγ with γ >0 ] , then we find interesting crossover effects in the mixing effectiveness of the diffusion process when the characteristic exponent γ is varied. Crossover effects are also found at the level of the survival probability and of the moments of the first passage-time distribution with two different regimes separated by the critical value γ =1 /2 . The case of an exponential scale factor is analyzed separately both for expanding and contracting media. In the latter situation, a stationary probability distribution arises in the long-time limit.

Light and Life in Baltimore—and Beyond

PubMed Central

Edidin, Michael

2015-01-01

Baltimore has been the home of numerous biophysical studies using light to probe cells. One such study, quantitative measurement of lateral diffusion of rhodopsin, set the standard for experiments in which recovery after photobleaching is used to measure lateral diffusion. Development of this method from specialized microscopes to commercial scanning confocal microscopes has led to widespread use of the technique to measure lateral diffusion of membrane proteins and lipids, and as well diffusion and binding interactions in cell organelles and cytoplasm. Perturbation of equilibrium distributions by photobleaching has also been developed into a robust method to image molecular proximity in terms of fluorescence resonance energy transfer between donor and acceptor fluorophores. PMID:25650914

Lateral mobility of plasma membrane proteins in dividing eggs of the loach (Misgurnus fossilis): Regional differences and changes during the cell cycle.

PubMed

Bozhkova, V P; Budayova, M; Kvasnicka, P; Cigankova, N; Chorvat, D

1994-12-01

Regional differences in lateral diffusion rates of fluorescence-labeled proteins have been studied in the plasma membrane of dividing eggs of the loach (Misgurnus fossilis) by fluorescence recovery after photobleaching (FRAP). Apparent animal-vegetal differences in fluorescence intensity, lateral diffusion coefficients, and fractions of mobile proteins have been found, with all these quantities being higher in the animal pole region than in the yolk region. Cyclic changes in protein diffusion coefficients and mobile fractions during the first few cell cycles have also been recorded. Soon after the end of a cleavage, the diffusion coefficient reaches its minimal value and increases rapidly before the next cleavage.

Lateral carrier diffusion and current gain in terahertz InGaAs/InP double-heterojunction bipolar transistors

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

Chiang, Han-Wei; Rode, Johann C.; Choudhary, Prateek

2014-01-21

The DC current gain in In{sub 0.53}Ga{sub 0.47}As/InP double-heterojunction bipolar transistors is computed based on a drift-diffusion model, and is compared with experimental data. Even in the absence of other scaling effects, lateral diffusion of electrons to the base Ohmic contacts causes a rapid reduction in DC current gain as the emitter junction width and emitter-base contact spacing are reduced. The simulation and experimental data are compared in order to examine the effect of carrier lateral diffusion on current gain. The impact on current gain due to device scaling and approaches to increase current gain are discussed.

Thermal imaging measurement of lateral diffusivity and non-invasive material defect detection

DOEpatents

Sun, Jiangang; Deemer, Chris

2003-01-01

A system and method for determining lateral thermal diffusivity of a material sample using a heat pulse; a sample oriented within an orthogonal coordinate system; an infrared camera; and a computer that has a digital frame grabber, and data acquisition and processing software. The mathematical model used within the data processing software is capable of determining the lateral thermal diffusivity of a sample of finite boundaries. The system and method may also be used as a nondestructive method for detecting and locating cracks within the material sample.

Effects of Interfacial Translation-rotation Coupling for Confined Ferrofluids

NASA Astrophysics Data System (ADS)

Fang, Angbo

2011-03-01

Ferrofluids have wide applications ranging from semiconductor fabrications to biomedical processes. The hydrodynamic spin diffusion theory for ferrofluids has been successful in explaining many experimental data, but it suffers from some fatal flaws. For example, it fails to predict the incorrect flow direction for a ferrofluid confined in a concentric cylinder channel in the presence of a rotating magnetic field. In this work we develop a method to establish the general hydrodynamic boundary conditions (BCs) for micro-polar fluids such as ferrofluids. Through a dynamic generalization of the mesoscopic diffuse interface model, we are able to obtain the surface dissipation functional, in which the interfacial translation-rotation coupling plays a significant role. The generalized hydrodynamic BCs can be obtained straightforwardly by using Onsager's variational approach. The resulted velocity profile and other quantities compares well with the experimental data, strikingly different from traditional theories. The methodology can be applied to study the hydrodynamic behavior of other structured fluids in confined channels or multi-phase flows. The work is supported by a research award made by the King Abdullah University of Science and Technology.

Limitations of the commonly used simplified laterally uniform optical fiber probe-tissue interface in Monte Carlo simulations of diffuse reflectance

PubMed Central

Naglič, Peter; Pernuš, Franjo; Likar, Boštjan; Bürmen, Miran

2015-01-01

Light propagation models often simplify the interface between the optical fiber probe tip and tissue to a laterally uniform boundary with mismatched refractive indices. Such simplification neglects the precise optical properties of the commonly used probe tip materials, e.g. stainless steel or black epoxy. In this paper, we investigate the limitations of the laterally uniform probe-tissue interface in Monte Carlo simulations of diffuse reflectance. In comparison to a realistic probe-tissue interface that accounts for the layout and properties of the probe tip materials, the simplified laterally uniform interface is shown to introduce significant errors into the simulated diffuse reflectance. PMID:26504647

Membrane Orientation and Lateral Diffusion of BODIPY-Cholesterol as a Function of Probe Structure

PubMed Central

Solanko, Lukasz M.; Honigmann, Alf; Midtiby, Henrik Skov; Lund, Frederik W.; Brewer, Jonathan R.; Dekaris, Vjekoslav; Bittman, Robert; Eggeling, Christian; Wüstner, Daniel

2013-01-01

Cholesterol tagged with the BODIPY fluorophore via the central difluoroboron moiety of the dye (B-Chol) is a promising probe for studying intracellular cholesterol dynamics. We synthesized a new BODIPY-cholesterol probe (B-P-Chol) with the fluorophore attached via one of its pyrrole rings to carbon-24 of cholesterol (B-P-Chol). Using two-photon fluorescence polarimetry in giant unilamellar vesicles and in the plasma membrane (PM) of living intact and actin-disrupted cells, we show that the BODIPY-groups in B-Chol and B-P-Chol are oriented perpendicular and almost parallel to the bilayer normal, respectively. B-Chol is in all three membrane systems much stronger oriented than B-P-Chol. Interestingly, we found that the lateral diffusion in the PM was two times slower for B-Chol than for B-P-Chol, although we found no difference in lateral diffusion in model membranes. Stimulated emission depletion microscopy, performed for the first time, to our knowledge, with fluorescent sterols, revealed that the difference in lateral diffusion of the BODIPY-cholesterol probes was not caused by anomalous subdiffusion, because diffusion of both analogs in the PM was free but not hindered. Our combined measurements show that the position and orientation of the BODIPY moiety in cholesterol analogs have a severe influence on lateral diffusion specifically in the PM of living cells. PMID:24209853

Growth of monodisperse mesoscopic metal-oxide colloids under constant monomer supply

NASA Astrophysics Data System (ADS)

Nozawa, Koh; Delville, Marie-Hélène; Ushiki, Hideharu; Panizza, Pascal; Delville, Jean-Pierre

2005-07-01

In closed systems, control over the size of monodisperse metal-oxide colloids is generally limited to submicrometric dimensions. To overcome this difficulty, we explore the formation and growth of silica particles under constant monomer supply. The monomer source is externally driven by the progressive addition into the system of one of the precursors. Monodisperse spherical particles are produced up to a mesoscopic size. We analyze their growth versus the monomer addition rate at different temperatures. Our results show that in the presence of a continuous monomer addition, growth is limited by diffusion over the investigated temporal window. Using the temperature variation of the growth rate, we prove that rescaling leads to a data reduction onto a single master curve. Contrary to the growth process, the final particle’s size reached after the end of the reagent supply strongly depends on the addition rate. The variation of the final particle size versus addition rate can be deduced from an analogy with crystal formation in jet precipitation. Within this framework, and using the temperature dependences of both the particle growth law and the final size, we determine the value of the molecular heat of dissolution associated to the silica solubility. These observations support the fact that classical theories of phase-ordering dynamics can be extended to the synthesis of inorganic particles. The emergence of a master behavior in the presence of continuous monomer addition also suggests the extension of these theories to open systems.

Mobility Effect on Poroelastic Seismic Signatures in Partially Saturated Rocks With Applications in Time-Lapse Monitoring of a Heavy Oil Reservoir

NASA Astrophysics Data System (ADS)

Zhao, Luanxiao; Yuan, Hemin; Yang, Jingkang; Han, De-hua; Geng, Jianhua; Zhou, Rui; Li, Hui; Yao, Qiuliang

2017-11-01

Conventional seismic analysis in partially saturated rocks normally lays emphasis on estimating pore fluid content and saturation, typically ignoring the effect of mobility, which decides the ability of fluids moving in the porous rocks. Deformation resulting from a seismic wave in heterogeneous partially saturated media can cause pore fluid pressure relaxation at mesoscopic scale, thereby making the fluid mobility inherently associated with poroelastic reflectivity. For two typical gas-brine reservoir models, with the given rock and fluid properties, the numerical analysis suggests that variations of patchy fluid saturation, fluid compressibility contrast, and acoustic stiffness of rock frame collectively affect the seismic reflection dependence on mobility. In particular, the realistic compressibility contrast of fluid patches in shallow and deep reservoir environments plays an important role in determining the reflection sensitivity to mobility. We also use a time-lapse seismic data set from a Steam-Assisted Gravity Drainage producing heavy oil reservoir to demonstrate that mobility change coupled with patchy saturation possibly leads to seismic spectral energy shifting from the baseline to monitor line. Our workflow starts from performing seismic spectral analysis on the targeted reflectivity interface. Then, on the basis of mesoscopic fluid pressure diffusion between patches of steam and heavy oil, poroelastic reflectivity modeling is conducted to understand the shift of the central frequency toward low frequencies after the steam injection. The presented results open the possibility of monitoring mobility change of a partially saturated geological formation from dissipation-related seismic attributes.

Introscopy in nano- and mesoscopic physics: Single electronics and quantum ballistics

NASA Astrophysics Data System (ADS)

Tkachenko, V. A.; Tkachenko, O. A.; Kvon, Z. D.; Latyshev, A. V.; Aseev, A. L.

2016-09-01

A method is presented to be used in a computational experiment aimed at studying the internal structure of nano- and mesoscopic objects, i.e., conducting subsystems and quantum phenomena in solid submicron objects, which demonstrate an individual behavior of low-temperature resistance.

Fermi edge singularities in the mesoscopic regime: Photoabsorption spectra

NASA Astrophysics Data System (ADS)

Hentschel, Martina; Ullmo, Denis; Baranger, Harold U.

2007-12-01

We study Fermi edge singularities in photoabsorption spectra of generic mesoscopic systems such as quantum dots or nanoparticles. We predict deviations from macroscopic-metallic behavior and propose experimental setups for the observation of these effects. The theory is based on the model of a localized, or rank one, perturbation caused by the (core) hole left behind after the photoexcitation of an electron into the conduction band. The photoabsorption spectra result from the competition between two many-body responses, Anderson’s orthogonality catastrophe and the Mahan-Nozières-DeDominicis contribution. Both mechanisms depend on the system size through the number of particles and, more importantly, fluctuations produced by the coherence characteristic of mesoscopic samples. The latter lead to a modification of the dipole matrix element and trigger one of our key results: a rounded K -edge typically found in metals will turn into a (slightly) peaked edge on average in the mesoscopic regime. We consider in detail the effect of the “bound state” produced by the core hole.

Fracture of disordered solids in compression as a critical phenomenon. I. Statistical mechanics formalism.

PubMed

Toussaint, Renaud; Pride, Steven R

2002-09-01

This is the first of a series of three articles that treats fracture localization as a critical phenomenon. This first article establishes a statistical mechanics based on ensemble averages when fluctuations through time play no role in defining the ensemble. Ensembles are obtained by dividing a huge rock sample into many mesoscopic volumes. Because rocks are a disordered collection of grains in cohesive contact, we expect that once shear strain is applied and cracks begin to arrive in the system, the mesoscopic volumes will have a wide distribution of different crack states. These mesoscopic volumes are the members of our ensembles. We determine the probability of observing a mesoscopic volume to be in a given crack state by maximizing Shannon's measure of the emergent-crack disorder subject to constraints coming from the energy balance of brittle fracture. The laws of thermodynamics, the partition function, and the quantification of temperature are obtained for such cracking systems.

Efficient reactive Brownian dynamics

DOE PAGES

Donev, Aleksandar; Yang, Chiao-Yu; Kim, Changho

2018-01-21

We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently processmore » reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.« less

Efficient reactive Brownian dynamics

NASA Astrophysics Data System (ADS)

Donev, Aleksandar; Yang, Chiao-Yu; Kim, Changho

2018-01-01

We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently process reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.

Efficient reactive Brownian dynamics

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

Donev, Aleksandar; Yang, Chiao-Yu; Kim, Changho

We develop a Split Reactive Brownian Dynamics (SRBD) algorithm for particle simulations of reaction-diffusion systems based on the Doi or volume reactivity model, in which pairs of particles react with a specified Poisson rate if they are closer than a chosen reactive distance. In our Doi model, we ensure that the microscopic reaction rules for various association and dissociation reactions are consistent with detailed balance (time reversibility) at thermodynamic equilibrium. The SRBD algorithm uses Strang splitting in time to separate reaction and diffusion and solves both the diffusion-only and reaction-only subproblems exactly, even at high packing densities. To efficiently processmore » reactions without uncontrolled approximations, SRBD employs an event-driven algorithm that processes reactions in a time-ordered sequence over the duration of the time step. A grid of cells with size larger than all of the reactive distances is used to schedule and process the reactions, but unlike traditional grid-based methods such as reaction-diffusion master equation algorithms, the results of SRBD are statistically independent of the size of the grid used to accelerate the processing of reactions. We use the SRBD algorithm to compute the effective macroscopic reaction rate for both reaction-limited and diffusion-limited irreversible association in three dimensions and compare to existing theoretical predictions at low and moderate densities. We also study long-time tails in the time correlation functions for reversible association at thermodynamic equilibrium and compare to recent theoretical predictions. Finally, we compare different particle and continuum methods on a model exhibiting a Turing-like instability and pattern formation. Our studies reinforce the common finding that microscopic mechanisms and correlations matter for diffusion-limited systems, making continuum and even mesoscopic modeling of such systems difficult or impossible. We also find that for models in which particles diffuse off lattice, such as the Doi model, reactions lead to a spurious enhancement of the effective diffusion coefficients.« less

Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach

NASA Astrophysics Data System (ADS)

Kim, Changho; Nonaka, Andy; Bell, John B.; Garcia, Alejandro L.; Donev, Aleksandar

2017-03-01

We develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuating hydrodynamics (FHD). For hydrodynamic systems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i.e., each mesoscopic cell has few (reactive) molecules, to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the severe restriction on time step size that limits all methods based on explicit treatments of diffusion and construct numerical methods that are more efficient than RDME methods, without compromising accuracy. Guided by an analysis of the accuracy of the distribution of steady-state fluctuations for the linearized reaction-diffusion model, we construct several two-stage (predictor-corrector) schemes, where diffusion is treated using a stochastic Crank-Nicolson method, and reactions are handled by the stochastic simulation algorithm of Gillespie or a weakly second-order tau leaping method. We find that an implicit midpoint tau leaping scheme attains second-order weak accuracy in the linearized setting and gives an accurate and stable structure factor for a time step size of an order of magnitude larger than the hopping time scale of diffusing molecules. We study the numerical accuracy of our methods for the Schlögl reaction-diffusion model both in and out of thermodynamic equilibrium. We demonstrate and quantify the importance of thermodynamic fluctuations to the formation of a two-dimensional Turing-like pattern and examine the effect of fluctuations on three-dimensional chemical front propagation. By comparing stochastic simulations to deterministic reaction-diffusion simulations, we show that fluctuations accelerate pattern formation in spatially homogeneous systems and lead to a qualitatively different disordered pattern behind a traveling wave.

Stochastic simulation of reaction-diffusion systems: A fluctuating-hydrodynamics approach

DOE PAGES

Kim, Changho; Nonaka, Andy; Bell, John B.; ...

2017-03-24

Here, we develop numerical methods for stochastic reaction-diffusion systems based on approaches used for fluctuating hydrodynamics (FHD). For hydrodynamic systems, the FHD formulation is formally described by stochastic partial differential equations (SPDEs). In the reaction-diffusion systems we consider, our model becomes similar to the reaction-diffusion master equation (RDME) description when our SPDEs are spatially discretized and reactions are modeled as a source term having Poisson fluctuations. However, unlike the RDME, which becomes prohibitively expensive for an increasing number of molecules, our FHD-based description naturally extends from the regime where fluctuations are strong, i.e., each mesoscopic cell has few (reactive) molecules,more » to regimes with moderate or weak fluctuations, and ultimately to the deterministic limit. By treating diffusion implicitly, we avoid the severe restriction on time step size that limits all methods based on explicit treatments of diffusion and construct numerical methods that are more efficient than RDME methods, without compromising accuracy. Guided by an analysis of the accuracy of the distribution of steady-state fluctuations for the linearized reaction-diffusion model, we construct several two-stage (predictor-corrector) schemes, where diffusion is treated using a stochastic Crank-Nicolson method, and reactions are handled by the stochastic simulation algorithm of Gillespie or a weakly second-order tau leaping method. We find that an implicit midpoint tau leaping scheme attains second-order weak accuracy in the linearized setting and gives an accurate and stable structure factor for a time step size of an order of magnitude larger than the hopping time scale of diffusing molecules. We study the numerical accuracy of our methods for the Schlögl reaction-diffusion model both in and out of thermodynamic equilibrium. We demonstrate and quantify the importance of thermodynamic fluctuations to the formation of a two-dimensional Turing-like pattern and examine the effect of fluctuations on three-dimensional chemical front propagation. Furthermore, by comparing stochastic simulations to deterministic reaction-diffusion simulations, we show that fluctuations accelerate pattern formation in spatially homogeneous systems and lead to a qualitatively different disordered pattern behind a traveling wave.« less

Light and life in Baltimore--and beyond.

PubMed

Edidin, Michael

2015-02-03

Baltimore has been the home of numerous biophysical studies using light to probe cells. One such study, quantitative measurement of lateral diffusion of rhodopsin, set the standard for experiments in which recovery after photobleaching is used to measure lateral diffusion. Development of this method from specialized microscopes to commercial scanning confocal microscopes has led to widespread use of the technique to measure lateral diffusion of membrane proteins and lipids, and as well diffusion and binding interactions in cell organelles and cytoplasm. Perturbation of equilibrium distributions by photobleaching has also been developed into a robust method to image molecular proximity in terms of fluorescence resonance energy transfer between donor and acceptor fluorophores. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Hydrodynamic Electron Flow and Hall Viscosity

NASA Astrophysics Data System (ADS)

Scaffidi, Thomas; Moll, Philip; Kushwaha, Pallavi; Nandi, Nabhanila; Schmidt, Burkhard; MacKenzie, Andrew; Moore, Joel

In metallic samples of small enough size and sufficiently strong electron-electron scattering, the viscosity of the electron gas can become the dominant process governing transport. In this regime, momentum is a long-lived quantity whose evolution is described by an emergent hydrodynamical theory for which bounds on diffusion were conjectured based on an holographic correspondence. Furthermore, breaking time-reversal symmetry can lead to the appearance of an odd component to the viscosity called the Hall viscosity which has attracted a lot of attention recently due to its quantized nature in gapped systems but still eludes experimental confirmation. Based on microscopic calculations, we discuss how to measure the effects of both the even and odd components of the viscosity using hydrodynamic electronic transport in mesoscopic samples under applied magnetic fields. Gordon and Betty Moore Foundation.

Lattice Boltzmann model capable of mesoscopic vorticity computation

NASA Astrophysics Data System (ADS)

Peng, Cheng; Guo, Zhaoli; Wang, Lian-Ping

2017-11-01

It is well known that standard lattice Boltzmann (LB) models allow the strain-rate components to be computed mesoscopically (i.e., through the local particle distributions) and as such possess a second-order accuracy in strain rate. This is one of the appealing features of the lattice Boltzmann method (LBM) which is of only second-order accuracy in hydrodynamic velocity itself. However, no known LB model can provide the same quality for vorticity and pressure gradients. In this paper, we design a multiple-relaxation time LB model on a three-dimensional 27-discrete-velocity (D3Q27) lattice. A detailed Chapman-Enskog analysis is presented to illustrate all the necessary constraints in reproducing the isothermal Navier-Stokes equations. The remaining degrees of freedom are carefully analyzed to derive a model that accommodates mesoscopic computation of all the velocity and pressure gradients from the nonequilibrium moments. This way of vorticity calculation naturally ensures a second-order accuracy, which is also proven through an asymptotic analysis. We thus show, with enough degrees of freedom and appropriate modifications, the mesoscopic vorticity computation can be achieved in LBM. The resulting model is then validated in simulations of a three-dimensional decaying Taylor-Green flow, a lid-driven cavity flow, and a uniform flow passing a fixed sphere. Furthermore, it is shown that the mesoscopic vorticity computation can be realized even with single relaxation parameter.

Integrated corridor management (ICM) analysis, modeling, and simulation (AMS) for Minneapolis site : model calibration and validation report.

DOT National Transportation Integrated Search

2010-02-01

This technical report documents the calibration and validation of the baseline (2008) mesoscopic model for the I-394 Minneapolis, Minnesota, Pioneer Site. DynusT was selected as the mesoscopic model for analyzing operating conditions in the I-394 cor...

Developing mesoscopic models for the before and after study of the inter-county connector : phase-one.

DOT National Transportation Integrated Search

2013-03-01

This study developed a mesoscopic model for the before and after study of MD 200, the Inter-County Connector. It is in line with : recent efforts by the Maryland State Highway Administration (SHA) in developing effective modeling tools for traffic an...

Mesoscopic Rings with Spin-Orbit Interactions

ERIC Educational Resources Information Center

Berche, Bertrand; Chatelain, Christophe; Medina, Ernesto

2010-01-01

A didactic description of charge and spin equilibrium currents on mesoscopic rings in the presence of spin-orbit interaction is presented. Emphasis is made on the non-trivial construction of the correct Hamiltonian in polar coordinates, the calculation of eigenvalues and eigenfunctions and the symmetries of the ground-state properties. Spin…

Membrane orientation and lateral diffusion of BODIPY-cholesterol as a function of probe structure.

PubMed

Solanko, Lukasz M; Honigmann, Alf; Midtiby, Henrik Skov; Lund, Frederik W; Brewer, Jonathan R; Dekaris, Vjekoslav; Bittman, Robert; Eggeling, Christian; Wüstner, Daniel

2013-11-05

Cholesterol tagged with the BODIPY fluorophore via the central difluoroboron moiety of the dye (B-Chol) is a promising probe for studying intracellular cholesterol dynamics. We synthesized a new BODIPY-cholesterol probe (B-P-Chol) with the fluorophore attached via one of its pyrrole rings to carbon-24 of cholesterol (B-P-Chol). Using two-photon fluorescence polarimetry in giant unilamellar vesicles and in the plasma membrane (PM) of living intact and actin-disrupted cells, we show that the BODIPY-groups in B-Chol and B-P-Chol are oriented perpendicular and almost parallel to the bilayer normal, respectively. B-Chol is in all three membrane systems much stronger oriented than B-P-Chol. Interestingly, we found that the lateral diffusion in the PM was two times slower for B-Chol than for B-P-Chol, although we found no difference in lateral diffusion in model membranes. Stimulated emission depletion microscopy, performed for the first time, to our knowledge, with fluorescent sterols, revealed that the difference in lateral diffusion of the BODIPY-cholesterol probes was not caused by anomalous subdiffusion, because diffusion of both analogs in the PM was free but not hindered. Our combined measurements show that the position and orientation of the BODIPY moiety in cholesterol analogs have a severe influence on lateral diffusion specifically in the PM of living cells. Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Diffusion tensor imaging analysis of sequential spreading of disease in amyotrophic lateral sclerosis confirms patterns of TDP-43 pathology.

PubMed

Kassubek, Jan; Müller, Hans-Peter; Del Tredici, Kelly; Brettschneider, Johannes; Pinkhardt, Elmar H; Lulé, Dorothée; Böhm, Sarah; Braak, Heiko; Ludolph, Albert C

2014-06-01

Diffusion tensor imaging can identify amyotrophic lateral sclerosis-associated patterns of brain alterations at the group level. Recently, a neuropathological staging system for amyotrophic lateral sclerosis has shown that amyotrophic lateral sclerosis may disseminate in a sequential regional pattern during four disease stages. The objective of the present study was to apply a new methodological diffusion tensor imaging-based approach to automatically analyse in vivo the fibre tracts that are prone to be involved at each neuropathological stage of amyotrophic lateral sclerosis. Two data samples, consisting of 130 diffusion tensor imaging data sets acquired at 1.5 T from 78 patients with amyotrophic lateral sclerosis and 52 control subjects; and 55 diffusion-tensor imaging data sets at 3.0 T from 33 patients with amyotrophic lateral sclerosis and 22 control subjects, were analysed by a tract of interest-based fibre tracking approach to analyse five tracts that become involved during the course of amyotrophic lateral sclerosis: the corticospinal tract (stage 1); the corticorubral and the corticopontine tracts (stage 2); the corticostriatal pathway (stage 3); the proximal portion of the perforant path (stage 4); and two reference pathways. The statistical analyses of tracts of interest showed differences between patients with amyotrophic lateral sclerosis and control subjects for all tracts. The significance level of the comparisons at the group level was lower, the higher the disease stage with corresponding involved fibre tracts. Both the clinical phenotype as assessed by the amyotrophic lateral sclerosis functional rating scale-revised and disease duration correlated significantly with the resulting staging scheme. In summary, the tract of interest-based technique allowed for individual analysis of predefined tract structures, thus making it possible to image in vivo the disease stages in amyotrophic lateral sclerosis. This approach can be used not only for individual clinical work-up purposes, but enlarges the spectrum of potential non-invasive surrogate markers as a neuroimaging-based read-out for amyotrophic lateral sclerosis studies within a clinical context. © The Author (2014). Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Joint Services Electronics Program

NASA Astrophysics Data System (ADS)

Tinkham, Michael

1989-07-01

Topics addressed include: Electronic Theory of Semiconductor Alloys and Superlattices; Pressure Dependence of Photo Luminescence Excitation in GaAs/Al(x)Ga(1-x)As Multi-Quantum Wells; X Ray Surface Characterization; High Temperature Superconductivity; Quantum and Charging Phenomena in Mesoscopic Josephson Junctions; Nonlinear Dynamics of Electronic Neural Networks; Structural and Electronic Studies of Semiconductor Interfaces and Surfaces; Interaction of Ultrashort Laser Pulses with Semiconductor Surfaces; Multiphoton Vibrational Excitation of Molecules; Analytical and Numerical Determination of the Fields of Antennas near an Interface Between Two Half-Spaces with Significantly Different Wave Numbers; Theoretical Study of Lateral-Wave Propagation in Horizontally-Layered Media; Lateral Electromagnetic Waves from a Horizontal Antenna for Remote Sensing in the Ocean; Lateral Electromagnetic Pulses Generated by Horizontal and Vertical Dipoles on the Boundary Between Two Dielectrics; Theoretical Study of Isolated and Coupled Strip Antennas; Theoretical Study of Electromagnetic Pulses with a Slow Rate of Decay; Experimental Study of Electromagnetic Pulses with a Slow Rate of Decay; Properties of Closed Loops of Pseudodipoles; Asymptotic Solution for the Charge and Current Near the Open End of a Linear Tubular Antenna; Closed Loops of Parallel Coplanar Dipoles - Electrically Short Elements; Harmonic Generation in High-Temperature Superconductors and Resonant Closed Loops of Dipoles.

Lateral Membrane Diffusion Modulated by a Minimal Actin Cortex

PubMed Central

Heinemann, Fabian; Vogel, Sven K.; Schwille, Petra

2013-01-01

Diffusion of lipids and proteins within the cell membrane is essential for numerous membrane-dependent processes including signaling and molecular interactions. It is assumed that the membrane-associated cytoskeleton modulates lateral diffusion. Here, we use a minimal actin cortex to directly study proposed effects of an actin meshwork on the diffusion in a well-defined system. The lateral diffusion of a lipid and a protein probe at varying densities of membrane-bound actin was characterized by fluorescence correlation spectroscopy (FCS). A clear correlation of actin density and reduction in mobility was observed for both the lipid and the protein probe. At high actin densities, the effect on the protein probe was ∼3.5-fold stronger compared to the lipid. Moreover, addition of myosin filaments, which contract the actin mesh, allowed switching between fast and slow diffusion in the minimal system. Spot variation FCS was in accordance with a model of fast microscopic diffusion and slower macroscopic diffusion. Complementing Monte Carlo simulations support the analysis of the experimental FCS data. Our results suggest a stronger interaction of the actin mesh with the larger protein probe compared to the lipid. This might point toward a mechanism where cortical actin controls membrane diffusion in a strong size-dependent manner. PMID:23561523

Centerband-only-detection-of-exchange (31)P nuclear magnetic resonance and phospholipid lateral diffusion: theory, simulation and experiment.

PubMed

Lai, Angel; Saleem, Qasim; Macdonald, Peter M

2015-10-14

Centerband-only-detection-of-exchange (CODEX) (31)P NMR lateral diffusion measurements were performed on dimyristoylphosphatidylcholine (DMPC) assembled into large unilamellar spherical vesicles. Optimization of sample and NMR acquisition conditions provided significant sensitivity enhancements relative to an earlier first report (Q. Saleem, A. Lai, H. Morales, and P. M. Macdonald, Chem. Phys. Lipids, 2012, 165, 721). An analytical description was developed that permitted the extraction of lateral diffusion coefficients from CODEX data, based on a Gaussian-diffusion-on-a-sphere model (A. Ghosh, J. Samuel, and S. Sinha, Europhys. Lett., 2012, 98, 30003-p1) as relevant to CODEX (31)P NMR measurements on a population of spherical unilamellar phospholipid bilayer vesicles displaying a distribution of vesicle radii.

Statistics of the quantized microwave electromagnetic field in mesoscopic elements at low temperature

NASA Astrophysics Data System (ADS)

Virally, Stéphane; Olivier Simoneau, Jean; Lupien, Christian; Reulet, Bertrand

2018-03-01

The quantum behavior of the electromagnetic field in mesoscopic elements is intimately linked to the quantization of the charge. In order to probe nonclassical aspects of the field in those elements, it is essential that thermal noise be reduced to the quantum level, i.e. to scales where kT ≲ hν. This is easily achieved in dilution refrigerators for frequencies of a few GHz, i.e. in the microwave domain. Several recent experiments have highlighted the link between discrete charge transport and discrete photon emission in simple mesoscopic elements such as a tunnel junction. Photocount statistics are inferred from the measurement of continuous variables such as the quadratures of the field.

Mesoscopic Magnetic Resonance Spectroscopy with a Remote Spin Sensor

NASA Astrophysics Data System (ADS)

Xie, Tianyu; Shi, Fazhan; Chen, Sanyou; Guo, Maosen; Chen, Yisheng; Zhang, Yixing; Yang, Yu; Gao, Xingyu; Kong, Xi; Wang, Pengfei; Tateishi, Kenichiro; Uesaka, Tomohiro; Wang, Ya; Zhang, Bo; Du, Jiangfeng

2018-06-01

Quantum sensing based on nitrogen-vacancy (N -V ) centers in diamond has been developed as a powerful tool for microscopic magnetic resonance. However, the reported sensor-to-sample distance is limited within tens of nanometers resulting from the cubic decrease of the signal of spin fluctuation with the increasing distance. Here we extend the sensing distance to tens of micrometers by detecting spin polarization rather than spin fluctuation. We detect the mesoscopic magnetic resonance spectra of polarized electrons of a pentacene-doped crystal, measure its two typical decay times, and observe the optically enhanced spin polarization. This work paves the way for the N -V -based mesoscopic magnetic resonance spectroscopy and imaging at ambient conditions.

Effects of epitaxial structure and processing on electrical characteristics of InAs-based nBn infrared detectors

NASA Astrophysics Data System (ADS)

Du, X.; Savich, G. R.; Marozas, B. T.; Wicks, G. W.

2017-02-01

The conventional processing of the III-V nBn photodetectors defines mesa devices by etching the contact n-layer and stopping immediately above the barrier, i.e., a shallow etch. This processing enables great suppression of surface leakage currents without having to explore surface passivation techniques. However, devices that are made with this processing scheme are subject to lateral diffusion currents. To address the lateral diffusion current, we compare the effects of different processing approaches and epitaxial structures of nBn detectors. The conventional solution for eliminating lateral diffusion current, a deep etch through the barrier and the absorber, creates increased dark currents and an increased device failure rate. To avoid deep etch processing, a new device structure is proposed, the inverted-nBn structure. By comparing with the conventional nBn structure, the results show that the lateral diffusion current is effectively eliminated in the inverted-nBn structure without elevating the dark currents.

An asymmetric mesoscopic model for single bulges in RNA

NASA Astrophysics Data System (ADS)

de Oliveira Martins, Erik; Weber, Gerald

2017-10-01

Simple one-dimensional DNA or RNA mesoscopic models are of interest for their computational efficiency while retaining the key elements of the molecular interactions. However, they only deal with perfectly formed DNA or RNA double helices and consider the intra-strand interactions to be the same on both strands. This makes it difficult to describe highly asymmetric structures such as bulges and loops and, for instance, prevents the application of mesoscopic models to determine RNA secondary structures. Here we derived the conditions for the Peyrard-Bishop mesoscopic model to overcome these limitations and applied it to the calculation of single bulges, the smallest and simplest of these asymmetric structures. We found that these theoretical conditions can indeed be applied to any situation where stacking asymmetry needs to be considered. The full set of parameters for group I RNA bulges was determined from experimental melting temperatures using an optimization procedure, and we also calculated average opening profiles for several RNA sequences. We found that guanosine bulges show the strongest perturbation on their neighboring base pairs, considerably reducing the on-site interactions of their neighboring base pairs.

Fano effect in the transport of an artificial molecule

NASA Astrophysics Data System (ADS)

Norimoto, Shota; Nakamura, Shuji; Okazaki, Yuma; Arakawa, Tomonori; Asano, Kenichi; Onomitsu, Koji; Kobayashi, Kensuke; Kaneko, Nobu-hisa

2018-05-01

The Fano effect is a ubiquitous phenomenon arising from interference between a discrete energy state and an energy continuum. We explore this effect in an artificial molecule, namely, two lateral quantum dots (QDs) fabricated from a two-dimensional electron gas system and coupled in series. When the coupling between the leads and QDs is small, the charge stability diagram of the system shows a honeycomb lattice structure that is characteristic of a double QD system. As the coupling increases, a honeycomb structure consisting of the Fano resonances emerges. A numerical simulation based on the T-matrix method can satisfactorily reproduce our experimental observation. This report constitutes a clear example of the ubiquitous nature of the Fano effect in mesoscopic transport.

Insight into the CH3NH3PbI3/C interface in hole-conductor-free mesoscopic perovskite solar cells

NASA Astrophysics Data System (ADS)

Li, Jiangwei; Niu, Guangda; Li, Wenzhe; Cao, Kun; Wang, Mingkui; Wang, Liduo

2016-07-01

Perovskite solar cells (PSCs) with hole-conductor-free mesoscopic architecture have shown superb stability and great potential in practical application. The printable carbon counter electrodes take full responsibility of extracting holes from the active CH3NH3PbI3 absorbers. However, an in depth study of the CH3NH3PbI3/C interface properties, such as the structural formation process and the effect of interfacial conditions on hole extraction, is still lacking. Herein, we present, for the first time, an insight into the spatial confinement induced CH3NH3PbI3/C interface formation by in situ photoluminescence observations during the crystallization process of CH3NH3PbI3. The derived reaction kinetics allows a quantitative description of the perovskite formation process. In addition, we found that the interfacial contact between carbon and perovskite was dominant for hole extraction efficiency and associated with the photovoltaic parameter of short circuit current density (JSC). Consequently, we conducted a solvent vapor assisted process of PbI2 diffusion to carefully control the CH3NH3PbI3/C interface with less unreacted PbI2 barrier. The improvement of interface conditions thereby contributes to a high hole extraction proved by the charge extraction resistance and PL lifetime change, resulting in the increased JSC valve.Perovskite solar cells (PSCs) with hole-conductor-free mesoscopic architecture have shown superb stability and great potential in practical application. The printable carbon counter electrodes take full responsibility of extracting holes from the active CH3NH3PbI3 absorbers. However, an in depth study of the CH3NH3PbI3/C interface properties, such as the structural formation process and the effect of interfacial conditions on hole extraction, is still lacking. Herein, we present, for the first time, an insight into the spatial confinement induced CH3NH3PbI3/C interface formation by in situ photoluminescence observations during the crystallization process of CH3NH3PbI3. The derived reaction kinetics allows a quantitative description of the perovskite formation process. In addition, we found that the interfacial contact between carbon and perovskite was dominant for hole extraction efficiency and associated with the photovoltaic parameter of short circuit current density (JSC). Consequently, we conducted a solvent vapor assisted process of PbI2 diffusion to carefully control the CH3NH3PbI3/C interface with less unreacted PbI2 barrier. The improvement of interface conditions thereby contributes to a high hole extraction proved by the charge extraction resistance and PL lifetime change, resulting in the increased JSC valve. Electronic supplementary information (ESI) available: Fig. S1-S11, Tables S1, S2 and details of the Avrami model for reaction kinetics. See DOI: 10.1039/c6nr03359h

PREFACE: Advanced many-body and statistical methods in mesoscopic systems

NASA Astrophysics Data System (ADS)

Anghel, Dragos Victor; Sabin Delion, Doru; Sorin Paraoanu, Gheorghe

2012-02-01

It has increasingly been realized in recent times that the borders separating various subfields of physics are largely artificial. This is the case for nanoscale physics, physics of lower-dimensional systems and nuclear physics, where the advanced techniques of many-body theory developed in recent times could provide a unifying framework for these disciplines under the general name of mesoscopic physics. Other fields, such as quantum optics and quantum information, are increasingly using related methods. The 6-day conference 'Advanced many-body and statistical methods in mesoscopic systems' that took place in Constanta, Romania, between 27 June and 2 July 2011 was, we believe, a successful attempt at bridging an impressive list of topical research areas: foundations of quantum physics, equilibrium and non-equilibrium quantum statistics/fractional statistics, quantum transport, phases and phase transitions in mesoscopic systems/superfluidity and superconductivity, quantum electromechanical systems, quantum dissipation, dephasing, noise and decoherence, quantum information, spin systems and their dynamics, fundamental symmetries in mesoscopic systems, phase transitions, exactly solvable methods for mesoscopic systems, various extension of the random phase approximation, open quantum systems, clustering, decay and fission modes and systematic versus random behaviour of nuclear spectra. This event brought together participants from seventeen countries and five continents. Each of the participants brought considerable expertise in his/her field of research and, at the same time, was exposed to the newest results and methods coming from the other, seemingly remote, disciplines. The talks touched on subjects that are at the forefront of topical research areas and we hope that the resulting cross-fertilization of ideas will lead to new, interesting results from which everybody will benefit. We are grateful for the financial and organizational support from IFIN-HH, Ovidius University (where the conference took place), the Academy of Romanian Scientists and the Romanian National Authority for Scientific Research. This conference proceedings volume brings together some of the invited and contributed talks of the conference. The hope of the editors is that they will constitute reference material for applying many-body techniques to problems in mesoscopic and nuclear physics. We thank all the participants for their contribution to the success of this conference. D V Anghel and D S Delion IFIN-HH, Bucharest, Romania G S Paraoanu Aalto University, Finland Conference photograph

Ultrafast charge separation dynamics in opaque, operational dye-sensitized solar cells revealed by femtosecond diffuse reflectance spectroscopy

PubMed Central

Ghadiri, Elham; Zakeeruddin, Shaik M.; Hagfeldt, Anders; Grätzel, Michael; Moser, Jacques-E.

2016-01-01

Efficient dye-sensitized solar cells are based on highly diffusive mesoscopic layers that render these devices opaque and unsuitable for ultrafast transient absorption spectroscopy measurements in transmission mode. We developed a novel sub-200 femtosecond time-resolved diffuse reflectance spectroscopy scheme combined with potentiostatic control to study various solar cells in fully operational condition. We studied performance optimized devices based on liquid redox electrolytes and opaque TiO2 films, as well as other morphologies, such as TiO2 fibers and nanotubes. Charge injection from the Z907 dye in all TiO2 morphologies was observed to take place in the sub-200 fs time scale. The kinetics of electron-hole back recombination has features in the picosecond to nanosecond time scale. This observation is significantly different from what was reported in the literature where the electron-hole back recombination for transparent films of small particles is generally accepted to occur on a longer time scale of microseconds. The kinetics of the ultrafast electron injection remained unchanged for voltages between +500 mV and –690 mV, where the injection yield eventually drops steeply. The primary charge separation in Y123 organic dye based devices was clearly slower occurring in two picoseconds and no kinetic component on the shorter femtosecond time scale was recorded. PMID:27095505

Strain partitioning and deformation mode analysis of the normal faults at Red Mountain, Birmingham, Alabama

NASA Astrophysics Data System (ADS)

Wu, Schuman

1989-12-01

In a low-temperature environment, the thin-section scale rock-deformation mode is primarily a function of confining pressure and total strain at geological strain rates. A deformation mode diagram is constructed from published experimental data by plotting the deformation mode on a graph of total strain versus the confining pressure. Four deformation modes are shown on the diagram: extensional fracturing, mesoscopic faulting, incipient faulting, and uniform flow. By determining the total strain and the deformation mode of a naturally deformed sample, the confining pressure and hence the depth at which the rock was deformed can be evaluated. The method is applied to normal faults exposed on the gently dipping southeast limb of the Birmingham anticlinorium in the Red Mountain expressway cut in Birmingham, Alabama. Samples of the Ordovician Chickamauga Limestone within and adjacent to the faults contain brittle structures, including mesoscopic faults and veins, and ductile deformation features including calcite twins, intergranular and transgranular pressure solution, and deformed burrows. During compaction, a vertical shortening of about 45 to 80% in shale is indicated by deformed burrows and relative compaction of shale to burrows, about 6% in limestone by stylolites. The normal faults formed after the Ordovician rocks were consolidated because the faults and associated veins truncate the deformed burrows and stylolites, which truncate the calcite cement. A total strain of 2.0% was caused by mesoscopic faults during normal faulting. A later homogenous deformation, indicated by the calcite twins in veins, cement and fossil fragments, has its major principal shortening strain in the dip direction at a low angle (about 22°) to bedding. The strain magnitude is about 2.6%. By locating the observed data on the deformation mode diagram, it is found that the normal faulting characterized by brittle deformation occurred under low confining pressure (< 18 MPa) at shallow depth (< 800 m), and the homogenous horizontal compression characterized by uniform flow occurred under higher confining pressure (at least 60 MPa) at greater depth (> 2.5 km).

Opposing Effects of cAMP and T259 Phosphorylation on Plasma Membrane Diffusion of the Water Channel Aquaporin-5 in Madin-Darby Canine Kidney Cells

PubMed Central

Koffman, Jennifer S.; Arnspang, Eva C.; Marlar, Saw; Nejsum, Lene N.

2015-01-01

Aquaporin-5 (AQP5) facilitates passive water transport in glandular epithelia in response to secretory stimuli via intracellular pathways involving calcium release, cAMP and protein kinase A (PKA). In epithelial plasma membranes, AQP5 may be acutely regulated to facilitate water transport in response to physiological stimuli by changes in protein modifications, interactions with proteins and lipids, nanoscale membrane domain organization, and turnover rates. Such regulatory mechanisms could potentially be associated with alteration of diffusion behavior, possibly resulting in a change in the plasma membrane diffusion coefficient of AQP5. We aimed to test the short-term regulatory effects of the above pathways, by measuring lateral diffusion of AQP5 and an AQP5 phospho-mutant, T259A, using k-space Image Correlation Spectroscopy of quantum dot- and EGFP-labeled AQP5. Elevated cAMP and PKA inhibition significantly decreased lateral diffusion of AQP5, whereas T259A mutation showed opposing effects; slowing diffusion without stimulation and increasing diffusion to basal levels after cAMP elevation. Thus, lateral diffusion of AQP5 is significantly regulated by cAMP, PKA, and T259 phosphorylation, which could be important for regulating water flow in glandular secretions. PMID:26218429

Communication: Anion-specific response of mesoscopic organization in ionic liquids upon pressurization

NASA Astrophysics Data System (ADS)

Lo Celso, Fabrizio; Triolo, Alessandro; Gontrani, Lorenzo; Russina, Olga

2018-06-01

One of the outstanding features of ionic liquids is their inherently hierarchical structural organization at mesoscopic spatial scales. Recently experimental and computational studies showed the fading of this feature when pressurising. Here we use simulations to show that this effect is not general: appropriate anion choice leads to an obstinate resistance against pressurization.

Many-Worlds Interpretation of Quantum Theory and Mesoscopic Anthropic Principle

NASA Astrophysics Data System (ADS)

Kamenshchik, A. Yu.; Teryaev, O. V.

2008-10-01

We suggest to combine the Anthropic Principle with Many-Worlds Interpretation of Quantum Theory. Realizing the multiplicity of worlds it provides an opportunity of explanation of some important events which are assumed to be extremely improbable. The Mesoscopic Anthropic Principle suggested here is aimed to explain appearance of such events which are necessary for emergence of Life and Mind. It is complementary to Cosmological Anthropic Principle explaining the fine tuning of fundamental constants. We briefly discuss various possible applications of Mesoscopic Anthropic Principle including the Solar Eclipses and assembling of complex molecules. Besides, we address the problem of Time's Arrow in the framework of Many-World Interpretation. We suggest the recipe for disentangling of quantities defined by fundamental physical laws and by an anthropic selection.

Mesoscopic fluctuations of the population of a qubit in a strong alternating field

NASA Astrophysics Data System (ADS)

Denisenko, M. V.; Satanin, A. M.

2016-12-01

Fluctuations of the population of a Josephson qubit in an alternating field, which is a superposition of electromagnetic pulses with large amplitudes, are studied. It is shown that the relative phase of pulses is responsible for the rate of Landau-Zener transitions and, correspondingly, for the frequency of transitions between adiabatic states. The durations of pulses incident on the qubit are controlled with an accuracy of the field period, which results in strong mesoscopic fluctuations of the population of the qubit. Similar to the magnetic field in mesoscopic physics, the relative phase of pulses can destroy the interference pattern of the population of the qubit. The influence of the duration of the pulse and noise on the revealed fluctuation effects is studied.

Static and Dynamic Effects of Lateral Carrier Diffusion in Semiconductor Lasers

NASA Technical Reports Server (NTRS)

Li, Jian-Zhong; Cheung, Samson H.; Ning, C. Z.; Biegel, Bryan A. (Technical Monitor)

2002-01-01

Electron and hole diffusions in the plane of semiconductor quantum wells play an important part in the static and dynamic operations of semiconductor lasers. It is well known that the value of diffusion coefficients affects the threshold pumping current of a semiconductor laser. At the same time, the strength of carrier diffusion process is expected to affect the modulation bandwidth of an AC-modulated laser. It is important not only to investigate the combined DC and AC effects due to carrier diffusion, but also to separate the AC effects from that of the combined effects in order to provide design insights for high speed modulation. In this presentation, we apply a hydrodynamic model developed by the present authors recently from the semiconductor Bloch equations. The model allows microscopic calculation of the lateral carrier diffusion coefficient, which is a nonlinear function of the carrier density and plasma temperature. We first studied combined AC and DC effects of lateral carrier diffusion by studying the bandwidth dependence on diffusion coefficient at a given DC current under small signal modulation. The results show an increase of modulation bandwidth with decrease in the diffusion coefficient. We simultaneously studied the effects of nonlinearity in the diffusion coefficient. To clearly identify how much of the bandwidth increase is a result of decrease in the threshold pumping current for smaller diffusion coefficient, thus an effective increase of DC pumping, we study the bandwidth dependence on diffusion coefficient at a given relative pumping. A detailed comparison of the two cases will be presented.

Thermal coupling effect on the vortex dynamics of superconducting thin films: time-dependent Ginzburg–Landau simulations

NASA Astrophysics Data System (ADS)

Jing, Ze; Yong, Huadong; Zhou, Youhe

2018-05-01

In this paper, vortex dynamics of superconducting thin films are numerically investigated by the generalized time-dependent Ginzburg–Landau (TDGL) theory. Interactions between vortex motion and the motion induced energy dissipation is considered by solving the coupled TDGL equation and the heat diffusion equation. It is found that thermal coupling has significant effects on the vortex dynamics of superconducting thin films. Branching in the vortex penetration path originates from the coupling between vortex motion and the motion induced energy dissipation. In addition, the environment temperature, the magnetic field ramp rate and the geometry of the superconducting film also greatly influence the vortex dynamic behaviors. Our results provide new insights into the dynamics of superconducting vortices, and give a mesoscopic understanding on the channeling and branching of vortex penetration paths during flux avalanches.

Near-band-edge optical responses of solution-processed organic-inorganic hybrid perovskite CH3NH3PbI3 on mesoporous TiO2 electrodes

NASA Astrophysics Data System (ADS)

Yamada, Yasuhiro; Nakamura, Toru; Endo, Masaru; Wakamiya, Atsushi; Kanemitsu, Yoshihiko

2014-03-01

We studied the near-band-edge optical responses of solution-processed CH3NH3PbI3 on mesoporous TiO2 electrodes, which is utilized in mesoscopic heterojunction solar cells. Photoluminescence (PL) and PL excitation spectra peaks appear at 1.60 and 1.64 eV, respectively. The transient absorption spectrum shows a negative peak at 1.61 eV owing to photobleaching at the band-gap energy, indicating a direct band-gap semiconductor. On the basis of the temperature-dependent PL and diffuse reflectance spectra, we clarified that the absorption tail at room temperature is explained in terms of an Urbach tail and consistently determined the band-gap energy to be ˜1.61 eV at room temperature.

Dynamic cross-correlations between entangled biofilaments as they diffuse

PubMed Central

Tsang, Boyce; Dell, Zachary E.; Jiang, Lingxiang; Schweizer, Kenneth S.; Granick, Steve

2017-01-01

Entanglement in polymer and biological physics involves a state in which linear interthreaded macromolecules in isotropic liquids diffuse in a spatially anisotropic manner beyond a characteristic mesoscopic time and length scale (tube diameter). The physical reason is that linear macromolecules become transiently localized in directions transverse to their backbone but diffuse with relative ease parallel to it. Within the resulting broad spectrum of relaxation times there is an extended period before the longest relaxation time when filaments occupy a time-averaged cylindrical space of near-constant density. Here we show its implication with experiments based on fluorescence tracking of dilutely labeled macromolecules. The entangled pairs of aqueous F-actin biofilaments diffuse with separation-dependent dynamic cross-correlations that exceed those expected from continuum hydrodynamics up to strikingly large spatial distances of ≈15 µm, which is more than 104 times the size of the solvent water molecules in which they are dissolved, and is more than 50 times the dynamic tube diameter, but is almost equal to the filament length. Modeling this entangled system as a collection of rigid rods, we present a statistical mechanical theory that predicts these long-range dynamic correlations as an emergent consequence of an effective long-range interpolymer repulsion due to the de Gennes correlation hole, which is a combined consequence of chain connectivity and uncrossability. The key physical assumption needed to make theory and experiment agree is that solutions of entangled biofilaments localized in tubes that are effectively dynamically incompressible over the relevant intermediate time and length scales. PMID:28283664

Lateral diffusion and signaling of receptor for advanced glycation end-products (RAGE): a receptor involved in chronic inflammation.

PubMed

Syed, Aleem; Zhu, Qiaochu; Smith, Emily A

2018-01-01

Membrane diffusion is one of the key mechanisms in the cellular function of receptors. The signaling of receptors for advanced glycation end-products (RAGE) has been extensively studied in the context of several pathological conditions, however, very little is known about RAGE diffusion. To fill this gap, RAGE lateral diffusion is probed in native, cholesterol-depleted, and cytoskeleton-altered cellular conditions. In native GM07373 cellular conditions, RAGE has a 90% mobile fraction and an average diffusion coefficient of 0.3 μm 2 /s. When depolymerization of the actin cytoskeleton is inhibited with the small molecule jasplakinolide (Jsp), the RAGE mobile fraction and diffusion coefficient decrease by 22 and 37%, respectively. In contrast, depolymerizing the filamentous actin cytoskeleton using the small molecule cytochalasin D (CD) does not alter the RAGE diffusion properties. There is a 70 and 50% decrease in phosphorylation of extracellular signal-regulated kinase (p-ERK) when the actin cytoskeleton is disrupted by CD or Jsp, respectively, in RAGE-expressing GM07373 cells. Disrupting the actin cytoskeleton in GM07373 cells that do not express detectable amounts of RAGE results in no change in p-ERK. Cholesterol depletion results in no statistically significant change in the diffusion properties of RAGE or p-ERK. This work presents a strong link between the actin cytoskeleton and RAGE diffusion and downstream signaling, and serves to further our understanding of the factors influencing RAGE lateral diffusion.

2D Lattice Boltzmann Simulation Of Chemical Reactions Within Rayleigh-Bénard And Poiseuille-Bénard Convection Systems

NASA Astrophysics Data System (ADS)

Amaya-Ventura, Gilberto; Rodríguez-Romo, Suemi

2011-09-01

This paper deals with the computational simulation of the reaction-diffusion-advection phenomena emerging in Rayleigh-Bénard (RB) and Poiseuille-Bénard reactive convection systems. We use the Boussinesq's approximation for buoyancy forces and the Lattice Boltzmann method (LBM). The first kinetic mesoscopic model proposed here is based on the discrete Boltzmann equation needed to solve the momentum balance coupled with buoyancy forces. Then, a second lattice Boltzmann algorithm is applied to solve the reaction-diffusion-advection equation to calculate the evolution of the chemical species concentration. We use a reactive system composed by nitrous oxide (so call laughing gas) in air as an example; its spatio-temporal decomposition is calculated. Two cases are considered, a rectangular enclosed cavity and an open channel. The simulations are performed at low Reynolds numbers and in a steady state between the first and second thermo-hydrodynamic instabilities. The results presented here, for the thermo-hydrodynamic behavior, are in good agreement with experimental data; while our| chemical kinetics simulation yields expected results. Some applications of our approach are related to chemical reactors and atmospheric phenomena, among others.

Entropic trapping of macromolecules by mesoscopic periodic voids in a polymer hydrogel

NASA Astrophysics Data System (ADS)

Liu, Lei; Li, Pusheng; Asher, Sanford A.

1999-01-01

The separation of macromolecules such as polymers and DNA by means of electrophoresis, gel permeation chromatography or filtration exploits size-dependent differences in the time it takes for the molecules to migrate through a random porous network. Transport through the gel matrices, which usually consist of full swollen crosslinked polymers, depends on the relative size of the macromolecule compared with the pore radius. Sufficiently small molecules are thought to adopt an approximately spherical conformation when diffusing through the gel matrix, whereas larger ones are forced to migrate in a snake-like fashion. Molecules of intermediate size, however, can get temporarily trapped in the largest pores of the matrix, where the molecule can extend and thus maximize its conformational entropy. This `entropic trapping' is thought to increase the dependence of diffusion rate on molecular size. Here we report the direct experimental verification of this phenomenon. Bragg diffraction from a hydrogel containing a periodic array of monodisperse water voids confirms that polymers of different weights partition between the hydrogel matrix and the water voids according to the predictions of the entropic trapping theory. Our approach might also lead to the design of improved separation media based on entropic trapping.

Notch-mediated lateral inhibition regulates proneural wave propagation when combined with EGF-mediated reaction diffusion

PubMed Central

Sato, Makoto; Yasugi, Tetsuo; Minami, Yoshiaki; Miura, Takashi; Nagayama, Masaharu

2016-01-01

Notch-mediated lateral inhibition regulates binary cell fate choice, resulting in salt and pepper patterns during various developmental processes. However, how Notch signaling behaves in combination with other signaling systems remains elusive. The wave of differentiation in the Drosophila visual center or “proneural wave” accompanies Notch activity that is propagated without the formation of a salt and pepper pattern, implying that Notch does not form a feedback loop of lateral inhibition during this process. However, mathematical modeling and genetic analysis clearly showed that Notch-mediated lateral inhibition is implemented within the proneural wave. Because partial reduction in EGF signaling causes the formation of the salt and pepper pattern, it is most likely that EGF diffusion cancels salt and pepper pattern formation in silico and in vivo. Moreover, the combination of Notch-mediated lateral inhibition and EGF-mediated reaction diffusion enables a function of Notch signaling that regulates propagation of the wave of differentiation. PMID:27535937

Mesoscopic Physics of Electronic and Optical Systems

NASA Astrophysics Data System (ADS)

Hentschel, Martina

2005-10-01

The progress in fabricating and controlling mesoscopic samples opens the possibility to investigate many-body phenomena on the nanoscopic scale, for example in quantum dots or nanoparticles. We recently studied the many-body signatures in the photoabsorption cross-section of those systems. Two counteracting many-body effects (Anderson's orthogonality catastrophe and Mahan's exciton) lead to deviations from the naively expected cross-section and to Fermi-edge singularities in the form of a peaked or rounded edge. We found that mesoscopic-coherent systems can show a many-body response that differs considerably from macroscopic samples. The reason for this lies in the finite number of particles and the lack of rotational symmetry in generic mesoscopic systems. The properties of mesoscopic systems crucially depend on whether the corresponding classical systems possess chaotic or integrable dynamics. Signatures of the underlying classical dynamics in quantum-mechanical behavior are searched for in the field of quantum chaos. We study it in the context of optical microresonators-billiards where reflection at hard walls is replaced by confinement due to total internal reflection. The relation between the simple ray model and the wave description (that has to be used when the wavelength becomes comparable to the system size) is called ``ray-wave correspondence.'' It can be established in both real and phase space. For the latter we generalized the concept of Husimi functions to dielectric boundaries. Although the ray model provides a qualitative understanding of the system properties even into the wave limit, semiclassical corrections of the ray picture are necessary in order to establish quantitative correspondence.

Final Report

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

Stinis, Panos

2016-08-07

This is the final report for the work conducted at the University of Minnesota (during the period 12/01/12-09/18/14) by PI Panos Stinis as part of the "Collaboratory on Mathematics for Mesoscopic Modeling of Materials" (CM4). CM4 is a multi-institution DOE-funded project whose aim is to conduct basic and applied research in the emerging field of mesoscopic modeling of materials.

Mesoscopic interactions and species coexistence in evolutionary game dynamics of cyclic competitions.

PubMed

Cheng, Hongyan; Yao, Nan; Huang, Zi-Gang; Park, Junpyo; Do, Younghae; Lai, Ying-Cheng

2014-12-15

Evolutionary dynamical models for cyclic competitions of three species (e.g., rock, paper, and scissors, or RPS) provide a paradigm, at the microscopic level of individual interactions, to address many issues in coexistence and biodiversity. Real ecosystems often involve competitions among more than three species. By extending the RPS game model to five (rock-paper-scissors-lizard-Spock, or RPSLS) mobile species, we uncover a fundamental type of mesoscopic interactions among subgroups of species. In particular, competitions at the microscopic level lead to the emergence of various local groups in different regions of the space, each involving three species. It is the interactions among the groups that fundamentally determine how many species can coexist. In fact, as the mobility is increased from zero, two transitions can occur: one from a five- to a three-species coexistence state and another from the latter to a uniform, single-species state. We develop a mean-field theory to show that, in order to understand the first transition, group interactions at the mesoscopic scale must be taken into account. Our findings suggest, more broadly, the importance of mesoscopic interactions in coexistence of great many species.

Lead iodide perovskite sensitized all-solid-state submicron thin film mesoscopic solar cell with efficiency exceeding 9%.

PubMed

Kim, Hui-Seon; Lee, Chang-Ryul; Im, Jeong-Hyeok; Lee, Ki-Beom; Moehl, Thomas; Marchioro, Arianna; Moon, Soo-Jin; Humphry-Baker, Robin; Yum, Jun-Ho; Moser, Jacques E; Grätzel, Michael; Park, Nam-Gyu

2012-01-01

We report on solid-state mesoscopic heterojunction solar cells employing nanoparticles (NPs) of methyl ammonium lead iodide (CH(3)NH(3))PbI(3) as light harvesters. The perovskite NPs were produced by reaction of methylammonium iodide with PbI(2) and deposited onto a submicron-thick mesoscopic TiO(2) film, whose pores were infiltrated with the hole-conductor spiro-MeOTAD. Illumination with standard AM-1.5 sunlight generated large photocurrents (J(SC)) exceeding 17 mA/cm(2), an open circuit photovoltage (V(OC)) of 0.888 V and a fill factor (FF) of 0.62 yielding a power conversion efficiency (PCE) of 9.7%, the highest reported to date for such cells. Femto second laser studies combined with photo-induced absorption measurements showed charge separation to proceed via hole injection from the excited (CH(3)NH(3))PbI(3) NPs into the spiro-MeOTAD followed by electron transfer to the mesoscopic TiO(2) film. The use of a solid hole conductor dramatically improved the device stability compared to (CH(3)NH(3))PbI(3) -sensitized liquid junction cells.

Lead Iodide Perovskite Sensitized All-Solid-State Submicron Thin Film Mesoscopic Solar Cell with Efficiency Exceeding 9%

PubMed Central

Kim, Hui-Seon; Lee, Chang-Ryul; Im, Jeong-Hyeok; Lee, Ki-Beom; Moehl, Thomas; Marchioro, Arianna; Moon, Soo-Jin; Humphry-Baker, Robin; Yum, Jun-Ho; Moser, Jacques E.; Grätzel, Michael; Park, Nam-Gyu

2012-01-01

We report on solid-state mesoscopic heterojunction solar cells employing nanoparticles (NPs) of methyl ammonium lead iodide (CH3NH3)PbI3 as light harvesters. The perovskite NPs were produced by reaction of methylammonium iodide with PbI2 and deposited onto a submicron-thick mesoscopic TiO2 film, whose pores were infiltrated with the hole-conductor spiro-MeOTAD. Illumination with standard AM-1.5 sunlight generated large photocurrents (JSC) exceeding 17 mA/cm2, an open circuit photovoltage (VOC) of 0.888 V and a fill factor (FF) of 0.62 yielding a power conversion efficiency (PCE) of 9.7%, the highest reported to date for such cells. Femto second laser studies combined with photo-induced absorption measurements showed charge separation to proceed via hole injection from the excited (CH3NH3)PbI3 NPs into the spiro-MeOTAD followed by electron transfer to the mesoscopic TiO2 film. The use of a solid hole conductor dramatically improved the device stability compared to (CH3NH3)PbI3 -sensitized liquid junction cells. PMID:22912919

The development of a 3D mesoscopic model of metallic foam based on an improved watershed algorithm

NASA Astrophysics Data System (ADS)

Zhang, Jinhua; Zhang, Yadong; Wang, Guikun; Fang, Qin

2018-06-01

The watershed algorithm has been used widely in the x-ray computed tomography (XCT) image segmentation. It provides a transformation defined on a grayscale image and finds the lines that separate adjacent images. However, distortion occurs in developing a mesoscopic model of metallic foam based on XCT image data. The cells are oversegmented at some events when the traditional watershed algorithm is used. The improved watershed algorithm presented in this paper can avoid oversegmentation and is composed of three steps. Firstly, it finds all of the connected cells and identifies the junctions of the corresponding cell walls. Secondly, the image segmentation is conducted to separate the adjacent cells. It generates the lost cell walls between the adjacent cells. Optimization is then performed on the segmentation image. Thirdly, this improved algorithm is validated when it is compared with the image of the metallic foam, which shows that it can avoid the image segmentation distortion. A mesoscopic model of metallic foam is thus formed based on the improved algorithm, and the mesoscopic characteristics of the metallic foam, such as cell size, volume and shape, are identified and analyzed.

Microscopic theory of linear light scattering from mesoscopic media and in near-field optics.

PubMed

Keller, Ole

2005-08-01

On the basis of quantum mechanical response theory a microscopic propagator theory of linear light scattering from mesoscopic systems is presented. The central integral equation problem is transferred to a matrix equation problem by discretization in transitions between pairs of (many-body) energy eigenstates. The local-field calculation which appears from this approach is valid down to the microscopic region. Previous theories based on the (macroscopic) dielectric constant concept make use of spatial (geometrical) discretization and cannot in general be trusted on the mesoscopic length scale. The present theory can be applied to light scattering studies in near-field optics. After a brief discussion of the macroscopic integral equation problem a microscopic potential description of the scattering process is established. In combination with the use of microscopic electromagnetic propagators the formalism allows one to make contact to the macroscopic theory of light scattering and to the spatial photon localization problem. The quantum structure of the microscopic conductivity response tensor enables one to establish a clear physical picture of the origin of local-field phenomena in mesoscopic and near-field optics. The Huygens scalar propagator formalism is revisited and its generality in microscopic physics pointed out.

Lipid diffusion in alcoholic environment.

PubMed

Rifici, Simona; Corsaro, Carmelo; Crupi, Cristina; Nibali, Valeria Conti; Branca, Caterina; D'Angelo, Giovanna; Wanderlingh, Ulderico

2014-08-07

We have studied the effects of a high concentration of butanol and octanol on the phase behavior and on the lateral mobility of 1,2-palmitoyl-sn-glycero-3-phosphocholine (DPPC) by means of differential scanning calorimetry and pulsed-gradient stimulated-echo (PGSTE) NMR spectroscopy. A lowering of the lipid transition from the gel to the liquid-crystalline state for the membrane-alcohol systems has been observed. NMR measurements reveal three distinct diffusions in the DPPC-alcohol systems, characterized by a high, intermediate, and slow diffusivity, ascribed to the water, the alcohol, and the lipid, respectively. The lipid diffusion process is promoted in the liquid phase while it is hindered in the interdigitated phase due to the presence of alcohols. Furthermore, in the interdigitated phase, lipid lateral diffusion coefficients show a slight temperature dependence. To the best of our knowledge, this is the first time that lateral diffusion coefficients on alcohol with so a long chain, and at low temperatures, are reported. By the Arrhenius plots of the temperature dependence of the diffusion coefficients, we have evaluated the apparent activation energy in both the liquid and in the interdigitated phase. The presence of alcohol increases this value in both phases. An explanation in terms of a free volume model that takes into account also for energy factors is proposed.

The Generalized Hellmann-Feynman Theorem Approach to Quantum Effects of Mesoscopic Complicated Coupling Circuit at Finite Temperature

NASA Astrophysics Data System (ADS)

Wang, Xiu-Xia

2016-02-01

By employing the generalized Hellmann-Feynman theorem, the quantization of mesoscopic complicated coupling circuit is proposed. The ensemble average energy, the energy fluctuation and the energy distribution are investigated at finite temperature. It is shown that the generalized Hellmann-Feynman theorem plays the key role in quantizing a mesoscopic complicated coupling circuit at finite temperature, and when the temperature is lower than the specific temperature, the value of (\\vartriangle {hat {H}})2 is almost zero and the values of e and (\\vartriangle hat {{H}})2are basically constant, but while the temperature rises to the specific temperature, both of them move upward rapidly. The energy fluctuation of the system becomes larger when the coupling inductance is larger or the coupling capacitance is smaller.

Phoretic self-propulsion: a mesoscopic description of reaction dynamics that powers motion.

PubMed

de Buyl, Pierre; Kapral, Raymond

2013-02-21

The fabrication of synthetic self-propelled particles and the experimental investigations of their dynamics have stimulated interest in self-generated phoretic effects that propel nano- and micron-scale objects. Theoretical modeling of these phenomena is often based on a continuum description of the solvent for different phoretic propulsion mechanisms, including, self-electrophoresis, self-diffusiophoresis and self-thermophoresis. The work in this paper considers various types of catalytic chemical reaction at the motor surface and in the bulk fluid that come into play in mesoscopic descriptions of the dynamics. The formulation is illustrated by developing the mesoscopic reaction dynamics for exothermic and dissociation reactions that are used to power motor motion. The results of simulations of the self-propelled dynamics of composite Janus particles by these mechanisms are presented.

Mesoscopic fluctuations of the population of a qubit in a strong alternating field

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

Denisenko, M. V., E-mail: mar.denisenko@gmail.com; Satanin, A. M.

Fluctuations of the population of a Josephson qubit in an alternating field, which is a superposition of electromagnetic pulses with large amplitudes, are studied. It is shown that the relative phase of pulses is responsible for the rate of Landau–Zener transitions and, correspondingly, for the frequency of transitions between adiabatic states. The durations of pulses incident on the qubit are controlled with an accuracy of the field period, which results in strong mesoscopic fluctuations of the population of the qubit. Similar to the magnetic field in mesoscopic physics, the relative phase of pulses can destroy the interference pattern of themore » population of the qubit. The influence of the duration of the pulse and noise on the revealed fluctuation effects is studied.« less

Harvesting dissipated energy with a mesoscopic ratchet

NASA Astrophysics Data System (ADS)

Roche, B.; Roulleau, P.; Jullien, T.; Jompol, Y.; Farrer, I.; Ritchie, D. A.; Glattli, D. C.

2015-04-01

The search for new efficient thermoelectric devices converting waste heat into electrical energy is of major importance. The physics of mesoscopic electronic transport offers the possibility to develop a new generation of nanoengines with high efficiency. Here we describe an all-electrical heat engine harvesting and converting dissipated power into an electrical current. Two capacitively coupled mesoscopic conductors realized in a two-dimensional conductor form the hot source and the cold converter of our device. In the former, controlled Joule heating generated by a voltage-biased quantum point contact results in thermal voltage fluctuations. By capacitive coupling the latter creates electric potential fluctuations in a cold chaotic cavity connected to external leads by two quantum point contacts. For unequal quantum point contact transmissions, a net electrical current is observed proportional to the heat produced.

Macroscopic and mesoscopic approach to the alkali-silica reaction in concrete

NASA Astrophysics Data System (ADS)

Grymin, Witold; Koniorczyk, Marcin; Pesavento, Francesco; Gawin, Dariusz

2018-01-01

A model of the alkali-silica reaction, which takes into account couplings between thermal, hygral, mechanical and chemical phenomena in concrete, has been discussed. The ASR may be considered at macroscopic or mesoscopic scale. The main features of each approach have been summarized and development of the model for both scales has been briefly described. Application of the model to experimental results for both scales has been presented. Even though good accordance of the model has been obtained for both approaches, consideration of the model at the mesoscopic scale allows to model different mortar mixes, prepared with the same aggregate, but of different grain size, using the same set of parameters. It enables also to predict reaction development assuming different alkali sources, such as de-icing salts or alkali leaching.

Mapping Ionic Currents and Reactivity on the Nanoscale: Electrochemical Strain Microscopy

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

Kalinin, S.V.

2010-10-19

Solid-state electrochemical processes in oxides underpin a broad spectrum of energy and information storage devices, ranging from Li-ion and Li-air batteries, to solid oxide fuel cells (SOFC) to electroresistive and memristive systems. These functionalities are controlled by the bias-driven diffusive and electromigration transport of mobile ionic species, as well as intricate a set of electrochemical and defect-controlled reactions at interfaces and in bulk. Despite the wealth of device-level and atomistic studies, little is known on the mesoscopic mechanisms of ion diffusion and electronic transport on the level of grain clusters, individual grains, and extended defects. The development of the capabilitymore » for probing ion transport on the nanometer scale is a key to deciphering complex interplay between structure, functionality, and performance in these systems. Here we introduce Electrochemical Strain Microscopy, a scanning probe microscopy technique based on strong strain-bias coupling in the systems in which local ion concentrations are changed by electrical fields. The imaging capability, as well as time- and voltage spectroscopies analogous to traditional current based electrochemical characterization methods are developed. The reversible intercalation of Li and mapping electrochemical activity in LiCoO2 is demonstrated, illustrating higher Li diffusivity at non-basal planes and grain boundaries. In Si-anode device structure, the direct mapping of Li diffusion at extended defects and evolution of Li-activity with charge state is explored. The electrical field-dependence of Li mobility is studied to determine the critical bias required for the onset of electrochemical transformation, allowing reaction and diffusion processes in the battery system to be separated at each location. Finally, the applicability of ESM for probing oxygen vacancy diffusion and oxygen reduction/evolution reactions is illustrated, and the high resolution ESM maps are correlated with aberration corrected scanning transmission electron microscopy imaging. The future potential for deciphering mechanisms of electrochemical transformations on an atomically-defined single-defect level is discussed.« less

Thermodynamics of the general diffusion process: Equilibrium supercurrent and nonequilibrium driven circulation with dissipation

NASA Astrophysics Data System (ADS)

Qian, H.

2015-07-01

Unbalanced probability circulation, which yields cyclic motions in phase space, is the defining characteristics of a stationary diffusion process without detailed balance. In over-damped soft matter systems, such behavior is a hallmark of the presence of a sustained external driving force accompanied with dissipations. In an under-damped and strongly correlated system, however, cyclic motions are often the consequences of a conservative dynamics. In the present paper, we give a novel interpretation of a class of diffusion processes with stationary circulation in terms of a Maxwell-Boltzmann equilibrium in which cyclic motions are on the level set of stationary probability density function thus non-dissipative, e.g., a supercurrent. This implies an orthogonality between stationary circulation J ss ( x) and the gradient of stationary probability density f ss ( x) > 0. A sufficient and necessary condition for the orthogonality is a decomposition of the drift b( x) = j( x) + D( x)∇φ( x) where ∇ṡ j( x) = 0 and j( x) ṡ∇φ( x) = 0. Stationary processes with such Maxwell-Boltzmann equilibrium has an underlying conservative dynamics , and a first integral ϕ( x) ≡ -ln f ss (x) = const, akin to a Hamiltonian system. At all time, an instantaneous free energy balance equation exists for a given diffusion system; and an extended energy conservation law among an entire family of diffusion processes with different parameter α can be established via a Helmholtz theorem. For the general diffusion process without the orthogonality, a nonequilibrium cycle emerges, which consists of external driven φ-ascending steps and spontaneous φ-descending movements, alternated with iso-φ motions. The theory presented here provides a rich mathematical narrative for complex mesoscopic dynamics, with contradistinction to an earlier one [H. Qian et al., J. Stat. Phys. 107, 1129 (2002)]. This article is supplemented with comments by H. Ouerdane and a final reply by the author.

Increased Accuracy of Ligand Sensing by Receptor Internalization and Lateral Receptor Diffusion

NASA Astrophysics Data System (ADS)

Aquino, Gerardo; Endres, Robert

2010-03-01

Many types of cells can sense external ligand concentrations with cell-surface receptors at extremely high accuracy. Interestingly, ligand-bound receptors are often internalized, a process also known as receptor-mediated endocytosis. While internalization is involved in a vast number of important functions for the life of a cell, it was recently also suggested to increase the accuracy of sensing ligand as overcounting of the same ligand molecules is reduced. A similar role may be played by receptor diffusion om the cell membrane. Fast, lateral receptor diffusion is known to be relevant in neurotransmission initiated by release of neurotransmitter glutamate in the synaptic cleft between neurons. By binding ligand and removal by diffusion from the region of release of the neurotransmitter, diffusing receptors can be reasonably expected to reduce the local overcounting of the same ligand molecules in the region of signaling. By extending simple ligand-receptor models to out-of-equilibrium thermodynamics, we show that both receptor internalization and lateral diffusion increase the accuracy with which cells can measure ligand concentrations in the external environment. We confirm this with our model and give quantitative predictions for experimental parameters values. We give quantitative predictions, which compare favorably to experimental data of real receptors.

Investigating axial diffusion in cylindrical pores using confocal single-particle fluorescence correlation spectroscopy.

PubMed

Chen, Fang; Neupane, Bhanu; Li, Peiyuan; Su, Wei; Wang, Gufeng

2016-08-01

We explored the feasibility of using confocal fluorescence correlation spectroscopy to study small nanoparticle diffusion in hundred-nanometer-sized cylindrical pores. By modeling single particle diffusion in tube-like confined three-dimensional space aligned parallel to the confocal optical axis, we showed that two diffusion dynamics can be observed in both original intensity traces and the autocorrelation functions (ACFs): the confined two-dimensional lateral diffusion and the unconfined one-dimensional (1D) axial diffusion. The separation of the axial and confined lateral diffusion dynamics provides an opportunity to study diffusions in different dimensions separately. We further experimentally studied 45 nm carboxylated polystyrene particles diffusing in 300 nm alumina pores. The experimental data showed consistency with the simulation. To extract the accurate axial diffusion coefficient, we found that a 1D diffusion model with a Lorentzian axial collection profile needs to be used to analyze the experimental ACFs. The diffusion of the 45 nm nanoparticles in polyethyleneglycol-passivated 300 nm pores slowed down by a factor of ∼2, which can be satisfactorily explained by hydrodynamic frictions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Current driven transition from Abrikosov-Josephson to Josephson-like vortex in mesoscopic lateral S/S’/S superconducting weak links

PubMed Central

Carapella, G.; Sabatino, P.; Barone, C.; Pagano, S.; Gombos, M.

2016-01-01

Vortices are topological defects accounting for many important effects in superconductivity, superfluidity, and magnetism. Here we address the stability of a small number of such excitations driven by strong external forces. We focus on Abrikosov-Josephson vortex that appears in lateral superconducting S/S’/S weak links with suppressed superconductivity in S’. In such a system the vortex is nucleated and confined in the narrow S’ region by means of a small magnetic field and moves under the effect of a force proportional to an applied electrical current with a velocity proportional to the measured voltage. Our numerical simulations show that when a slow moving Abrikosov-Josephson vortex is driven by a strong constant current it becomes unstable with respect to a faster moving excitation: the Josephon-like vortex. Such a current-driven transition explains the structured dissipative branches that we observe in the voltage-current curve of the weak link. When vortex matter is strongly confined phenomena as magnetoresistance oscillations and reentrance of superconductivity can possibly occur. We experimentally observe these phenomena in our weak links. PMID:27752137

Non-Linear Meissner Effect in Mesoscopic Superconductors

DTIC Science & Technology

1998-06-01

6525 ED Nijmegen, the Netherlands Abstract. Magnetization measurements on superconducting bulk samples and large radius cylinders had resulted in the...Phenomenological London’s theory that is found to be violated in recent magnetization measurements in superconducting mesoscopic discs that exhibit a...quantity. Recently Geim et al [1] used sub-micron Hall probes to detect the magnetization of thin (thickness down to d - 0.07 pm) single superconducting

Using Models at the Mesoscopic Scale in Teaching Physics: Two Experimental Interventions in Solid Friction and Fluid Statics

ERIC Educational Resources Information Center

Besson, Ugo; Viennot, Laurence

2004-01-01

This article examines the didactic suitability of introducing models at an intermediate (i.e. mesoscopic) scale in teaching certain subjects, at an early stage. The design and evaluation of two short sequences based on this rationale will be outlined: one bears on propulsion by solid friction, the other on fluid statics in the presence of gravity.…

Fabrication methods for mesoscopic flying vehicle

NASA Astrophysics Data System (ADS)

Cheng, Yih-Lin

2001-10-01

Small-scale flying vehicles are attractive tools for atmospheric science research. A centimeter-size mesoscopic electric helicopter, the mesicopter, has been developed at Stanford University for these applications. The mesoscopic scale implies a design with critical features between tens of microns and several millimeters. Three major parts in the mesicopter are challenging to manufacture. Rotors require smooth 3D surfaces and a blade thickness of less than 100 mum. Components in the DC micro-motor must be made of engineering materials, which is difficult on the mesoscopic scale. Airframe fabrication has to integrate complex 3D geometry into one single structure at this scale. In this research, material selection and manufacturing approaches have been investigated and implemented. In rotor fabrication, high-strength polymers manufactured by the Shape Deposition Manufacturing (SDM) technique were the top choice. Aluminum alloys were only considered as the second choice because the fabrication process is more involved. Lift tests showed that the 4-blade polymer and aluminum rotors could deliver about 90% of the expected lift (4g). To explain the rotor performance, structural analyses of spinning rotors were performed and the fabricated geometry was investigated. The bending deflections and the torsional twists were found to be too small to degrade aerodynamic performance. The rotor geometry was verified by laser scanning and by cross-section observations. Commercially available motors are used in the prototypes but a smaller DC micro-motor was designed for future use. Components of the DC micro-motors were fabricated by the Mesoscopic Additive/Subtractive Material Processing technique, which is capable of shaping engineering materials on the mesoscopic scale. The approaches are described in this thesis. The airframe was manufactured using the SDM process, which is capable of building complex parts without assembly. Castable polymers were chosen and mixed with glass microspheres to reduce their density. The finished airframe (65.5 mm x 65.5 mm) weighed only 1.5g. Two mesicopter prototypes, weighing 3g and 17g, have illustrated that powered flight at this scale is feasible. This research provides solutions to manufacture the challenging parts for the mesicopter. The manufacturing approaches discussed here are applicable to other small flying vehicles in similar and even smaller size regimes.

Water diffusion-exchange effect on the paramagnetic relaxation enhancement in off-resonance rotating frame

NASA Astrophysics Data System (ADS)

Zhang, Huiming; Xie, Yang; Ji, Tongyu

2007-06-01

The off-resonance rotating frame technique based on the spin relaxation properties of off-resonance T1 ρ can significantly increase the sensitivity of detecting paramagnetic labeling at high magnetic fields by MRI. However, the in vivo detectable dimension for labeled cell clusters/tissues in T1 ρ-weighted images is limited by the water diffusion-exchange between mesoscopic scale compartments. An experimental investigation of the effect of water diffusion-exchange between compartments on the paramagnetic relaxation enhancement of paramagnetic agent compartment is presented for in vitro/ in vivo models. In these models, the size of paramagnetic agent compartment is comparable to the mean diffusion displacement of water molecules during the long RF pulses that are used to generate the off-resonance rotating frame. The three main objectives of this study were: (1) to qualitatively correlate the effect of water diffusion-exchange with the RF parameters of the long pulse and the rates of water diffusion, (2) to explore the effect of water diffusion-exchange on the paramagnetic relaxation enhancement in vitro, and (3) to demonstrate the paramagnetic relaxation enhancement in vivo. The in vitro models include the water permeable dialysis tubes or water permeable hollow fibers embedded in cross-linked proteins gels. The MWCO of the dialysis tubes was chosen from 0.1 to 15 kDa to control the water diffusion rate. Thin hollow fibers were chosen to provide sub-millimeter scale compartments for the paramagnetic agents. The in vivo model utilized the rat cerebral vasculatures as a paramagnetic agent compartment, and intravascular agents (Gd-DTPA) 30-BSA were administrated into the compartment via bolus injections. Both in vitro and in vivo results demonstrate that the paramagnetic relaxation enhancement is predominant in the T1 ρ-weighted image in the presence of water diffusion-exchange. The T1 ρ contrast has substantially higher sensitivity than the conventional T1 contrast in detecting paramagnetic agents, especially at low paramagnetic agent volumetric fractions, low paramagnetic agent concentrations, and low RF amplitudes. Short pulse duration, short pulse recycle delay and efficient paramagnetic relaxation can reduce the influence of water diffusion-exchange on the paramagnetic enhancement. This study paves the way for the design of off-resonance rotating experiments to detect labeled cell clusters/tissue compartments in vivo at a sub-millimeter scale.

Realizing Controllable Quantum States

NASA Astrophysics Data System (ADS)

Takayanagi, Hideaki; Nitta, Junsaku

1. Entanglement in solid states. Orbital entanglement and violation of bell inequalities in mesoscopic conductors / M. Büttiker, P. Samuelsson and E. V. Sukhoruk. Teleportation of electron spins with normal and superconducting dots / O. Sauret, D. Feinberg and T. Martin. Entangled state analysis for one-dimensional quantum spin system: singularity at critical point / A. Kawaguchi and K. Shimizu. Detecting crossed Andreev reflection by cross-current correlations / G. Bignon et al. Current correlations and transmission probabilities for a Y-shaped diffusive conductor / S. K. Yip -- 2. Mesoscopic electronics. Quantum bistability, structural transformation, and spontaneous persistent currents in mesoscopic Aharonov-Bohm loops / I. O. Kulik. Many-body effects on tunneling of electrons in magnetic-field-induced quasi one-dimensional systems in quantum wells / T. Kubo and Y. Tokura. Electron transport in 2DEG narrow channel under gradient magnetic field / M. Hara et al. Transport properties of a quantum wire with a side-coupled quantum dot / M. Yamaguchi et al. Photoconductivity- and magneto-transport studies of single InAs quantum wires / A. Wirthmann et al. Thermoelectric transports in charge-density-wave systems / H. Yoshimoto and S. Kurihara -- 3. Mesoscopic superconductivity. Parity-restricted persistent currents in SNS nanorings / A. D. Zaikin and S. V. Sharov. Large energy dependence of current noise in superconductingh/normal metal junctions / F. Pistolesi and M. Houzet. Generation of photon number states and their superpositions using a superconducting qubit in a microcavity / Yu-Xi Liu, L. F. Wei and F. Nori. Andreev interferometry for pumped currents / F. Taddei, M. Governale and R. Fazio. Suppression of Cooper-pair breaking against high magnetic fields in carbon nanotubes / J. Haruyama et al. Impact of the transport supercurrent on the Josephson effect / S. N. Shevchenko. Josephson current through spin-polarized Luttinger liquid / N. Yokoshi and S. Kurihara -- 4. Mesoscopic superconductivity with unconventional superconductor or ferromagnet. Ultraefficient microrefrigerators realized with ferromagnet-superconductor junctions / F. Giazotto et al. Anomalous charge transport in triplet superconductor junctions by the synergy effect of the proximity effect and the mid gap Andreev resonant states / Y. Tanaka and S. Kashiwaya. Paramagnetic and glass states in superconductive YBa[symbol]Cu[symbol]O[symbol] ceramics of sub-micron scale grains / H. Deguchi et al. Quantum properties of single-domain triplet superconductors / A. M. Gulian and K. S. Wood. A numerical study of Josephson current in p wave superconducting junctions / Y. Asano et al. Tilted bi-crystal sapphire substrates improve properties of grain boundary YBa[symbol]Cu[symbol]O[symbol] junctions and extend their Josephson response to THZ frequencies / E. Stepantsov et al. Circuit theory analysis of AB-plane tunnel junctions of unconventional superconductor Bi[symbol]Sr[symbol]Ca[symbol]Cu[symbol]O[symbol] / I. Shigeta et al. Transport properties of normal metal/anisotropic superconductor junctions in the eutectic system Sr[symbol]RuO[symbol]Ru / M. Kawamura et al. Macroscopic quantum tunneling in d-wave superconductor Josephson / S. Kawabata et al. Quasiparticle states of high-T[symbol] oxides observed by a Zeeman magnetic field response / S. Kashiwaya et al. Experimentally realizable devices for controlling the motion of magnetic flux quanta in anisotropic superconductors: vortex lenses, vortex diodes and vortex pumps / S. Savel'ev and F. Nori. Stability of vortex-antivortex "molecules" in mesoscopic superconducting triangles / V. R. Misko et al. Superconducting network with magnetic decoration - Hofstadter butterfly in spatially modulated magnetic field / Y. Iye et al. Observation of paramagnetic supercurrent in mesoscopic superconducting rings and disks using multiple-small-tunnel-junction method / A. Kanda et al. Guidance of vortices in high-T[stmbol] superconducting thin films with special arrangements of antidots / R. Wöerdenweber, P. Dymashevski and V. R. Misko. Quantum tunneling of relativistic fluxons / K. Konno et al. -- 6. Quantum information processing in solid states. Qubit decoherence by low-frequency noise / K. Rabenstein, V. A. Sverdlov and D. V. Averin. A critique of two-level approximation / K. Savran and T. Hakioǧlu. Josephson arrays as quantum channels / A. Romito, C. Bruder and R. Fazio. Fighting decoherence in a Josephson qubit circuit / E. Collin et al. Fast switching current detection at low critical currents / J. Walter, S. Corlevi and D. Haviland. Asymmetric flux bias for coupled qubits to observe entangled states / Y. Shimazu. Interaction of Josephson qubits with strong QED cavity modes: dynamical entanglement transfer and navigation / G. Falci et al. Controlling decoherence of transported quantum spin information in semiconductor spintronics / B. Nikolic and S. Souma. Decoherence due to telegraph and 1/f noise in Josephson qubits / E. Paladino et al. Detection of entanglement in NMR quantum information processing / R. Rahimi, K. Takeda and M. Kitagawa. Multiphoton absorption and SQUID switching current behaviors in superconducting flux-qubit experiments / H. Takayanagi et al. -- 7. Quantum information theory. Quantum query complexities / K. Iwama. A construction for non-stabilizer Clifford codes / M. Hagiwara and H. Imai. Quantum pushdown automata that can deterministically solve a certain problem / Y. Murakami et al. Trading classical for quantum computation using indirection / R. van Meter. Intractability of the initial arrangement of input data on qubits / Y. Kawano et al. Reversibility of modular squaring / N. Kunihiro, Y. Takahashi and Y. Kawano. Study of proximity effect at D-wave superconductors in quasiclassical methods / Y. Tanuma, Y. Tanaka and S. Kashiwaya -- 8. Spintronics in band electrons. Triplet superconductors: exploitable basis for scalable quantum computing / K. S. Wood et al. Spin excitations in low-dimensional electron gases studied by far-infrared photoconductivity spectroscopy / C.-M. Hu. Control of photogenerated carriers and spins using surface acoustic waves / P. V. Santos, J. A. H. Stotz and R. Hey. PbTe nanostructures for spin filtering and detecting / G. Grabecki. G-factor control in an Ids-inserted InGaAs/InAlAs heterostructure / J. Nitta et al. Spin hall effect in p-type semiconductors / S. Murakami. Spin diffusion in mesoscopic superconducting A1 wires / Y.-S. Shin. H.-J. Lee and H.-W. Lee. Magnetization processes revealed by in-plane DC magnetoresistance measurements on manganite bicrystal thin film devices / R. Gunnarsson. M. Hanson and T. Claeson. Giant magnetoconductance at interface between a two-dimensional hole system and a magnetic semiconductor (Ga, Mn)As / Y. Hashimoto, S. Katsumoto and Y. Iye. Diffusion modes of the transport in diluted magnetic semiconductors / I. Kanazawa. Effect of an invasive voltage probe on the spin polarized current / J. Ohe and T. Ohtsuki -- 9. Spintronics in quantum dots. Tunable exchange interaction and Kondo screening in quantum dot devices / H. Tamura et al. Kondo effect in quantum dots in presence of itinerant-electron magnetism / J. Martinek et al. Optical band edge of II-VI and III-V based diluted magnetic semiconductors / M. Takahashi. Spin-polarized transport properties through double quantum dots / Y. Tanaka and N. Kawakami. RKKY interaction between two quantum dots embedded in an Aharonov-Bohm ring / Y. Utsumi et al. Fabrication and characterization of quantum dot single electron spin resonance devices / T. Kodera et al. Kondo effect in quantum dots with two orbitals and spin 1/2 - crossover from SU (4) to SU (2) symmetry / M. Eto. Detecting spin polarization of electrons in quantum dot edge channels by photoluminescence / S. Nomura. Manipulation of exchange interaction in a double quantum dot / M. Stopa, S. Tarucha and T. Hatano. Electron-density dependence of photoluminescence from Be-[symbol]-doped GaAs quantum wells with a back gate / M. Yamaguchi et al. Direct observation of [symbol]Si nuclear-spin decoherence process / S. Sasaki and S. Watanabe.

Mesoscopic model for binary fluids

NASA Astrophysics Data System (ADS)

Echeverria, C.; Tucci, K.; Alvarez-Llamoza, O.; Orozco-Guillén, E. E.; Morales, M.; Cosenza, M. G.

2017-10-01

We propose a model for studying binary fluids based on the mesoscopic molecular simulation technique known as multiparticle collision, where the space and state variables are continuous, and time is discrete. We include a repulsion rule to simulate segregation processes that does not require calculation of the interaction forces between particles, so binary fluids can be described on a mesoscopic scale. The model is conceptually simple and computationally efficient; it maintains Galilean invariance and conserves the mass and energy in the system at the micro- and macro-scale, whereas momentum is conserved globally. For a wide range of temperatures and densities, the model yields results in good agreement with the known properties of binary fluids, such as the density profile, interface width, phase separation, and phase growth. We also apply the model to the study of binary fluids in crowded environments with consistent results.

Seismoelectric effects due to mesoscopic heterogeneities

NASA Astrophysics Data System (ADS)

Jougnot, Damien; Rubino, J. GermáN.; Carbajal, Marina Rosas; Linde, Niklas; Holliger, Klaus

2013-05-01

While the seismic effects of wave-induced fluid flow due to mesoscopic heterogeneities have been studied for several decades, the role played by these types of heterogeneities on seismoelectric phenomena is largely unexplored. To address this issue, we have developed a novel methodological framework which allows for the coupling of wave-induced fluid flow, as inferred through numerical oscillatory compressibility tests, with the pertinent seismoelectric conversion mechanisms. Simulating the corresponding response of a water-saturated sandstone sample containing mesoscopic fractures, we demonstrate for the first time that these kinds of heterogeneities can produce measurable seismoelectric signals under typical laboratory conditions. Given that this phenomenon is sensitive to key hydraulic and mechanical properties, we expect that the results of this pilot study will stimulate further exploration on this topic in several domains of the Earth, environmental, and engineering sciences.

Magnetic disorder in superconductors: Enhancement by mesoscopic fluctuations

NASA Astrophysics Data System (ADS)

Burmistrov, I. S.; Skvortsov, M. A.

2018-01-01

We study the density of states (DOS) and the transition temperature Tc in a dirty superconducting film with rare classical magnetic impurities of an arbitrary strength described by the Poissonian statistics. We take into account that the potential disorder is a source of mesoscopic fluctuations of the local DOS, and, consequently, of the effective strength of magnetic impurities. We find that these mesoscopic fluctuations result in a nonzero DOS for all energies in the region of the phase diagram where without this effect the DOS is zero within the standard mean-field theory. This mechanism can be more efficient in filling the mean-field superconducting gap than rare fluctuations of the potential disorder (instantons). Depending on the magnetic impurity strength, the suppression of Tc by spin-flip scattering can be faster or slower than in the standard mean-field theory.

MEG Coherence and DTI Connectivity in mTLE

PubMed Central

Nazem-Zadeh, Mohammad-Reza; Bowyer, Susan M.; Moran, John E.; Davoodi-Bojd, Esmaeil; Zillgitt, Andrew; Weiland, Barbara J.; Bagher-Ebadian, Hassan; Mahmoudi, Fariborz; Elisevich, Kost; Soltanian-Zadeh, Hamid

2017-01-01

Purpose Magnetoencephalography (MEG) is a noninvasive imaging method for localization of focal epileptiform activity in patients with epilepsy. Diffusion tensor imaging (DTI) is a noninvasive imaging method for measuring the diffusion properties of the underlying white matter tracts through which epileptiform activity is propagated. This study investigates the relationship between the cerebral functional abnormalities quantified by MEG coherence and structural abnormalities quantified by DTI in mesial temporal lobe epilepsy (mTLE). Methods Resting state MEG data was analyzed using MEG coherence source imaging (MEG-CSI) method to determine the coherence in 54 anatomical sites in 17 adult mTLE patients with surgical resection and Engel class I outcome, and 17 age- and gender- matched controls. DTI tractography identified the fiber tracts passing through these same anatomical sites of the same subjects. Then, DTI nodal degree and laterality index were calculated and compared with the corresponding MEG coherence and laterality index. Results MEG coherence laterality, after Bonferroni adjustment, showed significant differences for right versus left mTLE in insular cortex and both lateral orbitofrontal and superior temporal gyri (p<0.017). Likewise, DTI nodal degree laterality, after Bonferroni adjustment, showed significant differences for right versus left mTLE in gyrus rectus, insular cortex, precuneus and superior temporal gyrus (p<0.017). In insular cortex, MEG coherence laterality correlated with DTI nodal degree laterality (R2 = 0.46; p = 0.003) in the cases of mTLE. None of these anatomical sites showed statistically significant differences in coherence laterality between right and left sides of the controls. Coherence laterality was in agreement with the declared side of epileptogenicity in insular cortex (in 82% of patients) and both lateral orbitofrontal (88%) and superior temporal gyri (88%). Nodal degree laterality was also in agreement with the declared side of epileptogenicity in gyrus rectus (in 88% of patients), insular cortex (71%), precuneus (82%) and superior temporal gyrus (94%). Combining all significant laterality indices improved the lateralization accuracy to 94% and 100% for the coherence and nodal degree laterality indices, respectively. Conclusion The associated variations in diffusion properties of fiber tracts quantified by DTI and coherence measures quantified by MEG with respect to epileptogenicity possibly reflect the chronic microstructural cerebral changes associated with functional interictal activity. The proposed methodology for using MEG and DTI to investigate diffusion abnormalities related to focal epileptogenicity and propagation may provide a further means of noninvasive lateralization. PMID:27060092

Lateral carrier diffusion in InGaAs/GaAs coupled quantum dot-quantum well system

NASA Astrophysics Data System (ADS)

Pieczarka, M.; Syperek, M.; Biegańska, D.; Gilfert, C.; Pavelescu, E. M.; Reithmaier, J. P.; Misiewicz, J.; Sek, G.

2017-05-01

The lateral carrier diffusion process is investigated in coupled InGaAs/GaAs quantum dot-quantum well (QD-QW) structures by means of spatially resolved photoluminescence spectroscopy at low temperature. Under non-resonant photo-excitation above the GaAs bandgap, the lateral carrier transport reflected in the distorted electron-hole pair emission profiles is found to be mainly governed by high energy carriers created within the 3D density of states of GaAs. In contrast, for the case of resonant excitation tuned to the QW-like ground state of the QD-QW system, the emission profiles remain unaffected by the excess kinetic energy of carriers and local phonon heating within the pump spot. The lateral diffusion lengths are determined and present certain dependency on the coupling strength between QW and QDs. While for a strongly coupled structure the diffusion length is found to be around 0.8 μm and monotonically increases up to 1.4 μm with the excitation power density, in weakly coupled structures, it is determined to ca. 1.6 μm and remained virtually independent of the pumping power density.

Analytical network-averaging of the tube model: Strain-induced crystallization in natural rubber

NASA Astrophysics Data System (ADS)

Khiêm, Vu Ngoc; Itskov, Mikhail

2018-07-01

In this contribution, we extend the analytical network-averaging concept (Khiêm and Itskov, 2016) to phase transition during strain-induced crystallization of natural rubber. To this end, a physically-based constitutive model describing the nonisothermal strain-induced crystallization is proposed. Accordingly, the spatial arrangement of polymer subnetworks is driven by crystallization nucleation and consequently alters the mesoscopic deformation measures. The crystallization growth is elucidated by diffusion of chain segments into crystal nuclei. The crystallization results in a change of temperature and an evolution of heat source. By this means, not only the crystallization kinetics but also the Gough-Joule effect are thoroughly described. The predictive capability of the constitutive model is illustrated by comparison with experimental data for natural rubbers undergoing strain-induced crystallization. All measurable values such as stress, crystallinity and heat source are utilized for the comparison.

Pattern Transitions in Bacterial Oscillating System under Nanofluidic Confinement

NASA Astrophysics Data System (ADS)

Shen, Jie-Pan; Chou, Chia-Fu

2011-03-01

Successful binary fission in E. coli relies on remarkable oscillatory behavior of the MinCDE protein system to determine the exact division site. The most favorable models to explain this fascinating spatiotemporal regulation on dynamic MinDE pattern formation in cells are based on reaction-diffusion scenario. Although not fully understood, geometric factors caused by bacterial morphology play a crucial role in MinDE dynamics. In the present study, bacteria were cultured, confined and reshaped in various micro/nanofluidic devices, to mimic either curvature changes of cell peripherals. Fluorescence imaging was utilized to detail the mode transitions in multiple MinDE patterns. The understanding of the physics in multiple pattern formations is further complemented via in silico modeling. The study synergizes the join merits of in vivo, in vitro and in silico approaches, to grasp the insight of stochastic dynamics inherited from the noisy mesoscopic biophysics. We acknowledge support from the Foresight Project, Academia Sinica.

Postcoalescence evolution of growth stress in polycrystalline films.

PubMed

González-González, A; Polop, C; Vasco, E

2013-02-01

The growth stress generated once grains coalesce in Volmer-Weber-type thin films is investigated by time-multiscale simulations comprising complementary modules of (i) finite-element modeling to address the interactions between grains happening at atomic vibration time scales (~0.1 ps), (ii) dynamic scaling to account for the surface stress relaxation via morphology changes at surface diffusion time scales (~μs-ms), and (iii) the mesoscopic rate equation approach to simulate the bulk stress relaxation at deposition time scales (~sec-h). On the basis of addressing the main experimental evidence reported so far on the topic dealt with, the simulation results provide key findings concerning the interplay between anisotropic grain interactions at complementary space scales, deposition conditions (such as flux and mobility), and mechanisms of stress accommodation-relaxation, which underlies the origin, nature and spatial distribution, and the flux dependence of the postcoalescence growth stress.

Multiscale simulations of anisotropic particles combining molecular dynamics and Green's function reaction dynamics

NASA Astrophysics Data System (ADS)

Vijaykumar, Adithya; Ouldridge, Thomas E.; ten Wolde, Pieter Rein; Bolhuis, Peter G.

2017-03-01

The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems. We present the novel algorithm focusing on Brownian dynamics only, although the methodology is generic. We illustrate the novel algorithm using a simple patchy particle model. After validation of the algorithm, we discuss its performance. The rotational Brownian dynamics MD-GFRD multiscale method will open up the possibility for large scale simulations of protein signalling networks.

Physicochemical Study of Viral Nanoparticles at the Air/Water Interface.

PubMed

Torres-Salgado, Jose F; Comas-Garcia, Mauricio; Villagrana-Escareño, Maria V; Durán-Meza, Ana L; Ruiz-García, Jaime; Cadena-Nava, Ruben D

2016-07-07

The assembly of most single-stranded RNA (ssRNA) viruses into icosahedral nucleocapsids is a spontaneous process driven by protein-protein and RNA-protein interactions. The precise nature of these interactions results in the assembly of extremely monodisperse and structurally indistinguishable nucleocapsids. In this work, by using a ssRNA plant virus (cowpea chlorotic mottle virus [CCMV]) as a charged nanoparticle we show that the diffusion of these nanoparticles from the bulk solution to the air/water interface is an irreversible adsorption process. By using the Langmuir technique, we measured the diffusion and adsorption of viral nucleocapsids at the air/water interface at different pH conditions. The pH changes, and therefore in the net surface charge of the virions, have a great influence in the diffusion rate from the bulk solution to the air/water interface. Moreover, assembly of mesoscopic and microscopic viral aggregates at this interface depends on the net surface charge of the virions and the surface pressure. By using Brewster's angle microscopy we characterized these structures at the interface. Most common structures observed were clusters of virions and soap-frothlike micron-size structures. Furthermore, the CCMV films were compressed to form monolayers and multilayers from moderate to high surface pressures, respectively. After transferring the films from the air/water interface onto mica by using the Langmuir-Blodgett technique, their morphology was characterized by atomic force microscopy. These viral monolayers showed closed-packing nano- and microscopic arrangements.

Dynamic density functional theory with hydrodynamic interactions and fluctuations

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

Donev, Aleksandar, E-mail: donev@courant.nyu.edu; Vanden-Eijnden, Eric, E-mail: eve2@courant.nyu.edu

2014-06-21

We derive a closed equation for the empirical concentration of colloidal particles in the presence of both hydrodynamic and direct interactions. The ensemble average of our functional Langevin equation reproduces known deterministic Dynamic Density Functional Theory (DDFT) [M. Rex and H. Löwen, “Dynamical density functional theory with hydrodynamic interactions and colloids in unstable traps,” Phys. Rev. Lett. 101(14), 148302 (2008)], and, at the same time, it also describes the microscopic fluctuations around the mean behavior. We suggest separating the ideal (non-interacting) contribution from additional corrections due to pairwise interactions. We find that, for an incompressible fluid and in the absencemore » of direct interactions, the mean concentration follows Fick's law just as for uncorrelated walkers. At the same time, the nature of the stochastic terms in fluctuating DDFT is shown to be distinctly different for hydrodynamically-correlated and uncorrelated walkers. This leads to striking differences in the behavior of the fluctuations around Fick's law, even in the absence of pairwise interactions. We connect our own prior work [A. Donev, T. G. Fai, and E. Vanden-Eijnden, “A reversible mesoscopic model of diffusion in liquids: from giant fluctuations to Fick's law,” J. Stat. Mech.: Theory Exp. (2014) P04004] on fluctuating hydrodynamics of diffusion in liquids to the DDFT literature, and demonstrate that the fluid cannot easily be eliminated from consideration if one wants to describe the collective diffusion in colloidal suspensions.« less

Quantum gambling using mesoscopic ring qubits

NASA Astrophysics Data System (ADS)

Pakuła, Ireneusz

2007-07-01

Quantum Game Theory provides us with new tools for practising games and some other risk related enterprices like, for example, gambling. The two party gambling protocol presented by Goldenberg {\\it et al} is one of the simplest yet still hard to implement applications of Quantum Game Theory. We propose potential physical realisation of the quantum gambling protocol with use of three mesoscopic ring qubits. We point out problems in implementation of such game.

Intrinsic behavior of face-centered-cubic supra-crystals of nanocrystals self-organized on mesoscopic scale

NASA Astrophysics Data System (ADS)

Pileni, M. P.

2005-12-01

We describe intrinsic behavior due to the high ordering of nanocrystals at the mesoscopic scale. The first example shows well-defined columns in the formation of cobalt nanocrystals when an applied magnetic field is applied during the evaporation process. Collective breathing properties between nanocrystals are demonstrated. In both cases, these features are observed when the nanocrystals are highly ordered in fcc supra-crystals.

1997 Technical Digest Series. Volume 9: Quantum Optoelectronics

DTIC Science & Technology

1997-03-01

Program Co-Chair Shigehisa Arai, Tokyo Institute of Technology, Japan Yasuhiko Arakawa, University of Tokyo, Japan Israel Bar-Joseph, Weizmann...assembly formed quantum dot active layers, (p. 3) 2:30pm (Invited) QWA3 • Optical probing of mesoscopic and nano-structures, Yasuhiko Arakawa, Univ...80, 3466 (1996). 6/QWA3-1 Optical Probing of Mesoscopic and Nano-Structures Yasuhiko Arakawa University of Tokyo, Japan We investigate the

Lateral diffusion of inositol 1,4,5-trisphosphate receptor type 1 in Purkinje cells is regulated by calcium and actin filaments.

PubMed

Fukatsu, Kazumi; Bannai, Hiroko; Inoue, Takafumi; Mikoshiba, Katsuhiko

2010-09-01

Inositol 1,4,5-trisphosphate receptor type 1 (IP(3) R1) is an intracellular Ca(2+) release channel that plays crucial roles in the functions of Purkinje cells. The dynamics of IP(3) R1 on the endoplasmic reticulum membrane and the distribution of IP(3) R1 in neurons are thought to be important for the spatial regulation of Ca(2+) release. In this study, we analyzed the lateral diffusion of IP(3) R1 in Purkinje cells in cerebellar slice cultures using fluorescence recovery after photobleaching. In the dendrites of Purkinje cells, IP(3) R1 showed lateral diffusion with an effective diffusion constant of approximately 0.30 μm(2) /s, and the diffusion of IP(3) R1 was negatively regulated by actin filaments. We found that actin filaments were also involved in the regulation of IP(3) R1 diffusion in the spine of Purkinje cells. Glutamate or quisqualic acid stimulation, which activates glutamate receptors and leads to a Ca(2+) transient in Purkinje cells, decreased the diffusion of IP(3) R1 and increased the density of actin in spines. These findings indicate that the neuronal activity-dependent augmentation of actin contributes to the stabilization of IP(3) R1 in spines. © 2010 The Authors. Journal Compilation © 2010 International Society for Neurochemistry.

Polymorphism of Lysozyme Condensates.

PubMed

Safari, Mohammad S; Byington, Michael C; Conrad, Jacinta C; Vekilov, Peter G

2017-10-05

Protein condensates play essential roles in physiological processes and pathological conditions. Recently discovered mesoscopic protein-rich clusters may act as crucial precursors for the nucleation of ordered protein solids, such as crystals, sickle hemoglobin polymers, and amyloid fibrils. These clusters challenge settled paradigms of protein condensation as the constituent protein molecules present features characteristic of both partially misfolded and native proteins. Here we employ the antimicrobial enzyme lysozyme and examine the similarities between mesoscopic clusters, amyloid structures, and disordered aggregates consisting of chemically modified protein. We show that the mesoscopic clusters are distinct from the other two classes of aggregates. Whereas cluster formation and amyloid oligomerization are both reversible, aggregation triggered by reduction of the intramolecular S-S bonds is permanent. In contrast to the amyloid structures, protein molecules in the clusters retain their enzymatic activity. Furthermore, an essential feature of the mesoscopic clusters is their constant radius of less than 50 nm. The amyloid and disordered aggregates are significantly larger and rapidly grow. These findings demonstrate that the clusters are a product of limited protein structural flexibility. In view of the role of the clusters in the nucleation of ordered protein solids, our results suggest that fine-tuning the degree of protein conformational stability is a powerful tool to control and direct the pathways of protein condensation.

Non-equilibrium phase transition in mesoscopic biochemical systems: from stochastic to nonlinear dynamics and beyond

PubMed Central

Ge, Hao; Qian, Hong

2011-01-01

A theory for an non-equilibrium phase transition in a driven biochemical network is presented. The theory is based on the chemical master equation (CME) formulation of mesoscopic biochemical reactions and the mathematical method of large deviations. The large deviations theory provides an analytical tool connecting the macroscopic multi-stability of an open chemical system with the multi-scale dynamics of its mesoscopic counterpart. It shows a corresponding non-equilibrium phase transition among multiple stochastic attractors. As an example, in the canonical phosphorylation–dephosphorylation system with feedback that exhibits bistability, we show that the non-equilibrium steady-state (NESS) phase transition has all the characteristics of classic equilibrium phase transition: Maxwell construction, a discontinuous first-derivative of the ‘free energy function’, Lee–Yang's zero for a generating function and a critical point that matches the cusp in nonlinear bifurcation theory. To the biochemical system, the mathematical analysis suggests three distinct timescales and needed levels of description. They are (i) molecular signalling, (ii) biochemical network nonlinear dynamics, and (iii) cellular evolution. For finite mesoscopic systems such as a cell, motions associated with (i) and (iii) are stochastic while that with (ii) is deterministic. Both (ii) and (iii) are emergent properties of a dynamic biochemical network. PMID:20466813

Mesoscopic Framework Enables Facile Ionic Transport in Solid Electrolytes for Li Batteries

DOE PAGES

Ma, Cheng; Cheng, Yongqiang; Chen, Kai; ...

2016-03-29

In Li-ion-conducting solid electrolytes can simultaneously overcome two grand challenges for Li-ion batteries: the severe safety concerns that limit the large-scale application and the poor electrolyte stability that forbids the use of high-voltage cathodes. Nevertheless, the ionic conductivity of solid electrolytes is typically low, compromising the battery performances. Precisely determining the ionic transport mechanism(s) is a prerequisite for the rational design of highly conductive solid electrolytes. For decades, the research on this subject has primarily focused on the atomic and microscopic scales, where the main features of interest are unit cells and microstructures, respectively. We show that the largely overlookedmore » mesoscopic scale lying between these extremes could be the key to fast ionic conduction. In a prototype system, (Li 0.33La 0.56)TiO 3, a mesoscopic framework is revealed for the first time by state-of-the-art scanning transmission electron microscopy. Corroborated by theoretical calculations and impedance measurements, it is demonstrated that such a unique configuration maximizes the number of percolation directions and thus most effectively improves the ionic conductivity. Finally, this discovery reconciles the long-standing structure–property inconsistency in (Li 0.33La 0.56)TiO 3 and also identifies mesoscopic ordering as a promising general strategy for optimizing Li+ conduction.« less

Transforming Mesoscopic (Bio)materials with Holographic Optical Tweezers

NASA Astrophysics Data System (ADS)

Grier, David

2004-03-01

An optical tweezer uses the forces exerted by a strongly focused beam of light to trap and move objects ranging in size from tens of nanometers to tens of micrometers. Since their introduction in 1986, optical tweezers have become a mainstay of research in biology, physical chemistry, and soft condensed matter physics. This talk highlights recent advances made possible by new classes of optical traps created with computer-designed holograms, a technique we call holographic optical trapping. Holographic optical tweezers can trap hundreds of mesoscopic objects simultaneously and move them independently in three dimensions. Arrays of optical traps can be used to continuously sort heterogeneous samples into selected fractions, a process we call optical fractionation. The same holograms can transform optical traps into optical scalpels and scissors that photochemically transform mesoscopic samples with exquisite spatial resolution. They also can impose arbitrary phase profiles onto the trapping beams, thereby creating optical vortices and related optical machines capable of actuating MEMS devices and driving mesoscale pumps and mixers. These new applications for laser light promise to take optical tweezers out of the laboratory and into real-world applications including manufacturing, diagnostics, and even consumer products. The unprecedented access to the mesoscopic world provided by holographic optical tweezers also offers revolutionary new opportunities for fundamental and applied research.

Fractal analysis of lateral movement in biomembranes.

PubMed

Gmachowski, Lech

2018-04-01

Lateral movement of a molecule in a biomembrane containing small compartments (0.23-μm diameter) and large ones (0.75 μm) is analyzed using a fractal description of its walk. The early time dependence of the mean square displacement varies from linear due to the contribution of ballistic motion. In small compartments, walking molecules do not have sufficient time or space to develop an asymptotic relation and the diffusion coefficient deduced from the experimental records is lower than that measured without restrictions. The model makes it possible to deduce the molecule step parameters, namely the step length and time, from data concerning confined and unrestricted diffusion coefficients. This is also possible using experimental results for sub-diffusive transport. The transition from normal to anomalous diffusion does not affect the molecule step parameters. The experimental literature data on molecular trajectories recorded at a high time resolution appear to confirm the modeled value of the mean free path length of DOPE for Brownian and anomalous diffusion. Although the step length and time give the proper values of diffusion coefficient, the DOPE speed calculated as their quotient is several orders of magnitude lower than the thermal speed. This is interpreted as a result of intermolecular interactions, as confirmed by lateral diffusion of other molecules in different membranes. The molecule step parameters are then utilized to analyze the problem of multiple visits in small compartments. The modeling of the diffusion exponent results in a smooth transition to normal diffusion on entering a large compartment, as observed in experiments.

Mesoscopic spin Hall effect in semiconductor nanostructures

NASA Astrophysics Data System (ADS)

Zarbo, Liviu

The spin Hall effect (SHE) is a name given to a collection of diverse phenomena which share two principal features: (i) longitudinal electric current flowing through a paramagnetic semiconductor or metallic sample leads to transverse spin current and spin accumulation of opposite sign at opposing lateral edges; (ii) SHE does not require externally applied magnetic field or magnetic ordering in the equilibrium state of the sample, instead it relies on the presence of spin-orbit (SO) couplings within the sample. This thesis elaborates on a new type of phenomenon within the SHE family, predicted in our recent studies [Phys. Rev. B 72, 075361 (2005); Phys. Rev. Lett. 95, 046601 (2005); Phys. Rev. B 72, 075335 (2005); Phys. Rev. B 73 , 075303 (2006); and Europhys. Lett. 77, 47004 (2007)], where pure spin current flows through the transverse electrodes attached to a clean finitesize two-dimensional electron gas (2DEG) due to unpolarized charge current injected through its longitudinal leads. If transverse leads are removed, the effect manifests as nonequilibrium spin Hall accumulation at the lateral edges of 2DEG wires. The SO coupling driving this SHE effect is of the Rashba type, which arises due to structural inversion asymmetry of semiconductor heterostructure hosting the 2DEG. We term the effect "mesoscopic" because the spin Hall currents and accumulations reach optimal value in samples of the size of the spin precession length---the distance over which the spin of an electron precesses by an angle pi. In strongly SO-coupled structures this scale is of the order of ˜100 nm, and, therefore, mesoscopic in the sense of being much larger than the characteristic microscopic scales (such as the Fermi wavelength, screening length, or the mean free path in disordered systems), but still much smaller than the macroscopic ones. Although the first theoretical proposal for SHE, driven by asymmetry in SO-dependent scattering of spin-up and spin-down electrons off impurities, appeared in 1970s, it is only in the past few years that advances in optical detection of nonequilibrium magnetization in semiconductors have made possible the detection of such extrinsic SHE in groundbreaking experiments. The experimental pursuits of SHE have, in fact, been largely motivated by very recent theoretical speculations for several order of magnitude greater spin Hall currents driven by intrinsic SO mechanisms due to SO couplings existing not only around the impurity but also throughout the sample. The homogeneous intrinsic SO couplings are capable of spin-splitting the band structure and appear as momentum-dependent magnetic field within the sample which causes spin non-conservation due to precession of injected spins which are not in the eigenstates of the corresponding Zeeman term. Besides deepening our understanding of subtle relativistic effects in solids, SHE has attracted a lot of attention since it offers an all-electrical way of generating pure spin currents in semiconductors. (Abstract shortened by UMI.)

Theoretical approach to oxygen atom degradation of silver

NASA Technical Reports Server (NTRS)

Fromhold, Albert T., Jr.; Noh, Seung; Beshears, Ronald; Whitaker, Ann F.; Little, Sally A.

1987-01-01

Based on available Rutherford backscattering spectrometry (RBS), proton induced X-ray emission (PIXE) and ellipsometry data obtained on silver specimens subjected to atomic oxygen attack in low Earth orbit STS flight 41-G, a theory was developed to model the oxygen atom degradation of silver. The diffusion of atomic oxygen in a microscopically nonuniform medium is an essential constituent of the theory. The driving force for diffusion is the macroscopic electrochemical potential gradient developed between the specimen surface exposed to the ambient and the bulk of the silver specimen. The longitudinal electric effect developed parallel to the gradient is modified by space charge of the diffusing charged species. Lateral electric fields and concentration differences also exist due to the nonuniform nature of the medium. The lateral concentration differences are found to be more important than the lateral electric fields in modifying the diffusion rate. The model was evaluated numerically. Qualitative agreement exists between the kinetics predicted by the theory and kinetic data taken in ground-based experiments utilizing a plasma asher.

A sphingolipid-dependent diffusion barrier confines ER stress to the yeast mother cell

PubMed Central

Clay, Lori; Caudron, Fabrice; Denoth-Lippuner, Annina; Boettcher, Barbara; Buvelot Frei, Stéphanie; Snapp, Erik Lee; Barral, Yves

2014-01-01

In many cell types, lateral diffusion barriers compartmentalize the plasma membrane and, at least in budding yeast, the endoplasmic reticulum (ER). However, the molecular nature of these barriers, their mode of action and their cellular functions are unclear. Here, we show that misfolded proteins of the ER remain confined into the mother compartment of budding yeast cells. Confinement required the formation of a lateral diffusion barrier in the form of a distinct domain of the ER-membrane at the bud neck, in a septin-, Bud1 GTPase- and sphingolipid-dependent manner. The sphingolipids, but not Bud1, also contributed to barrier formation in the outer membrane of the dividing nucleus. Barrier-dependent confinement of ER stress into the mother cell promoted aging. Together, our data clarify the physical nature of lateral diffusion barriers in the ER and establish the role of such barriers in the asymmetric segregation of proteotoxic misfolded proteins during cell division and aging. DOI: http://dx.doi.org/10.7554/eLife.01883.001 PMID:24843009

The role of mass transport in protein crystallization.

PubMed

García-Ruiz, Juan Manuel; Otálora, Fermín; García-Caballero, Alfonso

2016-02-01

Mass transport takes place within the mesoscopic to macroscopic scale range and plays a key role in crystal growth that may affect the result of the crystallization experiment. The influence of mass transport is different depending on the crystallization technique employed, essentially because each technique reaches supersaturation in its own unique way. In the case of batch experiments, there are some complex phenomena that take place at the interface between solutions upon mixing. These transport instabilities may drastically affect the reproducibility of crystallization experiments, and different outcomes may be obtained depending on whether or not the drop is homogenized. In diffusion experiments with aqueous solutions, evaporation leads to fascinating transport phenomena. When a drop starts to evaporate, there is an increase in concentration near the interface between the drop and the air until a nucleation event eventually takes place. Upon growth, the weight of the floating crystal overcomes the surface tension and the crystal falls to the bottom of the drop. The very growth of the crystal then triggers convective flow and inhomogeneities in supersaturation values in the drop owing to buoyancy of the lighter concentration-depleted solution surrounding the crystal. Finally, the counter-diffusion technique works if, and only if, diffusive mass transport is assured. The technique relies on the propagation of a supersaturation wave that moves across the elongated protein chamber and is the result of the coupling of reaction (crystallization) and diffusion. The goal of this review is to convince protein crystal growers that in spite of the small volume of the typical protein crystallization setup, transport plays a key role in the crystal quality, size and phase in both screening and optimization experiments.

The occurrence of macro- and mesoscopic methane hydrate in the eastern margin of Japan Sea

NASA Astrophysics Data System (ADS)

Matsumoto, R.; Kakuwa, Y.; Tanahashi, M.; Hiruta, A.

2016-12-01

Shallow methane hydrate is known to occur in muddy sediments that were deposited in the eastern margin of Japan Sea. In such settings, the hydrate occurs just below the seabed or is exposed directly on the seabed. Its presence is quite different from the pore-filling type of hydrate typically found in sandstone of the Pacific Ocean side of the Japanese islands. This presentation focuses on categorizing the distribution of gas hydrate in Japan Sea which, until recently, has been poorly understood. Macroscopic occurrence: Numerous gas chimney structures, which are characterized by an acoustic blanking on sub-bottom profiler images, have been discovered in the eastern margin of Japan Sea. We carried out seafloor drilling at several topographic highs that showed gas chimney structures. The results confirm that, while methane hydrate does not occur in the well-stratified part of SBP images, it does occur uniquely in the gas chimney structure-bearing mounds and pockmarks. Several horizons of methane hydrate-concentrated layers are identified by our LWD data and are traceable over lateral distances of as much as a kilometer.. In another case, the methane hydrate-concentrated layers occur stratigraphically in a regular manner with methane-derived carbonate nodules. We interpret the second case as one in which methane gas was supplied by regularly repeated movements of active fault(s). Mesoscopic occurrence: Methane hydrate is classified into 5 types that are readily observable in drilled cores: granular, nodular, platy, veiny and massive. The granular type is common over shallower intervals, while platy and veiny types are more common in the deeper intervals. Nevertheless, a significant fraction of the granular type may have possibly originated from the destruction and dissociation of other types during drilling and recovery. The massive type hydrate that characterizes highly-concentrated layers transitions to other types laterally as methane hydrate becomes poorly concentrated. This study was conducted under the commission from AIST as a part of the methane hydrate research project funded by METI (the Ministry of Economy, Trade and Industry, Japan).

Diffusion tensor imaging demonstrates brainstem and cerebellar abnormalities in congenital central hypoventilation syndrome.

PubMed

Kumar, Rajesh; Macey, Paul M; Woo, Mary A; Alger, Jeffry R; Harper, Ronald M

2008-09-01

Congenital central hypoventilation syndrome (CCHS) patients show reduced breathing drive during sleep, decreased hypoxic and hypercapnic ventilatory responses, and autonomic and affective deficits, suggesting both brainstem and forebrain injuries. Forebrain damage was previously described in CCHS, but methodological limitations precluded detection of brainstem injury, a concern because genetic mutations in CCHS target brainstem autonomic nuclei. To assess brainstem and cerebellar areas, we used diffusion tensor imaging-based measures, namely axial diffusivity, reflecting water diffusion parallel to fibers, and sensitive to axonal injury, and radial diffusivity, measuring diffusion perpendicular to fibers, and indicative of myelin injury. Diffusion tensor imaging was performed in 12 CCHS and 26 controls, and axial and radial diffusivity maps were compared between groups using analysis of covariance (covariates; age and gender). Increased axial diffusivity in CCHS appeared within the lateral medulla and clusters with injury extended from the dorsal midbrain through the periaqueductal gray, raphé, and superior cerebellar decussation, ventrally to the basal-pons. Cerebellar cortex and deep nuclei, and the superior and inferior cerebellar peduncles showed increased radial diffusivity. Midbrain, pontine, and lateral medullary structures, and the cerebellum and its fiber systems are injured in CCHS, likely contributing to the characteristics found in the syndrome.

Paleokarst and reservoir porosity in the Ordovician Beekmantown Dolomite of the central Appalachian basin

USGS Publications Warehouse

Smosna, R.; Bruner, K.R.; Riley, R.A.

2005-01-01

A karst-unconformity play at the top of the Ordovician Beekmantown Dolomite is judged to have great petroleum potential in Ohio and adjacent states; wells have high ultimate reserves and large areas remain untested. To better understand the origin, development, and distribution of Beekmantown porosity, we conducted a petrologic-stratigraphic study of cores and thin sections from 15 oil and gas wells. The massive dolomite, characterized by a hypidiotopic-idiotopic texture, formed by the replacement of stacked peritidal carbonate cycles. Secondary porosity occurs at two scales: (1) mesoscopic - breccia porosity, solution-enlarged fractures, large vugs, and caverns, and (2) microscopic - intercrystalline, intracrystalline, molds, small vugs, and microfractures. Mesoscopic pores (providing the major storage capacity in this reservoir) were produced by intrastratal solution and collapse of carbonate layers, whereas microscopic pores (connecting the larger pores) generally formed by the leaching of individual carbonate grains and crystals. Most pore types developed during periods of subaerial exposure across the carbonate bank, tied to either the numerous, though brief falls of relative sea level during Beekmantown deposition or more importantly the prolonged Knox unconformity at the close of sedimentation. The distribution of reservoir-quality porosity is quite heterogeneous, being confined vertically to a zone immediately below the unconformity and best developed laterally beneath buried hills and noses of this erosion surface. The inferred, shallow flow of ground water in the Beekmantown karst, primarily below topographic highs and above a diagenetic base level close to the water table, led to this irregular distribution of porosity.

LATERAL HEAT FLOW INFRARED THERMOGRAPHY FOR THICKNESS INDEPENDENT DETERMINATION OF THERMAL DIFFUSIVITY IN CFRP

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

Tralshawala, Nilesh; Howard, Don; Knight, Bryon

2008-02-28

In conventional infrared thermography, determination of thermal diffusivity requires thickness information. Recently GE has been experimenting with the use of lateral heat flow to determine thermal diffusivity without thickness information. This work builds on previous work at NASA Langley and Wayne State University but we incorporate thermal time of flight (tof) analysis rather than curve fitting to obtain quantitative information. We have developed appropriate theoretical models and a tof based data analysis framework to experimentally determine all components of thermal diffusivity from the time-temperature measurements. Initial validation was carried out using finite difference simulations. Experimental validation was done using anisotropicmore » carbon fiber reinforced polymer (CFRP) composites. We found that in the CFRP samples used, the in-plane component of diffusivity is about eight times larger than the through-thickness component.« less

Observational Inferences of Lateral Eddy Diffusivity in the Halocline of the Beaufort Gyre

NASA Astrophysics Data System (ADS)

Meneghello, Gianluca; Marshall, John; Cole, Sylvia T.; Timmermans, Mary-Louise

2017-12-01

Using Ekman pumping rates mediated by sea ice in the Arctic Ocean's Beaufort Gyre (BG), the magnitude of lateral eddy diffusivities required to balance downward pumping is inferred. In this limit—that of vanishing residual-mean circulation—eddy-induced upwelling exactly balances downward pumping. The implied eddy diffusivity varies spatially and decays with depth, with values of 50-400 m2/s. Eddy diffusivity estimated using mixing length theory applied to BG mooring data exhibits a similar decay with depth and range of values from 100 m2/s to more than 600 m2/s. We conclude that eddy diffusivities in the BG are likely large enough to balance downward Ekman pumping, arresting the deepening of the gyre and suggesting that eddies play a zero-order role in buoyancy and freshwater budgets of the BG.

Dynamics, Stability, and Evolutionary Patterns of Mesoscale Intrathermocline Vortices

DTIC Science & Technology

2016-12-01

physical oceanography, namely, the link between the basin-scale forcing of the ocean by air-sea fluxes and the dissipation of energy and thermal variance...at the microscale. 14. SUBJECT TERMS Meddy, intrathermocline, double diffusion, energy cascade, eddy, MITgcm, numerical simulation, interleaving...lateral intrusions, lateral diffusivity, heat flux 15. NUMBER OF PAGES 69 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT Unclassified 18

Mesoscopic monodisperse ferromagnetic colloids enable magnetically controlled photonic crystals.

PubMed

Xu, Xiangling; Majetich, Sara A; Asher, Sanford A

2002-11-20

We report here the first synthesis of mesoscopic, monodisperse particles which contain nanoscopic inclusions of ferromagnetic cobalt ferrites. These monodisperse ferromagnetic composite particles readily self-assemble into magnetically responsive photonic crystals that efficiently Bragg diffract incident light. Magnetic fields can be used to control the photonic crystal orientation and, thus, the diffracted wavelength. We demonstrate the use of these ferromagnetic particles to fabricate magneto-optical diffracting fluids and magnetically switchable diffracting mirrors.

Vortex-slip transitions in superconducting a-NbGe mesoscopic channels

NASA Astrophysics Data System (ADS)

Kokubo, N.; Sorop, T. G.; Besseling, R.; Kes, P. H.

2006-06-01

Intriguing and novel physical aspects related to the vortex flow dynamics have been recently observed in mesoscopic channel devices of a-NbGe with NbN channel edges. In this work we have systematically studied the flow properties of vortices confined in such mesoscopic channels as a function of the magnetic field history, using dc-transport and mode-locking (ML) measurements. As opposed to the field-down situation, in the field-up case a kink anomaly in the dc I-V curves is detected. The mode-locking measurements reveal that this anomaly is, in fact, a flow induced vortex slip transition: by increasing the external drive (either dc or ac) a sudden change occurs from n to n+2 moving vortex rows in the channel. The observed features can be explained in terms of an interplay between field focusing due to screening currents and a change in the predominant pinning mechanism.

Mesoscopic Fluctuations for the Thinned Circular Unitary Ensemble

NASA Astrophysics Data System (ADS)

Berggren, Tomas; Duits, Maurice

2017-09-01

In this paper we study the asymptotic behavior of mesoscopic fluctuations for the thinned Circular Unitary Ensemble. The effect of thinning is that the eigenvalues start to decorrelate. The decorrelation is stronger on the larger scales than on the smaller scales. We investigate this behavior by studying mesoscopic linear statistics. There are two regimes depending on the scale parameter and the thinning parameter. In one regime we obtain a CLT of a classical type and in the other regime we retrieve the CLT for CUE. The two regimes are separated by a critical line. On the critical line the limiting fluctuations are no longer Gaussian, but described by infinitely divisible laws. We argue that this transition phenomenon is universal by showing that the same transition and their laws appear for fluctuations of the thinned sine process in a growing box. The proofs are based on a Riemann-Hilbert problem for integrable operators.

Applicability of a diffusion model to lateral transport in the terrestrial and lunar exospheres.

NASA Technical Reports Server (NTRS)

Hodges, R. R., Jr.

1972-01-01

Kinetic theory is used to determine a series expansion of the vertical flux of particles in an exosphere in terms of time and space derivatives of particle concentration, exobase velocity, and temperature. For sufficiently large scale variations of these parameters in time and space, the series can be truncated to a form that is similar to a diffusion equation. Owing to this analogy, it is possible to unite the mathematical description of molecular diffusion, which governs thermospheric flow, and the corresponding exospheric equation by using effective transport coefficients which change smoothly with altitude through the transition from thermosphere to exosphere. A new definition of the exobase for lateral flow emerges from the analogy of exospheric and thermospheric diffusion, as the altitude where the horizontal mean free path length equals the mean horizontal extent of ballistic trajectories of the transported gas, as opposed to the scale height of the dominant gas which determines the exobase for escape. It is shown that the approximation of exospheric lateral flow as a diffusion process is applicable to global scale problems concerning terrestrial helium and heavier gases, and lunar gases heavier than helium.

Application of Lattice Boltzmann Methods in Complex Mass Transfer Systems

NASA Astrophysics Data System (ADS)

Sun, Ning

Lattice Boltzmann Method (LBM) is a novel computational fluid dynamics method that can easily handle complex and dynamic boundaries, couple local or interfacial interactions/reactions, and be easily parallelized allowing for simulation of large systems. While most of the current studies in LBM mainly focus on fluid dynamics, however, the inherent power of this method makes it an ideal candidate for the study of mass transfer systems involving complex/dynamic microstructures and local reactions. In this thesis, LBM is introduced to be an alternative computational method for the study of electrochemical energy storage systems (Li-ion batteries (LIBs) and electric double layer capacitors (EDLCs)) and transdermal drug design on mesoscopic scale. Based on traditional LBM, the following in-depth studies have been carried out: (1) For EDLCs, the simulation of diffuse charge dynamics is carried out for both the charge and the discharge processes on 2D systems of complex random electrode geometries (pure random, random spheres and random fibers). Steric effect of concentrated solutions is considered by using modified Poisson-Nernst-Plank (MPNP) equations and compared with regular Poisson-Nernst-Plank (PNP) systems. The effects of electrode microstructures (electrode density, electrode filler morphology, filler size, etc.) on the net charge distribution and charge/discharge time are studied in detail. The influence of applied potential during discharging process is also discussed. (2) For the study of dendrite formation on the anode of LIBs, it is shown that the Lattice Boltzmann model can capture all the experimentally observed features of microstructure evolution at the anode, from smooth to mossy to dendritic. The mechanism of dendrite formation process in mesoscopic scale is discussed in detail and compared with the traditional Sand's time theories. It shows that dendrite formation is closely related to the inhomogeneous reactively at the electrode-electrolyte interface. When the inhomogeneity is small, dendrites form mainly under high current densities, in which the mass transfer is dominated by electromigration; when the inhomogeneity is very large, dendrites may form under both high and low current densities, which is dominated by electromigration in high current density and by surface reactivity in low current density. We show that the critical current density for dendrite formation is sensitive to surface inhomogeneous reactivity and the onset time of dendrite formation is sensitive to the initial roughness of electrode. A new analysis method is introduced, which can predict the formation of dendrites in batteries at a very early stage even before large dendrites form. Charge/discharge cyclic properties of the system are also studied, which shows that electrode roughness will increase during cycles and the break-off of dendritic structures is inevitable once big dendrites form; however, it is possible to minimize the amount of break-off materials by optimizing the rate of discharge. (3) The LBM is also used to simulate intercalation reactions in a Li-Ion battery with graphite as anode and pure Li metal as counter electrode. Both galvanostatic and potentiostatic conditions were studied. The relation between operation parameters (current and potential) and electrode parameters (porosity, thickness and diffusivity) and plating times were discussed. Different equilibrium potentials forms (empirical fitting, fitting of SONY 18650 cell, and staged profiles) were also compared. By modifying the morphology of electrode with a density gradient, it was shown that much better electrode performance can be obtained, which can be helpful for the designing and manufacturing of better batteries. (4) The transdermal drug delivery system is also simulated by using LBM. Two kinds of transdermal structures are discussed: "brick and mortar" structure and a simple homogenized structure. It is demonstrated that the homogenized system is able to obtain similar steady state flux as the "brick and mortar" structure; however, in the early transient region, their flux value can be different. The influence of different system parameters (amount of drug in patch, patch thickness, partition coefficient at patch/ Stratum Corneum (SC) interface, and the diffusion coefficient of drug in each component) is discussed in details. It turns out that in this system, the rate-determine step for mass transfer should be the partition between patch and SC layers and the diffusion in the SC layer. The influence of enhancer is also tested. It is shown that by adding enhancers, the drug flux can be significantly increased. However, the peak time of drug does not necessarily match the peak flux time of enhancer. The peak time of drug could be adjusted (pushed earlier or dragged later) by using different kinds of enhancers, which has higher/smaller diffusivity than drug in the SC layer.

Tritium Fluxes through the Shallow Unsaturated Zone adjacent to a Radioactive Waste Disposal Facility in an Arid Environment

NASA Astrophysics Data System (ADS)

Maples, S.; Andraski, B. J.; Stonestrom, D. A.; Cooper, C. A.; Pohll, G.

2011-12-01

Studies at the U.S. Geological Survey's Amargosa Desert Research Site (ADRS) in southern Nevada have documented long-distance (>400-m) tritium (3H) transport adjacent to a commercial, low-level radioactive waste disposal facility. Transport at this scale is orders of magnitude greater than anticipated; however, lateral 3H fluxes through the shallow unsaturated zone (UZ) have not been investigated in detail. The objective of this study is to estimate and compare lateral and vertical tritiated water-vapor (3HHOg) fluxes in the shallow UZ and their relation to the observed plume migration. Previous studies have recognized two distinct plumes of 3H emanating from the facility. Shallow (0.5 and 1.5-m depth) soil-water vapor samples were collected yearly along 400-m long transects through both plumes from 2003-09. Within the south plume, 3H concentrations at 1.5-m depth have decreased by 44 ± 0.3% during this period, and plume advancement there has effectively ceased (i.e., rate of advance equals rate of decay). During the same period, the west plume showed a net decrease in concentration of 34 ± 0.9% within 100-m of the facility; however, plume advancement is observed at the leading edge of the plume, and concentrations 200-300-m from the facility show an increase in 3H concentration of 64 ± 28.4%. Lateral and vertical diffusive fluxes within both plumes were calculated using 3HHOg concentrations from 2006. Lateral 3HHOg diffusive fluxes within both plumes have been estimated 25-300-m from the facility at 1.5-m depth. Mean lateral 3HHOg diffusive fluxes are 10-14 g m-2 yr-1 within the south plume, and 10-13 g m-2 yr-1 within the west plume. Mean lateral fluxes in the south plume are an order of magnitude lower than in the west plume. This behavior corresponds with the observed relative immobility of the south plume, while the elevated west plume fluxes agree with the plume advancement seen there. Shallow, upward directed, mean vertical 3HHOg fluxes 25-300-m from the facility are estimated to be 10-12 g m-2 yr-1 in the south plume and 10-11 g m-2 yr-1 in the west plume. Within both plumes, mean vertical diffusive fluxes are two orders of magnitude greater than mean lateral diffusive fluxes. Lateral diffusive 3HHOg fluxes have been calculated similarly using 2001 south plume data and were compared to 2001 south plume vertical diffusive 3HHOg fluxes published by Andraski et al. (2005). Here, too, mean vertical fluxes dwarf mean lateral fluxes (10-11 g m-2 yr-1 vs. 10-14 g m-2 yr-1). This behavior highlights the importance of upward movement and release of 3H to the atmosphere. The potential role of advective lateral transport and its contribution to observed plume migration is also under investigation.

Temperature and chain length dependence of ultrafast vibrational dynamics of thiocyanate in alkylimidazolium ionic liquids: A random walk on a rugged energy landscape.

PubMed

Brinzer, Thomas; Garrett-Roe, Sean

2017-11-21

Ultrafast two-dimensional infrared spectroscopy of a thiocyanate vibrational probe (SCN - ) was used to investigate local dynamics in alkylimidazolium bis-[trifluoromethylsulfonyl]imide ionic liquids ([Im n,1 ][Tf 2 N], n = 2, 4, 6) at temperatures from 5 to 80 °C. The rate of frequency fluctuations reported by SCN - increases with increasing temperature and decreasing alkyl chain length. Temperature-dependent correlation times scale proportionally to temperature-dependent bulk viscosities of each ionic liquid studied. A multimode Brownian oscillator model demonstrates that very low frequency (<10 cm -1 ) modes primarily drive the observed spectral diffusion and that these modes broaden and blue shift on average with increasing temperature. An Arrhenius analysis shows activation barriers for local motions around the probe between 5.5 and 6.5 kcal/mol that are very similar to those for translational diffusion of ions. [Im 6,1 ][Tf 2 N] shows an unexpected decrease in activation energy compared to [Im 4,1 ][Tf 2 N] that may be related to mesoscopically ordered polar and nonpolar domains. A model of dynamics on a rugged potential energy landscape provides a unifying description of the observed Arrhenius behavior and the Brownian oscillator model of the low frequency modes.

The Stability Analysis Method of the Cohesive Granular Slope on the Basis of Graph Theory.

PubMed

Guan, Yanpeng; Liu, Xiaoli; Wang, Enzhi; Wang, Sijing

2017-02-27

This paper attempted to provide a method to calculate progressive failure of the cohesivefrictional granular geomaterial and the spatial distribution of the stability of the cohesive granular slope. The methodology can be divided into two parts: the characterization method of macro-contact and the analysis of the slope stability. Based on the graph theory, the vertexes, the edges and the edge sequences are abstracted out to characterize the voids, the particle contact and the macro-contact, respectively, bridging the gap between the mesoscopic and macro scales of granular materials. This paper adopts this characterization method to extract a graph from a granular slope and characterize the macro sliding surface, then the weighted graph is analyzed to calculate the slope safety factor. Each edge has three weights representing the sliding moment, the anti-sliding moment and the braking index of contact-bond, respectively, . The safety factor of the slope is calculated by presupposing a certain number of sliding routes and reducing Weight repeatedly and counting the mesoscopic failure of the edge. It is a kind of slope analysis method from mesoscopic perspective so it can present more detail of the mesoscopic property of the granular slope. In the respect of macro scale, the spatial distribution of the stability of the granular slope is in agreement with the theoretical solution.

Integrodifferential formulations of the continuous-time random walk for solute transport subject to bimolecular A +B →0 reactions: From micro- to mesoscopic

NASA Astrophysics Data System (ADS)

Hansen, Scott K.; Berkowitz, Brian

2015-03-01

We develop continuous-time random walk (CTRW) equations governing the transport of two species that annihilate when in proximity to one another. In comparison with catalytic or spontaneous transformation reactions that have been previously considered in concert with CTRW, both species have spatially variant concentrations that require consideration. We develop two distinct formulations. The first treats transport and reaction microscopically, potentially capturing behavior at sharp fronts, but at the cost of being strongly nonlinear. The second, mesoscopic, formulation relies on a separation-of-scales technique we develop to separate microscopic-scale reaction and upscaled transport. This simplifies the governing equations and allows treatment of more general reaction dynamics, but requires stronger smoothness assumptions of the solution. The mesoscopic formulation is easily tractable using an existing solution from the literature (we also provide an alternative derivation), and the generalized master equation (GME) for particles undergoing A +B →0 reactions is presented. We show that this GME simplifies, under appropriate circumstances, to both the GME for the unreactive CTRW and to the advection-dispersion-reaction equation. An additional major contribution of this work is on the numerical side: to corroborate our development, we develop an indirect particle-tracking-partial-integro-differential-equation (PIDE) hybrid verification technique which could be applicable widely in reactive anomalous transport. Numerical simulations support the mesoscopic analysis.

Observational Inferences of Lateral Eddy Diffusivity in the Halocline of the Beaufort Gyre

NASA Astrophysics Data System (ADS)

Meneghello, G.; Marshall, J.; Cole, S. T.; Timmermans, M. L.

2017-12-01

Using Ekman pumping rates mediated by sea-ice in the Arctic Ocean's Beaufort Gyre (BG), the magnitude of lateral eddy diffusivities required to balance downward pumping is inferred. In this limit — that of vanishing residual-mean circulation — eddy-induced upwelling exactly balances downward pumping. The implied eddy diffusivity varies spatially with values of 50-400 m2/s, and decays with depth. Eddy diffusivity estimated using mixing length theory applied to BG mooring data exhibits a similar range of values from 100 m2/s to more than 600 m2/s, and also decays with depth. We conclude that eddy diffusivities in the BG are likely large enough to balance downward Ekman pumping, arresting the deepening of the gyre and suggesting that eddies play a zero-order role in buoyancy and freshwater budgets of the BG.

Assessing lateral flows and solute transport during floods in a conduit-flow-dominated karst system using the inverse problem for the advection-diffusion equation

NASA Astrophysics Data System (ADS)

Cholet, Cybèle; Charlier, Jean-Baptiste; Moussa, Roger; Steinmann, Marc; Denimal, Sophie

2017-07-01

The aim of this study is to present a framework that provides new ways to characterize the spatio-temporal variability of lateral exchanges for water flow and solute transport in a karst conduit network during flood events, treating both the diffusive wave equation and the advection-diffusion equation with the same mathematical approach, assuming uniform lateral flow and solute transport. A solution to the inverse problem for the advection-diffusion equations is then applied to data from two successive gauging stations to simulate flows and solute exchange dynamics after recharge. The study site is the karst conduit network of the Fourbanne aquifer in the French Jura Mountains, which includes two reaches characterizing the network from sinkhole to cave stream to the spring. The model is applied, after separation of the base from the flood components, on discharge and total dissolved solids (TDSs) in order to assess lateral flows and solute concentrations and compare them to help identify water origin. The results showed various lateral contributions in space - between the two reaches located in the unsaturated zone (R1), and in the zone that is both unsaturated and saturated (R2) - as well as in time, according to hydrological conditions. Globally, the two reaches show a distinct response to flood routing, with important lateral inflows on R1 and large outflows on R2. By combining these results with solute exchanges and the analysis of flood routing parameters distribution, we showed that lateral inflows on R1 are the addition of diffuse infiltration (observed whatever the hydrological conditions) and localized infiltration in the secondary conduit network (tributaries) in the unsaturated zone, except in extreme dry periods. On R2, despite inflows on the base component, lateral outflows are observed during floods. This pattern was attributed to the concept of reversal flows of conduit-matrix exchanges, inducing a complex water mixing effect in the saturated zone. From our results we build the functional scheme of the karst system. It demonstrates the impact of the saturated zone on matrix-conduit exchanges in this shallow phreatic aquifer and highlights the important role of the unsaturated zone on storage and transfer functions of the system.

Characteristics of Superjunction Lateral-Double-Diffusion Metal Oxide Semiconductor Field Effect Transistor and Degradation after Electrical Stress

NASA Astrophysics Data System (ADS)

Lin, Jyh‑Ling; Lin, Ming‑Jang; Lin, Li‑Jheng

2006-04-01

The superjunction lateral double diffusion metal oxide semiconductor field effect has recently received considerable attention. Introducing heavily doped p-type strips to the n-type drift region increases the horizontal depletion capability. Consequently, the doping concentration of the drift region is higher and the conduction resistance is lower than those of conventional lateral-double-diffusion metal oxide semiconductor field effect transistors (LDMOSFETs). These characteristics may increase breakdown voltage (\\mathit{BV}) and reduce specific on-resistance (Ron,sp). In this study, we focus on the electrical characteristics of conventional LDMOSFETs on silicon bulk, silicon-on-insulator (SOI) LDMOSFETs and superjunction LDMOSFETs after bias stress. Additionally, the \\mathit{BV} and Ron,sp of superjunction LDMOSFETs with different N/P drift region widths and different dosages are discussed. Simulation tools, including two-dimensional (2-D) TSPREM-4/MEDICI and three-dimensional (3-D) DAVINCI, were employed to determine the device characteristics.

Mesoscopic entanglement induced by spontaneous emission in solid-state quantum optics.

PubMed

González-Tudela, Alejandro; Porras, Diego

2013-02-22

Implementations of solid-state quantum optics provide us with devices where qubits are placed at fixed positions in photonic or plasmonic one-dimensional waveguides. We show that solely by controlling the position of the qubits and with the help of a coherent driving, collective spontaneous decay may be engineered to yield an entangled mesoscopic steady state. Our scheme relies on the realization of pure superradiant Dicke models by a destructive interference that cancels dipole-dipole interactions in one dimension.

Modeling off-resonant nonlinear-optical cascading in mesoscopic thin films and guest-host molecular systems

NASA Astrophysics Data System (ADS)

Dawson, Nathan J.; Andrews, James H.; Crescimanno, Michael

2013-12-01

A model for off-resonant microscopic cascading of (hyper)polarizabilities is developed using a self-consistent field approach to study mesoscopic systems of nonlinear polarizable atoms and molecules. We find enhancements in the higher-order susceptibilities resulting from geometrical and boundary orientation effects. We include an example of the dependence on excitation beam cross sectional structure and a simplified derivation of the microscopic cascading of the nonlinear-optical response in guest-host systems.

Mesoscopic Vortex–Meissner currents in ring ladders

NASA Astrophysics Data System (ADS)

Haug, Tobias; Amico, Luigi; Dumke, Rainer; Kwek, Leong-Chuan

2018-07-01

Recent experimental progress have revealed Meissner and Vortex phases in low-dimensional ultracold atoms systems. Atomtronic setups can realize ring ladders, while explicitly taking the finite size of the system into account. This enables the engineering of quantized chiral currents and phase slips in between them. We find that the mesoscopic scale modifies the current. Full control of the lattice configuration reveals a reentrant behavior of Vortex and Meissner phases. Our approach allows a feasible diagnostic of the currents’ configuration through time-of-flight measurements.

Fractal Tomlinson model for mesoscopic friction: from microscopic velocity-dependent damping to macroscopic Coulomb friction.

PubMed

Filippov, A E; Popov, V L

2007-02-01

A modified Tomlinson equation with fractal potential is studied. The effective potential is numerically generated and its mesoscopic structure is gradually adjusted to different scales by a number of Fourier modes. It is shown that with the change of scale the intensity of velocity-dependent damping in an effective Langevin equation can be gradually substituted by an equivalent constant "dry friction." For smooth macrosopic surfaces the effective equation completely reduces to the well known Coulomb law.

Quantum Device Applications of Mesoscopic Superconductivity

NASA Astrophysics Data System (ADS)

Hakonen, P. J.

2006-08-01

A brief account is given on the possibilities of mesoscopic superconductivity in low-noise amplifier and detector applications. In particular, three devices will be described: 1) Bloch oscillating transistor (BOT), 2) Inductively-read superconducting Cooper pair transistor (L-SET), and 3) Quantum capacitive phase detector (C-SET). The BOT is a low-noise current amplifier while the L-SET and C-SET act as ultra-sensitive charge and phase detectors, respectively. The basic operating principles and the main characteristics of these devices will be reviewed and discussed.

Superconductivity in disordered thin films: giant mesoscopic fluctuations.

PubMed

Skvortsov, M A; Feigel'man, M V

2005-07-29

We discuss the intrinsic inhomogeneities of superconductive properties of uniformly disordered thin films with a large dimensionless conductance g. It is shown that mesoscopic fluctuations, which usually contain a small factor 1/g, are crucially enhanced near the critical conductance g(cF) > 1 where superconductivity is destroyed at T = 0 due to Coulomb suppression of the Cooper attraction. This leads to strong spatial fluctuations of the local transition temperature and thus to the percolative nature of the thermal superconductive transition.

Universal broadening of the Bardeen-Cooper-Schrieffer coherence peak of disordered superconducting films.

PubMed

Feigel'man, M V; Skvortsov, M A

2012-10-05

In disordered superconductors, the local pairing field fluctuates in space, leading to the smearing of the BCS peak in the density of states and the appearance of the subgap tail states. We analyze the universal mesoscopic contributions to these effects and show that they are enhanced by the Coulomb repulsion. In the vicinity of the quantum critical point, where superconductivity is suppressed by the "fermionic mechanism," strong smearing of the peak due to mesoscopic fluctuations is predicted.

Disorder-Enhanced Dielectric Response of Nanoscale and Mesoscopic Insulators

NASA Astrophysics Data System (ADS)

Onoda, Shigeki; Chern, Chyh-Hong; Murakami, Shuichi; Ogimoto, Yasushi; Nagaosa, Naoto

2006-12-01

Enhancement of the dielectric response of insulators by disorder is theoretically proposed, where the quantum interference of electronic waves through the nanoscale or mesoscopic system and its change due to external perturbations control the polarization. In the disordered case with all the states being localized, the resonant tunneling, which is topologically protected, plays a crucial role, and enhances the dielectric response by a factor 30 40 compared with the pure case. The realization of this idea with accessible materials or structures is also discussed.

An extended model of vesicle fusion at the plasma membrane to estimate protein lateral diffusion from TIRF microscopy images.

PubMed

Basset, Antoine; Bouthemy, Patrick; Boulanger, Jérôme; Waharte, François; Salamero, Jean; Kervrann, Charles

2017-07-24

Characterizing membrane dynamics is a key issue to understand cell exchanges with the extra-cellular medium. Total internal reflection fluorescence microscopy (TIRFM) is well suited to focus on the late steps of exocytosis at the plasma membrane. However, it is still a challenging task to quantify (lateral) diffusion and estimate local dynamics of proteins. A new model was introduced to represent the behavior of cargo transmembrane proteins during the vesicle fusion to the plasma membrane at the end of the exocytosis process. Two biophysical parameters, the diffusion coefficient and the release rate parameter, are automatically estimated from TIRFM image sequences, to account for both the lateral diffusion of molecules at the membrane and the continuous release of the proteins from the vesicle to the plasma membrane. Quantitative evaluation on 300 realistic computer-generated image sequences demonstrated the efficiency and accuracy of the method. The application of our method on 16 real TIRFM image sequences additionally revealed differences in the dynamic behavior of Transferrin Receptor (TfR) and Langerin proteins. An automated method has been designed to simultaneously estimate the diffusion coefficient and the release rate for each individual vesicle fusion event at the plasma membrane in TIRFM image sequences. It can be exploited for further deciphering cell membrane dynamics.

Tract-Specific Diffusion Tensor Imaging Reveals Laterality of Neurological Symptoms in Patients with Cervical Compression Myelopathy.

PubMed

Maki, Satoshi; Koda, Masao; Saito, Junya; Takahashi, Sho; Inada, Taigo; Kamiya, Koshiro; Ota, Mitsutoshi; Iijima, Yasushi; Masuda, Yoshitada; Matsumoto, Koji; Kojima, Masatoshi; Takahashi, Kazuhisa; Obata, Takayuki; Yamazaki, Masashi; Furuya, Takeo

2016-12-01

Patients with cervical compression myelopathy (CCM) generally present bilateral neurological symptoms in their extremities. However, a substantial portion of patients with CCM exhibit laterality of neurological symptoms. The aim of this study was to assess the correlation between intrinsic structural damage and laterality of symptoms using spinal cord diffusion tensor imaging (DTI) of the corticospinal tract. We enrolled 10 healthy volunteers and 40 patients with CCM in this study. We evaluated motor function using the American Spinal Injury Association (ASIA) motor score for left and right extremities. For DTI acquisitions, a 3.0-T magnetic resonance imaging system with diffusion-weighted spin-echo sequence was used. Regions-of-interest in the lateral column tracts were determined. We determined the correlations between fractional anisotropy (FA) and ASIA motor scores. An FA asymmetry index was calculated using left and right regions-of-interest. Four patients exhibited laterality of symptoms in their extremities, for which left and right ASIA scores correlated moderately with FA in the left and right lateral columns, respectively (left: ρ = 0.64, P < 0.001; right: ρ = 0.67, P < 0.001). The area under the receiver-operator characteristic curve showed that the FA asymmetry index indicated laterality of symptoms. Using tract-specific DTI, we demonstrated that microstructural damages in the left and right corticospinal tracts correlated with corresponding neurological symptoms in the ipsilateral side and the FA asymmetry index could indicate laterality in neurological symptoms of patients with CCM. Copyright © 2016 Elsevier Inc. All rights reserved.

Contributions of Microtubule Dynamic Instability and Rotational Diffusion to Kinetochore Capture.

PubMed

Blackwell, Robert; Sweezy-Schindler, Oliver; Edelmaier, Christopher; Gergely, Zachary R; Flynn, Patrick J; Montes, Salvador; Crapo, Ammon; Doostan, Alireza; McIntosh, J Richard; Glaser, Matthew A; Betterton, Meredith D

2017-02-07

Microtubule dynamic instability allows search and capture of kinetochores during spindle formation, an important process for accurate chromosome segregation during cell division. Recent work has found that microtubule rotational diffusion about minus-end attachment points contributes to kinetochore capture in fission yeast, but the relative contributions of dynamic instability and rotational diffusion are not well understood. We have developed a biophysical model of kinetochore capture in small fission-yeast nuclei using hybrid Brownian dynamics/kinetic Monte Carlo simulation techniques. With this model, we have studied the importance of dynamic instability and microtubule rotational diffusion for kinetochore capture, both to the lateral surface of a microtubule and at or near its end. Over a range of biologically relevant parameters, microtubule rotational diffusion decreased capture time, but made a relatively small contribution compared to dynamic instability. At most, rotational diffusion reduced capture time by 25%. Our results suggest that while microtubule rotational diffusion can speed up kinetochore capture, it is unlikely to be the dominant physical mechanism for typical conditions in fission yeast. In addition, we found that when microtubules undergo dynamic instability, lateral captures predominate even in the absence of rotational diffusion. Counterintuitively, adding rotational diffusion to a dynamic microtubule increases the probability of end-on capture. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Studying microstructure and microstructural changes in plant tissues by advanced diffusion magnetic resonance imaging techniques

PubMed Central

Morozov, Darya; Tal, Iris; Pisanty, Odelia; Shani, Eilon

2017-01-01

Abstract As sessile organisms, plants must respond to the environment by adjusting their growth and development. Most of the plant body is formed post-embryonically by continuous activity of apical and lateral meristems. The development of lateral adventitious roots is a complex process, and therefore the development of methods that can visualize, non-invasively, the plant microstructure and organ initiation that occur during growth and development is of paramount importance. In this study, relaxation-based and advanced diffusion magnetic resonance imaging (MRI) methods including diffusion tensor (DTI), q-space diffusion imaging (QSI), and double-pulsed-field-gradient (d-PFG) MRI, at 14.1 T, were used to characterize the hypocotyl microstructure and the microstructural changes that occurred during the development of lateral adventitious roots in tomato. Better contrast was observed in relaxation-based MRI using higher in-plane resolution but this also resulted in a significant reduction in the signal-to-noise ratio of the T2-weighted MR images. Diffusion MRI revealed that water diffusion is highly anisotropic in the vascular cylinder. QSI and d-PGSE MRI showed that in the vascular cylinder some of the cells have sizes in the range of 6–10 μm. The MR images captured cell reorganization during adventitious root formation in the periphery of the primary vascular bundles, adjacent to the xylem pole that broke through the cortex and epidermis layers. This study demonstrates that MRI and diffusion MRI methods allow the non-invasive study of microstructural features of plants, and enable microstructural changes associated with adventitious root formation to be followed. PMID:28398563

Elastic properties of magnetorheological elastomer: description with the two-particle mesoscopic model

NASA Astrophysics Data System (ADS)

Biller, A. M.; Stolbov, O. V.; Raikher, Yu L.

2017-06-01

A pair of magnetizable solid particles embedded in a cylinder made of high-elasticity material is considered as a model of a mesoscopic structure element of a magnetorheological elastomer. An applied magnetic field induces ponderomotive interaction of the particles making them to move relative to one another so as to balance the counteracting magnetic and elastic forces. In a certain parameter range, the system exhibits bistability due to which under the increase / decrease of the field, the interparticle distance changes in a hysteretic manner. This behavior has a significant effect on the ability of the mesoscopic element to resist external load. Using the developed two-particle model prone to the magnetomechanical hysteresis, we extend it to the case of a virtually macroscopic sample presenting the latter as a superposition of such elements with distributed interparticle distances. In spite of its simplicity, this scheme in a generally correct way describes the field-induced changes of the internal structure and elastic modulus of the magnetorheological composites.

Mesohysteresis model for ferromagnetic materials by minimization of the micromagnetic free energy

NASA Astrophysics Data System (ADS)

van den Berg, A.; Dupré, L.; Van de Wiele, B.; Crevecoeur, G.

2009-04-01

To study the connection between macroscopic hysteretic behavior and the microstructural properties, this paper presents and validates a new material dependent three-dimensional mesoscopic magnetic hysteresis model. In the presented mesoscopic description, the different micromagnetic energy terms are reformulated on the space scale of the magnetic domains. The sample is discretized in cubic cells, each with a local stress state, local bcc crystallographic axes, etc. The magnetization is assumed to align with one of the three crystallographic axes, in positive or negative sense, defining six volume fractions within each cell. The micromagnetic Gibbs free energy is described in terms of these volume fractions. Hysteresis loops are computed by minimizing the mesoscopic Gibbs free energy using a modified gradient search for a sequence of external applied fields. To validate the mesohysteresis model, we studied the magnetic memory properties. Numerical experiments reveal that (1) minor hysteresis loops are indeed closed and (2) the closed minor loops are erased from the memory.

Interface Engineering Based on Liquid Metal for Compact-Layer-free, Fully Printable Mesoscopic Perovskite Solar Cells.

PubMed

Zhang, Yumin; Zhao, Jianhong; Zhang, Jin; Jiang, Xixi; Zhu, Zhongqi; Liu, Qingju

2018-05-09

A printing process for the fabrication of perovskite solar cells (PSCs) exhibits promising future application in the photovoltaic industry due to its low-cost and eco-friendly preparation. In mesoscopic carbon-based PSCs, however, compared to conventional ones, the hole-transport-layer-free PSCs often lead to inefficient hole extraction. Here, we used liquid metal (LM, Galinstan) as an interface modifier material in combination with a carbon electrode. Considering the high conductivity and room-temperature fluidity, it is found that LMs are superior in improving hole extraction and, more importantly, LMs tend to be reserved at the interface between ZrO 2 and carbon for enhancing the contact property. Correspondingly, the carrier transfer resistance was decreased at the carbon/perovskite interface. As optimized content, the triple mesoscopic PSCs based on mixed-cation perovskite with a power conversion efficiency of 13.51% was achieved, involving a 26% increase compared to those without LMs. This work opens new techniques for LMs in optoelectronics and printing.

Quantum mechanics and the second law of thermodynamics: an insight gleaned from magnetic hysteresis in the first order phase transition of an isolated mesoscopic-size type I superconductor

NASA Astrophysics Data System (ADS)

Keefe, Peter D.

2012-11-01

J Bardeen proposed that the adiabatic phase transition of mesoscopic-size type I superconductors must be accompanied by magnetic hysteresis in the critical magnetic field of sufficient magnitude to satisfy the second law of thermodynamics, herein referred to as ‘Bardeen Hysteresis’. Bardeen Hysteresis remains speculative in that it has not been reported in the literature. This paper investigates Bardeen Hysteresis as a possible accompaniment to the adiabatic phase transition of isolated mesoscopic-size type I superconductors and its implications with respect to the second law of thermodynamics. A causal mechanism for Bardeen Hysteresis is discussed which contrasts with the long accepted causal mechanism of magnetic hysteresis, as first summarized by Pippard, herein referred to as ‘Pippard Hysteresis’. The paper offers guidance for an experimental verification and comments on how the existence of Bardeen Hysteresis has relation to a quantum mechanical basis for the second law of thermodynamics.

Mesoscopic superconductivity and high spin polarization coexisting at metallic point contacts on Weyl semimetal TaAs

PubMed Central

Aggarwal, Leena; Gayen, Sirshendu; Das, Shekhar; Kumar, Ritesh; Süß, Vicky; Felser, Claudia; Shekhar, Chandra; Sheet, Goutam

2017-01-01

A Weyl semimetal is a topologically non-trivial phase of matter that hosts mass-less Weyl fermions, the particles that remained elusive for more than 80 years since their theoretical discovery. The Weyl semimetals exhibit unique transport properties and remarkably high surface spin polarization. Here we show that a mesoscopic superconducting phase with critical temperature Tc=7 K can be realized by forming metallic point contacts with silver (Ag) on single crystals of TaAs, while neither Ag nor TaAs are superconductors. Andreev reflection spectroscopy of such point contacts reveals a superconducting gap of 1.2 meV that coexists with a high transport spin polarization of 60% indicating a highly spin-polarized supercurrent flowing through the point contacts on TaAs. Therefore, apart from the discovery of a novel mesoscopic superconducting phase, our results also show that the point contacts on Weyl semimetals are potentially important for applications in spintronics. PMID:28071685

Multimodel analysis of anisotropic diffusive tracer-gas transport in a deep arid unsaturated zone

USGS Publications Warehouse

Green, Christopher T.; Walvoord, Michelle Ann; Andraski, Brian J.; Striegl, Robert G.; Stonestrom, David A.

2015-01-01

Gas transport in the unsaturated zone affects contaminant flux and remediation, interpretation of groundwater travel times from atmospheric tracers, and mass budgets of environmentally important gases. Although unsaturated zone transport of gases is commonly treated as dominated by diffusion, the characteristics of transport in deep layered sediments remain uncertain. In this study, we use a multimodel approach to analyze results of a gas-tracer (SF6) test to clarify characteristics of gas transport in deep unsaturated alluvium. Thirty-five separate models with distinct diffusivity structures were calibrated to the tracer-test data and were compared on the basis of Akaike Information Criteria estimates of posterior model probability. Models included analytical and numerical solutions. Analytical models provided estimates of bulk-scale apparent diffusivities at the scale of tens of meters. Numerical models provided information on local-scale diffusivities and feasible lithological features producing the observed tracer breakthrough curves. The combined approaches indicate significant anisotropy of bulk-scale diffusivity, likely associated with high-diffusivity layers. Both approaches indicated that diffusivities in some intervals were greater than expected from standard models relating porosity to diffusivity. High apparent diffusivities and anisotropic diffusivity structures were consistent with previous observations at the study site of rapid lateral transport and limited vertical spreading of gas-phase contaminants. Additional processes such as advective oscillations may be involved. These results indicate that gases in deep, layered unsaturated zone sediments can spread laterally more quickly, and produce higher peak concentrations, than predicted by homogeneous, isotropic diffusion models.

The Stability Analysis Method of the Cohesive Granular Slope on the Basis of Graph Theory

PubMed Central

Guan, Yanpeng; Liu, Xiaoli; Wang, Enzhi; Wang, Sijing

2017-01-01

This paper attempted to provide a method to calculate progressive failure of the cohesive-frictional granular geomaterial and the spatial distribution of the stability of the cohesive granular slope. The methodology can be divided into two parts: the characterization method of macro-contact and the analysis of the slope stability. Based on the graph theory, the vertexes, the edges and the edge sequences are abstracted out to characterize the voids, the particle contact and the macro-contact, respectively, bridging the gap between the mesoscopic and macro scales of granular materials. This paper adopts this characterization method to extract a graph from a granular slope and characterize the macro sliding surface, then the weighted graph is analyzed to calculate the slope safety factor. Each edge has three weights representing the sliding moment, the anti-sliding moment and the braking index of contact-bond, respectively, E1E2E3E1E2E3. The safety factor of the slope is calculated by presupposing a certain number of sliding routes and reducing Weight E3 repeatedly and counting the mesoscopic failure of the edge. It is a kind of slope analysis method from mesoscopic perspective so it can present more detail of the mesoscopic property of the granular slope. In the respect of macro scale, the spatial distribution of the stability of the granular slope is in agreement with the theoretical solution. PMID:28772596

Effect of integral membrane proteins on the lateral mobility of plastoquinone in phosphatidylcholine proteoliposomes.

PubMed

Blackwell, M F; Whitmarsh, J

1990-11-01

PYRENE FLUORESCENCE QUENCHING BY PLASTOQUINONE WAS USED TO ESTIMATE THE RATE OF PLASTOQUINONE LATERAL DIFFUSION IN SOYBEAN PHOSPHATIDYLCHOLINE PROTEOLIPOSOMES CONTAINING THE FOLLOWING INTEGRAL MEMBRANE PROTEINS: gramicidin D, spinach cytochrome bf complex, spinach cytochrome f, reaction centers from Rhodobacter sphaeroides, beef heart mitochondrial cytochrome bc(1), and beef heart mitochondrial cytochrome oxidase. The measured plastoquinone lateral diffusion coefficient varied between 1 and 3 . 10(-7) cm(2) s(-1) in control liposomes that lacked protein. When proteins were added, these values decreased: a 10-fold decrease was observed when 16-26% of the membrane surface area was occupied by protein for all the proteins but gramicidin. The larger protein complexes (cytochrome bf, Rhodobacter sphaeroides reaction centers, cytochrome bc(1), and cytochrome oxidase), whose hydrophobic volumes were 15-20 times as large as that of cytochrome f and the gramicidin transmembrane dimer, were 15-20 times as effective in decreasing the lateral-diffusion coefficient over the range of concentrations studied. These proteins had a much stronger effect than that observed for bacteriorhodopsin in fluorescence photobleaching recovery measurements. The effect of high-protein concentrations in gramicidin proteoliposomes was in close agreement with fluorescence photobleaching measurements. The results are compared with the predictions of several theoretical models of lateral mobility as a function of integral membrane concentration.

Effect of integral membrane proteins on the lateral mobility of plastoquinone in phosphatidylcholine proteoliposomes

PubMed Central

Blackwell, Mary F.; Whitmarsh, John

1990-01-01

Pyrene fluorescence quenching by plastoquinone was used to estimate the rate of plastoquinone lateral diffusion in soybean phosphatidylcholine proteoliposomes containing the following integral membrane proteins: gramicidin D, spinach cytochrome bf complex, spinach cytochrome f, reaction centers from Rhodobacter sphaeroides, beef heart mitochondrial cytochrome bc1, and beef heart mitochondrial cytochrome oxidase. The measured plastoquinone lateral diffusion coefficient varied between 1 and 3 · 10-7 cm2 s-1 in control liposomes that lacked protein. When proteins were added, these values decreased: a 10-fold decrease was observed when 16-26% of the membrane surface area was occupied by protein for all the proteins but gramicidin. The larger protein complexes (cytochrome bf, Rhodobacter sphaeroides reaction centers, cytochrome bc1, and cytochrome oxidase), whose hydrophobic volumes were 15-20 times as large as that of cytochrome f and the gramicidin transmembrane dimer, were 15-20 times as effective in decreasing the lateral-diffusion coefficient over the range of concentrations studied. These proteins had a much stronger effect than that observed for bacteriorhodopsin in fluorescence photobleaching recovery measurements. The effect of high-protein concentrations in gramicidin proteoliposomes was in close agreement with fluorescence photobleaching measurements. The results are compared with the predictions of several theoretical models of lateral mobility as a function of integral membrane concentration. PMID:19431774

Arcuate fasciculus laterality by diffusion tensor imaging correlates with language laterality by functional MRI in preadolescent children.

PubMed

Sreedharan, Ruma Madhu; Menon, Amitha C; James, Jija S; Kesavadas, Chandrasekharan; Thomas, Sanjeev V

2015-03-01

Language lateralization is unique to humans. Functional MRI (fMRI) and diffusion tensor imaging (DTI) enable the study of language areas and white matter fibers involved in language, respectively. The objective of this study was to correlate arcuate fasciculus (AF) laterality by diffusion tensor imaging with that by fMRI in preadolescent children which has not yet been reported. Ten children between 8 and 12 years were subjected to fMRI and DTI imaging using Siemens 1.5 T MRI. Two language fMRI paradigms--visual verb generation and word pair task--were used. Analysis was done using SPM8 software. In DTI, the fiber volume of the arcuate fasciculus (AFV) and fractional anisotropy (FA) was measured. The fMRI Laterality Index (fMRI-LI) and DTI Laterality Index (DTI-LI) were calculated and their correlation assessed using the Pearson Correlation Index. Of ten children, mean age 10.6 years, eight showed left lateralization while bilateral language lateralization was seen in two. AFV by DTI was more on the left side in seven of the eight children who had left lateralization by fMRI. DTI could not trace the AF in one child. Of the two with bilateral language lateralization on fMRI, one showed larger AFV on the right side while the other did not show any asymmetry. There was a significant correlation (p < 0.02) between fMRI-LI and DTI-LI. Group mean of AFV by DTI was higher on the left side (2659.89 ± 654.75 mm(3)) as compared to the right (1824.11 ± 582.81 mm(3)) (p < 0.01). Like fMRI, DTI also reveals language laterality in children with a high degree of correlation between the two imaging modalities.

Vertical eddy diffusion coefficient from the LANDSAT imagery

NASA Technical Reports Server (NTRS)

Viswanadham, Y. (Principal Investigator); Torsani, J. A.

1982-01-01

Analysis of five stable cases of the smoke plumes that originated in eastern Cabo Frio (22 deg 59'S; 42 deg 02'W), Brazil using LANDSAT imagery is presented for different months and years. From these images the lateral standard deviation (sigma sub y) and the lateral eddy diffusion coefficient (K sub y) are obtained from the formula based on Taylor's theory of diffusion by continuous moment. The rate of kinetic energy dissipation (e) is evaluated from the diffusion parameters sigma sub y and K sub y. Then, the vertical diffusion coefficient (K sub z) is estimated using Weinstock's formulation. These results agree well with the previous experimental values obtained over water surfaces by various workers. Values of e and K sub z show the weaker mixing processes in the marine stable boundary layer. The data sample is apparently to small to include representative active turbulent regions because such regions are so intermittent in time and in space. These results form a data base for use in the development and validation of mesoscale atmospheric diffusion models.

Influence of impeller and diffuser geometries on the lateral fluid forces of whirling centrifugal impeller

NASA Technical Reports Server (NTRS)

Ohashi, Hideo; Sakurai, Akira; Nishihama, Jiro

1989-01-01

Lateral fluid forces on two-dimensional centrifugal impellers, which whirl on a circular orbit in a vaneless diffuser, were reported. Experiments were further conducted for the cases in which a three-dimensional centrifugal impeller, a model of the boiler feed pump, whirls in vaneless and vaned diffusers. The influence of the clearance configuration between the casing and front shroud of the impeller was also investigated. The result indicated that the fluid dynamic interaction between the impeller and the guide vanes induces quite strong fluctuating fluid forces to the impeller, but nevertheless its influence on radial and tangential force components averaged over a whirling orbit is relatively small.

Electronic Phase Separation in the Slightly Underdoped Iron Pnictide Superconductor Ba{sub 1-x}K{sub x}Fe{sub 2}As{sub 2}

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

Park, J. T.; Inosov, D. S.; Sun, G. L.

2009-03-20

Here we present a combined study of the slightly underdoped novel pnictide superconductor Ba{sub 1-x}K{sub x}Fe{sub 2}As{sub 2} by means of x-ray powder diffraction, neutron scattering, muon-spin rotation ({mu}SR), and magnetic force microscopy (MFM). Static antiferromagnetic order sets in below T{sub m}{approx_equal}70 K as inferred from the neutron scattering and zero-field-{mu}SR data. Transverse-field {mu}SR below T{sub c} shows a coexistence of magnetically ordered and nonmagnetic states, which is also confirmed by MFM imaging. We explain such coexistence by electronic phase separation into antiferromagnetic and superconducting- or normal-state regions on a lateral scale of several tens of nanometers. Our findings indicatemore » that such mesoscopic phase separation can be considered an intrinsic property of some iron pnictide superconductors.« less

Breakdown of the independent electron picture in mesoscopic samples at low temperatures: The hunt for the Unicorn

NASA Astrophysics Data System (ADS)

Webb, R. A.

1998-03-01

A variety of experiments are discussed where, at low temperatures, it appears that the non-interacting picture of electrons in a Fermi liquid description of a mesoscopic sample is breaking down. Specifically, experiments on the temperature dependence of the phase-coherence time, energy relaxation rate, spin-flip scattering time, persistent currents in normal metals and transmission through a barrier in the fractional quantum Hall regime all display low-temperature properties which can not be accounted for in the independent electron picture.

Mesoscopic Free Path of Nonthermalized Photogenerated Carriers in a Ferroelectric Insulator.

PubMed

Gu, Zongquan; Imbrenda, Dominic; Bennett-Jackson, Andrew L; Falmbigl, Matthias; Podpirka, Adrian; Parker, Thomas C; Shreiber, Daniel; Ivill, Mathew P; Fridkin, Vladimir M; Spanier, Jonathan E

2017-03-03

We show how finite-size scaling of a bulk photovoltaic effect-generated electric field in epitaxial ferroelectric insulating BaTiO_{3}(001) films and a photo-Hall response involving the bulk photovoltaic current reveal a large room-temperature mean free path of photogenerated nonthermalized electrons. Experimental determination of mesoscopic ballistic optically generated carrier transport opens a new paradigm for hot electron-based solar energy conversion, and for facile control of ballistic transport distinct from existing low-dimensional semiconductor interfaces, surfaces, layers, or other structures.

Cluster growth mechanisms in Lennard-Jones fluids: A comparison between molecular dynamics and Brownian dynamics simulations

NASA Astrophysics Data System (ADS)

Jung, Jiyun; Lee, Jumin; Kim, Jun Soo

2015-03-01

We present a simulation study on the mechanisms of a phase separation in dilute fluids of Lennard-Jones (LJ) particles as a model of self-interacting molecules. Molecular dynamics (MD) and Brownian dynamics (BD) simulations of the LJ fluids are employed to model the condensation of a liquid droplet in the vapor phase and the mesoscopic aggregation in the solution phase, respectively. With emphasis on the cluster growth at late times well beyond the nucleation stage, we find that the growth mechanisms can be qualitatively different: cluster diffusion and coalescence in the MD simulations and Ostwald ripening in the BD simulations. We also show that the rates of the cluster growth have distinct scaling behaviors during cluster growth. This work suggests that in the solution phase the random Brownian nature of the solute dynamics may lead to the Ostwald ripening that is qualitatively different from the cluster coalescence in the vapor phase.

Suspended sub-50 nm vanadium dioxide membrane transistors: fabrication and ionic liquid gating studies

NASA Astrophysics Data System (ADS)

Sim, Jai S.; Zhou, You; Ramanathan, Shriram

2012-10-01

We demonstrate a robust lithographic patterning method to fabricate self-supported sub-50 nm VO2 membranes that undergo a phase transition. Utilizing such self-supported membranes, we directly observed a shift in the metal-insulator transition temperature arising from stress relaxation and consistent opening of the hysteresis. Electric double layer transistors were then fabricated with the membranes and compared to thin film devices. The ionic liquid allowed reversible modulation of channel resistance and distinguishing bulk processes from the surface effects. From the shift in the metal-insulator transition temperature, the carrier density doped through electrolyte gating is estimated to be 1 × 1020 cm-3. Hydrogen annealing studies showed little difference in resistivity between the film and the membrane indicating rapid diffusion of hydrogen in the vanadium oxide rutile lattice consistent with previous observations. The ability to fabricate electrically-wired, suspended VO2 ultra-thin membranes creates new opportunities to study mesoscopic size effects on phase transitions and may also be of interest in sensor devices.

Operational properties of fluctuation X-ray scattering data

DOE PAGES

Malmerberg, Erik; Kerfeld, Cheryl A.; Zwart, Petrus H.

2015-03-20

X-ray scattering images collected on timescales shorter than rotation diffusion times using a (partially) coherent beam result in a significant increase in information content in the scattered data. These measurements, named fluctuation X-ray scattering (FXS), are typically performed on an X-ray free-electron laser (XFEL) and can provide fundamental insights into the structure of biological molecules, engineered nanoparticles or energy-related mesoscopic materials beyond what can be obtained with standard X-ray scattering techniques. In order to understand, use and validate experimental FXS data, the availability of basic data characteristics and operational properties is essential, but has been absent up to this point.more » In this communication, an intuitive view of the nature of FXS data and their properties is provided, the effect of FXS data on the derived structural models is highlighted, and generalizations of the Guinier and Porod laws that can ultimately be used to plan experiments and assess the quality of experimental data are presented.« less

Flux-induced Nernst effect in low-dimensional superconductors

NASA Astrophysics Data System (ADS)

Berger, Jorge

2017-02-01

A method is available that enables consistent study of the stochastic behavior of a system that obeys purely diffusive evolution equations. This method has been applied to a superconducting loop with nonuniform temperature, with average temperature close to Tc. It is found that a flux-dependent average potential difference arises along the loop, proportional to the temperature gradient and most pronounced in the direction perpendicular to this gradient. The largest voltages were obtained for fluxes close to 0.3Φ0, average temperatures slightly below the critical temperature, thermal coherence length of the order of the perimeter of the ring, BCS coherence length that is not negligible in comparison to the thermal coherence length, and short inelastic scattering time. This effect is entirely due to thermal fluctuations. It differs essentially from the usual Nernst effect in bulk superconductors, that is induced by magnetic field rather than by magnetic flux. We also study the effect of confinement in a 2D mesoscopic film.

Lateral Hydrogen Diffusion at p-GaN Layers in Nitride-Based Light Emitting Diodes with Tunnel Junctions

NASA Astrophysics Data System (ADS)

Kuwano, Yuka; Kaga, Mitsuru; Morita, Takatoshi; Yamashita, Kouji; Yagi, Kouta; Iwaya, Motoaki; Takeuchi, Tetsuya; Kamiyama, Satoshi; Akasaki, Isamu

2013-08-01

We demonstrated lateral Mg activation along p-GaN layers underneath n-GaN surface layers in nitride-based light emitting diodes (LEDs) with GaInN tunnel junctions. A high temperature thermal annealing was effective for the lateral Mg activation when the p-GaN layers were partly exposed to an oxygen ambient as etched sidewalls. The activated regions gradually extended from the etched sidewalls to the centers with an increase of annealing time, observed as emission regions with current injection. These results suggest that hydrogen diffuses not vertically thorough the above n-GaN but laterally through the exposed portions of the p-GaN. The lowest voltage drop at the GaInN tunnel junction was estimated to be 0.9 V at 50 mA with the optimized annealing condition.

A Potential Biomarker in Amyotrophic Lateral Sclerosis: Can Assessment of Brain Iron Deposition with SWI and Corticospinal Tract Degeneration with DTI Help?

PubMed

Sheelakumari, R; Madhusoodanan, M; Radhakrishnan, A; Ranjith, G; Thomas, B

2016-02-01

Iron-mediated oxidative stress plays a pivotal role in the pathogenesis of amyotrophic lateral sclerosis. This study aimed to assess iron deposition qualitatively and quantitatively by using SWI and microstructural changes in the corticospinal tract by using DTI in patients with amyotrophic lateral sclerosis. Seventeen patients with amyotrophic lateral sclerosis and 15 age- and sex-matched controls underwent brain MR imaging with SWI and DTI. SWI was analyzed for both signal-intensity scoring and quantitative estimation of iron deposition in the anterior and posterior banks of the motor and sensory cortices and deep gray nuclei. The diffusion measurements along the corticospinal tract at the level of pons and medulla were obtained by ROI analysis. Patients with amyotrophic lateral sclerosis showed reduced signal-intensity grades in the posterior bank of the motor cortex bilaterally. Quantitative analysis confirmed significantly higher iron content in the posterior bank of the motor cortex in patients with amyotrophic lateral sclerosis. In contrast, no significant differences were noted for the anterior bank of the motor cortex, anterior and posterior banks of the sensory cortex, and deep nuclei. Receiver operating characteristic comparison showed a cutoff of 35μg Fe/g of tissue with an area under the curve of 0.78 (P = .008) for the posterior bank of the motor cortex in discriminating patients with amyotrophic lateral sclerosis from controls. Fractional anisotropy was lower in the pyramidal tracts of patients with amyotrophic lateral sclerosis at the pons and medulla on either side, along with higher directionally averaged mean diffusivity values. The combination of SWI and DTI revealed an area under the curve of 0.784 for differentiating patients with amyotrophic lateral sclerosis from controls. Measurements of motor cortex iron deposition and diffusion tensor parameters of the corticospinal tract may be useful biomarkers for the diagnosis of clinically suspected amyotrophic lateral sclerosis. © 2016 by American Journal of Neuroradiology.

Modeling growth kinetics of thin films made by atomic layer deposition in lateral high-aspect-ratio structures

NASA Astrophysics Data System (ADS)

Ylilammi, Markku; Ylivaara, Oili M. E.; Puurunen, Riikka L.

2018-05-01

The conformality of thin films grown by atomic layer deposition (ALD) is studied using all-silicon test structures with long narrow lateral channels. A diffusion model, developed in this work, is used for studying the propagation of ALD growth in narrow channels. The diffusion model takes into account the gas transportation at low pressures, the dynamic Langmuir adsorption model for the film growth and the effect of channel narrowing due to film growth. The film growth is calculated by solving the diffusion equation with surface reactions. An efficient analytic approximate solution of the diffusion equation is developed for fitting the model to the measured thickness profile. The fitting gives the equilibrium constant of adsorption and the sticking coefficient. This model and Gordon's plug flow model are compared. The simulations predict the experimental measurement results quite well for Al2O3 and TiO2 ALD processes.

Diffusion of molecules and macromolecules in thylakoid membranes.

PubMed

Kirchhoff, Helmut

2014-04-01

The survival and fitness of photosynthetic organisms is critically dependent on the flexible response of the photosynthetic machinery, harbored in thylakoid membranes, to environmental changes. A central element of this flexibility is the lateral diffusion of membrane components along the membrane plane. As demonstrated, almost all functions of photosynthetic energy conversion are dependent on lateral diffusion. The mobility of both small molecules (plastoquinone, xanthophylls) as well as large protein supercomplexes is very sensitive to changes in structural boundary conditions. Knowledge about the design principles that govern the mobility of photosynthetic membrane components is essential to understand the dynamic response of the photosynthetic machinery. This review summarizes our knowledge about the factors that control diffusion in thylakoid membranes and bridges structural membrane alterations to changes in mobility and function. This article is part of a Special Issue entitled: Dynamic and ultrastructure of bioenergetic membranes and their components. Copyright © 2013 Elsevier B.V. All rights reserved.

Tetraspanin Tspan9 regulates platelet collagen receptor GPVI lateral diffusion and activation

PubMed Central

Haining, Elizabeth J.; Matthews, Alexandra L.; Noy, Peter J.; Romanska, Hanna M.; Harris, Helen J.; Pike, Jeremy; Morowski, Martina; Gavin, Rebecca L.; Yang, Jing; Milhiet, Pierre-Emmanuel; Berditchevski, Fedor; Nieswandt, Bernhard; Poulter, Natalie S.; Watson, Steve P.; Tomlinson, Michael G.

2017-01-01

Abstract The tetraspanins are a superfamily of four-transmembrane proteins, which regulate the trafficking, lateral diffusion and clustering of the transmembrane proteins with which they interact. We have previously shown that tetraspanin Tspan9 is expressed on platelets. Here we have characterised gene-trap mice lacking Tspan9. The mice were viable with normal platelet numbers and size. Tspan9-deficient platelets were specifically defective in aggregation and secretion induced by the platelet collagen receptor GPVI, despite normal surface GPVI expression levels. A GPVI activation defect was suggested by partially impaired GPVI-induced protein tyrosine phosphorylation. In mechanistic experiments, Tspan9 and GPVI co-immunoprecipitated and co-localised, but super-resolution imaging revealed no defects in collagen-induced GPVI clustering on Tspan9-deficient platelets. However, single particle tracking using total internal reflection fluorescence microscopy showed that GPVI lateral diffusion was reduced by approximately 50% in the absence of Tspan9. Therefore, Tspan9 plays a fine-tuning role in platelet activation by regulating GPVI membrane dynamics. PMID:28032533

Probability distribution of financial returns in a model of multiplicative Brownian motion with stochastic diffusion coefficient

NASA Astrophysics Data System (ADS)

Silva, Antonio

2005-03-01

It is well-known that the mathematical theory of Brownian motion was first developed in the Ph. D. thesis of Louis Bachelier for the French stock market before Einstein [1]. In Ref. [2] we studied the so-called Heston model, where the stock-price dynamics is governed by multiplicative Brownian motion with stochastic diffusion coefficient. We solved the corresponding Fokker-Planck equation exactly and found an analytic formula for the time-dependent probability distribution of stock price changes (returns). The formula interpolates between the exponential (tent-shaped) distribution for short time lags and the Gaussian (parabolic) distribution for long time lags. The theoretical formula agrees very well with the actual stock-market data ranging from the Dow-Jones index [2] to individual companies [3], such as Microsoft, Intel, etc. [] [1] Louis Bachelier, ``Th'eorie de la sp'eculation,'' Annales Scientifiques de l''Ecole Normale Sup'erieure, III-17:21-86 (1900).[] [2] A. A. Dragulescu and V. M. Yakovenko, ``Probability distribution of returns in the Heston model with stochastic volatility,'' Quantitative Finance 2, 443--453 (2002); Erratum 3, C15 (2003). [cond-mat/0203046] [] [3] A. C. Silva, R. E. Prange, and V. M. Yakovenko, ``Exponential distribution of financial returns at mesoscopic time lags: a new stylized fact,'' Physica A 344, 227--235 (2004). [cond-mat/0401225

Sensing and enumerating rare circulating cells with diffuse light

NASA Astrophysics Data System (ADS)

Zettergren, Eric; Vickers, Dwayne; Niedre, Mark

2011-02-01

Detection and quantification of circulating cells in live animals is a challenging and important problem in many areas of biomedical research. Current methods involve extraction of blood samples and counting of cells ex-vivo. Since only small blood volumes are analyzed at specific time points, monitoring of changes in cell populations over time is difficult and rare cells often escape detection. The goal of this research is to develop a method for enumerating very rare circulating cells in the bloodstream non-invasively. This would have many applications in biomedical research, including monitoring of cancer metastasis and tracking of hematopoietic stem cells. In this work we describe the optical configuration of our instrument which allows fluorescence detection of single cells in diffusive media at the mesoscopic scale. Our instrument design consists of two continuous wave laser diode sources and an 8-channel fiber coupled multi-anode photon counting PMT. Fluorescence detector fibers were arranged circularly around the target in a miniaturized ring configuration. Cell-simulating fluorescent microspheres and fluorescently-labeled cells were passed through a limb mimicking phantom with similar optical properties and background fluorescence as a limb of a mouse. Our data shows that we are able to successfully detect and count these with high quantitative accuracy. Future work includes characterization of our instrument using fluorescently labeled cells in-vivo. If successful, this technique would allow several orders of magnitude in vivo detection sensitivity improvement versus current approaches.

Correlation between hierarchical structure of crystal networks and macroscopic performance of mesoscopic soft materials and engineering principles.

PubMed

Lin, Naibo; Liu, Xiang Yang

2015-11-07

This review examines how the concepts and ideas of crystallization can be extended further and applied to the field of mesoscopic soft materials. It concerns the structural characteristics vs. the macroscopic performance, and the formation mechanism of crystal networks. Although this subject can be discussed in a broad sense across the area of mesoscopic soft materials, our main focus is on supramolecular materials, spider and silkworm silks, and biominerals. First, the occurrence of a hierarchical structure, i.e. crystal network and domain network structures, will facilitate the formation kinetics of mesoscopic phases and boost up the macroscopic performance of materials in some cases (i.e. spider silk fibres). Second, the structure and performance of materials can be correlated in some way by the four factors: topology, correlation length, symmetry/ordering, and strength of association of crystal networks. Moreover, four different kinetic paths of crystal network formation are identified, namely, one-step process of assembly, two-step process of assembly, mixed mode of assembly and foreign molecule mediated assembly. Based on the basic mechanisms of crystal nucleation and growth, the formation of crystal networks, such as crystallographic mismatch (or noncrystallographic) branching (tip branching and fibre side branching) and fibre/polymeric side merging, are reviewed. This facilitates the rational design and construction of crystal networks in supramolecular materials. In this context, the (re-)construction of a hierarchical crystal network structure can be implemented by thermal, precipitate, chemical, and sonication stimuli. As another important class of soft materials, the unusual mechanical performance of spider and silkworm silk fibres are reviewed in comparison with the regenerated silk protein derivatives. It follows that the considerably larger breaking stress and unusual breaking strain of spider silk fibres vs. silkworm silk fibres can be interpreted according to the synergistically correlated hierarchical structures of the domain and crystal networks, which can be quantified by the hierarchical structural correlation and the four structural parameters. Based on the concept of crystal networks, the new understanding acquired will transfer the research and engineering of mesoscopic materials, particularly, soft functional materials, to a new phase.

Role of insulin receptor and insulin signaling on αPS2CβPS integrins' lateral diffusion.

PubMed

Mainali, Dipak; Syed, Aleem; Arora, Neha; Smith, Emily A

2014-12-01

Integrins are ubiquitous transmembrane receptors with adhesion and signaling properties. The influence of insulin receptor and insulin signaling on αPS2CβPS integrins' lateral diffusion was studied using single particle tracking in S2 cells before and after reducing the insulin receptor expression or insulin stimulation. Insulin signaling was monitored by Western blotting for phospho-Akt expression. The expression of the insulin receptor was reduced using RNA interference (RNAi). After insulin receptor RNAi, four significant changes were measured in integrin diffusion properties: (1) there was a 24% increase in the mobile integrin population, (2) 14% of the increase was represented by integrins with Brownian diffusion, (3) for integrins that reside in confined zones of diffusion, there was a 45% increase in the diameter of the confined zone, and (4) there was a 29% increase in the duration integrins spend in confined zones of diffusion. In contrast to reduced expression of the insulin receptor, which alters integrin diffusion properties, insulin stimulation alone or insulin stimulation under conditions of reduced insulin receptor expression have minimal effects on altering the measured integrin diffusion properties. The differences in integrin diffusion measured after insulin receptor RNAi in the presence or absence of insulin stimulation may be the result of other insulin signaling pathways that are activated at reduced insulin receptor conditions. No change in the average integrin diffusion coefficient was measured for any conditions included in this study.

Mesoscopic bar magnet based on ε-Fe2O3 hard ferrite.

PubMed

Ohkoshi, Shin-Ichi; Namai, Asuka; Yamaoka, Takehiro; Yoshikiyo, Marie; Imoto, Kenta; Nasu, Tomomichi; Anan, Shizuka; Umeta, Yoshikazu; Nakagawa, Kosuke; Tokoro, Hiroko

2016-06-07

Ferrite magnets have a long history. They are used in motors, magnetic fluids, drug delivery systems, etc. Herein we report a mesoscopic ferrite bar magnet based on rod-shaped ε-Fe2O3 with a large coercive field (>25 kOe). The ε-Fe2O3-based bar magnet is a single crystal with a single magnetic domain along the longitudinal direction. A wide frequency range spectroscopic study shows that the crystallographic a-axis of ε-Fe2O3, which corresponds to the longitudinal direction of the bar magnet, plays an important role in linear and non-linear magneto-optical transitions, phonon modes, and the magnon (Kittel mode). Due to its multiferroic property, a magnetic-responsive non-linear optical sheet is manufactured as an application using an ε-Fe2O3-based bar magnet, resin, and polyethylene terephthalate. Furthermore, from the viewpoint of the large coercive field property, we demonstrate that a mesoscopic ε-Fe2O3 bar magnet can be used as a magnetic force microscopy probe.

Mesoscopic bar magnet based on ɛ-Fe2O3 hard ferrite

NASA Astrophysics Data System (ADS)

Ohkoshi, Shin-Ichi; Namai, Asuka; Yamaoka, Takehiro; Yoshikiyo, Marie; Imoto, Kenta; Nasu, Tomomichi; Anan, Shizuka; Umeta, Yoshikazu; Nakagawa, Kosuke; Tokoro, Hiroko

2016-06-01

Ferrite magnets have a long history. They are used in motors, magnetic fluids, drug delivery systems, etc. Herein we report a mesoscopic ferrite bar magnet based on rod-shaped ɛ-Fe2O3 with a large coercive field (>25 kOe). The ɛ-Fe2O3-based bar magnet is a single crystal with a single magnetic domain along the longitudinal direction. A wide frequency range spectroscopic study shows that the crystallographic a-axis of ɛ-Fe2O3, which corresponds to the longitudinal direction of the bar magnet, plays an important role in linear and non-linear magneto-optical transitions, phonon modes, and the magnon (Kittel mode). Due to its multiferroic property, a magnetic-responsive non-linear optical sheet is manufactured as an application using an ɛ-Fe2O3-based bar magnet, resin, and polyethylene terephthalate. Furthermore, from the viewpoint of the large coercive field property, we demonstrate that a mesoscopic ɛ-Fe2O3 bar magnet can be used as a magnetic force microscopy probe.

Spatial and mesoscopic fluctuations in glassy dynamics

NASA Astrophysics Data System (ADS)

Chamon, Claudio C.; Cugliandolo, Leticia F.

2004-05-01

One of the striking properties of a glassy system is that many material properties depend on its age, i.e., the time since the system entered its glassy phase. In this this talk we shall review some recent progress (work in collaboration with H. E. Castillo, P. Charbonneau, J. L. Iguain, M. P. Kennett, D. R. Reichman and M. Sellitto) in understanding local aging, through the study of local observable quantities, which reveal that there are spatial heterogeneities and fluctuations in the aging process of macroscopic systems. We show that a number of universal properties are shared by many non-equilibrium systems, both with and without quenched disorder, such as the 3D Edwards-Anderson model and some kinetically constrained non-interacting 2D and 3D spin models, for example. Similar scaling relations are found for mesoscopic sample-to-sample fluctuations of global quantities in small size systems. We discuss how the emergence of a symmetry in aging systems, time-reparametrization invariance, could be responsible for the observed universal behavior of the local and mesoscopic non-equilibrium fluctuations.

Can mutation-mediated effects occurring early in development cause long-term seizure susceptibility in genetic generalized epilepsies?

PubMed

Reid, Christopher Alan; Rollo, Ben; Petrou, Steven; Berkovic, Samuel F

2018-05-01

Epilepsy has a strong genetic component, with an ever-increasing number of disease-causing genes being discovered. Most epilepsy-causing mutations are germ line and thus present from conception. These mutations are therefore well positioned to have a deleterious impact during early development. Here we review studies that investigate the role of genetic lesions within the early developmental window, specifically focusing on genetic generalized epilepsy (GGE). Literature on the potential pathogenic role of sub-mesoscopic structural changes in GGE is also reviewed. Evidence from rodent models of genetic epilepsy support the idea that functional and structural changes can occur in early development, leading to altered seizure susceptibility into adulthood. Both animal and human studies suggest that sub-mesoscopic structural changes occur in GGE. The existence of sub-mesoscopic structural changes prior to seizure onset may act as biomarkers of excitability in genetic epilepsies. We also propose that presymptomatic treatment may be essential for limiting the long-term consequences of disease-causing mutations in genetic epilepsies. Wiley Periodicals, Inc. © 2018 International League Against Epilepsy.

Mesoscopic structure conditions the emergence of cooperation on social networks

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

Lozano, S.; Arenas, A.; Sanchez, A.

We study the evolutionary Prisoner's Dilemma on two social networks substrates obtained from actual relational data. We find very different cooperation levels on each of them that cannot be easily understood in terms of global statistical properties of both networks. We claim that the result can be understood at the mesoscopic scale, by studying the community structure of the networks. We explain the dependence of the cooperation level on the temptation parameter in terms of the internal structure of the communities and their interconnections. We then test our results on community-structured, specifically designed artificial networks, finding a good agreement withmore » the observations in both real substrates. Our results support the conclusion that studies of evolutionary games on model networks and their interpretation in terms of global properties may not be sufficient to study specific, real social systems. Further, the study allows us to define new quantitative parameters that summarize the mesoscopic structure of any network. In addition, the community perspective may be helpful to interpret the origin and behavior of existing networks as well as to design structures that show resilient cooperative behavior.« less

White-matter microstructure and language lateralization in left-handers: a whole-brain MRI analysis.

PubMed

Perlaki, Gabor; Horvath, Reka; Orsi, Gergely; Aradi, Mihaly; Auer, Tibor; Varga, Eszter; Kantor, Gyongyi; Altbäcker, Anna; John, Flora; Doczi, Tamas; Komoly, Samuel; Kovacs, Norbert; Schwarcz, Attila; Janszky, Jozsef

2013-08-01

Most people are left-hemisphere dominant for language. However the neuroanatomy of language lateralization is not fully understood. By combining functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI), we studied whether language lateralization is associated with cerebral white-matter (WM) microstructure. Sixteen healthy, left-handed women aged 20-25 were included in the study. Left-handers were targeted in order to increase the chances of involving subjects with atypical language lateralization. Language lateralization was determined by fMRI using a verbal fluency paradigm. Tract-based spatial statistics analysis of DTI data was applied to test for WM microstructural correlates of language lateralization across the whole brain. Fractional anisotropy and mean diffusivity were used as indicators of WM microstructural organization. Right-hemispheric language dominance was associated with reduced microstructural integrity of the left superior longitudinal fasciculus and left-sided parietal lobe WM. In left-handed women, reduced integrity of the left-sided language related tracts may be closely linked to the development of right hemispheric language dominance. Our results may offer new insights into language lateralization and structure-function relationships in human language system. Copyright © 2013 Elsevier Inc. All rights reserved.

Molecular, mesoscopic and microscopic structure evolution during amylase digestion of maize starch granules.

PubMed

Shrestha, Ashok K; Blazek, Jaroslav; Flanagan, Bernadine M; Dhital, Sushil; Larroque, Oscar; Morell, Matthew K; Gilbert, Elliot P; Gidley, Michael J

2012-09-01

Cereal starch granules with high (>50%) amylose content are a promising source of nutritionally desirable resistant starch, i.e. starch that escapes digestion in the small intestine, but the structural features responsible are not fully understood. We report the effects of partial enzyme digestion of maize starch granules on amylopectin branch length profiles, double and single helix contents, gelatinisation properties, crystallinity and lamellar periodicity. Comparing results for three maize starches (27, 57, and 84% amylose) that differ in both structural features and amylase-sensitivity allows conclusions to be drawn concerning the rate-determining features operating under the digestion conditions used. All starches are found to be digested by a side-by-side mechanism in which there is no major preference during enzyme attack for amylopectin branch lengths, helix form, crystallinity or lamellar organisation. We conclude that the major factor controlling enzyme susceptibility is granule architecture, with shorter length scales not playing a major role as inferred from the largely invariant nature of numerous structural measures during the digestion process (XRD, NMR, SAXS, DSC, FACE). Results are consistent with digestion rates being controlled by restricted diffusion of enzymes within densely packed granular structures, with an effective surface area for enzyme attack determined by external dimensions (57 or 84% amylose - relatively slow) or internal channels and pores (27% amylose - relatively fast). Although the process of granule digestion is to a first approximation non-discriminatory with respect to structure at molecular and mesoscopic length scales, secondary effects noted include (i) partial crystallisation of V-type helices during digestion of 27% amylose starch, (ii) preferential hydrolysis of long amylopectin branches during the early stage hydrolysis of 27% and 57% but not 84% amylose starches, linked with disruption of lamellar repeating structure and (iii) partial B-type recrystallisation after prolonged enzyme incubation for 57% and 84% amylose starches but not 27% amylose starch. Copyright © 2012 Elsevier Ltd. All rights reserved.

Magnetic nanostructures.

PubMed

Bennemann, K

2010-06-23

Characteristic results of magnetism in small particles, thin films and tunnel junctions are presented. As a consequence of the reduced atomic coordination in small clusters and thin films the electronic states and density of states are modified. Thus, magnetic moments and magnetization are affected. Generally, in clusters and thin films magnetic anisotropy plays a special role. In tunnel junctions the interplay of magnetism, spin currents and superconductivity are of particular interest. In ring-like mesoscopic systems Aharonov-Bohm-induced currents are studied. Results are given for single transition metal clusters, cluster ensembles, thin films, mesoscopic structures and tunnel systems. © 2010 IOP Publishing Ltd

Universal shape characteristics for the mesoscopic star-shaped polymer via dissipative particle dynamics simulations

NASA Astrophysics Data System (ADS)

Kalyuzhnyi, O.; Ilnytskyi, J. M.; Holovatch, Yu; von Ferber, C.

2018-05-01

In this paper we study the shape characteristics of star-like polymers in various solvent quality using a mesoscopic level of modeling. The dissipative particle dynamics simulations are performed for the homogeneous and four different heterogeneous star polymers with the same molecular weight. We analyse the gyration radius and asphericity at the poor, good and θ-solvent regimes. Detailed explanation based on interplay between enthalpic and entropic contributions to the free energy and analyses on of the asphericity of individual branches are provided to explain the increase of the apsphericity in θ-solvent regime.

Physics at the FMQT’08 conference

NASA Astrophysics Data System (ADS)

Špička, V.; Nieuwenhuizen, Th. M.; Keefe, P. D.

2010-01-01

This paper summarizes the recent state of the art of the following topics presented at the FQMT’08 conference: Foundations of quantum physics, Quantum measurement; Quantum noise, decoherence and dephasing; Cold atoms and Bose-Einstein condensation; Physics of quantum computing and information; Nonequilibrium quantum statistical mechanics; Quantum, mesoscopic and partly classical thermodynamics; Mesoscopic, nano-electro-mechanical systems and optomechanical systems; Spins systems and their dynamics, Brownian motion and molecular motors; Physics of biological systems, and Relevant experiments from the nanoscale to the macroscale. To all these subjects an introduction is given and the recent literature is overviewed. The paper contains some 680 references in total.

Corticospinal tract asymmetry and handedness in right- and left-handers by diffusion tensor tractography.

PubMed

Seizeur, Romuald; Magro, Elsa; Prima, Sylvain; Wiest-Daesslé, Nicolas; Maumet, Camille; Morandi, Xavier

2014-03-01

Cerebral hemispheres represent both structural and functional asymmetry, which differs among right- and left-handers. The left hemisphere is specialised for language and task execution of the right hand in right-handers. We studied the corticospinal tract in right- and left-handers by diffusion tensor imaging and tractography. The present study aimed at revealing a morphological difference resulting from a region of interest (ROI) obtained by functional MRI (fMRI). Twenty-five healthy participants (right-handed: 15, left-handed: 10) were enrolled in our assessment of morphological, functional and diffusion tensor MRI. Assessment of brain fibre reconstruction (tractography) was done using a deterministic algorithm. Fractional anisotropy (FA) and mean diffusivity (MD) were studied on the tractography traces of the reference slices. We observed a significant difference in number of leftward fibres based on laterality. The significant difference in regard to FA and MD was based on the slices obtained at different levels and the laterality index. We found left-hand asymmetry and right-hand asymmetry, respectively, for the MD and FA. Our study showed the presence of hemispheric asymmetry based on laterality index in right- and left-handers. These results are inconsistent with some studies and consistent with others. The reported difference in hemispheric asymmetry could be related to dexterity (manual skill).

A first principles kinetic Monte Carlo investigation of the adsorption and mobility of gadolinium on the (100) surface of tungsten

NASA Astrophysics Data System (ADS)

Samin, Adib J.; Zhang, Jinsuo

2017-05-01

An accurate characterization of lanthanide adsorption and mobility on tungsten surfaces is important for pyroprocessing. In the present study, the adsorption and diffusion of gadolinium on the (100) surface of tungsten was investigated. It was found that the hollow sites were the most energetically favorable for the adsorption. It was further observed that a magnetic moment was induced following the adsorption of gadolinium on the tungsten surface and that the system with adsorbed hollow sites had the largest magnetization. A pathway for the surface diffusion of gadolinium was determined to occur by hopping between the nearest neighbor hollow sites via the bridge site and the activation energy for the hop was calculated to be 0.75 eV. The surface diffusion process was further assessed using two distinct kinetic Monte Carlo models; one that accounted for lateral adsorbate interactions up to the second nearest neighbor and one that did not account for such interatomic interactions in the adlayer. When the lateral interactions were included in the simulations, the diffusivity was observed to have a strong dependence on coverage (for the coverage values being studied). The effects of lateral interactions were further observed in a one-dimensional simulation of the diffusion equation where the asymmetry in the surface coverage profile upon its approach to a steady state distribution was clear in comparison with the simulations which did not account for those interactions.

Electrochemical measurement of lateral diffusion coefficients of ubiquinones and plastoquinones of various isoprenoid chain lengths incorporated in model bilayers.

PubMed Central

Marchal, D; Boireau, W; Laval, J M; Moiroux, J; Bourdillon, C

1998-01-01

The long-range diffusion coefficients of isoprenoid quinones in a model of lipid bilayer were determined by a method avoiding fluorescent probe labeling of the molecules. The quinone electron carriers were incorporated in supported dimyristoylphosphatidylcholine layers at physiological molar fractions (<3 mol%). The elaborate bilayer template contained a built-in gold electrode at which the redox molecules solubilized in the bilayer were reduced or oxidized. The lateral diffusion coefficient of a natural quinone like UQ10 or PQ9 was 2.0 +/- 0.4 x 10(-8) cm2 s(-1) at 30 degrees C, two to three times smaller than the diffusion coefficient of a lipid analog in the same artificial bilayer. The lateral mobilities of the oxidized or reduced forms could be determined separately and were found to be identical in the 4-13 pH range. For a series of isoprenoid quinones, UQ2 or PQ2 to UQ10, the diffusion coefficient exhibited a marked dependence on the length of the isoprenoid chain. The data fit very well the quantitative behavior predicted by a continuum fluid model in which the isoprenoid chains are taken as rigid particles moving in the less viscous part of the bilayer and rubbing against the more viscous layers of lipid heads. The present study supports the concept of a homogeneous pool of quinone located in the less viscous region of the bilayer. PMID:9545054

Modulation of Membrane Protein Lateral Mobility by Polyphosphates and Polyamines

NASA Astrophysics Data System (ADS)

Schindler, Melvin; Koppel, Dennis E.; Sheetz, Michael P.

1980-03-01

The lateral mobility of fluorescein-labeled membrane glycoproteins was measured in whole unlysed erythrocytes and erythrocyte ghosts by the technique of ``fluorescence redistribution after fusion.'' Measurements were made on polyethylene glycol-fused cell pairs in which only one member of the couplet was initially fluorescently labeled. Diffusion coefficients were estimated from the rate of fluorescence redistribution determined from successive scans with a focused laser beam across individual fused pairs. This technique allows for the analysis of diffusion within cell membranes without the possible damaging photochemical events caused by photobleaching. It was found that lateral mobility of erythrocyte proteins can be increased by the addition of polyphosphates (i.e., ATP and 2,3-diphosphoglycerate) and decreased by the addition of organic polyamines (i.e., neomycin and spermine). This control is exerted by these molecules only when they contact the cytoplasmic side of the membrane and is not dependent upon high-energy phosphates. Microviscosity experiments employing diphenylhexatriene demonstrated no changes in membrane lipid state as a function of these reagents. Our results, in conjunction with data on the physical interactions of cytoskeletal proteins, suggest that the diffusion effector molecules alter the lateral mobility of erythrocyte membrane proteins through modifications of interactions in the shell, which is composed of spectrin, actin, and component 4.1.

Phospholipid lateral diffusion in phosphatidylcholine-sphingomyelin-cholesterol monolayers; effects of oxidatively truncated phosphatidylcholines.

PubMed

Parkkila, Petteri; Stefl, Martin; Olżyńska, Agnieszka; Hof, Martin; Kinnunen, Paavo K J

2015-01-01

Oxidative stress is involved in a number of pathological conditions and the generated oxidatively modified lipids influence membrane properties and functions, including lipid-protein interactions and cellular signaling. Brewster angle microscopy demonstrated oxidatively truncated phosphatidylcholines to promote phase separation in monolayers of 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (POPC), sphingomyelin (SM) and cholesterol (Chol). More specifically, 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PazePC), was found to increase the miscibility transition pressure of the SM/Chol-phase. Lateral diffusion of lipids is influenced by a variety of membrane properties, thus making it a sensitive parameter to observe the coexistence of different lipid phases, for instance. The dependence on lipid lateral packing of the lateral diffusion of fluorophore-containing phospholipid analogs was investigated in Langmuir monolayers composed of POPC, SM, and Chol and additionally containing oxidatively truncated phosphatidylcholines, using fluorescence correlation spectroscopy (FCS). To our knowledge, these are the first FCS results on miscibility transition in ternary lipid monolayers, confirming previous results obtained using Brewster angle microscopy on such lipid monolayers. Wide-field fluorescence microscopy was additionally employed to verify the transition, i.e. the loss and reformation of SM/Chol domains. Copyright © 2014. Published by Elsevier B.V.

CHAIRMEN'S FOREWORD: The Seventh International Conference on New Phenomena in Mesoscopic Structures & The Fifth International Conference on Surfaces and Interfaces of Mesoscopic Devices

NASA Astrophysics Data System (ADS)

Aoyagi, Yoshinobu; Goodnick, Stephen M.

2006-05-01

This special issue of the Journal of Physics: Conference Series contains the proceedings of the joint Seventh International Conference on New Phenomena in Mesoscopic Structures and Fifth International Conference on Surfaces and Interfaces of Mesoscopic Devices, which was held from November 27th - December 2nd, 2005, at the Ritz Carlton Kapalua, Maui, Hawaii. The string of these conferences dates back to the first one in 1989. Of special importance is that this year's conference was dedicated to Professor Gottfried Landwehr, in recognition of his many outstanding contributions to semiconductor physics. A personal tribute to Prof Landwehr by Dr K von Klitzing leads off this issue. The scope of NPMS-7/SIMD-5 spans nano-fabrication through complex phase coherent mesoscopic systems including nano-transistors and nano-scale characterization. Topics of interest include: •Nanoscale fabrication: high-resolution electron lithography, FIB nano-patterning, scanning- force-microscopy (SFM) lithography, SFM-stimulated growth, novel patterning, nano-imprint lithography, special etching, and self-assembled monolayers •Nanocharacterization: SFM characterization, ballistic-electron emission microscopy (BEEM), optical studies of nanostructures, tunneling, properties of discrete impurities, phase coherence, noise, THz studies, and electro-luminescence in small structures •Nanodevices: ultra-scaled FETs, quantum single-electron transistors (SETS), resonant tunneling diodes, ferromagnetic and spin devices, superlattice arrays, IR detectors with quantum dots and wires, quantum point contacts, non-equilibrium transport, simulation, ballistic transport, molecular electronic devices, carbon nanotubes, spin selection devices, spin-coupled quantum dots, and nanomagnetics •Quantum-coherent transport: the quantum Hall effect, ballistic quantum systems, quantum-computing implementations and theory, and magnetic spin systems •Mesoscopic structures: quantum wires and dots, quantum chaos, non-equilibrium transport, instabilities, nano-electro-mechanical systems, mesoscopic Josephson effects, phase coherence and breaking, and the Kondo effect •Systems of nanodevices: Quantum cellular automata, systolic SET processors, quantum neural nets, adaptive effects in circuits, and molecular circuits •Nanomaterials: nanotubes, nanowires, organic and molecular materials, self-assembled nano wires, and organic devices •Nanobioelectronics: electronic properties of biological structures on the nanoscale. This year's conference was organized by Prof Stephen Goodnick, Arizona State University, and Prof Yoshinobu Aoyagi, Tokyo Institute of Technology. The conference benefited from 14 invited speakers, whose topics spanned the above list, and a total of 97 registered attendees. The largest contingent was from Japan, followed closely by the US. In total, there were 49 from Japan, 31 fiom the US, and 17 from Europe. The organizers want to especially thank the sponsors for the meeting: The Office of Naval Research, the Army Research Office, and Arizona State University on the US side, and the Japan Society for the Promotion of Science, through their 151 Committee, on the Japanese side. PROGRAM COMMITTEE •Prof Gerhard Abstreiter, Technical University of Munich •Prof Tsuneya Ando, Tokyo Institute of Technology •Prof John Barker, University of Glasgow •Prof Jonathan Bird, the University at Buffalo •Prof Robert Blick, University of Wisconsin •Prof David Ferry, Chair, Arizona State University •Dr Yoshiro Hirayama, NTT Basic Research Laboratories •Dr Koji Ishibashi, RIKEN •Prof Carlo Jacoboni, University of Modena •Prof David Janes, Purdue University •Prof Friedl Kuchar, University of Leoben •Prof K. Matsumoto, Osaka University •Prof Wolfgang Porod, Notre Dame University •Prof Michiharu Tabe, Shizuoka University •Prof Joachim Wolter, Eindhoven Institute of Technology •Prof Lukas Worschech, University of Würzburg •Dr Naoki Yokoyama, Fujitsu Research

Active learning of constitutive relation from mesoscopic dynamics for macroscopic modeling of non-Newtonian flows

NASA Astrophysics Data System (ADS)

Zhao, Lifei; Li, Zhen; Caswell, Bruce; Ouyang, Jie; Karniadakis, George Em

2018-06-01

We simulate complex fluids by means of an on-the-fly coupling of the bulk rheology to the underlying microstructure dynamics. In particular, a continuum model of polymeric fluids is constructed without a pre-specified constitutive relation, but instead it is actively learned from mesoscopic simulations where the dynamics of polymer chains is explicitly computed. To couple the bulk rheology of polymeric fluids and the microscale dynamics of polymer chains, the continuum approach (based on the finite volume method) provides the transient flow field as inputs for the (mesoscopic) dissipative particle dynamics (DPD), and in turn DPD returns an effective constitutive relation to close the continuum equations. In this multiscale modeling procedure, we employ an active learning strategy based on Gaussian process regression (GPR) to minimize the number of expensive DPD simulations, where adaptively selected DPD simulations are performed only as necessary. Numerical experiments are carried out for flow past a circular cylinder of a non-Newtonian fluid, modeled at the mesoscopic level by bead-spring chains. The results show that only five DPD simulations are required to achieve an effective closure of the continuum equations at Reynolds number Re = 10. Furthermore, when Re is increased to 100, only one additional DPD simulation is required for constructing an extended GPR-informed model closure. Compared to traditional message-passing multiscale approaches, applying an active learning scheme to multiscale modeling of non-Newtonian fluids can significantly increase the computational efficiency. Although the method demonstrated here obtains only a local viscosity from the polymer dynamics, it can be extended to other multiscale models of complex fluids whose macro-rheology is unknown.

Perceptual thresholds for non-ideal diffuse field reverberation.

PubMed

Romblom, David; Guastavino, Catherine; Depalle, Philippe

2016-11-01

The objective of this study is to understand listeners' sensitivity to directional variations in non-ideal diffuse field reverberation. An ABX discrimination test was conducted using a semi-spherical 28-loudspeaker array; perceptual thresholds were estimated by systematically varying the level of a segment of loudspeakers for lateral, height, and frontal conditions. The overall energy was held constant using a gain compensation scheme. When compared to an ideal diffuse field, the perceptual threshold for detection is -2.5 dB for the lateral condition, -6.8 dB for the height condition, and -3.2 dB for the frontal condition. Measurements of the experimental stimuli were analyzed using a Head and Torso Simulator as well as with opposing cardioid microphones aligned on the three Cartesian axes. Additionally, opposing cardioid measurements made in an acoustic space demonstrate that level differences corresponding to the perceptual thresholds can be found in practice. These results suggest that non-ideal diffuse field reverberation may be a previously unrecognized component of spatial impression.

On an aggregation in birth-and-death stochastic dynamics

NASA Astrophysics Data System (ADS)

Finkelshtein, Dmitri; Kondratiev, Yuri; Kutoviy, Oleksandr; Zhizhina, Elena

2014-06-01

We consider birth-and-death stochastic dynamics of particle systems with attractive interaction. The heuristic generator of the dynamics has a constant birth rate and density-dependent decreasing death rate. The corresponding statistical dynamics is constructed. Using the Vlasov-type scaling we derive the limiting mesoscopic evolution and prove that this evolution propagates chaos. We study a nonlinear non-local kinetic equation for the first correlation function (density of population). The existence of uniformly bounded solutions as well as solutions growing inside of a bounded domain and expanding in the space are shown. These solutions describe two regimes in the mesoscopic system: regulation and aggregation.

Probing eukaryotic cell mechanics via mesoscopic simulations

NASA Astrophysics Data System (ADS)

Pivkin, Igor V.; Lykov, Kirill; Nematbakhsh, Yasaman; Shang, Menglin; Lim, Chwee Teck

2017-11-01

We developed a new mesoscopic particle based eukaryotic cell model which takes into account cell membrane, cytoskeleton and nucleus. The breast epithelial cells were used in our studies. To estimate the viscoelastic properties of cells and to calibrate the computational model, we performed micropipette aspiration experiments. The model was then validated using data from microfluidic experiments. Using the validated model, we probed contributions of sub-cellular components to whole cell mechanics in micropipette aspiration and microfluidics experiments. We believe that the new model will allow to study in silico numerous problems in the context of cell biomechanics in flows in complex domains, such as capillary networks and microfluidic devices.

Observable consequences of zero-point energy

NASA Astrophysics Data System (ADS)

Sen, Siddhartha; Gupta, Kumar S.

2017-12-01

Spectral line widths, the Lamb shift and the Casimir effect are generally accepted to be observable consequences of the zero-point electromagnetic (ZPEM) fields. A new class of observable consequences of ZPEM field at the mesoscopic scale were recently proposed and observed. Here, we extend this class of observable effects and predict that mesoscopic water layers should have a high value for its solid-liquid phase transition temperature, as illustrated by water inside a single-walled carbon nanotube (CNT). For this case, our analysis predicts that the phase transition temperature scales inversely with the square of the effective radius available for the water flow within the CNT.

A mesoscopic approach for draping simulation of preforms manufactured by direct fibre placement

NASA Astrophysics Data System (ADS)

Engelfried, Mathias; Fial, Julian; Tartler, Manuel; Böhler, Patrick; Hägele, Dominik; Middendorf, Peter

2017-10-01

The draping of preforms made by automated fibre placement is a suitable way to generate complex, three-dimensional preforms. The absence of weaving or sewing yarns leads to a high tendency towards defects, such as gaps. To predict those defects a detailed simulation model of the material is necessary. This work deals with a method to describe the inter-ply friction of preforms that consists of carbon fibre yarns joined by a thermoplastic binder. Therefore, a friction model which is customised to the partial presence of molten binder is proposed. This model is used in a mesoscopic draping simulation and is validated by draping experiments.

Equilibrium finite-frequency noise of an interacting mesoscopic capacitor studied in time-dependent density functional theory

NASA Astrophysics Data System (ADS)

Dittmann, Niklas; Splettstoesser, Janine; Helbig, Nicole

2018-03-01

We calculate the frequency-dependent equilibrium noise of a mesoscopic capacitor in time-dependent density functional theory (TDDFT). The capacitor is modeled as a single-level quantum dot with on-site Coulomb interaction and tunnel coupling to a nearby reservoir. The noise spectra are derived from linear-response conductances via the fluctuation-dissipation theorem. Thereby, we analyze the performance of a recently derived exchange-correlation potential with time-nonlocal density dependence in the finite-frequency linear-response regime. We compare our TDDFT noise spectra with real-time perturbation theory and find excellent agreement for noise frequencies below the reservoir temperature.

A novel grid-based mesoscopic model for evacuation dynamics

NASA Astrophysics Data System (ADS)

Shi, Meng; Lee, Eric Wai Ming; Ma, Yi

2018-05-01

This study presents a novel grid-based mesoscopic model for evacuation dynamics. In this model, the evacuation space is discretised into larger cells than those used in microscopic models. This approach directly computes the dynamic changes crowd densities in cells over the course of an evacuation. The density flow is driven by the density-speed correlation. The computation is faster than in traditional cellular automata evacuation models which determine density by computing the movements of each pedestrian. To demonstrate the feasibility of this model, we apply it to a series of practical scenarios and conduct a parameter sensitivity study of the effect of changes in time step δ. The simulation results show that within the valid range of δ, changing δ has only a minor impact on the simulation. The model also makes it possible to directly acquire key information such as bottleneck areas from a time-varied dynamic density map, even when a relatively large time step is adopted. We use the commercial software AnyLogic to evaluate the model. The result shows that the mesoscopic model is more efficient than the microscopic model and provides more in-situ details (e.g., pedestrian movement pattern) than the macroscopic models.

Thermodynamics of the mesoscopic thermoelectric heat engine beyond the linear-response regime.

PubMed

Yamamoto, Kaoru; Hatano, Naomichi

2015-10-01

Mesoscopic thermoelectric heat engine is much anticipated as a device that allows us to utilize with high efficiency wasted heat inaccessible by conventional heat engines. However, the derivation of the heat current in this engine seems to be either not general or described too briefly, even inappropriately in some cases. In this paper, we give a clear-cut derivation of the heat current of the engine with suitable assumptions beyond the linear-response regime. It resolves the confusion in the definition of the heat current in the linear-response regime. After verifying that we can construct the same formalism as that of the cyclic engine, we find the following two interesting results within the Landauer-Büttiker formalism: the efficiency of the mesoscopic thermoelectric engine reaches the Carnot efficiency if and only if the transmission probability is finite at a specific energy and zero otherwise; the unitarity of the transmission probability guarantees the second law of thermodynamics, invalidating Benenti et al.'s argument in the linear-response regime that one could obtain a finite power with the Carnot efficiency under a broken time-reversal symmetry [Phys. Rev. Lett. 106, 230602 (2011)]. These results demonstrate how quantum mechanics constrains thermodynamics.

Mesoscopic Rigid Body Modelling of the Extracellular Matrix Self-Assembly.

PubMed

Wong, Hua; Prévoteau-Jonquet, Jessica; Baud, Stéphanie; Dauchez, Manuel; Belloy, Nicolas

2018-06-11

The extracellular matrix (ECM) plays an important role in supporting tissues and organs. It even has a functional role in morphogenesis and differentiation by acting as a source of active molecules (matrikines). Many diseases are linked to dysfunction of ECM components and fragments or changes in their structures. As such it is a prime target for drugs. Because of technological limitations for observations at mesoscopic scales, the precise structural organisation of the ECM is not well-known, with sparse or fuzzy experimental observables. Based on the Unity3D game and physics engines, along with rigid body dynamics, we propose a virtual sandbox to model large biological molecules as dynamic chains of rigid bodies interacting together to gain insight into ECM components behaviour in the mesoscopic range. We have preliminary results showing how parameters such as fibre flexibility or the nature and number of interactions between molecules can induce different structures in the basement membrane. Using the Unity3D game engine and virtual reality headset coupled with haptic controllers, we immerse the user inside the corresponding simulation. Untrained users are able to navigate a complex virtual sandbox crowded with large biomolecules models in a matter of seconds.

Quasi-lattice of qubits and its mesoscopic features

NASA Astrophysics Data System (ADS)

Ian, Hou; Liu, Yu-Xi

2014-03-01

In a circuit quantum electrodynamic system, both the size of superconducting qubits and the length scale of the inter-qubit spacing in a chain of such qubits are mesoscopic. As a result, the qubit-field coupling is inhomogeneous. The excitation on the qubits is described by a projection-deformation model and this set of qubits exhibit unique mesoscopic features of what we termed a quasi-lattice. A quasi-lattice in a circuit cavity has a spacing-dependent excitation spectrum. Inhomogeneous coupling giving rise to asynchronously excited qubits, the probability of multi-photon resonance on the quasi-lattice as a whole has increased. This induces simultaneous generations of GHZ-type and W-type entanglements among the qubits. Moreover, the polaritons formed by the mixing of the quasi-lattice excitation and the cavity photon has a selective spontaneous radiation. The spectrum of the radiation has a periodicity governed by the spacing and the variation of the decay rate over the spacing coincides with the cooperation of atoms predicted by Dicke model. We present the theory behinds these effects of the quasi-lattice and discuss how the spacing affects the delay and life time of a superfluorescent pulse arising from it. Supported by Univ. of Macau and FDCT Macau.

Thouless dephasing and amplitude modulation of Aharonov-Bohm oscillations in mesoscopic InGaAs/InAlAs interferometers

NASA Astrophysics Data System (ADS)

Heremans, J. J.; Ren, S. L.; Zhang, Yao; Gaspe, C. K.; Vijeyaragunathan, S.; Mishima, T. D.; Santos, M. B.

2014-03-01

Aharonov-Bohm oscillations in the low-temperature magnetoresistance of mesoscopic interferometric rings are investigated for their dependence on bias current and temperature, and to explore origins of the observed amplitude modulation in magnetic field. Single-ring interferometers of radius 650 nm and lithographic arm width 300 nm were fabricated on a high-mobility high-density InGaAs/InAlAs heterostructure. The rings show interference oscillations over a wide range of magnetic fields, with amplitudes subject to modulation with applied magnetic field. The quantum phase coherence length is extracted by analysis of the fundamental and higher Fourier components of the oscillations, and by comparative study of the amplitude. The variation of the amplitude with bias current and temperature shows the existence of a critical excitation energy consistent with the Thouless energy for quantum phase smearing. Autocorrelation and Fourier analysis are used to determine the quasi-period of the amplitude modulation, which is found to be consistent with an origin in the magnetic flux threading the finite width of the interferometer arms, changing the mesoscopic realization of the system. Supported by DOE DE-FG02-08ER46532 (VT) and NSF DMR-0520550 (UoO).

CHAIRMAN'S FOREWORD: First International Symposium on Advanced Nanodevices and Nanotechnology

NASA Astrophysics Data System (ADS)

Aoyagi, Yoshinobu; Goodnick, Stephen M.

2008-03-01

This volume of Journal of Physics: Conference Series contains selected papers from the First International Symposium on Advanced Nanodevices and Nanotechnology. This conference is a merging of the two previous series New Phenomena in Mesoscopic Structures and the Surfaces and Interfaces of Mesoscopic Devices. This year's conference was held 2-7 December 2007 at the Waikoloa Beach Marriott on the Kohala coast of the big island of Hawaii. The scope of ISANN spans nano-fabrication through complex phase coherent mesoscopic systems including nano-transistors and nano-scale characterization. Topics of interest included: Nano-scale fabrication (high-resolution electron lithography, FIB nano-patterning SFM lithography, SFM stimulated growth, novel patterning, nano-imprint lithography, special etching, and SAMs) Nano-characterization (SFM characterization, BEEM, optical studies of nanostructures, tunneling, properties of discrete impurities, phase coherence, noise, THz studies, electro-luminescence in small structures) Nano-devices (ultra-scaled FETs, quantum SETs, RTDs, ferromagnetic, and spin devices, superlattice arrays, IR detectors with quantum dots and wires, quantum point contacts, non-equilibrium transport, simulation, ballistic transport, molecular electronic devices, carbon nanotubes, spin selection devices, spin-coupled quantum dots, nano-magnetics) Quantum coherent transport (quantum Hall effect, ballistic quantum systems, quantum computing implementations and theory, magnetic spin systems, quantum NEMs) Mesoscopic structures (quantum wires and dots, chaos, non-equilibrium transport, instabilities, nano-electro-mechanical systems, mesoscopic Josephson effects, phase coherence and breaking, Kondo effect) Systems of nano-devices (QCAs, systolic SET processors, quantum neural nets, adaptive effects in circuits, molecular circuits, NEMs) Nanomaterials (nanotubes, nanowires, organic and molecular materials, self-assembled nanowires, organic devices) Nano-bio-electronics (electronic properties of biological structures on the nanoscale) We were very pleased and honored to have the opportunity to organize the first International Symposium on Advanced Nanodevices and Nanotechnology. The conference benefited from 14 invited speakers, whose topics spanned the above list, and a total of 90 registered attendees. The largest contingent was from Japan, followed closely by the USA. We wish to particularly thank the sponsors for the meeting: Arizona State University on the US side, and the Japan Society for the Promotion of Science, through their 151 Committee, on the Japanese side. We would also like to thank Dr Koji Ishibashi, of RIKEN, for his assistance in the organization of the conference, and Professor David K Ferry for serving as the Editor for the ISANN Proceedings. Yoshinobu Aoyagi and Stephen M Goodnick Conference Co-Chairs

Nanoscopic dynamics of bicontinous microemulsions: effect of membrane associated protein

DOE PAGES

Sharma, V. K.; Hayes, Douglas G.; Urban, Volker S.; ...

2017-06-12

Bicontinous microemulsions (BμE) generally consist of nanodomains formed by surfactant in a mixture of water and oil at nearly equal proportions and are potential candidates for the solubilization and purification of membrane proteins. In this paper, we present the first time report of nanoscopic dynamics of surfactant monolayers within BμEs formed by the anionic surfactant sodium dodecyl sulfate (SDS) measured on the nanosecond to picosecond time scale using quasielastic neutron scattering (QENS). BμEs investigated herein consisted of middle phases isolated from Winsor-III microemulsion systems that were formed by mixing aqueous and oil solutions under optimal conditions. QENS data indicates thatmore » surfactants undergo two distinct motions, namely (i) lateral motion along the surface of the oil nanodomains and (ii) localized internal motion. Lateral motion can be described using a continuous diffusion model, from which the lateral diffusion coefficient is obtained. Internal motion of surfactant is described using a model which assumes that a fraction of the surfactants’ hydrogens undergoes localized translational diffusion that could be considered confined within a spherical volume. The effect of cytochrome c, an archetypal membrane-associated protein known to strongly partition near the surfactant head groups in BμEs (a trend supported by small-angle X-ray scattering [SAXS] analysis), on the dynamics of BμE has also been investigated. QENS results demonstrated that cytochrome c significantly hindered both the lateral and the internal motions of surfactant. The lateral motion was more strongly affected: a reduction of the lateral diffusion coefficient by 33% was measured. This change is mainly attributable to the strong association of cytochrome c with oppositely charged SDS. In contrast, analysis of SAXS data suggested that thermal fluctuations (for a longer length and slower time scale compared to QENS) were increased upon incorporation of cytochrome c. Finally, this study demonstrates the utility of QENS for evaluating dynamics of BμEs in nanoscopic region, and that proteins directly affect the microscopic dynamics, which is of relevance for evaluating release kinetics of encapsulated drugs from BμE delivery systems and the use of BμEs as biomembrane mimetic systems for investigating membrane protein–biomembrane interactions.« less

Lateralization of the arcuate fasciculus and its differential correlation with reading ability between young learners and experienced readers: a diffusion tensor tractography study in a Chinese cohort.

PubMed

Qiu, Deqiang; Tan, Li-Hai; Siok, Wai-Ting; Zhou, Ke; Khong, Pek-Lan

2011-12-01

As Chinese reading engages a different neural network from alphabetic language reading, we investigate whether leftward lateralization of the arcuate fasciculus (AF), as observed in the Western population, is also present in the Chinese population and if it does, whether it is associated with better reading ability. Diffusion tensor tractography analysis on 75 Chinese subjects of three age groups (first graders, fourth graders, and college students) showed that 70-83% of them had leftward lateralization of the AF. The pattern of lateralization did not differ significantly among the three groups, suggesting that lateralization of the AF is formed at an early age and before one enters first grade. Among the first graders, who had just started to learn to read, subjects with strongly leftward lateralized AF scored significantly higher than those with other defined lateralization patterns in Chinese (P = 0.001) and English (P = 0.036) reading tasks. This association was not observed among the fourth graders and college students who were experienced Chinese readers. Among the fourth graders, females were found to obtain significantly higher Chinese (P = 0.033) and English reading scores than males (P = 0.002). Our study suggests a differential effect of leftward lateralization of the AF on reading ability at different stages of reading development in the Chinese population. Copyright © 2011 Wiley Periodicals, Inc.

Diffusion-Weighted Magnetic Resonance Imaging Characterization of White Matter Injury Produced by Axon-Sparing Demyelination and Severe Contusion Spinal Cord Injury in Rats

PubMed Central

Nout-Lomas, Yvette S.; Wendland, Michael F.; Mukherjee, Pratik; Huie, J. Russell; Hess, Christopher P.; Mabray, Marc C.; Bresnahan, Jacqueline C.; Beattie, Michael S.

2016-01-01

Abstract Alterations in magnetic resonance imaging (MRI)–derived measurements of water diffusion parallel (D∥) and perpendicular (D⊥) to white matter tracts have been specifically attributed to pathology of axons and myelin, respectively. We test the hypothesis that directional diffusion measurements can distinguish between axon-sparing chemical demyelination and severe contusion spinal cord white matter injury. Adult rats received either unilateral ethidium bromide (EB) microinjections (chemical demyelination) into the lateral funiculus of the spinal cord at C5 or were subjected to unilateral severe contusion spinal cord injury (SCI). Diffusion MRI metrics in the lateral funiculus were analyzed at early and late time-points following injury and correlated with histology. Early EB-demyelination resulted in a significant elevation in D⊥ and significant reduction in D∥ at the injury epicenter, with histological evidence of uniform axon preservation. Alterations in D⊥ and D∥ at the epicenter of early EB-demyelination were not significantly different from those observed with severe contusion at the epicenter, where histology demonstrated severe combined axonal and myelin injury. Diffusion abnormalities away from the injury epicenter were seen with contusion injury, but not with EB-demyelination. Chronic EB lesions underwent endogenous remyelination with normalization of diffusion metrics, whereas chronic contusion resulted in persistently altered diffusivities. In the early setting, directional diffusion measurements at the injury epicenter associated with chemical demyelination are indistinguishable from those seen with severe contusive SCI, despite dramatic pathologic differences between injury models. Caution is advised in interpretation of diffusion metrics with respect to specific white matter structural alterations. Diffusion analysis should not be limited to the epicenter of focal spinal lesions as alterations marginal to the epicenter are useful for assessing the nature of focal white matter injury. PMID:26483094

The absence of chlorophyll b affects lateral mobility of photosynthetic complexes and lipids in grana membranes of Arabidopsis and barley chlorina mutants.

PubMed

Tyutereva, Elena V; Evkaikina, Anastasiia I; Ivanova, Alexandra N; Voitsekhovskaja, Olga V

2017-09-01

The lateral mobility of integral components of thylakoid membranes, such as plastoquinone, xanthophylls, and pigment-protein complexes, is critical for the maintenance of efficient light harvesting, high rates of linear electron transport, and successful repair of damaged photosystem II (PSII). The packaging of the photosynthetic pigment-protein complexes in the membrane depends on their size and stereometric parameters which in turn depend on the composition of the complexes. Chlorophyll b (Chlb) is an important regulator of antenna size and composition. In this study, the lateral mobility (the mobile fraction size) of pigment-protein complexes and lipids in grana membranes was analyzed in chlorina mutants of Arabidopsis and barley lacking Chlb. In the Arabidopsis ch1-3 mutant, diffusion of membrane lipids decreased as compared to wild-type plants, but the diffusion of photosynthetic complexes was not affected. In the barley chlorina f2 3613 mutant, the diffusion of pigment-protein complexes significantly decreased, while the diffusion of lipids increased, as compared to wild-type plants. We propose that the size of the mobile fractions of pigment-protein complexes in grana membranes in vivo is higher than reported previously. The data are discussed in the context of the protein composition of antennae, characteristics of the plastoquinone pool, and production of reactive oxygen species in leaves of chlorina mutants.

Age at First Exposure to Football Is Associated with Altered Corpus Callosum White Matter Microstructure in Former Professional Football Players

PubMed Central

Stamm, Julie M.; Koerte, Inga K.; Muehlmann, Marc; Pasternak, Ofer; Bourlas, Alexandra P.; Baugh, Christine M.; Giwerc, Michelle Y.; Zhu, Anni; Coleman, Michael J.; Bouix, Sylvain; Fritts, Nathan G.; Martin, Brett M.; Chaisson, Christine; McClean, Michael D.; Lin, Alexander P.; Cantu, Robert C.; Tripodis, Yorghos; Shenton, Martha E.

2015-01-01

Abstract Youth football players may incur hundreds of repetitive head impacts (RHI) in one season. Our recent research suggests that exposure to RHI during a critical neurodevelopmental period prior to age 12 may lead to greater later-life mood, behavioral, and cognitive impairments. Here, we examine the relationship between age of first exposure (AFE) to RHI through tackle football and later-life corpus callosum (CC) microstructure using magnetic resonance diffusion tensor imaging (DTI). Forty retired National Football League (NFL) players, ages 40–65, were matched by age and divided into two groups based on their AFE to tackle football: before age 12 or at age 12 or older. Participants underwent DTI on a 3 Tesla Siemens (TIM-Verio) magnet. The whole CC and five subregions were defined and seeded using deterministic tractography. Dependent measures were fractional anisotropy (FA), trace, axial diffusivity, and radial diffusivity. Results showed that former NFL players in the AFE <12 group had significantly lower FA in anterior three CC regions and higher radial diffusivity in the most anterior CC region than those in the AFE ≥12 group. This is the first study to find a relationship between AFE to RHI and later-life CC microstructure. These results suggest that incurring RHI during critical periods of CC development may disrupt neurodevelopmental processes, including myelination, resulting in altered CC microstructure. PMID:26200068

Water at hydrophobic interfaces delays proton surface-to-bulk transfer and provides a pathway for lateral proton diffusion

PubMed Central

Zhang, Chao; Knyazev, Denis G.; Vereshaga, Yana A.; Ippoliti, Emiliano; Nguyen, Trung Hai; Carloni, Paolo; Pohl, Peter

2012-01-01

Fast lateral proton migration along membranes is of vital importance for cellular energy homeostasis and various proton-coupled transport processes. It can only occur if attractive forces keep the proton at the interface. How to reconcile this high affinity to the membrane surface with high proton mobility is unclear. Here, we tested whether a minimalistic model interface between an apolar hydrophobic phase (n-decane) and an aqueous phase mimics the biological pathway for lateral proton migration. The observed diffusion span, on the order of tens of micrometers, and the high proton mobility were both similar to the values previously reported for lipid bilayers. Extensive ab initio simulations on the same water/n-decane interface reproduced the experimentally derived free energy barrier for the excess proton. The free energy profile GH+ adopts the shape of a well at the interface, having a width of two water molecules and a depth of 6 ± 2RT. The hydroniums in direct contact with n-decane have a reduced mobility. However, the hydroniums in the second layer of water molecules are mobile. Their in silico diffusion coefficient matches that derived from our in vitro experiments, (5.7 ± 0.7) × 10-5 cm2 s-1. Conceivably, these are the protons that allow for fast diffusion along biological membranes. PMID:22675120

Age at First Exposure to Football Is Associated with Altered Corpus Callosum White Matter Microstructure in Former Professional Football Players.

PubMed

Stamm, Julie M; Koerte, Inga K; Muehlmann, Marc; Pasternak, Ofer; Bourlas, Alexandra P; Baugh, Christine M; Giwerc, Michelle Y; Zhu, Anni; Coleman, Michael J; Bouix, Sylvain; Fritts, Nathan G; Martin, Brett M; Chaisson, Christine; McClean, Michael D; Lin, Alexander P; Cantu, Robert C; Tripodis, Yorghos; Stern, Robert A; Shenton, Martha E

2015-11-15

Youth football players may incur hundreds of repetitive head impacts (RHI) in one season. Our recent research suggests that exposure to RHI during a critical neurodevelopmental period prior to age 12 may lead to greater later-life mood, behavioral, and cognitive impairments. Here, we examine the relationship between age of first exposure (AFE) to RHI through tackle football and later-life corpus callosum (CC) microstructure using magnetic resonance diffusion tensor imaging (DTI). Forty retired National Football League (NFL) players, ages 40-65, were matched by age and divided into two groups based on their AFE to tackle football: before age 12 or at age 12 or older. Participants underwent DTI on a 3 Tesla Siemens (TIM-Verio) magnet. The whole CC and five subregions were defined and seeded using deterministic tractography. Dependent measures were fractional anisotropy (FA), trace, axial diffusivity, and radial diffusivity. Results showed that former NFL players in the AFE <12 group had significantly lower FA in anterior three CC regions and higher radial diffusivity in the most anterior CC region than those in the AFE ≥12 group. This is the first study to find a relationship between AFE to RHI and later-life CC microstructure. These results suggest that incurring RHI during critical periods of CC development may disrupt neurodevelopmental processes, including myelination, resulting in altered CC microstructure.

Stochastic dynamics and non-equilibrium thermodynamics of a bistable chemical system: the Schlögl model revisited.

PubMed

Vellela, Melissa; Qian, Hong

2009-10-06

Schlögl's model is the canonical example of a chemical reaction system that exhibits bistability. Because the biological examples of bistability and switching behaviour are increasingly numerous, this paper presents an integrated deterministic, stochastic and thermodynamic analysis of the model. After a brief review of the deterministic and stochastic modelling frameworks, the concepts of chemical and mathematical detailed balances are discussed and non-equilibrium conditions are shown to be necessary for bistability. Thermodynamic quantities such as the flux, chemical potential and entropy production rate are defined and compared across the two models. In the bistable region, the stochastic model exhibits an exchange of the global stability between the two stable states under changes in the pump parameters and volume size. The stochastic entropy production rate shows a sharp transition that mirrors this exchange. A new hybrid model that includes continuous diffusion and discrete jumps is suggested to deal with the multiscale dynamics of the bistable system. Accurate approximations of the exponentially small eigenvalue associated with the time scale of this switching and the full time-dependent solution are calculated using Matlab. A breakdown of previously known asymptotic approximations on small volume scales is observed through comparison with these and Monte Carlo results. Finally, in the appendix section is an illustration of how the diffusion approximation of the chemical master equation can fail to represent correctly the mesoscopically interesting steady-state behaviour of the system.

A spin current rectifier

NASA Astrophysics Data System (ADS)

Eyni, Zahra; Mohammadpour, Hakimeh

2017-12-01

Current modulation and rectification is an important subject of electronics as well as spintronics. In this paper, an efficient rectifying mesoscopic device is introduced. The device is a two terminal device on the 2D plane of electron gas. The lateral contacts are half-metal ferromagnetic with antiparallel magnetizations and the central channel region is taken as ferromagnetic or normal in the presence of an applied magnetic field. The device functionality is based on the modification of spin-current by tuning the strength of the magnetic field or equivalently by the exchange coupling of the channel to the substrate. The result is that the (spin-) current depends on the polarity of the bias voltage. Converting an alternating bias voltage to direct current is the main achievement of this model device with an additional profit of rectified spin-current. We analyze the results in terms of the spin-dependent barrier in the channel. Detecting the strength of the magnetic field by spin polarization is also suggested.

Stepwise self-assembly of C60 mediated by atomic scale moiré magnifiers

NASA Astrophysics Data System (ADS)

Gruznev, D. V.; Matetskiy, A. V.; Bondarenko, L. V.; Utas, O. A.; Zotov, A. V.; Saranin, A. A.; Chou, J. P.; Wei, C. M.; Lai, M. Y.; Wang, Y. L.

2013-04-01

Self-assembly of atoms or molecules on a crystal surface is considered one of the most promising methods to create molecular devices. Here we report a stepwise self-assembly of C60 molecules into islands with unusual shapes and preferred sizes on a gold-indium-covered Si(111) surface. Specifically, 19-mer islands prefer a non-compact boomerang shape, whereas hexagonal 37-mer islands exhibit extraordinarily enhanced stability and abundance. The stepwise self-assembly is mediated by the moiré interference between an island with its underlying lattice, which essentially maps out the adsorption-energy landscape of a C60 on different positions of the surface with a lateral magnification factor and dictates the probability for the subsequent attachment of C60 to an island’s periphery. Our discovery suggests a new method for exploiting the moiré interference to dynamically assist the self-assembly of particles and provides an unexplored tactic of engineering atomic scale moiré magnifiers to facilitate the growth of monodispersed mesoscopic structures.

Imaging Findings Associated with Cognitive Performance in Primary Lateral Sclerosis and Amyotrophic Lateral Sclerosis

PubMed Central

Meoded, Avner; Kwan, Justin Y.; Peters, Tracy L.; Huey, Edward D.; Danielian, Laura E.; Wiggs, Edythe; Morrissette, Arthur; Wu, Tianxia; Russell, James W.; Bayat, Elham; Grafman, Jordan; Floeter, Mary Kay

2013-01-01

Introduction Executive dysfunction occurs in many patients with amyotrophic lateral sclerosis (ALS), but it has not been well studied in primary lateral sclerosis (PLS). The aims of this study were to (1) compare cognitive function in PLS to that in ALS patients, (2) explore the relationship between performance on specific cognitive tests and diffusion tensor imaging (DTI) metrics of white matter tracts and gray matter volumes, and (3) compare DTI metrics in patients with and without cognitive and behavioral changes. Methods The Delis-Kaplan Executive Function System (D-KEFS), the Mattis Dementia Rating Scale (DRS-2), and other behavior and mood scales were administered to 25 ALS patients and 25 PLS patients. Seventeen of the PLS patients, 13 of the ALS patients, and 17 healthy controls underwent structural magnetic resonance imaging (MRI) and DTI. Atlas-based analysis using MRI Studio software was used to measure fractional anisotropy, and axial and radial diffusivity of selected white matter tracts. Voxel-based morphometry was used to assess gray matter volumes. The relationship between diffusion properties of selected association and commissural white matter and performance on executive function and memory tests was explored using a linear regression model. Results More ALS than PLS patients had abnormal scores on the DRS-2. DRS-2 and D-KEFS scores were related to DTI metrics in several long association tracts and the callosum. Reduced gray matter volumes in motor and perirolandic areas were not associated with cognitive scores. Conclusion The changes in diffusion metrics of white matter long association tracts suggest that the loss of integrity of the networks connecting fronto-temporal areas to parietal and occipital areas contributes to cognitive impairment. PMID:24052798

Outer Hair Cell Lateral Wall Structure Constrains the Mobility of Plasma Membrane Proteins

PubMed Central

Yamashita, Tetsuji; Hakizimana, Pierre; Wu, Siva; Hassan, Ahmed; Jacob, Stefan; Temirov, Jamshid; Fang, Jie; Mellado-Lagarde, Marcia; Gursky, Richard; Horner, Linda; Leibiger, Barbara; Leijon, Sara; Centonze, Victoria E.; Berggren, Per-Olof; Frase, Sharon; Auer, Manfred; Brownell, William E.; Fridberger, Anders; Zuo, Jian

2015-01-01

Nature’s fastest motors are the cochlear outer hair cells (OHCs). These sensory cells use a membrane protein, Slc26a5 (prestin), to generate mechanical force at high frequencies, which is essential for explaining the exquisite hearing sensitivity of mammalian ears. Previous studies suggest that Slc26a5 continuously diffuses within the membrane, but how can a freely moving motor protein effectively convey forces critical for hearing? To provide direct evidence in OHCs for freely moving Slc26a5 molecules, we created a knockin mouse where Slc26a5 is fused with YFP. These mice and four other strains expressing fluorescently labeled membrane proteins were used to examine their lateral diffusion in the OHC lateral wall. All five proteins showed minimal diffusion, but did move after pharmacological disruption of membrane-associated structures with a cholesterol-depleting agent and salicylate. Thus, our results demonstrate that OHC lateral wall structure constrains the mobility of plasma membrane proteins and that the integrity of such membrane-associated structures are critical for Slc26a5’s active and structural roles. The structural constraint of membrane proteins may exemplify convergent evolution of cellular motors across species. Our findings also suggest a possible mechanism for disorders of cholesterol metabolism with hearing loss such as Niemann-Pick Type C diseases. PMID:26352669

Differential equation of exospheric lateral transport and its application to terrestrial hydrogen

NASA Technical Reports Server (NTRS)

Hodges, R. R., Jr.

1973-01-01

The differential equation description of exospheric lateral transport of Hodges and Johnson is reformulated to extend its utility to light gases. Accuracy of the revised equation is established by applying it to terrestrial hydrogen. The resulting global distributions for several static exobase models are shown to be essentially the same as those that have been computed by Quessette using an integral equation approach. The present theory is subsequently used to elucidate the effects of nonzero lateral flow, exobase rotation, and diurnal tidal winds on the hydrogen distribution. Finally it is shown that the differential equation of exospheric transport is analogous to a diffusion equation. Hence it is practical to consider exospheric transport as a continuation of thermospheric diffusion, a concept that alleviates the need for an artificial exobase dividing thermosphere and exosphere.

Micro-Hall devices for magnetic, electric and photo-detection

NASA Astrophysics Data System (ADS)

Gilbertson, A.; Sadeghi, H.; Panchal, V.; Kazakova, O.; Lambert, C. J.; Solin, S. A.; Cohen, L. F.

Multifunctional mesoscopic sensors capable of detecting local magnetic (B) , electric (E) , and optical fields can greatly facilitate image capture in nano-arrays that address a multitude of disciplines. The use of micro-Hall devices as B-field sensors and, more recently as E-field sensors is well established. Here we report the real-space voltage response of InSb/AlInSb micro-Hall devices to not only local E-, and B-fields but also to photo-excitation using scanning probe microscopy. We show that the ultrafast generation of localised photocarriers results in conductance perturbations analogous to those produced by local E-fields. Our experimental results are in good agreement with tight-binding transport calculations in the diffusive regime. At room temperature, samples exhibit a magnetic sensitivity of >500 nT/ √Hz, an optical noise equivalent power of >20 pW/ √Hz (λ = 635 nm) comparable to commercial photoconductive detectors, and charge sensitivity of >0.04 e/ √Hz comparable to that of single electron transistors. Work done while on sabbatical from Washington University. Co-founder of PixelEXX, a start-up whose focus is imaging nano-arrays.

Gene regulatory networks: a coarse-grained, equation-free approach to multiscale computation.

PubMed

Erban, Radek; Kevrekidis, Ioannis G; Adalsteinsson, David; Elston, Timothy C

2006-02-28

We present computer-assisted methods for analyzing stochastic models of gene regulatory networks. The main idea that underlies this equation-free analysis is the design and execution of appropriately initialized short bursts of stochastic simulations; the results of these are processed to estimate coarse-grained quantities of interest, such as mesoscopic transport coefficients. In particular, using a simple model of a genetic toggle switch, we illustrate the computation of an effective free energy Phi and of a state-dependent effective diffusion coefficient D that characterize an unavailable effective Fokker-Planck equation. Additionally we illustrate the linking of equation-free techniques with continuation methods for performing a form of stochastic "bifurcation analysis"; estimation of mean switching times in the case of a bistable switch is also implemented in this equation-free context. The accuracy of our methods is tested by direct comparison with long-time stochastic simulations. This type of equation-free analysis appears to be a promising approach to computing features of the long-time, coarse-grained behavior of certain classes of complex stochastic models of gene regulatory networks, circumventing the need for long Monte Carlo simulations.

Prenatal and Neonatal Brain Structure and White Matter Maturation in Children at High Risk for Schizophrenia

PubMed Central

Gilmore, John H.; Kang, Chaeryon; Evans, Dianne D.; Wolfe, Honor M.; Smith, J. Keith; Lieberman, Jeffrey A.; Lin, Weili; Hamer, Robert M.; Styner, Martin; Gerig, Guido

2011-01-01

Objective Schizophrenia is a neurodevelopmental disorder associated with abnormalities of brain structure and white matter, although little is known about when these abnormalities arise. This study was conducted to identify structural brain abnormalities in the prenatal and neonatal periods associated with genetic risk for schizophrenia. Method Prenatal ultrasound scans and neonatal structural magnetic resonance imaging (MRI) and diffusion tensor imaging were prospectively obtained in the offspring of mothers with schizophrenia or schizoaffective disorder (N=26) and matched comparison mothers without psychiatric illness (N=26). Comparisons were made for prenatal lateral ventricle width and head circumference, for neonatal intracranial, CSF, gray matter, white matter, and lateral ventricle volumes, and for neonatal diffusion properties of the genu and splenium of the corpus callosum and corticospinal tracts. Results Relative to the matched comparison subjects, the offspring of mothers with schizophrenia did not differ in prenatal lateral ventricle width or head circumference. Overall, the high-risk neonates had nonsignificantly larger intracranial, CSF, and lateral ventricle volumes. Subgroup analysis revealed that male high-risk infants had significantly larger intracranial, CSF, total gray matter, and lateral ventricle volumes; the female high-risk neonates were similar to the female comparison subjects. There were no group differences in white matter diffusion tensor properties. Conclusions Male neonates at genetic risk for schizophrenia had several larger than normal brain volumes, while females did not. To the authors' knowledge, this study provides the first evidence, in the context of its limitations, that early neonatal brain development may be abnormal in males at genetic risk for schizophrenia. PMID:20516153

Right hemispheric reversible cerebral vasoconstriction syndrome in a patient with left hemispheric partial seizures.

PubMed

Perez, Gina S; McCaslin, Justin; Shamim, Sadat

2017-04-01

We report a right-handed 19-year-old girl who developed reversible cerebral vasoconstriction syndrome (RCVS) lateralized to the right hemisphere with simultaneous new-onset left hemispheric seizures. RCVS, typically more diffuse, was lateralized to one of the cerebral hemispheres.

Quantitative Examination of Corrosion Damage by Means of Thermal Response Measurements

NASA Technical Reports Server (NTRS)

Rajic, Nik

1998-01-01

Two computational methods are presented that enable a characterization of corrosion damage to be performed from thermal response measurements derived from a standard flash thermographic inspection. The first is based upon a one dimensional analytical solution to the heat diffusion equation and presumes the lateral extent of damage is large compared to the residual structural thickness, such that lateral heat diffusion effects can be considered insignificant. The second proposed method, based on a finite element optimization scheme, addresses the more general case where these conditions are not met. Results from an experimental application are given to illustrate the precision, robustness and practical efficacy of both methods.

Estimates of the lateral eddy diffusivity in the Indian Ocean as derived from drifter data

NASA Astrophysics Data System (ADS)

Zhurbas, V. M.; Lyzhkov, D. A.; Kuzmina, N. P.

2014-05-01

The Global Drifter Program data set is applied to develop 2° × 2° bin estimates of the lateral eddy diffusivity K in the Indian Ocean (IO) by means of a modification of the Davis approach. The calculations were performed relative to the seasonal change in the mean currents, which is especially important in the case of monsoon-driven circulation in the IO. Estimates of K were found to be below 1 × 104 m2/s almost every-where in the IO. The spatial variations of K were analyzed in relation to the instabilities of the ocean circulation.

Towards large-scale, human-based, mesoscopic neurotechnologies.

PubMed

Chang, Edward F

2015-04-08

Direct human brain recordings have transformed the scope of neuroscience in the past decade. Progress has relied upon currently available neurophysiological approaches in the context of patients undergoing neurosurgical procedures for medical treatment. While this setting has provided precious opportunities for scientific research, it also has presented significant constraints on the development of new neurotechnologies. A major challenge now is how to achieve high-resolution spatiotemporal neural recordings at a large scale. By narrowing the gap between current approaches, new directions tailored to the mesoscopic (intermediate) scale of resolution may overcome the barriers towards safe and reliable human-based neurotechnology development, with major implications for advancing both basic research and clinical translation. Copyright © 2015 Elsevier Inc. All rights reserved.

Ballistic pulse propagation in quantum wire waveguides: Toward localization and control of electron wave packets in space and time

NASA Astrophysics Data System (ADS)

Hayata, K.; Tsuji, Y.; Koshiba, M.

1992-10-01

A theoretical formulation of electron pulse propagation in quantum wire structures with mesoscopic scale cross sections is presented, assuming quantum ballistic transport of electron wave packets over a certain characteristic length. As typical mesoscopic structures for realizing coherent electron transmission, two traveling-wave configurations are considered: straight quantum wire waveguides and quantum wire bend structures (quantum whispering galleries). To estimate temporal features of the pulse during propagation, the walk off, the dispersion, and the pulse coherence lengths are defined as useful characteristic lengths. Numerical results are shown for ultrashort pulse propagation through rectangular wire waveguides. Effects due to an external electric field are discussed as well.

Controlling morphology, mesoporosity, crystallinity, and photocatalytic activity of ordered mesoporous TiO2 films prepared at low temperature

NASA Astrophysics Data System (ADS)

Elgh, Björn; Yuan, Ning; Cho, Hae Sung; Magerl, David; Philipp, Martine; Roth, Stephan V.; Yoon, Kyung Byung; Müller-Buschbaum, Peter; Terasaki, Osamu; Palmqvist, Anders E. C.

2014-11-01

Partly ordered mesoporous titania films with anatase crystallites incorporated into the pore walls were prepared at low temperature by spin-coating a microemulsion-based reaction solution. The effect of relative humidity employed during aging of the prepared films was studied using SEM, TEM, and grazing incidence small angle X-ray scattering to evaluate the mesoscopic order, porosity, and crystallinity of the films. The study shows unambiguously that crystal growth occurs mainly during storage of the films and proceeds at room temperature largely depending on relative humidity. Porosity, pore size, mesoscopic order, crystallinity, and photocatalytic activity of the films increased with relative humidity up to an optimum around 75%.

Balanced double-loop mesoscopic interferometer based on Josephson proximity nanojunctions

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

Ronzani, Alberto, E-mail: alberto.ronzani@nano.cnr.it; Altimiras, Carles; Giazotto, Francesco

We report on the fabrication and characterization of a two-terminal mesoscopic interferometer based on three V/Cu/V Josephson junctions having nanoscale cross-section. The junctions have been arranged in a double-ring geometry realized by metallic thin film deposition through a suspended mask defined by electron beam lithography. Although a significant amount of asymmetry between the critical current of each junction is observed, we show that the interferometer is able to suppress the supercurrent to a level lower than 6 parts per thousand, being here limited by measurement resolution. The present nano-device is suitable for low-temperature magnetometric and gradiometric measurements over the micrometricmore » scale.« less

Structure and rheology of star polymers in confined geometries: a mesoscopic simulation study.

PubMed

Zheng, Feiwo; Goujon, Florent; Mendonça, Ana C F; Malfreyt, Patrice; Tildesley, Dominic J

2015-11-28

Mesoscopic simulations of star polymer melts adsorbed onto solid surfaces are performed using the dissipative particle dynamics (DPD) method. A set of parameters is developed to study the low functionality star polymers under shear. The use of a new bond-angle potential between the arms of the star creates more rigid chains and discriminates between different functionalities at equilibrium, but still allows the polymers to deform appropriately under shear. The rheology of the polymer melts is studied by calculating the kinetic friction and viscosity and there is good agreement with experimental properties of these systems. The study is completed with predictive simulations of star polymer solutions in an athermal solvent.

Modeling of electrical and mesoscopic circuits at quantum nanoscale from heat momentum operator

NASA Astrophysics Data System (ADS)

El-Nabulsi, Rami Ahmad

2018-04-01

We develop a new method to study electrical circuits at quantum nanoscale by introducing a heat momentum operator which reproduces quantum effects similar to those obtained in Suykens's nonlocal-in-time kinetic energy approach for the case of reversible motion. The series expansion of the heat momentum operator is similar to the momentum operator obtained in the framework of minimal length phenomenologies characterized by the deformation of Heisenberg algebra. The quantization of both LC and mesoscopic circuits revealed a number of motivating features like the emergence of a generalized uncertainty relation and a minimal charge similar to those obtained in the framework of minimal length theories. Additional features were obtained and discussed accordingly.

Chrysocolla Redefined as Spertiniite

NASA Astrophysics Data System (ADS)

Farges, François; Benzerara, Karim; Brown, Gordon E.

2007-02-01

XAFS and μ-XAFS spectra were collected at the Cu K-edge for seven chrysocolla samples (Peru, USA, and Congo). The results suggest that that the local structure around Cu is similar to that in Cu(OH)2 (spertiniite). Cu-L3 STXM imaging and spectroscopy confirm that the chrysocolla samples examined here consist of mesoscopic Cu(II)-rich domains surrounded by Si-rich domains (in agreement with results from infra-red spectroscopy). Hence, we suggest that chrysocolla, which is generally considered to be orthorhombic with composition (Cu,Al)2H2Si2O5(OH)4ṡnH2O, is in actually a mesoscopic assemblage composed dominantly of spertiniite (Cu(OH)2), water and amorphous silica (SiO2).

Mesoscopic modeling of multi-physicochemical transport phenomena in porous media

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

Kang, Qinjin; Wang, Moran; Mukherjee, Partha P

2009-01-01

We present our recent progress on mesoscopic modeling of multi-physicochemical transport phenomena in porous media based on the lattice Boltzmann method. Simulation examples include injection of CO{sub 2} saturated brine into a limestone rock, two-phase behavior and flooding phenomena in polymer electrolyte fuel cells, and electroosmosis in homogeneously charged porous media. It is shown that the lattice Boltzmann method can account for multiple, coupled physicochemical processes in these systems and can shed some light on the underlying physics occuning at the fundamental scale. Therefore, it can be a potential powerful numerical tool to analyze multi-physicochemical processes in various energy, earth,more » and environmental systems.« less

Quantum solitonic wave-packet of a meso-scopic system in singularity free gravity

NASA Astrophysics Data System (ADS)

Buoninfante, Luca; Lambiase, Gaetano; Mazumdar, Anupam

2018-06-01

In this paper we will discuss how to localise a quantum wave-packet due to self-gravitating meso-scopic object by taking into account gravitational self-interaction in the Schrödinger equation beyond General Relativity. In particular, we will study soliton-like solutions in infinite derivative ghost free theories of gravity, which resolves the gravitational 1 / r singularity in the potential. We will show a unique feature that the quantum spread of such a gravitational system is larger than that of the Newtonian gravity, therefore enabling us a window of opportunity to test classical and quantum properties of such theories of gravity in the near future at a table-top experiment.

Energy utilization in fluctuating biological energy converters

PubMed Central

Szőke, Abraham; Hajdu, Janos

2016-01-01

We have argued previously [Szoke et al., FEBS Lett. 553, 18–20 (2003); Curr. Chem. Biol. 1, 53–57 (2007)] that energy utilization and evolution are emergent properties based on a small number of established laws of physics and chemistry. The relevant laws constitute a framework for biology on a level intermediate between quantum chemistry and cell biology. There are legitimate questions whether these concepts are valid at the mesoscopic level. Such systems fluctuate appreciably, so it is not clear what their efficiency is. Advances in fluctuation theorems allow the description of such systems on a molecular level. We attempt to clarify this topic and bridge the biochemical and physical descriptions of mesoscopic systems. PMID:27191009

Effects of finite size on spin glass dynamics

NASA Astrophysics Data System (ADS)

Sato, Tetsuya; Komatsu, Katsuyoshi

2010-12-01

In spite of comprehensive studies to clarify a variety of interesting phenomena of spin glasses, their understanding has been insufficiently established. To overcome such a problem, fabrication of a mesoscopic spin glass system, whose dynamics can be observed over the entire range to the equilibrium, is useful. In this review the challenges of research that has been performed up to now in this direction and our recent related studies are introduced. We have established to study the spin glass behaviour in terms of droplet picture using nanofabricated mesoscopic samples to some extent, but some problems that should be clarified have been left. Finally, the direction of some new studies is proposed to solve the problems.

The Environmental Protection Agency's brownfields pilot program.

PubMed

Greenberg, Michael R; Hollander, Justin

2006-02-01

We studied the diffusion of the US Environmental Protection Agency's national brownfields pilot innovation to more than 300 local governments between 1993 through 2002 to determine why some local governments received grants very early in the process while other awardees received funding later. We did an ordinal regression analysis of the characteristics of all local government award recipients, and we conducted interviews with early-award recipients. The first set of local government awardees had lost much of their manufacturing base, had large concentrations of economically disadvantaged minority residents, and had local capacity to compete for funding. Federal and state officials catalyzed the diffusion of the innovation by working with local governments. The widely praised program was diffused selectively at first and then more widely later on the basis of local need, local capacity to compete, and networks of contacts among entrepreneurs and local governments. The economic, social, political, and public health impacts must be monitored and reviewed.

Diffusive boundary layers at the bottom of gaps and cracks

NASA Astrophysics Data System (ADS)

Etzold, Merlin A.; Landel, Julien R.; Dalziel, Stuart B.

2017-11-01

This work is motivated by the chemical decontamination of droplets of chemical warfare agents trapped in the gaps and cracks found in most man-made objects. We consider axial laminar flow within gaps with both straight and angled walls. We study the diffusive mass transfer from a source (e.g. a droplet surface) located at the bottom of the gap. This problem is similar to boundary layers and Graetz-type problems (heat transfer in pipe flow) with the added complication of a non-uniform lateral concentration profile due to the lateral variation of the velocity profile. We present 3D solutions for the diffusive boundary layer and demonstrate that a 2D mean-field model, for which we calculate series and similarity solutions, captures the essential physics. We demonstrate the immediate practical relevance of our findings by comparing decontamination of a droplet located in a gap and on an exposed surface.

Contributions of microtubule rotation and dynamic instability to kinetochore capture

NASA Astrophysics Data System (ADS)

Sweezy-Schindler, Oliver; Edelmaier, Christopher; Blackwell, Robert; Glaser, Matt; Betterton, Meredith

2014-03-01

The capture of lost kinetochores (KCs) by microtubules (MTs) is a crucial part of prometaphase during mitosis. Microtubule dynamic instability has been considered the primary mechanism of KC capture, but recent work discovered that lateral KC attachment to pivoting MTs enabled rapid capture even with significantly reduced MT dynamics. We aim to understand the relative contributions of MT rotational diffusion and dynamic instability to KC capture, as well as KC capture through end-on and/or lateral attachment. Our model consists of rigid MTs and a spherical KC, which are allowed to diffuse inside a spherical nuclear envelope consistent with the geometry of fission yeast. For simplicity, we include a single spindle pole body, which is anchored to the nuclear membrane, and its associated polar MTs. Brownian dynamics treats the diffusion of the MTs and KC and kinetic Monte Carlo models stochastic processes such as dynamic instability. NSF 1546021.

Two-dimensional enzyme diffusion in laterally confined DNA monolayers.

PubMed

Castronovo, Matteo; Lucesoli, Agnese; Parisse, Pietro; Kurnikova, Anastasia; Malhotra, Aseem; Grassi, Mario; Grassi, Gabriele; Scaggiante, Bruna; Casalis, Loredana; Scoles, Giacinto

2011-01-01

Addressing the effects of confinement and crowding on biomolecular function may provide insight into molecular mechanisms within living organisms, and may promote the development of novel biotechnology tools. Here, using molecular manipulation methods, we investigate restriction enzyme reactions with double-stranded (ds)DNA oligomers confined in relatively large (and flat) brushy matrices of monolayer patches of controlled, variable density. We show that enzymes from the contacting solution cannot access the dsDNAs from the top-matrix interface, and instead enter at the matrix sides to diffuse two-dimensionally in the gap between top- and bottom-matrix interfaces. This is achieved by limiting lateral access with a barrier made of high-density molecules that arrest enzyme diffusion. We put forward, as a possible explanation, a simple and general model that relates these data to the steric hindrance in the matrix, and we briefly discuss the implications and applications of this strikingly new phenomenon.

Right hemispheric reversible cerebral vasoconstriction syndrome in a patient with left hemispheric partial seizures

PubMed Central

Perez, Gina S.; McCaslin, Justin

2017-01-01

We report a right-handed 19-year-old girl who developed reversible cerebral vasoconstriction syndrome (RCVS) lateralized to the right hemisphere with simultaneous new-onset left hemispheric seizures. RCVS, typically more diffuse, was lateralized to one of the cerebral hemispheres. PMID:28405089

Conceptual techniques for reducing parasitic current gain of lateral pnp transistors

NASA Technical Reports Server (NTRS)

Gallagher, R. C.; Scott, J. M.

1969-01-01

Two techniques have been conceptually proposed as possible means of reducing parasitic beta in lateral p-n-p transistors. One method uses a degenerate substrate and high concentration P /plus/ guard-ring diffusion, another places the base contact at the center of an annular ring structure.

Convergence of lateral dynamic measurements in the plasma membrane of live cells from single particle tracking and STED-FCS

NASA Astrophysics Data System (ADS)

Lagerholm, B. Christoffer; Andrade, Débora M.; Clausen, Mathias P.; Eggeling, Christian

2017-02-01

Fluorescence correlation spectroscopy (FCS) in combination with the super-resolution imaging method STED (STED-FCS), and single-particle tracking (SPT) are able to directly probe the lateral dynamics of lipids and proteins in the plasma membrane of live cells at spatial scales much below the diffraction limit of conventional microscopy. However, a major disparity in interpretation of data from SPT and STED-FCS remains, namely the proposed existence of a very fast (unhindered) lateral diffusion coefficient, ⩾5 µm2 s-1, in the plasma membrane of live cells at very short length scales, ≈⩽ 100 nm, and time scales, ≈1-10 ms. This fast diffusion coefficient has been advocated in several high-speed SPT studies, for lipids and membrane proteins alike, but the equivalent has not been detected in STED-FCS measurements. Resolving this ambiguity is important because the assessment of membrane dynamics currently relies heavily on SPT for the determination of heterogeneous diffusion. A possible systematic error in this approach would thus have vast implications in this field. To address this, we have re-visited the analysis procedure for SPT data with an emphasis on the measurement errors and the effect that these errors have on the measurement outputs. We subsequently demonstrate that STED-FCS and SPT data, following careful consideration of the experimental errors of the SPT data, converge to a common interpretation which for the case of a diffusing phospholipid analogue in the plasma membrane of live mouse embryo fibroblasts results in an unhindered, intra-compartment, diffusion coefficient of  ≈0.7-1.0 µm2 s-1, and a compartment size of about 100-150 nm.

Convergence of lateral dynamic measurements in the plasma membrane of live cells from single particle tracking and STED-FCS

PubMed Central

Lagerholm, B Christoffer; Andrade, Débora M; Clausen, Mathias P; Eggeling, Christian

2017-01-01

Abstract Fluorescence correlation spectroscopy (FCS) in combination with the super-resolution imaging method STED (STED-FCS), and single-particle tracking (SPT) are able to directly probe the lateral dynamics of lipids and proteins in the plasma membrane of live cells at spatial scales much below the diffraction limit of conventional microscopy. However, a major disparity in interpretation of data from SPT and STED-FCS remains, namely the proposed existence of a very fast (unhindered) lateral diffusion coefficient, ⩾5 µm2 s−1, in the plasma membrane of live cells at very short length scales, ≈⩽ 100 nm, and time scales, ≈1–10 ms. This fast diffusion coefficient has been advocated in several high-speed SPT studies, for lipids and membrane proteins alike, but the equivalent has not been detected in STED-FCS measurements. Resolving this ambiguity is important because the assessment of membrane dynamics currently relies heavily on SPT for the determination of heterogeneous diffusion. A possible systematic error in this approach would thus have vast implications in this field. To address this, we have re-visited the analysis procedure for SPT data with an emphasis on the measurement errors and the effect that these errors have on the measurement outputs. We subsequently demonstrate that STED-FCS and SPT data, following careful consideration of the experimental errors of the SPT data, converge to a common interpretation which for the case of a diffusing phospholipid analogue in the plasma membrane of live mouse embryo fibroblasts results in an unhindered, intra-compartment, diffusion coefficient of  ≈0.7–1.0 µm2 s−1, and a compartment size of about 100–150 nm. PMID:28458397

The initial stage of uranium oxidation: mechanism of UO(2) scale formation in the presence of a native lateral stress field.

PubMed

Chernia, Z; Ben-Eliyahu, Y; Kimmel, G; Braun, G; Sariel, J

2006-11-23

In this work, an oxidation model for alpha-uranium is presented. It describes the internally lateral stress field built in the oxide scale during the reaction. The thickness of the elastic, stress-preserving oxide (UO(2+x)) scale is less than 0.5 microm. A lateral, 6.5 GPa stress field has been calculated from strains derived from line shifts (delta(2theta)) as measured by the X-ray diffraction of UO(2). It is shown that in the elastic growth domain, (110) is the main UO(2) growth plane for gas-solid oxidation. The diffusion-limited oxidation mechanism discussed here is based on the known "2:2:2" cluster theory which describes the mechanism of fluorite-based hyperstoichiometric oxides. In this study, it is adapted to describe oxygen-anion hopping. Anion hopping toward the oxide-metal interface proceeds at high rates in the [110] direction, hence making this pipeline route the principal growth direction in UO(2) formation. It is further argued that growth in the pure elastic domain of the oxide scale should be attributed entirely to anion hopping in 110. Anions, diffusing isotropically via grain boundaries and cracks, are shown to have a significant impact on the overall oxidation rate in relatively thick (>0.35 microm) oxide scales if followed by an avalanche break off in the postelastic regime. Stress affects oxidation in the elastic domain by controlling the hopping rate directly. In the postelastic regime, stress weakens hopping, indirectly, by enhancing isotropic diffusion. Surface roughness presents an additional hindering factor for the anion hopping. In comparison to anisotropic hopping, diffusion of isotropic hopping has a lower activation energy barrier. Therefore, a relatively stronger impact at lower temperatures due to isotropic diffusion is displayed.

Lateral diffusion of rhodopsin in photoreceptor membrane: a reappraisal.

PubMed

Govardovskii, Victor I; Korenyak, Darya A; Shukolyukov, Sergei A; Zueva, Lidia V

2009-08-28

In a series of works between 1972 and 1984, it was established that rhodopsin undergoes rotational and lateral Brownian motion in the plane of photoreceptor membrane. The concept of free movement of proteins of phototransduction cascade is an essential principle of the present scheme of vertebrate phototransduction. This has recently been challenged by findings that show that in certain conditions rhodopsin in the membrane may be dimeric and form extended areas of paracrystalline organization. Such organization seems incompatible with earlier data on free rhodopsin diffusion. Thus we decided to reinvestigate lateral diffusion of rhodopsin and products of its photolysis in photoreceptor membrane specifically looking for indications of possible oligomeric organization. Diffusion exchange by rhodopsin and its photoproducts between bleached and unbleached halves of rod outer segment was traced using high-speed dichroic microspectrophotometer. Measurements were conducted on amphibian (frog, toad, and salamander) and gecko rods. We found that the curves that are supposed to reflect the process of diffusion equilibration of rhodopsin in nonuniformly bleached outer segment largely show production of long-lived bleaching intermediate, metarhodopsin III (Meta III). After experimental elimination of Meta III contribution, we observed rhodopsin equilibration time constant was threefold to tenfold longer than estimated previously. However, after proper correction for the geometry of rod discs, it translates into generally accepted value of diffusion constant of approximately 5 x 10(-9) cm(2) s(-1). Yet, we found that there exists an immobile rhodopsin fraction whose size can vary from virtually zero to 100%, depending on poorly defined factors. Controls suggest that the formation of the immobile fraction is not due to fragmentation of rod outer segment discs but supposedly reflects oligomerization of rhodopsin. Implications of the new findings for the present model of phototransduction are discussed. We hypothesize that formation of paracrystalline areas, if controlled physiologically, could be an extra mechanism of cascade regulation.

Thermodynamics of the mesoscopic thermoelectric heat engine beyond the linear-response regime

NASA Astrophysics Data System (ADS)

Yamamoto, Kaoru; Hatano, Naomichi

2015-10-01

Mesoscopic thermoelectric heat engine is much anticipated as a device that allows us to utilize with high efficiency wasted heat inaccessible by conventional heat engines. However, the derivation of the heat current in this engine seems to be either not general or described too briefly, even inappropriately in some cases. In this paper, we give a clear-cut derivation of the heat current of the engine with suitable assumptions beyond the linear-response regime. It resolves the confusion in the definition of the heat current in the linear-response regime. After verifying that we can construct the same formalism as that of the cyclic engine, we find the following two interesting results within the Landauer-Büttiker formalism: the efficiency of the mesoscopic thermoelectric engine reaches the Carnot efficiency if and only if the transmission probability is finite at a specific energy and zero otherwise; the unitarity of the transmission probability guarantees the second law of thermodynamics, invalidating Benenti et al.'s argument in the linear-response regime that one could obtain a finite power with the Carnot efficiency under a broken time-reversal symmetry [Phys. Rev. Lett. 106, 230602 (2011), 10.1103/PhysRevLett.106.230602]. These results demonstrate how quantum mechanics constrains thermodynamics.

Spontaneous and persistent currents in superconductive and mesoscopic structures (Review)

NASA Astrophysics Data System (ADS)

Kulik, I. O.

2004-07-01

We briefly review aspects of superconductive persistent currents in Josephson junctions of the S/I/S, S/O/S and S/N/S types, focusing on the origin of jumps in the current versus phase dependences, and discuss in more detail the persistent and the "spontaneous" currents in Aharonov-Bohm mesoscopic and nanoscopic (macromolecular) structures. A fixed-number-of-electrons mesoscopic or macromolecular conducting ring is shown to be unstable against structural transformation removing spatial symmetry (in particular, azimuthal periodicity) of its electron-lattice Hamiltonian. In the case when the transformation is blocked by strong coupling to an external azimuthally symmetric environment, the system becomes bistable in its electronic configuration at a certain number of electrons. Under such a condition, the persistent current has a nonzero value even at an (almost) zero applied Aharonov-Bohm flux and results in very high magnetic susceptibility dM/dH at small nonzero fields, followed by an oscillatory dependence at larger fields. We tentatively assume that previously observed oscillatory magnetization in cyclic metallo-organic molecules by Gatteschi et al. can be attributed to persistent currents. If this proves correct, it may present an opportunity for (and, more generally, macromolecular cyclic structures may suggest the possibility of) engineering quantum computational tools based on the Aharonov-Bohm effect in ballistic nanostructures and macromolecular cyclic aggregates.

Equilibrium state of a cylindrical particle with flat ends in nematic liquid crystals.

PubMed

Hashemi, S Masoomeh; Ejtehadi, Mohammad Reza

2015-01-01

A continuum theory is employed to numerically study the equilibrium orientation and defect structures of a circular cylindrical particle with flat ends under a homeotropic anchoring condition in a uniform nematic medium. Different aspect ratios of this colloidal geometry from thin discotic to long rodlike shapes and several colloidal length scales ranging from mesoscale to nanoscale are investigated. We show that the equilibrium state of this colloidal geometry is sensitive to the two geometrical parameters: aspect ratio and length scale of the particle. For a large enough mesoscopic particle, there is a specific asymptotic equilibrium angle associated to each aspect ratio. Upon reducing the particle size to nanoscale, the equilibrium angle follows a descending or ascending trend in such a way that the equilibrium angle of a particle with the aspect ratio bigger than 1:1 (a discotic particle) goes to a parallel alignment with respect to the far-field nematic, whereas the equilibrium angle for a particle with the aspect ratio 1:1 and smaller (a rodlike particle) tends toward a perpendicular alignment to the uniform nematic direction. The discrepancy between the equilibrium angles of the mesoscopic and nanoscopic particles originates from the significant differences between their defect structures. The possible defect structures related to mesoscopic and nanoscopic colloidal particles of this geometry are also introduced.

Cavity QED with hybrid nanocircuits: from atomic-like physics to condensed matter phenomena

NASA Astrophysics Data System (ADS)

Cottet, Audrey; Dartiailh, Matthieu C.; Desjardins, Matthieu M.; Cubaynes, Tino; Contamin, Lauriane C.; Delbecq, Matthieu; Viennot, Jérémie J.; Bruhat, Laure E.; Douçot, Benoit; Kontos, Takis

2017-11-01

Circuit QED techniques have been instrumental in manipulating and probing with exquisite sensitivity the quantum state of superconducting quantum bits coupled to microwave cavities. Recently, it has become possible to fabricate new devices in which the superconducting quantum bits are replaced by hybrid mesoscopic circuits combining nanoconductors and metallic reservoirs. This mesoscopic QED provides a new experimental playground to study the light-matter interaction in electronic circuits. Here, we present the experimental state of the art of mesoscopic QED and its theoretical description. A first class of experiments focuses on the artificial atom limit, where some quasiparticles are trapped in nanocircuit bound states. In this limit, the circuit QED techniques can be used to manipulate and probe electronic degrees of freedom such as confined charges, spins, or Andreev pairs. A second class of experiments uses cavity photons to reveal the dynamics of electron tunneling between a nanoconductor and fermionic reservoirs. For instance, the Kondo effect, the charge relaxation caused by grounded metallic contacts, and the photo-emission caused by voltage-biased reservoirs have been studied. The tunnel coupling between nanoconductors and fermionic reservoirs also enable one to obtain split Cooper pairs, or Majorana bound states. Cavity photons represent a qualitatively new tool to study these exotic condensed matter states.

Time-dependent photon heat transport through a mesoscopic Josephson device

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

Lu, Wen-Ting; Zhao, Hong-Kang, E-mail: zhaohonk@bit.edu.cn

The time-oscillating photon heat current through a dc voltage biased mesoscopic Josephson Junction (MJJ) has been investigated by employing the nonequilibrium Green’s function approach. The Landauer-like formula of photon heat current has been derived in both of the Fourier space and its time-oscillating versions, where Coulomb interaction, self inductance, and magnetic flux take effective roles. Nonlinear behaviors are exhibited in the photon heat current due to the quantum nature of MJJ and applied external dc voltage. The magnitude of heat current decreases with increasing the external bias voltage, and subtle oscillation structures appear as the superposition of different photon heatmore » branches. The overall period of heat current with respect to time is not affected by Coulomb interaction, however, the magnitude and phase of it vary considerably by changing the Coulomb interaction. - Highlights: • The time-oscillating photon heat current through a mesoscopic Josephson Junction has been investigated. • The Landauer-like formula of photon heat current has been derived by the nonequilibrium Green’s function approach. • Nonlinear behaviors are exhibited in the photon heat current resulting from the self inductance and Coulomb interaction. • The oscillation structure of heat current is composed of the superposition of oscillations with different periods.« less

Functional energy nanocomposites surfaces based on mesoscopic microspheres, polymers and graphene flakes

NASA Astrophysics Data System (ADS)

Alekseev, S. A.; Dmitriev, A. S.; Dmitriev, A. A.; Makarov, P. G.; Mikhailova, I. A.

2017-11-01

In recent years, there has been a great interest in the development and creation of new functional energy materials, including for improving the energy efficiency of power equipment and for effectively removing heat from energy devices, microelectronics and optoelectronics (power micro electronics, supercapacitors, cooling of processors, servers and Data centers). In this paper, the technology of obtaining a new nanocomposite based on mesoscopic microspheres, polymers and graphene flakes is considered. The methods of sequential production of functional materials from graphite flakes of different volumetric concentration using polymers based on epoxy resins and polyimide, as well as the addition of a mesoscopic medium in the form of monodisperse microspheres are described. The data of optical and electron microscopy of such nanocomposites are presented, the main problems in the appearance of defects in such materials are described, the possibilities of their elimination by the selection of different concentrations and sizes of the components. Data are given on the measurement of the hysteresis of the contact angle and the evaporation of droplets on similar substrates. The results of studying the mechanical, electrophysical and thermal properties of such nanocomposites are presented. Particular attention is paid to the investigation of the thermal conductivity of these nanocomposites with respect to the creation of thermal interface materials for cooling devices of electronics, optoelectronics and power engineering.

Poroelastic finite difference modeling of seismic attenuation and dispersion due to mesoscopic-scale heterogeneity

NASA Astrophysics Data System (ADS)

Masson, Y. J.; Pride, S. R.

2007-03-01

Seismic attenuation and dispersion are numerically determined for computer-generated porous materials that contain arbitrary amounts of mesoscopic-scale heterogeneity in the porous continuum properties. The local equations used to determine the poroelastic response within such materials are those of Biot (1962). Upon applying a step change in stress to samples containing mesoscopic-scale heterogeneity, the poroelastic response is determined using finite difference modeling, and the average strain throughout the sample computed, along with the effective complex and frequency-dependent elastic moduli of the sample. The ratio of the imaginary and real parts of these moduli determines the attenuation as a function of frequency associated with the modes of applied stress (pure compression and pure shear). By having a wide range of heterogeneity present, there exists a wide range of relaxation frequencies in the response with the result that the curves of attenuation as a function of frequency are broader than in existing analytical theories based on a single relaxation frequency. Analytical explanations are given for the various high-frequency and low-frequency asymptotic behavior observed in the numerical simulations. It is also shown that the overall level of attenuation of a given sample is proportional to the square of the incompressibility contrasts locally present.

Thermal-mechanical-chemical responses of polymer-bonded explosives using a mesoscopic reactive model under impact loading.

PubMed

Wang, XinJie; Wu, YanQing; Huang, FengLei

2017-01-05

A mesoscopic framework is developed to quantify the thermal-mechanical-chemical responses of polymer-bonded explosive (PBX) samples under impact loading. A mesoscopic reactive model is developed for the cyclotetramethylenetetranitramine (HMX) crystal, which incorporates nonlinear elasticity, crystal plasticity, and temperature-dependent chemical reaction. The proposed model was implemented in the finite element code ABAQUS by the user subroutine VUMAT. A series of three-dimensional mesoscale models were constructed and calculated under low-strength impact loading scenarios from 100m/s to 600m/s where only the first wave transit is studied. Crystal anisotropy and microstructural heterogeneity are responsible for the nonuniform stress field and fluctuations of the stress wave front. At a critical impact velocity (≥300m/s), a chemical reaction is triggered because the temperature contributed by the volumetric and plastic works is sufficiently high. Physical quantities, including stress, temperature, and extent of reaction, are homogenized from those across the microstructure at the mesoscale to compare with macroscale measurements, which will advance the continuum-level models. The framework presented in this study has important implications in understanding hot spot ignition processes and improving predictive capabilities in energetic materials. Copyright © 2016 Elsevier B.V. All rights reserved.

A mesoscopic reaction rate model for shock initiation of multi-component PBX explosives.

PubMed

Liu, Y R; Duan, Z P; Zhang, Z Y; Ou, Z C; Huang, F L

2016-11-05

The primary goal of this research is to develop a three-term mesoscopic reaction rate model that consists of a hot-spot ignition, a low-pressure slow burning and a high-pressure fast reaction terms for shock initiation of multi-component Plastic Bonded Explosives (PBX). Thereinto, based on the DZK hot-spot model for a single-component PBX explosive, the hot-spot ignition term as well as its reaction rate is obtained through a "mixing rule" of the explosive components; new expressions for both the low-pressure slow burning term and the high-pressure fast reaction term are also obtained by establishing the relationships between the reaction rate of the multi-component PBX explosive and that of its explosive components, based on the low-pressure slow burning term and the high-pressure fast reaction term of a mesoscopic reaction rate model. Furthermore, for verification, the new reaction rate model is incorporated into the DYNA2D code to simulate numerically the shock initiation process of the PBXC03 and the PBXC10 multi-component PBX explosives, and the numerical results of the pressure histories at different Lagrange locations in explosive are found to be in good agreements with previous experimental data. Copyright © 2016 Elsevier B.V. All rights reserved.

Cavity QED with hybrid nanocircuits: from atomic-like physics to condensed matter phenomena.

PubMed

Cottet, Audrey; Dartiailh, Matthieu C; Desjardins, Matthieu M; Cubaynes, Tino; Contamin, Lauriane C; Delbecq, Matthieu; Viennot, Jérémie J; Bruhat, Laure E; Douçot, Benoit; Kontos, Takis

2017-11-01

Circuit QED techniques have been instrumental in manipulating and probing with exquisite sensitivity the quantum state of superconducting quantum bits coupled to microwave cavities. Recently, it has become possible to fabricate new devices in which the superconducting quantum bits are replaced by hybrid mesoscopic circuits combining nanoconductors and metallic reservoirs. This mesoscopic QED provides a new experimental playground to study the light-matter interaction in electronic circuits. Here, we present the experimental state of the art of mesoscopic QED and its theoretical description. A first class of experiments focuses on the artificial atom limit, where some quasiparticles are trapped in nanocircuit bound states. In this limit, the circuit QED techniques can be used to manipulate and probe electronic degrees of freedom such as confined charges, spins, or Andreev pairs. A second class of experiments uses cavity photons to reveal the dynamics of electron tunneling between a nanoconductor and fermionic reservoirs. For instance, the Kondo effect, the charge relaxation caused by grounded metallic contacts, and the photo-emission caused by voltage-biased reservoirs have been studied. The tunnel coupling between nanoconductors and fermionic reservoirs also enable one to obtain split Cooper pairs, or Majorana bound states. Cavity photons represent a qualitatively new tool to study these exotic condensed matter states.

Turbulent flow near the wall of a conical diffuser

NASA Astrophysics Data System (ADS)

Satyaprakash, B. R.; Azad, R. S.; Nagabushana, K. A.; Kassab, S. Z.

The turbulent flow in a conical diffuser is predicted adapting the boundary layer calculation method of Bradshaw, Ferris and Atwell. The predicted mean velocity and shear stress profiles, using the experimental data as initial input, agree well with the measured profiles. The universal low of the wall present at the inlet vahishes in the initial region and reappears later, but the width of validity is diminished considerably. The effect of divergence is present in the initial region of the diffuser only. This technique fails to predict beyond one half the total length of the diffuser.

Depth estimation of multi-layered impact damage in PMC using lateral thermography

NASA Astrophysics Data System (ADS)

Whitlow, Travis; Kramb, Victoria; Reibel, Rick; Dierken, Josiah

2018-04-01

Characterization of impact damage in polymer matrix composites (PMCs) continues to be a challenge due to the complex internal structure of the material. Nondestructive characterization approaches such as normal incident immersion ultrasound and flash thermography are sensitive to delamination damage, but do not provide information regarding damage obscured by the delaminations. Characterization of material state below a delamination requires a technique which is sensitive to in-plane damage modes such as matrix cracking and fiber breakage. Previous studies of the lateral heat flow through a composite laminate showed that the diffusion time was sensitive to the depth of the simulated damage zone. The current study will further evaluate the lateral diffusion model to provide sensitivity limits for the modeled flaw dimensions. Comparisons between the model simulations and experimental data obtained using a concentrated heat source and machined targets will also be presented.

The effect of ligand affinity on integrins' lateral diffusion in cultured cells.

PubMed

Mainali, Dipak; Smith, Emily A

2013-04-01

The role of ligand affinity in altering αPS2CβPS integrins' lateral mobility was studied using single particle tracking (SPT) with ligand-functionalized quantum dots (QDs) and fluorescence recovery after photobleaching (FRAP) with fluorescent protein tagged integrins. Integrins are ubiquitous transmembrane proteins that are vital for numerous cellular functions, including bidirectional signaling and cell anchorage. Wild-type and high ligand affinity mutant (αPS2CβPS-V409D) integrins were studied in S2 cells. As measured by SPT, the integrin mobile fraction decreased by 22% and had a 4× slower diffusion coefficient for αPS2CβPS-V409D compared to wild-type integrins. These differences are partially the result of αPS2CβPS-V409D integrins' increased clustering. For the wild-type integrins, the average of all diffusion coefficients measured by SPT was statistically similar to the ensemble FRAP results. A 75% slower average diffusion coefficient was measured by SPT compared to FRAP for αPS2CβPS-V409D integrins, and this may be the result of SPT measuring only ligand-bound integrins, in contrast all ligand-bound and ligand-unbound integrins are averaged in FRAP measurements. Specific binding of the ligand-functionalized QDs was 99% for integrin expressing cells. The results prove that the ligand binding affinity affects the lateral dynamics of a subset of integrins based on the complementary SPT and FRAP data.

Interactions between electrons, mesoscopic Josephson effect and asymmetric current fluctuations

NASA Astrophysics Data System (ADS)

Huard, B.

2006-07-01

This article discusses three experiments on the properties of electronic transport at the mesoscopic scale. The first one allowed to measure the energy exchange rate between electrons in a metal contaminated by a very weak concentration of magnetic impurities. The role played by magnetic impurities in the Kondo regime on those energy exchanges is quantitatively investigated, and the global measured exchange rate is larger than expected. The second experiment is a measurement of the current-phase relation in a system made of two superconductors linked through a single atom. We thus provide quantitative support for the recent description of the mesoscopic Josephson effect. The last experiment is a measurement of the asymmetry of the current fluctuations in a mesoscopic conductor, using a Josephson junction as a threshold detector. Cet ouvrage décrit trois expériences portant sur les propriétés du transport électronique à l'échelle mésoscopique. La première a permis de mesurer le taux d'échange d'énergie entre électrons dans un métal contenant une très faible concentration d'impuretés magnétiques. Nous avons validé la description quantitative du rôle des impuretés magnétiques dans le régime Kondo sur ces échanges énergétiques et aussi montré que le taux global d'échange est plus fort que prévu. La seconde expérience est une mesure de la relation courant-phase dans un système constitué de deux supraconducteurs couplés par un seul atome. Elle nous a permis de conforter quantitativement la récente description de l'effet Josephson mésoscopique. La dernière expérience est unemesure de l'asymétrie des fluctuations du courant dans un conducteur mésoscopique en utilisant une Jonction Josephson comme détecteur de seuil.

Elastic tunneling identification through crossings, anti-crossings and splitting of states in the complex electronic current of systems based on mesoscopic molecules

NASA Astrophysics Data System (ADS)

López, Luis I. A.; Mendoza, Michel; Ujevic, Sebastian

2013-09-01

We have systematically studied the conductance σ( E,B) and the electronic current line shapes J( V ex ) through complex mesoscopic molecules in an elastic resonant tunneling regime. The studied systems are based on GaAs/AlGaAs hetero-structures, with several discrete states in each coupled mesoscopic molecule. The molecules were formed using different wells and barrier widths. These systems allow effective couplings and uncouplings that lead to elastic processes as a function of the electronic potential V ex and magnetic field B. In this situation, the J( V ex ) and σ( E, B) curves exhibit a sequence of peaks of difficult interpretation, in which crossings and anti-crossings (a splitting if it is generated in the resonance condition) of states contribute in a way that they cannot be easily identified. Performing a systematic analysis of the evolution of these states (before the resonance condition), we were able to determine the origin of these current peaks. We have found that the coupling of states (anti-crossing) around the resonance region can be identified as a broad mirrored- D line shape in the J( V ex ) curves. The mirrored- D line shape peaks can be clearly differentiated from the neighboring peaks because the last ones follow a very defined increasing sequence in their intensities and widths. Also, this behavior (fingerprint) can be used to identify possible splitting of states in the J( V ex ). The splittings that are generated between states with different quantum numbers (quantum numbers associated to the individual well) follow an unexpected opposite behavior when compared with those generated between states with the same quantum numbers (quasi-miniband). All these results are also observed in the conductance σ( E, B) associated with complex mesoscopic molecules based on a two-dimensional electron gas.

Analysis of the diffusion of Ras2 in Saccharomyces cerevisiae using fluorescence recovery after photobleaching

NASA Astrophysics Data System (ADS)

Vinnakota, Kalyan C.; Mitchell, David A.; Deschenes, Robert J.; Wakatsuki, Tetsuro; Beard, Daniel A.

2010-06-01

Binding, lateral diffusion and exchange are fundamental dynamic processes involved in protein association with cellular membranes. In this study, we developed numerical simulations of lateral diffusion and exchange of fluorophores in membranes with arbitrary bleach geometry and exchange of the membrane-localized fluorophore with the cytosol during fluorescence recovery after photobleaching (FRAP) experiments. The model simulations were used to design FRAP experiments with varying bleach region sizes on plasma membrane-localized wild-type GFP-Ras2 with a dual lipid anchor and mutant GFP-Ras2C318S with a single lipid anchor in live yeast cells to investigate diffusional mobility and the presence of any exchange processes operating in the time scale of our experiments. Model parameters estimated using data from FRAP experiments with a 1 µm × 1 µm bleach region-of-interest (ROI) and a 0.5 µm × 0.5 µm bleach ROI showed that GFP-Ras2, single or dual lipid modified, diffuses as single species with no evidence of exchange with a cytoplasmic pool. This is the first report of Ras2 mobility in the yeast plasma membrane. The methods developed in this study are generally applicable for studying diffusion and exchange of membrane-associated fluorophores using FRAP on commercial confocal laser scanning microscopes.

Single file diffusion into a semi-infinite tube.

PubMed

Farrell, Spencer G; Brown, Aidan I; Rutenberg, Andrew D

2015-11-23

We investigate single file diffusion (SFD) of large particles entering a semi-infinite tube, such as luminal diffusion of proteins into microtubules or flagella. While single-file effects have no impact on the evolution of particle density, we report significant single-file effects for individually tracked tracer particle motion. Both exact and approximate ordering statistics of particles entering semi-infinite tubes agree well with our stochastic simulations. Considering initially empty semi-infinite tubes, with particles entering at one end starting from an initial time t = 0, tracked particles are initially super-diffusive after entering the system, but asymptotically diffusive at later times. For finite time intervals, the ratio of the net displacement of individual single-file particles to the average displacement of untracked particles is reduced at early times and enhanced at later times. When each particle is numbered, from the first to enter (n = 1) to the most recent (n = N), we find good scaling collapse of this distance ratio for all n. Experimental techniques that track individual particles, or local groups of particles, such as photo-activation or photobleaching of fluorescently tagged proteins, should be able to observe these single-file effects. However, biological phenomena that depend on local concentration, such as flagellar extension or luminal enzymatic activity, should not exhibit single-file effects.

Protein Diffusion on Charged Membranes: A Dynamic Mean-Field Model Describes Time Evolution and Lipid Reorganization

PubMed Central

Khelashvili, George; Weinstein, Harel; Harries, Daniel

2008-01-01

As charged macromolecules adsorb and diffuse on cell membranes in a large variety of cell signaling processes, they can attract or repel oppositely charged lipids. This results in lateral membrane rearrangement and affects the dynamics of protein function. To address such processes quantitatively we introduce a dynamic mean-field scheme that allows self-consistent calculations of the equilibrium state of membrane-protein complexes after such lateral reorganization of the membrane components, and serves to probe kinetic details of the process. Applicable to membranes with heterogeneous compositions containing several types of lipids, this comprehensive method accounts for mobile salt ions and charged macromolecules in three dimensions, as well as for lateral demixing of charged and net-neutral lipids in the membrane plane. In our model, the mobility of membrane components is governed by the diffusion-like Cahn-Hilliard equation, while the local electrochemical potential is based on nonlinear Poisson-Boltzmann theory. We illustrate the method by applying it to the adsorption of the anionic polypeptide poly-Lysine on negatively charged lipid membranes composed of binary mixtures of neutral and monovalent lipids, or onto ternary mixtures of neutral, monovalent, and multivalent lipids. Consistent with previous calculations and experiments, our results show that at steady-state multivalent lipids (such as PIP2), but not monovalent lipid (such as phosphatidylserine), will segregate near the adsorbing macromolecules. To address the corresponding diffusion of the adsorbing protein in the membrane plane, we couple lipid mobility with the propagation of the adsorbing protein through a dynamic Monte Carlo scheme. We find that due to their higher mobility dictated by the electrochemical potential, multivalent lipids such as PIP2 more quickly segregate near oppositely charged proteins than do monovalent lipids, even though their diffusion constants may be similar. The segregation, in turn, slows protein diffusion, as lipids introduce an effective drag on the motion of the adsorbate. In contrast, monovalent lipids such as phosphatidylserine only weakly segregate, and the diffusions of protein and lipid remain largely uncorrelated. PMID:18065451

Multiscale model of metal alloy oxidation at grain boundaries

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

Sushko, Maria L.; Alexandrov, Vitali Y.; Schreiber, Daniel K.

2015-06-07

High temperature intergranular oxidation and corrosion of metal alloys is one of the primary causes of materials degradation in nuclear systems. In order to gain insights into grain boundary oxidation processes, a mesoscale metal alloy oxidation model at experimentally relevant length scales is established by combining quantum Density Functional Theory (DFT) and mesoscopic Poisson-Nernst-Planck/classical DFT with predictions focused on Ni alloyed with either Cr or Al. Analysis of species and fluxes at steady-state conditions indicates that the oxidation process involves vacancy-mediated transport of Ni and the minor alloying element to the oxidation front and the formation of stable metal oxides.more » The simulations further demonstrate that the mechanism of oxidation for Ni-5Cr and Ni-4Al is qualitatively different. Intergranular oxidation of Ni-5Cr involves the selective oxidation of the minor element and not matrix Ni, due to slower diffusion of Ni relative to Cr in the alloy and due to the significantly smaller energy gain upon the formation of nickel oxide compared to that of Cr2O3. This essentially one-component oxidation process results in continuous oxide formation and a monotonic Cr vacancy distribution ahead of the oxidation front, peaking at alloy/oxide interface. In contrast, Ni and Al are both oxidized in Ni-4Al forming a mixed spinel NiAl2O4. Different diffusivities of Ni and Al give rise to a complex elemental distribution in the vicinity of the oxidation front. Slower diffusing Ni accumulates in the oxide and metal within 3 nm of the interface, while Al penetrates deeper into the oxide phase. Ni and Al are both depleted from the region 3–10 nm ahead of the oxidation front creating voids. The oxide microstructure is also different. Cr2O3 has a plate-like structure with 1.2 - 1.7 nm wide pores running along the grain boundary, while NiAl2O4 has 1.5 nm wide pores in the direction parallel to the grain boundary and 0.6 nm pores in the perpendicular direction providing an additional pathway for oxygen diffusion through the oxide.« less

Diffuse consolidation form of bronchoalveolar carcinoma.

PubMed

Khalil, Kanwal Fatima; Saeed, Waseem; Zill-e-Hamayun

2010-03-01

This case report describes a patient with diffuse consolidation form of bronchoalveolar carcinoma (BAC) which is a rare type of adenocarcinoma of lung. He was diagnosed on the basis of findings on X-ray and high resolution CT(HRCT) chest later confirmed by open lung biopsy and immuno-histochemical staining. Only supportive treatment could be provided and the patient expired during the subsequent month of follow-up. Traditionally, diffuse consolidation is the radiological presentation in only 20% of patients with bronchoalveolar carcinoma.

Lateral diffusion contributes to FRET from lanthanide-tagged membrane proteins

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

Lan, Tien-Hung; Wu, Guangyu; Lambert, Nevin A., E-mail: nelambert@gru.edu

2015-08-14

Diffusion can enhance Förster resonance energy transfer (FRET) when donors or acceptors diffuse distances that are similar to the distances separating them during the donor's excited state lifetime. Lanthanide donors remain in the excited state for milliseconds, which makes them useful for time-resolved FRET applications but also allows time for diffusion to enhance energy transfer. Here we show that diffusion dramatically enhances FRET between membrane proteins labeled with lanthanide donors. This phenomenon complicates interpretation of experiments that use long-lived donors to infer association or proximity of mobile membrane proteins, but also offers a method of monitoring diffusion in membrane domainsmore » in real time in living cells. - Highlights: • Diffusion enhances TR-FRET from membrane proteins labeled with lanthanide donors. • Diffusion-dependent FRET can overshadow FRET due to oligomerization or clustering. • FRET studies using lanthanide-tagged membrane proteins should consider diffusion. • FRET from lanthanide donors can be used to monitor membrane protein diffusion.« less

Frontoparietal Tracts Linked to Lateralized Hand Preference and Manual Specialization.

PubMed

Howells, Henrietta; Thiebaut de Schotten, Michel; Dell'Acqua, Flavio; Beyh, Ahmad; Zappalà, Giuseppe; Leslie, Anoushka; Simmons, Andrew; Murphy, Declan G; Catani, Marco

2018-04-21

Humans show a preference for using the right hand over the left for tasks and activities of everyday life. While experimental work in non-human primates has identified the neural systems responsible for reaching and grasping, the neural basis of lateralized motor behavior in humans remains elusive. The advent of diffusion imaging tractography for studying connectional anatomy in the living human brain provides the possibility of understanding the relationship between hemispheric asymmetry, hand preference, and manual specialization. In this study, diffusion tractography was used to demonstrate an interaction between hand preference and the asymmetry of frontoparietal tracts, specifically the dorsal branch of the superior longitudinal fasciculus, responsible for visuospatial integration and motor planning. This is in contrast to the corticospinal tract and the superior cerebellar peduncle, for which asymmetry was not related to hand preference. Asymmetry of the dorsal frontoparietal tract was also highly correlated with the degree of lateralization in tasks requiring visuospatial integration and fine motor control. These results suggest a common anatomical substrate for hand preference and lateralized manual specialization in frontoparietal tracts important for visuomotor processing.

Lateralization of Temporal Lobe Epilepsy using a Novel Uncertainty Analysis of MR Diffusion in Hippocampus, Cingulum, and Fornix, and Hippocampal Volume and FLAIR Intensity

PubMed Central

Nazem-Zadeh, Mohammad-Reza; Schwalb, Jason M.; Elisevich, Kost V.; Bagher-Ebadian, Hassan; Hamidian, Hajar; Akhondi-Asl, Ali-Reza; Jafari-Khouzani, Kourosh; Soltanian-Zadeh, Hamid

2014-01-01

Purpose To analyze the utility of a quantitative uncertainty analysis approach for evaluation and comparison of various MRI findings for lateralization of epileptogenicity in mesial temporal lobe epilepsy (mTLE), including novel diffusion-based analyses. Methods We estimated the hemispheric variation uncertainty (HVU) of hippocampal T1 volumetry and FLAIR (Fluid Attenuated Inversion Recovery) intensity. Using diffusion tensor images of 23 nonepileptic subjects, we estimated the HVU levels of mean diffusivity (MD) in the hippocampus, and fractional anisotropy (FA) in the posteroinferior cingulum and crus of fornix. Imaging from a retrospective cohort of 20 TLE patients who had undergone surgical resection with Engel class I outcomes was analyzed to determine whether asymmetry of preoperative volumetrics, FLAIR intensities, and MD values in hippocampi, as well as FA values in posteroinferior cingula and fornix crura correctly predicted laterality of seizure onset. Ten of the cohort had pathologically proven mesial temporal sclerosis (MTS). Seven of these patients had undergone extra-operative electrocorticography (ECoG) for lateralization or to rule out extra-temporal foci. Results HVU was estimated to be 3.1 × 10−5 for hippocampal MD, 0.027 for FA in posteroinferior cingulum, 0.018 for FA in crus of fornix, 0.069 for hippocampal normalized volume, and 0.099 for hippocampal normalized FLAIR intensity. Using HVU analysis, a higher hippocampal MD value, lower FA within the posteroinferior cingulum and crus of fornix, shrinkage in hippocampal volume, and higher hippocampal FLAIR intensity were observed beyond uncertainty on the side ipsilateral to seizure onset for 10, 10, 9, 9, and 10 out of 10 pathology-proven MTS patients, respectively. Considering all 20 TLE patients, these numbers were 18, 15, 14, 13, and 16, respectively. However, consolidating lateralization results of HVU analysis on these quantities by majority voting detected the epileptogenic side for 19 out of 20 cases with no wrong lateralization. Conclusion The presence of MTS in TLE patients is associated with an elevated MD value in the ipsilateral hippocampus and a reduced FA value in the posteroinferior subregion of the ipsilateral cingulum and crus of ipsilateral fornix. When considering all TLE patients, among the mentioned biomarkers the hippocampal MD had the best performance with true detection rate of 90% without any wrong lateralization. The proposed uncertainty based analyses hold promise for improving decision-making for surgical resection. PMID:24857759

Lateralization of temporal lobe epilepsy using a novel uncertainty analysis of MR diffusion in hippocampus, cingulum, and fornix, and hippocampal volume and FLAIR intensity.

PubMed

Nazem-Zadeh, Mohammad-Reza; Schwalb, Jason M; Elisevich, Kost V; Bagher-Ebadian, Hassan; Hamidian, Hajar; Akhondi-Asl, Ali-Reza; Jafari-Khouzani, Kourosh; Soltanian-Zadeh, Hamid

2014-07-15

To analyze the utility of a quantitative uncertainty analysis approach for evaluation and comparison of various MRI findings for the lateralization of epileptogenicity in mesial temporal lobe epilepsy (mTLE), including novel diffusion-based analyses. We estimated the hemispheric variation uncertainty (HVU) of hippocampal T1 volumetry and FLAIR (Fluid Attenuated Inversion Recovery) intensity. Using diffusion tensor images of 23 nonepileptic subjects, we estimated the HVU levels of mean diffusivity (MD) in the hippocampus, and fractional anisotropy (FA) in the posteroinferior cingulum and crus of fornix. Imaging from a retrospective cohort of 20 TLE patients who had undergone surgical resection with Engel class I outcomes was analyzed to determine whether asymmetry of preoperative volumetrics, FLAIR intensities, and MD values in hippocampi, as well as FA values in posteroinferior cingula and fornix crura correctly predicted laterality of seizure onset. Ten of the cohort had pathologically proven mesial temporal sclerosis (MTS). Seven of these patients had undergone extraoperative electrocorticography (ECoG) for lateralization or to rule out extra-temporal foci. HVU was estimated to be 3.1×10(-5) for hippocampal MD, 0.027 for FA in posteroinferior cingulum, 0.018 for FA in crus of fornix, 0.069 for hippocampal normalized volume, and 0.099 for hippocampal normalized FLAIR intensity. Using HVU analysis, a higher hippocampal MD value, lower FA within the posteroinferior cingulum and crus of fornix, shrinkage in hippocampal volume, and higher hippocampal FLAIR intensity were observed beyond uncertainty on the side ipsilateral to seizure onset for 10, 10, 9, 9, and 10 out of 10 pathology-proven MTS patients, respectively. Considering all 20 TLE patients, these numbers were 18, 15, 14, 13, and 16, respectively. However, consolidating the lateralization results of HVU analysis on these quantities by majority voting has detected the epileptogenic side for 19 out of 20 cases with no wrong lateralization. The presence of MTS in TLE patients is associated with an elevated MD value in the ipsilateral hippocampus and a reduced FA value in the posteroinferior subregion of the ipsilateral cingulum and crus of ipsilateral fornix. When considering all TLE patients, among the mentioned biomarkers the hippocampal MD had the best performance with true detection rate of 90% without any wrong lateralization. The proposed uncertainty based analyses hold promise for improving decision-making for surgical resection. Copyright © 2014 Elsevier B.V. All rights reserved.

Reaction-diffusion basis of retroviral infectivity

NASA Astrophysics Data System (ADS)

Sadiq, S. Kashif

2016-11-01

Retrovirus particle (virion) infectivity requires diffusion and clustering of multiple transmembrane envelope proteins (Env3) on the virion exterior, yet is triggered by protease-dependent degradation of a partially occluding, membrane-bound Gag polyprotein lattice on the virion interior. The physical mechanism underlying such coupling is unclear and only indirectly accessible via experiment. Modelling stands to provide insight but the required spatio-temporal range far exceeds current accessibility by all-atom or even coarse-grained molecular dynamics simulations. Nor do such approaches account for chemical reactions, while conversely, reaction kinetics approaches handle neither diffusion nor clustering. Here, a recently developed multiscale approach is considered that applies an ultra-coarse-graining scheme to treat entire proteins at near-single particle resolution, but which also couples chemical reactions with diffusion and interactions. A model is developed of Env3 molecules embedded in a truncated Gag lattice composed of membrane-bound matrix proteins linked to capsid subunits, with freely diffusing protease molecules. Simulations suggest that in the presence of Gag but in the absence of lateral lattice-forming interactions, Env3 diffuses comparably to Gag-absent Env3. Initial immobility of Env3 is conferred through lateral caging by matrix trimers vertically coupled to the underlying hexameric capsid layer. Gag cleavage by protease vertically decouples the matrix and capsid layers, induces both matrix and Env3 diffusion, and permits Env3 clustering. Spreading across the entire membrane surface reduces crowding, in turn, enhancing the effect and promoting infectivity. This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

High-b-value diffusion-weighted MR imaging for pretreatment prediction and early monitoring of tumor response to therapy in mice.

PubMed

Roth, Yiftach; Tichler, Thomas; Kostenich, Genady; Ruiz-Cabello, Jesus; Maier, Stephan E; Cohen, Jack S; Orenstein, Arie; Mardor, Yael

2004-09-01

To evaluate the use of diffusion-weighted magnetic resonance (MR) imaging with standard and high b values for pretreatment prediction and early detection of tumor response to various antineoplastic therapies in an animal model. Mice bearing C26 colon carcinoma tumors were treated with doxorubicin (n = 25) and with aminolevulinic acid-based photodynamic therapy (n = 23). Fourteen mice served as controls. Conventional T2-weighted fast spin-echo and diffusion-weighted MR images were acquired once before therapy and at 6, 24, and 48 hours after treatment. Pretreatment and early (1-2 days) posttreatment water diffusion parameters were calculated and compared with later changes in tumor volumes measured on conventional MR images by using the Pearson correlation test. In chemotherapy-treated tumors, a significant correlation (P <.002, r = 0.6) was observed between diffusion parameters that reflected tumor viability, measured prior to treatment, and changes in tumor volumes after therapy. This correlation implies that tumors with high pretreatment viability will respond better to chemotherapy than more necrotic tumors. In tumors treated with photodynamic therapy, no such correlation was found. Changes observed in water diffusion 1-2 days after treatment significantly correlated with later tumor growth rate for both therapies (P <.002, r = 0.54 for photodynamic therapy; P <.0003, r = 0.61 for chemotherapy). High-b-value diffusion-weighted MR imaging has potential use for the early detection of response to therapy and for predicting treatment outcome prior to initiation of chemotherapy. Copyright RSNA, 2004

Early detection of response to radiation therapy in patients with brain malignancies using conventional and high b-value diffusion-weighted magnetic resonance imaging.

PubMed

Mardor, Yael; Pfeffer, Raphael; Spiegelmann, Roberto; Roth, Yiftach; Maier, Stephan E; Nissim, Ouzi; Berger, Raanan; Glicksman, Ami; Baram, Jacob; Orenstein, Arie; Cohen, Jack S; Tichler, Thomas

2003-03-15

To study the feasibility of using diffusion-weighted magnetic resonance imaging (DWMRI), which is sensitive to the diffusion of water molecules in tissues, for detection of early tumor response to radiation therapy; and to evaluate the additional information obtained from high DWMRI, which is more sensitive to low-mobility water molecules (such as intracellular or bound water), in increasing the sensitivity to response. Standard MRI and DWMRI were acquired before and at regular intervals after initiating radiation therapy for 10 malignant brain lesions in eight patients. One week posttherapy, three of six responding lesions showed an increase in the conventional DWMRI parameters. Another three responding lesions showed no change. Four nonresponding lesions showed a decrease or no change. The early change in the diffusion parameters was enhanced by using high DWMRI. When high DWMRI was used, all responding lesions showed increase in the diffusion parameter and all nonresponding lesions showed no change or decrease. Response was determined by standard MRI 7 weeks posttherapy. The changes in the diffusion parameters measured 1 week after initiating treatment were correlated with later tumor response or no response (P <.006). This correlation was increased to P <.0006 when high DWMRI was used. The significant correlation between changes in diffusion parameters 1 week after initiating treatment and later tumor response or no response suggests the feasibility of using DWMRI for early, noninvasive prediction of tumor response. The ability to predict response may enable early termination of treatment in nonresponding patients, prevent additional toxicity, and allow for early changes in treatment.

Asymmetric Differential Resistance of Current Biased Mesoscopic AuFe Wires

NASA Astrophysics Data System (ADS)

Eom, J.; Chandrasekhar, V.; Neuttiens, G.; Strunk, C.; van Haesendonck, C.; Bruynseraede, Y.

1996-03-01

An anomalous asymmetry is found in the differential resistance dV/dI of mesoscopic AuFe wires as a function of dc bias current at low temperatures. The samples are fabricated by ion implanting Au wires of length 1.0 - 35.0 μ m and of width 0.1 - 1.0 μ m with Fe at two different concentrations, 0.2 at.% and 0.4 at.%. The asymmetry is more pronounced in narrow and short samples. The asymmetric component of dV/dI increases with decreasing temperature, and saturates below the maximum in the spin glass resistance. It is found that the lead configuration for the four-terminal measurement also affects the asymmetric component of dV/dI.

A Mesoscopic Electromechanical Theory of Ferroelectric Films and Ceramics

NASA Astrophysics Data System (ADS)

Li, Jiangyu; Bhattacharya, Kaushik

2002-08-01

We present a multi-scale modelling framework to predict the effective electromechanical behavior of ferroelectric ceramics and thin films. This paper specifically focuses on the mesoscopic scale and models the effects of domains and domain switching taking into account intergranular constraints. Starting from the properties of the single crystal and the pre-poling granular texture, the theory predicts the domain patterns, the post-poling texture, the saturation polarization, saturation strain and the electromechanical moduli. We demonstrate remarkable agreement with experimental data. The theory also explains the superior electromechanical property of PZT at the morphotropic phase boundary. The paper concludes with the application of the theory to predict the optimal texture for enhanced electromechanical coupling factors and high-strain actuation in selected materials.

Giant mesoscopic fluctuations of the elastic cotunneling thermopower of a single-electron transistor

NASA Astrophysics Data System (ADS)

Vasenko, A. S.; Basko, D. M.; Hekking, F. W. J.

2015-02-01

We study the thermoelectric transport of a small metallic island weakly coupled to two electrodes by tunnel junctions. In the Coulomb blockade regime, in the case when the ground state of the system corresponds to an even number of electrons on the island, the main mechanism of electron transport at the lowest temperatures is elastic cotunneling. In this regime, the transport coefficients strongly depend on the realization of the random impurity potential or the shape of the island. Using random-matrix theory, we calculate the thermopower and the thermoelectric kinetic coefficient and study the statistics of their mesoscopic fluctuations in the elastic cotunneling regime. The fluctuations of the thermopower turn out to be much larger than the average value.

Electron teleportation via Majorana bound states in a mesoscopic superconductor.

PubMed

Fu, Liang

2010-02-05

Zero-energy Majorana bound states in superconductors have been proposed to be potential building blocks of a topological quantum computer, because quantum information can be encoded nonlocally in the fermion occupation of a pair of spatially separated Majorana bound states. However, despite intensive efforts, nonlocal signatures of Majorana bound states have not been found in charge transport. In this work, we predict a striking nonlocal phase-coherent electron transfer process by virtue of tunneling in and out of a pair of Majorana bound states. This teleportation phenomenon only exists in a mesoscopic superconductor because of an all-important but previously overlooked charging energy. We propose an experimental setup to detect this phenomenon in a superconductor-quantum-spin-Hall-insulator-magnetic-insulator hybrid system.

Mesoscopic Simulations of Crosslinked Polymer Networks

NASA Astrophysics Data System (ADS)

Megariotis, Grigorios; Vogiatzis, Georgios G.; Schneider, Ludwig; Müller, Marcus; Theodorou, Doros N.

2016-08-01

A new methodology and the corresponding C++ code for mesoscopic simulations of elastomers are presented. The test system, crosslinked ds-1’4-polyisoprene’ is simulated with a Brownian Dynamics/kinetic Monte Carlo algorithm as a dense liquid of soft, coarse-grained beads, each representing 5-10 Kuhn segments. From the thermodynamic point of view, the system is described by a Helmholtz free-energy containing contributions from entropic springs between successive beads along a chain, slip-springs representing entanglements between beads on different chains, and non-bonded interactions. The methodology is employed for the calculation of the stress relaxation function from simulations of several microseconds at equilibrium, as well as for the prediction of stress-strain curves of crosslinked polymer networks under deformation.

Transport mechanisms of contaminants released from fine sediment in rivers

NASA Astrophysics Data System (ADS)

Cheng, Pengda; Zhu, Hongwei; Zhong, Baochang; Wang, Daozeng

2015-12-01

Contaminants released from sediment into rivers are one of the main problems to study in environmental hydrodynamics. For contaminants released into the overlying water under different hydrodynamic conditions, the mechanical mechanisms involved can be roughly divided into convective diffusion, molecular diffusion, and adsorption/desorption. Because of the obvious environmental influence of fine sediment (D_{90}= 0.06 mm), non-cohesive fine sediment, and cohesive fine sediment are researched in this paper, and phosphorus is chosen for a typical adsorption of a contaminant. Through theoretical analysis of the contaminant release process, according to different hydraulic conditions, the contaminant release coupling mathematical model can be established by the N-S equation, the Darcy equation, the solute transport equation, and the adsorption/desorption equation. Then, the experiments are completed in an open water flume. The simulation results and experimental results show that convective diffusion dominates the contaminant release both in non-cohesive and cohesive fine sediment after their suspension, and that they contribute more than 90 % of the total release. Molecular diffusion and desorption have more of a contribution for contaminant release from unsuspended sediment. In unsuspension sediment, convective diffusion is about 10-50 times larger than molecular diffusion during the initial stages under high velocity; it is close to molecular diffusion in the later stages. Convective diffusion is about 6 times larger than molecular diffusion during the initial stages under low velocity, it is about a quarter of molecular diffusion in later stages, and has a similar level with desorption/adsorption. In unsuspended sediment, a seepage boundary layer exists below the water-sediment interface, and various release mechanisms in that layer mostly dominate the contaminant release process. In non-cohesive fine sediment, the depth of that layer increases linearly with shear stress. In cohesive fine sediment, the range seepage boundary is different from that in non-cohesive sediment, and that phenomenon is more obvious under a lower shear stress.

Surface pressure and elasticity of hydrophobin HFBII layers on the air-water interface: rheology versus structure detected by AFM imaging.

PubMed

Stanimirova, Rumyana D; Gurkov, Theodor D; Kralchevsky, Peter A; Balashev, Konstantin T; Stoyanov, Simeon D; Pelan, Eddie G

2013-05-21

Here, we combine experiments with Langmuir trough and atomic force microscopy (AFM) to investigate the reasons for the special properties of layers from the protein HFBII hydrophobin spread on the air-water interface. The hydrophobin interfacial layers possess the highest surface dilatational and shear elastic moduli among all investigated proteins. The AFM images show that the spread HFBII layers are rather inhomogeneous, (i.e., they contain voids, monolayer and multilayer domains). A continuous compression of the layer leads to filling the voids and transformation of a part of the monolayer into a trilayer. The trilayer appears in the form of large surface domains, which can be formed by folding and subduction of parts from the initial monolayer. The trilayer appears also in the form of numerous submicrometer spots, which can be obtained by forcing protein molecules out of the monolayer and their self-assembly into adjacent pimples. Such structures are formed because not only the hydrophobic parts, but also the hydrophilic parts of the HFBII molecules can adhere to each other in the water medium. If a hydrophobin layer is subjected to oscillations, its elasticity considerably increases, up to 500 mN/m, which can be explained with compaction. The relaxation of the layer's tension after expansion or compression follows the same relatively simple law, which refers to two-dimensional diffusion of protein aggregates within the layer. The characteristic diffusion time after compression is longer than after expansion, which can be explained with the impedence of diffusion in the more compact interfacial layer. The results shed light on the relation between the mesoscopic structure of hydrophobin interfacial layers and their unique mechanical properties that find applications for the production of foams and emulsions of extraordinary stability; for the immobilization of functional molecules at surfaces, and as coating agents for surface modification.

Electron and proton transfer in chloroplasts in silico. 2: The effect of diffusion limitations on the process of photosynthesis in spatially inhomogeneous thylakoids

NASA Astrophysics Data System (ADS)

Vershubskii, A. V.; Tikhonov, A. N.

2017-07-01

The lateral mobility of protons and mobile electron carriers (plastoquinone and plastocyanin) is subjected to diffusion limitations; the effect of these limitations on the kinetics of photoinduced pH i changes has been investigated in the present work for metabolic states 3 (conditions of intensive ATP synthesis) and 4 (the state of photosynthetic control). Computer simulations were based on a mathematical model of electron and proton transport in chloroplasts developed earlier by the authors. Non-uniform distribution of electron carriers and ATP synthase complexes in the membranes of grana and intergranal thylakoids was taken into account in the model. The kinetics of intrathylakoid pH i changes and the lateral profiles of distribution of the mobile electron transporters in granal and intergranal thylakoids were studied. The formation of non-uniform pH i profiles (with lumen acidification in the central parts of the grana being substantially slower than in the stromal thylakoids) was shown to occur under the conditions of ATP synthesis. Variation of the diffusion coefficients of intrathylakoid hydrogen ions and mobile electron carriers (plastoquinone and plastocyanin) can have substantial effects on the lateral pH i profiles and the redox state of the mobile electron carriers.

Comparison of Diffusion MRI Acquisition Protocols for the In Vivo Characterization of the Mouse Spinal Cord: Variability Analysis and Application to an Amyotrophic Lateral Sclerosis Model

PubMed Central

Marcuzzo, Stefania; Bonanno, Silvia; Padelli, Francesco; Moreno-Manzano, Victoria; García-Verdugo, José Manuel; Bernasconi, Pia; Mantegazza, Renato; Bruzzone, Maria Grazia; Zucca, Ileana

2016-01-01

Diffusion-weighted Magnetic Resonance Imaging (dMRI) has relevant applications in the microstructural characterization of the spinal cord, especially in neurodegenerative diseases. Animal models have a pivotal role in the study of such diseases; however, in vivo spinal dMRI of small animals entails additional challenges that require a systematical investigation of acquisition parameters. The purpose of this study is to compare three acquisition protocols and identify the scanning parameters allowing a robust estimation of the main diffusion quantities and a good sensitivity to neurodegeneration in the mouse spinal cord. For all the protocols, the signal-to-noise and contrast-to noise ratios and the mean value and variability of Diffusion Tensor metrics were evaluated in healthy controls. For the estimation of fractional anisotropy less variability was provided by protocols with more diffusion directions, for the estimation of mean, axial and radial diffusivity by protocols with fewer diffusion directions and higher diffusion weighting. Intermediate features (12 directions, b = 1200 s/mm2) provided the overall minimum inter- and intra-subject variability in most cases. In order to test the diagnostic sensitivity of the protocols, 7 G93A-SOD1 mice (model of amyotrophic lateral sclerosis) at 10 and 17 weeks of age were scanned and the derived diffusion parameters compared with those estimated in age-matched healthy animals. The protocols with an intermediate or high number of diffusion directions provided the best differentiation between the two groups at week 17, whereas only few local significant differences were highlighted at week 10. According to our results, a dMRI protocol with an intermediate number of diffusion gradient directions and a relatively high diffusion weighting is optimal for spinal cord imaging. Further work is needed to confirm these results and for a finer tuning of acquisition parameters. Nevertheless, our findings could be important for the optimization of acquisition protocols for preclinical and clinical dMRI studies on the spinal cord. PMID:27560686

Biological plywood film formation from para-nematic liquid crystalline organization.

PubMed

Aguilar Gutierrez, Oscar F; Rey, Alejandro D

2017-11-15

In vitro non-equilibrium chiral phase ordering processes of biomacromolecular solutions offer a systematic and reproducible way of generating material architectures found in Nature, such as biological plywoods. Accelerated progress in biomimetic engineering of mesoscopic plywoods and other fibrous structures requires a fundamental understanding of processing and transport principles. In this work we focus on collagen I based materials and structures to find processing conditions that lead to defect-free collagen films displaying the helicoidal plywood architecture. Here we report experimentally-guided theory and simulations of the chiral phase ordering of collagen molecules through water solvent evaporation of pre-aligned dilute collagen solutions. We develop, implement and a posteriori validate an integrated liquid crystal chiral phase ordering-water transport model that captures the essential features of spatio-temporal chiral structure formation in shrinking film domains due to directed water loss. Three microstructural (texture) modes are identified depending on the particular value of the time-scale ratio defined by collagen rotational diffusion to water translational diffusion. The magnitude of the time scale ratio provides the conditions for the synchronization of the helical axis morphogenesis with the increase in the mesogen concentration due to water loss. Slower than critical water removal rates leads to internal multiaxial cellular patterns, reminiscent of the classical columnar-equiaxed metallurgical casting structures. Excessive water removal rates lead to destabilization of the chiral axis and multidomain defected films. The predictions of the integrated model are in qualitative agreement with experimental results and can potentially guide solution processing of other bio-related mesogenic solutions that seek to mimic the architecture of biological fibrous composites.

Multiscale modeling of particle in suspension with smoothed dissipative particle dynamics

NASA Astrophysics Data System (ADS)

Bian, Xin; Litvinov, Sergey; Qian, Rui; Ellero, Marco; Adams, Nikolaus A.

2012-01-01

We apply smoothed dissipative particle dynamics (SDPD) [Español and Revenga, Phys. Rev. E 67, 026705 (2003)] to model solid particles in suspension. SDPD is a thermodynamically consistent version of smoothed particle hydrodynamics (SPH) and can be interpreted as a multiscale particle framework linking the macroscopic SPH to the mesoscopic dissipative particle dynamics (DPD) method. Rigid structures of arbitrary shape embedded in the fluid are modeled by frozen particles on which artificial velocities are assigned in order to satisfy exactly the no-slip boundary condition on the solid-liquid interface. The dynamics of the rigid structures is decoupled from the solvent by solving extra equations for the rigid body translational/angular velocities derived from the total drag/torque exerted by the surrounding liquid. The correct scaling of the SDPD thermal fluctuations with the fluid-particle size allows us to describe the behavior of the particle suspension on spatial scales ranging continuously from the diffusion-dominated regime typical of sub-micron-sized objects towards the non-Brownian regime characterizing macro-continuum flow conditions. Extensive tests of the method are performed for the case of two/three dimensional bulk particle-system both in Brownian/ non-Brownian environment showing numerical convergence and excellent agreement with analytical theories. Finally, to illustrate the ability of the model to couple with external boundary geometries, the effect of confinement on the diffusional properties of a single sphere within a micro-channel is considered, and the dependence of the diffusion coefficient on the wall-separation distance is evaluated and compared with available analytical results.

Minority carrier diffusion and defects in InGaAsN grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Kurtz, Steven R.; Klem, J. F.; Allerman, A. A.; Sieg, R. M.; Seager, C. H.; Jones, E. D.

2002-02-01

To gain insight into the nitrogen-related defects of InGaAsN, nitrogen vibrational mode spectra, Hall mobilities, and minority carrier diffusion lengths are examined for InGaAsN (1.1 eV band gap) grown by molecular beam epitaxy (MBE). Annealing promotes the formation of In-N bonding, and lateral carrier transport is limited by large scale (≫mean free path) material inhomogeneities. Comparing solar cell quantum efficiencies with our earlier results for devices grown by metalorganic chemical vapor deposition (MOCVD), we find significant electron diffusion in the MBE material (reversed from the hole diffusion in MOCVD material), and minority carrier diffusion in InGaAsN cannot be explained by a "universal," nitrogen-related defect.

Isotope Fractionation by Diffusion in Liquids (Final Technical Report)

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

Richter, Frank

The overall objective of the DOE-funded research by grant DE-FG02-01ER15254 was document and quantify kinetic isotope fractionations during chemical and thermal (i.e., Soret) diffusion in liquids (silicate melts and water) and in the later years to include alloys and major minerals such as olivine and pyroxene. The research involved both laboratory experiments and applications to natural settings. The key idea is that major element zoning on natural geologic materials is common and can arise for either changes in melt composition during cooling and crystallization or from diffusion. The isotope effects associated with diffusion that we have documented are the keymore » for determining whether or not the zoning observed in a natural system was the result of diffusion. Only in those cases were the zoning is demonstrably due to diffusion can use independently measured rates of diffusion to constrain the thermal evolution of the system.« less

Recipes for lateral spin transport between magnetic contacts, advantage of carbon-based materials.

NASA Astrophysics Data System (ADS)

Fert, Albert

2010-03-01

After the presentation of magneto-transport results [1] on metallic carbon nanotubes (CNT) between LSMO electrodes (MR 60-70%, [VAP -- VP] 60mV), I will discuss the general problem of spin transport in a nonmagnetic lateral channel between spin-polarized contacts in both the diffusive and ballistic regimes. In the diffusive regime, a treatment by the classical drift-diffusion equations applied to a multi-terminal structure is used to calculate what can be expected for the output signal with local or non-local voltage probes. A general result is that the output signal (δR = δV/I where δV is the local or non-local output voltage), directly related to the spin accumulation splitting in the channel, scales with the smallest of the relevant spin and interfaces resistances. In the best situation, that is with only tunnel contacts having the same (large) resistance RT and separated by less than the spin diffusion length (λ) in a lateral channel limited to the zone of the contacts, the signal δR increases in proportion of RT as long as the dwell time is smaller than the spin lifetime. δR can be thus much larger than the spin resistance of the channel (product of its resistivity by the ratio λ/section ). This explain why, in the experiments of Ref.[1] on CNT, δR can be as large as 90 Mφ, that is of the order of the tunnel contact resistances and much larger than the spin resistance of the CNT (smaller signals in experiments with CNT or graphene are often due the leak of spin accumulation in lateral channels extending too far outside the contacts). The relative disadvantage for semiconductors comes from the too long dwell time due to much smaller electron velocities than in metallic CNTs (and graphene). We will conclude by a similar analysis of the ballistic regime and a discussion of experiments with graphene. [4pt] [1] Hueso et al, Nature 445, 410 (2007).

Language Laterality in Autism Spectrum Disorder and Typical Controls: A Functional, Volumetric, and Diffusion Tensor MRI Study

ERIC Educational Resources Information Center

Knaus, Tracey A.; Silver, Andrew M.; Kennedy, Meaghan; Lindgren, Kristen A.; Dominick, Kelli C.; Siegel, Jeremy; Tager-Flusberg, Helen

2010-01-01

Language and communication deficits are among the core features of autism spectrum disorder (ASD). Reduced or reversed asymmetry of language has been found in a number of disorders, including ASD. Studies of healthy adults have found an association between language laterality and anatomical measures but this has not been systematically…

Kinetic Monte Carlo simulations of electrodeposition: Crossover from continuous to instantaneous homogeneous nucleation within Avrami’s law

NASA Astrophysics Data System (ADS)

Frank, Stefan; Rikvold, Per Arne

2006-06-01

The influence of lateral adsorbate diffusion on the dynamics of the first-order phase transition in a two-dimensional Ising lattice gas with attractive nearest-neighbor interactions is investigated by means of kinetic Monte Carlo simulations. For example, electrochemical underpotential deposition proceeds by this mechanism. One major difference from adsorption in vacuum surface science is that under control of the electrode potential and in the absence of mass-transport limitations, local adsorption equilibrium is approximately established. We analyze our results using the theory of Kolmogorov, Johnson and Mehl, and Avrami (KJMA), which we extend to an exponentially decaying nucleation rate. Such a decay may occur due to a suppression of nucleation around existing clusters in the presence of lateral adsorbate diffusion. Correlation functions prove the existence of such exclusion zones. By comparison with microscopic results for the nucleation rate I and the interface velocity of the growing clusters v, we can show that the KJMA theory yields the correct order of magnitude for Iv2. This is true even though the spatial correlations mediated by diffusion are neglected. The decaying nucleation rate causes a gradual crossover from continuous to instantaneous nucleation, which is complete when the decay of the nucleation rate is very fast on the time scale of the phase transformation. Hence, instantaneous nucleation can be homogeneous, producing negative minima in the two-point correlation functions. We also present in this paper an n-fold way Monte Carlo algorithm for a square lattice gas with adsorption/desorption and lateral diffusion.

The Environmental Protection Agency’s Brownfields Pilot Program

PubMed Central

Greenberg, Michael R.; Hollander, Justin

2006-01-01

Objective. We studied the diffusion of the US Environmental Protection Agency’s national brownfields pilot innovation to more than 300 local governments between 1993 through 2002 to determine why some local governments received grants very early in the process while other awardees received funding later. Methods. We did an ordinal regression analysis of the characteristics of all local government award recipients, and we conducted interviews with early-award recipients. Results. The first set of local government awardees had lost much of their manufacturing base, had large concentrations of economically disadvantaged minority residents, and had local capacity to compete for funding. Federal and state officials catalyzed the diffusion of the innovation by working with local governments. Conclusions. The widely praised program was diffused selectively at first and then more widely later on the basis of local need, local capacity to compete, and networks of contacts among entrepreneurs and local governments. The economic, social, political, and public health impacts must be monitored and reviewed. PMID:16380572

Imaging carbon nanotube interactions, diffusion, and stability in nanopores.

PubMed

Eichmann, Shannon L; Smith, Billy; Meric, Gulsum; Fairbrother, D Howard; Bevan, Michael A

2011-07-26

We report optical microscopy measurements of three-dimensional trajectories of individual multiwalled carbon nanotubes (MWCNTs) in nanoscale silica slit pores. Trajectories are analyzed to nonintrusively measure MWCNT interactions, diffusion, and stability as a function of pH and ionic strength. Evanescent wave scattering is used to track MWCNT positions normal to pore walls with nanometer-scale resolution, and video microscopy is used to track lateral positions with spatial resolution comparable to the diffraction limit. Analysis of MWCNT excursions normal to pore walls yields particle-wall potentials that agree with theoretical electrostatic and van der Waals potentials assuming a rotationally averaged potential of mean force. MWCNT lateral mean square displacements are used to quantify translational diffusivities, which are comparable to predictions based on the best available theories. Finally, measured MWCNT pH and ionic strength dependent stabilities are in excellent agreement with predictions. Our findings demonstrate novel measurement and modeling tools to understand the behavior of confined MWCNTs relevant to a broad range of applications.

Henoch–Schönlein purpura: a clinical case with dramatic presentation

PubMed Central

Bento, João; Magalhães, Adriana; Moura, Conceição Souto; Hespanhol, Venceslau

2010-01-01

A case study involving a 55-year-old Caucasian male with end-stage glomerulosclerosis is presented here. Kidney biopsies showed no deposits on imunofluorescent microscopy. Relapsing massive haemoptysis and suspected bronchovascular malformation required lung lobectomy which revealed malformative and tortuous small blood vessels, with no vasculitis. Blood antinuclear antibodies, antineutrophil cytoplasmic antibodies and antiglomerular basement membrane antibodies were undetectable. Seric immunoglobulins and complement levels were normal. Three months later, arthralgia and joint oedema first appeared. Skin biopsy revealed vasculitis immune-reactive to immunoglobulin A. Systemic corticotherapy was then started. Two weeks later, the patient presented with abdominal pain melena and rectal bleeding (haematoquesia). Endoscopic study showed diffuse gastrointestinal haemorrhage. Angiographic study revealed diffuse lesions compatible with vasculitis and haemorrhage from multiple spots. Cyclophosphamide and then intravenous immunoglobulin were associated to treatment without response. Increasing blood loss occurred, with massive gastrointestinal haemorrhage and haemorrhagic ascitis. Death occurred due to uncontrolled diffuse bleeding. Necropsy findings showed generalised small vessels vasculitis compatible with Henoch–Schönlein purpura. PMID:22778211

Diffusion tensor imaging and voxel based morphometry study in amyotrophic lateral sclerosis: relationships with motor disability

PubMed Central

Thivard, Lionel; Pradat, Pierre‐François; Lehéricy, Stéphane; Lacomblez, Lucette; Dormont, Didier; Chiras, Jacques; Benali, Habib; Meininger, Vincent

2007-01-01

The aim of this study was to investigate the extent of cortical and subcortical lesions in amyotrophic lateral sclerosis (ALS) using, in combination, voxel based diffusion tensor imaging (DTI) and voxel based morphometry (VBM). We included 15 patients with definite or probable ALS and 25 healthy volunteers. Patients were assessed using the revised ALS Functional Rating Scale (ALSFRS‐R). In patients, reduced fractional anisotropy was found in bilateral corticospinal tracts, the left insula/ventrolateral premotor cortex, the right parietal cortex and the thalamus, which correlated with the ALSFRS‐R. Increased mean diffusivity (MD) was found bilaterally in the motor cortex, the ventrolateral premotor cortex/insula, the hippocampal formations and the right superior temporal gyrus, which did not correlate with the ALSFRS‐R. VBM analysis showed no changes in white matter but widespread volume decreases in grey matter in several regions exhibiting MD abnormalities. In ALS patients, our results show that subcortical lesions extend beyond the corticospinal tract and are clinically relevant. PMID:17635981

Diffusion tensor imaging and voxel based morphometry study in amyotrophic lateral sclerosis: relationships with motor disability.

PubMed

Thivard, Lionel; Pradat, Pierre-François; Lehéricy, Stéphane; Lacomblez, Lucette; Dormont, Didier; Chiras, Jacques; Benali, Habib; Meininger, Vincent

2007-08-01

The aim of this study was to investigate the extent of cortical and subcortical lesions in amyotrophic lateral sclerosis (ALS) using, in combination, voxel based diffusion tensor imaging (DTI) and voxel based morphometry (VBM). We included 15 patients with definite or probable ALS and 25 healthy volunteers. Patients were assessed using the revised ALS Functional Rating Scale (ALSFRS-R). In patients, reduced fractional anisotropy was found in bilateral corticospinal tracts, the left insula/ventrolateral premotor cortex, the right parietal cortex and the thalamus, which correlated with the ALSFRS-R. Increased mean diffusivity (MD) was found bilaterally in the motor cortex, the ventrolateral premotor cortex/insula, the hippocampal formations and the right superior temporal gyrus, which did not correlate with the ALSFRS-R. VBM analysis showed no changes in white matter but widespread volume decreases in grey matter in several regions exhibiting MD abnormalities. In ALS patients, our results show that subcortical lesions extend beyond the corticospinal tract and are clinically relevant.

Resting State and Diffusion Neuroimaging Predictors of Clinical Improvements Following Constraint-Induced Movement Therapy in Children With Hemiplegic Cerebral Palsy.

PubMed

Manning, Kathryn Y; Fehlings, Darcy; Mesterman, Ronit; Gorter, Jan Willem; Switzer, Lauren; Campbell, Craig; Menon, Ravi S

2015-10-01

The aim was to identify neuroimaging predictors of clinical improvements following constraint-induced movement therapy. Resting state functional magnetic resonance and diffusion tensor imaging data was acquired in 7 children with hemiplegic cerebral palsy. Clinical and magnetic resonance imaging (MRI) data were acquired at baseline and 1 month later following a 3-week constraint therapy regimen. A more negative baseline laterality index characterizing an atypical unilateral sensorimotor resting state network significantly correlated with an improvement in the Canadian Occupational Performance Measure score (r = -0.81, P = .03). A more unilateral network with decreased activity in the affected hemisphere was associated with greater improvements in clinical scores. Higher mean diffusivity in the posterior limb of the internal capsule of the affect tract correlated significantly with improvements in the Jebsen-Taylor score (r = -0.83, P = .02). Children with more compromised networks and tracts improved the most following constraint therapy. © The Author(s) 2015.

Towards a theory of cortical columns: From spiking neurons to interacting neural populations of finite size.

PubMed

Schwalger, Tilo; Deger, Moritz; Gerstner, Wulfram

2017-04-01

Neural population equations such as neural mass or field models are widely used to study brain activity on a large scale. However, the relation of these models to the properties of single neurons is unclear. Here we derive an equation for several interacting populations at the mesoscopic scale starting from a microscopic model of randomly connected generalized integrate-and-fire neuron models. Each population consists of 50-2000 neurons of the same type but different populations account for different neuron types. The stochastic population equations that we find reveal how spike-history effects in single-neuron dynamics such as refractoriness and adaptation interact with finite-size fluctuations on the population level. Efficient integration of the stochastic mesoscopic equations reproduces the statistical behavior of the population activities obtained from microscopic simulations of a full spiking neural network model. The theory describes nonlinear emergent dynamics such as finite-size-induced stochastic transitions in multistable networks and synchronization in balanced networks of excitatory and inhibitory neurons. The mesoscopic equations are employed to rapidly integrate a model of a cortical microcircuit consisting of eight neuron types, which allows us to predict spontaneous population activities as well as evoked responses to thalamic input. Our theory establishes a general framework for modeling finite-size neural population dynamics based on single cell and synapse parameters and offers an efficient approach to analyzing cortical circuits and computations.

Mesoscopic Fluorescence Molecular Tomography for Evaluating Engineered Tissues.

PubMed

Ozturk, Mehmet S; Chen, Chao-Wei; Ji, Robin; Zhao, Lingling; Nguyen, Bao-Ngoc B; Fisher, John P; Chen, Yu; Intes, Xavier

2016-03-01

Optimization of regenerative medicine strategies includes the design of biomaterials, development of cell-seeding methods, and control of cell-biomaterial interactions within the engineered tissues. Among these steps, one paramount challenge is to non-destructively image the engineered tissues in their entirety to assess structure, function, and molecular expression. It is especially important to be able to enable cell phenotyping and monitor the distribution and migration of cells throughout the bulk scaffold. Advanced fluorescence microscopic techniques are commonly employed to perform such tasks; however, they are limited to superficial examination of tissue constructs. Therefore, the field of tissue engineering and regenerative medicine would greatly benefit from the development of molecular imaging techniques which are capable of non-destructive imaging of three-dimensional cellular distribution and maturation within a tissue-engineered scaffold beyond the limited depth of current microscopic techniques. In this review, we focus on an emerging depth-resolved optical mesoscopic imaging technique, termed laminar optical tomography (LOT) or mesoscopic fluorescence molecular tomography (MFMT), which enables longitudinal imaging of cellular distribution in thick tissue engineering constructs at depths of a few millimeters and with relatively high resolution. The physical principle, image formation, and instrumentation of LOT/MFMT systems are introduced. Representative applications in tissue engineering include imaging the distribution of human mesenchymal stem cells embedded in hydrogels, imaging of bio-printed tissues, and in vivo applications.

Elaboration of highly hydrophobic polymeric surface--a potential strategy to reduce the adhesion of pathogenic bacteria?

PubMed

Poncin-Epaillard, F; Herry, J M; Marmey, P; Legeay, G; Debarnot, D; Bellon-Fontaine, M N

2013-04-01

Different polymeric surfaces have been modified in order to reach a high hydrophobic character, indeed the superhydrophobicity property. For this purpose, polypropylene and polystyrene have been treated by RF or μwaves CF4 plasma with different volumes, the results were compared according to the density of injected power. The effect of pretreatment such as mechanical abrasion or plasma activation was also studied. The modified surfaces were shown as hydrophobic, or even superhydrophobic depending of defects density. They were characterized by measurement of wettability and roughness at different scales, i.e. macroscopic, mesoscopic and atomic. It has been shown that a homogeneous surface at the macroscopic scale could be heterogeneous at lower mesoscopic scale. This was associated with the crystallinity of the material. The bioadhesion tests were performed with Gram positive and negative pathogenic strains: Listeria monocytogenes, Pseudomonas aeruginosa and Hafnia alvei. They have demonstrated an antibacterial efficiency of very hydrophobic and amorphous PS treated for all strains tested and a strain-dependent efficiency with modified PP surface being very heterogeneous at the mesoscopic scale. Thus, these biological results pointed out not only the respective role of the surface chemistry and topography in bacterial adhesion, but also the dependence on the peaks and valley distribution at bacteria dimension scale. Copyright © 2012 Elsevier B.V. All rights reserved.

Note: A simple picture of subdiffusive polymer motion from stochastic simulations

NASA Astrophysics Data System (ADS)

Gniewek, Pawel; Kolinski, Andrzej

2011-02-01

Entangled polymer solutions and melts exhibit unusual frictional properties. In the entanglement limit self-diffusion coefficient of long flexible polymers decays with the second power of chain length and viscosity increases with 3-3.5 power of chain length.1 It is very difficult to provide detailed molecular-level explanation of the entanglement effect.2 Perhaps, the problem of many entangled polymer chains is the most complex multibody issue of classical physics. There are different approaches to polymer melt dynamics. Some of these recognize hydrodynamic interactions as a dominant term, while topological constraints for polymer chains are assumed as a secondary factor. Other theories consider the topological constraints as the most important factors controlling polymer dynamics. Herman and co-workers describe polymer dynamics in melts, as a lateral sliding of a chain along other chains until complete mutual disentanglement. Despite the success in explaining the power-laws for viscosity, the model has some limitations. First of all, memory effects are ignored, that is, polymer segments are treated independently. Also, each entanglement/obstacle is treated as a separate entity, which is certainly a simplification of the memory effect problem. In addition to that, correlated motions of segments are addressed within the framework of renormalized Rouse-chain theory,7 without calling any topological entanglements in advance. This approach leads to the generalized Langevin equation characterized by distinct memory kernels describing local and nonlocal segment correlations or to the Smoluchowski equation in which the segments' mobility is treated as a stochastic variable.11 Both models describe the polymer segments motion at a microscopic level. An interesting alternative is to solve the integrodifferential equation for the chain relaxation with a sophisticated kernel function.12 The design of the kernel function is based on a mesoscopic description of the polymer melt. These theories explain some experimental data, although the description of the crossover between the Rouse and non-Rouse behavior is not satisfactory. Obviously, within the scope of a short note we cannot review all theoretical concepts of the polymer melt dynamics. Here we focus just on the interpretation of the observed single segment autocorrelation function.

Quantum transport in mesoscopic 3He films: experimental study of the interference of bulk and boundary scattering.

PubMed

Sharma, P; Córcoles, A; Bennett, R G; Parpia, J M; Cowan, B; Casey, A; Saunders, J

2011-11-04

We discuss the mass transport of a degenerate Fermi liquid ^{3}He film over a rough surface, and the film momentum relaxation time, in the framework of theoretical predictions. In the mesoscopic regime, the anomalous temperature dependence of the relaxation time is explained in terms of the interference between elastic boundary scattering and inelastic quasiparticle-quasiparticle scattering within the film. We exploit a quasiclassical treatment of quantum size effects in the film in which the surface roughness, whose power spectrum is experimentally determined, is mapped into an effective disorder potential within a film of uniform thickness. Confirmation is provided by the introduction of elastic scattering centers within the film. The improved understanding of surface roughness scattering may impact on enhancing the conductivity in thin metallic films.

Microstructure-based hyperelastic models for closed-cell solids

PubMed Central

Wyatt, Hayley

2017-01-01

For cellular bodies involving large elastic deformations, mesoscopic continuum models that take into account the interplay between the geometry and the microstructural responses of the constituents are developed, analysed and compared with finite-element simulations of cellular structures with different architecture. For these models, constitutive restrictions for the physical plausibility of the material responses are established, and global descriptors such as nonlinear elastic and shear moduli and Poisson’s ratio are obtained from the material characteristics of the constituents. Numerical results show that these models capture well the mechanical responses of finite-element simulations for three-dimensional periodic structures of neo-Hookean material with closed cells under large tension. In particular, the mesoscopic models predict the macroscopic stiffening of the structure when the stiffness of the cell-core increases. PMID:28484340

Microstructure-based hyperelastic models for closed-cell solids.

PubMed

Mihai, L Angela; Wyatt, Hayley; Goriely, Alain

2017-04-01

For cellular bodies involving large elastic deformations, mesoscopic continuum models that take into account the interplay between the geometry and the microstructural responses of the constituents are developed, analysed and compared with finite-element simulations of cellular structures with different architecture. For these models, constitutive restrictions for the physical plausibility of the material responses are established, and global descriptors such as nonlinear elastic and shear moduli and Poisson's ratio are obtained from the material characteristics of the constituents. Numerical results show that these models capture well the mechanical responses of finite-element simulations for three-dimensional periodic structures of neo-Hookean material with closed cells under large tension. In particular, the mesoscopic models predict the macroscopic stiffening of the structure when the stiffness of the cell-core increases.

Microstructure-based hyperelastic models for closed-cell solids

NASA Astrophysics Data System (ADS)

Mihai, L. Angela; Wyatt, Hayley; Goriely, Alain

2017-04-01

For cellular bodies involving large elastic deformations, mesoscopic continuum models that take into account the interplay between the geometry and the microstructural responses of the constituents are developed, analysed and compared with finite-element simulations of cellular structures with different architecture. For these models, constitutive restrictions for the physical plausibility of the material responses are established, and global descriptors such as nonlinear elastic and shear moduli and Poisson's ratio are obtained from the material characteristics of the constituents. Numerical results show that these models capture well the mechanical responses of finite-element simulations for three-dimensional periodic structures of neo-Hookean material with closed cells under large tension. In particular, the mesoscopic models predict the macroscopic stiffening of the structure when the stiffness of the cell-core increases.

Connection between two statistical approaches for the modelling of particle velocity and concentration distributions in turbulent flow: The mesoscopic Eulerian formalism and the two-point probability density function method

NASA Astrophysics Data System (ADS)

Simonin, Olivier; Zaichik, Leonid I.; Alipchenkov, Vladimir M.; Février, Pierre

2006-12-01

The objective of the paper is to elucidate a connection between two approaches that have been separately proposed for modelling the statistical spatial properties of inertial particles in turbulent fluid flows. One of the approaches proposed recently by Février, Simonin, and Squires [J. Fluid Mech. 533, 1 (2005)] is based on the partitioning of particle turbulent velocity field into spatially correlated (mesoscopic Eulerian) and random-uncorrelated (quasi-Brownian) components. The other approach stems from a kinetic equation for the two-point probability density function of the velocity distributions of two particles [Zaichik and Alipchenkov, Phys. Fluids 15, 1776 (2003)]. Comparisons between these approaches are performed for isotropic homogeneous turbulence and demonstrate encouraging agreement.

The role of community structure on the nature of explosive synchronization.

PubMed

Lotfi, Nastaran; Rodrigues, Francisco A; Darooneh, Amir Hossein

2018-03-01

In this paper, we analyze explosive synchronization in networks with a community structure. The results of our study indicate that the mesoscopic structure of the networks could affect the synchronization of coupled oscillators. With the variation of three parameters, the degree probability distribution exponent, the community size probability distribution exponent, and the mixing parameter, we could have a fast or slow phase transition. Besides, in some cases, we could have communities which are synchronized inside but not with other communities and vice versa. We also show that there is a limit in these mesoscopic structures which suppresses the transition from the second-order phase transition and results in explosive synchronization. This could be considered as a tuning parameter changing the transition of the system from the second order to the first order.

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

Farges, Francois; /Museum Nat. Hist., Paris /Stanford U., Geo. Environ. Sci.; Benzerara, Karim

XAFS and {mu}-XAFS spectra were collected at the Cu K-edge for seven chrysocolla samples (Peru, USA, and Congo). The results suggest that the local structure around Cu is similar to that in Cu(OH){sub 2} (spertiniite). Cu-L{sub 3} STXM imaging and spectroscopy confirm that the chrysocolla samples examined here consist of mesoscopic Cu(II)-rich domains surrounded by Si-rich domains (in agreement with results from infra-red spectroscopy). Hence, we suggest that chrysocolla, which is generally considered to be orthorhombic with composition (Cu,Al){sub 2}H{sub 2}Si{sub 2}O{sub 5}(OH){sub 4} {center_dot} nH{sub 2}O, is in actually a mesoscopic assemblage composed dominantly of spertiniite (Cu(OH){sub 2}), watermore » and amorphous silica (SiO{sub 2}).« less

Effect of hydrodynamic interactions on the diffusion of integral membrane proteins: diffusion in plasma membranes.

PubMed Central

Bussell, S J; Koch, D L; Hammer, D A

1995-01-01

Tracer diffusion coefficients of integral membrane proteins (IMPs) in intact plasma membranes are often much lower than those found in blebbed, organelle, and reconstituted membranes. We calculate the contribution of hydrodynamic interactions to the tracer, gradient, and rotational diffusion of IMPs in plasma membranes. Because of the presence of immobile IMPs, Brinkman's equation governs the hydrodynamics in plasma membranes. Solutions of Brinkman's equation enable the calculation of short-time diffusion coefficients of IMPs. There is a large reduction in particle mobilities when a fraction of them is immobile, and as the fraction increases, the mobilities of the mobile particles continue to decrease. Combination of the hydrodynamic mobilities with Monte Carlo simulation results, which incorporate excluded area effects, enable the calculation of long-time diffusion coefficients. We use our calculations to analyze results for tracer diffusivities in several different systems. In erythrocytes, we find that the hydrodynamic theory, when combined with excluded area effects, closes the gap between existing theory and experiment for the mobility of band 3, with the remaining discrepancy likely due to direct obstruction of band 3 lateral mobility by the spectrin network. In lymphocytes, the combined hydrodynamic-excluded area theory provides a plausible explanation for the reduced mobility of sIg molecules induced by binding concanavalin A-coated platelets. However, the theory does not explain all reported cases of "anchorage modulation" in all cell types in which receptor mobilities are reduced after binding by concanavalin A-coated platelets. The hydrodynamic theory provides an explanation of why protein lateral mobilities are restricted in plasma membranes and why, in many systems, deletion of the cytoplasmic tail of a receptor has little effect on diffusion rates. However, much more data are needed to test the theory definitively. We also predict that gradient and tracer diffusivities are the same to leading order. Finally, we have calculated rotational diffusion coefficients in plasma membranes. They decrease less rapidly than translational diffusion coefficients with increasing protein immobilization, and the results agree qualitatively with the limited experimental data available. PMID:7612825

Postural headache in a patient with Marfan's syndrome.

PubMed

Ferrante, E; Citterio, A; Savino, A; Santalucia, P

2003-09-01

A 26-year-old man with Marfan's syndrome had postural headache. Brain MRI with gadolinium showed diffuse pachymeningeal enhancement. MRI myelography revealed bilateral multiple large meningeal diverticula at sacral nerve roots level. He was suspected to have spontaneous intracranial hypotension syndrome. Eight days later headache improved with bed rest and hydration. One month after the onset he was asymptomatic and 3 months later brain MRI showed no evidence of diffuse pachymeningeal enhancement. The 1-year follow-up revealed no neurological abnormalities. The intracranial hypotension syndrome likely resulted from a CSF leak from one of the meningeal diverticula. In conclusion patients with spinal meningeal diverticula (frequently seen in Marfan's syndrome) might be at increased risk of developing CSF leaks, possibly secondary to Valsalva maneuver or minor unrecognized trauma.

Dynamics of two-dimensional monolayer water confined in hydrophobic and charged environments.

PubMed

Kumar, Pradeep; Han, Sungho

2012-09-21

We perform molecular dynamics simulations to study the effect of charged surfaces on the intermediate and long time dynamics of water in nanoconfinements. Here, we use the transferable interaction potential with five points (TIP5P) model of a water molecule confined in both hydrophobic and charged surfaces. For a single molecular layer of water between the surfaces, we find that the temperature dependence of the lateral diffusion constant of water up to very high temperatures remains Arrhenius with a high activation energy. In case of charged surfaces, however, the dynamics of water in the intermediate time regime is drastically modified presumably due to the transient coupling of dipoles of water molecules with electric field fluctuations induced by charges on the confining surfaces. Specifically, the lateral mean square displacements display a distinct super-diffusive behavior at intermediate time scale, defined as the time scale between ballistic and diffusive regimes. This change in the intermediate time-scale dynamics in the charged confinement leads to the enhancement of long-time dynamics as reflected in increasing diffusion constant. We introduce a simple model for a possible explanation of the super-diffusive behavior and find it to be in good agreement with our simulation results. Furthermore, we find that confinement and the surface polarity enhance the low frequency vibration in confinement compared to bulk water. By introducing a new effective length scale of coupling between translational and orientational motions, we find that the length scale increases with the increasing strength of the surface polarity. Further, we calculate the correlation between the diffusion constant and the excess entropy and find a disordering effect of polar surfaces on the structure of water. Finally, we find that the empirical relation between the diffusion constant and the excess entropy holds for a monolayer of water in nanoconfinement.

Navier-Stokes calculations for 3D gaseous fuel injection with data comparisons

NASA Technical Reports Server (NTRS)

Fuller, E. J.; Walters, R. W.

1991-01-01

Results from a computational study and experiments designed to further expand the knowledge of gaseous injection into supersonic cross-flows are presented. Experiments performed at Mach 6 included several cases of gaseous helium injection with low transverse angles and injection with low transverse angles coupled with a low yaw angle. Both experimental and computational data confirm that injector yaw has an adverse effect on the helium core decay rate. An array of injectors is found to give higher penetration into the freestream without loss of core injectant decay as compared to a single injector. Lateral diffusion plays a major role in lateral plume spreading, eddy viscosity, injectant plume, and injectant-freestream mixing. Grid refinement makes it possible to capture the gradients in the streamwise direction accurately and to vastly improve the data comparisons. Computational results for a refined grid are found to compare favorably with experimental data on injectant overall and core penetration provided laminar lateral diffusion was taken into account using the modified Baldwin-Lomax turbulence model.

A review of progress in the physics of open quantum systems: theory and experiment.

PubMed

Rotter, I; Bird, J P

2015-11-01

This report on progress explores recent advances in our theoretical and experimental understanding of the physics of open quantum systems (OQSs). The study of such systems represents a core problem in modern physics that has evolved to assume an unprecedented interdisciplinary character. OQSs consist of some localized, microscopic, region that is coupled to an external environment by means of an appropriate interaction. Examples of such systems may be found in numerous areas of physics, including atomic and nuclear physics, photonics, biophysics, and mesoscopic physics. It is the latter area that provides the main focus of this review, an emphasis that is driven by the capacity that exists to subject mesoscopic devices to unprecedented control. We thus provide a detailed discussion of the behavior of mesoscopic devices (and other OQSs) in terms of the projection-operator formalism, according to which the system under study is considered to be comprised of a localized region (Q), embedded into a well-defined environment (P) of scattering wavefunctions (with Q   +   P   =   1). The Q subspace must be treated using the concepts of non-Hermitian physics, and of particular interest here is: the capacity of the environment to mediate a coupling between the different states of Q; the role played by the presence of exceptional points (EPs) in the spectra of OQSs; the influence of EPs on the rigidity of the wavefunction phases, and; the ability of EPs to initiate a dynamical phase transition (DPT). EPs are singular points in the continuum, at which two resonance states coalesce, that is where they exhibit a non-avoided crossing. DPTs occur when the quantum dynamics of the open system causes transitions between non-analytically connected states, as a function of some external control parameter. Much like conventional phase transitions, the behavior of the system on one side of the DPT does not serve as a reliable indicator of that on the other. In addition to discussing experiments on mesoscopic quantum point contacts that provide evidence of the environmentally-mediated coupling of quantum states, we also review manifestations of DPTs in mesoscopic devices and other systems. These experiments include observations of resonance-trapping behavior in microwave cavities and open quantum dots, phase lapses in tunneling through single-electron transistors, and spin swapping in atomic ensembles. Other possible manifestations of this phenomenon are presented, including various superradiant phenomena in low-dimensional semiconductors. From these discussions a generic picture of OQSs emerges in which the environmentally-mediated coupling between different quantum states plays a critical role in governing the system behavior. The ability to control or manipulate this interaction may even lead to new applications in photonics and electronics.

Electrodiffusion of lipids on membrane surfaces.

PubMed

Zhou, Y C

2012-05-28

Lateral translocation of lipids and proteins is a universal process on membrane surfaces. Local aggregation or organization of lipids and proteins can be induced when the random lateral motion is mediated by the electrostatic interactions and membrane curvature. Although the lateral diffusion rates of lipids on membranes of various compositions are measured and the electrostatic free energies of predetermined protein-membrane-lipid systems can be computed, the process of the aggregation and the evolution to the electrostatically favorable states remain largely undetermined. Here we propose an electrodiffusion model, based on the variational principle of the free energy functional, for the self-consistent lateral drift-diffusion of multiple species of charged lipids on membrane surfaces. Finite sizes of lipids are modeled to enforce the geometrical constraint of the lipid concentration on membrane surfaces. A surface finite element method is developed to appropriate the Laplace-Beltrami operators in the partial differential equations of the model. Our model properly describes the saturation of lipids on membrane surfaces, and correctly predicts that the MARCKS peptide can consistently sequester three multivalent phosphatidylinositol 4,5-bisphosphate lipids through its basic amino acid residues, regardless of a wide range of the percentage of monovalent phosphatidylserine in the membrane.

Electrodiffusion of lipids on membrane surfaces

NASA Astrophysics Data System (ADS)

Zhou, Y. C.

2012-05-01

Lateral translocation of lipids and proteins is a universal process on membrane surfaces. Local aggregation or organization of lipids and proteins can be induced when the random lateral motion is mediated by the electrostatic interactions and membrane curvature. Although the lateral diffusion rates of lipids on membranes of various compositions are measured and the electrostatic free energies of predetermined protein-membrane-lipid systems can be computed, the process of the aggregation and the evolution to the electrostatically favorable states remain largely undetermined. Here we propose an electrodiffusion model, based on the variational principle of the free energy functional, for the self-consistent lateral drift-diffusion of multiple species of charged lipids on membrane surfaces. Finite sizes of lipids are modeled to enforce the geometrical constraint of the lipid concentration on membrane surfaces. A surface finite element method is developed to appropriate the Laplace-Beltrami operators in the partial differential equations of the model. Our model properly describes the saturation of lipids on membrane surfaces, and correctly predicts that the MARCKS peptide can consistently sequester three multivalent phosphatidylinositol 4,5-bisphosphate lipids through its basic amino acid residues, regardless of a wide range of the percentage of monovalent phosphatidylserine in the membrane.

Why Non-Equilibrium is Different

NASA Astrophysics Data System (ADS)

Dorfman, J. Robert; Kirkpatrick, Theodore R.; Sengers, Jan V.

The 1970 paper, "Decay of the Velocity Correlation Function" [Phys. Rev. A1, 18 (1970), see also Phys. Rev. Lett. 18, 988, (1967)] by Berni Alder and Tom Wainwright, demonstrated, by means of computer simulations, that the velocity autocorrelation function for a particle moving diffusively in a gas of hard disks decays algebraically in time as t-1, and as t-3/2 for a gas of hard spheres. These decays appear in non-equilibrium fluids and have no counterpart in fluids in thermodynamic equilibrium. The work of Alder and Wainwright stimulated theorists to find explanations for these "long time tails" using kinetic theory or a mesoscopic mode-coupling theory. This paper has had a profound influence on our understanding of the non-equilibrium properties of fluid systems. Here we discuss the kinetic origins of the long time tails, the microscopic foundations of modecoupling theory, and the implications of these results for the physics of fluids. We also mention applications of the long time tails and mode-coupling theory to other, seemingly unrelated, fields of physics. We are honored to dedicate this short review to Berni Alder on the occasion of his 90th birthday!

Theories of binary fluid mixtures: from phase-separation kinetics to active emulsions

NASA Astrophysics Data System (ADS)

Cates, Michael E.; Tjhung, Elsen

2018-02-01

Binary fluid mixtures are examples of complex fluids whose microstructure and flow are strongly coupled. For pairs of simple fluids, the microstructure consists of droplets or bicontinuous demixed domains and the physics is controlled by the interfaces between these domains. At continuum level, the structure is defined by a composition field whose gradients which are steep near interfaces drive its diffusive current. These gradients also cause thermodynamic stresses which can drive fluid flow. Fluid flow in turn advects the composition field, while thermal noise creates additional random fluxes that allow the system to explore its configuration space and move towards the Boltzmann distribution. This article introduces continuum models of binary fluids, first covering some well-studied areas such as the thermodynamics and kinetics of phase separation, and emulsion stability. We then address cases where one of the fluid components has anisotropic structure at mesoscopic scales creating nematic (or polar) liquid-crystalline order; this can be described through an additional tensor (or vector) order parameter field. We conclude by outlining a thriving area of current research, namely active emulsions, in which one of the binary components consists of living or synthetic material that is continuously converting chemical energy into mechanical work.

Mesoscopic Simulations of Adsorption and Association of PEO-PPO-PEO Triblock Copolymers on a Hydrophobic Surface: From Mushroom Hemisphere to Rectangle Brush.

PubMed

Song, Xianyu; Zhao, Shuangliang; Fang, Shenwen; Ma, Yongzhang; Duan, Ming

2016-11-08

The dissipative particle dynamics (DPD) method is used to investigate the adsorption behavior of PEO-PPO-PEO triblock copolymers at the liquid/solid interface. The effect of molecular architecture on the self-assembled monolayer adsorption of PEO-PPO-PEO triblock copolymers on hydrophobic surfaces is elucidated by the adsorption process, film properties, and adsorption morphologies. The adsorption thicknesses on hydrophobic surfaces and the diffusion coefficient as well as the aggregation number of Pluronic copolymers in aqueous solution observed in our simulations agree well with previous experimental and numerical observations. The radial distribution function revealed that the ability of self-assembly on hydrophobic surfaces is P123 > P84 > L64 > P105 > F127, which increased with the EO ratio of the Pluronic copolymers. Moreover, the shape parameter and the degree of anisotropy increase with increasing molecular weight and mole ratio of PO of the Pluronic copolymers. Depending on the conformation of different Pluronic copolymers, the morphology transition of three regimes on hydrophobic surfaces is present: mushroom or hemisphere, progressively semiellipsoid, and rectangle brush regimes induced by decreasing molecular weight and mole ratio of EO of Pluronic copolymers.

A laminar optical tomography system for the early cervical cancer diagnosis

NASA Astrophysics Data System (ADS)

Cui, Shanshan; Jia, Mengyu; Chen, Xueying; Meng, Wei; Gao, Feng; Zhao, Huijuan

2014-03-01

Laminar optical tomography (LOT) is a new mesoscopic functional optical imaging technique, which is an extension of a confocal microscope and diffuse optical tomography to acquire both the coaxial and off-axis scattered light at the same time. In this paper, a LOT system with a larger detection area aiming at the in vivo detection of early cervical cancer is developed. The field of view of our system is 10 mm x 10 mm. In order to improve the image quality of the system, two methods were performed: the correction of image distortion and the restriction of returning light. The performance of the system with aperture stop was assessed by liquid phantom experiments. Comparing with the Monte Carlo simulation, the measurement results show that the average relative errors of eight different source-detector distances corresponding to 4 source points are lower than the errors of the system taking the frame of objective lens as the aperture stop by 5.7%, 4.8%, 6.1%, 6.1% respectively. Moreover, the experiment based on the phantom with specified structure and optical parameters to simulate the cervix demonstrates that the system perform well for the cervix measurement.

Three-dimensional resistivity and switching between correlated electronic states in 1T-TaS2

NASA Astrophysics Data System (ADS)

Svetin, Damjan; Vaskivskyi, Igor; Brazovskii, Serguei; Mihailovic, Dragan

2017-04-01

Recent demonstrations of controlled switching between different ordered macroscopic states by impulsive electromagnetic perturbations in complex materials have opened some fundamental questions on the mechanisms responsible for such remarkable behavior. Here we experimentally address the question of whether two-dimensional (2D) Mott physics can be responsible for unusual switching between states of different electronic order in the layered dichalcogenide 1T-TaS2, or it is a result of subtle inter-layer “orbitronic” re-ordering of its stacking structure. We report on in-plane (IP) and out-of-plane (OP) resistance switching by current-pulse injection at low temperatures. Elucidating the controversial theoretical predictions, we also report on measurements of the anisotropy of the electrical resistivity below room temperature. From the T-dependence of ρ⊥ and ρ||, we surmise that the resistivity is more consistent with collective motion than single particle diffusive or band-like transport. The relaxation dynamics of the metastable state for both IP and OP electron transport are seemingly governed by the same mesoscopic quantum re-ordering process. We conclude that 1T-TaS2 shows resistance switching arising from an interplay of both IP and OP correlations.

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

NASA Astrophysics Data System (ADS)

Oganesov, Armen

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

Critical role for mesoscale eddy diffusion in supplying oxygen to hypoxic ocean waters

NASA Astrophysics Data System (ADS)

Gnanadesikan, Anand; Bianchi, Daniele; Pradal, Marie-Aude

2013-10-01

of the oceanic lateral eddy diffusion coefficient Aredi vary by more than an order of magnitude, ranging from less than a few hundred m2/s to thousands of m2/s. This uncertainty has first-order implications for the intensity of oceanic hypoxia, which is poorly simulated by the current generation of Earth System Models. Using satellite-based estimate of oxygen consumption in hypoxic waters to estimate the required diffusion coefficient for these waters gives a value of order 1000 m2/s. Varying Aredi across a suite of Earth System Models yields a broadly consistent result given a thermocline diapycnal diffusion coefficient of 1 × 10-5 m2/s.

Quantifying structural alterations in Alzheimer's disease brains using quantitative phase imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lee, Moosung; Lee, Eeksung; Jung, JaeHwang; Yu, Hyeonseung; Kim, Kyoohyun; Yoon, Jonghee; Lee, Shinhwa; Jeong, Yong; Park, YongKeun

2017-02-01

Imaging brain tissues is an essential part of neuroscience because understanding brain structure provides relevant information about brain functions and alterations associated with diseases. Magnetic resonance imaging and positron emission tomography exemplify conventional brain imaging tools, but these techniques suffer from low spatial resolution around 100 μm. As a complementary method, histopathology has been utilized with the development of optical microscopy. The traditional method provides the structural information about biological tissues to cellular scales, but relies on labor-intensive staining procedures. With the advances of illumination sources, label-free imaging techniques based on nonlinear interactions, such as multiphoton excitations and Raman scattering, have been applied to molecule-specific histopathology. Nevertheless, these techniques provide limited qualitative information and require a pulsed laser, which is difficult to use for pathologists with no laser training. Here, we present a label-free optical imaging of mouse brain tissues for addressing structural alteration in Alzheimer's disease. To achieve the mesoscopic, unlabeled tissue images with high contrast and sub-micrometer lateral resolution, we employed holographic microscopy and an automated scanning platform. From the acquired hologram of the brain tissues, we could retrieve scattering coefficients and anisotropies according to the modified scattering-phase theorem. This label-free imaging technique enabled direct access to structural information throughout the tissues with a sub-micrometer lateral resolution and presented a unique means to investigate the structural changes in the optical properties of biological tissues.

Postoperative Posterior Ischemic Optic Neuropathy After Left Far-Lateral Craniectomy for Resection of Craniocervical Meningioma.

PubMed

Eli, Ilyas M; Kim, Robert B; Kilburg, Craig; Pecha, Travis J; Couldwell, William T; Menacho, Sarah T

2018-06-01

Postoperative posterior ischemic optic neuropathy (PION) is a rare cause of postoperative vision loss, most often seen when surgical patients are placed in the prone position for a prolonged period of time. We report a case of bilateral PION after far-lateral craniectomy in the lateral position. A 36-year-old man presented with a history of right extremity numbness, weakness, and muscle atrophy, and a craniocervical meningioma was diagnosed. Surgery in the lateral position lasted 9 hours, 52 minutes; the patient had 2 L of blood loss. On postoperative day 1, the patient had bilateral vision loss, which prompted further work-up. Diffusion-weighted imaging of the orbits demonstrated restricted diffusion within the bilateral optic nerves. The clinical presentation of painless vision loss after surgery with these imaging findings led to a diagnosis of PION. At the time of discharge, he had not recovered any visual function. This case suggests that PION can occur in the lateral position where there is no direct pressure on the orbits. PION is often not discussed as a potential complication during the preoperative consent process. This case suggests it may be prudent to discuss PION in similar neurosurgical cases. Intraoperative blood transfusion should be considered in prolonged surgeries in the lateral position, where slow blood loss over a long period could be a contributing factor to development of PION. Copyright © 2018 Elsevier Inc. All rights reserved.

Many-body Effects in a Laterally Inhomogeneous Semiconductor Quantum Well

NASA Technical Reports Server (NTRS)

Ning, Cun-Zheng; Li, Jian-Zhong; Biegel, Bryan A. (Technical Monitor)

2002-01-01

Many body effects on conduction and diffusion of electrons and holes in a semiconductor quantum well are studied using a microscopic theory. The roles played by the screened Hartree-Fock (SHE) terms and the scattering terms are examined. It is found that the electron and hole conductivities depend only on the scattering terms, while the two-component electron-hole diffusion coefficients depend on both the SHE part and the scattering part. We show that, in the limit of the ambipolax diffusion approximation, however, the diffusion coefficients for carrier density and temperature are independent of electron-hole scattering. In particular, we found that the SHE terms lead to a reduction of density-diffusion coefficients and an increase in temperature-diffusion coefficients. Such a reduction or increase is explained in terms of a density-and temperature dependent energy landscape created by the bandgap renormalization.

Enhanced truncated-correlation photothermal coherence tomography with application to deep subsurface defect imaging and 3-dimensional reconstructions

NASA Astrophysics Data System (ADS)

Tavakolian, Pantea; Sivagurunathan, Koneswaran; Mandelis, Andreas

2017-07-01

Photothermal diffusion-wave imaging is a promising technique for non-destructive evaluation and medical applications. Several diffusion-wave techniques have been developed to produce depth-resolved planar images of solids and to overcome imaging depth and image blurring limitations imposed by the physics of parabolic diffusion waves. Truncated-Correlation Photothermal Coherence Tomography (TC-PCT) is the most successful class of these methodologies to-date providing 3-D subsurface visualization with maximum depth penetration and high axial and lateral resolution. To extend the depth range and axial and lateral resolution, an in-depth analysis of TC-PCT, a novel imaging system with improved instrumentation, and an optimized reconstruction algorithm over the original TC-PCT technique is developed. Thermal waves produced by a laser chirped pulsed heat source in a finite thickness solid and the image reconstruction algorithm are investigated from the theoretical point of view. 3-D visualization of subsurface defects utilizing the new TC-PCT system is reported. The results demonstrate that this method is able to detect subsurface defects at the depth range of ˜4 mm in a steel sample, which exhibits dynamic range improvement by a factor of 2.6 compared to the original TC-PCT. This depth does not represent the upper limit of the enhanced TC-PCT. Lateral resolution in the steel sample was measured to be ˜31 μm.

Evaluation of glymphatic system activity with the diffusion MR technique: diffusion tensor image analysis along the perivascular space (DTI-ALPS) in Alzheimer's disease cases.

PubMed

Taoka, Toshiaki; Masutani, Yoshitaka; Kawai, Hisashi; Nakane, Toshiki; Matsuoka, Kiwamu; Yasuno, Fumihiko; Kishimoto, Toshifumi; Naganawa, Shinji

2017-04-01

The activity of the glymphatic system is impaired in animal models of Alzheimer's disease (AD). We evaluated the activity of the human glymphatic system in cases of AD with a diffusion-based technique called diffusion tensor image analysis along the perivascular space (DTI-ALPS). Diffusion tensor images were acquired to calculate diffusivities in the x, y, and z axes of the plane of the lateral ventricle body in 31 patients. We evaluated the diffusivity along the perivascular spaces as well as projection fibers and association fibers separately, to acquire an index for diffusivity along the perivascular space (ALPS-index) and correlated them with the mini mental state examinations (MMSE) score. We found a significant negative correlation between diffusivity along the projection fibers and association fibers. We also observed a significant positive correlation between diffusivity along perivascular spaces shown as ALPS-index and the MMSE score, indicating lower water diffusivity along the perivascular space in relation to AD severity. Activity of the glymphatic system may be evaluated with diffusion images. Lower diffusivity along the perivascular space on DTI-APLS seems to reflect impairment of the glymphatic system. This method may be useful for evaluating the activity of the glymphatic system.

Narrow groove welding gas diffuser assembly and welding torch

DOEpatents

Rooney, Stephen J.

2001-01-01

A diffuser assembly is provided for narrow groove welding using an automatic gas tungsten arc welding torch. The diffuser assembly includes a manifold adapted for adjustable mounting on the welding torch which is received in a central opening in the manifold. Laterally extending manifold sections communicate with a shield gas inlet such that shield gas supplied to the inlet passes to gas passages of the manifold sections. First and second tapered diffusers are respectively connected to the manifold sections in fluid communication with the gas passages thereof. The diffusers extend downwardly along the torch electrode on opposite sides thereof so as to release shield gas along the length of the electrode and at the distal tip of the electrode. The diffusers are of a transverse width which is on the order of the thickness of the electrode so that the diffusers can, in use, be inserted into a narrow welding groove before and after the electrode in the direction of the weld operation.

Thermodynamics of pairing in mesoscopic systems

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

Sumaryada, Tony; Volya, Alexander

Using numerical and analytical methods implemented for different models, we conduct a systematic study of the thermodynamic properties of pairing correlations in mesoscopic nuclear systems. Various quantities are calculated and analyzed using the exact solution of pairing. An in-depth comparison of canonical, grand canonical, and microcanonical ensembles is conducted. The nature of the pairing phase transition in a small system is of a particular interest. We discuss the onset of discontinuity in the thermodynamic variables, fluctuations, and evolution of zeros of the canonical and grand canonical partition functions in the complex plane. The behavior of the invariant correlational entropy ismore » also studied in the transitional region of interest. The change in the character of the phase transition due to the presence of a magnetic field is discussed along with studies of superconducting thermodynamics.« less

Low-noise current amplifier based on mesoscopic Josephson junction.

PubMed

Delahaye, J; Hassel, J; Lindell, R; Sillanpää, M; Paalanen, M; Seppä, H; Hakonen, P

2003-02-14

We used the band structure of a mesoscopic Josephson junction to construct low-noise amplifiers. By taking advantage of the quantum dynamics of a Josephson junction, i.e., the interplay of interlevel transitions and the Coulomb blockade of Cooper pairs, we created transistor-like devices, Bloch oscillating transistors, with considerable current gain and high-input impedance. In these transistors, the correlated supercurrent of Cooper pairs is controlled by a small base current made up of single electrons. Our devices reached current and power gains on the order of 30 and 5, respectively. The noise temperature was estimated to be around 1 kelvin, but noise temperatures of less than 0.1 kelvin can be realistically achieved. These devices provide quantum-electronic building blocks that will be useful at low temperatures in low-noise circuit applications with an intermediate impedance level.

Manipulating mesoscopic multipartite entanglement with atom-light interfaces

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

Stasinska, J.; Rodo, C.; Paganelli, S.

2009-12-15

Entanglement between two macroscopic atomic ensembles induced by measurement on an ancillary light system has proven to be a powerful method for engineering quantum memories and quantum state transfer. Here we investigate the feasibility of such methods for generation, manipulation, and detection of genuine multipartite entanglement (Greenberger-Horne-Zeilinger and clusterlike states) between mesoscopic atomic ensembles without the need of individual addressing of the samples. Our results extend in a nontrivial way the Einstein-Podolsky-Rosen entanglement between two macroscopic gas samples reported experimentally in [B. Julsgaard, A. Kozhekin, and E. Polzik, Nature (London) 413, 400 (2001)]. We find that under realistic conditions, amore » second orthogonal light pulse interacting with the atomic samples, can modify and even reverse the entangling action of the first one leaving the samples in a separable state.« less

Probing eukaryotic cell mechanics via mesoscopic simulations

PubMed Central

Shang, Menglin; Lim, Chwee Teck

2017-01-01

Cell mechanics has proven to be important in many biological processes. Although there is a number of experimental techniques which allow us to study mechanical properties of cell, there is still a lack of understanding of the role each sub-cellular component plays during cell deformations. We present a new mesoscopic particle-based eukaryotic cell model which explicitly describes cell membrane, nucleus and cytoskeleton. We employ Dissipative Particle Dynamics (DPD) method that provides us with the unified framework for modeling of a cell and its interactions in the flow. Data from micropipette aspiration experiments were used to define model parameters. The model was validated using data from microfluidic experiments. The validated model was then applied to study the impact of the sub-cellular components on the cell viscoelastic response in micropipette aspiration and microfluidic experiments. PMID:28922399

Mesoscopic Metal-Insulator Transition at Ferroelastic Domain Walls in VO2

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

Jones, Keith M; Kalinin, Sergei V; Kolmakov, Andrei

2010-01-01

The novel phenomena induced by symmetry breaking at homointerfaces between ferroic variants in ferroelectric and ferroelastic materials have attracted recently much attention. Using variable temperature scanning microwave microscopy, we demonstrate the mesoscopic strain-induced metal-insulator phase transitions in the vicinity of ferroelastic domain walls in the semiconductive VO2 that nucleated at temperatures as much as 10-12 C below bulk transition, resulting in the formation of conductive channels in the material. Density functional theory is used to rationalize the process low activation energy. This behavior, linked to the strain inhomogeneity inherent in ferroelastic materials, can strongly affect interpretation of phase-transition studies inmore » VO2 and similar materials with symmetry-lowering transitions, and can also be used to enable new generations of electronic devices though strain engineering of conductive and semiconductive regions.« less

Imaging stem cell distribution, growth, migration, and differentiation in 3-D scaffolds for bone tissue engineering using mesoscopic fluorescence tomography.

PubMed

Tang, Qinggong; Piard, Charlotte; Lin, Jonathan; Nan, Kai; Guo, Ting; Caccamese, John; Fisher, John; Chen, Yu

2018-01-01

Regenerative medicine has emerged as an important discipline that aims to repair injury or replace damaged tissues or organs by introducing living cells or functioning tissues. Successful regenerative medicine strategies will likely depend upon a simultaneous optimization strategy for the design of biomaterials, cell-seeding methods, cell-biomaterial interactions, and molecular signaling within the engineered tissues. It remains a challenge to image three-dimensional (3-D) structures and functions of the cell-seeded scaffold in mesoscopic scale (>2 ∼ 3 mm). In this study, we utilized angled fluorescence laminar optical tomography (aFLOT), which allows depth-resolved molecular characterization of engineered tissues in 3-D to investigate cell viability, migration, and bone mineralization within bone tissue engineering scaffolds in situ. © 2017 Wiley Periodicals, Inc.

Out-of-equilibrium spin transport in mesoscopic superconductors.

PubMed

Quay, C H L; Aprili, M

2018-08-06

The excitations in conventional superconductors, Bogoliubov quasi-particles, are spin-[Formula: see text] fermions but their charge is energy-dependent and, in fact, zero at the gap edge. Therefore, in superconductors (unlike normal metals) spin and charge degrees of freedom may be separated. In this article, we review spin injection into conventional superconductors and focus on recent experiments on mesoscopic superconductors. We show how quasi-particle spin transport and out-of-equilibrium spin-dependent superconductivity can be triggered using the Zeeman splitting of the quasi-particle density of states in thin-film superconductors with small spin-mixing scattering. Finally, we address the spin dynamics and the feedback of quasi-particle spin imbalances on the amplitude of the superconducting energy gap.This article is part of the theme issue 'Andreev bound states'. © 2018 The Author(s).

Micro- and mesoscopic process interactions in protein coagulation

NASA Astrophysics Data System (ADS)

San Biagio, P. L.; Martorana, V.; Emanuele, A.; Vaiana, S. M.; Manno, M.; Bulone, D.; Palma-Vittorelli, M. B.; Palma, M. U.

2000-04-01

It has recently been recognized that pathological protein coagulation is responsible for lethal pathologies as diverse as amyloidosis, Alzheimer and TSE. Understanding the coagulation mechanisms is therefore stirring great interest. In previous studies we have shown that on profoundly different systems coagulation is the result of a strong interaction between two processes on different length scales (mesoscopic and microscopic). Here we report experiments on bovine serum albumin (BSA) showing that the overall mechanism is the result of at least 3 distinct and strongly intertwined processes, on both length scales: molecular conformational changes, solution demixing and intermolecular crosslinking. This mechanism involves the statistical mechanics of protein-solvent interaction, its relation to the protein's landscape of configurational free energy and to the solution's thermodynamic stability, and its relation to the topological problem of crosslink-percolation, responsible for coagulation.

New nanocomposite surfaces and thermal interface materials based on mesoscopic microspheres, polymers and graphene flakes

NASA Astrophysics Data System (ADS)

Dmitriev, Alex A.; Dmitriev, Alex S.; Makarov, Petr; Mikhailova, Inna

2018-04-01

In recent years, there has been a great interest in the development and creation of new functional energy mate-rials, including for improving the energy efficiency of power equipment and for effectively removing heat from energy devices, microelectronics and optoelectronics (power micro electronics, supercapacitors, cooling of processors, servers and data centers). In this paper, the technology of obtaining new nanocomposites based on mesoscopic microspheres, polymers and graphene flakes is considered. The methods of sequential production of functional materials from graphene flakes of different volumetric concentration using epoxy polymers, as well as the addition of monodisperse microspheres are described. Data are given on the measurement of the contact angle and thermal conductivity of these nanocomposites with respect to the creation of thermal interface materials for cooling devices of electronics, optoelectronics and power engineering.

Broadband giant-refractive-index material based on mesoscopic space-filling curves

NASA Astrophysics Data System (ADS)

Chang, Taeyong; Kim, Jong Uk; Kang, Seung Kyu; Kim, Hyowook; Kim, Do Kyung; Lee, Yong-Hee; Shin, Jonghwa

2016-08-01

The refractive index is the fundamental property of all optical materials and dictates Snell's law, propagation speed, wavelength, diffraction, energy density, absorption and emission of light in materials. Experimentally realized broadband refractive indices remain <40, even with intricately designed artificial media. Herein, we demonstrate a measured index >1,800 resulting from a mesoscopic crystal with a dielectric constant greater than three million. This gigantic enhancement effect originates from the space-filling curve concept from mathematics. The principle is inherently very broad band, the enhancement being nearly constant from zero up to the frequency of interest. This broadband giant-refractive-index medium promises not only enhanced resolution in imaging and raised fundamental absorption limits in solar energy devices, but also compact, power-efficient components for optical communication and increased performance in many other applications.

In situ ESEM imaging of the vapor-pressure-dependent sublimation-induced morphology of ice

NASA Astrophysics Data System (ADS)

Nair, Malavika; Husmann, Anke; Cameron, Ruth E.; Best, Serena M.

2018-04-01

Sublimation is a fundamental phase transition that has a profound impact on both natural phenomena and advanced manufacturing technologies. Although great strides have been made in the study of ice growth from melt and vapor, little consideration has been given to the effect of sublimation on the morphological features that develop in the ice microstructure. In this experimental study, we demonstrate the effect of vapor pressure on the mesoscopic faceting observed and show that a vapor-pressure-specific wavelength characterizes the periodic features that arise during sublimation. The ability to control the length scale of these features not only provides us with new insights into the mesoscopic roughness of ice crystals, but also presents the potential to exploit this effect in a plethora of applications from comet dating to ice-templated tissue engineering scaffolds.

Time-dependent photon heat transport through a mesoscopic Josephson device

NASA Astrophysics Data System (ADS)

Lu, Wen-Ting; Zhao, Hong-Kang

2017-02-01

The time-oscillating photon heat current through a dc voltage biased mesoscopic Josephson Junction (MJJ) has been investigated by employing the nonequilibrium Green's function approach. The Landauer-like formula of photon heat current has been derived in both of the Fourier space and its time-oscillating versions, where Coulomb interaction, self inductance, and magnetic flux take effective roles. Nonlinear behaviors are exhibited in the photon heat current due to the quantum nature of MJJ and applied external dc voltage. The magnitude of heat current decreases with increasing the external bias voltage, and subtle oscillation structures appear as the superposition of different photon heat branches. The overall period of heat current with respect to time is not affected by Coulomb interaction, however, the magnitude and phase of it vary considerably by changing the Coulomb interaction.

Towards a theory of cortical columns: From spiking neurons to interacting neural populations of finite size

PubMed Central

Gerstner, Wulfram

2017-01-01

Neural population equations such as neural mass or field models are widely used to study brain activity on a large scale. However, the relation of these models to the properties of single neurons is unclear. Here we derive an equation for several interacting populations at the mesoscopic scale starting from a microscopic model of randomly connected generalized integrate-and-fire neuron models. Each population consists of 50–2000 neurons of the same type but different populations account for different neuron types. The stochastic population equations that we find reveal how spike-history effects in single-neuron dynamics such as refractoriness and adaptation interact with finite-size fluctuations on the population level. Efficient integration of the stochastic mesoscopic equations reproduces the statistical behavior of the population activities obtained from microscopic simulations of a full spiking neural network model. The theory describes nonlinear emergent dynamics such as finite-size-induced stochastic transitions in multistable networks and synchronization in balanced networks of excitatory and inhibitory neurons. The mesoscopic equations are employed to rapidly integrate a model of a cortical microcircuit consisting of eight neuron types, which allows us to predict spontaneous population activities as well as evoked responses to thalamic input. Our theory establishes a general framework for modeling finite-size neural population dynamics based on single cell and synapse parameters and offers an efficient approach to analyzing cortical circuits and computations. PMID:28422957

Flexible histone tails in a new mesoscopic oligonucleosome model.

PubMed

Arya, Gaurav; Zhang, Qing; Schlick, Tamar

2006-07-01

We describe a new mesoscopic model of oligonucleosomes that incorporates flexible histone tails. The nucleosome cores are modeled using the discrete surface-charge optimization model, which treats the nucleosome as an electrostatic surface represented by hundreds of point charges; the linker DNAs are treated using a discrete elastic chain model; and the histone tails are modeled using a bead/chain hydrodynamic approach as chains of connected beads where each bead represents five protein residues. Appropriate charges and force fields are assigned to each histone chain so as to reproduce the electrostatic potential, structure, and dynamics of the corresponding atomistic histone tails at different salt conditions. The dynamics of resulting oligonucleosomes at different sizes and varying salt concentrations are simulated by Brownian dynamics with complete hydrodynamic interactions. The analyses demonstrate that the new mesoscopic model reproduces experimental results better than its predecessors, which modeled histone tails as rigid entities. In particular, our model with flexible histone tails: correctly accounts for salt-dependent conformational changes in the histone tails; yields the experimentally obtained values of histone-tail mediated core/core attraction energies; and considers the partial shielding of electrostatic repulsion between DNA linkers as a result of the spatial distribution of histone tails. These effects are crucial for regulating chromatin structure but are absent or improperly treated in models with rigid histone tails. The development of this model of oligonucleosomes thus opens new avenues for studying the role of histone tails and their variants in mediating gene expression through modulation of chromatin structure.

The Complexity of Dynamics in Small Neural Circuits

PubMed Central

Panzeri, Stefano

2016-01-01

Mean-field approximations are a powerful tool for studying large neural networks. However, they do not describe well the behavior of networks composed of a small number of neurons. In this case, major differences between the mean-field approximation and the real behavior of the network can arise. Yet, many interesting problems in neuroscience involve the study of mesoscopic networks composed of a few tens of neurons. Nonetheless, mathematical methods that correctly describe networks of small size are still rare, and this prevents us to make progress in understanding neural dynamics at these intermediate scales. Here we develop a novel systematic analysis of the dynamics of arbitrarily small networks composed of homogeneous populations of excitatory and inhibitory firing-rate neurons. We study the local bifurcations of their neural activity with an approach that is largely analytically tractable, and we numerically determine the global bifurcations. We find that for strong inhibition these networks give rise to very complex dynamics, caused by the formation of multiple branching solutions of the neural dynamics equations that emerge through spontaneous symmetry-breaking. This qualitative change of the neural dynamics is a finite-size effect of the network, that reveals qualitative and previously unexplored differences between mesoscopic cortical circuits and their mean-field approximation. The most important consequence of spontaneous symmetry-breaking is the ability of mesoscopic networks to regulate their degree of functional heterogeneity, which is thought to help reducing the detrimental effect of noise correlations on cortical information processing. PMID:27494737

Acrosome reaction inducers impose alterations in repulsive strain and hydration barrier in human sperm membranes.

PubMed

Purohit, S B; Laloraya, M; Kumar, G P

1998-06-01

Spin labeling studies of the lipophilic domains of human spermatozoa during capacitation and during acrosome reaction (AR) under the influence of selected AR-inducers were performed. Significantly enhanced rotational function of molecules was obvious during capacitation, with no significant changes in membrane packaging or the lateral diffusion of molecules. The AR inducers appeared to restrict the rotational freedom of molecules, dramatically enhancing the lateral diffusion and ordering coefficients. A significant decrease in superoxide anion generation was observed in the acrosome reacted groups when compared to the non-acrosome reacted groups. A high level of superoxide anion radical (O2.-) level maintained in capacitated spermatozoa would add to the Van der Waal's repulsive forces at the polar head of phospholipids, holding the membrane in strain where the molecular enjoy little freedom for lateral motion. A sudden drop in the levels of O2.- in spermatozoa upon addition of AR inducers could abruptly release the local hydrophobic repulsive strain within the membrane. This loss of hydration barrier explains the observed enhancement in lateral diffusion profiles of lipids and the packaging of molecules. It is reasonable to assume that these phenomena could be amplified further by interplay of Ca2+ by modifying the local charge aggregation. Thus, we would conclude that AR inducers release the oxyradical load in capacitated spermatozoa, which would modify the repulsive strain and hydration barrier forces in the lipophilic domains permitting vesiculation of the membranes. It appears that various acrosome reaction inducers act as effectors of grossly similar physical alterations in sperm membranes and that the resulting signal cascades proceed through intercalating biochemical sequences.

Cortical Terminations of the Inferior Fronto-Occipital and Uncinate Fasciculi: Anatomical Stem-Based Virtual Dissection

PubMed Central

Hau, Janice; Sarubbo, Silvio; Perchey, Guy; Crivello, Fabrice; Zago, Laure; Mellet, Emmanuel; Jobard, Gaël; Joliot, Marc; Mazoyer, Bernard M.; Tzourio-Mazoyer, Nathalie; Petit, Laurent

2016-01-01

We combined the neuroanatomists’ approach of defining a fascicle as all fibers passing through its compact stem with diffusion-weighted tractography to investigate the cortical terminations of two association tracts, the inferior fronto-occipital fasciculus (IFOF) and the uncinate fasciculus (UF), which have recently been implicated in the ventral language circuitry. The aim was to provide a detailed and quantitative description of their terminations in 60 healthy subjects and to do so to apply an anatomical stem-based virtual dissection, mimicking classical post-mortem dissection, to extract with minimal a priori the IFOF and UF from tractography datasets. In both tracts, we consistently observed more extensive termination territories than their conventional definitions, within the middle and superior frontal, superior parietal and angular gyri for the IFOF and the middle frontal gyrus and superior, middle and inferior temporal gyri beyond the temporal pole for the UF. We revealed new insights regarding the internal organization of these tracts by investigating for the first time the frequency, distribution and hemispheric asymmetry of their terminations. Interestingly, we observed a dissociation between the lateral right-lateralized and medial left-lateralized fronto-occipital branches of the IFOF. In the UF, we observed a rightward lateralization of the orbito-frontal and temporal branches. We revealed a more detailed map of the terminations of these fiber pathways that will enable greater specificity for correlating with diseased populations and other behavioral measures. The limitations of the diffusion tensor model in this study are also discussed. We conclude that anatomical stem-based virtual dissection with diffusion tractography is a fruitful method for studying the structural anatomy of the human white matter pathways. PMID:27252628

Hemispheric Differences in White Matter Microstructure between Two Profiles of Children with High Intelligence Quotient vs. Controls: A Tract-Based Spatial Statistics Study

PubMed Central

Nusbaum, Fanny; Hannoun, Salem; Kocevar, Gabriel; Stamile, Claudio; Fourneret, Pierre; Revol, Olivier; Sappey-Marinier, Dominique

2017-01-01

Objectives: The main goal of this study was to investigate and compare the neural substrate of two children's profiles of high intelligence quotient (HIQ). Methods: Two groups of HIQ children were included with either a homogeneous (Hom-HIQ: n = 20) or a heterogeneous IQ profile (Het-HIQ: n = 24) as defined by a significant difference between verbal comprehension index and perceptual reasoning index. Diffusion tensor imaging was used to assess white matter (WM) microstructure while tract-based spatial statistics (TBSS) analysis was performed to detect and localize WM regional differences in fractional anisotropy (FA), mean diffusivity, axial (AD), and radial diffusivities. Quantitative measurements were performed on 48 regions and 21 fiber-bundles of WM. Results: Hom-HIQ children presented higher FA than Het-HIQ children in widespread WM regions including central structures, and associative intra-hemispheric WM fasciculi. AD was also greater in numerous WM regions of Total-HIQ, Hom-HIQ, and Het-HIQ groups when compared to the Control group. Hom-HIQ and Het-HIQ groups also differed by their hemispheric lateralization in AD differences compared to Controls. Het-HIQ and Hom-HIQ groups showed a lateralization ratio (left/right) of 1.38 and 0.78, respectively. Conclusions: These findings suggest that both inter- and intra-hemispheric WM integrity are enhanced in HIQ children and that neural substrate differs between Hom-HIQ and Het-HIQ. The left hemispheric lateralization of Het-HIQ children is concordant with their higher verbal index while the relative right hemispheric lateralization of Hom-HIQ children is concordant with their global brain processing and adaptation capacities as evidenced by their homogeneous IQ. PMID:28420955

Mobility measurement by analysis of fluorescence photobleaching recovery kinetics.

PubMed Central

Axelrod, D; Koppel, D E; Schlessinger, J; Elson, E; Webb, W W

1976-01-01

Fluorescence photobleaching recovery (FPR) denotes a method for measuring two-dimensional lateral mobility of fluorescent particles, for example, the motion of fluorescently labeled molecules in approximately 10 mum2 regions of a single cell surface. A small spot on the fluorescent surface is photobleached by a brief exposure to an intense focused laser beam, and the subsequent recovery of the fluorescence is monitored by the same, but attenuated, laser beam. Recovery occurs by replenishment of intact fluorophore in the bleached spot by lateral transport from the surrounding surface. We present the theoretical basis and some practical guidelines for simple, rigorous analysis of FPR experiments. Information obtainable from FPR experiments includes: (a) identification of transport process type, i.e. the admixture of random diffusion and uniform directed flow; (b) determination of the absolute mobility coefficient, i.e. the diffusion constant and/or flow velocity; and (c) the fraction of total fluorophore which is mobile. To illustrate the experimental method and to verify the theory for diffusion, we describe some model experiments on aqueous solutions of rhodamine 6G. PMID:786399

Temperature dependence of magneto-transport properties in Co{sub 2}Fe(Ga{sub 0.5}Ge{sub 0.5})/Cu lateral spin valves

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

Ikhtiar,; Mitani, S.; Hono, K.

2016-02-08

The non-local spin signals of Co{sub 2}Fe(Ga{sub 0.5}Ge{sub 0.5})/Cu lateral spin valves with sub-micron size dimensions were measured with varying temperatures. The non-local spin signal reaches 54 mΩ at 4 K, while it degrades down to 13 mΩ at room temperature. Analysis based on the one-dimensional spin diffusion model clarifies the dominant source for degrading of the spin signal is suppression of the spin diffusion length in Cu, not the spin polarization, indicating Co{sub 2}Fe(Ga{sub 0.5}Ge{sub 0.5}) keeps half-metallic nature even at room temperature. The temperature dependence of non-local spin signal was found to exhibit a downturn at 36 K. The presence of magneticmore » impurities, detrimental effect of which becomes more pronounced for diffusive transport in long Cu wires, is suggested to cause the observed downturn in non-local spin signals.« less

Micromechanical analysis of volumetric growth in the context of open systems thermodynamics and configurational mechanics. Application to tumor growth

NASA Astrophysics Data System (ADS)

Ganghoffer, J. F.; Boubaker, M. B.

2017-03-01

We adopt in this paper the physically and micromechanically motivated point of view that growth (resp. resorption) occurs as the expansion (resp. contraction) of initially small tissue elements distributed within a host surrounding matrix, due to the interfacial motion of their boundary. The interface motion is controlled by the availability of nutrients and mechanical driving forces resulting from the internal stresses that built in during the growth. A general extremum principle of the zero potential for open systems witnessing a change of their mass due to the diffusion of nutrients is constructed, considering the framework of open systems thermodynamics. We postulate that the shape of the tissue element evolves in such a way as to minimize the zero potential among all possible admissible shapes of the growing tissue elements. The resulting driving force for the motion of the interface sets a surface growth models at the scale of the growing tissue elements, and is conjugated to a driving force identified as the interfacial jump of the normal component of an energy momentum tensor, in line with Hadamard's structure theorem. The balance laws associated with volumetric growth at the mesoscopic level result as the averaging of surface growth mechanisms occurring at the microscopic scale of the growing tissue elements. The average kinematics has been formulated in terms of the effective growth velocity gradient and elastic rate of deformation tensor, both functions of time. This formalism is exemplified by the simulation of the avascular growth of multicell spheroids in the presence of diffusion of nutrients, showing the respective influence of mechanical and chemical driving forces in relation to generation of internal stresses.

Particle-based membrane model for mesoscopic simulation of cellular dynamics

NASA Astrophysics Data System (ADS)

Sadeghi, Mohsen; Weikl, Thomas R.; Noé, Frank

2018-01-01

We present a simple and computationally efficient coarse-grained and solvent-free model for simulating lipid bilayer membranes. In order to be used in concert with particle-based reaction-diffusion simulations, the model is purely based on interacting and reacting particles, each representing a coarse patch of a lipid monolayer. Particle interactions include nearest-neighbor bond-stretching and angle-bending and are parameterized so as to reproduce the local membrane mechanics given by the Helfrich energy density over a range of relevant curvatures. In-plane fluidity is implemented with Monte Carlo bond-flipping moves. The physical accuracy of the model is verified by five tests: (i) Power spectrum analysis of equilibrium thermal undulations is used to verify that the particle-based representation correctly captures the dynamics predicted by the continuum model of fluid membranes. (ii) It is verified that the input bending stiffness, against which the potential parameters are optimized, is accurately recovered. (iii) Isothermal area compressibility modulus of the membrane is calculated and is shown to be tunable to reproduce available values for different lipid bilayers, independent of the bending rigidity. (iv) Simulation of two-dimensional shear flow under a gravity force is employed to measure the effective in-plane viscosity of the membrane model and show the possibility of modeling membranes with specified viscosities. (v) Interaction of the bilayer membrane with a spherical nanoparticle is modeled as a test case for large membrane deformations and budding involved in cellular processes such as endocytosis. The results are shown to coincide well with the predicted behavior of continuum models, and the membrane model successfully mimics the expected budding behavior. We expect our model to be of high practical usability for ultra coarse-grained molecular dynamics or particle-based reaction-diffusion simulations of biological systems.

Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering

PubMed Central

2015-01-01

The lateral heterogeneity of cellular membranes plays an important role in many biological functions such as signaling and regulating membrane proteins. This heterogeneity can result from preferential interactions between membrane components or interactions with membrane proteins. One major difficulty in molecular dynamics simulations aimed at studying the membrane heterogeneity is that lipids diffuse slowly and collectively in bilayers, and therefore, it is difficult to reach equilibrium in lateral organization in bilayer mixtures. Here, we propose the use of the replica exchange with solute tempering (REST) approach to accelerate lateral relaxation in heterogeneous bilayers. REST is based on the replica exchange method but tempers only the solute, leaving the temperature of the solvent fixed. Since the number of replicas in REST scales approximately only with the degrees of freedom in the solute, REST enables us to enhance the configuration sampling of lipid bilayers with fewer replicas, in comparison with the temperature replica exchange molecular dynamics simulation (T-REMD) where the number of replicas scales with the degrees of freedom of the entire system. We apply the REST method to a cholesterol and 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayer mixture and find that the lateral distribution functions of all molecular pair types converge much faster than in the standard MD simulation. The relative diffusion rate between molecules in REST is, on average, an order of magnitude faster than in the standard MD simulation. Although REST was initially proposed to study protein folding and its efficiency in protein folding is still under debate, we find a unique application of REST to accelerate lateral equilibration in mixed lipid membranes and suggest a promising way to probe membrane lateral heterogeneity through molecular dynamics simulation. PMID:25328493

A new mechanism for spatial pattern formation via lateral and protrusion-mediated lateral signalling

PubMed Central

Hunter, Ginger L.; Baum, Buzz

2016-01-01

Tissue organization and patterning are critical during development when genetically identical cells take on different fates. Lateral signalling plays an important role in this process by helping to generate self-organized spatial patterns in an otherwise uniform collection of cells. Recent data suggest that lateral signalling can be mediated both by junctional contacts between neighbouring cells and via cellular protrusions that allow non-neighbouring cells to interact with one another at a distance. However, it remains unclear precisely how signalling mediated by these distinct types of cell–cell contact can physically contribute to the generation of complex patterns without the assistance of diffusible morphogens or pre-patterns. To explore this question, in this work we develop a model of lateral signalling based on a single receptor/ligand pair as exemplified by Notch and Delta. We show that allowing the signalling kinetics to differ at junctional versus protrusion-mediated contacts, an assumption inspired by recent data which show that the cleavage of Notch in several systems requires both Delta binding and the application of mechanical force, permits individual cells to act to promote both lateral activation and lateral inhibition. Strikingly, under this model, in which Delta can sequester Notch, a variety of patterns resembling those typical of reaction–diffusion systems is observed, together with more unusual patterns that arise when we consider changes in signalling kinetics, and in the length and distribution of protrusions. Importantly, these patterns are self-organizing—so that local interactions drive tissue-scale patterning. Together, these data show that protrusions can, in principle, generate different types of patterns in addition to contributing to long-range signalling and to pattern refinement. PMID:27807273

Acceleration of Lateral Equilibration in Mixed Lipid Bilayers Using Replica Exchange with Solute Tempering.

PubMed

Huang, Kun; García, Angel E

2014-10-14

The lateral heterogeneity of cellular membranes plays an important role in many biological functions such as signaling and regulating membrane proteins. This heterogeneity can result from preferential interactions between membrane components or interactions with membrane proteins. One major difficulty in molecular dynamics simulations aimed at studying the membrane heterogeneity is that lipids diffuse slowly and collectively in bilayers, and therefore, it is difficult to reach equilibrium in lateral organization in bilayer mixtures. Here, we propose the use of the replica exchange with solute tempering (REST) approach to accelerate lateral relaxation in heterogeneous bilayers. REST is based on the replica exchange method but tempers only the solute, leaving the temperature of the solvent fixed. Since the number of replicas in REST scales approximately only with the degrees of freedom in the solute, REST enables us to enhance the configuration sampling of lipid bilayers with fewer replicas, in comparison with the temperature replica exchange molecular dynamics simulation (T-REMD) where the number of replicas scales with the degrees of freedom of the entire system. We apply the REST method to a cholesterol and 1,2-dipalmitoyl- sn -glycero-3-phosphocholine (DPPC) bilayer mixture and find that the lateral distribution functions of all molecular pair types converge much faster than in the standard MD simulation. The relative diffusion rate between molecules in REST is, on average, an order of magnitude faster than in the standard MD simulation. Although REST was initially proposed to study protein folding and its efficiency in protein folding is still under debate, we find a unique application of REST to accelerate lateral equilibration in mixed lipid membranes and suggest a promising way to probe membrane lateral heterogeneity through molecular dynamics simulation.

Multiscale model of metal alloy oxidation at grain boundaries

NASA Astrophysics Data System (ADS)

Sushko, Maria L.; Alexandrov, Vitaly; Schreiber, Daniel K.; Rosso, Kevin M.; Bruemmer, Stephen M.

2015-06-01

High temperature intergranular oxidation and corrosion of metal alloys is one of the primary causes of materials degradation in nuclear systems. In order to gain insights into grain boundary oxidation processes, a mesoscale metal alloy oxidation model is established by combining quantum Density Functional Theory (DFT) and mesoscopic Poisson-Nernst-Planck/classical DFT with predictions focused on Ni alloyed with either Cr or Al. Analysis of species and fluxes at steady-state conditions indicates that the oxidation process involves vacancy-mediated transport of Ni and the minor alloying element to the oxidation front and the formation of stable metal oxides. The simulations further demonstrate that the mechanism of oxidation for Ni-5Cr and Ni-4Al is qualitatively different. Intergranular oxidation of Ni-5Cr involves the selective oxidation of the minor element and not matrix Ni, due to slower diffusion of Ni relative to Cr in the alloy and due to the significantly smaller energy gain upon the formation of nickel oxide compared to that of Cr2O3. This essentially one-component oxidation process results in continuous oxide formation and a monotonic Cr vacancy distribution ahead of the oxidation front, peaking at alloy/oxide interface. In contrast, Ni and Al are both oxidized in Ni-4Al forming a mixed spinel NiAl2O4. Different diffusivities of Ni and Al give rise to a complex elemental distribution in the vicinity of the oxidation front. Slower diffusing Ni accumulates in the oxide and metal within 3 nm of the interface, while Al penetrates deeper into the oxide phase. Ni and Al are both depleted from the region 3-10 nm ahead of the oxidation front creating voids. The oxide microstructure is also different. Cr2O3 has a plate-like structure with 1.2-1.7 nm wide pores running along the grain boundary, while NiAl2O4 has 1.5 nm wide pores in the direction parallel to the grain boundary and 0.6 nm pores in the perpendicular direction providing an additional pathway for oxygen diffusion through the oxide. The proposed theoretical methodology provides a framework for modeling metal alloy oxidation processes from first principles and on the experimentally relevant length scales.

Multiscale model of metal alloy oxidation at grain boundaries

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

Sushko, Maria L., E-mail: maria.sushko@pnnl.gov; Alexandrov, Vitaly; Schreiber, Daniel K.

2015-06-07

High temperature intergranular oxidation and corrosion of metal alloys is one of the primary causes of materials degradation in nuclear systems. In order to gain insights into grain boundary oxidation processes, a mesoscale metal alloy oxidation model is established by combining quantum Density Functional Theory (DFT) and mesoscopic Poisson-Nernst-Planck/classical DFT with predictions focused on Ni alloyed with either Cr or Al. Analysis of species and fluxes at steady-state conditions indicates that the oxidation process involves vacancy-mediated transport of Ni and the minor alloying element to the oxidation front and the formation of stable metal oxides. The simulations further demonstrate thatmore » the mechanism of oxidation for Ni-5Cr and Ni-4Al is qualitatively different. Intergranular oxidation of Ni-5Cr involves the selective oxidation of the minor element and not matrix Ni, due to slower diffusion of Ni relative to Cr in the alloy and due to the significantly smaller energy gain upon the formation of nickel oxide compared to that of Cr{sub 2}O{sub 3}. This essentially one-component oxidation process results in continuous oxide formation and a monotonic Cr vacancy distribution ahead of the oxidation front, peaking at alloy/oxide interface. In contrast, Ni and Al are both oxidized in Ni-4Al forming a mixed spinel NiAl{sub 2}O{sub 4}. Different diffusivities of Ni and Al give rise to a complex elemental distribution in the vicinity of the oxidation front. Slower diffusing Ni accumulates in the oxide and metal within 3 nm of the interface, while Al penetrates deeper into the oxide phase. Ni and Al are both depleted from the region 3–10 nm ahead of the oxidation front creating voids. The oxide microstructure is also different. Cr{sub 2}O{sub 3} has a plate-like structure with 1.2–1.7 nm wide pores running along the grain boundary, while NiAl{sub 2}O{sub 4} has 1.5 nm wide pores in the direction parallel to the grain boundary and 0.6 nm pores in the perpendicular direction providing an additional pathway for oxygen diffusion through the oxide. The proposed theoretical methodology provides a framework for modeling metal alloy oxidation processes from first principles and on the experimentally relevant length scales.« less

Analytical approach for collective diffusion: One-dimensional lattice with the nearest neighbor and the next nearest neighbor lateral interactions

NASA Astrophysics Data System (ADS)

Tarasenko, Alexander

2018-01-01

Diffusion of particles adsorbed on a homogeneous one-dimensional lattice is investigated using a theoretical approach and MC simulations. The analytical dependencies calculated in the framework of approach are tested using the numerical data. The perfect coincidence of the data obtained by these different methods demonstrates that the correctness of the approach based on the theory of the non-equilibrium statistical operator.

Isopycnal diffusivity in the tropical North Atlantic oxygen minimum zone

NASA Astrophysics Data System (ADS)

Köllner, Manuela; Visbeck, Martin; Tanhua, Toste; Fischer, Tim

2017-04-01

Isopycnal diffusivity plays an important role in the ventilation of the Eastern Tropical North Atlantic (ETNA) Oxygen Minimum Zone (OMZ). Lateral tracer transport is described by isopycnal diffusivity and mean advection of the tracer (e.g. oxygen), together they account for up to 70% of the oxygen supply for the OMZ. One of the big challenges is to separate diffusivity from advection. Isopycnal diffusivity was estimated to be Ky=(500 ± 200) m2 s-1 and Kx=(1200 ± 600) m2 s-1 by Banyte et. al (2013) from a Tracer Release Experiment (TRE). Hahn et al. (2014) estimated a meridional eddy diffusivity of 1350 m2 s-1 at 100 m depth decaying to less than 300 m2 s-1 below 800 m depth from repeated ship sections of CTD and ADCP data in addition with hydrographic mooring data. Uncertainties of the estimated diffusivities were still large, thus the Oxygen Supply Tracer Release Experiment (OSTRE) was set up to estimate isopycnal diffusivity in the OMZ using a newly developed sampling strategy of a control volume. The tracer was released in 2012 in the core of the OMZ at approximately 410 m depth and mapped after 6, 15 and 29 months in a regular grid. In addition to the calculation of tracer column integrals from vertical tracer profiles a new sampling method was invented and tested during two of the mapping cruises. The mean eddy diffusivity during OSTRE was found to be about (300 ± 130) m2 s-1. Additionally, the tracer has been advected further to the east and west by zonal jets. We compare different analysis methods to estimate isopycnal diffusivity from tracer spreading and show the advantage of the control volume surveys and control box approach. From the control box approach we are estimating the strength of the zonal jets within the OMZ core integrated over the TRE time period. References: Banyte, D., Visbeck, M., Tanhua, T., Fischer, T., Krahmann, G.,Karstensen, J., 2013. Lateral Diffusivity from Tracer Release Experiments in the Tropical North Atlantic Thermocline. Journal of Geophysical Research 118. Hahn, J., Brandt, P., Greatbatch, R., Krahmann, G., Körtzinger, A., 2014. Oxygen variance and meridional oxygen supply in the Tropical North East Atlantic oxygen minimum zone. Climate Dynamics 43, 2999-3024.

Numerical Modeling of Pulsed Electrical Discharges for High-Speed Flow Control

DTIC Science & Technology

2012-02-01

dimensions , and later on more complex problems. Subsequent work compared different physical models for pulsed discharges: one-moment (drift-diffusion with...two dimensions , and later on more complex problems. Subsequent work compared different physical models for pulsed discharges: one-moment (drift...The state of a particle can be specified by its position and velocity. In principal, the motion of a large group of particles can be predicted from

From Philharmonic Hall to number theory: The way to more diffusion

NASA Astrophysics Data System (ADS)

Schroeder, Manfred R.

2005-09-01

In September 1962, in the presence of Mrs. Jacqueline Kennedy, Philharmonic Hall in New York was inaugurated-the first building of the new Lincoln Center for the Performing Arts. To address the soon-apparent acoustic problems, Lincoln Center turned to Bell Laboratories for help, and I was asked to join a ``committee of experts,'' chaired by Vern O. Knudsen of UCLA. My work on Philharmonic Hall, assisted by B.S. Atal, G.M. Sessler, and J.E. West, and later, after my move to Göttingen, by my students D. Gottlob, F.K. Siebrasse, and U. Eysholdt, indicated a need for energetic early lateral sound. It was clear that better lateral diffusion could improve the acoustic quality and the feeling of ``envelopment'' by the sound. Knowing some Galois field mathematics, I lucked upon the design of diffusors which scattered incident waves into broad lateral patterns-but only for a single musical octave. Then, in 1977, during a celebration of the 200th anniversary of Gauss's birth, I heard a talk by André Weil on Gauss sums and quadratic residues and, in a flash, it became clear to me that diffusors based on quadratic residues were the answer to broadly scattering waves comprising many musical octaves.

A morphological study of diffuse axonal injury in a rat model by lateral head rotation trauma.

PubMed

Xiaoshengi, He; Guitao, Yang; Xiang, Zhang; Zhou, Fei

2010-03-01

Morphology in diffuse axonal injury (DAI) by lateral head rotation was investigated. SD rats were divided into injury (n=9) and sham (n=3) groups. A device was used to produce lateral rotational acceleration of the rats' heads. At different survival times three rats were killed for light and electron microscopic examination of the brain tissue. Sagittal sections were made from medulla oblongata and immunolabelled for NF68. At post-traumatic 30 min, NF68 immunolabelling showed a small number ofswollen and irregular axons. Ultrastructurally slightly-separated myelin lamellae and disorderly arranged neurofilaments occurred. At 2 and 24 h axonal damage became more severe. Increases in immunolabelled axonal swellings, disconnected axons and axonal retraction bulbs appeared. EM provided evidence of myelin separation, peri-axonal spaces, blank areas in axoplasm, loss of microtubules, peripheral accumulation of mitochondria and clumped neurofilaments for DAI. A tendency was noted for greater labelling with NF68 as axonal damage increased. The disorderly arrangement of NFs occurred at early stage of post-traumatic axonal changes.

Mesoscopic and continuum modelling of angiogenesis

PubMed Central

Spill, F.; Guerrero, P.; Alarcon, T.; Maini, P. K.; Byrne, H. M.

2016-01-01

Angiogenesis is the formation of new blood vessels from pre-existing ones in response to chemical signals secreted by, for example, a wound or a tumour. In this paper, we propose a mesoscopic lattice-based model of angiogenesis, in which processes that include proliferation and cell movement are considered as stochastic events. By studying the dependence of the model on the lattice spacing and the number of cells involved, we are able to derive the deterministic continuum limit of our equations and compare it to similar existing models of angiogenesis. We further identify conditions under which the use of continuum models is justified, and others for which stochastic or discrete effects dominate. We also compare different stochastic models for the movement of endothelial tip cells which have the same macroscopic, deterministic behaviour, but lead to markedly different behaviour in terms of production of new vessel cells. PMID:24615007

Aharonov-Bohm oscillations, quantum decoherence and amplitude modulation in mesoscopic InGaAs/InAlAs rings.

PubMed

Ren, S L; Heremans, J J; Gaspe, C K; Vijeyaragunathan, S; Mishima, T D; Santos, M B

2013-10-30

Low-temperature Aharonov-Bohm oscillations in the magnetoresistance of mesoscopic interferometric rings patterned on an InGaAs/InAlAs heterostructure are investigated for their dependence on excitation current and temperature. The rings have an average radius of 650 nm, and a lithographic arm width of 300 nm, yielding pronounced interference oscillations over a wide range of magnetic fields. Apart from a current and temperature dependence, the oscillation amplitude also shows a quasi-periodic modulation with applied magnetic field. The phase coherence length is extracted by analysis of the fundamental and higher Fourier components of the oscillations, and by direct analysis of the amplitude and its dependence on parameters. It is concluded that the Thouless energy forms the measure of excitation energies for quantum decoherence. The amplitude modulation finds an explanation in the effect of the magnetic flux threading the finite width of the interferometer arms.

Controlling the quantum dynamics of a mesoscopic spin bath in diamond

PubMed Central

de Lange, Gijs; van der Sar, Toeno; Blok, Machiel; Wang, Zhi-Hui; Dobrovitski, Viatcheslav; Hanson, Ronald

2012-01-01

Understanding and mitigating decoherence is a key challenge for quantum science and technology. The main source of decoherence for solid-state spin systems is the uncontrolled spin bath environment. Here, we demonstrate quantum control of a mesoscopic spin bath in diamond at room temperature that is composed of electron spins of substitutional nitrogen impurities. The resulting spin bath dynamics are probed using a single nitrogen-vacancy (NV) centre electron spin as a magnetic field sensor. We exploit the spin bath control to dynamically suppress dephasing of the NV spin by the spin bath. Furthermore, by combining spin bath control with dynamical decoupling, we directly measure the coherence and temporal correlations of different groups of bath spins. These results uncover a new arena for fundamental studies on decoherence and enable novel avenues for spin-based magnetometry and quantum information processing. PMID:22536480

In vivo excitation of nanoparticles using luminescent bacteria

PubMed Central

Dragavon, Joe; Blazquez, Samantha; Rekiki, Abdessalem; Samson, Chelsea; Theodorou, Ioanna; Rogers, Kelly L.; Tournebize, Régis; Shorte, Spencer L.

2012-01-01

The lux operon derived from Photorhabdus luminescens incorporated into bacterial genomes, elicits the production of biological chemiluminescence typically centered on 490 nm. The light-producing bacteria are widely used for in vivo bioluminescence imaging. However, in living samples, a common difficulty is the presence of blue-green absorbers such as hemoglobin. Here we report a characterization of fluorescence by unbound excitation from luminescence, a phenomenon that exploits radiating luminescence to excite nearby fluorophores by epifluorescence. We show that photons from bioluminescent bacteria radiate over mesoscopic distances and induce a red-shifted fluorescent emission from appropriate fluorophores in a manner distinct from bioluminescence resonance energy transfer. Our results characterizing fluorescence by unbound excitation from luminescence, both in vitro and in vivo, demonstrate how the resulting blue-to-red wavelength shift is both necessary and sufficient to yield contrast enhancement revealing mesoscopic proximity of luminescent and fluorescent probes in the context of living biological tissues. PMID:22615349

Band and Correlated Insulators of Cold Fermions in a Mesoscopic Lattice

NASA Astrophysics Data System (ADS)

Lebrat, Martin; Grišins, Pjotrs; Husmann, Dominik; Häusler, Samuel; Corman, Laura; Giamarchi, Thierry; Brantut, Jean-Philippe; Esslinger, Tilman

2018-01-01

We investigate the transport properties of neutral, fermionic atoms passing through a one-dimensional quantum wire containing a mesoscopic lattice. The lattice is realized by projecting individually controlled, thin optical barriers on top of a ballistic conductor. Building an increasingly longer lattice, one site after another, we observe and characterize the emergence of a band insulating phase, demonstrating control over quantum-coherent transport. We explore the influence of atom-atom interactions and show that the insulating state persists as contact interactions are tuned from moderately to strongly attractive. Using bosonization and classical Monte Carlo simulations, we analyze such a model of interacting fermions and find good qualitative agreement with the data. The robustness of the insulating state supports the existence of a Luther-Emery liquid in the one-dimensional wire. Our work realizes a tunable, site-controlled lattice Fermi gas strongly coupled to reservoirs, which is an ideal test bed for nonequilibrium many-body physics.

p-type Mesoscopic nickel oxide/organometallic perovskite heterojunction solar cells.

PubMed

Wang, Kuo-Chin; Jeng, Jun-Yuan; Shen, Po-Shen; Chang, Yu-Cheng; Diau, Eric Wei-Guang; Tsai, Cheng-Hung; Chao, Tzu-Yang; Hsu, Hsu-Cheng; Lin, Pei-Ying; Chen, Peter; Guo, Tzung-Fang; Wen, Ten-Chin

2014-04-23

In this article, we present a new paradigm for organometallic hybrid perovskite solar cell using NiO inorganic metal oxide nanocrystalline as p-type electrode material and realized the first mesoscopic NiO/perovskite/[6,6]-phenyl C61-butyric acid methyl ester (PC61BM) heterojunction photovoltaic device. The photo-induced transient absorption spectroscopy results verified that the architecture is an effective p-type sensitized junction, which is the first inorganic p-type, metal oxide contact material for perovskite-based solar cell. Power conversion efficiency of 9.51% was achieved under AM 1.5 G illumination, which significantly surpassed the reported conventional p-type dye-sensitized solar cells. The replacement of the organic hole transport materials by a p-type metal oxide has the advantages to provide robust device architecture for further development of all-inorganic perovskite-based thin-film solar cells and tandem photovoltaics.

p-type Mesoscopic Nickel Oxide/Organometallic Perovskite Heterojunction Solar Cells

PubMed Central

Wang, Kuo-Chin; Jeng, Jun-Yuan; Shen, Po-Shen; Chang, Yu-Cheng; Diau, Eric Wei-Guang; Tsai, Cheng-Hung; Chao, Tzu-Yang; Hsu, Hsu-Cheng; Lin, Pei-Ying; Chen, Peter; Guo, Tzung-Fang; Wen, Ten-Chin

2014-01-01

In this article, we present a new paradigm for organometallic hybrid perovskite solar cell using NiO inorganic metal oxide nanocrystalline as p-type electrode material and realized the first mesoscopic NiO/perovskite/[6,6]-phenyl C61-butyric acid methyl ester (PC61BM) heterojunction photovoltaic device. The photo-induced transient absorption spectroscopy results verified that the architecture is an effective p-type sensitized junction, which is the first inorganic p-type, metal oxide contact material for perovskite-based solar cell. Power conversion efficiency of 9.51% was achieved under AM 1.5 G illumination, which significantly surpassed the reported conventional p-type dye-sensitized solar cells. The replacement of the organic hole transport materials by a p-type metal oxide has the advantages to provide robust device architecture for further development of all-inorganic perovskite-based thin-film solar cells and tandem photovoltaics. PMID:24755642

Large spin accumulation and crystallographic dependence of spin transport in single crystal gallium nitride nanowires

PubMed Central

Park, Tae-Eon; Park, Youn Ho; Lee, Jong-Min; Kim, Sung Wook; Park, Hee Gyum; Min, Byoung-Chul; Kim, Hyung-jun; Koo, Hyun Cheol; Choi, Heon-Jin; Han, Suk Hee; Johnson, Mark; Chang, Joonyeon

2017-01-01

Semiconductor spintronics is an alternative to conventional electronics that offers devices with high performance, low power and multiple functionality. Although a large number of devices with mesoscopic dimensions have been successfully demonstrated at low temperatures for decades, room-temperature operation still needs to go further. Here we study spin injection in single-crystal gallium nitride nanowires and report robust spin accumulation at room temperature with enhanced spin injection polarization of 9%. A large Overhauser coupling between the electron spin accumulation and the lattice nuclei is observed. Finally, our single-crystal gallium nitride samples have a trigonal cross-section defined by the (001), () and () planes. Using the Hanle effect, we show that the spin accumulation is significantly different for injection across the (001) and () (or ()) planes. This provides a technique for increasing room temperature spin injection in mesoscopic systems. PMID:28569767

Non-metal spintronics: study of spin-dependent transport in InSb- and InAs-based nanopatterned heterostructures

NASA Astrophysics Data System (ADS)

Heremans, J. J.; Chen, Hong; Peters, J. A.; Goel, N.; Chung, S. J.; Santos, M. B.; van Roy, W.; Borghs, G.

2006-03-01

Spin-orbit interaction in semiconductor heterostructures can lead to various spin-dependent electronic transport effects without the presence of magnetic materials. Mesoscopic samples were fabricated on InSb/InAlSb and InAs/AlGaSb two-dimensional electron systems, where spin-orbit interaction is strong. In mesoscopic devices, the effects of spin-orbit interaction are not averaged out over the geometry, and lead to observable electronic properties. We experimentally demonstrate spin-split ballistic transport and the creation of fully spin-polarized electron beams using spin-dependent reflection geometries and transverse magnetic focusing geometries. Spin-dependent transport properties in the semiconductor materials are also investigated using antidot lattices. Spin-orbit interaction effects in high-mobility semiconductor devices may be utilized toward the design of novel spintronics implementations. We acknowledge NSF DMR-0094055 (JJH), DMR-0080054, DMR-0209371 (MBS).

Evaluation of calcium hydrogen carbonate mesoscopic crystals as a disinfectant for influenza A viruses

PubMed Central

NAKASHIMA, Ryuji; KAWAMOTO, Masaomi; MIYAZAKI, Shigeru; ONISHI, Rumiko; FURUSAKI, Koichi; OSAKI, Maho; KIRISAWA, Rikio; SAKUDO, Akikazu; ONODERA, Takashi

2017-01-01

In this study, the virucidal effect of a novel electrically charged disinfectant CAC-717 was investigated. CAC-717 is produced by applying an electric field to mineral water containing calcium hydrogen carbonate to generate mesoscopic crystals. Virus titration analysis showed a >3 log reduction of influenza A viruses after treatment with CAC-717 for 1 min in room temperature, while infectivity was undetectable after 15 min treatment. Adding bovine serum albumin to CAC-717 solution did not affect the disinfectant effect. Although CAC-717 is an alkaline solution (pH=12.39), upon contact with human tissue, its pH becomes almost physiological (pH 8.84) after accelerated electric discharge, which enables its use against influenza viruses. Therefore, CAC-717 may be used as a preventative measure against influenza A viruses and for biosecurity in the environment. PMID:28392537

Role of weakest links and system-size scaling in multiscale modeling of stochastic plasticity

NASA Astrophysics Data System (ADS)

Ispánovity, Péter Dusán; Tüzes, Dániel; Szabó, Péter; Zaiser, Michael; Groma, István

2017-02-01

Plastic deformation of crystalline and amorphous matter often involves intermittent local strain burst events. To understand the physical background of the phenomenon a minimal stochastic mesoscopic model was introduced, where details of the microstructure evolution are statistically represented in terms of a fluctuating local yield threshold. In the present paper we propose a method for determining the corresponding yield stress distribution for the case of crystal plasticity from lower scale discrete dislocation dynamics simulations which we combine with weakest link arguments. The success of scale linking is demonstrated by comparing stress-strain curves obtained from the resulting mesoscopic and the underlying discrete dislocation models in the microplastic regime. As shown by various scaling relations they are statistically equivalent and behave identically in the thermodynamic limit. The proposed technique is expected to be applicable to different microstructures and also to amorphous materials.

Variable speed limit strategies analysis with mesoscopic traffic flow model based on complex networks

NASA Astrophysics Data System (ADS)

Li, Shu-Bin; Cao, Dan-Ni; Dang, Wen-Xiu; Zhang, Lin

As a new cross-discipline, the complexity science has penetrated into every field of economy and society. With the arrival of big data, the research of the complexity science has reached its summit again. In recent years, it offers a new perspective for traffic control by using complex networks theory. The interaction course of various kinds of information in traffic system forms a huge complex system. A new mesoscopic traffic flow model is improved with variable speed limit (VSL), and the simulation process is designed, which is based on the complex networks theory combined with the proposed model. This paper studies effect of VSL on the dynamic traffic flow, and then analyzes the optimal control strategy of VSL in different network topologies. The conclusion of this research is meaningful to put forward some reasonable transportation plan and develop effective traffic management and control measures to help the department of traffic management.

Effect of Phase-Breaking Events on Electron Transport in Mesoscopic and Nanodevices

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

Meunier, Vincent; Mintmire, John W; Thushari, Jayasekera

2008-01-01

Existing ballistic models for electron transport in mesoscopic and nanoscale systems break down as the size of the device becomes longer than the phase coherence length of electrons in the system. Krstic et al. experimentally observed that the current in single-wall carbon nanotube systems can be regarded as a combination of a coherent part and a noncoherent part. In this article, we discuss the use of Buettiker phase-breaking technique to address partially coherent electron transport, generalize that to a multichannel problem, and then study the effect of phase-breaking events on the electron transport in two-terminal graphene nanoribbon devices. We alsomore » investigate the difference between the pure-phase randomization and phase/momentum randomization boundary conditions. While momentum randomization adds an extra resistance caused by backward scattering, pure-phase randomization smooths the conductance oscillations because of interference.« less

Spatial confinement governs orientational order in patchy particles

NASA Astrophysics Data System (ADS)

Iwashita, Yasutaka; Kimura, Yasuyuki

2016-06-01

Orientational order in condensed matter plays a key role in determining material properties such as ferromagnetism, viscoelasticity or birefringence. We studied purely orientational ordering in closely-packed one-patch colloidal particles confined between flat substrates, where the particles can only rotate and are ordered via the sticky interaction between the patches. For the first time, we experimentally realized a rich variety of mesoscopic patterns through orientational ordering of colloids by controlling patch size and confinement thickness. The combination of experiment and numerical simulation reveals the decisive role of confinement: An ordered state(s) is selected from the (meta)stable options in bulk when it is commensurate with the system geometry and boundary conditions; otherwise, frustration induces a unique order. Our study offers a new means of systematic control over mesoscopic structures via orientational ordering in patchy particles. The system would also possess unique functionalities through the rotational response of the particles to external stimuli.

Simulating the flow of entangled polymers.

PubMed

Masubuchi, Yuichi

2014-01-01

To optimize automation for polymer processing, attempts have been made to simulate the flow of entangled polymers. In industry, fluid dynamics simulations with phenomenological constitutive equations have been practically established. However, to account for molecular characteristics, a method to obtain the constitutive relationship from the molecular structure is required. Molecular dynamics simulations with atomic description are not practical for this purpose; accordingly, coarse-grained models with reduced degrees of freedom have been developed. Although the modeling of entanglement is still a challenge, mesoscopic models with a priori settings to reproduce entangled polymer dynamics, such as tube models, have achieved remarkable success. To use the mesoscopic models as staging posts between atomistic and fluid dynamics simulations, studies have been undertaken to establish links from the coarse-grained model to the atomistic and macroscopic simulations. Consequently, integrated simulations from materials chemistry to predict the macroscopic flow in polymer processing are forthcoming.

Compartmentalization of the outer hair cell demonstrated by slow diffusion in the extracisternal space.

PubMed

Gliko, Olga; Saggau, Peter; Brownell, William E

2009-08-19

In the outer hair cell (OHC), the extracisternal space (ECiS) is a conduit and reservoir of the molecular and ionic substrates of the lateral wall, including those necessary for electromotility. To determine the mechanisms through which molecules are transported in the ECiS of the OHC, we selectively imaged the time-dependent spatial distribution of fluorescent molecules in a <100 nm layer near the cell/glass interface of the recording chamber after their photolytic activation in a diffraction-limited volume. The effective diffusion coefficient was calculated using the analytical solution of the diffusion equation. It was found that diffusion in the ECiS is isotropic and not affected by depolarizing the OHC. Compared with free solution, the diffusion of 10 kDa dextran was slowed down in both the ECiS and the axial core by a factor of 4.6 and 1.6, respectively.

Diffusion barriers

NASA Technical Reports Server (NTRS)

Nicolet, M. A.

1983-01-01

The choice of the metallic film for the contact to a semiconductor device is discussed. One way to try to stabilize a contact is by interposing a thin film of a material that has low diffusivity for the atoms in question. This thin film application is known as a diffusion barrier. Three types of barriers can be distinguished. The stuffed barrier derives its low atomic diffusivity to impurities that concentrate along the extended defects of a polycrystalline layer. Sacrificial barriers exploit the fact that some (elemental) thin films react in a laterally uniform and reproducible fashion. Sacrificial barriers have the advantage that the point of their failure is predictable. Passive barriers are those most closely approximating an ideal barrier. The most-studied case is that of sputtered TiN films. Stuffed barriers may be viewed as passive barriers whose low diffusivity material extends along the defects of the polycrystalline host.

Anomalous cation diffusion in salt-doped confined bilayer ice.

PubMed

Qiu, Hu; Xue, Minmin; Shen, Chun; Guo, Wanlin

2018-05-17

The diffusive dynamics of aqueous electrolyte solutions in nanoconfined spaces has attracted considerable attention due to their potential applications in desalination, biosensors and supercapacitors. Here we show by molecular dynamics simulations that lithium and sodium ions diffuse at a rate at least an order of magnitude higher than that of water molecules when the ions are trapped in an ice bilayer confined between two parallel plates. This novel picture is in sharp contrast to the prevailing view that the diffusion rate of ions is comparable to or even lower than that of water in both bulk and confined solutions. The predicted high ion mobility stems from frequent lateral hopping of ions along the coordination sites inside the hydrogen-bonding network connecting the two water layers of the ice bilayer. This anomalous diffusion should provide new insights into the physics of confined aqueous electrolytes.

Diffusion lengths of silicon solar cells from luminescence images

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

Wuerfel, P.; Trupke, T.; Puzzer, T.

A method for spatially resolved measurement of the minority carrier diffusion length in silicon wafers and in silicon solar cells is introduced. The method, which is based on measuring the ratio of two luminescence images taken with two different spectral filters, is applicable, in principle, to both photoluminescence and electroluminescence measurements and is demonstrated experimentally by electroluminescence measurements on a multicrystalline silicon solar cell. Good agreement is observed with the diffusion length distribution obtained from a spectrally resolved light beam induced current map. In contrast to the determination of diffusion lengths from one single luminescence image, the method proposed heremore » gives absolute values of the diffusion length and, in comparison, it is much less sensitive to lateral voltage variations across the cell area as caused by local variations of the series resistance. It is also shown that measuring the ratio of two luminescence images allows distinguishing shunts or surface defects from bulk defects.« less

Lateral gas phase diffusion length of boron atoms over Si/B surfaces during CVD of pure boron layers

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

Mohammadi, V., E-mail: V.Mohammadi@tudelft.nl; Nihtianov, S.

The lateral gas phase diffusion length of boron atoms, L{sub B}, along silicon and boron surfaces during chemical vapor deposition (CVD) using diborane (B{sub 2}H{sub 6}) is reported. The value of L{sub B} is critical for reliable and uniform boron layer coverage. The presented information was obtained experimentally and confirmed analytically in the boron deposition temperature range from 700 °C down to 400 °C. For this temperature range the local loading effect of the boron deposition is investigated on the micro scale. A L{sub B} = 2.2 mm was determined for boron deposition at 700 °C, while a L{sub B}more » of less than 1 mm was observed at temperatures lower than 500 °C.« less

Lateral Diffusion in a DMPC:DMPE-EO Binary Monolayer at the Air/Water Interface

NASA Astrophysics Data System (ADS)

Adalsteinsson, Thorsteinn; Porter, Ryan; Yu, Hyuk

2002-03-01

Polyethylene glycol tethered phospholipids (lipo-polymers) have recently attracted attention for improving the stability of liposomes and other bilayer delivery systems. Here, we report a study of surface pressure measurement and diffusion measurements of a probe lipid (NBD-DMPC) in a binary monolayer of DMPC and DMPE-EO at the Air/Water interface. Our findings are that the DMPE-EO lipo-polymer desorbs from the interface at intermediate surface pressures if the EO tail is sufficiently large (i.e. EO_45) and does not interfere with the diffusion of the probe thereafter. In the case where the EO tail is short (i.e. EO_17) the lipo-polymer retards the diffusion of the probe, but as the surface pressure increases, the diffusion behavior approaches that of pure DMPC monolayer independent of lipo-polymer. Thus, we conclude that the surface pressure and EO molar mass dependent desorption of the lipo-polymer modulates the probe diffusion retardation.